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Li CY, Cao HY, Payet RD, Todd JD, Zhang YZ. Dimethylsulfoniopropionate (DMSP): From Biochemistry to Global Ecological Significance. Annu Rev Microbiol 2024; 78:513-532. [PMID: 39231449 DOI: 10.1146/annurev-micro-041222-024055] [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] [Indexed: 09/06/2024]
Abstract
Dimethylsulfoniopropionate (DMSP) is one of Earth's most abundant organosulfur compounds with important roles in stress tolerance, chemotaxis, global carbon and sulfur cycling, and climate-active gas production. Diverse marine prokaryotes and eukaryotes produce DMSP via three known pathways (methylation, transamination, and decarboxylation) and metabolize DMSP via three further pathways (demethylation, cleavage, and oxidation). Over 20 key enzymes from these pathways have been identified that demonstrate the biodiversity and importance of DMSP cycling. The last dozen years have seen significant changes in our understanding of the enzymology and molecular mechanisms of these DMSP cycling enzymes through the application of biochemistry and structural biology. This has yielded more than 10 crystal structures and, in many cases, detailed explanations as to how and why organisms synthesis and metabolize DMSP. In this review, we describe recent progress in biochemical and mechanistic understandings of DMSP synthesis and metabolism, highlighting the important knowledge gleaned and current challenges that warrant further exploration.
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Affiliation(s)
- Chun-Yang Li
- Joint Research Center for Marine Microbial Science and Technology, Shandong University and Ocean University of China, Qingdao, China
- MOE Key Laboratory of Evolution and Marine Biodiversity; Frontiers Science Center for Deep Ocean Multispheres and Earth System; and College of Marine Life Sciences, Ocean University of China, Qingdao, China;
| | - Hai-Yan Cao
- Joint Research Center for Marine Microbial Science and Technology, Shandong University and Ocean University of China, Qingdao, China
- MOE Key Laboratory of Evolution and Marine Biodiversity; Frontiers Science Center for Deep Ocean Multispheres and Earth System; and College of Marine Life Sciences, Ocean University of China, Qingdao, China;
| | - Rocky D Payet
- School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
| | - Jonathan D Todd
- School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
- MOE Key Laboratory of Evolution and Marine Biodiversity; Frontiers Science Center for Deep Ocean Multispheres and Earth System; and College of Marine Life Sciences, Ocean University of China, Qingdao, China;
| | - Yu-Zhong Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China;
- MOE Key Laboratory of Evolution and Marine Biodiversity; Frontiers Science Center for Deep Ocean Multispheres and Earth System; and College of Marine Life Sciences, Ocean University of China, Qingdao, China;
- Joint Research Center for Marine Microbial Science and Technology, Shandong University and Ocean University of China, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, China
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Lin Y, Zhang M, Lai YX, Liu T, Meng M, Sun Y, Wang Y, Dong QY, Li CX, Yu MX, Cheng J, Liu SJ, Shao X, Zhang N, Li CY. Genomic analysis of Alteromonas sp. M12 isolated from the Mariana Trench reveals its role in dimethylsulfoniopropionate cycling. Mar Genomics 2024; 76:101112. [PMID: 39009493 DOI: 10.1016/j.margen.2024.101112] [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: 04/19/2024] [Revised: 05/02/2024] [Accepted: 05/03/2024] [Indexed: 07/17/2024]
Abstract
Dimethylsulfoniopropionate (DMSP) is a ubiquitous organosulfur molecule in marine environments with important roles in stress tolerance, global carbon and sulfur cycling, and chemotaxis. It is the main precursor of the climate active gas dimethyl sulfide (DMS), which is the greatest natural source of bio‑sulfur transferred from ocean to atmosphere. Alteromonas sp. M12, a Gram-negative and aerobic bacterium, was isolated from the seawater samples collected from the Mariana Trench at the depth of 2500 m. Here, we report the complete genome sequence of strain M12 and its genomic characteristics to import and utilize DMSP. The genome of strain M12 contains one circular chromosome (5,012,782 bp) with the GC content of 40.88%. Alteromonas sp. M12 can grow with DMSP as a sole carbon source, and produced DMS with DMSP as a precursor. Genomic analysis showed that strain M12 contained a set of genes involved in the downstream steps of DMSP cleavage, but no known genes encoding DMSP transporters or DMSP lyases. The results indicated that this strain contained novel DMSP transport and cleavage genes in its genome which warrants further investigation. The import of DMSP into cells may be a strategy of strain M12 to adapt the hydrostatic pressure environment in the Mariana Trench, as DMSP can be used as a hydrostatic pressure protectant. This study sheds light on the catabolism of DMSP by deep-sea bacteria.
