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Yang X, Garuglieri E, Van Goethem MW, Marasco R, Fusi M, Daffonchio D. Mangrovimonas cancribranchiae sp. nov., a novel bacterial species associated with the gills of the fiddler crab Cranuca inversa (Brachyura, Ocypodidae) from Red Sea mangroves. Int J Syst Evol Microbiol 2024; 74:006415. [PMID: 38865172 PMCID: PMC11261673 DOI: 10.1099/ijsem.0.006415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Accepted: 05/27/2024] [Indexed: 06/13/2024] Open
Abstract
Two bacteria, UG2_1T and UG2_2, were isolated from the gill tissues of the mangrove fiddler crab Cranuca inversa collected on the east coast of the Red Sea (Thuwal, Saudi Arabia). The cells are Gram-negative, rod-shaped, orange-pigmented, motile by gliding with no flagella, strictly aerobic, and grow at 20-37 °C (optimum, 28-35 °C), at pH 5.0-9.0 (optimum, pH 6.0-7.0), and with 1-11 % (w/v) NaCl (optimum, 2-4 %). They were positive for oxidase and catalase activity. Phylogenetic analysis based on 16S rRNA gene sequences indicated that isolates UG2_1T and UG2_2 belong to the genus Mangrovimonas, showing the highest similarity to Mangrovimonas spongiae HN-E26T (99.4 %). Phylogenomic analysis based on the whole genomes, independently using 49 and 120 concatenated genes, showed that strains UG2_1T and UG2_2 formed a monophyletic lineage in a different cluster from other type strain species within the genus Mangrovimonas. The genome sizes were 3.08 and 3.07 Mbp for UG2_1T and UG2_2, respectively, with a G+C content of 33.8 mol% for both strains. Values of average nucleotide identity and digital DNA-DNA hybridization between the strains and closely related species were 91.0 and 43.5 %, respectively. Chemotaxonomic analysis indicated that both strains had iso-C15 : 0 and iso-C15 : 1 G as dominant fatty acids, and the primary respiratory quinone was identified as MK-6. The major polar lipids comprised phosphatidylethanolamine, one unidentified glycolipid, one unidentified phospholipid, two unidentified aminolipids, and four unidentified lipids. Based on phylogenetic, phylogenomic, genome relatedness, phenotypic, and chemotaxonomical data, the two isolates represent a novel species within the genus Mangrovimonas, with the proposed name Mangrovimonas cancribranchiae sp. nov., and the type strain UG2_1T (=KCTC 102158T=DSM 117025T).
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Affiliation(s)
- Xinyuan Yang
- Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Elisa Garuglieri
- Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Marc W. Van Goethem
- Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Ramona Marasco
- Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Marco Fusi
- Dove Marine Laboratory, School of Natural and Environmental Sciences Newcastle University, Newcastle-Upon-Tyne, NE1 7RU, UK
| | - Daniele Daffonchio
- Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
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2
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Liu Y, Pei T, Du J, Zhang M, Zhu H. Altererythrobacter litoralis sp. nov., a New Carotenoid-Producing Member of the Family Erythrobacteraceae, Isolated from a Tidal Flat Sediment. Curr Microbiol 2024; 81:191. [PMID: 38797770 DOI: 10.1007/s00284-024-03714-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Accepted: 04/21/2024] [Indexed: 05/29/2024]
Abstract
A new isolate designated as 1XM1-14T was isolated from a tidal flat sediment of Xiamen Island. The yellow-pigmented colonies and rod-shaped cells were observed. Strain 1XM1-14T could hydrolyze Tweens 20, 40, 60, aesculin, and skim milk, and was chemoheterotrophic and mesophilic, required NaCl for the growth. The 16S rRNA gene-based phylogenetic analysis indicated that strain 1XM1-14T was the most closely related to Altererythrobacter epoxidivorans CGMCC 1.7731T (97.0%), followed by other type strain of the genus Altererythrobacter with identities below 97.0%. The DNA-DNA hybridization and average nucleotide identity values between strain 1XM1-14T and its relatives of the genus Altererythrobacter were below the respective thresholds for prokaryotic species demarcation. The phylogenomic inference further revealed that strain 1XM1-14T formed a separate branch distinct from the type strains of the recognized species within the genus Altererythrobacter. The major cellular fatty acids of strain 1XM1-14T were identified as summed feature 8 (C18:1 ω6c and/or C18:1 ω7c), C17:1 ω6c, and C16:0; the profile of polar lipids comprised diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, sphingoglycolipid, an unidentified glycolipid, and two unidentified lipids; the respiratory quinone was determined to ubiquinone-10. The genomic size and DNA G+C content of strain 1XM1-14T were 2.5 Mbp and 62.71%. The key carotenoid biosynthetic genes were determined in the genome of strain 1XM1-14T and the generated carotenoids were detected. The combined genotypic and phenotypic characteristics supported the classification of strain 1XM1-14T (= GDMCC 1.2383T = KCTC 82612T) as a novel species in the genus Altererythrobacter, for which the name Altererythrobacter litoralis sp. nov. is proposed.
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Affiliation(s)
- Yang Liu
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Building 66, Xianlie Middle Road 100, Guangzhou, 510070, Guangdong, People's Republic of China
| | - Tao Pei
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Building 66, Xianlie Middle Road 100, Guangzhou, 510070, Guangdong, People's Republic of China
| | - Juan Du
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Building 66, Xianlie Middle Road 100, Guangzhou, 510070, Guangdong, People's Republic of China
| | - Mingxia Zhang
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Building 66, Xianlie Middle Road 100, Guangzhou, 510070, Guangdong, People's Republic of China
| | - Honghui Zhu
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Building 66, Xianlie Middle Road 100, Guangzhou, 510070, Guangdong, People's Republic of China.
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3
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Montecillo JAV, Billacura MP, Billacura MDG. Reclassification of Aestuariicella albida as Pseudomaricurvus albidus comb. nov. and Aestuariicella hydrocarbonica as Pseudomaricurvus hydrocarbonicus comb. nov. Based on Comparative Genomics and Molecular Synapomorphies. Curr Microbiol 2024; 81:159. [PMID: 38689166 DOI: 10.1007/s00284-024-03683-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 03/30/2024] [Indexed: 05/02/2024]
Abstract
The genus Aestuariicella has been recently reclassified as a member of the family Cellvibrionaceae. However, the taxonomic position of the genus as a distinct member of the family has not been clarified. In the present study, we performed multilayered analyses anchored on genome sequences to clarify the relationship between the genera Aestuariicella and Pseudomaricurvus within the family Cellvibrionaceae. Phylogenetic analyses based on 16S rRNA gene, RNA polymerase beta subunit (RpoB) protein, and core gene sequences showed a well-supported tight cluster formed by the members of the two genera. Moreover, the analysis of the average amino acid identity (AAI) revealed that the members of the two genera shared 68.16-79.48% AAI, values which were within the range of observed AAI (≥ 67.23%) among the members of the same genus within the family Cellvibrionaceae. Members of the two genera also shared several common characteristics. Furthermore, molecular synapomorphies in a form of conserved signature indels were identified in six protein sequences that were exclusively shared by the members of the two genera. Based on the phylogenetic and molecular evidence presented here, we propose the reclassification of the species Aestuariicella albida and Aestuariicella hydrocarbonica as Pseudomaricurvus albidus comb. nov. and Pseudomaricurvus hydrocarbonicus comb. nov., respectively.
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Affiliation(s)
- Jake Adolf V Montecillo
- Department of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk, 38541, Republic of Korea.
| | - Merell P Billacura
- Department of Chemistry, Mindanao State University-Main Campus, 9700, Marawi, Lanao del Sur, Philippines
| | - Maria Distressa G Billacura
- Department of Chemistry, Mindanao State University-Iligan Institute of Technology, Andres Bonifacio Avenue, Tibanga, 9200, Iligan, Lanao del Norte, Philippines
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Yang K, Tan J, Jiang G, Ni Z, Lin Q, Chao Y, Ruan Z, Qiu R. Description and Genomic Characteristics of Diaphorobacter limosus sp. nov., Isolated from a Sewage-Treatment Plant. Curr Microbiol 2024; 81:155. [PMID: 38652318 DOI: 10.1007/s00284-024-03659-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 03/03/2024] [Indexed: 04/25/2024]
Abstract
A Gram-stain-negative, rod-shaped, non-motile, catalase-positive, denitrifying bacterium, designated strain Y-1T, was isolated from an aeration tank of a sewage treatment plant in China and characterized using polyphasic taxonomic approaches. Strain Y-1T could grow at 10-37 °C (optimum 25 °C), at pH 5.0-10.0 (optimum 7.0) and in the presence of 0-3.0% (w/v) NaCl (optimum 0.5%). The phylogenetic tree based on the 16S rRNA gene sequences revealed that strain Y-1T was a member of genus Diaphorobacter, and showed the highest sequence similarities with Diaphorobacter oryzae RF3T (97.50%), Diaphorobacter nitroreducens NA10BT (97.38%) and Diaphorobacter aerolatus 8604S-37T (96.56%). In terms of carbon source utilization and enzyme activities, strain Y-1T was significantly different from its similar strains. The major respiratory quinone was Q-8, and the main polar lipid was phosphatidylethanolamine. Comparative genomic analysis of strain Y-1T and other Diaphorobacter species was conducted to explore the mechanisms underlying the differences among these strains. Strain Y-1T encoded 3957 genes, consisting of 3813 protein-coding genes and 144 RNA coding genes, and encoded 652 enzymes with 31 unique enzymes compared with other related species. The DNA G + C content was 69.95 mol%. Strain Y-1T exhibited 41.71% DNA-DNA relatedness and 95% ANIb with the most related type strains.On the basis of the evidence presented from polyphasic analysis, strain Y-1T was suggested as a novel species within the genus Diaphorobacter, for which the name Diaphorobacter limosus sp. nov. is proposed, with the type strain Y-1T (= KCTC 92852T = CCTCC AB 2023032T).
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Affiliation(s)
- Kaiqing Yang
- Heyuan Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Provincial Key Laboratory of Agricultural and Rural Pollution Abatement and Environmental Safety, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, China
| | - Jialin Tan
- Heyuan Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Provincial Key Laboratory of Agricultural and Rural Pollution Abatement and Environmental Safety, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, China
| | - Gengbo Jiang
- School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou, 510006, China
| | - Zhuobiao Ni
- Heyuan Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Provincial Key Laboratory of Agricultural and Rural Pollution Abatement and Environmental Safety, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, China
| | - Qingqi Lin
- Heyuan Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Provincial Key Laboratory of Agricultural and Rural Pollution Abatement and Environmental Safety, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, China
| | - Yuanqing Chao
- School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou, 510006, China
| | - Zhepu Ruan
- Heyuan Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Provincial Key Laboratory of Agricultural and Rural Pollution Abatement and Environmental Safety, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, China.
| | - Rongliang Qiu
- Heyuan Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Provincial Key Laboratory of Agricultural and Rural Pollution Abatement and Environmental Safety, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, China.
- School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou, 510006, China.
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Jing F, Chen K, Yandeau-Nelson MD, Nikolau BJ. Machine learning model of the catalytic efficiency and substrate specificity of acyl-ACP thioesterase variants generated from natural and in vitro directed evolution. Front Bioeng Biotechnol 2024; 12:1379121. [PMID: 38665811 PMCID: PMC11043601 DOI: 10.3389/fbioe.2024.1379121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 03/28/2024] [Indexed: 04/28/2024] Open
Abstract
Modulating the catalytic activity of acyl-ACP thioesterase (TE) is an important biotechnological target for effectively increasing flux and diversifying products of the fatty acid biosynthesis pathway. In this study, a directed evolution approach was developed to improve the fatty acid titer and fatty acid diversity produced by E. coli strains expressing variant acyl-ACP TEs. A single round of in vitro directed evolution, coupled with a high-throughput colorimetric screen, identified 26 novel acyl-ACP TE variants that convey up to a 10-fold increase in fatty acid titer, and generate altered fatty acid profiles when expressed in a bacterial host strain. These in vitro-generated variant acyl-ACP TEs, in combination with 31 previously characterized natural variants isolated from diverse phylogenetic origins, were analyzed with a random forest classifier machine learning tool. The resulting quantitative model identified 22 amino acid residues, which define important structural features that determine the catalytic efficiency and substrate specificity of acyl-ACP TE.
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Affiliation(s)
- Fuyuan Jing
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA, United States
- Center for Metabolic Biology, Iowa State University, Ames, IA, United States
- Engineering Research Center for Biorenewable Chemicals, Iowa State University, Ames, IA, United States
| | - Keting Chen
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA, United States
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, United States
| | - Marna D. Yandeau-Nelson
- Center for Metabolic Biology, Iowa State University, Ames, IA, United States
- Engineering Research Center for Biorenewable Chemicals, Iowa State University, Ames, IA, United States
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, United States
| | - Basil J. Nikolau
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA, United States
- Center for Metabolic Biology, Iowa State University, Ames, IA, United States
- Engineering Research Center for Biorenewable Chemicals, Iowa State University, Ames, IA, United States
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Wei HM, Xu L, Zhang X, Sun JQ. Three novel Luteimonas species from a root and rhizosphere soil of Kalidium cuspidatum: Luteimonas endophytica sp. nov., Luteimonas rhizosphaericola sp. nov. and Luteimonas kalidii sp. nov. Int J Syst Evol Microbiol 2024; 74. [PMID: 38284380 DOI: 10.1099/ijsem.0.006257] [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: 01/30/2024] Open
Abstract
Three Gram-stain-negative, aerobic and rod-shaped bacterial strains, designated RD2P54T, M1R5S18T and M1R5S59T, were isolated from a root and rhizosphere soil of Kalidium cuspidatum, in Baotou, PR China. The three strains showed 94.1–98.7 % 16S rRNA gene sequence similarities to
Luteimonas
strains, indicating they belonged to the genus
Luteimonas
. The phylogenomic tree based on core genomes showed that strain RD2P54T tightly clustered with
Luteimonas salinisoli
SJ-92T, while strains M1R5S18T and M1R5S59T clustered with each other and with Luteimonas viscosa XBU10T and
Luteimonas saliphila
SJ-9T. Though strains M1R5S18T and M1R5S59T showed high 16S rRNA similarity (99.4 %) to each other, the low average nucleotide identity based on blast (ANIb; 88.6 %) and digital DNA–DNA hybridization (dDDH; 31.6 %) values between them indicated that they belonged to two different species. The ANIb and dDDH values of strains RD2P54T, M1R5S18T and M1R5S59T with their closely neighbours are well below the delineation threshold values for identifying strains as representing different species. All three strains take iso-C15 : 0 and summed feature 9 (C16 : 0 10-methyl and/or iso-C17 : 1
ω9c) as major fatty acids, and ubiquinone-8 as the sole respiratory quinone. The major polar lipids of all three strains are diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. Based on phenotypic and phylogenetic data, these three strains should be considered to represent three novel species of the genus
Luteimonas
, for which the names Luteimonas endophytica sp. nov. (type strain RD2P54T=CGMCC 1.61535T =KCTC 92470T), Luteimonas rhizosphaericola sp. nov. (type strain M1R5S18T=CGMCC 1.61537T =KCTC 92469T) and Luteimonas kalidii sp. nov. (type strain M1R5S59T=CGMCC 1.61536T =KCTC 92471T) are proposed.
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Affiliation(s)
- Hua-Mei Wei
- Laboratory for Microbial Resources, School of Ecology and Environment, Inner Mongolia University, Hohhot, 010021, PR China
| | - Lian Xu
- Jiangsu Key Laboratory for Organic Solid Waste Utilization, Educational Ministry Engineering Center of Resource-saving Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Xu Zhang
- Laboratory for Microbial Resources, School of Ecology and Environment, Inner Mongolia University, Hohhot, 010021, PR China
| | - Ji-Quan Sun
- Laboratory for Microbial Resources, School of Ecology and Environment, Inner Mongolia University, Hohhot, 010021, PR China
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Ye L, Zhang G, Yang J, Yang C, Liu Y, Pu J, Huang Y, Zhang S, Jin D, Lu S, Liu L, Xu J. Taxonomic descriptions of Aeromicrobium duanguangcaii sp. nov., Aeromicrobium wangtongii sp. nov. and Aeromicrobium senzhongii sp. nov. Int J Syst Evol Microbiol 2023; 73. [PMID: 37917124 DOI: 10.1099/ijsem.0.006118] [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: 11/03/2023] Open
Abstract
Six Gram-stain-positive, facultative anaerobic, nonmotile and rod-shaped strains, designated zg-Y50T, zg-Y1362, zg-Y1379T, zg-Y869, zg-629T and zg-Y636, were isolated from the intestinal contents of Marmota himalayana in Qinghai Province, PR China. Strains zg-Y50T, zg-Y1379T and zg-629T exhibited the highest 16S rRNA gene sequence similarities of 99.2, 98.9 and 98.8 % to Aeromicrobium choanae 9 H-4T, Aeromicrobium ginsengisoli JCM 14732T and Aeromicrobium flavum TYLN1T, respectively. Phylogenetic and phylogenomic analyses based on the 16S rRNA gene and genomic sequences, respectively, revealed that the six strains formed three distinct clades within the genus Aeromicrobium. The genome sizes of strains zg-Y50T, zg-Y1379T and zg-629T were 3.1-3.7 Mb, with DNA G+C contents of 69.6-70.4 mol%. Average nucleotide identity and digital DNA-DNA hybridization values between each novel strain and available members of the genus Aeromicrobium were all below species thresholds. All novel strains contained MK-9 (H4) as the major menaquinone and diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol as the polar lipids. The predominant fatty acid of the six isolates was C18 : 1 ω9c. The cell-wall peptidoglycan contained ʟʟ-diaminopimelic acid as the diagnostic diamino acid. Based on the results from this polyphasic taxonomic study, three novel species in the genus Aeromicrobium are proposed, namely, Aeromicrobium duanguangcaii sp. nov. (zg-Y50T=GDMCC 1.2981T=KCTC 49764T), Aeromicrobium wangtongii sp. nov. (zg-Y1379T=GDMCC 1.2982T=KCTC 49765T) and Aeromicrobium senzhongii sp. nov. (zg-629T=CGMCC 1.17414T=JCM 33888T).
