Print PageSoil microbial communities are a critical component of terrestrial ecosystems and the global carbon cycle. Their astounding complexity and the limitations of inferring function from single gene-based (SSU rRNA) inventories pose challenges for mechanistically describing the myriad roles soil microbes perform in ecosystem processes.
We used shotgun metagenomics via second-generation sequencing (454) and high-throughput annotation (MetaGenome Rapid Annotation using Subsystems Technology [MG-RAST]) to explore drivers of microbial function across North American ecosystems in the National Ecological Observatory Network (NEON). This unprecedented characterization of soil microbial communities and their environments sought to (1) determine the relative importance of edaphic and climatic drivers on soil metagenomes (microbial community functional gene sets) across ecosystems and (2) pinpoint aspects of metagenomes that vary with particular edaphic or ecosystem properties.
Results/Conclusions
Combining the increasingly lower cost of second-generation DNA sequencing technologies (compared to first-generation-based approaches) with high-volume data analysis platforms like MG-RAST provides a new level of observational resolution for environmental metagenomics. The increased volume of sequence data produced with these sequencing technologies, the ecoclimatic representation of terrestrial ecosystems provided by NEON core sites, and corresponding extensive metadata allowed us to meaningfully partition functional sequence data within the single “biome” of terrestrial soils.
At the broadest level, universal patterns in the ~888.6 Mb of metagenomic DNA demonstrated that metabolic constraints drive the genetic foundation of soil communities independent of biome, whereas biome-specific patterns emerged with higher resolution analyses. These communities have distinct gene repertoires that clearly segregate by biome (forest vs. grassland) regardless of climate or geography. Nitrogen (N) and pH were significant drivers of patterns within biomes, and we identified >24 metabolic subsystems that ostensibly are responsible for these relationships.
Harnessing the enhanced resolution of shotgun metagenomics, we found that within distinct biome clusters, edaphic factors (N and pH) drive the functional gene repertoires of soil microbial communities regardless of climate or geography. Our findings demonstrate the basis from which soil microbial ecology can advance to hypothesis-based experiments capable of testing cause-and-effect relationships between measureable soil parameters and greenhouse gas-producing microbial metabolic processes.
