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Fu L, Liu Y, Wang M, Lian C, Cao L, Wang W, Sun Y, Wang N, Li C. The diversification and potential function of microbiome in sediment-water interface of methane seeps in South China Sea. Front Microbiol 2024; 15:1287147. [PMID: 38380093 PMCID: PMC10878133 DOI: 10.3389/fmicb.2024.1287147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 01/11/2024] [Indexed: 02/22/2024] Open
Abstract
The sediment-water interfaces of cold seeps play important roles in nutrient transportation between seafloor and deep-water column. Microorganisms are the key actors of biogeochemical processes in this interface. However, the knowledge of the microbiome in this interface are limited. Here we studied the microbial diversity and potential metabolic functions by 16S rRNA gene amplicon sequencing at sediment-water interface of two active cold seeps in the northern slope of South China Sea, Lingshui and Site F cold seeps. The microbial diversity and potential functions in the two cold seeps are obviously different. The microbial diversity of Lingshui interface areas, is found to be relatively low. Microbes associated with methane consumption are enriched, possibly due to the large and continuous eruptions of methane fluids. Methane consumption is mainly mediated by aerobic oxidation and denitrifying anaerobic methane oxidation (DAMO). The microbial diversity in Site F is higher than Lingshui. Fluids from seepage of Site F are mitigated by methanotrophic bacteria at the cyclical oxic-hypoxic fluctuating interface where intense redox cycling of carbon, sulfur, and nitrogen compounds occurs. The primary modes of microbial methane consumption are aerobic methane oxidation, along with DAMO, sulfate-dependent anaerobic methane oxidation (SAMO). To sum up, anaerobic oxidation of methane (AOM) may be underestimated in cold seep interface microenvironments. Our findings highlight the significance of AOM and interdependence between microorganisms and their environments in the interface microenvironments, providing insights into the biogeochemical processes that govern these unique ecological systems.
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Affiliation(s)
- Lulu Fu
- Center of Deep Sea Research and Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laoshan Laboratory, Qingdao, China
| | - Yanjun Liu
- Center of Deep Sea Research and Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Minxiao Wang
- Center of Deep Sea Research and Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laoshan Laboratory, Qingdao, China
| | - Chao Lian
- Center of Deep Sea Research and Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Lei Cao
- Center of Deep Sea Research and Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Weicheng Wang
- State Key Laboratory of Mariculture Breeding, Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, College of Marine Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yan Sun
- Center of Deep Sea Research and Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laoshan Laboratory, Qingdao, China
| | - Nan Wang
- Center of Deep Sea Research and Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laoshan Laboratory, Qingdao, China
| | - Chaolun Li
- Center of Deep Sea Research and Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laoshan Laboratory, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
- South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
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2
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Kawagucci S, Sakai S, Tasumi E, Hirai M, Takaki Y, Nunoura T, Saitoh M, Ueno Y, Yoshida N, Shibuya T, Clifford Sample J, Okumura T, Takai K. Deep Subseafloor Biogeochemical Processes and Microbial Populations Potentially Associated with the 2011 Tohoku-oki Earthquake at the Japan Trench Accretionary Wedge (IODP Expedition 343). Microbes Environ 2023; 38:n/a. [PMID: 37331792 DOI: 10.1264/jsme2.me22108] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2023] Open
Abstract
Post-mega-earthquake geochemical and microbiological properties in subseafloor sediments of the Japan Trench accretionary wedge were investigated using core samples from Hole C0019E, which was drilled down to 851 m below seafloor (mbsf) at a water depth of 6,890 m. Methane was abundant throughout accretionary prism sediments; however, its concentration decreased close to the plate boundary decollement. Methane isotope systematics indicated a biogenic origin. The content of mole-cular hydrogen (H2) was low throughout core samples, but markedly increased at specific depths that were close to potential faults predicted by logging-while-drilling ana-lyses. Based on isotopic systematics, H2 appeared to have been abundantly produced via a low-temperature interaction between pore water and the fresh surface of crushed rock induced by earthquakes. Subseafloor microbial cell density remained constant at approximately 105 cells mL-1. Amplicon sequences revealed that predominant members at the phylum level were common throughout the units tested, which also included members frequently found in anoxic subseafloor sediments. Metabolic potential assays using radioactive isotopes as tracers revealed homoacetogenic activity in H2-enriched core samples collected near the fault. Furthermore, homoacetogenic bacteria, including Acetobacterium carbinolicum, were isolated from similar samples. Therefore, post-earthquake subseafloor microbial communities in the Japan Trench accretionary prism appear to be episodically dominated by homoacetogenic populations and potentially function due to the earthquake-induced low-temperature generation of H2. These post-earthquake microbial communities may eventually return to the steady-state communities dominated by oligotrophic heterotrophs and hydrogenotrophic and methylotrophic methanogens that are dependent on refractory organic matter in the sediment.
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Affiliation(s)
- Shinsuke Kawagucci
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-STAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
- Marine Biodiversity and Environmental Assessment Research Center (BioEnv), Research Institute for Global Change (RIGC), Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | - Sanae Sakai
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-STAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | - Eiji Tasumi
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-STAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | - Miho Hirai
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-STAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | - Yoshihiro Takaki
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-STAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | - Takuro Nunoura
- Research Center for Bioscience and Nanoscience (CeBN), Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | | | - Yuichiro Ueno
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-STAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
- Department of Earth and Planetary Sciences, Tokyo Institute of Technology
- Earth-Life Science Institute, Tokyo Institute of Technology
| | - Naohiro Yoshida
- Earth-Life Science Institute, Tokyo Institute of Technology
- National Institute of Information and Communications Technology
| | - Takazo Shibuya
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-STAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | | | - Tomoyo Okumura
- Center for Advanced Marine Core Research, Kochi University
| | - Ken Takai
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-STAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
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3
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Medvedeva S, Sun J, Yutin N, Koonin EV, Nunoura T, Rinke C, Krupovic M. Three families of Asgard archaeal viruses identified in metagenome-assembled genomes. Nat Microbiol 2022; 7:962-973. [PMID: 35760839 PMCID: PMC11165672 DOI: 10.1038/s41564-022-01144-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 05/04/2022] [Indexed: 02/07/2023]
Abstract
Asgardarchaeota harbour many eukaryotic signature proteins and are widely considered to represent the closest archaeal relatives of eukaryotes. Whether similarities between Asgard archaea and eukaryotes extend to their viromes remains unknown. Here we present 20 metagenome-assembled genomes of Asgardarchaeota from deep-sea sediments of the basin off the Shimokita Peninsula, Japan. By combining a CRISPR spacer search of metagenomic sequences with phylogenomic analysis, we identify three family-level groups of viruses associated with Asgard archaea. The first group, verdandiviruses, includes tailed viruses of the class Caudoviricetes (realm Duplodnaviria); the second, skuldviruses, consists of viruses with predicted icosahedral capsids of the realm Varidnaviria; and the third group, wyrdviruses, is related to spindle-shaped viruses previously identified in other archaea. More than 90% of the proteins encoded by these viruses of Asgard archaea show no sequence similarity to proteins encoded by other known viruses. Nevertheless, all three proposed families consist of viruses typical of prokaryotes, providing no indication of specific evolutionary relationships between viruses infecting Asgard archaea and eukaryotes. Verdandiviruses and skuldviruses are likely to be lytic, whereas wyrdviruses potentially establish chronic infection and are released without host cell lysis. All three groups of viruses are predicted to play important roles in controlling Asgard archaea populations in deep-sea ecosystems.
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Affiliation(s)
- Sofia Medvedeva
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, Paris, France
- Center of Life Science, Skolkovo Institute of Science and Technology, Moscow, Russia
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Evolutionary Biology of the Microbial Cell Unit, Paris, France
| | - Jiarui Sun
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia
| | - Natalya Yutin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Takuro Nunoura
- Research Center for Bioscience and Nanoscience, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan.
| | - Christian Rinke
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia.
