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Jung YH, Kwon YM, Chung D, Yu WJ, Choi G, Kim TW, Bae SS. Lutimonas zeaxanthinifaciens sp. nov. , a zeaxanthin-producing marine bacterium isolated from coastal sediment. Int J Syst Evol Microbiol 2024; 74. [PMID: 38743481 DOI: 10.1099/ijsem.0.006386] [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: 05/16/2024] Open
Abstract
A Gram-stain-negative, yellow-pigmented, strictly aerobic, non-flagellated, motile by gliding, rod-shaped bacterium, designated strain YSD2104T, was isolated from a coastal sediment sample collected from the southeastern part of the Yellow Sea. Phylogenetic analysis based on the 16S rRNA gene sequences revealed that strain YSD2104T was closely related to three type strains, Lutimonas vermicola IMCC1616T (97.4 %), Lutimonas saemankumensis SMK-142T (96.9 %), and Lutimonas halocynthiae RSS3-C1T (96.8 %). Strain YSD2104T has a single circular chromosome of 3.54 Mbp with a DNA G+C content of 38.3 mol%. The average nucleotide identity and digital DNA-DNA hybridization values between strain YSD2104T and the three type strains (L. vermicola IMCC1616 T, L. saemankumensis SMK-142T, and L. halocynthiae RSS3-C1T) were 74.0, 86.2 and 73.6 %, and 17.9, 30.3 and 17.8 %, respectively. Growth was observed at 20-30 °C (optimum, 30 °C), at pH 6.5-8.5 (optimum, pH 7.0), and with NaCl concentrations of 1.5-3.5 % (optimum, 2.5 %). The major carotenoid was zeaxanthin, and flexirubin-type pigment was not produced. The major respiratory quinone was menaquinone-6. The major fatty acids (>10 %) were iso-C15 : 0, iso-C15 : 1 G, iso-C17 : 0 3-OH, summed feature 3 (C16 : 1 ω6c and/or C16 : 1 ω7c), and summed feature 9 (iso-C17 : 1 ω9c and/or 10-methyl C16 : 0). The major polar lipids were phosphatidylethanolamine, one unidentified aminophospholipid, two unidentified aminolipids, and eight unidentified lipids. Conclusively, based on this polyphasic approach, we classified strain YSD2104T (=KCTC 102008T=JCM 36287T) as representing a novel species of the genus Lutimonas and proposed the name Lutimonas zeaxanthinifaciens sp. nov.
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Affiliation(s)
- Yoon-Hee Jung
- National Marine Biodiversity Institute of Korea, 101-75, Jangsan-ro, Janghang-eup, Seocheon-gun Chungcheongnam-do 33662, Republic of Korea
- Department of Biotechnology and Bioengineering, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Yong Min Kwon
- National Marine Biodiversity Institute of Korea, 101-75, Jangsan-ro, Janghang-eup, Seocheon-gun Chungcheongnam-do 33662, Republic of Korea
| | - Dawoon Chung
- National Marine Biodiversity Institute of Korea, 101-75, Jangsan-ro, Janghang-eup, Seocheon-gun Chungcheongnam-do 33662, Republic of Korea
| | - Woon-Jong Yu
- National Marine Biodiversity Institute of Korea, 101-75, Jangsan-ro, Janghang-eup, Seocheon-gun Chungcheongnam-do 33662, Republic of Korea
| | - Grace Choi
- National Marine Biodiversity Institute of Korea, 101-75, Jangsan-ro, Janghang-eup, Seocheon-gun Chungcheongnam-do 33662, Republic of Korea
| | - Tae Wan Kim
- Department of Biotechnology and Bioengineering, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Seung Seob Bae
- National Marine Biodiversity Institute of Korea, 101-75, Jangsan-ro, Janghang-eup, Seocheon-gun Chungcheongnam-do 33662, Republic of Korea
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Li J, Luo J, Li M, Wang C, Hu S, Lu K, Wang G. Splendidivirga corallicola gen. nov., sp. nov. and Agaribacillus aureus gen. nov., sp. nov., two bacteria isolated from coral Porites lutea, and proposal of Splendidivirgaceae fam. nov. Int J Syst Evol Microbiol 2024; 74. [PMID: 38739684 DOI: 10.1099/ijsem.0.006376] [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: 05/16/2024] Open
Abstract
The Bacteroidota is one of the dominant bacterial phyla in corals. However, the exact taxa of those coral bacteria under the Bacteroidota are still unclear. Two aerobic, Gram-stain-negative, non-motile rods, designated strains BMA10T and BMA12T, were isolated from stony coral Porites lutea collected from Weizhou Island, PR China. Global alignment of 16S rRNA gene sequences indicated that both strains are closest to species of Fulvivirga with the highest identities being lower than 93 %, and the similarity value between these two strains was 92.3 %. Phylogenetic analysis based on 16S rRNA gene and genome sequences indicated that these two strains form an monophylogenetic lineage alongside the families Fulvivirgaceae, Reichenbachiellaceae, Roseivirgaceae, Marivirgaceae, Cyclobacteriaceae, and Cesiribacteraceae in the order Cytophagales, phylum Bacteroidota. The genomic DNA G+C contents of BMA10T and BMA12T were 38.4 and 41.9 