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Su Y, Zhang W, Liang Y, Wang H, Liu Y, Zheng K, Liu Z, Yu H, Ren L, Shao H, Sung YY, Mok WJ, Wong LL, Zhang YZ, McMinn A, Wang M. Identification and genomic analysis of temperate Halomonas bacteriophage vB_HmeY_H4907 from the surface sediment of the Mariana Trench at a depth of 8,900 m. Microbiol Spectr 2023; 11:e0191223. [PMID: 37728551 PMCID: PMC10580944 DOI: 10.1128/spectrum.01912-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 08/04/2023] [Indexed: 09/21/2023] Open
Abstract
Viruses play crucial roles in the ecosystem by modulating the host community structure, mediating biogeochemical cycles, and compensating for the metabolism of host cells. Mariana Trench, the world's deepest hadal habitat, harbors a variety of unique microorganisms that have adapted to its extreme conditions of low temperatures, high pressure, and nutrient scarcity. However, our knowledge about isolated hadal phage strains in the hadal trench is still limited. This study reported the discovery of a temperate phage, vB_HmeY_H4907, infecting Halomonas meridiana H4907, isolated from surface sediment from the Mariana Trench at a depth of 8,900 m. To our best knowledge, it is the deepest isolated siphovirus from the ocean. Its 40,452 bp linear dsDNA genome has 57.64% GC content and 55 open reading frames, and it is highly homologous to its host. Phylogenetic analysis and average nucleotide sequence identification reveal that vB_HmeY_H4907 is separated from the isolated phages and represents a new family, Suviridae, with eight predicted proviruses and six uncultured viral genomes. They are widely distributed in the ocean, suggesting a prevalence of this viral family in the deep sea. These findings expand our understanding of the phylogenetic diversity and genomic features of hadal lysogenic phages, provide essential information for further studies of phage-host interactions and evolution, and may reveal new insights into the lysogenic lifestyles of viruses inhabiting the hadal ocean. IMPORTANCE Halomonas phage vB_HmeY_H4907 is the deepest isolated siphovirus from the ocean, and it represents a novel abundant viral family in the ocean. This study provides insights into the genomic, phylogenetic, and ecological characteristics of the new viral family, namely, Suviridae.
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Affiliation(s)
- Yue Su
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Wenjing Zhang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
| | - Yantao Liang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
- UMT-OUC Joint Academic Centre for Marine Studies, Qingdao, China
| | - Hongmin Wang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Yundan Liu
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Kaiyang Zheng
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Ziqi Liu
- Department of Integrated Global Studies, School of Integrated Arts and Sciences, Hiroshima University, Hiroshima, Japan
| | - Hao Yu
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Linyi Ren
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Hongbing Shao
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
- UMT-OUC Joint Academic Centre for Marine Studies, Qingdao, China
| | - Yeong Yik Sung
- UMT-OUC Joint Academic Centre for Marine Studies, Qingdao, China
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, Kuala Terengganu, Malaysia
| | - Wen Jye Mok
- UMT-OUC Joint Academic Centre for Marine Studies, Qingdao, China
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, Kuala Terengganu, Malaysia
| | - Li Lian Wong
- UMT-OUC Joint Academic Centre for Marine Studies, Qingdao, China
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, Kuala Terengganu, Malaysia
| | - Yu-Zhong Zhang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Andrew McMinn
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania, Australia
| | - Min Wang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
- UMT-OUC Joint Academic Centre for Marine Studies, Qingdao, China
- Haide College, Ocean University of China, Qingdao, China
- The Affiliated Hospital of Qingdao University, Qingdao, China
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Ecogenomics reveals viral communities across the Challenger Deep oceanic trench. Commun Biol 2022; 5:1055. [PMID: 36192584 PMCID: PMC9529941 DOI: 10.1038/s42003-022-04027-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 09/23/2022] [Indexed: 11/23/2022] Open
Abstract
