PNNL

Abstract

Soil organic matter decomposition is a complex process that depends on microbial composition and environmental conditions. Moisture plays a significant role in modulating connectivity and interactions of microbes involved in organic matter metabolism. Due to heterogeneity in microbial connectivity in soil, a deeper understanding of soil moisture’s influence on the dynamics and resultant phenotypes remains a challenge. We conducted laboratory incubations to investigate the response of a soil microbiome on organic matter decomposition under low and high moisture using chitin as a model substrate. By combining enzymatic assays, biomass measurements, and microbial enrichment via activity-based probes, we determined the functional response of the microbial community to chitin and moisture treatments at both community and individual cell scales. Chitinolytic activities showed greater response to the amendment of chitin than to differences in soil moisture. However, for other measurements of carbon metabolism and cellular functions, high moisture caused greater potential enzyme activity. We used a novel cell tagging approach to enrich microbes producing a suite of chitin degrading enzymes and observed differences in members actively decomposing chitin and N-acetyl-glucosamine. Our findings demonstrate that, despite the broad phylogenetic distribution of genes encoding chitinase enzymes, a few keystone species are responsible for the majority of enzyme activity. In the absence of substrate amendments, decomposition activity increased with soil moisture, which impacts carbon use efficiency and carbon storage in drying soils. By combining molecular and ecosystem approaches, we reveal that bulk measurements of potential enzymes capture collective responses that are driven by a few organisms.