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Affiliation(s)
- Lin Ye
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan 030001, PR China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
- Department of Endocrinology, The second hospital of Shanxi Medical University, Taiyuan 030001, PR China
| | - Gui Zhang
- Infection Management Office, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan 250021, PR China
| | - Jing Yang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 102206, PR China
| | - Caixin Yang
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan 030001, PR China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Yue Liu
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan 030001, PR China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Ji Pu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Yuyuan Huang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Sihui Zhang
- Department of Laboratorial Science and Technology & Vaccine Research Center, School of Public Health, Peking University, 38th Xueyuan Road, Haidian District, Beijing 100191, PR China
| | - Dong Jin
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 102206, PR China
| | - Shan Lu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 102206, PR China
| | - Liyun Liu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 102206, PR China
| | - Jianguo Xu
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan 030001, PR China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 102206, PR China
- Department of Laboratorial Science and Technology & Vaccine Research Center, School of Public Health, Peking University, 38th Xueyuan Road, Haidian District, Beijing 100191, PR China
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8
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Ying Y, Yuan B, Liu T, Bai X, Zhao H. Leucobacter tenebrionis sp. nov., isolated from the gut of Tenebrio molitor. Int J Syst Evol Microbiol 2023; 73. [PMID: 37823785 DOI: 10.1099/ijsem.0.006081] [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: 10/13/2023] Open
Abstract
A novel Gram-stain-positive bacterium, designated NB10T, was isolated from the gut of Tenebrio molitor. The isolate was rod-shaped, aerobic, non-motile and non-spore-forming. Colonies of strain NB10T were light yellow, circular and smooth. Phylogenetic analysis based on 16S rRNA gene sequence comparisons indicated that the isolate was related to the genus Leucobacter. Its closest relatives were Leucobacter holotrichiae T14T (97.8 % 16S rRNA gene sequence similarity), Leucobacter zeae CC-MF41T (97.0%) and Leucobacter salsicius M1-8T (96.4%). The DNA G+C content of strain NB10T was 68.8 mol%. The average nucleotide identity (ANI) and digital DNA-DNA hybridization values among strain NB10T and the selected Leucobacter species were ≤83.8 % (ANI-blast), 87.6 % (ANI-MUMmer) and 29.6%, which were below the recommended cutoff values for species delineation. The predominant cellular fatty acids were anteiso-C15 : 0 (39.0%), anteiso-C17 : 0 (35.5%) and iso-C16 : 0 (17.0%). The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and glycolipids. The predominant respiratory quinones were MK-11 and MK-10. The cell wall amino acids were Gly, Glu, Tr, Ala, and DAB. Based on these phylogenetic and phenotypic results, strain NB10T can be clearly distinguished from all of the recognized species of the genus Leucobacter and is considered to represent a novel species of that genus. The name Leucobacter tenebrionis sp. nov. is proposed, with the type strain NB10T (=MCCC 1K07072T=KCTC 49728T).
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Affiliation(s)
- Yu Ying
- Qingdao Institute for Food and Drug Control 266071, Qingdao, PR China
| | - Bo Yuan
- College of Life Science and Technology, Inner Mongolia Normal University, Hohhot, 010022, Inner Mongolia, PR China
| | - Tingting Liu
- Qingdao Institute for Food and Drug Control 266071, Qingdao, PR China
| | - Xiaoshuan Bai
- College of Life Science and Technology, Inner Mongolia Normal University, Hohhot, 010022, Inner Mongolia, PR China
| | - Haifeng Zhao
- Qingdao Institute for Food and Drug Control 266071, Qingdao, PR China
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Zhu GX, Chen X, Wu YJ, Wang HL, Jiao Y, Liu ZC, Zhang Y, Tang SK, Kong DJ, Cao YR. Chryseobacterium luquanense sp. nov., a casein-hydrolysing bacterium from the Jiaozi Mountain in Yunnan, PR China. Int J Syst Evol Microbiol 2023; 73. [PMID: 37728599 DOI: 10.1099/ijsem.0.006031] [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: 09/21/2023] Open
Abstract
Strain KC 927T was isolated during an investigation of the soil bacteria diversity on Jiaozi Mountain, central Yunnan, Southwest China. The strain was Gram-stain-negative, rod-shaped, non-motile, oxidase-negative, catalase-positive and aerobic. Results of 16S rRNA gene alignment and phylogenetic analysis indicated that strain KC 927T was a member of the genus Chryseobacterium and closely related to Chryseobacterium caseinilyticum GCR10T (98.4%), Chryseobacterium piscicola DSM 21068T (98.3 %) and 'Chryseobacterium formosus' CCTCC AB 2015118T (97.9 %). With a genome size of 4 348 708 bp, strain KC 927T had 33.5 mol% DNA G+C content and contained 4012 protein-coding genes and 77 RNA genes. The average nucleotide identity and digital DNA-DNA hybridization values between strain KC 927T and C. caseinilyticum GCR10T, C. piscicola DSM 21068T and 'C. formosus' CCTCC AB 2015118T were 80.1, 79.6 and 90.7 %, and 25.5, 23.6 and 42.0 %, respectively. The main polar lipid of strain KC 927T was phosphatidylethanolamine and the respiratory quinone was MK-6. The major fatty acids (≥10 %) were iso-C15 : 0, iso-C17 : 1 ω9c and iso-C17 : 0 3-OH. Evidence from phenotypic, phylogenetic and chemotaxonomic analyses support that strain KC 927T represents a new species of the genus Chryseobacterium, for which the name Chryseobacterium luquanense sp. nov. is proposed. The type strain is KC 927T (=CGMCC 1.18760T=JCM 35707T).
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Affiliation(s)
- Guo-Xing Zhu
- College of Agriculture and Life Sciences, Kunming University, Kunming, Yunnan, PR China
| | - Xiu Chen
- College of Agriculture and Life Sciences, Kunming University, Kunming, Yunnan, PR China
- School of Medicine, Kunming University, Kunming, Yunnan, PR China
| | - Ya-Jie Wu
- College of Agriculture and Life Sciences, Kunming University, Kunming, Yunnan, PR China
| | - Hai-Long Wang
- College of Agriculture and Life Sciences, Kunming University, Kunming, Yunnan, PR China
| | - Yu Jiao
- College of Agriculture and Life Sciences, Kunming University, Kunming, Yunnan, PR China
| | - Zi-Chao Liu
- College of Agriculture and Life Sciences, Kunming University, Kunming, Yunnan, PR China
| | - Yue Zhang
- College of Agriculture and Life Sciences, Kunming University, Kunming, Yunnan, PR China
| | - Shu-Kun Tang
- Yunnan Institute of Microbiology, Key Laboratory for Conservation and Utilization of Bio-Resource, and Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, Yunnan, PR China
| | - De-Jun Kong
- School of Ecology and Environmental Science, Yunnan University, Kunming, Yunnan, PR China
| | - Yan-Ru Cao
- College of Agriculture and Life Sciences, Kunming University, Kunming, Yunnan, PR China
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Han JR, Li S, Lu CY, Lian WH, Shi GY, Feng CY, Li WJ, Dong L. Rubellimicrobium arenae sp. nov., isolated from desert soil. Int J Syst Evol Microbiol 2023; 73. [PMID: 37490404 DOI: 10.1099/ijsem.0.005990] [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: 07/27/2023] Open
Abstract
Two Gram-stain-negative strains, designated as SYSU D00286T and SYSU D00782, were isolated from a sand sample collected from the Kumtag Desert in Xinjiang, north-west China. Cells were aerobic, non-motile and positive for both oxidase and catalase. Growth occurred at 4-37 °C (optimum, 28-30 °C), pH 6.0-7.0 (optimum, pH 7.0) and NaCl concentration of 0-1.5 % (w/v; optimum, 0%). Growth was observed on Reasoner's 2A agar and nutrient agar, but not on Luria-Bertani agar and trypticase soy agar. The polar lipids were identified as diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol, three unidentified aminolipids, one unidentified glycolipid and two unidentified phospholipids. The major respiratory quinone was ubiquinone-10 and the major fatty acids (>10 %) were C16 : 0 and summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c). The 16S rRNA gene sequence similarity between strains SYSU D00286T and SYSU D00782 was 100%, and their average nucleotide identity (ANI), average amino acid identity and (AAI) digital DNA-DNA hybridization (dDDH) values were all 100.0 %. Phylogenetic analysis indicated that these two strains belong to the same species of the genus Rubellimicrobium and show the highest sequence similarity to Rubellimicrobium rubrum KCTC 72461T (98.2 %) and Rubellimicrobium roseum CCTCC AA 208029T (97.5 %). The ANI, AAI and dDDH values between SYSU D00286T (as well as SYSU D00782) and the other five Rubellimicrobium type strains were all less than or equal to 83.2, 80.1 and 23.6 %, respectively. Based on their phylogenetic, phenotypic and chemotaxonomical features, strains SYSU D00286T and SYSU D00782 represent a novel species of the genus Rubellimicrobium, for which the name Rubellimicrobium arenae sp. nov. is proposed. The type strain is SYSU D00286T (=MCCC 1K04981T=CGMCC 1.8626T=KCTC 82271T).
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Affiliation(s)
- Jia-Rui Han
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Shuai Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
- School of Life Sciences, Jiaying University, Meizhou, 514015, PR China
| | - Chun-Yan Lu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Wen-Hui Lian
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Guo-Yuan Shi
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Chu-Ying Feng
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, PR China
| | - Lei Dong
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
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11
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Shen L, An M, Liang R, Li Y, He X, Zhao G. Polyphase taxonomy and genome analysis reveal the adaptability of Luteolibacter rhizosphaerae sp. nov. to the rhizosphere soil of Ulmus pumila L. Antonie Van Leeuwenhoek 2023:10.1007/s10482-023-01845-w. [PMID: 37222844 DOI: 10.1007/s10482-023-01845-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 05/15/2023] [Indexed: 05/25/2023]
Abstract
A Gram-stain-negative, rod-shaped, non-flagellated, pale-yellow bacterium, designated GHJ8T, was isolated from the rhizosphere soil of Ulmus pumila L., Shanxi Province, China. Growth occurred at 20-37 °C (optimum, 28 °C), pH 6.0-11.0 (optimum, pH 8.0), and 0-1% NaCl (optimum, 0%). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain GHJ8T was related to members of the genus Luteolibacter, and close to Luteolibacter flavescens GKXT (98.5%), Luteolibacter luteus G-1-1-1T (97.3%), Luteolibacter arcticus MC 3726T (97.2%), and Luteolibacter marinus NBU1238T (96.0%). The genome size of strain GHJ8T was 6.2 Mbp, with a G + C content of 62.5%. Genomic mining revealed that the strain contained antibiotic resistance genes and secondary metabolic gene clusters, indicating that it had adaptation mechanisms to environmental stress. Comparative genomic analyses clearly separated strain GHJ8T from the recognized species of the genus Luteolibacter based on average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values below the thresholds for species delineation. The major cellular fatty acids were iso-C14:0 (30.8%), C16:1 ω9c (23.0%), C16:0 (17.3%), and C14:0 (13.4%). The quinone system was composed of the major menaquinones MK-8, MK-9, and MK-10, and the principal polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, an unidentified aminophospholipid, an unidentified glycolipid, two unidentified phospholipids, and three unidentified lipids. Based on its phenotypic and genotypic properties and phylogenetic inference, strain GHJ8T is a novel species of the genus Luteolibacter, for which the name Luteolibacter rhizosphaerae sp. nov. is proposed. The type strain is GHJ8T (= GDMCC 1.2160T = KCTC 82452T = JCM 34400T).
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Affiliation(s)
- Lei Shen
- College of Biological Sciences and Technology, National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Forestry University, Beijing, 100083, China
- College of Life Sciences, Langfang Normal University, Langfang, 065000, China
| | - Miaomiao An
- College of Biological Sciences and Technology, National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Forestry University, Beijing, 100083, China
| | - Ruina Liang
- College of Biological Sciences and Technology, National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Forestry University, Beijing, 100083, China
| | - Ying Li
- College of Biological Sciences and Technology, National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Forestry University, Beijing, 100083, China
| | - Xiangwei He
- College of Biological Sciences and Technology, National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Forestry University, Beijing, 100083, China
| | - Guozhu Zhao
- College of Biological Sciences and Technology, National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Forestry University, Beijing, 100083, China.
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Perween N, Pekhale K, Haval G, Bose GS, Mittal SPK, Ghaskadbi S, Ghaskadbi SS. Glutaredoxin 1 from Evolutionary Ancient Hydra: Characteristics of the Enzyme and Its Possible Functions in Cell. BIOCHEMISTRY. BIOKHIMIIA 2023; 88:667-678. [PMID: 37331712 DOI: 10.1134/s0006297923050097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Revised: 02/20/2023] [Accepted: 02/20/2023] [Indexed: 06/20/2023]
Abstract
Glutaredoxin (Grx) is an antioxidant redox protein that uses glutathione (GSH) as an electron donor. Grx plays a crucial role in various cellular processes, such as antioxidant defense, control of cellular redox state, redox control of transcription, reversible S-glutathionylation of specific proteins, apoptosis, cell differentiation, etc. In the current study, we have isolated and characterized dithiol glutaredoxin from Hydra vulgaris Ind-Pune (HvGrx1). Sequence analysis showed that HvGrx1 belongs to the Grx family with the classical Grx motif (CPYC). Phylogenetic analysis and homology modeling revealed that HvGrx1 is closely related to Grx2 from zebrafish. HvGrx1 gene was cloned and expressed in Escherichia coli cells; the purified protein had a molecular weight of 11.82 kDa. HvGrx1 efficiently reduced β-hydroxyethyl disulfide (HED) with the temperature optimum of 25°C and pH optimum 8.0. HvGrx1 was ubiquitously expressed in all body parts of Hydra. Expression of HvGrx1 mRNA and enzymatic activity of HvGrx1 were significantly upregulated post H2O2 treatment. When expressed in human cells, HvGrx1 protected the cells from oxidative stress and enhanced cell proliferation and migration. Although Hydra is a simple invertebrate, HvGrx1 is evolutionary closer to its homologs from higher vertebrates (similar to many other Hydra proteins).
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Affiliation(s)
- Nusrat Perween
- Department of Zoology, Savitribai Phule Pune University, Pune, 411007, India.
- Department of Zoology, M. C. E. Society's Abeda Inamdar Senior College, Pune, 411001, India
| | - Komal Pekhale
- Department of Zoology, Savitribai Phule Pune University, Pune, 411007, India.
| | - Gauri Haval
- Department of Zoology, Savitribai Phule Pune University, Pune, 411007, India.
- Department of Zoology, Abasaheb Garware College, Pune, 411004, India
| | - Ganesh S Bose
- Department of Biotechnology, Savitribai Phule Pune University, Pune, 411007, India.
| | - Smriti P K Mittal
- Department of Biotechnology, Savitribai Phule Pune University, Pune, 411007, India.
| | - Surendra Ghaskadbi
- Developmental Biology Group, Agharkar Research Institute, Pune, 411004, India.
| | - Saroj S Ghaskadbi
- Department of Zoology, Savitribai Phule Pune University, Pune, 411007, India.
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13
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Li J, Liang Y, He Z, An L, Liu Y, Zhong M, Hu Z. Tamlana laminarinivorans sp. nov. and Tamlana sargassicola sp. nov., two novel species isolated from Sargassum, show genomic and physiological adaptations for a Sargassum-associated lifestyle. Int J Syst Evol Microbiol 2023; 73. [PMID: 36884369 DOI: 10.1099/ijsem.0.005706] [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: 03/09/2023] Open
Abstract
The genus Tamlana from the Bacteroidota currently includes six validated species. Two strains designated PT2-4T and 62-3T were isolated from Sargassum abundant at the Pingtan island coast in the Fujian Province of China. 16S rRNA gene sequence analysis showed that the closest described relative of strains PT2-4T and 62-3T is Tamlana sedimentorum JCM 19808T with 98.40 and 97.98% sequence similarity, respectively. The 16S rRNA gene sequence similarity between strain PT2-4T and strain 62-3T was 98.68 %. Furthermore, the highest average nucleotide identity values were 87.34 and 88.97 % for strains PT2-4T and 62-3T, respectively. The highest DNA-DNA hybridization (DDH) value of strain PT2-4T was 35.2 % with strain 62-3T, while the DDH value of strain 62-3T was 37.7 % with T. sedimentorum JCM 19808T. Growth of strains PT2-4T and 62-3T occurs at 15-40 °C (optimum, 30 °C) with 0-4 % (w/v) NaCl (optimum 0-1 %). Strains PT2-4T and 62-3T can grow from pH 5.0 to 10.0 (optimum, pH 7.0). The major fatty acids of strains PT2-4T and 62-3T are iso-C15 : 0 and iso G-C15 : 1. MK-6 is the sole respiratory quinone. Genomic and physiological analyses of strains PT2-4T and 62-3T showed corresponding adaptive features. Significant adaptation to the growth environment of macroalgae includes the degradation of brown algae-derived diverse polysaccharides (alginate, laminarin and fucoidan). Notably, strain PT2-4T can utilize laminarin, fucoidan and alginate via specific carbohydrate-active enzymes encoded in polysaccharide utilization loci, rarely described for the genus Tamlana to date. Based on their distinct physiological characteristics and the traits of utilizing polysaccharides from Sargassum, strains PT2-4T and 62-3T are suggested to be classified into two novel species, Tamlana laminarinivorans sp. nov. and Tamlana sargassicola sp. nov. (type strain PT2-4T=MCCC 1K04427T=KCTC 92183T and type strain 62-3T=MCCC 1K04421T=KCTC 92182T).
