1
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Liu X, Zhang Y, Sun H, Tan S, Zhang XH. Highly active bacterial DMSP metabolism in the surface microlayer of the eastern China marginal seas. Front Microbiol 2023; 14:1135083. [PMID: 37032870 PMCID: PMC10076866 DOI: 10.3389/fmicb.2023.1135083] [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: 12/31/2022] [Accepted: 03/06/2023] [Indexed: 04/11/2023] Open
Abstract
The microbial cycling of dimethylsulfoniopropionate (DMSP) and the resulting gaseous catabolites dimethylsulfide (DMS) or methylmercaptan (MeSH) play key roles in the global sulfur cycle and potentially climate regulation. As the ocean-atmosphere boundary, the sea surface microlayer (SML) is important for the generation and emission of DMS and MeSH. However, understanding of the microbial DMSP metabolism remains limited in the SML. Here, we studied the spatiotemporal differences for DMS/DMSP, bacterial community structure and the key bacterial DMSP metabolic genes between SML and subsurface seawater (SSW) samples in the eastern China marginal seas (the East China Sea and Yellow Sea). In general, DMSPd and DMSPt concentrations, and the abundance of total, free-living and particle-associated bacteria were higher in SML than that in SSW. DMSP synthesis (~7.81-fold for dsyB, ~2.93-fold for mmtN) and degradation genes (~5.38-fold for dmdA, ~6.27-fold for dddP) detected in SML were more abundant compared with SSW samples. Free-living bacteria were the main DMSP producers and consumers in eastern Chinese marginal sea. Regionally, the bacterial community structure was distinct between the East China Sea and the Yellow Sea. The abundance of DMSP metabolic genes (dsyB, dmdA, and dddP) and genera in the East China Sea were higher than those of the Yellow Sea. Seasonally, DMSP/DMS level and DMSP metabolic genes and bacteria were more abundant in SML of the East China Sea in summer than in spring. Different from those in spring, Ruegeria was the dominant DMSP metabolic bacteria. In conclusion, the DMSP synthesis and degradation showed significant spatiotemporal differences in the SML of the eastern China marginal seas, and were consistently more active in the SML than in the SSW.
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Affiliation(s)
- Xiujie Liu
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yunhui Zhang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao, China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Hao Sun
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Siyin Tan
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Xiao-Hua Zhang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao, China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
- *Correspondence: Xiao-Hua Zhang,
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2
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Seong HJ, Roux S, Hwang CY, Sul WJ. Marine DNA methylation patterns are associated with microbial community composition and inform virus-host dynamics. MICROBIOME 2022; 10:157. [PMID: 36167684 PMCID: PMC9516812 DOI: 10.1186/s40168-022-01340-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 07/28/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND DNA methylation in prokaryotes is involved in many different cellular processes including cell cycle regulation and defense against viruses. To date, most prokaryotic methylation systems have been studied in culturable microorganisms, resulting in a limited understanding of DNA methylation from a microbial ecology perspective. Here, we analyze the distribution patterns of several microbial epigenetics marks in the ocean microbiome through genome-centric metagenomics across all domains of life. RESULTS We reconstructed 15,056 viral, 252 prokaryotic, 56 giant viral, and 6 eukaryotic metagenome-assembled genomes from northwest Pacific Ocean seawater samples using short- and long-read sequencing approaches. These metagenome-derived genomes mostly represented novel taxa, and recruited a majority of reads. Thanks to single-molecule real-time (SMRT) sequencing technology, base modification could also be detected for these genomes. This showed that DNA methylation can readily be detected across dominant oceanic bacterial, archaeal, and viral populations, and microbial epigenetic changes correlate with population differentiation. Furthermore, our genome-wide epigenetic analysis of Pelagibacter suggests that GANTC, a DNA methyltransferase target motif, is related to the cell cycle and is affected by environmental conditions. Yet, the presence of this motif also partitions the phylogeny of the Pelagibacter phages, possibly hinting at a competitive co-evolutionary history and multiple effects of a single methylation mark. CONCLUSIONS Overall, this study elucidates that DNA methylation patterns are associated with ecological changes and virus-host dynamics in the ocean microbiome. Video Abstract.
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Affiliation(s)
- Hoon Je Seong
- Department of Systems Biotechnology, Chung-Ang University, Anseong, Republic of Korea
| | - Simon Roux
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Chung Yeon Hwang
- School of Earth and Environmental Sciences and Research Institute of Oceanography, Seoul National University, Seoul, Republic of Korea
| | - Woo Jun Sul
- Department of Systems Biotechnology, Chung-Ang University, Anseong, Republic of Korea
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3
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O’Brien J, McParland EL, Bramucci AR, Ostrowski M, Siboni N, Ingleton T, Brown MV, Levine NM, Laverock B, Petrou K, Seymour J. The Microbiological Drivers of Temporally Dynamic Dimethylsulfoniopropionate Cycling Processes in Australian Coastal Shelf Waters. Front Microbiol 2022; 13:894026. [PMID: 35783424 PMCID: PMC9240709 DOI: 10.3389/fmicb.2022.894026] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 05/20/2022] [Indexed: 01/04/2023] Open
Abstract
The organic sulfur compounds dimethylsulfoniopropionate (DMSP) and dimethyl sulfoxide (DMSO) play major roles in the marine microbial food web and have substantial climatic importance as sources and sinks of dimethyl sulfide (DMS). Seasonal shifts in the abundance and diversity of the phytoplankton and bacteria that cycle DMSP are likely to impact marine DMS (O) (P) concentrations, but the dynamic nature of these microbial interactions is still poorly resolved. Here, we examined the relationships between microbial community dynamics with DMS (O) (P) concentrations during a 2-year oceanographic time series conducted on the east Australian coast. Heterogenous temporal patterns were apparent in chlorophyll a (chl a) and DMSP concentrations, but the relationship between these parameters varied over time, suggesting the phytoplankton and bacterial community composition were affecting the net DMSP concentrations through differential DMSP production and degradation. Significant increases in DMSP were regularly measured in spring blooms dominated by predicted high DMSP-producing lineages of phytoplankton (Heterocapsa, Prorocentrum, Alexandrium, and Micromonas), while spring blooms that were dominated by predicted low DMSP-producing phytoplankton (Thalassiosira) demonstrated negligible increases in DMSP concentrations. During elevated DMSP concentrations, a significant increase in the relative abundance of the key copiotrophic bacterial lineage Rhodobacterales was accompanied by a three-fold increase in the gene, encoding the first step of DMSP demethylation (dmdA). Significant temporal shifts in DMS concentrations were measured and were significantly correlated with both fractions (0.2-2 μm and >2 μm) of microbial DMSP lyase activity. Seasonal increases of the bacterial DMSP biosynthesis gene (dsyB) and the bacterial DMS oxidation gene (tmm) occurred during the spring-summer and coincided with peaks in DMSP and DMSO concentration, respectively. These findings, along with significant positive relationships between dsyB gene abundance and DMSP, and tmm gene abundance with DMSO, reinforce the significant role planktonic bacteria play in producing DMSP and DMSO in ocean surface waters. Our results highlight the highly dynamic nature and myriad of microbial interactions that govern sulfur cycling in coastal shelf waters and further underpin the importance of microbial ecology in mediating important marine biogeochemical processes.