Despite the environmental challenges and nutrient scarcity, the geographically isolated Challenger Deep in Mariana trench, is considered a dynamic hotspot of microbial activity. Hadal viruses are the least explored microorganisms in Challenger Deep, while their taxonomic and functional diversity and ecological impact on deep-sea biogeochemistry are poorly described. Here, we collect 13 sediment cores from slope and bottom-axis sites across the Challenger Deep (down to ~11 kilometers depth), and identify 1,628 previously undescribed viral operational taxonomic units at species level. Community-wide analyses reveals 1,299 viral genera and distinct viral diversity across the trench, which is significantly higher at the bottom-axis vs. slope sites of the trench. 77% of these viral genera have not been previously identified in soils, deep-sea sediments and other oceanic settings. Key prokaryotes involved in hadal carbon and nitrogen cycling are predicted to be potential hosts infected by these viruses. The detected putative auxiliary metabolic genes suggest that viruses at Challenger Deep could modulate the carbohydrate and sulfur metabolisms of their potential hosts, and stabilize host’s cell membranes under extreme hydrostatic pressures. Our results shed light on hadal viral metabolic capabilities, contribute to understanding deep sea ecology and on functional adaptions of hadal viruses for future research. Analysis of 13 sediment cores from the Challenger Deep of Marian Trench (down to 11 kilometers depth) identified distinct operational taxonomic units and relevant auxiliary metabolic genes, providing further insight into deep-sea viral metabolic capabilities and ecology.
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Wirth J, Young M. Viruses in Subsurface Environments. Annu Rev Virol 2022; 9:99-119. [PMID: 36173700 DOI: 10.1146/annurev-virology-093020-015957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Over the past 20 years, our knowledge of virus diversity and abundance in subsurface environments has expanded dramatically through application of quantitative metagenomic approaches. In most subsurface environments, viral diversity and abundance rival viral diversity and abundance observed in surface environments. Most of these viruses are uncharacterized in terms of their hosts and replication cycles. Analysis of accessory metabolic genes encoded by subsurface viruses indicates that they evolved to replicate within the unique features of their environments. The key question remains: What role do these viruses play in the ecology and evolution of the environments in which they replicate? Undoubtedly, as more virologists examine the role of viruses in subsurface environments, new insights will emerge.
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Affiliation(s)
- Jennifer Wirth
- Department of Plant Science and Plant Pathology and Thermal Biology Institute, Montana State University, Bozeman, Montana, USA;
| | - Mark Young
- Department of Plant Science and Plant Pathology and Thermal Biology Institute, Montana State University, Bozeman, Montana, USA;
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Zhao J, Jing H, Wang Z, Wang L, Jian H, Zhang R, Xiao X, Chen F, Jiao N, Zhang Y. Novel Viral Communities Potentially Assisting in Carbon, Nitrogen, and Sulfur Metabolism in the Upper Slope Sediments of Mariana Trench. mSystems 2022; 7:e0135821. [PMID: 35089086 PMCID: PMC8725595 DOI: 10.1128/msystems.01358-21] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 12/08/2021] [Indexed: 01/12/2023] Open
Abstract
Viruses are ubiquitous in the oceans. Even in the deep sediments of the Mariana Trench, viruses have high productivity. However, little is known about their species composition and survival strategies in that environment. Here, we uncovered novel viral communities (3,206 viral scaffolds) in the upper slope sediments of the Mariana Trench via metagenomic analysis of 15 sediment samples. Most (99%) of the viral scaffolds lack known viral homologs, and ca. 59% of the high-quality viral genomes (total of 111 with completeness of >90%) represent novel genera, including some Phycodnaviridae and jumbo phages. These viruses contain various auxiliary metabolic genes (AMGs) potentially involved in organic carbon degradation, inorganic carbon fixation, denitrification, and assimilatory sulfate reduction, etc. This study provides novel insight into the almost unknown benthic viral communities in the Mariana Trench. IMPORTANCE The Mariana Trench harbors a substantial number of infective viral particles. However, very little is known about the identity, survival strategy, and potential functions of viruses in the trench sediments. Here, through metagenomic analysis, unusual benthic viral communities with high diversity and novelty were discovered. Among them, 59% of the viruses with a genome completeness of >90% represent novel genera. Various auxiliary metabolic genes carried by these viruses reflect the potential adaptive characteristics of viruses in this extreme environment and the biogeochemical cycles that they may participate in. This study gives us a deeper understanding of the peculiarities of viral communities in deep-sea/hadal sediments.
