1
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Xu N, Wang W, Xu K, Xu Y, Ji D, Chen C, Xie C. Cultivation of different seaweed species and seasonal changes cause divergence of the microbial community in coastal seawaters. Front Microbiol 2022; 13:988743. [PMID: 36160253 PMCID: PMC9490310 DOI: 10.3389/fmicb.2022.988743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 08/17/2022] [Indexed: 12/02/2022] Open
Abstract
Although the effects of certain species of seaweed on the microbial community structure have long been a research focus in marine ecology, the response of the microbial community to seasons and different seaweed species is poorly understood. In the present study, a total of 39 seawater samples were collected during 3 months from three zones: Neoporphyra haitanensis cultivation zones (P), Gracilaria lemaneiformis-Saccharina japonica mixed cultivation zones (G), and control zones (C). These samples were then analyzed using 18S and 16S rRNA gene sequencing to ascertain the fungal and bacterial communities, respectively, along with the determination of environmental factors. Our results showed that increased dissolved oxygen (DO), decreased inorganic nutrients, and released dissolved organic matter (DOM) in seaweed cultivation zone predominantly altered the variability of eukaryotic and prokaryotic microbial communities. Certain microbial groups such as Aurantivirga, Pseudomonas, and Woeseia were stimulated and enriched in response to seaweed cultivation, and the enriched microorganisms varied across seaweed cultivation zones due to differences in the composition of released DOM. In addition, seasonal changes in salinity and temperature were strongly correlated with microbial community composition and structure. Our study provides new insights into the interactions between seaweed and microbial communities.
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Affiliation(s)
- Ningning Xu
- Fisheries College, Jimei University, Xiamen, China
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Xiamen, China
- Fujian Engineering Research Center of Aquatic Breeding and Healthy Aquaculture, Xiamen, China
| | - Wenlei Wang
- Fisheries College, Jimei University, Xiamen, China
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Xiamen, China
- Fujian Engineering Research Center of Aquatic Breeding and Healthy Aquaculture, Xiamen, China
| | - Kai Xu
- Fisheries College, Jimei University, Xiamen, China
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Xiamen, China
- Fujian Engineering Research Center of Aquatic Breeding and Healthy Aquaculture, Xiamen, China
| | - Yan Xu
- Fisheries College, Jimei University, Xiamen, China
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Xiamen, China
- Fujian Engineering Research Center of Aquatic Breeding and Healthy Aquaculture, Xiamen, China
| | - Dehua Ji
- Fisheries College, Jimei University, Xiamen, China
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Xiamen, China
- Fujian Engineering Research Center of Aquatic Breeding and Healthy Aquaculture, Xiamen, China
| | - Changsheng Chen
- Fisheries College, Jimei University, Xiamen, China
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Xiamen, China
- Fujian Engineering Research Center of Aquatic Breeding and Healthy Aquaculture, Xiamen, China
| | - Chaotian Xie
- Fisheries College, Jimei University, Xiamen, China
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Xiamen, China
- Fujian Engineering Research Center of Aquatic Breeding and Healthy Aquaculture, Xiamen, China
- *Correspondence: Chaotian Xie,
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2
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Description of Polaribacter batillariae sp. nov., Polaribacter cellanae sp. nov., and Polaribacter pectinis sp. nov., novel bacteria isolated from the gut of three types of South Korean shellfish. J Microbiol 2022; 60:576-584. [DOI: 10.1007/s12275-022-1604-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 02/21/2022] [Accepted: 03/02/2022] [Indexed: 10/18/2022]
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3
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Najafpour B, Pinto PIS, Canario AVM, Power DM. Quantifying dominant bacterial genera detected in metagenomic data from fish eggs and larvae using genus-specific primers. Microbiologyopen 2022; 11:e1274. [PMID: 35765179 PMCID: PMC9055463 DOI: 10.1002/mbo3.1274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 03/05/2022] [Indexed: 12/03/2022] Open
Abstract
The goal of this study was to design genus-specific primers for rapid evaluation of the most abundant bacterial genera identified using amplicon-based sequencing of the 16S rRNA gene in fish-related samples and surrounding water. Efficient genus-specific primers were designed for 11 bacterial genera including Alkalimarinus, Colwellia, Enterovibrio, Marinomonas, Massilia, Oleispira, Phaeobacter, Photobacterium, Polarbacerium, Pseudomonas, and Psychrobium. The specificity of the primers was confirmed by the phylogeny of the sequenced polymerase chain reaction (PCR) amplicons that indicated primers were genus-specific except in the case of Colwellia and Phaeobacter. Copy number of the 16S rRNA gene obtained by quantitative PCR using genus-specific primers and the relative abundance obtained by 16S rRNA gene sequencing using universal primers were well correlated for the five analyzed abundant bacterial genera. Low correlations between quantitative PCR and 16S rRNA gene sequencing for Pseudomonas were explained by the higher coverage of known Pseudomonas species by the designed genus-specific primers than the universal primers used in 16S rRNA gene sequencing. The designed genus-specific primers are proposed as rapid and cost-effective tools to evaluate the most abundant bacterial genera in fish-related or potentially other metagenomics samples.
