1
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Graham OJ, Adamczyk EM, Schenk S, Dawkins P, Burke S, Chei E, Cisz K, Dayal S, Elstner J, Hausner ALP, Hughes T, Manglani O, McDonald M, Mikles C, Poslednik A, Vinton A, Wegener Parfrey L, Harvell CD. Manipulation of the seagrass-associated microbiome reduces disease severity. Environ Microbiol 2024; 26:e16582. [PMID: 38195072 DOI: 10.1111/1462-2920.16582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 12/27/2023] [Indexed: 01/11/2024]
Abstract
Host-associated microbes influence host health and function and can be a first line of defence against infections. While research increasingly shows that terrestrial plant microbiomes contribute to bacterial, fungal, and oomycete disease resistance, no comparable experimental work has investigated marine plant microbiomes or more diverse disease agents. We test the hypothesis that the eelgrass (Zostera marina) leaf microbiome increases resistance to seagrass wasting disease. From field eelgrass with paired diseased and asymptomatic tissue, 16S rRNA gene amplicon sequencing revealed that bacterial composition and richness varied markedly between diseased and asymptomatic tissue in one of the two years. This suggests that the influence of disease on eelgrass microbial communities may vary with environmental conditions. We next experimentally reduced the eelgrass microbiome with antibiotics and bleach, then inoculated plants with Labyrinthula zosterae, the causative agent of wasting disease. We detected significantly higher disease severity in eelgrass with a native microbiome than an experimentally reduced microbiome. Our results over multiple experiments do not support a protective role of the eelgrass microbiome against L. zosterae. Further studies of these marine host-microbe-pathogen relationships may continue to show new relationships between plant microbiomes and diseases.
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Affiliation(s)
- Olivia J Graham
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
| | - Emily M Adamczyk
- Department of Zoology and Biodiversity Research Centre, Unceded xʷməθkʷəy̓əm (Musqueam) Territory, University of British Columbia, Vancouver, British Columbia, Canada
| | - Siobhan Schenk
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Phoebe Dawkins
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
| | - Samantha Burke
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
| | - Emily Chei
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
| | - Kaitlyn Cisz
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
| | - Sukanya Dayal
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
| | - Jack Elstner
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
| | | | - Taylor Hughes
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
| | - Omisha Manglani
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
| | - Miles McDonald
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
| | - Chloe Mikles
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
| | - Anna Poslednik
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
| | - Audrey Vinton
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
| | - Laura Wegener Parfrey
- Department of Zoology and Biodiversity Research Centre, Unceded xʷməθkʷəy̓əm (Musqueam) Territory, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - C Drew Harvell
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
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2
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Lucas-Elío P, ElAlami T, Martínez A, Sanchez-Amat A. Marinomonas mediterranea synthesizes an R-type bacteriocin. Appl Environ Microbiol 2024; 90:e0127323. [PMID: 38169292 PMCID: PMC10870725 DOI: 10.1128/aem.01273-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 11/17/2023] [Indexed: 01/05/2024] Open
Abstract
Prophages integrated into bacterial genomes can become cryptic or defective prophages, which may evolve to provide various traits to bacterial cells. Previous research on Marinomonas mediterranea MMB-1 demonstrated the production of defective particles. In this study, an analysis of the genomes of three different strains (MMB-1, MMB-2, and MMB-3) revealed the presence of a region named MEDPRO1, spanning approximately 52 kb, coding for a defective prophage in strains MMB-1 and MMB-2. This prophage seems to have been lost in strain MMB-3, possibly due to the presence of spacers recognizing this region in an I-F CRISPR array in this strain. However, all three strains produce remarkably similar defective particles. Using strain MMB-1 as a model, mass spectrometry analyses indicated that the structural proteins of the defective particles are encoded by a second defective prophage situated within the MEDPRO2 region, spanning approximately 13 kb. This finding was further validated through the deletion of this second defective prophage. Genomic region analyses and the detection of antimicrobial activity of the defective prophage against other Marinomonas species suggest that it is an R-type bacteriocin. Marinomonas mediterranea synthesizes antimicrobial proteins with lysine oxidase activity, and the synthesis of an R-type bacteriocin constitutes an additional mechanism in microbial competition for the colonization of habitats such as the surface of marine plants.IMPORTANCEThe interactions between bacterial strains inhabiting the same environment determine the final composition of the microbiome. In this study, it is shown that some extracellular defective phage particles previously observed in Marinomonas mediterranea are in fact R-type bacteriocins showing antimicrobial activity against other Marinomonas strains. The operon coding for the R-type bacteriocin has been identified.
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Affiliation(s)
- Patricia Lucas-Elío
- Department of Genetics and Microbiology, University of Murcia, Murcia, Spain
| | - Tarik ElAlami
- Department of Genetics and Microbiology, University of Murcia, Murcia, Spain
| | - Alicia Martínez
- Department of Genetics and Microbiology, University of Murcia, Murcia, Spain
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3
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Cui N, Zhang Y, Fan J, Liu X, Li Y, Zhang X, Guan J, Li T, Wang Y. Marinomonas transparens sp. nov. and Marinomonas sargassi sp. nov., isolated from marine alga. Int J Syst Evol Microbiol 2023; 73. [PMID: 38112722 DOI: 10.1099/ijsem.0.005879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2023] Open
Abstract
Two Gram-stain-negative, rod-shaped, non-spore-forming, strictly aerobic, motile bacteria with a single polar flagellum, designated strains C1424T and C2222T, were isolated from marine alga collected from the sea shore at Yantai, PR China. Strain C1424T grew at 4-37 °C and in the presence of 1-9 % (w/v) NaCl, while strain C2222T grew at 4-32 °C with 1-6 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences and concatenated amino acid sequences of 120 ubiquitous single-copy proteins showed that both strains C1424T and C2222T belonged to the genus Marinomonas, showing highest 16S rRNA gene sequence similarities to the type strains of Marinomonas primoryensis (98.1 %) and Marinomonas dokdonensis (98.1 %), respectively. The major fatty acids of the two strains were C18 : 1 ω6c and/or C18 : 1 ω7c, C16 : 1 ω6c and/or C16 : 1 ω7c and C16 : 0, their predominant polar lipids were phosphatidylethanolamine and phosphatidylglycerol, and their sole respiratory quinone was Q8. On the basis of polyphasic analyses, strains C1424T and C2222T are considered to represent two novel species within the genus Marinomonas, for which the names Marinomonas transparens sp. nov. and Marinomonas sargassi sp. nov. are proposed. The type strains are C1424T (=KCTC 72119T=MCCC 1K03601T) and C2222T (=KCTC 72120T=MCCC 1K03602T), respectively.
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Affiliation(s)
- Ning Cui
- Synthetic Biology Engineering Lab of Henan Province, School of Life Sciences and Technology, Xinxiang Medical University, 601 Jinsui Avenue, Xinxiang 453003, PR China
| | - Yao Zhang
- Synthetic Biology Engineering Lab of Henan Province, School of Life Sciences and Technology, Xinxiang Medical University, 601 Jinsui Avenue, Xinxiang 453003, PR China
| | - Jiwu Fan
- Synthetic Biology Engineering Lab of Henan Province, School of Life Sciences and Technology, Xinxiang Medical University, 601 Jinsui Avenue, Xinxiang 453003, PR China
| | - Xinqi Liu
- Synthetic Biology Engineering Lab of Henan Province, School of Life Sciences and Technology, Xinxiang Medical University, 601 Jinsui Avenue, Xinxiang 453003, PR China
| | - Yang Li
- Synthetic Biology Engineering Lab of Henan Province, School of Life Sciences and Technology, Xinxiang Medical University, 601 Jinsui Avenue, Xinxiang 453003, PR China
| | - Xiuhua Zhang
- Synthetic Biology Engineering Lab of Henan Province, School of Life Sciences and Technology, Xinxiang Medical University, 601 Jinsui Avenue, Xinxiang 453003, PR China
| | - Jianyi Guan
- Synthetic Biology Engineering Lab of Henan Province, School of Life Sciences and Technology, Xinxiang Medical University, 601 Jinsui Avenue, Xinxiang 453003, PR China
| | - Tao Li
- Synthetic Biology Engineering Lab of Henan Province, School of Life Sciences and Technology, Xinxiang Medical University, 601 Jinsui Avenue, Xinxiang 453003, PR China
| | - Yan Wang
- Synthetic Biology Engineering Lab of Henan Province, School of Life Sciences and Technology, Xinxiang Medical University, 601 Jinsui Avenue, Xinxiang 453003, PR China
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4
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Kristyanto S, Jung J, Kim JM, Choi BJ, Han DM, Lee SC, Jeon CO. Psychroserpens ponticola sp. nov. and Marinomonas maritima sp. nov., isolated from seawater. Int J Syst Evol Microbiol 2023; 73. [PMID: 37830909 DOI: 10.1099/ijsem.0.006090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2023] Open
Abstract
Two Gram-stain-negative, catalase- and oxidase-positive, aerobic non-motile and motile rod bacteria, strains MSW6T and RSW2T, were isolated from surface seawater. Strain MSW6T optimally grew at 20 °C, pH 7.0 and 3 % NaCl, while strain RSW2T optimally grew at 25 °C, pH 7.0-8.0 and 2 % NaCl. Strain MSW6T possessed menaquinone-6 as the major respiratory quinone, and its major fatty acids were iso-C15 : 1 G, iso-C15 : 0 and iso-C15 : 0 3-OH. The major polar lipid identified in strain MSW6T was phosphatidylethanolamine (PE). On the other hand, strain RSW2T had ubiquinone-8 as the predominant respiratory quinone, and its major fatty acids consisted of summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c) and C16 : 0. The major polar lipids identified in strain RSW2T were PE and phosphatidylglycerol. As the sole respiratory quinone, strain MSW6T possessed menaquinone-6, while strain RSW2T had ubiquinone-8. The DNA G+C contents of strains MSW6T and RSW2T were 31.9 and 43.4 mol%, respectively. Phylogenetic analyses based on 16S rRNA and core gene sequences showed that strain MSW6T formed a phylogenic lineage with Psychroserpens mesophilus KOPRI 13649T, while strain RSW2T formed a phylogenic lineage with Marinomonas primoryensis KMM 3633T. Strain MSW6T shared 97.9 % 16S rRNA gene sequence similarity and 80.7 % average nucleotide identity (ANI) ith P. mesophilus KOPRI 13649T, and strain RSW2T shared 99.1 % 16S rRNA gene sequence similarity and 93.1 % ANI with M. primoryensis KMM 3633T. Based on the results of phenotypic, chemotaxonomic and phylogenetic analyses, strains MSW6T and RSW2T represent novel species of the genera Psychroserpens and Marinomonas, respectively, for which the names Psychroserpens ponticola sp. nov. and Marinomonas maritima sp. nov. are proposed, respectively. The type strain of P. ponticola is MSW6T (=KACC 22338T=JCM 35022T) and the type strain of M. maritima is RSW2T (=KACC 22716T=JCM 35550T).