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Affiliation(s)
- James O’Brien
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, Australia
- School of Life Sciences, University of Technology Sydney, Ultimo, NSW, Australia
| | - Erin L. McParland
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, United States
| | - Anna R. Bramucci
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, Australia
| | - Martin Ostrowski
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, Australia
| | - Nachshon Siboni
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, Australia
| | - Timothy Ingleton
- Water, Wetlands and Coastal Science, NSW Department of Planning, Industry and Environment, Lidcombe, NSW, Australia
| | - Mark V. Brown
- School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW, Australia
| | - Naomi M. Levine
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States
| | - Bonnie Laverock
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, Australia
| | - Katherina Petrou
- School of Life Sciences, University of Technology Sydney, Ultimo, NSW, Australia
| | - Justin Seymour
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, Australia
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4
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Shaw DK, Sekar J, Ramalingam PV. Recent insights into oceanic dimethylsulfoniopropionate biosynthesis and catabolism. Environ Microbiol 2022; 24:2669-2700. [PMID: 35611751 DOI: 10.1111/1462-2920.16045] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 05/07/2022] [Accepted: 05/09/2022] [Indexed: 11/29/2022]
Abstract
Dimethylsulfoniopropionate (DMSP), a globally important organosulfur compound is produced in prodigious amounts (2.0 Pg sulfur) annually in the marine environment by phytoplankton, macroalgae, heterotrophic bacteria, some corals and certain higher plants. It is an important marine osmolyte and a major precursor molecule for the production of climate-active volatile gas dimethyl sulfide (DMS). DMSP synthesis take place via three pathways: a transamination 'pathway-' in some marine bacteria and algae, a Met-methylation 'pathway-' in angiosperms and bacteria and a decarboxylation 'pathway-' in the dinoflagellate, Crypthecodinium. The enzymes DSYB and TpMMT are involved in the DMSP biosynthesis in eukaryotes while marine heterotrophic bacteria engage key enzymes such as DsyB and MmtN. Several marine bacterial communities import DMSP and degrade it via cleavage or demethylation pathways or oxidation pathway, thereby generating DMS, methanethiol, and dimethylsulfoxonium propionate, respectively. DMSP is cleaved through diverse DMSP lyase enzymes in bacteria and via Alma1 enzyme in phytoplankton. The demethylation pathway involves four different enzymes, namely DmdA, DmdB, DmdC and DmdD/AcuH. However, enzymes involved in the oxidation pathway have not been yet identified. We reviewed the recent advances on the synthesis and catabolism of DMSP and enzymes that are involved in these processes.
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Affiliation(s)
- Deepak Kumar Shaw
- Microbiology Lab, Department of Biotechnology, M. S. Swaminathan Research Foundation, Taramani, Chennai, 600113, Tamil Nadu, India
| | - Jegan Sekar
- Microbiology Lab, Department of Biotechnology, M. S. Swaminathan Research Foundation, Taramani, Chennai, 600113, Tamil Nadu, India
| | - Prabavathy Vaiyapuri Ramalingam
- Microbiology Lab, Department of Biotechnology, M. S. Swaminathan Research Foundation, Taramani, Chennai, 600113, Tamil Nadu, India
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5
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Zhang Y, Sun K, Sun C, Shi X, Todd JD, Zhang XH. Dimethylsulfoniopropionate Biosynthetic Bacteria in the Subseafloor Sediments of the South China Sea. Front Microbiol 2021; 12:731524. [PMID: 34707588 PMCID: PMC8543147 DOI: 10.3389/fmicb.2021.731524] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Accepted: 09/17/2021] [Indexed: 11/13/2022] Open
Abstract
Dimethylsulfoniopropionate (DMSP) is one of Earth’s most abundant organosulfur molecules, and bacteria in marine sediments have been considered significant producers. However, the vertical profiles of DMSP content and DMSP-producing bacteria in subseafloor sediment have not been described. Here, we used culture-dependent and -independent methods to investigate microbial DMSP production and cycling potential in South China Sea (SCS) sediment. The DMSP content of SCS sediment decreased from 11.25 to 20.90 nmol g–1 in the surface to 0.56–2.08 nmol g–1 in the bottom layers of 8-m-deep subseafloor sediment cores (n = 10). Very few eukaryotic plastid sequences were detected in the sediment, supporting bacteria and not algae as important sediment DMSP producers. Known bacterial DMSP biosynthesis genes (dsyB and mmtN) were only predicted to be in 0.0007–0.0195% of sediment bacteria, but novel DMSP-producing isolates with potentially unknown DMSP synthesis genes and/or pathways were identified in these sediments, including Marinobacter (Gammaproteobacteria) and Erythrobacter (Alphaproteobacteria) sp. The abundance of bacteria with the potential to produce DMSP decreased with sediment depth and was extremely low at 690 cm. Furthermore, distinct DMSP-producing bacterial groups existed in surface and subseafloor sediment samples, and their abundance increased when samples were incubated under conditions known to enrich for DMSP-producing bacteria. Bacterial DMSP catabolic genes were also most abundant in the surface oxic sediments with high DMSP concentrations. This study extends the current knowledge of bacterial DMSP biosynthesis in marine sediments and implies that DMSP biosynthesis is not only confined to the surface oxic sediment zones. It highlights the importance of future work to uncover the DMSP biosynthesis genes/pathways in novel DMSP-producing bacteria.