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Affiliation(s)
- Babak Najafpour
- Centro de Ciências do Mar (CCMAR/CIMAR)Universidade do AlgarveFaroPortugal
| | - Patricia I. S. Pinto
- Centro de Ciências do Mar (CCMAR/CIMAR)Universidade do AlgarveFaroPortugal
- International Center for Marine StudiesShanghai Ocean UniversityShanghaiChina
| | - A. V. M. Canario
- Centro de Ciências do Mar (CCMAR/CIMAR)Universidade do AlgarveFaroPortugal
- International Center for Marine StudiesShanghai Ocean UniversityShanghaiChina
| | - Deborah M. Power
- Centro de Ciências do Mar (CCMAR/CIMAR)Universidade do AlgarveFaroPortugal
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4
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A deep dive into the epibiotic communities on aquacultured sugar kelp Saccharina latissima in Southern New England. ALGAL RES 2022. [DOI: 10.1016/j.algal.2022.102654] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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5
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Heins A, Reintjes G, Amann RI, Harder J. Particle Collection in Imhoff Sedimentation Cones Enriches Both Motile Chemotactic and Particle-Attached Bacteria. Front Microbiol 2021; 12:643730. [PMID: 33868201 PMCID: PMC8047139 DOI: 10.3389/fmicb.2021.643730] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 03/01/2021] [Indexed: 11/13/2022] Open
Abstract
Marine heterotrophic microorganisms remineralize about half of the annual primary production, with the microbiomes on and around algae and particles having a major contribution. These microbiomes specifically include free-living chemotactic and particle-attached bacteria, which are often difficult to analyze individually, as the standard method of size-selective filtration only gives access to particle-attached bacteria. In this study, we demonstrated that particle collection in Imhoff sedimentation cones enriches microbiomes that included free-living chemotactic bacteria and were distinct from particle microbiomes obtained by filtration or centrifugation. Coastal seawater was collected during North Sea phytoplankton spring blooms, and the microbiomes were investigated using 16S rRNA amplicon sequencing and fluorescence microscopy. Enrichment factors of individual operational taxonomic units (OTUs) were calculated for comparison of fractionated communities after separation with unfractionated seawater communities. Filtration resulted in a loss of cells and yielded particle fractions including bacterial aggregates, filaments, and large cells. Centrifugation had the lowest separation capacity. Particles with a sinking rate of >2.4 m day-1 were collected in sedimentation cones as a bottom fraction and enriched in free-living chemotactic bacteria, i.e., Sulfitobacter, Pseudoalteromonas, and Vibrio. Subfractions of these bottom fractions, obtained by centrifugation, showed enrichment of either free-living or particle-attached bacteria. We identified five distinct enrichment patterns across all separation techniques: mechano-sensitive and mechano-stable free-living bacteria and three groups of particle-attached bacteria. Simultaneous enrichment of particle-attached and chemotactic free-living bacteria in Imhoff sedimentation cones is a novel experimental access to these groups providing more insights into the diversity, structure, and function of particle-associated microbiomes, including members of the phycosphere.
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Affiliation(s)
- Anneke Heins
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Greta Reintjes
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany.,Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Rudolf I Amann
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Jens Harder
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
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6
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Alcamán-Arias ME, Fuentes-Alburquenque S, Vergara-Barros P, Cifuentes-Anticevic J, Verdugo J, Polz M, Farías L, Pedrós-Alió C, Díez B. Coastal Bacterial Community Response to Glacier Melting in the Western Antarctic Peninsula. Microorganisms 2021; 9:microorganisms9010088. [PMID: 33401391 PMCID: PMC7823458 DOI: 10.3390/microorganisms9010088] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 12/20/2020] [Accepted: 12/21/2020] [Indexed: 01/04/2023] Open
Abstract
Current warming in the Western Antarctic Peninsula (WAP) has multiple effects on the marine ecosystem, modifying the trophic web and the nutrient regime. In this study, the effect of decreased surface salinity on the marine microbial community as a consequence of freshening from nearby glaciers was investigated in Chile Bay, Greenwich Island, WAP. In the summer of 2016, samples were collected from glacier ice and transects along the bay for 16S rRNA gene sequencing, while in situ dilution experiments were conducted and analyzed using 16S rRNA gene sequencing and metatranscriptomic analysis. The results reveal that certain common seawater genera, such as Polaribacter, Pseudoalteromonas and HTCC2207, responded positively to decreased salinity in both the bay transect and experiments. The relative abundance of these bacteria slightly decreased, but their functional activity was maintained and increased the over time in the dilution experiments. However, while ice bacteria, such as Flavobacterium and Polaromonas, tolerated the increased salinity after mixing with seawater, their gene expression decreased considerably. We suggest that these bacterial taxa could be defined as sentinels of freshening events in the Antarctic coastal system. Furthermore, these results suggest that a significant portion of the microbial community is resilient and can adapt to disturbances, such as freshening due to the warming effect of climate change in Antarctica.
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Affiliation(s)
- María Estrella Alcamán-Arias
- Department of Oceanography, Universidad de Concepcion, Concepcion 4030000, Chile; (M.E.A.-A.); (L.F.)
- Center for Climate and Resilience Research (CR)2, Santiago 8320000, Chile
- Escuela de Medicina, Universidad Espíritu Santo, Guayaquil 0901952, Ecuador
| | - Sebastián Fuentes-Alburquenque
- Centro de Investigación en Recursos Naturales y Sustentabilidad, Universidad Bernardo O’Higgins, Santiago 8370993, Chile;
- Facultad de Ingeniería, Ciencia y Tecnología, Universidad Bernardo O’Higgins, Santiago 8370993, Chile
| | - Pablo Vergara-Barros
- Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile; (P.V.-B.); (J.C.-A.)
| | - Jerónimo Cifuentes-Anticevic
- Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile; (P.V.-B.); (J.C.-A.)
| | - Josefa Verdugo
- Alfred-Wegener-Institute, Helmholtz-Centre for Polar and Marine Research, 27570 Bremerhaven, Germany;
| | - Martin Polz
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA;
| | - Laura Farías
- Department of Oceanography, Universidad de Concepcion, Concepcion 4030000, Chile; (M.E.A.-A.); (L.F.)
- Center for Climate and Resilience Research (CR)2, Santiago 8320000, Chile
| | - Carlos Pedrós-Alió
- Departamento de Biología de Sistemas, Centro Nacional de Biotecnología (CSIC), Darwin 3, 28049 Madrid, Spain;
| | - Beatriz Díez
- Center for Climate and Resilience Research (CR)2, Santiago 8320000, Chile
- Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile; (P.V.-B.); (J.C.-A.)
- Correspondence:
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7
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Choo S, Borchert E, Wiese J, Saha M, Künzel S, Weinberger F, Hentschel U. Polaribacter septentrionalilitoris sp. nov., isolated from the biofilm of a stone from the North Sea. Int J Syst Evol Microbiol 2020; 70:4305-4314. [PMID: 32579104 DOI: 10.1099/ijsem.0.004290] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A new member of the family Flavobacteriaceae was isolated from the biofilm of a stone at Nordstrand, a peninsula at the German North Sea shore. Phylogenetic analysis of the 16S rRNA gene sequence showed that strain ANORD1T was most closely related to the validly described type strains Polaribacter porphyrae LNM-20T (97.0 %) and Polaribacter reichenbachii KMM 6386T (96.9 % 16S rRNA gene sequence similarity) and clustered with Polaribacter gangjinensis K17-16T (96.0 %). Strain ANORD1T was determined to be mesophilic, Gram-negative, non-motile and strictly aerobic. Optimal growth was observed at 20-30 °C, within a salinity range of 2-7 % sea salt and from pH 7-10. Like other type strains of the genus Polaribacter, ANORD1T was tested negative for flexirubin-type pigments, while carotenoid-type pigments were detected. The DNA G+C content of strain ANORD1T was 30.6 mol%. The sole respiratory quinone detected was menaquinone 6 (MK-6). The major fatty acids identified were C15 : 0, iso-C15 : 0, C15 : 1 ω6c and iso-C15 : 0 3-OH. Based on the polyphasic approach, strain ANORD1T represents a novel species in the genus Polaribacter, with the name Polaribacter septentrionalilitoris sp. nov. being proposed. The type strain is ANORD1T (=DSM 110039T=NCIMB 15081T=MTCC 12685T).
