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Wang C, Zheng R, Sun C. Multi-omics analyses provide insights into the sulfur metabolism of a novel deep-sea sulfate-reducing bacterium. iScience 2024; 27:110095. [PMID: 38947506 PMCID: PMC11214288 DOI: 10.1016/j.isci.2024.110095] [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: 01/24/2024] [Revised: 04/02/2024] [Accepted: 05/21/2024] [Indexed: 07/02/2024] Open
Abstract
Sulfate-reducing bacteria (SRB) are ubiquitously distributed across various biospheres and play key roles in global sulfur and carbon cycles. However, few deep-sea SRB have been cultivated and studied in situ, limiting our understanding of the true metabolism of deep-sea SRB. Here, we firstly clarified the high abundance of SRB in deep-sea sediments and successfully isolated a sulfate-reducing bacterium (zrk46) from a cold seep sediment. Our genomic, physiological, and phylogenetic analyses indicate that strain zrk46 is a novel species, which we propose as Pseudodesulfovibrio serpens. We found that supplementation with sulfate, thiosulfate, or sulfite promoted strain zrk46 growth by facilitating energy production through the dissimilatory sulfate reduction, which was coupled to the oxidation of organic matter in both laboratory and deep-sea conditions. Moreover, in situ metatranscriptomic results confirmed that other deep-sea SRB also performed the dissimilatory sulfate reduction, strongly suggesting that SRB may play undocumented roles in deep-sea sulfur cycling.
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Affiliation(s)
- Chong Wang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology & Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
- Center of Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Rikuan Zheng
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology & Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
- Center of Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Chaomin Sun
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology & Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
- Center of Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
- College of Earth Science, University of Chinese Academy of Sciences, Beijing 100049, China
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Yadav S, Koenen M, Bale NJ, Reitsma W, Engelmann JC, Stefanova K, Damsté JSS, Villanueva L. Organic matter degradation in the deep, sulfidic waters of the Black Sea: insights into the ecophysiology of novel anaerobic bacteria. MICROBIOME 2024; 12:98. [PMID: 38797849 PMCID: PMC11129491 DOI: 10.1186/s40168-024-01816-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 04/15/2024] [Indexed: 05/29/2024]
Abstract
BACKGROUND Recent studies have reported the identity and functions of key anaerobes involved in the degradation of organic matter (OM) in deep (> 1000 m) sulfidic marine habitats. However, due to the lack of available isolates, detailed investigation of their physiology has been precluded. In this study, we cultivated and characterized the ecophysiology of a wide range of novel anaerobes potentially involved in OM degradation in deep (2000 m depth) sulfidic waters of the Black Sea. RESULTS We have successfully cultivated a diverse group of novel anaerobes belonging to various phyla, including Fusobacteriota (strain S5), Bacillota (strains A1T and A2), Spirochaetota (strains M1T, M2, and S2), Bacteroidota (strains B1T, B2, S6, L6, SYP, and M2P), Cloacimonadota (Cloa-SY6), Planctomycetota (Plnct-SY6), Mycoplasmatota (Izemo-BS), Chloroflexota (Chflx-SY6), and Desulfobacterota (strains S3T and S3-i). These microorganisms were able to grow at an elevated hydrostatic pressure of up to 50 MPa. Moreover, this study revealed that different anaerobes were specialized in degrading specific types of OM. Strains affiliated with the phyla Fusobacteriota, Bacillota, Planctomycetota, and Mycoplasmatota were found to be specialized in the degradation of cellulose, cellobiose, chitin, and DNA, respectively, while strains affiliated with Spirochaetota, Bacteroidota, Cloacimonadota, and Chloroflexota preferred to ferment less complex forms of OM. We also identified members of the phylum Desulfobacterota as terminal oxidizers, potentially involved in the consumption of hydrogen produced during fermentation. These results were supported by the identification of genes in the (meta)genomes of the cultivated microbial taxa which encode proteins of specific metabolic pathways. Additionally, we analyzed the composition of membrane lipids of selected taxa, which could be critical for their survival in the harsh environment of the deep sulfidic waters and could potentially be used as biosignatures for these strains in the sulfidic waters of the Black Sea. CONCLUSIONS This is the first report that demonstrates the cultivation and ecophysiology of such a diverse group of microorganisms from any sulfidic marine habitat. Collectively, this study provides a step forward in our understanding of the microbes thriving in the extreme conditions of the deep sulfidic waters of the Black Sea. Video Abstract.
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Affiliation(s)
- Subhash Yadav
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, 1797AB Den Burg, P.O. Box 59, Texel, The Netherlands
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, The Netherlands
| | - Michel Koenen
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, 1797AB Den Burg, P.O. Box 59, Texel, The Netherlands
| | - Nicole J Bale
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, 1797AB Den Burg, P.O. Box 59, Texel, The Netherlands
| | - Wietse Reitsma
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, 1797AB Den Burg, P.O. Box 59, Texel, The Netherlands
| | - Julia C Engelmann
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, 1797AB Den Burg, P.O. Box 59, Texel, The Netherlands
| | - Kremena Stefanova
- Institute of Oceanology "Fridtjof Nansen", Bulgarian Academy of Sciences, Varna, Bulgaria
| | - Jaap S Sinninghe Damsté
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, 1797AB Den Burg, P.O. Box 59, Texel, The Netherlands
- Faculty of Geosciences, Department of Earth Sciences, Utrecht University, P.O. Box 80.021, 3508 TA, Utrecht, The Netherlands
| | - Laura Villanueva
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, 1797AB Den Burg, P.O. Box 59, Texel, The Netherlands.
- Faculty of Geosciences, Department of Earth Sciences, Utrecht University, P.O. Box 80.021, 3508 TA, Utrecht, The Netherlands.
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Yin X, Zhou G, Wang H, Han D, Maeke M, Richter-Heitmann T, Wunder LC, Aromokeye DA, Zhu QZ, Nimzyk R, Elvert M, Friedrich MW. Unexpected carbon utilization activity of sulfate-reducing microorganisms in temperate and permanently cold marine sediments. THE ISME JOURNAL 2024; 18:wrad014. [PMID: 38365251 PMCID: PMC10811731 DOI: 10.1093/ismejo/wrad014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 11/21/2023] [Accepted: 11/29/2023] [Indexed: 02/18/2024]
Abstract
Significant amounts of organic carbon in marine sediments are degraded, coupled with sulfate reduction. However, the actual carbon and energy sources used in situ have not been assigned to each group of diverse sulfate-reducing microorganisms (SRM) owing to the microbial and environmental complexity in sediments. Here, we probed microbial activity in temperate and permanently cold marine sediments by using potential SRM substrates, organic fermentation products at very low concentrations (15-30 μM), with RNA-based stable isotope probing. Unexpectedly, SRM were involved only to a minor degree in organic fermentation product mineralization, whereas metal-reducing microbes were dominant. Contrastingly, distinct SRM strongly assimilated 13C-DIC (dissolved inorganic carbon) with H2 as the electron donor. Our study suggests that canonical SRM prefer autotrophic lifestyle, with hydrogen as the electron donor, while metal-reducing microorganisms are involved in heterotrophic organic matter turnover, and thus regulate carbon fluxes in an unexpected way in marine sediments.
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Affiliation(s)
- Xiuran Yin
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, 58 Renmin Avenue, Haikou 570228, China
- Faculty of Biology/Chemistry, University of Bremen, Leobener Strasse 3, Bremen D-28359, Germany
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Leobener Strasse 8, Bremen D-28359, Germany
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, Bremen D-28359, Germany
| | - Guowei Zhou
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, 58 Renmin Avenue, Haikou 570228, China
- School of Resources and Environmental Engineering, Anhui University, 111 Jiulong Road, Hefei, Anhui 230601, China
| | - Haihua Wang
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, 58 Renmin Avenue, Haikou 570228, China
- Faculty of Biology/Chemistry, University of Bremen, Leobener Strasse 3, Bremen D-28359, Germany
- College of Urban and Environmental Sciences, Peking University, No. 5 Yiheyuan Road, Beijing 100871, China
| | - Dukki Han
- Department of Marine Bioscience, Gangneung-Wonju National University, 7 Jukheon-gil, Gangneung-si 25457, Republic of Korea
| | - Mara Maeke
- Faculty of Biology/Chemistry, University of Bremen, Leobener Strasse 3, Bremen D-28359, Germany
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, Bremen D-28359, Germany
| | - Tim Richter-Heitmann
- Faculty of Biology/Chemistry, University of Bremen, Leobener Strasse 3, Bremen D-28359, Germany
| | - Lea C Wunder
- Faculty of Biology/Chemistry, University of Bremen, Leobener Strasse 3, Bremen D-28359, Germany
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, Bremen D-28359, Germany
| | - David A Aromokeye
- Faculty of Biology/Chemistry, University of Bremen, Leobener Strasse 3, Bremen D-28359, Germany
| | - Qing-Zeng Zhu
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Leobener Strasse 8, Bremen D-28359, Germany
| | - Rolf Nimzyk
- Faculty of Biology/Chemistry, University of Bremen, Leobener Strasse 3, Bremen D-28359, Germany
| | - Marcus Elvert
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Leobener Strasse 8, Bremen D-28359, Germany
- Faculty of Geosciences, University of Bremen, Klagenfurter Strasse 2-4, Bremen D-28359, Germany
| | - Michael W Friedrich
- Faculty of Biology/Chemistry, University of Bremen, Leobener Strasse 3, Bremen D-28359, Germany
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Leobener Strasse 8, Bremen D-28359, Germany
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Jiang Q, Jing H, Li X, Wan Y, Chou IM, Hou L, Dong H, Niu Y, Gao D. Active pathways of anaerobic methane oxidization in deep-sea cold seeps of the South China Sea. Microbiol Spectr 2023; 11:e0250523. [PMID: 37916811 PMCID: PMC10715046 DOI: 10.1128/spectrum.02505-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 10/08/2023] [Indexed: 11/03/2023] Open
Abstract
IMPORTANCE Cold seeps occur in continental margins worldwide and are deep-sea oases. Anaerobic oxidation of methane is an important microbial process in the cold seeps and plays an important role in regulating methane content. This study elucidates the diversity and potential activities of major microbial groups in dependent anaerobic methane oxidation and sulfate-dependent anaerobic methane oxidation processes and provides direct evidence for the occurrence of nitrate-/nitrite-dependent anaerobic methane oxidation (Nr-/N-DAMO) as a previously overlooked microbial methane sink in the hydrate-bearing sediments of the South China Sea. This study provides direct evidence for occurrence of Nr-/N-DAMO as an important methane sink in the deep-sea cold seeps.
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Affiliation(s)
- Qiuyun Jiang
- 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
| | - 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
- Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, Guangdong, China
- HKUST-CAS Sanya Joint Laboratory of Marine Science Research, Chinese Academy of Sciences, Sanya, China
| | - Xuegong Li
- CAS Key Laboratory for Experimental Study under Deep-sea Extreme Conditions, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Ye Wan
- CAS Key Laboratory for Experimental Study under Deep-sea Extreme Conditions, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - I-Ming Chou
- CAS Key Laboratory for Experimental Study under Deep-sea Extreme Conditions, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Lijun Hou
- State Key Laboratory of Estuarine and Costal Research, East China Normal University, Shanghai, China
| | - Hongpo Dong
- State Key Laboratory of Estuarine and Costal Research, East China Normal University, Shanghai, China
| | - Yuhui Niu
- State Key Laboratory of Estuarine and Costal Research, East China Normal University, Shanghai, China
| | - Dengzhou Gao
- State Key Laboratory of Estuarine and Costal Research, East China Normal University, Shanghai, China
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Thangaraj S, Kim HR, Heo JM, Son S, Ryu J, Park JW, Kim JH, Kim SY, Jung HK, Kim IN. Unraveling prokaryotic diversity distribution and functional pattern on nitrogen and methane cycling in the subtropical Western North Pacific Ocean. MARINE POLLUTION BULLETIN 2023; 196:115569. [PMID: 37922593 DOI: 10.1016/j.marpolbul.2023.115569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 09/15/2023] [Accepted: 09/20/2023] [Indexed: 11/07/2023]
Abstract
Prokaryotes play an important role in marine nitrogen and methane cycles. However, their community changes and metabolic modifications to the concurrent impact of ocean warming (OW), acidification (OA), deoxygenation (OD), and anthropogenic‑nitrogen-deposition (AND) from the surface to the deep ocean remains unknown. We examined here the amplicon sequencing approach across the surface (0-200 m; SL), intermediate (200-1000 m; IL), and deep layers (1000-2200 m; DL), and characterized the simultaneous impacts of OW, OA, OD, and AND on the Western North Pacific Ocean prokaryotic changes and their functional pattern in nitrogen and methane cycles. Results showed that SL possesses higher ammonium oxidation community/metabolic composition assumably the reason for excess nitrogen input from AND and modification of their kinetic properties to OW adaptation. Expanding OD at IL showed hypoxic conditions in the oxygen minimum layer, inducing higher microbial respiration that elevates the dimerization of nitrification genes for higher nitrous oxide production. The aerobic methane-oxidation composition was dominant in SL presumably the reason for adjustment in prokaryotic optimal temperature to OW, while anaerobic oxidation composition was dominant at IL due to the evolutionary changes coupling with higher nitrification. Our findings refocus on climate-change impacts on the open ocean ecosystem from the surface to the deep-environment integrating climate-drivers as key factors for higher nitrous-oxide and methane emissions.
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Affiliation(s)
- Satheeswaran Thangaraj
- Department of Marine Science, Incheon National University, Incheon, South Korea; Freddy and Nadine Herrmann Institute of Earth Sciences, Hebrew University of Jerusalem, Jerusalem, Israel; Interuniversity Institute for Marine Sciences, Eilat, Israel; Department of Physiology, Saveetha Dental College and Hospital, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, India
| | - Hyo-Ryeon Kim
- Department of Marine Science, Incheon National University, Incheon, South Korea
| | - Jang-Mu Heo
- Department of Marine Science, Incheon National University, Incheon, South Korea
| | - Seunghyun Son
- Cooperative Institute for Satellite Earth System Studies (CISESS) / Earth System Science Interdisciplinary Center (ESSIC), University of Maryland, USA
| | - Jongseong Ryu
- Department of Marine Biotechnology, Anyang University, Incheon, South Korea
| | - Jong-Woo Park
- Tidal Flat Research Center, National Institute of Fisheries Science, Gunsan, South Korea
| | - Ju-Hyoung Kim
- Department of Aquaculture and Aquatic Science, Kunsan National University, Gunsan, South Korea
| | - Seo-Young Kim
- Department of Marine Science, Incheon National University, Incheon, South Korea
| | - Hae-Kun Jung
- Environment and Fisheries Resources Research Division, East Sea Fisheries Institute, National Institute of Fisheries Science, Gangneung, South Korea
| | - Il-Nam Kim
- Department of Marine Science, Incheon National University, Incheon, South Korea.
