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Cheng J, Wang P, Ghiglione JF, Liu L, Cai Z, Zhou J, Zhu X. Bacterial pathogens associated with the plastisphere of surgical face masks and their dispersion potential in the coastal marine environment. J Hazard Mater 2024; 462:132741. [PMID: 37827107 DOI: 10.1016/j.jhazmat.2023.132741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 10/05/2023] [Accepted: 10/06/2023] [Indexed: 10/14/2023]
Abstract
Huge numbers of face masks (FMs) were discharged into the ocean during the coronavirus pandemic. These polymer-based artificial surfaces can support the growth of specific bacterial assemblages, pathogens being of particular concern. However, the potential risks from FM-associated pathogens in the marine environment remain poorly understood. Here, FMs were deployed in coastal seawater for two months. PacBio circular consensus sequencing of the full-length 16S rRNA was used for pathogen identification, providing enhanced taxonomic resolution. Selective enrichment of putative pathogens (e.g., Ralstonia pickettii) was found on FMs, which provided a new niche for these pathogens rarely detected in the surrounding seawater or the stone controls. The total relative abundance of the putative pathogens in FMs was higher than in seawater but lower than in the stone controls. FM exposure during the two months resulted in 3% weight loss and the release of considerable amounts of microfibers. The ecological assembly process of the putative FM-associated pathogens was less impacted by the dispersal limitation, indicating that FM-derived microplastics can serve as vectors of most pathogens for their regional transport. Our results indicate a possible ecological risk of FMs for marine organisms or humans in the coastal and potentially in the open ocean.
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Affiliation(s)
- Jingguang Cheng
- Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, PR China
| | - Pu Wang
- Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, PR China
| | - Jean-François Ghiglione
- CNRS, Sorbonne Université, Laboratoire d'Océanographie Microbienne (LOMIC), Observatoire Océanologique de Banyuls, Banyuls sur mer 66650, France
| | - Lu Liu
- Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, PR China
| | - Zhonghua Cai
- Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, PR China
| | - Jin Zhou
- Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, PR China.
| | - Xiaoshan Zhu
- Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, PR China; College of Ecology and Environment, Hainan University, Haikou 570228, PR China.
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Tasdemir D, Scarpato S, Utermann-Thüsing C, Jensen T, Blümel M, Wenzel-Storjohann A, Welsch C, Echelmeyer VA. Epiphytic and endophytic microbiome of the seagrass Zostera marina: Do they contribute to pathogen reduction in seawater? Sci Total Environ 2024; 908:168422. [PMID: 37956849 DOI: 10.1016/j.scitotenv.2023.168422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 10/27/2023] [Accepted: 11/06/2023] [Indexed: 11/15/2023]
Abstract
Seagrass meadows provide crucial ecosystem services for coastal environments and were shown to reduce the abundance of waterborne pathogens linked to infections in humans and marine organisms in their vicinity. Among potential drivers, seagrass phenolics released into seawater have been linked to pathogen suppression, but the potential involvement of the seagrass microbiome has not been investigated. We hypothesized that the microbiome of the eelgrass Zostera marina, especially the leaf epiphytes that are at direct interface between the seagrass host and the surrounding seawater, inhibit waterborne pathogens thereby contributing to their removal. Using a culture-dependent approach, we isolated 88 bacteria and fungi associated with the surfaces and inner tissues of the eelgrass leaves (healthy and decaying) and the roots. We assessed the antibiotic activity of microbial extracts against a large panel of common aquatic, human (fecal) and plant pathogens, and mined the metabolome of the most active extracts. The healthy leaf epibiotic bacteria, particularly Streptomyces sp. strain 131, displayed broad-spectrum antibiotic activity superior to some control drugs. Gram-negative bacteria abundant on healthy leaf surfaces, and few endosphere-associated bacteria and fungi also displayed remarkable activities. UPLC-MS/MS-based untargeted metabolomics analyses showed rich specialized metabolite repertoires with low annotation rates, indicating the presence of many undescribed antimicrobials in the extracts. This study contributes to our understanding on microbial and chemical ecology of seagrasses, implying potential involvement of the seagrass microbiome in suppression of pathogens in seawater. Such effect is beneficial for the health of ocean and human, especially in the context of climate change that is expected to exacerbate all infectious diseases. It may also assist future seagrass conservation and management strategies.
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Affiliation(s)
- Deniz Tasdemir
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel 24106, Germany; Faculty of Mathematics and Natural Sciences, Kiel University, Kiel 24118, Germany.
| | - Silvia Scarpato
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel 24106, Germany
| | - Caroline Utermann-Thüsing
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel 24106, Germany
| | - Timo Jensen
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel 24106, Germany
| | - Martina Blümel
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel 24106, Germany
| | - Arlette Wenzel-Storjohann
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel 24106, Germany
| | - Claudia Welsch
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel 24106, Germany
| | - Vivien Anne Echelmeyer
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel 24106, Germany
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Miyazaki U, Mizutani D, Hashimoto Y, Tame A, Sawayama S, Miyazaki J, Takai K, Nakagawa S. Helicovermis profundi gen. nov., sp. nov., a novel mesophilic, asporogenous bacterium within the Clostridia isolated from a deep-sea hydrothermal vent chimney. Antonie Van Leeuwenhoek 2024; 117:24. [PMID: 38217723 DOI: 10.1007/s10482-023-01919-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 12/12/2023] [Indexed: 01/15/2024]
Abstract
A novel mesophilic bacterial strain, designated S502T, was isolated from a deep-sea hydrothermal vent at Suiyo Seamount, Japan. Cells were Gram-positive, asporogenous, motile, and curved rods, measuring 1.6-5.6 µm in length. The strain was an obligate anaerobe that grew fermentatively on complex substrates such as yeast extract and Bacto peptone. Elemental sulfur stimulated the growth of the strain, and was reduced to hydrogen sulfide. The strain grew within a temperature range of 10-23 °C (optimum at 20 °C), pH range of 4.8-8.3 (optimum at 7.4), and a NaCl concentration range of 1.0-4.0% (w/v) (optimum at 3.0%, w/v). Phylogenetic analysis based on the 16S rRNA gene sequence revealed that the isolate was a member of the class Clostridia, with Fusibacter paucivorans strain SEBR 4211T (91.1% sequence identity) being its closest relative. The total size of the genome of the strain was 3.12 Mbp, and a G + C content was 28.2 mol%. The highest values for average nucleotide identity (ANI), average amino acid identity (AAI), and digital DNA-DNA hybridization (dDDH) value of strain S502T with relatives were 67.5% (with Marinisporobacter balticus strain 59.4MT), 51.5% (with M. balticus strain 59.4MT), and 40.9% (with Alkaliphilus serpentinus strain LacTT), respectively. Based on a combination of phylogenetic, genomic, and phenotypic characteristics, we propose strain S502T to represent a novel genus and species, Helicovermis profundi gen. nov., sp. nov., with the type strain S502T (= DSM 112048T = JCM 39167T).
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Affiliation(s)
- Urara Miyazaki
- Laboratory of Marine Environmental Microbiology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Oiwake-Cho, Kitashirakawa, Sakyo-Ku, Kyoto, 606-8502, Japan
| | - Daiki Mizutani
- Laboratory of Marine Environmental Microbiology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Oiwake-Cho, Kitashirakawa, Sakyo-Ku, Kyoto, 606-8502, Japan
| | - Yurina Hashimoto
- Laboratory of Marine Environmental Microbiology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Oiwake-Cho, Kitashirakawa, Sakyo-Ku, Kyoto, 606-8502, Japan
| | - Akihiro Tame
- Depertment of Marine and Earth Sciences, Marine Works Japan Ltd, 3-54-1 Oppamahigashi, Yokosuka, 237-0063, Japan
- General Affairs Department, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-Cho, Yokosuka, 237-0061, Japan
| | - Shigeki Sawayama
- Laboratory of Marine Environmental Microbiology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Oiwake-Cho, Kitashirakawa, Sakyo-Ku, Kyoto, 606-8502, Japan
| | - Junichi Miyazaki
- Institute for Extra-Cutting-Edge Science and Technology Avant-Garde Research (X-Star), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2-15 Natsushima-Cho, Yokosuka, 237-0061, Japan
| | - Ken Takai
- Institute for Extra-Cutting-Edge Science and Technology Avant-Garde Research (X-Star), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2-15 Natsushima-Cho, Yokosuka, 237-0061, Japan
- Section for Exploration of Life in Extreme Environments, Exploratory Research Center On Life and Living Systems (ExCELLS), National Institute of Natural Sciences, 5-1 Higashiyama, Myodaiji-Cho, Okazaki, 444-8787, Japan
| | - Satoshi Nakagawa
- Laboratory of Marine Environmental Microbiology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Oiwake-Cho, Kitashirakawa, Sakyo-Ku, Kyoto, 606-8502, Japan.
- Institute for Extra-Cutting-Edge Science and Technology Avant-Garde Research (X-Star), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2-15 Natsushima-Cho, Yokosuka, 237-0061, Japan.
- Section for Exploration of Life in Extreme Environments, Exploratory Research Center On Life and Living Systems (ExCELLS), National Institute of Natural Sciences, 5-1 Higashiyama, Myodaiji-Cho, Okazaki, 444-8787, Japan.
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Miksch S, Orellana LH, Oggerin de Orube M, Vidal-Melgosa S, Solanki V, Hehemann JH, Amann R, Knittel K. Taxonomic and functional stability overrules seasonality in polar benthic microbiomes. ISME J 2024; 18:wrad005. [PMID: 38365229 PMCID: PMC10811738 DOI: 10.1093/ismejo/wrad005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 11/06/2023] [Accepted: 11/07/2023] [Indexed: 02/18/2024]
Abstract
Coastal shelf sediments are hot spots of organic matter mineralization. They receive up to 50% of primary production, which, in higher latitudes, is strongly seasonal. Polar and temperate benthic bacterial communities, however, show a stable composition based on comparative 16S rRNA gene sequencing despite different microbial activity levels. Here, we aimed to resolve this contradiction by identifying seasonal changes at the functional level, in particular with respect to algal polysaccharide degradation genes, by combining metagenomics, metatranscriptomics, and glycan analysis in sandy surface sediments from Isfjorden, Svalbard. Gene expressions of diverse carbohydrate-active enzymes changed between winter and spring. For example, β-1,3-glucosidases (e.g. GH30, GH17, GH16) degrading laminarin, an energy storage molecule of algae, were elevated in spring, while enzymes related to α-glucan degradation were expressed in both seasons with maxima in winter (e.g. GH63, GH13_18, and GH15). Also, the expression of GH23 involved in peptidoglycan degradation was prevalent, which is in line with recycling of bacterial biomass. Sugar extractions from bulk sediments were low in concentrations during winter but higher in spring samples, with glucose constituting the largest fraction of measured monosaccharides (84% ± 14%). In porewater, glycan concentrations were ~18-fold higher than in overlying seawater (1107 ± 484 vs. 62 ± 101 μg C l-1) and were depleted in glucose. Our data indicate that microbial communities in sandy sediments digest and transform labile parts of photosynthesis-derived particulate organic matter and likely release more stable, glucose-depleted residual glycans of unknown structures, quantities, and residence times into the ocean, thus modulating the glycan composition of marine coastal waters.
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Affiliation(s)
- Sebastian Miksch
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
| | - Luis H Orellana
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
| | - Monike Oggerin de Orube
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
| | - Silvia Vidal-Melgosa
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
- MARUM MPG Bridge Group Marine Glycobiology, Center for Marine Environmental Sciences, University of Bremen, 28359 Bremen, Germany
| | - Vipul Solanki
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
| | - Jan-Hendrik Hehemann
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
- MARUM MPG Bridge Group Marine Glycobiology, Center for Marine Environmental Sciences, University of Bremen, 28359 Bremen, Germany
| | - Rudolf Amann
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
| | - Katrin Knittel
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
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55
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Lang-Yona N, Flores JM, Nir-Zadock TS, Nussbaum I, Koren I, Vardi A. Impact of airborne algicidal bacteria on marine phytoplankton blooms. ISME J 2024; 18:wrae016. [PMID: 38442732 PMCID: PMC10944695 DOI: 10.1093/ismejo/wrae016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 01/18/2024] [Accepted: 01/24/2024] [Indexed: 03/07/2024]
Abstract
Ocean microbes are involved in global processes such as nutrient and carbon cycling. Recent studies indicated diverse modes of algal-bacterial interactions, including mutualism and pathogenicity, which have a substantial impact on ecology and oceanic carbon sequestration, and hence, on climate. However, the airborne dispersal and pathogenicity of bacteria in the marine ecosystem remained elusive. Here, we isolated an airborne algicidal bacterium, Roseovarius nubinhibens, emitted to the atmosphere as primary marine aerosol (referred also as sea spray aerosols) and collected above a coccolithophore bloom in the North Atlantic Ocean. The aerosolized bacteria retained infective properties and induced lysis of Gephyrocapsa huxleyi cultures.This suggests that the transport of marine bacteria through the atmosphere can effectively spread infection agents over vast oceanic regions, highlighting its significance in regulating the cell fate in algal blooms.
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Affiliation(s)
- Naama Lang-Yona
- Department of Plant and Environmental Science, Weizmann Institute of Science, Rehovot 7610001, Israel
- Technion - Israel Institute of Technology, Environmental, Water and Agricultural Engineering, Haifa 3200003, Israel
| | - J Michel Flores
- Department of Earth and Planetary Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Tal Sharon Nir-Zadock
- Department of Plant and Environmental Science, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Inbal Nussbaum
- Department of Plant and Environmental Science, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ilan Koren
- Department of Earth and Planetary Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Assaf Vardi
- Department of Plant and Environmental Science, Weizmann Institute of Science, Rehovot 7610001, Israel
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56
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Manck LE, Coale TH, Stephens BM, Forsch KO, Aluwihare LI, Dupont CL, Allen AE, Barbeau KA. Iron limitation of heterotrophic bacteria in the California Current System tracks relative availability of organic carbon and iron. ISME J 2024; 18:wrae061. [PMID: 38624181 PMCID: PMC11069385 DOI: 10.1093/ismejo/wrae061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 04/09/2024] [Accepted: 04/10/2024] [Indexed: 04/17/2024]
Abstract
Iron is an essential nutrient for all microorganisms of the marine environment. Iron limitation of primary production has been well documented across a significant portion of the global surface ocean, but much less is known regarding the potential for iron limitation of the marine heterotrophic microbial community. In this work, we characterize the transcriptomic response of the heterotrophic bacterial community to iron additions in the California Current System, an eastern boundary upwelling system, to detect in situ iron stress of heterotrophic bacteria. Changes in gene expression in response to iron availability by heterotrophic bacteria were detected under conditions of high productivity when carbon limitation was relieved but when iron availability remained low. The ratio of particulate organic carbon to dissolved iron emerged as a biogeochemical proxy for iron limitation of heterotrophic bacteria in this system. Iron stress was characterized by high expression levels of iron transport pathways and decreased expression of iron-containing enzymes involved in carbon metabolism, where a majority of the heterotrophic bacterial iron requirement resides. Expression of iron stress biomarkers, as identified in the iron-addition experiments, was also detected insitu. These results suggest iron availability will impact the processing of organic matter by heterotrophic bacteria with potential consequences for the marine biological carbon pump.