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Affiliation(s)
- Yunhui Zhang
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Kai Sun
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Chuang Sun
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Xiaochong Shi
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Jonathan D Todd
- School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
| | - Xiao-Hua Zhang
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
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6
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Sun H, Liu J, Tan S, Zheng Y, Wang X, Liang J, Todd JD, Zhang XH. Spatiotemporal distribution of bacterial dimethylsulfoniopropionate producing and catabolic genes in the Changjiang Estuary. Environ Microbiol 2021; 23:7073-7092. [PMID: 34693622 DOI: 10.1111/1462-2920.15813] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 09/05/2021] [Accepted: 10/05/2021] [Indexed: 11/28/2022]
Abstract
The osmolyte dimethylsulfoniopropionate (DMSP) is produced in petagram amounts by marine microorganisms. Estuaries provide natural gradients in salinity and nutrients, factors known to regulate DMSP production; yet there have been no molecular studies of DMSP production and cycling across these gradients. Here, we study the abundance, distribution and transcription of key DMSP synthesis (e.g. dsyB and mmtN) and catabolic (e.g. dddP and dmdA) genes along the salinity gradient of the Changjiang Estuary. DMSP levels did not correlate with Chl a across the salinity gradient. In contrast, DMSP concentration, abundance of bacterial DMSP producers and their dsyB and mmtN transcripts were lowest in the freshwater samples and increased abruptly with salinity in the transitional and seawater samples. Metagenomics analysis suggests bacterial DMSP-producers were more abundant than their algal equivalents and were more prominent in summer than winter samples. Bacterial DMSP catabolic genes and their transcripts followed the same trend of being greatly enhanced in transitional and seawater samples with higher DMSP levels than freshwater samples. DMSP cleavage was likely the dominant catabolic pathway, with DMSP lyase genes being ~4.3-fold more abundant than the demethylase gene dmdA. This is an exemplar study for future research on microbial DMSP cycling in estuary environments.
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Affiliation(s)
- Hao Sun
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
| | - Ji Liu
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China
| | - Siyin Tan
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China
| | - Yanfen Zheng
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China
| | - Xiaolei Wang
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China
| | - Jinchang Liang
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China
| | - Jonathan D Todd
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR47TJ, UK
| | - Xiao-Hua Zhang
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China.,Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
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7
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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. Biogeographic traits of dimethyl sulfide and dimethylsulfoniopropionate cycling in polar oceans. MICROBIOME 2021; 9:207. [PMID: 34654476 PMCID: PMC8520302 DOI: 10.1186/s40168-021-01153-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 08/04/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Dimethyl sulfide (DMS) is the dominant volatile organic sulfur in global oceans. The predominant source of oceanic DMS is the cleavage of dimethylsulfoniopropionate (DMSP), which can be produced by marine bacteria and phytoplankton. Polar oceans, which represent about one fifth of Earth's surface, contribute significantly to the global oceanic DMS sea-air flux. However, a global overview of DMS and DMSP cycling in polar oceans is still lacking and the key genes and the microbial assemblages involved in DMSP/DMS transformation remain to be fully unveiled. RESULTS Here, we systematically investigated the biogeographic traits of 16 key microbial enzymes involved in DMS/DMSP cycling in 60 metagenomic samples from polar waters, together with 174 metagenome and 151 metatranscriptomes from non-polar Tara Ocean dataset. Our analyses suggest that intense DMS/DMSP cycling occurs in the polar oceans. DMSP demethylase (DmdA), DMSP lyases (DddD, DddP, and DddK), and trimethylamine monooxygenase (Tmm, which oxidizes DMS to dimethylsulfoxide) were the most prevalent bacterial genes involved in global DMS/DMSP cycling. Alphaproteobacteria (Pelagibacterales) and Gammaproteobacteria appear to play prominent roles in DMS/DMSP cycling in polar oceans. The phenomenon that multiple DMS/DMSP cycling genes co-occurred in the same bacterial genome was also observed in metagenome assembled genomes (MAGs) from polar oceans. The microbial assemblages from the polar oceans were significantly correlated with water depth rather than geographic distance, suggesting the differences of habitats between surface and deep waters rather than dispersal limitation are the key factors shaping microbial assemblages involved in DMS/DMSP cycling in polar oceans. CONCLUSIONS Overall, this study provides a global overview of the biogeographic traits of known bacterial genes involved in DMS/DMSP cycling from the Arctic and Antarctic oceans, laying a solid foundation for further studies of DMS/DMSP cycling in polar ocean microbiome at the enzymatic, metabolic, and processual levels. Video Abstract.
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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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8
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Fernandez E, Ostrowski M, Siboni N, Seymour JR, Petrou K. Uptake of Dimethylsulfoniopropionate (DMSP) by Natural Microbial Communities of the Great Barrier Reef (GBR), Australia. Microorganisms 2021; 9:microorganisms9091891. [PMID: 34576786 PMCID: PMC8471478 DOI: 10.3390/microorganisms9091891] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 08/17/2021] [Accepted: 09/01/2021] [Indexed: 01/04/2023] Open
Abstract
Dimethylsulfoniopropionate (DMSP) is a key organic sulfur compound that is produced by many phytoplankton and macrophytes and is ubiquitous in marine environments. Following its release into the water column, DMSP is primarily metabolised by heterotrophic bacterioplankton, but recent evidence indicates that non-DMSP producing phytoplankton can also assimilate DMSP from the surrounding environment. In this study, we examined the uptake of DMSP by communities of bacteria and phytoplankton within the waters of the Great Barrier Reef (GBR), Australia. We incubated natural GBR seawater with DMSP and quantified the uptake of DMSP by different fractions of the microbial community (>8 µm, 3-8 µm, <3 µm). We also evaluated how microbial community composition and the abundances of DMSP degrading genes are influenced by elevated dissolved DMSP levels. Our results showed uptake and accumulation of DMSP in all size fractions of the microbial community, with the largest fraction (>8 µm) forming the dominant sink, increasing in particulate DMSP by 44-115% upon DMSP enrichment. Longer-term incubations showed however, that DMSP retention was short lived (<24 h) and microbial responses to DMSP enrichment differed depending on the community carbon and sulfur demand. The response of the microbial communities from inside the reef indicated a preference towards cleaving DMSP into the climatically active aerosol dimethyl sulfide (DMS), whereas communities from the outer reef were sulfur and carbon limited, resulting in more DMSP being utilised by the cells. Our results show that DMSP uptake is shared across members of the microbial community, highlighting larger phytoplankton taxa as potentially relevant DMSP reservoirs and provide new information on sulfur cycling as a function of community metabolism in deeper, oligotrophic GBR waters.
