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Zhong Y, Li Y, Wang Z, Cui L, Lv S, Zhu H, Yuan Q, Lai Q, Wang S, Jiang L. Sulfurimonas microaerophilic sp. nov. and Sulfurimonas diazotrophicus sp. nov.: Two Novel Nitrogen-Fixing and Hydrogen- and Sulfur-Oxidizing Chemolithoautotrophs Within the Campylobacteria Isolated from Mangrove Sediments. Microorganisms 2025; 13:713. [PMID: 40284549 PMCID: PMC12029903 DOI: 10.3390/microorganisms13040713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2025] [Revised: 03/06/2025] [Accepted: 03/19/2025] [Indexed: 04/29/2025] Open
Abstract
Two novel marine hydrogen- and sulfur-oxidizing bacteria, designated HSL1-7T and HSL3-1T, were isolated from mangrove sediments from Fujian Province, China. Strain HSL1-7T exhibited Gram-negative, rod-shaped to slightly curved morphology with polar flagellum-driven motility, whereas strain HSL3-1T was Gram-negative, rod-shaped and non-motile. Strain HSL1-7T and HSL3-1T were obligate chemolithoautotrophs, capable of using molecular hydrogen and thiosulfate as an energy source, and molecular oxygen and elemental sulfur as the electron acceptors for growth. Cellular fatty acid profiles revealed similar predominant components (C16:1ω7c, C16:0, C18:1ω7c, and C14:0) in both strains. Strains HSL1-7T and HSL3-1T were strongly diazotrophic, as demonstrated by 15N2 fixation when a fixed nitrogen source was absent from the growth medium. The DNA G+C contents of strains HSL1-7T and HSL3-1T were determined to be 36.1% and 57.3%, respectively. Based on the 16S rRNA gene sequences, strains HSL1-7T and HSL3-1T exhibited the highest sequence similarities with Sulfurimonas marina B2T (98.5% and 94.45%, respectively). Notably, the 16S rRNA gene sequence similarity between strains HSL1-7T and HSL3-1T was 93.19%, indicating that they represent distinct species within the genus Sulfurimonas. Comparative genomic analyses revealed the presence of diverse metabolic profiles in strains HSL1-7T and HSL3-1T, including carbon fixation, hydrogen oxidation, sulfur oxidation, and nitrogen fixation. The combined phenotypic, chemotaxonomic, and phylogenetic evidence, including average nucleotide identity and in silico DNA-DNA hybridization values, shows that strains HSL1-7T and HSL3-1T represent two novel species of the genus Sulfurimonas for which the names Sulfurimonas microaerophilic sp. nov. and Sulfurimonas diazotrophicus sp. nov. are proposed, with the type strains HSL1-7T (=MCCC 1A18899T = KCTC 25640T) and HSL3-1T (=MCCC 1A18844T), respectively.
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Affiliation(s)
- Yangsheng Zhong
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen 361005, China; (Y.Z.); (Y.L.); (Z.W.); (L.C.); (S.L.); (Q.Y.); (Q.L.)
- Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, China
| | - Yufei Li
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen 361005, China; (Y.Z.); (Y.L.); (Z.W.); (L.C.); (S.L.); (Q.Y.); (Q.L.)
- Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, China
| | - Zhaodi Wang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen 361005, China; (Y.Z.); (Y.L.); (Z.W.); (L.C.); (S.L.); (Q.Y.); (Q.L.)
- Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, China
| | - Liang Cui
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen 361005, China; (Y.Z.); (Y.L.); (Z.W.); (L.C.); (S.L.); (Q.Y.); (Q.L.)
- Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, China
| | - Shiwei Lv
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen 361005, China; (Y.Z.); (Y.L.); (Z.W.); (L.C.); (S.L.); (Q.Y.); (Q.L.)
- Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, China
| | - Han Zhu
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen 361005, China; (Y.Z.); (Y.L.); (Z.W.); (L.C.); (S.L.); (Q.Y.); (Q.L.)
- Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, China
| | - Qing Yuan
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen 361005, China; (Y.Z.); (Y.L.); (Z.W.); (L.C.); (S.L.); (Q.Y.); (Q.L.)
- Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, China
| | - Qiliang Lai
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen 361005, China; (Y.Z.); (Y.L.); (Z.W.); (L.C.); (S.L.); (Q.Y.); (Q.L.)
- Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, China
| | - Shasha Wang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen 361005, China; (Y.Z.); (Y.L.); (Z.W.); (L.C.); (S.L.); (Q.Y.); (Q.L.)
- Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, China
| | - Lijing Jiang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen 361005, China; (Y.Z.); (Y.L.); (Z.W.); (L.C.); (S.L.); (Q.Y.); (Q.L.)
- Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, China
- School of Marine Biology, Xiamen Ocean Vocational College, Xiamen 361012, China
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Li Y, Ye Z, Lai MC, Liu CS, Paull CK, Lin S, Lai SJ, You YT, Wu SY, Hung CC, Ding JY, Shih CJ, Wu YC, Zhao J, Xiao W, Wu CH, Dong G, Zhang H, Qiu W, Wang S, Chen SC. Microbial Communities in and Around the Siboglinid Tubeworms from the South Yungan East Ridge Cold Seep Offshore Southwestern Taiwan at the Northern South China Sea. Microorganisms 2024; 12:2452. [PMID: 39770655 PMCID: PMC11676240 DOI: 10.3390/microorganisms12122452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2024] [Revised: 11/22/2024] [Accepted: 11/26/2024] [Indexed: 01/11/2025] Open
Abstract
To date, only a few microbial community studies of cold seeps at the South China Sea (SCS) have been reported. The cold seep dominated by tubeworms was discovered at South Yungan East Ridge (SYER) offshore southwestern Taiwan by miniROV. The tubeworms were identified and proposed as Paraescarpia formosa sp. nov. through morphological and phylogenetic analyses. The endosymbionts in the trunk of P. formosa analyzed by a 16S rRNA gene clone library represented only one phylotype, which belonged to the family Sedimenticolaceae in Gammaproteobacteria. In addition, the archaeal and bacterial communities in the habitat of tubeworm P. formosa were investigated by using high-phylogenetic-resolution full-length 16S rRNA gene amplicon sequencing. The results showed that anerobic methane-oxidizing archaea (ANME)-1b was most abundant and ANME-2ab was minor in a consortia of the anerobic oxidation of methane (AOM). The known sulfate-reducing bacteria (SRB) partners in AOM consortia, such as SEEP-SRB1, -SRB2, and -SRB4, Desulfococcus and Desulfobulbus, occurred in a small population (0-5.7%) at the SYER cold seep, and it was suggested that ANME-1b and ANME-2ab might be coupled with multiple SRB in AOM consortia. Besides AOM consortia, various methanogenic archaea, including Bathyarchaeota (Subgroup-8), Methanocellales, Methanomicrobiales, Methanosarcinales, Methanofastidiosales and Methanomassiliicoccales, were identified, and sulfur-oxidizing bacteria Sulfurovum and Sulfurimonas in phylum Epsilonbacteraeota were dominant. This study revealed the first investigation of microbiota in and around tubeworm P. formosa discovered at the SYER cold seep offshore southwestern Taiwan. We could gain insights into the chemosynthetic communities in the deep sea, especially regarding the cold seep ecosystems at the SCS.
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Affiliation(s)
- Yin Li
- School of Resources and Chemical Engineering, Sanming University, Sanming 365004, China; (Y.L.); (Z.Y.); (J.Z.); (W.X.); (C.-H.W.); (G.D.); (H.Z.); (W.Q.); (S.W.)
- Fujian Provincial Key Laboratory of Resources and Environmental Monitoring and Sustainable Management and Utilization, Sanming University, Sanming 365004, China
- College of Environment and Safety Engineering, Fuzhou University, Fuzhou 350108, China
| | - Zhiwei Ye
- School of Resources and Chemical Engineering, Sanming University, Sanming 365004, China; (Y.L.); (Z.Y.); (J.Z.); (W.X.); (C.-H.W.); (G.D.); (H.Z.); (W.Q.); (S.W.)
- Fujian Provincial Key Laboratory of Resources and Environmental Monitoring and Sustainable Management and Utilization, Sanming University, Sanming 365004, China
| | - Mei-Chin Lai
- Department of Life Sciences, National Chung Hsing University, Taichung 402202, Taiwan; (S.-J.L.); (Y.-T.Y.); (S.-Y.W.); (C.-C.H.); (J.-Y.D.)
| | - Char-Shine Liu
- Institute of Oceanography, National Taiwan University, Taipei 106319, Taiwan; (C.-S.L.); (S.L.)
| | - Charles K. Paull
- Monterey Bay Aquarium Research Institute, Moss Landing, CA 95039-9644, USA;
| | - Saulwood Lin
- Institute of Oceanography, National Taiwan University, Taipei 106319, Taiwan; (C.-S.L.); (S.L.)
| | - Shu-Jung Lai
- Department of Life Sciences, National Chung Hsing University, Taichung 402202, Taiwan; (S.-J.L.); (Y.-T.Y.); (S.-Y.W.); (C.-C.H.); (J.-Y.D.)