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Affiliation(s)
- Lauren E Manck
- Geosciences Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, United States
- Flathead Lake Biological Station, University of Montana, Polson, MT 59860, United States
| | - Tyler H Coale
- Integrative Oceanography Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, United States
- Ocean Sciences Department, University of California Santa Cruz, Santa Cruz, CA 95064, United States
- Department of Environment and Sustainability, J. Craig Venter Institute, La Jolla, CA 92037, United States
| | - Brandon M Stephens
- Geosciences Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, United States
- Institute of Oceanography, National Taiwan University, Taipei, 106, Taiwan
| | - Kiefer O Forsch
- Geosciences Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, United States
| | - Lihini I Aluwihare
- Geosciences Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, United States
| | - Christopher L Dupont
- Department of Environment and Sustainability, J. Craig Venter Institute, La Jolla, CA 92037, United States
- Department of Human Health, J. Craig Venter Institute, La Jolla, CA 92037, United States
- Department of Synthetic Biology, J. Craig Venter Institute, La Jolla, CA 92037, United States
| | - Andrew E Allen
- Integrative Oceanography Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, United States
- Department of Environment and Sustainability, J. Craig Venter Institute, La Jolla, CA 92037, United States
| | - Katherine A Barbeau
- Geosciences Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, United States
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Deutschmann IM, Delage E, Giner CR, Sebastián M, Poulain J, Arístegui J, Duarte CM, Acinas SG, Massana R, Gasol JM, Eveillard D, Chaffron S, Logares R. Disentangling microbial networks across pelagic zones in the tropical and subtropical global ocean. Nat Commun 2024; 15:126. [PMID: 38168083 PMCID: PMC10762198 DOI: 10.1038/s41467-023-44550-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 12/18/2023] [Indexed: 01/05/2024] Open
Abstract
Microbial interactions are vital in maintaining ocean ecosystem function, yet their dynamic nature and complexity remain largely unexplored. Here, we use association networks to investigate possible ecological interactions in the marine microbiome among archaea, bacteria, and picoeukaryotes throughout different depths and geographical regions of the tropical and subtropical global ocean. Our findings reveal that potential microbial interactions change with depth and geographical scale, exhibiting highly heterogeneous distributions. A few potential interactions were global, meaning they occurred across regions at the same depth, while 11-36% were regional within specific depths. The bathypelagic zone had the lowest proportion of global associations, and regional associations increased with depth. Moreover, we observed that most surface water associations do not persist in deeper ocean layers despite microbial vertical dispersal. Our work contributes to a deeper understanding of the tropical and subtropical global ocean interactome, which is essential for addressing the challenges posed by global change.
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Affiliation(s)
| | - Erwan Delage
- Nantes Université, CNRS UMR 6004, LS2N, F-44000, Nantes, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
| | | | | | - Julie Poulain
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Javier Arístegui
- Instituto de Oceanografía y Cambio Global, IOCAG, Universidad de Las Palmas de Gran Canaria, ULPGC, Gran Canaria, Spain
| | - Carlos M Duarte
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center (RSRC), Thuwal, Saudi Arabia
| | | | - Ramon Massana
- Institute of Marine Sciences (ICM), CSIC, Barcelona, Spain
| | - Josep M Gasol
- Institute of Marine Sciences (ICM), CSIC, Barcelona, Spain
| | - Damien Eveillard
- Nantes Université, CNRS UMR 6004, LS2N, F-44000, Nantes, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
| | - Samuel Chaffron
- Nantes Université, CNRS UMR 6004, LS2N, F-44000, Nantes, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
| | - Ramiro Logares
- Institute of Marine Sciences (ICM), CSIC, Barcelona, Spain.
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58
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Zhao HW, Yi Y, Li JQ, Wang JH. Two new mohangic acid derivatives from the deep-sea bacteria Alcanivorax dieselolei BC-5. Nat Prod Res 2024; 38:206-210. [PMID: 35975783 DOI: 10.1080/14786419.2022.2112578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 08/03/2022] [Accepted: 08/09/2022] [Indexed: 10/15/2022]
Abstract
Mohangic acids are a class of p-aminoacetophenonic acids that contain a conjugated triene or diene moiety. Herein, this paper reports two new mohangic acids E and F (1-2) together with a known compound mohangic acid A (3), which were isolated from the deep-sea sediment-derived bacteria Alcanivorax dieselolei BC-5. The structures of 1 and 2 were established by HRESIMS, 1 D and 2 D NMR, and IR spectroscopy.
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Affiliation(s)
- Hao-Wen Zhao
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan, China
| | - Yan Yi
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan, China
| | - Jia-Qi Li
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan, China
| | - Jin-Hui Wang
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan, China
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Lo LSH, Liu X, Qian PY, Häggblom MM, Cheng J. Microbial colonization and chemically influenced selective enrichment of bacterial pathogens on polycarbonate plastic. Environ Sci Pollut Res Int 2024; 31:8061-8071. [PMID: 38175506 DOI: 10.1007/s11356-023-31752-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 12/23/2023] [Indexed: 01/05/2024]
Abstract
Plastic pollution in aquatic environments poses significant concerns due to its potential to serve as a refuge for aquatic pathogens. However, the role of plastic surfaces and microbial biofilm interfaces in facilitating pathogen development remains poorly understood. In this study, a microcosm setup was employed to investigate the interactions between plastics and the microbial community and examine the differences in bacterial community composition and potential pathogen occurrences between the plastisphere-biofilm and surrounding seawater. Community composition analysis combined with SEM observations over time indicated that biofilm extracellular polymeric substance formation over 14 days had a link with the relative abundance and succession patterns of pathogen taxa. Colony clusters were observed on biofilms from day 7 and coincided with higher bacterial pathogen dominance. On day 14, pathogen abundance overall decreased with a potentially degrading biofilm. Pseudomonas and Pseudoalteromonas were the dominant potential pathogen groups observed in the microcosm. When further subjected to chemical treatment as an imposed environmental stress over time, biofilm-associated Psuedoalteromonas sharply increased in abundance after three days of exposure, but quickly diminished by 14 days in favor of genera such as Acinetobacter, Pseudomonas, and Staphylococcus. These results suggest that environmental plastisphere-biofilms can promote the early selection, enrichment, and spread of pathogenic bacteria in the aquatic environment and could be later worsened under chemical and long-term pressure. This study provided new insights into the succession of pathogens in plastisphere biofilms, contributing to the understanding of pathogen risks involved in emerging plastisphere biofilms in light of global plastic pollution.
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Affiliation(s)
- Linus Shing Him Lo
- Department of Science and Environmental Studies and State Key Laboratory of Marine Pollution, The Education University of Hong Kong, New Territories, Hong Kong, China
- The Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
| | - Xuan Liu
- The Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
- Department of Ocean Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Hong Kong University of Science and Technology, Kowloon, Hong Kong, China
| | - Pei-Yuan Qian
- The Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
- Department of Ocean Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Hong Kong University of Science and Technology, Kowloon, Hong Kong, China
| | - Max M Häggblom
- Department of Biochemistry and Microbiology, School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey, 76 Lipman Drive, New Brunswick, NJ, 08901-8525, USA
| | - Jinping Cheng
- Department of Science and Environmental Studies and State Key Laboratory of Marine Pollution, The Education University of Hong Kong, New Territories, Hong Kong, China.
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Couceiro JF, Marques M, Silva SG, Keller-Costa T, Costa R. Aquimarina aquimarini sp. nov. and Aquimarina spinulae sp. nov., novel bacterial species with versatile natural product biosynthesis potential isolated from marine sponges. Int J Syst Evol Microbiol 2024; 74. [PMID: 38240740 DOI: 10.1099/ijsem.0.006228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2024] Open
Abstract
This study describes two Gram-negative, flexirubin-producing, biofilm-forming, motile-by-gliding and rod-shaped bacteria, isolated from the marine sponges Ircinia variabilis and Sarcotragus spinosulus collected off the coast of Algarve, Portugal. Both strains, designated Aq135T and Aq349T, were classified into the genus Aquimarina by means of 16S rRNA gene sequencing. We then performed phylogenetic, phylogenomic and biochemical analyses to determine whether these strains represent novel Aquimarina species. Whereas the closest 16S rRNA gene relatives to strain Aq135T were Aquimarina macrocephali JAMB N27T (97.8 %) and Aquimarina sediminis w01T (97.1 %), strain Aq349T was more closely related to Aquimarina megaterium XH134T (99.2 %) and Aquimarina atlantica 22II-S11-z7T (98.1 %). Both strains showed genome-wide average nucleotide identity scores below the species level cut-off (95 %) with all Aquimarina type strains with publicly available genomes, including their closest relatives. Digital DNA-DNA hybridization further suggested a novel species status for both strains since values lower than 70 % hybridization level with other Aquimarina type strains were obtained. Strains Aq135T and Aq349T grew from 4 to 30°C and with between 1-5 % (w/v) NaCl in marine broth. The most abundant fatty acids were iso-C17 : 03-OH and iso-C15 : 0 and the only respiratory quinone was MK-6. Strain Aq135T was catalase-positive and β-galactosidase-negative, while Aq349T was catalase-negative and β-galactosidase-positive. These strains hold unique sets of secondary metabolite biosynthetic gene clusters and are known to produce the peptide antibiotics aquimarins (Aq135T) and the trans-AT polyketide cuniculene (Aq349T), respectively. Based on the polyphasic approach employed in this study, we propose the novel species names Aquimarina aquimarini sp. nov. (type strain Aq135T=DSM 115833T=UCCCB 169T=ATCC TSD-360T) and Aquimarina spinulae sp. nov. (type strain Aq349T=DSM 115834T=UCCCB 170T=ATCC TSD-361T).
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Affiliation(s)
- Joana F Couceiro
- iBB-Institute for Bioengineering and Biosciences and i4HB-Institute for Health and Bioeconomy, Instituto Superior Técnico, University of Lisbon, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
- Department of Bioengeneering, Instituto Superior Técnico, University of Lisbon, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
| | - Matilde Marques
- iBB-Institute for Bioengineering and Biosciences and i4HB-Institute for Health and Bioeconomy, Instituto Superior Técnico, University of Lisbon, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
- Department of Bioengeneering, Instituto Superior Técnico, University of Lisbon, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
| | - Sandra G Silva
- iBB-Institute for Bioengineering and Biosciences and i4HB-Institute for Health and Bioeconomy, Instituto Superior Técnico, University of Lisbon, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
- Department of Bioengeneering, Instituto Superior Técnico, University of Lisbon, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
| | - Tina Keller-Costa
- iBB-Institute for Bioengineering and Biosciences and i4HB-Institute for Health and Bioeconomy, Instituto Superior Técnico, University of Lisbon, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
- Department of Bioengeneering, Instituto Superior Técnico, University of Lisbon, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
| | - Rodrigo Costa
- iBB-Institute for Bioengineering and Biosciences and i4HB-Institute for Health and Bioeconomy, Instituto Superior Técnico, University of Lisbon, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
- Department of Bioengeneering, Instituto Superior Técnico, University of Lisbon, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
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de Oliveira BFR, Yusuff Y. Culturing enigmatic marine bacteria. Nat Microbiol 2024; 9:6-7. [PMID: 38177298 DOI: 10.1038/s41564-023-01567-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2024]
Affiliation(s)
| | - Yahyah Yusuff
- Department of Microbiology, University of Ilorin, Ilorin, Nigeria.
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Zhang Y, Liu J, Song D, Yao P, Zhu S, Zhou Y, Jin J, Zhang XH. Stochasticity-driven weekly fluctuations distinguished the temporal pattern of particle-associated microorganisms from its free-living counterparts in temperate coastal seawater. Water Res 2024; 248:120849. [PMID: 37979570 DOI: 10.1016/j.watres.2023.120849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 11/03/2023] [Accepted: 11/07/2023] [Indexed: 11/20/2023]
Abstract
Microbial community dynamics directly determine their ecosystem functioning. Despite the well-known annual recurrence pattern, little is known how different lifestyles affect the temporal variation and how community assembly mechanisms change over different temporal scales. Here, through a high-resolution observation of size fractionated samples over 60 consecutive weeks, we investigate the distinction in weekly distribution pattern and assembly mechanism between free-living (FL) and particle-associated (PA) communities in highly dynamic coastal environments. A clear pattern of annual recurrence was observed, which was more pronounced in FL compared to PA, resulting in higher temporal specificity in the former samples. Both the two size fractions displayed significant temporal distance-decay patterns, yet the PA community showed a higher magnitude of community variation between adjacent weeks, likely caused by sudden, drastic and long-lived blooms of heterotrophic bacteria. Generally, determinism (environmental selection) had a greater effect on the community assembly than stochasticity (random birth, death, and dispersal events), with significant contributions from temperature and inorganic nutrients. However, a clear shift in the temporal assembly pattern was observed, transitioning from a prevalence of stochastic processes driving short-term (within a month) fluctuations to a dominance of deterministic processes over longer time intervals. Between adjacent weeks, stochasticity was more important in the community assembly of PA than FL. This study revealed that stochastic processes can lead to rapid, dramatic and irregular PA community fluctuations, indicating weak resistance and resilience to disturbances, which considering the role of PA microbes in carbon processing would significantly affect the coastal carbon cycle. Our results provided a new insight into the microbial community assembly mechanisms in the temporal dimension.
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Affiliation(s)
- Yulin Zhang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Jiwen Liu
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; Laboratory for Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao 266237, China; Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Derui Song
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Peng Yao
- Laboratory for Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao 266237, China; Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao 266100, China
| | - Shaodong Zhu
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Yi Zhou
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Jian Jin
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Xiao-Hua Zhang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; Laboratory for Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao 266237, China; Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China.
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Yuasa K, Mekata T, Kiryu I, Nomura K, Sudo R, Satomi M. Aureispira anguillae sp. nov., isolated from Japanese eel Anguilla japonica leptocephali. Arch Microbiol 2023; 206:47. [PMID: 38160217 DOI: 10.1007/s00203-023-03771-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 11/16/2023] [Accepted: 11/24/2023] [Indexed: 01/03/2024]
Abstract
A novel filamentous eel-leptocephalus pathogenic marine bacterium, designated strain EL160426T, was isolated from Japanese eel, Anguilla japonica, leptocephali reared at a laboratory in Mie, Japan. In experimental infection studies on eel larvae, the strain EL160426T caused massive larval mortality and was reisolated from moribund leptocephali. Characteristically, observations of infected larvae found that EL160426T forms columnar colonies on the cranial surface of larvae. The novel isolate exhibited growth at 15-30 °C, pH 7-9, and seawater concentrations of 60-150% (W/V). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain EL160426T was most closely related to Aureispira maritima 59SAT with 97.7% sequence similarity. The whole genome sequence analysis of the strain EL160426T showed that the strain maintained a circular chromosome with a size of approximately 7.58 Mbp and the DNA G + C content was 36.2%. The major respiratory quinone was MK-7 and the predominant cellular fatty acids were 16:0, 20:4 w6c (arachidonic acid), 17:0 iso and 16:0 N alcohol. DNA relatedness between the closest phylogenetic neighbor strain EL160426T and A. maritima (JCM23207T) was less than 13%. On the basis of the polyphasic taxonomic data, the strain represents a novel species of the genus Aureispira, for which the name Aureispira anguillae sp. nov. is proposed. The type strain is EL160426T (= JCM 35024 T = TSD-286 T).
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Affiliation(s)
- Kei Yuasa
- Planning and Coordination Department, Fisheries Technology Institute, Japan Fisheries Research and Education Agency, Miyako, 027-0097, Japan
| | - Tohru Mekata
- Faculty of Veterinary Medicine, Okayama University of Science, Imabari, Ehime, 794-8555, Japan
| | - Ikunari Kiryu
- Pathology Division, Fisheries Technology Institute, Japan Fisheries Research and Education Agency, Minamiise, Watarai, Mie, 516-0193, Japan
| | - Kazuharu Nomura
- Glass Eel Production Division, Fisheries Technology Institute, Japan Fisheries Research and Education Agency, Minamiise, Watarai, Mie, 516-0193, Japan
| | - Ryusuke Sudo
- Glass Eel Production Division, Fisheries Technology Institute, Minamiizu Field Station, Japan Fisheries Research and Education Agency, Minamiizu, Kamo, Shizuoka, 415-0156, Japan
| | - Masataka Satomi
- Glass Eel Production Division, Fisheries Technology Institute, Minamiizu Field Station, Japan Fisheries Research and Education Agency, Minamiizu, Kamo, Shizuoka, 415-0156, Japan.