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Affiliation(s)
- Eva Fernandez
- School of Life Sciences, University of Technology Sydney, Ultimo, NSW 2007, Australia;
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW 2007, Australia; (M.O.); (N.S.); (J.R.S.)
| | - Martin Ostrowski
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW 2007, Australia; (M.O.); (N.S.); (J.R.S.)
| | - Nachshon Siboni
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW 2007, Australia; (M.O.); (N.S.); (J.R.S.)
| | - Justin R. Seymour
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW 2007, Australia; (M.O.); (N.S.); (J.R.S.)
| | - Katherina Petrou
- School of Life Sciences, University of Technology Sydney, Ultimo, NSW 2007, Australia;
- Correspondence:
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9
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Liu J, Zhang Y, Liu J, Zhong H, Williams BT, Zheng Y, Curson ARJ, Sun C, Sun H, Song D, Wagner Mackenzie B, Bermejo Martínez A, Todd JD, Zhang XH. Bacterial Dimethylsulfoniopropionate Biosynthesis in the East China Sea. Microorganisms 2021; 9:microorganisms9030657. [PMID: 33810191 PMCID: PMC8004995 DOI: 10.3390/microorganisms9030657] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 03/14/2021] [Accepted: 03/19/2021] [Indexed: 12/16/2022] Open
Abstract
Dimethylsulfoniopropionate (DMSP) is one of Earth's most abundant organosulfur molecules. Recently, many marine heterotrophic bacteria were shown to produce DMSP, but few studies have combined culture-dependent and independent techniques to study their abundance, distribution, diversity and activity in seawater or sediment environments. Here we investigate bacterial DMSP production potential in East China Sea (ECS) samples. Total DMSP (DMSPt) concentration in ECS seawater was highest in surface waters (SW) where phytoplankton were most abundant, and it decreased with depth to near bottom waters. However, the percentage of DMSPt mainly apportioned to bacteria increased from the surface to the near bottom water. The highest DMSP concentration was detected in ECS oxic surface sediment (OSS) where phytoplankton were not abundant. Bacteria with the genetic potential to produce DMSP and relevant biosynthesis gene transcripts were prominent in all ECS seawater and sediment samples. Their abundance also increased with depth and was highest in the OSS samples. Microbial enrichments for DMSP-producing bacteria from sediment and seawater identified many novel taxonomic groups of DMSP-producing bacteria. Different profiles of DMSP-producing bacteria existed between seawater and sediment samples and there are still novel DMSP-producing bacterial groups to be discovered in these environments. This study shows that heterotrophic bacteria significantly contribute to the marine DMSP pool and that their contribution increases with water depth and is highest in seabed surface sediment where DMSP catabolic potential is lowest. Furthermore, distinct bacterial groups likely produce DMSP in seawater and sediment samples, and many novel producing taxa exist, especially in the sediment.
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Affiliation(s)
- Ji Liu
- College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; (J.L.); (Y.Z.); (J.L.); (H.Z.); (Y.Z.); (C.S.); (H.S.); (D.S.)
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK; (B.T.W.); (A.R.J.C.); (A.B.M.)
| | - Yunhui Zhang
- College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; (J.L.); (Y.Z.); (J.L.); (H.Z.); (Y.Z.); (C.S.); (H.S.); (D.S.)
| | - Jingli Liu
- College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; (J.L.); (Y.Z.); (J.L.); (H.Z.); (Y.Z.); (C.S.); (H.S.); (D.S.)
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK; (B.T.W.); (A.R.J.C.); (A.B.M.)
| | - Haohui Zhong
- College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; (J.L.); (Y.Z.); (J.L.); (H.Z.); (Y.Z.); (C.S.); (H.S.); (D.S.)
| | - Beth T. Williams
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK; (B.T.W.); (A.R.J.C.); (A.B.M.)
| | - Yanfen Zheng
- College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; (J.L.); (Y.Z.); (J.L.); (H.Z.); (Y.Z.); (C.S.); (H.S.); (D.S.)
| | - Andrew R. J. Curson
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK; (B.T.W.); (A.R.J.C.); (A.B.M.)
| | - Chuang Sun
- College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; (J.L.); (Y.Z.); (J.L.); (H.Z.); (Y.Z.); (C.S.); (H.S.); (D.S.)
| | - Hao Sun
- College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; (J.L.); (Y.Z.); (J.L.); (H.Z.); (Y.Z.); (C.S.); (H.S.); (D.S.)
| | - Delei Song
- College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; (J.L.); (Y.Z.); (J.L.); (H.Z.); (Y.Z.); (C.S.); (H.S.); (D.S.)
| | - Brett Wagner Mackenzie
- Department of Surgery, School of Medicine, The University of Auckland, Auckland 1142, New Zealand;
| | - Ana Bermejo Martínez
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK; (B.T.W.); (A.R.J.C.); (A.B.M.)
| | - Jonathan D. Todd
- College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; (J.L.); (Y.Z.); (J.L.); (H.Z.); (Y.Z.); (C.S.); (H.S.); (D.S.)
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK; (B.T.W.); (A.R.J.C.); (A.B.M.)
- Correspondence: (J.D.T.); (X.-H.Z.)
| | - Xiao-Hua Zhang
- College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; (J.L.); (Y.Z.); (J.L.); (H.Z.); (Y.Z.); (C.S.); (H.S.); (D.S.)
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
- Correspondence: (J.D.T.); (X.-H.Z.)
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10
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11
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Zheng Y, Wang J, Zhou S, Zhang Y, Liu J, Xue CX, Williams BT, Zhao X, Zhao L, Zhu XY, Sun C, Zhang HH, Xiao T, Yang GP, Todd JD, Zhang XH. Bacteria are important dimethylsulfoniopropionate producers in marine aphotic and high-pressure environments. Nat Commun 2020; 11:4658. [PMID: 32938931 PMCID: PMC7494906 DOI: 10.1038/s41467-020-18434-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 08/21/2020] [Indexed: 11/17/2022] Open
Abstract
Dimethylsulfoniopropionate (DMSP) is an important marine osmolyte. Aphotic environments are only recently being considered as potential contributors to global DMSP production. Here, our Mariana Trench study reveals a typical seawater DMSP/dimethylsulfide (DMS) profile, with highest concentrations in the euphotic zone and decreased but consistent levels below. The genetic potential for bacterial DMSP synthesis via the dsyB gene and its transcription is greater in the deep ocean, and is highest in the sediment.s DMSP catabolic potential is present throughout the trench waters, but is less prominent below 8000 m, perhaps indicating a preference to store DMSP in the deep for stress protection. Deep ocean bacterial isolates show enhanced DMSP production under increased hydrostatic pressure. Furthermore, bacterial dsyB mutants are less tolerant of deep ocean pressures than wild-type strains. Thus, we propose a physiological function for DMSP in hydrostatic pressure protection, and that bacteria are key DMSP producers in deep seawater and sediment. Dimethylsulfoniopropionate (DMSP) is an osmolyte produced by marine microbes that plays an important role in nutrient cycling and atmospheric chemistry. Here the authors go to the Mariana Trench—the deepest point in the ocean—and find bacteria are key DMSP producers, and that DMSP has a role in protection against high pressure.
