It was suggested that genetic and phenotypic details of trench microbial communities would ultimately require whole metagenome studies, but not just 16S rRNA gene analyses. However, our understanding of the hadal microbial diversity and association of environmental factors has largely relied on the technology of 16 s rRNA gene profiling, and the studies of limited number of cultured microbes. In a comparison of microbes between Mariana and Kermadec trench habitats, they comprised cosmopolitan taxa with different abundances, in addition to some autochthonous microbes associated with unique and rare OTUs. Investigation on microbiome from abyssal water to bottom sediment in the Mariana Trench via the 16 s rRNA gene profiling found that Proteobacteria, Bacteroidetes, Actinobacteria, Gemmatimonadetes, Thaumarchaeota, and Planctomycetes were dominant in the Mariana Trench habitats. Recent technological advances using 16S ribosomal RNA (rRNA) gene profiling expanded studies on ocean microbes by circumventing the limitation of culture dependency. Characterization of the microbial species in the hadal habitat began in the 1950s using culture-based techniques. It contains the deepest habitat known on earth, the Challenger Deep, ~ 11,000 m below the ocean surface. Ī great deal of effort has been focused on the Mariana Trench system in the Western Pacific ocean where two tectonic plates, the Philippine Sea plate and the Pacific plate, collide. The microbial abundance in hadal trenches was related to the availability of sedimentary organic matter, which reached the deep hadal environments by sinking via the funneling effect and by occasional landslides induced by deep ocean earthquakes. Hadal trenches were proposed to comprise specialized biodiversity related to their geographic isolation and unique environment characteristics. Despite the harsh conditions, abundant microorganisms and metabolic activities were found to exist in both the hadal water columns and hadal sediments. In addition to elevated hydrostatic pressure (60–110 MPa), the trench environments are characterized as near-freezing temperatures, total darkness, poor nutrient availability, and isolation in topography. The hadal trench represents the deepest habitat for living organisms on the surface of the earth and accounts for a significant portion of the global benthic area. The deep metagenomics approach fills the knowledge gaps in structure and diversity of the hadal microbiome, and provides novel insight into the ecology and metabolism of eukaryotic and viral components in the deepest biosphere on earth. Our hadal MAGs and isolates increase the diversity of the Challenger Deep sediment microbial genomes and isolates present in the public. The hadal microbiome is further investigated by large-scale cultivation that cataloged 1070 bacterial and 19 fungal isolates from the Challenger Deep sediment, many of which are found to be new species specialized in the hadal habitat. By metaviromic analysis, we reveal novel hadal Caudovirales clades, distinctive virus-host interactions, and specialized auxiliary metabolic genes for modulating hosts’ nitrogen/sulfur metabolism. The microeukaryotic community is found to be dominated by six fungal groups that are characterized for the first time in hadal sediment to possess the assimilatory and dissimilatory nitrate/sulfate reduction, and hydrogen sulfide oxidation pathways. Based on the MAGs, we find the microbial community functions are marked by enrichment and prevalence of mixotrophy and facultative anaerobic metabolism. We construct 178 metagenome-assembled genomes (MAGs) representing 26 phyla, 16 of which are reported from hadal sediment for the first time. We adopt a deep metagenomics approach to investigate the microbiome in the sediment of Challenger Deep, Mariana Trench. The full biosphere structure and functional exploration of the microbial communities of the Challenger Deep of the Mariana Trench, the deepest known hadal zone on Earth, lag far behind that of other marine realms.
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