Integrating environmental 
DNA science into Australia’s 
marine parks: a roadmap



Copyright

© Commonwealth Scientific and Industrial Research 
Organisation 2023. To the extent permitted by law, 
all rights are reserved and no part of this publication 
covered by copyright may be reproduced or copied 
in any form or by any means except with the written 
permission of CSIRO.

Citation and authorship

De Brauwer M, Deagle B, Dunstan P & Berry O (2023). 
Integrating environmental DNA science into Australia’s 
marine parks: a roadmap. CSIRO, Hobart.

ISBN (online): 978-1-4863-1917-6

ISBN (print): 978-1-4863-1918-3

Acknowledgements

CSIRO acknowledges the Traditional Owners of the 
land, sea and waters of the area that we live and work 
on across Australia. We acknowledge their continuing 
connection to their culture, and we pay our respects to 
their Elders past and present.

The roadmap was created in close consultation with 
Parks Australia; the authors would like to specifically 
thank Steffan Howe, Cath Samson, and Alex Tomlinson 
for their valuable input. The authors would also like 
to thank the many people who provided advice, 
information, and feedback: Neville Barret, Cindy 
Bessey, Danny Brock, Simon Bryars, Michael Bunce, 
Kerry Cameron, Kris Cooling, Pascal Craw, Vanessa 
Crowe, Joseph DiBattista, Jon Emmet, Francisco 
Encinas-Viso, Jenny Giles, Madeline Green, Erin 
Hahn, David Harasti, Jamie Hicks, Jessica Hoey, Tom 
Holmes, Josephine Hyde, Florian Leese, Rich Little, 
Craig Meakin, Nicole Middleton, Karen Moloney, Tom 
Mooney, Barbara Musso, Kristian Peters, Meaghan 
Rourke, Michael Sams, Chloe Schauble, Nicole Strehling, 
Alejandro Trujillo-González, Nicola Udy, Sven Uthicke, 
Jodie Van De Kamp, David Wachenfeld, Mark Wallace, 
Katrina West, Andrea Wild, Shaun Wilson, and 
Anastasija Zaiko.

Editing and design: Biotext Pty Ltd.

Important disclaimers

CSIRO advises that the information contained in this 
publication comprises general statements based on 
scientific research. The reader is advised and needs 
to be aware that such information may be incomplete 
or unable to be used in any specific situation. 
No reliance or actions must therefore be made on that 
information without seeking prior expert professional, 
scientific and technical advice. To the extent 
permitted by law, CSIRO (including its employees and 
consultants) excludes all liability to any person for any 
consequences, including but not limited to all losses, 
damages, costs, expenses and any other compensation, 
arising directly or indirectly from using this publication 
(in part or in whole) and any information or material 
contained in it. The views expressed in this document 
do not necessarily reflect those of Parks Australia or 
other management agencies.

CSIRO is committed to providing web accessible 
content wherever possible. If you are having 
difficulties with accessing this document please 
contact csiro.au/contact.


Contents


Executive summary

Environmental DNA technologies can contribute 
to the long-term monitoring and management 
of Australia’s vast marine environment.

This roadmap is a guide for marine resource 
managers seeking to understand the value of 
environmental DNA (eDNA) for monitoring. 
It explains eDNA technologies and empowers 
resource managers to assess the feasibility of 
using eDNA to address their monitoring and 
research needs. It highlights eDNA technologies 
that need further development before they can 
benefit marine monitoring programs.

The roadmap is also a guide for eDNA 
researchers who work in Australian Marine 
Parks. It describes marine park monitoring 
requirements and provides background 
information on existing monitoring programs.

Monitoring Australia’s 
marine environment

Australia has one of the world’s largest 
marine estates, with a network of more than 
160 marine parks exceeding 4 million km2. 
The marine environment contributes 
an estimated $105 billion per year to 
Australia’s GDP by providing food, mineral 
resources, recreation and cultural value, 
as well as supporting shipping and defence. 
However, the environment faces local and 
global threats that may have significant 
ecological and socioeconomic impacts.

Effective management is vital to addressing 
these threats and protecting the health of 
the marine environment. Many jurisdictions 
and stakeholders are involved in managing 
Australia’s marine environment, and data are 
critical to support evidence-based decisions. 
But with its wide geographic extent, diverse 
habitats and remoteness, Australia’s marine 
environment poses unique monitoring 
challenges. Effective monitoring of the 
Australian marine estate requires a broad 
toolset and expertise. The challenge now is to 
develop appropriate monitoring frameworks 
to assess impacts on marine environments and 
deliver information to support management 
and policymakers.

Decision-makers, proponents and the 
community do not have access to the best 
available data, information and science. 
This results in sub-optimal decision-making, 
inefficiency and additional cost for business, 
and poor transparency for the community.

Independent review of the 
Environment Protection and Biodiversity 
Conservation Act 1999, 2020

How eDNA can help

Environmental DNA refers to the traces 
of DNA present in environmental samples 
(soil, sediment, water, air and more), 
which can be detected without observing the 
original organism. Environmental DNA surveys 
offer a new and useful capability for marine 
monitoring. Environmental DNA technologies 
collect, sequence and match traces of DNA 
to the species present at a site. They are a 
powerful, non-destructive, cost-effective, and 
fast complement to traditional monitoring 
approaches such as visual surveys, video, 
multibeam sonar or fisheries catch records.



The rapid uptake of eDNA methods globally 
signals its huge potential in environmental 
monitoring (Box 1). There are opportunities 
to integrate eDNA into marine reporting and 
management to:

• detect pest species

• detect rare and threatened species

• provide data on multiple species to 
characterise ecosystems

• detect changes in environmental condition.

Once established, eDNA surveys are fast, 
cost‑effective and non-lethal, with higher 
detection probabilities and fewer personal 
safety risks than many other methods 
(Beng & Corlett 2020, Richards et al. 2022). 
Australian researchers have been a part of 
the eDNA revolution. As a nation, Australia 
has strong expertise in eDNA research and 
increasing capacity to meet monitoring needs.

Purpose of the 
roadmap

This roadmap suggests pathways for 
integrating eDNA technologies into Australian 
monitoring programs to adaptively manage 
the sustainable use and conservation of the 
marine environment.

The roadmap describes how eDNA technologies 
with high technology readiness levels can be 
integrated into routine monitoring. It also 
looks ahead to emerging methods that will 
allow management bodies to anticipate future 
monitoring scenarios. While the roadmap 
focuses on monitoring programs for marine 
parks in Australia, its methods and timelines are 
likely to be transferrable to marine protected 
areas elsewhere.



Short-term roadmap recommendations

Diagram summarising the short-term roadmap recommendations (adopt, scale, standardize, calibrate, include, embed)
Adopt eDNA technologies off er a powerful approach that is ready to address 
policy and management needs and improve monitoring in marine 
parks. The methods are being adopted globally and Australia is ready 
to begin implementation.
Scale Increase eDNA capacity. Upskill staff and molecular researchers in 
eDNA use to support marine park management. Invest in the transition 
to integrate eDNA technologies in marine park monitoring programs to 
ensure continuity of high-quality data series. Test and deploy emerging 
eDNA approaches.
Standardise Provide best practice standards and user guides for national marine 
monitoring using eDNA. Develop standard operating procedures. 
Include park-specific eDNA strategies. Formalise eDNA workfl ows.
Calibrate Run parallel surveys. Use traditional monitoring methods to calibrate 
and ground truth new eDNA approaches and add value through 
creating additional data.
Include Work with Traditional Owners, citizen scientists, and other stakeholders 
to deploy eDNA technologies across Australia’s marine environment.
Embed Scale up successful eDNA monitoring systems and coordinate between 
jurisdictions. Complete reference databases for matching eDNA to 
species. Develop automated eDNA collection, analysis, and reporting in 
marine parks.




Guide to this document

This document has 5 sections:

• The roadmap: integrating eDNA science 
into marine parks in Australia – identifies 
current and future pathways for large-scale 
integration of eDNA methods into Australian 
marine monitoring and applied research 
programs. This section is for those interested 
in current needs and opportunities to use 
eDNA methods in monitoring programs, 
as well as future technical developments 
relevant to marine park management.

• The context: understanding eDNA and 
marine parks in Australia provides 
background information about 
environmental DNA technologies to allow 
resource managers to assess the feasibility of 
using eDNA methods to address monitoring 
and science needs. It also provides 
information on monitoring programs in 
Australia’s national marine reserve system to 
allow molecular scientists to understand the 
aims and needs of resource managers.

• How eDNA can be used in marine 
parks: applications, benefits, challenges 
and opportunities answers questions 
about the practical applications of eDNA, 
and discusses both the benefits and 
the challenges of eDNA technologies. 
It looks at how eDNA could be used in 
existing monitoring programs, and eDNA 
opportunities beyond monitoring.

• Action plan for managers: practical steps 
to integrate eDNA in individual projects 
presents a practical action plan for marine 
park managers who are considering using 
eDNA technologies. The framework can 
inform managers’ decision-making about 
whether and how to incorporate eDNA 
methods into monitoring programs.

• Research priorities and future 
developments: supporting integration 
into monitoring programs considers 
the research activities that should be 
prioritised to improve the integration of 
eDNA technologies in marine monitoring 
programs, based on existing needs and 
priorities in Australian Marine Parks.

Box 1 A vision for the future

Imagine a fleet of automated samplers transmitting real-time eDNA data from the marine 
environment, supported by on-ground sampling teams where they are most needed. 
Automated systems integrate this eDNA data with physical and chemical data.

Analyses based on machine learning quickly detect changes in ecosystem health, pinpointing 
the cause and predicting the impacts on different species. Biosecurity threats are detected 
before critical population thresholds are reached, while detailed provenance and spatial 
information identifies the source of the incursion. Rangers and community groups feel 
more connected to marine management and contribute data from local samples to a shared 
national database.

The data feeds into an online platform where anyone, from marine scientists to holiday‑makers, 
can check the condition of the ocean. The platform provides scientists and managers with 
data they can analyse or use to direct on-ground monitoring teams to collect targeted 
information using conventional methods. Simultaneously, the platform offers non-experts 
user-friendly information so that they can monitor the ocean in their area, just as they 
monitor the weather through weather forecasts.

continues



Box 1 continued

Infographic of current survey methods and emerging DNA methods. Current methods include acoustic surveys, diver visual surveys and catch-based methods. Emerging methods include eDNA collecting devices, biosecurity screening and eDNA water sampling


Infographic of future eDNA methods, showing a data integration platform linked to a drone sampler, a laboratory on a boat using various monitoring methods including deep water sampling and deep tow cameras, and a network of eDNA samplers including autonomous samplers, passive eDNA sampling and hand-held DNA sequencing.

The roadmap: integrating eDNA 
science into marine parks 
in Australia

The rapid adoption of eDNA technologies in 
natural resource management means a national 
roadmap for their integration in the Australian 
context is timely and necessary. Environmental 
DNA and other molecular methods can 
complement and improve existing science and 
monitoring programs in marine parks (Stepien 
et al. 2022). The opportunities are far-ranging 
and likely to be transformative.

Effective governance and coordination are 
needed to take full advantage of eDNA 
technologies and to transform marine 
monitoring (Turrell 2018, Kelly et al. 2023). 
Globally, multiple jurisdictions are taking 
a strategic approach to the integration 
of eDNA into environmental monitoring 
(Kelly et al. 2023).

European roadmaps optimistically forecast 
that eDNA will become a standard monitoring 
method within 2 to 10 years (Norros et al. 
2022). In the USA, the National Oceanic 
and Atmospheric Administration (NOAA) 
Omics strategic plan aims to accelerate the 
integration of eDNA and other transformational 
‘omics’ tools by 2025 (Goodwin et al. 2020). 
Closer to home, New Zealand’s Department 
of Conservation expects eDNA to have an 
important place in the long-term monitoring 
of the country’s biodiversity (DOC & Toitū Te 
Whenua Land Information New Zealand 2023).

While these international plans are informative, 
Australia’s unique marine park management 
context requires bespoke consideration. 
The next decade offers a window of 
opportunity for Australia to shape the future 
of eDNA science in monitoring: Australia has 
eDNA capability; eDNA technologies have 
reached high technology readiness levels; 
and global and national interest in genomic 
methods mean a higher chance of uptake from 
policy makers. The Australian eDNA roadmap 
aims to facilitate and streamline the integration 
of eDNA methods, maximising their benefits for 
marine park management.

The roadmap identifies short-, mid- and 
long-term integration opportunities tailored 
to the Australian marine park management 
context (Figure 1). For the short term (until 
2030), the roadmap sets out recommendations 
for integrating eDNA methods. It then 
canvasses expectations for the development 
of eDNA methods over the medium term 
(2030 to 2040), and projections for the longer 
term (2040 to 2050).

The roadmap investigates how eDNA methods 
can address marine park monitoring goals 
based on the needs of marine resource 
managers. Australia’s marine parks encompass 
a vast spectrum of environments; their science 
and monitoring programs therefore have varied 
requirements. Some of the roadmap’s general 
recommendations will not be relevant to every 
marine park jurisdiction.



Diagram summarising the projected timeline for integration of eDNA methods in monitoring programs, showing the present to 2030 recommendations, the 2030 to 2040 expectations, and the 2040 to 2050 projections
Design park-specific 
strategies for eDNA 
integration 
Develop national marine 
monitoring SOPs and 
metadata standardsIncrease eDNA 
capacity through 
targeted training and 
employment Commence eDNA 
monitoring projectsIncrease eDNA method 
uptake and deployment, 
including by completing 
a fish reference librarySustain investment and 
formalise workflows 
Fine-tune existing 
applications Create decision 
frameworks to guide 
management Test and deploy new 
technologies 
eDNA is integrated in 
monitoring programs Ecosystem health 
indices are used to 
monitor changes in 
ecosystems Large-scale automated 
sampling systems are 
deployed Assay validation scales 
are developed for 
relevant monitoring 
programs Assays deliver 
abundance metrics 
comparable to other 
methods 
Capacity for big data 
and advanced analytics 
is increased Reference libraries are 
complete for significant 
taxa All Australian species are 
in reference librariesA fleet of automated 
testing devices are in 
place Data from testing are 
uploaded to central 
database in real time Data analysis is 
automated to provide 
trend information and 
flag issues in real time Population genetics 
information is readily 
available Data enable insights 
about the physiological 
state of species of 
interest Long-term data are used 
to assess management 
effects Present–2030 
Recommendations 2030–2040 
Expectations 2040–2050 
Projections


Figure 1 Projected timeline for integration of eDNA methods in monitoring programs



Short-term 
recommendations 
(present–2030)

The roadmap’s short-term recommendations 
can be summarised as:

1. Adopt: Environmental DNA technologies 
offer a powerful approach that is ready to 
improve monitoring and address policy and 
management needs. The methods are being 
adopted globally and Australia is ready to 
begin implementation.

2. Scale: Increase eDNA capacity. Upskill 
staff and molecular researchers in eDNA 
use to support marine park management. 
Invest in the transition to integrate 
eDNA technologies in marine park 
monitoring programs to ensure continuity 
of high‑quality data series. Test and deploy 
emerging eDNA approaches.

3. Standardise: Provide best practice 
standards and user guides for national 
marine monitoring using eDNA. Develop 
standard operating procedures (SOPs). 
Include park‑specific eDNA strategies. 
Formalise eDNA workflows.

4. Calibrate: Run parallel surveys. 
Use conventional monitoring methods 
to calibrate and ground truth new eDNA 
approaches and add value by creating 
additional data.

5. Include: Work with Traditional Owners, 
citizen scientists and other stakeholders to 
deploy eDNA technologies across Australia’s 
marine environment.

6. Embed: Scale up successful eDNA 
monitoring systems and coordinate 
between jurisdictions. Complete reference 
databases for matching eDNA to species. 
Develop automated eDNA collection, 
analysis and reporting in marine parks.

Short-term – immediate 
recommendations 
(present–2025)

In the immediate term, the recommendations 
are to:

• design park-specific strategies for eDNA 
integration

• develop national marine monitoring eDNA 
SOPs and metadata standards

• increase eDNA capacity

• begin eDNA monitoring projects.

Design park-specific strategies 
for eDNA integration

So that eDNA methods can be incorporated 
into monitoring programs efficiently, marine 
park managers should identify the most 
impactful integration opportunities. Analysis 
of management goals, stakeholder needs, 
department capacities and local environmental 
factors will help managers to direct resources 
and plan monitoring programs (see Action 
plan for managers). Parks should design their 
eDNA monitoring strategies in consultation 
with molecular experts to guarantee achievable 
goals at a realistic scale.

Strategic, coordinated policy action on 
governmental and departmental levels could 
expedite the integration of molecular survey 
methods (Lodge 2022). Regional management 
groups would benefit from a national vision of 
how eDNA fits within Parks Australia’s strategy. 
Strategies should be aligned with international 
initiatives promoting inter-operable eDNA 
monitoring data (see Global perspectives and 
the inter-operability of eDNA data).



Develop national marine monitoring 
eDNA SOPs and metadata standards

Developing SOPs will ensure:

• data is findable, accessible, inter-operable 
and reusable (FAIR)

• metadata is comprehensive

• future inter-operability between regions 
and time series.

The National Marine Science Committee 
has recommended that national guidelines 
for data collection, management, sharing 
and delivery be developed (NMSC 2021). 
Although National Environmental Science 
Program (NESP) initiatives are working to 
standardise marine data collection methods, 
eDNA methods are not included. Future efforts 
in this area should include eDNA methods 
(Trujillo-González et al. 2021).

SOPs for the collection of eDNA samples 
should be designed as soon as possible. 
Sample collection is executed in the field, 
often by non-experts. Without quality 
standards, there is a high risk of generating 
unreliable data due to issues such as 
contamination and poor alignment between 
collection methods and project goals. In the 
absence of SOPs, eDNA projects should follow 
current best practice guidelines to ensure 
quality (De Brauwer et al. 2022a,b).

Increase eDNA capacity through 
targeted training and employment

The uptake of eDNA methods in monitoring 
will require capacity building (Kelly et al. 
2023). Parks personnel will need to build 
their eDNA literacy, while molecular scientists 
must deepen their understanding of marine 
park management. Molecular methods 
are specialised and to integrate them 
successfully, parks will either need to employ 
staff with relevant expertise or consult with 
external experts.

Begin eDNA monitoring projects

The first eDNA projects will reflect local 
capacities and priorities. Generally, eDNA 
can be used immediately to monitor regions 
that are not easily accessible for divers, and 
to complement other data for a more holistic 
characterisation of the environment.

Comparing eDNA and conventional monitoring 
methods will help to calibrate methods and 
collect baseline data. To interpret temporal 
variation, method comparisons should ideally 
be conducted for at least 3 monitoring seasons, 
although duration could differ depending 
on local variability. Improving existing DNA 
reference libraries will be vital to establish clear 
baselines and allow for better comparisons 
between methods.

Some other applications of eDNA, such as 
detecting invasive or endangered species, are 
already well established at high technology 
readiness levels. Such projects would require 
limited investment beyond the development 
of species-specific assays (see Current 
uses of eDNA methods in Australia’s 
marine environment).

A dedicated budget for eDNA integration 
would support the deployment of new 
methods and the continuity of high-quality 
data series. Funding for eDNA monitoring 
projects should focus on areas where eDNA 
results can meaningfully inform monitoring 
goals or improve the efficiency of future 
eDNA monitoring.

New eDNA projects should follow best 
practices. Experts in eDNA methods in the 
marine environment should be included 
at all stages of project design and analysis 
(De Brauwer et al. 2022a).



Short-term – near future 
recommendations (2025–2030)

In the near future, the recommendations are to:

• increase eDNA method uptake and wider 
deployment

• sustain investment and formalise workflows

• fine-tune existing applications

• create decision frameworks to guide 
management

• test and deploy new technologies.

Increase eDNA method uptake 
and deployment

The second half of this decade is likely to see 
increased use of eDNA methods and their 
wider integration into marine park monitoring. 
Timely establishment of eDNA survey protocols 
and preparing for anticipated scientific advances 
will ensure their integration in monitoring and 
research programs is optimised. Technological 
developments and method improvements – 
such as more complete DNA reference libraries, 
faster and inter-operable bioinformatics 
pipelines, and new analytical methods – will 
start to become operational. By this time, DNA 
reference databases should be complete for all 
Australian fishes and a significant proportion 
of invertebrates, improving the species 
identification of eDNA surveys (CSIRO 2023). 
The projected evolution in portable eDNA 
devices will enable rapid assessment of the 
presence of species in the field.