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Affiliation(s)
- Sylvia Kristyanto
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Jaejoon Jung
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Jeong Min Kim
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Byeong Jun Choi
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Dong Min Han
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Sung Chul Lee
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Che Ok Jeon
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
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5
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Akter S, Rahman MS, Ali H, Minch B, Mehzabin K, Siddique MM, Galib SM, Yesmin F, Azmuda N, Adnan N, Hasan NA, Rahman SR, Moniruzzaman M, Ahmed MF. Phylogenetic diversity and functional potential of the microbial communities along the Bay of Bengal coast. Sci Rep 2023; 13:15976. [PMID: 37749192 PMCID: PMC10520010 DOI: 10.1038/s41598-023-43306-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 09/21/2023] [Indexed: 09/27/2023] Open
Abstract
The Bay of Bengal, the world's largest bay, is bordered by populous countries and rich in resources like fisheries, oil, gas, and minerals, while also hosting diverse marine ecosystems such as coral reefs, mangroves, and seagrass beds; regrettably, its microbial diversity and ecological significance have received limited research attention. Here, we present amplicon (16S and 18S) profiling and shotgun metagenomics data regarding microbial communities from BoB's eastern coast, viz., Saint Martin and Cox's Bazar, Bangladesh. From the 16S barcoding data, Proteobacteria appeared to be the dominant phylum in both locations, with Alteromonas, Methylophaga, Anaerospora, Marivita, and Vibrio dominating in Cox's Bazar and Pseudoalteromonas, Nautella, Marinomonas, Vibrio, and Alteromonas dominating the Saint Martin site. From the 18S barcoding data, Ochrophyta, Chlorophyta, and Protalveolata appeared among the most abundant eukaryotic divisions in both locations, with significantly higher abundance of Choanoflagellida, Florideophycidae, and Dinoflagellata in Cox's Bazar. The shotgun sequencing data reveals that in both locations, Alteromonas is the most prevalent bacterial genus, closely paralleling the dominance observed in the metabarcoding data, with Methylophaga in Cox's Bazar and Vibrio in Saint Martin. Functional annotations revealed that the microbial communities in these samples harbor genes for biofilm formation, quorum sensing, xenobiotics degradation, antimicrobial resistance, and a variety of other processes. Together, these results provide the first molecular insight into the functional and phylogenetic diversity of microbes along the BoB coast of Bangladesh. This baseline understanding of microbial community structure and functional potential will be critical for assessing impacts of climate change, pollution, and other anthropogenic disturbances on this ecologically and economically vital bay.
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Affiliation(s)
- Salma Akter
- Department of Microbiology, Jahangirnagar University, Savar, Dhaka, Bangladesh
| | - M Shaminur Rahman
- Department of Microbiology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Hazrat Ali
- Department of Microbiology, Jahangirnagar University, Savar, Dhaka, Bangladesh
| | - Benjamin Minch
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, Coral Gables, FL, USA
| | - Kaniz Mehzabin
- Department of Microbiology, Jahangirnagar University, Savar, Dhaka, Bangladesh
| | - Md Moradul Siddique
- Department of Computer Science and Engineering, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Syed Md Galib
- Department of Computer Science and Engineering, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Farida Yesmin
- Department of Microbiology, Jahangirnagar University, Savar, Dhaka, Bangladesh
| | - Nafisa Azmuda
- Department of Microbiology, Jahangirnagar University, Savar, Dhaka, Bangladesh
| | - Nihad Adnan
- Department of Microbiology, Jahangirnagar University, Savar, Dhaka, Bangladesh
| | - Nur A Hasan
- University of Maryland, College Park, MD, USA
| | | | - Mohammad Moniruzzaman
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, Coral Gables, FL, USA.
| | - Md Firoz Ahmed
- Department of Microbiology, Jahangirnagar University, Savar, Dhaka, Bangladesh.
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6
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Marchetti A, Orlando M, Mangiagalli M, Lotti M. A cold‐active esterase enhances mesophilic properties through Mn
2+
binding. FEBS J 2022; 290:2394-2411. [PMID: 36266734 DOI: 10.1111/febs.16661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 09/20/2022] [Accepted: 10/19/2022] [Indexed: 12/12/2022]
Abstract
A key aspect of adaptation to cold environments is the production of cold-active enzymes by psychrophilic organisms. These enzymes not only have high activity at low temperatures, but also exhibit remarkable structural flexibility and thermolability. In this context, the role of metal ions has been little explored, and the few available studies seem to suggest that metal binding counteracts structural flexibility. This article reports an investigation into the role of the binding of manganese ion (Mn2+ ) in the thermal adaptation of an esterase (M-Est) of the GDSx family, identified in the genome of the Antarctic bacterium Marinomonas sp. ef1. M-Est is specific for esters containing acetate groups and turned out to be a highly thermolabile cold-active enzyme, with a catalysis optimum temperature of 5 °C and a melting temperature of 31.7 °C. A combination of biochemical and computational analyses, including molecular dynamics simulations, revealed that M-Est binds Mn2+ ions via a single binding site located on the surface of the enzyme, close to the active site. Although the interaction between M-Est and Mn2+ induces only local conformational changes involving the active site, quite surprisingly they trigger an improvement in both thermal stability and catalytic efficiency under mild temperature conditions. These results, together with the conservation of the Mn2+ binding site among psychrophilic and psychrotolerant homologues, suggest that Mn2+ binding may be a useful, albeit atypical, strategy to mitigate the detrimental effects of temperature on true cold-active enzymes.
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Affiliation(s)
| | - Marco Orlando
- Department of Biotechnology and Biosciences University of Milano‐Bicocca Italy
- Department of Biotechnology and Life Sciences University of Insubria Varese Italy
| | - Marco Mangiagalli
- Department of Biotechnology and Biosciences University of Milano‐Bicocca Italy
| | - Marina Lotti
- Department of Biotechnology and Biosciences University of Milano‐Bicocca Italy
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7
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Gao Y, Wei Y, Wang P. Marinomonas lutimaris sp. nov., isolated from a tidal flat sediment of the East China Sea. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005368] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative bacterial strain, designated as E165T, was isolated from a tidal flat sediment of the East China Sea. Strain E165T grew optimally at pH 6, at 32 °C and with 1–2 % (w/v) NaCl. The 16S rRNA gene sequence similarity results revealed that strain E165T was most closely related to
Marinomonas rhizomae
IVIA-Po-145T,
Marinomonas polaris
CK13T,
Marinomonas foliarum
IVIA-Po-155T,
Marinomonas hwangdonensis
HDW-15T,
Marinomonas pontica
46-16T,
Marinomonas mangrovi
B20-1T and
Marinomonas shanghaiensis
DSL-35T with values of 97.0–98.5 %. The digital DNA–DNA hybridization and average nucleotide identity values between strain E165T and the reference strains were 21.9–34.3 % and 77.6–87.3 %, respectively. The DNA G+C content of the isolate was 42.9 mol%. Strain E165T contained Q-8 as the sole ubiquinone and C16 : 0, summed feature 8 (C18 : 1
ω7c and/or C18 : 1
ω6c) and summed feature 3 (C16 : 1
ω7c and/or C16 : 1
ω6c) as the major fatty acids. The major polar lipids of strain E165T were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, aminolipid and aminophospholipid. On the basis of phenotypic characteristics, phylogenetic analysis and DNA–DNA relatedness, a novel species, Marinomonas lutimaris sp. nov., is proposed with E165T (=MCCC 1K06241T=KCTC 82809T) as the type strain.
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Affiliation(s)
- Yuxin Gao
- State Key Laboratory of Marine Geology, Tongji University, Shanghai 200092, PR China
| | - Yuli Wei
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, PR China
| | - Peng Wang
- State Key Laboratory of Marine Geology, Tongji University, Shanghai 200092, PR China
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8
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Ying JJ, Fang YC, Ye YL, Wu ZC, Xu L, Han BN, Sun C. Marinomonas vulgaris sp. nov., a marine bacterium isolated from seawater in a coastal intertidal zone of Zhoushan island. Arch Microbiol 2021; 203:5133-5139. [PMID: 34319420 DOI: 10.1007/s00203-021-02500-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 07/01/2021] [Accepted: 07/19/2021] [Indexed: 10/20/2022]
Abstract
A Marinomonas-like, Gram-stain-negative, strictly aerobic and rod to ovoid-shaped bacterium, designated as strain A79T, was isolated from the seawater mixtures of oyster shells and brown algae in a coastal intertidal zone of Zhoushan, China. The strain was positive for oxidase and catalase. Colonies grown on marine agar for 48 h were round, milky white, smooth and moist with the diameter of 2-3 mm. Growth was observed at 15-30 °C (optimum, 25℃), pH 5.5-9.5 (optimum, pH 8.5) and with 0.5-8% (w/v) NaCl (optimum, 2-2.5%). The G + C content based on the genome sequence was 46.0%. The only respiratory quinone was Q-8. The main polar lipids contained phosphatidylglycerol, phosphatidylethanolamine, unidentified glycolipids, unidentified phospholipid and three unidentified lipids. The major fatty acids (> 10%) were C16:0, Summed feature 3 (comprising C16:1 ω6c and/or C16:1 ω7c) and summed feature 8 (comprising C18:1 ω6c and/or C18:1 ω7c). The 16S rRNA gene sequence similarity between strain A79T and Marinomonas pollencensis IVIA-Po-185T was 97.4%, the similarities with other type strains of the genus Marinomonas were 93.8-96.7%. Based on the results, Marinomonas vulgaris sp. nov. was proposed as a novel species. The type strain is A79T (= MCCC 1K05799T = KCTC 82519T = JCM 34473T).
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Affiliation(s)
- Jun-Jie Ying
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China
| | - Yuan-Chun Fang
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China
| | - Yong-Lian Ye
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China
| | - Zhi-Cheng Wu
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, 310012, People's Republic of China.,Ocean College, Zhejiang University, Zhoushan, 316021, People's Republic of China
| | - Lin Xu
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China.,Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, 310012, People's Republic of China
| | - Bing-Nan Han
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China
| | - Cong Sun
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China. .,Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, 310012, People's Republic of China.