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung 406040, Taiwan
- Research Center for Cancer Biology, China Medical University, Taichung 406040, Taiwan
| | - Yi-Ting You
- Department of Life Sciences, National Chung Hsing University, Taichung 402202, Taiwan; (S.-J.L.); (Y.-T.Y.); (S.-Y.W.); (C.-C.H.); (J.-Y.D.)
| | - Sue-Yao Wu
- Department of Life Sciences, National Chung Hsing University, Taichung 402202, Taiwan; (S.-J.L.); (Y.-T.Y.); (S.-Y.W.); (C.-C.H.); (J.-Y.D.)
| | - Chuan-Chuan Hung
- Department of Life Sciences, National Chung Hsing University, Taichung 402202, Taiwan; (S.-J.L.); (Y.-T.Y.); (S.-Y.W.); (C.-C.H.); (J.-Y.D.)
| | - Jiun-Yan Ding
- Department of Life Sciences, National Chung Hsing University, Taichung 402202, Taiwan; (S.-J.L.); (Y.-T.Y.); (S.-Y.W.); (C.-C.H.); (J.-Y.D.)
| | - Chao-Jen Shih
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu 300193, Taiwan; (C.-J.S.); (Y.-C.W.)
| | - Yen-Chi Wu
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu 300193, Taiwan; (C.-J.S.); (Y.-C.W.)
| | - Jingjing Zhao
- School of Resources and Chemical Engineering, Sanming University, Sanming 365004, China; (Y.L.); (Z.Y.); (J.Z.); (W.X.); (C.-H.W.); (G.D.); (H.Z.); (W.Q.); (S.W.)
- Fujian Provincial Key Laboratory of Resources and Environmental Monitoring and Sustainable Management and Utilization, Sanming University, Sanming 365004, China
- College of Chemistry and Materials Science, Fujian Normal University, Fuzhou 350117, China
| | - Wangchuan Xiao
- School of Resources and Chemical Engineering, Sanming University, Sanming 365004, China; (Y.L.); (Z.Y.); (J.Z.); (W.X.); (C.-H.W.); (G.D.); (H.Z.); (W.Q.); (S.W.)
- Fujian Provincial Key Laboratory of Resources and Environmental Monitoring and Sustainable Management and Utilization, Sanming University, Sanming 365004, China
| | - Chih-Hung Wu
- School of Resources and Chemical Engineering, Sanming University, Sanming 365004, China; (Y.L.); (Z.Y.); (J.Z.); (W.X.); (C.-H.W.); (G.D.); (H.Z.); (W.Q.); (S.W.)
- Fujian Provincial Key Laboratory of Resources and Environmental Monitoring and Sustainable Management and Utilization, Sanming University, Sanming 365004, China
- College of Environment and Safety Engineering, Fuzhou University, Fuzhou 350108, China
| | - Guowen Dong
- School of Resources and Chemical Engineering, Sanming University, Sanming 365004, China; (Y.L.); (Z.Y.); (J.Z.); (W.X.); (C.-H.W.); (G.D.); (H.Z.); (W.Q.); (S.W.)
- Fujian Provincial Key Laboratory of Resources and Environmental Monitoring and Sustainable Management and Utilization, Sanming University, Sanming 365004, China
- College of Environment and Safety Engineering, Fuzhou University, Fuzhou 350108, China
| | - Hangying Zhang
- School of Resources and Chemical Engineering, Sanming University, Sanming 365004, China; (Y.L.); (Z.Y.); (J.Z.); (W.X.); (C.-H.W.); (G.D.); (H.Z.); (W.Q.); (S.W.)
- Fujian Provincial Key Laboratory of Resources and Environmental Monitoring and Sustainable Management and Utilization, Sanming University, Sanming 365004, China
- Medical Plant Exploitation and Utilization Engineering Research Center, Sanming University, Sanming 365004, China
| | - Wanling Qiu
- School of Resources and Chemical Engineering, Sanming University, Sanming 365004, China; (Y.L.); (Z.Y.); (J.Z.); (W.X.); (C.-H.W.); (G.D.); (H.Z.); (W.Q.); (S.W.)
- Fujian Provincial Key Laboratory of Resources and Environmental Monitoring and Sustainable Management and Utilization, Sanming University, Sanming 365004, China
- College of Environment and Safety Engineering, Fuzhou University, Fuzhou 350108, China
| | - Song Wang
- School of Resources and Chemical Engineering, Sanming University, Sanming 365004, China; (Y.L.); (Z.Y.); (J.Z.); (W.X.); (C.-H.W.); (G.D.); (H.Z.); (W.Q.); (S.W.)
- Fujian Provincial Key Laboratory of Resources and Environmental Monitoring and Sustainable Management and Utilization, Sanming University, Sanming 365004, China
- College of Chemistry and Materials Science, Fujian Normal University, Fuzhou 350117, China
| | - Sheng-Chung Chen
- School of Resources and Chemical Engineering, Sanming University, Sanming 365004, China; (Y.L.); (Z.Y.); (J.Z.); (W.X.); (C.-H.W.); (G.D.); (H.Z.); (W.Q.); (S.W.)
- Fujian Provincial Key Laboratory of Resources and Environmental Monitoring and Sustainable Management and Utilization, Sanming University, Sanming 365004, China
- College of Environment and Safety Engineering, Fuzhou University, Fuzhou 350108, China
- Department of Life Sciences, National Chung Hsing University, Taichung 402202, Taiwan; (S.-J.L.); (Y.-T.Y.); (S.-Y.W.); (C.-C.H.); (J.-Y.D.)
- College of Chemistry and Materials Science, Fujian Normal University, Fuzhou 350117, China
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Yuan Q, Wang S, Wang S, Zhong Y, Jiang L. Genome sequence of Sulfurimonas sp. C5, a potential chemolithoautotrophic, sulfur-oxidizing bacterium isolated from a mangrove sediment. Microbiol Resour Announc 2024; 13:e0047424. [PMID: 39315832 PMCID: PMC11556096 DOI: 10.1128/mra.00474-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2024] [Accepted: 09/06/2024] [Indexed: 09/25/2024] Open
Abstract
Sulfurimonas sp. strain C5 (MCCC 1A19556) is a strain with potential chemolithoautotrophic sulfur-oxidizing function, which is isolated from a mangrove sediment sample collected from Quanzhou Bay, Fujian Province, China. This report describes the genome sequence of strain C5, which possesses the gene sets for the sulfur-oxidizing pathway.
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Affiliation(s)
- Qing Yuan
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China; Fujian Key Laboratory of Marine Genetic Resources, Xiamen, China
- School of Marine Science and Fisheries, Jiangsu Ocean University, Lianyungang, China
| | - Shufang Wang
- School of Marine Science and Fisheries, Jiangsu Ocean University, Lianyungang, China
| | - ShaSha Wang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China; Fujian Key Laboratory of Marine Genetic Resources, Xiamen, China
| | - Yangsheng Zhong
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China; Fujian Key Laboratory of Marine Genetic Resources, Xiamen, China
| | - Lijing Jiang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China; Fujian Key Laboratory of Marine Genetic Resources, Xiamen, China
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Xu JM, Dong H, Xu HR, Sun YL, Yu Y, Zhang LY, Yi GP, He WK, Wu CM, Wang AJ, Cheng HY. Water flush boosts performance of elemental sulfur-based denitrification packed-bed systems: Optimization and mechanisms. BIORESOURCE TECHNOLOGY 2024; 408:131158. [PMID: 39059589 DOI: 10.1016/j.biortech.2024.131158] [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: 06/24/2024] [Revised: 07/17/2024] [Accepted: 07/23/2024] [Indexed: 07/28/2024]
Abstract
Despite the promising potential of elemental sulfur-based denitrification (ESDeN) packed-bed progresses, challenges such as excessive biofilm growth and gas entrapment persist, leading to denitrification deterioration. Water flush (WF) is recognized as an effective strategy, yet its effects remain underexplored. To address this knowledge gap, this study systematically investigated WF effects on ESDeN packed-bed denitrification. Results demonstrated that controlling WF effectively regulated denitrification, achieving superior and stable rates. Compared to no WF (0.45 kgN·m-3·d-1), rates improved by 1.20 ∼ 1.56 times under low-frequency (weekly WF, 0.54 kgN·m-3·d-1) and low-intensity WF (0.54 ∼ 0.70 kgN·m-3·d-1). High-frequency (hours WF) and high-intensity WF (30 & 50 m/h) further amplified denitrification rates by 1.73 ∼ 2.29 times. The enhanced denitrifications under low-frequency/intensity WF were mainly attributed to prolonged actual hydraulic retention time (AHRT), while high-frequency/intensity WF improved both AHRT prolonging and biofilm thinning, facilitating mass transfer. This study offers a promising avenue for fine-tuning denitrification rates via strategic WF adjustments.