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Affiliation(s)
- Simeon Choo
- GEOMAR Helmholtz Centre for Ocean Research Kiel, RD3 Marine Symbioses, Düsternbrooker Weg 20, 24105 Kiel, Germany
| | - Erik Borchert
- GEOMAR Helmholtz Centre for Ocean Research Kiel, RD3 Marine Symbioses, Düsternbrooker Weg 20, 24105 Kiel, Germany
| | - Jutta Wiese
- GEOMAR Helmholtz Centre for Ocean Research Kiel, RD3 Marine Symbioses, Düsternbrooker Weg 20, 24105 Kiel, Germany
| | - Mahasweta Saha
- Present address: Marine Ecology and Biodiversity, Plymouth Marine Laboratory, Prospect Place, PL1 3DH, Plymouth, UK.,GEOMAR Helmholtz Centre for Ocean Research Kiel, RD3 Benthic Ecology, Hohenbergstraße 2, 24105 Kiel, Germany
| | - Sven Künzel
- Max Planck Institute for Evolutionary Biology, 24306 Plön, Germany
| | - Florian Weinberger
- GEOMAR Helmholtz Centre for Ocean Research Kiel, RD3 Benthic Ecology, Hohenbergstraße 2, 24105 Kiel, Germany
| | - Ute Hentschel
- Christian-Albrechts-University (CAU) of Kiel, Kiel, Germany.,GEOMAR Helmholtz Centre for Ocean Research Kiel, RD3 Marine Symbioses, Düsternbrooker Weg 20, 24105 Kiel, Germany
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8
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García-López M, Meier-Kolthoff JP, Tindall BJ, Gronow S, Woyke T, Kyrpides NC, Hahnke RL, Göker M. Analysis of 1,000 Type-Strain Genomes Improves Taxonomic Classification of Bacteroidetes. Front Microbiol 2019; 10:2083. [PMID: 31608019 PMCID: PMC6767994 DOI: 10.3389/fmicb.2019.02083] [Citation(s) in RCA: 190] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 08/23/2019] [Indexed: 11/25/2022] Open
Abstract
Although considerable progress has been made in recent years regarding the classification of bacteria assigned to the phylum Bacteroidetes, there remains a need to further clarify taxonomic relationships within a diverse assemblage that includes organisms of clinical, piscicultural, and ecological importance. Bacteroidetes classification has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees and a limited number of phenotypic features. Here, draft genome sequences of a greatly enlarged collection of genomes of more than 1,000 Bacteroidetes and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa proposed long ago such as Bacteroides, Cytophaga, and Flavobacterium but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which can be considered valuable taxonomic markers. We detected many incongruities when comparing the results of the present study with existing classifications, which appear to be caused by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. The few significant incongruities found between 16S rRNA gene and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences and the impediment in using ordinary bootstrapping in phylogenomic studies, particularly when combined with too narrow gene selections. While a significant degree of phylogenetic conservation was detected in all phenotypic characters investigated, the overall fit to the tree varied considerably, which is one of the probable causes of misclassifications in the past, much like the use of plesiomorphic character states as diagnostic features.
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Affiliation(s)
- Marina García-López
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Jan P. Meier-Kolthoff
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Brian J. Tindall
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Sabine Gronow
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Tanja Woyke
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, United States
| | - Nikos C. Kyrpides
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, United States
| | - Richard L. Hahnke
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Markus Göker
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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9
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Park S, Park JM, Lee JS, Yoon JH. Description of Polaribacter aestuariivivens sp. nov., isolated from a tidal flat. FEMS Microbiol Lett 2019; 366:5567180. [PMID: 31504481 DOI: 10.1093/femsle/fnz185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 09/06/2019] [Indexed: 11/12/2022] Open
Abstract
A bacterial strain, DBTF-3T, was isolated from a tidal flat of Republic of Korea. Phylogenetic trees of 16S rRNA gene sequences showed that strain DBTF-3T belonged to the genus Polaribacter. Strain DBTF-3T exhibited 16S rRNA gene sequence similarities of 97.1-98.1% to type strains of P. dokdonensis, P. haliotis, P. marinaquae, P. insulae, P. vadi, P. glomeratus, P. irgensii and P. reichenbachii, and 94.0-96.9% to those of the other Polaribacter species. DNA-DNA relatedness values of strain DBTF-3T with type strains of P. marinaquae and P. insulae were 14-19%. Average nucleotide identity and digital DNA-DNA hybridization values between strain DBTF-3T and type strains of six other Polaribacter species were 76.5-83.5% and 20.9-27.1%, respectively. Strain DBTF-3T contained MK-6 as the predominant menaquinone, and iso-C15:0, summed feature 3, iso-C15:1 G and iso-C15:0 3-OH as the major fatty acids. The major polar lipids were phosphatidylethanolamine and one unidentified lipid. Differential phenotypic properties, together with its phylogenetic and genetic distinctiveness, revealed that strain DBTF-3T is separated from Polaribacter species. On the basis of the data presented, strain DBTF-3T (= KACC 19612T = NBRC 113191T) represents a novel species of the genus Polaribacter, for which the name Polaribacter aestuariivivens sp. nov. is proposed.