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Affiliation(s)
- Yanfen Zheng
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Jinyan Wang
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Shun Zhou
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Yunhui Zhang
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Ji Liu
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Chun-Xu Xue
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Beth T Williams
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Xiuxiu Zhao
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Li Zhao
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Xiao-Yu Zhu
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Chuang Sun
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Hong-Hai Zhang
- MOE Key Laboratory of Marine Chemistry Theory and Technology, College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao, 266100, China
| | - Tian Xiao
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Gui-Peng Yang
- MOE Key Laboratory of Marine Chemistry Theory and Technology, College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao, 266100, China
| | - Jonathan D Todd
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK.
| | - Xiao-Hua Zhang
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China. .,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
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12
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Cui Y, Wong SK, Kaneko R, Mouri A, Tada Y, Nagao I, Chun SJ, Lee HG, Ahn CY, Oh HM, Sato-Takabe Y, Suzuki K, Fukuda H, Nagata T, Kogure K, Hamasaki K. Distribution of Dimethylsulfoniopropionate Degradation Genes Reflects Strong Water Current Dependencies in the Sanriku Coastal Region in Japan: From Mesocosm to Field Study. Front Microbiol 2020; 11:1372. [PMID: 32754122 PMCID: PMC7370799 DOI: 10.3389/fmicb.2020.01372] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 05/27/2020] [Indexed: 11/23/2022] Open
Abstract
Dimethyl sulfide (DMS) is an important component of the global sulfur cycle as it is the most abundant sulfur compound that is emitted via the ocean surface to the atmosphere. Dimethylsulfoniopropionate (DMSP), the precursor of DMS, is mainly produced by phytoplankton and is degraded by marine bacteria. To reveal the role of bacteria in the regulation of DMSP degradation and DMS production, mesocosm and field studies were performed in the Sanriku Coast on the Pacific Ocean in northeast Japan. The responsible bacteria for the transformation of DMSP to DMS and the assimilation of DMSP were monitored, and the genes encoding DMSP lyase (dddD and dddP) and DMSP demethylase (dmdA) were analyzed. The mesocosm study showed that the dmdA subclade D was the dominant DMSP degradation gene in the free-living (FL) and particle-associated (PA) fractions. The dddD gene was found in higher abundance than the dddP gene in all the tested samples. Most importantly, DMS concentration was positively correlated with the abundance of the dddD gene. These results indicated that bacteria possessing dmdA and dddD genes were the major contributors to the DMSP degradation and DMS production, respectively. The genes dmdA subclade D and dddP were abundant in the Tsugaru Warm (TW) Current, while the dmdA subclade C/2 and dddD genes were dominant in the Oyashio (OY) Current. Functional gene network analysis also showed that the DMSP degradation genes were divided into OY and TW Current-related modules, and genes sharing similar functions were clustered in the same module. Our data suggest that environmental fluctuations resulted in habitat filtering and niche partitioning of bacteria possessing DMSP degradation genes. Overall, our findings provide novel insights into the distribution and abundance of DMSP degradation genes in a coastal region with different water current systems.
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Affiliation(s)
- Yingshun Cui
- Marine Microbiology, Department of Marine Ecosystem Dynamics, Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Japan
| | - Shu-Kuan Wong
- Marine Microbiology, Department of Marine Ecosystem Dynamics, Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Japan
| | - Ryo Kaneko
- National Institute of Polar Research, Tachikawa, Japan
| | - Ayako Mouri
- Marine Microbiology, Department of Marine Ecosystem Dynamics, Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Japan
| | - Yuya Tada
- Marine Microbiology, Department of Marine Ecosystem Dynamics, Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Japan.,National Institute for Minamata Disease, Kumamoto, Japan
| | - Ippei Nagao
- Graduate School of Environmental Studies, Nagoya University, Nagoya, Japan
| | - Seong-Jun Chun
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea.,National Institute of Ecology, Seocheon-gun, South Korea
| | - Hyung-Gwan Lee
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea
| | - Chi-Yong Ahn
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea
| | - Hee-Mock Oh
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea
| | - Yuki Sato-Takabe
- Coastal Conservation, International Coastal Research Center, Atmosphere and Ocean Research Institute, The University of Tokyo, Tokyo, Japan
| | - Koji Suzuki
- Faculty of Environmental Earth Science, Hokkaido University, Sapporo, Japan
| | - Hideki Fukuda
- Coastal Conservation, International Coastal Research Center, Atmosphere and Ocean Research Institute, The University of Tokyo, Tokyo, Japan
| | - Toshi Nagata
- Marine Biogeochemistry, Department of Chemical Oceanography, Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Japan
| | - Kazuhiro Kogure
- Marine Microbiology, Department of Marine Ecosystem Dynamics, Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Japan
| | - Koji Hamasaki
- Marine Microbiology, Department of Marine Ecosystem Dynamics, Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan
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13
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Sun H, Zhang Y, Tan S, Zheng Y, Zhou S, Ma QY, Yang GP, Todd JD, Zhang XH. DMSP-Producing Bacteria Are More Abundant in the Surface Microlayer than Subsurface Seawater of the East China Sea. MICROBIAL ECOLOGY 2020; 80:350-365. [PMID: 32335713 DOI: 10.1007/s00248-020-01507-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 03/18/2020] [Indexed: 06/11/2023]
Abstract
Microbial production and catabolism of dimethylsulfoniopropionate (DMSP), generating the climatically active gases dimethyl sulfide (DMS) and methanethiol (MeSH), have key roles in global carbon and sulfur cycling, chemotaxis, and atmospheric chemistry. Microorganisms in the sea surface microlayer (SML), the interface between seawater and atmosphere, likely play an important role in the generation of DMS and MeSH and their exchange to the atmosphere, but little is known about these SML microorganisms. Here, we investigated the differences between bacterial community structure and the distribution and transcription profiles of the key bacterial DMSP synthesis (dsyB and mmtN) and catabolic (dmdA and dddP) genes in East China Sea SML and subsurface seawater (SSW) samples. Per equivalent volume, bacteria were far more abundant (~ 7.5-fold) in SML than SSW, as were those genera predicted to produce DMSP. Indeed, dsyB (~ 7-fold) and mmtN (~ 4-fold), robust reporters for bacterial DMSP production, were also far more abundant in SML than SSW. In addition, the SML had higher dsyB transcripts (~ 3-fold) than SSW samples, which may contribute to the significantly higher DMSP level observed in SML compared with SSW. Furthermore, the abundance of bacteria with dmdA and their transcription were higher in SML than SSW samples. Bacteria with dddP and transcripts were also prominent, but less than dmdA and presented at similar levels in both layers. These data indicate that the SML might be an important hotspot for bacterial DMSP production as well as generating the climatically active gases DMS and MeSH, a portion of which are likely transferred to the atmosphere.
