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Park M, Kim J. Arthrobacter horti sp. nov., isolated from mountain soil. Int J Syst Evol Microbiol 2024; 74. [PMID: 39008344 DOI: 10.1099/ijsem.0.006459] [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: 07/16/2024] Open
Abstract
Gram-stain-positive, aerobic, rod-shaped strains, YJM1T and YJM12S, were isolated from Maebong Mountain, Dogok-dong, Gangnam-gu, Seoul, Republic of Korea. Strains YJM1T and YJM12S exhibited growth at 5-35 °C (optimum, 20-30 °C) and pH 6-9 (optimum, pH 7) and in 0-4 % (w/v) NaCl. Strains YJM1T and YJM12S showed highest 16S rRNA gene sequence similarity to the following members of the genus Arthrobacter: A. nanjingensis A33T (98.3 %/98.2 % similarity), A. woluwensis NBRC 107840T (98.2 %/98.1 %), A. humicola KV-653T (97.3 %), A. oryzae KV-651T (97.3 %), and A. globiformis NBRC 12137T (97.2 %). The strains grew well on Reasoner's 2A, nutrient, Mueller-Hinton, yeast-dextrose, and glucose-peptone-meat extract agars. The major polar lipids of strain YJM1T were phosphatidylglycerol, diphosphatidylglycerol, and phosphatidylinositol. The primary respiratory quinone of strain YJM1T was MK-9(H2), and the major fatty acids of strains YJM1T and YJM12S were anteiso-C15 : 0, anteiso-C17 : 0, iso-C15 : 0, and iso-C16 : 0. The DNA G+C content, based on the whole genome sequence of strain YJM1T, was 68.3 mol%. Average nucleotide identity values and digital DNA-DNA hybridization values between strain YJM1T and the reference strains ranged from 75.0 to 92.7 % and from 21.0 to 65.3 %, respectively. Strain YJM1T exhibited antimicrobial activity against Bacillus subtilis and Escherichia coli. Considering the chemotaxonomic, phenotypic, genotypic, and phylogenetic results, we propose the strain YJM1T represents a novel species in the genus Arthrobacter and suggest the name Arthrobacter horti sp. nov. (type strain YJM1T=KACC 23300T=JCM 36483T).
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Affiliation(s)
- Mingyeong Park
- Department of Life Science, College of Natural Sciences, Kyonggi University, Suwon, Kyonggi-Do 16227, Republic of Korea
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Vodickova P, Suman J, Benesova E, Strejcek M, Neumann-Schaal M, Cajthaml T, Ridl J, Pajer P, Ulbrich P, Uhlik O, Lipovova P. Arthrobacter polaris sp. nov., a new cold-adapted member of the family Micrococcaceae isolated from Antarctic fellfield soil. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005541] [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
An aerobic, Gram-stain-positive and non-spore-forming strain, designated C1-1T, was isolated from a fellfield soil sample collected from frost-sorted polygons on Jane Col, Signy Island, Maritime Antarctic. Cells with a size of 0.65–0.9×1.2–1.7 µm have a flagellar motile apparatus and exhibit a rod–coccus growth cycle. Optimal growth conditions were observed at 15–20 °C, pH 7.0 and NaCl concentration up to 0.5 % (w/v) in the medium. The 16S rRNA gene sequence of C1-1T showed the highest pairwise similarity of 98.77 % to
Arthrobacter glacialis
NBRC 113092T. Phylogenetic trees based on the 16S rRNA and whole-genome sequences revealed that strain C1-1T belongs to the genus
Arthrobacter
and is most closely related to members of the ‘
Arthrobacter psychrolactophilus
group’. The G+C content of genomic DNA was 58.95 mol%. The original and orthologous average nucleotide identities between strain C1-1T and
A. glacialis
NBRC 113092T were 77.15 % and 77.38 %, respectively. The digital DNA–DNA relatedness values between strain C1-1T and
A. glacialis
NBRC 113092T was 21.6 %. The polar lipid profile was composed mainly of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and an unidentified glycolipid. The predominant cellular fatty acids were anteiso-C15 : 0 (75 %) and anteiso-C17 : 0 (15.2 %). Menaquinone MK-9(H2) (86.4 %) was the major respiratory quinone in strain C1-1T. The peptidoglycan type was determined as A3α (l-Lys–l-Ala3; A11.6). Based on all described phylogenetic, physiological and chemotaxonomic characteristics, we propose that strain C1-1T (=DSM 112353T=CCM 9148T) is the type strain of a novel species Arthrobacter polaris sp. nov.
