Soil sampling in Coober Pedy, South Australia

Soil sampling in Coober Pedy, South Australia.

A layer of life under your feet

The Biomes of Australian Soil Environments (BASE) project will provide the first comprehensive continent wide inventory of soil biodiversity.

  • 5 September 2012

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Glen Paul: G’day, and welcome to CSIROpod, I’m Glen Paul. Australian soils mirror the continent’s great age, and as a result are products of environmental conditions of this long history, such as climate, topography, parent material, and the organisms that make soils their home. Surprisingly far less is known about these microscopic communities of organisms compared to above ground biodiversity, and with them playing such a crucial role in ecosystem function, Scientists naturally want to know more.

Now with the help of new technology the Biomes of Australian Soil Environments, or BASE Project, has been established to bring together a number of agencies, including CSIRO, and the Victorian Department of Primary Industries, for a two year $3 million study of soil ecosystems across the entire Australian continent. Joining me on the line is the Director of the Centre for Australian National Biodiversity, CSIRO’s Professor Andrew Young.

Andrew, this is obviously a massive project, but is it just a matter of scientific curiosity, or is there something more to be gained by understanding all these different soil ecosystems?

Prof. Young: Yes, soil is probably the least understood environment we have across Australia, and one of the ones that perhaps has greatest ecological significance. Soil environments are important in nutrient cycling, in maintaining ecosystem stability, in underpinning the productivity of our agricultural systems, and up until now it’s been very difficult to look at the soil micro biome, all the microbes that make up that environment, using traditional lab techniques, and so being able to move into the world of metagenomics and use DNA technologies to understand the composition of those ecosystems is something that’s going to be really helpful in understanding what is one of our really important ecosystems.

Glen Paul: Hmm, sounds like it. But where did metagenomics kind of spring from?

Prof. Young: Metagenomics is really a product of a revolution in DNA sequencing technology. So 20 years ago when I was a PhD student it took several months to extract DNA from maybe 20 or 30 samples and sequence with short pieces. With the advent of two things really, very high throughput genotyping technologies called next-generation sequencing, which has come about over the last five years, and huge advances in bioinformatics, so the ability to handle very large sequence datasets, have meant that we can now isolate very large numbers of samples and analyse them to see what DNA there is in an environmental sample, and then we can take that sequence information, search it against a database of microbes, and use that to tell us what microbes are available.

So really it’s been a combination of sequencing technologies and big advances in bioinformatics, the handling of large numbers of sequence data.

Glen Paul: And 20 years ago you probably wouldn’t even contemplate undertaking something as vast as this. Just how much of Australia is going to be surveyed, and who’s involved?

Prof. Young: So having said we can do it because of the advances in these two fields, that’s true theoretically, but operationally we can only undertake the project by collaborating with colleagues at Bioplatforms Australia who are undertaking the large portion of the sequencing effort, and colleagues at the National Parks Service. So we’re using the National Reserve system, which is managed by Parks Australia, as a sampling framework to collect samples from, and also the NCRIS (National Collaborative Research Infrastructure Strategy) and TERN (Terrestrial Ecosystem Research Network) sites, the long term environmental monitoring sites, and ecological sites run by DECWA in W.A., so it’s bringing those three together, they give us the samples, Bioplatforms Australia is doing the sequencing, and CSIRO is doing the bioinformatics analysis. So really it’s the three large partners, those doing the environmental sampling, those doing the sequencing, and ourselves doing the bioinformatics, which is letting the project happen.

In terms of the scale of the sampling, we’re certainly in the first instance trying to sample 250 sites from as broad a range of Australian environments as possible. So we’ve built environmental models of the country that include both soil and vegetation, and then distributed those 250 samples as best we can to cover as much of the environmental amplitude as is possible.

Glen Paul: OK. And what about the samples themselves, how do you collect them? Is it just a matter of going out with a garden trowel and putting soil into a plastic bag, or do you take core samples? How does it work?

Prof. Young: Yeah, so taking environmental samples for DNA analysis, whether they’re soil samples, or water samples, or samples from sewerage pipes, which some of these are used for, is a difficult thing to do – you need to keep the samples very clean, because you don’t want contamination. So when we go to a site we put out a 25 by 25 metre plot, we take nine soil cores down to about 30 or 40 centimetres, and we divide them into the top ten centimetres and 20 centimetres and below, because you get quite different microbial communities in those two environments – one which has more oxygen than the other – and then we freeze them, bring them back to the lab, and we can do the metagenomic analysis.

Glen Paul: When the study is complete, how will the microbial information be used to better farming practices?

Prof. Young: So there’s really two bits to the project. The first part, which we’re largely involved in at the moment, is trying to set a bit of a baseline. We know so little about soil microbial communities, the initial questions are pretty simple – what do we have; how much is there; and how does that relate to environment? So they’re really the three big first questions we’re trying to ask. It’s sort of an audit of Australian soil, microbial diversity, and we can then compare that because we are part of what’s called the Earth Microbiome Project, we’re the Australasian node of that project, and we can compare what we have here in Australia to samples from all over the planet that have been taken by labs in other countries.

So some of it’s a bit phenomenological, we’re just trying to see what we have, where it is, how does that relate to environment, and then we’re using those data as a baseline and taking another 250 samples in a whole range of different agricultural sites, so cotton, wheat, forestry sites, horticultural sites, and by comparing those against the baselines we can start to understand how agricultural practices change the soil microbial community, and what that might mean for long term productivity and ecological sustainability.

And interesting also with there being a big push to look at restoration of native forests in some areas, and grasslands, so turning old unproductive agricultural land back into native ecosystems, we can start to get a feel for what kinds of microbes we might want to restore as part of that process, because managing the microbes in that way could really help us with the long term success of native revegetation projects as well.

Glen Paul: So are you expecting any surprises from it, perhaps an idea that might be confirmed, or maybe a new species that might turn up?

Prof. Young: I guess one of the really big things we’d like to know is whether soil microbes obey the same broad ecological rules that higher organisms like plants and animals do. So do you see changes in soil communities in the same sorts of way along energy gradients, along latitudinal and longitudinal gradients, across environmental gradients? So are they basically responding to the same kinds of cues as aboveground biodiversity?

And that’s something that we don’t know much about, so it’s a pretty important thing to try and find out. But I think it’s going to be full of surprises. I think it’s going to be full of surprises in understanding how these organisms behave ecologically, simply because we haven’t had the ability to look at them in detail before. And I think it’s going to be full of surprises in seeing for the first time suites of microbes that we just might not have seen before, that might even be completely new to science.

Glen Paul: That of course would be very exciting, so best of luck with the research, and thank you very much for discussing it with us today, Andrew.

Prof. Young: A pleasure.

Glen Paul: Prof. Andrew Young. And to find out more about the research being undertaken at CSIRO, and to follow us on other social media, go to

BASE participant organisations