To allow for ecosystem-scale comparability, 
the large quantities of data generated by 
metabarcoding should be made accessible via 
platforms such as the Atlas of Living Australia, 
the Global Biodiversity Information Facility, 
the Ocean Biodiversity Information System, 
or future custom-made platforms designed 
for marine parks data. Key to the usability of 
such systems will be the ability to access eDNA 
survey data alongside other data types or 
layers, such as geographical information and 
temperature data.

Sustain investment and formalise 
workflows

Sustained investment in eDNA capability 
will be needed. Investments could focus 
on embedding molecular scientists within 
departments; developing programs to improve 
eDNA literacy among marine park science 
managers and major science partners; or 
designing structures to increase molecular 
scientists’ understanding of policy drivers 
and marine park management needs.

Cost decreases, efficiency improvements 
and the growth of external service providers 
will make eDNA surveys more useful as 
a monitoring tool. Detailed cost–benefit 
analyses will help ensure the highest return on 
investment (Andres et al. 2022). For example, 
while some parks may benefit from investing 
in specific eDNA tools or infrastructure 
(e.g. sampler units, laboratory robots), 
for others it may be more cost-effective to 
outsource parts of the eDNA monitoring 
workflow that require the purchase of 
high‑cost assets.

Formalising end-to-end sample processing 
workflows will further improve monitoring 
efficiency (Minamoto et al. 2021). Such 
workflows could incorporate sampling 
SOPs, preferred lab protocols and assays, 
standardised analysis methods, and centralised 
data repositories.

Fine-tune existing applications

This phase will need continued, focused 
calibration and fine-tuning of existing eDNA 
methods. To make monitoring programs more 
effective, it will be important to understand 
technical issues such as assay sensitivity 
and the limits of detection for specific 
single‑species assays. Better knowledge of 
how metabarcoding assays compare with 
other methods will make eDNA more useful in 
informing management decisions.



Create decision frameworks 
to guide management

Improved analytical methods will inform clear 
management decision frameworks, unlocking 
the full potential of eDNA methods to answer 
monitoring questions and guide management 
decisions. Such frameworks and improved 
technologies are needed to act upon big eDNA 
datasets. They will also allow for increased 
integration and inter-operability of data 
from other survey methods in large, cross-
stakeholder projects.

Test and deploy new technologies

Around this time, novel methods such as 
automated samplers and AI-assisted analyses 
will start to reach maturity, becoming ready for 
testing and, eventually, large-scale deployment. 
The shift to automated sampling methods could 
scale up sampling and reduce OH&S risks. 
This could happen through facilities such as 
Integrated Marine Observing System (IMOS) or 
the deployment of temporary local sampling 
units and autonomous underwater vehicles 
(AUVs). Automated samplers could be installed 
on ’ships of opportunity’: vessels that repeat the 
same route could conduct routine sampling, 
while vessels that trace multiple routes could 
characterise species communities.

Developing and testing custom eDNA-based 
health indices for specific environments may 
allow detection and response to emerging 
ecosystem changes or anthropogenic stressors. 
Such indices can be based on microbial or 
metazoan communities or a combination 
of the two – or they can be taxonomy-free 
(van de Kamp et al. 2023, Wilkinson et al. 
2023). Finally, relative abundance indices will 
also likely become ready for calibration and 
feasibility testing.

Mid-term expectations 
(2030–2040)

Over the next decade, better understanding of 
the possibilities and limitations of molecular 
surveys will yield benefits. In this phase, 
eDNA methods should become standard in 
monitoring programs, used by a wide range of 
stakeholders to monitor different facets of the 
marine environment.

In the mid-term, the expectations are:

• practical – large-scale cross-stakeholder 
integration, automated sampling, ecosystem 
health indices, single-species assays in 
full use, complete reference database for 
Australian fishes

• analytical – used in spatial planning, 
automated bioinformatics, novel modelling 
approaches, real-time data reporting

• technological – abundance indices, 
cross-method applications, organismal health 
methods, population genetics.

Practical expectations

Large-scale deployment will see automated 
eDNA sampling systems covering a broader 
spatial scale. The customised health indices 
developed previously will now be used to 
monitor changes in ecosystems.

Monitoring of single species will become 
more refined as the ecological interpretation 
of targeted assay results is fully understood. 
Resource managers will go beyond testing for 
the presence of Threatened, Endangered and 
Protected (TEP) or pest species, using validated 
assays and sampling designs to assess relative 
abundance and detailed spatial distribution. 
This information will then be used to design 
targeted warnings or responses to concerns 
such as toxic algal blooms, Irukandji swarms 
and biosecurity threats.



The resolution of DNA reference databases 
for habitat forming species and mobile 
invertebrates will continue to increase and 
improve the resolution and analytical power 
of metabarcoding surveys. On-site sequencing 
technologies should become more commonly 
available, making rapid detections of full 
species assemblages a reality.

Analytical expectations

Increased eDNA integration into 
multidisciplinary programs will generate 
big monitoring datasets, offering new 
opportunities and challenges. To process the 
wealth of data now available, investment in 
data analysis and bioinformatics capability 
will be necessary. Similarly, data storage and 
computing infrastructure will be needed to 
support efficient data processing. Efficiency 
will be further improved by the development 
of automated bioinformatics and data analyses 
pipelines customised to local monitoring needs.

Such measures will allow for improved 
ecosystem modelling. Better access to 
biodiversity information will benefit spatial 
planning processes in both the design of new 
parks and the management of existing ones. 
Improved analytical methods will enable 
the development of reporting pipelines that 
use near-real-time data stored in central 
repositories or sent to relevant management 
bodies in line with pre-determined triggers, 
which are set out in eDNA decision frameworks.

Technological expectations

While eDNA monitoring methods are likely 
to become integrated into day-to-day 
management, technological improvements and 
development of new methods should continue. 
In this phase, multi-species assays could start 
to deliver abundance metrics comparable to 
other methods.

Investigating the links between remote sensing 
and eDNA datasets will improve ocean-scale 
understanding of ecosystems. With this data 
incorporated into ecosystem models, it may be 
possible to predict how global climate change, 
regional weather or local anthropogenic 
impacts will affect marine ecosystems – 
similarly to how weather is forecast today.

We can also expect more research into 
applications that monitor not only presence or 
abundance, but also the physiological state of 
species. This would facilitate the monitoring 
of, for example, coral bleaching, reproductive 
cycles and the age of organisms.

Long-term projections 
(2040–2050)

Predicting long-term developments for 
rapidly developing molecular technologies 
is challenging. However, by considering 
general trends and the expectations of eDNA 
practitioners, we can form an idea of the 
possibilities that might exist in 30 years.

In the long term, the projections are:

• practical – increased scaling up of eDNA 
monitoring systems, complete reference 
databases, automated sample collection, 
capability to respond quickly to emerging 
trends on all levels of biodiversity

• analytical – automated analysis and 
reporting, long-term eDNA data used to 
model management intervention effects

• technological – continued development of 
new technologies, population genetics data 
available, applications to understand the 
physiological state of species.



Practical projections

Technology costs will reduce, making it more 
practical to scale up molecular monitoring 
applications. Fleets of automated testing 
buoys and ocean gliders could be uploading 
biodiversity data in real time. Implementation 
of large-scale eDNA monitoring will allow 
conventional methods to be deployed 
for targeted research, or in response to 
specific ecosystem trends that require more 
detailed data.

By now, DNA reference libraries should be 
complete for all Australian species and a large 
proportion of global species. Consequently, all 
fauna and flora in Australian Marine Parks can 
be detected and identified in a consistent way 
using eDNA methods.

Analytical projections

Automated data analyses linked to central 
data repositories could provide information 
on real-time trends in marine park indicators; 
the presence and abundance of TEP species; 
and the state of important habitat-forming 
organisms. Emerging issues first apparent in 
fast-responding microbial communities can 
be flagged, allowing a rapid management 
response. As long-term eDNA datasets across 
nationwide spatial scales are now available, 
modelling future scenarios and outcomes of 
policy and management interventions will 
become easier and more accurate.

Technological projections

New and improved molecular technologies 
will continue to develop in ways that 
are hard to predict. It is likely that at this 
stage, technological advances in other 
fields of science will open complementary 
possibilities with developments in eDNA 
methods. Advanced eDNA technologies for 
the study of intraspecific genetic diversity or 
population genetic structures may become 
readily available. Such tools could support 
sustainable use and conservation planning and 
allow for more targeted management actions 
(Bani et al. 2020). Alongside developments 
in metagenomics and transcriptomics, better 
understanding of new biomarkers could make 
it possible to assess target species’ biological 
metrics and physiological states such as health, 
age, reproductive state and stress.



The context: understanding eDNA 
and marine parks in Australia

This section provides background information 
about environmental DNA technologies 
to allow resource managers to assess the 
feasibility of applying eDNA methods to 
monitoring and science needs. It also provides 
information on monitoring programs in 
Australia’s national marine reserve system to 
allow molecular scientists to understand the 
aims and needs of resource managers.

Understanding eDNA

What is environmental DNA 
(eDNA)?

The term ‘eDNA’ refers to the DNA 
present in environmental samples 
(water, sediment, air, etc.). This DNA 
can include whole cells, parts of cells 
or extracellular DNA, which are shed 
by organisms through skin, mucous, 
faeces, etc.

eDNA is not a survey method. Rather, 
it is a variable that can be measured 
using an array of molecular methods, 
each of which has specific applications 
and limitations.

Environmental DNA (eDNA) science offers new 
and useful capabilities for marine monitoring. 
Environmental DNA was first defined as 
‘DNA that can be extracted from environmental 
samples (such as soil, water or air), without 
first isolating any target organisms’ (Taberlet 
et al. 2012). Environmental DNA is a mixture 
of DNA molecules in the environment, which 
can be measured using a range of molecular 
methods. As such, eDNA is a measured variable, 
not a method. The different methods used to 
collect and analyse eDNA samples can be as 
distinct as the different visual methods used to 
measure marine biodiversity.

Present-day eDNA methods have their technical 
origins in microbiology and ancient DNA 
(Clark et al. 2018). However, the first use of 
eDNA to detect macro-organisms from water 
samples was just over a decade ago (Ficetola 
et al. 2008), while the first study to detect 
multiple marine taxa was conducted in 2012 
(Thomsen et al. 2012).

Environmental DNA methods have progressed 
much since Ficetola et al. first used water 
samples to detect invasive bullfrogs in 2008. 
In less than 15 years, the field of eDNA science 
has matured well beyond the proof-of-concept 
state to its current integration into research 
and monitoring projects globally. There have 
been considerable improvements at each 
step of the eDNA workflow: from sample 
collection through to laboratory analysis, 
bioinformatics, data analysis and visualisation. 
These advancements have enabled eDNA 
methods to address a vast range of applications 
in all biomes.

Below is a brief overview of recent 
developments and the current technological 
state of eDNA methods which are summarised 
in Figure 2. For more information, see recent 
reviews by Mathieu et al. 2020, Gilbey et al. 
2021, Rourke et al. 2021, and Takahashi 
et al. 2023.

Diagram showing 2 eDNA workflows. For multi-species detections or metabarcoding, the workflow is research question; sample collection; laboratory analyses including extraction, PCR and sequencing; bioinformatics; data analyses; and result interpretation. For single-species detections or qPCR, the workflow is research question; sample collection; laboratory analyses including extraction and qPCR; data analyses; and result interpretation.


Figure 2 Environmental DNA workflow for (left column) multi-species detections (metabarcoding); 
and (right column) single-species detections (qPCR)

Sample collection

Environmental DNA samples from the marine 
environment can be collected from sources 
including water, sediment and scat.

Water is the most frequently used substrate 
and can be collected with a range of methods. 
The simplest method, surface water collected 
with a container, is quick, easy, cheap and 
widely used. Water can also be collected from 
different depths and environments by scuba 
divers, or using technologies such as Niskin 
bottles, rosette samplers or remotely operated 
underwater vehicles (ROVs). These approaches 
allow eDNA to be collected from inaccessible or 
remote ecosystems, such as remote seamounts, 
or where direct human sampling is unsafe.

Factors such as water turbidity or species 
richness can influence results; research is 
ongoing into the water volume and number of 
replicates that maximise sampling accuracy and 
precision. Higher water volumes and replicate 
numbers generally yield higher richness, but 
may require more effort and increase cost 
(Bessey et al. 2020, Takahashi et al. 2023).

Once collected, samples need to be processed 
or preserved as soon as possible to reduce 
degradation of DNA (Goldberg et al. 2016). 
While entire water samples can be preserved 
by freezing or adding stabilising buffers 
(Villacorta-Rath & Burrows 2021), it is more 
common to filter water samples soon after 
collection, preserving the resulting filters 
containing DNA. Filtration methods can vary 
according to type of pump, type of filter 
material, or filter pore size. These can be 
adapted to fit survey aims, which should be 
considered during the design phase of any 
eDNA project (Takahashi et al. 2023).

DNA on the filters is still prone to degradation, 
and needs to be preserved to maintain its 
integrity. This can be done via freezing (ideally 
at −80° C), stabilising buffers or desiccation 
(De Brauwer et al. 2022a). Various commercially 
available sampling systems streamline the 
collection process, using a single device to 
collect, filter and preserve samples (e.g. Thomas 
et al. 2019).

Even simpler collection procedures are being 
trialled. One promising, low-cost avenue is 
passive sampling, where filters are directly 
submerged in water, eliminating the need 
to collect or filter water (Bessey et al. 2021, 
2022). The development of autonomous and 
potentially mobile eDNA samplers is another 
highly active research topic. These methods 
greatly reduce workload and might offer a cost-
effective solution for large-scale (temporal and 
geographical) monitoring projects. A range of 
autonomous samplers have been developed: 
from small stationary units that collect and filter 
water in situ, to integrated eDNA sampling units 
within ocean gliders, which sample transects 
at much larger scales (Flanigan et al. 2021, 
Truelove et al. 2022, Hendricks et al. 2023).

Other environmental substrates including 
sediment, stomach contents, scats, bulk 
plankton samples and scrapings of biofouling 
can also be valuable sources of eDNA. 
These substrates can be used to detect larger 
taxa or to address specific questions, such as 
species diet (Deagle et al. 2009, Berry et al. 
2015, Koziol et al. 2019). The choice of sample 
substrate can significantly affect which taxa are 
detected; it is therefore essential to understand 
both the survey objective and the dynamics of 
eDNA substrates in order to design a suitable 
eDNA monitoring method (Koziol et al. 2019, 
Kawakami et al. 2023).

To optimise sample collection, it is essential 
to understand the factors that influence how 
much DNA is present in a sample and where 
it comes from. Often termed ‘the ecology of 
eDNA’, this active field of research studies the 
various factors affecting DNA dynamics in the 
environment (Barnes & Turner 2016, Scriver 
et al. 2023, Kawakami et al. 2023). Research is 
testing how long eDNA can persist in different 
environments and how far it can travel from 
its source, as well as how eDNA signal might 
differ across diurnal or seasonal timescales, and 
between species or life history stages (Harrison 
et al. 2019, Collins et al. 2022, Richards et al. 
2022). This field is advancing rapidly and 
has already shown that the ecology of eDNA 
depends on local environmental factors.

Laboratory analysis

In the laboratory analysis phase, increased 
automatisation of methods is one of the 
biggest advances. Robotics platforms have 
allowed samples to be processed faster, more 
cheaply and more precisely, with less room for 
human error.

The first step of lab processing, the extraction 
of DNA from environmental samples, is 
routinely conducted using commercial kits, 
which offer comparability, quality assurance 
and reduced costs. However, in some cases, 
such as when working with samples from turbid 
environments or from materials like scats, 
custom extraction protocols might be needed 
to make eDNA extraction more efficient.

The subsequent processing of the extracted 
DNA can be broadly categorised by its 
purpose: detecting a single species (such as 
an invasive or threatened species) or detecting 
a community of multiple species (Nagarajan 
et al. 2022).

Targeted single-species detection can be 
conducted using a range of methods, most 
commonly quantitative polymerase chain 
reaction (qPCR) or digital droplet PCR (ddPCR). 



Species-specific assays must be designed 
and tested before targeting single species 
with eDNA methods (Thalinger et al. 2021, 
De Brauwer et al. 2022b), but once these 
assays have been validated, they are faster and 
cheaper than multi-species (metabarcoding) 
approaches. In limited situations and if 
sufficiently ground truthed, they can also 
produce relative abundance estimates (Rourke 
et al. 2021). In some cases, rapid in situ species 
detection can be achieved with new portable 
methods such as lateral flow (dipstick) assays 
or Nanopore MinION technology (Thomas et al. 
2019, Doyle & Uthicke 2021, Egeter et al. 2022).

Detection of species communities requires 
the use of metabarcoding methods. These have 
2 steps:

1. PCR amplification of the extracted DNA 
using primers designed to target a particular 
group of species.

2. High-throughput sequencing (HTS) of 
PCR products.

The primers used in the PCR step determine 
what information can be retrieved from the 
DNA sample (i.e. what group of taxa will be 
recovered and the degree to which species 
can be distinguished from one another). 
The primers bind to specific regions in the 
DNA, allowing for targeted amplification of the 
taxonomic group of interest (e.g. eukaryotes, 
fish, corals, elasmobranchs). A wide range of 
primers have been developed (see Takahashi 
et al. 2023 for a detailed database). The design 
and testing of primers can be time-consuming, 
but is important, as primer performance can 
affect results and needs to be considered 
when interpreting data (Deiner et al. 2017). 
These primer biases also mean metabarcoding 
is less reliable than single-species (qPCR) 
methods for assessing abundance (Deiner et al. 
2017) (see also Data analysis and Abundance).

During the subsequent HTS step, the DNA 
sequences amplified during the PCR phase are 
read and assembled ready for analyses. All the 
DNA sequences amplified by PCR are read 
separately, so the data produced is thousands 
of independent sequences, which can be 
matched back to their biological source.

Several HTS technologies have been used 
in eDNA studies, but most applications use 
Illumina sequencing, which is available at 
commercial laboratories and is ideal for the 
short DNA fragments typically found in eDNA. 
There are several new sequencing technologies 
that can produce longer sequences and, in 
some cases, use smaller sequencing machines 
(MinIon) that could be deployed in the field for 
specialised applications (Egeter et al. 2022).

Bioinformatics

The goal of bioinformatics is to transform 
the outputs of metabarcoding sequencing 
data (which often yields data from millions 
of DNA fragments) into data that is useful 
for biodiversity assessment. The millions of 
DNA sequences vary depending on which 
taxa they came from, so data processing 
involves cleaning data (including removing 
errors introduced during the laboratory 
steps) and assigning sequences to species by 
interrogating DNA sequence reference libraries 
(Mathon et al 2021).

During this stage, choices are made about 
quality control and the method used for 
taxonomic assignment. These decisions can 
impact the final dataset, but raw sequence data 
can be retained and reanalysed if required.

The bioinformatics process is run using 
pipelines of code. These can be custom-made 
for specific projects, but common, publicly 
available pipelines are widely used (Casas 
& Saborido-Rey 2022, Pauvert et al. 2019). 
Bioinformatics workflows are not needed when 
using single-species assays, because each assay 
targets a single taxon (De Brauwer et al. 2022b).

Complete DNA sequence reference libraries 
(also called reference databases) are crucial for 
the accurate assignment of eDNA sequences to 
taxonomic identities. Ideally, reference libraries 



provide DNA sequences from authoritatively 
identified specimens of all relevant 
species. However, the completeness and 
authoritativeness of available DNA reference 
libraries varies substantially depending on 
the taxon of interest (Weigand et al. 2019). 
This is a globally recognised issue, which can 
be resolved by concerted efforts to improve 
reference libraries (Weigand et al. 2019, Yao 
et al. 2022). CSIRO and partners are engaged in 
a major effort to create reference sequences for 
all Australian species, the National Biodiversity 
DNA Library (NBDL).

An alternative to conventional taxonomic 
annotation is to use uniquely recurring DNA 
sequences as a proxy for diversity. These 
sequence variants can be clustered based on 
similarity and are referred to as operational 
taxonomic units (OTUs), molecular operational 
taxonomic units (mOTUs), zero-radius 
operational taxonomic units (zOTUs), or 
amplicon sequence variants (ASVs).

The use of different clustering approaches 
can affect result interpretation (Pauvert et al. 
2019, Brandt et al. 2021). For non-experts, it 
is important to understand that while these 
non-taxonomic metrics can provide valuable 
insights on the diversity of a system, they are 
not an exact proxy for individual species, as 
intraspecific genetic variation can result in 
multiple OTUs per species and some recently 
separated species can share the same OTU 
(Blackman et al. 2023). Furthermore, it 
might not be possible to ascribe functional 
contributions to OTUs or ASVs.