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Affiliation(s)
- Sooyeon Park
- Department of Food Science and Biotechnology, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon 16419, Republic of Korea
| | - Ji-Min Park
- Department of Food Science and Biotechnology, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon 16419, Republic of Korea
| | - Jung-Sook Lee
- Korean Collection for Type Cultures (KCTC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), 181 Ipsin-gil, Jeongeup-si 56212, Republic of Korea
| | - Jung-Hoon Yoon
- Department of Food Science and Biotechnology, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon 16419, Republic of Korea
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10
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Zhang Z, Hu Z, Tang L, Wang Z, Zhang Y. Ulvibacterium marinum gen. nov., sp. nov., a novel marine bacterium of the family Flavobacteriaceae, isolated from a culture of the green alga Ulva prolifera. Antonie van Leeuwenhoek 2019; 112:1077-1085. [PMID: 30729398 DOI: 10.1007/s10482-019-01239-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 01/22/2019] [Indexed: 11/30/2022]
Abstract
A Gram-stain negative, aerobic, rod-shaped, and non-motile bacterium, designated strain CCMM003T, was isolated from a culture of the green alga Ulva prolifera. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain CCMM003T belongs to the family Flavobacteriaceae and exhibits a close relationship to Pseudozobellia thermophila DSM 19858T (92.5%). Optimal growth occurred in the presence of 4% (w/v) NaCl, at pH 7.0 and 30 °C. The polar lipids of strain CCMM003T consisted of phosphatidylethanolamine and six unidentified lipids. The predominant isoprenoid quinone was MK-6. The major fatty acids were iso-C15:0, iso-C15:1 G, iso-C17:0 3-OH and summed feature 3 (C16:1ω7c and/or iso-C15:0 2-OH). The DNA G + C content of strain CCMM003T calculated on the basis of the genome sequence was 41.2 mol% and the genome size was 5.9 Mbp. On the basis of data from this polyphasic study, strain CCMM003T is considered to represent a novel genus and species of the family Flavobacteriaceae, for which the name Ulvibacterium marinum gen. nov., sp. nov. is proposed. The type strain is CCMM003T (= MCCC 1K03244T =KCTC 52639T).
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Affiliation(s)
- Zenghu Zhang
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, People's Republic of China
| | - Zhenzhen Hu
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, People's Republic of China.,Institute of Marine Science and Technology, Shandong University, Qingdao, 266273, People's Republic of China
| | - Lili Tang
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Zengmeng Wang
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Yongyu Zhang
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, People's Republic of China.
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11
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Nedashkovskaya OI, Kim SG, Balabanova LA, Zhukova NV, Bakunina IY, Mikhailov VV. Polaribacter staleyi sp. nov., a polysaccharide-degrading marine bacterium isolated from the red alga Ahnfeltia tobuchiensis. Int J Syst Evol Microbiol 2018; 68:623-629. [DOI: 10.1099/ijsem.0.002554] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Olga I. Nedashkovskaya
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry of the Far-Eastern Branch of the Russian Academy of Sciences, Pr. 100 Let Vladivostoku 159, 690022, Vladivostok, Russia
| | - Song-Gun Kim
- Korean Collection for Type Cultures, Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, 181 Ipsin-gil, Jeongeup, Jeollabuk-do 56212, Republic of Korea
| | - Larissa A. Balabanova
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry of the Far-Eastern Branch of the Russian Academy of Sciences, Pr. 100 Let Vladivostoku 159, 690022, Vladivostok, Russia
- Far Eastern Federal University, Sukhanova St. 8, 690950, Vladivostok, Russia
| | - Natalia V. Zhukova
- Far Eastern Federal University, Sukhanova St. 8, 690950, Vladivostok, Russia
- National Scientific Center of Marine Biology, Russian Academy of Science, Palchevskogo 17, Vladivostok 690041, Russia
| | - Irina Y. Bakunina
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry of the Far-Eastern Branch of the Russian Academy of Sciences, Pr. 100 Let Vladivostoku 159, 690022, Vladivostok, Russia
| | - Valery V. Mikhailov
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry of the Far-Eastern Branch of the Russian Academy of Sciences, Pr. 100 Let Vladivostoku 159, 690022, Vladivostok, Russia
- Far Eastern Federal University, Sukhanova St. 8, 690950, Vladivostok, Russia
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12
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Han JR, Wang K, Zhang J, Chen GJ, Du ZJ. Polaribacter tangerinus sp. nov., isolated from sediment in a sea cucumber culture pond. Int J Syst Evol Microbiol 2017; 67:4736-4741. [DOI: 10.1099/ijsem.0.002369] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Ji-Ru Han
- State key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China
- College of Marine Science, Shandong University, Weihai 264209, PR China
| | - Kan Wang
- State key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China
- College of Marine Science, Shandong University, Weihai 264209, PR China
| | - Jing Zhang
- State key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China
- College of Marine Science, Shandong University, Weihai 264209, PR China
| | - Guan-Jun Chen
- State key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China
- College of Marine Science, Shandong University, Weihai 264209, PR China
| | - Zong-Jun Du
- State key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China
- College of Marine Science, Shandong University, Weihai 264209, PR China
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13
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Park S, Yoon SY, Park JM, Yoon JH. Polaribacter insulae sp. nov., isolated from a tidal flat. Int J Syst Evol Microbiol 2017; 67:4013-4019. [PMID: 28893356 DOI: 10.1099/ijsem.0.002236] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [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, non-motile and ovoid or rod-shaped bacterial strain, designated OITF-22T, was isolated from a tidal flat of Oido, an island of South Korea, and subjected to a polyphasic taxonomic study. Strain OITF-22T grew optimally at 25 °C, at pH 7.0-8.0 and in the presence of 2.0-3.0 % (w/v) NaCl. The phylogenetic trees based on 16S rRNA gene sequences showed that strain OITF-22T fell within the clade comprising the type strains of Polaribacter species. Strain OITF-22T exhibited 16S rRNA gene sequence similarity values of 97.2-99.4 % to the type strains of Polaribacter vadi, P. haliotis, P. atrinae, P. dokdonensis, P. litorisediminis,P. reichenbachii, P. irgensii and P. marinaquae, and of 93.0-96.9 % to the type strains of the other Polaribacter species. Strain OITF-22T contained MK-6 as the predominant menaquinone and iso-C15 : 0 and iso-C15 : 0 3-OH as the major fatty acids. The major polar lipids detected in strain OITF-22T were phosphatidylethanolamine and one unidentified lipid. The DNA G+C content of strain OITF-22T was 32.3 mol% and its DNA-DNA relatedness values with the type strains of the eight phylogenetically most closely related Polaribacter species were 9-32 %. Differential phenotypic properties, together with phylogenetic and genetic distinctiveness, revealed that strain OITF-22T is separated from recognized species of the genus Polaribacter. On the basis of the data presented, strain OITF-22T is considered to represent a novel species of the genus Polaribacter, for which the name Polaribacter insulae sp. nov. is proposed. The type strain is OITF-22T (=KCTC 52658T=NBRC 112706T).