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Hribovšek P, Olesin Denny E, Dahle H, Mall A, Øfstegaard Viflot T, Boonnawa C, Reeves EP, Steen IH, Stokke R. Putative novel hydrogen- and iron-oxidizing sheath-producing Zetaproteobacteria thrive at the Fåvne deep-sea hydrothermal vent field. mSystems 2023; 8:e0054323. [PMID: 37921472 PMCID: PMC10734525 DOI: 10.1128/msystems.00543-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 10/02/2023] [Indexed: 11/04/2023] Open
Abstract
IMPORTANCE Knowledge on microbial iron oxidation is important for understanding the cycling of iron, carbon, nitrogen, nutrients, and metals. The current study yields important insights into the niche sharing, diversification, and Fe(III) oxyhydroxide morphology of Ghiorsea, an iron- and hydrogen-oxidizing Zetaproteobacteria representative belonging to Zetaproteobacteria operational taxonomic unit 9. The study proposes that Ghiorsea exhibits a more extensive morphology of Fe(III) oxyhydroxide than previously observed. Overall, the results increase our knowledge on potential drivers of Zetaproteobacteria diversity in iron microbial mats and can eventually be used to develop strategies for the cultivation of sheath-forming Zetaproteobacteria.
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Affiliation(s)
- Petra Hribovšek
- Centre for Deep Sea Research, University of Bergen, Bergen, Norway
- Department of Earth Science, University of Bergen, Bergen, Norway
| | - Emily Olesin Denny
- Centre for Deep Sea Research, University of Bergen, Bergen, Norway
- Department of Biological Sciences, University of Bergen, Bergen, Norway
- Computational Biology Unit, University of Berge, Bergen, Norway
| | - Håkon Dahle
- Centre for Deep Sea Research, University of Bergen, Bergen, Norway
- Department of Biological Sciences, University of Bergen, Bergen, Norway
- Computational Biology Unit, University of Berge, Bergen, Norway
| | - Achim Mall
- Centre for Deep Sea Research, University of Bergen, Bergen, Norway
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Thomas Øfstegaard Viflot
- Centre for Deep Sea Research, University of Bergen, Bergen, Norway
- Department of Earth Science, University of Bergen, Bergen, Norway
| | - Chanakan Boonnawa
- Centre for Deep Sea Research, University of Bergen, Bergen, Norway
- Department of Earth Science, University of Bergen, Bergen, Norway
| | - Eoghan P. Reeves
- Centre for Deep Sea Research, University of Bergen, Bergen, Norway
- Department of Earth Science, University of Bergen, Bergen, Norway
| | - Ida Helene Steen
- Centre for Deep Sea Research, University of Bergen, Bergen, Norway
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Runar Stokke
- Centre for Deep Sea Research, University of Bergen, Bergen, Norway
- Department of Biological Sciences, University of Bergen, Bergen, Norway
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Molina-Pardines C, Haro-Moreno JM, López-Pérez M. Phosphate-related genomic islands as drivers of environmental adaptation in the streamlined marine alphaproteobacterial HIMB59. mSystems 2023; 8:e0089823. [PMID: 38054740 PMCID: PMC10734472 DOI: 10.1128/msystems.00898-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 10/17/2023] [Indexed: 12/07/2023] Open
Abstract
IMPORTANCE These results shed light on the evolutionary strategies of microbes with streamlined genomes to adapt and survive in the oligotrophic conditions that dominate the surface waters of the global ocean. At the individual level, these microbes have been subjected to evolutionary constraints that have led to a more efficient use of nutrients, removing non-essential genes named as "streamlining theory." However, at the population level, they conserve a highly diverse gene pool in flexible genomic islands resulting in polyclonal populations on the same genomic background as an evolutionary response to environmental pressures. Localization of these islands at equivalent positions in the genome facilitates horizontal transfer between clonal lineages. This high level of environmental genomic heterogeneity could explain their cosmopolitan distribution. In the case of the order HIMB59 within the class Alphaproteobacteria, two factors exert evolutionary pressure and determine this intraspecific diversity: phages and the concentration of P in the environment.
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Affiliation(s)
- Carmen Molina-Pardines
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, San Juan, Alicante, Spain
| | - Jose M. Haro-Moreno
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, San Juan, Alicante, Spain
| | - Mario López-Pérez
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, San Juan, Alicante, Spain
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66
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Zhang Y, Liu H, Huang N, Peng X, Jing H. Geographical distribution and driving force of micro-eukaryotes in the seamount sediments along the island arc of the Yap and Mariana trenches. Microbiol Spectr 2023; 11:e0206923. [PMID: 37943079 PMCID: PMC10714776 DOI: 10.1128/spectrum.02069-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 09/26/2023] [Indexed: 11/10/2023] Open
Abstract
IMPORTANCE A distinct distribution pattern was shaped by a deterministic process. Enhanced vertical connectivity expanded the previous understanding of seamount effects. Parasitism and predation were prevalent in the seamounts.
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Affiliation(s)
- Yue Zhang
- CAS Key Lab for Experimental Study under Deep-sea Extreme Conditions, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Hongbin Liu
- Department of Ocean Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
- HKUST-CAS Sanya Joint Laboratory of Marine Science Research, Chinese Academy of Sciences, Sanya, China
| | - Ning Huang
- CAS Key Lab for Experimental Study under Deep-sea Extreme Conditions, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Xiaotong Peng
- CAS Key Lab for Experimental Study under Deep-sea Extreme Conditions, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Hongmei Jing
- CAS Key Lab for Experimental Study under Deep-sea Extreme Conditions, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
- Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
- HKUST-CAS Sanya Joint Laboratory of Marine Science Research, Chinese Academy of Sciences, Sanya, China
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Vipindas PV, Venkatachalam S, Jabir T, Yang EJ, Jung J, Jain A, Krishnan KP. Salinity-controlled distribution of prokaryotic communities in the Arctic sea-ice melt ponds. World J Microbiol Biotechnol 2023; 40:25. [PMID: 38057653 DOI: 10.1007/s11274-023-03850-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 11/22/2023] [Indexed: 12/08/2023]
Abstract
The thawing of snow and sea ice produces distinctive melt ponds on the surface of the Arctic sea ice, which covers a significant portion of the surface sea ice during summer. Melt-pond salinity impacts heat transfer to the ice below and the melting rate. It is widely known that melt ponds play a significant role in heat fluxes, ice-albedo feedback, and sea-ice energy balance. However, not much attention has been given to the fact that melt ponds also serve as a unique microbial ecosystem where microbial production begins as soon as they are formed. Here, we investigated the role of melt pond salinity in controlling the diversity and distribution of prokaryotic communities using culture-dependent and -independent approaches. The 16 S rRNA gene amplicon based next generation sequencing analysis retrieved a total of 14 bacterial phyla, consisting of 146 genera, in addition to two archaeal phyla. Further, the culture-dependent approaches of the study allowed for the isolation and identification of twenty-four bacterial genera in pure culture. Flavobacterium, Candidatus_Aquiluna, SAR11 clade, Polaribacter, Glaciecola, and Nonlabens were the dominant genera observed in the amplicon analysis. Whereas Actimicrobium, Rhodoglobus, Flavobacterium, and Pseudomonas were dominated in the culturable fraction. Our results also demonstrated that salinity, chlorophyll a, and dissolved organic carbon were the significant environmental variables controlling the prokaryotic community distribution in melt ponds. A significant community shift was observed in melt ponds when the salinity changed with the progression of melting and deepening of ponds. Different communities were found to be dominant in melt ponds with different salinity ranges. It was also observed that melt pond prokaryotic communities significantly differed from the surface ocean microbial community. Our observations suggest that complex prokaryotic communities develop in melt ponds immediately after its formation using dissolved organic carbon generated through primary production in the oligotrophic water.
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Affiliation(s)
- Puthiya Veettil Vipindas
- Arctic Ecology and Biogeochemistry Division, National Centre for Polar and Ocean Research, Ministry of Earth Sciences, Vasco-da-Gama, Goa, 403 804, India.
| | - Siddarthan Venkatachalam
- Arctic Ecology and Biogeochemistry Division, National Centre for Polar and Ocean Research, Ministry of Earth Sciences, Vasco-da-Gama, Goa, 403 804, India
| | - Thajudeen Jabir
- Arctic Ecology and Biogeochemistry Division, National Centre for Polar and Ocean Research, Ministry of Earth Sciences, Vasco-da-Gama, Goa, 403 804, India
| | - Eun Jin Yang
- Division of Polar Ocean Sciences, Korea Polar Research Institute, 26 Songdo-dong, Yeonsu-gu, Incheon, 21990, Republic of Korea
| | - Jinyoung Jung
- Division of Polar Ocean Sciences, Korea Polar Research Institute, 26 Songdo-dong, Yeonsu-gu, Incheon, 21990, Republic of Korea
| | - Anand Jain
- Arctic Ecology and Biogeochemistry Division, National Centre for Polar and Ocean Research, Ministry of Earth Sciences, Vasco-da-Gama, Goa, 403 804, India
| | - Kottekkatu Padinchati Krishnan
- Arctic Ecology and Biogeochemistry Division, National Centre for Polar and Ocean Research, Ministry of Earth Sciences, Vasco-da-Gama, Goa, 403 804, India
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Cha QQ, Liu SS, Dang YR, Ren XB, Xu F, Li PY, Chen XL, Wang P, Zhang XY, Zhang YZ, Qin QL. Ecological function and interaction of different bacterial groups during alginate processing in coastal seawater community. Environ Int 2023; 182:108325. [PMID: 37995388 DOI: 10.1016/j.envint.2023.108325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 11/10/2023] [Accepted: 11/11/2023] [Indexed: 11/25/2023]
Abstract
The degradation of high molecular weight organic matter (HMWOM) is a core process of oceanic carbon cycle, which is determined by the activity of microbial communities harboring hundreds of different species. Illustrating the active microbes and their interactions during HMWOM processing can provide key information for revealing the relationship between community composition and its ecological functions. In this study, the genomic and transcriptional responses of microbial communities to the availability of alginate, an abundant HMWOM in coastal ecosystem, were elucidated. The main degraders transcribing alginate lyase (Aly) genes came from genera Alteromonas, Psychrosphaera and Colwellia. Meanwhile, some strains, mainly from the Rhodobacteraceae family, did not transcribe Aly gene but could utilize monosaccharides to grow. The co-culture experiment showed that the activity of Aly-producing strain could promote the growth of Aly-non-producing strain when alginate was the sole carbon source. Interestingly, this interaction did not reduce the alginate degradation rate, possibly due to the easily degradable nature of alginate. This study can improve our understanding of the relationship between microbial community activity and alginate metabolism function as well as further manipulation of microbial community structure for alginate processing.
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Affiliation(s)
- Qian-Qian Cha
- State Key Laboratory of Microbial Technology, Shandong Provincial Hospital, Shandong University, Qingdao, China
| | - Sha-Sha Liu
- State Key Laboratory of Microbial Technology, Shandong Provincial Hospital, Shandong University, Qingdao, China
| | - Yan-Ru Dang
- State Key Laboratory of Microbial Technology, Shandong Provincial Hospital, Shandong University, Qingdao, China
| | - Xue-Bing Ren
- State Key Laboratory of Microbial Technology, Shandong Provincial Hospital, Shandong University, Qingdao, China
| | - Fei Xu
- State Key Laboratory of Microbial Technology, Shandong Provincial Hospital, Shandong University, Qingdao, China
| | - Ping-Yi Li
- State Key Laboratory of Microbial Technology, Shandong Provincial Hospital, Shandong University, Qingdao, China
| | - Xiu-Lan Chen
- State Key Laboratory of Microbial Technology, Shandong Provincial Hospital, Shandong University, Qingdao, China; Laboratory for Marine Biology and Biotechnology, National Laboratory for Marine Science and Technology, Qingdao, 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, China
| | - Xi-Ying Zhang
- State Key Laboratory of Microbial Technology, Shandong Provincial Hospital, Shandong University, Qingdao, China; Laboratory for Marine Biology and Biotechnology, National Laboratory for Marine Science and Technology, Qingdao, China
| | - Yu-Zhong Zhang
- State Key Laboratory of Microbial Technology, Shandong Provincial Hospital, Shandong University, Qingdao, China; Laboratory for Marine Biology and Biotechnology, National Laboratory for Marine Science and Technology, Qingdao, China; 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, China
| | - Qi-Long Qin
- State Key Laboratory of Microbial Technology, Shandong Provincial Hospital, Shandong University, Qingdao, China; Laboratory for Marine Biology and Biotechnology, National Laboratory for Marine Science and Technology, Qingdao, China.
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69
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van der Loos LM, D'hondt S, Engelen AH, Pavia H, Toth GB, Willems A, Weinberger F, De Clerck O, Steinhagen S. Salinity and host drive Ulva-associated bacterial communities across the Atlantic-Baltic Sea gradient. Mol Ecol 2023; 32:6260-6277. [PMID: 35395701 DOI: 10.1111/mec.16462] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 02/21/2022] [Accepted: 03/30/2022] [Indexed: 11/28/2022]
Abstract
The green seaweed Ulva is a model system to study seaweed-bacteria interactions, but the impact of environmental drivers on the dynamics of these interactions is little understood. In this study, we investigated the stability and variability of the seaweed-associated bacteria across the Atlantic-Baltic Sea salinity gradient. We characterized the bacterial communities of 15 Ulva sensu lato species along 2,000 km of coastline in a total of 481 samples. Our results demonstrate that the Ulva-associated bacterial composition was strongly structured by both salinity and host species (together explaining between 34% and 91% of the variation in the abundance of the different bacterial genera). The largest shift in the bacterial consortia coincided with the horohalinicum (5-8 PSU, known as the transition zone from freshwater to marine conditions). Low-salinity communities especially contained high relative abundances of Luteolibacter, Cyanobium, Pirellula, Lacihabitans and an uncultured Spirosomaceae, whereas high-salinity communities were predominantly enriched in Litorimonas, Leucothrix, Sulfurovum, Algibacter and Dokdonia. We identified a small taxonomic core community (consisting of Paracoccus, Sulfitobacter and an uncultured Rhodobacteraceae), which together contributed to 14% of the reads per sample, on average. Additional core taxa followed a gradient model, as more core taxa were shared between neighbouring salinity ranges than between ranges at opposite ends of the Atlantic-Baltic Sea gradient. Our results contradict earlier statements that Ulva-associated bacterial communities are taxonomically highly variable across individuals and largely stochastically defined. Characteristic bacterial communities associated with distinct salinity regions may therefore facilitate the host's adaptation across the environmental gradient.