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Affiliation(s)
- Jiulong Zhao
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hongmei Jing
- CAS Key Laboratory for Experimental Study under Deep-Sea Extreme Conditions, Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zengmeng Wang
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Long Wang
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- State Key Laboratory for Marine Environmental Science, Xiamen University, Xiamen, China
| | - Huahua Jian
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Rui Zhang
- State Key Laboratory for Marine Environmental Science, Xiamen University, Xiamen, China
| | - Xiang Xiao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Feng Chen
- University of Maryland Center for Environmental Science, Baltimore, Maryland, USA
| | - Nianzhi Jiao
- State Key Laboratory for Marine Environmental Science, Xiamen University, Xiamen, China
| | - Yongyu Zhang
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
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A holistic genome dataset of bacteria, archaea and viruses of the Pearl River estuary. Sci Data 2022; 9:49. [PMID: 35165305 PMCID: PMC8844013 DOI: 10.1038/s41597-022-01153-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 01/12/2022] [Indexed: 12/21/2022] Open
Abstract
Estuaries are one of the most important coastal ecosystems. While microbiomes and viromes have been separately investigated in some estuaries, few studies holistically deciphered the genomes and connections of viruses and their microbial hosts along an estuarine salinity gradient. Here we applied deep metagenomic sequencing on microbial and viral communities in surface waters of the Pearl River estuary, one of China’s largest estuaries with strong anthropogenic impacts. Overall, 1,205 non-redundant prokaryotic genomes with ≥50% completeness and ≤10% contamination, and 78,502 non-redundant viral-like genomes were generated from samples of three size fractions and five salinity levels. Phylogenomic analysis and taxonomy classification show that majority of these estuarine prokaryotic and viral genomes are novel at species level according to public databases. Potential connections between the microbial and viral populations were further investigated by host-virus matching. These combined microbial and viral genomes provide an important complement of global marine genome datasets and should greatly facilitate our understanding of microbe-virus interactions, evolution and their implications in estuarine ecosystems. Measurement(s) | bacteria • Archaea • viruses | Technology Type(s) | Shotgun Sequencing | Sample Characteristic - Organism | estuary metagenome | Sample Characteristic - Environment | subtropical estuarine | Sample Characteristic - Location | Pearl river estuary |
Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.17139998
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Fan S, Wang M, Ding W, Li YX, Zhang YZ, Zhang W. Scientific and technological progress in the microbial exploration of the hadal zone. MARINE LIFE SCIENCE & TECHNOLOGY 2022; 4:127-137. [PMID: 37073349 PMCID: PMC10077178 DOI: 10.1007/s42995-021-00110-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 05/11/2021] [Indexed: 05/03/2023]
Abstract
The hadal zone is the deepest point in the ocean with a depth that exceeds 6000 m. Exploration of the biological communities in hadal zone began in the 1950s (the first wave of hadal exploration) and substantial advances have been made since the turn of the twenty-first century (the second wave of hadal exploration), resulting in a focus on the hadal sphere as a research hotspot because of its unique physical and chemical conditions. A variety of prokaryotes are found in the hadal zone. The mechanisms used by these prokaryotes to manage the high hydrostatic pressures and acquire energy from the environment are of substantial interest. Moreover, the symbioses between microbes and hadal animals have barely been studied. In addition, equipment has been developed that can now mimic hadal environments in the laboratory and allow cultivation of microbes under simulated in situ pressure. This review provides a brief summary of recent progress in the mechanisms by which microbes adapt to high hydrostatic pressures, manage limited energy resources and coexist with animals in the hadal zone, as well as technical developments in the exploration of hadal microbial life.