Data analysis

The data analysis options for eDNA methods 
depend on whether qPCR (single-species, 
semi‑quantitative) or metabarcoding 
(multi-species, rarely quantitative) approaches 
were used in the lab. Surveys using qPCR 
methods can result in presence/absence or 
semi-quantitative data, depending on the 
level of calibration of specific workflows 
(Thalinger et al. 2021). These data can then be 
analysed as conventional single‑species data to 
directly inform management needs.

Metabarcoding data provides information on 
the number of DNA sequences recovered from 
each taxon in each sample, but data is almost 
always converted to presence/absence due to 
biases in sequence recovery. In some instances, 
however, where sampling effort was sufficiently 
extensive, inferences can be made about the 
abundance of species (e.g. common species 
tend to be present in more samples than 
rare species).

This is a developing field of research where a 
variety of analytical approaches are increasingly 
applied to provide more relevant ecological 
information (see Analytical improvements). 
Furthermore, presence/absence data is 
sufficient for some uses such as biotic indices 
(Beentjes et al. 2018, see Applied research). 
Examples of novel analytical approaches that 
use metabarcoding data include multi‑species 
occupancy models (e.g. McClenaghan et al. 
2020, Holmes et al. 2022) and network analysis 
methods (e.g. DiBattista et al. 2020, Djurhuus 
et al. 2020). These methods can make it 
possible to infer broad ecological trends 
without the need for abundance data, but often 
need higher replication levels and rigorous 
experimental design (Ficetola et al. 2015, 
Fukaya et al. 2022).

Metabarcoding data can be analysed using 
taxonomic information (i.e. comparing 
identities of species or other taxa), but this 
approach can be limiting when incomplete 
taxonomic reference databases yield 
poor resolution (i.e. a small percentage of 
sequences can be assigned to known taxa). 
Analysing recurring genetic sequences 
(e.g. ASVs, OTUs) as species-equivalent 
units maximises the use of available genetic 
information without the need to assign all 
sequences to a taxonomic level.



This approach has benefits when studying 
ecosystems as high-level ecological 
assemblages. Compared with conventional 
methods, it allows researchers to use much 
more biological data, such as for groups where 
taxonomy is less resolved (including microbial 
communities, small-bodied invertebrates and 
cryptic fish species). As it does not rely on 
taxonomic expertise or visual observations, 
this approach eliminates common biases 
towards charismatic and highly visible species, 
providing insights that might be missed with 
other methods. However, OTUs are not easily 
transferable between eDNA studies, nor easily 
combined with other observation data, which 
can limit spatial comparisons or long-term 
temporal studies.

Applications

Single-species assays

In the marine environment, eDNA-based 
methods have had a variety of monitoring 
and research applications (Gilbey et al. 2021). 
Single-species analyses have mainly been 
applied in biosecurity and the detection of TEP 
species. Globally and in Australia, there are 
well-developed surveillance programs for pest 
species, including invasive and native nuisance 
species (see Box 2; McDonald et al. 2019, Bolte 
et al. 2021, Uthicke et al. 2022). Indeed, the first 
published paper to use eDNA methods (Ficetola 
et al. 2008), aimed to detect invasive bullfrogs 
in Europe. Surveys using qPCR methods have 
been applied to the detection of TEP species 
including sharks, seahorses and cetaceans in 
Australia and across the world (Simpfendorfer 
et al. 2016, Nester et al. 2020, West et al. 2021).

Metabarcoding

Multi-species (metabarcoding) methods have a 
wider range of applications than single‑species 
methods. The ability to survey a wide range 
of taxa using a single sample has given rise to 
so-called ‘tree of life’ metabarcoding, where 
marine taxa ranging from protozoans and 
plants to corals, fishes and crustaceans can 
be detected from a single sample (Stat et al. 
2017). In monitoring, these methods allow 
the study of changes in species assemblages 
over time (Berry et al. 2019, Chrismas et al. 
2023), between habitats, across large and 
small spatial scales (West et al. 2020, 2021, 
DiBattista et al. 2022) and across human 
impacts gradients (DiBattista et al. 2020), or to 
inform spatial planning decisions (Bani et al. 
2020). A wide body of literature addresses how 
eDNA metabarcoding methods differ from 
and complement conventional monitoring 
methods. Reviews indicate that eDNA 
metabarcoding generally shows similar results, 
but detects slightly different aspects of species 
assemblages, with eDNA methods more likely 
to detect small, rare, or cryptic species than 
conventional methods (Richards et al. 2022). 
This suggests eDNA metabarcoding surveys can 
complement conventional surveys (Gilbey et al. 
2021, Guri et al. 2023).

Indices of environmental health

There is growing interest in the development 
of biotic indices of ecosystem health 
(Pawlowski et al. 2022, DiBattista et al. 
2020). Conventional biotic indices are based 
on visual observations and rely heavily on 
dwindling taxonomic expertise, and getting 
results can be time‑consuming (Borja et al. 
2000, Pawlowski et al. 2018). Incorporating 
eDNA methods into biotic indices allows 
for a wider range of taxa to be detected 
without the need for extensive morphological 
identification. If designed correctly, such 
molecular indices do not need abundance data 
to be accurate (Beentjes et al. 2018). Examples 
from New Zealand and Norway show that 
such eDNA indices are quicker, cheaper and 
more efficient in detecting anthropogenic 
pressures than morphometric approaches 
(Lanzén et al. 2021, Pochon et al. 2015). 
These indices are incorporated into routine 
monitoring, such as monitoring of the benthic 
impacts of salmon farming practices in New 
Zealand (Pochon et al. 2019).



Alternative molecular indices, such as 
taxonomy-free indices or indices developed 
through supervised machine learning, are being 
trialled globally. Promisingly, these indices 
can use a much broader range of available 
DNA sequences associated with differently 
impacted ecosystems (Cordier et al. 2017, 
Apothéloz‑Perret-Gentil et al. 2017, Wilkinson 
et al. 2023).

Microbial communities

The Australian Microbiome project, a 
collaboration between Parks Australia, 
IMOS, Bioplatforms Australia and CSIRO, 
has developed standardised methods for the 
collection, processing and analysis of samples 
and baseline data on microbial communities 
across the Australian continent and 
surrounding oceans (Bissett et al. 2016, Brown 
et al. 2018). A core dataset within the Australian 
Microbiome project is the long-term timeseries 
data from Australia’s IMOS, which has been 
using microbial eDNA technology since 2012 
to deliver microbial community observations 
in the marine environment at national scale. 
These observations were used to assess 
marine microbial communities in the marine 
chapter of the 2021 State of the Environment 
Report (Brown et al. 2018, Brown & Bodrossy, 
2021). Combining data from the Australian 
Microbiome project and macro-organismal 
eDNA has the potential to provide valuable 
information about, for example, the base of 
the marine food chain. It could also be used to 
develop comprehensive environmental indices 
for marine parks (Berry et al. 2023).

Fisheries management applications

The practical applications of eDNA methods 
in fisheries management are becoming 
increasingly clear, and have received extensive 
attention in the literature (Jerde 2021, Gilbey 
et al. 2021). In particular, eDNA methods can 
be used where focal species are hard to survey 
using conventional methods (e.g. rare or 
invasive species), or where extractive methods 
are not desirable (e.g. threatened species) 
(Nester et al. 2023). Environmental DNA 
methods can also help managers understand 
important stages in the life cycle of target 
species by detecting spawning aggregations, 
or characterise feeding preferences (Takahashi 
et al. 2020, Holmes et al. 2022). There are 
promising applications under development in 
post-catch compliance, such as detecting catch 
composition, biosecurity threats and illegal 
catches in the live fish trade (Green et al. 2021, 
Maiello et al. 2022, Urban et al. 2022).

Metrics such as abundance, biomass and 
target species’ condition are vital to fisheries 
management, but cannot yet be measured 
reliably with eDNA methods (see Abundance). 
Improving the understanding of how relative 
abundance metrics from eDNA surveys 
correlate with abundance from catch data is 
a highly active field of research and in some 
cases, estimates are strongly correlated 
(Rourke et al. 2021). In Australia, eDNA surveys 
are already being applied in freshwater fish 
monitoring (e.g. by the New South Wales 
Department of Primary Industries), but formal 
integration in the marine environment 
remains limited.

Historical environmental change

Environmental DNA methods, particularly 
metabarcoding, are also being used in 
paleogenomics. This field uses ancient DNA, 
often extracted from sediment cores, to study 
how past marine communities changed over 
large temporal scales (Capo et al. 2021). While it 
is possible to study communities as far back as 
2 million years (Kjær et al. 2022), reconstructing 
more recent community baselines to study 
historical and current impacts on marine 
ecosystems has more direct relevance to 
resource managers (Shaw et al. 2019, Siano 
et al. 2021, Williams et al. 2023).



Australian eDNA 
research community

Australia has strong and increasing capacity 
to deliver eDNA research and monitoring 
activities. Australian researchers have been 
a central part of the eDNA revolution and 
Australia has a strong expertise in eDNA 
research. The national eDNA community 
continues to produce groundbreaking 
research and is at the leading edge of 
many developments in the field. In the past 
10 years, publications such as Furlan et al. 
2016, Stat et al. 2017, DiBattista et al. 2020 
and many others have set the standards in 
the field for quality control, metabarcoding 
applications and ecological inference. At the 
time of writing, Australia has an estimated 45 
laboratories and sequencing facilities active in 
the broader field of environmental genomics 
(marine and terrestrial).

The Southern eDNA Society (SeDNAS), 
the official eDNA society for Australia and 
New Zealand, was formally established in 
2023. SeDNAS aims to promote science and 
industry collaboration, promote adoption 
and advance best practice eDNA methods. 
It will connect researchers and end users, 
lead the establishment of best practice, and 
be an important source of advice on future 
developments in the field.

The recently published Best practice guidelines 
for environmental DNA biomonitoring in 
Australia and New Zealand (De Brauwer et al. 
2023) were created by SeDNAS and partner 
institutions, with the support of the Australian 
Government Department of Agriculture, 
Fisheries, and Forestry. The guidelines outline 
minimum standard considerations for eDNA 
surveys across the complete project workflow 
(De Brauwer et al. 2023).

Understanding marine 
park management

Australia’s exclusive economic zone (EEZ) has 
more than 160 marine parks, which represent 
a wide diversity of ecosystems ranging 
from tropical coral reefs to sub-Antarctic 
sea canyons. Successful monitoring and 
management are vital to the conservation and 
sustainable use of the marine environment. 
Management of marine parks is a key 
component of management of Australia’s 
marine estate.

Marine parks in Australia

Australia has one of the world’s largest marine 
estates and a large network of marine parks. 
This network includes a national network of 
Commonwealth parks, known as Australian 
Marine Parks, and other marine park 
networks in different jurisdictions (Table 1). 
Combined, there are more than 160 marine 
parks in Australia’s EEZ, covering a combined 
area of more than 4 million km2. They are 
home to multiple global biodiversity hotspots 
and some of the world’s highest marine 
biodiversity. Australia’s marine environment 
is expected to contribute up to $105 billion 
per year to GDP by 2025 through ecosystem 
services ranging from food provisioning and 
resource extraction to recreation, cultural 
values, shipping and defence (AIMS 2023, 
NMSC 2015, 2021).



Australian Marine Parks

The Australian Marine Parks were first 
proclaimed under the Environment Protection 
and Biodiversity Conservation Act 1999 (EPBC 
Act) in 2007 and revised in 2018. The parks 
are generally established in waters 3 nautical 
miles (5.5 km) from the shore up to the end of 
Australia’s EEZ, 200 nautical miles (370.4 km) 
from shore. There are currently 60 parks, 
which are organised in 5 regional networks 
(North, North-West, South-west, South-east, 
Temperate East), as well as the Coral Sea Marine 
Park and the Indian Ocean Territories (Figure 3). 
Combined, the Australian Marine Parks span 
more than 3.3 million km2, making the network 
one of the largest marine park networks 
globally. The smallest park is 4 km2 and the 
largest is 989,842 km2. The parks stretch from 
the tropics to the sub-Antarctic and contain a 
variety of marine habitats ranging from coral 
reefs and shallow sand-cays to deep canyons 
and sea mounts more than 6 km deep.

The Australian Marine Parks are managed 
centrally by the Marine and Island Parks Branch 
within Parks Australia in the Department of 
Climate Change, Energy, the Environment and 
Water (DCCEEW). Management of the parks is 
based on 2 objectives:

• Protection and conservation of biodiversity 
and other natural, cultural and heritage 
values of marine parks.

• Ecologically sustainable use and enjoyment 
of the natural resources within marine parks, 
where this is consistent with first objective.

The parks are designed as multiple-use parks, 
with specific zonation allowing a range of 
activities such as resource extraction, research, 
shipping and recreation. Specific no-take zones 
are also included within this zonation design. 
Parks Australia uses an adaptive management 
and evidence-based approach. It works closely 
with a range of other regulators, partners and 
stakeholders, including the Australian Marine 
Park Advisory Committees. The Marine and 
Island Parks Branch does not have internal 
monitoring capability, and monitoring is 
therefore outsourced through a system 
of grants and collaborations with science 
partners (e.g. NESP) and marine parks staff in 
other jurisdictions.

Table 1 Overview of marine parks in Australia

Component

Type of marine park

Australian 
Marine Parks

Heard & McDonald 
Islands Marine Reserve

Great Barrier 
Reef Marine Park

State and 
territory 
marine parks

Jurisdiction

Australian 
Government

Australian Government

Australian 
Government 
and Queensland 
Government

State and 
territory 
governments

Management 
agency

Parks Australia

Australian Antarctic 
Division

Great Barrier 
Reef Marine Park 
Authority

Different 
management 
agencies

Location

National: more 
than 3 nautical 
miles offshore

Heard & McDonald 
Islands

Queensland

Coastal waters: 
up to 3 nautical 
miles offshore



Map showing Australian Marine Parks around Australia, which include the Coral Sea Marine Park off Queensland; the Temperate East Network off New South Wales; the South-east Network off New South Wales, Victoria, Tasmania, Macquarie Island and South Australia; the South-west Network off South Australia and Western Australia; the North-west Network off Western Australia; the North Network off the Northern Territory and Queensland; and Indian Ocean Territories around Cocos, Keeling and Christmas Islands.
© Commonwealth of Australia, 2023


Figure 3 Map of Australian Marine Parks



Heard and McDonald Islands

The remote, uninhabited Heard and McDonald 
Islands are an external territory of the 
Commonwealth of Australia and consist of 
a 71,000 km2 large reserve, which is mainly 
marine. The Heard Island and McDonald 
Islands (HIMI) Marine Reserve hosts unique 
sub-Antarctic and Antarctic marine life of high 
conservation value. The entire reserve is a 
Category 1a Strict Nature Reserve, which means 
any extractive activities are prohibited and 
other uses are strictly controlled. As an external 
territory, the HIMI reserve is not part of the 
Australian Marine Parks; instead, it is managed 
by the Australian Antarctic Division (AAD) 
in collaboration with various stakeholders, 
including the Australian Border Force, the 
Australian Fisheries Management Authority and 
the Australian Marine Safety Authority.

Great Barrier Reef Marine Park

The Great Barrier Reef Marine Park (GBRMP) 
is one of Australia’s oldest marine protected 
areas. Established in 1975, the GBRMP spans 
344,440 km2 and is Australia’s best known 
marine park. The Great Barrier Reef (GBR) is 
a world heritage area and the world’s largest 
coral reef ecosystem. The park attracts tourism 
to Queensland and Australia, has cultural value 
for Traditional Owners and supports a fishing 
and aquaculture industry. Through its various 
direct and indirect ecosystem services, the total 
economic value of the GBR has been estimated 
to exceed $56 billion per year (Deloitte Access 
Economics 2017).

The GBRMP is also a Commonwealth park, 
but it is managed by the Great Barrier 
Reef Marine Park Authority (GBRMPA), an 
Australia Government agency that is part 
of DCCEEW. GBRMPA works closely with 
different stakeholders to manage the park, 
and currently uses a long-term sustainability 
plan as a framework to guide its management 
practices. The GBRMP is divided into different 
use zones with specific priorities and rules. 
Monitoring in the GBRMP is conducted 
by a range of stakeholders following the 
Reef 2050 Integrated Monitoring and 
Reporting Program (RIMReP).

State and territory marine parks

All Australian states and territories that border 
the ocean have marine parks. However, there 
are large jurisdictional differences in the 
number of parks, the area covered, zoning 
arrangements, and management priorities and 
approaches. State parks generally run from the 
high tide line up to 5.5 km (3 nautical miles) 
from shore. An estimated 98 state parks or 
reserves have been declared, covering more 
than 95,000 km2. The size of individual parks 
ranges from less than 1 km2 to 18,450 km2, 
with a median size of 673 km2. State and 
territory parks are coastal, and compared to 
parks managed by the Australian Government, 
the ecosystems represented in state parks 
more commonly include shallow habitats 
such as beaches, estuaries, mangroves and 
shallow reefs.

Management and monitoring approaches 
differ markedly between states and territories. 
Multiple state and territory governments have 
departments responsible for managing parks, 
which typically includes marine parks. In some 
states, however, marine park management 
is the responsibility of fisheries or primary 
industry departments.

State parks are typically smaller than those 
managed by the Australian Government, and 
see more recreational use. This is reflected in 
stronger interactions with stakeholders such 
as Traditional Owners, recreational fishers and 
tourism operators. Increasingly, state parks 
are co-managed by Traditional Owner groups, 
as is the case with the recently established 
Bardi Jawi Gaarra and Lalanggaddam marine 
parks in Western Australia (DBCA 2022a,b). 
Most state parks also consist of multi-use 
zones, but there is a stronger emphasis on the 
use of no-take zones than in Commonwealth 
marine parks. These no-take zones can be 
integrated within parks or, in some states, can 
be entirely separate parks, often called reserves 
or sanctuary zones.

Stakeholders in marine parks

Australia’s marine parks are used by a range 
of stakeholders (Table 2). Many stakeholders 
contribute directly or indirectly to monitoring 
or have strong interests in its outcomes and 
the resulting management actions. While state 
and Commonwealth marine parks are managed 
separately, many stakeholders are common 
to both.

Stakeholders active in the Australian marine 
environment include government agencies, 
industry bodies, Traditional Owner groups 
and research organisations. The nature and 
relevance of monitoring and the potential 
applications of eDNA methods vary greatly 
between stakeholders. Certain bodies are 
already using eDNA methods or planning 
to increase their use (e.g. biosecurity 
departments; McDonald et al. 2019), while 
eDNA methods might not be relevant to other 
agencies for the foreseeable future (e.g. marine 
heritage groups). The level of integration of 
monitoring activities between stakeholders 
and parks management likewise differs 
considerably. The activities of monitoring 
bodies can be closely aligned with the marine 
parks they take place in, but monitoring or 
research results do not always feed back into 
management practices.