mol%, respectively. The major polar lipids of BMA10T were phosphatidylethanolamine, unidentified aminophospholipid, four unidentified aminolipids, and five unidentified lipids. While those of BMA12T were phosphatidylethanolamine, two unidentified aminolipids, and five unidentified lipids. The major cellular fatty acids detected in both isolates were iso-C15 : 0 and C16 : 1 ω5c. Carbohydrate-active enzyme analysis indicated these two strains may utilize coral mucus or chitin. Based on above characteristics, these two strains are suggested to represent two new species in two new genera of a new family in the order Cytophagales, for which the name Splendidivirga corallicola gen. nov., sp. nov., Agaribacillus aureus gen. nov., sp. nov. and Splendidivirgaceae fam. nov. are proposed. The type strain of S. corallicola is BMA10T (=MCCC 1K08300T=KCTC 102045T), and that for A. aureus is BMA12T (=MCCC 1K08309T=KCTC 102046T).
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Affiliation(s)
- Jin Li
- Guangxi Key Laboratory on the Study of Coral Reefs in the South China Sea, Nanning 530004, PR China
- School of Marine Sciences, Guangxi University, Nanning 530004, PR China
| | - Jixin Luo
- Guangxi Key Laboratory on the Study of Coral Reefs in the South China Sea, Nanning 530004, PR China
- School of Marine Sciences, Guangxi University, Nanning 530004, PR China
| | - Mi Li
- Guangxi Key Laboratory on the Study of Coral Reefs in the South China Sea, Nanning 530004, PR China
- School of Marine Sciences, Guangxi University, Nanning 530004, PR China
| | - Chenyan Wang
- Guangxi Key Laboratory on the Study of Coral Reefs in the South China Sea, Nanning 530004, PR China
- School of Marine Sciences, Guangxi University, Nanning 530004, PR China
| | - Siyu Hu
- Guangxi Key Laboratory on the Study of Coral Reefs in the South China Sea, Nanning 530004, PR China
- School of Marine Sciences, Guangxi University, Nanning 530004, PR China
| | - Kun Lu
- Guangxi Key Laboratory on the Study of Coral Reefs in the South China Sea, Nanning 530004, PR China
- School of Marine Sciences, Guangxi University, Nanning 530004, PR China
| | - Guanghua Wang
- Guangxi Key Laboratory on the Study of Coral Reefs in the South China Sea, Nanning 530004, PR China
- School of Marine Sciences, Guangxi University, Nanning 530004, PR China
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Nguyen TTH, Vuong TQ, Han HL, Li Z, Lee YJ, Ko J, Nedashkovskaya OI, Kim SG. Three marine species of the genus Fulvivirga, rich sources of carbohydrate-active enzymes degrading alginate, chitin, laminarin, starch, and xylan. Sci Rep 2023; 13:6301. [PMID: 37072506 PMCID: PMC10113389 DOI: 10.1038/s41598-023-33408-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 04/12/2023] [Indexed: 05/03/2023] Open
Abstract
Bacteroidota is a group of marine polysaccharide degraders, which play a crucial role in the carbon cycle in the marine ecosystems. In this study, three novel gliding strains, designated as SS9-22T, W9P-11T, and SW1-E11T, isolated from algae and decaying wood were proposed to represent three novel species of the genus Fulvivirga. We identified a large number of genes encoding for carbohydrate-active enzymes, which potentially participate in polysaccharide degradation, based on whole genome sequencing. The 16S rRNA sequence similarities among them were 94.4-97.2%, and against existing species in the genus Fulvivirga 93.1-99.8%. The complete genomes of strains SS9-22T, W9P-11T, and SW1-E11T comprised one circular chromosome with size of 6.98, 6.52, and 6.39 Mb, respectively; the GC contents were 41.9%, 39.0%, and 38.1%, respectively. The average nucleotide identity and the digital DNA-DNA hybridization values with members in the genus Fulvivirga including the isolates were in a range of 68.9-85.4% and 17.1-29.7%, respectively, which are low for the proposal of novel species. Genomic mining in three genomes identified hundreds of carbohydrate-active enzymes (CAZymes) covering up to 93 CAZyme families and 58-70 CAZyme gene clusters, exceeding the numbers of genes present in the other species of the genus Fulvivirga. Polysaccharides of alginate, chitin, laminarin, starch, and xylan were degraded in vitro, highlighting that the three strains are rich sources of CAZymes of polysaccharide degraders for biotechnological applications. The phenotypic, biochemical, chemotaxonomic, and genomic characteristics supported the proposal of three novel species in the genus Fulvivirga, for which the names Fulvivirga ulvae sp. nov. (SS9-22T = KCTC 82072T = GDMCC 1.2804T), Fulvivirga ligni sp. nov. (W9P-11T = KCTC 72992T = GDMCC 1.2803T), and Fulvivirga maritima sp. nov. (SW1-E11T = KCTC 72832T = GDMCC 1.2802T) are proposed.