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, Paris, France.
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4
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Katayama T, Yoshioka H, Kaneko M, Amo M, Fujii T, Takahashi HA, Yoshida S, Sakata S. Cultivation and biogeochemical analyses reveal insights into methanogenesis in deep subseafloor sediment at a biogenic gas hydrate site. THE ISME JOURNAL 2022; 16:1464-1472. [PMID: 35105960 PMCID: PMC9038717 DOI: 10.1038/s41396-021-01175-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 11/30/2021] [Accepted: 12/08/2021] [Indexed: 11/09/2022]
Abstract
AbstractGas hydrates deposited in subseafloor sediments are considered to primarily consist of biogenic methane. However, little evidence for the occurrence of living methanogens in subseafloor sediments has been provided. This study investigated viable methanogen diversity, population, physiology and potential activity in hydrate-bearing sediments (1–307 m below the seafloor) from the eastern Nankai Trough. Radiotracer experiments, the quantification of coenzyme F430 and molecular sequencing analysis indicated the occurrence of potential methanogenic activity and living methanogens in the sediments and the predominance of hydrogenotrophic methanogens followed by methylotrophic methanogens. Ten isolates and nine representative culture clones of hydrogenotrophic, methylotrophic and acetoclastic methanogens were obtained from the batch incubation of sediments and accounted for 0.5–76% of the total methanogenic sequences directly recovered from each sediment. The hydrogenotrophic methanogen isolates of Methanocalculus and Methanoculleus that dominated the sediment methanogen communities produced methane at temperatures from 4 to 55 °C, with an abrupt decline in the methane production rate at temperatures above 40 °C, which is consistent with the depth profiles of potential methanogenic activity in the Nankai Trough sediments in this and previous studies. Our results reveal the previously overlooked phylogenetic and metabolic diversity of living methanogens, including methylotrophic methanogenesis.
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5
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Kerrigan Z, D’Hondt S. Patterns of Relative Bacterial Richness and Community Composition in Seawater and Marine Sediment Are Robust for Both Operational Taxonomic Units and Amplicon Sequence Variants. Front Microbiol 2022; 13:796758. [PMID: 35197949 PMCID: PMC8859096 DOI: 10.3389/fmicb.2022.796758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Accepted: 01/10/2022] [Indexed: 11/23/2022] Open
Abstract
To understand the relative influences of operational taxonomic units (OTUs) and amplicon sequence variants (ASVs) on patterns of marine microbial diversity and community composition, we examined bacterial diversity and community composition of seawater from 12 sites in the North Atlantic Ocean and Canadian Arctic and sediment from two sites in the North Atlantic. For the seawater analyses, we included samples from three to six zones in the water column of each site. For the sediment analyses, we included over 20 sediment horizons at each of two sites. For all samples, we amplified the V4-V5 hypervariable region of the 16S ribosomal RNA (rRNA) gene. We analyzed each sample in two different ways: (i) by clustering its reads into 97%-similar OTUs and (ii) by assigning sequences to unique ASVs. OTU richness is much higher than ASV richness for every sample, but both OTUs and ASVs exhibit similar vertical patterns of relative diversity in both the water column and the sediment. Bacterial richness is highest just below the photic zone in the water column and at the seafloor in the sediment. For both OTUs and ASVs, richness estimates depend on the number of sequences analyzed. Both methods yield broadly similar community compositions for each sample at the taxonomic levels of phyla to families. While the two methods yield different richness values, broad-scale patterns of relative richness and community composition are similar with both methods.
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Affiliation(s)
- Zak Kerrigan
- Graduate School of Oceanography, University of Rhode Island, Narragansett, RI, United States
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6
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Westmeijer G, Mehrshad M, Turner S, Alakangas L, Sachpazidou V, Bunse C, Pinhassi J, Ketzer M, Åström M, Bertilsson S, Dopson M. Connectivity of Fennoscandian Shield terrestrial deep biosphere microbiomes with surface communities. Commun Biol 2022; 5:37. [PMID: 35017653 PMCID: PMC8752596 DOI: 10.1038/s42003-021-02980-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 12/15/2021] [Indexed: 12/20/2022] Open
Abstract
The deep biosphere is an energy constrained ecosystem yet fosters diverse microbial communities that are key in biogeochemical cycling. Whether microbial communities in deep biosphere groundwaters are shaped by infiltration of allochthonous surface microorganisms or the evolution of autochthonous species remains unresolved. In this study, 16S rRNA gene amplicon analyses showed that few groups of surface microbes infiltrated deep biosphere groundwaters at the Äspö Hard Rock Laboratory, Sweden, but that such populations constituted up to 49% of the microbial abundance. The dominant persisting phyla included Patescibacteria, Proteobacteria, and Epsilonbacteraeota. Despite the hydrological connection of the Baltic Sea with the studied groundwaters, infiltrating microbes predominantly originated from deep soil groundwater. Most deep biosphere groundwater populations lacked surface representatives, suggesting that they have evolved from ancient autochthonous populations. We propose that deep biosphere groundwater communities in the Fennoscandian Shield consist of selected infiltrated and indigenous populations adapted to the prevailing conditions. Westmeijer et al. employ high-throughput sequencing to investigate the connection between deep biosphere groundwaters and surface microbial communities. They suggest that the microbial communities of deep biosphere groundwaters in the Fennoscandian Shield are mostly comprised of autochthonous species, rather than migratory surface representatives.
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Affiliation(s)
- George Westmeijer
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Stuvaregatan 4, 39 231, Kalmar, Sweden.
| | - Maliheh Mehrshad
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, P.O. Box 7050, 75 007, Uppsala, Sweden
| | - Stephanie Turner
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Stuvaregatan 4, 39 231, Kalmar, Sweden
| | - Linda Alakangas
- Swedish Nuclear Fuel and Waste Management Co (SKB), 57 229, Oskarshamn, Sweden
| | - Varvara Sachpazidou
- Department of Biology and Environmental Sciences, Linnaeus University, 39 231, Kalmar, Sweden
| | - Carina Bunse
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Stuvaregatan 4, 39 231, Kalmar, Sweden.,Helmholtz-Institute for Functional Marine Biodiversity at the University of Oldenburg (HIFMB), 26129, Oldenburg, Germany
| | - Jarone Pinhassi
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Stuvaregatan 4, 39 231, Kalmar, Sweden
| | - Marcelo Ketzer
- Department of Biology and Environmental Sciences, Linnaeus University, 39 231, Kalmar, Sweden
| | - Mats Åström
- Department of Biology and Environmental Sciences, Linnaeus University, 39 231, Kalmar, Sweden
| | - Stefan Bertilsson
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, P.O. Box 7050, 75 007, Uppsala, Sweden
| | - Mark Dopson
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Stuvaregatan 4, 39 231, Kalmar, Sweden
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7
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Hu Y, Jiang X, Shao K, Tang X, Qin B, Gao G. Convergency and Stability Responses of Bacterial Communities to Salinization in Arid and Semiarid Areas: Implications for Global Climate Change in Lake Ecosystems. Front Microbiol 2022; 12:741645. [PMID: 35058891 PMCID: PMC8764409 DOI: 10.3389/fmicb.2021.741645] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 11/30/2021] [Indexed: 11/13/2022] Open
Abstract
Climate change has given rise to salinization and nutrient enrichment in lake ecosystems of arid and semiarid areas, which have posed the bacterial communities not only into an ecotone in lake ecosystems but also into an assemblage of its own unique biomes. However, responses of bacterial communities to climate-related salinization and nutrient enrichment remain unclear. In September 2019, this study scrutinized the turnover of bacterial communities along gradients of increasing salinity and nutrient by a space-for-time substitution in Xinjiang Uyghur Autonomous Region, China. We find that salinization rather than nutrient enrichment primarily alters bacterial communities. The homogenous selection of salinization leads to convergent response of bacterial communities, which is revealed by the combination of a decreasing β-nearest taxon index (βNTI) and a pronounced negative correlation between niche breadth and salinity. Furthermore, interspecific interactions within bacterial communities significantly differed among distinct salinity levels. Specifically, mutualistic interactions showed an increase along the salinization. In contrast, topological parameters show hump-shaped curves (average degree and density) and sunken curves (modularity, density, and average path distance), the extremums of which all appear in the high-brackish environment, hinting that bacterial communities are comparatively stable at freshwater and brine environments but are unstable in moderately high-brackish lake.