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Affiliation(s)
- Hao Sun
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Yunhui Zhang
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Siyin Tan
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Yanfen Zheng
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Shun Zhou
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Qian-Yao Ma
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education/Institute for Advanced Ocean Study, Ocean University of China, Qingdao, 266100, China
| | - Gui-Peng Yang
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education/Institute for Advanced Ocean Study, Ocean University of China, Qingdao, 266100, China
- Institute of Marine Chemistry, Ocean University of China, Qingdao, 266100, China
| | - Jonathan D Todd
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.
| | - Xiao-Hua Zhang
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China.
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, 266100, China.
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14
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Dixon JL, Hopkins FE, Stephens JA, Schäfer H. Seasonal Changes in Microbial Dissolved Organic Sulfur Transformations in Coastal Waters. Microorganisms 2020; 8:E337. [PMID: 32120978 PMCID: PMC7143303 DOI: 10.3390/microorganisms8030337] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 02/14/2020] [Accepted: 02/24/2020] [Indexed: 11/16/2022] Open
Abstract
The marine trace gas dimethylsulfide (DMS) is the single most important biogenic source of atmospheric sulfur, accounting for up to 80% of global biogenic sulfur emissions. Approximately 300 million tons of DMS are produced annually, but the majority is degraded by microbes in seawater. The DMS precursor dimethylsulfoniopropionate (DMSP) and oxidation product dimethylsulphoxide (DMSO) are also important organic sulfur reservoirs. However, the marine sinks of dissolved DMSO remain unknown. We used a novel combination of stable and radiotracers to determine seasonal changes in multiple dissolved organic sulfur transformation rates to ascertain whether microbial uptake of dissolved DMSO was a significant loss pathway. Surface concentrations of DMS ranged from 0.5 to 17.0 nM with biological consumption rates between 2.4 and 40.8 nM·d-1. DMS produced from the reduction of DMSO was not a significant process. Surface concentrations of total DMSO ranged from 2.3 to 102 nM with biological consumption of dissolved DMSO between 2.9 and 111 nM·d-1. Comparisons between 14C2-DMSO assimilation and dissimilation rates suggest that the majority of dissolved DMSO was respired (>94%). Radiotracer microbial consumption rates suggest that dissimilation of dissolved DMSO to CO2 can be a significant loss pathway in coastal waters, illustrating the significance of bacteria in controlling organic sulfur seawater concentrations.
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Affiliation(s)
- Joanna L Dixon
- Plymouth Marine Laboratory, Prospect Place, West Hoe, Plymouth, Devon PL1 3DH, UK; (F.E.H.); (J.A.S.)
| | - Frances E Hopkins
- Plymouth Marine Laboratory, Prospect Place, West Hoe, Plymouth, Devon PL1 3DH, UK; (F.E.H.); (J.A.S.)
| | - John A Stephens
- Plymouth Marine Laboratory, Prospect Place, West Hoe, Plymouth, Devon PL1 3DH, UK; (F.E.H.); (J.A.S.)
| | - Hendrik Schäfer
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK;
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15
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Song D, Zhang Y, Liu J, Zhong H, Zheng Y, Zhou S, Yu M, Todd JD, Zhang XH. Metagenomic Insights Into the Cycling of Dimethylsulfoniopropionate and Related Molecules in the Eastern China Marginal Seas. Front Microbiol 2020; 11:157. [PMID: 32132981 PMCID: PMC7039863 DOI: 10.3389/fmicb.2020.00157] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 01/22/2020] [Indexed: 11/13/2022] Open
Abstract
The microbial cycling of dimethylsulfoniopropionate (DMSP) and its gaseous catabolites dimethylsulfide (DMS) and methanethiol (MeSH) are important processes in the global sulfur cycle, marine microbial food webs, signaling pathways, atmospheric chemistry, and potentially climate regulation. Many functional genes have been identified and used to study the genetic potential of microbes to produce and catabolize these organosulfur compounds in different marine environments. Here, we sampled seawater, marine sediment and hydrothermal sediment, and polymetallic sulfide in the eastern Chinese marginal seas and analyzed their microbial communities for the genetic potential to cycle DMSP, DMS, and MeSH using metagenomics. DMSP was abundant in all sediment samples, but was fivefold less prominent in those from hydrothermal samples. Indeed, Yellow Sea (YS) sediment samples had DMSP concentrations two orders of magnitude higher than in surface water samples. Bacterial genetic potential to synthesize DMSP (mainly in Rhodobacteraceae bacteria) was far higher than for phytoplankton in all samples, but particularly in the sediment where no algal DMSP synthesis genes were detected. Thus, we propose bacteria as important DMSP producers in these marine sediments. DMSP catabolic pathways mediated by the DMSP lyase DddP (prominent in Pseudomonas and Mesorhizobium bacteria) and DMSP demethylase DmdA enzymes (prominent in Rhodobacteraceae bacteria) and MddA-mediated MeSH S-methylation were very abundant in Bohai Sea and Yellow Sea sediments (BYSS) samples. In contrast, the genetic potential for DMSP degradation was very low in the hydrothermal sediment samples-dddP was the only catabolic gene detected and in only one sample. However, the potential for DMS production from MeSH (mddA) and DMS oxidation (dmoA and ddhA) was relatively abundant. This metagenomics study does not provide conclusive evidence for DMSP cycling; however, it does highlight the potential importance of bacteria in the synthesis and catabolism of DMSP and related compounds in diverse sediment environments.
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Affiliation(s)
- Delei Song
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yunhui Zhang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Ji Liu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Haohui Zhong
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yanfen Zheng
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Shun Zhou
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Min Yu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Jonathan D. Todd
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Xiao-Hua Zhang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
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16
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The water depth-dependent co-occurrence patterns of marine bacteria in shallow and dynamic Southern Coast, Korea. Sci Rep 2019; 9:9176. [PMID: 31235719 PMCID: PMC6591218 DOI: 10.1038/s41598-019-45512-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 06/04/2019] [Indexed: 01/05/2023] Open
Abstract
To investigate the interactions between bacterial species in relation to the biotic and abiotic environmental fluctuations, free-living (FL), nanoparticle-associated (NP), and microparticle-associated (MP) bacterial community compositions (BCCs) were analyzed. A total of 267 samples were collected from July to December 2016 in the dynamic and shallow southern coastal water of Korea. The variations in BCC mostly depended on planktonic size fraction. Network analysis revealed water depth-dependent co-occurrence patterns of coastal bacterial communities. Higher interspecies connectivity was observed within FL bacteria than NP/MP bacteria, suggesting that FL bacteria with a streamlined genome may need other bacterial metabolites for survival, while the NP/MP copiotrophs may have the self-supporting capacity to produce the vital nutrients. The analysis of topological roles of individual OTUs in the network revealed that several groups of metabolically versatile bacteria (the marine Roseobacters, Flavobacteriales, Desulfobacterales, and SAR406 clade) acted as module hubs in different water depth. In conclusion, interspecies interactions dominated in FL bacteria, compared to NP and MP bacteria; modular structures of bacterial communities and keystone species strongly depended on the water depth-derived environmental factors. Furthermore, the multifunctional, versatile FL bacteria could play pivotal roles in dynamic shallow coastal ecosystems.
