Microbial regulation of the soil carbon cycle: evidence from gene–enzyme relationships

Abstract

A lack of empirical evidence for the microbial regulation of ecosystem processes, including carbon (C) degradation, hinders our ability to develop a framework to directly incorporate the genetic composition of microbial communities in the enzyme-driven Earth system models. Herein we evaluated the linkage between microbial functional genes and extracellular enzyme activity in soil samples collected across three geographical regions of Australia. We found a strong relationship between different functional genes and their corresponding enzyme activities. This relationship was maintained after considering microbial community structure, total C and soil pH using structural equation modelling. Results showed that the variations in the activity of enzymes involved in C degradation were predicted by the functional gene abundance of the soil microbial community (R 2 40.90 in all cases). Our findings provide a strong framework for improved predictions on soil C dynamics that could be achieved by adopting a gene-centric approach incorporating the abundance of functional genes into process models.

Mammalian engineers drive soil microbial communities and ecosystem functions across a disturbance gradient

“…Trivedi et al . ). Thus, changes in microbial composition resulting from disturbance by mammals can markedly alter both microbial community composition and therefore ecosystem functioning.…”

Effect of permafrost thaw on plant and soil fungal community in a boreal forest: Does fungal community change mediate plant productivity response?

“…This covariance approach allows tests of potential causal paths while accounting for other factors in the experimental design (Bever, Broadhurst, & Thrall, ). Interpretations were confirmed using structured equation modelling on reduced datasets (Trivedi et al, ; Waldrop et al, ). As NMDS visualizes overall differences in microbial communities across different habitats or experimental treatments, we used the scores for each NMDS axis as covariates representing the overall fungal community composition.…”

Microbial energy and matter transformation in agricultural soils

“…Thus for certain ecosystem functions a combination of functional gene diversity, taxonomic diversity and knowledge of the conditions which induce protein expression between species may be necessary to elucidate a relationship between function and diversity. This may explain why relationships are more readily apparent for some functions, such as enzymes involved in decomposition (Trivedi et al, 2016) but not necessarily with others, such as methane oxidation (Rocca et al, 2015). In short, much scope remains for appropriate ecological hypothesis testing of the role of functional diversity in soil geochemical processes .…”

“…The activity of C degrading enzymes can be explained by functional gene abundance, the taxonomic composition of the microbial community and the quantity of SOM in situ (Allison and Vitousek, 2005;Sinsabaugh et al, 2005;Trivedi et al, 2016). Total OC (%) plays a strong role in shaping the relative abundance of GH families in situ, as shown by greater richness of GH families involved in cellulose, hemicellulose, lignin and pectin degradation in relatively C rich organic soil layers compared to a greater relative abundance of phenol and protein degradation in C poor mineral soil layers (Cardenas et al, 2015;de Menezes et al, 2015;Uroz et al, 2013).…”