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Affiliation(s)
- Luna M van der Loos
- Phycology Research Group, Department of Biology, Ghent University, Ghent, Belgium
- Laboratory of Microbiology, Department Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Sofie D'hondt
- Phycology Research Group, Department of Biology, Ghent University, Ghent, Belgium
| | - Aschwin H Engelen
- Marine Microbial Ecology & Biotechnology, CCMAR, University of Algarve, Faro, Portugal
| | - Henrik Pavia
- Department of Marine Sciences-Tjärnö, University of Gothenburg, Strömstad, Sweden
| | - Gunilla B Toth
- Department of Marine Sciences-Tjärnö, University of Gothenburg, Strömstad, Sweden
| | - Anne Willems
- Laboratory of Microbiology, Department Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | | | - Olivier De Clerck
- Phycology Research Group, Department of Biology, Ghent University, Ghent, Belgium
| | - Sophie Steinhagen
- Department of Marine Sciences-Tjärnö, University of Gothenburg, Strömstad, Sweden
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70
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Arrington EC, Tarn J, Kittner HE, Kivenson V, Liu RM, Valentine DL. Methylated cycloalkanes fuel a novel genus in the Porticoccaceae family (Ca. Reddybacter gen. nov). Environ Microbiol 2023; 25:2958-2971. [PMID: 37599091 DOI: 10.1111/1462-2920.16474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Accepted: 07/19/2023] [Indexed: 08/22/2023]
Abstract
Cycloalkanes are abundant and toxic compounds in subsurface petroleum reservoirs and their fate is important to ecosystems impacted by natural oil seeps and spills. This study focuses on the microbial metabolism of methylcyclohexane (MCH) and methylcyclopentane (MCP) in the deep Gulf of Mexico. MCH and MCP are often abundant cycloalkanes observed in petroleum and will dissolve into the water column when introduced at the seafloor via a spill or natural seep. We conducted incubations with deep Gulf of Mexico (GOM) seawater amended with MCH and MCP at four stations. Within incubations with active respiration of MCH and MCP, we found that a novel genus of bacteria belonging to the Porticoccaceae family (Candidatus Reddybacter) dominated the microbial community. Using metagenome-assembled genomes, we reconstructed the central metabolism of Candidatus Reddybacter, identifying a novel clade of the particulate hydrocarbon monooxygenase (pmo) that may play a central role in MCH and MCP metabolism. Through comparative analysis of 174 genomes, we parsed the taxonomy of the Porticoccaceae family and found evidence suggesting the acquisition of pmo and other genes related to the degradation of cyclic and branched hydrophobic compounds were likely key events in the ecology and evolution of this group of organisms.
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Affiliation(s)
- Eleanor C Arrington
- Marine Science Institute, University of California-Santa Barbara, Santa Barbara, California, USA
| | - Jonathan Tarn
- Interdepartmental Graduate Program in Marine Science, University of California-Santa Barbara, Santa Barbara, California, USA
| | - Hailie E Kittner
- Interdepartmental Graduate Program in Marine Science, University of California-Santa Barbara, Santa Barbara, California, USA
| | - Veronika Kivenson
- Innovative Genomics Institute, University of California-Berkeley, Berkeley, California, USA
| | - Rachel M Liu
- School of Oceanography, University of Washington, Seattle, Washington, USA
| | - David L Valentine
- Marine Science Institute, University of California-Santa Barbara, Santa Barbara, California, USA
- Department of Earth Science, University of California-Santa Barbara, Santa Barbara, California, USA
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71
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Rong JC, Cui LL, Yang XC, Yi ML, Zhao Q. Complete genome analysis of type strain of a novel bacterial family Temperatibacteraceae fam. nov., isolated from surface seawater. Mar Genomics 2023; 72:101073. [PMID: 38008532 DOI: 10.1016/j.margen.2023.101073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 10/31/2023] [Accepted: 10/31/2023] [Indexed: 11/28/2023]
Abstract
Novel bacterial resources are valuable for studying bacterial taxonomy, bacterial evolution, and genome mining of novel antibiotics, antitumor agents, and immune modulators. In this study, we de novo sequenced the type strain of a novel bacterial family, Temperatibacteraceae fam. Nov., belonging to class Alphaproteobacteria of phylum Pseudomonadota. The type strain, Temperatibacter marinus NBRC 110045T, is mesophilic and was isolated from surface seawater around Muroto city of Japan at a depth of 0.5 m. Here, the sequenced complete genome of strain NBRC 110045T is composed of a circular chromosome of 3,184,799 bp with a mean G + C content of 43.71%. Genome analysis was applied to reveal the genetic basis of its cellular activities. Cellular regulation and signaling was analyzed to infer the regulatory mechanism of its limited growth temperature range. Genomic features of the novel family Temperatibacteraceae may expand our knowledge on environmental adaptation, genetic evolution and natural product discovery of marine bacteria.
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Affiliation(s)
- Jin-Cheng Rong
- Department of Medical Laboratory, Yantai Yuhuangding Hospital, Qingdao University, Yantai 264000, China
| | - Lin-Lin Cui
- Weihai Second Municipal Hospital, Qingdao University, Weihai 264200, China
| | - Xiao-Chen Yang
- Department of Medical Laboratory, Yantai Yuhuangding Hospital, Qingdao University, Yantai 264000, China
| | - Mao-Li Yi
- Department of Medical Laboratory, Yantai Yuhuangding Hospital, Qingdao University, Yantai 264000, China
| | - Qi Zhao
- Department of Medical Laboratory, Yantai Yuhuangding Hospital, Qingdao University, Yantai 264000, China.
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72
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Wang YW, Wang XH, Zhang J, Du ZJ, Mu DS. Cerina litoralis gen. nov., sp. nov., a novel potential polysaccharide degrading bacterium of the family Flavobacteriaceae, isolated from marine sediment. Antonie Van Leeuwenhoek 2023; 116:1447-1455. [PMID: 37899393 DOI: 10.1007/s10482-023-01888-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 09/14/2023] [Indexed: 10/31/2023]
Abstract
The Gram-strain-negative, facultative anaerobic, chemoheterotrophic, short-rod-shaped, non-motile, forming yellow colonies strain, designated F89T, was isolated from marine sediment of Xiaoshi Island, Weihai. Strain F89T grew at 15-37 °C (optimally at 28 °C), at pH 6.0-8.5 (optimally at pH 7.0) and in the presence of 1-5% (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain F89T was related to the family Flavobacteriaceae. F89T had highest 16S rRNA gene sequence similarity to Maribacter cobaltidurans MCCC 1K03318T (93.3%). The predominant cellular fatty acids of F89T were iso-C15:0, iso-C15:0 G and Summed Feature 3. The main respiratory quinone of F89T was menaquinone 6 (MK-6), consistent with that observed for all related strains. The polar lipid profile of strain F89T contained phosphatidylethanolamine, two aminolipids and three unidentified polar lipids. The genomic DNA G + C content of strain F89T was 42.7%. Strain F89T encoded 121 glycoside hydrolases and was a potential polysaccharide degrading bacterium. Differential phenotypic and genotypic characteristics of the strain showed that F89T should be classified as a novel genus in Flavobacteriaceae, for which the name Cerina litoralis is proposed. The type strain is F89T (= MCCC 1H00510T = KCTC 92203T).
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Affiliation(s)
- Ya-Wei Wang
- Marine College, Shandong University, Weihai, 264209, Shandong, China
| | - Xin-Hui Wang
- ANU Joint Science College, Shandong University, Weihai, 264209, Shandong, China
| | - Jing Zhang
- Marine College, Shandong University, Weihai, 264209, Shandong, China
| | - Zong-Jun Du
- Marine College, Shandong University, Weihai, 264209, Shandong, China
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, Shandong, China
- Weihai Research Institute of Industrial Technology of Shandong University, Weihai, China
| | - Da-Shuai Mu
- Marine College, Shandong University, Weihai, 264209, Shandong, China.
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, Shandong, China.
- Weihai Research Institute of Industrial Technology of Shandong University, Weihai, China.
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73
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Hwang K, Choe H, Kim KM. Complete genome of Polaribacter huanghezhanensis KCTC 32516 T isolated from glaciomarine fjord sediment of Svalbard. Mar Genomics 2023; 72:101068. [PMID: 38008528 DOI: 10.1016/j.margen.2023.101068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 08/17/2023] [Accepted: 08/18/2023] [Indexed: 11/28/2023]
Abstract
Polaribacter huanghezhanensis KCTC 32516T is an aerobic, non-flagellated, Gram-negative, orange-colony-forming bacterium that was isolated from the surficial glaciomarine sediment of inner basin of Kongsfjorden, Svalbard. The sampling site is characterized by a sedimentation of organic depleted lithogenous particles from the nearby glaciers, resulting in reduction of organic matter concentration. In order to understand microbial adaptation to the oligotrophic environment, we here sequenced the complete genome of the P. huanghezhanensis KCTC 32516T. The genome consists of 2,587,874 bp (G + C content of 31.5%) with a single chromosome, 2391 protein-coding genes, 39 tRNAs, and 2 rRNA operons. Our comparative analysis revealed that the P. huanghezhanensis possess the smallest genome in fifteen Polaribacter species with genome. The streamlined genome of this species, required less resource in replication, could evolved by the nutrient deficiency in surrounding environment. Simultaneously, the 15 KOs involved in amino acid biosynthesis and anaplerotic carbon fixation is uniquely absent in the P. huanghezhanensis. In addition, although the advantage of small genome, other 15 KOs involved in resource recycling and stress resistance is uniquely present in sequenced genome. This result demonstrates that the sequenced genome serves as a valuable model for further studies aimed at elucidating the molecular mechanisms associated with adaptation to oligotrophic habitat.
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Affiliation(s)
- Kyuin Hwang
- Division of Polar Life Sciences, Korea Polar Research Institute, 26 Songdomirae-ro, Yeonsu-gu, Incheon 21990, Republic of Korea.
| | - Hanna Choe
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, 181 Ipsin-gil, Jeongeup 56212, Republic of Korea
| | - Kyung Mo Kim
- Division of Polar Life Sciences, Korea Polar Research Institute, 26 Songdomirae-ro, Yeonsu-gu, Incheon 21990, Republic of Korea
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74
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Zhou K, Wong TY, Long L, Anantharaman K, Zhang W, Wong WC, Zhang R, Qian PY. Genomic and transcriptomic insights into complex virus-prokaryote interactions in marine biofilms. ISME J 2023; 17:2303-2312. [PMID: 37875603 PMCID: PMC10689801 DOI: 10.1038/s41396-023-01546-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 10/12/2023] [Accepted: 10/16/2023] [Indexed: 10/26/2023]
Abstract
Marine biofilms are complex communities of microorganisms that play a crucial ecological role in oceans. Although prokaryotes are the dominant members of these biofilms, little is known about their interactions with viruses. By analysing publicly available and newly sequenced metagenomic data, we identified 2446 virus-prokaryote connections in 84 marine biofilms. Most of these connections were between the bacteriophages in the Uroviricota phylum and the bacteria of Proteobacteria, Cyanobacteria and Bacteroidota. The network of virus-host pairs is complex; a single virus can infect multiple prokaryotic populations or a single prokaryote is susceptible to several viral populations. Analysis of genomes of paired prokaryotes and viruses revealed the presence of 425 putative auxiliary metabolic genes (AMGs), 239 viral genes related to restriction-modification (RM) systems and 38,538 prokaryotic anti-viral defence-related genes involved in 15 defence systems. Transcriptomic evidence from newly established biofilms revealed the expression of viral genes, including AMGs and RM, and prokaryotic defence systems, indicating the active interplay between viruses and prokaryotes. A comparison between biofilms and seawater showed that biofilm prokaryotes have more abundant defence genes than seawater prokaryotes, and the defence gene composition differs between biofilms and the surrounding seawater. Overall, our study unveiled active viruses in natural biofilms and their complex interplay with prokaryotes, which may result in the blooming of defence strategists in biofilms. The detachment of bloomed defence strategists may reduce the infectivity of viruses in seawater and result in the emergence of a novel role of marine biofilms.
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Affiliation(s)
- Kun Zhou
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Tin Yan Wong
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Lexin Long
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | | | - Weipeng Zhang
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Wai Chuen Wong
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Rui Zhang
- Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China.
| | - Pei-Yuan Qian
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China.
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75
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Pereira TJ, Walters TL, El-Shaffey HM, Bik HM, Frischer ME. The microbiome of the pelagic tunicate Dolioletta gegenbauri: A potential link between the grazing and microbial food web. Mol Ecol 2023; 32:6564-6579. [PMID: 35989550 DOI: 10.1111/mec.16668] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 08/10/2022] [Accepted: 08/15/2022] [Indexed: 11/28/2022]
Abstract
Bloom-forming gelatinous zooplankton occur circumglobally and significantly influence the structure of pelagic marine food webs and biogeochemical cycling through interactions with microbial communities. During bloom conditions especially, gelatinous zooplankton are keystone taxa that help determine the fate of primary production, nutrient remineralization, and carbon export. Using the pelagic tunicate Dolioletta gegenbauri as a model system for gelatinous zooplankton, we carried out a laboratory-based feeding experiment to investigate the potential ecosystem impacts of doliolid gut microbiomes and microbial communities associated with doliolid faecal pellets and the surrounding seawater. Metabarcoding targeting Bacteria and Archaea 16S rRNA genes/Archaea) and qPCR approaches were used to characterize microbiome assemblages. Comparison between sample types revealed distinct patterns in microbial diversity and biomass that were replicable across experiments. These observations support the hypothesis that through their presence and trophic activity, doliolids influence the structure of pelagic food webs and biogeochemical cycling in subtropical continental shelf systems where tunicate blooms are common. Bacteria associated with starved doliolids (representative of the resident gut microbiome) possessed distinct low-biomass and low-diversity microbial assemblages, suggesting that the doliolid microbiome is optimized to support a detrital trophic mode. Bacterial genera Pseudoalteromomas and Shimia were the most abundant potential core microbiome taxa, similar to patterns observed in other marine invertebrates. Exploratory bioinformatic analyses of predicted functional genes suggest that doliolids, via their interactions with bacterial communities, may affect important biogeochemical processes including nitrogen, sulphur, and organic matter cycling.
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Affiliation(s)
- Tiago J Pereira
- Department of Marine Sciences and Institute of Bioinformatics, University of Georgia, Athens, Georgia, USA
| | - Tina L Walters
- Department of Marine Sciences, University of Georgia Skidaway Institute of Oceanography, Savannah, Georgia, USA
| | - Hisham M El-Shaffey
- Department of Marine Sciences, University of Georgia Skidaway Institute of Oceanography, Savannah, Georgia, USA
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina, USA
| | - Holly M Bik
- Department of Marine Sciences and Institute of Bioinformatics, University of Georgia, Athens, Georgia, USA
| | - Marc E Frischer
- Department of Marine Sciences, University of Georgia Skidaway Institute of Oceanography, Savannah, Georgia, USA
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76
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Fuchsman CA, Hays MD. Increased cyanophage infection at the bottom of the euphotic zone, especially in the fall. Environ Microbiol 2023; 25:3349-3363. [PMID: 37861083 DOI: 10.1111/1462-2920.16525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 10/03/2023] [Indexed: 10/21/2023]
Abstract
Picocyanobacteria contribute greatly to offshore primary production with cells extending through the deep euphotic zone. Literature indicates high viral infection of cyanobacteria in ocean transition zones. We postulate that the bottom of the euphotic zone is a transition zone, where communities transition from phototrophic to aphotic processes. We use single-copy core genes to examine cyanophage to cyanobacteria ratios in cellular metagenomes in the subtropical North Atlantic and Pacific. Cyanophage to cyanobacteria terL/rpoB ratios generally increase to >10 in the deep euphotic zone. As light levels decrease in the fall, Prochlorococcus in the deep euphotic zone experience reduced light levels. We find clear differences between spring (Geotraces GA02) and fall (GA03) in the North Atlantic, with terL/rpoB ratios increasing to >40 in the fall. When examining 23 months of the North Pacific Hawaii Ocean Timeseries, the depth of elevated cyanophage to cyanobacteria ratios in cellular metagenomes negatively correlated with surface photosynthetic radiation (PAR), particularly with the change in PAR, which reflected the season. In fall, all picocyanobacteria ecotypes were found at depths enriched with viruses, while in summer, only low light ecotypes were affected. Thus, we find high cyanophage infection both in the deep euphotic zone and during seasonal transitions.