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9
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Arcos SC, Lira F, Robertson L, González MR, Carballeda-Sangiao N, Sánchez-Alonso I, Zamorano L, Careche M, Jiménez-Ruíz Y, Ramos R, Llorens C, González-Muñoz M, Oliver A, Martínez JL, Navas A. Metagenomics Analysis Reveals an Extraordinary Inner Bacterial Diversity in Anisakids (Nematoda: Anisakidae) L3 Larvae. Microorganisms 2021; 9:1088. [PMID: 34069371 PMCID: PMC8158776 DOI: 10.3390/microorganisms9051088] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/05/2021] [Accepted: 05/10/2021] [Indexed: 11/28/2022] Open
Abstract
L3 larvae of anisakid nematodes are an important problem for the fisheries industry and pose a potential risk for human health by acting as infectious agents causing allergies and as potential vectors of pathogens and microrganisms. In spite of the close bacteria-nematode relationship very little is known of the anisakids microbiota. Fresh fish could be contaminated by bacteria vectored in the cuticle or in the intestine of anisakids when the L3 larvae migrate through the muscles. As a consequence, the bacterial inoculum will be spread, with potential effects on the quality of the fish, and possible clinical effects cannot be discarded. A total of 2,689,113 16S rRNA gene sequences from a total of 113 L3 individuals obtained from fish captured along the FAO 27 fishing area were studied. Bacteria were taxonomically characterized through 1803 representative operational taxonomic units (OTUs) sequences. Fourteen phyla, 31 classes, 52 orders, 129 families and 187 genera were unambiguously identified. We have found as part of microbiome an average of 123 OTUs per L3 individual. Diversity indices (Shannon and Simpson) indicate an extraordinary diversity of bacteria at an OTU level. There are clusters of anisakids individuals (samples) defined by the associated bacteria which, however, are not significantly related to fish hosts or anisakid taxa. This suggests that association or relationship among bacteria in anisakids, exists without the influence of fishes or nematodes. The lack of relationships with hosts of anisakids taxa has to be expressed by the association among bacterial OTUs or other taxonomical levels which range from OTUs to the phylum level. There are significant biological structural associations of microbiota in anisakid nematodes which manifest in clusters of bacteria ranging from phylum to genus level, which could also be an indicator of fish contamination or the geographic zone of fish capture. Actinobacteria, Aquificae, Firmicutes, and Proteobacteria are the phyla whose abundance value discriminate for defining such structures.
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Affiliation(s)
- Susana C. Arcos
- Museo Nacional de Ciencias Naturales, Dpto Biodiversidad y Biología Evolutiva, CSIC, 28006 Madrid, Spain; (S.C.A.); (L.R.); (M.R.G.); (Y.J.-R.)
| | - Felipe Lira
- Centro Nacional de Biotecnología, Departamento de Biotecnología Microbiana, CSIC, 28049 Madrid, Spain; (F.L.); (J.L.M.)
| | - Lee Robertson
- Museo Nacional de Ciencias Naturales, Dpto Biodiversidad y Biología Evolutiva, CSIC, 28006 Madrid, Spain; (S.C.A.); (L.R.); (M.R.G.); (Y.J.-R.)
- Departamento de Protección Vegetal, INIA, 28040 Madrid, Spain
| | - María Rosa González
- Museo Nacional de Ciencias Naturales, Dpto Biodiversidad y Biología Evolutiva, CSIC, 28006 Madrid, Spain; (S.C.A.); (L.R.); (M.R.G.); (Y.J.-R.)
| | | | - Isabel Sánchez-Alonso
- Instituto de Ciencia y Tecnología de Alimentos y Nutrición, CSIC, 28040 Madrid, Spain; (I.S.-A.); (M.C.)
| | - Laura Zamorano
- Servicio de Microbiología y Unidad de Investigación, Hospital Son Espases, (IdISPa), 07120 Palma de Mallorca, Spain; (L.Z.); (A.O.)
| | - Mercedes Careche
- Instituto de Ciencia y Tecnología de Alimentos y Nutrición, CSIC, 28040 Madrid, Spain; (I.S.-A.); (M.C.)
| | - Yolanda Jiménez-Ruíz
- Museo Nacional de Ciencias Naturales, Dpto Biodiversidad y Biología Evolutiva, CSIC, 28006 Madrid, Spain; (S.C.A.); (L.R.); (M.R.G.); (Y.J.-R.)
| | - Ricardo Ramos
- Unidad de Genómica, “Scientific Park of Madrid”, Campus de Cantoblanco, 28049 Madrid, Spain;
| | - Carlos Llorens
- Biotechvana, “Scientific Park”, University of Valencia, 46980 Valencia, Spain;
| | - Miguel González-Muñoz
- Servicio de Immunología, Hospital Universitario La Paz, 28046 Madrid, Spain; (N.C.-S.); (M.G.-M.)
| | - Antonio Oliver
- Servicio de Microbiología y Unidad de Investigación, Hospital Son Espases, (IdISPa), 07120 Palma de Mallorca, Spain; (L.Z.); (A.O.)
| | - José L. Martínez
- Centro Nacional de Biotecnología, Departamento de Biotecnología Microbiana, CSIC, 28049 Madrid, Spain; (F.L.); (J.L.M.)
| | - Alfonso Navas
- Museo Nacional de Ciencias Naturales, Dpto Biodiversidad y Biología Evolutiva, CSIC, 28006 Madrid, Spain; (S.C.A.); (L.R.); (M.R.G.); (Y.J.-R.)
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10
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Sun XM, Chen C, Xue Z, He XY, Liu NH, Chen XL, Zhang YZ, Fan SJ, Zhang XY. Marinomonas algicola sp. nov. and Marinomonas colpomeniae sp. nov., isolated from marine macroalgae. Int J Syst Evol Microbiol 2021; 71. [PMID: 33661091 DOI: 10.1099/ijsem.0.004730] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two Gram-stain-negative, aerobic, rod-shaped bacteria, polar flagellated, designated strains SM2066T and SM1966T, were respectively isolated from the surfaces of Colpomenia sinuosa and Ulva pertusa macroalgae collected off the coastal areas of Rongcheng, PR China. Strain SM2066T grew at 8-37 °C and with 0.5-7.0 % (w/v) NaCl, while strain SM1966T grew at 5-30 °C and with 0.5-8.5% (w/v) NaCl. Both of them reduced nitrate to nitrite and required Na+ for growth but neither of them hydrolysed starch and DNA. Phylogenetic analysis based on 16S rRNA gene and single-copy orthologous cluster sequences revealed that both strains SM2066T and SM1966T were affiliated with the genus Marinomonas but formed distinct phylogenetic branches from known Marinomonas species, respectively sharing the highest 16S rRNA gene sequence similarities with type strains of Marinomonas ushuaiensis (97.9 %) and Marinomonas blandensis (96.7 %). The digital DNA-DNA hybridization and average nucleotide identity values between strains SM2066T and SM1966T and type strains of closely related Marinomonas species were all below 22.9 and 79.9 mol%, respectively. The major fatty acids of the two strains were summed feature 3 (C16 : 1 ω6c/C16 : 1 ω7c), summed feature 8 (C18 : 1 ω7c) and C16 : 0, with their predominant polar lipids being phosphatidylethanolamine and phosphatidylglycerol, and their sole respiratory quinone being Q-8. The genomic DNA G+C contents of strains SM2066T and SM1966T determined from genomic sequences were 40.3 and 41.6 mol%, respectively. On the basis of the polyphasic evidence presented in this study, strains SM2066T and SM1966T are considered to represent two novel species within the genus Marinomonas, for which the names Marinomonas colpomeniae sp. nov. and Marinomonas algicola sp. nov. are proposed. The type strains are SM2066T (=MCCC 1K04390T= KCTC 82372T) and SM1966T (=MCCC 1K04387T= KCTC 72848T), respectively.
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Affiliation(s)
- Xiao-Meng Sun
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao 266237, PR China.,Life Science College, Shandong Normal University, Jinan 250014, PR China
| | - Cui Chen
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao 266237, PR China.,Life Science College, Shandong Normal University, Jinan 250014, PR China
| | - Zhao Xue
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, PR China.,Life Science College, Shandong Normal University, Jinan 250014, PR China
| | - Xiao-Yan He
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, PR China.,State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao 266237, PR China
| | - Ning-Hua Liu
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, PR China.,State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao 266237, PR China
| | - Xiu-Lan Chen
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, PR China.,State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao 266237, PR China
| | - Yu-Zhong Zhang
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, 266003, PR China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, PR China.,State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao 266237, PR China
| | - Shou-Jin Fan
- Life Science College, Shandong Normal University, Jinan 250014, PR China
| | - Xi-Ying Zhang
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, PR China.,State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao 266237, PR China
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11
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Discovering symbiosis in the supralittoral: bacterial metabarcoding analysis from the hepatopancreas of Orchestia and Tylos (Crustacea). Symbiosis 2021. [DOI: 10.1007/s13199-021-00749-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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12
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Sanders-Smith R, Segovia BT, Forbes C, Hessing-Lewis M, Morien E, Lemay MA, O'Connor MI, Parfrey LW. Host-Specificity and Core Taxa of Seagrass Leaf Microbiome Identified Across Tissue Age and Geographical Regions. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.605304] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The seagrass Zostera marina is a widespread foundational species in temperate coastal ecosystems that supports diverse communities of epiphytes and grazers. Bacteria link the production of seagrass to higher trophic levels and are thought to influence seagrass biology and health. Yet, we lack a clear understanding of the factors that structure the seagrass microbiome, or whether there is a consistent microbial community associated with seagrass that underpins functional roles. We sampled surface microbiome (epibiota) from new and old growth seagrass leaves and the surrounding seawater in eight meadows among four regions along the Central Coast of British Columbia, Canada to assess microbiome variability across space and as leaves age. We found that the seagrass leaf microbiome differs strongly from seawater. Microbial communities in new and old growth leaves are different from each other and from artificial seagrass leaves we deployed in one meadow. The microbiome on new leaves is less diverse and there is a small suite of core OTUs (operational taxonomic units) consistently present across regions. The overall microbial community for new leaves is more dispersed but with little regional differentiation, while the epiphytes on old leaves are regionally distinct. Many core OTUs on old leaves are commonly associated with marine biofilms. Together these observations suggest a stronger role for host filtering in new compared to old leaves, and a stronger influence of the environment and environmental colonization in old leaves. We found 11 core microbial taxa consistently present on old and new leaves and at very low relative abundance on artificial leaves and in the water column. These 11 taxa appear to be strongly associated with Z. marina. These core taxa may perform key functions important for the host such as detoxifying seagrass waste products, enhancing plant growth, and controlling epiphyte cover.
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13
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Li Y, Sun XM, Li J, Song XY, Qin QL, Su HN, Chen XL, Zhang YZ, Fan SJ, Zhang XY. Marinomonas profundi sp. nov., isolated from deep seawater of the Mariana Trench. Int J Syst Evol Microbiol 2020; 70:5747-5752. [PMID: 32945763 DOI: 10.1099/ijsem.0.004472] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, aerobic, polarly flagellated, straight or curved rod-shaped bacterium, designated strain M1K-6T, was isolated from deep seawater samples collected from the Mariana Trench. The strain grew at -4 to 37 °C (optimum, 25-30 °C), at pH 5.5-10.0 (optimum, pH 7.0) and with 0.5-14.0 % (w/v) NaCl (optimum, 2.0 %). It did not reduce nitrate to nitrite nor hydrolyse gelatin or starch. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain M1K-6T was affiliated with the genus Marinomonas, sharing 93.1-97.0 % sequence similarity with the type strains of recognized Marinomonas species. The major cellular fatty acids were summed feature 3 (C16 : 1 ω6c/C16 : 1 ω7c), summed feature 8 (C18 : 1 ω7c/C18 : 1 ω6c), C16 : 0, C10 : 0 3-OH and C18 : 0. The predominant respiratory quinone was ubiquinone-8. Polar lipids of strain M1K-6T included phosphatidylethanolamine, phosphatidylglycerol and two unidentified lipids. The genomic G+C content of strain M1K-6T was 46.0 mol%. Based on data from the present polyphasic study, strain M1K-6T was considered to represent a novel species within the genus Marinomonas, for which the name Marinomonas profundi sp. nov. is proposed. The type strain is M1K-6T (=KCTC 72501T=MCCC 1K03890T).