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Affiliation(s)
- Yue Lin
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Min Zhang
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Yu-Xiang Lai
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Teng Liu
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Meng Meng
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Yan Sun
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Yu Wang
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Qing-Yu Dong
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Chen-Xi Li
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Meng-Xue Yu
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Jin Cheng
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Shu-Jun Liu
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Xuan Shao
- Key Laboratory on Agricultural Microorganism Resources Development of Shangqiu, Shangqiu Normal University, Shangqiu 476000, China
| | - Nan Zhang
- School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, China.
| | - Chun-Yang Li
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.
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Teng ZJ, Li J, Wang P, Li CY, Peng M, Qin QL, Chen XL, Chen Y, Fu HH, Wang N, Zhang YZ. Meta-omics analysis reveals the marine arsenic cycle driven by bacteria. JOURNAL OF HAZARDOUS MATERIALS 2024; 476:135137. [PMID: 39024770 DOI: 10.1016/j.jhazmat.2024.135137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 06/16/2024] [Accepted: 07/05/2024] [Indexed: 07/20/2024]
Abstract
Arsenic is a toxic element widely distributed in the Earth's crust and ranked as a class I human carcinogen. Microbial metabolism makes significant contributions to arsenic detoxification, migration and transformation. Nowadays, research on arsenic is primarily in areas affected by arsenic pollution associated with human health activities. However, the biogeochemical traits of arsenic in the global marine ecosystem remain to be explicated. In this study, we revealed that seawater environments were primarily governed by the process of arsenate reduction to arsenite, while arsenite methylation was predominant in marine sediments which may serve as significant sources of arsenic emission into the atmosphere. Significant disparities existed in the distribution patterns of the arsenic cycle between surface and deep seawaters at middle and low latitudes, whereas these situations tend to be similar in the Arctic and Antarctic oceans. Significant variations were also observed in the taxonomic diversity and core microbial community of arsenic cycling across different marine environments. Specifically, γ-proteobacteria played a pivotal role in the arsenic cycle in the whole marine environment. Temperature, dissolved oxygen and phosphate were the crucial factors that related to these differentiations in seawater environments. Overall, our study contributes to a deeper understanding of the marine arsenic cycle.
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Affiliation(s)
- Zhao-Jie Teng
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China.
| | - Jian Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Peng Wang
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; Joint Research Center for Marine Microbial Science and Technology, Shandong University and Ocean University of China, Qingdao 266003, China; Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, 266373, China
| | - Chun-Yang Li
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; Joint Research Center for Marine Microbial Science and Technology, Shandong University and Ocean University of China, Qingdao 266003, China; Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, 266373, China
| | - Ming Peng
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Qi-Long Qin
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China; Joint Research Center for Marine Microbial Science and Technology, Shandong University and Ocean University of China, Qingdao 266003, China; Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, 266373, China
| | - Xiu-Lan Chen
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China; Joint Research Center for Marine Microbial Science and Technology, Shandong University and Ocean University of China, Qingdao 266003, China; Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, 266373, China
| | - Yin Chen
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; School of Life Sciences, The University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Hui-Hui Fu
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; Joint Research Center for Marine Microbial Science and Technology, Shandong University and Ocean University of China, Qingdao 266003, China; Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, 266373, China
| | - Ning Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China.
| | - Yu-Zhong Zhang
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; Joint Research Center for Marine Microbial Science and Technology, Shandong University and Ocean University of China, Qingdao 266003, China; Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, 266373, China; Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China.
