Microbial proteins for organic material degradation in the deep ocean.

Organic material is synthesized in the sunlit surface layer of the oceans and that is where most of it is decomposed back to carbon dioxide and other inorganic constituents. However, a small fraction escapes immediate degradation and makes its way into deeper waters, some as far as the bottom thousands of meters below the surface. This sinking organic material contributes to sequestering atmospheric carbon dioxide and to feeding the biota of the deep ocean. Degradation is carried out by a complex microbial community whose taxonomic composition and metabolic potential vary greatly along the kilometer-long trip to the ocean floor. The metabolic potential of microbial communities has been deduced from metagenomics, genomic information gained by sequencing the entire community. In PNAS, Bergauer et al. (1) use metagenomics and another omic approach to explore changes in microbial communities and metabolism from 100-m to over 4,000-m deep in the Atlantic Ocean. They find many changes, but more surprising were the similarities in the cellular proteins used by microbes to degrade organic material along this depth profile and to support microbial life in the deep ocean. In the surface layer, bacteria use dissolved organic material (DOM) from phytoplankton, either produced directly or indirectly via release by grazers and viral lysis. The source for deep oceanic microbes is less obvious. One source is the organisms and particulate organic detritus produced in the surface layer that then sink to deeper waters. Because the biomass production of microbes on particles is much less than that by their free-living counterparts (2, 3), it is thought that sinking particulate organic material is broken up and solubilized to DOM (4) before being taken up by free-living heterotrophic bacteria and archaea (Fig. 1). Another potential source, albeit smaller than sinking particles, is the export of surface-layer DOM to deeper waters (5). The exported DOM differs from freshly produced DOM because only the compounds surviving immediate degradation are exported to deep waters. So the DOM components used by deep-sea bacteria and archaea could be similar to those in the surface layer if the main source is DOM from fresh detritus, or they could be quite different if the composition of the organic material has changed during its descent from the surface layer. Before the work by Bergauer et al. (1), most signs pointed to deep-sea DOM being quite different. Geochemical analyses indicate that the amount and chemical make-up of organic material change greatly with depth (6, 7), and large changes in microbial communities are also evident in metagenomic data and studies of 16S rRNA genes (8, 9). The omic approach used by Bergauer et al. (1) to address this questionwasmetaproteomics, complemented DOM1 DOM3 Phytoplankton