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6
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Jaussi M, Jørgensen BB, Kjeldsen KU, Lomstein BA, Pearce C, Seidenkantz MS, Røy H. Cell-specific rates of sulfate reduction and fermentation in the sub-seafloor biosphere. Front Microbiol 2023; 14:1198664. [PMID: 37555068 PMCID: PMC10405931 DOI: 10.3389/fmicb.2023.1198664] [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: 04/01/2023] [Accepted: 07/05/2023] [Indexed: 08/10/2023] Open
Abstract
Microorganisms in subsurface sediments live from recalcitrant organic matter deposited thousands or millions of years ago. Their catabolic activities are low, but the deep biosphere is of global importance due to its volume. The stability of deeply buried sediments provides a natural laboratory where prokaryotic communities that live in steady state with their environments can be studied over long time scales. We tested if a balance is established between the flow of energy, the microbial community size, and the basal power requirement needed to maintain cells in sediments buried meters below the sea floor. We measured rates of carbon oxidation by sulfate reduction and counted the microbial cells throughout ten carefully selected sediment cores with ages from years to millions of years. The rates of carbon oxidation were converted to power (J s-1 i.e., Watt) using the Gibbs free energy of the anaerobic oxidation of complex organic carbon. We separated energy dissipation by fermentation from sulfate reduction. Similarly, we separated the community into sulfate reducers and non-sulfate reducers based on the dsrB gene, so that sulfate reduction could be related to sulfate reducers. We found that the per-cell sulfate reduction rate was stable near 10-2 fmol C cell-1 day-1 right below the zone of bioturbation and did not decrease with increasing depth and sediment age. The corresponding power dissipation rate was 10-17 W sulfate-reducing cell-1. The cell-specific power dissipation of sulfate reducers in old sediments was similar to the slowest growing anaerobic cultures. The energy from mineralization of organic matter that was not dissipated by sulfate reduction was distributed evenly to all cells that did not possess the dsrB gene, i.e., cells operationally defined as fermenting. In contrast to sulfate reducers, the fermenting cells had decreasing catabolism as the sediment aged. A vast difference in power requirement between fermenters and sulfate reducers caused the microbial community in old sediments to consist of a minute fraction of sulfate reducers and a vast majority of fermenters.
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Affiliation(s)
- Marion Jaussi
- Department of Biology, Aarhus University, Aarhus, Denmark
| | | | | | | | - Christof Pearce
- Department of Geoscience, Aarhus University, Aarhus, Denmark
| | | | - Hans Røy
- Department of Biology, Aarhus University, Aarhus, Denmark
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Zhang P, Yang F, Dai W, Wei C. Variation of sulfate reducing bacteria communities in ionic rare earth tailings and the potential of a single cadmium resistant strain in bioremediation. CHEMOSPHERE 2023; 328:138615. [PMID: 37023895 DOI: 10.1016/j.chemosphere.2023.138615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 02/14/2023] [Accepted: 04/03/2023] [Indexed: 06/19/2023]
Abstract
Heap leaching ionic rare earth tailings might be prone to nourish sulfate reducing bacteria (SRB), but the SRB community in terrestrial ecosystems, such as tailings, has never been studied. This work was conducted to investigate the SRB communities in revegetated and bare tailings in Dingnan county, Jiangxi province, China, incorporating with indoor experiments to isolate SRB strain in bioremediation of Cd contamination. Significant increases in richness, accompanied by reductions in evenness and diversity, were found in the SRB community in revegetated tailings compared to bare tailings. At genus taxonomic level, two distinct dominant SRB were observed in samples from bare and revegetated tailings, with Desulfovibrio dominating in the former and Streptomyces dominating in the latter, respectively. A single SRB strain was screened out from the bare tailings (REO-01). The cell of REO-01 was rod-shaped and belonged to family Desulfuricans and genus Desulfovibrio. The Cd resistance of the strain was further examined, no changes in cell morphology were observed at 0.05 mM Cd, additionally, the atomic ratios of S, Cd, and Fe changed with the increase in Cd dosages, indicating FeS and CdS were produced simultaneously, XRD results further confirmed the production changed gradually from FeS to CdS with increasing Cd dosages from 0.05 to 0.2 mM. FT-IR analysis showed that functional groups containing amide, polysaccharide glycosidic linkage, hydroxyl, carboxy, methyl, phosphodiesters and sulfhydryl groups in extracellular polymeric substances (EPS) of REO-01 might have affinity with Cd. This study demonstrated the potential of a single SRB strain isolated from ionic rare earth tailings in bioremediation of Cd contamination.
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Affiliation(s)
- Ping Zhang
- Key Laboratory of Land Surface Pattern and Simulation, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fen Yang
- Key Laboratory of Land Surface Pattern and Simulation, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, 100101, China
| | - Weijie Dai
- Key Laboratory of Land Surface Pattern and Simulation, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chaoyang Wei
- Key Laboratory of Land Surface Pattern and Simulation, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, 100101, China.
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Liang QY, Zhang JY, Ning D, Yu WX, Chen GJ, Tao X, Zhou J, Du ZJ, Mu DS. Niche Modification by Sulfate-Reducing Bacteria Drives Microbial Community Assembly in Anoxic Marine Sediments. mBio 2023; 14:e0353522. [PMID: 36988509 PMCID: PMC10128000 DOI: 10.1128/mbio.03535-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 02/27/2023] [Indexed: 03/30/2023] Open
Abstract
Sulfate-reducing bacteria (SRB) are essential functional microbial taxa for degrading organic matter (OM) in anoxic marine environments. However, there are little experimental data regarding how SRB regulates microbial communities. Here, we applied a top-down microbial community management approach by inhibiting SRB to elucidate their contributions to the microbial community during OM degradation. Based on the highly replicated microcosms (n = 20) of five different incubation stages, we found that many microbial community properties were influenced after inhibiting SRB, including the composition, structure, network, and community assembly processes. We also found a strong coexistence pattern between SRB and other abundant phylogenetic lineages via positive frequency-dependent selection. The relative abundances of the families Synergistaceae, Peptostreptococcaceae, Dethiosulfatibacteraceae, Prolixibacteraceae, Marinilabiliaceae, and Marinifilaceae were simultaneously suppressed after inhibiting SRB during OM degradation. A close association between SRB and the order Marinilabiliales among coexisting taxa was most prominent. They contributed to preserved modules during network successions, were keystone nodes mediating the networked community, and contributed to homogeneous ecological selection. The molybdate tolerance test of the isolated strains of Marinilabiliales showed that inhibited SRB (not the inhibitor of SRB itself) triggered a decrease in the relative abundance of Marinilabiliales. We also found that inhibiting SRB resulted in reduced pH, which is unsuitable for the growth of most Marinilabiliales strains, while the addition of pH buffer (HEPES) in SRB-inhibited treatment microcosms restored the pH and the relative abundances of these bacteria. These data supported that SRB could modify niches to affect species coexistence. IMPORTANCE Our model offers insight into the ecological properties of SRB and identifies a previously undocumented dimension of OM degradation. This targeted inhibition approach could provide a novel framework for illustrating how functional microbial taxa associate the composition and structure of the microbial community, molecular ecological network, and community assembly processes. These findings emphasize the importance of SRB during OM degradation. Our results proved the feasibility of the proposed study framework, inhibiting functional taxa at the community level, for illustrating when and to what extent functional taxa can contribute to ecosystem services.
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Affiliation(s)
- Qi-Yun Liang
- Marine College, Shandong University, Weihai, People’s Republic of China
| | - Jin-Yu Zhang
- Marine College, Shandong University, Weihai, People’s Republic of China
| | - Daliang Ning
- Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, USA
| | - Wen-Xing Yu
- Marine College, Shandong University, Weihai, People’s Republic of China
| | - Guan-Jun Chen
- Marine College, Shandong University, Weihai, People’s Republic of China
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Xuanyu Tao
- Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, USA
| | - Jizhong Zhou
- Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, USA
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Zong-Jun Du
- Marine College, Shandong University, Weihai, People’s Republic of China
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Da-Shuai Mu
- Marine College, Shandong University, Weihai, People’s Republic of China
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
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Qian L, Yu X, Gu H, Liu F, Fan Y, Wang C, He Q, Tian Y, Peng Y, Shu L, Wang S, Huang Z, Yan Q, He J, Liu G, Tu Q, He Z. Vertically stratified methane, nitrogen and sulphur cycling and coupling mechanisms in mangrove sediment microbiomes. MICROBIOME 2023; 11:71. [PMID: 37020239 PMCID: PMC10074775 DOI: 10.1186/s40168-023-01501-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 02/20/2023] [Indexed: 06/19/2023]
Abstract
BACKGROUND Mangrove ecosystems are considered as hot spots of biogeochemical cycling, yet the diversity, function and coupling mechanism of microbially driven biogeochemical cycling along the sediment depth of mangrove wetlands remain elusive. Here we investigated the vertical profile of methane (CH4), nitrogen (N) and sulphur (S) cycling genes/pathways and their potential coupling mechanisms using metagenome sequencing approaches. RESULTS Our results showed that the metabolic pathways involved in CH4, N and S cycling were mainly shaped by pH and acid volatile sulphide (AVS) along a sediment depth, and AVS was a critical electron donor impacting mangrove sediment S oxidation and denitrification. Gene families involved in S oxidation and denitrification significantly (P < 0.05) decreased along the sediment depth and could be coupled by S-driven denitrifiers, such as Burkholderiaceae and Sulfurifustis in the surface sediment (0-15 cm). Interestingly, all S-driven denitrifier metagenome-assembled genomes (MAGs) appeared to be incomplete denitrifiers with nitrate/nitrite/nitric oxide reductases (Nar/Nir/Nor) but without nitrous oxide reductase (Nos), suggesting such sulphide-utilizing groups might be an important contributor to N2O production in the surface mangrove sediment. Gene families involved in methanogenesis and S reduction significantly (P < 0.05) increased along the sediment depth. Based on both network and MAG analyses, sulphate-reducing bacteria (SRB) might develop syntrophic relationships with anaerobic CH4 oxidizers (ANMEs) by direct electron transfer or zero-valent sulphur, which would pull forward the co-existence of methanogens and SRB in the middle and deep layer sediments. CONCLUSIONS In addition to offering a perspective on the vertical distribution of microbially driven CH4, N and S cycling genes/pathways, this study emphasizes the important role of S-driven denitrifiers on N2O emissions and various possible coupling mechanisms of ANMEs and SRB along the mangrove sediment depth. The exploration of potential coupling mechanisms provides novel insights into future synthetic microbial community construction and analysis. This study also has important implications for predicting ecosystem functions within the context of environmental and global change. Video Abstract.
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Affiliation(s)
- Lu Qian
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-Sen University, Guangzhou, 510006 China
| | - Xiaoli Yu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-Sen University, Guangzhou, 510006 China
| | - Hang Gu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-Sen University, Guangzhou, 510006 China
| | - Fei Liu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-Sen University, Guangzhou, 510006 China
| | - Yijun Fan
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-Sen University, Guangzhou, 510006 China
| | - Cheng Wang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-Sen University, Guangzhou, 510006 China
| | - Qiang He
- Department of Civil and Environmental Engineering, the University of Tennessee, Knoxville, TN 37996 USA
| | - Yun Tian
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen, 361005 China
| | - Yisheng Peng
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-Sen University, Guangzhou, 510006 China
| | - Longfei Shu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-Sen University, Guangzhou, 510006 China
| | - Shanquan Wang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-Sen University, Guangzhou, 510006 China
| | - Zhijian Huang
- School of Marine Science, Sun Yat-Sen University, Zhuhai, 519080 China
| | - Qingyun Yan
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-Sen University, Guangzhou, 510006 China
| | - Jianguo He
- School of Life Science, Sun Yat-Sen University, Guangzhou, 510275 China
| | - Guangli Liu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-Sen University, Guangzhou, 510006 China
| | - Qichao Tu
- Institute of Marine Science and Technology, Shandong University, Qingdao, 266237 China
| | - Zhili He
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-Sen University, Guangzhou, 510006 China
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10
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Botti A, Biagi E, Musmeci E, Breglia A, Degli Esposti M, Fava F, Zanaroli G. Effect of polyhydroxyalkanoates on the microbial reductive dechlorination of polychlorinated biphenyls and competing anaerobic respirations in a marine microbial culture. MARINE POLLUTION BULLETIN 2023; 186:114458. [PMID: 36493518 DOI: 10.1016/j.marpolbul.2022.114458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 10/26/2022] [Accepted: 11/28/2022] [Indexed: 06/17/2023]
Abstract
The effect of polyhydroxyalkanoates (PHAs) with different composition on the reductive dechlorination activity of a polychlorinated biphenyls (PCBs) dechlorinating marine microbial community and on the activity of sulfate-reducing (SRB) and methanogenic bacteria (MB), were investigated in marine sediment microcosms and compared with the main monomer, 3-hydroxybutyric acid (3HB). Despite PHAs were fermented more slowly than 3HB, all electron donors stimulated constantly sulfate-reduction, methanogenesis and, only transiently, PCB reductive dechlorination. No relevant differences were observed with different compositions of PHAs. According to electron balances, the majority of the supplied electrons (50 %) were consumed by SRB and to less extent by MB (9-31 %), while a small percentage (0.01 %) was delivered to OHRB. In the studied conditions PHAs were confirmed as potential slow‑hydrogen releasing compounds in marine environment but their fermentation rate was sufficiently high to mainly stimulate the competitors of organohalide respring bacteria for electron donors.
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Affiliation(s)
- Alberto Botti
- Dept. of Civil, Chemical, Environmental and Material Engineering (DICAM), Alma Mater Studiorum University of Bologna, Via Terracini 28, 40131 Bologna, Italy
| | - Elena Biagi
- Dept. of Civil, Chemical, Environmental and Material Engineering (DICAM), Alma Mater Studiorum University of Bologna, Via Terracini 28, 40131 Bologna, Italy
| | - Eliana Musmeci
- Dept. of Civil, Chemical, Environmental and Material Engineering (DICAM), Alma Mater Studiorum University of Bologna, Via Terracini 28, 40131 Bologna, Italy
| | - Alessia Breglia
- Dept. of Civil, Chemical, Environmental and Material Engineering (DICAM), Alma Mater Studiorum University of Bologna, Via Terracini 28, 40131 Bologna, Italy
| | - Micaela Degli Esposti
- Dept. of Civil, Chemical, Environmental and Material Engineering (DICAM), Alma Mater Studiorum University of Bologna, Via Terracini 28, 40131 Bologna, Italy
| | - Fabio Fava
- Dept. of Civil, Chemical, Environmental and Material Engineering (DICAM), Alma Mater Studiorum University of Bologna, Via Terracini 28, 40131 Bologna, Italy
| | - Giulio Zanaroli
- Dept. of Civil, Chemical, Environmental and Material Engineering (DICAM), Alma Mater Studiorum University of Bologna, Via Terracini 28, 40131 Bologna, Italy.