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Cao Q, Liu X, Wang Q, Liu Z, Xia Y, Xun L, Liu H. Rhodobacteraceae methanethiol oxidases catalyze methanethiol degradation to produce sulfane sulfur other than hydrogen sulfide. mBio 2024; 15:e0290723. [PMID: 38329332 PMCID: PMC10936201 DOI: 10.1128/mbio.02907-23] [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: 10/26/2023] [Accepted: 01/09/2024] [Indexed: 02/09/2024] Open
Abstract
Methanethiol (MT) is a sulfur-containing compound produced during dimethylsulfoniopropionate (DMSP) degradation by marine bacteria. The C-S bond of MT can be cleaved by methanethiol oxidases (MTOs) to release a sulfur atom. However, the cleaving process remains unclear, and the species of sulfur product is uncertain. It has long been assumed that MTOs produce hydrogen sulfide (H2S) from MT. Herein, we studied the MTOs in the Rhodobacteraceae family-whose members are important DMSP degraders ubiquitous in marine environments. We identified 57 MTOs from 1,904 Rhodobacteraceae genomes. These MTOs were grouped into two major clusters. Cluster 1 members share three conserved cysteine residues, while cluster 2 members contain one conserved cysteine residue. We examined the products of three representative MTOs both in vitro and in vivo. All of them produced sulfane sulfur other than H2S from MT. Their conserved cysteines are substrate-binding sites in which the MTO-S-S-CH3 complex is formed. This finding clarified the sulfur product of MTOs and enlightened the MTO-catalyzing process. Moreover, this study connected DMSP degradation with sulfane sulfur metabolism, filling a critical gap in the DMSP degradation pathway and representing new knowledge in the marine sulfur cycle field. IMPORTANCE This study overthrows a long-time assumption that methanethiol oxidases (MTOs) cleave the C-S bond of methanethiol to produce both H2S and H2O2-the former is a strong reductant and the latter is a strong oxidant. From a chemistry viewpoint, this reaction is difficult to happen. Investigations on three representative MTOs indicated that sulfane sulfur (S0) was the direct product, and no H2O2 was produced. Finally, the products of MTOs were corrected to be S0 and H2O. This finding connected dimethylsulfoniopropionate (DMSP) degradation with sulfane sulfur metabolism, filling a critical gap in the DMSP degradation pathway and representing new knowledge in the marine sulfur cycle field.
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Affiliation(s)
- Qun Cao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Xuanyu Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Qingda Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Zongzheng Liu
- Qingdao Institute of Animal Husbandry and Veterinary Medicine, Qingdao, China
| | - Yongzhen Xia
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Luying Xun
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- School of Molecular Biosciences, Washington State University, Pullman, Washington, USA
| | - Huaiwei Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
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Wang S, Zhang N, Teng Z, Wang X, Todd JD, Zhang Y, Cao H, Li C. A new dimethylsulfoniopropionate lyase of the cupin superfamily in marine bacteria. Environ Microbiol 2023; 25:1238-1249. [PMID: 36808192 PMCID: PMC11497337 DOI: 10.1111/1462-2920.16355] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 02/16/2023] [Indexed: 02/23/2023]
Abstract
Dimethylsulfoniopropionate (DMSP) is a marine organosulfur compound with important roles in stress protection, marine biogeochemical cycling, chemical signalling and atmospheric chemistry. Diverse marine microorganisms catabolize DMSP via DMSP lyases to generate the climate-cooling gas and info-chemical dimethyl sulphide. Abundant marine heterotrophs of the Roseobacter group (MRG) are well known for their ability to catabolize DMSP via diverse DMSP lyases. Here, a new DMSP lyase DddU within the MRG strain Amylibacter cionae H-12 and other related bacteria was identified. DddU is a cupin superfamily DMSP lyase like DddL, DddQ, DddW, DddK and DddY, but shares <15% amino acid sequence identity with these enzymes. Moreover, DddU proteins forms a distinct clade from these other cupin-containing DMSP lyases. Structural prediction and mutational analyses suggested that a conserved tyrosine residue is the key catalytic amino acid residue in DddU. Bioinformatic analysis indicated that the dddU gene, mainly from Alphaproteobacteria, is widely distributed in the Atlantic, Pacific, Indian and polar oceans. For reference, dddU is less abundant than dddP, dddQ and dddK, but much more frequent than dddW, dddY and dddL in marine environments. This study broadens our knowledge on the diversity of DMSP lyases, and enhances our understanding of marine DMSP biotransformation.