Table 2 Stakeholders active in Australia’s marine parks and their monitoring roles

Agency

Type

Role

Monitoring 
capability

Parks Australia

Parks 
management 
agency

Manage Australia’s Commonwealth 
Marine Parks

Commissions 
monitoring

Great Barrier Reef 
Marine Park Authority

Parks 
management 
agency

Manage the Great Barrier Reef Marine 
Park

In-house 
capability

Commissions 
monitoring

State parks agencies

Parks 
management 
agency

Manage state marine parks

In-house 
capability

Commissions 
monitoring

State fisheries agencies 
and

primary industries 
agencies

Government 
agency

Manage state-based fisheries 
(e.g. Western Australian Department 
of Primary Industries and Regional 
Development, South Australian 
Research and Development Institute, 
New South Wales Department of 
Primary Industries)

In-house 
capability

Australian Fisheries 
Management Authority

Government 
agency

Manage Commonwealth fisheries

Commissions 
monitoring

Australian Maritime 
Safety Authority

Government 
agency

Oversee maritime safety, protect the 
marine environment and operate 
maritime aviation search and rescue

Commissions 
monitoring

Biosecurity departments

Government 
agency

Monitor and respond to biosecurity 
threats

In-house 
capability

Commissions 
monitoring

Environmental 
Protection Agencies

Government 
agency

Protect, restore and enhance the 
environment through the regulation of 
pollution, waste, noise and radiation

Variable

Australian Antarctic 
Division

Government 
agency: 
research 
organisation

Coordinate Australia’s activities in 
Antarctica, from scientific research 
through to logistics and transport

In-house 
capability

Commissions 
monitoring







Agency

Type

Role

Monitoring 
capability

Australian Institute of 
Marine Science

Government 
agency: 
research 
organisation

Australia’s tropical marine research 
agency: conduct research

Supplies 
capability

CSIRO

Government 
agency: 
research 
organisation

Australia’s national science research 
agency: conduct research

Supplies 
capability

National Environmental 
Science Program

Government 
agency: 
research 
funding body

Fund research

Supplies 
capability

Integrated Marine 
Observing System

Research 
organisation

Provide open access marine 
observation data

Supplies 
capability

Universities

Research 
organisation

Conduct research

Supplies 
capability

Industry research 
organisations 
(e.g. Western Australian 
Marine Science 
Institution)

Research 
organisation

Industry body

Investigate and inform governments, 
industry and the wider community 
about the management of specific 
industries

In-house 
capability

Fisheries Research 
and Development 
Corporation

Industry body

Research 
funding body

Manage research and development 
investment by the Australian 
Government and the Australian fishing 
and aquaculture sectors

Supplies 
capability

Australian Petroleum 
Production & 
Exploration Association

Industry body

Represent the interests of the oil and 
gas industry

No monitoring

Clean Energy Council

Industry body

Represent the interests of companies 
that work in or support the clean 
energy sector

No monitoring

Commercial shipping 
bodies

(e.g. Shipping Australia 
Limited, Australian Peak 
Shippers Association)

Industry body

Represent the interests of shipowners, 
shippers, and shipping agents

No monitoring







Agency

Type

Role

Monitoring 
capability

National Offshore 
Petroleum Safety 
and Environmental 
Management Authority

Industry body

Regulate health and safety, well 
integrity, and environmental 
management for all oil and gas 
operations, offshore renewable 
infrastructure and greenhouse gas 
storage activities

No monitoring

Ports Australia

Industry body

Represent the port sector and 
associated maritime services

Commissions 
monitoring

Recreational fishing 
bodies
(e.g. OzFish, 
RecFishWest)

Industry body

Represent recreational fishers’ 
interests

Commissions 
monitoring

Tourism bodies
(e.g. Association of 
Marine Park Tourism 
Operators, Tourism 
Australia)

Industry body

Represent tourism industry interests

No monitoring

Scientific organisations
(e.g. Australian Coral 
Reef Society, Australian 
Marine Science 
Association, Australian 
Society for Fish Biology)

Industry body

Represent research fields active in 
Australia’s marine estate

Supplies 
capability

Seafood industry 
associations 
(e.g. Commonwealth 
Fisheries Association, 
Seafood Industry 
Australia, Seafood 
Industry Victoria)

Industry body

Represent fishery, aquaculture and 
seafood industry interests

No monitoring

Traditional Owner 
groups

Private

Represent the interests of Traditional 
Owners

Variable

The Minderoo 
Foundation

Philanthropic 
research 
organisation

Conduct research and promote marine 
conservation activities

In-house 
capability







Agency

Type

Role

Monitoring 
capability

Conservation 
organisations
(e.g. Australian Marine 
Science Conservation 
Society, Surfrider 
Foundation)

NGOs

Promote ocean conservation

Variable

Limited current relevance for eDNA methods

Geosciences Australia

Government 
agency
Research 
organisation

Conduct geoscientific research, 
provide technical geoscience advice 
and act as custodian of geographic 
and geological data and knowledge

Supplies 
capability

Australian Border Force

Government 
agency

Protect Australia’s border and enable 
legitimate travel and trade

N/A

Australian Defence 
Force

Government 
agency

Defend the Commonwealth of 
Australia and its national interests

N/A

Maritime Heritage 
organisations

Government 
agency

Manage and protect marine heritage 
and their associated artefacts

N/A

DCCEEW Underwater 
Cultural Heritage

Government 
agency

Manage and protect underwater 
heritage and their associated artefacts

N/A







Marine park monitoring 
priorities

Biodiversity monitoring principles

Successful resource management relies on 
realistic predictions about future conditions, 
which in turn requires a clear understanding 
of past and current states. To achieve such 
understanding, well-designed monitoring and 
research programs are essential. Monitoring 
is defined as the systematic collection 
of data over time to detect changes in a 
system (Gerber et al. 2005) and can include 
information on a range of factors, including 
environmental (e.g. temperature), ecological 
(e.g. species abundance), biological (e.g. health 
of organisms), social (e.g. visitor rates) and 
economic (e.g. ecosystem value). Monitoring of 
physical and chemical environmental data, and 
socioeconomic data are beyond the scope of 
this roadmap.

Scientific activities in marine parks extend 
beyond typical monitoring-only surveys and 
include a range of applied research programs. 
Applied research directly relevant to the 
management of marine parks mainly focuses 
on the characterisation of marine communities 
(i.e. biodiversity surveys) for purposes such as 
establishing baselines or approving permits for 
activities in marine parks. The suggestions in 
this roadmap are equally applicable to these 
applied research activities as to the more 
typical mandated monitoring programs.

For monitoring to be successful in the 
long term, it needs to be well designed 
with clear priorities (Hedge et al. 2022). 
Monitoring priorities are set by management 
and policy makers, who often commission 
external stakeholders to undertake the 
actual monitoring. In other cases, external 
stakeholders conduct their own question-driven 
monitoring or applied research, with results fed 
back to management indirectly.

Many marine parks are moving towards 
an adaptive management approach, which 
integrates program design, management and 
monitoring and allows systematic testing of 
assumptions. The exact application of this 
framework varies between parks, and the 
variables being monitored differ depending on 
each park’s nature, use and current pressures.

Priorities in federally managed 
marine parks

To manage the Australian Marine Parks 
(Commonwealth) network, Parks Australia 
uses an adaptive management approach based 
on a monitoring and evaluation framework 
(Figure 4) and informed by targeted monitoring 
and applied research programs. 

Diagram showing the Adaptive management cycles in Australian Marine Parks, with 1 Scope, 2 Plan, 3 Do, 4 Evaluate, and 5 Report and improve.

Figure 4 Adaptive management cycles 
in Australian Marine Parks

This framework aims to address the most 
pressing management issues and questions and 
increase the effectiveness of park management 
(Hayes et al. 2021). Science plays a critical role 
in each step of the adaptive management cycle. 
The marine science program also underpins 
Parks Australia’s management effectiveness 
approach, which helps measure implementation 
of management strategies, evaluate 
effectiveness and identify opportunities for 
improvement. Within this framework, the 
monitoring cycle uses a standardised approach 
(Hayes et al. 2021).

In the Heard and McDonald Islands, monitoring 
objectives are written into the general 
management plan and aim to increase baseline 
knowledge, assess impacts and changes in the 
reserve’s ecosystems, and inform management 
decisions (DOE 2014). A recently released eDNA 
biosecurity framework outlines how eDNA 
methods can be used to monitor biosecurity 
threats to the Heard and McDonald Islands and 
other Antarctic regions (Clarke et al. 2023).

Monitoring in the GBRMP is directed and 
managed by the GBRMPA through RIMReP, 
which is part of the strategic Reef 2050 
Long‑Term Sustainability Plan (Commonwealth 
of Australia 2015, GBRMPA & Queensland 
Government 2015). RIMPReP aims to measure 
the condition and trends of key values in the 
park; inform the evaluation of management 
effectiveness; and inform stakeholders of 
progress relative to the Reef 2050 Plan 
(GBRMPA & Queensland Government 2015). 
As part of RIMReP, the Great Barrier Reef 
Outlook Report is published every 5 years, 
most recently in 2019. These reports present:

• the current state of key park 
environmental values

• threats, management responses, 
resilience and risk

• the long-term outlook for the 
GBR Marine Park.

Monitoring priorities within RIMReP include 
specific habitats such as coral reefs and 
mangrove forests, as well as population 
dynamics of taxa such as bony fishes, 
seagrasses and dugongs (GBRMPA 2019).

Priorities in state and territory 
marine parks

State and territory management bodies set 
monitoring priorities for their marine parks. 
These can be detailed and prescriptive, as is 
the case for New South Wales, which recently 
established a new Integrated monitoring and 
evaluation framework for the Marine Integrated 
Monitoring Program (MIMP). This framework, 
similar to RIMReP, was co‑designed with key 
stakeholders and is managed by the New 
South Wales Department of Primary Industries. 
The program’s aims are to monitor the 
condition of the environmental assets and the 
community benefits from these; evaluate the 
effectiveness of management initiatives and 
actions; and fill knowledge gaps in the parks. 
MIMP has specific monitoring indicators that 
inform a 5-year health check, which will be 
reported publicly.

The Department of Biodiversity, Conservation 
and Attractions (DBCA) in Western Australia 
uses a different approach to address similar 
monitoring goals. DBCA has individual 
management plans for each of its marine parks, 
but a coordinated framework that considers 
all marine reserves as a part of a network. 
Monitoring evaluates park-specific KPIs, with a 
monitoring prioritised based on a framework 
designed by Simpson et al. 2015. Monitoring 
activities are further influenced by factors 
such as the natural variability in ecological 
values, current conditions and trends, existing 
pressures on ecological values and the 
availability of internal expertise.

South Australia’s marine park network was 
proclaimed in 2012 and a 10-year evaluation 
of the marine program is currently underway. 
Marine park management plans include a 
monitoring, evaluation and reporting (MER) 
component that describes how to assess 
whether the park is achieving the aims of the 
Marine Parks Act 2007.



The Marine Science Team (within the 
Department for Environment and Water) 
implements the MER program, which focuses 
on 6 questions that evaluate conservation 
outcomes, ecological processes, management 
effectiveness, public engagement and cultural 
heritage. The individual management plans for 
South Australia’s marine parks use the same 
strategies that are applied to the network, but 
each focuses implementation on local needs 
and capacity. Monitoring predominantly occurs 
in sanctuary zones and comparison sites.

Parks Victoria has adopted an adaptive 
management framework and conservation 
planning process to manage natural assets and 
threats to marine parks. Challenges include 
limited baseline knowledge and addressing 
practical management questions. Parks Victoria 
uses its Signs of Healthy Parks (SHP) program 
to monitor the health of marine protected 
areas and inform management (Ierodiaconou 
et al. 2022). The SHP monitoring program 
uses environmental indicators of natural 
values and ecological processes, as well as 
potential threats within the parks. Indicators for 
marine ecosystems and key habitats in parks 
are outlined under the SHP program, with 
monitoring activities focusing on key ecological 
attributes and threats within at least one 
marine park with each bioregion in the state.

Among all Australian states, Tasmania has the 
lowest proportion of marine parks (1.1% of 
state waters). Tasmania’s marine parks do not 
have official monitoring programs or published 
management priorities, and there are no active 
marine parks management activities in place. 
Monitoring occurs solely through research 
initiatives of parks stakeholders (e.g. Reef Life 
Survey), without a formal government strategy.

Marine parks in Queensland are divided into 
2 management units: the GBRMP, managed 
by the GBRMPA (see above), and state marine 
parks, which are managed by the Queensland 
Government Department of Environment and 
Science. The department is working towards 
an improved framework based on monitoring, 
evaluation, reporting and improvement 
principles, which will complement current 
zoning plan reviews. Monitoring programs in 
Queensland’s state marine parks are primarily 
set through a risk-based approach, with 
monitoring focused on vulnerable habitats 
(e.g. seagrass, coral), threatened species 
(e.g. turtles, dugongs, grey nurse sharks, 
migratory shorebirds), and areas of high and 
competing uses.

The context for marine parks in the Northern 
Territory is strongly shaped by Traditional 
Owner stakeholders. Indigenous peoples own 
more than 78% of the Territory’s coastline, 
including the waters that overlay them. 
This is recognised in the Coastal and marine 
management strategy 2019–2029, which 
outlines a 10-year vision for managing and 
protecting the territory’s marine environment. 
The strategy aims to enable activities 
that address knowledge gaps by building 
on existing monitoring initiatives while 
maximising participation from stakeholders. 
Of the 5 high‑level objectives in the strategy, 
objectives 2 (‘Safeguard our coasts and 
seas’) and 5 (‘Build our knowledge’) are most 
relevant to monitoring programs. These 
objectives include actions such as developing 
and implementing an integrated monitoring 
program; identifying knowledge gaps and 
research priorities to support decision-making; 
and improving knowledge about key ecological 
processes, impacts and threats.

Regulatory monitoring needs

In addition to the priorities set by marine park 
management bodies, the different regulatory 
stakeholders active in parks may have specific 
monitoring needs (Table 2). For example, 
resource industries conduct environmental 
baseline surveys prior to starting activities 
and are regulated by the National Offshore 
Petroleum Safety and Environmental 
Management Authority (NOPSEMA); the 
Australian Fisheries Management Authority 



regulates fisheries and has strong interest in 
the abundance and condition of target species; 
and biosecurity departments closely monitor 
incursions of invasive pests (Table 2).

Despite the differences in priorities and 
management approaches, stakeholders in 
Australia’s state and Commonwealth marine 
parks share 4 general monitoring goals:

• Provide baseline data, including through 
applied research programs, to fill 
knowledge gaps (e.g. characterising 
marine communities, effective regulation 
of activities).

• Measure the current condition of natural 
values such as ecosystems, ecosystem 
components and species.

• Monitor changes in environmental 
values over time in response to 
management actions, human impacts 
and natural fluctuations.

• Report results to inform management 
and stakeholders.

The natural values or assets that are monitored 
differ between parks according to local 
ecosystem-dependent variation. Frequently, 
monitoring programs focus on:

• key species that sustain ecosystem 
functioning (e.g. habitat-forming species, 
key invertebrate communities)

• threatened species (e.g. handfish, skates)

• charismatic species (e.g. turtles, whales)

• pest species (introduced and native)

• harvested species (commercially and 
recreationally).

Monitoring of these natural values can measure 
a range of variables or indicators depending on 
the type of value, its function, known impacts, 
and so on. Commonly measured variables are:

• species diversity

• species abundance

• percent cover (sessile organisms)

• organism size or size distribution across 
populations

• patchiness or fragmentation.

Marine park monitoring 
strategies

Monitoring programs in marine parks measure 
a wide range of ecosystem characteristics 
relevant to management priorities, requiring 
a broad range of expertise and techniques 
(DCCEEW 2022, Hedge et al. 2022). Monitoring 
often includes non-biological metrics such 
physical (e.g. temperature, wave height), 
chemical (e.g. pH, salinity), and geological 
metrics (e.g. depth, benthic structure). Here, 
however, we focus solely on strategies used to 
monitor biological and ecological metrics, that 
is, ‘biomonitoring’.

Metrics

Monitoring strategies vary according to 
site‑specific priorities, but most aim to measure 
trends in the status of species and ecosystems 
of interest. Commonly used metrics include the 
abundance of mobile species or percent cover 
for benthic, habitat-forming species such as 
corals or macro-algae. Data on biological or 
physiological characteristics (e.g. size, weight, 
disease status) are also frequently collected. 
Budgetary and logistical considerations mean 
that monitoring efforts usually focus either on 
recognised keystone species or species that are 
of importance to managers or stakeholders, 
such as TEP species and charismatic or easily 
detected macro-organisms. For these reasons, 
small, cryptic species in remote or hard-to-
access locations are monitored less frequently.

Methods

Marine park managers use a variety of 
established methods to achieve their 
monitoring objectives. While managers 
recognise that innovative methods can offer 
considerable benefits, budgetary restrictions 
may leave limited room for experimentation. 
At present, monitoring strategies across 
Australia most commonly rely on visual, indirect 
or collection-based methods (e.g. Bryars et al. 
2017, Ierodiaconou et al. 2022). Commonly 
used methods include direct observational 



techniques (e.g. underwater visual census 
[UVC], photo-quadrats, manta tows), video 
methods (e.g. baited remote underwater 
video [BRUV], diver operated video [DOV], 
ROV), remote sensing, sediment grabs and 
multibeam sonar (Przeslawski & Foster 2020, 
Young et al. 2022). The use of well-established 
methods facilitates data inter-operability. 
For example, the NESP field manuals 
allow for improved spatial and temporal 
comparisons to support management decisions 
(Przeslawski & Foster 2020).

Capacity and implementation

Which organisation carries out monitoring 
depends on the location and aim of monitoring 
programs. None of Australia’s marine park 
agencies rely solely on in-house monitoring 
capacity. Complementary monitoring data is 
frequently sourced from external agencies or 
stakeholders to support management (Table 2). 
For example, Parks Australia, which manages 
Australia’s largest marine parks network, does 
not have in-house monitoring capacity and 
commissions its monitoring activities.

Regions differ in the types and number 
of science partners and stakeholders, 
methodological approach and the level of 
monitoring input provided. There is a wide 
spectrum of involvement with external 
organisations. For example, in Tasmania, 
monitoring is designed and conducted wholly 
by independent external partners, whereas 
Western Australia and New South Wales 
both have centrally coordinated regional 
monitoring teams.

However, even parks with strong internal 
monitoring capacity often collaborate with 
local stakeholders. Compared to the larger 
Australian Marine Parks, state parks tend to 
involve local stakeholders (e.g. universities, 
Traditional Owner groups, citizen scientists) 
more directly due to their proximity to the 
coastline (e.g. Scholz et al. 2017, Browne et al. 
2018, Northern Territory Government 2019, 
DBCA 2022a,b). Parks Australia does work more 
closely with Traditional Owners in the North 
network, and is set to begin an Indigenous 
science program for the Australian Marine 
Parks. Collaboration with Traditional Owners 
is evolving from solely employing people 
as park rangers towards co-management 
(DBCA 2022a,b). While larger networks such 
as the GBRMP still work closely with small 
stakeholder groups, large-scale and long-term 
monitoring activities are often conducted 
in collaboration with large agencies such as 
Australian Institute of Marine Science (AIMS) 
or CSIRO.



How eDNA can be used in marine 
parks: applications, benefits, 
challenges and opportunities

Monitoring Australia’s marine environment is 
challenging. Successful adaptive management 
depends upon well-designed monitoring 
programs to meet mandated monitoring 
requirements and fulfil specific, research-driven 
goals. However, the extent, diversity and 
remoteness of the Australian marine estate 
make it difficult to design monitoring 
frameworks that can effectively assess impacts 
and support management and policy decisions.

This section answers questions about the 
practical applications of eDNA, and discusses 
the benefits and challenges of eDNA 
technologies. It looks at how eDNA could be 
used in existing monitoring programs, and at 
eDNA opportunities beyond monitoring.

How eDNA can be 
used in monitoring

To be used in monitoring programs, eDNA 
technology must be reliable. The growing 
scientific consensus is that eDNA methods 
are ready for deployment in typical marine 
monitoring applications, although different 
management needs might require additional 
validation processes (Hajibabaei 2022). 
Decisions with more consequential implications 
(e.g. legal use in biosecurity) require a stronger 
level of evidence and method validation (as is 
also the case with conventional methods). 
The recently published Best practice guidelines 
for environmental DNA biomonitoring in 
Australia and New Zealand and eDNA test 
validation protocols provide a framework 
for designing such validation processes that 
is accepted by the Australian Government 
(De Brauwer et al. 2022a,b).

Environmental DNA methods have the potential 
to answer questions relevant to monitoring 
goals. In aquatic environments, eDNA has even 
been shown to be more sensitive for detecting 
pest species than conventional approaches 
(Dejean et al. 2012, Zaiko et al. 2016). Presently 
available eDNA methods can readily be applied 
to monitor:

• ecosystem biodiversity

• temporal and spatial changes in species 
assemblages

• the presence of TEP species

• the presence of pest species.

Once calibrated to the local environment and 
monitoring needs, eDNA methods can also 
be deployed to model species distributions 
or measure anthropogenic impacts and 
ecosystem health.

Monitoring approaches fit within a larger 
management framework, and are not solely 
determined by scientific evidence. To be 
integrated into day-to-day management 
practice, eDNA methods must adhere to the 
tenets of successful marine park management 
(Table 3) (Elliot 2013).

Technological advancements, improved 
cost-effectiveness and increased public 
understanding of molecular methods due 
to COVID-19 pandemic reporting mean 
that there are now few practical barriers 
to the integration of eDNA methods into 
management practices.



