Microbial Metagenomics Reveals Climate-Relevant Subsurface Biogeochemical Processes

Microorganisms play key roles in terrestrial system processes, including the turnover of natural organic carbon, such as leaf litter and woody debris that accumulate in soils and subsurface sediments. What has emerged from a series of recent DNA sequencing-based studies is recognition of the enormous variety of little known and previously unknown microorganisms that mediate recycling of these vast stores of buried carbon in subsoil compartments of the terrestrial system. More importantly, the genome resolution achieved in these studies has enabled association of specific members of these microbial communities with carbon compound transformations and other linked biogeochemical processes–such as the nitrogen cycle–that can impact the quality of groundwater, surface water, and atmospheric trace gas concentrations. The emerging view also emphasizes the importance of organism interactions through exchange of metabolic byproducts (e.g., within the carbon, nitrogen, and sulfur cycles) and via symbioses since many novel organisms exhibit restricted metabolic capabilities and an associated extremely small cell size. New, genome-resolved information reshapes our view of subsurface microbial communities and provides critical new inputs for advanced reactive transport models. These inputs are needed for accurate prediction of feedbacks in watershed biogeochemical functioning and their influence on the climate via the fluxes of greenhouse gases, CO2, CH4, and N2O.

TrendsDatasets from subsurface samples can now be resolved into collections of complete or near-complete microbial genomes, yielding information about biogeochemical roles and mechanisms by which surface- and groundwater quality and atmospheric compositions are impacted.Deep sequencing reveals extremely high levels of diversity in both the vadose zone and groundwater.Many novel organisms have an extremely small cell size and small genome size, with restricted metabolic capability. Their growth is likely tightly linked to that of other community members.Genomic analyses suggest that subsurface geochemical processes reflect the functioning of complex communities as opposed to a few dominant species.Newly discovered microorganisms catalyze transformations relevant to greenhouse gases and processing of biologically critical elements.