Microblitz - Mapping Soil Biota in WA
You don't need a PhD to do science of global significance; that's according to microbiologist Andy Whiteley. When he was in the UK he mapped the microbes hidden in the soil nationwide by hiring scientists to send him samples from across the country. But when he moved recently to the University of Western Australia and wanted to repeat the project he knew it was never going to be possible without some help from the public; so he's started a project that launched this month called Microblitz.
Chris Smith met up with him to discuss the project.
Andy - MicroBlitz is basically a science for 21st century. We're looking at what microbes are hidden away in the sun and where are they? This is important for a couple of reasons. The first one really is, is that when plants grow, and basically, we have productivity above ground, half of that cycle is actually below ground. So, these are the microbes that are sitting there in the ground that are helping. And it's really about asking the question, where are they and what are they doing? And these microbes are actually really diverse. So for example, when you put your footprint down in a paddock or a field, there's about 10 trillion individual bacterial cells in that.
Chris - 10 trillion!
Andy - 10 trillion in that footprint and about 10,000 species of bacterias where we think - that's an estimate and it's probably an underestimate. So, this whole world of biodiversity is hidden away below the ground and this project is to empower the general public's helpers to take samples out in their natural environment to help work out in terms of the microbes, what's there and where are they?
Chris - If I put my foot down on the beach here because we're looking at the Swan River in Perth, will I get different bacteria in the soils beside this river compared with somewhere else in the world?
Andy - We think there are some common bacteria that are present all over the world, so globally distributed. But yes, in terms of different habitats and different environments, we do see different species and different relative proportions of those species as well. So, there are what we call biomes of bacteria. There are certain types of bacteria that always associate with soil. Certain types would, for example, associate with sandy beach wave standing and for example, certain types of bacteria that will associate with the waters actually flowing down Swan River just in front of us.
Chris - So, what gave you the idea for doing this project in the first place?
Andy - The original mapping part of the project was a project that was happening in the UK in 2007 when I worked at the Centre for Ecology and Hydrology. The project when it came about asking the question, okay, we have this landmass in the UK and this has very different uses in terms of agriculture and various other grasslands and things such as that. And asking the question, "Well, do those different uses of the landscape actually change the microbial communities that are present within the different types of soils and landscapes."
Chris - So, if I have farmland that's been intensively farmed over many years, I get different bacteria there than for instance, if I've got a lawn in someone's garden?
Andy - For sure. We think naturally that we are manipulating some landscape quite a lot and so, the original idea really was, "Well, let's just go and sample out in the UK. So, we have this survey which piggybacked a survey called Countryside Survey 2007. That was the first time anybody was trying to do a microbial map of a country.
Chris - So, how did you map Britain? Did you get someone to send in samples of soil from the entire country that you could look at with DNA in there then?
Andy - It was actually a formal scientific survey done at 5 kilometres resolution. So, it was people trained as scientists who actually went out there and take samples for us. The problem came in terms of taking that map that we did in the UK and trying for example to do in Australia and Western Australia especially is the size and scale. So, it's 22 times the size of the UK and it's also 1/20 of the population. So, it would take us 60 - 150 years to actually do this similar effort of sampling however here. So, that's where the real idea came to make it into a citizen science project where we engage with the local public to help us out with a large scale mapping. Okay, so we're down to about 10 centimetres. Essentially what we do is dig straight down that side of the soil and put a strike into - we need about 300 grams of sample. That's important because it gives us enough sample for the molecular analysis. But also, it gives us enough sample for chemical analysis. So, measure things like pH, carbon. phosphorus sample. Once the sample is mixed, we'll remove anything that's large in terms of roots or rocks or shoots. So, there's a bit there that we're just going to throw away. The first thing we do is load one of the tubes for DNA extraction and analysis. So, these are very small, screw top 2ml tubes. Half a gramme, there we go, screw the top back on. And there's a second which is our backup sample. So, this will go in the freezer. If the first extraction doesn't work for whatever reason, we have a backup sample. So, we have about 300 grams of soil in the back, we have 2 tubes which are the DNA extraction tubes. In the meantime, while somebody is doing this, somebody else can be filling in some of the shipping form which essentially tells where a sample was, time, date, everything then goes into the pretty paid nvelope. There you go. You just become MicroBlitzer.
Chris - That arrives back in the laboratory. How do you then process that and marry all of these data together?
Andy - Samples arrive back in the laboratory. They are first of all determined for dry weight. So, we weigh a portion of it and then basically weigh again. So, that gives us moisture content which we think is quite important in samples. The samples then go into a freezer. So, we store them all frozen until we basically take them out as batches of say, 96. Once the DNA is extracted then we use various molecular biological means which is PCR to work out and sequencing to work out the microbes are present in the sample.
Chris - And because you are keeping a version of the sample in pristine condition in the freezer, I suppose that in the long term, if you have further questions subsequently you want to ask of that sample, you can go back to it and ask those questions as technology and science evolves and moves forward.
Andy - Exactly. One of the key things on MicroBlitz is not just the data that we get back from it now. It's actually the legacy in the future. So essentially, we have a biological bank of samples which is a snapshot when we did the samples. As different questions become more relevant, we can always go back to that bio bank and ask those questions again without having to do the extra effort.
Chris - Andy Whiteley from the University of Western Australia and microblitz.com.au is the web address to find out a bit more.