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Affiliation(s)
- Yi Li
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao 266237, PR China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, PR China.,College of Life Sciences, Shanxi Agricultural University, Taigu 030801, PR China
| | - Xiao-Meng Sun
- College of Life Science, Shandong Normal University, Jinan 250014, PR China.,State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao 266237, PR China
| | - Jian Li
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao 266237, PR China
| | - Xiao-Yan Song
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao 266237, PR China
| | - Qi-Long Qin
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao 266237, PR China
| | - Hai-Nan Su
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao 266237, PR China
| | - Xiu-Lan Chen
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, PR China.,State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao 266237, PR China
| | - Yu-Zhong Zhang
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266003, PR China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, PR China.,State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao 266237, PR China
| | - Shou-Jin Fan
- College of Life Science, Shandong Normal University, Jinan 250014, PR China
| | - Xi-Ying Zhang
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, PR China.,State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao 266237, PR China
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14
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Porin from Marine Bacterium Marinomonas primoryensis KMM 3633 T: Isolation, Physico-Chemical Properties, and Functional Activity. Molecules 2020; 25:molecules25143131. [PMID: 32650591 PMCID: PMC7397200 DOI: 10.3390/molecules25143131] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 07/01/2020] [Accepted: 07/03/2020] [Indexed: 01/29/2023] Open
Abstract
Marinomonas primoryensis KMM 3633T, extreme living marine bacterium was isolated from a sample of coastal sea ice in the Amursky Bay near Vladivostok, Russia. The goal of our investigation is to study outer membrane channels determining cell permeability. Porin from M. primoryensis KMM 3633T (MpOmp) has been isolated and characterized. Amino acid analysis and whole genome sequencing were the sources of amino acid data of porin, identified as Porin_4 according to the conservative domain searching. The amino acid composition of MpOmp distinguished by high content of acidic amino acids and low content of sulfur-containing amino acids, but there are no tryptophan residues in its molecule. The native MpOmp existed as a trimer. The reconstitution of MpOmp into black lipid membranes demonstrated its ability to form ion channels whose conductivity depends on the electrolyte concentration. The spatial structure of MpOmp had features typical for the classical gram-negative porins. However, the oligomeric structure of isolated MpOmp was distinguished by very low stability: heat-modified monomer was already observed at 30 °C. The data obtained suggest the stabilizing role of lipids in the natural membrane of marine bacteria in the formation of the oligomeric structure of porin.
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15
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Tarquinio F, Hyndes GA, Laverock B, Koenders A, Säwström C. The seagrass holobiont: understanding seagrass-bacteria interactions and their role in seagrass ecosystem functioning. FEMS Microbiol Lett 2020; 366:5382495. [PMID: 30883643 DOI: 10.1093/femsle/fnz057] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 03/16/2019] [Indexed: 12/27/2022] Open
Abstract
This review shows that the presence of seagrass microbial community is critical for the development of seagrasses; from seed germination, through to phytohormone production and enhanced nutrient availability, and defence against pathogens and saprophytes. The tight seagrass-bacterial relationship highlighted in this review supports the existence of a seagrass holobiont and adds to the growing evidence for the importance of marine eukaryotic microorganisms in sustaining vital ecosystems. Incorporating a micro-scale view on seagrass ecosystems substantially expands our understanding of ecosystem functioning and may have significant implications for future seagrass management and mitigation against human disturbance.
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Affiliation(s)
- Flavia Tarquinio
- Centre for Marine Ecosystems Research, Edith Cowan University, Joondalup, Western Australia, Australia.,Commonwealth Scientific and Industrial Research Organization, Crawley, 6009, Western Australia, Australia
| | - Glenn A Hyndes
- Centre for Marine Ecosystems Research, Edith Cowan University, Joondalup, Western Australia, Australia
| | - Bonnie Laverock
- Plant Functional Biology and Climate Change Cluster, University of Technology Sydney, Sydney, 2007, Australia.,School of Science, Auckland University of Technology, Auckland, 1010, New Zealand
| | - Annette Koenders
- Centre for Ecosystem Management, Edith Cowan University, Joondalup, 6027, Western Australia, Australia
| | - Christin Säwström
- Centre for Marine Ecosystems Research, Edith Cowan University, Joondalup, Western Australia, Australia
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16
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Hu M, Zhai Y, Zhang Y, Han X, Fang W, Fang Z, Xiao Y. Marinomonas flavescens sp. nov., isolated from seawater adjacent to Fildes Peninsula, Antarctica. Int J Syst Evol Microbiol 2019; 69:3414-3419. [DOI: 10.1099/ijsem.0.003631] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Miaomiao Hu
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, Anhui 230601, PR China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, Anhui 230601, PR China
- School of Life Sciences, Anhui University, Hefei, Anhui 230601, PR China
| | - Yanwu Zhai
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, Anhui 230601, PR China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, Anhui 230601, PR China
- School of Life Sciences, Anhui University, Hefei, Anhui 230601, PR China
| | - Yanfeng Zhang
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, Anhui 230601, PR China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, Anhui 230601, PR China
- School of Life Sciences, Anhui University, Hefei, Anhui 230601, PR China
| | - Xiaoyan Han
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, Anhui 230601, PR China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, Anhui 230601, PR China
- School of Life Sciences, Anhui University, Hefei, Anhui 230601, PR China
| | - Wei Fang
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, Anhui 230601, PR China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, Anhui 230601, PR China
- School of Life Sciences, Anhui University, Hefei, Anhui 230601, PR China
| | - Zemin Fang
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, Anhui 230601, PR China
- School of Life Sciences, Anhui University, Hefei, Anhui 230601, PR China
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, Anhui 230601, PR China
| | - Yazhong Xiao
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, Anhui 230601, PR China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, Anhui 230601, PR China
- School of Life Sciences, Anhui University, Hefei, Anhui 230601, PR China
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17
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Inaba N, Trainer VL, Nagai S, Kojima S, Sakami T, Takagi S, Imai I. Dynamics of seagrass bed microbial communities in artificial Chattonella blooms: A laboratory microcosm study. HARMFUL ALGAE 2019; 84:139-150. [PMID: 31128798 DOI: 10.1016/j.hal.2018.12.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 12/17/2018] [Accepted: 12/17/2018] [Indexed: 06/09/2023]
Abstract
The influence of algicidal and growth-inhibiting bacteria in a seagrass (Zostera marina) bed, and their capability of controlling blooms of the fish-killing raphidophyte flagellate, Chattonella antiqua, were examined in laboratory microcosm experiments. Bacterial communities in seawater collected from the seagrass bed and Z. marina biofilm suppressed artificial Chattonella blooms in the presence of their natural competitors and predators. Phylogenetic analysis suggest that considerable numbers of bacteria that suppress Chattonella, including algicidal or growth-inhibiting bacteria isolated from seagrass biofilm and seawater from the seagrass bed, are members of Proteobacteria that can decompose lignocellulosic compounds. A direct comparison of partial 16S rRNA gene sequences (500 bp) revealed that the growth-limiting bacterium (strain ZM101) isolated from Z. marina biofilm belonged to the genus Phaeobacter (Alphaproteobacteria) showed 100% similarity with strains of growth-limiting bacteria isolated from seawater of both the seagrass bed and nearshore region, suggesting that the origin of these growth-limiting bacteria are the seagrass biofilm or seawater surrounding the seagrass bed. This study demonstrates that Chattonella growth-limiting bacteria living on seagrass biofilm and in the adjacent seawater can suppress Chattonella blooms, suggesting the possibility of Chattonella bloom prevention through restoration, protection, or introduction of seagrass in coastal areas.
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Affiliation(s)
- Nobuharu Inaba
- Civil Engineering Research Institute for Cold Region, Public Works Research Institute, Hiragishi 1-3-1-34, Toyohira-ku, Sapporo, Hokkaido, 062-8602, Japan.
| | - Vera L Trainer
- Environmental and Fisheries Science Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, 2725 Montlake Blvd. E., Seattle, WA, 98112, United States
| | - Satoshi Nagai
- National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, 2-12-4 Fukuura, Kanazawa-ku, Yokohama, Kanagawa 236-8648, Japan
| | - Senri Kojima
- Plankton Laboratory, Graduate School of Fisheries Sciences, Hokkaido University, 3-1-1 Minato-cho Hokkaido, Hakodate, 041-8611, Japan
| | - Tomoko Sakami
- National Research Institute of Aquaculture, Japan Fisheries Research and Education Agency, 422-1 Nakatsuhama-ura, Minami-ise, Mie 516-0193, Japan
| | - Shuzo Takagi
- Research Institute for Fisheries Science, Okayama Prefectural Technology Center for Agriculture, Forestry and Fisheries, Kashino 6641-6, Ushimado, Setouchi, Okayama 701-4303, Japan
| | - Ichiro Imai
- Plankton Laboratory, Graduate School of Fisheries Sciences, Hokkaido University, 3-1-1 Minato-cho Hokkaido, Hakodate, 041-8611, Japan
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18
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Wei Y, Cao J, Mao H, Pei J, Liu R, Fang J. Marinomonas shanghaiensis sp. nov., isolated from the junction between an ocean and a freshwater lake. Int J Syst Evol Microbiol 2019; 69:805-810. [DOI: 10.1099/ijsem.0.003241] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Yuli Wei
- 2National Engineering Research Centre for Oceanic Fisheries, Shanghai Ocean University, Shanghai 201306, PR China
- 3The Key Laboratory of Sustainable Exploitation of Oceanic Fisheries Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, PR China
- 1Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, PR China
| | - Junwei Cao
- 1Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, PR China
| | - Haiyan Mao
- 1Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, PR China
| | - Jiahao Pei
- 1Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, PR China
| | - Rulong Liu
- 1Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, PR China
| | - Jiasong Fang
- 5Department of Natural Sciences, Hawaii Pacific University, Honolulu, HI 96813, USA
- 4Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, PR China
- 1Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, PR China
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19
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Lucas-Elio P, Silas S, Sanchez-Amat A. Isolation of Phages Infecting Marinomonas mediterranea by an Enrichment Protocol. Bio Protoc 2018. [DOI: 10.21769/bioprotoc.2921] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
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20
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Kristyanto S, Chaudhary DK, Lee SS, Kim J. Characterization of Marinomonas algicida sp. nov., a novel algicidal marine bacterium isolated from seawater. Int J Syst Evol Microbiol 2017; 67:4777-4784. [DOI: 10.1099/ijsem.0.002374] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Sylvia Kristyanto
- Department of Life Science, College of Natural Sciences, Kyonggi University, Suwon 16227, Republic of Korea
| | - Dhiraj Kumar Chaudhary
- Department of Life Science, College of Natural Sciences, Kyonggi University, Suwon 16227, Republic of Korea
| | - Sang-Seob Lee
- Department of Life Science, College of Natural Sciences, Kyonggi University, Suwon 16227, Republic of Korea
| | - Jaisoo Kim
- Department of Life Science, College of Natural Sciences, Kyonggi University, Suwon 16227, Republic of Korea
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21
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Silas S, Lucas-Elio P, Jackson SA, Aroca-Crevillén A, Hansen LL, Fineran PC, Fire AZ, Sánchez-Amat A. Type III CRISPR-Cas systems can provide redundancy to counteract viral escape from type I systems. eLife 2017; 6:27601. [PMID: 28826484 PMCID: PMC5576922 DOI: 10.7554/elife.27601] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2017] [Accepted: 08/07/2017] [Indexed: 12/26/2022] Open
Abstract
CRISPR-Cas-mediated defense utilizes information stored as spacers in CRISPR arrays to defend against genetic invaders. We define the mode of target interference and role in antiviral defense for two CRISPR-Cas systems in Marinomonas mediterranea. One system (type I-F) targets DNA. A second system (type III-B) is broadly capable of acquiring spacers in either orientation from RNA and DNA, and exhibits transcription-dependent DNA interference. Examining resistance to phages isolated from Mediterranean seagrass meadows, we found that the type III-B machinery co-opts type I-F CRISPR-RNAs. Sequencing and infectivity assessments of related bacterial and phage strains suggests an ‘arms race’ in which phage escape from the type I-F system can be overcome through use of type I-F spacers by a horizontally-acquired type III-B system. We propose that the phage-host arms race can drive selection for horizontal uptake and maintenance of promiscuous type III interference modules that supplement existing host type I CRISPR-Cas systems.