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Affiliation(s)
- Tra T H Nguyen
- Biological Resource Center, Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, 56212, Republic of Korea
- Department of Biotechnology, KRIBB School, University of Science and Technology (UST), Daejeon, 34113, Republic of Korea
| | - Tien Q Vuong
- Hanoi University of Science, Vietnam National University, Hanoi, 10000, Vietnam
| | - Ho Le Han
- The University of Danang, University of Science and Technology, 54 Nguyen Luong Bang St., Da Nang, 550000, Vietnam
| | - Zhun Li
- Biological Resource Center, Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, 56212, Republic of Korea
- Department of Biotechnology, KRIBB School, University of Science and Technology (UST), Daejeon, 34113, Republic of Korea
| | - Yong-Jae Lee
- Biological Resource Center, Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, 56212, Republic of Korea
| | - Jaeho Ko
- Biological Resource Center, Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, 56212, Republic of Korea
| | - Olga I Nedashkovskaya
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry of the Far-Eastern Branch of the Russian Academy of Sciences, Vladivostok, Russia, 690022
| | - Song-Gun Kim
- Biological Resource Center, Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, 56212, Republic of Korea.
- Department of Biotechnology, KRIBB School, University of Science and Technology (UST), Daejeon, 34113, Republic of Korea.
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Jiang Y, Guan Y, Kang S, Lee MK, Kim KH, Li Z. Dasania phycosphaerae sp. nov., isolated from phytoplankton sample from the south coast of the Republic of Korea. Int J Syst Evol Microbiol 2023; 73. [PMID: 37185061 DOI: 10.1099/ijsem.0.005768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023] Open
Abstract
A novel bacterial strain, designated as GY-18T, was isolated from particulate material sampled from the Korean south coast. The bacterium was Gram-stain-negative, aerobic and rod-shaped. Oxidase and catalase were positive. Optimal growth was observed at 30 °C, pH 7.0, in the presence of 1 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene and whole-genome sequences suggested that strain GY-18T was a member of the genus
Dasania
, but represented a separate lineage. The 16S rRNA gene sequence of strain GY-18T showed high similarities to
Dasania marina
KCTC 12566T (98.4 %),
Halioglobus japonicus
KCTC 23429T (92.2 %),
Marimicrobium arenosum
KCTC 42300T (92.4 %) and
Seongchinamella unica
KCTC 62383T (92.2 %), respectively. The genome length of strain GY-18T was 3 808 450 bp with a DNA G+C content of 47.8 mol %. The major cellular fatty acids of strain GY-18T were summed feature 3 (comprising C16 : 1
ω7c and/or C16 : 1
ω6c), C16 : 0 and C10 : 0 3-OH (>10 %). Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phospholipids were shown to be the major polar lipids. The predominant isoprenoid quinone was Q-8. Based on phylogenetic, phenotypic, chemotaxonomic and genomic features, we propose that strain GY-18T represents a novel species in the genus
Dasania
of the family
Spongiibacteraceae
, with the proposed name Dasania phycosphaerae sp. nov. The type strain is GY-18T (=KCTC 92290T=GDMCC 1.3586T).
