What makes soil, soil? Researchers find hidden clues in DNA

Netherlands Institute of Ecology (NIOO-KNAW)
28-NOV-2017 - Ever wonder what makes soil, soil? And could soil from the Amazon rainforest really be the same as soil from your garden? Researchers from the University of Manchester and the Netherlands Institute of Ecology (NIOO-KNAW) are using DNA sequencing to unlock the secrets of the world’s soils, and analyse ecological patterns and microbial communities on a global scale.
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The research team, made up of 36 scientists from around the world, collated and analysed data on soil bacteria from 21 different countries. In all, they looked at over 1900 soils, containing over 8000 bacterial groups.

The study, published advanced online in Nature Microbiology, gives new insight into the bacteria that make a soil a soil, and how our soils are functioning and responding to global challenges such as climate change.

Picky bacteria

The researchers found that some groups of bacteria always show up in soil, no matter where it is collected from on the planet: wether it's a field in the UK or the forest floor in the Amazon rainforest, they remain constant.

But other bacteria are pickier, and those are the ones we should pay attention to, say the researchers. That’s because these bacteria could hold clues to what makes some soils more fertile and suitable for planting crops than others. Dr Kelly Ramirez, from NIOO-KNAW, explains:

"When we see a cactus, we know we're in a desert, when we see a palm tree we know we're in the tropics and when we see a grass we could be almost anywhere."

This same idea, that species indicate a habitat, is true for soils, she says. "Only instead of using plants, we use soil bacteria. But if you were to pick up a handful of soil from your garden, from a forest, or even a meadow it would probably be hard to tell the difference."

Consolidating research

However, the microbial communities that live within the world’s soils are more diverse and contain more individuals than any other species groups on the planet, and can tell us a lot about a their origins. Dr Franciska de Vries, from The University of Manchester’s School of Earth and Environmental Sciences (SEES), adds:

"In the soil these bacteria help plants grow, cycle carbon and keep our ecosystems functioning. Scientists all over the world are studying these important bacteria, but they are all using different techniques and keeping all the information organized is a challenge. So we decided to try and find a way to consolidate all the research and bring it together."

That's when Dr Chris Knight, also from SEES and the paper’s co-author, brought his expertise to the study. An expert in microbial and computational modelling, he used a specific technique that could accommodate thousands of bacterial species. The ‘machine learning’ method allowed the team to evaluate all the species and match them to different environmental factors and to each other.

Clearer picture

"What resulted was a new and clearer picture of the roles of particular groups of bacteria in shaping communities of soil bacteria," says Dr. Knight.

"Some bacteria are common, but how many turn up in any particular soil has more to do with the details of how they were measured than any real differences among soils. Some are so rare that you only ever see them in a handful of soils of any sort, which doesn’t say much. But in between there are informative families of bacteria that indicate real differences among types of soil."

Text: NIOO-KNAW
Photos: David Elliot, Flickr; NIOO-KNAW

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