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Hong W, Wang X, Yuan Y, Liu R, Zhao W, Xue CX, Zhang XH. Photobacterium obscurum sp. nov., a marine bacterium isolated from the coast of Qingdao. Int J Syst Evol Microbiol 2023; 73. [PMID: 37889564 DOI: 10.1099/ijsem.0.006096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2023] Open
Abstract
A Gram-stain-negative, facultative anaerobic, rod-shaped strain, named SDRW27T, was isolated from offshore seawater collected near Qingdao. Strain SDRW27T was able to grow at 16-37 °C (optimum, 28 °C), pH 6.0-9.0 (optimum, pH 6.0) and in the presence of 1-7 % (w/v) NaCl (optimum, 3 %). Phylogenetic analysis using 16S rRNA gene sequences indicated that strain SDRW27T was most closely related to Photobacterium toruni H01100410BT (97.89 % sequence similarity), Photobacterium andalusiense H01100409BT (97.89 %) and Photobacterium leiognathi ATCC 25521T (97.82 %). The predominant fatty acids were summed feature 3 (C16 : 1 ω7c and/or iso-C15 : 0 2-OH), summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c) and C16 : 0. The polar lipids of strain SDRW27T comprised phosphatidylglycerol, phosphatidylinositol dimannoside, phosphatidylcholine, phosphatidylethanolamine and three unidentified lipids. The major respiratory quinone was ubiquinone-8. The G+C content was 47.71 mol%. The genome size was 5.84 Mbp, including 85 contigs with an N50 value of 223 542. The average nucleotide identity (ANI) values of SDRW27T with its three most similar strains, P. toruni H01100410BT, P. andalusiense H01100409BT and P. leiognathi ATCC 25521T, were 71.36, 71.58 and 72.23 %, respectively (all lower than the 95-96 % ANI threshold), and the DNA-DNA hybridization (DDH) values were 20.4, 20.8 and 20.4 % (all lower than the 70 % DDH threshold). The obtained results of polyphasic analysis demonstrate that strain SDRW27T represents a novel species, for which the name Photobacterium obscurum sp. nov. is proposed. The type strain is SDRW27T (=MCCC 1K06286T=KCTC 82892T).
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Affiliation(s)
- Wen Hong
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, PR China
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, PR China
| | - Xiaolei Wang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, PR China
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, PR China
| | - Yalin Yuan
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, PR China
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, PR China
| | - Ronghua Liu
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, PR China
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, PR China
| | - Wenbin Zhao
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, PR China
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, PR China
| | - Chun-Xu Xue
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, PR China
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, PR China
| | - Xiao-Hua Zhang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, PR China
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, PR China
- Laboratory for Marine Ecology and Environmental Science, Qingdao Laoshan Laboratory for Marine Science and Technology, Qingdao 266071, PR China
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Lau NS, Heng WL, Miswan N, Azami NA, Furusawa G. Comparative Genomic Analyses of the Genus Photobacterium Illuminate Biosynthetic Gene Clusters Associated with Antagonism. Int J Mol Sci 2022; 23:ijms23179712. [PMID: 36077108 PMCID: PMC9456166 DOI: 10.3390/ijms23179712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 08/20/2022] [Accepted: 08/24/2022] [Indexed: 11/16/2022] Open
Abstract
The genus Photobacterium is known for its ecophysiological versatility encompassing free-living, symbiotic, and pathogenic lifestyles. Photobacterium sp. CCB-ST2H9 was isolated from estuarine sediment collected at Matang Mangrove, Malaysia. In this study, the genome of CCB-ST2H9 was sequenced, and the pan-genome of 37 Photobacterium strains was analysed. Phylogeny based on core genes showed that CCB-ST2H9 clustered with P. galatheae, forming a distinct clade with P. halotolerans, P. salinisoli, and P. arenosum. The core genome of Photobacterium was conserved in housekeeping functions, while the flexible genome was well represented by environmental genes related to energy production and carbohydrate metabolism. Genomic metrics including 16S rRNA sequence similarity, average nucleotide identity, and digital DNA–DNA hybridization values were below the cut-off for species delineation, implying that CCB-ST2H9 potentially represents a new species. Genome mining revealed that biosynthetic gene clusters (BGCs) involved in producing antimicrobial compounds such as holomycin in CCB-ST2H9 could contribute to the antagonistic potential. Furthermore, the EtOAc extract from the culture broth of CCB-ST2H9 exhibited antagonistic activity against Vibrio spp. Intriguingly, clustering based on BGCs profiles grouped P. galatheae, P. halotolerans, P. salinisoli, P. arenosum, and CCB-ST2H9 together in the heatmap by the presence of a large number of BGCs. These BGCs-rich Photobacterium strains represent great potential for bioactive secondary metabolites production and sources for novel compounds.