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Affiliation(s)
- Patricie Vodickova
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Technická 5, 16628, Prague 6, Czech Republic
| | - Jachym Suman
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Technická 5, 16628, Prague 6, Czech Republic
| | - Eva Benesova
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Technická 5, 16628, Prague 6, Czech Republic
| | - Michal Strejcek
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Technická 5, 16628, Prague 6, Czech Republic
| | - Meina Neumann-Schaal
- Bacterial Metabolomics, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124, Braunschweig, Germany
| | - Tomas Cajthaml
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Prague 4, Czech Republic
- Institute for Environmental Studies, Faculty of Science, Charles University, Benátská 2, 12801, Prague 2, Czech Republic
| | - Jakub Ridl
- Department of Zoology, Faculty of Science, Charles University, Viničná 1594, 128 00, Prague 2, Czech Republic
- Laboratory of Genomics and Bioinformatics, Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, 14220, Prague 4, Czech Republic
| | - Petr Pajer
- Military Health Institute, Military Medical Agency, Tychonova 1, 16001, Prague 6, Czech Republic
| | - Pavel Ulbrich
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Technická 5, 16628, Prague 6, Czech Republic
| | - Ondrej Uhlik
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Technická 5, 16628, Prague 6, Czech Republic
| | - Petra Lipovova
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Technická 5, 16628, Prague 6, Czech Republic
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Fang Z, Zhao X, Wu Q, Li S, Liu Q, Tan L, Weng Q. Arthrobacter cavernae sp. nov., a novel actinobacterium isolated from sediment of karst cave. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005445] [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 novel, Gram-stain-positive, aerobic, non-endospore-forming, non-motile and rod-shaped bacterium designated PO-11T was isolated from sediment of karst cave collected in Libo county, Guizhou Province, PR China. The isolate grew optimally on R2A agar at 25 °C, pH 8.0 and with 0.5 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that PO-11T belonged to the genus
Arthrobacter
and was most closely related to
Arthrobacter methylotrophus
TGAT (98.3 % sequence similarity),
Arthrobacter alkaliphilus
LC6T (97.7 %) and
Arthrobacter ramosus
CCM1646T (97.1 %). Genome sequencing revealed a genome size of 4 073 119 bp and the genomic DNA G+C content was 66.16 mol%. Its DNA–DNA relatedness values with
A. methylotrophus
TGAT,
A. alkaliphilus
LC6T and
A. ramosus
CCM1646T were 23.0, 22.9 and 23.2 %, respectively. The main fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0. The major respiratory quinone was MK-9(H2). The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, glycolipid, phosphatidylethanolamine, phosphatidylinositol and unidentified lipids. Thus, based on phylogenetic and phenotypic and chemotaxonomic data, strain PO-11T represents a novel species of the genus
Arthrobacter
, for which the name Arthrobacter cavernae sp. nov. is proposed. The type strain is strain PO-11T (=CCTCC AB 2021070T=LMG 32459T).
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Affiliation(s)
- Zheng Fang
- School of Life Sciences, Guizhou Normal University, Guiyang 550025, PR China
| | - Xiaoyong Zhao
- School of Life Sciences, Guizhou Normal University, Guiyang 550025, PR China
| | - Qingshan Wu
- School of Life Sciences, Guizhou Normal University, Guiyang 550025, PR China
| | - Shixia Li
- School of Life Sciences, Guizhou Normal University, Guiyang 550025, PR China
| | - Qiuping Liu
- School of Life Sciences, Guizhou Normal University, Guiyang 550025, PR China
| | - Leitao Tan
- School of Life Sciences, Guizhou Normal University, Guiyang 550025, PR China
| | - Qingbei Weng
- Qiannan Normal University for Nationalities, Duyun 558000, PR China
- School of Life Sciences, Guizhou Normal University, Guiyang 550025, PR China
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Sun YC, Sun P, Xue J, Du Y, Yan H, Wang LW, Yi XX, Sun JG, Zhang X, Gao JL. Arthrobacter wenxiniae sp. nov., a novel plant growth-promoting rhizobacteria species harbouring a carotenoids biosynthetic gene cluster. Antonie van Leeuwenhoek 2022; 115:353-364. [PMID: 35088183 DOI: 10.1007/s10482-021-01701-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 12/10/2021] [Indexed: 10/19/2022]
Abstract