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Affiliation(s)
- Jin Li
- Department of Biology, College of Science, Shantou University, Shantou, 515063, PR China
| | - Yumei Liang
- Department of Biology, College of Science, Shantou University, Shantou, 515063, PR China
| | - Zhixiao He
- Department of Biology, College of Science, Shantou University, Shantou, 515063, PR China
| | - Lu An
- Department of Biology, College of Science, Shantou University, Shantou, 515063, PR China
| | - Yongjin Liu
- Department of Biology, College of Science, Shantou University, Shantou, 515063, PR China
| | - Mingqi Zhong
- Department of Biology, College of Science, Shantou University, Shantou, 515063, PR China
| | - Zhong Hu
- Department of Biology, College of Science, Shantou University, Shantou, 515063, PR China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, 511458, PR China
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14
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A novel nitrogen-fixing bacterium, Propionivibrio soli sp. nov. isolated from paddy soil. Arch Microbiol 2023; 205:68. [PMID: 36662302 DOI: 10.1007/s00203-023-03413-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 01/04/2023] [Accepted: 01/10/2023] [Indexed: 01/21/2023]
Abstract
A facultative anaerobic nitrogen-fixing bacterium, designated SG131T, was isolated from paddy soil. Strain SG131T showed high 16S rRNA gene sequence similarities with type strains Propionivibrio limicola DSM 6832T (96.9%), Propionivibrio pelophilus asp 66T (96.0%) and Propionivibrio dicarboxylicus DSM 5885T (95.7%). The phylogenetic trees (based on 16S rRNA gene sequences and 120 conserved genes from genomes, respectively) indicated that strain SG131T clustered with members of the genus Propionivibrio. Growth of strain SG131T was observed at 25-40 °C, pH 5.5-10.5 and 0-0.5% (w/v) NaCl. The quinone was Q-7, and the main fatty acids were C16:1 ω6c and/or C16:1 ω7c (25.9%), C16:0 (23.3%), C17:0-cyclo (11.7%), C12:0 (6.0%) and C17:0 (5.9%). The genomic DNA G + C content of strain SG131T was 60.3%. The average nucleotide identity (ANI) values between strain SG131T and its most closely related species P. limicola DSM 6832T, P. pelophilus DSM 12018T and P. dicarboxylicus DSM 5885T were 74.4%, 74.9% and 75.6%, respectively. The digital DNA-DNA hybridization (dDDH) values between strain SG131T and its most closely related species P. limicola DSM 6832T, P. pelophilus DSM 12018T and P. dicarboxylicus DSM 5885T were 19.9%, 20.6% and 20.5%, respectively. All these values were lower than the recommended species delineation thresholds of ANI (95-96%) and dDDH (70%). Strain SG131T possessed core genes (nifHDK) of nitrogen fixation and was confirmed its nitrogen-fixing ability by the ARA method. According to the above-described analysis, strain SG131T represents a novel species of the genus Propionivibrio, for which the name Propionivibrio soli sp. nov. is proposed. The type strain is SG131T (= GDMCC 1.3313T = JCM 35595T).
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Ling K, Yi-ning D, Majeed A, Zi-jiang Y, Jun-wen C, Li-lian H, Xian-hong W, Lu-feng L, Zhen-feng Q, Dan Z, Shu-jie G, Rong X, Lin-yan X, Fu X, Yang D, Fu-sheng L. Evaluation of genome size and phylogenetic relationships of the Saccharum complex species. 3 Biotech 2022; 12:327. [PMID: 36276474 PMCID: PMC9582063 DOI: 10.1007/s13205-022-03338-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 08/16/2022] [Indexed: 11/29/2022] Open
Abstract
"Saccharum complex" is a hypothetical group of species, which is supposed to be involved in the origin of modern sugarcane, and displays large genomes and complex chromosomal alterations. The utilization of restricted parents in breeding programs of modern cultivated sugarcane has resulted in a genetic blockage, which controlled its improvement because of the limited genetic diversity. The use of wild relatives is an effective way to broaden the genetic composition of cultivated sugarcane. Due to the infrequent characterization of genomes, the potential of wild relatives is diffused in improving the cultivated sugarcane. To characterize the genomes of the wild relatives, the genome size and phylogenetic relationships among eight species, including Saccharum spontaneum, Erianthus arundinaceus, E. fulvus, E. rockii, Narenga porphyrocoma, Miscanthus floridulus, Eulalia quadrinervis, and M. sinensis were evaluated based on flow cytometry, genome surveys, K-mer analysis, chloroplast genome sequencing, and whole-genome SNPs analysis. We observed highly heterozygous genomes of S. spontaneum, E. rockii, and E. arundinaceus and the highly repetitive genome of E. fulvus. The genomes of Eulalia quadrinervis, N. porphyrocoma, M. sinensis, and M. floridulus were highly complex. Phylogenetic results of the two approaches were dissimilar, however, both indicate E. fulvus displayed closer relationships to Miscanthus and Saccharum than other species of Saccharum complex. Eulalia quadrinervis was more closely related to M. floridulus than M. sinensis; E. arundinaceus differ significantly from Miscanthus, Narenga, and Saccharum, but was relatively close to Erianthus. We proved the point of E. rockii and E. fulvus should not be classified as one genus, and E. fulvus should be classified as the Saccharum genus. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-022-03338-5.
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Affiliation(s)
- Kui Ling
- The Key Laboratory for Crop Production and Intelligent Agriculture of Yunnan Province, Kunming, 650201 Yunnan China
- Shenzhen Qianhai Shekou Free Trade Zone Hospital, Shenzhen, 518067 China
| | - Di Yi-ning
- The Key Laboratory for Crop Production and Intelligent Agriculture of Yunnan Province, Kunming, 650201 Yunnan China
| | - Aasim Majeed
- School of Agricultural Biotechnology, Punjab Agriculture University, Ludhiana, 141004 India
| | - Yang Zi-jiang
- Applied Genomics Technology Laboratory, Yunnan Agricultural University, Kunming, 650201 Yunnan China
| | - Chen Jun-wen
- The Key Laboratory for Crop Production and Intelligent Agriculture of Yunnan Province, Kunming, 650201 Yunnan China
| | - He Li-lian
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201 Yunnan China
| | - Wang Xian-hong
- The Key Laboratory for Crop Production and Intelligent Agriculture of Yunnan Province, Kunming, 650201 Yunnan China
| | - Liu Lu-feng
- Sugarcane Research Institute, Yunnan Agricultural University, Kunming, 650201 Yunnan China
| | - Qian Zhen-feng
- The Key Laboratory for Crop Production and Intelligent Agriculture of Yunnan Province, Kunming, 650201 Yunnan China
| | - Zeng Dan
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201 Yunnan China
| | - Gu Shu-jie
- The Key Laboratory for Crop Production and Intelligent Agriculture of Yunnan Province, Kunming, 650201 Yunnan China
| | - Xu Rong
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201 Yunnan China
| | - Xie Lin-yan
- The Key Laboratory for Crop Production and Intelligent Agriculture of Yunnan Province, Kunming, 650201 Yunnan China
| | - Xu Fu
- Sugarcane Research Institute, Yunnan Agricultural University, Kunming, 650201 Yunnan China
| | - Dong Yang
- Applied Genomics Technology Laboratory, Yunnan Agricultural University, Kunming, 650201 Yunnan China
| | - Li Fu-sheng
- The Key Laboratory for Crop Production and Intelligent Agriculture of Yunnan Province, Kunming, 650201 Yunnan China
- Sugarcane Research Institute, Yunnan Agricultural University, Kunming, 650201 Yunnan China
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201 Yunnan China
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16
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Zhang G, Yang J, Lai XH, Jin D, Lu S, Liu L, Cheng Y, Pu J, Yang C, Liu Y, Ye L, Xu J. Cellulomonas dongxiuzhuiae sp. nov., Cellulomonas wangleii sp. nov. and Cellulomonas fengjieae sp. nov., isolated from the intestinal contents of Marmota himalayana. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Six Gram-stain-positive, aerobic or facultative anaerobic, catalase-positive, urease- and oxidase-negative, rod-shaped bacteria (zg-ZUI157T/zg-ZUI40, zg-ZUI222T/zg-ZUI199 and zg-ZUI188T/ zg-ZUI168) were characterized by a polyphasic approach. Optimal growth of the six strains was observed at pH 7.0 and 28 °C. Phylogenetic analyses based on the 16S rRNA gene and 247 core genes revealed that they belong to genus
Cellulomonas
. The three type strains have low digital DNA-DNA hybridization (19.3–30.1%) and average nucleotide identity values (78.0-85.5%) with all available genomes in the genus
Cellulomonas
, and a DNA G+C content range of 73.0-74.6 mol%. The major fatty acids detected in strain pairs zg-ZUI157T/zg-ZUI40 and zg-ZUI 222T/zg-ZUI199 were C16:0, anteiso-C15:0 and anteiso A-C15:1, and C16:0, anteiso-C15:0, anteiso A-C15:1 and anteiso-C17:0 in strain pair zg-ZUI188T/zg-ZUI168. Diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol mannosides were the major polar lipids detected in the three novel species. MK-9(H4) was the predominant quinone detected in strains zg-ZUI222T (87.4 %) and zg-ZUI188T (91.4 %), and MK-9(H4) (49.1 %) and MK-8 (43.4 %) in strain zg-ZUI157T. The cell-wall sugars detected in the three novel species mainly contained rhamnose. The cell-wall peptidoglycan type of the three novel species was A4β, with an inferred l-Orn–d-Asp interpeptide bridge for strains zg-ZUI157T and zg-ZUI222T, and l-Orn–d-Glu for strain zg-ZUI188T. Based on the results of the phenotypic, phylogenetic, genomic hybridization, average nucleotide identity and chemotaxonomic analyses, the six strains should be classified as belonging to three novel
Cellulomonas
species, for which the names Cellulomonas dongxiuzhuiae sp. nov. (zg-ZUI157T=GDMCC 1.2559T=KCTC 49678T), Cellulomonas wangleii sp. nov. (zg-ZUI222T=GDMCC 1.2501T=KCTC 49675T) and Cellulomonas fengjieae sp. nov. (zg-ZUI188T=GDMCC 1.2563T=KCTC 49674T) are proposed.
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Affiliation(s)
- Gui Zhang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Jing Yang
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 102206, PR China
- Shanghai Institute for Emerging and Re-emerging Infectious Diseases, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, PR China
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Xin-He Lai
- Henan Key Laboratory of Biomolecular Recognition and Sensing, College of Chemistry and Chemical Engineering, Henan Joint International Research Laboratory of Chemo/Biosensing and Early Diagnosis of Major Diseases, Shangqiu Normal University, Shangqiu 476000, PR China
| | - Dong Jin
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 102206, PR China
- Shanghai Institute for Emerging and Re-emerging Infectious Diseases, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, PR China
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Shan Lu
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 102206, PR China
- Shanghai Institute for Emerging and Re-emerging Infectious Diseases, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, PR China
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Liyun Liu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Yanpeng Cheng
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Ji Pu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Caixin Yang
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan 030001, PR China
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Yue Liu
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan 030001, PR China
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Lin Ye
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan 030001, PR China
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Jianguo Xu
- Institute of Public Health, Nankai University, Tianjin 300071, PR China
- Shanghai Institute for Emerging and Re-emerging Infectious Diseases, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, PR China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 102206, PR China
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan 030001, PR China
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
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17
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Streptomyces plumbidurans sp. nov., a Pb2+-tolerant actinomycete. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005505] [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 novel actinobacterium, designated KC 17012T, was isolated from lead zinc tailings collected from Lanping, Yunnan, PR China. Comparative 16S rRNA gene sequencing showed that KC 17012T belonged to the genus
Streptomyces
and was most closely related to the type strains of
Streptomyces neyagawaensis
(98.34%),
Streptomyces panaciradicis
(98.34%) and
Streptomyces heilongjiangensis
(98.27%). Phylogenetic tree analysis revealed strain KC 17012T formed a distinct clade. The genome size was 8.64 Mbp with a DNA G+C content of 70.8%. Digital DNA–DNA hybridization and average nucleotide identity values between the genome sequence of strain KC 17012T and those of
S. neyagawaensis
JCM 4796T (25.3 and 81.5 %) and
S. panaciradicis
NBRC 109811T (30.1 and 85.7 %) were below the thresholds of 70 and 96% for prokaryotic conspecific assignation. The strain formed long straight aerial hyphae which generated regular short rod spores with spiny surfaces. Growth occurred at 10–45 °C, pH 6–8 and with 0–9 % NaCl (w/v). Strain KC 17012T contained ll-diaminopimelic acid and the major whole-cell hydrolysates included glucose, mannose and ribose. The menaquinones were MK-9(H4), MK-9(H6) and MK-9(H8). The major cellular fatty acids were iso-C15 : 0, anteiso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside, one unidentified lipid and one unidentified phospholipid. On the basis of the results of a polyphasic taxonomic study, it is concluded that KC 17012T represents a novel species of the genus
Streptomyces
, for which the name Streptomyces plumbidurans sp. nov., is proposed. The type strain is KC 17012T (CGMCC 4.7704T=JCM 35204T).
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18
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Zhu GX, Wu YJ, Cao YR, Fan BJ, Jiao Y, Hou XL, Liu ZC, Zhang Y, He JB, Liang LM. Siccirubricoccus soli sp. nov., a novel bacterial species isolated from Jiaozi Mountain soil. Antonie Van Leeuwenhoek 2022; 115:1285-1295. [PMID: 35998006 DOI: 10.1007/s10482-022-01771-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 08/11/2022] [Indexed: 11/30/2022]
Abstract
An isolate of Gram-stain-negative and strictly aerobic bacterium, designated KC 17139T, was isolated from Jiaozi Mountain sample in Yunnan, China. Cells were non-motile cocci to oval, catalase-positive and oxidase-positive. Growth occurred at 0-7% NaCl (w/v; optimum, 0%), pH 6.0-8.0 (optimum, pH 7.0) and 15-45 °C (optimum, 28-37 °C). The polar lipids were diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), phosphatidylglycerol (PG), phosphatidylcholine (PC) and four unidentified aminolipids (UALs). Strain KC 17139T contained summed feature 8 (comprising C18:1 ω7c and/or C18:1 ω6c), C18:1 2OH and C16:0 as major cellular fatty acids (> 5%) and ubiquinone-10 as the sole isoprenoid quinone. The 16S rRNA gene sequence analysis indicated that strain KC 17139T shared highest similarities with Siccirubricoccus phaeus 1-3T (96.7%) and Siccirubricoccus deserti SYSU D8009T (95.0%). Strain KC 17139T clustered with the two Siccirubricoccus type strains, but formed a separate branch in both 16S rRNA gene and genome-scale phylogenetic dendrograms. The genomic DNA G + C content of strain KC 17139T was 71.2%. Genomic comparisons between strain KC 17139T and its close relatives showed the highest digital DNA-DNA hybridisation to S. phaeus (35.5%), highest average nucleotide identity to S. phaeus (88.2%), indicating that strain KC 17139T represents a novel species. On the basis of results of phenotypic, chemotaxonomic and molecular analysis, we report a new bacterium strain KC 17139T belonged to genus Siccirubricoccus, for which the name Siccirubricoccus soli sp. nov. is proposed. The type strain is KC 17139T (= CGMCC 1.18756T = JCM 35132T).
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Affiliation(s)
- Guo-Xing Zhu
- College of Agriculture and Life Sciences, Kunming University, Kunming, People's Republic of China
| | - Ya-Jie Wu
- College of Agriculture and Life Sciences, Kunming University, Kunming, People's Republic of China
| | - Yan-Ru Cao
- College of Agriculture and Life Sciences, Kunming University, Kunming, People's Republic of China.
| | - Bing-Jun Fan
- College of Agriculture and Life Sciences, Kunming University, Kunming, People's Republic of China
| | - Yu Jiao
- College of Agriculture and Life Sciences, Kunming University, Kunming, People's Republic of China
| | - Xiu-Li Hou
- College of Agriculture and Life Sciences, Kunming University, Kunming, People's Republic of China
| | - Zi-Chao Liu
- College of Agriculture and Life Sciences, Kunming University, Kunming, People's Republic of China
| | - Yue Zhang
- College of Agriculture and Life Sciences, Kunming University, Kunming, People's Republic of China
| | - Jiang-Bo He
- Medical College, Kunming University, Kunming, People's Republic of China
| | - Lian-Ming Liang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, People's Republic of China.