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Affiliation(s)
- Shu‐Yan Wang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life SciencesOcean University of ChinaQingdaoChina
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research CenterShandong UniversityQingdaoChina
- Laboratory for Marine Biology and BiotechnologyPilot National Laboratory for Marine Science and TechnologyQingdaoChina
| | - Nan Zhang
- School of BioengineeringQilu University of Technology (Shandong Academy of Sciences)JinanChina
| | - Zhao‐Jie Teng
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research CenterShandong UniversityQingdaoChina
| | - Xiao‐Di Wang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life SciencesOcean University of ChinaQingdaoChina
| | | | - Yu‐Zhong Zhang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life SciencesOcean University of ChinaQingdaoChina
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research CenterShandong UniversityQingdaoChina
- Laboratory for Marine Biology and BiotechnologyPilot National Laboratory for Marine Science and TechnologyQingdaoChina
| | - Hai‐Yan Cao
- Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life SciencesOcean University of ChinaQingdaoChina
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research CenterShandong UniversityQingdaoChina
| | - Chun‐Yang Li
- Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life SciencesOcean University of ChinaQingdaoChina
- Laboratory for Marine Biology and BiotechnologyPilot National Laboratory for Marine Science and TechnologyQingdaoChina
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Carrión O, Zhu XY, Williams BT, Wang J, Zhang XH, Todd JD. Molecular discoveries in microbial DMSP synthesis. Adv Microb Physiol 2023; 83:59-116. [PMID: 37507162 DOI: 10.1016/bs.ampbs.2023.03.001] [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] [Indexed: 07/30/2023]
Abstract
Dimethylsulfoniopropionate (DMSP) is one of the Earth's most abundant organosulfur compounds because many marine algae, bacteria, corals and some plants produce it to high mM intracellular concentrations. In these organisms, DMSP acts an anti-stress molecule with purported roles to protect against salinity, temperature, oxidative stress and hydrostatic pressure, amongst many other reported functions. However, DMSP is best known for being a major precursor of the climate-active gases and signalling molecules dimethylsulfide (DMS), methanethiol (MeSH) and, potentially, methane, through microbial DMSP catabolism. DMSP catabolism has been extensively studied and the microbes, pathways and enzymes involved have largely been elucidated through the application of molecular research over the last 17 years. In contrast, the molecular biology of DMSP synthesis is a much newer field, with the first DMSP synthesis enzymes only being identified in the last 5 years. In this review, we discuss how the elucidation of key DMSP synthesis enzymes has greatly expanded our knowledge of the diversity of DMSP-producing organisms, the pathways used, and what environmental factors regulate production, as well as to inform on the physiological roles of DMSP. Importantly, the identification of key DMSP synthesis enzymes in the major groups of DMSP producers has allowed scientists to study the distribution and predict the importance of different DMSP-producing organisms to global DMSP production in diverse marine and sediment environments. Finally, we highlight key challenges for future molecular research into DMSP synthesis that need addressing to better understand the cycling of this important marine organosulfur compound, and its magnitude in the environment.
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Affiliation(s)
- Ornella Carrión
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom.
| | - Xiao-Yu Zhu
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Beth T Williams
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Jinyan Wang
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Xiao-Hua Zhang
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Jonathan D Todd
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom.
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Shu Y, Wang Y, Wei Z, Gao N, Wang S, Li C, Xing Q, Hu X, Zhang X, Zhang Y, Zhang W, Bao Z, Ding W. A bacterial symbiont in the gill of the marine scallop Argopecten irradians irradians metabolizes dimethylsulfoniopropionate. MLIFE 2023; 2:178-189. [PMID: 38817626 PMCID: PMC10989825 DOI: 10.1002/mlf2.12072] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 04/23/2023] [Accepted: 05/15/2023] [Indexed: 06/01/2024]
Abstract
Microbial lysis of dimethylsulfoniopropionate (DMSP) is a key step in marine organic sulfur cycling and has been recently demonstrated to play an important role in mediating interactions between bacteria, algae, and zooplankton. To date, microbes that have been found to lyse DMSP are largely confined to free-living and surface-attached bacteria. In this study, we report for the first time that a symbiont (termed "Rhodobiaceae bacterium HWgs001") in the gill of the marine scallop Argopecten irradians irradians can lyse and metabolize DMSP. Analysis of 16S rRNA gene sequences suggested that HWgs001 accounted for up to 93% of the gill microbiota. Microscopic observations suggested that HWgs001 lived within the gill tissue. Unlike symbionts of other bivalves, HWgs001 belongs to Alphaproteobacteria rather than Gammaproteobacteria, and no genes for carbon fixation were identified in its small genome. Moreover, HWgs001 was found to possess a dddP gene, responsible for the lysis of DMSP to acrylate. The enzymatic activity of dddP was confirmed using the heterologous expression, and in situ transcription of the gene in scallop gill tissues was demonstrated using reverse-transcription PCR. Together, these results revealed a taxonomically and functionally unique symbiont, which represents the first-documented DMSP-metabolizing symbiont likely to play significant roles in coastal marine ecosystems.
