Illuminating microbial metabolic activities in the dark deep ocean with metaproteomics

Abstract

24The deep ocean is the largest habitat on earth and holds diverse microbial life forms. Significant 25 advances have been made in microbial diversity and their genomic potential in the deep ocean, 26 however, little is known about microbial metabolic activity that is crucial to regulate the 27 bathypelagic carbon sequestration. Here, we characterized proteomes covering large particulate 28 (>0.7 m), small particulate (0.2-0.7 m) and dissolved (10 kDa-0.2 m) fractions collected at a 29 depth of 3000 m in the South China Sea. The Rhodospirillales, SAR324, SAR11, 30 Nitrosinae/Tectomicrobia were the major contributors in the particulate fraction whereas 31 Alteromonadales and viruses dominated the dissolved counterpart. Frequent detection of 32 transcription or translation proteins in the particulate fractions indicated active metabolism of 33 SAR324, Archaea, SAR11, and possible viable surface microbes, e.g. Prochlorococcus. 34 Transporters for diverse substrates were the most abundant functional groups, and numerous 35 spectra of formate dehydrogenases and glycine betaine transporters unveiled the importance of 36 methylated compounds for the survival of deep-sea microbes. Notably, abundant non-viral 37 proteins, especially transporters and cytoplasmic proteins, were detected in the dissolved fraction, 38 indicating their potential roles in nutrient scavenging and the stress response. Our size-based 39 proteomic study implied the holistic microbial activity mostly acting on the labile dissolved 40 organic matter as well as the potential activities of surface microbes and dissolved non-viral 41 proteins in the deep ocean. 42 43 Importance 44The deep ocean produces one third of the biological CO 2 in the ocean. However, little is known 45 about metabolic activity of the bathypelagic microbial community which is crucial for 46 3 understanding the biogeochemical cycling of organic matter, especially the formation of bulk 47 refractory dissolved organic matter (DOM), one of the largest reservoirs of reduced carbon on 48 Earth. This study provided the protein evidence firstly including both particulate and dissolved 49 fractions to comprehensively decipher the active microbes and metabolic processes involved in 50 the DOM recycling in the deep ocean. Our data supported the hypothesis of the carbon and 51 energy supply from the labile DOM after the solution of sinking particles to the bathypelagic 52 microbial community. 53 54 55The vast areas of deep ocean, characterized by low temperature, high hydrostatic pressure and 56 complete darkness, is the most unexplored biome on Earth and produces one third of the 57 biological CO 2 in the ocean (1). However, this habitat has not yet been greatly explored. 58 Recently culture independent sequencing techniques, i.e. 16S rRNA gene sequencing (2-7) and 59 metagenomics (8-11), have been applied to explore the phylogenetic diversity and genomic 60 potential of microbial communities in the deep ocean. Bacterial (5), archaeal (12) and small 61 eukaryotic (3) popul...