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Affiliation(s)
- Shen Fan
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003 China
| | - Meng Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003 China
| | - Wei Ding
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003 China
- Department of Chemistry, The University of Hong Kong, Hong Kong, China
| | - Yong-Xin Li
- Department of Chemistry, The University of Hong Kong, Hong Kong, China
| | - Yu-Zhong Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003 China
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237 China
| | - Weipeng Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003 China
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7
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Nomaki H, Rastelli E, Ogawa NO, Matsui Y, Tsuchiya M, Manea E, Corinaldesi C, Hirai M, Ohkouchi N, Danovaro R, Nunoura T, Amaro T. In situ experimental evidences for responses of abyssal benthic biota to shifts in phytodetritus compositions linked to global climate change. GLOBAL CHANGE BIOLOGY 2021; 27:6139-6155. [PMID: 34523189 PMCID: PMC9293103 DOI: 10.1111/gcb.15882] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 08/04/2021] [Accepted: 08/30/2021] [Indexed: 06/13/2023]
Abstract
Abyssal plains cover more than half of Earth's surface, and the main food source in these ecosystems is phytodetritus, mainly originating from primary producers in the euphotic zone of the ocean. Global climate change is influencing phytoplankton abundance, productivity, and distribution. Increasing importance of picoplankton over diatom as primary producers in surface oceans (especially projected for higher latitudes) is projected and hence altering the quantity of organic carbon supplied to the abyssal seafloor as phytodetritus, consequences of which remain largely unknown. Here, we investigated the in situ responses of abyssal biota from viruses to megafauna to different types of phytoplankton input (diatoms or cyanobacteria which were labeled with stable isotopes) at equatorial (oligotrophic) and temperate (eutrophic) benthic sites in the Pacific Ocean (1°N at 4277 m water depth and 39°N at 5260 m water depth, respectively). Our results show that meiofauna and macrofauna generally preferred diatoms as a food source and played a relatively larger role in the consumption of phytodetritus at higher latitudes (39°N). Contrarily, prokaryotes and viruses showed similar or even stronger responses to cyanobacterial than to diatom supply. Moreover, the response of prokaryotes and viruses was very rapid (within 1-2 days) at both 1°N and 39°N, with quickest responses reported in the case of cyanobacterial supply at higher latitudes. Overall, our results suggest that benthic deep-sea eukaryotes will be negatively affected by the predicted decrease in diatoms in surface oceans, especially at higher latitudes, where benthic prokaryotes and viruses will otherwise likely increase their quantitative role and organic carbon cycling rates. In turn, such changes can contribute to decrease carbon transfer from phytodetritus to higher trophic levels, with strong potential to affect oceanic food webs, their biodiversity and consequently carbon sequestration capacity at the global scale.
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Affiliation(s)
- Hidetaka Nomaki
- X‐starJapan Agency for Marine‐Earth Science and Technology (JAMSTEC)YokosukaJapan
| | - Eugenio Rastelli
- Department of Marine BiotechnologyStazione Zoologica Anton DohrnFano Marine CentreFanoItaly
| | | | - Yohei Matsui
- X‐starJapan Agency for Marine‐Earth Science and Technology (JAMSTEC)YokosukaJapan
| | | | - Elisabetta Manea
- Institute of Marine SciencesNational Research Council (ISMAR‐CNR)VeniceItaly
| | - Cinzia Corinaldesi
- Department of Materials, Environmental Sciences and Urban PlanningPolytechnic University of MarcheAnconaItaly
| | - Miho Hirai
- X‐starJapan Agency for Marine‐Earth Science and Technology (JAMSTEC)YokosukaJapan
| | | | - Roberto Danovaro
- Department of Environmental and Life SciencesPolytechnic University of MarcheAnconaItaly
- Stazione Zoologica Anton DohrnNaplesItaly
| | - Takuro Nunoura
- Research Center for Bioscience and Nanoscience (CeBN)JAMSTECYokosukaJapan
| | - Teresa Amaro