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Affiliation(s)
- Jia-Min Xu
- State Key Laboratory of Urban Water Resources and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen 518055, China
| | - Heng Dong
- State Key Laboratory of Urban Water Resources and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen 518055, China; CSD (Jiangsu) Environmental Construction Co., Ltd., Nanjing 211134, China; CSD Water Service Co., Ltd. R&D Branch, Yixing 214214, China
| | - Hao-Ran Xu
- State Key Laboratory of Urban Water Resources and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen 518055, China
| | - Yi-Lu Sun
- Cas Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Yang Yu
- State Key Laboratory of Urban Water Resources and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen 518055, China
| | - Li-Ying Zhang
- State Key Laboratory of Urban Water Resources and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen 518055, China
| | - Gen-Ping Yi
- State Key Laboratory of Urban Water Resources and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen 518055, China
| | - Wen-Ke He
- State Key Laboratory of Urban Water Resources and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen 518055, China
| | - Chang-Min Wu
- CSD (Jiangsu) Environmental Construction Co., Ltd., Nanjing 211134, China; CSD Water Service Co., Ltd. R&D Branch, Yixing 214214, China
| | - Ai-Jie Wang
- State Key Laboratory of Urban Water Resources and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen 518055, China; Cas Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Hao-Yi Cheng
- State Key Laboratory of Urban Water Resources and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen 518055, China.
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Wang L, Liu J, Li Y, Liu Z, Zhang L, Che H, Cui H, Zhang Y. Elemental sulfur-driven autotrophic denitrification process for effective removal of nitrate in mariculture wastewater: Performance, kinetics and microbial community. CHEMOSPHERE 2023; 337:139354. [PMID: 37394184 DOI: 10.1016/j.chemosphere.2023.139354] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 05/29/2023] [Accepted: 06/25/2023] [Indexed: 07/04/2023]
Abstract
To date, there is a lack of systematic investigation on the elemental sulfur-driven autotrophic denitrification (SDAD) process for removing nitrate (NO3--N) from mariculture wastewater deficient in organic carbon sources. Therefore, a packed-bed reactor was established and continuously operated for 230 days to investigate the operation performance, kinetic characteristics and microbial community of SDAD biofilm process. Results indicate that the NO3--N removal efficiencies and rates varied with the operational conditions including HRT (1-4 h), influent concentrations of NO3--N (25-100 mg L-1) and DO (0.2-7.0 mg L-1), and temperature (10oC-30 °C), in the ranges of 51.4%-98.6% and 0.054-0.546 g L-1 d-1, respectively. Limestone could partially neutralize the produced acidity. Small portions of NO3--N were converted to nitrite (<4.5%) and ammonia (<2.8%) in the reactor. Operational conditions also influenced the production of acidity, nitrite and ammonia as well as sulfate. Shortening HRT and increasing influent NO3--N concentration turned the optimal fitting model depicting the NO3--N removal along the reactor from half-order to zero-order. Furthermore, the NO3--N removal was accelerated by a higher temperature and influent NO3--N concentration and a lower HRT and influent DO concentration. Microbial richness, evenness and diversity gradually decreased during the autotrophic denitrifier enrichment cultivation and the reactor start-up and operation. Sulfurimonas constituted the predominate genus and the primary functional bacteria in the reactor. This study highlights the SDAD as a promising way to control the coastal eutrophication associated with mariculture wastewater discharge.
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Affiliation(s)
- Lu Wang
- Laoshan Laboratory, Qingdao, 266237, China
| | - Jun Liu
- Laoshan Laboratory, Qingdao, 266237, China; First Institute of Oceanography, Ministry of Natural Resources, Qingdao, 266061, China
| | - Yongfu Li
- College of Oceanography, Hohai University, Nanjing, 210098, China
| | - Zhihao Liu
- Laoshan Laboratory, Qingdao, 266237, China
| | - Long Zhang
- National Fisheries Technology Extension Center, China Society of Fisheries, Beijing, 100125, China
| | - Hong Che
- Laoshan Laboratory, Qingdao, 266237, China
| | - Hongwu Cui
- Laoshan Laboratory, Qingdao, 266237, China; Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China.
| | - Ying Zhang
- Ocean University of China, Qingdao, 266100, China.
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Sun QL, Xu K, Cao L, Du Z, Wang M, Sun L. Nitrogen and sulfur cycling driven by Campylobacterota in the sediment-water interface of deep-sea cold seep: a case in the South China Sea. mBio 2023; 14:e0011723. [PMID: 37409803 PMCID: PMC10470523 DOI: 10.1128/mbio.00117-23] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 05/11/2023] [Indexed: 07/07/2023] Open
Abstract
Chemoautotrophs within Campylobacterota, especially Sulfurovum and Sulfurimonas, are abundant in the seawater-sediment interface of the Formosa cold seep in the South China Sea. However, the in situ activity and function of Campylobacterota are unknown. In this study, the geochemical role of Campylobacterota in the Formosa cold seep was investigated with multiple means. Two members of Sulfurovum and Sulfurimonas were isolated for the first time from deep-sea cold seep. These isolates are new chemoautotrophic species that can use molecular hydrogen as an energy source and CO2 as a sole carbon source. Comparative genomics identified an important hydrogen-oxidizing cluster in Sulfurovum and Sulfurimonas. Metatranscriptomic analysis detected high expression of hydrogen-oxidizing gene in the RS, suggesting that H2 was likely an energy source in the cold seep. Genomic analysis indicated that the Sulfurovum and Sulfurimonas isolates possess a truncated sulfur-oxidizing system, and metatranscriptomic analysis revealed that Sulfurovum and Sulfurimonas with this genotype were active in the surface of RS and likely contributed to thiosulfate production. Furthermore, geochemical and in situ analyses revealed sharply decreased nitrate concentration in the sediment-water interface due to microbial consumption. Consistently, the denitrification genes of Sulfurimonas and Sulfurovum were highly expressed, suggesting an important contribution of these bacteria to nitrogen cycling. Overall, this study demonstrated that Campylobacterota played a significant role in the cycling of nitrogen and sulfur in a deep-sea cold seep. IMPORTANCE Chemoautotrophs within Campylobacterota, in particular Sulfurovum and Sulfurimonas, are ubiquitous in deep-sea cold seeps and hydrothermal vents. However, to date, no Sulfurovum or Sulfurimonas has been isolated from cold seeps, and the ecological roles of these bacteria in cold seeps remain to be investigated. In this study, we obtained two isolates of Sulfurovum and Sulfurimonas from Formosa cold seep, South China Sea. Comparative genomics, metatranscriptomics, geochemical analysis, and in situ experimental study indicated collectively that Campylobacterota played a significant part in nitrogen and sulfur cycling in cold seep and was the cause of thiosulfate accumulation and sharp reduction of nitrate level in the sediment-water interface. The findings of this study promoted our understanding of the in situ function and ecological role of deep-sea Campylobacterota.
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Affiliation(s)
- Qing-lei Sun
- College of Life Science, Qingdao Agricultural University, Qingdao, China
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao, China.
| | - Ke Xu
- College of Life Science, Qingdao Agricultural University, Qingdao, China
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Lei Cao
- Deep Sea Research Center, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Zengfeng Du
- Deep Sea Research Center, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Key Laboratory of Marine Geology and Environment, Institute of Oceanology, Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Minxiao Wang
- Deep Sea Research Center, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- CAS Key Laboratory of Marine Ecology and Environmental Science, Institute of Oceanology, Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Li Sun
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao, China.
