Hadal ocean biosphere, that is, the deepest part of the world's oceans, harbors a unique microbial community, suggesting a potential uncovered co-occurring virioplankton assemblage. Herein, we reveal the unique virioplankton assemblages of the Challenger Deep, comprising 95,813 non-redundant viral contigs from the surface to the hadal zone. Almost all of the dominant viral contigs in the hadal zone were unclassified, potentially related to Alteromonadales and Oceanospirillales. 2,586 viral auxiliary metabolic genes from 132 different KEGG orthologous groups were mainly related to the carbon, nitrogen, sulfur, and arsenic metabolism. Lysogenic viral production and integrase genes were augmented in the hadal zone, suggesting the prevalence of viral lysogenic life strategy. Abundant rve genes in the hadal zone, which function as transposase in the caudoviruses, further suggest the prevalence of viral-mediated horizontal gene transfer. This study provides fundamental insights into the virioplankton assemblages of the hadal zone, reinforcing the necessity of incorporating virioplankton into the hadal biogeochemical cycles.
Abstract The diversity and spatiotemporal dynamics of a coastal RNA virus community, was investigated focusing on the effects of a bloom of the macroalgae U. prolifera through a metatranscriptomic reconstruction of ~ 880Gb of Qingdao Coastal RNA sequences from May 2019 to December 2020. 6,079 RNA viral contigs were identified and these generated 2,351 viral operational taxonomic units within known orders. The analysis found that structural components of the coastal marine RNA virus community are diverse, abundant and stable. The viruses were mainly associated with eukaryotes from Intramacronucleata, Chlorophyta, Bacillariophyta and Dinophyceae, bacteria from Flavobacteriales and Rhodobacterales and MGII and Nitrosopumilales from archaea. The viral auxiliary metabolic genes indicate that coastal RNA viruses manipulate reprogramming of diverse host metabolisms, including carbon cycling, signaling pathways, membrane transport, transcription and translation. Together these results provide critical insights for incorporating RNA viruses into marine ecological and epidemiological models.
Abstract The intertidal sediment environment is dynamic and the biofilm bacterial community within it must constantly adjust, but an understanding of the differences in the biofilm bacterial community within sediments of different types is still relatively limited. In this study, the structure of the bacterial community in Jiaozhou Bay sediment biofilms are described using high-throughput 16S rRNA gene sequencing and the effects of temporal change and different sediment environment types are discussed. The Shannon index was significantly higher in sandy samples than in muddy samples. The co-occurrence network was tighter and more species were involved in community building in sandy samples. The principal coordinates analysis identified a significant separation between different sediment types and between stations (LiCun estuary, LC and ZhanQiao Pier, ZQ). Proteobacteria, which had a relative abundance of approximately 50% at all phylum levels, was significantly more abundant at ZQ, while Campilobacterota and Firmicutes were significantly more abundant at LC. The relative abundances of Bacteroidetes, Campilobacterota, Firmicutes, and Chloroflexi were significantly higher in the muddy samples, while Actinobacteria and Proteobacteria were higher in the sandy samples. There were different phylum-level biomarkers between sediment types at different stations. There were also different patterns of functional enrichment in biogeochemical cycles between sediment types and stations with the former having more gene families that differed significantly, highlighting their greater role in determining bacterial function. The RDA results, where each month’s samples were concentrated individually, showed reduced variation between months when the amplicon sequence variant was replaced by KEGG orthologs, presumably the temporal change had an impact on shaping the intertidal sediment bacterial community, although this was less clear at the gene family level. Random forest prediction yielded a combination of 43 family-level features that responded well to temporal change, reflecting the influence of temporal change on sediment biofilm bacteria. Highlights Sandy sediments have more bacterial species involved in community building. Different substrates from different stations have their own phylum biomarkers. Substrates have a greater influence on shaping bacterial function. Temporal changes have a greater shaping power on bacteria than on gene families. Graphic abstract
Abstract Background Polar sea ice is one of the largest ecosystems on Earth, harboring a vast and unexplored microbial diversity, which sustains the polar ecosystems during the long dark winters. Viruses are the most abundant “life forms” in the sea and are considered the main manipulators of microorganisms. However, little is known about the viral assemblages inhabiting Antarctic sea ice and under ice seawater or their biogeochemical roles. Results Here we establish an Antarctic sea ice and water DNA virome (ASIWV) dataset by analyzing 11 viral metagenomes derived from sea ice and seawater from below the melting ice in spring. A total of 28,169 viral contigs were identified and classified into 17,284 nonredundant viral Operational Taxonomic Units (vOTUs). Most of vOTUs could not be classified and so are considered probably endemic to Antarctic marine environments. Compared with those from sea water, viruses from within the sea ice preferentially adopted a lysogenic infection strategy, comprising more than 20% of viruses in multiple sea ice samples. The vOTUs in sea ice and sea water were quite similar, but there was still a distinction between their relative abundances. Potential hosts of 222 vOTUs were predicted, mainly linked to the dominant bacterial classes Gammaproteobacteria and Flavobacteriia . Notably, 220 virus-encoded auxiliary metabolic genes from 28 categories were identified, suggesting that viruses mediate microbial metabolism of carbon, sulfur, nitrogen, lipids and cold adaption. Conclusions This study is the first to reveal the unique taxonomic characteristics of viruses from polar sea ice and the under ice seawater, provides a baseline for sea ice DNA viral assemblages, highlights an unexplored hotspot of viral diversity and enhances our understanding of the viral contribution to the regulation microbial ecology and biogeochemistry.
Abstract Background: The hadal ocean biosphere, i.e the deepest part of the world’s oceans, harbors a unique community of cellular microbes, implying that there is also a novel assemblage of co-occurring viruses. However, the diversity and lifestyle of viroplanktons in hadal zone is poorly studied. Results: Herein, we show the unique nature of the Mariana Trench DNA virome (MTV) comprising a dataset of 95,813 non-redundant assembled viral sequences (contigs) from the ocean’s surface (2m) to the hadal zone at 8727 m below the surface. We assigned 29% of the contigs into 236 viral taxa, of which all but 3% belonged to groups with no cultured representatives. The remaining 71% of the contigs could not be assigned to a taxonomic group. The dominant viral contigs were almost more abundant in deep even hadal zone than in surface zone. The MTV is unlike any other viral assemblage described to date, and presents a novel viral ecological zone in the global ocean. The dominant viral contigs in the MTV were abundant and significantly specific in the “Trench” zone, and were associated with viruses that had signature genes indicative of a lysogenic life strategy, suggesting that horizontal gene transfer by viruses among bacteria is likely more prevelant in hadal zone than in the overlying waters. Conclusions: This study demonstrates that viruses dominating the hadal zone of the Mariana Trench are unlike those associated with other marine viral assemblages sampled to date, representing a unique ecological assemblage characterized by a lysogenic life style and horizontal gene transfer events. These results establish a foundation against which viral assemblages from other deep trenches can be compared. Keywords: Challenger Deep, Mariana Trench, ocean viromes, viral metagenomics, lysogenic life strategy, horizontal gene transfer
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