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11
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Jiang Q, Jing H, Liu H, Du M. Biogeographic distributions of microbial communities associated with anaerobic methane oxidation in the surface sediments of deep-sea cold seeps in the South China Sea. Front Microbiol 2022; 13:1060206. [PMID: 36620029 PMCID: PMC9822730 DOI: 10.3389/fmicb.2022.1060206] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 12/02/2022] [Indexed: 12/24/2022] Open
Abstract
Cold seeps are oasis for the microbes in the deep-sea ecosystems, and various cold seeps are located along the northern slope of the South China Sea (SCS). However, by far most microbial ecological studies were limited to specific cold seep in the SCS, and lack of comparison between different regions. Here, the surface sediments (0-4 cm) from the Site F/Haima cold seeps and the Xisha trough in the SCS were used to elucidate the biogeography of microbial communities, with particular interest in the typical functional groups involved in the anaerobic oxidation of methane (AOM) process. Distinct microbial clusters corresponding to the three sampling regions were formed, and significantly higher gene abundance of functional groups were present in the cold seeps than the trough. This biogeographical distribution could be explained by the geochemical characteristics of sediments, such as total nitrogen (TN), total phosphorus (TP), nitrate (NO3 -), total sulfur (TS) and carbon to nitrogen ratios (C/N). Phylogenetic analysis demonstrated that mcrA and pmoA genotypes were closely affiliated with those from wetland and mangroves, where denitrifying anaerobic methane oxidation (DAMO) process frequently occurred; and highly diversified dsrB genotypes were revealed as well. In addition, significantly higher relative abundance of NC10 group was found in the Xisha trough, suggesting that nitrite-dependent DAMO (N-DAMO) process was more important in the hydrate-bearing trough, although its potential ecological contribution to AOM deserves further investigation. Our study also further demonstrated the necessity of combining functional genes and 16S rRNA gene to obtain a comprehensive picture of the population shifts of natural microbial communities among different oceanic regions.
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Affiliation(s)
- Qiuyun Jiang
- 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
| | - 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,HKUST-CAS Sanya Joint Laboratory of Marine Science Research, Chinese Academy of Sciences, Sanya, China,Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China,*Correspondence: Hongmei Jing,
| | - Hao Liu
- CAS Key Laboratory for Experimental Study Under Deep-sea Extreme Conditions, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Mengran Du
- CAS Key Laboratory for Experimental Study Under Deep-sea Extreme Conditions, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
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12
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Wang T, van Dijk L, Rijnaarts I, Hermes GDA, de Roos NM, Witteman BJM, de Wit NJW, Govers C, Smidt H, Zoetendal EG. Methanogen Levels Are Significantly Associated with Fecal Microbiota Composition and Alpha Diversity in Healthy Adults and Irritable Bowel Syndrome Patients. Microbiol Spectr 2022; 10:e0165322. [PMID: 36321894 PMCID: PMC9769613 DOI: 10.1128/spectrum.01653-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 10/14/2022] [Indexed: 11/07/2022] Open
Abstract
Hydrogenotrophic microbes, primarily including the three functional groups methanogens, sulfate-reducing bacteria, and reductive acetogens, use hydrogen as an energy source and play an important role in maintaining the hydrogen balance in gut ecosystems. A distorted hydrogen balance has been associated with irritable bowel syndrome (IBS). However, the role of hydrogenotrophic microbes in overall microbiota composition and function remains largely unknown. This study aims to assess the distribution and stability of hydrogenotrophic functional groups in healthy adults (HAs) and IBS patients and their association with overall microbiota composition and IBS symptoms. A two-time-point study with 4 weeks in between was performed with 27 HAs and 55 IBS patients included. Our observations revealed that methanogens showed a bimodal distribution across samples. A high-level methanogen microbiota was consistently associated with higher alpha diversity, and its composition was significantly different from that of individuals with a low-level methanogen microbiota. In general, these associations were more pronounced in IBS patients than in HAs. The differences in the copy numbers of genes indicative of total bacteria and acetogens between HAs and IBS patients and their correlations with IBS symptom severity, anxiety, depression, and quality of life (QoL) were sampling time dependent. Hydrogenotrophic functional groups did not show negative abundance correlations with each other in HAs and IBS patients. These findings suggest that methanogen levels in the gut have a pronounced association with microbiota alpha diversity and composition, and the interactions between hydrogenotrophic functional groups are complex in gut ecosystems. IMPORTANCE Hydrogenotrophic microbes play an essential role in the disposal of hydrogen and the maintenance of the hydrogen balance in gut ecosystems. Their abundances vary between individuals and have been reported to be associated with human gut disorders such as irritable bowel disease. This study confirms that methanogen levels show a bimodal distribution. Moreover, a high-level methanogen microbiota was associated with higher alpha diversity, and its composition was different from that of individuals with a low-level methanogen microbiota. These associations are more pronounced in IBS patients than in healthy subjects. In addition, associations between hydrogenotrophic microbes and IBS symptom scores vary over time, which argues for the use of longitudinal study designs. Last but not least, this study suggests that the different hydrogenotrophic microbes coexist with each other and do not necessarily compete for hydrogen in the gut. The findings in this study highlight the impact of methanogens on overall microbiota composition and function.
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Affiliation(s)
- Taojun Wang
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, the Netherlands
| | - Leander van Dijk
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, the Netherlands
| | - Iris Rijnaarts
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, the Netherlands
- Division of Human Nutrition and Health, Wageningen University and Research, Wageningen, the Netherlands
- Wageningen Food and Biobased Research, Wageningen University and Research, Wageningen, the Netherlands
| | - Gerben D. A. Hermes
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, the Netherlands
| | - Nicole M. de Roos
- Division of Human Nutrition and Health, Wageningen University and Research, Wageningen, the Netherlands
| | - Ben J. M. Witteman
- Division of Human Nutrition and Health, Wageningen University and Research, Wageningen, the Netherlands
- Department of Gastroenterology and Hepatology, Hospital Gelderse Vallei, Ede, the Netherlands
| | - Nicole J. W. de Wit
- Wageningen Food and Biobased Research, Wageningen University and Research, Wageningen, the Netherlands
| | - Coen Govers
- Wageningen Food and Biobased Research, Wageningen University and Research, Wageningen, the Netherlands
- Cell Biology and Immunology, Wageningen University and Research, Wageningen, the Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, the Netherlands
| | - Erwin G. Zoetendal
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, the Netherlands
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13
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Quang NX, Yen NTM, Thai TT, Yen NTH, Van Dong N, Hoai PN, Lins L, Vanreusel A, Veettil BK, Hiep ND, Bang HQ, Quan NH, Prozorova L. Impact of a dam construction on the intertidal environment and free-living nematodes in the Ba Lai, Mekong Estuaries, Vietnam. ENVIRONMENTAL MONITORING AND ASSESSMENT 2022; 194:770. [PMID: 36255542 DOI: 10.1007/s10661-022-10187-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 05/28/2022] [Indexed: 06/16/2023]
Abstract
The impact of high siltation and accumulation of organic and waste material in the intertidal of the dammed Ba Lai River in Vietnam as part of the Mekong estuarine system was investigated by means of marine free-living nematodes. Nutrients content (nitrate, ammonium, total phosphorus, total nitrogen), total suspended solids, total organic carbon, coliform, bacteria E. coli, pH, dissolved oxygen, total dissolved solids, methane and hydrogen sulfide concentration, and the nematode communities were characterized in sediment at selected stations along the river above and below the dam. Our results found elevated methane concentrations at the upstream side of the dam while hydrogen sulfide concentrations found to be highest in the downstream side of the dam. Furthermore, methane and hydrogen sulfide concentrations were correlated to nematode community characteristics such as trophic composition densities and genera composition. There was a clear difference between the communities above and below the dam. The discontinuous nematode community distribution indicated that the Ba Lai River is impacted by dam construction. Potentially the high deposition and eutrophication could turn the area into a methane-rich area related to predicted impact on nematodes.
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Affiliation(s)
- Ngo Xuan Quang
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, 18, Hoang Quoc Viet, Cau Giay, Ha Noi, Vietnam.
- Department of Environmental Management and Technology, Institute of Tropical Biology, Vietnam Academy of Science and Technology, 85, Tran Quoc Toan, Dist.3, Ho Chi Minh city, Vietnam.
| | - Nguyen Thi My Yen
- Department of Environmental Management and Technology, Institute of Tropical Biology, Vietnam Academy of Science and Technology, 85, Tran Quoc Toan, Dist.3, Ho Chi Minh city, Vietnam
| | - Tran Thanh Thai
- Department of Environmental Management and Technology, Institute of Tropical Biology, Vietnam Academy of Science and Technology, 85, Tran Quoc Toan, Dist.3, Ho Chi Minh city, Vietnam
| | | | - Nguyen Van Dong
- Faculty of Chemistry, Ho Chi Minh City University of Science, Vietnam National University, Nguyen Van Cu Str., Dist. 5, Ho Chi Minh City, Vietnam
| | - Pham Ngoc Hoai
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, 18, Hoang Quoc Viet, Cau Giay, Ha Noi, Vietnam
- Thu Dau Mot University, Binh Duong, Vietnam
| | - Lidia Lins
- Marine Biology Research Group, Biology Department, Ghent University, Krijgslaan 281, S8, B-9000, Ghent, Belgium
| | - Ann Vanreusel
- Marine Biology Research Group, Biology Department, Ghent University, Krijgslaan 281, S8, B-9000, Ghent, Belgium
| | - Bijeesh Kozhikkodan Veettil
- Institute of Fundamental and Applied Sciences, Duy Tan University, Ho Chi Minh City, 700000, Vietnam
- Faculty of Information Technology, Duy Tan University, Da Nang, 550000, Vietnam
| | - Nguyen Duc Hiep
- Environmental Quality, Atmospheric Science and Climate Change Research Group, Ton Duc Thang University, Ho Chi Minh City, Vietnam
| | - Ho Quoc Bang
- Institute for Environment and Resources, National University, Ho Chi Minh City, Vietnam
| | - Nguyen Hong Quan
- Institute for Circular Economy Development, National University, Ho Chi Minh City, Vietnam
| | - Larisa Prozorova
- Far Eastern Branch of Russian Academy of Sciences, Federal Scientific Center of the East Asia Terrestrial Biodiversity, Vladivostok, Russia
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14
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Beulig F, Schubert F, Adhikari RR, Glombitza C, Heuer VB, Hinrichs KU, Homola KL, Inagaki F, Jørgensen BB, Kallmeyer J, Krause SJE, Morono Y, Sauvage J, Spivack AJ, Treude T. Rapid metabolism fosters microbial survival in the deep, hot subseafloor biosphere. Nat Commun 2022; 13:312. [PMID: 35078973 PMCID: PMC8789916 DOI: 10.1038/s41467-021-27802-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 12/10/2021] [Indexed: 11/25/2022] Open
Abstract
A fourth of the global seabed sediment volume is buried at depths where temperatures exceed 80 °C, a previously proposed thermal barrier for life in the subsurface. Here, we demonstrate, utilizing an extensive suite of radiotracer experiments, the prevalence of active methanogenic and sulfate-reducing populations in deeply buried marine sediment from the Nankai Trough subduction zone, heated to extreme temperature (up to ~120 °C). The small microbial community subsisted with high potential cell-specific rates of energy metabolism, which approach the rates of active surface sediments and laboratory cultures. Our discovery is in stark contrast to the extremely low metabolic rates otherwise observed in the deep subseafloor. As cells appear to invest most of their energy to repair thermal cell damage in the hot sediment, they are forced to balance delicately between subsistence near the upper temperature limit for life and a rich supply of substrates and energy from thermally driven reactions of the sedimentary organic matter. In the deep sedimentary biosphere, 80 °C has been proposed as an upper thermal barrier for life. Using a suite of radiotracer experiments, this study reports active methanogenic and sulfate-reducing microbial populations with high cell-specific metabolic rates in deeply buried marine sediments from the Nankai Trough subduction zone, which reach temperatures up to 120 °C.
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15
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Response to substrate limitation by a marine sulfate-reducing bacterium. THE ISME JOURNAL 2022; 16:200-210. [PMID: 34285365 PMCID: PMC8692349 DOI: 10.1038/s41396-021-01061-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 07/04/2021] [Accepted: 07/06/2021] [Indexed: 02/07/2023]
Abstract
Sulfate-reducing microorganisms (SRM) in subsurface sediments live under constant substrate and energy limitation, yet little is known about how they adapt to this mode of life. We combined controlled chemostat cultivation and transcriptomics to examine how the marine sulfate reducer, Desulfobacterium autotrophicum, copes with substrate (sulfate or lactate) limitation. The half-saturation uptake constant (Km) for lactate was 1.2 µM, which is the first value reported for a marine SRM, while the Km for sulfate was 3 µM. The measured residual lactate concentration in our experiments matched values observed in situ in marine sediments, supporting a key role of SRM in the control of lactate concentrations. Lactate limitation resulted in complete lactate oxidation via the Wood-Ljungdahl pathway and differential overexpression of genes involved in uptake and metabolism of amino acids as an alternative carbon source. D. autotrophicum switched to incomplete lactate oxidation, rerouting carbon metabolism in response to sulfate limitation. The estimated free energy was significantly lower during sulfate limitation (-28 to -33 kJ mol-1 sulfate), suggesting that the observed metabolic switch is under thermodynamic control. Furthermore, we detected the upregulation of putative sulfate transporters involved in either high or low affinity uptake in response to low or high sulfate concentration.