- Department of Biology & CESAMUniversity of AveiroAveiroPortugal
- Hellenic Center for Marine Research (HCMR)HeraklionGreece
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Diversity and distribution of viruses inhabiting the deepest ocean on Earth. THE ISME JOURNAL 2021; 15:3094-3110. [PMID: 33972725 PMCID: PMC8443753 DOI: 10.1038/s41396-021-00994-y] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 04/08/2021] [Accepted: 04/20/2021] [Indexed: 02/01/2023]
Abstract
As the most abundant biological entities on the planet, viruses significantly influence the overall functioning of marine ecosystems. The abundance, distribution, and biodiversity of viral communities in the upper ocean have been relatively well studied, but our understanding of viruses in the hadal biosphere remains poor. Here, we established the oceanic trench viral genome dataset (OTVGD) by analysing 19 microbial metagenomes derived from seawater and sediment samples of the Mariana, Yap, and Kermadec Trenches. The trench viral communities harbored remarkably high novelty, and they were predicted to infect ecologically important microbial clades, including Thaumarchaeota and Oleibacter. Significant inter-trench and intra-trench exchange of viral communities was proposed. Moreover, viral communities in different habitats (seawater/sediment and depth-stratified ocean zones) exhibited distinct niche-dependent distribution patterns and genomic properties. Notably, microbes and viruses in the hadopelagic seawater seemed to preferably adopt lysogenic lifestyles compared to those in the upper ocean. Furthermore, niche-specific auxiliary metabolic genes were identified in the hadal viral genomes, and a novel viral D-amino acid oxidase was functionally and phylogenetically characterized, suggesting the contribution of these genes in the utilization of refractory organic matter. Together, these findings highlight the genomic novelty, dynamic movement, and environment-driven diversification of viral communities in oceanic trenches, and suggest that viruses may influence the hadal ecosystem by reprogramming the metabolism of their hosts and modulating the community of keystone microbes.
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Zhang WJ, Zhang C, Zhou S, Li XG, Mangenot S, Fouteau S, Guerin T, Qi XQ, Yang J, Bartlett DH, Wu LF. Comparative genomic analysis of obligately piezophilic Moritella yayanosii DB21MT-5 reveals bacterial adaptation to the Challenger Deep, Mariana Trench. Microb Genom 2021; 7:000591. [PMID: 34319226 PMCID: PMC8477399 DOI: 10.1099/mgen.0.000591] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 04/20/2021] [Indexed: 01/19/2023] Open
Abstract
Hadal trenches are the deepest but underexplored ecosystems on the Earth. Inhabiting the trench bottom is a group of micro-organisms termed obligate piezophiles that grow exclusively under high hydrostatic pressures (HHP). To reveal the genetic and physiological characteristics of their peculiar lifestyles and microbial adaptation to extreme high pressures, we sequenced the complete genome of the obligately piezophilic bacterium Moritella yayanosii DB21MT-5 isolated from the deepest oceanic sediment at the Challenger Deep, Mariana Trench. Through comparative analysis against pressure sensitive and deep-sea piezophilic Moritella strains, we identified over a hundred genes that present exclusively in hadal strain DB21MT-5. The hadal strain encodes fewer signal transduction proteins and secreted polysaccharases, but has more abundant metal ion transporters and the potential to utilize plant-derived saccharides. Instead of producing osmolyte betaine from choline as other Moritella strains, strain DB21MT-5 ferments on choline within a dedicated bacterial microcompartment organelle. Furthermore, the defence systems possessed by DB21MT-5 are distinct from other Moritella strains but resemble those in obligate piezophiles obtained from the same geographical setting. Collectively, the intensive comparative genomic analysis of an obligately piezophilic strain Moritella yayanosii DB21MT-5 demonstrates a depth-dependent distribution of energy metabolic pathways, compartmentalization of important metabolism and use of distinct defence systems, which likely contribute to microbial adaptation to the bottom of hadal trench.
