Simplifying Microbial Consortia Opens a Path to Understanding Soil Community Ecology

Representative communities of reduced complexity provide new experimental context for investigating how soil microbial communities function.

The Science

Soil microbiomes are among the most diverse communities of microbes on Earth. They play a huge role in cycling soil carbon, nitrogen, and other nutrients. These cycles underpin land-based food webs. Soil microbes also regulate many of the planet’s other biogeochemical cycles. It is notoriously difficult to study how these natural microbial communities interact, function, and respond to changing environments. New research demonstrates that microbial communities that are simplified but still representative may offer a way to explore more complex ones. In particular, they can help scientists uncover the mechanisms that drive the ecology of groups of soil microbes.

The Impact

Soil microbial communities that are simpler than real ones but still represent their basic functions can be useful tools for scientists. They can offer insights into how the microbes in these communities remain stable or change over time. They provide scientists with new contexts to understand how environments shape soil microbiomes. These communities can also reveal how the different types of microbes and their environment can influence the community’s stability. By observing these simplified communities, scientists can learn more about how to potentially control similar ones in complex native soils.


Scientists need a deeper understanding of the ecological properties that control the structure and function of soil microbiomes. These communities are globally consequential and are now undergoing little-known pressures in a changing world environment. Understanding them is difficult because of the sheer number of species present. In addition, scientists have cultivated and thoroughly studied very few soil microbes in laboratory conditions. Now a team of researchers report on representative, reduced-complexity microbial communities that can serve as tools for better understanding soil microbiology. To cultivate their simplified soil microbiomes, the researchers looked at both bacteria and fungi. Many other studies use only liquid and focus only on bacteria, making it impossible to simulate a full view of the soil microbiome in its native environment.

They found that an environment of soil, rather than liquid, leads to a community of microbes that is representative of native soil sites. The researchers used a dilution procedure to obtain simplified, naturally adapted cohorts to serve as an experimental resource that recapitulates at least some soil microbiome behaviors. Finally, they showed that such reduced-complexity communities are reproducible and that the communities are stable across time.

Principal Investigator

Elias Zegeye
Pacific Northwest National Laboratory
[email protected]

Co-Principal Investigator

Janet Jansson
Pacific Northwest National Laboratory
[email protected]

BER Program Manager

Dawn Adin

U.S. Department of Energy, Biological and Environmental Research (SC-33)
Biological Systems Science Division
[email protected]


This work was supported by the Office of Biological and Environmental Research (BER), within the U.S. Department of Energy (DOE) Office of Science, and is a contribution of the Scientific Focus Area Phenotypic Response of the Soil Microbiome to Environmental Perturbations (70880). The Pacific Northwest National Laboratory (PNNL) is operated for DOE by Battelle Memorial Institute.


Zegeye, E. K., C. J. Brislawn, Y. Ferris, S. J. Fansler, K. S. Hofmockel, J. K. Jansson, A. T. Wright, E. B. Graham, D. Naylor, R. S. McClure, and H. C. Bernstein. 2019. “Selection, Succession, and Stabilization of Soil Microbial Consortia,” mSystems 4, e00055-19. DOI:10.1128/mSystems.00055-19.