A bacterial strain, designated AETb3-4T was isolated from the rhizosphere of lily. Comparison of 16S rRNA gene sequences showed that the sequence from strain AETb3-4T exhibits high sequence similarity with those of Arthrobacter silviterrae KIS14-16T (97.9%), Arthrobacter livingstonensis LI2T (97.2%) and Arthrobacter stackebrandtii CCM 2783T (97.0%). Whole genome average nucleotide identity (ANI) and the digital DNA-DNA hybridization (dDDH) values between strain AETb3-4T and the reference strains A. silviterrae DSM 27180T, A. livingstonensis L12T and A. stackebrandtii DSM 16005T were below 83.6% and 27.7%, respectively, values which are considerably below the proposed thresholds for the species delineation, consistent with the proposal that strain AETb3-4T represents a novel species. The genome size of strain AETb3-4T is 4.33 Mb and the genomic DNA G + C content is 67.3%. The main polar lipids were identified as phosphatidylglycerol, diphosphatidylglycero, phosphatidylinositol and an unidentified glycolipid. The major fatty acids (> 10%) were identified as anteiso-C15: 0 and anteiso-C17: 0. The predominant menaquinone was found to be menaquinone 9 (MK-9) (H2) (82.2%). Phenotypic tests allowed the strain to be differentiated from its close phylogenetic neighbors. Based on the results obtained, it is proposed that the strain AETb3-4T (= CFCC 16390T = LMG 31708T) represents a novel species in the genus Arthrobacter, for which the names Arthrobacter wenxiniae sp. nov. is proposed. In addition, the novel strain AETb3-4T has multiple plant growth-promoting characters including ACC-deaminase activity and production of IAA. Furthermore, the genome contains secondary metabolite biosynthesis gene clusters, including a carotenoid biosynthetic gene cluster, suggesting potential capacities for secondary metabolite synthesis. These data suggest that strain AETb3-4T may have potential applications both in medicine and sustainable agriculture.
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Affiliation(s)
- Yu-Chen Sun
- Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, People's Republic of China.,College of Food Science and Engineering, Beijing University of Agriculture, Beijing, 102206, People's Republic of China
| | - Pengbo Sun
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,German Cancer Consortium(DKTK), German Cancer Research Center(DKFZ), 69120, Heidelberg, Germany
| | - Jing Xue
- Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, People's Republic of China
| | - Yunpeng Du
- Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, People's Republic of China
| | - Hui Yan
- College of Animal Science and Technology, Hebei Agricultural University, Baoding, 071001, People's Republic of China
| | - Li-Wei Wang
- Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, People's Republic of China
| | - Xin-Xin Yi
- College of Food Science and Engineering, Beijing University of Agriculture, Beijing, 102206, People's Republic of China
| | - Jian-Guang Sun
- Key Laboratory of Microbial Resources, Ministry of Agriculture/Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China
| | - Xiuhai Zhang
- Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, People's Republic of China.
| | - Jun-Lian Gao
- Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, People's Republic of China.
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Abstract
A Gram-stain-positive, aerobic and rod-shaped bacterial strain, designated JH1-1T, was isolated from a forest soil sample collected in Suwon, Gyeonggi-do, Republic of Korea. Strain JH1-1T could grow at 10-35 °C (optimum, 28-30 °C), pH 4.5-8.5 and tolerated 5 % (w/v) NaCl. Strain JH1-1T was most closely related to members of the genus Arthrobacter, namely Arthrobacter alkaliphilus LC6T (98.5 % similarity), Arthrobacter methylotrophus TGAT (98.4 %), Arthrobacter ramosus CCM 1646T (97.8 %), Arthrobacter bambusae THG-GM18T (97.5 %) and Arthrobacter pokkalii P3B162T (97.3 %). The strain grew well on Reasoner's 2A agar, tryptone soya agar, nutrient agar, Mueller-Hinton agar and Luria-Bertani agar. The major polar lipid profile comprised phosphatidylglycerol, diphosphatidylglycerol, unidentified phospholipid and unidentified glycolipids. The major respiratory quinone was MK-9(H2). The main fatty acids were C15 : 0 anteiso, C15 : 0 iso, C16 : 0 iso and C17 :0 anteiso. The DNA G+C content of the isolated strain based on the whole genome sequence was 63.6 mol%. The average nucleotide identity and digital DNA-DNA hybridization values between strain JH1-1T and its reference type strains ranged from 81.3 to 85.4 % and from 21.1 to 29.1 %, respectively. Based on phenotypic, chemotypic and genotypic evidence, strain JH1-1T could be differentiated phylogenetically and phenotypically from the recognized species of the genus Arthrobacter. Therefore, strain JH1-1T is considered to represent a novel species, for which the name Arthrobacter terricola sp. nov. is proposed. The type strain is JH1-1T (=KACC 21385T=JCM 33641T).