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Kong D, Wang Y, Li Q, Zhou Y, Jiang X, Xing Z, Wang Z, Ruan Z. Chryseobacterium subflavum sp. nov., isolated from soil. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005345] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, aerobic, non-motile, rod-shaped bacterium, designated LAMRS1T, was isolated from a soil sample collected in Hebei Province, PR China. Strain LAMRS1T was able to grow optimally in the presence of 0.5 % (w/v) NaCl, at pH 7.5 and at 30 °C. On the basis of 16S rRNA gene sequence analysis, strain LAMRS1T was closely related to members of the genus
Chryseobacterium
, with highest levels of sequence similarity to
Chryseobacterium soli
DSM 19298T (97.9 %),
Chryseobacterium soldanellicola
DSM 17072T (97.6%) and
Chryseobacterium piperi
CTMT (97.5 %). The average nucleotide identity and digital DNA–DNA hybridization values between LAMRS1T and the closely related species of
C. soli
DSM 19298T,
C. soldanellicola
DSM 17072T and
C. piperi
CTMT were 78.1, 78.2 and 80.7 %, and 21.7, 22.0 and 23.7 %, respectively. The draft genome sequence of LAMRS1T was 4.61 Mb, with DNA G+C content of 36.2 mol%. The major isoprenoid quinone was menaquinone-6 and iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1
ω6c and/or C16 : 1
ω7c) constituted the major cellular fatty acids. The main polar lipids were phosphatidylethanolamine, four aminolipids, three glycolipids and seven unidentified lipids. On the basis of evidence presented in this study, strain LAMRS1T represents a novel species of the genus
Chryseobacterium
, for which the name Chryseobacterium subflavum sp. nov. is proposed. The type strain is LAMRS1T (=JCM 33868T=KCTC 72823T).
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Affiliation(s)
- Delong Kong
- College of Resources and Environment, Tibet Agricultural and Animal Husbandry University, Linzhi 860000, PR China
| | - Yan Wang
- CAAS-CIAT Joint Laboratory in Advanced Technologies for Sustainable Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
- College of Resources and Environment, Tibet Agricultural and Animal Husbandry University, Linzhi 860000, PR China
| | - Qingqing Li
- CAAS-CIAT Joint Laboratory in Advanced Technologies for Sustainable Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Yanzheng Zhou
- Jining Academy of Agricultural Sciences, Jining 272000, PR China
| | - Xu Jiang
- CAAS-CIAT Joint Laboratory in Advanced Technologies for Sustainable Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Zhen Xing
- College of Resources and Environment, Tibet Agricultural and Animal Husbandry University, Linzhi 860000, PR China
| | - Zhiye Wang
- Key Laboratory of Microbial Resources Exploitation and Application of Gansu Province, Institute of Biology, Gansu Academy of Sciences, Lanzhou 730000, PR China
| | - Zhiyong Ruan
- CAAS-CIAT Joint Laboratory in Advanced Technologies for Sustainable Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
- College of Resources and Environment, Tibet Agricultural and Animal Husbandry University, Linzhi 860000, PR China
- College of Life Sciences, Yantai University, Yantai 264005, PR China
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Kong D, Li Q, Zhou Y, Wang Y, Jiang X, Wang Z, Ruan Z. Pseudomonas tumuqii sp. nov., isolated from greenhouse soil. Arch Microbiol 2022; 204:249. [PMID: 35396979 DOI: 10.1007/s00203-022-02869-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 03/22/2022] [Accepted: 03/23/2022] [Indexed: 11/02/2022]
Abstract
A Gram-stain-negative, aerobic, rod-shaped and motile bacterium, named LAMW06T, was isolated from greenhouse soil in Beijing, China. In the 16S rRNA gene sequence comparison, strain LAMW06T had the highest similarity with Pseudomonas cuatrocienegasensis 1NT. Phylogenetic analysis based on the 16S rRNA and three housekeeping gene sequences (gyrB, rpoB and rpoD) indicated that strain represented a member of the genus Pseudomonas. The genome sequence size of the isolate was 5.5 Mb, with a DNA G + C content of 63.5 mol%. The average nucleotide identity and DNA-DNA hybridization values between strain LAMW06T and closely related members of Pseudomonas borbori R-20821T, Pseudomonas taeanensis MS-3T and P. cuatrocienegasensis 1NT were 90.9%, 82.4%, 81.5% and 43.0%, 25.9%, 24.6% respectively. The major fatty acids contained summed feature 3 (C16:1 ω6c and/or C16:1 ω7c), C18:1 ω7c and C16:0. The primary respiratory quinone was ubiquinone-9. The main polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, six aminophospholipids, six phospholipids, one aminolipid and one glycolipid. According to the genotypic, phylogenetic and chemotaxonomic data, strain LAMW06T represents a novel species within the genus Pseudomonas, for which the name Pseudomonas tumuqii sp. nov. is proposed. The type strain is LAMW06T (= GDMCC 1.2003T = KCTC 72829T).