Frequently asked questions 
about the applications 
of eDNA

• Can eDNA provide data about species 
abundance or density?
Currently, eDNA methods cannot provide 
measures of abundance in terms of numbers 
of individuals, although this is an active area 
of research. It is possible to estimate the 
relative abundance of some species using 
qPCR (single-species assays). This approach 
requires case-by-case, species-specific assay 
design, extensive validation of limits of 
detection and quantification.
The recent literature suggests that in some 
cases, abundance estimates obtained from 
metabarcoding (multi-species) assays are 
correlated to those from conventional survey 
methods. However, these correlations do not 
hold across all studies (see Abundance and 
Long-term future developments).

• How long does eDNA last in the 
environment? Is it possible that eDNA 
detects species that are no longer present?
It depends. In general, eDNA degrades 
quickly in the marine environment. Studies 
that measured eDNA persistence in the 
ocean found that in most cases eDNA can no 
longer be detected after 48 hours. However, 
the rate of degradation can vary depending 
on a range of environmental and biological 
factors such as temperature and UV radiation 
(see Sample collection).

Table 3 10 tenets of successful marine management and their relevance to eDNA technology

Tenet

Relevance to eDNA technology

Ecologically sustainable

Can deliver ecological information relevant to management

Technologically feasible

Technology is feasible for species detection

Economically viable

Cost-effective, but may need initial additional funding

Socially desirable or tolerable

Non-invasive and can be safely deployed, likely to be accepted by 
stakeholders and general public

Legally permissible

Best practice guidelines provide a framework for the design of legal 
validation processes

Administratively achievable

Only minor adaptations required to existing systems

Politically expedient

Can contribute to Australia’s image as leader in cutting-edge science 
and best practice resource and conservation management

Ethically defensible

More suitable than many conventional methods as it is a non-
destructive method

Culturally inclusive

Non-eDNA experts can collect samples so possible to include 
Traditional Owner groups and the general public

Effectively communicable

Possible if done well, as shown by science communication during 
COVID-19 wastewater detections and PCR testing





Source: Elliot 2013



• How far can eDNA travel in the marine 
environment?
The dispersion of eDNA through the water 
column depends on factors such as currents, 
waves and thermoclines. While eDNA could 
theoretically travel long distances, studies 
in the marine environment repeatedly show 
highly localised eDNA signatures often less 
than 500 m from the sampling source. This is 
likely due to factors such as dilution and 
degradation. In certain environments, such 
as rivers, eDNA can sometimes travel further 
and be detected multiple kilometres from its 
source (see Sample collection).

• Can eDNA methods be used to detect TEP 
species or invasive and pest species?
Yes. In cases where detecting a species 
would be highly significant, it is important 
to develop and validate eDNA assays to 
ensure they have appropriate sensitivity 
and accuracy (see eDNA opportunities in 
existing monitoring programs and Assay 
development and calibration).

• Do different species shed different amounts 
of DNA?
Yes, eDNA shedding rates can vary 
significantly between species, according to 
life stage, physiological activity and other 
factors. Understanding how much or how 
little DNA different species shed can be 
important for designing sampling strategies 
with sufficient power to detect target species 
(see Sample collection).

• How many eDNA samples should I take?
This can vary depending on the purpose 
of the study, the type of environment, the 
characteristics of the target species or 
communities, and the known abundance 
of target species. An absolute minimum 
of 3 replicate samples per site is advised, 
but higher replication is often desirable 
for environments with high biodiversity 
or to accommodate analytical approaches 
such as occupancy modelling.
A pilot study may be needed to determine 
minimum sample size for long-term 
monitoring projects, particularly in novel 
habitats or with target taxa for which limited 
empirical eDNA data exist.

• Can eDNA methods be used for population 
genetics studies?
While studies have shown eDNA can 
provide some information about levels of 
population genetic diversity and geographic 
differentiation in specific situations, at 
present it is largely a topic of research 
rather than a routine monitoring approach 
(see Long-term future developments).

• Is there a risk of obtaining false negatives?
Yes, like other survey methods, eDNA 
analyses can produce false negatives. 
To minimise the risk of false negatives and 
correctly interpret results, it is important 
to understand method-specific limitations, 
use assays that are fit for purpose and 
suitably validated, and take sufficient 
samples (see Result interpretation and 
Long-term future developments).

• Is there a risk of obtaining false positives?
Yes, false positives can occur, but 
their causes are well understood. The 
risks can be mitigated by using strict 
contamination controls and well-validated 
assays (see Result interpretation and 
Long-term future developments).

• How long does it take to process 
eDNA samples?
Sample processing times depend on 
which method is used (e.g. qPCR or 
metabarcoding); whether assays already 
exist and have been validated; and whether 
processing is done in-house or through 
commercial service providers.
In general, single-species approaches can 
be finished in as few as 2–3 days, or even in 
the field if suitable equipment is available. 
In the metabarcoding process, completing 
laboratory and bioinformatics procedures 
can take weeks to months.
Depending on the project aims, novel assays 
might need to be developed and validated 
before sampling. This process can take 
several months to years, depending on 
species and validation requirements.



Current uses of eDNA 
methods in Australia’s 
marine environment

Various agencies are already using eDNA 
methods to monitor Australia’s marine 
environment (Table 4). So far, most 
eDNA projects in parks have been 
limited to biosecurity applications and to 
research‑focused or short-term pilot projects. 
However, there are examples of successful 
long‑term monitoring projects that have 
integrated eDNA methodology in the workflow, 
or will do so in the near future. 

For example, the recently announced 
collaboration between Parks Australia and 
the Minderoo Foundation aims to use eDNA 
methods to monitor marine parks in the future. 
These existing programs highlight the 
recognised potential of eDNA methods and 
can help guide wider integration into future 
monitoring programs.

Table 4 Examples of active and planned environmental DNA monitoring projects in the Australian 
marine estate

Agency

Location

Project

Reference

Western Australian 
Department of Primary 
Industries and Regional 
Development

Western 
Australian 
ports

Biosecurity monitoring: State 
Wide Array Surveillance 
Program

McDonald et al. 
2019

Queensland Department of 
Agriculture and Fisheries

Queensland 
ports

Biosecurity monitoring: 
Q-SEAS project

Biosecurity 
Queensland

Victorian Department of 
Primary Industries

Victorian 
ports

Victorian Ports Marine 
Surveillance Pilot Program

Agriculture Victoria 
2023

Great Barrier Reef Marine 
Park Authority and the 
Australian Institute of Marine 
Science

Great Barrier 
Reef Marine 
Park

Crown of thorns seastar 
monitoring (see Box 2)

Uthicke et al. 2022

Australian Antarctic Division

Antarctica

eDNA biosecurity framework

Clarke et al. 2023

Parks Australia

Norfolk Island

Norfolk Marine Park habitat 
mapping project

Australian Marine 
Parks 2021

Minderoo Foundation

Australian 
Marine Parks

Ocean Discovery and 
Restoration Program

Australian Marine 
Parks 2023

UNESCO

Ningaloo, 
Shark Bay and 
Lord Howe 
Island

Environmental DNA 
Expeditions in UNESCO World 
Heritage Marine Sites

UNESCO 2023







Benefits of integrating 
eDNA methods in 
marine parks

Scaling up

Australia’s marine park network is one of 
the world’s largest, and covers a diversity 
of habitats and ecosystems. Managing 
marine environments on such a large scale 
is challenging. Typically, conventional survey 
methods can only cover a small geographic 
area. Commonly used methods such as visual 
surveys, ROVs, AUVs, towed video and even 
BRUVs can take hours to investigate the 
biodiversity of even small reefs. Large-scale 
ocean observation is possible through remote 
sensing, though it lacks resolution to address 
many monitoring requirements.

One of the biggest benefits of eDNA methods 
is that samples can potentially be collected 
across a large area more quickly and with 
fewer monitoring personnel (Mori et al. 2023). 
Staff can be trained more quickly to collect 
eDNA samples than to conduct visual surveys, 
handle ROVs, or use other field data collection 
methods. Advances in automated collections 
systems and linking eDNA data to remote 
sensing data will make scaling up monitoring 
programs over large spatial and temporal time 
scales even easier (Budd et al. 2023).

Scaling up any monitoring program depends 
on standardised methods across spatial 
and temporal scales. Environmental DNA 
collection methods can be standardised 
easily, and the development of national best 
practice guidelines and SOPs mean spatial 
inter-operability and temporal continuity of 
eDNA-derived data are realistic near-future 
prospects (Mori et al. 2023). Introducing 
formal certifications for eDNA laboratories 
or developing measures to validate eDNA 
processes used in marine park monitoring will 
increase trust in methods and facilitate their 
broader use.

Accessing the inaccessible 
– health and safety

Marine monitoring comes with risks associated 
with going out onto, and often into, the 
ocean. Scuba diving and snorkelling surveys 
require extensive training and risk mitigation 
protocols to manage environmental risks 
(e.g. hypothermia, currents, depth limits) and 
dangerous marine life (e.g. jellyfish, sharks, 
crocodiles) (DiBattista et al. 2019, West et al. 
2021, Muff et al. 2023). Conversely, eDNA 
samples can be collected without entering 
the water, removing the risks associated with 
in-water surveys.

These risks can also be avoided by using 
remote video survey systems such as BRUVs 
or ROVs. However, systems such as BRUVs are 
usually heavy and bulky, requiring winches 
and additional care to avoid manual handling 
injuries. The risks of handling injuries are 
smaller when collecting water samples for 
eDNA analysis. Furthermore, while video 
methods are efficient in clear waters, they 
are less effective in waters with low visibility. 
While turbid waters can also complicate eDNA 
methods when sediments clog up filters or 
inhibit PCR reactions, such limitations can be 
addressed by optimising methods (e.g. Williams 
et al. 2017, Takasaki et al. 2021).

Cost

The initial uptake of eDNA methods in 
monitoring programs will require extra 
investments, but once established, operational 
costs of eDNA surveys are lower than those 
of many conventional methods (Gilbey et al. 
2021). Studies have shown that compared to 
other methods, metabarcoding monitoring 
methods can reduce costs by 55% and lower 
monitoring time by 72% (Aylagas et al. 2018). 
Single-species surveys can be up to 67% less 
expensive, depending on which methods are 
used (Evans et al. 2017).

The average per sample cost for eDNA surveys 
is lower than conventional methods, largely 



because of boat times are reduced and fewer 
trained staff are needed in the field. While the 
costs of lab processing, sample sequencing 
and bioinformatics are substantial, costs are 
similar for taxonomic experts to analyse videos 
or process bulk samples. Using automation, 
sequencing DNA can process hundreds 
of samples in a short time frame, further 
increasing cost-effectiveness.

Ethical considerations

Because eDNA can detect species at low 
concentrations, it has been used to detect 
rare, threatened, or endangered species. 
Environmental DNA sample collection is 
non-lethal and non-invasive, making it 
particularly relevant for monitoring threatened 
species. In Australian Marine Parks, destructive 
sampling methods (e.g. ichthyocides) are 
generally prohibited or subject to strict 
regulation. Methods such as seine netting 
or long lining also come with the inherent 
risk of decreased survival of the species 
studied, and removing the need to catch, 
handle or euthanise organisms to detect their 
presence is advantageous when species are 
rare or threatened (Simpfendorfer et al. 2016, 
Nester et al. 2023). Recent advances in eDNA 
technologies also open the future possibility 
of better understanding population structure 
of threatened species without the need for 
invasive sampling (Sigsgaard et al. 2016, 
Adams et al. 2022).

Stakeholder inclusion

Marine parks aim to educate the public, 
communicate the state of the marine 
environment and sometimes even co-manage 
parks with stakeholders. As COVID-19 pandemic 
communications have shown, molecular 
methods can be clearly communicated to the 
public. Practical international examples of clear 
eDNA communication include New Zealand’s 
Wai Tuwhera o te Taiao – Open Waters 
Aotearoa program and the ANEMONE program 
in Japan (Box 3; EPA 2023, Suzuki‑Ohno 
et al. 2023). For marine parks, focusing on the 
potential to discover charismatic or endangered 
species can be a particularly valuable 
engagement approach.

Furthermore, if well designed, monitoring 
programs can include stakeholders such as 
industry and community groups directly in 
sample collection (see Engagement with the 
general public). Collecting eDNA water samples 
to detect single species or monitor a suite of 
species is relatively simple, and as a result, this 
approach has been used in various successful 
citizen science projects both nationally and 
abroad (Biggs et al. 2015, Griffiths et al. 2022).

Challenges to 
integration of 
eDNA methods 
in marine parks

Fragmented monitoring 
landscape

One of the biggest challenges to the successful 
integration of novel eDNA methods in 
monitoring programs is the heterogeneity 
of monitoring approaches across Australian 
Marine Parks. Jurisdictional differences in 
monitoring frameworks are recognised as 
a challenge, particularly when monitoring 
priorities would benefit from a coordinated 
approach (e.g. large-scale ecological processes) 
(Addison et al. 2018). These differences reflect 
the large geographic extent, wide range of 
stakeholders and differences in monitoring 
needs. Management in different states and 
territories have different priorities, funding 
sources and research capacities, which are 
different still from those associated with the 
even larger parks and reserves managed by 
the Commonwealth. Designing a national 
approach to establish baselines and marine 



monitoring was a key recommendation of 
the National Marine Science Plan and a lack 
of harmonisation across disciplines and 
jurisdictions is seen as a significant challenge to 
achieving this (NMSC 2015, Hedge et al. 2022).

These challenges make standardised and 
comparable monitoring on a large scale 
difficult to achieve (Hedge et al. 2022). While 
integrating eDNA into individual management 
zones can have local benefits, without strategic 
national coordination, the full potential of the 
methods may not be realised (Kelly et al. 2023).

The fundamental solutions to these challenges 
are beyond the scope of this roadmap. 
However, the effectiveness of eDNA methods 
can be maximised by harmonising their 
adoption across parks, as occurred with 
the development of SOPs for marine park 
monitoring (Przeslawski & Foster 2020, 
Hedge et al. 2022). Harmonised integration 
of eDNA methods may create opportunities 
for inter-operability. Method standardisation 
is preferable, provided it does not reduce 
the power to detect a change of interest or 
answer a specific monitoring question. Failure 
to align methods will inevitably incur a loss of 
data comparability on small and large scales. 
The recent development of national best 
practice guidelines can act as a focal point for 
a unified, trusted approach.

Cost

Increasing the cost-effectiveness of marine park 
monitoring and research is universally seen 
as desirable. It is therefore challenging to add 
new methods to existing programs, particularly 
where this entails extra costs. Environmental 
DNA methods have repeatedly been shown 
to be cost-efficient on large scales (Aylagas 
et al. 2018). However, for the foreseeable 
future, these methods will be complementary, 
entailing increased costs, including the cost of 
establishing protocols and calibrating eDNA 
methods with existing monitoring methods.

Given the evidence that eDNA analysis can 
yield cost-effective monitoring data, there 
may be an argument for strategic investment 
to establish operational monitoring protocols 
and programs, as occurred with the eDNA 
program to detect crown of thorns seastars 
(CoTS) at the GBRMP (Uthicke et al. 2022, see 
Box 2). Such investment could happen through 
local or cross-jurisdictional collaborations 
that address shared needs, such as IMOS, ARC 
linkage projects or even philanthropic projects 
(Forrest 2020).

In the absence of investment, there are 
avenues to maximise the cost-effectiveness 
of eDNA-based monitoring. For example, 
scaling up projects through cross-park or 
cross-stakeholder collaboration can reduce 
the cost per sample while increasing data 
output. The rapid evolution of automated 
eDNA workflows, from sample collecting 
to data analyses, means costs will decrease 
further in the future. Finally, where the 
costs of immediate analysis are too high, 
samples could be stored in biobanks (Jarman 
et al. 2018). Baseline samples collected now 
could be analysed in future projects, when 
budgets allow.

Expertise

Although the collection of eDNA samples 
is straightforward, downstream processing 
is highly specialised and relatively novel, 
meaning most monitoring teams currently lack 
relevant expertise. In regional areas, relevant 
expertise may be even more scarce. Lack of 
understanding of the capabilities and limits 
of eDNA methods may hinder the uptake and 
effective use of eDNA approaches.

These challenges can be addressed in multiple 
ways. To enable clearer communication, eDNA 
researchers should build their management 
and policy literacy, while MPA science 
managers should develop their understanding 
of eDNA. This could be supported by the 
newly established SeDNAS, which advises 
stakeholders on the best-practice application 



and interpretation of eDNA methods. 
Developing mutual understanding and shared 
language will help managers and eDNA experts 
to collaborate more closely.

Alternatively, molecular experts could be 
employed into monitoring program teams for 
some jurisdictions. Existing eDNA research 
activities within the DBCA, New South Wales 
Department of Primary Industries and the 
AAD show how this can be achieved. When it 
is not feasible to employ molecular experts, 
critical eDNA workflows can be outsourced 
to molecular experts. Finally, eDNA experts 
could be embedded in major initiatives and 
consortiums such as NESP or the National 
Marine Science Committee to provide oversight 
and advice.

Reference sequence libraries

To characterise species assemblages, DNA 
sequences collected from the environment are 
assigned to a species by interrogating DNA 
reference libraries. The quality of eDNA results 
depends on the completeness of reference 
libraries; yet global and Australian DNA 
reference libraries are incomplete (Weigand 
et al. 2019, Yao et al. 2022, CSIRO 2023). As a 
result, most sequences obtained through eDNA 
analysis cannot be assigned to species level, but 
are limited to higher taxonomic ranks such as 
genus or, more commonly, family or even order 
(Weigand et al. 2019). 

The construction of DNA reference libraries 
faces 2 main hindrances: the difficulty of 
extracting sequences from known species 
and making the sequences publicly accessible; 
and the lack of taxonomic expertise to link 
sequences to the correct species. The lack of 
complete reference libraries is most strongly 
felt in poorly studied regions (e.g. deep sea 
canyons) or taxa (e.g. invertebrates), and areas 
with high biodiversity (e.g. coral reefs).

This challenge links taxonomy, the most 
fundamental biological science, with 
cutting-edge technology, and as such, 
the solution must involve both fields.

New methods to more rapidly extract 
sequences from species are being developed 
and improved (e.g. CSIRO’s NBDL). However, 
these still need taxonomic expertise to ensure 
accuracy – a concern which is addressed 
through the NBDL project (CSIRO 2023). 
Investment is needed in both taxonomy and 
sequencing programs for the creation of 
reference sequences. Recognising this, the 
European Union aims to publish the DNA 
sequences of 50% of the organisms in its 
ecosystems by 2030 (Lamy et al. 2020).

An alternative already in use by eDNA 
researchers is the application of 
taxonomy-independent analyses. The use of 
OTUs or ASVs (see Bioinformatics) removes 
the need for taxonomic identification, but still 
has the potential to measure changes in the 
ecosystem through, for example, custom health 
indices. It is important to note, however, that 
without translation to taxonomic identities, 
OTUs have limited ability to inform practical 
management interventions.

Abundance

Most environmental monitoring programs 
include a focus on measuring abundance and 
trends in abundance for species of interest. 
At present, eDNA methods cannot provide 
measures of abundance in terms of numbers 
of individuals. This can be perceived as a major 
challenge to the integration of eDNA methods 
into monitoring projects (Jerde 2021, Rourke 
et al. 2021, Norros et al. 2022). Addressing this 
challenge is the subject of extensive research. 
A potential way forward would be to examine 
methods that provide trends without requiring 
absolute estimates of abundance.

In relation to abundance measures, however, 
2 important observations must be made. 
Firstly, most conventional survey methods 
only offer a relative measure of abundance, 
such as MaxN or estimated percentage cover 
(McCormick & Choat 1987, Benedetti-Cecchi 
et al. 1996, Campbell et al. 2015). Whether 
visual, video or catch methods are used, each 



method has limitations that affect how well 
estimates of abundance reflect true abundance. 
Secondly, the goal of monitoring abundance 
is generally to measure how it changes over 
time or in response to management, so that 
the effects of impacts or interventions can 
be determined. Precise knowledge of exact 
population numbers is rarely needed (with 
some exceptions, such as highly threatened 
species) (IUCN 2012).

Environmental DNA methods can address some 
of the challenges around abundance measures 
by using the relative abundance of DNA 
sequences as a proxy for species abundance. 
When conducting single-species assays, it is 
possible to estimate relative abundance for 
some species using qPCR (see Laboratory 
analysis). This approach, however, requires 
case-by-case, species-specific assay design, 
extensive validation of limits of detection and 
quantification. Multiple environmental and 
species-specific variables can influence whether 
quantification is feasible. While estimations 
of relative abundance are possible for many 
species, they do not work for all species 
(Rourke et al. 2021, 2023). However, when 
assays can be validated, the relative abundance 
results from qPCR methods can be used to 
measure changes in the population of interest. 
If necessary, this approach can then be backed 
up by conventional methods.