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Affiliation(s)
- Yue Jiang
- Biological Resource Center/Korean Collection for Type Cultures (KCTC), Korea Research Institute of Bioscience and Biotechnology, Jeongeup 56212, Republic of Korea
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Yong Guan
- Biological Resource Center/Korean Collection for Type Cultures (KCTC), Korea Research Institute of Bioscience and Biotechnology, Jeongeup 56212, Republic of Korea
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Sungmo Kang
- Biological Resource Center/Korean Collection for Type Cultures (KCTC), Korea Research Institute of Bioscience and Biotechnology, Jeongeup 56212, Republic of Korea
| | - Mi-Kyung Lee
- Biological Resource Center/Korean Collection for Type Cultures (KCTC), Korea Research Institute of Bioscience and Biotechnology, Jeongeup 56212, Republic of Korea
- Department of Environmental Biotechnology, University of Science and Technology (UST), Daejeon 34113, Republic of Korea
| | - Ki-Hyun Kim
- Biological Resource Center/Korean Collection for Type Cultures (KCTC), Korea Research Institute of Bioscience and Biotechnology, Jeongeup 56212, Republic of Korea
| | - Zhun Li
- Biological Resource Center/Korean Collection for Type Cultures (KCTC), Korea Research Institute of Bioscience and Biotechnology, Jeongeup 56212, Republic of Korea
- Department of Environmental Biotechnology, University of Science and Technology (UST), Daejeon 34113, Republic of Korea
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Burbick CR, Munson E, Lawhon SD, Zapp A, Villaflor M, Thelen E. An Update on Novel Taxa and Revised Taxonomic Status of Bacteria (Including Members of the Phylum Planctomycetota) Isolated from Aquatic Host Species Described in 2018 to 2021. J Clin Microbiol 2023; 61:e0142622. [PMID: 36719221 PMCID: PMC9945501 DOI: 10.1128/jcm.01426-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Increased interest in farmed aquatic species, aquatic conservation measures, and microbial metabolic end-product utilization have translated into a need for awareness and recognition of novel microbial species and revisions to bacterial taxonomy. Because this need has largely been unmet, through a 4-year literature review, we present lists of novel and revised bacterial species (including members of the phylum Planctomycetota) derived from aquatic hosts that can serve as a baseline for future biennial summaries of taxonomic revisions in this field. Most new and revised taxa were noted within oxidase-positive and/or nonglucose fermentative Gram-negative bacilli, including members of the Tenacibaculum, Flavobacterium, and Vibrio genera. Valid and effectively published novel members of the Streptococcus, Erysipelothrix, and Photobacterium genera are additionally described from disease pathogenesis perspectives.
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Affiliation(s)
- Claire R. Burbick
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, Washington, USA
| | - Erik Munson
- Department of Medical Laboratory Science, Marquette University, Milwaukee, Wisconsin, USA
| | - Sara D. Lawhon
- Department of Veterinary Pathobiology, Texas A&M University, College Station, Texas, USA
| | - Amanda Zapp
- Department of Medical Laboratory Science, Marquette University, Milwaukee, Wisconsin, USA
| | - Maia Villaflor
- Department of Medical Laboratory Science, Marquette University, Milwaukee, Wisconsin, USA
| | - Elizabeth Thelen
- Department of Medical Laboratory Science, Marquette University, Milwaukee, Wisconsin, USA
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Marinigracilibium pacificum gen. nov., sp. nov., a starch-degrading bacterium isolated from tropical western Pacific. Antonie Van Leeuwenhoek 2023; 116:185-192. [PMID: 36374402 DOI: 10.1007/s10482-022-01792-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 11/01/2022] [Indexed: 11/16/2022]
Abstract
The Gram-stain-negative, golden-yellow-colored, non-spore-forming, strictly aerobic, slender rod-shaped bacterial strain, designated KN852T, was isolated from a seamount in the tropical western Pacific. The predominant respiratory quinone was MK-7 and the polar lipid profiles contained phosphatidylethanolamine, one unidentified phospholipid and six unidentified polar lipids. The predominant cellular fatty acids were iso-C15:0, summed feature 3(C16:1ω7c and/or iso-C15:0 2OH), iso-C17:0 3OH and iso-C15:1 G. Phylogenetic analyses of 16S rRNA gene sequence revealed that strain KN852T was affiliated with the family Flammeovirgaceae of the phylum Bacteroidota and formed a distinct lineage. The genomic DNA G + C content of strain KN852T was 34.8%. Collectively, based on phenotypic, chemotaxonomic, phylogenetic and genomic evidence presented, strain KN852T represents a novel species of a novel genus of the family Flammeovirgaceae, for which the name Marinigracilibium pacificum gen. nov., sp. nov. is proposed. The type strain is KN852T (= CGMCC 1.17119T = KCTC 72433T).