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17
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Zhang XH, Liu J, Liu J, Yang G, Xue CX, Curson ARJ, Todd JD. Biogenic production of DMSP and its degradation to DMS-their roles in the global sulfur cycle. SCIENCE CHINA-LIFE SCIENCES 2019; 62:1296-1319. [PMID: 31231779 DOI: 10.1007/s11427-018-9524-y] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 03/16/2019] [Indexed: 01/08/2023]
Abstract
Dimethyl sulfide (DMS) is the most abundant form of volatile sulfur in Earth's oceans, and is mainly produced by the enzymatic clevage of dimethylsulfoniopropionate (DMSP). DMS and DMSP play important roles in driving the global sulfur cycle and may affect climate. DMSP is proposed to serve as an osmolyte, a grazing deterrent, a signaling molecule, an antioxidant, a cryoprotectant and/or as a sink for excess sulfur. It was long believed that only marine eukaryotes such as phytoplankton produce DMSP. However, we recently discovered that marine heterotrophic bacteria can also produce DMSP, making them a potentially important source of DMSP. At present, one prokaryotic and two eukaryotic DMSP synthesis enzymes have been identified. Marine heterotrophic bacteria are likely the major degraders of DMSP, using two known pathways: demethylation and cleavage. Many phytoplankton and some fungi can also cleave DMSP. So far seven different prokaryotic and one eukaryotic DMSP lyases have been identified. This review describes the global distribution pattern of DMSP and DMS, the known genes for biosynthesis and cleavage of DMSP, and the physiological and ecological functions of these important organosulfur molecules, which will improve understanding of the mechanisms of DMSP and DMS production and their roles in the environment.
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Affiliation(s)
- Xiao-Hua Zhang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China.
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
| | - Ji Liu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Jingli Liu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Guipeng Yang
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
- College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao, 266071, China
| | - Chun-Xu Xue
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Andrew R J Curson
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Jonathan D Todd
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
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Liu J, Liu J, Zhang SH, Liang J, Lin H, Song D, Yang GP, Todd JD, Zhang XH. Novel Insights Into Bacterial Dimethylsulfoniopropionate Catabolism in the East China Sea. Front Microbiol 2018; 9:3206. [PMID: 30622530 PMCID: PMC6309047 DOI: 10.3389/fmicb.2018.03206] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 12/11/2018] [Indexed: 11/18/2022] Open
Abstract
The compatible solute dimethylsulfoniopropionate (DMSP), made by many marine organisms, is one of Earth's most abundant organosulfur molecules. Many marine bacteria import DMSP and can degrade it as a source of carbon and/or sulfur via DMSP cleavage or DMSP demethylation pathways, which can generate the climate active gases dimethyl sulfide (DMS) or methanthiol (MeSH), respectively. Here we used culture-dependent and -independent methods to study bacteria catabolizing DMSP in the East China Sea (ECS). Of bacterial isolates, 42.11% showed DMSP-dependent DMS (Ddd+) activity, and 12.28% produced detectable levels of MeSH. Interestingly, although most Ddd+ isolates were Alphaproteobacteria (mainly Roseobacters), many gram-positive Actinobacteria were also shown to cleave DMSP producing DMS. The mechanism by which these Actinobacteria cleave DMSP is unknown, since no known functional ddd genes have been identified in genome sequences of Ddd+Microbacterium and Agrococcus isolates or in any other sequenced Actinobacteria genomes. Gene probes to the DMSP demethylation gene dmdA and the DMSP lyase gene dddP demonstrated that these DMSP-degrading genes are abundant and widely distributed in ECS seawaters. dmdA was present in relatively high proportions in both surface (19.53% ± 6.70%) and bottom seawater bacteria (16.00% ± 8.73%). In contrast, dddP abundance positively correlated with chlorophyll a, and gradually decreased with the distance from land, which implies that the bacterial DMSP lyase gene dddP might be from bacterial groups that closely associate with phytoplankton. Bacterial community analysis showed positive correlations between Rhodobacteraceae abundance and concentrations of DMS and DMSP, further confirming the link between this abundant bacterial class and the environmental DMSP cycling.
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Affiliation(s)
- Jingli Liu
- College of Marine Life Sciences, Ocean University of China, Qingdao, China.,School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
| | - Ji Liu
- College of Marine Life Sciences, Ocean University of China, Qingdao, China.,School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
| | - Sheng-Hui Zhang
- College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao, China
| | - Jinchang Liang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Heyu Lin
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Delei Song
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Gui-Peng Yang
- College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Jonathan D Todd
- School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
| | - Xiao-Hua Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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Djurhuus A, Boersch-Supan PH, Mikalsen SO, Rogers AD. Microbe biogeography tracks water masses in a dynamic oceanic frontal system. ROYAL SOCIETY OPEN SCIENCE 2017; 4:170033. [PMID: 28405400 PMCID: PMC5383857 DOI: 10.1098/rsos.170033] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 02/14/2017] [Indexed: 05/11/2023]
Abstract
Dispersal limitation, not just environmental selection, plays an important role in microbial biogeography. The distance-decay relationship is thought to be weak in habitats where dispersal is high, such as in the pelagic environment, where ocean currents facilitate microbial dispersal. Most studies of microbial community composition to date have observed little geographical heterogeneity on a regional scale (100 km). We present a study of microbial communities across a dynamic frontal zone in the southwest Indian Ocean and investigate the spatial structure of the microbes with respect to the different water masses separated by these fronts. We collected 153 samples of free-living microorganisms from five seamounts located along a gradient from subtropical to subantarctic waters and across three depth layers: (i) the sub-surface chlorophyll maximum (approx. 40 m), (ii) the bottom of the euphotic zone (approx. 200 m), and (iii) the benthic boundary layer (300-2000 m). Diversity and abundance of microbial operational taxonomic units (OTUs) were assessed by amplification and sequencing of the 16S rRNA gene on an Illumina MiSeq platform. Multivariate analyses showed that microbial communities were structured more strongly by depth than by latitude, with similar phyla occurring within each depth stratum across seamounts. The deep layer was homogeneous across the entire survey area, corresponding to the spread of Antarctic intermediate water. However, within both the sub-surface layer and the intermediate depth stratum there was evidence for OTU turnover across fronts. The microbiome of these layers appears to be divided into three distinct biological regimes corresponding to the subantarctic surface water, the convergence zone and subtropical. We show that microbial biogeography across depth and latitudinal gradients is linked to the water masses the microbes persist in, resulting in regional patterns of microbial biogeography that correspond to the regional scale physical oceanography.
