Soil Microbial Community Responses to a Decade of Warming as Revealed by Comparative Metagenomics

Abstract

Soil microbial communities are extremely complex, being composed of thousands of low-abundance species (<0.1% of total). How such complex communities respond to natural or human-induced fluctuations, including major perturbations such as global climate change, remains poorly understood, severely limiting our predictive ability for soil ecosystem functioning and resilience. In this study, we compared 12 whole-community shotgun metagenomic data sets from a grassland soil in the Midwestern United States, half representing soil that had undergone infrared warming by 2°C for 10 years, which simulated the effects of climate change, and the other half representing the adjacent soil that received no warming and thus, served as controls. Our analyses revealed that the heated communities showed significant shifts in composition and predicted metabolism, and these shifts were community wide as opposed to being attributable to a few taxa. Key metabolic pathways related to carbon turnover, such as cellulose degradation (ϳ13%) and CO 2 production (ϳ10%), and to nitrogen cycling, including denitrification (ϳ12%), were enriched under warming, which was consistent with independent physicochemical measurements. These community shifts were interlinked, in part, with higher primary productivity of the aboveground plant communities stimulated by warming, revealing that most of the additional, plant-derived soil carbon was likely respired by microbial activity. Warming also enriched for a higher abundance of sporulation genes and genomes with higher G؉C content. Collectively, our results indicate that microbial communities of temperate grassland soils play important roles in mediating feedback responses to climate change and advance the understanding of the molecular mechanisms of community adaptation to environmental perturbations.

Nitrogen Cycling Potential of a Grassland Litter Microbial Community

“…A few studies highlight mixed responses by pathway (85)(86)(87); for instance, burning tended to increase the relative abundance of dissimilatory processes and decrease that of assimilatory processes (88).…”

Investigating microbial transformations of soil organic matter: synthesizing knowledge from disparate fields to guide new experimentation

“…However, as outlined by Schimel and Schaeffer (2012), using modern molecular tools to better understand SOM decay is challenging given the lack of specificity of decay-related genes; unlike processes like methanogenesis and methanotrophy or denitrification, SOM decay is governed by a relatively large number of genes residing in a greater diversity of organisms. Despite the seemingly daunting level of microbial genetic diversity, soil metagenomes can be mined for their annotated and functionally assigned genes, and then used to assess how potential metabolic pathways can shift with changes in the environment such as soil warming (Luo et al, 2014). New tools such as Functional Ontology Assignments for Metagenomes (FOAM, Prestat et al, 2014) are making it even easier to use metagenomic data to group microbial communities based on broadly categorized metabolic processes.…”

Biofilms on Hospital Shower Hoses: Characterization and Implications for Nosocomial Infections

“…Hence, metagenome sequencing (i.e., random sequencing of total community DNA extracts) has recently been used to examine the functional network of complex microbial communities (28,29). In spite of the rise of infections by opportunistic premise plumbing pathogens, relatively few studies have assessed the diversity of biofilms growing in DWDS at the metagenome level, especially in health care units (30)(31)(32)(33).…”