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Affiliation(s)
| | | | | | | | | | - Guang Gao
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
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8
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Kaneko M, Takano Y, Kamo M, Morimoto K, Nunoura T, Ohkouchi N. Insights into the Methanogenic Population and Potential in Subsurface Marine Sediments Based on Coenzyme F430 as a Function-Specific Biomarker. JACS AU 2021; 1:1743-1751. [PMID: 34723277 PMCID: PMC8549059 DOI: 10.1021/jacsau.1c00307] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Indexed: 06/13/2023]
Abstract
Coenzyme F430, the prosthetic group of methyl coenzyme M reductase (MCR), is a key compound in methane metabolism. We applied coenzyme F430 as a function-specific biomarker of methanogenesis to subsurface marine sediments collected below the sulfate reduction zone to investigate the distribution and activity of methanogens. In addition, we examined the kinetics of the epimerization of coenzyme F430, which is the first stage of the degradation process after cell death, at various temperatures (4, 15, 34, 60 °C) and pH (5, 7, 9) conditions, which cover in situ conditions of drilled sediments used in this study. The degradation experiments revealed that the kinetics of the epimerization well follow the thermodynamic laws, and the half-life of coenzyme F430 is decreasing from 304 days to 11 h with increasing the in situ temperature. It indicates that the native F430 detected in the sediments is derived from living methanogens, because the abiotic degradation of F430 is much faster than the sedimentation rate and will not be fossilized. Based on coenzyme F430 analysis and degradation experiments, the native form of F430 detected in subseafloor sediments off the Shimokita Peninsula originates from living methanogen cells, which is protected from degradation in cells but disappears soon after cell death. The biomass of methanogens calculated from in situ F430 concentration and F430 contents in cultivable methanogen species decreases by 2 orders of magnitude up to a sediment depth of 2.5 km, with a maximum value at ∼70 m below the seafloor (mbsf), while the proportion of methanogens to the total prokaryotic cell abundance increases with the depth, which is 1 to 2 orders of magnitude higher than expected previously. Our results indicate the presence of undetectable methanogens using conventional techniques.
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Affiliation(s)
- Masanori Kaneko
- Geological
Survey of Japan, National Institute of Advanced
Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba 305-8567, Japan
- Biogeochemistry
Research Center, Japan Agency for Marine-Earth
Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Yoshinori Takano
- Biogeochemistry
Research Center, Japan Agency for Marine-Earth
Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Masashi Kamo
- Research
Institute of Science for Safety and Sustainability, National Institute of Advanced Industrial Science and Technology
(AIST), 16-1 Onogawa, Tsukuba 305-8569, Japan
| | - Kazuya Morimoto
- Geological
Survey of Japan, National Institute of Advanced
Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba 305-8567, Japan
| | - Takuro Nunoura
- Research
Center for Bioscience and Nanoscience, Japan
Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Naohiko Ohkouchi
- Biogeochemistry
Research Center, Japan Agency for Marine-Earth
Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
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9
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Zhang Y, Yao P, Sun C, Li S, Shi X, Zhang XH, Liu J. Vertical diversity and association pattern of total, abundant and rare microbial communities in deep-sea sediments. Mol Ecol 2021; 30:2800-2816. [PMID: 33960545 PMCID: PMC8251536 DOI: 10.1111/mec.15937] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 04/21/2021] [Accepted: 04/22/2021] [Indexed: 12/16/2022]
Abstract
Microbial abundance and community composition in marine sediments have been widely explored. However, high‐resolution vertical changes of benthic microbial diversity and co‐occurrence patterns are poorly described. The ecological contributions of abundant and rare species in sediments also remain largely unknown. Here, by analysing microbial populations at 14 depth layers of 10 subseafloor sediment cores (water depth 1,250–3,530 m) obtained in the South China Sea, we provided the vertical profiles of microbial β‐diversity and co‐occurrence influenced by subcommunities of different abundance. These 134 sediment samples were clustered into four groups according to sediment depth (1–2, 6–10, 30–90 and 190–790 cm) with obvious shifts in microbial community compositions. The vertical succession of microorganisms was consistent with redox zonation and influenced by terrestrial inputs. Partitioning of vertical β‐diversity showed extremely high species replacement between deep layers and the surface layer, indicating selection‐induced loss of rare species and dispersal of dormant cells and spores. By contrast, for horizontal β‐diversity, richness of rare species became increasingly significant in deep sediments. Accompanying this β‐diversity profile were clear changes in the association pattern, with microorganisms being less connected in deeper sediment layers, probably reflecting reduced syntrophic interactions. Rare species accounted for an indispensable proportion in the co‐occurrence network, and tended to form complex “small worlds.” The rare subcommunity also responded differently to various environmental factors compared with the abundant subcommunity. Our findings expand current knowledge on vertical changes of marine benthic microbial diversity and their association patterns, emphasizing the potential roles of rare species.
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Affiliation(s)
- Yunhui Zhang
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Peng Yao
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao, China
| | - Chuang Sun
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Sanzhong Li
- Key Laboratory of Submarine Geosciences and Prospecting Techniques, Ministry of Education/College of Marine Geosciences, Ocean University of China, Qingdao, China.,Laboratory for Marine Geology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Xiaochong Shi
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Xiao-Hua Zhang
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Jiwen Liu
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, China
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10
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Lv X, Ma B, Cologgi D, Lee K, Ulrich A. Naphthenic acid anaerobic biodegrading consortia enriched from pristine sediments underlying oil sands tailings ponds. JOURNAL OF HAZARDOUS MATERIALS 2020; 394:122546. [PMID: 32203719 DOI: 10.1016/j.jhazmat.2020.122546] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 03/06/2020] [Accepted: 03/14/2020] [Indexed: 06/10/2023]
Abstract
Seepage from oil sands tailings ponds (OSTP), which contain toxic naphthenic acids (NAs), can infiltrate into groundwater. Clay sediment layer beneath is a critical barrier for reducing the infiltration of NAs into the sand sediment layer, where groundwater channels reside. Biodegradation has great potential as a strategy for NAs removal, but little is known about NAs biodegradability and potential functional microbes in these pristine sediments. This study investigated the potential for anaerobic biodegradation of NAs by microbial consortia enriched from clay and sand sediments underlying OSTP, amended with either acid extracted organics or Merichem NAs, under nitrate- and sulfate-reducing conditions. Degradation of NAs only be detected after DOC concentration reached to steady state after 163 days. Microbial community analysis shows that different electron acceptors, sediment types, and NAs sources associated with specific microbial taxa and can explain 14.8, 13.9 % and 5% of variation of microbial community structures, respectively. The DOC and methane were the most important geochemical properties for microbial community variations. This study approved the potential capability of indigenous microbial communities from the pristine sediments in NA degradation, demonstrating the barrier function of pristine clay sediments underlying OSTP in prohibiting organic contaminants from entering into groundwater.