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16
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Yadav S, Koenen M, Bale N, Sinninghe Damsté JS, Villanueva L. The physiology and metabolic properties of a novel, low-abundance Psychrilyobacter species isolated from the anoxic Black Sea shed light on its ecological role. ENVIRONMENTAL MICROBIOLOGY REPORTS 2021; 13:899-910. [PMID: 34668338 DOI: 10.1111/1758-2229.13012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 08/26/2021] [Accepted: 09/17/2021] [Indexed: 06/13/2023]
Abstract
Members of the Psychrilyobacter spp. of the phylum Fusobacteria have been recently suggested to be amongst the most significant primary degraders of the detrital organic matter in sulfidic marine habitats, despite representing only a small proportion (<0.1%) of the microbial community. In this study, we have isolated a previously uncultured Psychrilyobacter species (strains SD5T and BL5; Psychrilyobacter piezotolerans sp. nov.) from the sulfidic waters (i.e., 2000 m depth) of the Black Sea and investigated its physiology and genomic capability in order to better understand potential ecological adaptation strategies. P. piezotolerans utilized a broad range of organic substituents (carbohydrates and proteins) and, remarkably, grew at sulfide concentrations up to 32 mM. These flexible physiological properties were supported by the presence of the respective metabolic pathways in the genomes of both strains. Growth at varying hydrostatic pressure (0.1-50 MPa) was sustained by modifying its membrane lipid composition. Thus, we have isolated a novel member of the 'rare biosphere', which endures the extreme conditions and may play a significant role in the degradation of detrital organic matter sinking into the sulfidic waters of the Black Sea.
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Affiliation(s)
- Subhash Yadav
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, P.O. Box 59, 1797AB, Den Burg, Texel, The Netherlands
| | - Michel Koenen
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, P.O. Box 59, 1797AB, Den Burg, Texel, The Netherlands
| | - Nicole Bale
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, P.O. Box 59, 1797AB, Den Burg, Texel, The Netherlands
| | - Jaap S Sinninghe Damsté
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, P.O. Box 59, 1797AB, Den Burg, Texel, The Netherlands
- Faculty of Geosciences, Department of Earth Sciences, Utrecht University, P.O. Box 80.021, 3508 TA, Utrecht, The Netherlands
| | - Laura Villanueva
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, P.O. Box 59, 1797AB, Den Burg, Texel, The Netherlands
- Faculty of Geosciences, Department of Earth Sciences, Utrecht University, P.O. Box 80.021, 3508 TA, Utrecht, The Netherlands
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17
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Niu ZS, Yan J, Guo XP, Xu M, Sun Y, Tou FY, Yin GY, Hou LJ, Liu M, Yang Y. Human activities can drive sulfate-reducing bacteria community in Chinese intertidal sediments by affecting metal distribution. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 786:147490. [PMID: 33975107 DOI: 10.1016/j.scitotenv.2021.147490] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 04/28/2021] [Accepted: 04/28/2021] [Indexed: 06/12/2023]
Abstract
Sulfate-reducing bacteria (SRB), which are ubiquitous in intertidal sediments, play an important role in global sulfur and carbon cycles, and in the bioremediation of toxic metalloids/metals. Pollution from human activities is now a major challenge to the sustainable development of the intertidal zone, but little is known about how and to what extent various anthropic and/or natural factors affect the SRB community. In the current study, based on the dsrB gene, we investigated the SRB community in intertidal sediment along China's coastline. The results showed that dsrB gene abundances varied among different sampling sites, with the highest average abundance of SRB at XHR (near the Bohai Sea). The SRB community structures showed obvious spatial distribution patterns with latitude along the coastal areas of China, with Desulfobulbus generally being the dominant genus. Correlation analysis and redundancy discriminant analysis revealed that total organic carbon (TOC) and pH were significantly correlated with the richness of the SRB community, and salinity, pH, sulfate and climatic parameters could be the important natural factors influencing the composition of the SRB community. Moreover, metals, especially bioavailable metals, could regulate the diversity and composition of the SRB communities. Importantly, according to structural equation model (SEM) analysis, anthropic factors (e.g., population, economy and industrial activities) could drive SRB community diversity directly or by significantly affecting the concentrations of metals. This study provides the first comprehensive investigation of the direct and indirect anthropic factors on the SRB community in intertidal sediments on a continental scale.
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Affiliation(s)
- Zuo-Shun Niu
- Key Laboratory of Geographic Information Science of the Ministry of Education, School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Jia Yan
- Key Laboratory of Geographic Information Science of the Ministry of Education, School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Xing-Pan Guo
- Key Laboratory of Geographic Information Science of the Ministry of Education, School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Miao Xu
- Key Laboratory of Geographic Information Science of the Ministry of Education, School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Yuan Sun
- Key Laboratory of Geographic Information Science of the Ministry of Education, School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Fei-Yun Tou
- Key Laboratory of Geographic Information Science of the Ministry of Education, School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Guo-Yu Yin
- Key Laboratory of Geographic Information Science of the Ministry of Education, School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Li-Jun Hou
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, 3663 North Zhongshan Road, Shanghai 200062, China; Yangtze Delta Estuarine Wetland Ecosystem Observation and Research Station, Ministry of Education & Shanghai, East China Normal University, 3663 North Zhongshan Road, Shanghai 200062, China.
| | - Min Liu
- Key Laboratory of Geographic Information Science of the Ministry of Education, School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China; Institute of Eco-Chongming, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Yi Yang
- Key Laboratory of Geographic Information Science of the Ministry of Education, School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China; State Key Laboratory of Estuarine and Coastal Research, East China Normal University, 3663 North Zhongshan Road, Shanghai 200062, China; Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China; Yangtze Delta Estuarine Wetland Ecosystem Observation and Research Station, Ministry of Education & Shanghai, East China Normal University, 3663 North Zhongshan Road, Shanghai 200062, China.
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18
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Kong Y, Lei H, Zhang Z, Cheng W, Wang B, Pan F, Huang F, Huang F, Li W. Depth profiles of geochemical features, geochemical activities and biodiversity of microbial communities in marine sediments from the Shenhu area, the northern South China Sea. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 779:146233. [PMID: 34030248 DOI: 10.1016/j.scitotenv.2021.146233] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 02/25/2021] [Accepted: 02/26/2021] [Indexed: 06/12/2023]
Abstract
The biogeochemical processes, anaerobic oxidation of methane (AOM) and methanogenesis, control methane emission and create distinct geochemical profiles with depth in marine sediments. Correlating the capacities and biodiversity of the microbial communities in marine sediments remains challenging. We therefore investigated the geochemical constituents and the capabilities and diversity of microbial communities in sediments at different depths in two cores from the Shenhu area in the northern South China Sea, which is characterized by underlying gas hydrates. The geochemical features, sulfate concentration decreased linearly and the acid volatile sulfur accumulated from 4 m below the seafloor (mbsf) to the bottom, indicating significant sulfate reduction. However, the methane concentration was relatively low and showed irregular trends, indicating that our study cores did not reach the sulfate-methane transition zone (SMTZ). Nevertheless, incubation experiments showed that the microbial groups in sediments performed AOM and methanogenesis in the region where sulfate decreased linearly above the SMTZ. We mapped the diversity and abundance of microbial communities in sediments with depth using high-throughput sequencing. A small proportion of known methanogens (<0.3%) may have been responsible for the methanogenesis during incubation. No classical archaeal anaerobic methanotroph (ANME) sequences were detected across all samples; only a small amount of SEEP-SRB1 were detected, and their abundance did not increase with increasing depth. Thus, unknown or unconventional phylotypes may have participated in AOM during the incubation, and the dominant phylum Bathyarchaeota or the small number of detected methanogens are the most likely performers of AOM.
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Affiliation(s)
- Yuan Kong
- Department of Geological Oceanography, College of Ocean & Earth Science, Xiamen University, Xiamen 361102, PR China
| | - Huaiyan Lei
- Department of Geological Oceanography, College of Ocean & Earth Science, Xiamen University, Xiamen 361102, PR China.
| | - Zilian Zhang
- Department of Geological Oceanography, College of Ocean & Earth Science, Xiamen University, Xiamen 361102, PR China
| | - Weidong Cheng
- Department of Geological Oceanography, College of Ocean & Earth Science, Xiamen University, Xiamen 361102, PR China
| | - Bin Wang
- Department of Geological Oceanography, College of Ocean & Earth Science, Xiamen University, Xiamen 361102, PR China
| | - Fulong Pan
- Department of Geological Oceanography, College of Ocean & Earth Science, Xiamen University, Xiamen 361102, PR China
| | - Fanfan Huang
- Department of Geological Oceanography, College of Ocean & Earth Science, Xiamen University, Xiamen 361102, PR China
| | - Fanli Huang
- Department of Geological Oceanography, College of Ocean & Earth Science, Xiamen University, Xiamen 361102, PR China
| | - Wenqing Li
- Key Laboratory of Mineral Resources Evaluation in Northeast China, Ministry of Land and Resources, Changchun 130061, PR China
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19
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Ueno A, Tamazawa S, Tamamura S, Murakami T, Kiyama T, Inomata H, Amano Y, Miyakawa K, Tamaki H, Naganuma T, Kaneko K. Desulfovibrio subterraneus sp. nov., a mesophilic sulfate-reducing deltaproteobacterium isolated from a deep siliceous mudstone formation. Int J Syst Evol Microbiol 2021; 71. [PMID: 33588983 DOI: 10.1099/ijsem.0.004683] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel mesophilic sulfate-reducing bacterium, strain HN2T, was isolated from groundwater sampled from the subsurface siliceous mudstone of the Wakkanai Formation located in Horonobe, Hokkaido, Japan. The bacterium was Gram-negative and vibrio-shaped, and its motility was conferred by a single polar flagellum. Cells had desulfoviridin. Catalase and oxidase activities were not detected. It grew in the temperature range of 25-40 °C (optimum, 35 °C) and pH range of 6.3-8.1 (optimum, pH 7.2-7.6). It used sulfate, thiosulfate, dimethyl sulfoxide, anthraquinone-2,6-disulfonate, Fe3+, and manganese oxide, but not elemental sulfur, nitrite, nitrate, or fumarate as electron acceptors. The strain showed weak growth with sulfite as the electron acceptor. Fermentative growth with pyruvate, lactate and cysteine was observed in the absence of sulfate, but not with malate or fumarate. NaCl was not required, but the strain tolerated up to 40 g l-1. Strain HN2T did not require vitamins. The major cellular fatty acids were iso-C15 : 0 (23.8 %), C18 : 1 ω9t (18.4 %), C18 : 0 (15.0 %), C16 : 0 (14.5 %), and anteiso-C17 :0 (10.1 %). The major respiratory quinone was menaquinone MK-6(H2). The G+C content of the genomic DNA was 56.7 mol%. Based on 16S rRNA gene sequence analysis, the closest phylogenetic relative of strain HN2T is Desulfovibrio psychrotolerans JS1T (97.0 %). Digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values of the strains HN2T and D. psychrotolerans JS1T were 22.2 and 79.8 %, respectively. Based on the phenotypic and molecular genetic evidence, we propose a novel species, D. subterraneus sp. nov. with the type strain HN2T (=DSM 101010T=NBRC 112213T).
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Affiliation(s)
- Akio Ueno
- Horonobe Research Institute for the Subsurface Environment (H-RISE) Northern Advancement Centre for Science and Technology (NOASTEC), Sakae-machi, Horonobe-cho, Teshio-gun, Hokkaido, Japan
| | - Satoshi Tamazawa
- Horonobe Research Institute for the Subsurface Environment (H-RISE) Northern Advancement Centre for Science and Technology (NOASTEC), Sakae-machi, Horonobe-cho, Teshio-gun, Hokkaido, Japan
| | - Shuji Tamamura
- Horonobe Research Institute for the Subsurface Environment (H-RISE) Northern Advancement Centre for Science and Technology (NOASTEC), Sakae-machi, Horonobe-cho, Teshio-gun, Hokkaido, Japan
| | - Takuma Murakami
- Horonobe Research Institute for the Subsurface Environment (H-RISE) Northern Advancement Centre for Science and Technology (NOASTEC), Sakae-machi, Horonobe-cho, Teshio-gun, Hokkaido, Japan
| | - Tamotsu Kiyama
- Horonobe Research Institute for the Subsurface Environment (H-RISE) Northern Advancement Centre for Science and Technology (NOASTEC), Sakae-machi, Horonobe-cho, Teshio-gun, Hokkaido, Japan
| | - Hidenori Inomata
- Horonobe Research Institute for the Subsurface Environment (H-RISE) Northern Advancement Centre for Science and Technology (NOASTEC), Sakae-machi, Horonobe-cho, Teshio-gun, Hokkaido, Japan
| | - Yuki Amano
- Horonobe Underground Research Center, Japan Atomic Energy Agency (JAEA), Hokushin 432-2, Horonobe-cho, Hokkaido 098-3224, Japan
| | - Kazuya Miyakawa
- Horonobe Underground Research Center, Japan Atomic Energy Agency (JAEA), Hokushin 432-2, Horonobe-cho, Hokkaido 098-3224, Japan
| | - Hideyuki Tamaki
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1, Higashi, Tsukuba 305-856, Japan
| | - Takeshi Naganuma
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-4-4, Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8528, Japan
| | - Katsuhiko Kaneko
- Horonobe Research Institute for the Subsurface Environment (H-RISE) Northern Advancement Centre for Science and Technology (NOASTEC), Sakae-machi, Horonobe-cho, Teshio-gun, Hokkaido, Japan
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20
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Influence of Temperature and Sulfate Concentration on the Sulfate/Sulfite Reduction Prokaryotic Communities in the Tibetan Hot Springs. Microorganisms 2021; 9:microorganisms9030583. [PMID: 33809110 PMCID: PMC8002027 DOI: 10.3390/microorganisms9030583] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 03/05/2021] [Accepted: 03/09/2021] [Indexed: 11/18/2022] Open
Abstract
The distribution and diversity of sulfate/sulfite reduction prokaryotic (SRP) communities in hot springs from the Quzhuomu and Daggyai Geothermal Zone of Tibetan, China, was reported for the first time. In hot springs that are naturally hyperthermal and anoxic, the sulfur cycle is one of the most active cycles of the elements. The distribution of SRP in response to temperature is of great importance to the understanding of biogeochemical cycling of sulfur in geothermal features. Little is known about the SRP in geothermal zone. In this study, the diversity of SRP was investigated in the sediments from the Daggyai and Quzhuomu geothermal zone using PCR amplification, cloning and sequencing of the dissimilatory sulfite reductase beta subunit gene (dsrB). The abundance of dsrB and 16S rRNA genes, were determined by quantitative polymerase chain reactions. In addition, correlations of the SRP assemblages with environmental factors were analyzed by the aggregated boosted tree (ABT) statistical analysis. The results showed that SRP populations were diverse, but were mainly composed of Desulfobacterales, Desulfovibrionales, Syntrophobacterales, Clostridia and Nitrospirales, and large fraction (25%) of novel sequences have branched groups in the dsrB phylogenetic tree. In Quzhuomu geothermal zone, sulfate-rich hot springs are characterized by thick bacterial mats that are green or red and the SRP populations mainly appear at mid-temperature (50 °C to 70 °C). In low-sulfate hot springs in the Daggyai geothermal zone, although gray or pink streamers are widely formed at 60 °C to 80 °C, they prefer to inhabit in green mat at lower temperature (30 °C to 50 °C). With increasing temperature, the diversity of the dsrB gene at the OTU level (cutoff 97%) decreased, while its relative abundance increased. This result suggests that temperature played an important role in affecting dsrB gene distribution.