Measuring relative abundance for 
metabarcoding (multi-species) methods is more 
difficult than conducting single-species assays. 
The relative abundance reads in metabarcoding 
results can be affected by a range of technical 
issues, which complicate their interpretation. 
A number of studies and reviews have shown 
strong correlations between relative eDNA 
abundance and the abundance estimated by 
conventional methods such as UVCs, BRUVs, 
trawls and acoustic surveys (Fediajevaite et al. 
2021, Keck et al. 2022). However, other studies 
have failed to find such correlations.

As an alternative to measuring relative 
abundance, statistical approaches are being 
developed to infer abundance from eDNA 
presence/absence data (see Applications). 
Methods such as multi-species occupancy 
models use high levels of spatial sampling to 
infer overall abundance of species and how 
they might be affected by environmental 
variables (McClenaghan et al. 2020).

Organismal biology and health

Life history attributes such as the size, life stage, 
age, weight and health of monitored species 
are other metrics used when monitoring 
ecosystems. For example, monitoring organism 
health, fecundity and size is standard practice 
for fisheries species. Similarly, in pest species 
surveillance it is important to be able to 
distinguish between established populations 
and the brief presence of larvae. Currently, 
eDNA methods cannot provide such biological 
information.

A potential solution is measuring 
environmental RNA (eRNA) rather than eDNA, 
or investigating other biomarkers for, for 
example, age (Mayne et al. 2021). RNA, which 
is only shed by living organisms, transfers 
information within cells to produce specific 
proteins. Theoretically, measuring eRNA offers 
the potential to study which proteins are 
being expressed and how these relate to the 
biological state of an organism (e.g. disease, 
fecundity, age). The potential applications of 
eRNA could be significant, and are increasingly 
the subject of research. However, it is unlikely 
that such methods will be operational in the 
short-to-medium term (5–10 years).

Result interpretation

Marine resource managers are accustomed 
to interpreting estimates of species numbers, 
percent cover and other similar abundance 
metrics. The methodological limitations of 
survey techniques are understood well enough 
to help interpret the ecological meaning of 
such monitoring results.



The results of eDNA technologies, however, 
pose new challenges, such as interpreting 
data that only conveys presence or absence; 
determining if ecological interpretations can 
be made when taxonomic units are presented 
at the resolution of genus or family, or are 
replaced entirely by units such as OTUs or 
ASVs; and understanding how much confidence 
can be placed in eDNA-based detections or 
non-detections if it is not possible to visually 
confirm the presence of a species.

False negatives can occur in eDNA analyses. 
False negatives are also commonly encountered 
when using other survey methods (e.g. UVC and 
BRUV methods generally ignore cryptobenthic 
species as they cannot be reliably detected) 
(Samoilys & Carlos 2000, Watson et al. 2010, 
De Brauwer et al. 2018). Understanding 
method-specific limitations is therefore key to 
correct data interpretation. For eDNA, a large 
body of research has studied the factors 
influencing false negatives, such as primer 
design, laboratory protocols and the ecology 
of eDNA prior to collection. Limitations are 
increasingly well understood, and will only 
become clearer in the future.

While there is always a risk of false 
positives, their causes are also well 
understood and can be mitigated by strict 
contamination controls throughout the eDNA 
workflow (Burian et al. 2021). To further 
decrease the risk of contamination, eDNA 
monitoring should ideally be done by experts. 
At minimum, staff collecting samples should 
be adequately trained.

Limited taxonomic resolution is not unique to 
eDNA: methods such as invertebrate surveys 
regularly identify morphological groups 
rather than species or even genus or family 
(Berman et al. 2013). Improved reference 
libraries will increasingly improve resolution in 
eDNA metabarcoding studies, alleviating this 
challenge (see Reference sequence libraries). 
However, methods that bypass taxonomy 
such as taxonomy-free biotic indices can be 
developed to assess the health of ecosystems 
or indicate specific anthropogenic impacts, 
allowing for targeted management action 
(e.g. Cordier et al. 2018, Wilkinson et al. 2023).

Addressing results interpretation challenges 
will require continued research in method 
limitations and the ecology of eDNA; stringent 
contamination controls; and well-designed 
training protocols for sample collection. Many 
of these challenges already being addressed 
through innovations in the field, and there 
are national guidelines to help non-experts 
address contamination concerns (De Brauwer 
et al. 2023). Particularly when monitoring single 
species, it can be helpful to collaborate with 
an expert to design a management decision 
framework that sets out decision triggers linked 
to specific results (De Brauwer et al. 2022a).

Spatial and temporal 
comparability of eDNA 
datasets

Environmental DNA practices and capabilities 
can differ considerably between users and 
laboratories. This variability is present in all 
scientific disciplines, but may be particularly 
acute for eDNA, since it is developing so rapidly. 
The use of different protocols has the potential 
to limit the inter-operability of independently 
collected data, including time series. Variations 
in collection methods, bioinformatic protocols 
and laboratory and service provider procedures 
can all reduce comparability between studies.

In response, countries around the world 
are establishing national guidelines for best 
practice in the use of eDNA in different 
circumstances (Loeza-Quintana et al. 2020, 
De Brauwer et al. 2023, Gagné et al. 2021). 
Creating SOPs for eDNA applications within 
and between parks is an important first step. 
Where SOPs are not yet possible, following 
best practice guidelines and collecting 
comprehensive metadata should be mandatory. 
Complete metadata will improve current 



inter-operability of data and allow future 
comparisons when methods have improved 
(Fediajevaite et al. 2021). Developing a 
national system to store standardised (meta)
data, like the recently developed platform for 
fish survey image annotation, would greatly 
improve inter-operability and comparability 
(Langlois & Friedman 2018).

A long-term solution could be to design a 
nationally coordinated system to guarantee 
eDNA samples from monitoring activities 
across all parks are processed in a reliable, 
comparable manner, as has been suggested 
for other countries (Norros et al. 2022, Kelly 
et al. 2023). Service providers should be 
given clear guidelines on sample processing 
standards. Designing proficiency testing 
systems for service providers, as has been done 
for the crested newt eDNA project in the UK, 
would ensure quality and reliability of results 
(Biggs et al. 2015). Existing testing programs 
in Australia, such as those for biosecurity 
applications run through the National eDNA 
Reference Centre, could potentially be adapted 
for this purpose in the future (Trujillo-González 
et al. 2021).

Existing and new 
opportunities

eDNA opportunities in existing 
monitoring programs

Environmental DNA methods are already used 
for monitoring in Australian Marine Parks, and 
there is opportunity for wider deployment 
under suitable circumstances. It is likely 
that initially, eDNA methods will be used to 
complement existing methods and to establish 
comparability for future inter-operability. 
Below is an overview of how existing eDNA 
capacity in Australia could be used to address 
the 4 goals of monitoring programs in marine 
parks (Table 5).

Ecosystem characterisation

Available eDNA applications can generate 
biodiversity data to fill knowledge gaps 
in marine parks, particularly in areas 
where conventional methods are not 
feasible due to, for example, poor visibility, 
remoteness or OH&S risks (Table 4). 
Ecosystem characterisation to establish baseline 
data is often a condition for approval of 
activities inside marine parks. Furthermore, 
in well-known parks, eDNA methods can 
provide baseline information about a range 
of cryptic taxa that cannot be detected using 
conventional survey methods. This use of eDNA 
is currently limited by the quality of available 
reference databases (Table 5) and presently only 
produces reliable presence/absence data, not 
abundance data.



Measuring the current condition of 
natural values

There is capacity in Australia to use eDNA 
methods to monitor the condition of 
ecosystems through the presence of specific 
species (Tables 4, 5). This is particularly relevant 
for pest or TEP species. The AAD’s eDNA 
biosecurity framework identifies benefits 
from surveillance of, for example, nearshore 
environments and biofouling species on boats 
in the Antarctic region (Clarke et al. 2023). 
Successful ongoing biosecurity monitoring 
programs, such as the State Wide Array 
Surveillance Program in Western Australia 
(McDonald et al. 2019), have been used as 
a template for different regions (Table 4). 
With relatively minor adjustments to current 
systems, eDNA methods could be applied to 
detect native pest species such as CoTS (Box 2) 
or TEP species such as sharks or seahorses, 
as demonstrated by recent research and 
successful programs in the GBRMP (Uthicke 
et al. 2022, van Rooyen et al. 2021, Nester 
et al. 2023). Integrating genetic methods has 
the potential to reduce costs and increase the 
scale of monitoring programs, but will require 
the development and validation of relevant 
species‑specific assays (Table 4; De Brauwer 
et al. 2022a).

Monitoring changes in environmental 
values over time

eDNA methods can be used to detect 
changes in the environment over time, across 
geographic scales, or through anthropogenic 
drivers (Berry et al. 2019, DiBattista et al. 
2020, West et al. 2021). Environmental 
DNA methods can detect a wider range of 
taxa, especially short-lived indicator taxa 
(e.g. bacteria or cryptobenthic fishes). Because 
these indicator taxa are more responsive to 
changing conditions, eDNA methods can 
detect environmental changes more quickly 
than monitoring of highly visible but slower 
growing species.

Report results to inform 
management and stakeholders

For reporting, eDNA methods offer both 
challenges and benefits. The sophisticated 
laboratory methods are highly technical and 
can be challenging to fully understand, even for 
those with scientific training. Classic reporting 
of detailed procedures with extensive results 
and caveats are unlikely to be understood by 
management and the public.

However, the COVID-19 pandemic has increased 
public understanding of certain molecular 
methods and demonstrated that these methods 
and their results can be conveyed clearly 
with the right communication. Furthermore, 
the core results of most eDNA methods, that 
is, the presence or absence of species in a 
location, are easily explained. Interactive maps 
in the Wai Tuwhera o te Taiao – Open Waters 
Aotearoa program are an example of how 
eDNA monitoring data can be communicated 
effectively to the general public (EPA 2023, 
Suzuki-Ohno et al. 2023; see also Box 3).



Box 2 Detecting crown of thorn seastars using eDNA methods

Author: Sven Uthicke, Principal Research Scientist, AIMS

Coral-eating crown of thorn seastars 
(CoTS) on the GBR and elsewhere in the 
Indo–Pacific region are natural members 
of coral reef ecosystems, but are prone to 
extreme population explosions (Uthicke 
et al. 2015). During these outbreaks the 
number of corals they consume outweighs 
coral growth rates, resulting in reef 
degradation. Overfishing of predators or 
increased larval survival triggered by high 
food (plankton algae) through increased 
land-runoff (‘eutrophication’) alone or in 
combination are the most likely causes of 
outbreaks (Babcock et al. 2016).

Given other reef stressors such as climate 
change need global long-term effort to 
address, management authorities endorse 
and support culling of CoTS as one way to 
directly protect corals. There are 6–7 vessels 
involved in culling, with > 1 million CoTS 
culled in the last 10 years.

To understand outbreaks and guide culling 
activities, outbreaks need to be detected 
early. This is difficult to achieve with standard 
monitoring techniques because CoTS are 
often cryptic juveniles only visible by experts, 
and outside active outbreaks, densities are 
less than 10 animals per hectare.

To assist with these issues, scientists at 
AIMS developed CoTS-specific DNA markers 
initially used to detect and quantify CoTS 
larvae (Uthicke et al. 2015, Doyle et al. 2017). 
This larvae work is ongoing and supported 
by tourism operators and CoTS control 
boats collecting plankton samples. New 
eDNA techniques, developed later, use these 
markers to detect post-settlement CoTS in 
small water samples. The new methods 
can detect very low densities, and sample 
occupancy and concentration show a direct 
relationship to CoTS densities (Uthicke 
et al. 2018, Uthicke et al. 2022). Method 
development and testing was supported 
by the Australian Government through 
funding to the AIMS and NESP funding, 
but also by grants from the GBRMPA and 
the tourism industry.

AIMS is part of the CoTS control innovation 
program (CCIP) which seeks to improve 
monitoring and control of CoTS. The project 
is tasked with operationalising an 
eDNA-based CoTS monitoring program. 
Although eDNA will not be the only 
monitoring tool, the ongoing close 
collaboration with managers and reef users 
allows scientists to identify where methods 
are most efficient and can most effectively 
guide management effort. The most likely 
areas for eDNA methods will be in early 
detection of outbreaks on individual reefs 
and in monitoring potential population 
growth after culling on specific reefs has 
pushed densities below outbreak levels. 
Other methods for achieving this would 
require significantly more time and financial 
effort, and thus more reefs can be surveyed 
with eDNA methods in less time. In addition, 
the ease with which samples can be obtained 
by citizen scientist or managers/enforcement 
makes eDNA monitoring for CoTS attractive 
for citizen scientists.



Table 5 Opportunities to integrate eDNA methods in existing marine monitoring frameworks

Attributes

Monitoring goals

Characterise 
communities 
(baseline studies)

Measure current 
condition

Monitor 
environmental 
change

Report

Technical 
feasibility

• Possible for single 
species and whole 
communities


• Possible 
depending on 
which values or 
indicators are 
measured


• Needs method 
calibration and 
baseline data


• Feasible


Potential 
monitoring 
applications

• Areas unsafe or 
difficult to access 
using conventional 
methods
• Biosecurity 
surveillance
• Complementary 
with existing 
methods


• Presence of 
Threatened, 
Endangered and 
Protected species
• Species 
assemblages
• Biosecurity 
applications
• Native pest 
species presence


• Temporal studies
• Measure effects of 
management
• Rapid data 
collection after 
disasters and 
human impact 
events


• Novel data 
visualisation 
options
• Wider range 
of taxa to 
report than 
conventional 
monitoring


Benefits

• Samples easy and 
safe to collect
• Possible to conduct 
large-scale surveys
• Can monitor wider 
range of species 
compared to other 
methods (including 
cryptic species and 
microbial diversity)
• Non-lethal data 
collection
• Reduced vessel and 
fieldwork costs


• Samples easy and 
safe to collect
• Can monitor 
wider range of 
target species 
compared to 
other methods
• Non-lethal data 
collection
• Potential multi-
species health 
indices
• Reduced vessel 
and fieldwork 
costs


• Samples easy and 
safe to collect
• Can monitor 
wider range of 
species compared 
to other methods
• Sensitive to detect 
rapid changes in 
cryptic organisms
• Potential multi-
species health 
indices
• Reduced vessel 
and fieldwork 
costs


• Presence/
absence data 
is easy to 
understand
• Can easily be 
visualised in 
map form
• Can be done 
rapidly








Environmental DNA 
opportunities beyond 
monitoring

Co-management with 
Traditional Owners

First Nations peoples’ long history of caring 
for country is increasingly recognised in the 
management and monitoring of marine parks. 
Parks Australia and many state and territory 
marine parks are beginning to incorporate 
the knowledge of First Nations peoples in 
management decisions and the co-design 
of projects and programs on Sea Country. 
Some jurisdictions are also moving towards 
co‑managed parks with local Traditional 
Owners, such as the Bardi Jawi Gaarra and 
Maiyalam parks in WA, or the ongoing 
partnership approaches of AIMS (Evans-Illidge 
et al. 2020, DBCA 2022a,b). For First Nations 
groups in remote regions, eDNA methods 
offer a way of collecting data on the entire 
ecosystem without the need for expensive, 
hard-to-deploy equipment or expert training. 
Indigenous ranger groups are already using 
eDNA methods in the Torres Strait Islands 
and the Kimberley to detect invasive and 
threatened species (Villacorta-Rath et al. 2021, 
Villacorta‑Rath & Burrows 2021). Increased 
uptake of eDNA methods could further improve 
the quantity and quality of data provided by 
and to First Nations peoples.

While new methods provide new opportunities 
for co-management, they also present new 
challenges. To improve sample collection and 
minimise contamination, training is needed. 
The remoteness of some regions co-managed 
by Traditional Owner groups increases the 
risk of degradation before samples reach 
processing facilities. To maximise uptake 
and efficiency, collection methods should be 
adapted to local conditions and needs, for 
example, with adapted protocols or mobile 
facilities (Villacorta-Rath & Burrows 2021, 
Forrest 2020).

Attributes

Monitoring goals

Characterise 
communities 
(baseline studies)

Measure current 
condition

Monitor 
environmental 
change

Report

Limitations

• Incomplete 
reference 
databases mean 
not all taxa 
identifiable to 
species
• Currently no 
abundance data


• Incomplete 
reference 
databases mean 
not all taxa 
identifiable to 
species
• Species-specific 
assays need to be 
developed and 
validated
• Limited 
information 
on abundance 
and population 
structure


• Incomplete 
reference 
databases mean 
not all taxa 
identifiable to 
species
• Limited 
information 
on abundance 
and population 
structure
• Indices need to 
be developed and 
ground truthed
• No information 
on size/biomass/
health of species


• Molecular 
underpinnings 
hard to explain 
to non-experts
• Workflows 
for specific 
visualisation 
applications 
need to be 
developed








Engagement with the general public

Most if not all marine parks aim to engage with 
the general public (e.g. GBRMPA & Queensland 
Government 2015, Director of National Parks 
2018, Aither 2021). This engagement can be 
limited to simply communicating park rules, 
but is often more involved. Many marine 
parks aim to educate the public about local 
marine life and how parks can help conserve 
it. Other parks have gone further, engaging 
with the public through citizen science – the 
results of which are sometimes used to inform 
park management (e.g. Browne et al. 2018). 
Engagement with the public also helps marine 
parks to maintain productive relationships 
with certain stakeholders, such as tourism or 
recreational fishing bodies. Redmap Australia 
is one example of successful engagement 
with recreational fishers to inform both 
climate change researchers and the public 
(Pecl et al. 2019).

The ease of collecting eDNA samples has 
led to the development of numerous eDNA 
citizen science projects in Australia and across 
the world. In one of the earliest established 
projects, eDNA methods have been used by 
citizen scientists since 2015 to detect the great 
crested newt (Triturus cristatus) in the UK. 
Government has sanctioned use of the 
resulting data for planning applications 
(Biggs et al. 2015). A more recent Japanese 
project worked with 168 volunteers to map 
coastal fish assemblages across the country 
(Suzuki-Ohno et al. 2023). The Wai Tuwhera 
o te Taiao – Open Waters Aotearoa program in 
New Zealand exemplifies how eDNA methods 
can be effectively used by and communicated 
with the public (Box 3). On an even larger 
scale, the new eBioAtlas is an international 
partnership between the IUCN and a UK-based 
service provider that has the ambitious goal 
of filling critical conservation knowledge 
gaps by mapping global riverine biodiversity 
with local stakeholders and citizen scientists 
(IUCN & NatureMetrics 2023).

In Australia, notable citizen science projects 
that use eDNA include the Great Australian 
Platypus Search, which collected samples 
from 1,649 sites to improve knowledge of 
platypus distribution across Victoria (Griffiths 
et al. 2022). Recreational fishing bodies have 
also run eDNA projects to help recreational 
fishers detect threatened freshwater species 
in New South Wales, Queensland and Victoria 
(OzFish Unlimited 2022).



Box 3 Wai Tuwhera o te Taiao – Open Waters Aotearoa

Author: Vanessa Crowe, Principal Community Engagement Lead, Environmental Protection Authority, New Zealand

Wai Tuwhera o te Taiao – Open Waters 
Aotearoa is a nationwide community science 
program designed by the New Zealand 
Environmental Protection Authority (EPA). 
The project supports and empowers 
collaborative environmental protection at 
the flax roots of Aotearoa. The program has 
supported over 300 community groups, 
schools and Māori-led groups to undertake 
eDNA testing.

Participants can use eDNA findings to 
advocate for their local environment and 
make connections with science, technology 
and mātauranga (Māori knowledge) 
to inform environmental management 
decisions. This can include collecting 
baseline data, comparing sites, monitoring 
the distribution of species within a 
catchment or area, and tracking changes 
over time. The test results can provide useful 
evidence that can be used in submissions, 
advocacy and environmental decision-
making, such as the extension to trapping 
zones and reserve areas and improvements 
to fish passage. The EPA encourages 
match‑funding and collaboration with other 
support organisations such as councils 
to increase resources and strengthen 
place‑based relationships.

We prioritise Māori participation and 
acknowledge the inherent rights and 
interests that Māori have in relation to the 
collection, ownership and application of 
Māori data, including data relating to te 
taiao (the environment). Some steps we 
have taken so far towards recognising Māori 
rights to data and involvement in how that 
data is managed include:

• ensuring collected samples stay 
within Aotearoa

• encouraging participants to talk with 
mana whenua (the indigenous people 
who have historic and territorial rights 
over the land) before taking samples

• making sure data is password-protected, 
unless people wish to make it public

• ensuring full ownership and rights to the 
sample data sit with the participant

• taking time to speak transparently about 
how data is stored, used, and managed.