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Affiliation(s)
- Clara A Fuchsman
- Horn Point Laboratory, University of Maryland Center for Environmental Science, Cambridge, Maryland, USA
| | - Matthew D Hays
- Horn Point Laboratory, University of Maryland Center for Environmental Science, Cambridge, Maryland, USA
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77
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Zhang MD, Zhou ZY, Kou YY, Lu DC, Du ZJ. Brumimicrobium oceani sp. nov., isolated from coastal sediment saline lake and environmental adaptability analysis. Antonie Van Leeuwenhoek 2023; 116:1375-1384. [PMID: 37843738 DOI: 10.1007/s10482-023-01892-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 09/25/2023] [Indexed: 10/17/2023]
Abstract
A novel Gram-stain-negative, aerobic, non-motile, rod-shaped and orange-colored bacterium, designated as strain C305T, was isolated from marine sediment of the coast area of Weihai, China. Strain C305T growth occurs at 4-40 °C (optimally at 30-33 °C), pH 6.0-9.0 (optimally at pH 8.0) and with 0.5-10.0% (w/v) NaCl (optimum 1.5-3.0%). No growth is observed without NaCl. The major cellular fatty acids of strain C305T were identified as iso-C15:0, iso-C15:1G and iso-C17:0 3-OH. The major respiratory quinone was found to be MK-6, and the DNA G + C content was determined to be 35.5 mol%. The predominant polar lipids were mainly phosphatidylethanolamines (PE), unidentified aminophospholipids (APL), andunidentified lipid (L2). Phylogenetic analysis based on 16S rRNA gene sequences revealed that C305T was a member of the genus Brumimicrobium and had a 16S rRNA gene sequence similarity values of 96.9-98.0% with recognized Brumimicrobium species. On the basis of the phylogenetic and phenotypic evidences, strain C305T represents a novel species of the genus Brumimicrobium, for which the name Brumimicrobium oceani sp. nov. is proposed. The type strain is C305T (= KCTC 62371 T = MCCC 1H00297T).
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Affiliation(s)
- Meng-Di Zhang
- Marine College, Shandong University, Weihai, 264209, Shandong, People's Republic of China
- Joint Science College, Shandong University, Weihai, 264209, Shandong, People's Republic of China
| | - Zi-Yang Zhou
- Marine College, Shandong University, Weihai, 264209, Shandong, People's Republic of China
| | - Yi-Yu Kou
- Marine College, Shandong University, Weihai, 264209, Shandong, People's Republic of China
| | - De-Chen Lu
- Marine College, Shandong University, Weihai, 264209, Shandong, People's Republic of China
| | - Zong-Jun Du
- Marine College, Shandong University, Weihai, 264209, Shandong, People's Republic of China.
- Weihai Research Institute of Industrial Technology of Shandong University, Weihai, 264209, People's Republic of China.
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78
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Marietou A, Schmidt JS, Rasmussen MR, Scoma A, Rysgaard S, Vergeynst L. The effect of hydrostatic pressure on the activity and community composition of hydrocarbon-degrading bacteria in Arctic seawater. Appl Environ Microbiol 2023; 89:e0098723. [PMID: 37943057 PMCID: PMC10686064 DOI: 10.1128/aem.00987-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 10/05/2023] [Indexed: 11/10/2023] Open
Abstract
IMPORTANCE Increased ship traffic in the Arctic region raises the risk of oil spills. With an average sea depth of 1,000 m, there is a growing concern over the potential release of oil sinking in the form of marine oil snow into deep Arctic waters. At increasing depth, the oil-degrading community is exposed to increasing hydrostatic pressure, which can reduce microbial activity. However, microbes thriving in polar regions may adapt to low temperature by modulation of membrane fluidity, which is also a well-known adaptation to high hydrostatic pressure. At mild hydrostatic pressures up to 8-12 MPa, we did not observe an altered microbial activity or community composition, whereas comparable studies using deep-sea or sub-Arctic microbial communities with in situ temperatures of 4-5°C showed pressure-induced effects at 10-15 MPa. Our results suggest that the psychrophilic nature of the underwater microbial communities in the Arctic may be featured by specific traits that enhance their fitness at increasing hydrostatic pressure.
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Affiliation(s)
- Angeliki Marietou
- Department of Biology, Section for Microbiology, Aarhus University, Aarhus, Denmark
- Department of Biological and Chemical Engineering, Aarhus University, Aarhus, Denmark
| | | | - Martin R. Rasmussen
- Department of Biology, Section for Microbiology, Aarhus University, Aarhus, Denmark
| | - Alberto Scoma
- Department of Biology, Section for Microbiology, Aarhus University, Aarhus, Denmark
- Department of Biological and Chemical Engineering, Aarhus University, Aarhus, Denmark
| | - Søren Rysgaard
- Arctic Research Centre, Department of Biology, Aarhus University, Aarhus, Denmark
| | - Leendert Vergeynst
- Department of Biological and Chemical Engineering, Aarhus University, Aarhus, Denmark
- Arctic Research Centre, Department of Biology, Aarhus University, Aarhus, Denmark
- Centre for Water Technology (WATEC), Aarhus University, Aarhus, Denmark
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79
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Fernández-Juárez V, Hallstrøm S, Pacherres CO, Wang J, Coll-Garcia G, Kühl M, Riemann L. Biofilm formation and cell plasticity drive diazotrophy in an anoxygenic phototrophic bacterium. Appl Environ Microbiol 2023; 89:e0102723. [PMID: 37882569 PMCID: PMC10686084 DOI: 10.1128/aem.01027-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 09/14/2023] [Indexed: 10/27/2023] Open
Abstract
IMPORTANCE The contribution of non-cyanobacterial diazotrophs (NCDs) to total N2 fixation in the marine water column is unknown, but their importance is likely constrained by the limited availability of dissolved organic matter and low O2 conditions. Light could support N2 fixation and growth by NCDs, yet no examples from bacterioplankton exist. In this study, we show that the phototrophic NCD, Rhodopseudomonas sp. BAL398, which is a member of the diazotrophic community in the surface waters of the Baltic Sea, can utilize light. Our study highlights the significance of biofilm formation for utilizing light and fixing N2 under oxic conditions and the role of cell plasticity in regulating these processes. Our findings have implications for the general understanding of the ecology and importance of NCDs in marine waters.
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Affiliation(s)
- Víctor Fernández-Juárez
- Marine Biological Section, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Søren Hallstrøm
- Marine Biological Section, Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Cesar O. Pacherres
- Marine Biological Section, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Jiaqi Wang
- Marine Biological Section, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Guillem Coll-Garcia
- Microbiology, Biology Department, University of the Balearic Islands, Palma de Mallorca, Spain
- Environmental Microbiology Group, Mediterranean Institute for Advanced Studies (CSIC-UIB), Esporles, Spain
| | - Michael Kühl
- Marine Biological Section, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Lasse Riemann
- Marine Biological Section, Department of Biology, University of Copenhagen, Copenhagen, Denmark
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80
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Liu Y, Brinkhoff T, Berger M, Poehlein A, Voget S, Paoli L, Sunagawa S, Amann R, Simon M. Metagenome-assembled genomes reveal greatly expanded taxonomic and functional diversification of the abundant marine Roseobacter RCA cluster. Microbiome 2023; 11:265. [PMID: 38007474 PMCID: PMC10675870 DOI: 10.1186/s40168-023-01644-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 08/07/2023] [Indexed: 11/27/2023]
Abstract
BACKGROUND The RCA (Roseobacter clade affiliated) cluster belongs to the family Roseobacteracea and represents a major Roseobacter lineage in temperate to polar oceans. Despite its prevalence and abundance, only a few genomes and one described species, Planktomarina temperata, exist. To gain more insights into our limited understanding of this cluster and its taxonomic and functional diversity and biogeography, we screened metagenomic datasets from the global oceans and reconstructed metagenome-assembled genomes (MAG) affiliated to this cluster. RESULTS The total of 82 MAGs, plus five genomes of isolates, reveal an unexpected diversity and novel insights into the genomic features, the functional diversity, and greatly refined biogeographic patterns of the RCA cluster. This cluster is subdivided into three genera: Planktomarina, Pseudoplanktomarina, and the most deeply branching Candidatus Paraplanktomarina. Six of the eight Planktomarina species have larger genome sizes (2.44-3.12 Mbp) and higher G + C contents (46.36-53.70%) than the four Pseudoplanktomarina species (2.26-2.72 Mbp, 42.22-43.72 G + C%). Cand. Paraplanktomarina is represented only by one species with a genome size of 2.40 Mbp and a G + C content of 45.85%. Three novel species of the genera Planktomarina and Pseudoplanktomarina are validly described according to the SeqCode nomenclature for prokaryotic genomes. Aerobic anoxygenic photosynthesis (AAP) is encoded in three Planktomarina species. Unexpectedly, proteorhodopsin (PR) is encoded in the other Planktomarina and all Pseudoplanktomarina species, suggesting that this light-driven proton pump is the most important mode of acquiring complementary energy of the RCA cluster. The Pseudoplanktomarina species exhibit differences in functional traits compared to Planktomarina species and adaptations to more resource-limited conditions. An assessment of the global biogeography of the different species greatly expands the range of occurrence and shows that the different species exhibit distinct biogeographic patterns. They partially reflect the genomic features of the species. CONCLUSIONS Our detailed MAG-based analyses shed new light on the diversification, environmental adaptation, and global biogeography of a major lineage of pelagic bacteria. The taxonomic delineation and validation by the SeqCode nomenclature of prominent genera and species of the RCA cluster may be a promising way for a refined taxonomic identification of major prokaryotic lineages and sublineages in marine and other prokaryotic communities assessed by metagenomics approaches. Video Abstract.
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Affiliation(s)
- Yanting Liu
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Carl Von Ossietzky Str. 9-11, 26129, Oldenburg, Germany.
- Max Planck Institute for Marine Microbiology, Bremen, Germany.
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, People's Republic of China.
| | - Thorsten Brinkhoff
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Carl Von Ossietzky Str. 9-11, 26129, Oldenburg, Germany.
| | - Martine Berger
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Carl Von Ossietzky Str. 9-11, 26129, Oldenburg, Germany
| | - Anja Poehlein
- Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Georg-August University Göttingen, Grisebachstr. 8, 37077, Göttingen, Germany
| | - Sonja Voget
- Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Georg-August University Göttingen, Grisebachstr. 8, 37077, Göttingen, Germany
| | - Lucas Paoli
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zurich, Switzerland
| | - Shinichi Sunagawa
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zurich, Switzerland
| | - Rudolf Amann
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Meinhard Simon
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Carl Von Ossietzky Str. 9-11, 26129, Oldenburg, Germany.
- Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg (HIFMB), Ammerländer Heerstr. 231, 26129, Oldenburg, Germany.
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Kling JD, Lee MD, Walworth NG, Webb EA, Coelho JT, Wilburn P, Anderson SI, Zhou Q, Wang C, Phan MD, Fu F, Kremer CT, Litchman E, Rynearson TA, Hutchins DA. Dual thermal ecotypes coexist within a nearly genetically identical population of the unicellular marine cyanobacterium Synechococcus. Proc Natl Acad Sci U S A 2023; 120:e2315701120. [PMID: 37972069 PMCID: PMC10665897 DOI: 10.1073/pnas.2315701120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 10/11/2023] [Indexed: 11/19/2023] Open
Abstract
The extent and ecological significance of intraspecific functional diversity within marine microbial populations is still poorly understood, and it remains unclear if such strain-level microdiversity will affect fitness and persistence in a rapidly changing ocean environment. In this study, we cultured 11 sympatric strains of the ubiquitous marine picocyanobacterium Synechococcus isolated from a Narragansett Bay (RI) phytoplankton community thermal selection experiment. Thermal performance curves revealed selection at cool and warm temperatures had subdivided the initial population into thermotypes with pronounced differences in maximum growth temperatures. Curiously, the genomes of all 11 isolates were almost identical (average nucleotide identities of >99.99%, with >99% of the genome aligning) and no differences in gene content or single nucleotide variants were associated with either cool or warm temperature phenotypes. Despite a very high level of genomic similarity, sequenced epigenomes for two strains showed differences in methylation on genes associated with photosynthesis. These corresponded to measured differences in photophysiology, suggesting a potential pathway for future mechanistic research into thermal microdiversity. Our study demonstrates that present-day marine microbial populations can harbor cryptic but environmentally relevant thermotypes which may increase their resilience to future rising temperatures.
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Affiliation(s)
- Joshua D. Kling
- Department of Biological Sciences, University of Southern California, Los Angeles, CA90007
| | - Michael D. Lee
- ZOLL Medical Corporation, Chelmsford, MA01824
- Blue Marble Space Institute of Science, Seattle, WA98154
| | - Nathan G. Walworth
- Department of Biological Sciences, University of Southern California, Los Angeles, CA90007
| | - Eric A. Webb
- Department of Biological Sciences, University of Southern California, Los Angeles, CA90007
| | - Jordan T. Coelho
- Department of Biological Sciences, University of Southern California, Los Angeles, CA90007
| | - Paul Wilburn
- ZOLL Medical Corporation, Chelmsford, MA01824
- Kellogg Biological Station, College of Natural Science, Michigan State University, Hickory Corners, MI49060
| | - Stephanie I. Anderson
- Graduate School of Oceanography, The University of Rhode Island, Narragansett, RI02882
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Qianqian Zhou
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, Fujian361005, China
| | - Chunguang Wang
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, Fujian361005, China
| | - Megan D. Phan
- Department of Biological Sciences, University of Southern California, Los Angeles, CA90007
| | - Feixue Fu
- Department of Biological Sciences, University of Southern California, Los Angeles, CA90007
| | - Colin T. Kremer
- Kellogg Biological Station, College of Natural Science, Michigan State University, Hickory Corners, MI49060
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT06269
| | - Elena Litchman
- Kellogg Biological Station, College of Natural Science, Michigan State University, Hickory Corners, MI49060
- Department of Global Ecology, Carnegie Institution, Stanford University, Palo Alto, CA94305
| | - Tatiana A. Rynearson
- Graduate School of Oceanography, The University of Rhode Island, Narragansett, RI02882
| | - David A. Hutchins
- Department of Biological Sciences, University of Southern California, Los Angeles, CA90007
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82
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Jiang Z, Liu S, Zhang D, Sha Z. The Diversity and Metabolism of Culturable Nitrate-Reducing Bacteria from the Photic Zone of the Western North Pacific Ocean. Microb Ecol 2023; 86:2781-2789. [PMID: 37552473 PMCID: PMC10640468 DOI: 10.1007/s00248-023-02284-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 07/31/2023] [Indexed: 08/09/2023]
Abstract
To better understand bacterial communities and metabolism under nitrogen deficiency, 154 seawater samples were obtained from 5 to 200 m at 22 stations in the photic zone of the Western North Pacific Ocean. Total 634 nitrate-utilizing bacteria were isolated using selective media and culture-dependent methods, and 295 of them were positive for nitrate reduction. These nitrate-reducing bacteria belonged to 19 genera and 29 species and among them, Qipengyuania flava, Roseibium aggregatum, Erythrobacter aureus, Vibrio campbellii, and Stappia indica were identified from all tested seawater layers of the photic zone and at almost all stations. Twenty-nine nitrate-reducing strains representing different species were selected for further the study of nitrogen, sulfur, and carbon metabolism. All 29 nitrate-reducing isolates contained genes encoding dissimilatory nitrate reduction or assimilatory nitrate reduction. Six nitrate-reducing isolates can oxidize thiosulfate based on genomic analysis and activity testing, indicating that nitrate-reducing thiosulfate-oxidizing bacteria exist in the photic zone. Five nitrate-reducing isolates obtained near the chlorophyll a-maximum layer contained a dimethylsulfoniopropionate synthesis gene and three of them contained both dimethylsulfoniopropionate synthesis and cleavage genes. This suggests that nitrate-reducing isolates may participate in dimethylsulfoniopropionate synthesis and catabolism in photic seawater. The presence of multiple genes for chitin degradation and extracellular peptidases may indicate that almost all nitrate-reducing isolates (28/29) can use chitin and proteinaceous compounds as important sources of carbon and nitrogen. Collectively, these results reveal culturable nitrate-reducing bacterial diversity and have implications for understanding the role of such strains in the ecology and biogeochemical cycles of nitrogen, sulfur, and carbon in the oligotrophic marine photic zone.