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Affiliation(s)
- Delong Kong
- CAAS-CIAT Joint Laboratory in Advanced Technologies for Sustainable Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China
| | - Qingqing Li
- CAAS-CIAT Joint Laboratory in Advanced Technologies for Sustainable Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China
| | - Yanzheng Zhou
- Jining Academy of Agricultural Sciences, Jining, 272000, People's Republic of China
| | - Yan Wang
- CAAS-CIAT Joint Laboratory in Advanced Technologies for Sustainable Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China.,College of Resources and Environment, Tibet Agricultural and Animal Husbandry University, Linzhi, 860000, People's Republic of China
| | - Xu Jiang
- CAAS-CIAT Joint Laboratory in Advanced Technologies for Sustainable Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China
| | - Zhiye Wang
- Key Laboratory of Microbial Resources Exploitation and Application of Gansu Province, Institute of Biology, Gansu Academy of Sciences, Lanzhou, 730000, People's Republic of China
| | - Zhiyong Ruan
- CAAS-CIAT Joint Laboratory in Advanced Technologies for Sustainable Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China. .,College of Resources and Environment, Tibet Agricultural and Animal Husbandry University, Linzhi, 860000, People's Republic of China. .,College of Life Sciences, Yantai University, Yantai, 264005, People's Republic of China.
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Kong D, Xia Z, Gao Y, Zhou Y, Jiang X, Xu P, Guo W, Ruan Z. Sporosarcina jiandibaonis sp. nov., isolated from saline soil. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005244] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-positive, aerobic, motile, rod-shaped bacterium, designated strain LAM9210T, was isolated from a saline soil sample collected from Lingxian County, Shandong Province, PR China. Analysis of the 16S rRNA gene sequence of the isolate revealed highest sequence similarities to the type strain of
Sporosarcina pasteurii
NCIMB 8841T (97.6 % sequence similarity). The genomic G+C content was 40.4 mol%. The average nucleotide identity and in silico DNA–DNA hybridization values between strain LAM9210T and the type strain of the most closely related species
S. pasteurii
NCIMB 8841T were 73.6 and 20.6 %, respectively. Strain LAM9210T was found to grow at 10–40 °C (optimum, 30 °C), at pH 6.0–10.0 (optimum, pH 9.0) and with 0–6 % (w/v) NaCl (optimum, 0.5 %), respectively. The major fatty acids were anteiso-C15 : 0 and iso-C14 : 0. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and one unidentified phospholipid. Menaquinone-7 was detected as the predorminant respiratory quinone. Strain LAM9210T contained glycine, lysine, alanine and glutamic acid as the diagnostic amino acids in the cell-wall peptidoglycan. On the basis of phenotypic, phylogenetic and genotypic data, strain LAM9210T is considered to represent a novel species of the genus
Sporosarcina
, for which the name Sporosarcina jiandibaonis sp. nov. is proposed. The type strain is LAM9210T (=CGMCC 1.18607T=GDMCC 1.2002T=JCM 32514T).
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Affiliation(s)
- Delong Kong
- Institute of Agricultural Resources and Regional Planning, CAAS, Beijing 100081, PR China
- College of Life Science, Tarim University/Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin of Xinjiang Production & Construction Corps, Alar 843300, PR China
| | - Zhanfeng Xia
- College of Life Science, Tarim University/Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin of Xinjiang Production & Construction Corps, Alar 843300, PR China
| | - Yan Gao
- Institute of Applied Microbiology, Xinjiang Academy of Agriculture Science/Xinjiang Special Environmental Microbiology Laboratory, Urumqi 830091, PR China
| | - Yiqing Zhou
- Institute of Agricultural Resources and Regional Planning, CAAS, Beijing 100081, PR China
| | - Xu Jiang
- Institute of Agricultural Resources and Regional Planning, CAAS, Beijing 100081, PR China
| | - Piao Xu
- Guangxi Jiandibao Bio-Technology Limited, Nanning 530105, PR China
| | - Wei Guo
- Graduate School of Chinese Academy of Agriculture Sciences, Beijing 100081, PR China
| | - Zhiyong Ruan
- Institute of Agricultural Resources and Regional Planning, CAAS, Beijing 100081, PR China
- College of Resources and Environment, Tibet Agricultural and Animal Husbandry University, Linzhi 860000 Tibet, PR China
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6
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Weerawongwiwat V, Yoon S, Kim JH, Yoon JH, Lee JS, Sukhoom A, Kim W. Photobacterium arenosum sp. nov., isolated from marine sediment sand. Int J Syst Evol Microbiol 2021; 71. [PMID: 34605765 DOI: 10.1099/ijsem.0.005034] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, aerobic, motile, short rod-shaped, catalase-negative and oxidase-positive bacterium, strain CAU 1568T, was isolated from marine sediment sand sampled at Sido Island in the Republic of Korea. The optimum conditions for growth were at 25-30 °C, at pH 6.5-8.5 and with 0-4.0 % (w/v) NaCl. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain CAU 1568T was a member of the genus Photobacterium with high similarity to Photobacterium salinisoli JCM 30852T (97.7 %), Photobacterium halotolerans KACC 17089T (97.3 %) and Photobacterium galatheae LMG F28894T (97.3 %). The predominant cellular fatty acids were C16 : 0, summed feature 3 (C16 : 1 ω6c and/or C16 : 1 ω7c) and summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c), with Q-8 as the major of isoprenoid quinone. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerols, phosphatidylcholine, phosphatidylethanolamine, phospholipid, two aminophospholipids and three unidentified lipids. The whole genome size of strain CAU 1568T was 4.8 Mb with 50.1 mol% G+C content; including 38 contigs and 4233 protein-coding genes. These taxonomic data support CAU 1568T as representing a novel Photobacterium species, for which the name Photobacterium arenosum sp. nov. is proposed. The type strain of this novel species is CAU 1568T (=KCTC 82404T=MCCC 1K05668T).