Learn more about Wai Tuwhera o te Taiao.

Using eDNA technologies to engage with the 
public poses risks that should be considered 
before programs begin. Clear communication 
of methods and results is vital to optimise 
and sustain engagement with non-scientists. 
Messaging should be in plain language; focus 
on discovery or species of interest; and ideally 
include engaging images and video. Higher 
potential for sample contamination should be 
considered in downstream analyses for results 
to also be of use to management. Although 
some contamination is unavoidable when 
samples are taken by non-experts, steps can 
be taken to reduce the initial contamination 
risk, filter out doubtful samples, and follow up 
results of interest (Biggs et al. 2015, Griffiths 
et al. 2022).



Action plan for managers: 
practical steps to integrate 
eDNA in individual projects

Resource managers can use the following 
framework to inform decision-making and 
determine how eDNA methods could fit within 
their monitoring programs. The open access 
Best practice guidelines for environmental DNA 
biomonitoring in Australia and New Zealand 
provide detailed information about designing 
and executing eDNA projects in the Australian 
context (De Brauwer et al. 2023).

The framework steps begin with identifying 
priorities and opportunities, and then 
move from pilot study to implementation of 
monitoring in a cyclical approach (Figure 5).

Marine park objectives

First, assess existing monitoring objectives 
and budget (Hayes et al. 2021). This will ensure 
the adoption of a cost-effective, targeted 
approach with the highest chance of successful 
integration. Detailed monitoring objectives 
should be accompanied with clear metrics 
and expectations of which (if any) changes are 
expected to be detected.

eDNA opportunities

Next, cross-reference park-specific monitoring 
objectives with existing eDNA methods and 
capability. Simple decision frameworks can be 
used to assess the potential implementation 
of eDNA methods (Figure 6, Darling 2020). 
Consulting with eDNA experts is strongly 
recommended at this stage to ensure crucial 
technical nuances and region- or taxon-specific 
limitations are taken into account (Gleeson 
2021, Berry et al. 2023).

Use this information to identify the monitoring 
objectives to which eDNA methods are most 
applicable. The feasibility of different eDNA 
monitoring opportunities can then be assessed 
in reference to the existing monitoring 
framework. This assessment should consider 
logistical requirements, budgets, available 
in‑house expertise, added value and processing 
timelines. To reduce contamination risk and 
ensure sample quality, personnel must be 
trained in sample collection.

The assessment at this stage may identify 
multiple opportunities, which can then be 
prioritised in line with integration objectives 
or to maximise added value. Alternatively, the 
assessment may show that eDNA methods are 
not yet feasible for integration into the existing 
monitoring framework.



Diagram summarising the practical steps to integrate eDNA methods in monitoring programs. It starts with identifying park priorities by assessing monitoring objectives and budget; then exploring eDNA opportunities by identifying objectives where eDNA could be used, drawing up a budget, assessing the feasibility within existing management frameworks, and prioritising integration objectives. At this stage, a pilot study is recommended to calibrate results with existing monitoring methods. The final step is to implement monitoring, with appropriate experimental design and evaluation of results and benefits. 


Source: redrawn from Darling 2020, reused with permission.

Figure 5 Action plan: flowchart of the practical steps to integrate eDNA methods 
in monitoring programs



Diagram of a sample decision tree used when considering eDNA methods in species-specific monitoring programs. The decision tree works through the costs of false negatives and false positives, and the cost of conventional survey methods. In some cases conventional methods might be preferable, in some cases eDNA methods could be used for specific purposes, and in some cases eDNA methods are the most cost effective.


Figure 6 Example of a decision tree used when considering eDNA methods in species-specific 
monitoring programs (e.g. for endangered or pest species)



Pilot study

Strongly consider collaborating with eDNA 
experts to conduct a pilot study or eDNA 
method calibration test. This pilot study should 
be tailored to match the specific objective, 
including exact method, habitat and target 
species. Pilot studies might not be necessary 
where existing assays have been used and 
validated for target taxa in the intended 
ecosystem (Thalinger et al. 2021).

Monitoring

Monitoring programs need a well-designed 
workflow able to meet project goals. During 
project design, plan each step in the eDNA 
workflow, ensuring it is fit for purpose and 
can deliver the data required. Developing an 
appropriate experimental design suited for 
the monitoring objective, which considers 
strengths and limitations of the planned eDNA 
method, is essential at this stage. This should 
consider factors such as representative 
sampling, replication needs, spatial and 
temporal relevance, field logistics, data analysis 
needs, and data storage (De Brauwer et al. 
2022a – Table 1; Guri et al. 2023). If ongoing 
monitoring is planned, specific SOPs should 
be developed for the monitoring program. 
Consulting with molecular experts at this stage 
is advised to ensure planned methods are 
suitable and realistic.

Plan ahead for how eDNA results will inform 
management, before monitoring activities 
and data analyses. Decision frameworks 
can aid result interpretation, identify 
potential follow‑up surveys, or set trigger 
values for specific management actions 
(see Result interpretation, Sepulveda et al. 
2020, De Brauwer et al. 2022a). The decision 
framework can incorporate potential 
sources of error, management objectives or 
regional factors affecting monitoring actions. 
Also at this stage, define what will be 
considered successful outcomes from eDNA 
monitoring activities to facilitate method and 
result evaluation.

So that the effectiveness of eDNA surveys can 
be evaluated regularly, consider integrating 
eDNA technologies in adaptive management 
frameworks, such as the management 
effectiveness system. This approach ensures 
that improvements to eDNA monitoring 
programs can be implemented early.

Budget considerations

The costs of implementing molecular 
monitoring methods may be considerable. 
Recent research provides guidance on 
estimating eDNA survey costs and comparing 
them with other methods (Andres et al. 2022). 
Depending on project specifications, there may 
be eDNA-specific costs such as assay design and 
specialised sampling. Therefore, we strongly 
suggest consulting with molecular experts to 
assess budgetary needs.

Ideally, monitoring budgets would be designed 
to accommodate the integration of eDNA 
methods, but this might not be immediately 
feasible. Cost-effectiveness can be improved 
by designing cross-stakeholder or cross‑park 
monitoring programs to decrease the per‑unit 
processing cost of individual samples. 
Coordinating programs across jurisdictions 
could be used as leverage to decrease costs 
with eDNA service providers. If done correctly, 
samples can also be extracted and frozen 
to be analysed when budget is available or 
when there are enough samples to reduce 
the per‑unit cost. However, if samples are not 
stored in appropriate facilities, there is a risk of 
degraded sample quality or even sample loss.



Research priorities and future 
developments: supporting 
integration into monitoring 
programs

Ongoing research and development are 
needed if eDNA and other molecular methods 
are to reach their full potential as part of 
marine monitoring programs. To align method 
improvements with monitoring priorities, the 
needs of monitoring agencies must be clearly 
communicated to eDNA researchers.

This section considers eDNA research priorities, 
based on monitoring needs in Australian 
Marine Parks.

Research priorities

Based on the monitoring needs and priorities 
of different marine park jurisdictions and 
stakeholders, we consider research priorities 
that will support the uptake of eDNA 
technologies (Table 6). Although we expect 
this research to be conducted by molecular 
experts rather than marine park departments, 
collaboration between these two groups 
will maximise the benefits of advances in 
eDNA technology.

Infrastructure and logistics

Quality control

Optimising essential infrastructure and 
workflow logistics should be an important 
focus for development. For the foreseeable 
future, most laboratory processing of eDNA 
samples will likely be conducted by external 
service providers, not in-house. Designing 
systems for intercalibration and proficiency 
testing would help guarantee reliable results 
across different providers, increasing managers’ 
trust in sample quality (Trujillo-González et al. 
2021). A National eDNA Reference Centre 
has recently been established to provide 
these services for eDNA used in biosecurity 
monitoring, and could potentially be adapted 
as a model for marine monitoring programs 
(Trujillo-González et al. 2021). Countries such as 
the UK have developed laboratory certifications 
for specific eDNA applications. This approach 
could be of interest for certain monitoring 
activities in Australian Marine Parks, such as 
impact assessments. More simply, designing 
national standardised positive controls for 
metabarcoding studies could improve quality 
assessment of survey results.

Reference libraries

Recognised globally as a research priority, 
complete reference libraries are needed to 
optimise assays and accurately identify eDNA 
samples to species level (Beng & Corlett 2020, 
Norros et al. 2022, Takahashi et al. 2023). 
The NBDL is a collaborative initiative that will 
provide a comprehensive and authoritative 
data resource for all Australian species, based 
on expertly identified voucher specimens held 
in institutional collections. Complete reference 
sequences for all Australian marine vertebrates 
are expected by 2025 (CSIRO 2023). Efforts to 
create reference sequences for other marine 
species have been initiated but will require 
sustained investment and collaboration with 
stakeholders.



Table 6 Research priorities for environmental DNA methods to assist in monitoring

Focus area

Technology

Applications

Timeline*

Infrastructure 
and logistics

Quality control methods

Increased trust in results from service 
providers

2030

Passive sample collection 

All eDNA projects, particularly remote, 
long-term, large-scale

2030

Automatised sample 
collection

All eDNA projects, particularly remote, 
long-term, large-scale

2030

Point-of-need technologies 
for sample collection

Projects needing rapid turnaround times

2030

Assay 
development 
and 
calibration

National standards and 
SOPs

Spatial and temporal data comparability 
between park monitoring programs

2025

International reporting 
and analyses standards 
and SOPs

Increased international comparability

2030

Assay validation

Increased trust in results 

2025–2030

Technical improvements in 
assay validation

Improved understanding of limits and 
results interpretation

2025–2030

Calibration with 
conventional methods

Comparability across spatial and 
temporal scales

2025–2030

Ecology of eDNA 
(e.g. persistence, transport)

All eDNA projects: improved 
experimental design and interpretation 
of results

2025–2030

Applied 
research

Microbial ecosystem health 
indicators

Monitor base food chain and early 
indication impacts

2025

Custom parks ecosystem 
health indicators

Monitor changes in ecosystem health

2030

Early warning systems to 
detect health risks

Monitor presence of hazardous jellyfish, 
toxic algae blooms and other public 
health risks

2030

Early warning systems to 
detect pests and nuisance 
species

Monitor presence of species such as 
crown of thorns seastars or invasive pests

2025







Sample collection

Monitoring programs will benefit from 
continued efforts to simplify and improve 
sample collection methods (Formel et al. 2021, 
Truelove et al. 2022, Hendricks et al. 2023). 
Increased automatisation and methods such as 
passive sampling are particularly relevant when 
surveying remote or large areas, and when 
collection is done by non-experts. Portable 
point-of-need tools capable of providing near-
instant species identifications could be used to 
assess significant biosecurity risks or responses 
to catastrophic environmental impacts (Gleeson 
et al. 2022). These management needs could 
also be addressed by ships with mobile 
laboratory and sequencing facilities (Forrest 
2020). Incorporating eDNA monitoring into the 
existing IMOS framework of national ocean 
observations is feasible and would benefit long-
term observations. To further accommodate 
long-term comparisons of eDNA data, custom 
data platforms could be designed to allow 
Australian eDNA monitoring data to be stored 
and accessed for re-analysis.

Assay development 
and calibration

Standard operating procedures

Researchers are investigating how to improve 
the performance of eDNA assays that serve 
specific purposes, such as detection surveys 
of specific taxonomic groups. Establishing and 
regularly updating SOPs based on the latest 
research should be a priority. Implementing 
national SOPs for specific eDNA survey methods 
and metadata will improve the quality and 
inter-operability of eDNA monitoring programs 
(Samuel et al. 2021, Fediajevaite et al. 2021). 
NESP initiatives have developed standardised 
fieldwork protocols for a number of marine 
monitoring methods (Przeslawski & Foster 
2020). These initiatives illustrate how such 
protocols can be developed, but do not yet 
include eDNA methods. The Best practice 
guidelines for environmental DNA biomonitoring 
in Australia and New Zealand, which will be 
reviewed frequently, could be used to design 
SOPs to expert-approved quality standards 
(De Brauwer et al. 2023).

Focus area

Technology

Applications

Timeline*

Analyses

Data inter-operability for 
bioinformatics

Spatial and temporal data comparability 
between park monitoring programs 
studies

2030

Machine learning 
bioinformatics

Metabarcoding surveys, large-scale 
monitoring

2030

Novel modelling methods 
for analyses

Improved understanding of marine 
ecosystems

2030

Application-based 
packages for analyses

Improved efficiency for targeted surveys

2025

Reporting

Data visualisation and 
communication

All eDNA projects that need to be 
communicated with the public 

2030





* Timeline is based on expected technological readiness for widespread integration in management.



Assay validation

So that results can be interpreted correctly 
and used to inform management, assays 
used to detect single species of interest 
need to be adequately validated and their 
limitations well understood (Klymus et al. 
2020, De Brauwer et al. 2022b). Assays used 
to inform management should be validated to 
the level where limits of detection and assay 
sensitivity are well understood (i.e. levels 4–5, 
following Thalinger et al. 2021). It will also be 
important to continue calibrating single-species 
assays with conventional methods to inform 
quantitative measures and ensure temporal 
continuity of methods (Rourke et al. 2021).

Calibration with conventional 
methods

Calibration with existing methods is 
equally important for metabarcoding 
(multi-species) assays. A next step in calibrating 
metabarcoding methods is to investigate 
if, how and when conventional and eDNA 
methods can be combined for different 
monitoring purposes (Andres et al. 2022). 
To optimise the benefits of different survey 
methods, monitoring frameworks should 
include robust guidelines on the best use of 
available methods based on goals, budget, 
staff and other logistical considerations 
(Andres et al. 2022). An important area of 
research relevant to marine park management 
is understanding how estimates of abundance 
can be derived from eDNA data (see 
Long-term future developments).

Ecology of eDNA

Refining the understanding of the ecology 
of eDNA, that is, ‘the origin, state, transport, 
and fate of eDNA within the environment’ 
(Barnes & Turner 2016) is of relevance to all 
eDNA applications. While such studies can 
be highly technical with seemingly limited 
immediate benefits to management, they are 
essential to improve survey design, increase 
sampling efficiency and reduce sources of 
error from data analysis (Barnes & Turner 2016, 
Scriver et al. 2023). This is particularly relevant 
considering the size and diversity of Australia’s 
marine parks and the need to understand if and 
how the behaviour of eDNA molecules differs 
across the vast range of conditions in parks.

Applied research

A wide range of new practical eDNA 
applications are being developed globally. 
These range from highly specific applications 
designed to detect single species in a particular 
context (e.g. Uthicke et al. 2022, Griffiths et al. 
2022) to projects designed to detect multiple 
species relevant to nationwide monitoring 
(e.g. McDonald et al. 2019). Here, we consider 
promising developments relevant to large-scale 
marine monitoring programs.

Ecosystem health indices

Nearly all monitoring programs aim to detect 
changes in ecosystem health over time to 
help assess the effectiveness of policy and 
management interventions (Lindenmayer 
& Likens 2010). The complexity associated 
with managing large, highly biodiverse 
ecosystems can make it harder to determine 
which signals are important for detecting 
meaningful long-term trends or impacts. 
Ecosystem health indices based on a set of 
indicator taxa are commonly used to monitor 
freshwater habitats (Borja et al. 2015). Such 
indices can provide a reliable indication of the 
condition of an ecosystem, but morphological 
species identification is time-consuming and 
dependent on dwindling taxonomic expertise 
(Cordier et al. 2019, Wilkinson et al. 2023).

Multi-species molecular health indices could 
provide invaluable information for marine 
park managers to rapidly assess environmental 
changes (Hering et al. 2018, Cordier et al. 2019). 
By using metabarcoding methods, such indices 
could incorporate hundreds or even thousands 
of additional taxa with different sensitivities to 
a range of environmental pressures. A benefit 
of using molecular versus morphological 
indices is that data from macro‑organisms 



(e.g. fish or habitat-forming species), smaller 
cryptic invertebrates (e.g. meiofauna, 
plankton) and even bacteria can be collected 
simultaneously and included in the same 
index, providing a much more complete and 
sensitive measure of health than is currently 
possible (Chariton et al. 2015, Aylagas et al. 
2017). Importantly from a management 
perspective, biodiversity metrics alone are of 
limited use without the ability to link changes 
to pressures or management interventions 
(Hillebrand et al. 2018).

Current research in molecular biological 
indices has primarily focused on freshwater 
species assemblages or marine microbial 
communities (Aylagas et al. 2017, Borja 2018, 
Apothéloz-Perret-Gentil et al. 2020, Beale 
et al. 2022a). While metabarcoding studies 
of marine eukaryote species assemblages 
can accurately reflect anthropogenic impact 
gradients (e.g. Chariton et al. 2015, DiBattista 
et al. 2020), they have yet to be tested against 
existing conventional biological indices or 
put into practice in monitoring programs. 
The development of custom molecular assays 
and workflows for marine parks could be done 
relatively rapidly; however, this will require a 
standardised environmental health status rating 
for marine park sites as a reference.

Early warning systems

The ability to detect micro-organisms or cryptic 
species has other potential applications beyond 
health indices. Monitoring trends in cryptic 
species communities could serve as an early 
warning system for shifting ecosystem dynamics, 
potentially allowing for more rapid, successful 
interventions (Beale et al. 2022b). A better 
understanding of the dynamics of these species 
could allow researchers to diagnose how major 
impacts might have knock‑on effects through the 
food chain, or to closely monitor recovery after 
major disturbances (Lanzén et al. 2021, Wolfe 
et al. 2023).

The same approach could be applied as a 
warning system for public health threats from 
species that are currently hard to monitor. 
Standardised or automated systems could be 
designed to detect harmful algal blooms, the 
presence of nuisance species such Irukandji 
jellyfish, or even dangerous sharks (Bolte et al. 
2021, Rolton et al. 2022).

Applications could be developed to monitor 
compliance and the impacts of different 
industries active within parks. These could 
include improvements to existing methods 
for the early detection of invasive pest species 
in ballast water, as biofouling, or settling in 
new regions (Zaiko et al. 2016, Shaw et al. 
2019). Assays can also be developed to detect 
the presence of bacteria or other species 
indicative of oil spills or sediment run-off 
(Lanzén et al. 2021).

Analytical improvements

Environmental DNA methods have the potential 
to generate vast quantities of data. The datasets 
typical for eDNA surveys are challenging to 
analyse with standard ecological methods. 
Challenges include the large quantities of 
data generated, the complexity of assigning 
sequences to taxonomical species, and inferring 
ecological meaning from eDNA datasets. Novel 
analytical methods are already being developed 
to address some of these challenges.

Bioinformatics pipeline efficiency

The first, essential, step when analysing 
eDNA metabarcoding results is to process 
raw sequencing data using bioinformatics 
pipelines. However, there is a lack of consensus 
on best practice or standardised methods and 
a subsequent lack of consistency between 
pipelines (Pauvert et al. 2019). Bioinformatics 
pipelines are often designed for specific 
study goals or specific labs, which results in 
limited inter-operability between datasets. 
Data analysed using different bioinformatics 
protocols are rarely directly comparable, even 
if samples were processed with the same 
laboratory workflow (Pauvert et al. 2019, 
Mathon et al. 2021).



Project-specific needs mean that strict (inter)
nationally standardised bioinformatics pipelines 
are often not desirable or feasible. However, 
designing guidelines on minimal metadata 
reporting would be a first step towards 
increasing data inter-operability (Samuel et al. 
2021). More research is needed to clarify how 
specific steps in bioinformatics protocols affect 
data variability. Until these factors are better 
understood, raw data and scripts should be 
made available to allow for spatiotemporal 
comparisons, especially when samples 
were collected for monitoring purposes. 
Improved reference libraries are also essential 
(see Infrastructure and logistics).

Machine learning methods

Processing large quantities of data in 
metabarcoding workflows is computationally 
intensive (Mathon et al. 2021, Flück et al. 
2022). One way of improving the speed and 
accuracy of taxonomic assignation is applying 
machine learning methods, such as supervised 
and semi‑supervised models or convolutional 
neural networks (Crisci et al. 2012, Cordier 
et al. 2019, Flück et al. 2022). Different machine 
learning methods are increasingly used to 
process eDNA data and have been used to 
develop biological indices (Cordier et al. 2018, 
Wilkinson et al. 2023). The main benefits 
of machine learning methods are the much 
faster speed (minutes instead of hours), 
increased accuracy, and potential large-scale 
applications (Bohan et al. 2017, Cordier et al. 
2019, Flück et al. 2022). While these methods 
show promise, they require strong expertise 
in computational modelling and are not yet 
ready for use in routine monitoring programs. 
Future work should investigate how precision 
can be further optimised, and how methods 
can be used in user-friendly applications.