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19
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Yin YL, Li FL, Wang L. Halomonas salinarum sp. nov., a moderately halophilic bacterium isolated from saline soil in Yingkou, China. Arch Microbiol 2022; 204:466. [PMID: 35802152 PMCID: PMC9266089 DOI: 10.1007/s00203-022-03032-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 05/28/2022] [Accepted: 06/01/2022] [Indexed: 11/19/2022]
Abstract
Strain G5-11T, a Gram-negative, moderately halotolerant, facultatively aerobic, motile bacterium was isolated from saline soil collected from Yingkou, Liaoning, China. The cells of strain G5-11T grew in the presence of 3–15% (w/v) NaCl (optimum 5%), at between 4 and 35 °C (optimum 30 °C), and at a pH of 6.0–9.0 (optimum 8.0). The major respiratory quinone was Q-9 and the dominant cellular fatty acids were summed feature 8 (C18:1ω7c/C18:1ω6c), C16:0, and summed feature 3 (C16:1ω7c/C16:1ω6c). The major components of the polar lipid profile were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol and unidentified aminolipid. The G + C content of the strain G5-11T genome was 61.0 mol%. The isolated strain G5-11T showed the highest 16S rRNA gene similarity to Halomonas niordiana LMG 31227T and Halomonas taeanensis DSM 16463T, both reaching 98.3%, followed by Halomonas pacifica NBRC 102220T. The results from phenotypic, chemotaxonomic, and phylogenetic analyses showed that strain G5-11T represented a novel species of the genus Halomonas, for which the name Halomonas salinarum sp. nov. was proposed. The type strain of Halomonas salinarum is G5-11T (= CGMCC 1.12051T = LMG 31677T).
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Affiliation(s)
- Ya-Lin Yin
- MOA Key Laboratory of Soil Microbiology, Department of Microbiology and Immunology, College of Biological Sciences, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Fang-Ling Li
- MOA Key Laboratory of Soil Microbiology, Department of Microbiology and Immunology, College of Biological Sciences, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Lei Wang
- MOA Key Laboratory of Soil Microbiology, Department of Microbiology and Immunology, College of Biological Sciences, China Agricultural University, Beijing, 100193, People's Republic of China.
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20
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Identification of epithelial and mesenchymal circulating tumor cells in clonal lineage of an aggressive prostate cancer case. NPJ Precis Oncol 2022; 6:41. [PMID: 35729213 PMCID: PMC9213535 DOI: 10.1038/s41698-022-00289-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 05/19/2022] [Indexed: 01/01/2023] Open
Abstract
Little is known about the complexity and plasticity of circulating tumor cell (CTC) biology in different compartments of the fluid microenvironment during tumor metastasis. Here we integrated phenomics, genomics, and targeted proteomics to characterize CTC phenotypic and genotypic heterogeneity in paired peripheral blood (PB) and bone marrow aspirate (BMA) from a metastatic prostate cancer patient following the rapid disease progression, using the High-Definition Single Cell Assay 3.0 (HDSCA3.0). Uniquely, we identified a subgroup of genetically clonal CTCs that acquired a mesenchymal-like state and its presence was significantly associated with one subclone that emerged along the clonal lineage. Higher CTC abundance and phenotypic diversity were observed in the BMA than PB and differences in genomic alterations were also identified between the two compartments demonstrating spatial heterogeneity. Single cell copy number profiling further detected clonal heterogeneity within clusters of CTCs (also known as microemboli or aggregates) as well as phenotypic variations by targeted proteomics. Overall, these results identify epithelial and mesenchymal CTCs in the clonal lineage of an aggressive prostate cancer case and also demonstrate a single cell multi-omic approach to deconvolute the heterogeneity and association of CTC phenotype and genotype in multi-medium liquid biopsies of metastatic prostate cancer.
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21
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Du X, Ran Q, Wang J, Jiang H, Wang J, Li YZ. Microvirga roseola sp. nov. and Microvirga lenta sp. nov., isolated from Taklamakan Desert soil. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005409] [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 Gram-negative, rod-shaped, non-spore-forming bacteria, designated SM9T and SM2T, were isolated from Taklamakan Desert soil samples. Phylogenetic analysis based on the 16S rRNA gene sequences showed that strains SM9T and SM2T had the highest sequence similarity to the type strains
Microvirga indica
BCRC 80972T and
Microvirga soli
NBRC 112417T with similarity values of 98.2 and 97.7 %, respectively, and
Microvirga
was among the predominant genera in the desert soil. The draft genomes of these two strains were 4.56 Mbp (SM9T) and 5.08 Mbp (SM2T) long with 65.1 mol% (SM9T) and 63.5 mol% (SM2T) G+C content. To adapt to the desert environment, these two strains possessed pathways for the synthesis of stress metabolite trehalose. The major fatty acids (>5 %) included C18 : 1 ω9c in SM2T, but C16 : 0, C18 : 0 and C19 : 0 cyclo ω8c in SM9T, while the major menaquinone was ubiquinone 10 in both strains. The major polar lipids of SM9T and SM2T were phosphatidylglycerol, phosphatidylethanolamine and phospholipid. The average nucleotide identity and digital DNA–DNA hybridization results further indicated that strains SM9T and SM2T were distinguished from phylogenetically related species and represented two novel species within the genus
Microvirga
, for which the names Microvirga roseola sp. nov. (type strain SM2T=KCTC 72792T=CGMCC 1.17776T) and Microvirga lenta sp. nov. (type strain SM9T=KCTC 82729T=CCTCC AB 2021131T) are proposed.
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Affiliation(s)
- Xinran Du
- State Key Laboratory of Microbial Technology, Institute of Microbiology Technology, Shandong University, Qingdao 266237, PR China
| | - Qi Ran
- State Key Laboratory of Microbial Technology, Institute of Microbiology Technology, Shandong University, Qingdao 266237, PR China
| | - Jianing Wang
- State Key Laboratory of Microbial Technology, Institute of Microbiology Technology, Shandong University, Qingdao 266237, PR China
| | - Hong Jiang
- College of Food Science and Engineering, Ocean University of China, 266003 Qingdao, PR China
| | - Jingjing Wang
- State Key Laboratory of Microbial Technology, Institute of Microbiology Technology, Shandong University, Qingdao 266237, PR China
| | - Yue-zhong Li
- State Key Laboratory of Microbial Technology, Institute of Microbiology Technology, Shandong University, Qingdao 266237, PR China
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22
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Khanal S, Antony-Babu S, Gaire SP, Zhou XG. Multi-Locus Sequence Analysis Reveals Diversity of the Rice Kernel Smut Populations in the United States. Front Microbiol 2022; 13:874120. [PMID: 35602055 PMCID: PMC9116506 DOI: 10.3389/fmicb.2022.874120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 04/07/2022] [Indexed: 12/02/2022] Open
Abstract
Rice (Oryza sativa) is the second leading cereal crop in the world and is one of the most important field crops in the US, valued at approximately $2.5 billion. Kernel smut (Tilletia horrida Tak.), once considered as a minor disease, is now an emerging economically important disease in the US. In this study, we used multi-locus sequence analysis to investigate the genetic diversity of 63 isolates of T. horrida collected from various rice-growing areas across in the US. Three different phylogeny analyses (maximum likelihood, neighbor-joining, and minimum evolution) were conducted based on the gene sequence sets, consisting of all four genes concatenated together, two rRNA regions concatenated together, and only ITS region sequences. The results of multi-gene analyses revealed the presence of four clades in the US populations, with 59% of the isolates clustering together. The populations collected from Mississippi and Louisiana were found to be the most diverse, whereas the populations from Arkansas and California were the least diverse. Similarly, ITS region-based analysis revealed that there were three clades in the T. horrida populations, with a majority (76%) of the isolates clustering together along with the 22 Tilletia spp. from eight different countries (Australia, China, India, Korea, Pakistan, Taiwan, The US, and Vietnam) that were grouped together. Two of the three clades in the ITS region-based phylogeny consisted of the isolates reported from multiple countries, suggesting potential multiple entries of T. horrida into the US. This is the first multi-locus analysis of T. horrida populations. The results will help develop effective management strategies, especially breeding for resistant cultivars, for the control of kernel smut in rice.
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Affiliation(s)
- Sabin Khanal
- Texas A&M AgriLife Research Center, Beaumont, TX, United States
| | - Sanjay Antony-Babu
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, United States
| | - Shankar P Gaire
- Texas A&M AgriLife Research Center, Beaumont, TX, United States
| | - Xin-Gen Zhou
- Texas A&M AgriLife Research Center, Beaumont, TX, United States
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23
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Dong M, Feng H. Microbial Community Analysis and Food Safety Practice Survey-Based Hazard Identification and Risk Assessment for Controlled Environment Hydroponic/Aquaponic Farming Systems. Front Microbiol 2022; 13:879260. [PMID: 35663856 PMCID: PMC9161294 DOI: 10.3389/fmicb.2022.879260] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 04/21/2022] [Indexed: 11/26/2022] Open
Abstract
Hydroponic and aquaponic farming is becoming increasingly popular as a solution to address global food security. Plants in hydroponic systems are grown hydroponically under controlled environments and are considered to have fewer food safety concerns than traditional field farming. However, hydroponics and aquaponics might have very different sources of microbial food safety risks that remain under-examined. In this study, we investigated the microbiomes, microbial hazards, and potential bacterial transmission routes inside two commercial hydroponic and aquaponic farming systems using 16S-ITS-23S rRNA sequencing and a hydroponic food safety practice survey. The hydroponic farming system microbiome was analyzed from the fresh produce, nutrient solution, tools, and farmworkers. Proteobacteria, Actinobacteria, Cyanobacteria, Bacteroidetes, and Firmicutes were the main components of hydroponic/aquaponic farming systems, with Pseudomonas being the most abundant genus in fresh produce samples. We further identified the presence of multiple spoilage bacteria and potential human, plant, and fish pathogens at the subspecies level. Spoilage Pseudomonas spp. and spoilage Clostridium spp. were abundant in the hydroponic microgreen farm and aquaponic lettuce farm, respectively. Moreover, we demonstrated the mapping of Escherichia coli 16s-ITS-23s rRNA sequence reads (∼2,500 bp) to small or large subunit rRNA databases and whole-genome databases to confirm pathogenicity and showed the potential of using 16s-ITS-23s rRNA sequencing for pathogen identification. With the SourceTracker and overlapping amplicon sequence variants, we predicted the bidirectional transmission route between plants and the surrounding environment and constructed the bacteria transmission map, which can be implemented in future food safety risk control plans.
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Affiliation(s)
| | - Hao Feng
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, United States
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24
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Roseococcus pinisoli sp. nov., lacking pufL and pufM bacteriochlorophyll a: synthesizing genes. Arch Microbiol 2022; 204:293. [PMID: 35507236 DOI: 10.1007/s00203-022-02920-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 04/13/2022] [Accepted: 04/14/2022] [Indexed: 11/02/2022]
Abstract
A Gram-stain-negative, cocci-to-oval-shaped bacterial strain, designated XZZS9T, was isolated from the rhizosphere soil of Pinus sylvestris var. mongolica and characterized taxonomically using a polyphasic approach. Growth occurred at 20-35 °C (optimum, 28 °C), pH 6.0-11.0 (optimum, pH 7.0), and in 0-1% NaCl (optimum, 0%). Phylogenetic analysis based on 16S rRNA gene sequencing indicated that strain XZZS9T was related to members of the genus Roseococcus, with the highest sequence identity to Roseococcus microcysteis NIBR12T (96.9%). The major cellular fatty acids (> 5% of the total) were C18:1 ω7c and C19:0 cyclo ω8c. The major isoprenoid quinone was Q-9 and the polar lipid profile contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, an unidentified glycophospholipid, and an unidentified phospholipid. Genome sequencing revealed that had a genome size of 4.79 Mbp with a G + C content of 69.5%. Comparative genomic analyses clearly separated strain XZZS9T from the known species of the genus Roseococcus based on average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values below the thresholds for species delineation. Genome annotations did not find pufL and pufM genes in strain XZZS9T, suggesting a possible lack of photosynthetic reaction. Based on genotypic and phenotypic characteristics, strain XZZS9T represents a novel species of the genus Roseococcus, for which we propose the name Roseococcus pinisoli sp. nov. The type strain is XZZS9T (= KCTC 82435T = JCM 34402T = GDMCC 1.2158T).
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25
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Xu L, Huang XX, Wang HT, Tang SK, Shen B, Sun JQ. Description and characterization of three endophytic Bacillaceae from the halophyte Suaeda salsa: Paenalkalicoccus suaedae gen. nov., sp. nov. , Cytobacillus suaedae sp. nov. , and Bacillus suaedae sp. nov. Int J Syst Evol Microbiol 2022; 72. [PMID: 35550242 DOI: 10.1099/ijsem.0.005337] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Three strains of members of the family Bacillaceae, which can inhibit the growth of some Gram-stain-positive strains, designated M4U3P1T, HD4P25T and RD4P76T, were isolated from Suaeda salsa halophytes in Baotou, Inner Mongolia, PR China. A phylogenetic analysis based on the 16S rRNA gene and the whole genome sequences revealed that HD4P25T clustered with Cytobacillus luteolus YIM 93174T with a similarity of 98.4 %, and RD4P76T shared the highest similarity of 16S rRNA gene with Bacillus mesophilus SA4T (97.5 %). M4U3P1T clustered with strains of genera Salipaludibacillus and Alkalicoccus based on whole-genome sequence analyses, but its 16S rRNA gene had the highest similarity to 'Evansella tamaricis' EGI 80668 (96.1 %). The average nucleotide's identity by blast (ANIb) and digital DNA-DNA hybridization (dDDH) values of the three isolated strains to their close relatives were well below the threshold value for identifying a novel species.On the basis of the phylogenetic, physiological and phenotypic results, Paenalkalicoccus suaedae gen. nov., sp. nov. [type strain M4U3P1T (=CGMCC 1.17076T=JCM 33851T)], Cytobacillus suaedae sp. nov. [type strain HD4P25T (=CGMCC 1.18651T =JCM 34524T)], and Bacillus suaedae sp. nov. [type strain RD4P76T (=CGMCC 1.18659T=JCM 34525T)] were proposed, respectively. All three species are ubiquitous in the bulk saline-alkaline soils, but only the species represented by strain RD4P76T was widely distributed in the rhizosphere soil, the above-ground part and the roots of S. salsa. The species represented by M4U3P1T can be detected in the roots of S. salsa, and rarely detected in the above-ground parts of S. salsa. The species represented by HD4P25T was rarely detected in the interior of S. salsa. The three strains could inhibit some of the Gram-stain-positive bacteria (i.e. members of the genera Planococcus, Zhihengliuella and Sanguibacter) in the saline-alkali soil. A genomic analysis of these three strains revealed that they can synthesize different antagonistic compounds, such as aminobenzoate and bacitracin or subtilisin.
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Affiliation(s)
- Lian Xu
- Laboratory for Microbial Resources, Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, School of Ecology and Environment, Inner Mongolia University, Hohhot, 010021, PR China.,Jiangsu Key Laboratory for Organic Solid Waste Utilization, Educational Ministry Engineering Center of Resource-saving Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Xiao-Xian Huang
- Laboratory for Microbial Resources, Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, School of Ecology and Environment, Inner Mongolia University, Hohhot, 010021, PR China
| | - Hai-Tao Wang
- Laboratory for Microbial Resources, Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, School of Ecology and Environment, Inner Mongolia University, Hohhot, 010021, PR China
| | - Shu-Kun Tang
- Yunnan Institute of Microbiology, Key Laboratory for Conservation and Utilization of Bio-Resource, and Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, 650091, PR China
| | - Biao Shen
- Jiangsu Key Laboratory for Organic Solid Waste Utilization, Educational Ministry Engineering Center of Resource-saving Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Ji-Quan Sun
- Laboratory for Microbial Resources, Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, School of Ecology and Environment, Inner Mongolia University, Hohhot, 010021, PR China
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26
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Sun JQ, Huang XX, Xu L, Wei HM. Luteimonas saliphila sp. nov. and Luteimonas salinisoli sp. nov., two novel strains isolated from saline soils. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005334] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two Gram-stain-negative, motile with single polar flagellum, rod-shaped bacterial strains, named SJ-9T and SJ-92T, were isolated from saline soils from Inner Mongolia, PR China. SJ-9T and SJ-92T grew at pH 6.5–10.0 and 7.0–11.0, 10–35 °C, and in the presence of 0–5 % and 0–8 % NaCl, respectively. Both strains were positive for oxidase, and negative for catalase. The results of phylogenetic analysis based on 16S rRNA gene sequences indicated that SJ-9T clustered with
Luteimonas marina
FR1330T (sharing 97.9 % 16S rRNA gene similarity),
Luteimonas huabeiensis
HB2T (96.5 %), ‘Luteimonas wenzhouensis’ YD-1 (96.6 %), and
Luteimonas composti
CC-YY255T (95.1 %), and shared low 16S rRNA gene similarities (<97.0 %) with all the other type strains; while SJ-92T clustered with
Luteimonas aestuarii
B9T (98.2 %), and shared low 16S rRNA gene similarities (<98.0 %) with all the other type strains. The two strains shared 97.4 % 16S rRNA gene similarity with each other. The major cellular fatty acids of both strains are iso-C15 : 0 and summed feature 9 (C16 : 0 10-methyl and/or iso-C17 : 1ω9c). The major polar lipids of both strains are diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The only respiratory quinone for both strains is ubiquinone-8 (Q-8). The genomic DNA G+C contents are 69.3 and 70.4 mol%, respectively. The digital DNA–DNA hybridization (dDDH) and average nucleotide identity by blast (ANIb) values between the two strains were 22.6 and 77.5 %, while the values between SJ-9T and ‘L. wenzhouensis’ YD-1,
L. marina
FR1330T, and
L. huabeiensis
HB2T were 38.1, 39.2, and 21.9 %, and 82.5, 84.4, and 78.5 %, while those between SJ-92T and
L. aestuarii
B9T were 21.3 and 76.7 %. On the basis of the phenotypic, physiological and phylogenetic results, SJ-9T and SJ-92T represent two novel species of the genus
Luteimonas
, for which the names Luteimonas saliphila [type stain SJ-9T (=CGMCC 1.17377T=KCTC 82248T)] and Luteimonas salinisoli [type strain SJ-92T (=CGMCC 1.17695T=KCTC 82208T)] are proposed.