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Affiliation(s)
- Veeraya Weerawongwiwat
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul 06974, Republic of Korea
| | - Seokmin Yoon
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul 06974, Republic of Korea
| | - Jong-Hwa Kim
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul 06974, Republic of Korea
| | - Jung-Hoon Yoon
- Department of Food Science and Biotechnology, Sungkyunkwan University, Suwon, Republic of Korea
| | - Jung Sook Lee
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, Republic of Korea
| | - Ampaitip Sukhoom
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Thailand
| | - Wonyong Kim
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul 06974, Republic of Korea
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Li M, Ma Q, Kong D, Han X, Che J, Zhou Y, Jiang X, Ruan Z, Zhang Q. Pseudomonas nicosulfuronedens sp. nov., a nicosulfuron degrading bacterium, isolated from a microbial consortium. Int J Syst Evol Microbiol 2021; 71. [PMID: 33411665 DOI: 10.1099/ijsem.0.004632] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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, motile, short-rod-shaped bacterium with nicosulfuron-degrading ability, designated strain LAM1902T, was isolated from a microbial consortium enriched with nicosulfuron as a sole nitrogen and energy source. The optimal temperature and pH for growth of strain LAM1902T were 30 °C and pH 6.0, respectively. Strain LAM1902T could grow in the presence of NaCl with concentration up to 4.0 % (w/v). Comparative analysis of 16S rRNA gene sequences revealed that LAM1902T was closely related to the members of the family Pseudomonadaceae to the genus Pseudomonas, with the highest similarity to Pseudomonas nitroreducens DSM 14399T (99.6 %), Pseudomonas nitritireducens WZBFD3-5A2T (99.3 %) and Pseudomonas panipatensis Esp-1T (98.8 %). Multi-locus sequence analysis based on both concatenated sequences of the 16S rRNA gene and three housekeeping genes (gyrB, rpoB and rpoD) further confirmed the intrageneric phylogenetic position of strain LAM1902T. The genomic DNA G+C content of LAM1902T was 64.8 mol%. The low values of in silico DNA-DNA hybridization (less than 43.7 %) and average nucleotide identity (less than 90.9 %) also showed that the strain was distinctly different from known species of the genus Pseudomonas. The major fatty acids were C16 : 0, C17 : 0 cyclo and anteiso C15 : 0. Ubiquinone Q-9 was detected as the predorminant respiratory quinone. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and aminophospholipid. Based on phylogenetic, phenotypic and chemotaxonomic analyses and genome comparisons, we conclude that strain LAM1902T represents a novel species, for which the name Pseudomonas nicosulfuronedens sp. nov. is proposed. The type strain is LAM1902T (=JCM 33860T=KCTC 72830T).
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Affiliation(s)
- Miaomiao Li
- Institute of Agricultural Resources and Regional Planning, CAAS, Beijing 100081, PR China.,College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang 330045, PR China
| | - Qingyun Ma
- Institute of Agricultural Resources and Regional Planning, CAAS, Beijing 100081, PR China
| | - Delong Kong
- Institute of Agricultural Resources and Regional Planning, CAAS, Beijing 100081, PR China
| | - Xiaoyan Han
- Institute of Agricultural Resources and Regional Planning, CAAS, Beijing 100081, PR China.,College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang 330045, PR China
| | - Juan Che
- College of Life Science, Xinjiang Normal University, Urumqi, XinJiang, 830046, PR China.,Institute of Agricultural Resources and Regional Planning, CAAS, Beijing 100081, PR China
| | - Yiqing Zhou
- Institute of Agricultural Resources and Regional Planning, CAAS, Beijing 100081, PR China
| | - Xu Jiang
- Institute of Agricultural Resources and Regional Planning, CAAS, Beijing 100081, PR China
| | - Zhiyong Ruan
- Institute of Agricultural Resources and Regional Planning, CAAS, Beijing 100081, PR China.,College of Resources and Environment, Tibet Agricultural and Animal Husbandry University, Linzhi 860000, Tibet, PR China
| | - Qinghua Zhang
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang 330045, PR China
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Ma Q, Zhang Q, Jiang X, Kong D, Han X, Xue H, Zhou Y, Zhang Y, Zhang W, Ruan Z. Actinoplanes solisilvae sp. nov., Isolated from Birch Forest Soil. Curr Microbiol 2020; 77:3799-3806. [PMID: 32915290 DOI: 10.1007/s00284-020-02192-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 09/01/2020] [Indexed: 11/25/2022]
Abstract
A novel actinomycete, designated strain LAM7112T, was isolated from soil sample collected from a birch forest in Xinjiang Uygur Autonomous Region, China. The new isolate was found to be able to grow at 20-45 °C (optimum: 35 °C), pH 5.0-10.0 (optimum: 7.0) and in the presence of 0-10.0% (optimum: 3.0%) (w/v) NaCl. The isolate formed very scantily irregular sporangia containing motile spores on the substrate mycelium. Phylogenetic analysis of 16S rRNA gene sequences indicated that the new isolate was closely related to members of the family Micromonosporaceae, with highest similarites to Actinoplanes ferrugineus X-14695T (97.4%), Micromonospora zamorensis DSM 45600T (97.3%) and Micromonospora aurantiaca ATCC 27029T (97.3%). In the phylogenetic trees, strain LAM7112T formed a stable phylogenetic subclade within the genus Actinoplanes. The genomic DNA G + C content was 70.0 mol%. The major fatty acids (> 10%) were determined to be iso-C16:0, anteiso-C15:0 and anteiso-C17:0. The predominant menaquinones were identified as MK-9 (H2), MK-9 (H4) and MK-9 (H6). The major polar lipids were found to be diphosphatidylglycerol, phosphatidylinositol and phosphatidylethanolamine. The diagnostic amino acid of the cell wall peptidoglycan was determined to be meso-diaminopimelic acid. The diagnostic sugars in cell hydrolysates were determined to be glucose and ribose. On the basis of its phenotypic, phylogenetic and chemotaxonomic characteristics, strain LAM7112T (= CGMCC 4.7580T = JCM 32512T) is proposed to represent the type strain of a novel species of the genus Actinoplanes, for which the name Actinoplanes solisilvae is proposed.
