Soil microbes underpin a healthy planet. We've used next-gen DNA sequencing to map Australia's soil microbiome. Our map is being used for forensics, agriculture, conservation and more.

Four people taking soil samples with Uluru in the background.

Sampling soil at Uluru with National Parks staff.

Beneath our feet is a universe of microbes. The number of bacteria in Earth’s soils rivals the number of stars in the observable universe, and that’s not counting other microbes like fungi.

Soil microbes are vital for ecosystem health. They support soil fertility, agriculture, species diversity and resilience of our natural ecosystems.

You could even say that soil microbes run the planet. They take care of ecological processes like nutrient and carbon cycling and water purification. They help plants take in nitrogen from the soil. Like our own friendly gut bacteria they suppress plant diseases present in the soil.

How do we know what’s living in our soils? Until very recently, we didn’t. Counting microbes in the field, in the traditional way of surveying or collecting biodiversity, is obviously impossible. And while soil microbes are happy in the soil, try culturing them in the lab and you’ll find that most of them die while a few grow out of all proportion.

So over the last five years, we’ve run a project known as BASE – Biomes of Australian Soil Environments. Working with custodians and land owners, we sampled soils from more than 1500 sites across Australia, spanning deserts, agricultural lands, the tropics, alpine regions, coastal areas and beyond.

We then used next-generation DNA sequencing to identify the microbes present, handling more than 90 billion DNA sequences in the process. To make the resulting terabyte-scale data usable by real people, we built a map of Australia’s soil microbiome.

Map of Australia with soil sites marked and five photos of soil sites.

Map of soil sampling sites around Australia.

Our map is a world first, a globally unique resource for environmental research and management. It’s being used in many different ways: mineral exploration, land management, agriculture and even forensics.

One of BASE’s most interesting uses is in restoring landscapes. It turns out that areas with similar ecosystems have similar soil microbes, even if they are vast distances apart. You may have heard of a faecal transplant, where the gut microbiota of a healthy donor are transferred to a patient suffering an untreatable gut infection. The same can be done for soil, transplanting a little soil from a healthy ecosystem to help restore one that has been altered by farming, mining or other land uses, paving the way for successful plantings of local trees and other plants.

BASE continues to grow, with new contributors providing soil samples from across the continent. And the marine science community is adding data about our marine microbes to produce a national combined land and sea microbiome dataset for Australia.

The BASE dataset was published in the international data journal GigaScience and we are working on making it openly accessible on the Atlas of Living Australia, where it can be combined with other environmental data, such as climate data, geochemical information and vegetation type.

BASE has more than 25 research partners and is led by us in partnership with Bioplatforms Australia, Agriculture Victoria and the University of Adelaide.

You can find out more about our work with soil and see the dataset for yourself here.

13 comments

  1. Wonderful approach and great initiation. Keep sharing affirmative blogs.

  2. The article you have shared here very good. This is really interesting information for me. Thanks for sharing!

  3. This seems to be a very interesting area of research!
    I’m curious about urban environments and the microlife in soils there. How much of our urban soil contains a healthy amount and variety of microlife? What conditions help it to thrive? How do we best look after it?
    Even within a block or two the soil can be treated very differently:
    . nature strip mown & ignored,
    . sports field and park – grass may be fertilized, tree/shrub areas mulched,
    . urban garden (1) shurbs, trees and lawn occasionally bark mulched
    . urban garden (2) shrubs, trees and lawn bark mulch, chemical fertilizer
    . urban garden (3) shrubs, trees and lawn, sugarcane mulch & compost, organic fertilizer
    . urban garden (4) succulents and arid species, stone mulch
    And there are many other variants.
    There are other factors besides: does microlife vary between shaded and unshaded areas? Does it vary depending on the moisture content of the soil? Does it vary depending on what goes into your compost?
    I’m particularly interested in the latter because I have lately started using the bokashi system. This allows materials that you would not use in a regular compost system to be composted including cooked foods. Using the bokashi system means that my waste is now mostly unrecyclable plastics and fats/oils and much decreased in volume. If bokashi is also microlife friendly then it could potentially be used a lot more in urban areas.
    If there was an opt in system for the disposal of the kinds of waste that bokashi can handle, with many very local composting cells to avoid the spread of weeds and diseases I wonder how much we could cut the volume of our landfill. This could be a way that the local ‘green army’ idea could be put to work – collecting material from people who don’t wish, or in the case of apartments do not have the facilities, do their own composting.
    Using bokashi you can compost vegetable scraps, cooked food scraps, dirty paper including kitchen paper and tissues, used paper based cat litter etc. This can then be mixed with garden waste and composted a second time (that is also when I would add the cat litter to the compost tumbler). Bokaishi can also handle cloth. (I would not use the resultant compost on soil used for growing food for consumption if it contained cat litter etc.)
    But it does also raise questions about what kind of cooked food is not appropriate, I wouldn’t put in anything very salty, and would be cautious to add much food that had artificial flavouring. But I don’t know whether it would make any difference. In the case of cloth, it might be best limited to fabrics that don’t contain plastic. But I would like to know – not only for my own garden soil but because that could make a difference to whether an opt in scheme could work at a local level, as the less the user needs to remember the easier it would be to use.

  4. Thank you for posting the data..very informative

  5. That this information should be communicated to all levels of government, with requests that it be incorporated into their planning systems present coarse and inadequate considerations on environmental impacts of development

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