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Affiliation(s)
- Ji-Quan Sun
- Laboratory for Microbial Resources, Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, PR China
| | - Xiao-Xian Huang
- Laboratory for Microbial Resources, Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, PR China
| | - Lian Xu
- Jiangsu Key Laboratory for Organic Solid Waste Utilization, Educational Ministry Engineering Center of Resource-saving Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Hua-Mei Wei
- Laboratory for Microbial Resources, Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, PR China
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27
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Xue H, Piao CG, Lin YH, Li Y. Pinirhizobacter soli gen. nov., sp. nov., a novel low temperature resistant gammaproteobacterium in the family Rhodanobacteraceae isolated from rhizospheric soil of Larix gmelinii. Arch Microbiol 2022; 204:283. [PMID: 35474027 DOI: 10.1007/s00203-022-02867-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 03/22/2022] [Accepted: 03/23/2022] [Indexed: 11/27/2022]
Abstract
Three yellow-colored strains, NC2-4-308T, NC3-4-326 and NA3-4-109, were isolated from the rhizosphere soil of Larix gmelinii in Nanwenghe Nature Reserve, Great Khingan, China. These strains were oxidase- and catalase-positive and Gram-staining-negative. The cells were non-motile short rods that were aerobic and non-spore-forming. Growth occurred at pH values of 5.0-8.0 and at 0-4% (w/v) NaCl. The three strains were resistant to low temperature and grew at 2-35 °C. The principal fatty acids (> 5%) were summed feature 9, iso-C15:0, iso-C17:0 and anteiso-C15:0. The predominant quinone was ubiquinone-8. The polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine, two unidentified phospholipids, three unidentified lipids and three unidentified aminophospholipids. The DNA G + C content of the type species was 64.0 mol%. The 16S rRNA gene sequence similarities among the three strains are more than 99.9%, indicating they belong to the same species. Phylogenetic analysis of the 16S rRNA gene, whole-genome sequences, the low ANI (74.2-75.5%) and dDDH (19.3-20.1%) hybridization values enabled differentiation of strains NC2-4-308T, NC3-4-326 and NA3-4-109 from the members of related genera. The combined data from the morphological, physiological, biochemical and chemotaxonomic tests indicate the three strains as a novel genus and a novel species in the family Rhodanobacteraceae. Therefore, we propose a novel genus with the name Pinirhizobacter soli gen. nov., sp. nov., for which the type strain is NC2-4-308T (= CFCC 14693T = KCTC 72394T).
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Affiliation(s)
- Han Xue
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing, 100091, People's Republic of China
| | - Chun-Gen Piao
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing, 100091, People's Republic of China
| | - Ying-Hua Lin
- Institute of Wetland Research, Chinese Academy of Forestry, Beijing, 100091, People's Republic of China
| | - Yong Li
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing, 100091, People's Republic of China.
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28
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Yao L, Jia Y, Lai YH, Xue F, Wang JL. Pusillimonas minor sp. nov., a novel member of the genus Pusillimonas isolated from activated sludge. Int J Syst Evol Microbiol 2022; 72. [PMID: 35451948 DOI: 10.1099/ijsem.0.005323] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel pale white-pigmented bacterial strain designated YC-7-48T was isolated from activated sludge in China. Cells of the strain, which grew at 15-37 °C (optimum at 30 °C) and pH 6.0-9.0 (optimum at 7.0), were Gram-stain-negative, rod-shaped and motile. Strain YC-7-48T had 97.4-97.1% 16S rRNA gene sequence similarity to type strains of eight species in the genera Pusillimonas, Eoetvoesia, Paralcaligenes, Parapusillimonas and Paracandidimonas of the family Alcaligenaceae. Phylogenetic analysis based on 16S rRNA gene sequencing placed the strain on a separate branch in the genus Pusillimonas and showed that it exhibited 97.4, 97.3 and 96.6% similarity to Pusillimonas caeni EBR-8-1T, Pusillimonas noertemannii BN9T and Pusillimonas maritima 17-4AT, respectively. The genome size of strain YC-7-48T was 3202438 bp, with 54.3 mol% G+C content. According to the genome analysis, YC-7-48T encodes several heavy metal resistance proteins and enzymes related to the metabolism of nicotine and aromatic compounds. The results of digital DNA-DNA hybridization and average nucleotide identity analyses based on whole genome sequences between strain YC-7-48T and the closely related strains indicated that the strain represented a new species of the genus Pusillimonas. The chemotaxonomic results identified Q-8 as the predominant respiratory quinone, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, diphosphatidylglycerol and two unidentified aminolipids as the major polar lipids, and C16:0 (27.4 %), C17:0 cyclo (22.0 %), C18:0 (11.7 %) and C19:0 cyclo ω8c (9.5 %) as the major fatty acids. Thus, based on morphological, chemotaxonomic and phylogenetic characterization and genomic data, we proposed that the isolate is a representative of a novel species named Pusillimonas minor sp. nov., with the type strain YC-7-48T (=CGMCC 1.17466T=KACC 21349T).
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Affiliation(s)
- Li Yao
- College of Marine and Bio-Engineering, Yancheng Teachers University, Yancheng, Jiangsu 224000, PR China
| | - Yan Jia
- College of Marine and Bio-Engineering, Yancheng Teachers University, Yancheng, Jiangsu 224000, PR China.,College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, Jiangsu 210000, PR China
| | - Yu-Han Lai
- College of Marine and Bio-Engineering, Yancheng Teachers University, Yancheng, Jiangsu 224000, PR China
| | - Fei Xue
- College of Marine and Bio-Engineering, Yancheng Teachers University, Yancheng, Jiangsu 224000, PR China
| | - Jia-Lian Wang
- College of Marine and Bio-Engineering, Yancheng Teachers University, Yancheng, Jiangsu 224000, PR China
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29
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Sphingomonas quercus sp. nov., Isolated from Rhizosphere Soil of Quercus mongolica. Curr Microbiol 2022; 79:122. [PMID: 35239058 DOI: 10.1007/s00284-022-02819-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Accepted: 02/18/2022] [Indexed: 11/03/2022]
Abstract
Strain XMGL2T, isolated from rhizosphere soil of Quercus mongolica in China, was characterized using a polyphasic taxonomic approach. Cells were Gram-negative, aerobic, non-spore-forming, and rod-shaped. Growth occurred at 20-37 °C (optimum, 28 °C), pH 5.0-10.0 (optimum, pH 6.0), and with 0-1% NaCl (optimum, 1%). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain XMGL2T was related to members of the genus Sphingomonas and had the highest 16S rRNA gene sequence identity to Sphingomonas oleivorans FW-11 T (96.4%). The average nucleotide identity and digital DNA-DNA hybridization values between strain XMGL2T and the closely related taxa Sphingomonas oleivorans FW-11 T and Sphingomonas fennica K101T were 75.3/19.8% and 75.8/20.2%, respectively. The major cellular fatty acids were C18:1 ω7c, C14:0 2-OH, and C16:0. The major isoprenoid quinone was Q-10 and the polar lipid profile contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidyldimethylethanolamine, phosphatidylmonomethylethanolamine, an unidentified glycophospholipid and an unidentified phospholipid. The genomic DNA G + C content was 67.9%. Based on the phenotypic and genotypic properties and phylogenetic inference, strain XMGL2T represents a novel species of the genus Sphingomonas, for which the name Sphingomonas quercus sp. nov. is proposed. The type strain is XMGL2T (= JCM 34441 T = GDMCC 1.2153 T).
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30
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Zhang H, Wang H, Cao L, Chen H, Zhong Z, Wang M, Lian C, Liu R, Zhou L, Li C. Aequorivita iocasae sp. nov., a halophilic bacterium isolated from sediment collected at a cold seep field in the South China Sea. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005199] [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 moderately halophilic bacterium, designated strain KX20305T, was isolated from sediment collected from a cold seep field in the South China Sea. Cells of strain KX20305T were Gram-stain-negative, rod-shaped, non-motile, facultatively anaerobic, oxidase- and catalase-positive, and grew optimally at 25–30 °C, pH 6.0–8.0 and with 3–6 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain KX20305T grouped with members of the genus
Aequorivita
, including
Aequorivita aquimaris
D-24T (98.3 % sequence similarity),
Aequorivita vladivostokensis
KMM 3516T (98.1 %) and
Aequorivita echinoideorum
CC-CZW007T (97.5 %). Genome sequencing of strain KX20305T revealed a genome size of 3.35 Mb and a DNA G+C content of 38.71 mol%. Genomic average nucleotide identity (orthoANI) values of strain KX20305T with
A. aquimaris
D-24T,
A. vladivostokensis
KMM 3516T and
A. echinoideorum
JCM 30378T were 83.8, 81.7 and 75.4 %, respectively, while in silico DNA–DNA hybridization (GGDC) values for strain KX20305T with these strains were 27.2, 25.0 and 19.6 %, respectively. The major fatty acids of strain KX20305T were iso-C15 : 0, iso-C17 : 0 3-OH and 10-methyl C16 : 0/iso-C17 : 1
ω9c. The predominant respiratory quinone was menaquinone-6 (MK-6). The polar lipids mainly comprised phosphatidylethanolamine, two unidentified aminolipids and two unidentified lipids. Based on comparative analysis of phylogenetic, phylogenomic, phenotypic and chemotaxonomic characteristics, strain KX20305T represents a novel species of the genus
Aequorivita
, for which the name Aequorivita iocasae sp. nov. is proposed. The type strain is KX20305T (=KCTC 82699T=MCCC 1K06238T=JCM 34635T).
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Affiliation(s)
- Huan Zhang
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, PR China
- Center of Deep-Sea Research & CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, PR China
| | - Hao Wang
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, PR China
- Center of Deep-Sea Research & CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, PR China
| | - Lei Cao
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, PR China
- Center of Deep-Sea Research & CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, PR China
| | - Hao Chen
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, PR China
- Center of Deep-Sea Research & CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, PR China
| | - Zhaoshan Zhong
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, PR China
- Center of Deep-Sea Research & CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, PR China
| | - Minxiao Wang
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, PR China
- Center of Deep-Sea Research & CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, PR China
| | - Chao Lian
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, PR China
- Center of Deep-Sea Research & CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, PR China
| | - Rui Liu
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, PR China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, PR China
| | - Li Zhou
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, PR China
- Center of Deep-Sea Research & CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, PR China
| | - Chaolun Li
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, PR China
- Center of Deep-Sea Research & CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, PR China
- University of Chinese Academy of Sciences, Beijing 100049, PR China
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31
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Dong L, Li S, Lian WH, Wei QC, Mohamad OAA, Hozzein WN, Ahmed I, Li WJ. Sphingomonas arenae sp. nov., isolated from desert soil. Int J Syst Evol Microbiol 2022; 72. [PMID: 35060847 DOI: 10.1099/ijsem.0.005195] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024] Open
Abstract
Two bacterial strains, designated as SYSU D00720T and SYSU D00722, were isolated from a desert sandy soil sample collected from Gurbantunggut Desert in Xinjiang, north-west China. Cells were Gram-stain-negative, aerobic, non-motile, rod-shaped, oxidase-positive and catalase-negative. Colonies were circular, opaque, convex, smooth, orange on Reasoner's 2A (R2A) agar. The isolates were found to grow at 4-45 °C (optimum, 28-30 °C), at pH 6.0-7.0 (optimum, 7.0) and with 0-1.5 % (w/v) NaCl (optimum, 0%). Growth was observed on R2A agar, Luria-Bertani agar and nutrient agar, but not on trypticase soy agar. The polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, sphingoglycolipid, two unidentified aminolipids, one unidentified glycolipid, one unidentified aminoglycolipid, one unidentified aminophospholipid, one unidentified phospholipid and two unidentified lipids. The main fatty acids (>10%) were C17 : 1 ω6c, summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c) and C16 : 0. The major respiratory quinone was ubiquinone-10 and the major polyamine was sym-homospermidine. The genomic DNA G+C content was 66.0 mol%. Strains SYSU D00720T and SYSU D00722 were nearly identical with a 16S rRNA gene sequence similarity of 99.6 %, and 100.0 % average nucleotide identity (ANI), average amino acid identity (AAI) and digital DNA-DNA hybridization (dDDH) values. Phylogenetic analyses clearly demonstrated that these two strains belonged to the same species of the genus Sphingomonas, and had highest sequence similarity to Sphingomonas lutea KCTC 23642T (97.3 %). The ANI, AAI and dDDH values of strains SYSU D00720T and SYSU D00722 to S. lutea KCTC 23642T were both 73.2, 69.9 and 19.2 %, respectively. Based on phylogenetic, phenotypic and chemotaxonomic distinctiveness, strains SYSU D00720T and SYSU D00722 represent a novel species of the genus Sphingomonas, for which the name Sphingomonas arenae sp. nov. is proposed. The type strain is SYSU D00720T (=MCCC 1K05154T=NBRC 115061T).
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Affiliation(s)
- Lei Dong
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Shuai Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Wen-Hui Lian
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Qi-Chuang Wei
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Osama Abdalla Abdelshafy Mohamad
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, PR China
| | - Wael N Hozzein
- Zoology Department, College of Science, King Saud University, Riyadh 999088, Saudi Arabia
- Botany and Microbiology Department, Faculty of Science, Beni-Suef University, Beni-Suef 62511, Egypt
| | - Iftikhar Ahmed
- National Culture Collection of Pakistan (NCCP), Bio-Resources Conservation Institute (BCI), National Agricultural Research Centre (NARC), Park Road, Islamabad 45500, Pakistan
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, PR China
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32
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Shen L, Liu JJ, Liu PX, An MM, He XW, Zhao GZ. A non-symbiotic novel species, Rhizobium populisoli sp. nov., isolated from rhizosphere soil of Populus popularis. Arch Microbiol 2021; 204:50. [PMID: 34935074 DOI: 10.1007/s00203-021-02706-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 11/09/2021] [Accepted: 11/10/2021] [Indexed: 10/19/2022]
Abstract
Strain XQZ8T, isolated from the rhizosphere soil of a Populus popularis plant in China, was characterized using a polyphasic taxonomic approach. Cells were Gram-negative, aerobic, non-spore-forming, and rod-shaped. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain XQZ8T was related to members of the genus Rhizobium and had the highest 16S rRNA gene sequence similarity to Rhizobium smilacinae PTYR-5T (96.6%). The average nucleotide identity and digital DNA-DNA hybridization value between strain XQZ8T and R. smilacinae PTYR-5T were 77.5% and 21.4%, respectively. TYGS whole-genome-based taxonomic and multi-locus sequence analyses of three concatenated housekeeping genes (atpD-recA-glnII) further indicated that strain XQZ8T was a new member of the genus Rhizobium. The major cellular fatty acids included summed feature 8 (C18:1 ω7c/C18:1 ω6c), summed feature 2 (C12:0 aldehyde/unknown 10.928), C16:0, and C19:0 cyclo ω8c. The major respiratory quinones were Q-9 and Q-10. The polar lipids were phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidyldimethylethanolamine, phosphatidylmonomethylethanolamine, an unidentified glycophospholipid, and three unidentified lipids. The genomic DNA G + C content of the strain was 60.1 mol%. Based on the phylogenetic, phenotypic, and genotypic characteristics, strain XQZ8T represents a novel species of the genus Rhizobium, for which the name Rhizobium populisoli sp. nov. is proposed. The type strain is XQZ8T (= JCM 34442T = GDMCC 1.2201T).
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Affiliation(s)
- Lei Shen
- College of Biological Sciences and Biotechnology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing, 100083, People's Republic of China.,College of Life Sciences, Langfang Normal University, Langfang, 065000, People's Republic of China
| | - Jing-Ju Liu
- College of Biological Sciences and Biotechnology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing, 100083, People's Republic of China
| | - Peng-Xiao Liu
- College of Biological Sciences and Biotechnology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing, 100083, People's Republic of China
| | - Miao-Miao An
- College of Biological Sciences and Biotechnology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing, 100083, People's Republic of China
| | - Xiang-Wei He
- College of Biological Sciences and Biotechnology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing, 100083, People's Republic of China
| | - Guo-Zhu Zhao
- College of Biological Sciences and Biotechnology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing, 100083, People's Republic of China.