- College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, China
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7
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Molari M, Hassenrueck C, Laso-Pérez R, Wegener G, Offre P, Scilipoti S, Boetius A. A hydrogenotrophic Sulfurimonas is globally abundant in deep-sea oxygen-saturated hydrothermal plumes. Nat Microbiol 2023; 8:651-665. [PMID: 36894632 PMCID: PMC10066037 DOI: 10.1038/s41564-023-01342-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 02/10/2023] [Indexed: 03/11/2023]
Abstract
Members of the bacterial genus Sulfurimonas (phylum Campylobacterota) dominate microbial communities in marine redoxclines and are important for sulfur and nitrogen cycling. Here we used metagenomics and metabolic analyses to characterize a Sulfurimonas from the Gakkel Ridge in the Central Arctic Ocean and Southwest Indian Ridge, showing that this species is ubiquitous in non-buoyant hydrothermal plumes at Mid Ocean Ridges across the global ocean. One Sulfurimonas species, USulfurimonas pluma, was found to be globally abundant and active in cold (<0-4 °C), oxygen-saturated and hydrogen-rich hydrothermal plumes. Compared with other Sulfurimonas species, US. pluma has a reduced genome (>17%) and genomic signatures of an aerobic chemolithotrophic metabolism using hydrogen as an energy source, including acquisition of A2-type oxidase and loss of nitrate and nitrite reductases. The dominance and unique niche of US. pluma in hydrothermal plumes suggest an unappreciated biogeochemical role for Sulfurimonas in the deep ocean.
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Affiliation(s)
- Massimiliano Molari
- Max Planck Institute for Marine Microbiology, Bremen, Germany.
- Alfred Wegener Institute for Polar and Marine Research, Bremerhaven, Germany.
| | | | - Rafael Laso-Pérez
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Systems Biology Department, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Gunter Wegener
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Pierre Offre
- Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, Den Burg, the Netherlands
| | - Stefano Scilipoti
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- Center for Electromicrobiology, Department of Biology, Aarhus University, Aarhus, Denmark
| | - Antje Boetius
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- Alfred Wegener Institute for Polar and Marine Research, Bremerhaven, Germany
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
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8
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Wang Z, Wang S, Lai Q, Wei S, Jiang L, Shao Z. Sulfurimonas marina sp. nov., an obligately chemolithoautotrophic, sulphur-oxidizing bacterium isolated from a deep-sea sediment sample from the South China Sea. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A novel marine bacterium, designated strain B2T, was isolated from a deep-sea sediment sample collected from the South China Sea. Cells were observed to be Gram-stain negative, motile and rod shaped with a single polar flagellum. B2T could grow at 10–45 °C (optimum, 35 °C), pH 4.5–9.0 (optimum, pH 7.0) and in the presence of 1.0–8.0 % (w/v) NaCl (optimum, 3.0%). The isolate grew chemolithoautotrophically with sulphide, elemental sulphur and thiosulphate as electron donors, carbon dioxide as the sole carbon source, and molecular oxygen as the sole electron acceptor. Molecular hydrogen did not support growth. The predominant fatty acids of B2T were C16 : 1ω7c, C16 : 0 and C18 : 1ω7c. The results of phylogenetic analysis based on 16S rRNA gene sequence indicated that B2T represented a member of the genus
Sulfurimonas
, with the highest similarity to the 16S rRNA gene sequences of
Sulfurimonas indica
NW8NT (95.9 %),
Sulfurimonas crateris
SN118T (95.7 %),
Sulfurimonas xiamenensis
1-1NT (95.6 %) and
Sulfurimonas paralvinellae
GO25T (95.4 %). Sequence similarities to other members of the genus
Sulfurimonas
were less than 95.0 %. In addition, the average nucleotide identity (ANI) value and digital DNA–DNA hybridization (dDDH) estimate between B2T and
S. indica
NW8NT were 73.0 and 23.7 %, respectively. The size of the complete genome of B2T is 22 61 034 bp, with a DNA G+C content of 36.0 mol %. On the basis of the phenotypic, phylogenetic and genomic data presented here, strain B2T represent a novel species of the genus
Sulfurimonas
, for which the name Sulfurimonas marina sp. nov. is proposed, with the type strain B2T (=MCCC 1A14515T=KCTC 15852T).
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Affiliation(s)
- Zhaodi Wang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China; State Key Laboratory Breeding Base of Marine Genetic Resources; Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, PR China
- School of Marine Sciences, China University of Geosciences, Beijing 100083, PR China
| | - Shasha Wang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China; State Key Laboratory Breeding Base of Marine Genetic Resources; Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, PR China
| | - Qiliang Lai
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China; State Key Laboratory Breeding Base of Marine Genetic Resources; Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, PR China
| | - Shiping Wei
- School of Marine Sciences, China University of Geosciences, Beijing 100083, PR China
| | - Lijing Jiang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China; State Key Laboratory Breeding Base of Marine Genetic Resources; Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, PR China
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China; State Key Laboratory Breeding Base of Marine Genetic Resources; Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, PR China
- School of Marine Sciences, China University of Geosciences, Beijing 100083, PR China
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9
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Kojima H, Kato Y, Watanabe T, Fukui M. Sulfurimonas aquatica sp. nov., a sulfur-oxidizing bacterium isolated from water of a brackish lake. Arch Microbiol 2022; 204:559. [PMID: 35976522 DOI: 10.1007/s00203-022-03167-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/02/2022] [Accepted: 08/03/2022] [Indexed: 11/26/2022]
Abstract
A novel chemolithoautotrophic bacterium, strain H1576T, was isolated from water of a brackish lake. Strain H1576T grew aerobically on inorganic sulfur compounds. Hydrogen gas did not support autotrophic growth, and heterotrophic growth was not observed. Cells were rod shaped, motile, 1.5-2.7 μm in length and 0.6-0.7 μm in width. Growth was observed at 3-22 °C with an optimum growth temperature of 13-15 °C. The pH range for growth was 6.0-7.4 with an optimum pH of 6.6-6.8. Major fatty acids were summed feature 3 (C16: 1ω7c and/or C16: 1ω6c). The complete genome of strain H1576T consists of a circular chromosome and a plasmid, with total length of 2.8 Mbp and G+C content of 46.4 mol%. Phylogenetic analyses indicated that strain H1576T belongs to the genus Sulfurimonas but distinct from representatives of existing species. On the basis of genomic and phenotypic characteristics, a new species named Sulfurimonas aquatica sp. nov. is proposed with the type strain of strain H1576T (= BCRC 81254T = JCM 35004T).
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Affiliation(s)
- Hisaya Kojima
- The Institute of Low Temperature Science, Hokkaido University, Kita-19, Nishi-8, Kita-ku, Sapporo, 060-0819, Japan.
| | - Yukako Kato
- The Institute of Low Temperature Science, Hokkaido University, Kita-19, Nishi-8, Kita-ku, Sapporo, 060-0819, Japan
| | - Tomohiro Watanabe
- The Institute of Low Temperature Science, Hokkaido University, Kita-19, Nishi-8, Kita-ku, Sapporo, 060-0819, Japan
| | - Manabu Fukui
- The Institute of Low Temperature Science, Hokkaido University, Kita-19, Nishi-8, Kita-ku, Sapporo, 060-0819, Japan
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10
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Cordell GA, Lamahewage SNS. Ergothioneine, Ovothiol A, and Selenoneine-Histidine-Derived, Biologically Significant, Trace Global Alkaloids. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27092673. [PMID: 35566030 PMCID: PMC9103826 DOI: 10.3390/molecules27092673] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 04/15/2022] [Accepted: 04/16/2022] [Indexed: 11/16/2022]
Abstract
The history, chemistry, biology, and biosynthesis of the globally occurring histidine-derived alkaloids ergothioneine (10), ovothiol A (11), and selenoneine (12) are reviewed comparatively and their significance to human well-being is discussed.
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Affiliation(s)
- Geoffrey A. Cordell
- Natural Products Inc., Evanston, IL 60202, USA
- Department of Pharmaceutics, College of Pharmacy, University of Florida, Gainesville, FL 32610, USA
- Correspondence:
| | - Sujeewa N. S. Lamahewage
- Department of Chemistry, Iowa State University, Ames, IA 50011, USA;
- Department of Chemistry, University of Ruhuna, Matara 81000, Sri Lanka
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11
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Brancaccio M, Tangherlini M, Danovaro R, Castellano I. Metabolic adaptations to marine environments: molecular diversity and evolution of ovothiol biosynthesis in Bacteria. Genome Biol Evol 2021; 13:6323227. [PMID: 34272861 PMCID: PMC8433421 DOI: 10.1093/gbe/evab169] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/12/2021] [Indexed: 11/14/2022] Open
Abstract
Ovothiols are sulfur-containing amino acids synthesized by marine invertebrates, protozoans, and bacteria. They act as pleiotropic molecules in signaling and protection against oxidative stress. The discovery of ovothiol biosynthetic enzymes, sulfoxide synthase OvoA and β-lyase OvoB, paves the way for a systematic investigation of ovothiol distribution and molecular diversification in nature. In this work, we conducted genomic and metagenomics data mining to investigate the distribution and diversification of ovothiol biosynthetic enzymes in Bacteria. We identified the bacteria endowed with this secondary metabolic pathway, described their taxonomy, habitat and biotic interactions in order to provide insight into their adaptation to specific environments. We report that OvoA and OvoB are mostly encountered in marine aerobic Proteobacteria, some of them establishing symbiotic or parasitic relationships with other organisms. We identified a horizontal gene transfer event of OvoB from Bacteroidetes living in symbiosis with Hydrozoa. Our search within the Ocean Gene Atlas revealed the occurrence of ovothiol biosynthetic genes in Proteobacteria living in a wide range of pelagic and highly oxygenated environments. Finally, we tracked the evolutionary history of ovothiol biosynthesis from marine bacteria to unicellular eukaryotes and metazoans. Our analysis provides new conceptual elements to unravel the evolutionary and ecological significance of ovothiol biosynthesis.