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Affiliation(s)
- Wei-Jia Zhang
- Laboratory of Deep-Sea Microbial Cell Biology, Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, PR China
- France-China Joint Laboratory for Evolution and Development of Magnetotactic Multicellular Organisms (LIA-MagMC), Marseille, France / IDSSE-CAS, Sanya, PR China
- Institution of Deep-Sea Life Sciences, Hainan Deep-Sea Technology Laboratory, Sanya, PR China
| | - Chan Zhang
- Laboratory of Deep-Sea Microbial Cell Biology, Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, PR China
- Present address: College of Horticulture, Hainan University, No. 58, Renmin Avenue, Haikou, PR China
| | - Siyu Zhou
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, PR China
| | - Xue-Gong Li
- Laboratory of Deep-Sea Microbial Cell Biology, Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, PR China
- France-China Joint Laboratory for Evolution and Development of Magnetotactic Multicellular Organisms (LIA-MagMC), Marseille, France / IDSSE-CAS, Sanya, PR China
- Institution of Deep-Sea Life Sciences, Hainan Deep-Sea Technology Laboratory, Sanya, PR China
| | - Sophie Mangenot
- Génomique Métabolique, CEA, Genoscope, Institut François Jacob, Université d’Évry, Université Paris-Saclay, CNRS, Evry, France
| | - Stéphanie Fouteau
- Génomique Métabolique, CEA, Genoscope, Institut François Jacob, Université d’Évry, Université Paris-Saclay, CNRS, Evry, France
| | - Thomas Guerin
- Génomique Métabolique, CEA, Genoscope, Institut François Jacob, Université d’Évry, Université Paris-Saclay, CNRS, Evry, France
| | - Xiao-Qing Qi
- Laboratory of Deep-Sea Microbial Cell Biology, Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, PR China
- France-China Joint Laboratory for Evolution and Development of Magnetotactic Multicellular Organisms (LIA-MagMC), Marseille, France / IDSSE-CAS, Sanya, PR China
- Institution of Deep-Sea Life Sciences, Hainan Deep-Sea Technology Laboratory, Sanya, PR China
| | - Jian Yang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, PR China
| | - Douglas H. Bartlett
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093-0202, USA
| | - Long-Fei Wu
- France-China Joint Laboratory for Evolution and Development of Magnetotactic Multicellular Organisms (LIA-MagMC), Marseille, France / IDSSE-CAS, Sanya, PR China
- Aix-Marseille Université, CNRS, LCB UMR 7257, IMM, IM2B, Marseille, France
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Zhou H, Chen P, Zhang M, Chen J, Fang J, Li X. Revealing the Viral Community in the Hadal Sediment of the New Britain Trench. Genes (Basel) 2021; 12:genes12070990. [PMID: 34209474 PMCID: PMC8306916 DOI: 10.3390/genes12070990] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 06/07/2021] [Accepted: 06/09/2021] [Indexed: 12/24/2022] Open
Abstract
Marine viruses are widely distributed and influence matter and energy transformation in ecosystems by modulating hosts’ metabolism. The hadal trenches represent the deepest marine habitat on Earth, for which the viral communities and related biogeochemical functions are least explored and poorly understood. Here, using the sediment samples (8720 m below sea level) collected from the New Britain Trench (NBT), we investigated the viral community, diversity, and genetic potentials in the hadal sediment habitat for the first time by deep shotgun metagenomic sequencing. We found the NBT sediment viral community was dominated by Siphoviridae, Myoviridae, Podoviridae, Mimiviridae, and Phycodnaviridae, which belong to the dsDNA viruses. However, the large majority of them remained uncharacterized. We found the hadal sediment virome had some common components by comparing the hadal sediment viruses with those of hadal aquatic habitats and those of bathypelagic and terrestrial habitats. It was also distinctive in community structure and had many novel viral clusters not associated with the other habitual virome included in our analyses. Further phylogenetic analysis on its Caudovirales showed novel diversities, including new clades specially evolved in the hadal sediment habitat. Annotation of the NBT sediment viruses indicated the viruses might influence microbial hydrocarbon biodegradation and carbon and sulfur cycling via metabolic augmentation through auxiliary metabolic genes (AMGs). Our study filled in the knowledge gaps on the virome of the hadal sediment habitats and provided insight into the evolution and the potential metabolic functions of the hadal sediment virome.