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Affiliation(s)
- Qingyun Ma
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Qi Zhang
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- College of Life Science, Xinjiang Normal University, Ürümqi, 830046, Xinjiang, China
- Xinjiang Urumqi Maternal and Child Care Hospital, Ürümqi, 830001, Xinjiang, China
| | - Xu Jiang
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Delong Kong
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiaoyan Han
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Huiying Xue
- College of Resources and Environment, Tibet Agricultural and Animal Husbandry University, Linzhi, 860000, Tibet, China
| | - Yiqing Zhou
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yuqin Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Wei Zhang
- College of Life Science, Xinjiang Normal University, Ürümqi, 830046, Xinjiang, China.
| | - Zhiyong Ruan
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
- College of Resources and Environment, Tibet Agricultural and Animal Husbandry University, Linzhi, 860000, Tibet, China.
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Wang Z, Shi C, Wang H, Wan X, Zhang Q, Song X, Li G, Gong M, Ye S, Xie G, Huang J. A novel research on isolation and characterization of Photobacterium damselae subsp. damselae from Pacific white shrimp, Penaeus vannamei, displaying black gill disease cultured in China. JOURNAL OF FISH DISEASES 2020; 43:551-559. [PMID: 32196691 DOI: 10.1111/jfd.13153] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 02/15/2020] [Accepted: 02/18/2020] [Indexed: 06/10/2023]
Abstract
In June 2019, massive mortalities of cultured Penaeus vannamei occurred in a local farm in Hainan Province, China. The diseased shrimp displayed evident black gills. Three bacterial strains 20190611001, 20190611007 and 20190611022 were isolated from hepatopancreas and gills of the diseased shrimp and identified as Photobacterium damselae subsp. damselae based on the sequence analysis of 16S rRNA and toxR genes. These three isolates showed haemolytic activities. Of them, strain 20190611022 isolated from hepatopancreas was selected and processed for pathogenic analysis. The calculated median lethal dose (LD50 ) was 9.75 ± 4.29 × 105 CFU/g (body weight) by challenging P. vannameivia reverse gavage. The diseased shrimp displayed enlarged hepatopancreatic tubules and sloughing of epithelial cells in tubular lumens. The strain 20190611022 was also characterized by the testing of API 20NE systems and antibiotic susceptibility. The results of disc diffusion test showed that strain 20190611022 was sensitive to chloramphenicol, compound sulfamethoxazole, cefoperazone, ceftriaxone, ceftazidime and cefuroxime. To our knowledge, this is the first report of isolation and characterization of Photobacterium damselae subsp. damselae from natural diseased P. vannamei. Our findings can serve as a basis for further studies of its pathogenicity and provide technological support for disease controlling in shrimp aquaculture.