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Affiliation(s)
- Sooyeon Park
- Department of Food Science and Biotechnology, Sungkyunkwan University, Jangan-gu, Suwon, Republic of Korea
| | - Sun Young Yoon
- Department of Food Science and Biotechnology, Sungkyunkwan University, Jangan-gu, Suwon, Republic of Korea
| | - Ji-Min Park
- Department of Food Science and Biotechnology, Sungkyunkwan University, Jangan-gu, Suwon, Republic of Korea
| | - Jung-Hoon Yoon
- Department of Food Science and Biotechnology, Sungkyunkwan University, Jangan-gu, Suwon, Republic of Korea
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14
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Wu Y, Yu M, Zhang Z, Wang Y, Yang X, Wang X, Ren Q, Sun Z, Shi X, Zhang XH. Polaribacter pacificus sp. nov., isolated from a deep-sea polymetallic nodule from the Eastern Pacific Ocean. Int J Syst Evol Microbiol 2017; 67:3203-3208. [PMID: 28829019 DOI: 10.1099/ijsem.0.002082] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-staining-negative, yellow-colony-forming, rod-shaped, non-flagellated and facultatively aerobic strain, designed HRA130-1T, was isolated from a deep-sea polymetallic nodule from the Pacific Clarion-Clipperton Fracture Zone (CCFZ). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain HRA130-1T belonged to the genus Polaribacter (96.3-93.2 % 16S rRNA gene sequence similarity), and exhibited 94 % 16S rRNA gene sequence similarity to Polaribacter filamentus KCTC 23135T (type species) and the highest sequence similarity to Polaribacter huanghezhanensis KCTC 32516T (96.3 %). Optimal growth occurred in the presence of 4 % (w/v) NaCl, at pH 7.0 and 16 °C. The DNA G+C content of strain HRA130-1T was 35.9 mol%. The major fatty acid was iso-C15 : 0. The predominant respiratory quinone was menaquinone-6 (MK-6). The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, one unidentified phospholipid and an unidentified aminolipid. On the basis of data from the present taxonomic study using a polyphasic approach, strain HRA130-1T represents a novel species of the genus Polaribacter, for which the name Polaribacter pacificus sp. nov. is proposed. The type strain is HRA130-1T (=KCTC 52370T=MCCC 1K03199T=JCM 31460T=CGMCC 1.15763T).
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Affiliation(s)
- Yanhong Wu
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Min Yu
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Zenghu Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Yanan Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Xiaoting Yang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Xiaolei Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Qiaomeng Ren
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Zhongcheng Sun
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Xiaochong Shi
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Xiao-Hua Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China.,Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, PR China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, PR China
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15
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Park S, Yoon SY, Ha MJ, Yoon JH. Polaribacter litorisediminis sp. nov., isolated from a tidal flat. Int J Syst Evol Microbiol 2017; 67:2036-2042. [PMID: 28665265 DOI: 10.1099/ijsem.0.001919] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, aerobic, non-motile and ovoid or rod-shaped bacterial strain, designated OITF-11T, was isolated from a tidal flat in Oido, an island of South Korea, and subjected to a polyphasic taxonomic study. Strain OITF-11T grew optimally at 25 °C, at pH 7.0-8.0 and in the presence of 2.0 % (w/v) NaCl. The phylogenetic trees based on 16S rRNA gene sequences showed that strain OITF-11T belonged to the genus Polaribacter. Strain OITF-11T exhibited 16S rRNA gene sequence similarity values of 97.4-98.1 % to Polaribacter haliotis RA4-7T, Polaribacter atrinae KACC 17473T, Polaribacter dokdonensis DSW-5T and Polaribacter marinaquae KCTC 42664T, and of 94.1-96.9 % to the type strains of the other Polaribacter species. Strain OITF-11T contained menaquinone MK-6 as the predominant menaquinone and iso-C15 : 0, iso-C15 : 1 G, iso-C15 : 0 3-OH, iso-C17 : 0 3-OH and C15 : 1ω6c as the major fatty acids. The major polar lipids detected in strain OITF-11T were phosphatidylethanolamine, phosphatidylmonomethylethanolamine and one unidentified lipid. The DNA G+C content of strain OITF-11T was 32.2 mol% and its DNA-DNA relatedness values with the type strains of P. haliotis, P. atrinae, P. dokdonensis and P. marinaquae were 14-33 %. Differential phenotypic properties, together with its phylogenetic and genetic distinctiveness, revealed that strain OITF-11T is separated from recognized species of the genus Polaribacter. On the basis of the data presented, strain OITF-11T is considered to represent a novel species of the genus Polaribacter, for which the name Polaribacter litorisediminis sp. nov. is proposed. The type strain is OITF-11T (=KCTC 52500T=NBRC 112457T).
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Affiliation(s)
- Sooyeon Park
- Department of Food Science and Biotechnology, Sungkyunkwan University, Jangan-gu, Suwon, Republic of Korea
| | - Sun Young Yoon
- Department of Food Science and Biotechnology, Sungkyunkwan University, Jangan-gu, Suwon, Republic of Korea
| | - Min-Ji Ha
- Department of Food Science and Biotechnology, Sungkyunkwan University, Jangan-gu, Suwon, Republic of Korea
| | - Jung-Hoon Yoon
- Department of Food Science and Biotechnology, Sungkyunkwan University, Jangan-gu, Suwon, Republic of Korea
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16
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Kim E, Shin SK, Choi S, Yi H. Polaribacter vadi sp. nov., isolated from a marine gastropod. Int J Syst Evol Microbiol 2017; 67:144-147. [DOI: 10.1099/ijsem.0.001591] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Affiliation(s)
- Eunji Kim
- Department of Public Health Sciences, Graduate School, Korea University, Seoul, Republic of Korea
| | - Su-kyoung Shin
- Department of Public Health Sciences, Graduate School, Korea University, Seoul, Republic of Korea
| | - Sungmi Choi