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Affiliation(s)
- Mariarita Brancaccio
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy.,Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn Napoli, Naples, Italy
| | - Michael Tangherlini
- Department of Research Infrastructures for Marine Biological Resources, Stazione Zoologica Anton Dohrn, Fano Marine Centre, Fano, Italy
| | - Roberto Danovaro
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy.,Stazione Zoologica Anton Dohrn, Villa Comunale, Naples, Italy
| | - Immacolata Castellano
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy.,Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn Napoli, Naples, Italy
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12
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Sulfurimonas sediminis sp. nov., a novel hydrogen- and sulfur-oxidizing chemolithoautotroph isolated from a hydrothermal vent at the Longqi system, southwestern Indian ocean. Antonie Van Leeuwenhoek 2021; 114:813-822. [PMID: 33742343 DOI: 10.1007/s10482-021-01560-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 03/14/2021] [Indexed: 10/21/2022]
Abstract
A novel marine hydrogen- and sulfur-oxidizing bacterium, designated strain S2-6 T, was isolated from the deep-sea sediment samples at the Longqi hydrothermal system, southwestern Indian Ocean. Cells were Gram-stain-negative, motile, short rods with a single polar flagellum. Growth was observed at 10-45 °C (optimum 33 °C), pH 5.0-8.0 (optimum pH 7.0) and 1.5 to 6.0% (w/v) NaCl with an optimum at 3.0% (w/v). The isolate was an obligate chemolithoautotroph capable of growth using thiosulfate, tetrathionate, elemental sulfur or sodium sulfide as the energy source, and oxygen or nitrate as the sole electron acceptor. When hydrogen was used as the energy source, strain S2-6 T could respire oxygen, nitrate or element sulfur. The major cellular fatty acids of strain S2-6 T were summed feature 3 (C16:1ω7c and/or C16:1ω6c), C16:0 and summed feature 8 (C18:1ω7c and/or C18:1ω6c). The total size of its genome was 2,320,257 bp and the genomic DNA G + C content was 37.3 mol%. Phylogenetic analysis based on 16S rRNA gene sequences and core genes showed that the novel isolate belonged to the genus Sulfurimonas and was most closely related to Sulfurimonas paralvinellae GO25T (96.8% sequence identity) and Sulfurimonas autotrophica OK10T (95.8% sequence identity). The average nucleotide identity and DNA-DNA hybridization values between strain S2-6 T and S. paralvinellae GO25T and S. autotrophica OK10T were 74.6%-81.2% and 19.1%-24.6%, respectively. Based on the polyphase taxonomical data, strain S2-6 T represents a novel species of the genus Sulfurimonas, for which the name Sulfurimonas sediminis sp. nov. is proposed, with the type strain S2-6 T (= MCCC 1A14513T = KCTC 15854 T).
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13
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Wang S, Jiang L, Hu Q, Cui L, Zhu B, Fu X, Lai Q, Shao Z, Yang S. Characterization of Sulfurimonas hydrogeniphila sp. nov., a Novel Bacterium Predominant in Deep-Sea Hydrothermal Vents and Comparative Genomic Analyses of the Genus Sulfurimonas. Front Microbiol 2021; 12:626705. [PMID: 33717015 PMCID: PMC7952632 DOI: 10.3389/fmicb.2021.626705] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 02/11/2021] [Indexed: 11/13/2022] Open
Abstract
Bacteria of the genus Sulfurimonas within the class Campylobacteria are predominant in global deep-sea hydrothermal environments and widespread in global oceans. However, only few bacteria of this group have been isolated, and their adaptations for these extreme environments remain poorly understood. Here, we report a novel mesophilic, hydrogen- and sulfur-oxidizing bacterium, strain NW10T, isolated from a deep-sea sulfide chimney of Northwest Indian Ocean.16S rRNA gene sequence analysis showed that strain NW10T was most closely related to the vent species Sulfurimonas paralvinellae GO25T with 95.8% similarity, but ANI and DDH values between two strains were only 19.20 and 24.70%, respectively, indicating that strain NW10 represents a novel species. Phenotypic characterization showed strain NW10T is an obligate chemolithoautotroph utilizing thiosulfate, sulfide, elemental sulfur, or molecular hydrogen as energy sources, and molecular oxygen, nitrate, or elemental sulfur as electron acceptors. Moreover, hydrogen supported a better growth than reduced sulfur compounds. During thiosulfate oxidation, the strain can produce extracellular sulfur of elemental α-S8 with an unknown mechanism. Polyphasic taxonomy results support that strain NW10T represents a novel species of the genus Sulfurimonas, and named as Sulfurimonas hydrogeniphila sp. nov. Genome analyses revealed its diverse energy metabolisms driving carbon fixation via rTCA cycling, including pathways of sulfur/hydrogen oxidation, coupled oxygen/sulfur respiration and denitrification. Comparative analysis of the 11 available genomes from Sulfurimonas species revealed that vent bacteria, compared to marine non-vent strains, possess unique genes encoding Type V Sqr, Group II, and Coo hydrogenase, and are selectively enriched in genes related to signal transduction and inorganic ion transporters. These phenotypic and genotypic features of vent Sulfurimonas may explain their thriving in hydrothermal environments and help to understand the ecological role of Sulfurimonas bacteria in hydrothermal ecosystems.
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Affiliation(s)
- Shasha Wang
- Department of Bioengineering and Biotechnology, Huaqiao University, Xiamen, China
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China
- Fujian Key Laboratory of Marine Genetic Resources, Xiamen, China
| | - Lijing Jiang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China
- Fujian Key Laboratory of Marine Genetic Resources, Xiamen, China
| | - Qitao Hu
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China
- Fujian Key Laboratory of Marine Genetic Resources, Xiamen, China
| | - Liang Cui
- Department of Bioengineering and Biotechnology, Huaqiao University, Xiamen, China
| | - Bitong Zhu
- Department of Bioengineering and Biotechnology, Huaqiao University, Xiamen, China
| | - Xiaoteng Fu
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China
- Fujian Key Laboratory of Marine Genetic Resources, Xiamen, China
| | - Qiliang Lai
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China
- Fujian Key Laboratory of Marine Genetic Resources, Xiamen, China
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China
- Fujian Key Laboratory of Marine Genetic Resources, Xiamen, China
- Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
| | - Suping Yang
- Department of Bioengineering and Biotechnology, Huaqiao University, Xiamen, China
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14
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Hu Q, Wang S, Lai Q, Shao Z, Jiang L. Sulfurimonas indica sp. nov., a hydrogen- and sulfur-oxidizing chemolithoautotroph isolated from a hydrothermal sulfide chimney in the Northwest Indian Ocean. Int J Syst Evol Microbiol 2020; 71. [PMID: 33263512 DOI: 10.1099/ijsem.0.004575] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel mesophilic, hydrogen- and sulfur-oxidizing bacterium, designated strain NW8NT, was collected from a sulfide chimney at the deep-sea hydrothermal vent on the Carlsberg Ridge of the Northwest Indian Ocean. The cells were Gram-stain-negative, motile, short rods with a single polar flagellum. The temperature, pH and salinity ranges for growth of strain NW8NT were 4-40 °C (optimum, 33 °C), pH 4.5-7.5 (optimum, pH 5.5) and 340-680 mM NaCl (optimum, 510 mM). The isolate was an obligate chemolithoautotroph capable of growth using hydrogen, thiosulfate, sulfide or elemental sulphur as the sole energy source, carbon dioxide as the sole carbon source and molecular oxygen as the sole electron acceptor. The major cellular fatty acids of strain NW8NT were summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), C16 : 0 and summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c). The total size of its genome was 2 093 492 bp and the genomic DNA G+C content was 36.9 mol%. Phylogenetic analysis based on 16S rRNA gene sequences and core genes showed that the novel isolate belonged to the genus Sulfurimonas and was most closely related to Sulfurimonas paralvinellae GO25T (97.4 % sequence identity). The average nucleotide identity and DNA-DNAhybridization values between strain NW8NT and S. paralvinellae GO25T was 77.8 and 21.1 %, respectively. Based on the phylogenetic, genomic and phenotypic data presented here, strain NW8NT represents a novel species of the genus Sulfurimonas, for which the name Sulfurimonas indica sp. nov. is proposed, with the type strain NW8NT (=MCCC 1A13988T=KTCC 15780T).