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Affiliation(s)
- Ziyan Wang
- College of Fisheries and Life Science, Dalian Ocean University, Dalian, China
- Laboratory for Marine Fisheries Science and Food Production Processes, National Laboratory for Marine Science and Technology (Qingdao), Key Laboratory of Maricultural Organism Disease Control, Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Chengyin Shi
- Laboratory for Marine Fisheries Science and Food Production Processes, National Laboratory for Marine Science and Technology (Qingdao), Key Laboratory of Maricultural Organism Disease Control, Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Hailiang Wang
- Laboratory for Marine Fisheries Science and Food Production Processes, National Laboratory for Marine Science and Technology (Qingdao), Key Laboratory of Maricultural Organism Disease Control, Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Xiaoyuan Wan
- Laboratory for Marine Fisheries Science and Food Production Processes, National Laboratory for Marine Science and Technology (Qingdao), Key Laboratory of Maricultural Organism Disease Control, Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Qingli Zhang
- Laboratory for Marine Fisheries Science and Food Production Processes, National Laboratory for Marine Science and Technology (Qingdao), Key Laboratory of Maricultural Organism Disease Control, Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Xiaoling Song
- Laboratory for Marine Fisheries Science and Food Production Processes, National Laboratory for Marine Science and Technology (Qingdao), Key Laboratory of Maricultural Organism Disease Control, Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Ge Li
- Laboratory for Marine Fisheries Science and Food Production Processes, National Laboratory for Marine Science and Technology (Qingdao), Key Laboratory of Maricultural Organism Disease Control, Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Miao Gong
- Laboratory for Marine Fisheries Science and Food Production Processes, National Laboratory for Marine Science and Technology (Qingdao), Key Laboratory of Maricultural Organism Disease Control, Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Shigen Ye
- College of Fisheries and Life Science, Dalian Ocean University, Dalian, China
| | - Guosi Xie
- Laboratory for Marine Fisheries Science and Food Production Processes, National Laboratory for Marine Science and Technology (Qingdao), Key Laboratory of Maricultural Organism Disease Control, Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Jie Huang
- Laboratory for Marine Fisheries Science and Food Production Processes, National Laboratory for Marine Science and Technology (Qingdao), Key Laboratory of Maricultural Organism Disease Control, Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
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10
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Kong D, Zhang Q, Jiang X, Ma Q, Han X, Zhou Y, Xue H, Zhang Y, Zhang W, Ruan Z. Paenibacillus solisilvae sp. nov., isolated from birch forest soil. Int J Syst Evol Microbiol 2020; 70:2690-2695. [PMID: 32293556 DOI: 10.1099/ijsem.0.004093] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-positive, motile, rod-shaped bacterium, designated strain LAM7113T, was isolated from soil sample collected from a birch forest in Xinjiang Uygur Autonomous Region, PR China. Strain LAM7113T grew optimally at pH 8.0, 30 °C and in the presence of 1.0 % NaCl (w/v). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain LAM7113T was closely related to members of the genus Paenibacillus, with the highest similarity to Paenibacillus baekrokdamisoli Back-11T (96.2 %). The genomic DNA G+C content was 43.4 mol%. The values of average nucleotide identity and DNA-DNA hybridization were 66.1 and 27.0 %, respectively, by comparing the draft genome sequences of strain LAM7113T and P. baekrokdamisoli Back-11T. Anteiso-C15 : 0 and iso-C15 : 0 were identified as the major cellular fatty acids. Menaquinone-7 was detected as the predominant respiratory quinone. The major polar lipids were found to be diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, three unidentified aminophospholipids, three unidentified glycolipids, one unidentified phospholipid and two unknown polar lipids. Based on its phenotypic, phylogenetic and chemotaxonomic characteristics, strain LAM7113T is proposed to represent a novel species of the genus Paenibacillus with the name Paenibacillus solisilvae sp. nov. The type strain is LAM7113T (=CGMCC 1.16619T=JCM 32513T).
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Affiliation(s)
- Delong Kong
- Institute of Agricultural Resources and Regional Planning, CAAS, Beijing 100081, PR China
| | - Qi Zhang
- College of Life Science, Xinjiang Normal University, Urumqi, XinJiang, 830046, PR China
| | - Xu Jiang
- Institute of Agricultural Resources and Regional Planning, CAAS, Beijing 100081, PR China
| | - Qingyun Ma
- Institute of Agricultural Resources and Regional Planning, CAAS, Beijing 100081, PR China
| | - Xiaoyan Han
- Institute of Agricultural Resources and Regional Planning, CAAS, Beijing 100081, PR China
| | - Yiqing Zhou
- Institute of Agricultural Resources and Regional Planning, CAAS, Beijing 100081, PR China
| | - Huiying Xue
- College of Resources and Environment, Tibet Agricultural and Animal Husbandry University, Linzhi 860000, Tibet, PR China
| | - Yuqin Zhang
- Chinese Academy of Medical Sciences and Peking Union Medical College, Institute of Medicinal Biotechnology, Beijing 100050, PR China
| | - Wei Zhang
- College of Life Science, Xinjiang Normal University, Urumqi, XinJiang, 830046, PR China
| | - Zhiyong Ruan
- Institute of Agricultural Resources and Regional Planning, CAAS, Beijing 100081, PR China.,College of Resources and Environment, Tibet Agricultural and Animal Husbandry University, Linzhi 860000, Tibet, PR China
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11
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Xing J, Jiang X, Kong D, Zhou Y, Li M, Han X, Ma Q, Tan H, Ruan Z. Streptomyces soli sp. nov., isolated from birch forest soil. Arch Microbiol 2020; 202:1687-1692. [PMID: 32285167 DOI: 10.1007/s00203-020-01878-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Revised: 03/22/2020] [Accepted: 04/01/2020] [Indexed: 11/27/2022]
Abstract
A Gram-staining positive, aerobic, non-motile, rod-shaped bacterium, designated strain LAM7114T, was isolated from soil sample collected from a birch forest in Xinjiang Uygur Autonomous Region, China. The optimal temperature and pH for the growth of strain LAM7114T were 30 °C and 7.0, respectively. Strain LAM7114T could grow in the presence of NaCl up to 10% (w/v). Comparative analysis of the 16S rRNA gene sequences revealed that LAM7114T was closely related to the members of the family genus Streptomyces, with the highest similarity to Streptomyces urticae NEAU-PCY-1T (98.3%) and Streptomyces fildesensis GW25-5T (98.2%). The genomic G + C content was 70.0 mol%. The DNA-DNA hybridization values between strain LAM7114T and S. urticae CCTCC AA 2017015T, S. fildesensis CGMCC 4.5735T were 32.5 ± 1.8% and 27.5 ± 2.6%, respectively. The cell wall contained LL-diaminopimelic acid as the diagnostic diamino acid in the peptidoglycan. The whole-cell hydrolysates included glucose and mannose. The major fatty acids were anteiso-C15:0, iso-C15:0 and iso-C16:0. The predominant menaquinones were MK-9(H6), MK-9(H4) and MK-9(H8). The main polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, three unidentified aminophospholipids, three unidentified phospholipids, and an unidentified aminolipid. Based on the phenotypic characteristics and genotypic analyses, we propose that strain LAM7114T represents a novel species in the genus Streptomyces, for which the name Streptomyces soli sp. nov. is proposed. The type strain is LAM7114T (= CGMCC 4.7581T = JCM 32822T).