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Affiliation(s)
- Sukrit Silas
- Department of Pathology, Stanford University, Stanford, United States.,Department of Chemical and Systems Biology, Stanford University, Stanford, United States
| | - Patricia Lucas-Elio
- Department of Genetics and Microbiology, Universidad de Murcia, Murcia, Spain
| | - Simon A Jackson
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | | | - Loren L Hansen
- Department of Pathology, Stanford University, Stanford, United States
| | - Peter C Fineran
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand.,Bio-Protection Research Centre, University of Otago, Dunedin, New Zealand
| | - Andrew Z Fire
- Department of Pathology, Stanford University, Stanford, United States
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22
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Ojha AK, Verma A, Pal Y, Bhatt D, Mayilraj S, Krishnamurthi S. Marinomonas epiphytica sp. nov., isolated from a marine intertidal macroalga. Int J Syst Evol Microbiol 2017; 67:2746-2751. [PMID: 28771118 DOI: 10.1099/ijsem.0.002014] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-stain-negative, aerobic marine bacterial strain, SAB-3T, was isolated from brown macroalgae (Dictyota sp.) growing in the Arabian sea, Goa, India. The strain grew optimally at 30 °C, with 2.0-4.0 % (w/v) NaCl and at pH 7.0 on marine agar medium. Strain SAB-3T was unable to hydrolyse aesculin and did not grow in the presence of rifamycin but showed resistance to antibiotics such as cefadroxil and co-trimoxazole. The major fatty acids were summed feature 8 (C18 : 1ω7c/C18 : 1ω6c), summed feature 3 (C16 : 1ω7c/C16 : 1ω6c) and C16 : 0, and Q-8 was the major ubiquinone. The major polar lipids were phosphatidylglycerol and phosphatidylethanolamine. The DNA G+C content was 41.0 mol%. 16S rRNA gene sequencing and phylogenetic analysis indicated that the strain was a member of the genus Marinomonas with Marinomonas aquiplantarum IVIA-Po-159T (97.6 % similarity), Marinomonas posidonica IVIA-Po-181T (97.5 %) and Marinomonas dokdonensis DSM 17202T (97.4 %) as the closest relatives. Whole genome relatedness determined through DNA-DNA hybridization revealed values of 40-50 % (below the 70 % threshold recommended for species delineation) with the above three species, thus confirming it as representing a distinct and novel species of the genus Marinomonas for which the name Marinomonas epiphytica sp. nov. is proposed. The type strain is SAB-3T (=JCM 31365T=KCTC 52293T=MTCC 12569T).
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Affiliation(s)
- Anup Kumar Ojha
- Microbial Type Culture Collection and Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sec-39A, Chandigarh-160036, India
| | - Ashish Verma
- Microbial Type Culture Collection and Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sec-39A, Chandigarh-160036, India
| | - Yash Pal
- Microbial Type Culture Collection and Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sec-39A, Chandigarh-160036, India
| | - Deepak Bhatt
- Microbial Type Culture Collection and Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sec-39A, Chandigarh-160036, India
| | - Shanmugam Mayilraj
- Microbial Type Culture Collection and Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sec-39A, Chandigarh-160036, India
| | - Srinivasan Krishnamurthi
- Microbial Type Culture Collection and Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sec-39A, Chandigarh-160036, India
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Arahal DR, Lucena T, Macián MC, Ruvira MA, González JM, Lekumberri I, Pinhassi J, Pujalte MJ. Marinomonas blandensis sp. nov., a novel marine gammaproteobacterium. Int J Syst Evol Microbiol 2016; 66:5544-5549. [PMID: 27902199 DOI: 10.1099/ijsem.0.001554] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-staining-negative, chemoorganotrophic, moderately halophilic, strictly aerobic bacterium, strain MED121T, was isolated from a seawater sample collected at the Blanes Bay Microbial Observatory in the north-western Mediterranean Sea. Analysis of its 16S rRNA gene sequence, retrieved from the whole-genome sequence, showed that this bacterium was most closely related to Marinomonas dokdonensis and other Marinomonas species (96.3 and 93.3-95.7 % sequence similarities, respectively), within the family Oceanospirillaceae. Strain MED121T was included into a whole-genome sequencing study and, subsequently, it was characterized using a polyphasic taxonomic approach. It was found to be oxidase and catalase positive, its cells are cocci to short rods, it does not ferment carbohydrates and does not reduce nitrate to nitrite or gas and it requires at least 2.5 % (w/v) marine salts and tolerates up to 7 % (w/v) salts. Its major cellular fatty acids in order of abundance are C16 : 1ω7c/C16 : 1ω6c, C18 : 1ω7c, C16 : 0 and C10 : 0 3-OH. Its genome had an approximate length of 5.1 million bases and a DNA G+C content equal to 40.9 mol%. Analysis of the annotated genes reveals the capacity for the synthesis of ubiquinone 8 (Q8) and the polar lipids phosphatidylglycerol and phosphatidylethanolamine, in agreement with other members of the genus. All the data collected supported the creation of a novel species to accommodate this bacterium, for which the name Marinomonas blandensis sp. nov. is proposed. The type strain is MED121T (=CECT 7076T=LMG 29722T).
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Affiliation(s)
- David R Arahal
- Departamento de Microbiología y Ecología, Universitat de València, 46100 Burjassot (València), Spain.,Colección Española de Cultivos Tipo (CECT), Universitat de València, 46980 Paterna (València), Spain
| | - Teresa Lucena
- Colección Española de Cultivos Tipo (CECT), Universitat de València, 46980 Paterna (València), Spain
| | - M Carmen Macián
- Colección Española de Cultivos Tipo (CECT), Universitat de València, 46980 Paterna (València), Spain
| | - María A Ruvira
- Colección Española de Cultivos Tipo (CECT), Universitat de València, 46980 Paterna (València), Spain
| | - José M González
- Departament of Microbiology, University of La Laguna, La Laguna ES-38200, Spain
| | - Itziar Lekumberri
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona, Spain
| | - Jarone Pinhassi
- Centre for Ecology and Evolution in Microbial model Systems (EEMiS), Linnaeus University, Kalmar SE-39182, Sweden
| | - María J Pujalte
- Departamento de Microbiología y Ecología, Universitat de València, 46100 Burjassot (València), Spain.,Colección Española de Cultivos Tipo (CECT), Universitat de València, 46980 Paterna (València), Spain
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24
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Lasa A, Pichon P, Diéguez AL, Romalde JL. Marinomonas gallaica sp. nov. and Marinomonas atlantica sp. nov., isolated from reared clams (Ruditapes decussatus). Int J Syst Evol Microbiol 2016; 66:3183-3188. [DOI: 10.1099/ijsem.0.001170] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Aide Lasa
- Departamento de Microbiología y Parasitología, CIBUS-Facultad de Biología, Universidade de Santiago de Compostela, Campus Vida s/n. 15782, Santiago de Compostela, Spain
| | - Phillip Pichon
- Departamento de Microbiología y Parasitología, CIBUS-Facultad de Biología, Universidade de Santiago de Compostela, Campus Vida s/n. 15782, Santiago de Compostela, Spain
- Institute of Marine Sciences, School of Biological Sciences, University of Portsmouth, PO4 9LY, Portsmouth, UK
| | - Ana L. Diéguez
- Departamento de Microbiología y Parasitología, CIBUS-Facultad de Biología, Universidade de Santiago de Compostela, Campus Vida s/n. 15782, Santiago de Compostela, Spain
| | - Jesús L. Romalde
- Departamento de Microbiología y Parasitología, CIBUS-Facultad de Biología, Universidade de Santiago de Compostela, Campus Vida s/n. 15782, Santiago de Compostela, Spain
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25
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Mora-Ruiz MDR, Font-Verdera F, Orfila A, Rita J, Rosselló-Móra R. Endophytic microbial diversity of the halophyteArthrocnemum macrostachyumacross plant compartments. FEMS Microbiol Ecol 2016; 92:fiw145. [DOI: 10.1093/femsec/fiw145] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/22/2016] [Indexed: 11/13/2022] Open
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26
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Lucena T, Mesa J, Rodriguez-Llorente ID, Pajuelo E, Caviedes MÁ, Ruvira MA, Pujalte MJ. Marinomonas spartinae sp. nov., a novel species with plant-beneficial properties. Int J Syst Evol Microbiol 2016; 66:1686-1691. [PMID: 26821806 DOI: 10.1099/ijsem.0.000929] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two strains of Gram-stain-negative, chemo-organotrophic, aerobic and halophilic gammaproteobacteria, isolated from within the stem and roots of Spartina maritima in salt marshes from the south Atlantic Spanish coast, were found to represent a novel species in the genus Marinomonas through phylogenetic analysis of their 16S rRNA genes and phenotypic characterization. 16S rRNA gene sequences of the two strains shared < 96.2% similarity with other Marinomonas species, with Marimonas alcarazii being the most similar in sequence. They required sodium ions for growth, were able to thrive at low (4 °C) temperatures and at salinities of 12-15%, were unable to hydrolyse any tested macromolecule except casein, and grew with different monosaccharides, disaccharides, sugar alcohols, organic acids and amino acids. The novel species differed from other Marinomonas species in the use of several sole carbon sources, its temperature and salinity ranges for growth, ion requirements and cellular fatty acid composition, which included C16:0, C16:1 and C18:1 as major components and C10:0 3-OH, C12:0 and C12:0 3-OH as minor components. The name Marinomonas spartinae sp. nov. is proposed, with SMJ19T (=CECT 8886T=KCTC 42958T) as the type strain.