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33
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Pang FH, Yang HY, Sun J, Yu X, Zhang H. Ottowia caeni sp. nov., a novel phenylacetic acid degrading bacterium isolated from sludge. Int J Syst Evol Microbiol 2021; 71. [PMID: 34878373 DOI: 10.1099/ijsem.0.005144] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel bacterium, designated BD-1T, was isolated from a sludge sample. Cells of the novel Gram-stain-negative strain were identified to be facultative anaerobic, non-motile and short rod-shaped. Growth occurred at 15-37 °C (optimum, 30 °C), pH 5.0-10.0 (pH 7.0) and in 0-4.0 % NaCl (2.0 %, w/v). The 16S rRNA gene sequence of strain BD-1T showed the highest sequence similarity to Ottowia thiooxydans DSM 14619T (97.0 %), followed by Ottowia pentelensis DSM 21699T (96.3 %) and less than 96 % to other related strains. The phylogenetic trees revealed that strain BD-1T clustered within the genus Ottowia. Summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c, 48.2 %), C16 : 0 (23.2 %) and summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c, 8.6 %) were the major fatty acids (>5 %), and ubiquinone-8 was the respiratory quinone. Phosphatidylethanolamine, phosphatidylmethylethanolamine and phosphatidylglycerol were identified as the major polar lipids. Meanwhile, the G+C content of the DNA was 63.6 mol% based on the draft genome analysis. The average nucleotide identity and digital DNA-DNA hybridization values between strain BD-1T and DSM 14619T were 74.5 and 21.4 %, respectively. In addition, the novel strain completely degraded 500 mg l-1 phenylacetic acid within 72 h under the condition of 3 % NaCl. Given the results of genomic, phylogenetic, phenotypic and chemotaxonomic analyses, strain BD-1T was considered to represent a novel species of the genus Ottowia, for which the name Ottowia caeni sp. nov. is proposed. The strain is a potential resource for the bioremediation of phenylacetic acid contaminated water. The type strain is BD-1T (=CGMCC 1.18541T=KCTC 82183T).
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Affiliation(s)
- Fa-Hu Pang
- School of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang 473061, PR China
| | - Hui-Ying Yang
- School of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang 473061, PR China
| | - Jie Sun
- School of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang 473061, PR China
| | - Xing Yu
- Centre for Carbon, Water and Food, School of Life and Environmental Sciences, The University of Sydney, Camden, NSW, 2570, Australia
| | - Hao Zhang
- School of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang 473061, PR China.,Innovation Center of Water Security for Water Source Region of Mid-route Project of South-North Water Diversion of Henan Province, Nanyang Normal University, Nanyang 473061, PR China
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34
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Frolova M, Yudin S, Makarov V, Glazunova O, Alikina O, Markelova N, Kolzhetsov N, Dzhelyadin T, Shcherbakova V, Trubitsyn V, Panyukov V, Zaitsev A, Kiselev S, Shavkunov K, Ozoline O. Lacticaseibacillus paracasei: Occurrence in the Human Gut Microbiota and K-Mer-Based Assessment of Intraspecies Diversity. Life (Basel) 2021; 11:life11111246. [PMID: 34833122 PMCID: PMC8620312 DOI: 10.3390/life11111246] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 11/11/2021] [Accepted: 11/13/2021] [Indexed: 02/07/2023] Open
Abstract
Alignment-free approaches employing short k-mers as barcodes for individual genomes have created a new strategy for taxonomic analysis and paved a way for high-resolution phylogeny. Here, we introduce this strategy for the Lacticaseibacillus paracasei species as a taxon requiring barcoding support for precise systematics. Using this approach for phylotyping of L. paracasei VKM B-1144 at the genus level, we identified four L. paracasei phylogroups and found that L. casei 12A belongs to one of them, rather than to the L. casei clade. Therefore, we propose to change the specification of this strain. At the genus level we found only one relative of L. paracasei VKM B-1144 among 221 genomes, complete or available in contigs, and showed that the coding potential of the genome of this "rare" strain allows its consideration as a potential probiotic component. Four sets of published metagenomes were used to assess the dependence of L. paracasei presence in the human gut microbiome on chronic diseases, dietary changes and antibiotic treatment. Only antibiotics significantly affected their presence, and strain-specific barcoding allowed the identification of the main scenarios of the adaptive response. Thus, suggesting bacteria of this species for compensatory therapy, we also propose strain-specific barcoding for selecting optimal strains for target microbiomes.
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Affiliation(s)
- Maria Frolova
- Laboratory of Functional Genomics and Cellular Stress, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, Institute of Cell Biophysics of the Russian Academy of Sciences, 142290 Pushchino, Russia; (M.F.); (O.G.); (O.A.); (N.M.); (N.K.); (T.D.); (V.P.); (S.K.)
| | - Sergey Yudin
- Centre for Strategic Planning of Federal Medical-Biological Agency of Russia, 119121 Moscow, Russia; (S.Y.); (V.M.)
| | - Valentin Makarov
- Centre for Strategic Planning of Federal Medical-Biological Agency of Russia, 119121 Moscow, Russia; (S.Y.); (V.M.)
| | - Olga Glazunova
- Laboratory of Functional Genomics and Cellular Stress, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, Institute of Cell Biophysics of the Russian Academy of Sciences, 142290 Pushchino, Russia; (M.F.); (O.G.); (O.A.); (N.M.); (N.K.); (T.D.); (V.P.); (S.K.)
| | - Olga Alikina
- Laboratory of Functional Genomics and Cellular Stress, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, Institute of Cell Biophysics of the Russian Academy of Sciences, 142290 Pushchino, Russia; (M.F.); (O.G.); (O.A.); (N.M.); (N.K.); (T.D.); (V.P.); (S.K.)
| | - Natalia Markelova
- Laboratory of Functional Genomics and Cellular Stress, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, Institute of Cell Biophysics of the Russian Academy of Sciences, 142290 Pushchino, Russia; (M.F.); (O.G.); (O.A.); (N.M.); (N.K.); (T.D.); (V.P.); (S.K.)
| | - Nikolay Kolzhetsov
- Laboratory of Functional Genomics and Cellular Stress, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, Institute of Cell Biophysics of the Russian Academy of Sciences, 142290 Pushchino, Russia; (M.F.); (O.G.); (O.A.); (N.M.); (N.K.); (T.D.); (V.P.); (S.K.)
| | - Timur Dzhelyadin
- Laboratory of Functional Genomics and Cellular Stress, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, Institute of Cell Biophysics of the Russian Academy of Sciences, 142290 Pushchino, Russia; (M.F.); (O.G.); (O.A.); (N.M.); (N.K.); (T.D.); (V.P.); (S.K.)
| | - Viktoria Shcherbakova
- Laboratory of Anaerobic Microorganisms, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, Institute of Biochemistry and Physiology of Microorganisms of the Russian Academy of Sciences, 142290 Pushchino, Russia; (V.S.); (V.T.)
| | - Vladimir Trubitsyn
- Laboratory of Anaerobic Microorganisms, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, Institute of Biochemistry and Physiology of Microorganisms of the Russian Academy of Sciences, 142290 Pushchino, Russia; (V.S.); (V.T.)
| | - Valery Panyukov
- Laboratory of Functional Genomics and Cellular Stress, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, Institute of Cell Biophysics of the Russian Academy of Sciences, 142290 Pushchino, Russia; (M.F.); (O.G.); (O.A.); (N.M.); (N.K.); (T.D.); (V.P.); (S.K.)
- Institute of Mathematical Problems of Biology RAS—The Branch of Keldysh Institute of Applied Mathematics of the Russian Academy of Sciences, 142290 Pushchino, Russia;
| | - Alexandr Zaitsev
- Institute of Mathematical Problems of Biology RAS—The Branch of Keldysh Institute of Applied Mathematics of the Russian Academy of Sciences, 142290 Pushchino, Russia;
| | - Sergey Kiselev
- Laboratory of Functional Genomics and Cellular Stress, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, Institute of Cell Biophysics of the Russian Academy of Sciences, 142290 Pushchino, Russia; (M.F.); (O.G.); (O.A.); (N.M.); (N.K.); (T.D.); (V.P.); (S.K.)
| | - Konstantin Shavkunov
- Laboratory of Functional Genomics and Cellular Stress, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, Institute of Cell Biophysics of the Russian Academy of Sciences, 142290 Pushchino, Russia; (M.F.); (O.G.); (O.A.); (N.M.); (N.K.); (T.D.); (V.P.); (S.K.)
- Correspondence: (K.S.); (O.O.)
| | - Olga Ozoline
- Laboratory of Functional Genomics and Cellular Stress, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, Institute of Cell Biophysics of the Russian Academy of Sciences, 142290 Pushchino, Russia; (M.F.); (O.G.); (O.A.); (N.M.); (N.K.); (T.D.); (V.P.); (S.K.)
- Correspondence: (K.S.); (O.O.)
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Liu GM, Yuan LL, Zhang LL, Zeng H. Streptomyces blattellae, a novel actinomycete isolated from the in vivo of a Blattella germanica. Antonie van Leeuwenhoek 2021; 115:79-87. [PMID: 34775568 DOI: 10.1007/s10482-021-01681-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Accepted: 10/27/2021] [Indexed: 11/30/2022]
Abstract
During a screening for novel and useful actinobacteria in desert animal, a new actinomycete was isolated and designated strain TRM63209T. The strain was isolated from in vivo of a Blattella germanica in Tarim University in Alar City, Xinjiang, north-west China. The strain was found to exhibit an inhibitory effect on biofilm formation by Candida albicans ATCC 18,804. The strain was observed to form abundant aerial mycelium, occasionally twisted and which differentiated into spiral spore chains. Spores of TRM63209T were observed to be oval-shaped, with a smooth surface. Strain TRM63209T was found to grow optimally at 28 °C, pH 8 and in the presence of 1% (w/v) NaCl. The whole-cell sugars of strain TRM63209T were rhamnose ribose, xylose, mannose, galactose and glucose, and the principal polarlipids were found to be diphosphatidylglycerol, phos-phatidylethanolamine, phosphatidylcholine, phosphatidylinositol mannoside, phosphatidylinositol and an unknown phospholipid(L). The diagnostic cell wall amino acid was identified as LL-diaminopimelic acid. The predominant menaquinone was found to be MK-9(H6) (14.64%), MK-9(H2) (19.65%), MK-9(H8) (22.34%), MK-10(H2) (25.37%). The major cellular fatty acids were identified as iso-C16:0, 16:0, anteiso-C15:0, anteiso-C17:0, iso-C15:0 and Sum in Feature 3. Analysis of the 16S rRNA sequence showed that strain TRM63209T exhibits high sequence similarity to Streptomyces bungoensis strain DSM 41781T 98.20%. A multi-locus sequence analysis of five house-keeping genes (atpD, gyrB, rpoB, recA and trpB) and phylogenomic analysis also illustrated that strain TRM63209T should be assigned to the genus Streptomyces. The DNA G + C content of the strain was determined to be 70.2 mol%. Average nucleotide identity (ANI) between strain TRM63209T and S. bungoensis DSM 41781T, Streptomyces phyllanthi PA1-07T, Streptomyces longwoodensis DSM 41677T and Streptomyces caeruleatus NRRL B-24802T were 82.76%, 82.54%, 82.65%, 84.02%, respectively. Digtal DNA-DNA (dDDH) hybridization were 26.30%, 25.10%, 26.20%, 29.50%, respectively. Therefore, it is concluded that strain TRM63209T represents a novel species of the genus Streptomyces, for which the name Streptomyces blattelae is proposed. The type strain is TRM63209T (CCTCC AA 2018093T = LMG 31,403 = TRM63209T).
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Affiliation(s)
- Gui-Min Liu
- Xinjiang Production and Construction Corps Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin/College of Life Science, Tarim University, Alar, 843300, Xinjiang, People's Republic of China
| | - Lin-Lin Yuan
- Xinjiang Production and Construction Corps Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin/College of Life Science, Tarim University, Alar, 843300, Xinjiang, People's Republic of China
| | - Li-Li Zhang
- Xinjiang Production and Construction Corps Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin/College of Life Science, Tarim University, Alar, 843300, Xinjiang, People's Republic of China.
| | - Hong Zeng
- School of Basic Medicine, Youjiang Medical University for Nationalities, Baise, 533000, Guangxi, People's Republic of China.
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A sulfate-reducing bacterial genus, Desulfosediminicola gen. nov., comprising two novel species cultivated from tidal-flat sediments. Sci Rep 2021; 11:19978. [PMID: 34620953 PMCID: PMC8497536 DOI: 10.1038/s41598-021-99469-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 09/27/2021] [Indexed: 01/04/2023] Open
Abstract
Tidal-flat sediments harbor a diverse array of sulfate-reducing bacteria. To isolate novel sulfate-reducing bacteria and determine their abundance, a tidal-flat sediment sample collected off Ganghwa Island (Korea) was investigated using cultivation-based and culture-independent approaches. Two Gram-stain-negative, strictly anaerobic, rod-shaped, sulfate-reducing bacteria, designated IMCC35004T and IMCC35005T, were isolated from the sample. The two strains reduced sulfate, sulfite, elemental sulfur, thiosulfate, Fe(III) citrate, and Mn(IV) oxide by utilizing several carbon sources, including acetate. The 16S rRNA gene amplicon sequencing revealed that the tidal-flat sediment contained diverse members of the phylum Desulfobacterota, and the phylotypes related to IMCC35004T and IMCC35005T were < 1%. The two strains shared 97.6% similarity in 16S rRNA gene sequence and were closely related to Desulfopila aestuarii DSM 18488T (96.1-96.5%). The average nucleotide identity, level of digital DNA-DNA hybridization, average amino acid identity, and percentages of conserved proteins determined analyzing the whole-genome sequences, as well as the chemotaxonomic data showed that the two strains belong to two novel species of a novel genus. Additionally, genes related to dissimilatory sulfate reduction were detected in the genomes of the two strains. Unlike the genera Desulfopila and Desulfotalea, IMCC35004T and IMCC35005T contained menaquinone-5 as the major respiratory quinone. Collectively, IMCC35004T and IMCC35005T were concluded to represent two novel species of a novel genus within the family Desulfocapsaceae, for which the names Desulfosediminicola ganghwensis gen. nov., sp. nov. (IMCC35004T = KCTC 15826T = NBRC 114003T) and Desulfosediminicola flagellatus sp. nov. (IMCC35005T = KCTC 15827T = NBRC 114004T) are proposed.
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Im HS, Joung Y, Lee SS. Pedobacter riviphilus sp. nov., isolated from stream sediment. Int J Syst Evol Microbiol 2021; 71. [PMID: 34590995 DOI: 10.1099/ijsem.0.004989] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, aerobic, motile by gliding, rod-shaped and pink-coloured bacterium, designated strain SW-16T, was isolated from the sediment of small stream in the Republic of Korea. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain SW-16T formed a lineage within the genus Pedobacter of the family Sphingobacteriaceae. Phylogenetic analysis also showed that strain SW-16T was most closely related to Pedobacter soli 15-51T (98.0% 16S rRNA gene sequence similarity), Pedobacter humicola R135T (97.5%), Pedobacter suwonensis 15-52T (97.4%), Pedobacter sandarakinus DS-27T (97.0%) and Pedobacter kyungheensis THG-T17T (97.0%). Growth was observed at 10-37 °C (optimum at 30 °C), pH 6-8 (optimum at pH 7) and with 0-2.0 % NaCl (optimum at 0%). The major fatty acids of the bacterial strain were iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1 ω7c). The predominant respiratory quinone was menaquinone-7 and the major polar lipids were phosphatidylethanolamine, two unidentified amino lipids, one unidentified phospholipid and three unidentified lipids. The genome size of strain SW-16T was 5.8 Mbp and the G+C content was 38.5 mol%. Based on the results of phenotypic, genomic and phylogenetic analyses, strain SW-16T represents a novel species of the genus Pedobacter, for which the name Pedobacter riviphilus sp. nov. is proposed. The type strain is SW-16T (=KEMB 1602-396T=KCTC 82079T=JCM 34181T).
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Affiliation(s)
- Hong Sik Im
- Department of Life Science, Kyonggi University, 154-42 Gwanggyosan-ro Yeongtong-gu, Suwon-si, Gyeonggi-do 16227, Republic of Korea
| | - Yochan Joung
- KEMB, Kyonggi University, 154-42 Gwanggyosan-ro Yeongtong-gu, Suwon-si, Gyeonggi-do 16227, Republic of Korea
| | - Sang-Seob Lee
- Department of Life Science, Kyonggi University, 154-42 Gwanggyosan-ro Yeongtong-gu, Suwon-si, Gyeonggi-do 16227, Republic of Korea.,KEMB, Kyonggi University, 154-42 Gwanggyosan-ro Yeongtong-gu, Suwon-si, Gyeonggi-do 16227, Republic of Korea
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Pei T, Du J, Liu Y, Deng MR, Zhu H. Chitinilyticum piscinae sp. nov., isolated from aquaculture water. Int J Syst Evol Microbiol 2021; 71. [PMID: 34309506 DOI: 10.1099/ijsem.0.004899] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-stain-negative and rod-shaped bacterial strain, designated as 4Y14T, was isolated from aquaculture water and characterized by using a polyphasic taxonomic approach. Strain 4Y14T was found to grow at 10-40 °C (optimum, 28 °C), at pH 7.0-9.0 (optimum, 7.0-8.0) and with 0-2 % NaCl (optimum, 1 %, w/v). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain 4Y14T belonged to the genus Chitinilyticum with high levels of similarity to Chitinilyticum litopenaei c1T (97.8 %) and Chitinilyticum aquatile c14T (97.2 %). Phylogenomic analysis indicated that strain 4Y14T formed an independent branch distinct from the two type strains above. Digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values between strain 4Y14T and the two type strains were, respectively, 25.3 and 25.0 %, and 81.2 and 80.3 %, which were well below the thresholds of 70 % DDH and 95-96 % ANI for species definition, implying that strain 4Y14T should represent a novel genospecies. The predominant cellular fatty acids of strain 4Y14T were summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c) and iso-C16 : 0; the major polar lipids were diphosphatidylglycerol, phosphatidylcholine and phosphatidylethanolamine; and the sole respiratory quinone was Q-8. The genomic DNA G+C content was 60.1 mol%. Based on the phenotypic and genotypic analyses, strain 4Y14T is concluded to represent a novel species of the genus Chitinilyticum, for which the name Chitinilyticum piscinae sp. nov. is proposed. The type strain of the species is 4Y14T (=GDMCC 1.1934T=KACC 22080T).