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Affiliation(s)
- Zhichen Jiang
- Laboratory of Marine Organism Taxonomy and Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laoshan Laboratory, Qingdao, 266237, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Sizhen Liu
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Dechao Zhang
- Laboratory of Marine Organism Taxonomy and Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
- Laoshan Laboratory, Qingdao, 266237, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Zhongli Sha
- Laboratory of Marine Organism Taxonomy and Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laoshan Laboratory, Qingdao, 266237, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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83
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Karkanorachaki K, Syranidou E, Kalogerakis N. Extreme weather events as an important factor for the evolution of plastisphere but not for the degradation process. Water Res 2023; 246:120687. [PMID: 37801984 DOI: 10.1016/j.watres.2023.120687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 09/26/2023] [Accepted: 09/29/2023] [Indexed: 10/08/2023]
Abstract
Marine plastics, with their negative effects on marine life and the human health, have been recently recognized as a new niche for the colonization and development of marine biofilms. Members of the colonizing communities could possess the potential for plastic biodegradation. Thus, there is an urgent need to characterize these complex and geographically variable communities and elucidate the functionalities. In this work, we characterize the fungal and bacterial colonizers of 5 types of plastic films (High Density Polyethylene, Low Density Polyethylene, Polypropylene, Polystyrene and Polyethylene Terepthalate) over the course of a 242-day incubation in the south-eastern Mediterranean and relate them to the chemical changes observed on the surface of the samples via ATR-FTIR. The 16s rRNA and ITS2 ribosomal regions of the plastisphere communities were sequenced on four time points (35, 152, 202 and 242 days). The selection of the time points was dictated by the occurrence of a severe storm which removed biological fouling from the surface of the samples and initiated a second colonization period. The bacterial communities, dominated by Proteobacteria and Bacteroidetes, were the most variable and diverse. Fungal communities, characterized mainly by the presence of Ascomycota, were not significantly affected by the storm. Neither bacterial nor fungal community structure were related to the polymer type acting as substrate, while the surface of the plastic samples underwent weathering of oscillating degrees with time. This work examines the long-term development of Mediterranean epiplastic biofilms and is the first to examine how primary colonization influences the microbial community re-attachment and succession as a response to extreme weather events. Finally, it is one of the few studies to examine fungal communities, despite them containing putative plastic degraders.
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Affiliation(s)
- Katerina Karkanorachaki
- School of Chemical and Environmental Engineering, Technical University of Crete, GR-73100, Chania, Greece
| | - Evdokia Syranidou
- School of Chemical and Environmental Engineering, Technical University of Crete, GR-73100, Chania, Greece
| | - Nicolas Kalogerakis
- School of Chemical and Environmental Engineering, Technical University of Crete, GR-73100, Chania, Greece; Institute of GeoEnergy, Foundation for Research and Technology - Hellas, GR-73100, Chania, Greece.
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84
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85
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Li G, Wei M, Wei G, Chen Z, Shao Z. Efficient heterotrophic nitrification by a novel bacterium Sneathiella aquimaris 216LB-ZA1-12 T isolated from aquaculture seawater. Ecotoxicol Environ Saf 2023; 266:115588. [PMID: 37839193 DOI: 10.1016/j.ecoenv.2023.115588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Revised: 09/10/2023] [Accepted: 10/11/2023] [Indexed: 10/17/2023]
Abstract
High concentration of ammonia poses a common threat to the healthy breeding of marine aquaculture organisms. Since aquaculture water is rich in organic matter, heterotrophic nitrifying bacteria might play a crucial role in ammonia removal. However, their roles in ammonia oxidation remain unknown. Here, we report a novel strain isolated from shrimp aquaculture seawater, identified as Sneathiella aquimaris 216LB-ZA1-12T, capable of heterotrophic nitrification. It is the first characterized heterotrophic nitrifier of the order Sneathiellales in the class Alphaproteobacteria. It exhibits high activity in heterotrophic nitrification, removing nearly 94% of ammonium-N under carbon-constrained conditions in 8 days with no observed nitrite accumulation. The heterotrophic nitrification pathway, inferred based on detection and genomic data was as follows: NH4+→NH2OH→NO→NO2-→NO3-. While this pathway aligns with the classical nitrification pathway, while the significant difference lies in the absence of classical HAO and HOX encoding genes in the genome, which is common in heterotrophic nitrifying bacteria. In summary, this bacterium is not only valuable for studying the nitrifying mechanism, but also holds potential for practical applications in ammonia removal in marine aquaculture systems and saline wastewater.
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Affiliation(s)
- Guizhen Li
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, China; State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen 361005, China; Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, China
| | - Mengjiao Wei
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, China; State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen 361005, China; Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, China; College of Oceans and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Guangshan Wei
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, China; State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen 361005, China; Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, China; Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai)/School of Marine Sciences, Sun Yat-Sen University, Zhuhai 519082, China
| | - Zhen Chen
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, China; State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen 361005, China; Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, China
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, China; State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen 361005, China; Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, China; Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai)/School of Marine Sciences, Sun Yat-Sen University, Zhuhai 519082, China.
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86
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Mino S, Fukazawa S, Tsuchiya J, McNichol JC, Sievert SM, Yamaki S, Ando Y, Sawabe T. Hydrogenimonas cancrithermarum sp. nov., a hydrogen- and thiosulfate-oxidizing mesophilic chemolithoautotroph isolated from diffuse-flow fluids on the East Pacific Rise, and an emended description of the genus Hydrogenimonas. Int J Syst Evol Microbiol 2023; 73. [PMID: 37921642 DOI: 10.1099/ijsem.0.006132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2023] Open
Abstract
A novel mesophilic, hydrogen- and thiosulfate-oxidizing bacterium, strain ISO32T, was isolated from diffuse-flow hydrothermal fluids from the Crab Spa vent on the East Pacific Rise. Cells of ISO32T were rods, being motile by means of a single polar flagellum. The isolate grew at a temperature range between 30 and 55 °C (optimum, 43 °C), at a pH range between 5.3 and 7.6 (optimum, pH 5.8) and in the presence of 2.0-4.0 % NaCl (optimum, 2.5 %). The isolate was able to grow chemolithoautotrophically with molecular hydrogen, thiosulfate or elemental sulfur as the sole electron donor. Thiosulfate, elemental sulfur, nitrate and molecular oxygen were each used as a sole electron acceptor. Phylogenetic analysis of 16S rRNA gene sequences placed ISO32T in the genus Hydrogenimonas of the class Epsilonproteobacteria, with Hydrogenimonas thermophila EP1-55-1 %T as its closest relative (95.95 % similarity). On the basis of the phylogenetic, physiological and genomic characteristics, it is proposed that the organism represents a novel species within the genus Hydrogenimonas, Hydrogenimonas cancrithermarum sp. nov. The type strain is ISO32T (=JCM 39185T =KCTC 25252T). Furthermore, the genomic properties of members of the genus Hydrogenimonas are distinguished from those of members of other thermophilic genera in the orders Campylobacterales (Nitratiruptor and Nitrosophilus) and Nautiliales (Caminibacter, Nautilia and Lebetimonas), with larger genome sizes and lower 16S rRNA G+C content values. Comprehensive metabolic comparisons based on genomes revealed that genes responsible for the Pta-AckA pathway were observed exclusively in members of mesophilic genera in the order Campylobacterales and of the genus Hydrogenimonas. Our results indicate that the genus Hydrogenimonas contributes to elucidating the evolutionary history of Epsilonproteobacteria in terms of metabolism and transition from a thermophilic to a mesophilic lifestyle.
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Affiliation(s)
- Sayaka Mino
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan
| | - So Fukazawa
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan
| | - Jiro Tsuchiya
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan
| | - Jesse C McNichol
- Biology Department, Woods Hole Oceanographic Institution, MA, USA
- Department of Biology, St. Francis Xavier University, NS, Canada
| | - Stefan M Sievert
- Biology Department, Woods Hole Oceanographic Institution, MA, USA
| | - Shogo Yamaki
- Laboratory of Marine Food Science and Technology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan
| | - Yasuhiro Ando
- Laboratory of Marine Bioresources Chemistry, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan
| | - Tomoo Sawabe
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan
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87
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Fu ZY, Xue HP, He W, Ma GY, Zhang AH, Zhang DF, Li WJ. Marixanthotalea marina gen. nov., sp. nov., a bacterium in the family Flavobacteriaceae isolated from seawater. Int J Syst Evol Microbiol 2023; 73. [PMID: 37916703 DOI: 10.1099/ijsem.0.006107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2023] Open
Abstract
A Gram-stain-negative, yellow-pigmented, non-motile, rod-shaped, catalase-positive, strictly aerobic marine bacterium, designated XHP0103T, was isolated from seawater collected from the southern Yellow Sea, PR China (34° 45' 53″ N 119° 25' 30″ E). Strain XHP0103T grew optimally at 28 °C, pH 7.5 and in 1.0-3.0 % (w/v) sea salt. MK-6 was the major respiratory quinone. The major cellular fatty acids (>10%) were iso-C15 : 0, iso-C15 : 1 G and iso-C17 : 0 3-OH. The polar lipid profile contained phosphatidylethanolamine, an unidentified aminolipid, an unidentified glycolipid and an unidentified lipid. Results of 16S rRNA gene sequence analysis indicated that strain XHP0103T displayed highest sequence similarity to Aestuariibaculum marinum IP7T (94.1 %). However, the phylogenetic trees based on 16S rRNA gene sequences suggested that strain XHP0103T clustered with Tamlana crocina HST1-43T (93.4 % sequence similarity) and Aestuariivivens insulae AH-MY3T (93.5 %). Genome sequencing revealed that strain XHP0103T comprised 3 134 388 bp with 2770 protein-coding genes, and the DNA G+C content was 35.5 %. The average nucleotide identity and digital DNA-DNA hybridization values between strain XHP0103T and T. crocina HST1-43T were 73.6 and 17.3 %, respectively. Based on phylogenetic, phenotypic, genomic and chemotaxonomic evidence, strain XHP0103T represents a novel genus in the family Flavobacteriaceae, for which the name Marixanthotalea marina gen. nov., sp. nov. is proposed. The type strain is XHP0103T (=MCCC 1K06060T=JCM 34682T).
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Affiliation(s)
- Zi-Yue Fu
- Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization and College of Oceanography, Hohai University, Nanjing, PR China
| | - Hua-Peng Xue
- Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization and College of Oceanography, Hohai University, Nanjing, PR China
| | - Wei He
- Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization and College of Oceanography, Hohai University, Nanjing, PR China
| | - Guang-Yuan Ma
- Jiangsu Innovation Center of Marine Bioresources, Jiangsu Coast Development Group Co., Ltd, Nanjing, 210019, PR China
| | - Ai Hua Zhang
- Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization and College of Oceanography, Hohai University, Nanjing, PR China
| | - Dao-Feng Zhang
- Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization and College of Oceanography, Hohai University, Nanjing, PR China
| | - Wen-Jun Li
- Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization and College of Oceanography, Hohai University, Nanjing, PR China
- State Key Laboratory of Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, PR China
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88
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Zhang Z, Li D, Xie R, Guo R, Nair S, Han H, Zhang G, Zhao Q, Zhang L, Jiao N, Zhang Y. Plastoquinone synthesis inhibition by tetrabromo biphenyldiol as a widespread algicidal mechanism of marine bacteria. ISME J 2023; 17:1979-1992. [PMID: 37679430 PMCID: PMC10579414 DOI: 10.1038/s41396-023-01510-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 08/30/2023] [Accepted: 09/01/2023] [Indexed: 09/09/2023]
Abstract
Algae and bacteria have complex and intimate interactions in the ocean. Besides mutualism, bacteria have evolved a variety of molecular-based anti-algal strategies. However, limited by the unknown mechanism of synthesis and action of these molecules, these strategies and their global prevalence remain unknown. Here we identify a novel strategy through which a marine representative of the Gammaproteobacteria produced 3,3',5,5'-tetrabromo-2,2'-biphenyldiol (4-BP), that kills or inhibits diverse phytoplankton by inhibiting plastoquinone synthesis and its effect cascades to many other key metabolic processes of the algae. Through comparative genomic analysis between the 4-BP-producing bacterium and its algicidally inactive mutant, combined with gene function verification, we identified the gene cluster responsible for 4-BP synthesis, which contains genes encoding chorismate lyase, flavin-dependent halogenase and cytochrome P450. We demonstrated that in near in situ simulated algal blooming seawater, even low concentrations of 4-BP can cause changes in overall phytoplankton community structure with a decline in dinoflagellates and diatoms. Further analyses of the gene sequences from the Tara Oceans expeditions and 2750 whole genome sequences confirmed the ubiquitous presence of 4-BP synthetic genes in diverse bacterial members in the global ocean, suggesting that it is a bacterial tool potentially widely used in global oceans to mediate bacteria-algae antagonistic relationships.
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Affiliation(s)
- Zenghu Zhang
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- Shandong Energy Institute, Qingdao, 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, 266101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Dehai Li
- School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Ruize Xie
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
| | - Ruoyu Guo
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
| | - Shailesh Nair
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
| | - Huan Han
- School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Guojian Zhang
- School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Qun Zhao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. &A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Lihua Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. &A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361101, China
| | - Yongyu Zhang
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China.
- Shandong Energy Institute, Qingdao, 266101, China.
- Qingdao New Energy Shandong Laboratory, Qingdao, 266101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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89
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Dawson HM, Connors E, Erazo NG, Sacks JS, Mierzejewski V, Rundell SM, Carlson LT, Deming JW, Ingalls AE, Bowman JS, Young JN. Microbial metabolomic responses to changes in temperature and salinity along the western Antarctic Peninsula. ISME J 2023; 17:2035-2046. [PMID: 37709939 PMCID: PMC10579395 DOI: 10.1038/s41396-023-01475-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 06/28/2023] [Accepted: 06/30/2023] [Indexed: 09/16/2023]
Abstract
Seasonal cycles within the marginal ice zones in polar regions include large shifts in temperature and salinity that strongly influence microbial abundance and physiology. However, the combined effects of concurrent temperature and salinity change on microbial community structure and biochemical composition during transitions between seawater and sea ice are not well understood. Coastal marine communities along the western Antarctic Peninsula were sampled and surface seawater was incubated at combinations of temperature and salinity mimicking the formation (cold, salty) and melting (warm, fresh) of sea ice to evaluate how these factors may shape community composition and particulate metabolite pools during seasonal transitions. Bacterial and algal community structures were tightly coupled to each other and distinct across sea-ice, seawater, and sea-ice-meltwater field samples, with unique metabolite profiles in each habitat. During short-term (approximately 10-day) incubations of seawater microbial communities under different temperature and salinity conditions, community compositions changed minimally while metabolite pools shifted greatly, strongly accumulating compatible solutes like proline and glycine betaine under cold and salty conditions. Lower salinities reduced total metabolite concentrations in particulate matter, which may indicate a release of metabolites into the labile dissolved organic matter pool. Low salinity also increased acylcarnitine concentrations in particulate matter, suggesting a potential for fatty acid degradation and reduced nutritional value at the base of the food web during freshening. Our findings have consequences for food web dynamics, microbial interactions, and carbon cycling as polar regions undergo rapid climate change.