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Affiliation(s)
- Teresa Lucena
- Departamento de Microbiología y Ecología & Colección Española de Cultivos Tipo (CECT), Universitat de València, Spain
| | - Jennifer Mesa
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad de Sevilla, Spain
| | | | - Eloisa Pajuelo
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad de Sevilla, Spain
| | - Miguel Ángel Caviedes
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad de Sevilla, Spain
| | - María A Ruvira
- Departamento de Microbiología y Ecología & Colección Española de Cultivos Tipo (CECT), Universitat de València, Spain
| | - María J Pujalte
- Departamento de Microbiología y Ecología & Colección Española de Cultivos Tipo (CECT), Universitat de València, Spain
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Yoo AY, Park JK. Isolation and characterization of a serine protease-producing marine bacterium Marinomonas arctica PT-1. Bioprocess Biosyst Eng 2015; 39:307-14. [DOI: 10.1007/s00449-015-1514-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 11/24/2015] [Indexed: 10/22/2022]
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28
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A diverse group of halophilic bacteria exist in Lunsu, a natural salt water body of Himachal Pradesh, India. SPRINGERPLUS 2015; 4:274. [PMID: 26090321 PMCID: PMC4469599 DOI: 10.1186/s40064-015-1028-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Accepted: 05/12/2015] [Indexed: 11/10/2022]
Abstract
Five halophilic bacterial isolates namely SS1, SS2, SS3, SS5 and SS8 were isolated from soil sediments of Lunsu, a salty water body. All the bacterial isolates showed growth in LB medium containing up to 8.7% NaCl, pH 7-8 and at temperature range of 30-37°C. The bacterial isolates SS1 and SS3 require at least 3.8% NaCl for their growth, indicating their strict halophilic nature. Interestingly, bacterial isolates SS2, SS5 and SS8 but not SS1 and SS3 exhibited growth in medium supplemented with KCl. Accordingly, Na(+) and K(+) ions were detected at 1.39 and 0.0035%, respectively in Lunsu water. All the bacterial isolates were analyzed by random amplification of polymorphic DNA (RAPD) using four different random primers and produced PCR fragments ranging from 0.1 to 5 kb in size. Phylogenetic tree based on RAPD finger prints showed that SS1 and SS3 formed one group, while SS2 and SS5 formed the second group, whereas SS8 was out group. Sequence analysis of 16S rDNA identified SS1 and SS3 as Halobacillus trueperi, SS2 as Shewanella algae, SS5 as Halomonas venusta, and SS8 as Marinomonas sp. were deposited in GenBank with accession numbers of KM260166, KF751761, KF751760, KF751762 and KF751763, respectively. This is the first report on the presence of diverse halophilic bacteria in the foot hills of Himalayas.
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29
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Zhang DC, Margesin R. Marinomonas mangrovi sp. nov., isolated from mangrove sediment. Int J Syst Evol Microbiol 2015; 65:1537-1541. [DOI: 10.1099/ijs.0.000136] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, Na+-requiring bacterial strain, designated B20-1T, was isolated from soil of the root system of mangrove forest. Cells were curved rods and motile by means of a polar flagellum. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain B20-1T belonged to the genus
Marinomonas
, sharing highest sequence similarities with
Marinomonas rhizomae
IVIA-Po-145T (97.6 %),
Marinomonas dokdonensis
DSW10-10T (97.0 %) and
Marinomonas foliarum
IVIA-Po-155T (96.9 %). The predominant cellular fatty acids of strain B20-1T were C10 : 0 3-OH, C18 : 1ω7c, summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH) and C16 : 0. Phosphatidylethanolamine and phosphatidylglycerol were identified as the predominant phospholipids. The predominant ubiquinone was Q-8. The genomic DNA G+C content of strain B20-1T was 46.6 mol%. On the basis of phenotypic characteristics, phylogenetic analysis and DNA–DNA relatedness, a novel species, Marinomonas mangrovi sp. nov., is proposed with B20-1T ( = DSM 28136T = LMG 28077T) as the type strain.
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Affiliation(s)
- De-Chao Zhang
- Institute of Oceanology, Chinese Academy of Sciences, 266071, Qingdao, PR China
| | - Rosa Margesin
- Institute of Microbiology, University of Innsbruck, Technikerstrasse 25, A-6020 Innsbruck, Austria
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30
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Campillo-Brocal JC, Chacón-Verdú MD, Lucas-Elío P, Sánchez-Amat A. Distribution in microbial genomes of genes similar to lodA and goxA which encode a novel family of quinoproteins with amino acid oxidase activity. BMC Genomics 2015; 16:231. [PMID: 25886995 PMCID: PMC4417212 DOI: 10.1186/s12864-015-1455-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 03/09/2015] [Indexed: 11/16/2022] Open
Abstract
Background L-Amino acid oxidases (LAOs) have been generally described as flavoproteins that oxidize amino acids releasing the corresponding ketoacid, ammonium and hydrogen peroxide. The generation of hydrogen peroxide gives to these enzymes antimicrobial characteristics. They are involved in processes such as biofilm development and microbial competition. LAOs are of great biotechnological interest in different applications such as the design of biosensors, biotransformations and biomedicine. The marine bacterium Marinomonas mediterranea synthesizes LodA, the first known LAO that contains a quinone cofactor. LodA is encoded in an operon that contains a second gene coding for LodB, a protein required for the post-translational modification generating the cofactor. Recently, GoxA, a quinoprotein with sequence similarity to LodA but with a different enzymatic activity (glycine oxidase instead of lysine-ε-oxidase) has been described. The aim of this work has been to study the distribution of genes similar to lodA and/or goxA in sequenced microbial genomes and to get insight into the evolution of this novel family of proteins through phylogenetic analysis. Results Genes encoding LodA-like proteins have been detected in several bacterial classes. However, they are absent in Archaea and detected only in a small group of fungi of the class Agaromycetes. The vast majority of the genes detected are in a genome region with a nearby lodB-like gene suggesting a specific interaction between both partner proteins. Sequence alignment of the LodA-like proteins allowed the detection of several conserved residues. All of them showed a Cys and a Trp that aligned with the residues that are forming part of the cysteine tryptophilquinone (CTQ) cofactor in LodA. Phylogenetic analysis revealed that LodA-like proteins can be clustered in different groups. Interestingly, LodA and GoxA are in different groups, indicating that those groups are related to the enzymatic activity of the proteins detected. Conclusions Genome mining has revealed for the first time the broad distribution of LodA-like proteins containing a CTQ cofactor in many different microbial groups. This study provides a platform to explore the potentially novel enzymatic activities of the proteins detected, the mechanisms of post-translational modifications involved in their synthesis, as well as their biological relevance. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1455-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jonatan C Campillo-Brocal
- Department of Genetics and Microbiology, University of Murcia, Campus de Espinardo, Murcia, 30100, Spain.
| | - María Dolores Chacón-Verdú
- Department of Genetics and Microbiology, University of Murcia, Campus de Espinardo, Murcia, 30100, Spain.
| | - Patricia Lucas-Elío
- Department of Genetics and Microbiology, University of Murcia, Campus de Espinardo, Murcia, 30100, Spain.
| | - Antonio Sánchez-Amat
- Department of Genetics and Microbiology, University of Murcia, Campus de Espinardo, Murcia, 30100, Spain.
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Lee H, Yoshizawa S, Kogure K, Kim HS, Yoon J. Pelagitalea pacifica gen. nov., sp. nov., a New Marine Bacterium Isolated from Seawater. Curr Microbiol 2014; 70:514-9. [DOI: 10.1007/s00284-014-0750-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Accepted: 10/30/2014] [Indexed: 11/24/2022]
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32
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Marinomonas profundimaris sp. nov., isolated from deep-sea sediment sample of the Arctic Ocean. Antonie van Leeuwenhoek 2014; 106:449-55. [DOI: 10.1007/s10482-014-0213-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Accepted: 06/09/2014] [Indexed: 10/25/2022]
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Kumari P, Poddar A, Das SK. Marinomonas fungiae sp. nov., isolated from the coral Fungia echinata from the Andaman Sea. Int J Syst Evol Microbiol 2014; 64:487-494. [DOI: 10.1099/ijs.0.054809-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel aerobic marine bacterium, strain AN44T, was isolated from the coral Fungia echinata sampled from the Andaman Sea, India. Cells were Gram-negative, motile and rod-shaped. Oxidase and catalase tests were positive. Heterotrophic growth was observed at pH 5.5–10 and at 16–42 °C, with optimum growth at pH 7–8 and 28 °C. Strain AN44T grew in the presence of 0.5–11 % (w/v) NaCl; the optimal NaCl concentration for growth was 3–5 %. The DNA G+C content was 47.8 mol%. Predominant cellular fatty acids of strain AN44T were C18 : 1ω7c, C16 : 1ω7c/C16 : 1ω6c, C16 : 0, C10 : 0 3-OH, C12 : 0, C10 : 0, C14 : 0 and C18 : 0. The sole isoprenoid ubiquinone was Q-8. The polar lipids were an unidentified phospholipid, an unidentified aminophospholipid and two unidentified glycolipids. 16S rRNA gene sequence comparisons revealed that strain AN44T clustered within the radiation of the genus
Marinomonas
and showed similarity of 97.9 % with
Marinomonas ostreistagni
UST010306-043T, 97.8 % with
Marinomonas aquimarina
11SM4T, 97.1 % with
Marinomonas brasilensis
R-40503T and 97.0 % with
Marinomonas communis
8T. However, DNA–DNA relatedness between strain AN44T and closely related type strains was well below 70 %. On the basis of the data from the present polyphasic taxonomic study, strain AN44T is considered to represent a novel species of the genus
Marinomonas
, for which the name
Marinomonas
fungiae sp. nov. is proposed. The type strain is AN44T ( = JCM 18476T = LMG 27065T).