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Affiliation(s)
- Hui Zhou
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; (H.Z.); (P.C.); (M.Z.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ping Chen
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; (H.Z.); (P.C.); (M.Z.)
| | - Mengjie Zhang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; (H.Z.); (P.C.); (M.Z.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiawang Chen
- Ocean College, Zhejiang University, Zhoushan 316021, China
- Correspondence: (J.C.); (J.F.); (X.L.)
| | - Jiasong Fang
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China
- Correspondence: (J.C.); (J.F.); (X.L.)
| | - Xuan Li
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; (H.Z.); (P.C.); (M.Z.)
- University of Chinese Academy of Sciences, Beijing 100049, China
- Correspondence: (J.C.); (J.F.); (X.L.)
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11
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Schauberger C, Middelboe M, Larsen M, Peoples LM, Bartlett DH, Kirpekar F, Rowden AA, Wenzhöfer F, Thamdrup B, Glud RN. Spatial variability of prokaryotic and viral abundances in the Kermadec and Atacama Trench regions. LIMNOLOGY AND OCEANOGRAPHY 2021; 66:2095-2109. [PMID: 34239169 PMCID: PMC8248377 DOI: 10.1002/lno.11711] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 12/01/2020] [Accepted: 01/04/2021] [Indexed: 05/31/2023]
Abstract
Hadal trenches represent the deepest part of the ocean and are dynamic depocenters with intensified prokaryotic activity. Here, we explored the distribution and drivers of prokaryotic and viral abundance from the ocean surface and 40 cm into sediments in two hadal trench regions with contrasting surface productivity. In the water column, prokaryotic and viral abundance decreased with water depth before reaching a rather stable level at ~ 4000 m depth at both trench systems, while virus to prokaryote ratios were increasing with depth, presumably reflecting the declining availability of organic material. Prokaryotic and viral abundances in sediments were lower at the adjacent abyssal sites than at the hadal sites and declined exponentially with sediment depth, closely tracking the attenuation of total organic carbon (TOC) content. In contrast, hadal sediment exhibited erratic depth profiles of prokaryotes and viruses with many subsurface peaks. The prokaryotic abundance correlated well to extensive fluctuations in TOC content at centimeter scale, which were likely caused by recurring mass wasting events. Yet while prokaryotic and viral abundances cross correlated well in the abyssal sediments, there was no clear correlation in the hadal sites. The results suggested that dynamic depositional conditions and higher substrate availability result in a high spatial heterogeneity in viral and prokaryotic abundances in hadal sediments in comparison to more stable abyssal settings. We argue that these conditions enhance the relatively importance of viruses for prokaryotic mortality and carbon recycling in hadal settings.
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Affiliation(s)
- Clemens Schauberger
- Department of Biology, Nordcee and HADALUniversity of Southern DenmarkOdenseDenmark
| | - Mathias Middelboe
- Department of Biology, Nordcee and HADALUniversity of Southern DenmarkOdenseDenmark
- Marine Biological Section, Department of BiologyUniversity of CopenhagenHelsingørDenmark
| | - Morten Larsen
- Department of Biology, Nordcee and HADALUniversity of Southern DenmarkOdenseDenmark
| | - Logan M. Peoples
- Marine Biology Research Division, Scripps Institution of OceanographyUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Douglas H. Bartlett
- Marine Biology Research Division, Scripps Institution of OceanographyUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Finn Kirpekar
- Department of Biochemistry and Molecular BiologyUniversity of Southern DenmarkOdense MDenmark
| | - Ashley A. Rowden
- National Institute of Water and Atmospheric ResearchWellingtonNew Zealand
- School of Biological Sciences, Victoria University of WellingtonWellingtonNew Zealand
| | - Frank Wenzhöfer
- Alfred Wegener Institute, Helmholtz Center for Polar and Marine ResearchBremerhavenGermany
- Max Planck Institute for Marine Microbiology and EcologyBremenGermany
| | - Bo Thamdrup
- Department of Biology, Nordcee and HADALUniversity of Southern DenmarkOdenseDenmark
| | - Ronnie N. Glud
- Department of Biology, Nordcee and HADALUniversity of Southern DenmarkOdenseDenmark