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Fulvivirga sedimenti sp.nov, isolated from the sediment of oceanic tidal zone. Arch Microbiol 2022; 204:727. [DOI: 10.1007/s00203-022-03344-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 11/12/2022] [Accepted: 11/16/2022] [Indexed: 11/27/2022]
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Wang C, Lv Y, Li A, Yao Q, Zhu H. Parachryseolinea silvisoli gen. nov., sp. nov., isolated from forest soil, and reclassification of Chryseolinea flava as Pseudochryseolinea flava gen. nov., comb. nov. Int J Syst Evol Microbiol 2022; 72. [PMID: 36208420 DOI: 10.1099/ijsem.0.005523] [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: 06/16/2023] Open
Abstract
A lemon-chiffon strain, designated QH1ED-6-2T, was isolated from a soil sample collected from Qinghai Virgin Forests, Qinghai Province, PR China. The strain was Gram-stain-negative, aerobic, rod-shaped and motile by gliding. Phylogenetic analysis of 16S rRNA gene sequences revealed that strain QH1ED-6-2T belongs to the family Fulvivirgaceae, and has the highest similarity values of 93.6-92.0 % to Ohtaekwangia koreensis CCUG 58939T, Ohtaekwangia kribbensis CCUG 58938T, Chryseolinea flava SDU1-6T and Chryseolinea serpens DSM 24574T, respectively. The major cellular fatty acids included iso-C15 : 0, C16 : 1 ω5c, iso-C17 : 0 3-OH and summed feature 3. The major polar lipid was phosphatidylethanolamine. The predominant respiratory quinone was menaquinone-7. The average amino acid identity values and percentages of conserved proteins between QH1ED-6-2T and its closely related genera were 66.4-69.6 % and 58.9-64.9 %, respectively, which are interspersed in the intra-genera cutoff values. The digital DNA-DNA hybridization values were 17.6-19.2 %. The draft genome size of strain QH1ED-6-2T was 7.98 Mbp with a DNA G+C content of 51.4 mol%. Based on phenotypic, chemotaxonomic, phylogenetic data, genomic DNA G+C content, as well as AAI, POCP and dDDH results, strain QH1ED-6-2T represents a novel species of a new genus in the family Fulvivirgaceae, for which the name Parachryseolinea silvisoli sp. nov. is proposed. The type strain is QH1ED-6-2T (=GDMCC 1.2318T=JCM 35041T). We also propose the reclassification of Chryseolinea flava as Pseudochryseolinea flava gen. nov., comb. nov. (type strain SDU1-6T=CGMCC 1.13492T=JCM 32520T).
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Affiliation(s)
- Chunling Wang
- Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Microbial Culture Collection Center (GDMCC), Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, PR China
| | - Yingying Lv
- Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Microbial Culture Collection Center (GDMCC), Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, PR China
| | - Anzhang Li
- Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Microbial Culture Collection Center (GDMCC), Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, PR China
| | - Qing Yao
- College of Horticulture, South China Agricultural University, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Guangzhou 510642, PR China
| | - Honghui Zhu
- Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Microbial Culture Collection Center (GDMCC), Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, PR China
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Goldberg SR, Haltli BA, Correa H, Kerr RG. Pseudovibrio flavus sp. nov. isolated from the sea sponge Verongula gigantea. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005457] [Citation(s) in RCA: 0] [Impact Index Per Article: 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 marine bacterium, designated RKSG542T, was isolated from the sea sponge Verongula gigantea collected at a depth of 20 m off the west coast of San Salvador, The Bahamas. Phylogenetic analyses based on 16S rRNA gene and genome sequences place RKSG542T in a monophyletic clade with members of the genus
Pseudovibrio
. Strain RKSG542T shared <96.7 % 16S rRNA gene sequence similarity,<72.2 % average nucleotide identity,<66.7 % average amino acid identity, and <24.8 % digital DNA–DNA hybridization with type strains of the family
Stappiaceae
. Growth occurred at 22–37 °C (22–30 °C optimum), at pH 7–9 (pH 7 optimum), and with 0.5–5 % (w/v) NaCl (2 % optimum). The predominant fatty acids (>10 %) were summed feature 8 (C18 : 1
ω6c and/or C18 : 1
ω7c), C18 : 0 and C16 : 0, and the respiratory lipoquinone was Q-10. The polar lipid composition comprised phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, three unknown aminolipids, six unknown phospholipids and four unknown lipids. The DNA G+C content of the genome sequence was 52.5 mol%. Based on the results of biochemical, phylogenetic and genomic analyses, RKSG542T (=TSD-76T=LMG 29867T) is presented here as the type strain of a novel species within the genus
Pseudovibrio
(family
Stappiaceae
, order
Hyphomicrobiales
, class
Alphaproteobacteria
), for which the name Pseudovibrio flavus sp. nov. is proposed.