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Affiliation(s)
- Xiaofei Lv
- Department of Environmental Engineering, China Jiliang University, Hangzhou, 310018, China; Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Bin Ma
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China; Department of Civil and Environmental Engineering, University of Alberta, Edmonton, Alberta, T6G 2W2, Canada.
| | - Dena Cologgi
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, Alberta, T6G 2W2, Canada
| | - Korris Lee
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, Alberta, T6G 2W2, Canada
| | - Ania Ulrich
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, Alberta, T6G 2W2, Canada
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11
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Fu L, Li D, Mi T, Zhao J, Liu C, Sun C, Zhen Y. Characteristics of the archaeal and bacterial communities in core sediments from Southern Yap Trench via in situ sampling by the manned submersible Jiaolong. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 703:134884. [PMID: 31767325 DOI: 10.1016/j.scitotenv.2019.134884] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 10/03/2019] [Accepted: 10/06/2019] [Indexed: 06/10/2023]
Abstract
The hadal environment is the deepest part of the ocean and harbors a significant number of unique microbial communities. Here, we collected core sediment samples of Southern Yap Trench with the deep-sea manned submersible Jiaolong and analyzed the microbial community structure and abundance in the samples through high-throughput sequencing and real-time fluorescence quantitative PCR (qPCR), taking physicochemical parameters into account to explore potential environmental drivers and metabolic pathways therein. Considering the typical "V-shape" topography and frequent sediment collapses on trench walls, the core sediments of Southern Yap Trench harbored distinct microbial populations with fluctuating distributions and metabolic processes dominated by Proteobacteria and Thaumarchaeota. To discover the main potential metabolic processes of microbes, functional genes were detected by qPCR. The abundance of bacteria was greater than that of archaea in Southern Yap Trench sediments. The abundance of ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), sulfate-reducing bacteria (SRB) and denitrifying bacteria (denitrifier) decreased with increasing depth and decreasing total organic carbon (TOC%) and total nitrogen (TN%) and showed a positive and significant correlation with TOC% (P < 0.01), TN% (P < 0.01), TOC/TN molar ratio (C/N ratio) (P < 0.01) and median grain size (P < 0.01). From the perspective of function based on the 16S rRNA gene, aerobic ammonium oxidization, carbon assimilation, and chemoheterotrophic function may be the dominant processes in Southern Yap Trench sediments. Moreover, considering the isolated geomorphological and hydrological characteristics of Southern Yap Trench, we hypothesized that the distinct hadal microbial ecosystem was driven by the endogenous recycling of organic matter in the hadal sediments associated with the trench geomorphology.
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Affiliation(s)
- Lulu Fu
- Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Dong Li
- Key Laboratory of Marine Ecosystem and Biogeochemistry, State Oceanic Administration, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, China
| | - Tiezhu Mi
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Key Laboratory of Marine Environment and Ecology, Ministry of Education, Qingdao 266100, China; College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China
| | - Jun Zhao
- Key Laboratory of Marine Ecosystem and Biogeochemistry, State Oceanic Administration, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, China
| | - Chenggang Liu
- Key Laboratory of Marine Ecosystem and Biogeochemistry, State Oceanic Administration, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, China
| | - Chengjun Sun
- Marine Ecology Center, First Institute of Oceanography, Ministry of Natural Resources, Qingdao 266237, China
| | - Yu Zhen
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Key Laboratory of Marine Environment and Ecology, Ministry of Education, Qingdao 266100, China; College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China.
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12
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Yu T, Zhang M, Kang D, Zhao S, Ding A, Lin Q, Xu D, Hong Y, Wang L, Zheng P. Characteristics of Microbial Communities and Their Correlation With Environmental Substrates and Sediment Type in the Gas-Bearing Formation of Hangzhou Bay, China. Front Microbiol 2019; 10:2421. [PMID: 31708895 PMCID: PMC6819322 DOI: 10.3389/fmicb.2019.02421] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 10/07/2019] [Indexed: 12/02/2022] Open
Abstract
Shallow gas is a kind of natural gas buried in shallow strata, generally, with methane as the main component, endowing it a potential energy resource while also a potential risk to the safety of ground engineering and environment. Microbial activity is usually regarded as an important driving force to generate shallow gas via metabolizing the environmental substrates. Therefore, the research on the microbial communities will be helpful to reveal the distribution of shallow gas in the gas-bearing formation. In this study, 30 sediment samples below the seabed in Hangzhou Bay (China) from depths of 1.5 m to 55 m were collected to investigate their microbial community, environmental characteristics and sediment type (clay or sand). It turned out that the presence of shallow gas had a good correlation with the distribution of archaea rather than bacteria, with the dominant microbe of Bathyarchaeota, Thaumarchaeota, and Euryarchaeota in the formation. Methanosarcinaceae and ANME-1a with the capacity of methane metabolism occupied high proportions. The correlation analysis and redundancy analysis (RDA) suggested that ammonium was a key environmental substrate to indicate the microbial community in the formation. The sediment type was proposed to shape environmental substrates in the formation, thus further affecting the microbial communities. The clay strata were demonstrated to have an important role in the generation and distribution of shallow gas, and more attention should be paid in terms of its resource discovery and engineering safety assessment.
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Affiliation(s)
- Tao Yu
- Department of Environmental Engineering, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou, China
| | - Meng Zhang
- Department of Environmental Engineering, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou, China
- Advanced Environmental Biotechnology Centre, Nanyang Environment & Water Research Institute, Nanyang Technological University, Singapore, Singapore
| | - Da Kang
- Department of Environmental Engineering, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou, China
| | - Shuang Zhao
- Key Laboratory of Offshore Geotechnics and Material of Zhejiang Province, College of Civil Engineering and Architecture, Zhejiang University, Hangzhou, China
| | - Aqiang Ding
- Department of Environmental Science, College of Resources and Environmental Science, Chongqing University, Chongqing, China
| | - Qiujian Lin
- Department of Environmental Engineering, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou, China
| | - Dongdong Xu
- Department of Environmental Engineering, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou, China
| | - Yi Hong
- Key Laboratory of Offshore Geotechnics and Material of Zhejiang Province, College of Civil Engineering and Architecture, Zhejiang University, Hangzhou, China
| | - Lizhong Wang
- Key Laboratory of Offshore Geotechnics and Material of Zhejiang Province, College of Civil Engineering and Architecture, Zhejiang University, Hangzhou, China
| | - Ping Zheng
- Department of Environmental Engineering, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou, China
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13
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Shi R, Xu S, Qi Z, Zhu Q, Huang H, Weber F. Influence of suspended mariculture on vertical distribution profiles of bacteria in sediment from Daya Bay, Southern China. MARINE POLLUTION BULLETIN 2019; 146:816-826. [PMID: 31426223 DOI: 10.1016/j.marpolbul.2019.07.043] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 07/18/2019] [Accepted: 07/18/2019] [Indexed: 06/10/2023]
Abstract
Mariculture is known to contribute to oxygen depletion, pH decline and accumulation of nutrients and organic matter in sediments. However, studies on the bacterial vertical distribution of mariculture area are very limited. The bacterial abundance in the non-culture site (3.8 ± 0.8 × 109 copies g-1) was significantly higher than that in the three mariculture sites (1.2 ± 0.2 × 109 copies g-1), and bacterial diversity in the non-culture site was significantly higher than that in fish cage-TF (p < 0.05). The vertical distribution profiles of bacteria in non-culture and oyster culture sites were similar but very different from that of fish cage-TF. In addition, significant downward trends in bacterial abundance and diversity were observed as sediment depth increased (p < 0.05), and the most relevant environmental factors were moisture content, total nitrogen, total organic carbon and carbon/nitrogen. The dominant bacterial phyla in sediment were Proteobacteria, Chloroflexi and Bacteroidetes.
