Environomics, short for environmental genomics, is a technology platform to see beyond the landscape to its genescape, to reveal and make use of its genetic resources.

Mobilising collections through genomics

Natural history collections are vast biodiversity reference libraries, used for hundreds of years to help identify, understand and manage biodiversity. Until today, taxonomic classification of species relies on visual differences and we are still unable to identify most of the world’s species using DNA. This is a huge obstacle for life science researchers, whose work is largely driven by molecular data.

A scientist working with specimens stored at the Australian National Insect Collection.  ©CSIRO, Martin Ollman

Our goal is to create the capability and capacity to generate the DNA reference sequences needed to link modern research to existing knowledge of species.

We are developing workflows to mobilise the genomic information locked within our 15 million specimens that make up the National Research Collections Australia. We are focussing on: reducing costs per sample, building capacity to handle up to 1,000 samples per day, automating workflows from sample to analysis result, and reducing the risk of cross-contamination.

Our work will enable us to tackle big future science questions in evolution, ecology, biosecurity and conservation, helping us to better understand and manage the great biodiversity of Earth in an efficient way.

Project lead: Dr Andreas Zwick

Rapid assessment of environmental stress for major Australian plant groups

Rapid assessment of environmental stress will provide information that is important for managing and conserving Australian plants in rapidly changing environments.

Our research is looking at new ways to measure environmental stress in trees.  © Flickr CC2.0, Alex Proimos

One of the most popular approaches for studying plant stress involves the measurement of changes in the fluorescence emitted from chlorophyll pigments in leaves. Plant roots, which may be the first organ to experience environmental stress, are not amenable to this approach because they typically have little or no chlorophyll.

A very exciting alternative approach is to create a device for the detection of conserved microRNAs that increase in abundance in all organs when plants experience stress. MicroRNAs are becoming widely used as biomarkers of human disease and cancer. We will first identify a common set of microRNAs that increase under stress in all plant groups tested in glasshouse and field trials. Based on their known sequences, we will then design and test a novel microfluidic platform to detect changes in their abundance. Ultimately, we aim to produce a device for the on-the-spot, rapid detection of stress that can be used as an early alert tool for land managers.

Project Lead: Dr Sarah Mathews

Understanding stress in Australia’s animals and plants

Project lead: Clare Holleley

Environmental changes cause stress to our biodiversity, increasing the chances of disease outbreaks, extinctions, waves of invasive species and other environmental problems that can occur in stressed ecosystems.

Many plant specimens are carefully documented and stored at the Australian National Herbarium in Canberra.  ©CSIRO, Martin Ollman

We are developing new ways to detect stress responses in Australian animals and plants, looking into the genomes of specimens in CSIRO’s National Research Collections Australia to provide evidence of stress responses in the past. We’re also mapping species distributions again past, current and future stressors.

The results will help Australia identify areas at risk and monitor them for early warning signs of stress, predict disease outbreaks like influenza and help design early-interventions for natural resource management.

Project lead: Dr Clare Holleley

Mapping pollinator networks

Biodiversity and food security both depend on pollination of native plants and crops. But pollinators are in decline due to threats such as land clearing, habitat fragmentation, pesticides and climate change.

A blue-banded bee, Amegilla (Zonamegilla) asserta, from the Australian National Insect Collection. This specimen was collected in 1971 and still has pollen stuck to its legs. Photo by Juanita Rodriguez Arrieta.

We are researching pollinator networks in Australia to improve our knowledge of Australian biodiversity. We are building networks of interactions between plants and their pollinators using new DNA technologies, including pollen DNA metabarcoding.

Along with fresh specimens, we’re using native bees, wasps and flies in the Australian National Insect Collection that were collected as long as 50 years ago and have pollen still stuck to them. From the pollen DNA we’re identifying the plant species these insects visited and matching this with field data and plant specimens in the Australian National Herbarium.

Our work will reveal how plant-pollinator communities have changed in the last decades and identify keystone species for ecosystem functioning and crop pollination in different areas of Australia.

Project lead: Dr Francisco Encinas-Viso

Environmental DNA (eDNA) for mapping biodiversity, detecting pests and characterising food-webs

Understanding the distribution and abundance of organisms is a central focus of biological science, and underpins almost all environmental management. Yet, in practice detecting and identifying organisms in the environment remains extremely challenging, particularly across large ecosystems.

A tropical reef fish.  © CSIRO, Robert Kerton

Environmental DNA (eDNA) analysis is an emerging molecular technique for DNA-based identification of organisms.

Use of eDNA methods and analysis means that organisms can be detected and identified without capture or observation, even if they occur at low densities. These methods have the potential to transform the collection, analysis and use of biological data as well as increase our understanding of how ecosystems function and how they can be managed.

This project will showcase the application of eDNA methods using five case studies across freshwater and marine ecosystems and evaluate eDNA’s capacity to provide meaningful biological information to support practical decisions.

Project lead: Dr Olly Berry

Microbes and healthy waterways

What is the relationship between microbes and healthy waterways? We know that microbes influence ecosystem health in many fundamental ways, but their exact role in our marine environment is not well understood. This means that microbes are not well integrated into ecosystem health assessments and ecological models, which are relied on heavily in marine management.

We are assessing the relationship between the microbes present and their role in the ecosystem at several coastal sites around Australia. We are addressing a question fundamental to microbial ecology: what is the relationship between identity and function? Our project will also establish baseline data of microbial diversity and ecosystem health for use in ecosystem models.

Project lead: Mr Andrew Bissett

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