- Department of Public Health Sciences, Graduate School, Korea University, Seoul, Republic of Korea
| | - Hana Yi
- School of Biosystem and Biomedical Science, Korea University, Seoul, Republic of Korea
- Department of Public Health Sciences, Graduate School, Korea University, Seoul, Republic of Korea
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17
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Kim YO, Park IS, Park S, Nam BH, Park JM, Kim DG, Yoon JH. Polaribacter haliotis sp. nov., isolated from the gut of abalone Haliotis discus hannai. Int J Syst Evol Microbiol 2016; 66:5562-5567. [DOI: 10.1099/ijsem.0.001557] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Young-Ok Kim
- Biotechnology Research Division, National Institute of Fisheries Science (NIFS), Gijang, Busan 619-705, Republic of Korea
| | - In-Suk Park
- Biotechnology Research Division, National Institute of Fisheries Science (NIFS), Gijang, Busan 619-705, Republic of Korea
| | - Sooyeon Park
- Department of Food Science and Biotechnology, Sungkyunkwan University, Jangan-gu, Suwon, Republic of Korea
| | - Bo-Hye Nam
- Biotechnology Research Division, National Institute of Fisheries Science (NIFS), Gijang, Busan 619-705, Republic of Korea
| | - Ji-Min Park
- Department of Food Science and Biotechnology, Sungkyunkwan University, Jangan-gu, Suwon, Republic of Korea
| | - Dong-Gyun Kim
- Biotechnology Research Division, National Institute of Fisheries Science (NIFS), Gijang, Busan 619-705, Republic of Korea
| | - Jung-Hoon Yoon
- Department of Food Science and Biotechnology, Sungkyunkwan University, Jangan-gu, Suwon, Republic of Korea
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18
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Wang Y, Gao L, Ming H, Zhang P, Zhu W. Polaribacter marinaquae sp. nov., isolated from seawater. Int J Syst Evol Microbiol 2016; 66:4594-4599. [DOI: 10.1099/ijsem.0.001396] [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)
- Yan Wang
- Synthetic Biology Remaking Engineering and Applications Laboratory, School of Life Sciences and Technology, Xinxiang Medical University, 601 Jinsui Avenue, Xinxiang 453003, PR China
| | - Liyun Gao
- Department of Toxicology, School of Public Health, Xinxiang Medical University, 601 Jinsui Avenue, Xinxiang 453003, PR China
| | - Hong Ming
- Synthetic Biology Remaking Engineering and Applications Laboratory, School of Life Sciences and Technology, Xinxiang Medical University, 601 Jinsui Avenue, Xinxiang 453003, PR China
| | - Peng Zhang
- Synthetic Biology Remaking Engineering and Applications Laboratory, School of Life Sciences and Technology, Xinxiang Medical University, 601 Jinsui Avenue, Xinxiang 453003, PR China
| | - Wuling Zhu
- Synthetic Biology Remaking Engineering and Applications Laboratory, School of Life Sciences and Technology, Xinxiang Medical University, 601 Jinsui Avenue, Xinxiang 453003, PR China
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19
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Spongiiferula fulva gen. nov., sp. nov., a Bacterium of the Family Flavobacteriaceae Isolated from a Marine Sponge. Curr Microbiol 2016; 73:15-21. [PMID: 26960291 DOI: 10.1007/s00284-016-1022-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 02/05/2016] [Indexed: 10/22/2022]
Abstract
A Gram stain-negative, strictly aerobic, brown-pigmented, non-motile, rod-shaped, chemoheterotrophic bacterial strain-designated A6F-119(T) was isolated from a marine sponge (Rhabdastrella sp.). Phylogenetic analyses based on the 16S rRNA gene sequence revealed that the new strain represented a member of the family Flavobacteriaceae of the phylum Bacteroidetes and that it showed highest sequence similarity (93 %) to Tenacibaculum maritimum NBRC 15946(T). The strain could be differentiated phenotypically from the recognized members of the family Flavobacteriaceae. The DNA G + C content of strain A6F-119(T) was determined to be 30.8 mol%; MK-6 was identified as the major menaquinone; and the presence of iso-C15:0, iso-C17:0 3-OH, and C16:1 ω7c and/or C16:1 ω6c as the major (>10 %) cellular fatty acids. A polar lipid profile was present consisting of phosphatidylethanolamine, an unidentified aminolipid, and three unidentified lipids. From the distinct phylogenetic position and combination of genotypic and phenotypic characteristics, the strain is considered to represent a novel genus for which the name Spongiiferula fulva gen. nov., sp. nov. is proposed. The type strain of S. fulva is A6F-119(T) (= KCTC 42752(T) = NBRC 111402(T)).
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20
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Sun ML, Zhao F, Shi M, Zhang XY, Zhou BC, Zhang YZ, Chen XL. Characterization and Biotechnological Potential Analysis of a New Exopolysaccharide from the Arctic Marine Bacterium Polaribacter sp. SM1127. Sci Rep 2015; 5:18435. [PMID: 26688201 PMCID: PMC4685270 DOI: 10.1038/srep18435] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 11/18/2015] [Indexed: 11/21/2022] Open
Abstract
Although many kinds of exopolysaccharides (EPSs) from microorganisms have been used in industry, the exploration and utilization of EPSs from polar microorganisms is still rather rare. In this study, a flavobacterial strain, SM1127, from the Arctic brown alga Laminaria, was screened for its high EPS production (2.11 g/l) and was identified as belonging to the genus Polaribacter. The EPS secreted by strain SM1127 has a molecular mass of 220 kDa, and it mainly comprises N-acetyl glucosamine, mannose and glucuronic acid residues bound by heterogeneous linkages. Rheological studies on the aqueous EPS showed that it had a high viscosity and good shear-thinning property. Moreover, the EPS showed a high tolerance to high salinity and a wide pH range. The EPS also had good antioxidant activity. Particularly, its moisture-retention ability was superior to that of any other reported EPS or functional ingredient generally used in cosmetics. The EPS also showed a protective effect on human dermal fibroblasts at low temperature (4 °C). Safety assessment indicated that the EPS is safe for oral administration and external use. These results indicate the promising potential of the EPS from strain SM1127 in the food, cosmetic, pharmaceutical and biomedical fields.
