Microbial Metagenomics of Oxygen Minimum Zones
Frank J. Stewart and Osvaldo Ulloa
from: Metagenomics of the Microbial Nitrogen Cycle: Theory, Methods and Applications (Edited by: Diana Marco). Caister Academic Press, U.K. (2014)
Marine oxygen minimum zones (OMZs) support complex microbial assemblages with important roles in ocean biogeochemical cycles. The integration of genomic, metagenomic, and metatranscriptomic analyses has significantly enhanced our understanding of OMZ microbial communities, revealing a richness of metabolic processes structured along the OMZ redox gradient and previously unrecognized linkages between community members. Specifically, 'omics studies are clarifying the physiology, in situ activity, and evolutionary history of microbial groups mediating key steps of dissimilatory nitrogen cycling, including OMZ-specific clades of anaerobic ammonium oxidation (anammox) bacteria, aerobic ammonia-oxidizing Thaumarchaeota specialized for high-affinity substrate scavenging, and aerobic nitrite-oxidizing Nitrospina bacteria with adaptations for life under low oxygen conditions. Recent studies have also identified a diverse OMZ community of sulfur-oxidizing autotrophs whose activity appears coupled to reduced sulfur compounds generated by co-occurring sulphate-reducing heterotrophs. We discuss these and other OMZ metabolic processes in relationship to key environmental drivers, including water column nutrient and redox gradients and the microscale partitioning of communities between organic particle-associated and free-living microniches. Coupled ‘omic-biogeochemistry studies are critical for understanding how de-oxygenation structures microbial biogeochemistry in the ocean and for identifying key priorities for future OMZ research read more ...