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Affiliation(s)
- Anni Djurhuus
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
- College of Marine Science, University of South Florida, 830 1st St SE, St Petersburg, FL 33701, USA
- Author for correspondence: Anni Djurhuus e-mail:
| | - Philipp H. Boersch-Supan
- Department of Integrative Biology, University of South Florida, 4202 E Fowler Avenue, Tampa, FL 33620, USA
- Department of Geography, University of Florida, Gainesville, FL 32611, USA
| | - Svein-Ole Mikalsen
- Department of Science and Technology, University of the Faroe Islands, Noatun 3, Torshavn, Faroe Islands
| | - Alex D. Rogers
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
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Diversity of bacterial dimethylsulfoniopropionate degradation genes in surface seawater of Arctic Kongsfjorden. Sci Rep 2016; 6:33031. [PMID: 27604458 PMCID: PMC5015088 DOI: 10.1038/srep33031] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 08/19/2016] [Indexed: 11/08/2022] Open
Abstract
Dimethylsulfoniopropionate (DMSP), which is the major source of organic sulfur in the world's oceans, plays a significant role in the global sulfur cycle. This compound is rapidly degraded by marine bacteria either by cleavage to dimethylsulfide (DMS) or demethylation to 3-methylmercaptopropionate (MMPA). The diversity of genes encoding bacterial demethylation (dmdA) and DMS production (dddL and dddP) were measured in Arctic Kongsfjorden. Both dmdA and dddL genes were detected in all stations along a transect from the outer to the inner fjord, while dddP gene was only found in the outer and middle parts of the fjord. The dmdA gene was completely confined to the Roseobacter clade, while the dddL gene was confined to the genus Sulfitobacter. Although the dddP gene pool was also dominated by homologs from the Roseobacter clade, there were a few dddP genes showing close relationships to both Alphaproteobacter and Gammaproteobacter. The results of this study suggest that the Roseobacter clade may play an important role in DMSP catabolism via both demethylation and cleavage pathways in surface waters of Kongsfjorden during summer.
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Lidbury I, Kröber E, Zhang Z, Zhu Y, Murrell JC, Chen Y, Schäfer H. A mechanism for bacterial transformation of dimethylsulfide to dimethylsulfoxide: a missing link in the marine organic sulfur cycle. Environ Microbiol 2016; 18:2754-66. [PMID: 27114231 DOI: 10.1111/1462-2920.13354] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 04/19/2016] [Indexed: 11/30/2022]
Abstract
The volatile organosulfur compound, dimethylsulfide (DMS), plays an important role in climate regulation and global sulfur biogeochemical cycles. Microbial oxidation of DMS to dimethylsulfoxide (DMSO) represents a major sink of DMS in surface seawater, yet the underlying molecular mechanisms and key microbial taxa involved are not known. Here, we reveal that Ruegeria pomeroyi, a model marine heterotrophic bacterium, can oxidize DMS to DMSO using trimethylamine monooxygenase (Tmm). Purified Tmm oxidizes DMS to DMSO at a 1:1 ratio. Mutagenesis of the tmm gene in R. pomeroyi completely abolished DMS oxidation and subsequent DMSO formation. Expression of Tmm and DMS oxidation in R. pomeroyi is methylamine-dependent and regulated at the post-transcriptional level. Considering that Tmm is present in approximately 20% of bacterial cells inhabiting marine surface waters, particularly the marine Roseobacter clade and the SAR11 clade, our observations contribute to a mechanistic understanding of biological DMSO production in surface seawater.
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Affiliation(s)
- Ian Lidbury
- School of Life Sciences, Gibbet Hill Campus, University of Warwick, Coventry, CV4 7AL, UK
| | - Eileen Kröber
- School of Life Sciences, Gibbet Hill Campus, University of Warwick, Coventry, CV4 7AL, UK
| | - Zhidong Zhang
- Institute of Microbiology, Xinjiang Academy of Agriculture Sciences, Urumqi, 830091, China
| | - Yijun Zhu
- School of Life Sciences, Gibbet Hill Campus, University of Warwick, Coventry, CV4 7AL, UK
| | - J Colin Murrell
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, NR4 7TJ, Norwich, UK
| | - Yin Chen
- School of Life Sciences, Gibbet Hill Campus, University of Warwick, Coventry, CV4 7AL, UK
| | - Hendrik Schäfer
- School of Life Sciences, Gibbet Hill Campus, University of Warwick, Coventry, CV4 7AL, UK
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Microbial Surface Colonization and Biofilm Development in Marine Environments. Microbiol Mol Biol Rev 2015; 80:91-138. [PMID: 26700108 DOI: 10.1128/mmbr.00037-15] [Citation(s) in RCA: 462] [Impact Index Per Article: 51.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Biotic and abiotic surfaces in marine waters are rapidly colonized by microorganisms. Surface colonization and subsequent biofilm formation and development provide numerous advantages to these organisms and support critical ecological and biogeochemical functions in the changing marine environment. Microbial surface association also contributes to deleterious effects such as biofouling, biocorrosion, and the persistence and transmission of harmful or pathogenic microorganisms and their genetic determinants. The processes and mechanisms of colonization as well as key players among the surface-associated microbiota have been studied for several decades. Accumulating evidence indicates that specific cell-surface, cell-cell, and interpopulation interactions shape the composition, structure, spatiotemporal dynamics, and functions of surface-associated microbial communities. Several key microbial processes and mechanisms, including (i) surface, population, and community sensing and signaling, (ii) intraspecies and interspecies communication and interaction, and (iii) the regulatory balance between cooperation and competition, have been identified as critical for the microbial surface association lifestyle. In this review, recent progress in the study of marine microbial surface colonization and biofilm development is synthesized and discussed. Major gaps in our knowledge remain. We pose questions for targeted investigation of surface-specific community-level microbial features, answers to which would advance our understanding of surface-associated microbial community ecology and the biogeochemical functions of these communities at levels from molecular mechanistic details through systems biological integration.
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