November 10, 2022
Research Highlight

Keystone Functions of a Minority Species Drives Overall Soil Microbial Metabolism

Even microbes that can’t break down a plentiful food source can still be successful though interactions with fellow community members

Soil sample

Soil sample from the Washington State University field site in Prosser, Washington.

(Photo by Andrea Starr | Pacific Northwest National Laboratory)

The Science                                

Interactions among soil microorganisms lead to the release of nutrients derived from complex soil organic matter. This creates food for both microbes and plants. However, the specific nature of many of these interactions remains unclear. Researchers seek answers to why some microbes are more successful than others and what role individual members play in their communities. Researchers at the Pacific Northwest National Laboratory (PNNL) studied a model microbial community fed with chitin, a complex source of carbon and nitrogen commonly found in soil. They found that certain microbes drive specific steps of the chitin breakdown process, but the most abundant microbes are not necessarily the most important.

Microbes with the ability of breaking down chitin, are critical for the community’s success but do not necessarily grow the fastest. Instead, species with the ability to use a wide range of food sources grow to be the most abundant. This is because microbes that cannot break down the main food source of chitin feed on different nutrients produced by other members of the microbial community. They also found that although certain microbes drive specific steps of the chitin breakdown process, individual microbes can change their behavior when grown alone or in the community.

The Impact

Soil microorganisms promote plant growth by breaking down carbon and nutrients. The observation that microbes with the ability to use a wide range of carbon sources grow to be more abundant will help us to predict how microbial interactions and activity may respond as different nutrient sources become available in soil in response to environmental changes. Accurate predictions of this type will inform soil management to favor organisms and nutrient sources that best promote soil fertility through carbon and nutrient cycling and storage. These findings inform our understanding of how different microbial species interact to perform community processes that drive carbon and nitrogen cycling in soil.


Soil microorganisms provide key ecological functions that often rely on interactions among different members within a microbial community. To better understand these interactions and community processes, researchers used chitin, a major carbon, and nitrogen source in soil, to investigate microbial interactions that break down organic matter. The model microbial community used in this study included eight soil bacterial species—some chitin degraders and some non-degraders. Researchers observed that the species organized into distinct roles when it was time to break down the chitin. Intriguingly, the most abundant members of the model community were not those that were able to break down chitin itself, but rather those that were able to take full advantage of interactions with other community members to grow on chitin breakdown products. The study answered important questions about how complex carbon and nutrient sources are metabolized by interactions amongst microorganisms which in turn supports plant and microbial growth in soil ecosystems.

PNNL Contact

Kirsten Hofmockel, Joint appointee with Iowa State University and Pacific Northwest National Laboratory,


This research was supported by the Department of Energy’s Biological and Environmental Research (BER) program and is a contribution of the Scientific Focus Area “Phenotypic response of the soil microbiome to environmental perturbations” (FWP 70880). PNNL is operated for the DOE by Battelle Memorial Institute under contract DE-AC05-76RLO1830. A portion of this work was performed at EMSL, the Environmental Molecular Sciences Laboratory , a DOE Office of Science user facility at PNNL.

Published: November 10, 2022

McClure, R., Farris, Y., Danczak, R.E., Nelson, W.C., Couvillion, S.P., Jansson, J.K., Hofmockel, K.S. "Interaction Networks Are Driven by Community-Responsive Phenotypes in a Chitin-Degrading Consortium of Soil Microbes," mSystems. 7(5), e00372-00322 (2022). [DOI: 10.1128/msystems.00372-22]