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21
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Zheng R, Wu S, Sun C. Pseudodesulfovibrio cashew sp. Nov., a Novel Deep-Sea Sulfate-Reducing Bacterium, Linking Heavy Metal Resistance and Sulfur Cycle. Microorganisms 2021; 9:429. [PMID: 33669756 PMCID: PMC7922080 DOI: 10.3390/microorganisms9020429] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/17/2021] [Accepted: 02/17/2021] [Indexed: 11/17/2022] Open
Abstract
Sulfur cycling is primarily driven by sulfate reduction mediated by sulfate-reducing bacteria (SRB) in marine sediments. The dissimilatory sulfate reduction drives the production of enormous quantities of reduced sulfide and thereby the formation of highly insoluble metal sulfides in marine sediments. Here, a novel sulfate-reducing bacterium designated Pseudodesulfovibrio cashew SRB007 was isolated and purified from the deep-sea cold seep and proposed to represent a novel species in the genus of Pseudodesulfovibrio. A detailed description of the phenotypic traits, phylogenetic status and central metabolisms of strain SRB007 allowed the reconstruction of the metabolic potential and lifestyle of a novel member of deep-sea SRB. Notably, P. cashew SRB007 showed a strong ability to resist and remove different heavy metal ions including Co2+, Ni2+, Cd2+ and Hg2+. The dissimilatory sulfate reduction was demonstrated to contribute to the prominent removal capability of P. cashew SRB007 against different heavy metals via the formation of insoluble metal sulfides.
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Affiliation(s)
- Rikuan Zheng
- CAS Key Laboratory of Experimental Marine Biology & Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China;
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
- College of Earth Science, University of Chinese Academy of Sciences, Beijing 100049, China
- Center of Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Shimei Wu
- Department of Life Science, Qingdao University, Qingdao 266071, China;
| | - Chaomin Sun
- CAS Key Laboratory of Experimental Marine Biology & Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China;
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
- Center of Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
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22
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Chernyh NA, Neukirchen S, Frolov EN, Sousa FL, Miroshnichenko ML, Merkel AY, Pimenov NV, Sorokin DY, Ciordia S, Mena MC, Ferrer M, Golyshin PN, Lebedinsky AV, Cardoso Pereira IA, Bonch-Osmolovskaya EA. Dissimilatory sulfate reduction in the archaeon ‘Candidatus Vulcanisaeta moutnovskia’ sheds light on the evolution of sulfur metabolism. Nat Microbiol 2020; 5:1428-1438. [DOI: 10.1038/s41564-020-0776-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 07/16/2020] [Indexed: 02/07/2023]
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23
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Ziegler A, Gilligan AM, Dillon JG, Pernet B. Schizasterid Heart Urchins Host Microorganisms in a Digestive Symbiosis of Mesozoic Origin. Front Microbiol 2020; 11:1697. [PMID: 32793161 PMCID: PMC7387435 DOI: 10.3389/fmicb.2020.01697] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 06/29/2020] [Indexed: 01/04/2023] Open
Abstract
Because of their lifestyles, abundance, and feeding habits, infaunal marine deposit feeders have a significant impact on the ocean floor. As these animals also ingest microorganisms associated with their sediment and seawater diet, their digestive tract usually contains a diverse array of bacteria. However, while most of these microorganisms are transients, some may become part of a resident gut microbiome, in particular when sheltered from the main flow of digesta in specialized gut compartments. Here, we provide an in-depth analysis of the structure and contents of the intestinal caecum (IC), a hindgut diverticulum found exclusively in schizasterid heart urchins (Echinoidea: Spatangoida: Schizasteridae). Based on specimens of Brisaster townsendi, in addition to various other schizasterid taxa, our structural characterization of the IC shows that the organ is a highly specialized gut compartment with unique structural properties. Next generation sequencing shows that the IC contains a microbial population composed predominantly of Bacteroidales, Desulfobacterales, and Spirochaetales. The microbiome of this gut compartment is significantly different in composition and lower in diversity than the microbial population in the sediment-filled main digestive tract. Inferences on the function and evolution of the IC and its microbiome suggest that this symbiosis plays a distinct role in host nutrition and that it evolved at least 66 million years ago during the final phase of the Mesozoic.
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Affiliation(s)
- Alexander Ziegler
- Institut für Evolutionsbiologie und Ökologie, Rheinische Friedrich-Wilhelms-Universität, Bonn, Germany
| | - Ariel M. Gilligan
- Department of Biological Sciences, California State University, Long Beach, CA, United States
| | - Jesse G. Dillon
- Department of Biological Sciences, California State University, Long Beach, CA, United States
| | - Bruno Pernet
- Department of Biological Sciences, California State University, Long Beach, CA, United States
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24
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Tada Y, Marumoto K, Takeuchi A. Nitrospina-Like Bacteria Are Potential Mercury Methylators in the Mesopelagic Zone in the East China Sea. Front Microbiol 2020; 11:1369. [PMID: 32719662 PMCID: PMC7347909 DOI: 10.3389/fmicb.2020.01369] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 05/27/2020] [Indexed: 11/18/2022] Open
Abstract
In natural environments, the production of neurotoxic and bioaccumulative methylmercury (MeHg) is mediated by microorganisms carrying the genes hgcA and hgcB. However, the contribution of these microorganisms to mercury (Hg) methylation or MeHg accumulation in the ocean is poorly understood. Here we determined the total Hg (THg) and MeHg concentrations in seawater samples and conducted a metagenomic survey of the hgcAB genes and functional modules involved in metabolic pathways in the East China Sea (ECS). In the metagenomic analyses, we used paired-end reads and assembled contigs for hgcAB enumeration and phylogenetic analyses in the seawater column. To evaluate the relative abundance of hgcAB in the metagenomic data, we estimated the abundance of recA (single-copy gene of bacteria) as well and then compared them. Moreover, the profiles of prokaryotic community composition were analyzed by 16S rRNA gene (V4 region) deep-sequencing. In the mesopelagic layers, the hgcA sequences were detected, and there was a positive correlation between hgcA abundance relative to the recA and MeHg concentrations. Thus, the quantification of the hgcA sequences could provide valuable information to evaluate the potential environments of microbial MeHg accumulation in the seawater column. A phylogenetic analysis using the assembled contigs revealed that all of the hgcA sequences in the mesopelagic layers were affiliated with Nitrospina-like sequences. The 16S rRNA gene analysis revealed that Nitrospinae were abundant in the mesopelagic layers. Although the lineages of Deltaproteobacteria, Firmicutes, and Spirochaetes were detected in the seawater column, their hgcAB sequences were not detected in our metagenomes, despite the fact that they are closely related to previously identified Hg methylators. The metabolic pathway analysis revealed that the modules related to sulfur and methane metabolism were prominent in the mesopelagic layers. However, no hgcA sequences affiliated with sulfate-reducing bacteria (SRB) or methanogens were detected in these layers, suggesting that these bacteria could not be strongly involved in the Hg accumulation in the seawater column. Our results indicate that Nitrospina-like bacteria with hgcAB genes could play a critical role in microbial Hg accumulation in the oxygenated mesopelagic layers of the ECS.
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Affiliation(s)
- Yuya Tada
- Department of Environment and Public Health, National Institute for Minamata Disease, Kumamoto, Japan
| | - Kohji Marumoto
- Department of Environment and Public Health, National Institute for Minamata Disease, Kumamoto, Japan
| | - Akinori Takeuchi
- Center for Environmental Measurement and Analysis, National Institute for Environmental Studies, Ibaraki, Japan
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25
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Pellerin A, Antler G, Marietou A, Turchyn AV, Jørgensen BB. The effect of temperature on sulfur and oxygen isotope fractionation by sulfate reducing bacteria (Desulfococcus multivorans). FEMS Microbiol Lett 2020; 367:5817845. [PMID: 32267916 DOI: 10.1093/femsle/fnaa061] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 04/04/2020] [Indexed: 11/14/2022] Open
Abstract
Temperature influences microbiological growth and catabolic rates. Between 15 and 35 °C the growth rate and cell specific sulfate reduction rate of the sulfate reducing bacterium Desulfococcus multivorans increased with temperature. Sulfur isotope fractionation during sulfate reduction decreased with increasing temperature from 27.2 ‰ at 15 °C to 18.8 ‰ at 35 °C which is consistent with a decreasing reversibility of the metabolic pathway as the catabolic rate increases. Oxygen isotope fractionation, in contrast, decreased between 15 and 25 °C and then increased again between 25 and 35 °C, suggesting increasing reversibility in the first steps of the sulfate reducing pathway at higher temperatures. This points to a decoupling in the reversibility of sulfate reduction between the steps from the uptake of sulfate into the cell to the formation of sulfite, relative to the whole pathway from sulfate to sulfide. This observation is consistent with observations of increasing sulfur isotope fractionation when sulfate reducing bacteria are living near their upper temperature limit. The oxygen isotope decoupling may be a first signal of changing physiology as the bacteria cope with higher temperatures.
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Affiliation(s)
- André Pellerin
- Center for Geomicrobiology, Ny Munkegade 116, Aarhus C 8000, Aarhus University, Department of Bioscience, Denmark.,Department of Geological and Environmental Sciences, Ben-Gurion University of the Negev, P. O. Box 653, Beer-Sheva 84105, Israel
| | - Gilad Antler
- Department of Geological and Environmental Sciences, Ben-Gurion University of the Negev, P. O. Box 653, Beer-Sheva 84105, Israel.,The Interuniversity Institute for Marine Sciences of Eilat, PO Box 469, Eilat 88103, Israel
| | - Angeliki Marietou
- Center for Geomicrobiology, Ny Munkegade 116, Aarhus C 8000, Aarhus University, Department of Bioscience, Denmark
| | - Alexandra V Turchyn
- Cambridge University, Downing Street, Cambridge, CB2 3EQ, Departement of Earth Sciences, Cambridge, UK
| | - Bo Barker Jørgensen
- Center for Geomicrobiology, Ny Munkegade 116, Aarhus C 8000, Aarhus University, Department of Bioscience, Denmark
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26
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Ozuolmez D, Moore EK, Hopmans EC, Sinninghe Damsté JS, Stams AJM, Plugge CM. Butyrate Conversion by Sulfate-Reducing and Methanogenic Communities from Anoxic Sediments of Aarhus Bay, Denmark. Microorganisms 2020; 8:microorganisms8040606. [PMID: 32331369 PMCID: PMC7232339 DOI: 10.3390/microorganisms8040606] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 04/17/2020] [Accepted: 04/19/2020] [Indexed: 11/29/2022] Open
Abstract
The conventional perception that the zone of sulfate reduction and methanogenesis are separated in high- and low-sulfate-containing marine sediments has recently been changed by studies demonstrating their co-occurrence in sediments. The presence of methanogens was linked to the presence of substrates that are not used by sulfate reducers. In the current study, we hypothesized that both groups can co-exist, consuming common substrates (H2 and/or acetate) in sediments. We enriched butyrate-degrading communities in sediment slurries originating from the sulfate, sulfate–methane transition, and methane zone of Aarhus Bay, Denmark. Sulfate was added at different concentrations (0, 3, 20 mM), and the slurries were incubated at 10 °C and 25 °C. During butyrate conversion, sulfate reduction and methanogenesis occurred simultaneously. The syntrophic butyrate degrader Syntrophomonas was enriched both in sulfate-amended and in sulfate-free slurries, indicating the occurrence of syntrophic conversions at both conditions. Archaeal community analysis revealed a dominance of Methanomicrobiaceae. The acetoclastic Methanosaetaceae reached high relative abundance in the absence of sulfate, while presence of acetoclastic Methanosarcinaceae was independent of the sulfate concentration, temperature, and the initial zone of the sediment. This study shows that there is no vertical separation of sulfate reducers, syntrophs, and methanogens in the sediment and that they all participate in the conversion of butyrate.
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Affiliation(s)
- Derya Ozuolmez
- Laboratory of Microbiology, Wageningen University & Research, 6708 WE Wageningen, The Netherlands; (D.O.); (A.J.M.S.)
| | - Elisha K. Moore
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, and Utrecht University, P.O. Box 59, 1790 AB Den Burg, The Netherlands; (E.K.M.); (E.C.H.); (J.S.S.D.)
- Department of Environmental Science, Rowan University, 201 Mullica Hill Rd, Glassboro, NJ 08028, USA
| | - Ellen C. Hopmans
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, and Utrecht University, P.O. Box 59, 1790 AB Den Burg, The Netherlands; (E.K.M.); (E.C.H.); (J.S.S.D.)
| | - Jaap S. Sinninghe Damsté
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, and Utrecht University, P.O. Box 59, 1790 AB Den Burg, The Netherlands; (E.K.M.); (E.C.H.); (J.S.S.D.)
- Faculty of Geosciences, Utrecht University, P.O. Box 80.021, 3508 TA Utrecht, The Netherlands
| | - Alfons J. M. Stams
- Laboratory of Microbiology, Wageningen University & Research, 6708 WE Wageningen, The Netherlands; (D.O.); (A.J.M.S.)
| | - Caroline M. Plugge
- Laboratory of Microbiology, Wageningen University & Research, 6708 WE Wageningen, The Netherlands; (D.O.); (A.J.M.S.)
- Correspondence: ; Tel.: +31-317-483116
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27
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Propionate Converting Anaerobic Microbial Communities Enriched from Distinct Biogeochemical Zones of Aarhus Bay, Denmark under Sulfidogenic and Methanogenic Conditions. Microorganisms 2020; 8:microorganisms8030394. [PMID: 32168975 PMCID: PMC7143418 DOI: 10.3390/microorganisms8030394] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 03/10/2020] [Accepted: 03/10/2020] [Indexed: 11/17/2022] Open
Abstract
The relationship between predominant physiological types of prokaryotes in marine sediments and propionate degradation through sulfate reduction, fermentation, and methanogenesis was studied in marine sediments. Propionate conversion was assessed in slurries containing sediment from three different biogeochemical zones of Aarhus Bay, Denmark. Sediment slurries were amended with 0, 3, or 20 mM sulfate and incubated at 25 °C and 10 °C for 514-571 days. Methanogenesis in the sulfate zone and sulfate reduction in the methane zone slurries was observed. Both processes occurred simultaneously in enrichments originating from samples along the whole sediment. Bacterial community analysis revealed the dominance of Desulfobacteraceae and Desulfobulbaceae members in sulfate-amended slurries incubated at 25°C and 10°C. Cryptanaerobacter belonging to the Peptococcaceae family dominated sulfate-free methanogenic slurries at 25°C, whereas bacteria related to Desulfobacteraceae were dominant at 10°C. Archaeal community analysis revealed the prevalence of different genera belonging to Methanomicrobiales in slurries incubated at different temperatures and amended with different sulfate concentrations. Methanosarcinaceae were only detected in the absence of sulfate. In summary, Aarhus Bay sediment zones contain sulfate reducers, syntrophs, and methanogens interacting with each other in the conversion of propionate. Our results indicate that in Aarhus Bay sediments, Cryptanaerobacter degraded propionate in syntrophic association with methanogens.