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Affiliation(s)
- Mei-Ling Sun
- State Key Laboratory of Microbial Technology, Jinan 250100, China
- Marine Biotechnology Research Center, Shandong University, Jinan 250100, China
| | - Fang Zhao
- State Key Laboratory of Microbial Technology, Jinan 250100, China
- Marine Biotechnology Research Center, Shandong University, Jinan 250100, China
| | - Mei Shi
- State Key Laboratory of Microbial Technology, Jinan 250100, China
- Marine Biotechnology Research Center, Shandong University, Jinan 250100, China
| | - Xi-Ying Zhang
- State Key Laboratory of Microbial Technology, Jinan 250100, China
- Marine Biotechnology Research Center, Shandong University, Jinan 250100, China
| | - Bai-Cheng Zhou
- Marine Biotechnology Research Center, Shandong University, Jinan 250100, China
| | - Yu-Zhong Zhang
- State Key Laboratory of Microbial Technology, Jinan 250100, China
- Marine Biotechnology Research Center, Shandong University, Jinan 250100, China
| | - Xiu-Lan Chen
- State Key Laboratory of Microbial Technology, Jinan 250100, China
- Marine Biotechnology Research Center, Shandong University, Jinan 250100, China
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21
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Park S, Park JM, Jung YT, Lee KH, Yoon JH. Polaribacter undariae sp. nov., isolated from a brown alga reservoir. Int J Syst Evol Microbiol 2015; 65:1679-1685. [PMID: 25724747 DOI: 10.1099/ijs.0.000157] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, non-flagellated, non-gliding, aerobic and rod-shaped or ovoid bacterial strain, designated W-BA7(T), was isolated from a brown alga reservoir on the South Sea in South Korea. This strain grew optimally at 25 °C, at pH 7.0-8.0 and in the presence of approximately 2.0% (w/v) NaCl. A neighbour-joining phylogenetic tree based on 16S rRNA gene sequences showed that strain W-BA7(T) belonged to the genus Polaribacter, clustering coherently with the type strain of Polaribacter sejongensis, showing 99.3% sequence similarity. Strain W-BA7(T) exhibited 16S rRNA gene sequence similarity of 93.4-98.6% to the type strains of the other species of the genus Polaribacter. Strain W-BA7(T) contained MK-6 as the predominant menaquinone and iso-C15 : 0 3-OH and anteiso-C15 : 0 as the major fatty acids. The major polar lipids of strain W-BA7(T) were phosphatidylethanolamine, three unidentified lipids, one unidentified glycolipid, one unidentified aminolipid and one unidentified aminophospholipid. The DNA G+C content of strain W-BA7(T) was 31.9 mol%, and the mean DNA-DNA relatedness with the type strains of four phylogenetically related species of the genus Polaribacter was 12-27%. Differential phenotypic properties, together with its phylogenetic and genetic distinctiveness, revealed that strain W-BA7(T) is separated from recognized species of the genus Polaribacter. On the basis of the data presented, strain W-BA7(T) is considered to represent a novel species of the genus Polaribacter, for which the name Polaribacter undariae sp. nov. is proposed. The type strain is W-BA7(T) ( =KCTC 42175(T) =CECT 8670(T)).
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Affiliation(s)
- Sooyeon Park
- Department of Food Science and Biotechnology, Sungkyunkwan University, Jangan-gu, Suwon, South Korea
| | - Ji-Min Park
- Department of Food Science and Biotechnology, Sungkyunkwan University, Jangan-gu, Suwon, South Korea
| | - Yong-Taek Jung
- University of Science and Technology (UST), 113 Gwahangno, Yuseong, Daejeon, South Korea
- Department of Food Science and Biotechnology, Sungkyunkwan University, Jangan-gu, Suwon, South Korea
| | - Kang Hyun Lee
- Microbiological Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yuseong, Daejeon, South Korea
| | - Jung-Hoon Yoon
- Department of Food Science and Biotechnology, Sungkyunkwan University, Jangan-gu, Suwon, South Korea
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22
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Niches of two polysaccharide-degrading Polaribacter isolates from the North Sea during a spring diatom bloom. ISME JOURNAL 2014; 9:1410-22. [PMID: 25478683 DOI: 10.1038/ismej.2014.225] [Citation(s) in RCA: 123] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Revised: 10/06/2014] [Accepted: 10/23/2014] [Indexed: 11/08/2022]
Abstract
Members of the flavobacterial genus Polaribacter thrive in response to North Sea spring phytoplankton blooms. We analyzed two respective Polaribacter species by whole genome sequencing, comparative genomics, substrate tests and proteomics. Both can degrade algal polysaccharides but occupy distinct niches. The liquid culture isolate Polaribacter sp. strain Hel1_33_49 has a 3.0-Mbp genome with an overall peptidase:CAZyme ratio of 1.37, four putative polysaccharide utilization loci (PULs) and features proteorhodopsin, whereas the agar plate isolate Polaribacter sp. strain Hel1_85 has a 3.9-Mbp genome with an even peptidase:CAZyme ratio, eight PULs, a mannitol dehydrogenase for decomposing algal mannitol-capped polysaccharides but no proteorhodopsin. Unlike other sequenced Polaribacter species, both isolates have larger sulfatase-rich PULs, supporting earlier assumptions that Polaribacter take part in the decomposition of sulfated polysaccharides. Both strains grow on algal laminarin and the sulfated polysaccharide chondroitin sulfate. For strain Hel1_33_49, we identified by proteomics (i) a laminarin-induced PUL, (ii) chondroitin sulfate-induced CAZymes and (iii) a chondroitin-induced operon that likely enables chondroitin sulfate recognition. These and other data suggest that strain Hel1_33_49 is a planktonic flavobacterium feeding on proteins and a small subset of algal polysaccharides, while the more versatile strain Hel1_85 can decompose a broader spectrum of polysaccharides and likely associates with algae.
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Park S, Park JM, Jung YT, Lee KC, Lee JS, Yoon JH. Polaribacter marinivivus sp. nov., a member of the family Flavobacteriaceae isolated from seawater. Antonie van Leeuwenhoek 2014; 106:1139-46. [DOI: 10.1007/s10482-014-0283-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2014] [Accepted: 09/10/2014] [Indexed: 10/24/2022]
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Hyun DW, Shin NR, Kim MS, Kim PS, Jung MJ, Kim JY, Whon TW, Bae JW. Polaribacter atrinae sp. nov., isolated from the intestine of a comb pen shell, Atrina pectinata. Int J Syst Evol Microbiol 2014; 64:1654-1661. [DOI: 10.1099/ijs.0.060889-0] [Citation(s) in RCA: 25] [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 novel Gram-staining-negative, aerobic, non-motile, yellow-to-orange carotenoid-type-pigmented and rod-shaped bacterium, designated strain WP25T, was isolated from the intestine of a comb pen shell, Atrina pectinata, which was collected from the South Sea near Yeosu in Korea. The isolate grew optimally at 20 °C, at pH 7 and with 2 % (w/v) NaCl. 16S rRNA gene sequence analysis showed that strain WP25T belonged to the genus
Polaribacter
in the family
Flavobacteriaceae
and the highest sequence similarity was shared with the type strain of
Polaribacter sejongensis
(98.5 %). The major cellular fatty acids were iso-C15 : 0, anteiso-C15 : 0, C15 : 1ω6c and iso-C15 : 0 3-OH. The main respiratory quinone was menaquinone MK-6. The polar lipids of strain WP25T were phosphatidylethanolamine, two unidentified aminolipids, an unidentified phospholipid and four unidentified lipids. The genomic DNA G+C content was 31.2 mol%. DNA–DNA hybridization experiments indicated <12.6 % genomic relatedness with closely related strains. Based on phylogenetic, phenotypic and genotypic analyses, strain WP25T represents a novel species in the genus
Polaribacter
, for which the name
Polaribacter
atrinae sp. nov. is proposed, with the type strain WP25T ( = KACC 17473T = JCM 19202T).