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Affiliation(s)
- Prabla Kumari
- Institute of Life Sciences, Department of Biotechnology, Nalco Square, Bhubaneswar – 751 023, India
| | - Abhijit Poddar
- Institute of Life Sciences, Department of Biotechnology, Nalco Square, Bhubaneswar – 751 023, India
| | - Subrata K. Das
- Institute of Life Sciences, Department of Biotechnology, Nalco Square, Bhubaneswar – 751 023, India
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Siamer S, Gaubert S, Boureau T, Brisset MN, Barny MA. Mutational analysis of a predicted double β-propeller domain of the DspA/E effector of Erwinia amylovora. FEMS Microbiol Lett 2013; 342:54-61. [PMID: 23421848 DOI: 10.1111/1574-6968.12108] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Revised: 02/07/2013] [Accepted: 02/18/2013] [Indexed: 12/11/2022] Open
Abstract
The bacterium Erwinia amylovora causes fire blight, an invasive disease that threatens apple trees, pear trees and other plants of the Rosaceae family. Erwinia amylovora pathogenicity relies on a type III secretion system and on a single effector DspA/E. This effector belongs to the widespread AvrE family of effectors whose biological function is unknown. In this manuscript, we performed a bioinformatic analysis of DspA/E- and AvrE-related effectors. Motif search identified nuclear localization signals, peroxisome targeting signals, endoplasmic reticulum membrane retention signals and leucine zipper motifs, but none of these motifs were present in all the AvrE-related effectors analysed. Protein threading analysis, however, predicted a conserved double β-propeller domain in the N-terminal part of all the analysed effector sequences. We then performed a random pentapeptide mutagenesis of DspA/E, which led to the characterization of 13 new altered proteins with a five amino acids insertion. Eight harboured the insertion inside the predicted β-propeller domain and six of these eight insertions impaired DspA/E stability or function. Conversely, the two remaining insertions generated proteins that were functional and abundantly secreted in the supernatant suggesting that these two insertions stabilized the protein.
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Wilkins D, Yau S, Williams TJ, Allen MA, Brown MV, DeMaere MZ, Lauro FM, Cavicchioli R. Key microbial drivers in Antarctic aquatic environments. FEMS Microbiol Rev 2013; 37:303-35. [DOI: 10.1111/1574-6976.12007] [Citation(s) in RCA: 129] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2012] [Revised: 08/11/2012] [Accepted: 10/01/2012] [Indexed: 11/27/2022] Open
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Lucas-Elío P, Goodwin L, Woyke T, Pitluck S, Nolan M, Kyrpides NC, Detter JC, Copeland A, Lu M, Bruce D, Detter C, Tapia R, Han S, Land ML, Ivanova N, Mikhailova N, Johnston AWB, Sanchez-Amat A. Complete genome sequence of Marinomonas posidonica type strain (IVIA-Po-181(T)). Stand Genomic Sci 2012; 7:31-43. [PMID: 23458837 PMCID: PMC3577112 DOI: 10.4056/sigs.2976373] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Marinomonas posidonica IVIA-Po-181(T) Lucas-Elío et al. 2011 belongs to the family Oceanospirillaceae within the phylum Proteobacteria. Different species of the genus Marinomonas can be readily isolated from the seagrass Posidonia oceanica. M. posidonica is among the most abundant species of the genus detected in the cultured microbiota of P. oceanica, suggesting a close relationship with this plant, which has a great ecological value in the Mediterranean Sea, covering an estimated surface of 38,000 Km(2). Here we describe the genomic features of M. posidonica. The 3,899,940 bp long genome harbors 3,544 protein-coding genes and 107 RNA genes and is a part of the GenomicEncyclopedia ofBacteriaandArchaea project.
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Affiliation(s)
- Patricia Lucas-Elío
- Department of Genetics and Microbiology, Regional Campus of International Excellence “Campus Mare Nostrum”,University of Murcia, Murcia, Spain
| | - Lynne Goodwin
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Sam Pitluck
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Matt Nolan
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | | | | | - Alex Copeland
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Megan Lu
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - David Bruce
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Chris Detter
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Roxanne Tapia
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Shunsheng Han
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Miriam L. Land
- Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | | | | | - Andrew W. B. Johnston
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich,UK
| | - Antonio Sanchez-Amat
- Department of Genetics and Microbiology, Regional Campus of International Excellence “Campus Mare Nostrum”,University of Murcia, Murcia, Spain
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Abby SS, Rocha EPC. The non-flagellar type III secretion system evolved from the bacterial flagellum and diversified into host-cell adapted systems. PLoS Genet 2012; 8:e1002983. [PMID: 23028376 PMCID: PMC3459982 DOI: 10.1371/journal.pgen.1002983] [Citation(s) in RCA: 200] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2012] [Accepted: 08/09/2012] [Indexed: 12/20/2022] Open
Abstract
Type 3 secretion systems (T3SSs) are essential components of two complex bacterial machineries: the flagellum, which drives cell motility, and the non-flagellar T3SS (NF-T3SS), which delivers effectors into eukaryotic cells. Yet the origin, specialization, and diversification of these machineries remained unclear. We developed computational tools to identify homologous components of the two systems and to discriminate between them. Our analysis of >1,000 genomes identified 921 T3SSs, including 222 NF-T3SSs. Phylogenomic and comparative analyses of these systems argue that the NF-T3SS arose from an exaptation of the flagellum, i.e. the recruitment of part of the flagellum structure for the evolution of the new protein delivery function. This reconstructed chronology of the exaptation process proceeded in at least two steps. An intermediate ancestral form of NF-T3SS, whose descendants still exist in Myxococcales, lacked elements that are essential for motility and included a subset of NF-T3SS features. We argue that this ancestral version was involved in protein translocation. A second major step in the evolution of NF-T3SSs occurred via recruitment of secretins to the NF-T3SS, an event that occurred at least three times from different systems. In rhizobiales, a partial homologous gene replacement of the secretin resulted in two genes of complementary function. Acquisition of a secretin was followed by the rapid adaptation of the resulting NF-T3SSs to multiple, distinct eukaryotic cell envelopes where they became key in parasitic and mutualistic associations between prokaryotes and eukaryotes. Our work elucidates major steps of the evolutionary scenario leading to extant NF-T3SSs. It demonstrates how molecular evolution can convert one complex molecular machine into a second, equally complex machine by successive deletions, innovations, and recruitment from other molecular systems.
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Affiliation(s)
- Sophie S Abby
- Département Génomes et Génétique, Institut Pasteur, Microbial Evolutionary Genomics, Paris, France.
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38
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Garcias-Bonet N, Arrieta JM, de Santana CN, Duarte CM, Marbà N. Endophytic bacterial community of a Mediterranean marine angiosperm (Posidonia oceanica). Front Microbiol 2012; 3:342. [PMID: 23049528 PMCID: PMC3448135 DOI: 10.3389/fmicb.2012.00342] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2012] [Accepted: 09/04/2012] [Indexed: 11/24/2022] Open
Abstract
Bacterial endophytes are crucial for the survival of many terrestrial plants, but little is known about the presence and importance of bacterial endophytes of marine plants. We conducted a survey of the endophytic bacterial community of the long-living Mediterranean marine angiosperm Posidonia oceanica in surface-sterilized tissues (roots, rhizomes, and leaves) by Denaturing Gradient Gel Electrophoresis (DGGE). A total of 26 Posidonia oceanica meadows around the Balearic Islands were sampled, and the band patterns obtained for each meadow were compared for the three sampled tissues. Endophytic bacterial sequences were detected in most of the samples analyzed. A total of 34 OTUs (Operational Taxonomic Units) were detected. The main OTUs of endophytic bacteria present in P. oceanica tissues belonged primarily to Proteobacteria (α, γ, and δ subclasses) and Bacteroidetes. The OTUs found in roots significantly differed from those of rhizomes and leaves. Moreover, some OTUs were found to be associated to each type of tissue. Bipartite network analysis revealed differences in the bacterial endophyte communities present on different islands. The results of this study provide a pioneering step toward the characterization of the endophytic bacterial community associated with tissues of a marine angiosperm and reveal the presence of bacterial endophytes that differed among locations and tissue types.
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Litoribacillus peritrichatus gen. nov. sp. nov., isolated from coastal sediment of an amphioxus breeding zone in Qingdao, China. Antonie van Leeuwenhoek 2012; 103:357-66. [DOI: 10.1007/s10482-012-9815-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2012] [Accepted: 09/10/2012] [Indexed: 10/27/2022]
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40
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Jung YT, Oh TK, Yoon JH. Marinomonas hwangdonensis sp. nov., isolated from seawater. Int J Syst Evol Microbiol 2012; 62:2062-2067. [DOI: 10.1099/ijs.0.036582-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-negative, motile, rod-shaped bacterial strain, designated HDW-15T, was isolated from seawater of the Yellow Sea, Korea, and subjected to a polyphasic taxonomic study. Strain HDW-15T grew optimally at pH 7.0–8.0, at 25 °C and in the presence of 2 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain HDW-15T fell within the clade comprising
Marinomonas
species, joining the type strain of
Marinomonas arctica
, with which it exhibited highest 16S rRNA gene sequence similarity (97.7 %). The 16S rRNA gene sequence similarity values between strain HDW-15T and the type strains of other
Marinomonas
species were in the range 93.7–97.2 %. Mean DNA–DNA relatedness values between strain HDW-15T and the type strains of
M. arctica
,
Marinomonas polaris
and
Marinomonas pontica
were 5.0–9.9 %. The DNA G+C content of the isolate was 48.7 mol%. Strain HDW-15T contained Q-8 as the predominant ubiquinone and C18 : 1ω7c, summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH) and C16 : 0 as the major fatty acids. The major polar lipids found in strain HDW-15T were phosphatidylglycerol and phosphatidylethanolamine. Differential phenotypic properties, together with phylogenetic and genetic distinctiveness, showed that strain HDW-15T can be differentiated from other
Marinomonas
species. On the basis of the data presented, strain HDW-15T is considered to represent a novel species of the genus
Marinomonas
, for which the name Marinomonas hwangdonensis sp. nov. is proposed. The type strain is HDW-15T ( = KCTC 23661T = CCUG 61321T).