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28
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Bruckberger MC, Morgan MJ, Bastow TP, Walsh T, Prommer H, Mukhopadhyay A, Kaksonen AH, Davis GB, Puzon GJ. Investigation into the microbial communities and associated crude oil-contamination along a Gulf War impacted groundwater system in Kuwait. WATER RESEARCH 2020; 170:115314. [PMID: 31835139 DOI: 10.1016/j.watres.2019.115314] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 11/14/2019] [Accepted: 11/15/2019] [Indexed: 06/10/2023]
Abstract
During the First Gulf War (1991) a large number of oil wells were destroyed and oil fires subsequently extinguished with seawater. As a result Kuwait's sparse fresh groundwater resources were severely contaminated with crude oil. Since then limited research has focused on the microbial community ecology of the groundwater and their impact on the associated contamination. Here, the microbial community ecology (bacterial, archaeal and eukaryotic) and how it relates to the characteristics of the hydrocarbon contaminants were examined for the first time since the 1991 event. This study was conducted using 15 wells along the main groundwater flow direction and detected several potential hydrocarbon degrading microorganisms such as Hyphomicrobiaceae, Porphyromonadaceae and Eurotiomycetes. The beta diversity of the microbial communities correlated significantly with total petroleum hydrocarbon (TPH) concentrations and salinity. The TPH consisted mainly of polar compounds present as an unresolved complex mixture (UCM) of a highly recalcitrant nature. Based on the proportions of TPH to dissolved organic carbon (DOC), the results indicate that some minor biodegradation has occurred within highly contaminated aquifer zones. However, overall the results from this study suggest that the observed variations in TPH concentrations among the sampled wells are mainly induced by mixing/dilution with pristine groundwater rather than by biodegradation of the contaminants. The findings make an important contribution to better understand the fate of the groundwater pollution in Kuwait, with important implications for the design of future remediation efforts.
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Affiliation(s)
- Melanie C Bruckberger
- CSIRO Land and Water, Private Bag No. 5, Wembley, Western Australia, 6913, Australia; University of Western Australia, School of Agriculture and Environment, 35 Stirling Hwy, Crawley, WA, 6009, Australia
| | | | - Trevor P Bastow
- CSIRO Land and Water, Private Bag No. 5, Wembley, Western Australia, 6913, Australia
| | - Tom Walsh
- CSIRO Land and Water, Canberra, ACT, Australia
| | - Henning Prommer
- CSIRO Land and Water, Private Bag No. 5, Wembley, Western Australia, 6913, Australia; University of Western Australia, School of Earth Sciences, 35 Stirling Hwy, Crawley, WA, 6009, Australia
| | - Amitabha Mukhopadhyay
- Water Research Center, Kuwait Institute for Scientific Research, P.O. Box 24885, 13109, Safat, Kuwait
| | - Anna H Kaksonen
- CSIRO Land and Water, Private Bag No. 5, Wembley, Western Australia, 6913, Australia; School of Biomedical Sciences, University of Western Australia, 35 Stirling Highway, Crawley, Western Australia, 6009, Australia
| | - Greg B Davis
- CSIRO Land and Water, Private Bag No. 5, Wembley, Western Australia, 6913, Australia
| | - Geoffrey J Puzon
- CSIRO Land and Water, Private Bag No. 5, Wembley, Western Australia, 6913, Australia.
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29
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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: 19] [Impact Index Per Article: 4.8] [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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30
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Rylkova OA, Gulin SB, Pimenov NV. Determination of the Total Microbial Abundance in Black Sea Bottom Sediments Using Flow Cytometry. Microbiology (Reading) 2020. [DOI: 10.1134/s0026261719060158] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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31
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Polinski JM, Bucci JP, Gasser M, Bodnar AG. Metabarcoding assessment of prokaryotic and eukaryotic taxa in sediments from Stellwagen Bank National Marine Sanctuary. Sci Rep 2019; 9:14820. [PMID: 31616016 PMCID: PMC6794287 DOI: 10.1038/s41598-019-51341-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 09/27/2019] [Indexed: 12/30/2022] Open
Abstract
Stellwagen Bank National Marine Sanctuary (SBNMS) in the Gulf of Maine is a historic fishing ground renowned for remarkable productivity. Biodiversity conservation is a key management priority for SBNMS and yet data on the diversity of microorganisms, both prokaryotic and eukaryotic, is lacking. This study utilized next generation sequencing to characterize sedimentary communities within SBNMS at three sites over two seasons. Targeting 16S and 18S small subunit (SSU) rRNA genes and fungal Internal Transcribed Spacer (ITS) rDNA sequences, samples contained high diversity at all taxonomic levels and identified 127 phyla, including 115 not previously represented in the SBNMS Management Plan and Environmental Assessment. A majority of the diversity was bacterial, with 59 phyla, but also represented were nine Archaea, 18 Animalia, 14 Chromista, eight Protozoa, two Plantae, and 17 Fungi phyla. Samples from different sites and seasons were dominated by the same high abundance organisms but displayed considerable variation in rare taxa. The levels of biodiversity seen on this small spatial scale suggest that benthic communities of this area support a diverse array of micro- and macro-organisms, and provide a baseline for future studies to assess changes in community structure in response to rapid warming in the Gulf of Maine.
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Affiliation(s)
| | - John P Bucci
- Gloucester Marine Genomics Institute, Inc. Gloucester, Massachusetts, USA.,School of Marine Science and Ocean Engineering, University of New Hampshire, Durham, New Hampshire, USA
| | - Mark Gasser
- Gloucester Marine Genomics Institute, Inc. Gloucester, Massachusetts, USA.,The Johns Hopkins Applied Physics Laboratory, Laurel, Maryland, USA
| | - Andrea G Bodnar
- Gloucester Marine Genomics Institute, Inc. Gloucester, Massachusetts, USA
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32
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Cupit C, Lomstein BA, Kjeldsen KU. Contrasting community composition of endospores and vegetative Firmicutes in a marine sediment suggests both endogenous and exogenous sources of endospore accumulation. ENVIRONMENTAL MICROBIOLOGY REPORTS 2019; 11:352-360. [PMID: 30043505 DOI: 10.1111/1758-2229.12679] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 07/09/2018] [Accepted: 07/12/2018] [Indexed: 06/08/2023]
Abstract
Bacterial endospores are highly abundant in marine sediments, but their taxonomic identity and ecology is largely unknown. We selectively extracted DNA from endospores and vegetative cells and sequenced 16S rRNA genes to characterize the composition of the endospore and vegetative Firmicutes communities in the sediment and water column of Aarhus Bay (Denmark). The endospore community in the sediment was dominated by the families Bacillaceae, Lachnospiraceae, Clostridiaceae and Ruminoccocaceae. These families were also represented in the vegetative community in the sediment and the endospore community in the water column. OTUs of high relative abundance in the endospore community were also represented in the vegetative Firmicutes community. Other OTUs were exclusively found in the endospore communities. This suggests that endospores accumulate in marine sediments due to passive deposition from the water column and sporulation of vegetative cells in the sediment. Some OTUs were detected in the endospore community of the water column and the vegetative community the sediment indicating that endospores deposited from the water column may germinate upon burial/deposition in the sediment. We provide novel insight into the composition of endospore communities in marine sediments and highlight their role in microbial dispersal and as a seed bank in subsurface sediments.
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Affiliation(s)
- Carina Cupit
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Bente Aagaard Lomstein
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Kasper Urup Kjeldsen
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
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33
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Petro C, Zäncker B, Starnawski P, Jochum LM, Ferdelman TG, Jørgensen BB, Røy H, Kjeldsen KU, Schramm A. Marine Deep Biosphere Microbial Communities Assemble in Near-Surface Sediments in Aarhus Bay. Front Microbiol 2019; 10:758. [PMID: 31031732 PMCID: PMC6474314 DOI: 10.3389/fmicb.2019.00758] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 03/26/2019] [Indexed: 11/30/2022] Open
Abstract
Analyses of microbial diversity in marine sediments have identified a core set of taxa unique to the marine deep biosphere. Previous studies have suggested that these specialized communities are shaped by processes in the surface seabed, in particular that their assembly is associated with the transition from the bioturbated upper zone to the nonbioturbated zone below. To test this hypothesis, we performed a fine-scale analysis of the distribution and activity of microbial populations within the upper 50 cm of sediment from Aarhus Bay (Denmark). Sequencing and qPCR were combined to determine the depth distributions of bacterial and archaeal taxa (16S rRNA genes) and sulfate-reducing microorganisms (SRM) (dsrB gene). Mapping of radionuclides throughout the sediment revealed a region of intense bioturbation at 0-6 cm depth. The transition from bioturbated sediment to the subsurface below (7 cm depth) was marked by a shift from dominant surface populations to common deep biosphere taxa (e.g., Chloroflexi and Atribacteria). Changes in community composition occurred in parallel to drops in microbial activity and abundance caused by reduced energy availability below the mixed sediment surface. These results offer direct evidence for the hypothesis that deep subsurface microbial communities present in Aarhus Bay mainly assemble already centimeters below the sediment surface, below the bioturbation zone.
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Affiliation(s)
- Caitlin Petro
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Birthe Zäncker
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Piotr Starnawski
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Lara M. Jochum
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Timothy G. Ferdelman
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Bo Barker Jørgensen
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Hans Røy
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Kasper U. Kjeldsen
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Andreas Schramm
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
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34
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Cox TL, Gan HM, Moreau JW. Seawater recirculation through subducting sediments sustains a deeply buried population of sulfate-reducing bacteria. GEOBIOLOGY 2019; 17:172-184. [PMID: 30474350 DOI: 10.1111/gbi.12324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 10/10/2018] [Indexed: 06/09/2023]
Abstract
Subseafloor sulfate concentrations typically decrease with depth as this electron acceptor is consumed by respiring microorganisms. However, studies show that seawater can flow through hydraulically conductive basalt to deliver sulfate upwards into deeply buried overlying sediments. Our previous work on IODP Site C0012A (Nankai Trough, Japan) revealed that recirculation of sulfate through the subducting Philippine Sea Plate stimulated microbial activity near the sediment-basement interface (SBI). Here, we describe the microbial ecology, phylogeny, and energetic requirements of population of aero-tolerant sulfate-reducing bacteria in the deep subseafloor. We identified dissimilatory sulfite reductase gene (dsr) sequences 93% related to oxygen-tolerant Desulfovibrionales species across all reaction zones while no SRB were detected in drilling fluid control samples. Pore fluid chemistry revealed low concentrations of methane (<0.25 mM), while hydrogen levels were consistent with active bacterial sulfate reduction (0.51-1.52 nM). Solid phase total organic carbon (TOC) was also considerably low in these subseafloor sediments. Our results reveal the phylogenetic diversity, potential function, and physiological tolerance of a community of sulfate-reducing bacteria living at ~480 m below subducting seafloor.
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Affiliation(s)
- Toni L Cox
- School of Earth Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Han Ming Gan
- School of Life and Environmental Sciences, Centre for Integrative Ecology, Deakin University, Victoria, Australia
| | - John W Moreau
- School of Earth Sciences, The University of Melbourne, Parkville, Victoria, Australia
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35
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Beaton D, Pelletier P, Goulet RR. Microbial Degradation of Cellulosic Material and Gas Generation: Implications for the Management of Low- and Intermediate-Level Radioactive Waste. Front Microbiol 2019; 10:204. [PMID: 30814985 PMCID: PMC6381020 DOI: 10.3389/fmicb.2019.00204] [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: 09/26/2018] [Accepted: 01/24/2019] [Indexed: 11/13/2022] Open
Abstract
Deep geologic repositories (DGR) in Canada are designed to contain and isolate low- and intermediate-level radioactive waste. Microbial degradation of the waste potentially produces methane, carbon dioxide and hydrogen gas. The generation of these gases increase rock cavity pressure and limit water ingress which delays the mobility of water soluble radionuclides. The objective of this study was to measure gas pressure and composition over 7 years in experiments containing cellulosic material with various starting conditions relevant to a DGR and to identify micro-organisms generating gas. For this purpose, we conducted experiments in glass bottles containing (1) wet cellulosic material, (2) wet cellulosic material with compost Maker, and (3) wet cellulosic material with compost Accelerator. Results demonstrated that compost accelerated the pressure build-up in the containers and that methane gas was produced in one experiment with compost and one experiment without compost because the pH remained neutral for the duration of the 464 days experiment. Methane was not formed in the other experiment because the pH became acidic. Once the pressure became similar in all containers after 464 days, we then monitored gas pressure and composition in glass bottle containing wet cellulosic material in (1) acidic conditions, (2) neutral conditions, and (3) with an enzyme that accelerated degradation of cellulose over 1965 days. In these experiments, acetogenic bacteria degraded cellulose and produced acetic acid, which acidity suppressed methane production. Microbial community analyses suggested a diverse community of archaea, bacteria and fungi actively degrading cellulose. DNA analyses also confirmed the presence of methanogens and acetogens in our experiments. This study suggests that methane gas will be generated in DGRs if pH remains neutral. However, our results showed that microbial degradation of cellulose not only generated gas, but also generated acidity. This finding is important as acids can limit bentonite swelling and potentially degrade cement and rock barriers, thus this requires consideration in the safety case as appropriate.