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Affiliation(s)
- Tao Pei
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Open Laboratory of Applied Microbiology, Guangdong Microbial Culture Collection Center (GDMCC), Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, PR China
| | - Juan Du
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Open Laboratory of Applied Microbiology, Guangdong Microbial Culture Collection Center (GDMCC), Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, PR China
| | - Yang Liu
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Open Laboratory of Applied Microbiology, Guangdong Microbial Culture Collection Center (GDMCC), Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, PR China
| | - Ming-Rong Deng
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Open Laboratory of Applied Microbiology, Guangdong Microbial Culture Collection Center (GDMCC), Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, PR China
| | - Honghui Zhu
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Open Laboratory of Applied Microbiology, Guangdong Microbial Culture Collection Center (GDMCC), Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, PR China
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Du J, Liu Y, Pei T, Deng MR, Zhu H. Salipiger mangrovisoli sp. nov., isolated from mangrove soil and the proposal for the reclassification of Paraphaeobacter pallidus as Salipiger pallidus comb. nov. Int J Syst Evol Microbiol 2021; 71. [PMID: 34270400 DOI: 10.1099/ijsem.0.004892] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-stain-negative, aerobic and rod-shaped bacterial strain designated as 6D45AT was isolated from mangrove soil and characterized using a polyphasic taxonomic approach. Strain 6D45AT was found to grow at 10-37 °C (optimum, 28 °C), at pH 6.0-9.0 (optimum, 7.0) and in 0-5 % (w/v) NaCl (optimum, 2%). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain 6D45AT fell into the genus Salipiger and shared 99.1 % identity with the closest type strain Salipiger pacificus CGMCC 1.3455T and less than 97.2 % identity with other type strains of this genus. The 34.8 % digital DNA-DNA hybridization (dDDH) and 88.3 % average nucleotide identity (ANI) values between strain 6D45AT and the closest relative above were well below recognized thresholds of 70 % DDH and 95-96 % ANI for species definition, implying that strain 6D45AT should represent a novel genospecies. The phylogenomic analysis indicated that strain 6D45AT formed an independent branch distinct from reference strains. The predominant cellular fatty acid of strain 6D45AT was summed feature 8 (C18 : 1 ω6c and/or C18 : 1 ω7c, 66.9 %); the polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, two unidentified aminolipids, two unidentified glycolipids and an unknown lipid; the respiratory quinone was Q-10. The genomic DNA G+C content was 66.5 mol %. Based on the phenotypic and genotypic characteristics, strain 6D45AT is concluded to represent a novel species of the genus Salipiger, for which the name Salipiger mangrovisoli sp. nov., is proposed. The type strain of the species is 6D45AT (=GDMCC 1.1960T=KCTC 82334T). We also propose the reclassification of Paraphaeobacter pallidus as Salipiger pallidus comb. nov. and 'Pelagibaca abyssi' as a species of the genus Salipiger.
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Affiliation(s)
- Juan Du
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Open Laboratory of Applied Microbiology, Guangdong Microbial Culture Collection Center (GDMCC), Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, PR China
| | - Yang Liu
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Open Laboratory of Applied Microbiology, Guangdong Microbial Culture Collection Center (GDMCC), Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, PR China
| | - Tao Pei
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Open Laboratory of Applied Microbiology, Guangdong Microbial Culture Collection Center (GDMCC), Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, PR China
| | - Ming-Rong Deng
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Open Laboratory of Applied Microbiology, Guangdong Microbial Culture Collection Center (GDMCC), Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, PR China
| | - Honghui Zhu
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Open Laboratory of Applied Microbiology, Guangdong Microbial Culture Collection Center (GDMCC), Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, PR China
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Characterization and description of Faecalibacterium butyricigenerans sp. nov. and F. longum sp. nov., isolated from human faeces. Sci Rep 2021; 11:11340. [PMID: 34059761 PMCID: PMC8166934 DOI: 10.1038/s41598-021-90786-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Accepted: 05/07/2021] [Indexed: 02/07/2023] Open
Abstract
Exploiting a pure culture strategy to investigate the composition of the human gut microbiota, two novel anaerobes, designated strains AF52-21T and CM04-06T, were isolated from faeces of two healthy Chinese donors and characterized using a polyphasic approach. The two strains were observed to be gram-negative, non-motile, and rod-shaped. Both strains grew optimally at 37 °C and pH 7.0. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the two strains clustered with species of the genus Faecalibacterium and were most closely related to Faecalibacterium prausnitzii ATCC 27768T with sequence similarity of 97.18% and 96.87%, respectively. The two isolates shared a 16S rRNA gene sequence identity of 98.69%. Draft genome sequencing was performed for strains AF52-21T and CM04-06T, generating genome sizes of 2.85 Mbp and 3.01 Mbp. The calculated average nucleotide identity values between the genomes of the strains AF52-21T and CM04-06T compared to Faecalibacterium prausnitzii ATCC 27768T were 83.20% and 82.54%, respectively, and 90.09% when comparing AF52-21T and CM04-06T. Both values were below the previously proposed species threshold (95–96%), supporting their recognition as novel species in the genus Faecalibacterium. The genomic DNA G + C contents of strains AF52-21T and CM04-06T calculated from genome sequences were 57.77 mol% and 57.51 mol%, respectively. Based on the phenotypic, chemotaxonomic and phylogenetic characteristics, we conclude that both strains represent two new Faecalibacterium species, for which the names Faecalibacterium butyricigenerans sp. nov. (type strain AF52-21T = CGMCC 1.5206T = DSM 103434T) and Faecalibacterium longum sp. nov. (type strain CM04-06T = CGMCC 1.5208T = DSM 103432T) are proposed.
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Liu Y, Pei T, Deng MR, Zhu H. Qipengyuania soli sp. nov., Isolated from Mangrove Soil. Curr Microbiol 2021; 78:2806-2814. [PMID: 34047831 DOI: 10.1007/s00284-021-02538-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 05/05/2021] [Indexed: 11/26/2022]
Abstract
A novel Gram-stain-negative, non-motile, and rod-shaped bacterial strain, designated as 6D36T, was isolated from mangrove soil and characterized by using a polyphasic taxonomic approach. Strain 6D36T was found to grow at 10-37 °C (optimum, 28 °C), at pH 6.0-9.0 (optimum, 7.0) and in 0-8% (w/v) NaCl (optimum, 3%). The predominant cellular fatty acids of strain 6D36T were summed feature 8 (C19:1 ω7c and/or C18:1 ω6c) and C17:1 ω6c; the major polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, and sphingoglycolipid; the sole respiratory quinone was Q-10. The phylogenetic analysis based on 16S rRNA gene sequences showed that strain 6D36T fell into the genus Qipengyuania and was closely related to "Erythrobacter mangrovi" MCCC 1K03690T (98.5%), Qipengyuania citrea CGMCC 1.8703T (97.6%), and Qipengyuania pelagi JCM 17468T (97.4%). The phylogenomic analysis indicated that strain 6D36T formed an independent branch distinct from reference-type strains of species within this genus. The digital DNA-DNA hybridization and average nucleotide identity values between strain 6D36T and the three type strains above were, respectively, 20.2-21.3% and 79.5-81.5%, of which were far below their respective threshold for species definition, implying that the strain represents a novel genospecies. The genomic DNA G + C content was 63.3%. Based on phenotypic and genotypic characteristics, strain 6D36T is concluded to represent a novel species of the genus Qipengyuania, for which the name Qipengyuania soli sp. nov., is proposed. The type strain of the species is 6D36T (= GDMCC 1.1977T = KCTC 82333T).
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Affiliation(s)
- Yang Liu
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Open Laboratory of Applied Microbiology, Guangdong Microbial Culture Collection Center (GDMCC), Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, People's Republic of China
| | - Tao Pei
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Open Laboratory of Applied Microbiology, Guangdong Microbial Culture Collection Center (GDMCC), Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, People's Republic of China
| | - Ming-Rong Deng
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Open Laboratory of Applied Microbiology, Guangdong Microbial Culture Collection Center (GDMCC), Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, People's Republic of China
| | - Honghui Zhu
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Open Laboratory of Applied Microbiology, Guangdong Microbial Culture Collection Center (GDMCC), Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, People's Republic of China.
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Liu Y, Pei T, Du J, Deng MR, Zhu H. Inhella proteolytica sp. nov. and Inhella gelatinilytica sp. nov., two novel species of the genus Inhella isolated from aquaculture water. Arch Microbiol 2021; 203:3191-3200. [PMID: 33834272 DOI: 10.1007/s00203-021-02264-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 02/06/2021] [Accepted: 02/24/2021] [Indexed: 11/29/2022]
Abstract
The two novel bacterial strains designated 1Y17T and 4Y10T from aquaculture water were characterized using a polyphasic taxonomic approach. Phylogenetic analysis of 16S rRNA gene sequences revealed that strains 1Y17T and 4Y10T belonged to the genus Inhella and were close to Inhella crocodyli CCP-18T, Inhella inkyongensis IMCC1713T and Inhella fonticola TNR-25T. Strains 1Y17T and 4Y10T shared 98.6% identity with each other and less than 99.0% identity with their relatives above. The phylogenomic analysis indicated that the two strains formed two independent branches distinct from their relatives. The digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values between the two strains were 21.3 and 80.9% below the two thresholds of 70% dDDH and 95-96% ANI for species definition; those between the two novel strains and their relatives were far below thresholds for species definition, implying that they represent two novel genospecies. The predominant fatty acids of the two strains were summed feature 3 (C16:1 ω7c and/or C16:1 ω6c) and C16:0; the major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol; the major quinone and polyamine were Q-8 and putrescine. Their genomic DNA G + C contents were 69.3 and 65.0%. The two novel strains can produce poly-β-hydroxybutyrate, matching with the presence of the three synthetic related genes of the phaC-phaA-phaB in their genomes. Based on the genotypic and phenotypic characteristics such as aesculin and gelatin hydrolysis, strains 1Y17T and 4Y10T are concluded to represent two novel species of the genus Inhella, for which the names Inhella proteolytica sp. nov. (type strain 1Y17T = GDMCC 1.1830T = KACC 21948T) and Inhella gelatinilytica sp. (type strain 4Y10T = GDMCC 1.1829T = KCTC 82338T) are proposed.
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Affiliation(s)
- Yang Liu
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Open Laboratory of Applied Microbiology, Guangdong Microbial Culture Collection Center (GDMCC), Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, People's Republic of China
| | - Tao Pei
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Open Laboratory of Applied Microbiology, Guangdong Microbial Culture Collection Center (GDMCC), Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, People's Republic of China
| | - Juan Du
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Open Laboratory of Applied Microbiology, Guangdong Microbial Culture Collection Center (GDMCC), Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, People's Republic of China
| | - Ming-Rong Deng
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Open Laboratory of Applied Microbiology, Guangdong Microbial Culture Collection Center (GDMCC), Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, People's Republic of China
| | - Honghui Zhu
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Open Laboratory of Applied Microbiology, Guangdong Microbial Culture Collection Center (GDMCC), Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, People's Republic of China.
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Streptomyces polyasparticus sp. nov. isolated from cotton field soil by a medium applied with polyaspartic acid. Antonie Van Leeuwenhoek 2021; 114:777-786. [PMID: 33738648 DOI: 10.1007/s10482-021-01557-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Accepted: 03/06/2021] [Indexed: 10/21/2022]
Abstract
A novel Streptomyces strain (TRM66268-LWLT) was isolated from cotton field soil by a medium supplied with polyaspartic acid (PASP) at Alar, Xinjiang, Northwest PR China, and characterized using a polyphasic taxonomic approach. The strain was found to degrade PASP, and grow well on the medium to take PASP as the sole carbon source. The TRM66268-LWLT fermentation broth was applied to the surface of PASP, and there were pores on the surface of PASP after a period of time. The strain was observed to be Gram-stain-positive and to form greyish-white aerial mycelia that differentiated into straight spore chains with round spores. The whole-cell sugar pattern of TRM 66268-LWLT consisted of ribose, mannose and arabinose, and the principal phospholipids were found to be diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol mannoside, phosphatidylinositol and two undetermined polar lipids. The predominant menaquinones were MK-7, MK-7(H4), MK-9(H8), MK-10(H6). The diagnostic cell wall amino acid was identified as LL-diaminopimelic acid. The G+C content of strain TRM66268-LWLT was 70.11 mol%. The average nucleotide identity value between strain TRM66268-LWLT and the phylogenetically related strain Streptomyces indicus IH32-1T was calculated to be 85.49%. The digital DNA-DNA hybridization value between them was 30.40%. A multilocus sequence analysis of five house-keeping genes (atpD, gyrB, rpoB, recA and trpB) also illustrated that strain TRM66268-LWLT should be assigned to the genus Streptomyces. On the basis of evidence from polyphasic study, strain TRM66268-LWLT is designated as representing a novel species of the genus Streptomyces, for which the name Streptomyces polyasparticus sp. nov. is proposed. The type strain is TRM66268-LWLT (CCTCC AA 2020003T = LMG32106T).
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Liu Y, Pei T, Du J, Chao M, Deng MR, Zhu H. Roseibium litorale sp. nov., isolated from a tidal flat sediment and proposal for the reclassification of Labrenzia polysiphoniae as Roseibium polysiphoniae comb. nov. Int J Syst Evol Microbiol 2021; 71. [PMID: 33433309 DOI: 10.1099/ijsem.0.004634] [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 novel Gram-stain-negative, facultatively anaerobic, rod-shaped and non-motile bacterial strain, designated as 4C16AT, was isolated from a tidal flat sediment and characterized by using a polyphasic taxonomic approach. Strain 4C16AT was found to grow at 10-40 °C (optimum, 28 °C), at pH 5.0-10.0 (optimum, pH 6.0-7.0) and in 0-6 % (w/v) NaCl (optimum, 1 %). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain 4C16AT fell into the genus Roseibium, and shared the highest identity of 98.9 % with the closest type strain Roseibium suaedae KACC 13772T and less than 98.0 % identity with other type strains of recognized species within this genus. The phylogenomic analysis indicated that strain 4C16AT formed an independent branch within this genus. The 28.6 % digital DNA-DNA hybridization estimate and 85.0 % average nucleotide identity between strains 4C16AT and R. suaedae KACC 13772T were the highest, but still far below their respective threshold for species definition, implying that strain 4C16AT should represent a novel genospecies. The predominant cellular fatty acid was summed feature 8; the polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylmonomethylethanolamine; the respiratory quinones were Q-9 and Q-10. The genomic DNA G+C content was 59.8mol %. Based on phylogenetic analyses and phenotypic and chemotaxonomic characteristics, strain 4C16AT is concluded to represent a novel species of the genus Roseibium, for which the name Roseibium litorale sp. nov. is proposed. The type strain of the species is 4C16AT (=GDMCC 1.1932T=KACC 22078T). We also propose the reclassification of Labrenzia polysiphoniae as Roseibium polysiphoniae comb. nov. and 'Labrenzia callyspongiae' as Roseibium callyspongiae sp. nov.
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Affiliation(s)
- Yang Liu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, PR China
| | - Tao Pei
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, PR China
| | - Juan Du
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, PR China
| | - Meijie Chao
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, PR China
| | - Ming-Rong Deng
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, PR China
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Abstract
Phylogenetic trees inferred from sequence data often have branch lengths measured in the expected number of substitutions and therefore, do not have divergence times estimated. These trees give an incomplete view of evolutionary histories since many applications of phylogenies require time trees. Many methods have been developed to convert the inferred branch lengths from substitution unit to time unit using calibration points, but none is universally accepted as they are challenged in both scalability and accuracy under complex models. Here, we introduce a new method that formulates dating as a nonconvex optimization problem where the variance of log-transformed rate multipliers is minimized across the tree. On simulated and real data, we show that our method, wLogDate, is often more accurate than alternatives and is more robust to various model assumptions.