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Affiliation(s)
- Rongjun Shi
- Guangdong Provincial Key Laboratory of Fishery Ecology and Environment and Key Laboratory of Open-Sea Fishery Development, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou 510300, PR China
| | - Shumin Xu
- Guangdong Provincial Key Laboratory of Fishery Ecology and Environment and Key Laboratory of Open-Sea Fishery Development, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou 510300, PR China
| | - Zhanhui Qi
- Guangdong Provincial Key Laboratory of Fishery Ecology and Environment and Key Laboratory of Open-Sea Fishery Development, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou 510300, PR China.
| | - Qingzhi Zhu
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY 11794-5000, USA.
| | - Honghui Huang
- Guangdong Provincial Key Laboratory of Fishery Ecology and Environment and Key Laboratory of Open-Sea Fishery Development, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou 510300, PR China
| | - Felix Weber
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY 11794-5000, USA
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14
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D'Hondt S, Pockalny R, Fulfer VM, Spivack AJ. Subseafloor life and its biogeochemical impacts. Nat Commun 2019; 10:3519. [PMID: 31388058 PMCID: PMC6684631 DOI: 10.1038/s41467-019-11450-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 07/10/2019] [Indexed: 11/08/2022] Open
Abstract
Subseafloor microbial activities are central to Earth's biogeochemical cycles. They control Earth's surface oxidation and major aspects of ocean chemistry. They affect climate on long timescales and play major roles in forming and destroying economic resources. In this review, we evaluate present understanding of subseafloor microbes and their activities, identify research gaps, and recommend approaches to filling those gaps. Our synthesis suggests that chemical diffusion rates and reaction affinities play a primary role in controlling rates of subseafloor activities. Fundamental aspects of subseafloor communities, including features that enable their persistence at low catabolic rates for millions of years, remain unknown.
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Affiliation(s)
- Steven D'Hondt
- Graduate School of Oceanography, University of Rhode Island Narragansett Bay Campus, 215 South Ferry Road, Rhode Island, 02882, USA.
| | - Robert Pockalny
- Graduate School of Oceanography, University of Rhode Island Narragansett Bay Campus, 215 South Ferry Road, Rhode Island, 02882, USA
| | - Victoria M Fulfer
- Graduate School of Oceanography, University of Rhode Island Narragansett Bay Campus, 215 South Ferry Road, Rhode Island, 02882, USA
| | - Arthur J Spivack
- Graduate School of Oceanography, University of Rhode Island Narragansett Bay Campus, 215 South Ferry Road, Rhode Island, 02882, USA
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15
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Kerrigan Z, Kirkpatrick JB, D'Hondt S. Influence of 16S rRNA Hypervariable Region on Estimates of Bacterial Diversity and Community Composition in Seawater and Marine Sediment. Front Microbiol 2019; 10:1640. [PMID: 31379788 PMCID: PMC6646839 DOI: 10.3389/fmicb.2019.01640] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 07/02/2019] [Indexed: 11/13/2022] Open
Abstract
To assess the influence of 16S ribosomal RNA (rRNA) tag choice on estimates of microbial diversity and/or community composition in seawater and marine sediment, we examined bacterial diversity and community composition from a site in the Central North Atlantic and a site in the Equatorial Pacific. For each site, we analyzed samples from four zones in the water column, a seafloor sediment sample, and two subseafloor sediment horizons (with stratigraphic ages of 1.5 and 5.5 million years old). We amplified both the V4 and V6 hypervariable regions of the 16S rRNA gene and clustered the sequences into operational taxonomic units (OTUs) of 97% similarity to analyze for diversity and community composition. OTU richness is much higher with the V6 tag than with the V4 tag, and subsequently OTU-level community composition is quite different between the two tags. Vertical patterns of relative diversity are broadly the same for both tags, with maximum taxonomic richness in seafloor sediment and lowest richness in subseafloor sediment at both geographic locations. Genetic dissimilarity between sample locations is also broadly the same for both tags. Community composition is very similar for both tags at the class level, but very different at the level of 97% similar OTUs. Class-level diversity and community composition of water-column samples are very similar at each water depth between the Atlantic and Pacific. However, sediment communities differ greatly from the Atlantic site to the Pacific site. Finally, for relative patterns of diversity and class-level community composition, deep sequencing and shallow sequencing provide similar results.
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Affiliation(s)
- Zak Kerrigan
- Graduate School of Oceanography, The University of Rhode Island, Narragansett, RI, United States
| | | | - Steven D'Hondt
- Graduate School of Oceanography, The University of Rhode Island, Narragansett, RI, United States
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16
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Kirkpatrick JB, Walsh EA, D'Hondt S. Microbial Selection and Survival in Subseafloor Sediment. Front Microbiol 2019; 10:956. [PMID: 31139156 PMCID: PMC6527604 DOI: 10.3389/fmicb.2019.00956] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 04/16/2019] [Indexed: 01/23/2023] Open
Abstract
Many studies have examined relationships of microorganisms to geochemical zones in subseafloor sediment. However, responses to selective pressure and patterns of community succession with sediment depth have rarely been examined. Here we use 16S rDNA sequencing to examine the succession of microbial communities at sites in the Indian Ocean and the Bering Sea. The sediment ranges in depth from 0.16 to 332 m below seafloor and in age from 660 to 1,300,000 years. The majority of subseafloor taxonomic diversity is present in the shallowest depth sampled. The best predictor of sequence presence or absence in the oldest sediment is relative abundance in the near-seafloor sediment. This relationship suggests that perseverance of specific taxa into deep, old sediment is primarily controlled by the taxonomic abundance that existed when the sediment was near the seafloor. The operational taxonomic units that dominate at depth comprise a subset of the local seafloor community at each site, rather than a grown-in group of geographically widespread subseafloor specialists. At both sites, most taxa classified as abundant decrease in relative frequency with increasing sediment depth and age. Comparison of community composition to cell counts at the Bering Sea site indicates that the rise of the few dominant taxa in the deep subseafloor community does not require net replication, but might simply result from lower mortality relative to competing taxa on the long timescale of community burial.
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Affiliation(s)
- John B Kirkpatrick
- Graduate School of Oceanography, The University of Rhode Island, Narragansett, RI, United States.,The Evergreen State College, Olympia, WA, United States
| | - Emily A Walsh
- Graduate School of Oceanography, The University of Rhode Island, Narragansett, RI, United States
| | - Steven D'Hondt
- Graduate School of Oceanography, The University of Rhode Island, Narragansett, RI, United States
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17
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Dick JM, Yu M, Tan J, Lu A. Changes in Carbon Oxidation State of Metagenomes Along Geochemical Redox Gradients. Front Microbiol 2019; 10:120. [PMID: 30804909 PMCID: PMC6378307 DOI: 10.3389/fmicb.2019.00120] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 01/18/2019] [Indexed: 01/01/2023] Open
Abstract
There is widespread interest in how geochemistry affects the genomic makeup of microbial communities, but the possible impacts of oxidation-reduction (redox) conditions on the chemical composition of biomacromolecules remain largely unexplored. Here we document systematic changes in the carbon oxidation state, a metric derived from the chemical formulas of biomacromolecular sequences, using published metagenomic and metatranscriptomic datasets from 18 studies representing different marine and terrestrial environments. We find that the carbon oxidation states of DNA, as well as proteins inferred from coding sequences, follow geochemical redox gradients associated with mixing and cooling of hot spring fluids in Yellowstone National Park (USA) and submarine hydrothermal fluids. Thermodynamic calculations provide independent predictions for the environmental shaping of the gene and protein composition of microbial communities in these systems. On the other hand, the carbon oxidation state of DNA is negatively correlated with oxygen concentration in marine oxygen minimum zones. In this case, a thermodynamic model is not viable, but the low carbon oxidation state of DNA near the ocean surface reflects a low GC content, which can be attributed to genome reduction in organisms adapted to low-nutrient conditions. We also present evidence for a depth-dependent increase of oxidation state at the species level, which might be associated with alteration of DNA through horizontal gene transfer and/or selective degradation of relatively reduced (AT-rich) extracellular DNA by heterotrophic bacteria. Sediments exhibit even more complex behavior, where carbon oxidation state minimizes near the sulfate-methane transition zone and rises again at depth; markedly higher oxidation states are also associated with older freshwater-dominated sediments in the Baltic Sea that are enriched in iron oxides and have low organic carbon. This geobiochemical study of carbon oxidation state reveals a new aspect of environmental information in metagenomic sequences, and provides a reference frame for future studies that may use ancient DNA sequences as a paleoredox indicator.
