Genomic Science Program
U.S. Department of Energy | Office of Science | Biological and Environmental Research Program

Removal of Primary Nutrient Degraders Reduces Growth and Modifies Functional Pathways of Soil Microbial Communities with Genomic Redundancy


Ryan McClure1* (, Marci Garcia1, Sneha Couvillion1, Amy Zimmerman1, Yuliya Farris1, and Kirsten S. Hofmockel1,2


1Pacific Northwest National Laboratory (PNNL); and 2Iowa State University



PNNL’s Phenotypic Response of Soil Microbiomes Science Focus Area aims to achieve a systems-level understanding of the soil microbiome’s phenotypic response to changing moisture. Researchers perform multi-scale examinations of molecular and ecological interactions occurring within and between members of microbial consortia during organic carbon decomposition, using chitin as a model compound. Integrated experiments address spatial and inter-kingdom interactions among bacteria, fungi, viruses, and plants that regulate community functions throughout the soil profile. Data are used to parametrize individual- and population-based models for predicting interspecies and inter-kingdom interactions. Predictions are tested in laboratory and field experiments to reveal individual and community microbial phenotypes. Knowledge gained provides fundamental understanding of how soil microbes interact to decompose and sequester organic carbon and enable prediction of how biochemical reaction networks shift in response to changing moisture regimes.


Many ecosystem functions related to plant growth or carbon and nutrient cycling and stabilization rely on microbial metabolism. As a result, microbial communities are major drivers of carbon use efficiency (CUE). Furthermore, ecological theory indicates the importance of keystone community members that may carry out critical aspects of community functioning or interact with many other community members positively or negatively. Therefore, a quantitative assessment of species-specific responses within a community context is required to understand how microorganisms and keystone species within a soil community interact to support collective growth and community function related to carbon cycling.

To investigate how individual members of a microbial community contribute to decomposition, community growth, and CUE, researchers used a model substrate, chitin, and a Model Soil Consortium, MSC-2 (McClure et al. 2022). While MSC-2 can grow using chitin as the sole carbon source, the individual functions and metabolic contributions of the constituent species remain unknown. To quantify specific roles within this model community, researchers carried out experiments leaving out members of MSC-2 to test the implications for community biomass yields, CO2 production, proteomic and lipidomic profiles, and extracellular metabolites. Researchers chose two members to iteratively leave out: Streptomyces, as it is predicted via gene expression analysis to be a major chitin degrader in the community, and Rhodococcus as it is predicted via species co-abundance analysis to interact with several other members (McClure et al. 2020). The experiments revealed that when MSC-2 lacked Streptomyces, growth and respiration of the community was severely reduced, even though other members of MSC-2 can degrade chitin. Removal of Streptomyces also led to changes in abundance for several other species compared to the complete MSC-2 community, pointing to a comprehensive shifting of the community structure when important members are removed. In addition, while the absence of Streptomyces led to differences in microbial taxonomy compared to the complete MSC-2 community there were only minor changes compared to the community’s starting point, indicating minimal growth and activity when this keystone species is removed. In contrast, while the absence of Rhodococcus also led to taxonomic changes compared to the complete MSC-2 community, removal of this keystone species had little effect on community growth and respiration. A further multiomic analysis of communities lacking Streptomyces showed that without this member the proteomic profile of the community was distinct from the complete MSC-2. Proteins from Sinorhizobium and Ensifer were the most abundant in a community lacking Streptomyces while proteins from Ensifer and Sphingopyxis were more prevalent in the complete MSC-2. Major differences were also seen between the lipidomic profiles of MSC-2 with and without Streptomyces with the breakdown of triglycerides more prevalent in complete MSC-2 communities. As complete MSC-2 communities grow far better than those lacking Streptomyces this triglyceride breakdown may be a response to chitin being fully metabolized, forcing members to rely on other energy sources at the later timepoints of the experiments. Interestingly, polar metabolite abundances in the culture supernatants were relatively similar between communities with and without Streptomyces.

These results show that when keystone, chitin degrading members are removed, other members, even those with the ability to degrade chitin, do not fill the same metabolic niche to promote community growth. In addition, highly connected members may be removed with similar or even increased levels of community growth and respiration. This suggests that removal of keystone members can have positive or negative effects on overall community growth, an outcome driven not only by identity of the keystone member but the magnitude and type of the interactions it has with other members. The findings are critical to a better understanding of soil microbiology, specifically in how communities maintain activity when biotic or abiotic factors lead to changes in biodiversity in soil systems.


McClure, R., et al. 2022. “Interaction Networks Are Driven by Community-Responsive Phenotypes in a Chitin-Degrading Consortium of Soil ” Msystems 7(5), e00372-22.

McClure, R, et al. 2020. “Development and Analysis of a Stable, Reduced Complexity Model Soil Microbiome.” Frontiers in Microbiology 11, 1987.

Funding Information

PNNL is a multi-program national laboratory operated by Battelle for the DOE under Contract DE-AC05-76RLO 1830. This program is supported by the U. S. Department of Energy, Office of Science, through the Genomic Science program, Office of Biological and Environmental Research, under FWP 70880. A portion of this work was performed in the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL), a national scientific user facility sponsored by Office of Biological and Environmental Research and located at PNNL.