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Affiliation(s)
- H M Dawson
- School of Oceanography, University of Washington, Seattle, WA, 98195, USA.
| | - E Connors
- Scripps Institution of Oceanography, UC San Diego, La Jolla, CA, 92037, USA
| | - N G Erazo
- Scripps Institution of Oceanography, UC San Diego, La Jolla, CA, 92037, USA
- Center for Marine Biodiversity and Conservation, UC San Diego, La Jolla, CA, 92037, USA
| | - J S Sacks
- School of Oceanography, University of Washington, Seattle, WA, 98195, USA
| | - V Mierzejewski
- School of Earth and Space Exploration, Arizona State University, Tempe, AZ, 85287, USA
| | - S M Rundell
- School of Oceanography, University of Washington, Seattle, WA, 98195, USA
| | - L T Carlson
- School of Oceanography, University of Washington, Seattle, WA, 98195, USA
| | - J W Deming
- School of Oceanography, University of Washington, Seattle, WA, 98195, USA
| | - A E Ingalls
- School of Oceanography, University of Washington, Seattle, WA, 98195, USA
| | - J S Bowman
- Scripps Institution of Oceanography, UC San Diego, La Jolla, CA, 92037, USA
- Center for Marine Biodiversity and Conservation, UC San Diego, La Jolla, CA, 92037, USA
- Center for Microbiome Innovation, UC San Diego, La Jolla, CA, 92037, USA
| | - J N Young
- School of Oceanography, University of Washington, Seattle, WA, 98195, USA.
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90
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Turk-Kubo KA, Gradoville MR, Cheung S, Cornejo-Castillo FM, Harding KJ, Morando M, Mills M, Zehr JP. Non-cyanobacterial diazotrophs: global diversity, distribution, ecophysiology, and activity in marine waters. FEMS Microbiol Rev 2023; 47:fuac046. [PMID: 36416813 PMCID: PMC10719068 DOI: 10.1093/femsre/fuac046] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 09/15/2022] [Accepted: 11/17/2022] [Indexed: 12/17/2023] Open
Abstract
Biological dinitrogen (N2) fixation supplies nitrogen to the oceans, supporting primary productivity, and is carried out by some bacteria and archaea referred to as diazotrophs. Cyanobacteria are conventionally considered to be the major contributors to marine N2 fixation, but non-cyanobacterial diazotrophs (NCDs) have been shown to be distributed throughout ocean ecosystems. However, the biogeochemical significance of marine NCDs has not been demonstrated. This review synthesizes multiple datasets, drawing from cultivation-independent molecular techniques and data from extensive oceanic expeditions, to provide a comprehensive view into the diversity, biogeography, ecophysiology, and activity of marine NCDs. A NCD nifH gene catalog was compiled containing sequences from both PCR-based and PCR-free methods, identifying taxa for future studies. NCD abundances from a novel database of NCD nifH-based abundances were colocalized with environmental data, unveiling distinct distributions and environmental drivers of individual taxa. Mechanisms that NCDs may use to fuel and regulate N2 fixation in response to oxygen and fixed nitrogen availability are discussed, based on a metabolic analysis of recently available Tara Oceans expedition data. The integration of multiple datasets provides a new perspective that enhances understanding of the biology, ecology, and biogeography of marine NCDs and provides tools and directions for future research.
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Affiliation(s)
- Kendra A Turk-Kubo
- Ocean Sciences Department, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, United States
| | - Mary R Gradoville
- Ocean Sciences Department, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, United States
- Columbia River Inter-Tribal Fish Commission, Portland, OR, United States
| | - Shunyan Cheung
- Ocean Sciences Department, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, United States
| | - Francisco M Cornejo-Castillo
- Ocean Sciences Department, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, United States
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM-CSIC), Pg. Marítim Barceloneta, 37-49 08003 Barcelona, Spain
| | - Katie J Harding
- Ocean Sciences Department, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, United States
- Marine Biology Research Division, Scripps Institute of Oceanography, 9500 Gilman Drive, La Jolla, CA 92093, United States
| | - Michael Morando
- Ocean Sciences Department, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, United States
| | - Matthew Mills
- Department of Earth System Science, Stanford University, 473 Via Ortega, Stanford, CA 94305, United States
| | - Jonathan P Zehr
- Ocean Sciences Department, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, United States
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91
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Strauss J, Choi CJ, Grone J, Wittmers F, Jimenez V, Makareviciute-Fichtner K, Bachy C, Jaeger GS, Poirier C, Eckmann C, Spezzano R, Löscher CR, Sarma VVSS, Mahadevan A, Worden AZ. The Bay of Bengal exposes abundant photosynthetic picoplankton and newfound diversity along salinity-driven gradients. Environ Microbiol 2023; 25:2118-2141. [PMID: 37311449 DOI: 10.1111/1462-2920.16431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 05/13/2023] [Indexed: 06/15/2023]
Abstract
The Bay of Bengal (BoB) is a 2,600,000 km2 expanse in the Indian Ocean upon which many humans rely. However, the primary producers underpinning food chains here remain poorly characterized. We examined phytoplankton abundance and diversity along strong BoB latitudinal and vertical salinity gradients-which have low temperature variation (27-29°C) between the surface and subsurface chlorophyll maximum (SCM). In surface waters, Prochlorococcus averaged 11.7 ± 4.4 × 104 cells ml-1 , predominantly HLII, whereas LLII and 'rare' ecotypes, HLVI and LLVII, dominated in the SCM. Synechococcus averaged 8.4 ± 2.3 × 104 cells ml-1 in the surface, declined rapidly with depth, and population structure of dominant Clade II differed between surface and SCM; Clade X was notable at both depths. Across all sites, Ostreococcus Clade OII dominated SCM eukaryotes whereas communities differentiated strongly moving from Arabian Sea-influenced high salinity (southerly; prasinophytes) to freshwater-influenced low salinity (northerly; stramenopiles, specifically, diatoms, pelagophytes, and dictyochophytes, plus the prasinophyte Micromonas) surface waters. Eukaryotic phytoplankton peaked in the south (1.9 × 104 cells ml-1 , surface) where a novel Ostreococcus was revealed, named here Ostreococcus bengalensis. We expose dominance of a single picoeukaryote and hitherto 'rare' picocyanobacteria at depth in this complex ecosystem where studies suggest picoplankton are replacing larger phytoplankton due to climate change.
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Affiliation(s)
- Jan Strauss
- Ocean EcoSystems Biology Unit, RD3, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Chang Jae Choi
- Ocean EcoSystems Biology Unit, RD3, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Jonathan Grone
- Ocean EcoSystems Biology Unit, RD3, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
- Faculty of Mathematics and Natural Sciences, Christian-Albrecht University of Kiel, Kiel, Germany
| | - Fabian Wittmers
- Ocean EcoSystems Biology Unit, RD3, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
- Faculty of Mathematics and Natural Sciences, Christian-Albrecht University of Kiel, Kiel, Germany
| | - Valeria Jimenez
- Ocean EcoSystems Biology Unit, RD3, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | | | - Charles Bachy
- Ocean EcoSystems Biology Unit, RD3, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
- Sorbonne Université - CNRS, Roscoff Culture Collection, FR2424, Station Biologique de Roscoff, Roscoff, France
| | - Gualtiero Spiro Jaeger
- Physical Oceanography Department, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
| | - Camille Poirier
- Ocean EcoSystems Biology Unit, RD3, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Charlotte Eckmann
- Ocean EcoSystems Biology Unit, RD3, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Rachele Spezzano
- Ocean EcoSystems Biology Unit, RD3, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Carolin R Löscher
- Nordcee, DIAS, Department of Biology, University of Southern Denmark, Odense, Denmark
| | - V V S S Sarma
- Regional Centre, CSIR-National Institute of Oceanography, Visakhapatnam, India
| | - Amala Mahadevan
- Physical Oceanography Department, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
| | - Alexandra Z Worden
- Ocean EcoSystems Biology Unit, RD3, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
- Faculty of Mathematics and Natural Sciences, Christian-Albrecht University of Kiel, Kiel, Germany
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts, USA
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92
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Cleary DFR, de Voogd NJ, Stuij TM, Swierts T, Oliveira V, Polónia ARM, Louvado A, Gomes NCM, Coelho FJRC. A Study of Sponge Symbionts from Different Light Habitats. Microb Ecol 2023; 86:2819-2837. [PMID: 37597041 PMCID: PMC10640470 DOI: 10.1007/s00248-023-02267-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Accepted: 07/07/2023] [Indexed: 08/21/2023]
Abstract
The amount of available light plays a key role in the growth and development of microbial communities. In the present study, we tested to what extent sponge-associated prokaryotic communities differed between specimens of the sponge species Cinachyrella kuekenthali and Xestospongia muta collected in dimly lit (caves and at greater depths) versus illuminated (shallow water) habitats. In addition to this, we also collected samples of water, sediment, and another species of Cinachyrella, C. alloclada. Overall, the biotope (sponge host species, sediment, and seawater) proved the major driver of variation in prokaryotic community composition. The light habitat, however, also proved a predictor of compositional variation in prokaryotic communities of both C. kuekenthali and X. muta. We used an exploratory technique based on machine learning to identify features (classes, orders, and OTUs), which distinguished X. muta specimens sampled in dimly lit versus illuminated habitat. We found that the classes Alphaproteobacteria and Rhodothermia and orders Puniceispirillales, Rhodospirillales, Rhodobacterales, and Thalassobaculales were associated with specimens from illuminated, i.e., shallow water habitat, while the classes Dehalococcoidia, Spirochaetia, Entotheonellia, Nitrospiria, Schekmanbacteria, and Poribacteria, and orders Sneathiellales and Actinomarinales were associated with specimens sampled from dimly lit habitat. There was, however, considerable variation within the different light habitats highlighting the importance of other factors in structuring sponge-associated bacterial communities.
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Affiliation(s)
- D F R Cleary
- CESAM & Department of Biology, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal.
| | - N J de Voogd
- Naturalis Biodiversity Center, Leiden, The Netherlands.
- Institute of Environmental Sciences (CML), Leiden University, Leiden, The Netherlands.
| | - T M Stuij
- CESAM & Department of Biology, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| | - T Swierts
- Naturalis Biodiversity Center, Leiden, The Netherlands
| | - V Oliveira
- CESAM & Department of Biology, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| | - A R M Polónia
- CESAM & Department of Biology, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| | - A Louvado
- CESAM & Department of Biology, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| | - N C M Gomes
- CESAM & Department of Biology, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| | - F J R C Coelho
- CESAM & Department of Biology, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
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93
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Wang W, Liu M, Cao B, Liu Y, Huang K, Ding Y, Xu Z, Sun F, Zhang Y, Niu W, Tian P, Huang D, Wang X, Xiao J. Vibrio methylphosphonaticus sp. nov., a methylphosphonate-decomposing bacterium isolated from surface seawater in the Xisha Islands, PR China. Int J Syst Evol Microbiol 2023; 73. [PMID: 37997883 DOI: 10.1099/ijsem.0.006183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2023] Open
Abstract
A Gram-stain-negative, facultative anaerobic, methylphosphonate-decomposing, motile by a polar flagellum and rod-shaped marine bacterium, designated S4B1T, was isolated from the surface seawater collected from the Yongle Atoll (Xisha Islands, PR China). The pairwise alignment showed the highest sequence similarity of 97.5 and 96.6 % to Vibrio aestuarianus subsp. cardii 12_122_3T3T and Vibrio atypicus HHS02T, respectively. Phylogenetic analysis based on 16S rRNA gene and the phylogenomic analysis of single-copy genes showed that strain S4B1T belonged to the genus Vibrio and formed a close branch with Vibrio qingdaonensis ZSDZ65T. Growth of strain S4B1T occurred at 4-30 °C (optimum, 28 °C), at pH 6.0-8.0 (optimum, pH 7.0) and in the presence of 2-7 % (w/v) NaCl (optimum, 3 %). The predominant fatty acids (>10 %) were C16 : 0, iso-C16 : 0 and summed feature 3 (C16 : 1 ω7c or/and C16 : 1 ω6c). The DNA G+C content of the assembled genomic sequence was 44.3 mol%. Average nucleotide identity (ANI) values between S4B1T and its reference species were lower than the threshold for species delineation (95-96 %), in which its highest ANI value with V. qingdaonensis ZSDZ65T was 87.0 %. In silico DNA-DNA hybridization further showed that strain S4B1T had less than 70 % similarity to its relatives. On the basis of the polyphasic evidence, strain S4B1T is proposed to represent a novel species of the genus Vibrio, for which the name Vibrio methylphosphonaticus sp. nov. is proposed. The type strain is S4B1T (=KCTC 92311T=MCCC 1K06168T).
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Affiliation(s)
- Wei Wang
- Laboratory of Marine Biodiversity Research, Third Institute of Oceanography, Ministry of Natural Resources, 178 Daxue Road, Xiamen 361005, PR China
| | - Mei Liu
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Bingbing Cao
- Laboratory of Marine Biodiversity Research, Third Institute of Oceanography, Ministry of Natural Resources, 178 Daxue Road, Xiamen 361005, PR China
| | - Yi Liu
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Keyi Huang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Yunqi Ding
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Ziqing Xu
- Laboratory of Marine Biodiversity Research, Third Institute of Oceanography, Ministry of Natural Resources, 178 Daxue Road, Xiamen 361005, PR China
| | - Fucheng Sun
- Laboratory of Marine Biodiversity Research, Third Institute of Oceanography, Ministry of Natural Resources, 178 Daxue Road, Xiamen 361005, PR China
| | - Yunxiao Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Wentao Niu
- Laboratory of Marine Biodiversity Research, Third Institute of Oceanography, Ministry of Natural Resources, 178 Daxue Road, Xiamen 361005, PR China
| | - Peng Tian
- Laboratory of Marine Biodiversity Research, Third Institute of Oceanography, Ministry of Natural Resources, 178 Daxue Road, Xiamen 361005, PR China
| | - Dingyong Huang
- Key Laboratory of Marine Ecological Conservation and Restoration, Ministry of Natural Resources /Fujian Provincial Key Laboratory of Marine Ecological Conservation and Restoration, Fujian, PR China
| | - Xiaolei Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Jiaguang Xiao
- Laboratory of Marine Biodiversity Research, Third Institute of Oceanography, Ministry of Natural Resources, 178 Daxue Road, Xiamen 361005, PR China
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94
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Zhou ZY, An J, Jia YW, Xuan XQ, Du ZJ. Robiginitalea aurantiaca sp. nov. and Algoriphagus sediminis sp. nov., isolated from coastal sediment. Int J Syst Evol Microbiol 2023; 73. [PMID: 37942742 DOI: 10.1099/ijsem.0.006155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2023] Open
Abstract
Two novel rod-shaped, Gram-stain-negative, aerobic and non-motile bacterial strains, designated M39T and C2-7T, were isolated from the coastal sediment of Xiaoshi Island, Weihai, PR China. Growth of strain M39T occurred at 15-37 °C, at pH 6.0-9.0 and in the presence of 1.0-9.0 % (w/v) NaCl. Strain C2-7T grew at 15-40 °C, at pH 6.0-8.0 and in the presence of 0.5-8.0 % (w/v) NaCl. Phylogenetic analysis based 16S rRNA gene sequences revealed that strains M39T and C2-7T belong to the phylum Bacteroidota. Based on the results of 16S rRNA gene sequence analysis, the closest relative of strain M39T was Robiginitalea marina KCTC 92035T (95.4 %), and the closest relative of strain C2-7T was Algoriphagus namhaensis DPG-3T (97.0 %). The percentage of conserved protein and average nucleotide identity values between strain M39T and some species of the genus Robiginitalea were 66.9-77.6% and 69.3-71.0 %, respectively, while those between strain C2-7T and some species of the genus Algoriphagus were 68.0-70.1% and 56.1-72.6 %, respectively. The major cellular fatty acids (>10 %) of strain M39T consisted of iso-C15 : 1 F, iso-C15 : 0 and iso-C17 : 0 3-OH, while those of strain C2-7T were iso-C15 : 0 and C16 : 1 ω7c/C16 : 1 ω6c. MK-6 was the only respiratory quinone that was compatible with the genus of strain M39T. The predominant menaquinone of strain C2-7T was MK-7. The major polar lipids of strain M39T were phosphatidylethanolamine and glycolipids, and those of strain C2-7T were phosphatidylethanolamine, one unidentified aminolipid and four unidentified lipids. The DNA G+C contents of strains M39T and C2-7T were 46.9 and 40.8 mol%, respectively. Based upon the results presented in this study, strains M39T and C2-7T represent novel species of the genera Robiginitalea and Algoriphagus, respectively, for which the names Robiginitalea aurantiaca sp. nov. and Algoriphagus sediminis sp. nov. are proposed with the type strains M39T (=MCCC 1H00498T=KCTC 92014T) and C2-7T (=MCCC 1H00414T=KCTC 92027T).