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Affiliation(s)
- Jialing Xing
- Institute of Agricultural Resources and Regional Planning, CAAS, Beijing, 100081, China
| | - Xu Jiang
- Institute of Agricultural Resources and Regional Planning, CAAS, Beijing, 100081, China
| | - Delong Kong
- Institute of Agricultural Resources and Regional Planning, CAAS, Beijing, 100081, China
| | - Yiqing Zhou
- Institute of Agricultural Resources and Regional Planning, CAAS, Beijing, 100081, China
| | - Miaomiao Li
- Institute of Agricultural Resources and Regional Planning, CAAS, Beijing, 100081, China.,College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, 330045, People's Republic of China
| | - Xiaoyan Han
- Institute of Agricultural Resources and Regional Planning, CAAS, Beijing, 100081, China.,College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, 330045, People's Republic of China
| | - Qingyun Ma
- Institute of Agricultural Resources and Regional Planning, CAAS, Beijing, 100081, China
| | - Hao Tan
- Institute of Agricultural Resources and Regional Planning, CAAS, Beijing, 100081, China
| | - Zhiyong Ruan
- Institute of Agricultural Resources and Regional Planning, CAAS, Beijing, 100081, China.
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12
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Li B, Li Y, Liu R, Xue C, Zhu X, Tian X, Wang X, Liang J, Zheng Y, Zhang XH. Vibrio ouci sp. nov. and Vibrio aquaticus sp. nov., two marine bacteria isolated from the East China Sea. Int J Syst Evol Microbiol 2020; 70:172-179. [DOI: 10.1099/ijsem.0.003732] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Bei Li
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Yuying Li
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Ronghua Liu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Chunxu Xue
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Xiaoyu Zhu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Xiaorong Tian
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Xiaolei Wang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Jinchang Liang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Yanfen Zheng
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Xiao-Hua Zhang
- Institute of Evolution & 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
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
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13
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Fuertes-Perez S, Hauschild P, Hilgarth M, Vogel RF. Biodiversity of Photobacterium spp. Isolated From Meats. Front Microbiol 2019; 10:2399. [PMID: 31749770 PMCID: PMC6842964 DOI: 10.3389/fmicb.2019.02399] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 10/03/2019] [Indexed: 01/01/2023] Open
Abstract
Photobacteria are common psychrophilic bacteria found in marine environments. Recently, several studies revealed high numbers of Photobacterium (P.) spp. on packaged fresh meat. Their occurrence appears relevant for the spoilage of meat, since species of the genus are already known as potent fish spoilage organisms. Here we report on distribution, biodiversity, and specific traits of P. carnosum (n = 31), P. phosphoreum (n = 24), and P. iliopiscarium (n = 3) strains from different foods. Biodiversity was assessed by genomic fingerprinting, diversity index analysis, growth dynamics, comparison of metabolic activities, and antibiotic resistance. We observed a ubiquitous occurrence of the species on all common meats independent of packaging conditions and producer, suggesting contamination during an established processing or packaging step. Regarding biodiversity, the three species differed clearly in their growth properties and metabolic characteristics, with P. phosphoreum growing the fastest and showing the strongest alkalization of the media. On strain level we also recorded variations in enzymatic reactions, acid production, and antibiotic resistances not restricted to specific meat types. This depicts high biodiversity on species and strain level on each contaminated meat sample. Our analysis showed that meat-borne strains of P. phosphoreum and P. iliopiscarium clearly differ from their type strains from a marine habitat. Additionally, we report for the first time isolation of P. carnosum strains from packaged fish, which in contrast showed comparable phenotypic properties to meat-borne strains. This hints at different initial origins of P. phosphoreum/P. iliopiscarium (marine background) and P. carnosum (no demonstrated marine background) contaminations on fish and meat, respectively.