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Affiliation(s)
- Yi Shu
- MOE Key Laboratory of Marine Genetics and BreedingOcean University of ChinaQingdaoChina
- Laboratory of Tropical Marine Germplasm Resources and Breeding Engineering, Sanya Oceanographic InstitutionOcean University of ChinaSanyaChina
| | - Yongming Wang
- MOE Key Laboratory of Marine Genetics and BreedingOcean University of ChinaQingdaoChina
- Laboratory of Tropical Marine Germplasm Resources and Breeding Engineering, Sanya Oceanographic InstitutionOcean University of ChinaSanyaChina
| | - Zhongcheng Wei
- MOE Key Laboratory of Marine Genetics and BreedingOcean University of ChinaQingdaoChina
| | - Ning Gao
- MOE Key Laboratory of Marine Genetics and BreedingOcean University of ChinaQingdaoChina
- Laboratory of Tropical Marine Germplasm Resources and Breeding Engineering, Sanya Oceanographic InstitutionOcean University of ChinaSanyaChina
| | - Shuyan Wang
- College of Marine Life SciencesOcean University of ChinaQingdaoChina
| | - Chun‐Yang Li
- College of Marine Life SciencesOcean University of ChinaQingdaoChina
| | - Qiang Xing
- MOE Key Laboratory of Marine Genetics and BreedingOcean University of ChinaQingdaoChina
- College of Marine Life SciencesOcean University of ChinaQingdaoChina
| | - Xiaoli Hu
- MOE Key Laboratory of Marine Genetics and BreedingOcean University of ChinaQingdaoChina
- Laboratory of Tropical Marine Germplasm Resources and Breeding Engineering, Sanya Oceanographic InstitutionOcean University of ChinaSanyaChina
| | - Xiao‐Hua Zhang
- College of Marine Life SciencesOcean University of ChinaQingdaoChina
| | - Yu‐Zhong Zhang
- College of Marine Life SciencesOcean University of ChinaQingdaoChina
| | - Weipeng Zhang
- Institute of Evolution & Marine BiodiversityOcean University of ChinaQingdaoChina
| | - Zhenmin Bao
- MOE Key Laboratory of Marine Genetics and BreedingOcean University of ChinaQingdaoChina
- Laboratory of Tropical Marine Germplasm Resources and Breeding Engineering, Sanya Oceanographic InstitutionOcean University of ChinaSanyaChina
| | - Wei Ding
- MOE Key Laboratory of Marine Genetics and BreedingOcean University of ChinaQingdaoChina
- College of Marine Life SciencesOcean University of ChinaQingdaoChina
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8
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Zhao Y, Wang H, Wang H, Liu H, Zhang Y, Zhang J, Pi Y, Yang P, Wang Q. Sulfide causes histological damage, oxidative stress, metabolic disorders and gut microbiota dysbiosis in juvenile sea cucumber Apostichopus japonicus Selenka. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2023; 258:106439. [PMID: 36965428 DOI: 10.1016/j.aquatox.2023.106439] [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: 05/16/2022] [Revised: 12/01/2022] [Accepted: 02/16/2023] [Indexed: 06/18/2023]
Abstract
Sulfide is a common harmful substance in sediments, with an especially high risk for deposit feeder organisms. The sea cucumber Apostichopus japonicus is a typical benthic feeder, and its intestine is the first line of defense and serves as a crucial barrier function. In this study, histological, physiological, gut microbiota, and metabolomic analyses were performed to explore the toxic response in the intestine of juvenile A. japonicus exposed to 0, 0.8, and 1.6 mg/L sulfide stress for 96 h. The results revealed sulfide-induced intestinal inflammatory symptoms and oxidative stress. Moreover, gut bacterial composition was observed after sulfide exposure, with an increase in Proteobacteria and a decrease in Cyanobacteria and Planctomycetes. Specifically, sulfide increased a set of sulfide-removing bacteria and opportunistic pathogens while decreasing several putative beneficial substance-producing bacteria. The metabolomic analysis indicated that sulfide also disturbed metabolic homeostasis, especially lipid and energy metabolism, in intestine. Interestingly, several intestinal bacteria were further identified to be significantly correlated with metabolic changes; for example, the decreased abundance levels of Bacillus, Corynebacterium, and Psychromonas were positively correlated with important energy metabolites, including maleic acid, farnesyl pyrophosphate, thiamine, butynoic acid, and deoxycholic acid. Thus, our research provides new insights into the mechanisms associated with the intestinal metabolic and microbiota response involved in sulfide stress adaptation strategies of juvenile A. japonicus.