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Affiliation(s)
- Danielle Beaton
- Chalk River Laboratories, Canadian Nuclear Laboratories, Chalk River, ON, Canada
- Orillia Soldiers’ Memorial Hospital, Ottawa, ON, Canada
| | | | - Richard R. Goulet
- Orillia Soldiers’ Memorial Hospital, Ottawa, ON, Canada
- Canadian Nuclear Safety Commission, Ottawa, ON, Canada
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36
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Bradley JA, Amend JP, LaRowe DE. Survival of the fewest: Microbial dormancy and maintenance in marine sediments through deep time. GEOBIOLOGY 2019; 17:43-59. [PMID: 30248245 PMCID: PMC6585783 DOI: 10.1111/gbi.12313] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 07/17/2018] [Accepted: 08/21/2018] [Indexed: 06/01/2023]
Abstract
Microorganisms buried in marine sediments are known to endure starvation over geologic timescales. However, the mechanisms of how these microorganisms cope with prolonged energy limitation is unknown and therefore yet to be captured in a quantitative framework. Here, we present a novel mathematical model that considers (a) the physiological transitions between the active and dormant states of microorganisms, (b) the varying requirement for maintenance power between these phases, and (c) flexibility in the provenance (i.e., source) of energy from exogenous and endogenous catabolism. The model is applied to sediments underlying the oligotrophic South Pacific Gyre where microorganisms endure ultra-low fluxes of energy for tens of millions of years. Good fits between model simulations and measurements of cellular carbon and organic carbon concentrations are obtained and are interpreted as follows: (a) the unfavourable microbial habitat in South Pacific Gyre sediments triggers rapid mortality and a transition to dormancy; (b) there is minimal biomass growth, and organic carbon consumption is dominated by catabolism to support maintenance activities rather than new biomass synthesis; (c) the amount of organic carbon that microorganisms consume for maintenance activities is equivalent to approximately 2% of their carbon biomass per year; and (d) microorganisms must rely solely on exogenous rather than endogenous catabolism to persist in South Pacific Gyre sediments over long timescales. This leads us to the conclusion that under oligotrophic conditions, the fitness of an organism is determined by its ability to simply stay alive, rather than to grow. This modelling framework is designed to be flexible for application to other sites and habitats, and thus serves as a new quantitative tool for determining the habitability of and an ultimate limit for life in any environment.
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Affiliation(s)
- James A. Bradley
- Department of Earth SciencesUniversity of Southern CaliforniaLos AngelesCalifornia
| | - Jan P. Amend
- Department of Earth SciencesUniversity of Southern CaliforniaLos AngelesCalifornia
- Department of Biological SciencesUniversity of Southern CaliforniaLos AngelesCalifornia
| | - Douglas E. LaRowe
- Department of Earth SciencesUniversity of Southern CaliforniaLos AngelesCalifornia
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37
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Duarte AG, Catarino T, White GF, Lousa D, Neukirchen S, Soares CM, Sousa FL, Clarke TA, Pereira IAC. An electrogenic redox loop in sulfate reduction reveals a likely widespread mechanism of energy conservation. Nat Commun 2018; 9:5448. [PMID: 30575735 PMCID: PMC6303296 DOI: 10.1038/s41467-018-07839-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 11/27/2018] [Indexed: 02/02/2023] Open
Abstract
The bioenergetics of anaerobic metabolism frequently relies on redox loops performed by membrane complexes with substrate- and quinone-binding sites on opposite sides of the membrane. However, in sulfate respiration (a key process in the biogeochemical sulfur cycle), the substrate- and quinone-binding sites of the QrcABCD complex are periplasmic, and their role in energy conservation has not been elucidated. Here we show that the QrcABCD complex of Desulfovibrio vulgaris is electrogenic, as protons and electrons required for quinone reduction are extracted from opposite sides of the membrane, with a H+/e− ratio of 1. Although the complex does not act as a H+-pump, QrcD may include a conserved proton channel leading from the N-side to the P-side menaquinone pocket. Our work provides evidence of how energy is conserved during dissimilatory sulfate reduction, and suggests mechanisms behind the functions of related bacterial respiratory complexes in other bioenergetic contexts. The bacterial complex QrcABCD plays a key role in the bioenergetics of sulfate respiration. Here, Duarte et al. show that this complex is electrogenic, with protons and electrons required for quinone reduction being extracted from opposite sides of the membrane.
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Affiliation(s)
- Américo G Duarte
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | - Teresa Catarino
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal.,Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal
| | - Gaye F White
- Centre for Molecular and Structural Biochemistry, School of Biological Sciences and School of Chemistry, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Diana Lousa
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | - Sinje Neukirchen
- Division of Archaea Biology and Ecogenomics, Department of Ecogenomics and Systems Biology, University of Vienna, Althanstrasse 14 UZA I, 1090, Vienna, Austria
| | - Cláudio M Soares
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | - Filipa L Sousa
- Division of Archaea Biology and Ecogenomics, Department of Ecogenomics and Systems Biology, University of Vienna, Althanstrasse 14 UZA I, 1090, Vienna, Austria
| | - Thomas A Clarke
- Centre for Molecular and Structural Biochemistry, School of Biological Sciences and School of Chemistry, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Inês A C Pereira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal.
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38
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Authigenic and Detrital Minerals in Peat Environment of Vasyugan Swamp, Western Siberia. MINERALS 2018. [DOI: 10.3390/min8110500] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Studies of mineral-forming processes in modern peat bogs can shed light on metal concentrations and their cycling in similar environments, especially in geological paleoanalogs. In terms of the mineralogical and geochemical evolution of peat bog environments, the Vasyugan Swamp in Western Siberia is a unique scientific object. Twelve peat samples were collected from the Vasyugan Swamp up to the depth of 275 cm at 25 cm intervals. The studied peat deposit section is represented by oligotrophic (0–100 cm), mesotrophic (100–175 cm), and eutrophic (175–275 cm) peat, and this is underlain by basal sediments (from 275 cm). About 30 minerals were detected using scanning electron microscopy (SEM), X-ray diffraction (XRD), and Raman spectroscopy. The observed minerals are divided into detrital, clay, and authigenic phases. The detrital minerals found included quartz, feldspar, ilmenite, rutile, magnetite, zircon, and monazite. When passing from basal to oligotrophic bog sediments, the clay minerals changed from illite-smectite to kaolinite. Authigenic minerals are represented by carbonates (calcite and dolomite), iron (hydro-)oxides, galena, sphalerite, pyrite, chalcopyrite, Zn-Pb-S mineral, barite, baritocelestine, celestine, tetrahedrite, cassiterite, REE phosphate, etc. The regular distribution of mineral inclusions in peat is associated with the (bio)geochemical evolution of the environment. The formation of authigenic Zn, Pb and Sb sulfides is mainly confined to anaerobic conditions that exist in the eutrophic peat and basal sediments. The maximum amount of pyrite is associated with the interval of 225–250 cm, which is the zone of transition from basal sediments to eutrophic peat. The formation of carbonate minerals and the decreasing concentration of clay in the association with local sulfide formation (galena, sphalerite, chalcopyrite, stibnite) begins above this interval. The peak of specific carbonation appears in the 125–150 cm interval of the mesotrophic peat, which is characterized by pH 4.9–4.5 of pore water. Kaolinite is the dominant clay mineral in the oligotrophic peat. Gypsum, galena, chalcopyrite, sphalerite, and relicts of carbonate are noted in association with kaolinite. Changes in oxygen concentrations are reflected in newly formed mineral associations in corresponding intervals of the peat. This can be explained by the activity of microbiological processes such as the anaerobic oxidation of methane (AOM) and bacterial sulfate reduction (BSR), expressed in specific carbonatization (100–225 cm) and sulfidization (175–250 cm), respectively.
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Jochum LM, Schreiber L, Marshall IPG, Jørgensen BB, Schramm A, Kjeldsen KU. Single-Cell Genomics Reveals a Diverse Metabolic Potential of Uncultivated Desulfatiglans-Related Deltaproteobacteria Widely Distributed in Marine Sediment. Front Microbiol 2018; 9:2038. [PMID: 30233524 PMCID: PMC6129605 DOI: 10.3389/fmicb.2018.02038] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 08/13/2018] [Indexed: 11/13/2022] Open
Abstract
Desulfatiglans-related organisms comprise one of the most abundant deltaproteobacterial lineages in marine sediments where they occur throughout the sediment column in a gradient of increasing sulfate and organic carbon limitation with depth. Characterized Desulfatiglans isolates are dissimilatory sulfate reducers able to grow by degrading aromatic hydrocarbons. The ecophysiology of environmental Desulfatiglans-populations is poorly understood, however, possibly utilization of aromatic compounds may explain their predominance in marine subsurface sediments. We sequenced and analyzed seven Desulfatiglans-related single-cell genomes (SAGs) from Aarhus Bay sediments to characterize their metabolic potential with regard to aromatic compound degradation and energy metabolism. The average genome assembly size was 1.3 Mbp and completeness estimates ranged between 20 and 50%. Five of the SAGs (group 1) originated from the sulfate-rich surface part of the sediment while two (group 2) originated from sulfate-depleted subsurface sediment. Based on 16S rRNA gene amplicon sequencing group 2 SAGs represent the more frequent types of Desulfatiglans-populations in Aarhus Bay sediments. Genes indicative of aromatic compound degradation could be identified in both groups, but the two groups were metabolically distinct with regard to energy conservation. Group 1 SAGs carry a full set of genes for dissimilatory sulfate reduction, whereas the group 2 SAGs lacked any genetic evidence for sulfate reduction. The latter may be due to incompleteness of the SAGs, but as alternative energy metabolisms group 2 SAGs carry the genetic potential for growth by acetogenesis and fermentation. Group 1 SAGs encoded reductive dehalogenase genes, allowing them to access organohalides and possibly conserve energy by their reduction. Both groups possess sulfatases unlike their cultured relatives allowing them to utilize sulfate esters as source of organic carbon and sulfate. In conclusion, the uncultivated marine Desulfatiglans populations are metabolically diverse, likely reflecting different strategies for coping with energy and sulfate limitation in the subsurface seabed.
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Affiliation(s)
- Lara M Jochum
- Center for Geomicrobiology, Section for Microbiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Lars Schreiber
- Center for Geomicrobiology, Section for Microbiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Ian P G Marshall
- Center for Geomicrobiology, Section for Microbiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Bo B Jørgensen
- Center for Geomicrobiology, Section for Microbiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Andreas Schramm
- Center for Geomicrobiology, Section for Microbiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Kasper U Kjeldsen
- Center for Geomicrobiology, Section for Microbiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
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Nielsen G, Hatam I, Abuan KA, Janin A, Coudert L, Blais JF, Mercier G, Baldwin SA. Semi-passive in-situ pilot scale bioreactor successfully removed sulfate and metals from mine impacted water under subarctic climatic conditions. WATER RESEARCH 2018; 140:268-279. [PMID: 29723816 DOI: 10.1016/j.watres.2018.04.035] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 03/21/2018] [Accepted: 04/15/2018] [Indexed: 06/08/2023]
Abstract
Mine drainage contaminated with metals is a major environmental threat since it is a source of water pollution with devastating effects on aquatic ecosystems. Conventional active treatment technologies are prohibitively expensive and so there is increasing demand to develop reliable, cost-effective and sustainable passive or semi-passive treatment. These are promising alternatives since they leverage the metabolism of microorganisms native to the disturbed site at in situ or close to in situ conditions. Since this is a biological approach, it is not clear if semi-passive treatment would be effective in remote locations with extremely cold weather such as at mines in the subarctic. In this study we tested the hypothesis that sulfate-reducing bacteria, which are microorganisms that promote metal precipitation, exist in subarctic mine environments and their activity can be stimulated by adding a readily available carbon source. An experiment was setup at a closed mine in the Yukon Territory, Canada, where leaching of Zn and Cd occurs. To test if semi-passive treatment could precipitate these metals and prevent further leaching from waste rock, molasses as a carbon source was added to anaerobic bioreactors mimicking the belowground in-situ conditions. Microbial community analysis confirmed that sulfate-reducing bacteria became enriched in the bioreactors upon addition of molasses. The population composition remained fairly stable over the 14 month operating period despite temperature shifts from 17 to 5 °C. Sulfate reduction functionality was confirmed by quantification of the gene for dissimilatory sulfite reductase. Metals were removed from underground mine drainage fed into the bioreactors with Zn removal efficiency varying between 20.9% in winter and 89.3% in summer, and Cd removal efficiency between 39% in winter and 90.5% in summer. This study demonstrated that stimulation of native SRB in MIW was possible and that in situ semi-passive treatment can be effective in removing metals despite the cold climate.
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Affiliation(s)
- Guillaume Nielsen
- Institut national de la recherche scientifique (Centre Eau, Terre et Environnement), Université du Québec, 490 rue de la Couronne, Québec, QC G1K 9A9, Canada.
| | - Ido Hatam
- Chemical and Biological Engineering, UBC Vancouver Campus 2360 East Mall, Vancouver, BC V6T 1Z3, Canada
| | - Karl A Abuan
- Chemical and Biological Engineering, UBC Vancouver Campus 2360 East Mall, Vancouver, BC V6T 1Z3, Canada
| | - Amelie Janin
- Yukon Research Center, 500 College Drive, PO Box 2799, Whitehorse, YT Y1A 5K4, Canada
| | - Lucie Coudert
- Institut national de la recherche scientifique (Centre Eau, Terre et Environnement), Université du Québec, 490 rue de la Couronne, Québec, QC G1K 9A9, Canada
| | - Jean Francois Blais
- Institut national de la recherche scientifique (Centre Eau, Terre et Environnement), Université du Québec, 490 rue de la Couronne, Québec, QC G1K 9A9, Canada
| | - Guy Mercier
- Institut national de la recherche scientifique (Centre Eau, Terre et Environnement), Université du Québec, 490 rue de la Couronne, Québec, QC G1K 9A9, Canada
| | - Susan A Baldwin
- Chemical and Biological Engineering, UBC Vancouver Campus 2360 East Mall, Vancouver, BC V6T 1Z3, Canada.
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Katayama T, Yoshioka H, Yamanaka T, Takeuchi M, Muramoto Y, Usami J, Ikeda H, Sakata S. Microbial community structure in deep natural gas-bearing aquifers subjected to sulfate-containing fluid injection. J Biosci Bioeng 2018; 127:45-51. [PMID: 30082219 DOI: 10.1016/j.jbiosc.2018.06.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 06/15/2018] [Accepted: 06/18/2018] [Indexed: 10/28/2022]
Abstract
In the natural gas field located in central Japan, high concentrations of natural gases and iodide ions are dissolved in formation water and commercially produced in deep aquifers. In the iodine recovery process, the produced formation water is amended with sulfate, and this fluid is injected into gas-bearing aquifers, which may lead to infrastructure corrosion by hydrogen sulfide. In this study, we examined the microbial community in aquifers subjected to sulfate-containing fluid injection. Formation water samples were collected from production wells located at different distances from the injection wells. The chemical analysis showed that the injection fluid contained oxygen, nitrate, nitrite and sulfate, in contrast to the formation water, which had previously been shown to be depleted in these components. Sulfur isotopic analysis indicated that sulfate derived from the injection fluid was present in the sample collected from near the injection wells. Quantitative and sequencing analysis of dissimilatory sulfite reductase and 16S rRNA genes revealed that sulfate-reducing bacteria (SRB), sulfur-oxidizing bacteria, and anaerobic methanotrophic archaea (ANME) in the wells located near injection wells were more abundant than those in wells located far from the injection wells, suggesting that fluid injection stimulated these microorganisms through the addition of oxygen, nitrate, nitrite and sulfate to the methane-rich aquifers. The predominant taxa were assigned to the ANME-2 group, its sulfate-reducing partner SEEP-SRB1 cluster and sulfur-oxidizing Epsilonproteobacteria. These results provide important insights for future studies to support the development of natural gas and iodine resources in Japan.