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Affiliation(s)
- Ngoc Hoang Trinh
- Thai Nguyen University of Sciences, Thai Nguyen City, Thai Nguyen province 250000, Vietnam.,Department of Life Science, College of Natural Sciences, Kyonggi University, Suwon, Gyeonggi-Do 16227, Republic of Korea
| | - Jaisoo Kim
- Department of Life Science, College of Natural Sciences, Kyonggi University, Suwon, Gyeonggi-Do 16227, Republic of Korea
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Arthrobacter dokdonellae sp. nov., isolated from a plant of the genus Campanula. J Microbiol 2019; 57:732-737. [PMID: 31079331 DOI: 10.1007/s12275-019-8540-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 04/05/2019] [Accepted: 04/08/2019] [Indexed: 10/26/2022]
Abstract
A Gram-stain-positive, oxidase- and catalase-positive motile, aerobic, and rod-shaped bacterial strain, designated as DCT-5T, was isolated from a native plant belonging to the genus Campanula at Dokdo island, Republic of Korea. Growth of the strain DCT-5T was observed at 15-37°C (optimum 30°C) on R2A broth, pH 6.0-8.0 (optimum 7.0), and 0-5% (w/v) NaCl concentration (optimum 0%). The 16S rRNA gene sequence analysis revealed that strain DCT-5T was most closely related to Arthrobacter silviterrae KIS14-16T, Arthrobacter livingstonensis LI2T, Arthrobacter stackebrandtii CCM 2783T, Arthrobacter cryoconiti Cr6-08T, Arthrobacter ramosus CCM 1646T, and Arthrobacter psychrochitiniphilus GP3T with pairwise sequence similarities of 98.76%, 97.47%, 97.25%, 97.11%, 97.11%, and 97.00%, respectively. The DNA G+C content of strain DCT-5T was 64.7 mol%, and its DNA-DNA relatedness values with A. silviterrae KIS14-16T, A. livingstonensis LI2T, A. stackebrandtii CCM 2783T, A. psychrochitiniphilus GP3T, A. ramosus CCM 1646T, and A. cryoconiti Cr6-08T were 32.57 ± 2.02%, 28.75 ± 0.88%, 31.93 ± 1.15%, 34.73 ± 1.86%, 29.12 ± 1.56%, and 27.23 ± 0.88%, respectively. The major quinone was MK-9(H2) and major fatty acids were anteiso-C15:0, anteiso-C17:0, iso-C15:0, and iso-C16:0. The polar lipids were diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phosphatidylinositol (PI), unidentified glycolipid (GL), two unidentified aminophospholipids (APLs), and three unidentified lipids (Ls). The peptidoglycan type was A3α. On the basis of phenotypic, phylogenetic, genotypic, and chemotaxonomic characteristics, strain DCT-5T represents a novel species of the genus Arthrobacter, for which the name Arthrobacter dokdonellae sp. nov. is proposed. The type strain is DCT-5T (= KCTC 49189T = LMG 31284T).
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Tanner K, Martorell P, Genovés S, Ramón D, Zacarías L, Rodrigo MJ, Peretó J, Porcar M. Bioprospecting the Solar Panel Microbiome: High-Throughput Screening for Antioxidant Bacteria in a Caenorhabditis elegans Model. Front Microbiol 2019; 10:986. [PMID: 31134025 PMCID: PMC6514134 DOI: 10.3389/fmicb.2019.00986] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 04/18/2019] [Indexed: 01/11/2023] Open
Abstract
Microbial communities that are exposed to sunlight typically share a series of adaptations to deal with the radiation they are exposed to, including efficient DNA repair systems, pigment production and protection against oxidative stress, which makes these environments good candidates for the search of novel antioxidant microorganisms. In this research project, we isolated potential antioxidant pigmented bacteria from a dry and highly-irradiated extreme environment: solar panels. High-throughput in vivo assays using Caenorhabditis elegans as an experimental model demonstrated the high antioxidant and ultraviolet-protection properties of these bacterial isolates that proved to be rich in carotenoids. Our results suggest that solar panels harbor a microbial community that includes strains with potential applications as antioxidants.