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Affiliation(s)
- Dong-Wook Hyun
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Na-Ri Shin
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Min-Soo Kim
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Pil Soo Kim
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Mi-Ja Jung
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Joon Yong Kim
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Tae Woong Whon
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Jin-Woo Bae
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
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25
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Liu Y, Liu LZ, Liu HC, Zhou YG, Qi FJ, Liu ZP. Wenyingzhuangia marina gen. nov., sp. nov., a member of the family Flavobacteriaceae isolated from a recirculating mariculture system. Int J Syst Evol Microbiol 2014; 64:469-474. [DOI: 10.1099/ijs.0.055012-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, strictly aerobic and heterotrophic bacterial strain, designed strain D1T, was isolated from a recirculating mariculture system in Tianjin, China. Its taxonomic position was determined using a polyphasic approach. Cells of strain D1T were non-flagellated short rods, 0.3–0.5 µm wide and 0.5–1.0 µm long. Growth was observed at 15–30 °C (optimum, 25 °C), at pH 5.5–9.0 (optimum, pH 6.5–7.0) and in the presence of 1–8 % (w/v) NaCl (optimum, 2–3 %). Cells contained carotenoid pigments but not flexirubin-type pigments. Strain D1T contained MK-6 as the sole menaquinone and phosphatidylethanolamine (PE) as the sole phospholipid and four unidentified lipids. The major cellular fatty acids (>10 %) were iso-C15 : 0 (23.2 %), iso-C17 : 0 3-OH (15.2 %), C16 : 1ω7c/C16 : 1ω6c (14.3 %), iso-C15 : 0 3-OH (13.5 %) and iso-C15 : 1 G (10.8 %). 16S rRNA gene sequence analyses indicated that strain D1T belonged to the family
Flavobacteriaceae
and showed closest phylogenetic relationship to the genus
Lutibacter
, with highest sequence similarity to
Lutibacter aestuarii
MA-My1T (92.2 %). The DNA G+C content of strain D1T was 35.9 mol%. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain D1T was considered to represent a novel species in a new genus of the family
Flavobacteriaceae
, for which the name Wenyingzhuangia marina gen. nov., sp. nov. is proposed. The type strain of the type species is D1T ( = CGMCC 1.12162T = JCM 18494T).
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Affiliation(s)
- Ying Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Liang-Zi Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Hong-Can Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Yu-Guang Zhou
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Fang-Jun Qi
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, PR China
| | - Zhi-Pei Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
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26
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Li H, Zhang XY, Liu C, Lin CY, Xu Z, Chen XL, Zhou BC, Shi M, Zhang YZ. Polaribacter huanghezhanensis sp. nov., isolated from Arctic fjord sediment, and emended description of the genus Polaribacter. Int J Syst Evol Microbiol 2013; 64:973-978. [PMID: 24425815 DOI: 10.1099/ijs.0.056788-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-negative, orange-colony-forming, aerobic and non-flagellated bacterium, designated strain SM1202(T), was isolated from marine sediment of Kongsfjorden, Svalbard. Analysis of 16S rRNA gene sequences revealed that strain SM1202(T) was phylogenetically closely related to the genus Polaribacter. It shared the highest 16S rRNA gene sequence similarity with the type strain of Polaribacter dokdonensis (94.2 %) and 92.7-93.9 % sequence similarity with type strains of other known species of the genus Polaribacter. The strain grew at 4-35 °C and with 1.0-5.0 % (w/v) NaCl. It contained iso-C15 : 0, iso-C15 : 0 3-OH, iso-C13 : 0, C15 : 0, iso-C15 : 1 G, iso-C17 : 0 3-OH and C15 : 1ω6c as predominant cellular fatty acids and menaquinone-6 (MK-6) as the major respiratory quinone. The polar lipids of strain SM1202(T) were phosphatidylethanolamine, one unidentified lipid, two unidentified aminophospholipids and one unidentified aminolipid. The genomic DNA G+C content of strain SM1202(T) was 36.4 mol%. On the basis of the data from this polyphasic taxonomic study, strain SM1202(T) represents a novel species in the genus Polaribacter of the family Flavobacteriaceae, for which the name Polaribacter huanghezhanensis sp. nov. is proposed. The type strain of Polaribacter huanghezhanensis is SM1202(T) ( = CCTCC AB 2013148(T) = KCTC 32516(T)). An emended description of the genus Polaribacter is also presented.
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Affiliation(s)
- Hai Li
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Jinan 250100, China
| | - Xi-Ying Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Jinan 250100, China
| | - Chang Liu
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Jinan 250100, China
| | - Chao-Yi Lin
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Jinan 250100, China
| | - Zhong Xu
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Jinan 250100, China
| | - Xiu-Lan Chen
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Jinan 250100, China
| | - Bai-Cheng Zhou
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Jinan 250100, China
| | - Mei Shi
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Jinan 250100, China
| | - Yu-Zhong Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Jinan 250100, China
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27
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List of new names and new combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol 2013. [DOI: 10.1099/ijs.0.050948-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The purpose of this announcement is to effect the valid publication of the following effectively published new names and new combinations under the procedure described in the Bacteriological Code (1990 Revision). Authors and other individuals wishing to have new names and/or combinations included in future lists should send three copies of the pertinent reprint or photocopies thereof, or an electronic copy of the published paper, to the IJSEM Editorial Office for confirmation that all of the other requirements for valid publication have been met. It is also a requirement of IJSEM and the ICSP that authors of new species, new subspecies and new combinations provide evidence that types are deposited in two recognized culture collections in two different countries. It should be noted that the date of valid publication of these new names and combinations is the date of publication of this list, not the date of the original publication of the names and combinations. The authors of the new names and combinations are as given below, and these authors’ names will be included in the author index of the present issue. Inclusion of a name on these lists validates the publication of the name and thereby makes it available in the nomenclature of prokaryotes. The inclusion of a name on this list is not to be construed as taxonomic acceptance of the taxon to which the name is applied. Indeed, some of these names may, in time, be shown to be synonyms, or the organisms may be transferred to another genus, thus necessitating the creation of a new combination.
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