The dirty low-down

by Rebecca Priestley / 27 June, 2013
New soil-sampling techniques are revealing the presence of thousands of unrecognised species.
I spent a recent weekend clearing weeds, spreading compost and planting vegetables, and I got a good look at the range of species that live in my garden. In the vegetable patch I found worms, spiders and a few shield bugs hiding in the spinach. Spots on the leaves of a young quince tree showed there were fungi in the soil. In the wild parts, kowhai and karaka seedlings covered the ground.

I think I know my garden pretty well, but Allan Wilson Centre for Molecular Ecology & Evolution researchers could tell a lot more from just one small soil sample than I could ever see.

Image/Birgit Rhode, Landcare Research


The old way of studying ecology – interactions between plants, vertebrates, invertebrates and microbes and the environment they live in – involves many teams of specialist taxonomists and ecologists and lots of time, says Nicky Nelson, a Victoria University ecologist. “But we can get a reasonably accurate representation of what’s going on above the ground from what’s happening in the soil,” says Richard Newcomb from Plant & Food Research.

And that’s what the Hidden Treasures project is about. The main study area is Little Barrier/Hauturu, a volcanic island 80km north of Auckland that has an intact native ecosystem. Nelson and her colleagues have taken soil samples – about an icecream-container-full – from 28 plots on the island. Back in the lab, Newcomb and his team use newly affordable techniques – including the polymerase chain reaction and next-generation sequencing – to isolate and sequence segments of DNA from the soil. Alexei Drummond and his team at the University of Auckland then use computers to separate the gene sequences indicative of different groups, and look at the variation between sequences to get an indication of how many species are there.

Some of the genetic sequences can be matched to known species, but they are also indicating the presence of thousands of unrecognised species. Even one sample of soil, says Newcomb, can reveal DNA from thousands of bacteria species, thousands of fungi, thousands of invertebrates (including many insects) and hundreds of plants.

As well as being quick, this method of species identification is very effective. “Even using standard ecological methods, like pitfall traps, we miss stuff,” says Nelson. “Working at the DNA level is a way of getting at everything.” And a species doesn’t need to die in the plot to be counted. Plants drop seeds and pollen, fungi drop spores, and insects, birds and reptiles drop faeces – all of which contain DNA. A Little Barrier soil sample has even revealed evidence of an unknown fish species, something similar to an anchovy, that Nelson speculates may have arrived in a pile of “seabird vomit”.

This technique has “enormous potential for ecological monitoring and environmental restoration”, says Nelson. “At the moment, it’s super-expensive to monitor trends, you need lots of people on the ground and you need a lot of expertise. And many of the gene sequences we’re finding don’t tag to anything. There is so much diversity in New Zealand, but not enough people to figure out what there is. But we can’t afford to wait until all these species are named, we have to figure out a different way of cataloguing them and monitoring ecological trends.”

The Hidden Treasures project is focused on Little Barrier, but already includes plots on Raoul Island and in the Waitakere Ranges. And the soil sampling will only get easier. In the near future, says Nelson, there’s potential to do this sort of analysis in the field using hand-held DNA detectors. “We might also to able to use these techniques to detect rare species – the ones we think are out there but we just can’t find.”

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