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Affiliation(s)
- Zi-Yang Zhou
- Marine College, Shandong University, Weihai 264209, Shandong, PR China
| | - Jing An
- Marine College, Shandong University, Weihai 264209, Shandong, PR China
| | - Ya-Wei Jia
- Marine College, Shandong University, Weihai 264209, Shandong, PR China
| | - Xiao-Qi Xuan
- Marine College, Shandong University, Weihai 264209, Shandong, PR China
| | - Zong-Jun Du
- Marine College, Shandong University, Weihai 264209, Shandong, PR China
- Weihai Research Institute of Industrial Technology of Shandong University, Weihai, 264209, Shandong, PR China
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95
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Cai G, Yu X, Wang H, Zheng T, Azam F. Nutrient-dependent interactions between a marine copiotroph Alteromonas and a diatom Thalassiosira pseudonana. mBio 2023; 14:e0094023. [PMID: 37772817 PMCID: PMC10653928 DOI: 10.1128/mbio.00940-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 08/11/2023] [Indexed: 09/30/2023] Open
Abstract
IMPORTANCE As the major producers and consumers, phytoplankton and bacteria play central roles in marine ecosystems and their interactions show great ecological significance. Whether mutualistic or antagonistic, the interaction between certain phytoplankton and bacterial species is usually seen as a derivative of intrinsic physiological properties and rarely changes. This study demonstrated that the interactions between the ubiquitously co-occurring bacteria and diatom, Alteromonas and Thalassiosira pseudonana, varied with nutrient conditions. They overcame hardship together in oligotrophic seawater but showed antagonistic effects against each other under nutrient amendment. The contact-dependent algicidal behavior of Alteromonas based on protease activity solved the paradox among bacterial proliferation, nutrient viability, and algal demise haunting other known non-contact-dependent algicidal processes and might actually trigger the collapse of algal blooms in situ. The chemotactic and swarming movement of Alteromonas might also contribute greatly to the breakdown of "marine snow," which could redirect the carbon sequestration pathway in the ocean.
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Affiliation(s)
- Guanjing Cai
- Biology Department and Institute of Marine Sciences, College of Science, and Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China
- State Key Laboratory of Marine Environmental Science and Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen, China
| | - Xiaoqi Yu
- State Key Laboratory of Marine Environmental Science and Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen, China
| | - Hui Wang
- Biology Department and Institute of Marine Sciences, College of Science, and Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China
| | - Tianling Zheng
- State Key Laboratory of Marine Environmental Science and Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen, China
| | - Farooq Azam
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California, USA
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96
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Landry MR, Stukel MR, Selph KE, Goericke R. Coexisting picoplankton experience different relative grazing pressures across an ocean productivity gradient. Proc Natl Acad Sci U S A 2023; 120:e2220771120. [PMID: 37871180 PMCID: PMC10622918 DOI: 10.1073/pnas.2220771120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 08/30/2023] [Indexed: 10/25/2023] Open
Abstract
Picophytoplankton populations [Prochlorococcus, Synechococcus (SYN), and picoeukaryotes] are dominant primary producers in the open ocean and projected to become more important with climate change. Their fates can vary, however, with microbial food web complexities. In the California Current Ecosystem, picophytoplankton biomass and abundance peak in waters of intermediate productivity and decrease at higher production. Using experimental data from eight cruises crossing the pronounced CCE trophic gradient, we tested the hypothesis that these declines are driven by intensified grazing on heterotrophic bacteria (HBAC) passed to similarly sized picophytoplankton via shared predators. Results confirm previously observed distributions as well as significant increases in bacterial abundance, cell growth, and grazing mortality with primary production. Mortalities of picophytoplankton, however, diverge from the bacterial mortality trend such that relative grazing rates on SYN compared to HBAC decline by 12-fold between low and high productivity waters. The large shifts in mortality rate ratios for coexisting populations are not explained by size variability but rather suggest high selectivity of grazer assemblages or tightly coupled tradeoffs in microbial growth advantages and grazing vulnerabilities. These findings challenge the long-held view that protistan grazing mainly determines overall biomass of microbial communities while viruses uniquely regulate diversity by "killing the winners".
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Affiliation(s)
- Michael R. Landry
- Scripps Institution of Oceanography, University of California at San Diego, San Diego, CA92093
| | - Michael R. Stukel
- Earth, Ocean, and Atmospheric Science Department, Florida State University, Tallahassee, FL32306
| | - Karen E. Selph
- Department of Oceanography, University of Hawai’i at Manoa, Honolulu, HI96822
| | - Ralf Goericke
- Scripps Institution of Oceanography, University of California at San Diego, San Diego, CA92093
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97
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Kujawinski EB, Braakman R, Longnecker K, Becker JW, Chisholm SW, Dooley K, Kido Soule MC, Swarr GJ, Halloran K. Metabolite diversity among representatives of divergent Prochlorococcus ecotypes. mSystems 2023; 8:e0126122. [PMID: 37815355 PMCID: PMC10654061 DOI: 10.1128/msystems.01261-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 08/31/2023] [Indexed: 10/11/2023] Open
Abstract
IMPORTANCE Approximately half of the annual carbon fixation on Earth occurs in the surface ocean through the photosynthetic activities of phytoplankton such as the ubiquitous picocyanobacterium Prochlorococcus. Ecologically distinct subpopulations (or ecotypes) of Prochlorococcus are central conduits of organic substrates into the ocean microbiome, thus playing important roles in surface ocean production. We measured the chemical profile of three cultured ecotype strains, observing striking differences among them that have implications for the likely chemical impact of Prochlorococcus subpopulations on their surroundings in the wild. Subpopulations differ in abundance along gradients of temperature, light, and nutrient concentrations, suggesting that these chemical differences could affect carbon cycling in different ocean strata and should be considered in models of Prochlorococcus physiology and marine carbon dynamics.
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Affiliation(s)
- Elizabeth B. Kujawinski
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
| | - Rogier Braakman
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Krista Longnecker
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
| | - Jamie W. Becker
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Science Department, Alvernia University, Reading, Pennsylvania, USA
| | - Sallie W. Chisholm
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Keven Dooley
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, USA
| | - Melissa C. Kido Soule
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
| | - Gretchen J. Swarr
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
| | - Kathryn Halloran
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
- MIT/WHOI Joint Program in Oceanography/Applied Ocean Sciences and Engineering, Department of Marine Chemistry & Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
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98
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Siri Y, Precha N, Sirikanchana K, Haramoto E, Makkaew P. Antimicrobial resistance in southeast Asian water environments: A systematic review of current evidence and future research directions. Sci Total Environ 2023; 896:165229. [PMID: 37394072 DOI: 10.1016/j.scitotenv.2023.165229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 06/27/2023] [Accepted: 06/28/2023] [Indexed: 07/04/2023]
Abstract
Antimicrobial resistance has been a serious and complex issue for over a decade. Although research on antimicrobial resistance (AMR) has mainly focused on clinical and animal samples as essential for treatment, the AMR situation in aquatic environments may vary and have complicated patterns according to geographical area. Therefore, this study aimed to examine recent literature on the current situation and identify gaps in the AMR research on freshwater, seawater, and wastewater in Southeast Asia. The PubMed, Scopus, and ScienceDirect databases were searched for relevant publications published from January 2013 to June 2023 that focused on antimicrobial resistance bacteria (ARB) and antimicrobial resistance genes (ARGs) among water sources. Based on the inclusion criteria, the final screening included 41 studies, with acceptable agreement assessed using Cohen's inter-examiner kappa equal to 0.866. This review found that 23 out of 41 included studies investigated ARGs and ARB reservoirs in freshwater rather than in seawater and wastewater, and it frequently found that Escherichia coli was a predominant indicator in AMR detection conducted by both phenotypic and genotypic methods. Different ARGs, such as blaTEM, sul1, and tetA genes, were found to be at a high prevalence in wastewater, freshwater, and seawater. Existing evidence highlights the importance of wastewater management and constant water monitoring in preventing AMR dissemination and strengthening effective mitigation strategies. This review may be beneficial for updating current evidence and providing a framework for spreading ARB and ARGs, particularly region-specific water sources. Future AMR research should include samples from various water systems, such as drinking water or seawater, to generate contextually appropriate results. Robust evidence regarding standard detection methods is required for prospective-era work to raise practical policies and alerts for developing microbial source tracking and identifying sources of contamination-specific indicators in aquatic environment markers.
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Affiliation(s)
- Yadpiroon Siri
- Environmental, Safety Technology and Health Program, School of Public Health, Walailak University, Thaiburi, Thasala, Nakhon Si Thammarat 80160, Thailand
| | - Nopadol Precha
- Department of Environmental Health and Technology, School of Public Health, Walailak University, Nakhon Si Thammarat 80160, Thailand; One Health Research Center, Walailak University, Nakhon Si Thammarat 80160, Thailand
| | - Kwanrawee Sirikanchana
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok 10210, Thailand; Center of Excellence on Environmental Health and Toxicology (EHT), OPS, MHESI, Bangkok 10400, Thailand
| | - Eiji Haramoto
- Interdisciplinary Center for River Basin Environment, University of Yamanashi, Yamanashi 400-8511, Japan
| | - Prasert Makkaew
- Department of Environmental Health and Technology, School of Public Health, Walailak University, Nakhon Si Thammarat 80160, Thailand; One Health Research Center, Walailak University, Nakhon Si Thammarat 80160, Thailand.
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99
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von Arx JN, Kidane AT, Philippi M, Mohr W, Lavik G, Schorn S, Kuypers MMM, Milucka J. Methylphosphonate-driven methane formation and its link to primary production in the oligotrophic North Atlantic. Nat Commun 2023; 14:6529. [PMID: 37845220 PMCID: PMC10579326 DOI: 10.1038/s41467-023-42304-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 10/06/2023] [Indexed: 10/18/2023] Open
Abstract
Methylphosphonate is an organic phosphorus compound used by microorganisms when phosphate, a key nutrient limiting growth in most marine surface waters, becomes unavailable. Microbial methylphosphonate use can result in the formation of methane, a potent greenhouse gas, in oxic waters where methane production is traditionally unexpected. The extent and controlling factors of such aerobic methane formation remain underexplored. Here, we show high potential net rates of methylphosphonate-driven methane formation (median 0.4 nmol methane L-1 d-1) in the upper water column of the western tropical North Atlantic. The rates are repressed but still quantifiable in the presence of in-situ or added phosphate, suggesting that some methylphosphonate-driven methane formation persists in phosphate-replete waters. The genetic potential for methylphosphonate utilisation is present in and transcribed by key photo- and heterotrophic microbial taxa, such as Pelagibacterales, SAR116, and Trichodesmium. While the large cyanobacterial nitrogen-fixers dominate in the surface layer, phosphonate utilisation by Alphaproteobacteria appears to become more important in deeper depths. We estimate that at our study site, a substantial part (median 11%) of the measured surface carbon fixation can be sustained by phosphorus liberated from phosphonate utilisation, highlighting the ecological importance of phosphonates in the carbon cycle of the oligotrophic ocean.
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Affiliation(s)
- Jan N von Arx
- Max Planck Institute for Marine Microbiology, Bremen, Germany.
| | - Abiel T Kidane
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Miriam Philippi
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Wiebke Mohr
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Gaute Lavik
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Sina Schorn
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | | | - Jana Milucka
- Max Planck Institute for Marine Microbiology, Bremen, Germany
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100
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Wang SX, Wang YW, Ma L, An J, Gong Y, Du ZJ. Winogradskyella immobilis sp. nov., an Alginate-Hydrolyzing Bacterium Isolated from the Brown Algae Saccharina japonica. Curr Microbiol 2023; 80:370. [PMID: 37838638 DOI: 10.1007/s00284-023-03474-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 09/04/2023] [Indexed: 10/16/2023]
Abstract
A novel bacterium, designated E313T, was isolated from brown algae Saccharina japonica in Weihai, China. The strain is a Gram-stain-negative, non-flagellated, non-gliding, aerobic, rod-shaped bacterium that grows optimally at 28 °C with pH levels between 7.0 and 7.5 and in the presence of 2-3% (w/v) NaCl. Phylogenetic analyses based on its 16S rRNA gene sequence placed the strain within the monophyletic cluster of the genus Winogradskyella, exhibiting the highest similarity to Winogradskyella wandonensis KCTC 32579T (96.8%). Genome comparison of strain E313T with W. wandonensis KCTC 32579T and W. thalassocola KCTC 12221T revealed average nucleotide identity (ANI) values of 74.2% and 74.8%, and DNA-DNA hybridization (dDDH) values of 19.0% and 19.5%, respectively, lower than prokaryotic species delineation values. The strain E313T could hydrolyze alginate. A total of 123 carbohydrate-active enzymes were annotated according to the CAZy database. Especially, one oligo-alginate lyase and one poly(β-D-mannuronate) lyase were identified in the genome of strain E313T. Strain E313T possessed MK-6 quinone and iso-C15:0, iso-C15:1 G, iso-C17:0 3-OH, and iso-C15:0 3-OH as main fatty acids. Its major polar lipids were phosphatidylethanolamine (PE), one unidentified aminolipid, and two unknown lipids. Thus, based on phylogenetic, physiological, and chemotaxonomic analyses, we propose a novel species of the genus Winogradskyella, named Winogradskyella immobilis sp. nov., with E313T (= MCCC 1H00506T = KCTC 82731T) as the type strain.
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Affiliation(s)
- Shu-Xin Wang
- Marine College, Shandong University, Weihai, 264209, Shandong, China
| | - Ya-Wei Wang
- Marine College, Shandong University, Weihai, 264209, Shandong, China
| | - Lu Ma
- Marine College, Shandong University, Weihai, 264209, Shandong, China
| | - Jing An
- Marine College, Shandong University, Weihai, 264209, Shandong, China
| | - Ya Gong
- Marine College, Shandong University, Weihai, 264209, Shandong, China.
- WeiHai Research Institute of Industrial Technology of Shandong University, Weihai, 264209, Shandong, China.
| | - Zong-Jun Du
- Marine College, Shandong University, Weihai, 264209, Shandong, China.
- WeiHai Research Institute of Industrial Technology of Shandong University, Weihai, 264209, Shandong, China.
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