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Affiliation(s)
- Stacey R. Goldberg
- Department of Biomedical Science, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Prince Edward Island, Canada
| | - Brad A. Haltli
- Nautilus Biosciences Croda, Duffy Research Centre, Charlottetown, Prince Edward Island, Canada
- Department of Biomedical Science, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Prince Edward Island, Canada
| | - Hebelin Correa
- Nautilus Biosciences Croda, Duffy Research Centre, Charlottetown, Prince Edward Island, Canada
| | - Russell G. Kerr
- Nautilus Biosciences Croda, Duffy Research Centre, Charlottetown, Prince Edward Island, Canada
- Department of Biomedical Science, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Prince Edward Island, Canada
- Department of Chemistry, University of Prince Edward Island, Charlottetown, Prince Edward Island, Canada
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Qipengyuania pacifica sp. nov., a Novel Carotenoid-Producing Marine Bacterium of the Family Erythrobacteraceae, Isolated from Sponge (Demospongiae), and Antimicrobial Potential of Its Crude Extract. DIVERSITY 2022. [DOI: 10.3390/d14040295] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
A marine Alphaproteobacterium designated as strain NZ-96T was isolated in February 2021, from a sponge species (Demospongiae) collected in muddy sediments with boulders and old chimneys in Otago/Canterbury Slope, Pacific Ocean, New Zealand. The isolate was found to be Gram-negative, rod-shaped, aerobic, motile, and produced yellow-colored colonies. The isolate was positive for alkaline phosphatase, leucine arylamidase, trypsin, catalase, and oxidase and negative for α-galactosidase and urease. It was resistant to many antibiotics including hygromycin, trimethoprim, spectinomycin, ampicillin, oxytetracycline, cephalosporin, bacitracin, and polymyxin. The 16S rRNA gene-based phylogenetic analyses exhibited that strain NZ-96T belonged to the genus Qipengyuania and showed 98.3–98.8% 16S rRNA gene sequence similarity to its closest relatives. The major respiratory quinone was ubiquinone-10 (Q-10). The polar lipid profile consisted of phosphatidylcholine, sphingoglycolipid, phosphatidylglycerol, one unknown polar lipid, and three unknown glycolipids. The major fatty acids were C18:1ω12t, C16:0, C16:1ω7c, C17:1ω6c, C16:02-OH, and C14:0 2-OH. Carotenoid were produced. The crude extract showed pronounced activity against Staphylococcus aureus Newman and Bacillus subtilis DSM 10. Pairwise ANI and dDDH values of strain NZ-96T and closely related phylogenetic hits were below the threshold values of 95% and 70%, respectively. Genes for trehalose biosynthesis, aspartate-semialdehyde dehydrogenase, flagellar biosynthesis, fatty acid biosynthesis, and antibiotics resistance were present, which aids in isolate survival in a sea or ocean environment. The DNA G+C content was 60.8% (by genome). Based on data obtained by the polyphasic approach, strain NZ-96T (= DSM 112811T = NCCB 100842T) represents a novel species of the genus Qipengyuania, for which the name Qipengyuania pacifica sp. nov. is proposed.