Occupancy modelling

Species occupancy models aim to make 
inferences about alpha (local scale), beta 
(landscape scale), and gamma (macroscale) 
diversity and can be based on Bayesian 
or frequentist statistics (Bailey et al. 2014, 
Ferguson et al. 2015), with the former seen as 
more flexible (Burian et al. 2021). Although 
such models have predominantly been used 
to predict single-species dynamics to date, 
multispecies applications are increasingly being 
trialled (e.g. Fukaya et al. 2022).

Occupancy modelling applied to eDNA surveys 
aims to predict the probability of:

• species occurring at a site (occupancy)

• capturing the eDNA at a site (capture)

• detecting a species at a site (detection) 
(McClenaghan et al. 2020, Burian et al. 2021).

Advantages of this approach include the ease of 
incorporating covariates related to probability 
of detection (e.g. PCR amplification biases), 
false negative measurements errors, temporal 
dynamics of species-level occurrence, and 
species interactions (McClenaghan et al. 2020).

While these approaches show promise, further 
ground truthing across diverse systems is 
needed. The benefits of incorporating error 
measurement and capture probabilities can 
only be maximised if the data informing models 
is accurate (Willoughby et al. 2016). To achieve 
this accuracy, factors such as the ecology of 
eDNA (e.g. transport, degradation) and the 
effects of variations in lab protocols need to 
be better understood (Willoughby et al. 2016, 
McClenaghan et al. 2020).

Network analysis

Ecological network analyses are another class 
of models that have been applied to eDNA data 
(e.g. Evans et al. 2016, DiBattista et al. 2020, 
Seymour et al. 2020, Djurhuus et al. 2020). 
This approach assesses network properties 
that arise from analysing which taxa co-occur. 
Properties such as network connectivity, 
modularity and nestedness can convey 
information about the stability of ecological 
communities and how they respond to different 
impacts or management (Tulloch et al. 2018, 
DiBattista et al. 2020, Djurhuus et al. 2020).



The benefit of network analyses, particularly 
species co-occurrence networks, is that 
they do not necessarily require abundance 
data or taxonomic identification to describe 
communities and detect impacts or changes 
(Djurhuus et al. 2020, Seymour et al. 2020, 
Codello et al. 2022). However, to maximise 
these benefits, research is needed to determine 
which network properties (or combinations 
thereof) best predict community shifts or 
stability, how they correlate with conventional 
metrics, and how they can be used in real-
world predictive modelling (Codello et al. 2022).

Application-based software

Finally, there is increasing demand for 
user-friendly, application-based packages to 
speed up analyses for different monitoring 
purposes. Software packages or apps that 
directly address management needs without 
requiring specialist coding skills, specialist 
software or supercomputing resources would 
free up time and resources, which could instead 
be used to respond to the results.

One such application is Pest Alert, a new 
online app that automatically screens eDNA 
datasets for invasive species in New Zealand, 
even if the primary purpose of the dataset 
is not invasive species detection (Zaiko et al. 
2023). Applications that make it easier to re-use 
existing data for different purposes could be 
helpful to resource managers. For example, 
raw metabarcoding data initially collected to 
detect invasive taxa could be reanalysed for 
biodiversity studies, as a baseline to assess 
impacts, or to conduct long-term temporal 
studies. Such reanalysis would be supported 
by the development of custom data storage 
platforms that allow datasets to be archived, 
explored and extracted.

Reporting

Environmental DNA methods offer the potential 
to collect ever-larger amounts of monitoring 
data; however, this data only has value when 
used appropriately. Reporting is essential to 
ensure eDNA-based monitoring programs 
have real-world outcomes.

Depending on the audience, monitoring 
results are communicated in various formats. 
Reports written for management agencies are 
common, and publications in peer reviewed 
journals can be used to inform both the 
broader scientific community and marine park 
managers. Results can be shared with other 
stakeholders such as policy makers, industry 
and the public via white papers, public forums, 
websites and even social media.

Communicating detailed molecular results to 
non-experts can be challenging. Reporting 
must be clear and avoid jargon where possible, 
while still addressing the questions asked by 
the target audience. Examples of effective 
reporting to broad audiences include:

• the assessment summaries used in the GBR 
Outlook Reports (GBRMPA 2019)

• interactive survey maps, such as the 
Nonindigenous Aquatic Species map by the 
United States Geological Survey and the 
Reef Dashboard Monitoring Map by AIMS 
(Ferrante et al. 2022, AIMS 2023)

• biotic indices that clearly show ecosystem 
health (Wilkinson et al. 2023).

Developing clear communications often 
means engaging with professional science 
communicators to produce reports that are 
suited for the target audience.

Long-term future 
developments

The key to ensuring the integration of eDNA 
technologies into monitoring, is to ask what 
outcomes resource managers and policy 
makers (and by extension society) want to 
see from eDNA surveys. In other words, what 
does a finished eDNA product look like? In the 
long term, technological improvements must 
respond to societal needs and be developed as 
operational systems and tools.



Abundance: single species

Resource managers are interested in the ability 
to estimate the relative abundance of different 
species. Improvements in abundance estimates 
would increase the usefulness and uptake of 
eDNA methods in many marine parks.

The current literature suggests that 
relative measures of abundance can 
already be estimated from some, but not 
all, species-specific (qPCR) assays (Rourke 
et al. 2021, Skelton et al. 2022, Rourke et al. 
2023). Such assays need to be thoroughly 
validated and ideally compared to abundance 
estimates from conventional methods before 
operational use (Thalinger et al. 2021). Multiple 
environmental and species-specific biological 
factors can influence the appropriateness 
and effectiveness of abundance estimates for 
single-species assays. The routine use of eDNA 
methods to monitor single-species abundance 
is unlikely to become widespread without 
significant methodological developments. 
Better understanding of species-specific factors 
influencing DNA shedding rates (e.g. season, 
life stage, body size) and the ecology of eDNA 
(e.g. eDNA decay and transport) is needed 
to inform correlations through, for example, 
allometric scaling (linking organism biomass to 
eDNA shedding rates) (Yates et al. 2021)

Abundance: species 
communities

There has been comparatively less research 
into the abundance measures associated with 
metabarcoding (multi-species) assays (Rourke 
et al. 2021). The recent literature suggests that 
in some cases, abundance estimates obtained 
from metabarcoding assays are correlated 
to those from conventional survey methods 
(e.g. Yates et al. 2019, Fraija-Fernández et al. 
2020). However, these correlations do not 
hold across all studies (e.g. Lim et al. 2016) and 
scientific publishing bias means that failures to 
detect correlations could remain unpublished 
(Yates et al. 2019).

Therefore, the use of eDNA metabarcoding to 
reliably monitor multi-species abundance will 
require sustained research effort and method 
improvements over several years. Parallel 
surveys with conventional methods across 
temporal scales will aid calibration of these 
methods and might allow for operational use 
in the next decade. These should, however, be 
combined with controlled experiments and 
a better understanding of the mechanisms 
underlying the PCR process (e.g. PCR bias, 
amplification efficiencies) that might affect PCR 
read abundance (Kelly et al. 2019, Rourke et al. 
2021, Shelton et al. 2023).

Physiological condition

Being able to understand the physiological 
states of species of interest would assist marine 
resource managers in some circumstances, 
particularly when managing fisheries or 
endangered species. Early research is exploring 
how data such as the biomass, body size, 
age, fecundity or health of individuals can be 
derived from eDNA surveys. Some progress 
has been made using data based on eRNA 
to indicate gene expression state (i.e. animal 
condition; Yates et al. 2019). Also under 
development are methods for isolating and 
analysing individual cells from the environment 
(‘emCells’) to make inferences about abundance 
and other characteristics of target species 
(Miller et al. 2023).

Population genetics

Another long-term research frontier for eDNA 
monitoring is characterising the genetic 
population structure of species (Adams et al. 
2019). Studying population genetics can 
answer questions related to genetic diversity, 
the occurrence of hybridisation, effective 
population size and extent of dispersal, which 
can inform marine spatial planning decisions 
and restoration programs (Sigsgaard et al. 
2016, Bani et al. 2020). Environmental DNA 
methods have been used to survey genetic 
variation in populations of species such as 



abalone, porpoises, fishes and whale sharks 
(Parsons et al. 2018, Tsuji et al. 2020, Dugal 
et al. 2022, Adams et al. 2022). Extensive field 
and laboratory research is required to resolve 
questions such as: how can sequences be 
assigned to individual organisms? What DNA 
markers are most appropriate for these 
questions? How does allelic abundance reflect 
real abundance? And can current statistical 
assumptions (e.g. the ability to differentiate 
between individuals) be applied to eDNA 
data (Parsons et al. 2018, Adams et al. 2019)? 
Many of the advancements in other fields 
of eDNA research discussed in this section 
will also feed into eDNA applications in 
population genetics.

Cross-technological 
integration

The integration of large-scale eDNA monitoring 
programs with other survey methods, such as 
remote sensing, may offer opportunities for 
improved spatial planning and management 
(Bani et al. 2020). Automated eDNA monitoring 
systems could feed into spatial datasets to 
create nationwide, near-real-time monitoring 
networks (Bohan et al. 2017). Designing 
workflows that feed into online platforms 
or spatial planning frameworks would be of 
high relevance to dynamic ocean planning, 
incident responses and permit applications 
(Lewison et al. 2015, Dunn et al. 2016). 
New data management infrastructure will need 
to be designed to handle increasingly large 
volumes of data, but could be supported by 
novel data architecture developments such as 
data fabrics or meshes (Machado et al. 2022, 
Hechler et al. 2023).

Global perspectives 
and the inter-operability 
of eDNA data

The increased integration of molecular 
methods in monitoring and natural resource 
management is not restricted to Australia. 
Government and resource managers globally 
are adopting eDNA surveys as part of their 
monitoring toolbox, with levels of uptake 
varying from initial trials to standardised 
long‑term programs (Table 7).

Many developed countries have integrated 
or are planning to formally integrate eDNA 
and other omics methods into government 
monitoring programs in the next decade 
(Goodwin et al. 2020, Norros et al. 2022). 
The successful EU-funded DNAqua-Net program 
consisted of nearly 600 research and policy 
members from 36 European countries and 
aimed to improve eDNA methods and their 
uptake (Leese et al. 2016). Finland recently 
published a roadmap that aims to implement 
molecular monitoring methods (including 
eDNA) in national monitoring programs by 
2030 (Norros et al. 2022). In the USA, NOAA 
recently released a strategic 5-year plan 
to facilitate the uptake of various omics 
technologies in its monitoring programs 
(Goodwin et al. 2020).

Current applications centre around biosecurity 
(e.g. McDonald et al. 2019, Jerde 2021), 
single‑species monitoring (Biggs et al. 2015) and 
freshwater biodiversity (e.g. Leese et al. 2016, 
Hering et al. 2018). Standardisation of methods 
and results reporting is seen as central to the 
reliability and interoperability of this global 
movement towards omics-based monitoring 
(Berry et al. 2020, Samuel et al. 2021, Zaiko 
et al. 2022). Developing international initiatives 
that support best practices and help increase 
interoperability of the data generated by eDNA 
surveys would maximise the applications for 
management at both regional and international 
scales (Shea et al. 2023).



The need for such initiatives is recognised in 
the United Nations Ocean Decade framework 
(e.g.in relation to the challenge of expanding 
the global ocean observing system). 
International programs such as the Ocean 
Biomolecular Observing Network (OBON) are 
addressing the Ocean Decade challenges by 
hosting a suite of projects aimed at improving 
monitoring methods (Table 7). OBON projects 
of particular relevance to eDNA technologies 
include the NBDL, Better Biomolecular Ocean 
Practices and the Minderoo Foundation’s eDNA 
program, OceanOmics.

Standards and best practice guidelines are 
also being developed on national and regional 
levels (Table 6). The diversity in methods and 
applications used to detect eDNA means that 
standardisation attempts often focus on either 
broad principles or very specific workflows 
(e.g. metabarcoding in marine environment, 
diatom detection in freshwater systems). 
National initiatives tend to focus more on 
general best practice guidelines, with currently 
only a few initiatives aiming to develop formally 
accredited standards such as International 
Organization for Standardization standards 
(Table 7).

The establishment of national and 
international scientific societies focused on 
environmental omics methods reflects the 
increased use of eDNA methods and the 
demand for standardisation. These societies 
are well‑connected internationally and are 
likely to drive formalised standardisation and 
collaboration initiatives. SeDNAS aims to ensure 
that Australia and New Zealand guidelines are 
in harmony with international developments 
(De Brauwer et al. 2023).



Table 7 Recent global initiatives for eDNA standardisation and interoperability

Type

Region

Title

Goal

Organisation

Standard

Canada

Environmental DNA (eDNA) reporting 
requirements and terminology 
(Gagne et al. 2021)

Provide minimum reporting requirements 
for the planning, execution, analysis, 
interpretation, and reporting of eDNA projects

Canadian Standards 
Association

Standard

Europe

CEN/TC230/WG28 

Create ISO-approved standard for eDNA water 
sampling methods

DNAqua-Net and the 
European Standardisation 
Committees

Guidance 
document

Global

Minimum Information for an Omic 
Protocol (Samuel et al. 2021)

Orient protocols for the discovery of suitable 
protocol suites on the Ocean Best Practices 
System

Ocean Best Practices System 
Omics/eDNA Protocol 
Management Task team

Guidance 
document

Australia and 
New Zealand

Best Practice Guidelines for 
environmental DNA biomonitoring 
in Australia and New Zealand 
(De Brauwer et al. 2023)

Set minimum standards to support a consistent 
and best practice approach to eDNA testing

Southern eDNA Society

Guidance 
document

Canada

Environmental DNA Standardization 
Needs for Fish and Wildlife 
Population Assessments and 
Monitoring (Helbing & Hobbs 2019)

Guide, solicit support, and encourage 
development of rigorous standards by 
providing a comprehensive overview of current 
understanding and anticipated challenges

Canadian Standards 
Association

Guidance 
document

Canada

Guidance on the use of targeted 
environmental DNA (eDNA) analysis 
for the management of aquatic 
invasive species and species at risk 
(Abbott et al. 2021)

Provide a model for consistent and transparent 
communication and reporting of eDNA results 
aimed at fisheries and oceans managers

Department of Fisheries 
and Oceans Canada







Type

Region

Title

Goal

Organisation

Guidance 
document

Europe

A practical guide to DNA-based 
methods for biodiversity assessment 
(Bruce et al. 2021)

Summarise the scientific consensus relating 
to every step of the eDNA field and laboratory 
workflows involved in the most common types 
of samples and analyses

DNAqua-Net

Guidance 
document

Europe

A validation scale to determine the 
readiness of environmental DNA 
assays for routine species monitoring 
(Thalinger et al. 2021)

Describe the measures and tests necessary for 
successful validation of targeted eDNA assays 
to form the basis of guidelines

DNAqua-Net

Guidance 
document

Japan

Environmental DNA sampling and 
experiment manual 

Promote and standardise eDNA analysis 
methods

The eDNA Society

Guidance 
document

Switzerland

Environmental DNA applications in 
biomonitoring and bioassessment of 
aquatic ecosystems (Pawlowski et al. 
2020)

Provide detailed protocols and best practices 
for processing eDNA samples

Federal Office for the 
Environment 

Platform

Global

Ocean Best Practices System 

Enhance management of methods and support 
the development of ocean best practices 
through a global, sustained system comprising 
technological solutions and community 
approaches

Ocean Best Practices System

Platform

Global

Omic Biodiversity Observation 
Network 

Promote intercalibration of biomolecular 
observing technologies, the development of 
globally harmonised practices, standards and 
protocols to help establish global coordinated 
biomolecular observations

Biodiversity Observation 
Network








Type

Region

Title

Goal

Organisation

Platform

Global

Biomolecular Ocean Observing 
Network 

Develop a global system that will allow 
science and society to understand ocean using 
biomolecular methods

UN Ocean Decade action

Platform

Canada

Pathway to Increase Standards and 
Competency of eDNA Surveys 

Explore and inform public policy, industry 
strategies and future research on eDNA

University of Guelph

Platform

Europe

Bioscan Europe

Create a shared European perspective and 
framework for effective DNA-based biodiversity 
monitoring, connecting and enhancing 
national DNA barcoding infrastructures and 
initiatives

Bioscan Europe







Acronyms, initialisms and glossary

Term

Definition

AAD

Australian Antarctic Division

AIMS

Australian Institute of Marine Science

Assay

The laboratory workflow from DNA extraction to sequence outputs. Often refers 
more specifically to the target gene and taxonomic group (e.g. 16S_Fish, 18S 
universal, COI).

AUV

Autonomous underwater vehicle

ASV

Amplicon sequence variant

BRUV

Baited remote underwater video

CoTs

Crown of thorns seastar

CSIRO

Commonwealth Scientific and Industrial Research Organisation

DBCA

Department of Biodiversity, Conservation and Attractions

DCCEEW

Department of Climate Change, Energy, the Environment and Water

ddPCR

Digital Droplet PCR, a quantitative PCR method based on water-oil emulsion 
droplet technology.

DOV

Diver operated video

EEZ

Exclusive economic zone

Environmental 
DNA or RNA 
(eDNA or eRNA)

DNA or RNA present in environmental samples (soil, sediment, water, etc.), often 
without observation of the original organism. DNA carries genetic instructions for 
the development, functioning, growth and reproduction of organisms, while RNA 
transfers information within cells to produce specific proteins and is believed to be 
only shed by physiologically active (living) organisms.

EPA

Environmental Protection Authority

FAIR (data)

Findable, accessible, inter-operable, and reusable (data)

GBR

Great Barrier Reef

GBRMP

Great Barrier Reef Marine Park

GBRMPA

Great Barrier Reef Marine Park Authority







Term

Definition

HIMI

Heard Island and McDonald Islands

HTS

High-throughput sequencing

IMOS

Integrated Marine Observing System

IUCN

International Union for Conservation of Nature

Library (also 
Reference 
library, 
Reference 
database)

Database with DNA sequences of specific species

MER

Monitoring, evaluation and reporting

Metabarcoding

Simultaneous taxonomic identification of multiple species (or OTUs ASVs in eDNA 
samples with millions of sequences, generated by PCR amplification using high-
throughput sequencing techniques

MIMP

Marine Integrated Monitoring Program

MinION

A type of portable DNA and RNA sequencing device manufactured by Oxford 
Nanopore Technologies

mOTU

Molecular operational taxonomic units

NBDL

National Biodiversity DNA Library

NESP

National Environmental Science Program

NOAA

National Oceanic and Atmospheric Administration

NOPSEMA

National Offshore Petroleum Safety and Environmental Management Authority

OBON

UN Ocean Biomolecular Observing Network

Operational 
taxonomic unit 
(OTU)

Uniquely recurring DNA sequences used as a proxy for diversity. These 
taxonomically similar units are grouped according to their close DNA sequence 
similarity. Used a unit of diversity when conventional biological classification is not 
possible or desirable.

Polymerase 
chain reaction 
(PCR)

A molecular technique that allows the exponential amplification of a target 
fragment or region of DNA from a mixture of DNA fragments. The desired 
fragment is selected from the other fragments in the mixture by specific primers 
(small single-strand oligonucleotides) complementary to the desired sequence.







Term

Definition

Primer

Short DNA fragments used in PCR amplification that bind adjacent to the target 
region or gene. They enable the amplification and sequencing of specific parts of a 
genome and from specific groups of organisms.

Quantitative PCR 
(qPCR; also real-
time PCR)

A variant of PCR. The main difference is that qPCR quantifies the amount of DNA in 
the original sample.

RIMReP

Reef 2050 Integrated Monitoring and Reporting Program

ROV

Remotely operated underwater vehicle

SeDNAS

Southern eDNA Society

Sequencing

Determining the order of nucleotides in DNA or RNA; this can be done with a 
variety of methods

SHP

Signs of Healthy Parks

SOP

Standard operating procedure

TEP

Threatened, Endangered and Protected (species)

UNESCO

United Nations Educational, Scientific and Cultural Organization

UVC

Underwater visual census

zOTU

Zero-radius Operational Taxonomic Unit (see OTU)







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