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Affiliation(s)
| | | | | | | | - Lorenzo Zacarías
- Instituto de Agroquímica y Tecnología de Alimentos (IATA-CSIC), Paterna, Spain
| | - María Jesús Rodrigo
- Instituto de Agroquímica y Tecnología de Alimentos (IATA-CSIC), Paterna, Spain
| | - Juli Peretó
- Darwin Bioprospecting Excellence S.L., Paterna, Spain
- Institute for Integrative Systems Biology (I2SysBio), University of Valencia-CSIC, Paterna, Spain
- Department of Biochemistry and Molecular Biology, University of Valencia, Burjassot, Spain
| | - Manuel Porcar
- Darwin Bioprospecting Excellence S.L., Paterna, Spain
- Institute for Integrative Systems Biology (I2SysBio), University of Valencia-CSIC, Paterna, Spain
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Zhang Q, Oh M, Kim JH, Kanjanasuntree R, Konkit M, Sukhoom A, Kantachote D, Kim W. Arthrobacter paludis sp. nov., isolated from a marsh. Int J Syst Evol Microbiol 2018; 68:47-51. [DOI: 10.1099/ijsem.0.002426] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Qi Zhang
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul 06974, Republic of Korea
| | - Mihee Oh
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul 06974, Republic of Korea
| | - Jong-Hwa Kim
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul 06974, Republic of Korea
| | - Rungravee Kanjanasuntree
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul 06974, Republic of Korea
| | - Maytiya Konkit
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul 06974, Republic of Korea
| | - Ampaitip Sukhoom
- Department of Microbiology, Faculty of Science, Prince of Songkla University, Songkhla 90112, Thailand
| | - Duangporn Kantachote
- Department of Microbiology, Faculty of Science, Prince of Songkla University, Songkhla 90112, Thailand
| | - Wonyong Kim
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul 06974, Republic of Korea
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Lee JY, Hyun DW, Soo Kim P, Sik Kim H, Shin NR, Yun JH, Jung MJ, Kim MS, Woong Whon T, Bae JW. Arthrobacter echini sp. nov., isolated from the gut of a purple sea urchin, Heliocidaris crassispina. Int J Syst Evol Microbiol 2016; 66:1887-1893. [DOI: 10.1099/ijsem.0.000965] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- June-Young Lee
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul 130-701, Korea
| | - Dong-Wook Hyun
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul 130-701, Korea
| | - Pil Soo Kim
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul 130-701, Korea
| | - Hyun Sik Kim
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul 130-701, Korea
| | - Na-Ri Shin
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul 130-701, Korea
| | - Ji-Hyun Yun
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul 130-701, Korea
| | - Mi-Ja Jung
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul 130-701, Korea
| | - Min-Soo Kim
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul 130-701, Korea
| | - Tae Woong Whon
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul 130-701, Korea
| | - Jin-Woo Bae
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul 130-701, Korea
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Krishnan R, Menon RR, Tanaka N, Busse HJ, Krishnamurthi S, Rameshkumar N. Arthrobacter pokkalii sp nov, a Novel Plant Associated Actinobacterium with Plant Beneficial Properties, Isolated from Saline Tolerant Pokkali Rice, Kerala, India. PLoS One 2016; 11:e0150322. [PMID: 26963092 PMCID: PMC4786123 DOI: 10.1371/journal.pone.0150322] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 02/12/2016] [Indexed: 11/19/2022] Open
Abstract
A novel yellow colony-forming bacterium, strain P3B162T was isolated from the pokkali rice rhizosphere from Kerala, India, as part of a project study aimed at isolating plant growth beneficial rhizobacteria from saline tolerant pokkali rice and functionally evaluate their abilities to promote plant growth under saline conditions. The novel strain P3B162T possesses plant growth beneficial traits such as positive growth on 1-aminocyclopropane-1-carboxylic acid (ACC), production of indole acetic acid (IAA) and siderophore. In addition, it also showed important phenotypic characters such as ability to form biofilm and utilization of various components of plant root exudates (sugars, amino acids and organic acids), clearly indicating its lifestyle as a plant rhizosphere associated bacterium. Taxonomically, the novel strain P3B162T was affiliated to the genus Arthrobacter based on the collective results of phenotypic, genotypic and chemotaxonomic analyses. Moreover, molecular analysis using 16S rRNA gene showed Arthrobacter globiformis NBRC 12137T, Arthrobacter pascens DSM 20545T and Arthrobacter liuii DSXY973T as the closely related phylogenetic neighbours, showing more than 98% 16S rRNA similarity values, whereas the recA gene analysis displayed Arthrobacter liuii JCM 19864T as the nearest neighbour with 94.7% sequence similarity and only 91.7% to Arthrobacter globiformis LMG 3813T and 88.7% to Arthrobacter pascens LMG 16255T. However, the DNA-DNA hybridization values between strain P3B162T, Arthrobacter globiformis LMG 3813T, Arthrobacter pascens LMG 16255T and Arthrobacter liuii JCM 19864T was below 50%. In addition, the novel strain P3B162T can be distinguished from its closely related type strains by several phenotypic characters such as colony pigment, tolerance to NaCl, motility, reduction of nitrate, hydrolysis of DNA, acid from sucrose, cell wall sugars and cell wall peptidoglycan structure. In conclusion, the combined results of this study support the classification of strain P3B162T as a novel Arthrobacter species and we propose Arthrobacter pokkalii sp.nov.as its name. The type strain is P3B162T (= KCTC 29498T = MTCC 12358T).