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Zhao LH, Wang ZJ, Song C, Xing X, Liu YY, Shi LF, Yu TT, Zhang YM, Zhu Q, Du ZJ. Fulvivirga marina sp. nov. and Fulvivirga sediminis sp. nov., two novel Bacteroidetes isolated from the marine sediment. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005308] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two novel, designated strains 29W222T and 2943T, were isolated from the marine sediment from Aoshan Bay, Jimo, PR China. Growth was observed at pH 6.0–8.5 (optimum, pH 7.5) for strain 29W222T, and pH 5.5–8.5 (pH 7.0) for strain 2943T. Both strains displayed growth in 0.5–6 % NaCl with an optimum at 1 % for 29W222T; 0.5 % for 2943T. Both strains grew optimally at 33 °C. The results of phylogenetic analyses based on 16S rRNA gene sequences indicated that 29W222T and 2943T represented members of the genus
Fulvivirga
and strain 29W222T was most closely related to
Fulvivirga kasyanovii
KMM 6220T (97.9 % sequence similarity) and
Fulvivirga imtechensis
AK7T (95.0 %), and 2943T to
Fulvivirga imtechensis
AK7T (95.7 %) and
Fulvivirga kasyanovii
KMM 6220T (94.8 %). The genomic DNA G+C contents of 29W222T and 2943T were 39.9 and 37.7 mol%, respectively. The results of chemotaxonomic analysis indicated that the sole respiratory quinone was menaquinone 7 (MK-7), and the major fatty acid was iso-C15 : 0 for both strains. Average nucleotide identity and average amino acid identity values between strain 29W222T and
Fulvivirga kasyanovii
KMM 6220T were 78.9 and 83.6 %, respectively; the corresponding values between 2943T and
Fulvivirga imtechensis
AK7T were 69.8 and 63.6 %, respectively. Therefore, strains 29W222T and 2943T represent to two novel species of the genus
Fulvivirga
, for which the names Fulvivirga marina sp. nov. (29W222T=KCTC 62848T=MCCC 1K05194T) and Fulvivirga sediminis sp. nov. (2943T=KCTC 62847T= MCCC 1K05144T) are proposed, respectively.
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Affiliation(s)
- Li-Hua Zhao
- Marine College, Shandong University, Weihai, Shandong 264209, PR China
| | - Zong-Jie Wang
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China
- Marine College, Shandong University, Weihai, Shandong 264209, PR China
| | - Cui Song
- Marine College, Shandong University, Weihai, Shandong 264209, PR China
| | - Xiang Xing
- Marine College, Shandong University, Weihai, Shandong 264209, PR China
| | - Ying-Ying Liu
- Marine College, Shandong University, Weihai, Shandong 264209, PR China
| | - Li-Fang Shi
- Marine College, Shandong University, Weihai, Shandong 264209, PR China
| | - Tong-Tong Yu
- Marine College, Shandong University, Weihai, Shandong 264209, PR China
| | - You-Ming Zhang
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China
| | - Qian Zhu
- Marine College, Shandong University, Weihai, Shandong 264209, PR China
| | - Zong-Jun Du
- Marine College, Shandong University, Weihai, Shandong 264209, PR China
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Bae SS, Jung YH, Kwon YM, Chung D, Choi G, Cho K, Yu WJ, Baek K. Fulvivirga lutea sp. nov., a marine bacterium isolated from seawater. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005188] [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 strictly aerobic, Gram-stain-negative, gliding, rod-shaped bacteria, designated strain S481T, was isolated from a surface seawater sample collected at Gunsan marina, in the West Sea of the Republic of Korea. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain S481T formed a monophyletic clade with members of the genus
Fulvivirga
, showing 93.7–95.8% sequence similarity to the type strains. Strain S481T has a single circular chromosome of 4.13 Mbp with a DNA G+C content of 37.3 mol%. The values of average nucleotide identity, average amino acid identity and digital DNA–DNA hybridization between strain S481T and all genome-sequenced species of the genus
Fulvivirga
were below 71.2%, 68.6% and 18.9%, respectively, indicating lower values than the standard cut-offs for species delineation. Growth was observed at 20–42 °C (optimum, 37 °C), at pH 6–8 (optimum, pH 7) and with 0 – 6 % NaCl (optimum, 1–2 %). The major fatty acids (>10%) were iso-C15:0, iso-C15:1 G and C16:1ω5c. The respiratory quinone was MK-7. The major polar lipids were identified as phosphatidylethanolamine, three unidentified aminolipids and five unidentified lipids. Based on the results of phenotypic characterization, phylogenetic analysis and genome-based comparison, strain S481T represents a novel species in the genus
Fulvivirga
, for which we propose the name Fulvivirga lutea sp. nov. The type strain is S481T (=KCTC 82209T=JCM 34505T).
