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

Microbial Responses to Scaling Complexity in Chitin Decomposition with Changing Moisture and Structure Levels

Authors:

Nicholas J. Reichart1* (nicholas.reichart@pnnl.gov), Sheryl Bell1, Natalie Sadler1, Josué Rodríguez-Ramos1, Vanessa Garayburu-Caruso1, Sharon Zhao1, Kirsten S. Hofmockel1,2

Institutions:

1Biological Sciences Division, Pacific Northwest National Laboratory; 2Department of Agronomy, Iowa State University

URLs:

Goals

Pacific Northwest National Laboratory’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. Laboratory and field experiments test predictions to reveal individual and community microbial phenotypes. Knowledge gained provides a fundamental understanding of how soil microbes interact to decompose and sequester organic carbon and enables prediction of how biochemical reaction networks shift in response to changing moisture regimes.

Abstract

The complexity of the soil microbiome and its environment makes it difficult to understand the networks of interactions among community members, ranging from positive interactions, such as metabolite exchange, to negative interactions like competition. Moisture is a critical attribute of the soil environment that constrains access to resources and interactions within the community, impacting microbial metabolism and biogeochemical processes. Here, the group investigates microbial metabolic interactions and functions that govern organic matter decomposition under contrasting moisture conditions across three levels of biogeochemical complexity that use chitin as a model substrate. At the most reduced complexity, the team used a tractable Model Soil Consortium containing 8 members (MSC-2) to understand interspecies interactions governing degradation of chitin in a well-mixed system (McClure et al. 2022). The team expanded to an intermediate complexity consortium of 31 members (MSC-1) incubated in a spatially structured synthetic soil habitat to identify microbial interactions and metabolic pathways involved in chitin decomposition (McClure et al. 2020). At the highest level of biogeochemical complexity, researchers used laboratory incubations of soil with chitin amendments collected from the team’s Tall Wheatgrass Irrigation Field Trial in Prosser, WA, to understand how microbial interactions mediate the decomposition of organic substrates. By examining chitin decomposition in a series of experiments that scale in biological and chemical complexity, researchers test how outcomes from culturing experiments translate to soil environments.

Experiments from reduced complexity MSC-2 incubations demonstrate the importance of a subset of chitin degraders for promoting community function. Streptomyces was a key member responsible for most chitin degradation, while other organisms like Dyadobacter had small, realized niches, and low expression. Expanding on this complexity, MSC-1 was used to test impacts of structure and moisture on community interactions in synthetic soil habitats. Using genome-resolved metagenomics and metatranscriptomics, the study shows consistency across experimental scales, with members from MSC-2 retaining prevalent expression patterns in the unstructured broth incubations of MSC-1 (i.e., Streptomyces). In contrast, Dyadobacter was a highly active member of broth incubations in MSC-1. Introducing structure invoked significant treatment effects observed as a shift from Dyadobacter and Streptomyces dominated communities in broth to Ensifer in structured incubations. These patterns were likely a result of motility and transporter related gene expression present in Ensifer but not in Dyadobacter or Streptomyces. Microbial consortium responses to moisture and chitin amendment were tested in a soil-based experiment by screening for chitinolytic and carbon cycling enzymes. Chitin amendment increased chitinolytic response regardless of moisture level. For other carbon cycling enzymes, high moisture caused greater activity compared to low moisture soils. Activity-based probes (ABP) were used to identify organisms producing chitinolytic enzymes. Moisture status and chitin amendment impacted the recovery of chitinolytic genera, Chitinibacter, Cellvibrio, and Massilia, enriched using ABPs, leading to evidence for division of labor on carbon cycling and fitness variation for soil moisture.

These results highlight how genome-resolved multiomics and scaling experimental complexity aid researchers’ understanding of microbial communities and suggest a disconnect between broth-based incubations and native incubations of soil. Researchers aim to use this knowledge to move beyond lab-scale experiments and towards integrating in vivo experimentation to field-scale in- situ experiments.

References

McClure, R. et al. 2020. “Development and Analysis of a Stable, Reduced Complexity Model Soil Microbiome,” Frontiers in Microbiology 11, 1987. DOI:10.3389/fmicb.2020.01987.

McClure, R., et al. 2022. “Interaction Networks are Driven by Community-Responsive Phenotypes in a Chitin-Degrading Consortium of Soil Microbes,” mSystems 7. DOI:10.1128/msystems.00372-22.

Funding Information

Pacific Northwest National Laboratory (PNNL) is a multiprogram national laboratory operated by Battelle for the DOE under Contract DE-AC05-76RLO 1830. This program is supported by the U. S. DOE, Office of Science, through the GSP, BER program, 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 BER program and located at PNNL.