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Affiliation(s)
- Qitao Hu
- Fujian Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen 361005, PR China.,Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen 361005, PR China.,State Key Laboratory Breeding Base of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen 361005, PR China
| | - Shasha Wang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen 361005, PR China.,State Key Laboratory Breeding Base of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen 361005, PR China.,Fujian Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen 361005, PR China
| | - Qiliang Lai
- Fujian Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen 361005, PR China.,State Key Laboratory Breeding Base of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen 361005, PR China.,Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen 361005, PR China
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen 361005, PR China.,State Key Laboratory Breeding Base of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen 361005, PR China.,Fujian Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen 361005, PR China
| | - Lijing Jiang
- Fujian Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen 361005, PR China.,Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen 361005, PR China.,State Key Laboratory Breeding Base of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen 361005, PR China
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15
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Henkel JV, Vogts A, Werner J, Neu TR, Spröer C, Bunk B, Schulz-Vogt HN. Candidatus Sulfurimonas marisnigri sp. nov. and Candidatus Sulfurimonas baltica sp. nov., thiotrophic manganese oxide reducing chemolithoautotrophs of the class Campylobacteria isolated from the pelagic redoxclines of the Black Sea and the Baltic Sea. Syst Appl Microbiol 2020; 44:126155. [PMID: 33278714 DOI: 10.1016/j.syapm.2020.126155] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 10/27/2020] [Accepted: 11/02/2020] [Indexed: 10/23/2022]
Abstract
Species of the genus Sulfurimonas are reported and isolated from terrestrial habitats and marine sediments and water columns with steep redox gradients. Here we report on the isolation of strains SoZ1 and GD2 from the pelagic redoxcline of the Black Sea and the Baltic Sea, respectively. Both strains are gram-stain-negative and appear as short and slightly curved motile rods. The autecological preferences for growth of strain SoZ1 were 0-25°C (optimum 20°C), pH 6.5-9.0 (optimum pH 7.5-8.0) and salinity 10-40gL-1 (optimum 25gL-1). Preferences for growth of strain GD2 were 0-20°C (optimum 15°C), pH 7.0-8.0 (optimum pH 7.0-7.5) and salinity 5-40gL-1 (optimum 21gL-1). Strain SoZ1 grew chemolithoautotrophically, while strain GD2 also showed heterotrophic growth with short chained fatty acids as carbon source. Both species utilized hydrogen (H2), sulfide (H2S here taken as the sum of H2S, HS- and S2-), elemental sulfur (S0) and thiosulfate (S2O32-) as electron donors and nitrate (NO3-), oxygen (O2) and particulate manganese oxide (MnO2) as electron acceptors. Based on 16S rRNA gene sequence similarity, both strains cluster within the genus Sulfurimonas with Sulfurimonas gotlandica GD1T as the closest cultured relative species with a sequence similarity of 96.74% and 96.41% for strain SoZ1 and strain GD2, respectively. Strains SoZ1 and GD2 share a ribosomal 16S sequence similarity of 99.27% and were demarcated based on average nucleotide identity and average amino acid identity of the whole genome sequence. These calculations have been applied to the whole genus. We propose the names Candidatus Sulfurimonas marisnigri sp. nov. and Candidatus Sulfurimonas baltica sp. nov. for the thiotrophic manganese reducing culture isolates from the Black Sea and Baltic Sea, respectively.
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Affiliation(s)
- Jan V Henkel
- Leibniz Institute for Baltic Sea Research Warnemünde, 18119 Rostock, Germany.
| | - Angela Vogts
- Leibniz Institute for Baltic Sea Research Warnemünde, 18119 Rostock, Germany
| | - Johannes Werner
- Leibniz Institute for Baltic Sea Research Warnemünde, 18119 Rostock, Germany
| | - Thomas R Neu
- Helmholtz Centre for Environmental Research - UFZ, 39114 Magdeburg, Germany
| | - Cathrin Spröer
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Germany
| | - Boyke Bunk
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Germany
| | - Heide N Schulz-Vogt
- Leibniz Institute for Baltic Sea Research Warnemünde, 18119 Rostock, Germany
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16
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Wang S, Jiang L, Hu Q, Liu X, Yang S, Shao Z. Elemental sulfur reduction by a deep-sea hydrothermal vent Campylobacterium Sulfurimonas sp. NW10. Environ Microbiol 2020; 23:965-979. [PMID: 32974951 DOI: 10.1111/1462-2920.15247] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 09/22/2020] [Indexed: 01/10/2023]
Abstract
Sulfurimonas species (class Campylobacteria, phylum Campylobacterota) were globally distributed and especially predominant in deep-sea hydrothermal environments. They were previously identified as chemolithoautotrophic sulfur-oxidizing bacteria (SOB), whereas little is known about their potential in sulfur reduction. In this report, we found that the elemental sulfur reduction is quite common in different species of genus Sulfurimonas. To gain insights into the sulfur reduction mechanism, growth tests, morphology observation, as well as genomic and transcriptomic analyses were performed on a deep-sea hydrothermal vent bacterium Sulfurimonas sp. NW10. Scanning electron micrographs and dialysis tubing tests confirmed that elemental sulfur reduction occurred without direct contact of cells with sulfur particles while direct access strongly promoted bacterial growth. Furthermore, we demonstrated that most species of Sulfurimonas probably employ both periplasmic and cytoplasmic polysulfide reductases, encoded by genes psrA1 B1 CDE and psrA2 B2 , respectively, to accomplish cyclooctasulfur reduction. This is the first report showing two different sulfur reduction pathways coupled to different energy conservations could coexist in one sulfur-reducing microorganism, and demonstrates that most bacteria of Sulfurimonas could employ both periplasmic and cytoplasmic polysulfide reductases to perform cyclooctasulfur reduction. The capability of sulfur reduction coupling with hydrogen oxidation may partially explain the prevalenceof Sulfurimonas in deep-sea hydrothermal vent environments.
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Affiliation(s)
- Shasha Wang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, China.,State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, 361005, China.,Fujian Key Laboratory of Marine Genetic Resources, Xiamen, 361005, China.,Department of Bioengineering and Biotechnology, College of Chemical Engineering, Huaqiao University, Xiamen, 361021, China
| | - Lijing Jiang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, China.,State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, 361005, China.,Fujian Key Laboratory of Marine Genetic Resources, Xiamen, 361005, China
| | - Qitao Hu
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, China.,State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, 361005, China.,Fujian Key Laboratory of Marine Genetic Resources, Xiamen, 361005, China
| | - Xuewen Liu
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, China.,State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, 361005, China.,Fujian Key Laboratory of Marine Genetic Resources, Xiamen, 361005, China
| | - Suping Yang
- Department of Bioengineering and Biotechnology, College of Chemical Engineering, Huaqiao University, Xiamen, 361021, China
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, China.,State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, 361005, China.,Fujian Key Laboratory of Marine Genetic Resources, Xiamen, 361005, China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000, China
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17
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Wang JJ, Huang BC, Li J, Jin RC. Advances and challenges of sulfur-driven autotrophic denitrification (SDAD) for nitrogen removal. CHINESE CHEM LETT 2020. [DOI: 10.1016/j.cclet.2020.07.036] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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18
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Wang S, Jiang L, Liu X, Yang S, Shao Z. Sulfurimonas xiamenensis sp. nov. and Sulfurimonas lithotrophica sp. nov., hydrogen- and sulfur-oxidizing chemolithoautotrophs within the Epsilonproteobacteria isolated from coastal sediments, and an emended description of the genus Sulfurimonas. Int J Syst Evol Microbiol 2020; 70:2657-2663. [DOI: 10.1099/ijsem.0.004087] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strains 1-1NT and GYSZ_1T were isolated from marine sediments collected from the coast of Xiamen, PR China. Cells of the two strains were Gram-stain-negative, rod-shaped or slightly curved. Strain 1-1NT was non-motile, whereas strain GYSZ_1T was motile by means of one polar flagellum. The temperature, pH and salinity concentration ranges for growth of 1-1NT were 10–45 °C (optimum 30 °C), pH 5.5–8.0 (optimum 7.0) and 0–90 g l−1 NaCl (optimum 50 g l−1), while the growth of GYSZ_1T occurred at 4–45 °C (optimum 33 °C), pH 5.0–8.5 (optimum 6.5) and 5–90 g l−1 NaCl (optimum 20 g l−1). The two novel isolates were obligate chemolithoautotrophs capable of growth using hydrogen, thiosulfate, sulfide or elemental sulfur as the sole energy source, and nitrate, elemental sulfur or molecular oxygen as an electron acceptor. The major fatty acids of 1-1NT were C16 : 1ω7c, C16 : 0, C18 : 1ω7c and C18 : 0, while the predominant fatty acids of strain GYSZ_1T were C16 : 1ω7c, C16 : 0, C18 : 1ω7c and C14 : 0 3-OH. The DNA G+C contents of 1-1NT and GYSZ_1T were 34.5 mol% and 33.2 mol%, respectively. Phylogenetic analysis based on 16S rRNA gene sequences indicated that 1-1NT and GYSZ_1T represented members of the genus
Sulfurimonas
, with the highest sequence similarities to
Sulfurimonas crateris
SN118T (97.4 %) and
Sulfurimonas denitrificans
DSM 1251T (94.7 %), respectively. However, 1-1NT and GYSZ_1T shared 95.5 % similarity of 16S rRNA gene sequences, representing different species of the genus
Sulfurimonas
. On the basis of the physiological properties and the results of phylogenetic analyses, including average nucleotide identity and in silico DNA–DNA hybridization values, strains 1-1NT and GYSZ_1T represent two novel species within the genus
Sulfurimonas
, for which the names Sulfurimonas xiamenensis sp. nov. and Sulfurimonas lithotrophica sp. nov. are proposed, with the type strains 1-1NT (=MCCC 1A14514T=KCTC 15851T) and GYSZ_1T (=MCCC 1A14739T=KCTC 15853T), respectively. Our results also justify an emended description of the genus
Sulfurimonas
.
