Soil microbial community responses to warming as revealed by comparative metagenomics
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. Under a multi-institutional DOE-supported project, we have begun investigations on microbial communities from Alaskan tundra permafrost (AK) and Oklahoma temperate grassland (OK) soils, both of which have been experimentally warmed 2 to 4 °C for five years above ambient temperature in-situ. Here, we have employed 16S rRNA gene amplicon, meta-transcriptomic, and whole-community shotgun metagenomic analysis of well-replicated samples from these soils to document the responses of the indigenous microbial communities to the 1st year of warming (5 year data are forthcoming).
Our results showed small but significant shifts in community composition, gene expression, and functional metabolic potential compared to control (un-warmed) adjacent communities. Greater taxonomic composition differences were observed at the OK site relative to AK, presumably resulting from longer generation times due to the less optimal conditions for growth at permafrost soils. The most pronounced bacterial taxon shifts observed at OK site, which were somewhat also observed at the AK site, were an increase in abundance of Actinobacteria and decrease in Planctomycetes, both representing major phyla in soils, particularly in regards to C-cycling. In terms of functions, the communities of AK warmed plots were enriched in metabolic pathways related to labile carbon mobilization and oxidation whereas fewer of these patterns were observed in the OK communities, indicating that soil C is more vulnerable to microbial respiration at AK. These results, which were consistent with independent physicochemical measurements and process rates determined in-situ, were linked with higher primary productivity of the aboveground plant communities stimulated by warming. Collectively, our findings suggest that microbial communities of grassland soils play important roles in mediating feedback responses of the soil ecosystem to climate change and that even short periods of warming induce significant changes in microbial community function and composition. To enable this research, we have developed several bioinformatics tools that addressed practical limitations during the comparative analysis of the soil metagenomes such as how to assess the fraction of the community captured by a metagenomic dataset. These tools are available for online analysis through our lab website at: http://enve-omics.gatech.edu/