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Affiliation(s)
- Yong-Taek Jung
- University of Science and Technology (UST), 217 Gajungro, Yuseong, Daejeon 305-350, Republic of Korea
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yuseong, Daejeon, Republic of Korea
| | - Tae-Kwang Oh
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yuseong, Daejeon, Republic of Korea
| | - Jung-Hoon Yoon
- Department of Food Science and Biotechnology, Sungkyunkwan University, Jangan-gu, Suwon, Republic of Korea
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Lucas-Elío P, Goodwin L, Woyke T, Pitluck S, Nolan M, Kyrpides NC, Detter JC, Copeland A, Teshima H, Bruce D, Detter C, Tapia R, Han S, Land ML, Ivanova N, Mikhailova N, Johnston AWB, Sanchez-Amat A. Complete genome sequence of the melanogenic marine bacterium Marinomonas mediterranea type strain (MMB-1(T)). Stand Genomic Sci 2012; 6:63-73. [PMID: 22675599 PMCID: PMC3368407 DOI: 10.4056/sigs.2545743] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Marinomonas mediterranea MMB-1(T) Solano & Sanchez-Amat 1999 belongs to the family Oceanospirillaceae within the phylum Proteobacteria. This species is of interest because it is the only species described in the genus Marinomonas to date that can synthesize melanin pigments, which is mediated by the activity of a tyrosinase. M. mediterranea expresses other oxidases of biotechnological interest, such as a multicopper oxidase with laccase activity and a novel L-lysine-epsilon-oxidase. The 4,684,316 bp long genome harbors 4,228 protein-coding genes and 98 RNA genes and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
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Affiliation(s)
- Patricia Lucas-Elío
- Department of Genetics and Microbiology, University of Murcia, Murcia, Spain
| | - Lynne Goodwin
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Sam Pitluck
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Matt Nolan
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | | | | | - Alex Copeland
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Hazuki Teshima
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - David Bruce
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Chris Detter
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Roxanne Tapia
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Shunsheng Han
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Miriam L. Land
- Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | | | | | - Andrew W. B. Johnston
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
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Lucas-Elío P, Marco-Noales E, Espinosa E, Ordax M, López MM, Garcías-Bonet N, Marbà N, Duarte CM, Sanchez-Amat A. Marinomonas alcarazii sp. nov., M. rhizomae sp. nov., M. foliarum sp. nov., M. posidonica sp. nov. and M. aquiplantarum sp. nov., isolated from the microbiota of the seagrass Posidonia oceanica. Int J Syst Evol Microbiol 2011; 61:2191-2196. [DOI: 10.1099/ijs.0.027227-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Five novel Gram-reaction-negative aerobic marine bacterial strains with DNA G+C contents <50 mol% were isolated from the seagrass Posidonia oceanica. 16S rRNA sequence analysis indicated that they belonged to the genus Marinomonas. Major fatty acid compositions, comprising C10 : 0 3-OH, C16 : 0, C16 : 1ω7c and C18 : 1ω7c, supported the affiliation of these strains to the genus Marinomonas. Strains IVIA-Po-14bT, IVIA-Po-145T and IVIA-Po-155T were closely related to Marinomonas pontica 46-16T, according to phylogenetic analysis. However, DNA–DNA hybridization values <35 % among these strains revealed that they represented different species. Further differences in the phenotypes and minor fatty acid compositions were also found among the strains. Another two strains, designated IVIA-Po-181T and IVIA-Po-159T, were found to be closely related to M. dokdonensis DSW10-10T but DNA–DNA relatedness levels <40 % in pairwise comparisons, as well as some additional differences in phenotypes and fatty acid compositions supported the creation of two novel species. Accordingly, strains IVIA-Po-14bT ( = CECT 7730T = NCIMB 14671T), IVIA-Po-145T ( = CECT 7377T = NCIMB 14431T), IVIA-Po-155T ( = CECT 7731T = NCIMB 14672T), IVIA-Po-181T ( = CECT 7376T = NCIMB 14433T) and IVIA-Po-159T ( = CECT 7732T = NCIMB 14673T) represent novel species, for which the names Marinomonas alcarazii sp. nov., Marinomonas rhizomae sp. nov., Marinomonas foliarum sp. nov., Marinomonas posidonica sp. nov. and Marinomonas aquiplantarum sp. nov. are proposed, respectively.
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Affiliation(s)
- Patricia Lucas-Elío
- Department of Genetics and Microbiology, University of Murcia, Murcia 30100, Spain
| | - Ester Marco-Noales
- Centro de Protección Vegetal y Biotecnología, IVIA, 46113 Moncada (Valencia), Spain
| | - Elena Espinosa
- Department of Genetics and Microbiology, University of Murcia, Murcia 30100, Spain
| | - Mónica Ordax
- Centro de Protección Vegetal y Biotecnología, IVIA, 46113 Moncada (Valencia), Spain
| | - María M. López
- Centro de Protección Vegetal y Biotecnología, IVIA, 46113 Moncada (Valencia), Spain
| | - Neus Garcías-Bonet
- Department of Global Change Research, Instituto Mediterráneo de Estudios Avanzados (CSIC-UIB), 07190 Esporles, Mallorca, Spain
| | - Nuria Marbà
- Department of Global Change Research, Instituto Mediterráneo de Estudios Avanzados (CSIC-UIB), 07190 Esporles, Mallorca, Spain
| | - Carlos M. Duarte
- Department of Global Change Research, Instituto Mediterráneo de Estudios Avanzados (CSIC-UIB), 07190 Esporles, Mallorca, Spain
| | - Antonio Sanchez-Amat
- Department of Genetics and Microbiology, University of Murcia, Murcia 30100, Spain
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Marinomonas brasilensis sp. nov., isolated from the coral Mussismilia hispida, and reclassification of Marinomonas basaltis as a later heterotypic synonym of Marinomonas communis. Int J Syst Evol Microbiol 2011; 61:1170-1175. [DOI: 10.1099/ijs.0.024661-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-negative, aerobic bacterium, designated strain R-40503T, was isolated from mucus of the reef-builder coral Mussismilia hispida, located in the São Sebastião Channel, São Paulo, Brazil. Phylogenetic analyses revealed that strain R-40503T belongs to the genus Marinomonas. The 16S rRNA gene sequence similarity of R-40503T was above 97 % with the type strains of Marinomonas vaga, M. basaltis, M. communis and M. pontica, and below 97 % with type strains of the other Marinomonas species. Strain R-40503T showed less than 35 % DNA–DNA hybridization (DDH) with the type strains of the phylogenetically closest Marinomonas species, demonstrating that it should be classified into a novel species. Amplified fragment length polymorphism (AFLP), chemotaxonomic and phenotypic analyses provided further evidence for the proposal of a novel species. Concurrently, a close genomic relationship between M. basaltis and M. communis was observed. The type strains of these two species showed 78 % DDH and 63 % AFLP pattern similarity. Their phenotypic features were very similar, and their DNA G+C contents were identical (46.3 mol%). Collectively, these data demonstrate unambiguously that Marinomonas basaltis is a later heterotypic synonym of Marinomonas communis. Several phenotypic features can be used to discriminate between Marinomonas species. The novel strain R-40503T is clearly distinguishable from its neighbours. For instance, it shows oxidase and urease activity, utilizes l-asparagine and has the fatty acid C12 : 1 3-OH but lacks C10 : 0 and C12 : 0. The name Marinomonas brasilensis sp. nov. is proposed, with the type strain R-40503T ( = R-278T = LMG 25434T = CAIM 1459T). The DNA G+C content of strain R-40503T is 46.5 mol%.
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Molina-Quintero LR, Lucas-Elío P, Sanchez-Amat A. Regulation of the Marinomonas mediterranea antimicrobial protein lysine oxidase by L-lysine and the sensor histidine kinase PpoS. Appl Environ Microbiol 2010; 76:6141-9. [PMID: 20656878 PMCID: PMC2937512 DOI: 10.1128/aem.00690-10] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2010] [Accepted: 07/10/2010] [Indexed: 11/20/2022] Open
Abstract
Some Gram-negative bacteria express a novel enzyme with lysine-epsilon-oxidase (LOD) activity (EC 1.4.3.20). The oxidation of l-Lys generates, among other products, hydrogen peroxide, which confers antimicrobial properties to this kind of enzyme and has been shown to be involved in cell death during biofilm development and differentiation. In addition to LOD, the melanogenic marine bacterium Marinomonas mediterranea, which forms part of the microbiota of the marine plant Posidonia oceanica, expresses two other oxidases of biotechnological interest, a multicopper oxidase, PpoA, with laccase activity and a tyrosinase named PpoB, which is responsible for melanin synthesis. By using both lacZ fusions with the lodAB promoter and quantitative reverse transcription-PCR (qRT-PCR), this study shows that the hybrid sensor histidine kinase PpoS regulates LOD activity at the transcriptional level. Although PpoS also regulates PpoA and PpoB, in this case, the regulatory effect cannot be attributed only to a transcriptional regulation. Further studies indicate that LOD activity is induced at the posttranscriptional level by l-Lys as well as by two structurally similar compounds, l-Arg and meso-2,6-diaminopimelic acid (DAP), neither of which is a substrate of the enzyme. The inducing effect of these compounds is specific for LOD activity since PpoA and PpoB are not affected by them. This study offers, for the first time, insights into the mechanisms regulating the synthesis of the antimicrobial protein lysine-epsilon-oxidase in M. mediterranea, which could be important in the microbial colonization of the seagrass P. oceanica.
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Affiliation(s)
| | - Patricia Lucas-Elío
- Department of Genetics and Microbiology, University of Murcia, 30100 Murcia, Spain
| | - Antonio Sanchez-Amat
- Department of Genetics and Microbiology, University of Murcia, 30100 Murcia, Spain
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45
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Sanchez-Amat A, Solano F, Lucas-Elío P. Finding new enzymes from bacterial physiology: a successful approach illustrated by the detection of novel oxidases in Marinomonas mediterranea. Mar Drugs 2010; 8:519-41. [PMID: 20411113 PMCID: PMC2855505 DOI: 10.3390/md8030519] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2010] [Revised: 02/21/2010] [Accepted: 02/22/2010] [Indexed: 12/04/2022] Open
Abstract
The identification and study of marine microorganisms with unique physiological traits can be a very powerful tool discovering novel enzymes of possible biotechnological interest. This approach can complement the enormous amount of data concerning gene diversity in marine environments offered by metagenomic analysis, and can help to place the activities associated with those sequences in the context of microbial cellular metabolism and physiology. Accordingly, the detection and isolation of microorganisms that may be a good source of enzymes is of great importance. Marinomonas mediterranea, for example, has proven to be one such useful microorganism. This Gram-negative marine bacterium was first selected because of the unusually high amounts of melanins synthesized in media containing the amino acid L-tyrosine. The study of its molecular biology has allowed the cloning of several genes encoding oxidases of biotechnological interest, particularly in white and red biotechnology. Characterization of the operon encoding the tyrosinase responsible for melanin synthesis revealed that a second gene in that operon encodes a protein, PpoB2, which is involved in copper transfer to tyrosinase. This finding made PpoB2 the first protein in the COG5486 group to which a physiological role has been assigned. Another enzyme of interest described in M. mediterranea is a multicopper oxidase encoding a membrane-associated enzyme that shows oxidative activity on a wide range of substrates typical of both laccases and tyrosinases. Finally, an enzyme very specific for L-lysine, which oxidises this amino acid in epsilon position and that has received a new EC number (1.4.3.20), has also been described for M. mediterranea. Overall, the studies carried out on this bacterium illustrate the power of exploring the physiology of selected microorganisms to discover novel enzymes of biotechnological relevance.
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Affiliation(s)
- Antonio Sanchez-Amat
- Department of Genetics and Microbiology, Faculty of Biology, University of Murcia, Campus de Espinardo, Murcia 30100, Spain; E-Mail:
| | - Francisco Solano
- Department of Biochemistry and Molecular Biology B and Immunology, School of Medicine, University of Murcia, Murcia 30100, Spain; E-Mail:
| | - Patricia Lucas-Elío
- Department of Genetics and Microbiology, Faculty of Biology, University of Murcia, Campus de Espinardo, Murcia 30100, Spain; E-Mail:
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