Feeding frenzy: Linking soil chemistry and microbial community structure

A new study in Nature Communications integrates metabolomics and shotgun sequencing to functionally link microbial community structure with environmental chemistry in biological soil crust (biocrust).

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The corresponding Nature Communications paper can be found here: http://rdcu.be/DVgV

The following authors of the paper contributed to writing this blog: T. Swenson and T. Northen.

You may have seen ‘Don’t bust the crust’ signs on your last trip to the Southwest. While on the surface these soil biofilms known as ‘biocrusts’ may look like boring accumulations of minerals, they are actually a living microbial skin of the desert that’s extremely important in these sensitive ecosystems. Biocrusts are thought to be the most abundant biofilm on Earth and are important contributors to nutrient cycling (especially nitrogen and carbon), soil stability and water retention. These functions along with the fact that biocrusts cover enormous amounts of arid and semi-arid lands mean that biocrusts can uptake approximately 4 Pg of carbon from the atmosphere per year. This raises the exciting possibility that biocrust may be an important carbon sink in light of the inevitable atmospheric carbon increases.

Photo: Biocrust set amongst one of its many natural habitats, Moab UT.

Our lab became interested in these amazing communities that spend most of their time in a desiccated state, and then amazingly, resuscitate within minutes of becoming wet. These are whole microbial worlds constantly cycling through dormancy and growth- worlds that are dominated by Cyanobacteria, lichens, mosses, fungi and heterotrophic bacteria not to mention tardigrades, mites, and other fauna. For our studies, our samples are dominated by a Cyanobacterium, Microcoleus vaginatus. This organism is the key player for essential biocrust functioning: it fixes carbon and releases many metabolites that are consumed by its neighboring bacterial buddies. M. vaginatus is also central to holding biocrust soil particles together using exopolysaccharides, much like rebar does for buildings. Another interesting feature of M. vaginatus is that within its native biocrust environment, it grows fairly rapidly. However, when in liquid culture, it can take weeks. Based on recent evidence, this may be due to interactions with neighboring bacteria, forming a critical foodweb that is sustained by an elaborate exchange of nutrients.

Photo: Biocrust is held together primarily by exopolysaccharides produced by the filamentous Cyanobacterium, M. vaginatus.

This domination of a soil sample by just a few organisms, makes biocrust an excellent system for studying critical environmental processes such as carbon cycling and nutrient exchange. In our featured study, we examined the pulse of microbial activity set in motion by wetting dry biocrusts (from four different successional stages) to explore the linkages between microbes and metabolites.  We previously used exometabolomics to explore substrate preferences of M. vaginatus and several of its associated heterotrophic bacteria and found that these bacteria are ‘picky eaters’, selectively using largely non-overlapping substrates. Here, our primary focus was to determine the extent to which these culture-based observations are conserved in the intact biocrusts. Excitingly, we found that many of these culture-based microbe-metabolite relationships were indeed conserved in situ. This means, that at least for a relatively simplified system like biocrust, we can in fact use lab-based culture studies to glean insight into microbiome metabolite exchange. This may help us answer questions such as who is important in fixing carbon, maintaining soil fertility, or producing key metabolites.

Photo: Microbes in biocrust become metabolically active immediately upon wetting. Seen here, M. vaginatus turns green and releases oxygen.

We now have gigabytes of LC/MS and metagenomics data from our biocrust study to continue exploring this interesting soil community that is littered with key answers to critical questions concerning how these communities will respond to changes in rainfall frequency and duration. We hope that this study will inspire others to do the same. At the very least, we hope that next time you see a 'Don’t bust the crust' sign at a National Park, just remember how vital these little communities can be!

Tami Swenson

Scientific Engineering Associate, Lawrence Berkeley National Lab