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Affiliation(s)
- Jeffrey M. Dick
- Key Laboratory of Metallogenic Prediction of Nonferrous Metals and Geological Environment Monitoring, Ministry of Education, Central South University, Changsha, China
- School of Geosciences and Info-Physics, Central South University, Changsha, China
| | - Miao Yu
- Key Laboratory of Metallogenic Prediction of Nonferrous Metals and Geological Environment Monitoring, Ministry of Education, Central South University, Changsha, China
- School of Geosciences and Info-Physics, Central South University, Changsha, China
| | - Jingqiang Tan
- Key Laboratory of Metallogenic Prediction of Nonferrous Metals and Geological Environment Monitoring, Ministry of Education, Central South University, Changsha, China
- School of Geosciences and Info-Physics, Central South University, Changsha, China
| | - Anhuai Lu
- Key Laboratory of Metallogenic Prediction of Nonferrous Metals and Geological Environment Monitoring, Ministry of Education, Central South University, Changsha, China
- School of Geosciences and Info-Physics, Central South University, Changsha, China
- School of Earth and Space Sciences, Peking University, Beijing, China
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18
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Cui H, Su X, Chen F, Holland M, Yang S, Liang J, Su P, Dong H, Hou W. Microbial diversity of two cold seep systems in gas hydrate-bearing sediments in the South China Sea. MARINE ENVIRONMENTAL RESEARCH 2019; 144:230-239. [PMID: 30732863 DOI: 10.1016/j.marenvres.2019.01.009] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 12/29/2018] [Accepted: 01/14/2019] [Indexed: 05/05/2023]
Abstract
Cold seep is a unique habitat for microorganisms in deep marine sediments, and microbial communities and biogeochemical processes are still poorly understood, especially in relation to hydrate-bearing geo-systems. In this study, two cold seep systems were sampled and microbial diversity was studied at Site GMGS2-08 in the northern part of the South China Sea (SCS) during the GMGS2 gas hydrate expedition. The current cold seep system was composed of a sulfate methane transition zone (SMTZ) and an upper gas hydrate zone (UGHZ). The buried cold seep system was composed of an authigenic carbonate zone (ACZ) and a lower gas hydrate zone (LGHZ). These drill core samples provided an excellent opportunity for analyzing the microbial abundance and diversity based on quantitative polymerase chain reaction (qPCR) and high-throughput 16S rRNA gene sequencing. Compared to previous studies, the high relative abundance of ANME-1b, a clade of anaerobic methanotrophic archaea (ANME), may perform anaerobic oxidation of methane (AOM) in collaboration with ANME-2c and Desulfobacteraceae in the SMTZ, and the high relative abundances of Hadesarchaea, ANME-1b archaea and Aerophobetes bacteria were found in the gas hydrate zone (GHZ) at Site GMGS2-08. ANME-1b, detected in the GHZ, might mainly mediate the AOM process, and the process might occur in a wide depth range within the LGHZ. Moreover, bacterial communities were significantly different between the GHZ and non-GHZ sediments. In the ACZ, archaeal communities were different between the two samples from the upper and the lower layers, while bacterial communities shared similarities. Overall, this new record of cold seep microbial diversity at Site GMGS2-08 showed the complexity of the interaction between biogeochemical reactions and environmental conditions.
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Affiliation(s)
- Hongpeng Cui
- School of Ocean Sciences, China University of Geosciences, Beijing, 100083, China; State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, 100083, China
| | - Xin Su
- School of Ocean Sciences, China University of Geosciences, Beijing, 100083, China; State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, 100083, China.
| | - Fang Chen
- Guangzhou Marine Geological Survey, Guangzhou, 510075, China
| | | | - Shengxiong Yang
- Guangzhou Marine Geological Survey, Guangzhou, 510075, China
| | - Jinqiang Liang
- Guangzhou Marine Geological Survey, Guangzhou, 510075, China.
| | - Pibo Su
- Guangzhou Marine Geological Survey, Guangzhou, 510075, China
| | - Hailiang Dong
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, 100083, China; Department of Geology and Environmental Earth Science, Miami University, OH, 45056, USA
| | - Weiguo Hou
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, 100083, China
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19
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Lee YM, Hwang K, Lee JI, Kim M, Hwang CY, Noh HJ, Choi H, Lee HK, Chun J, Hong SG, Shin SC. Genomic Insight Into the Predominance of Candidate Phylum Atribacteria JS1 Lineage in Marine Sediments. Front Microbiol 2018; 9:2909. [PMID: 30555444 PMCID: PMC6281690 DOI: 10.3389/fmicb.2018.02909] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2018] [Accepted: 11/13/2018] [Indexed: 01/13/2023] Open
Abstract
Candidate phylum Atribacteria JS1 lineage is one of the predominant bacterial groups in anoxic subseafloor sediments, especially in organic-rich or gas hydrate-containing sediments. However, due to the lack of axenic culture representatives, metabolic potential and biogeochemical roles of this phylum have remained elusive. Here, we examined the microbial communities of marine sediments of the Ross Sea, Antarctica, and found candidate phylum Atribacteria JS1 lineage was the most abundant candidate phylum accounting for 9.8-40.8% of the bacterial communities with a single dominant operational taxonomic unit (OTU). To elucidate the metabolic potential and ecological function of this species, we applied a single-cell genomic approach and obtained 18 single-cell amplified genomes presumably from a single species that was consistent with the dominant OTU throughout the sediments. The composite genome constructed by co-assembly showed the highest genome completeness among available Atribacteria JS1 genomes. Metabolic reconstruction suggested fermentative potential using various substrates and syntrophic acetate oxidation coupled with hydrogen or formate scavenging methanogens. This metabolic potential supports the predominance of Atribacteria JS1 in anoxic environments expanding our knowledge of the ecological function of this uncultivated group.
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Affiliation(s)
- Yung Mi Lee
- Division of Polar Life Sciences, Korea Polar Research Institute, Incheon, South Korea
| | - Kyuin Hwang
- Division of Polar Life Sciences, Korea Polar Research Institute, Incheon, South Korea.,Department of Polar Science, University of Science and Technology, Daejeon, South Korea
| | - Jae Il Lee
- Division of Polar Paleoenvironment, Korea Polar Research Institute, Incheon, South Korea
| | - Mincheol Kim
- Division of Polar Life Sciences, Korea Polar Research Institute, Incheon, South Korea
| | - Chung Yeon Hwang
- Division of Polar Life Sciences, Korea Polar Research Institute, Incheon, South Korea
| | - Hyun-Ju Noh
- Division of Polar Life Sciences, Korea Polar Research Institute, Incheon, South Korea
| | - Hakkyum Choi
- Division of Polar Earth-System Sciences, Korea Polar Research Institute, Incheon, South Korea
| | - Hong Kum Lee
- Division of Polar Life Sciences, Korea Polar Research Institute, Incheon, South Korea
| | - Jongsik Chun
- School of Biological Sciences, College of Natural Sciences, Seoul National University, Seoul, South Korea
| | - Soon Gyu Hong
- Division of Polar Life Sciences, Korea Polar Research Institute, Incheon, South Korea
| | - Seung Chul Shin
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon, South Korea
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20
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Qiao Y, Liu J, Zhao M, Zhang XH. Sediment Depth-Dependent Spatial Variations of Bacterial Communities in Mud Deposits of the Eastern China Marginal Seas. Front Microbiol 2018; 9:1128. [PMID: 29904376 PMCID: PMC5990616 DOI: 10.3389/fmicb.2018.01128] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 05/14/2018] [Indexed: 12/17/2022] Open
Abstract
The mud sediments of the eastern China marginal seas (ECMS) are deposited under different hydrodynamic conditions with different organic matter sources. These events have been demonstrated to exert significant influences on microbial communities and biogeochemical processes in surface sediments. However, the extent to which such effects occur in subsurface microbial communities remains unclear. In this study, both horizontal and vertical (five sites, each for eight layers) distributions of bacterial abundance and community composition in mud deposits of the South Yellow Sea (SYS) and East China Sea (ECS) were investigated by quantitative PCR and Illumina sequencing of the 16S rRNA gene. Both bacterial abundance and diversity were higher in the ECS than in the SYS, and tended to be higher in up than in deep layers. Proteobacteria (JTB255 marine benthic group), Acidobacteria and Bacteroidetes were dominant in the upper layers, whereas Lactococcus, Pseudomonas, and Dehalococcoidia were enriched in the deep layers. The bacterial communities in surface and subsurface sediments showed different inter-taxa relationships, indicating contrasting co-occurrence patterns. The bacterial communities in the upper layer samples clustered in accordance with mud zones, whereas those in the deep layer samples of all sites tended to cluster together. TOC δ13C and TON δ15N significantly affected the bacterial community composition, suggesting that the abundance and composition of organic matter played critical roles in shaping of sedimentary bacterial communities. This study provides novel insights into the distribution of subsurface bacterial communities in mud deposits of the ECMS, and provides clues for understanding the biogeochemical cycles in this area.