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Affiliation(s)
- Ye Zhao
- Ocean school, Yantai University, Yantai, 264005, PR China.
| | - Han Wang
- Ocean school, Yantai University, Yantai, 264005, PR China
| | - Haona Wang
- Ocean school, Yantai University, Yantai, 264005, PR China
| | - Hui Liu
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, PR China
| | - Yanying Zhang
- Ocean school, Yantai University, Yantai, 264005, PR China
| | - Jianwei Zhang
- Shandong Anyuan Seed Technology Co. Ltd, Yantai, 265617, PR China
| | - Yongrui Pi
- Ocean school, Yantai University, Yantai, 264005, PR China
| | - Pei Yang
- Ocean school, Yantai University, Yantai, 264005, PR China
| | - Qing Wang
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, PR China.
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Lu J, Shu Y, Zhang H, Zhang S, Zhu C, Ding W, Zhang W. The Landscape of Global Ocean Microbiome: From Bacterioplankton to Biofilms. Int J Mol Sci 2023; 24:6491. [PMID: 37047466 PMCID: PMC10095273 DOI: 10.3390/ijms24076491] [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: 03/08/2023] [Revised: 03/26/2023] [Accepted: 03/27/2023] [Indexed: 04/01/2023] Open
Abstract
The development of metagenomics has opened up a new era in the study of marine microbiota, which play important roles in biogeochemical cycles. In recent years, the global ocean sampling expeditions have spurred this research field toward a deeper understanding of the microbial diversities and functions spanning various lifestyles, planktonic (free-living) or sessile (biofilm-associated). In this review, we deliver a comprehensive summary of marine microbiome datasets generated in global ocean expeditions conducted over the last 20 years, including the Sorcerer II GOS Expedition, the Tara Oceans project, the bioGEOTRACES project, the Micro B3 project, the Bio-GO-SHIP project, and the Marine Biofilms. These datasets have revealed unprecedented insights into the microscopic life in our oceans and led to the publication of world-leading research. We also note the progress of metatranscriptomics and metaproteomics, which are confined to local marine microbiota. Furthermore, approaches to transforming the global ocean microbiome datasets are highlighted, and the state-of-the-art techniques that can be combined with data analyses, which can present fresh perspectives on marine molecular ecology and microbiology, are proposed.
