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The challenge

Understanding soil microbes

Soil microbes are vital for ecosystem health, supporting soil fertility, species diversity and resilience in natural ecosystems.

The soil microbiome is one of the most genetically and ecologically diverse communities on Earth, but is poorly understood. Soil microbes are difficult to measure in the field or culture in the lab. This has severely limited Australia's ability to measure and manage soil microbial diversity to achieve positive outcomes for agriculture and the environment.

Our response

Mapping Australia’s microbiome

Working with custodians and land owners, we sampled soils from more than 1500 sites across Australia and the Antarctic, spanning deserts, agricultural lands, the tropics, alpine regions, coastal areas and beyond.

Sampling soil with National Parks staff near Uluru, Northern Territory.

To identify the microbial species present in each soil sample we used next-generation DNA sequencing, solving the challenge of handling more than 90 billion DNA sequences.

Using new analytical and visualisation tools to enable people to use the terabyte scale data that results from deep sequencing of environmental samples, we built a comprehensive reference database, or map, of the Australian soil microbiome: Biomes of Australian Soil Environments (BASE). It can be combined with other environmental data, including meteorological data, climate data, biological surveys, geochemical information and vegetation type.

We published the BASE dataset in the international data journal GigaScience and have made it openly accessible on the Biome of Australian Soil Environments, Bioplatforms Australia website.

The results

A national framework dataset

BASE solved a major national science challenge by measuring and modelling the biological and functional diversity of Australia's soil microbiome at a continental scale - a world first. It is a globally unique resource for environmental research and management.

Soil sampling sites across Australia.

BASE is now being used across the innovation sector, creating positive impact for Australia in mineral exploration, restoration biology, agricultural, land management and commercial development of soil-related products.

Forensic scientists are also using BASE as part of their work to develop a forensic framework of Australian soils, enabling better use of soil as a forensic tool and improved biosecurity assessments.

The Australian marine science community has adopted the BASE data management and public access model and is adding their data to produce a national combined land and sea microbiome dataset for Australia.

BASE continues to grow, with new contributors providing soil samples from across the continent. It continues to deliver value to diverse users across a broad sweep of sectors and, through this, positive impact for Australia.

BASE has more than 25 research partners and is led by:

  • Bioplatforms Australia
  • Agriculture Victoria
  • University of Adelaide.

BASE is now feeding into the Australian Microbiome initiative, which seeks to understand the function of microbes in the environment.

Our Collaborators

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