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Affiliation(s)
- Taiki Katayama
- Institute for Geo-Resources and Environment, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8567, Japan
| | - Hideyoshi Yoshioka
- Institute for Geo-Resources and Environment, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8567, Japan.
| | - Toshiro Yamanaka
- Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Tsushima-Naka, Kita-ku, Okayama 700-8530, Japan
| | - Mio Takeuchi
- Institute for Geo-Resources and Environment, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8567, Japan
| | - Yoshiyuki Muramoto
- Kanto Natural Gas Development Co., Ltd., 661 Mobara, Mobara City, Chiba 297-8550, Japan
| | - Jun Usami
- Kanto Natural Gas Development Co., Ltd., 661 Mobara, Mobara City, Chiba 297-8550, Japan
| | - Hidefumi Ikeda
- Kanto Natural Gas Development Co., Ltd., 661 Mobara, Mobara City, Chiba 297-8550, Japan
| | - Susumu Sakata
- Institute for Geo-Resources and Environment, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8567, Japan
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Bryukhanov AL, Vlasova MA, Malakhova TV, Perevalova AA, Pimenov NV. Phylogenetic Diversity of the Sulfur Cycle Bacteria in the Bottom Sediments of the Chersonesus Bay. Microbiology (Reading) 2018. [DOI: 10.1134/s0026261718030025] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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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: 21] [Impact Index Per Article: 3.5] [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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44
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Isoprenoid Quinones Resolve the Stratification of Redox Processes in a Biogeochemical Continuum from the Photic Zone to Deep Anoxic Sediments of the Black Sea. Appl Environ Microbiol 2018. [PMID: 29523543 DOI: 10.1128/aem.02736-17] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The stratified water column of the Black Sea serves as a model ecosystem for studying the interactions of microorganisms with major biogeochemical cycles. Here, we provide detailed analysis of isoprenoid quinones to study microbial redox processes in the ocean. In a continuum from the photic zone through the chemocline into deep anoxic sediments of the southern Black Sea, diagnostic quinones and inorganic geochemical parameters indicate niche segregation between redox processes and corresponding shifts in microbial community composition. Quinones specific for oxygenic photosynthesis and aerobic respiration dominate oxic waters, while quinones associated with thaumarchaeal ammonia oxidation and bacterial methanotrophy, respectively, dominate a narrow interval in suboxic waters. Quinone distributions indicate highest metabolic diversity within the anoxic zone, with anoxygenic photosynthesis being a major process in its photic layer. In the dark anoxic layer, quinone profiles indicate the occurrence of bacterial sulfur and nitrogen cycling, archaeal methanogenesis, and archaeal methanotrophy. Multiple novel ubiquinone isomers, possibly originating from unidentified intra-aerobic anaerobes, occur in this zone. The respiration modes found in the anoxic zone continue into shallow subsurface sediments, but quinone abundances rapidly decrease within the upper 50 cm below the sea floor, reflecting the transition to lower energy availability. In the deep subseafloor sediments, quinone distributions and geochemical profiles indicate archaeal methanogenesis/methanotrophy and potentially bacterial fermentative metabolisms. We observed that sedimentary quinone distributions track lithology, which supports prior hypotheses that deep biosphere community composition and metabolisms are determined by environmental conditions during sediment deposition.IMPORTANCE Microorganisms play crucial roles in global biogeochemical cycles, yet we have only a fragmentary understanding of the diversity of microorganisms and their metabolisms, as the majority remains uncultured. Thus, culture-independent approaches are critical for determining microbial diversity and active metabolic processes. In order to resolve the stratification of microbial communities in the Black Sea, we comprehensively analyzed redox process-specific isoprenoid quinone biomarkers in a unique continuous record from the photic zone through the chemocline into anoxic subsurface sediments. We describe an unprecedented quinone diversity that allowed us to detect distinct biogeochemical processes, including oxygenic photosynthesis, archaeal ammonia oxidation, aerobic methanotrophy, and anoxygenic photosynthesis in defined geochemical zones.
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45
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Guo XP, Lu DP, Niu ZS, Feng JN, Chen YR, Tou FY, Liu M, Yang Y. Bacterial community structure in response to environmental impacts in the intertidal sediments along the Yangtze Estuary, China. MARINE POLLUTION BULLETIN 2018; 126:141-149. [PMID: 29421081 DOI: 10.1016/j.marpolbul.2017.11.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 11/02/2017] [Accepted: 11/04/2017] [Indexed: 06/08/2023]
Abstract
This study was designed to investigate the characteristics of bacterial communities in intertidal sediments along the Yangtze Estuary and their responses to environmental factors. The results showed that bacterial abundance was significantly correlated with salinity, SO42- and total organic carbon, while bacterial diversity was significantly correlated with SO42- and total nitrogen. At different taxonomic levels, both the dominant taxa and their abundances varied among the eight samples, with Proteobacteria being the most dominant phylum in general. Cluster analysis revealed that the bacterial community structure was influenced by river runoff and sewerage discharge. Moreover, SO42-, salinity and total phosphorus were the vital environmental factors that influenced the bacterial community structure. Quantitative PCR and sequencing of sulphate-reducing bacteria indicated that the sulphate reduction process occurs frequently in intertidal sediments. These findings are important to understand the microbial ecology and biogeochemical cycles in estuarine environments.
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Affiliation(s)
- Xing-Pan Guo
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographical Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Da-Pei Lu
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographical Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Zuo-Shun Niu
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographical Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Jing-Nan Feng
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographical Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Yu-Ru Chen
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographical Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Fei-Yun Tou
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographical Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Min Liu
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographical Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Yi Yang
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographical Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China; State Key Laboratory of Estuarine and Coastal Research, East China Normal University, 3663 North Zhongshan Road, Shanghai 200062, China.
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Depth Distribution and Assembly of Sulfate-Reducing Microbial Communities in Marine Sediments of Aarhus Bay. Appl Environ Microbiol 2017; 83:AEM.01547-17. [PMID: 28939599 DOI: 10.1128/aem.01547-17] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2017] [Accepted: 09/14/2017] [Indexed: 11/20/2022] Open
Abstract
Most sulfate-reducing microorganisms (SRMs) present in subsurface marine sediments belong to uncultured groups only distantly related to known SRMs, and it remains unclear how changing geochemical zones and sediment depth influence their community structure. We mapped the community composition and abundance of SRMs by amplicon sequencing and quantifying the dsrB gene, which encodes dissimilatory sulfite reductase subunit beta, in sediment samples covering different vertical geochemical zones ranging from the surface sediment to the deep sulfate-depleted subsurface at four locations in Aarhus Bay, Denmark. SRMs were present in all geochemical zones, including sulfate-depleted methanogenic sediment. The biggest shift in SRM community composition and abundance occurred across the transition from bioturbated surface sediments to nonbioturbated sediments below, where redox fluctuations and the input of fresh organic matter due to macrofaunal activity are absent. SRM abundance correlated with sulfate reduction rates determined for the same sediments. Sulfate availability showed a weaker correlation with SRM abundances and no significant correlation with the composition of the SRM community. The overall SRM species diversity decreased with depth, yet we identified a subset of highly abundant community members that persists across all vertical geochemical zones of all stations. We conclude that subsurface SRM communities assemble by the persistence of members of the surface community and that the transition from the bioturbated surface sediment to the unmixed sediment below is a main site of assembly of the subsurface SRM community.IMPORTANCE Sulfate-reducing microorganisms (SRMs) are key players in the marine carbon and sulfur cycles, especially in coastal sediments, yet little is understood about the environmental factors controlling their depth distribution. Our results suggest that macrofaunal activity is a key driver of SRM abundance and community structure in marine sediments and that a small subset of SRM species of high relative abundance in the subsurface SRM community persists from the sulfate-rich surface sediment to sulfate-depleted methanogenic subsurface sediment. More generally, we conclude that SRM communities inhabiting the subsurface seabed assemble by the selective survival of members of the surface community.
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Wasmund K, Mußmann M, Loy A. The life sulfuric: microbial ecology of sulfur cycling in marine sediments. ENVIRONMENTAL MICROBIOLOGY REPORTS 2017; 9:323-344. [PMID: 28419734 PMCID: PMC5573963 DOI: 10.1111/1758-2229.12538] [Citation(s) in RCA: 162] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Almost the entire seafloor is covered with sediments that can be more than 10 000 m thick and represent a vast microbial ecosystem that is a major component of Earth's element and energy cycles. Notably, a significant proportion of microbial life in marine sediments can exploit energy conserved during transformations of sulfur compounds among different redox states. Sulfur cycling, which is primarily driven by sulfate reduction, is tightly interwoven with other important element cycles (carbon, nitrogen, iron, manganese) and therefore has profound implications for both cellular- and ecosystem-level processes. Sulfur-transforming microorganisms have evolved diverse genetic, metabolic, and in some cases, peculiar phenotypic features to fill an array of ecological niches in marine sediments. Here, we review recent and selected findings on the microbial guilds that are involved in the transformation of different sulfur compounds in marine sediments and emphasise how these are interlinked and have a major influence on ecology and biogeochemistry in the seafloor. Extraordinary discoveries have increased our knowledge on microbial sulfur cycling, mainly in sulfate-rich surface sediments, yet many questions remain regarding how sulfur redox processes may sustain the deep-subsurface biosphere and the impact of organic sulfur compounds on the marine sulfur cycle.
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Affiliation(s)
- Kenneth Wasmund
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Research Network “Chemistry meets Microbiology”University of ViennaAlthanstrasse 14ViennaA‐1090Austria
- Austrian Polar Research InstituteViennaAustria
| | - Marc Mußmann
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Research Network “Chemistry meets Microbiology”University of ViennaAlthanstrasse 14ViennaA‐1090Austria
| | - Alexander Loy
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Research Network “Chemistry meets Microbiology”University of ViennaAlthanstrasse 14ViennaA‐1090Austria
- Austrian Polar Research InstituteViennaAustria
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Climate oscillations reflected within the microbiome of Arabian Sea sediments. Sci Rep 2017; 7:6040. [PMID: 28729646 PMCID: PMC5519670 DOI: 10.1038/s41598-017-05590-9] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 06/13/2017] [Indexed: 11/08/2022] Open
Abstract
Selection of microorganisms in marine sediment is shaped by energy-yielding electron acceptors for respiration that are depleted in vertical succession. However, some taxa have been reported to reflect past depositional conditions suggesting they have experienced weak selection after burial. In sediments underlying the Arabian Sea oxygen minimum zone (OMZ), we performed the first metagenomic profiling of sedimentary DNA at centennial-scale resolution in the context of a multi-proxy paleoclimate reconstruction. While vertical distributions of sulfate reducing bacteria and methanogens indicate energy-based selection typical of anoxic marine sediments, 5-15% of taxa per sample exhibit depth-independent stratigraphies indicative of paleoenvironmental selection over relatively short geological timescales. Despite being vertically separated, indicator taxa deposited under OMZ conditions were more similar to one another than those deposited in bioturbated intervals under intervening higher oxygen. The genomic potential for denitrification also correlated with palaeo-OMZ proxies, independent of sediment depth and available nitrate and nitrite. However, metagenomes revealed mixed acid and Entner-Dourdoroff fermentation pathways encoded by many of the same denitrifier groups. Fermentation thus may explain the subsistence of these facultatively anaerobic microbes whose stratigraphy follows changing paleoceanographic conditions. At least for certain taxa, our analysis provides evidence of their paleoenvironmental selection over the last glacial-interglacial cycle.
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Sagheddu V, Patrone V, Miragoli F, Morelli L. Abundance and Diversity of Hydrogenotrophic Microorganisms in the Infant Gut before the Weaning Period Assessed by Denaturing Gradient Gel Electrophoresis and Quantitative PCR. Front Nutr 2017; 4:29. [PMID: 28695121 PMCID: PMC5483434 DOI: 10.3389/fnut.2017.00029] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 06/09/2017] [Indexed: 12/17/2022] Open
Abstract
Delivery mode (natural vs. cesarean) and feeding type (breast vs. formula feeding) are relevant factors for neonatal gut colonization. Biomolecular methods have shown that the ecological structure of infant microbiota is more complex than previously proposed, suggesting a relevant presence of unculturable bacteria. It has also been postulated that among unculturable bacteria, hydrogenotrophic populations might play a key role in infant health. Sulfate-reducing bacteria (SRB), acetogens, and methanogenic archaea use hydrogenotrophic pathways within the human colon. However, to date, few studies have reported detection of hydrogenotrophic microorganisms in newborns, possibly because of limitations on available group-specific, culture-independent quantification procedures. In the present work, we analyzed 16 fecal samples of healthy babies aged 1-6 months by means of quantitative PCR (qPCR) targeting the 16S rRNA or metabolic functional genes and by denaturing gradient gel electrophoresis (DGGE). qPCR data showed quantifiable levels of methanogens, SRB, and acetogens in all samples, indicating that the relative abundances of these microbial groups were not affected by delivery mode (natural vs. caesarian). DGGE revealed a high prevalence of the Blautia genus within the acetogenic bacteria despite strong interindividual variability. Our preliminary results suggest that hydrogenotrophic microorganisms, which have been a neglected group to date, should be included in future ecological and metabolic studies evaluating the infant intestinal microbiota.
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Affiliation(s)
- Valeria Sagheddu
- Facoltà di Scienze Agrarie, Alimentari e Ambientali, Istituto di Microbiologia, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Vania Patrone
- Facoltà di Scienze Agrarie, Alimentari e Ambientali, Istituto di Microbiologia, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Francesco Miragoli
- Facoltà di Scienze Agrarie, Alimentari e Ambientali, Istituto di Microbiologia, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Lorenzo Morelli
- Facoltà di Scienze Agrarie, Alimentari e Ambientali, Istituto di Microbiologia, Università Cattolica del Sacro Cuore, Piacenza, Italy
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50
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Tarpgaard IH, Jørgensen BB, Kjeldsen KU, Røy H. The marine sulfate reducer Desulfobacterium autotrophicum HRM2 can switch between low and high apparent half-saturation constants for dissimilatory sulfate reduction. FEMS Microbiol Ecol 2017; 93:2966865. [DOI: 10.1093/femsec/fix012] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 02/01/2017] [Indexed: 12/22/2022] Open
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