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Affiliation(s)
- Jie Lu
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266100, China
| | - Yi Shu
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao 266100, China;
| | - Heng Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266100, China
| | - Shangxian Zhang
- Haide College, Ocean University of China, Qingdao 266100, China
| | - Chengrui Zhu
- Haide College, Ocean University of China, Qingdao 266100, China
| | - Wei Ding
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao 266100, China;
- College of Marine Life Sciences, Ocean University of China, Qingdao 266100, China
- Haide College, Ocean University of China, Qingdao 266100, China
| | - Weipeng Zhang
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266100, China
- College of Marine Life Sciences, Ocean University of China, Qingdao 266100, China
- Haide College, Ocean University of China, Qingdao 266100, China
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Tian K, Meng Q, Li S, Chang M, Meng F, Yu Y, Li H, Qiu Q, Shao J, Huo H. Mechanism of 17β-estradiol degradation by Rhodococcus equi via the 4,5-seco pathway and its key genes. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 312:120021. [PMID: 36037852 DOI: 10.1016/j.envpol.2022.120021] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 08/04/2022] [Accepted: 08/17/2022] [Indexed: 06/15/2023]
Abstract
Steroid estrogens have been detected in oceans, rivers, lakes, groundwaters, soils, and even urban water supply systems, thereby inevitably imposing serious impacts on human health and ecological safety. Indeed, many estrogen-degrading bacterial strains and degradation pathways have been reported, with the 4,5-seco pathway being particularly important. However, few studies have evaluated the use of the 4,5-seco pathway by actinomycetes to degrade 17β-estradiol (E2). In this study, 5 genes involved in E2 degradation were identified in the Rhodococcus equi DSSKP-R-001 (R-001) genome and then heterologously expressed to confirm their functions. The transformation of E2 with hsd17b14 reached 63.7% within 30 h, resulting in transformation into estrone (E1). Furthermore, we found that At1g12200-encoded flavin-binding monooxygenase (FMOAt1g12200) can transform E1 at a rate of 51.6% within 30 h and can transform E1 into 4-hydroxyestrone (4-OH E1). In addition, catA and hsaC genes were identified to further transform 4-OH E1 at a rate of 97-99%, and this reaction was accomplished by C-C cleavage at the C4 position of the A ring of 4-OH E1. This study represents the first report on the roles of these genes in estrogen degradation and provides new insights into the mechanisms of microbial estrogen metabolism and a better understanding of E2 degradation via the 4,5-seco pathway by actinomycetes.
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Affiliation(s)
- Kejian Tian
- School of Environment, Northeast Normal University, No. 2555 Jingyue Avenue, Changchun City, Jilin Province, China
| | - Qi Meng
- School of Environment, Northeast Normal University, No. 2555 Jingyue Avenue, Changchun City, Jilin Province, China
| | - Shuaiguo Li
- School of Environment, Northeast Normal University, No. 2555 Jingyue Avenue, Changchun City, Jilin Province, China
| | - Menghan Chang
- School of Environment, Northeast Normal University, No. 2555 Jingyue Avenue, Changchun City, Jilin Province, China
| | - Fanxing Meng
- Jilin Province Water Resources and Hydropower Consultative Company of PR China, Changchun City, Jilin Province, China
| | - Yue Yu
- School of Environment, Northeast Normal University, No. 2555 Jingyue Avenue, Changchun City, Jilin Province, China
| | - Han Li
- School of Environment, Northeast Normal University, No. 2555 Jingyue Avenue, Changchun City, Jilin Province, China
| | - Qing Qiu
- School of Environment, Northeast Normal University, No. 2555 Jingyue Avenue, Changchun City, Jilin Province, China
| | - Junhua Shao
- School of Environment, Northeast Normal University, No. 2555 Jingyue Avenue, Changchun City, Jilin Province, China
| | - Hongliang Huo
- School of Environment, Northeast Normal University, No. 2555 Jingyue Avenue, Changchun City, Jilin Province, China; Jilin Province Laboratory of Water Pollution Control and Resource Engineering, Changchun, 130117, China.