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Affiliation(s)
- Ramya Krishnan
- Biotechnology Department, National Institute for Interdisciplinary Science and Technology (CSIR), Thiruvananthapuram, 695 019, Kerala, India
| | - Rahul Ravikumar Menon
- Biotechnology Department, National Institute for Interdisciplinary Science and Technology (CSIR), Thiruvananthapuram, 695 019, Kerala, India
| | - Naoto Tanaka
- NODAI Culture Collection Center, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo, 156–8502, Japan
| | - Hans-Jürgen Busse
- Institute of Microbiology, Veterinary University Vienna, A-1210, Vienna, Austria
| | - Srinivasan Krishnamurthi
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sec-39A, Chandigarh, 160036, India
| | - Natarajan Rameshkumar
- Biotechnology Department, National Institute for Interdisciplinary Science and Technology (CSIR), Thiruvananthapuram, 695 019, Kerala, India
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(Actino)Bacterial “intelligence”: using comparative genomics to unravel the information processing capacities of microbes. Curr Genet 2016; 62:487-98. [DOI: 10.1007/s00294-016-0569-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 01/20/2016] [Accepted: 01/22/2016] [Indexed: 01/24/2023]
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Environmental Sensing in Actinobacteria: a Comprehensive Survey on the Signaling Capacity of This Phylum. J Bacteriol 2015; 197:2517-35. [PMID: 25986905 DOI: 10.1128/jb.00176-15] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 05/12/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Signal transduction is an essential process that allows bacteria to sense their complex and ever-changing environment and adapt accordingly. Three distinct major types of signal-transducing proteins (STPs) can be distinguished: one-component systems (1CSs), two-component systems (2CSs), and extracytoplasmic-function σ factors (ECFs). Since Actinobacteria are particularly rich in STPs, we comprehensively investigated the abundance and diversity of STPs encoded in 119 actinobacterial genomes, based on the data stored in the Microbial Signal Transduction (MiST) database. Overall, we observed an approximately linear correlation between the genome size and the total number of encoded STPs. About half of all membrane-anchored 1CSs are protein kinases. For both 1CSs and 2CSs, a detailed analysis of the domain architectures identified novel proteins that are found only in actinobacterial genomes. Many actinobacterial genomes are particularly enriched for ECFs. As a result of this study, almost 500 previously unclassified ECFs could be classified into 18 new ECF groups. This comprehensive survey demonstrates that actinobacterial genomes encode previously unknown STPs, which may represent new mechanisms of signal transduction and regulation. This information not only expands our knowledge of the diversity of bacterial signal transduction but also provides clear and testable hypotheses about their mechanisms, which can serve as starting points for experimental studies. IMPORTANCE In the wake of the genomic era, with its enormous increase in the amount of available sequence information, the challenge has now shifted toward making sense and use of this treasure chest. Such analyses are a prerequisite to provide meaningful information that can help guide subsequent experimental efforts, such as mechanistic studies on novel signaling strategies. This work provides a comprehensive analysis of signal transduction proteins from 119 actinobacterial genomes. We identify, classify, and describe numerous novel and conserved signaling devices. Hence, our work serves as an important resource for any researcher interested in signal transduction of this important bacterial phylum, which contains organisms of ecological, biotechnological, and medical relevance.
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