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Affiliation(s)
- Seung Seob Bae
- National Marine Biodiversity Institute of Korea, 101-75, Jangsan-ro, Janghang-eup, Seocheon-gun Chungcheongnam-do 33662, Republic of Korea
| | - Yoon-Hee Jung
- National Marine Biodiversity Institute of Korea, 101-75, Jangsan-ro, Janghang-eup, Seocheon-gun Chungcheongnam-do 33662, Republic of Korea
| | - Yong Min Kwon
- National Marine Biodiversity Institute of Korea, 101-75, Jangsan-ro, Janghang-eup, Seocheon-gun Chungcheongnam-do 33662, Republic of Korea
| | - Dawoon Chung
- National Marine Biodiversity Institute of Korea, 101-75, Jangsan-ro, Janghang-eup, Seocheon-gun Chungcheongnam-do 33662, Republic of Korea
| | - Grace Choi
- National Marine Biodiversity Institute of Korea, 101-75, Jangsan-ro, Janghang-eup, Seocheon-gun Chungcheongnam-do 33662, Republic of Korea
| | - Kichul Cho
- National Marine Biodiversity Institute of Korea, 101-75, Jangsan-ro, Janghang-eup, Seocheon-gun Chungcheongnam-do 33662, Republic of Korea
| | - Woon-Jong Yu
- National Marine Biodiversity Institute of Korea, 101-75, Jangsan-ro, Janghang-eup, Seocheon-gun Chungcheongnam-do 33662, Republic of Korea
| | - Kyunghwa Baek
- National Marine Biodiversity Institute of Korea, 101-75, Jangsan-ro, Janghang-eup, Seocheon-gun Chungcheongnam-do 33662, Republic of Korea
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Alteriqipengyuania abyssalis sp. nov., a Novel Member of the Class Alphaproteobacteria Isolated from Sponge, and Emended Description of the Genus Alteriqipengyuania. DIVERSITY 2021. [DOI: 10.3390/d13120670] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
A novel Gram-negative, aerobic, motile, lemon-yellow-colored, and non-spore-forming rod-shaped bacterium designated strain NZ-12BT was isolated in February 2021 from a sponge species (Crateromorpha) collected at the southern Kermadec Ridge, Pacific Ocean, New Zealand. Comparative 16S rRNA gene-based analyses indicated that strain NZ-12BT shared 98.58%, 96.44%, 96.23%, and 94.78% 16S rRNA sequence similarity to Alteriqipengyuania lutimaris S-5T, Qipengyuania pelagi UST081027-248T, Qipengyuania citreus RE35F/1T, and Alteriqipengyuania halimionae CPA5T, respectively. The major respiratory quinone was ubiquinone-10(Q-10). The polar lipid profile of NZ-12BT was composed of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidyl-N-methyl-ethanolamine, phosphatidylcholine, sphingoglycolipid, phosphatidylglycerol, one unknown polar lipid, three unknown phospholipids, and three unknown glycolipids. The major fatty acids of strain NZ-12BT were C18:1ω12t, C16:0, C17:1ω6c, and C14:02-OH. Carotenoids were present. Genome mining analysis revealed a biosynthetic gene cluster encoding for the terpene biosynthesis. Pairwise ANI and dDDH values of strain NZ-12BT and closely related phylogenetic neighbors were below the threshold values of 95% and 70%, respectively. The DNA G+C content was 65.4 mol% (by genome). Based on data obtained by a polyphasic approach, type strain NZ-12BT (=DSM 112810T = NCCB 100841T) represents a novel species of the genus Alteriqipengyuania, for which the name Alteriqipengyuania abyssalis sp. nov. is proposed.
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Demko AM, Patin NV, Jensen PR. Microbial diversity in tropical marine sediments assessed using culture-dependent and culture-independent techniques. Environ Microbiol 2021; 23:6859-6875. [PMID: 34636122 DOI: 10.1111/1462-2920.15798] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 09/28/2021] [Indexed: 01/04/2023]
Abstract
The microbial communities associated with marine sediments are critical for ecosystem function yet remain poorly characterized. While culture-independent (CI) techniques capture the broadest perspective on community composition, culture-dependent (CD) methods can select for low abundance taxa that are missed using CI approaches. This study aimed to assess microbial diversity in tropical marine sediments at five shallow-water sites in Belize using both CD and CI techniques. The CD methods captured approximately 3% of the >800 genera detected across all sites using the CI approach. Additionally, 39 genera were only detected in culture, revealing rare taxa that were missed with the CI approach. Significantly different communities were detected across sites, with rare taxa playing an important role in distinguishing among communities. This study provides important baseline data describing shallow-water sediment microbial communities, evidence that standard cultivation techniques may be more effective than previously recognized, and the first steps towards identifying new taxa that are amenable to agar plate cultivation.
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Affiliation(s)
- Alyssa M Demko
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Nastassia V Patin
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Paul R Jensen
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.,Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
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