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Affiliation(s)
- Shasha Wang
- Department of Bioengineering and Biotechnology, College of Chemical Engineering, Huaqiao University, Xiamen 361021, PR China
- Fujian Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen 361005, PR China
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen 361005, PR China
- State Key Laboratory Breeding Base of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen 361005, PR China
| | - Lijing Jiang
- Fujian Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen 361005, PR China
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen 361005, PR China
- State Key Laboratory Breeding Base of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen 361005, PR China
| | - Xuewen Liu
- Fujian Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen 361005, PR China
- State Key Laboratory Breeding Base of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen 361005, PR China
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen 361005, PR China
| | - Suping Yang
- Department of Bioengineering and Biotechnology, College of Chemical Engineering, Huaqiao University, Xiamen 361021, PR China
| | - Zongze Shao
- State Key Laboratory Breeding Base of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen 361005, PR China
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen 361005, PR China
- Fujian Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen 361005, PR China
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19
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Ratnikova NM, Slobodkin AI, Merkel AY, Kopitsyn DS, Kevbrin VV, Bonch-Osmolovskaya EA, Slobodkina GB. Sulfurimonas crateris sp. nov., a facultative anaerobic sulfur-oxidizing chemolithoautotrophic bacterium isolated from a terrestrial mud volcano. Int J Syst Evol Microbiol 2020; 70:487-492. [PMID: 31639074 DOI: 10.1099/ijsem.0.003779] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel mesophilic facultative anaerobic bacterium, strain SN118T, was isolated from a terrestrial mud volcano in Taman Peninsula, Russia. The cells were Gram-negative, motile, short, straight or curved rods with a single polar flagellum. Growth was observed at 5-40 °C (optimum, 30 °C) and pH 5.5-9.5 (optimum, pH 8.0). Growth of strain SN118T was observed in NaCl concentrations ranging from 0.5 to 8.0 % (w/v) with an optimum at 2.0-3.0 % (w/v). The isolate grew chemolithoautotrophically with sulfide, elemental sulfur or thiosulfate as electron donor, oxygen, nitrate or nitrite as an electron acceptor and CO2/HCO3 - as a carbon source. Molecular hydrogen or organic substances did not support growth. Nitrate was reduced to N2. The dominant fatty acids were C16 : 1ω7c, C16 : 0 and C18 : 1ω7c. The total size of the genome of the novel isolate was 2 209 279 bp and the genomic DNA G+C content was 38.8 mol%. Results of phylogenetic analysis based on 16S rRNA gene sequences indicated that the novel isolate belonged to the genus Sulfurimonas and was most closely related to Sulfurimonas denitrificans DSM 1251T (96.74 %). Based on its physiological properties and results from phylogenetic analyses, including average nucleotide identity and in silico DNA-DNA hybridization values, the isolate is considered to represent a novel species of the genus Sulfurimonas, for which the name Sulfurimonas crateris sp. nov. is proposed. The type strain is SN118T (=DSM 109248T=VKM B-3378T).
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Affiliation(s)
- N M Ratnikova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Leninskiy Prospect, 33, bld. 2, 119071, Moscow, Russia
| | - A I Slobodkin
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Leninskiy Prospect, 33, bld. 2, 119071, Moscow, Russia
| | - A Y Merkel
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Leninskiy Prospect, 33, bld. 2, 119071, Moscow, Russia
| | - D S Kopitsyn
- Gubkin University, Leninsky Prospect, 65/1, 119991, Moscow, Russia
| | - V V Kevbrin
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Leninskiy Prospect, 33, bld. 2, 119071, Moscow, Russia
| | - E A Bonch-Osmolovskaya
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Leninskiy Prospect, 33, bld. 2, 119071, Moscow, Russia
| | - G B Slobodkina
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Leninskiy Prospect, 33, bld. 2, 119071, Moscow, Russia
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20
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Lahme S, Callbeck CM, Eland LE, Wipat A, Enning D, Head IM, Hubert CR. Comparison of sulfide‐oxidizing
Sulfurimonas
strains reveals a new mode of thiosulfate formation in subsurface environments. Environ Microbiol 2020; 22:1784-1800. [DOI: 10.1111/1462-2920.14894] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 12/02/2019] [Accepted: 12/11/2019] [Indexed: 01/18/2023]
Affiliation(s)
- Sven Lahme
- School of Natural and Environmental SciencesNewcastle University Devonshire Building (3rd floor) Newcastle upon Tyne NE1 7RU UK
| | | | - Lucy E. Eland
- School of ComputingNewcastle University Newcastle upon Tyne UK
| | - Anil Wipat
- School of ComputingNewcastle University Newcastle upon Tyne UK
| | - Dennis Enning
- ExxonMobil Upstream Research Company Spring Texas USA
| | - Ian M. Head
- School of Natural and Environmental SciencesNewcastle University Devonshire Building (3rd floor) Newcastle upon Tyne NE1 7RU UK
| | - Casey R.J. Hubert
- School of Natural and Environmental SciencesNewcastle University Devonshire Building (3rd floor) Newcastle upon Tyne NE1 7RU UK
- Department of Biological SciencesUniversity of Calgary Calgary Canada
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21
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Sposob M, Cydzik-Kwiatkowska A, Bakke R, Dinamarca C. Temperature-induced changes in a microbial community under autotrophic denitrification with sulfide. Process Biochem 2018. [DOI: 10.1016/j.procbio.2018.03.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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22
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Conte A, Papale M, Amalfitano S, Mikkonen A, Rizzo C, De Domenico E, Michaud L, Lo Giudice A. Bacterial community structure along the subtidal sandy sediment belt of a high Arctic fjord (Kongsfjorden, Svalbard Islands). THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 619-620:203-211. [PMID: 29149744 DOI: 10.1016/j.scitotenv.2017.11.077] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 11/07/2017] [Accepted: 11/07/2017] [Indexed: 06/07/2023]
Abstract
Open fjords are subject to contrasting environmental conditions, owing to meltwater glacial inputs, terrestrial runoff, and marine water mass exchanges, which are exacerbated by anthropogenic and climate perturbations. Following a slope-dependent water circulation, the subtidal sandy sediment belt regulates the convergent transport of nutrients downward the fjord depths, and the effective entrapment of suspended particles and microorganisms. In this study, we aimed at testing how glacial and seawater inputs may influence the bacterial community structure of subtidal sand deposits in the Kongsfjorden. Through total and viable cell counting and an amplicon sequencing approach, we found relevant differences in bacterial community structure along the glacio-marine sampling transect. Viable and high nucleic acid content (HNA) cells represented an important fraction of the total community, generally decreasing toward the glacier front. Besides the predominance of Alpha- and Gammaproteobacteria, Bacteroidetes, Firmicutes and Parcubacteria, the bacterial community structure was likely affected by the glacial activity in the inner fjord, with the occurrence of distinctive phylotypes belonging to Gemmatimonadates, Nitrospirae, Acidobacteria, and Chloroflexi. Overall, our outcomes highlighted that exploring the bacterial community distribution and structure can provide new insights into the active role of sand deposits in coastal cold environments.