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Affiliation(s)
- Yanlu Qiao
- Laboratory of Marine Microbiology, College of Marine Life Sciences, Ocean University of China, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Jiwen Liu
- Laboratory of Marine Microbiology, College of Marine Life Sciences, Ocean University of China, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Meixun Zhao
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao, China
| | - Xiao-Hua Zhang
- Laboratory of Marine Microbiology, College of Marine Life Sciences, Ocean University of China, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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21
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Nunoura T, Nishizawa M, Hirai M, Shimamura S, Harnvoravongchai P, Koide O, Morono Y, Fukui T, Inagaki F, Miyazaki J, Takaki Y, Takai K. Microbial Diversity in Sediments from the Bottom of the Challenger Deep, the Mariana Trench. Microbes Environ 2018; 33:186-194. [PMID: 29806625 PMCID: PMC6031389 DOI: 10.1264/jsme2.me17194] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The Challenger Deep is the deepest ocean on Earth. The present study investigated microbial community structures and geochemical cycles associated with the trench bottom sediments of the Challenger Deep, the Mariana Trench. The SSU rRNA gene communities found in trench bottom sediments were dominated by the bacteria Chloroflexi (SAR202 and other lineages), Bacteroidetes, Planctomycetes, "Ca. Marinimicrobia" (SAR406), and Gemmatimonadetes and by the archaeal α subgroup of MGI Thaumarchaeota and "Ca. Woesearchaeota" (Deep-sea Hydrothermal Vent Euryarchaeotic Group 6). The SSU rRNA gene sequencing analysis indicated that the dominant populations of the thaumarchaeal α group in hadal water and sediments were similar to each other at the species or genus level. In addition, the co-occurrence of nitrification and denitrification was revealed by the combination of pore water geochemical analyses and quantitative PCR for nitrifiers.
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Affiliation(s)
- Takuro Nunoura
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | - Manabu Nishizawa
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | - Miho Hirai
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | - Shigeru Shimamura
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | | | - Osamu Koide
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | - Yuki Morono
- Geomicrobiology Group, Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science Technology (JAMSTEC).,Geobiotechnology Group, Research and Development Center for Submarine Resources, Japan Agency for Marine-Earth Science Technology (JAMSTEC)
| | - Toshiaki Fukui
- School of Life Science and Technology, Tokyo Institute of Technology
| | - Fumio Inagaki
- Geomicrobiology Group, Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science Technology (JAMSTEC).,Geobiotechnology Group, Research and Development Center for Submarine Resources, Japan Agency for Marine-Earth Science Technology (JAMSTEC).,Research and Development Center for Ocean Drilling Science, Japan Agency for Marine-Earth Science Technology (JAMSTEC)
| | - Junichi Miyazaki
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | - Yoshihiro Takaki
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC).,Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | - Ken Takai
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
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22
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Graw MF, D'Angelo G, Borchers M, Thurber AR, Johnson JE, Zhang C, Liu H, Colwell FS. Energy Gradients Structure Microbial Communities Across Sediment Horizons in Deep Marine Sediments of the South China Sea. Front Microbiol 2018; 9:729. [PMID: 29696012 PMCID: PMC5905238 DOI: 10.3389/fmicb.2018.00729] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 03/28/2018] [Indexed: 01/28/2023] Open
Abstract
The deep marine subsurface is a heterogeneous environment in which the assembly of microbial communities is thought to be controlled by a combination of organic matter deposition, electron acceptor availability, and sedimentology. However, the relative importance of these factors in structuring microbial communities in marine sediments remains unclear. The South China Sea (SCS) experiences significant variability in sedimentation across the basin and features discrete changes in sedimentology as a result of episodic deposition of turbidites and volcanic ashes within lithogenic clays and siliceous or calcareous ooze deposits throughout the basin's history. Deep subsurface microbial communities were recently sampled by the International Ocean Discovery Program (IODP) at three locations in the SCS with sedimentation rates of 5, 12, and 20 cm per thousand years. Here, we used Illumina sequencing of the 16S ribosomal RNA gene to characterize deep subsurface microbial communities from distinct sediment types at these sites. Communities across all sites were dominated by several poorly characterized taxa implicated in organic matter degradation, including Atribacteria, Dehalococcoidia, and Aerophobetes. Sulfate-reducing bacteria comprised only 4% of the community across sulfate-bearing sediments from multiple cores and did not change in abundance in sediments from the methanogenic zone at the site with the lowest sedimentation rate. Microbial communities were significantly structured by sediment age and the availability of sulfate as an electron acceptor in pore waters. However, microbial communities demonstrated no partitioning based on the sediment type they inhabited. These results indicate that microbial communities in the SCS are structured by the availability of electron donors and acceptors rather than sedimentological characteristics.
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Affiliation(s)
- Michael F Graw
- College of Earth, Ocean, and Atmospheric Science, Oregon State University, Corvallis, OR, United States
| | - Grace D'Angelo
- Department of Microbiology, College of Science, Oregon State University, Corvallis, OR, United States
| | - Matthew Borchers
- Department of Biochemistry and Biophysics, College of Science, Oregon State University, Corvallis, OR, United States
| | - Andrew R Thurber
- College of Earth, Ocean, and Atmospheric Science, Oregon State University, Corvallis, OR, United States.,Department of Microbiology, College of Science, Oregon State University, Corvallis, OR, United States
| | - Joel E Johnson
- Department of Earth Sciences, University of New Hampshire, Durham, NH, United States
| | - Chuanlun Zhang
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, China
| | - Haodong Liu
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, China
| | - Frederick S Colwell
- College of Earth, Ocean, and Atmospheric Science, Oregon State University, Corvallis, OR, United States
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23
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Hirai M, Nishi S, Tsuda M, Sunamura M, Takaki Y, Nunoura T. Library Construction from Subnanogram DNA for Pelagic Sea Water and Deep-Sea Sediments. Microbes Environ 2017; 32:336-343. [PMID: 29187708 PMCID: PMC5745018 DOI: 10.1264/jsme2.me17132] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Shotgun metagenomics is a low biased technology for assessing environmental microbial diversity and function. However, the requirement for a sufficient amount of DNA and the contamination of inhibitors in environmental DNA leads to difficulties in constructing a shotgun metagenomic library. We herein examined metagenomic library construction from subnanogram amounts of input environmental DNA from subarctic surface water and deep-sea sediments using two library construction kits: the KAPA Hyper Prep Kit and Nextera XT DNA Library Preparation Kit, with several modifications. The influence of chemical contaminants associated with these environmental DNA samples on library construction was also investigated. Overall, shotgun metagenomic libraries were constructed from 1 pg to 1 ng of input DNA using both kits without harsh library microbial contamination. However, the libraries constructed from 1 pg of input DNA exhibited larger biases in GC contents, k-mers, or small subunit (SSU) rRNA gene compositions than those constructed from 10 pg to 1 ng DNA. The lower limit of input DNA for low biased library construction in this study was 10 pg. Moreover, we revealed that technology-dependent biases (physical fragmentation and linker ligation vs. tagmentation) were larger than those due to the amount of input DNA.