- Department of Ocean and Environmental SciencesTokyo University of Marine Science and TechnologyTokyoJapan
- Danish Institute for Advanced Study – DIAS, University of Southern DenmarkOdenseDenmark
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12
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Hiraoka S, Hirai M, Matsui Y, Makabe A, Minegishi H, Tsuda M, Juliarni, Rastelli E, Danovaro R, Corinaldesi C, Kitahashi T, Tasumi E, Nishizawa M, Takai K, Nomaki H, Nunoura T. Microbial community and geochemical analyses of trans-trench sediments for understanding the roles of hadal environments. ISME JOURNAL 2019; 14:740-756. [PMID: 31827245 PMCID: PMC7031335 DOI: 10.1038/s41396-019-0564-z] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 11/20/2019] [Accepted: 11/28/2019] [Indexed: 12/28/2022]
Abstract
Hadal trench bottom (>6000 m below sea level) sediments harbor higher microbial cell abundance compared with adjacent abyssal plain sediments. This is supported by the accumulation of sedimentary organic matter (OM), facilitated by trench topography. However, the distribution of benthic microbes in different trench systems has not been well explored yet. Here, we carried out small subunit ribosomal RNA gene tag sequencing for 92 sediment subsamples of seven abyssal and seven hadal sediment cores collected from three trench regions in the northwest Pacific Ocean: the Japan, Izu-Ogasawara, and Mariana Trenches. Tag-sequencing analyses showed specific distribution patterns of several phyla associated with oxygen and nitrate. The community structure was distinct between abyssal and hadal sediments, following geographic locations and factors represented by sediment depth. Co-occurrence network revealed six potential prokaryotic consortia that covaried across regions. Our results further support that the OM cycle is driven by hadal currents and/or rapid burial shapes microbial community structures at trench bottom sites, in addition to vertical deposition from the surface ocean. Our trans-trench analysis highlights intra- and inter-trench distributions of microbial assemblages and geochemistry in surface seafloor sediments, providing novel insights into ultradeep-sea microbial ecology, one of the last frontiers on our planet.
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Affiliation(s)
- Satoshi Hiraoka
- Research Center for Bioscience and Nanoscience (CeBN), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Kanagawa, Japan.
| | - Miho Hirai
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Kanagawa, Japan
| | - Yohei Matsui
- Project Team for Development of New-generation Research Protocol for Submarine Resources, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Kanagawa, Japan.,Research and Development Center for Submarine Resources, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Kanagawa, Japan.,Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8564, Japan
| | - Akiko Makabe
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Kanagawa, Japan
| | - Hiroaki Minegishi
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Kanagawa, Japan.,Faculty of Science and Engineering, Toyo University, 2100 Kujirai, Kawagoe, 350-8585, Saitama, Japan
| | - Miwako Tsuda
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Kanagawa, Japan
| | - Juliarni
- Project Team for Development of New-generation Research Protocol for Submarine Resources, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Kanagawa, Japan
| | - Eugenio Rastelli
- Stazione Zoologica Anton Dohrn, Villa Comunale, Naples, 80121, Italy
| | - Roberto Danovaro
- Stazione Zoologica Anton Dohrn, Villa Comunale, Naples, 80121, Italy.,Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, 60131, Italy
| | - Cinzia Corinaldesi
- Department of Materials, Environmental Sciences and Urban Planning, Polytechnic University of Marche, Ancona, 60131, Italy
| | - Tomo Kitahashi
- Marine Biodiversity and Environmental Assessment Research Center (BioEnv), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Kanagawa, Japan
| | - Eiji Tasumi
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Kanagawa, Japan
| | - Manabu Nishizawa
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Kanagawa, Japan
| | - Ken Takai
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Kanagawa, Japan
| | - Hidetaka Nomaki
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Kanagawa, Japan
| | - Takuro Nunoura
- Research Center for Bioscience and Nanoscience (CeBN), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Kanagawa, Japan.
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