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Affiliation(s)
- Antonella Conte
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy
| | - Maria Papale
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy
| | - Stefano Amalfitano
- Water Research Institute, National Research Council (IRSA-CNR), Monterotondo, Rome, Italy
| | - Anu Mikkonen
- Department of Biological and Environmental Sciences, University of Jyvaskyla, Jyvaskyla, Finland
| | - Carmen Rizzo
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy
| | - Emilio De Domenico
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy
| | - Luigi Michaud
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy
| | - Angelina Lo Giudice
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy; Institute for the Coastal Marine Environment, National Research Council (IAMC-CNR), Messina, Italy.
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23
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Sulfide Consumption in Sulfurimonas denitrificans and Heterologous Expression of Its Three Sulfide-Quinone Reductase Homologs. J Bacteriol 2016; 198:1260-7. [PMID: 26833414 DOI: 10.1128/jb.01021-15] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 01/28/2016] [Indexed: 12/29/2022] Open
Abstract
UNLABELLED Sulfurimonas denitrificans is a sulfur-oxidizing epsilonproteobacterium. It has been reported to grow with sulfide and to harbor genes that encode sulfide-quinone reductases (SQRs) (catalyze sulfide oxidation). However, the actual sulfide concentrations at which S. denitrificans grows and whether its SQRs are functional remain enigmatic. Here, we illustrate the sulfide concentrations at which S. denitrificans exhibits good growth, namely, 0.18 mM to roughly 1.7 mM. Around 2.23 mM, sulfide appears to inhibit growth. S. denitrificans harbors three SQR homolog genes on its genome (Suden_2082 for type II SQR, Suden_1879 for type III SQR, and Suden_619 for type IV SQR). They are all transcribed in S. denitrificans. According to our experiments, they appear to be loosely bound to the membrane. Each individual S. denitrificans SQR was heterologously expressed in the Rhodobacter capsulatus SB1003 sqr deletion mutant, and all exhibited SQR activities individually. This suggests that all of these three genes encode functional SQRs. This study also provides the first experimental evidence of a functional bacterial type III SQR. IMPORTANCE Although the epsilonproteobacterium Sulfurimonas denitrificans has been described as using many reduced sulfur compounds as electron donors, there is little knowledge about its growth with sulfide. In many bacteria, the sulfide-quinone reductase (SQR) is responsible for catalyzing sulfide oxidation. S. denitrificans has an array of different types of sqr genes on its genome and so do several other sulfur-oxidizing Epsilonproteobacteria. However, whether these SQRs are functional has remained unknown. Here, we shed light on sulfide metabolism in S. denitrificans. Our study provides the first experimental evidence of active epsilonproteobacterial SQRs and also gives the first report of a functional bacterial type III SQR.
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24
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Roalkvam I, Drønen K, Stokke R, Daae FL, Dahle H, Steen IH. Physiological and genomic characterization of Arcobacter anaerophilus IR-1 reveals new metabolic features in Epsilonproteobacteria. Front Microbiol 2015; 6:987. [PMID: 26441916 PMCID: PMC4584990 DOI: 10.3389/fmicb.2015.00987] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 09/04/2015] [Indexed: 01/18/2023] Open
Abstract
In this study we characterized and sequenced the genome of Arcobacter anaerophilus strain IR-1 isolated from enrichment cultures used in nitrate-amended corrosion experiments. A. anaerophilus IR-1 could grow lithoautotrophically on hydrogen and hydrogen sulfide and lithoheterothrophically on thiosulfate and elemental sulfur. In addition, the strain grew organoheterotrophically on yeast extract, peptone, and various organic acids. We show for the first time that Arcobacter could grow on the complex organic substrate tryptone and oxidize acetate with elemental sulfur as electron acceptor. Electron acceptors utilized by most Epsilonproteobacteria, such as oxygen, nitrate, and sulfur, were also used by A. anaerophilus IR-1. Strain IR-1 was also uniquely able to use iron citrate as electron acceptor. Comparative genomics of the Arcobacter strains A. butzleri RM4018, A. nitrofigilis CI and A. anaerophilus IR-1 revealed that the free-living strains had a wider metabolic range and more genes in common compared to the pathogen strain. The presence of genes for NAD(+)-reducing hydrogenase (hox) and dissimilatory iron reduction (fre) were unique for A. anaerophilus IR-1 among Epsilonproteobacteria. Finally, the new strain had an incomplete denitrification pathway where the end product was nitrite, which is different from other Arcobacter strains where the end product is ammonia. Altogether, our study shows that traditional characterization in combination with a modern genomics approach can expand our knowledge on free-living Arcobacter, and that this complementary approach could also provide invaluable knowledge about the physiology and metabolic pathways in other Epsilonproteobacteria from various environments.
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Affiliation(s)
- Irene Roalkvam
- Centre for Geobiology, University of Bergen Bergen, Norway ; Department of Biology, University of Bergen Bergen, Norway
| | - Karine Drønen
- UniResearch, Centre for Integrated Petroleum Research Bergen, Norway
| | - Runar Stokke
- Centre for Geobiology, University of Bergen Bergen, Norway ; Department of Biology, University of Bergen Bergen, Norway
| | - Frida L Daae
- Centre for Geobiology, University of Bergen Bergen, Norway ; Department of Biology, University of Bergen Bergen, Norway
| | - Håkon Dahle
- Centre for Geobiology, University of Bergen Bergen, Norway ; Department of Biology, University of Bergen Bergen, Norway
| | - Ida H Steen
- Centre for Geobiology, University of Bergen Bergen, Norway ; Department of Biology, University of Bergen Bergen, Norway
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25
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Han Y, Perner M. The globally widespread genus Sulfurimonas: versatile energy metabolisms and adaptations to redox clines. Front Microbiol 2015; 6:989. [PMID: 26441918 PMCID: PMC4584964 DOI: 10.3389/fmicb.2015.00989] [Citation(s) in RCA: 147] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 09/04/2015] [Indexed: 01/11/2023] Open
Abstract
Sulfurimonas species are commonly isolated from sulfidic habitats and numerous 16S rRNA sequences related to Sulfurimonas species have been identified in chemically distinct environments, such as hydrothermal deep-sea vents, marine sediments, the ocean's water column, and terrestrial habitats. In some of these habitats, Sulfurimonas have been demonstrated to play an important role in chemoautotrophic processes. Sulfurimonas species can grow with a variety of electron donors and acceptors, which may contribute to their widespread distribution. Multiple copies of one type of enzyme (e.g., sulfide:quinone reductases and hydrogenases) may play a pivotal role in Sulfurimonas' flexibility to colonize disparate environments. Many of these genes appear to have been acquired through horizontal gene transfer which has promoted adaptations to the distinct habitats. Here we summarize Sulfurimonas' versatile energy metabolisms and link their physiological properties to their global distribution.
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Affiliation(s)
| | - Mirjam Perner
- Molecular Biology of Microbial Consortia, Biocenter Klein Flottbek, University of HamburgHamburg, Germany
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26
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Klatt JM, Polerecky L. Assessment of the stoichiometry and efficiency of CO2 fixation coupled to reduced sulfur oxidation. Front Microbiol 2015; 6:484. [PMID: 26052315 PMCID: PMC4440400 DOI: 10.3389/fmicb.2015.00484] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Accepted: 05/02/2015] [Indexed: 11/13/2022] Open
Abstract
Chemolithoautotrophic sulfur oxidizing bacteria (SOB) couple the oxidation of reduced sulfur compounds to the production of biomass. Their role in the cycling of carbon, sulfur, oxygen, and nitrogen is, however, difficult to quantify due to the complexity of sulfur oxidation pathways. We describe a generic theoretical framework for linking the stoichiometry and energy conservation efficiency of autotrophic sulfur oxidation while accounting for the partitioning of the reduced sulfur pool between the energy generating and energy conserving steps as well as between the main possible products (sulfate vs. zero-valent sulfur). Using this framework, we show that the energy conservation efficiency varies widely among SOB with no apparent relationship to their phylogeny. Aerobic SOB equipped with reverse dissimilatory sulfite reductase tend to have higher efficiency than those relying on the complete Sox pathway, whereas for anaerobic SOB the presence of membrane-bound, as opposed to periplasmic, nitrate reductase systems appears to be linked to higher efficiency. We employ the framework to also show how limited rate measurements can be used to estimate the primary productivity of SOB without the knowledge of the sulfate-to-zero-valent-sulfur production ratio. Finally, we discuss how the framework can help researchers gain new insights into the activity of SOB and their niches.
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Affiliation(s)
| | - Lubos Polerecky
- Max Planck Institute for Marine MicrobiologyBremen, Germany
- Department of Earth Sciences – Geochemistry, Faculty of Geosciences, Utrecht UniversityUtrecht, Netherlands
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