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Affiliation(s)
- Miho Hirai
- Research and Development (R&D) Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | - Shinro Nishi
- Research and Development (R&D) Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC).,Ecosystem Observation and Evaluation Methodology Research Unit, Project Team for Development of New-generation Research Protocol for Submarine Resources, Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | - Miwako Tsuda
- Ecosystem Observation and Evaluation Methodology Research Unit, Project Team for Development of New-generation Research Protocol for Submarine Resources, Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | - Michinari Sunamura
- Ecosystem Observation and Evaluation Methodology Research Unit, Project Team for Development of New-generation Research Protocol for Submarine Resources, Japan Agency for Marine-Earth Science and Technology (JAMSTEC).,Department of Earth and Planetary Science, The University of Tokyo
| | - Yoshihiro Takaki
- Research and Development (R&D) Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC).,Ecosystem Observation and Evaluation Methodology Research Unit, Project Team for Development of New-generation Research Protocol for Submarine Resources, Japan Agency for Marine-Earth Science and Technology (JAMSTEC).,Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | - Takuro Nunoura
- Research and Development (R&D) Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC).,Ecosystem Observation and Evaluation Methodology Research Unit, Project Team for Development of New-generation Research Protocol for Submarine Resources, Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
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24
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Environmental factors shaping the archaeal community structure and ether lipid distribution in a subtropic river and estuary, China. Appl Microbiol Biotechnol 2017; 102:461-474. [PMID: 29103169 DOI: 10.1007/s00253-017-8595-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 10/11/2017] [Accepted: 10/12/2017] [Indexed: 10/18/2022]
Abstract
Archaea are widespread and abundant in aquatic and terrestrial habitats and play fundamental roles in global biogeochemical cycles. Archaeal lipids, such as isoprenoid glycerol diakyl glycerol tetraethers (iGDGTs), are important biomarkers tracing changes in archaeal community structure and biogeochemical processes in nature. However, the linkage between the archaeal populations and the GDGT distribution in the natural environment is poorly examined, which hindered the application and interpretation of GDGT-based climate or environmental proxies. We addressed this question by investigating changes in archaeal lipid composition and community structure in the context of environmental variables along the subtropical Jiulong River Watershed (JRW) and Jiulong River Estuary (JRE) in southern China. The results showed that both the archaeal cells and the polar GDGTs (P-GDGTs) in the JRW and JRE were mostly autochthonous rather than exogenous input from surrounding soils. We further found that only five (Methanobacteriales, Ca. Bathyarchaeota, Marine Benthic Groups A (MBGA), Marine Benthic Groups B (MBGB), and Marine Benthic Groups D (MBGD)) out of sixteen lineages showed significant impacts on the composition of P-GDGTs, suggesting the significant contribution of those archaea to the changes of P-GDGT compositions. Salinity and total phosphorus (TP) showed significant impact on the distribution of both genetic and P-GDGTs compositions of archaea; whereas, sand and silt contents only had significant impact on the P-GDGTs. MBGD archaea, which occur widely in marine sediments, showed positive correlations with P-TEX86 in the JRW and JRE, suggesting that uncultivated MBGD might also contribute to the variations in TEX86 signals in marine sediments. This study provided insight into the sources of P-GDGTs and the factors controlling their distributions in river-dominated continental margins, which has relevance to applications of GDGT-based proxies in paleoclimate studies.
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25
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Cerqueira T, Pinho D, Froufe H, Santos RS, Bettencourt R, Egas C. Sediment Microbial Diversity of Three Deep-Sea Hydrothermal Vents Southwest of the Azores. MICROBIAL ECOLOGY 2017; 74:332-349. [PMID: 28144700 DOI: 10.1007/s00248-017-0943-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 01/19/2017] [Indexed: 06/06/2023]
Abstract
Menez Gwen, Lucky Strike and Rainbow are the three most visited and well-known deep-sea hydrothermal vent fields in the Azores region, located in the Mid-Atlantic Ridge. Their distinct geological and ecological features allow them to support a diversity of vent communities, which are largely dependent on Bacteria and Archaea capable of anaerobic or microaerophilic metabolism. These communities play important ecological roles through chemoautotrophy, feeding and in establishing symbiotic associations. However, the occurrence and distribution of these microbes remain poorly understood, especially in deep-sea sediments. In this study, we provide for the first time a comparative survey of the sediment-associated microbial communities from these three neighbouring vent fields. Sediment samples collected in the Menez Gwen, Lucky Strike and Rainbow vent fields showed significant differences in trace-metal concentrations and associated microbiomes. The taxonomic profiles of bacterial, archaeal and eukaryotic representatives were assessed by rRNA gene-tag pyrosequencing, identified anaerobic methanogens and microaerobic Epsilonproteobacteria, particularly at the Menez Gwen site, suggesting sediment communities potentially enriched in sub-seafloor microbes rather than from pelagic microbial taxa. Cosmopolitan OTUs were also detected mostly at Lucky Strike and Rainbow sites and affiliated with the bacterial clades JTB255, Sh765B-TzT-29, Rhodospirillaceae and OCS155 marine group and with the archaeal Marine Group I. Some variations in the community composition along the sediment depth were revealed. Elemental contents and hydrothermal influence are suggested as being reflected in the composition of the microbial assemblages in the sediments of the three vent fields. Altogether, these findings represent valuable information for the understanding of the microbial distribution and potential ecological roles in deep-sea hydrothermal fields.
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Affiliation(s)
- Teresa Cerqueira
- Department of Oceanography and Fisheries, University of the Azores, Rua Prof. Dr. Frederico Machado, 4, 9901-862, Horta, Portugal.
- MARE-Marine and Environmental Sciences Centre-Azores, Rua Prof. Dr. Frederico Machado, 4, 9901-862, Horta, Portugal.
| | - Diogo Pinho
- Next Generation Sequencing Unit, UCBiotech-CNC, Parque Tecnológico de Cantanhede, Núcleo 04, Lote 8, 3060-197, Cantanhede, Portugal
| | - Hugo Froufe
- Next Generation Sequencing Unit, UCBiotech-CNC, Parque Tecnológico de Cantanhede, Núcleo 04, Lote 8, 3060-197, Cantanhede, Portugal
| | - Ricardo S Santos
- Department of Oceanography and Fisheries, University of the Azores, Rua Prof. Dr. Frederico Machado, 4, 9901-862, Horta, Portugal
- MARE-Marine and Environmental Sciences Centre-Azores, Rua Prof. Dr. Frederico Machado, 4, 9901-862, Horta, Portugal
- OKEANOS Centre, Department of Oceanography and Fisheries, Faculty of Sciences and Technology, University of the Azores, Rua Prof. Dr. Frederico Machado, 4, 9901-862, Horta, Portugal
| | - Raul Bettencourt
- MARE-Marine and Environmental Sciences Centre-Azores, Rua Prof. Dr. Frederico Machado, 4, 9901-862, Horta, Portugal
- OKEANOS Centre, Department of Oceanography and Fisheries, Faculty of Sciences and Technology, University of the Azores, Rua Prof. Dr. Frederico Machado, 4, 9901-862, Horta, Portugal
| | - Conceição Egas
- Next Generation Sequencing Unit, UCBiotech-CNC, Parque Tecnológico de Cantanhede, Núcleo 04, Lote 8, 3060-197, Cantanhede, Portugal
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