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11
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Novel Insights into Dimethylsulfoniopropionate Catabolism by Cultivable Bacteria in the Arctic Kongsfjorden. Appl Environ Microbiol 2021; 88:e0180621. [PMID: 34788071 DOI: 10.1128/aem.01806-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Dimethylsulfoniopropionate (DMSP) is one of the most abundant organic sulfur compounds in the oceans, which is mainly degraded by bacteria through two pathways, a cleavage pathway and a demethylation pathway. Its volatile catabolites dimethyl sulfide (DMS) and methanethiol (MT) in these pathways play important roles in the global sulfur cycle and have potential influences on the global climate. Intense DMS/DMSP cycling occurs in the Arctic. However, little is known about the diversity of cultivable DMSP-catabolizing bacteria in the Arctic and how they catabolize DMSP. Here, we screened DMSP-catabolizing bacteria from Arctic samples and found that bacteria of four genera (Psychrobacter, Pseudoalteromonas, Alteromonas and Vibrio) could grow with DMSP as the sole carbon source, among which Psychrobacter and Pseudoalteromonas are predominant. Four representative strains (Psychrobacter sp. K31L, Pseudoalteromonas sp. K222D, Alteromonas sp. K632G and Vibrio sp. G41H) from different genera were selected to probe their DMSP catabolic pathways. All these strains produce DMS and MT simultaneously during their growth on DMSP, indicating that all strains likely possess the two DMSP catabolic pathways. On the basis of genomic and biochemical analyses, the DMSP catabolic pathways in these strains were proposed. Bioinformatic analysis indicated that most bacteria of Psychrobacter and Vibrio have the potential to catabolize DMSP via the demethylation pathway, and that only a small portion of Psychrobacter strains may catabolize DMSP via the cleavage pathway. This study provides novel insights into DMSP catabolism in marine bacteria. IMPORTANCE Dimethylsulfoniopropionate (DMSP) is abundant in the oceans. The catabolism of DMSP is an important step of the global sulfur cycle. Although Gammaproteobacteria are widespread in the oceans, the contribution of Gammaproteobacteria in global DMSP catabolism is not fully understood. Here, we found that bacteria of four genera belonging to Gammaproteobacteria (Psychrobacter, Pseudoalteromonas, Alteromonas and Vibrio), which were isolated from Arctic samples, were able to grow on DMSP. The DMSP catabolic pathways of representative strains were proposed. Bioinformatic analysis indicates that most bacteria of Psychrobacter and Vibrio have the potential to catabolize DMSP via the demethylation pathway, and that only a small portion of Psychrobacter strains may catabolize DMSP via the cleavage pathway. Our results suggest that novel DMSP dethiomethylases/demethylases may exist in Pseudoalteromonas, Alteromonas and Vibrio, and that Gammaproteobacteria may be important participants in marine, especially in polar DMSP cycling.
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Teng ZJ, Qin QL, Zhang W, Li J, Fu HH, Wang P, Lan M, Luo G, He J, McMinn A, Wang M, Chen XL, Zhang YZ, Chen Y, Li CY. Correction to: Biogeographic traits of dimethyl sulfide and dimethylsulfoniopropionate cycling in polar oceans. MICROBIOME 2021; 9:221. [PMID: 34753519 PMCID: PMC8576990 DOI: 10.1186/s40168-021-01182-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Affiliation(s)
- Zhao-Jie Teng
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China
| | - Qi-Long Qin
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China
| | - Weipeng Zhang
- College of Marine Life Sciences, Institute for Advanced Ocean Study, Ocean University of China, Qingdao, 266003, China
| | - Jian Li
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China
| | - Hui-Hui Fu
- College of Marine Life Sciences, Institute for Advanced Ocean Study, Ocean University of China, Qingdao, 266003, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266373, China
| | - Peng Wang
- College of Marine Life Sciences, Institute for Advanced Ocean Study, Ocean University of China, Qingdao, 266003, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266373, China
| | - Musheng Lan
- The Key Laboratory for Polar Science MNR, Polar Research Institute of China, Shanghai, 200136, China
| | - Guangfu Luo
- The Key Laboratory for Polar Science MNR, Polar Research Institute of China, Shanghai, 200136, China
| | - Jianfeng He
- The Key Laboratory for Polar Science MNR, Polar Research Institute of China, Shanghai, 200136, China
| | - Andrew McMinn
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania, Australia
| | - Min Wang
- College of Marine Life Sciences, Institute for Advanced Ocean Study, Ocean University of China, Qingdao, 266003, China
| | - Xiu-Lan Chen
- College of Marine Life Sciences, Institute for Advanced Ocean Study, Ocean University of China, Qingdao, 266003, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266373, China
| | - Yu-Zhong Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China
- College of Marine Life Sciences, Institute for Advanced Ocean Study, Ocean University of China, Qingdao, 266003, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266373, China
| | - Yin Chen
- College of Marine Life Sciences, Institute for Advanced Ocean Study, Ocean University of China, Qingdao, 266003, China.
- School of Life Sciences, University of Warwick, Coventry, UK.
| | - Chun-Yang Li
- College of Marine Life Sciences, Institute for Advanced Ocean Study, Ocean University of China, Qingdao, 266003, China.
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266373, China.
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