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Affiliation(s)
- Sandra Fuertes-Perez
- Lehrstuhl Technische Mikrobiologie, Technische Universität München, Freising, Germany
| | - Philippa Hauschild
- Lehrstuhl Technische Mikrobiologie, Technische Universität München, Freising, Germany
| | - Maik Hilgarth
- Lehrstuhl Technische Mikrobiologie, Technische Universität München, Freising, Germany
| | - Rudi F Vogel
- Lehrstuhl Technische Mikrobiologie, Technische Universität München, Freising, Germany
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14
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Wang X, Li Y, Xue CX, Li B, Zhou S, Liu L, Zhang XH. Photobacterium chitinilyticum sp. nov., a marine bacterium isolated from seawater at the bottom of the East China Sea. Int J Syst Evol Microbiol 2019; 69:1477-1483. [PMID: 30860462 DOI: 10.1099/ijsem.0.003343] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, facultative aerobic, motile by a polar flagellum, rod-shaped strain, designated BEI247T, was isolated from seawater at the bottom of the East China Sea. Phylogenetic analysis of the 16S rRNA gene and whole genome data affiliated it with the genus Photobacterium. It was most closely related to Photobacterium alginatilyticum P03D4T (97.36 % 16S rRNA gene similarity). Multi-locus sequence analysis (MLSA) revealed a distinct lineage with P. alginatilyticum P03D4T as its closest relative. Strain BEI247T was found to have lower than 86.0 % similarities to the type strains of its most closely related species in MLSA, less than 82.3 % using genome average nucleotide identities, and less than 25.3 % in DNA-DNA relatedness studies. Growth occurred at 10-37 °C (optimum, 24 °C), pH 5.0-8.0 (pH 7.0) and in the presence of 1-5 % (w/v) NaCl (3 %). The dominant fatty acids were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0. The polar lipids of strain BEI247T comprised phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, two phospholipids and one unknown lipid. The major respiratory quinone was ubiquinone-8 (Q-8). The DNA G+C content of strain BEI247T was 46.45 mol%. On the basis of the polyphasic evidence, strain BEI247T is proposed as representing a novel species of the genus Photobacterium, for which the name Photobacterium chitinilyticum sp. nov. is proposed. The type strain is BEI247T (=JCM 32689T=MCCC 1K03517T=KCTC 62619T).
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Affiliation(s)
- Xiaolei Wang
- 1MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Yuying Li
- 1MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Chun-Xu Xue
- 1MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Bei Li
- 1MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Shun Zhou
- 1MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Lijun Liu
- 1MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Xiao-Hua Zhang
- 2Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, PR China.,3Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, PR China.,1MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
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15
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Abstract
Phylogenetic relationships between species in the genus Photobacterium have been poorly studied despite pathogenic and ecological relevance of some of its members. This is the first phylogenetic study that includes new species of Photobacterium (validated or not) that have not been included in any of the previously described clades, using 16S rRNA sequences and multilocus sequence analysis (MLSA) in concatenated sequences of gyrB, gapA, topA, ftsZ and mreB housekeeping genes. Sequence analysis has been implemented using Maximum-parsimony (MP), Neighbour-joining (NJ) and Maximum likelihood (ML) treeing methods and the predicted evolutionary relationship between the Photobacterium clades was established on the basis of bootstrap values of >75% for 16S rRNA sequences and MLSA. We have grouped 22 species of the genus Photobacterium into the following 5 clades: Phosphoreum (comprises P. aquimaris, “P. carnosum,” P. iliopiscarium, P. kishitanii, P. phosphoreum, “P. piscicola” and “P. toruni”); clade Profundum (composed of P. aestuarii, P. alginatilyticum, P. frigidiphilum, P. indicum, P. jeanii, P. lipolyticum, “P. marinum,” and P. profundum); clade Damselae (two subspecies of P. damselae, damselae and piscicida); and two new clades: clade Ganghwense (includes P. aphoticum, P. aquae, P. galatheae, P. ganghwense, P. halotolerans, P. panuliri and P. proteolyticum); and clade Leiognathi (composed by P. angustum, P. leiognathi subsp. leiognathi and “P. leiognathi subsp. mandapamensis”). Two additional clades, Rosenbergii and Swingsii, were formed using a phylogenetic method based on 16S rRNA gene, although they are not confirmed by any MLSA methods. Only P. aplysiae could not be included in none of the established clade, constituting an orphan clade.
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Affiliation(s)
- Alejandro M Labella
- Department of Microbiology, Faculty of Sciences, Universidad de Malaga, 29071 Malaga, Spain.
| | - M Dolores Castro
- Department of Microbiology, Faculty of Sciences, Universidad de Malaga, 29071 Malaga, Spain.
| | - Manuel Manchado
- Puerto de Santa María, Junta de Andalucía, IFAPA Centro El Toruño, 11500 Cadiz, Spain.
| | - Juan J Borrego
- Department of Microbiology, Faculty of Sciences, Universidad de Malaga, 29071 Malaga, Spain.
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