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Affiliation(s)
- Uyen Mai
- Department of Computer Science and Engineering, UC, San Diego, CA
| | - Siavash Mirarab
- Department of Electrical and Computer Engineering, UC, San Diego, CA
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Wang S, Yang R, Xu L, Xing YT, Sun JQ. Qingshengfaniella alkalisoli gen. nov., sp. nov., a p-hydroxybenzoate-degrading strain isolated from saline soil. Int J Syst Evol Microbiol 2021; 71. [PMID: 33629940 DOI: 10.1099/ijsem.0.004719] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
p-Hydroxybenzoate is an allelopathic compound commonly found in soil from long-term monoculture cropping systems. During the bacterial diversity analysis of saline soil, a Gram-negative, non-spore forming, non-motile, aerobic p-hydroxybenzoate-degrading bacterial strain, designated LN3S51T, was isolated from saline soil which was sampled from Tumd Right Banner, Inner Mongolia, northern China. Strain LN3S51T grew at 4-40 °C (optimum, 30 °C), pH 5.0-10.0 (optimum, pH 7.0) and 0-15 % NaCl (optimum 3.0 %). Though strain LN3S51T has the highest 16S rRNA gene similarities to Litoreibacter ponti GJSW-31T (96.0 %), the phylogenetic tree based on the 16S rRNA gene sequences showed that it clustered with Fluviibacterium aquatile SM1902T (95.8 %), Meridianimarinicoccus roseus TG-679T (93.9 %), and Phycocomes zhengii LMIT002T (93.9 %). Strain LN3S51T contained Q-10 as the major ubiquinone. Phosphatidylethanolamine (PE), phosphatidylglycerol (PG), phosphatidylcholine (PC), diphosphatidylglycerol (DPG), an unidentified aminolipid (AL), and two unidentified lipids (L) were the major polar lipids. The major fatty acids were sum feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c), C16 : 0, C18 : 0, and C18 : 1 ω7c 11-methyl. The genome of strain LN3S51T consisted of a 2 257 066 bp chromosome and four plasmids with a 59.1 mol% of genomic DNA G+C content. The average nucleotide identity (ANI) and digital DNA-DNA hybridization score (dDDH) values of strain LN3S51T to F. aquatile SM1902T, M. roseus TG-679T, P. zhengii LMIT002T, and L. ponti GJSW-31T were 69.6, 70.9, 70.6, and 69.5 %, and 20.0, 19.5, 19.0, and 20.0 %, respectively. Based on the results of phylogenetic, chemtaxonomic and phenotypic characterization, strain LN3S51T is considered to represent a novel species in a new genus within the family Rhodobacteraceae, for which Qingshengfaniella alkalisoli gen. nov., sp. nov. is proposed. The type strain is LN3S51T (=CGMCC 1.17099T=KCTC 72457T).
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Affiliation(s)
- Shuai Wang
- Department of Environmental Engineering, School of Ecology and Environment, Inner Mongolia University, Hohhot, 010021, PR China
| | - Rui Yang
- Department of Environmental Engineering, School of Ecology and Environment, Inner Mongolia University, Hohhot, 010021, PR China
| | - Lian Xu
- Department of Environmental Engineering, School of Ecology and Environment, Inner Mongolia University, Hohhot, 010021, PR China
| | - Ya-Ting Xing
- Department of Environmental Engineering, School of Ecology and Environment, Inner Mongolia University, Hohhot, 010021, PR China
| | - Ji-Quan Sun
- Department of Environmental Engineering, School of Ecology and Environment, Inner Mongolia University, Hohhot, 010021, PR China
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Zou Y, Xue W, Lin X, Hu T, Liu SW, Sun CH, Luo G, Lv M, Dai Y, Kristiansen K, Xiao L. Taxonomic Description and Genome Sequence of Christensenella intestinihominis sp. nov., a Novel Cholesterol-Lowering Bacterium Isolated From Human Gut. Front Microbiol 2021; 12:632361. [PMID: 33692769 PMCID: PMC7937921 DOI: 10.3389/fmicb.2021.632361] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 01/20/2021] [Indexed: 01/29/2023] Open
Abstract
A Gram-staining-negative, non-spore-forming, short, straight rod, non-motile, and obligate anaerobic bacterial strain, AF73-05CM02T, was isolated from a fecal sample of a 30 years old healthy male living in Shenzhen, China. Colonies were approximately 0.2 mm in diameter, beige, and circular after 4 days of incubation on PYG agar under anaerobic conditions at 37°C. Strain AF73-05CM02T grew in a temperature range between 30 and 42°C and a pH range from 6.0 to 8.5, with optimum growth at 37–42°C and pH 7.0. 16S rRNA gene sequence analysis demonstrated that strain AF73-05CM02T belongs to the genus Christensenella and showed the highest level of sequence similarity (98.68%) with Christensenella minuta DSM 22607T. The predominant fatty acids of strain AF73-05CM02T were C10:0 (7.5%), iso-C11:0 (5.6%), C12:0 (7.2%), C14:0 (46.6%), iso-C15:0 (7.4%), C16:0 (9.7%), and C18:1 ω9c (6.9%). Acetic acid, formic acid, butyric acid, and lactic acid were the end products of glucose fermentation. The strain was negative for catalase, indole production, and hydrolysis of gelatin. Genomic relatedness analyses based on average nucleotide identity (ANI) indicated that strain AF73-05CM02T significantly differed from other species of the genus Christensenella, showing ANI values less than 82.89% with the phylogenetically closest species. The G + C content of the genomic DNA was 52.07 mol% from the genome sequence, which differs from that of Christensenella minuta. Several physiological, biochemical, and genotypic properties differentiated the novel bacterial strain from the related species, indicating that the strain represents a new species of the genus Christensenella for which the name Christensenella intestinihominis sp. nov. is proposed, with strain AF73-05CM02T ( = CGMCC 1.5207T = DSM 103477T ) being the type strain. The following study explored the cholesterol-lowering function of strains AF73-05CM02T and Christensenella minuta DSM 22067T and revealed that the two strains exhibit the capacity for removing cholesterol with efficiency rates of 36.6 and 54.3% and produce exopolysaccharide of 234 and 271 mg/L, respectively.
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Affiliation(s)
- Yuanqiang Zou
- BGI-Shenzhen, Shenzhen, China.,Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark.,Shenzhen Engineering Laboratory of Detection and Intervention of Human Intestinal Microbiome, BGI-Shenzhen, Shenzhen, China.,Qingdao-Europe Advanced Institute for Life Sciences, BGI-Shenzhen, Qingdao, China
| | | | - Xiaoqian Lin
- BGI-Shenzhen, Shenzhen, China.,School of Bioscience and Biotechnology, South China University of Technology, Guangzhou, China
| | | | - Shao-Wei Liu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Cheng-Hang Sun
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | | | - Mei Lv
- BGI-Shenzhen, Shenzhen, China
| | | | - Karsten Kristiansen
- BGI-Shenzhen, Shenzhen, China.,Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark.,Qingdao-Europe Advanced Institute for Life Sciences, BGI-Shenzhen, Qingdao, China
| | - Liang Xiao
- BGI-Shenzhen, Shenzhen, China.,Shenzhen Engineering Laboratory of Detection and Intervention of Human Intestinal Microbiome, BGI-Shenzhen, Shenzhen, China.,Qingdao-Europe Advanced Institute for Life Sciences, BGI-Shenzhen, Qingdao, China.,BGI College and Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
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Iniyan AM, Wink J, Landwehr W, Ramprasad EVV, Sasikala C, Ramana CV, Schumann P, Spröer C, Bunk B, Joseph FJRS, Joshua SA, Shyl ENSGD, Kannan RR, Vincent SGP. Streptomyces marianii sp. nov., a novel marine actinomycete from southern coast of India. J Antibiot (Tokyo) 2021; 74:59-69. [PMID: 32788709 DOI: 10.1038/s41429-020-0360-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 07/15/2020] [Accepted: 07/17/2020] [Indexed: 12/25/2022]
Abstract
A novel marine actinomycete strain designated ICN19T was isolated from the subtidal sediment of Chinnamuttam coast of Kanyakumari, India and subjected to polyphasic taxonomic analysis. Neighbour-joining tree based on 16S rRNA gene sequences of validly described type strains had revealed the strain ICN19T formed distinct cluster with Streptomyces wuyuanensis CGMCC 4.7042T, Streptomyces tirandamycinicus HNM0039T and Streptomyces spongiicola HNM0071T. Morphological, physiological and chemotaxonomic characteristics were consistent with those of members of the genus Streptomyces. The strain possessed LL-diaminopimelic acid as the diagnostic diamino acid. The predominant isoprenoid quinone was identified as MK-9(H8) (70%), MK-9(H6) (20%) and MK-9(H2) (2%), with the major cellular fatty acids (>10%) being anteiso-C15:0, C16:0 and iso-C16:0. The main polar lipids were found to be diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol mannosides and three unidentified phospholipids. The dendrogram generated on the basis of MALDI-TOF mass spectra supports the strain differentiated from its neigbours. The genome sequence of strain ICN19T was 9,010,366 bp in size with a total of 7420 protein-coding genes and 98 RNA genes. The genomic G+C content of the novel strain was 71.27 mol%. The DNA-DNA relatedness between strain ICN19T and the reference strains with S. wuyuanensis CGMCC 4.7042T, S. tirandamycinicus HNM0039T and S. spongiicola HNM0071T were 42.8%, 39.5% and 38%, respectively. Based on differences in physiological, biochemical, chemotaxonomic differences and whole-genome characteristics the isolated strain represents a novel species of the genus Streptomyces, for which the name Streptomyces marianii sp. nov. is proposed. Type strain is ICN19T (=MCC 3599T = KCTC 39749T).
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Affiliation(s)
- Appadurai Muthamil Iniyan
- Centre for Marine Science and Technology (CMST), Manonmaniam Sundaranar University, Rajakkamangalam, Kanyakumari District, Tamil Nadu, 629502, India.
- Microbial Strain Collection, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, Braunschweig, D-38124, Germany.
| | - Joachim Wink
- Microbial Strain Collection, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, Braunschweig, D-38124, Germany
| | - Wiebke Landwehr
- Microbial Strain Collection, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, Braunschweig, D-38124, Germany
| | - Eedara Veera Venkata Ramprasad
- Bacterial Discovery Laboratory, Centre for Environment, Institute of Science and Technology, J.N.T. University Hyderabad, Kukatpally, Hyderabad, 500085, India
| | - Chintalapati Sasikala
- Bacterial Discovery Laboratory, Centre for Environment, Institute of Science and Technology, J.N.T. University Hyderabad, Kukatpally, Hyderabad, 500085, India
| | - Chintalapati Venkata Ramana
- Bacterial Discovery and Metabolomics Laboratory, Department of Plant Sciences, School of Life Sciences, University of Hyderabad, PO Central University, Hyderabad, 500046, India.
| | - Peter Schumann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Inhoffenstraße 7b, D-38124, Braunschweig, Germany
| | - Cathrin Spröer
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Inhoffenstraße 7b, D-38124, Braunschweig, Germany
| | - Boyke Bunk
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Inhoffenstraße 7b, D-38124, Braunschweig, Germany
| | | | - Sam Albert Joshua
- Centre for Marine Science and Technology (CMST), Manonmaniam Sundaranar University, Rajakkamangalam, Kanyakumari District, Tamil Nadu, 629502, India
| | - Eby-Nesar Stella-Glory Deepak Shyl
- Centre for Marine Science and Technology (CMST), Manonmaniam Sundaranar University, Rajakkamangalam, Kanyakumari District, Tamil Nadu, 629502, India
| | - Rajaretinam Rajesh Kannan
- Infectious Disease Biology Lab, Centre for Molecular and Nanomedical Sciences, Centre for Nanoscience and Nanotechnology, School of Bio and Chemical Engineering, Sathyabama Institute of Science and Technology, Jeppiaar Nagar, Chennai, Tamil Nadu, 600119, India
| | - Samuel Gnana Prakash Vincent
- Centre for Marine Science and Technology (CMST), Manonmaniam Sundaranar University, Rajakkamangalam, Kanyakumari District, Tamil Nadu, 629502, India.
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Xu Y, Li J, Hu Y, Li H, Peng T, Zhong M, Hu Z. Winogradskyella endarachnes sp. nov., a marine bacterium isolated from the brown alga Endarachne binghamiae. Int J Syst Evol Microbiol 2021; 71. [PMID: 33270004 DOI: 10.1099/ijsem.0.004577] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-negative, aerobic, rod-shaped, non-flagellated and motile by gliding bacterium HL2-2T, was isolated from the surface of the brown alga Endarachne binghamiae in China. The 16S rRNA gene sequence analysis showed that this strain was affiliated with the genus Winogradskyella in the family Flavobacteriaceae and presented great similarity with the type strain Winogradskyella litoriviva KMM 6491T (97.9 % sequence similarity). The whole genome of strain HL2-2T comprised 3.6 Mbp with a G+C content of 31.9 mol%. The average nucleotide identity between strain HL2-2T and Winogradskyella litoriviva KMM 6491T was 83.7 %. Growth of the isolated strain was observed from 20-40 °C (optimum, 30 °C), at pH ranged from 5.5 to 8.0 (optimum, pH 6.0) and in the presence of 0-5 % (w/v) NaCl (optimum, 0-2 %). The major fatty acids (>10 % of the total) were C16 : 0, iso-C15 : 0 and the predominant menaquinone was MK-6. The combined phylogenetic, physiological and chemotaxonomic analysis show that the strain HL2-2T represents a novel species belonging to the genus Winogradskyella, for which the name Winogradskyella endarachnes sp. nov. is proposed, and which the type strain is HL2-2T (=CICC 24857T=KCTC 72882T).
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Affiliation(s)
- Yan Xu
- Heyuan Polytechnic, Heyuan, 517000, PR China
- Department of Biology, College of Science, Shantou University, Shantou 515063, PR China
| | - Jin Li
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, 511458, PR China
- Department of Biology, College of Science, Shantou University, Shantou 515063, PR China
| | - Yu Hu
- School of Life Sciences, Xiamen University, Xiamen, 361102, PR China
| | - Haibin Li
- Department of Chemical Engineering, Jieyang Polytechnic, Jieyang, 522000, PR China
- Department of Biology, College of Science, Shantou University, Shantou 515063, PR China
| | - Tao Peng
- Department of Biology, College of Science, Shantou University, Shantou 515063, PR China
| | - Mingqi Zhong
- Department of Biology, College of Science, Shantou University, Shantou 515063, PR China
| | - Zhong Hu
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, 511458, PR China
- Department of Biology, College of Science, Shantou University, Shantou 515063, PR China
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Goh CBS, Wong LW, Parimannan S, Rajandas H, Loke S, Croft L, Yule CM, Pasbakhsh P, Lee SM, Tan JBL. Chitinophaga extrema sp. nov., isolated from subsurface soil and leaf litter in a tropical peat swamp forest. Int J Syst Evol Microbiol 2020; 70:6355-6363. [PMID: 33146596 DOI: 10.1099/ijsem.0.004539] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2023] Open
Abstract
A Gram-negative, filamentous aerobic bacterium designated as strain Mgbs1T was isolated on 12 April 2017 from the subsurface soil and leaf litter substrate at the base of a Koompassia malaccensis tree in a tropical peat swamp forest in the northern regions of the state of Selangor, Malaysia (3° 39' 04.7' N 101° 17' 43.7'' E). Phylogenetic analyses based on the full 16S rRNA sequence revealed that strain Mgbs1T belongs to the genus Chitinophaga with the greatest sequence similarity to Chitinophaga terrae KP01T (97.65 %), Chitinophaga jiangningensis DSM27406T (97.58 %), and Chitinophaga dinghuensis DHOC24T (97.17 %). The major fatty acids of strain Mgbs1T (>10 %) are iso-C15 : 0, C16 : 1 ω5c and iso-C17 : 0 3-OH while the predominant respiratory quinone is menaquinone-7. Strain Mgbs1T has a complete genome size of 8.03 Mb, with a G+C content of 48.5 mol%. The DNA-DNA hybridization (DDH) score between strain Mgbs1T and C. jiangningensis DSM27406T was 15.9 %, while in silico DDH values of strain Mgbs1T against C. dinghuensis DHOC24T and C. terrae KP01T were 20.0 and 19.10% respectively. Concurrently, Average Nucleotide Identity (ANI) scores between strain Mgbs1T against all three reference strains are 73.2 %. Based on the phenotypic, chemotaxonomic, and phylogenetic consensus, strain Mgbs1T represents a novel species of the genus Chitinophaga, for which the name Chitinophaga extrema sp. nov. is proposed (=DSM 108835T=JCM 33276T).
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Affiliation(s)
- Calvin Bok Sun Goh
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, 47500 Subang Jaya, Selangor, Malaysia
- Tropical Medicine and Biology Multidisciplinary Platform, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, 47500 Subang Jaya, Selangor, Malaysia
| | - Li Wen Wong
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, 47500 Subang Jaya, Selangor, Malaysia
| | - Sivachandran Parimannan
- Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, 08100 Bedong, Kedah, Malaysia
- Deakin Genomics Centre, School of Life and Environmental Sciences, Faculty of Science, Engineering and Built Environment, Deakin University, Waurn Ponds Campus, Victoria 3216, Australia
| | - Heera Rajandas
- Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, 08100 Bedong, Kedah, Malaysia
- Deakin Genomics Centre, School of Life and Environmental Sciences, Faculty of Science, Engineering and Built Environment, Deakin University, Waurn Ponds Campus, Victoria 3216, Australia
| | - Stella Loke
- Deakin Genomics Centre, School of Life and Environmental Sciences, Faculty of Science, Engineering and Built Environment, Deakin University, Waurn Ponds Campus, Victoria 3216, Australia
| | - Lawrence Croft
- Deakin Genomics Centre, School of Life and Environmental Sciences, Faculty of Science, Engineering and Built Environment, Deakin University, Waurn Ponds Campus, Victoria 3216, Australia
| | - Catherine Mary Yule
- School of Science and Engineering, University of the Sunshine Coast, Queensland 4556, Australia
| | - Pooria Pasbakhsh
- School of Engineering, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, 47500 Subang Jaya, Selangor, Malaysia
| | - Sui Mae Lee
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, 47500 Subang Jaya, Selangor, Malaysia
- Tropical Medicine and Biology Multidisciplinary Platform, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, 47500 Subang Jaya, Selangor, Malaysia
| | - Joash Ban Lee Tan
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, 47500 Subang Jaya, Selangor, Malaysia
- Tropical Medicine and Biology Multidisciplinary Platform, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, 47500 Subang Jaya, Selangor, Malaysia
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