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Woo C, Yamamoto N. Falling bacterial communities from the atmosphere. ENVIRONMENTAL MICROBIOME 2020; 15:22. [PMID: 33902752 PMCID: PMC8066439 DOI: 10.1186/s40793-020-00369-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 11/28/2020] [Indexed: 05/05/2023]
Abstract
BACKGROUND Bacteria emitted into the atmosphere eventually settle to the pedosphere via sedimentation (dry deposition) or precipitation (wet deposition), constituting a part of the global cycling of substances on Earth, including the water cycle. In this study, we aim to investigate the taxonomic compositions and flux densities of bacterial deposition, for which little is known regarding the relative contributions of each mode of atmospheric deposition, the taxonomic structures and memberships, and the aerodynamic properties in the atmosphere. RESULTS Precipitation was found to dominate atmospheric bacterial deposition, contributing to 95% of the total flux density at our sampling site in Korea, while bacterial communities in precipitation were significantly different from those in sedimentation, in terms of both their structures and memberships. Large aerodynamic diameters of atmospheric bacteria were observed, with an annual mean of 8.84 μm, which appears to be related to their large sedimentation velocities, with an annual mean of 1.72 cm s- 1 for all bacterial taxa combined. The observed mean sedimentation velocity for atmospheric bacteria was larger than the previously reported mean sedimentation velocities for fungi and plants. CONCLUSIONS Large aerodynamic diameters of atmospheric bacteria, which are likely due to the aggregation and/or attachment to other larger particles, are thought to contribute to large sedimentation velocities, high efficiencies as cloud nuclei, and large amounts of precipitation of atmospheric bacteria. Moreover, the different microbiotas between precipitation and sedimentation might indicate specific bacterial involvement and/or selective bacterial growth in clouds. Overall, our findings add novel insight into how bacteria participate in atmospheric processes and material circulations, including hydrological circulation, on Earth.
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Affiliation(s)
- Cheolwoon Woo
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, 08826, Republic of Korea
| | - Naomichi Yamamoto
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, 08826, Republic of Korea.
- Institute of Health and Environment, Seoul National University, Seoul, 08826, Republic of Korea.
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2
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Jiang LQ, Zhang K, Li GD, Wang XY, Shi SB, Li QY, An DF, Lang L, Wang LS, Jiang CL, Jiang Y. Naasia lichenicola sp. nov., an actinobacterium isolated from lichen. Int J Syst Evol Microbiol 2019; 70:1026-1030. [PMID: 31738159 DOI: 10.1099/ijsem.0.003865] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-positive, yellow-pigmented, catalase-positive and oxidase-negative, strictly aerobic actinobacterium, designated strain YIM 131853T, was isolated from lichen collected from the South Bank of the Baltic Sea. The novel strain was non-spore-forming, short rod-shaped and motile with a single polar flagellum. The strain could grow at 4-37 °C (optimum, 28 °C), at pH 4.0-12.0 (pH 6.0) and at 0-3 % (w/v) NaCl (1 %). The DNA G+C content of strain YIM 131853T based on the draft genome sequence was 68.3 mol%. Predominant cellular fatty acids (>10 %) were identified as anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0. The polar lipid profile included diphosphatidylglycerol, dimannosyldiacylglycerol, three unknown glycolipids, two unknown phospholipids and one unknown lipid. Strain YIM 131853T had 2,4-diaminobutyric acid as the diagnostic cell-wall diamino acid, galactose and glucose as whole-cell sugars, and MK-10, MK-14, MK-13 and MK-12 as the major menaquinones. Although strain YIM 131853T exhibited a highest 16S rRNA gene sequence similarity (96.6 %) to Amnibacterium kyonggiense NBRC 109360T, phylogenetic analysis based on 16S rRNA gene sequences indicated that the strain formed a tight lineage with Naasia aerilata NBRC 108725T (96.5 % 16S rRNA gene sequence similarity), which was the only species of genus Naasia. Based on the results of phenotypic, chemotaxonomic and phylogenetic analyses, strain YIM 131853T should belong to the genus Naasia and represents a novel species of the genus Naasia, for which the name Naasia lichenicola sp. nov. is proposed. The type strain is YIM 131853T (=CGMCC 4.7565T=NBRC 113605T).
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Affiliation(s)
- Long-Qian Jiang
- Yunnan Institute of Microbiology, Key Laboratory for Conservation and Utilization of Bio-resource, School of Life Sciences, Yunnan University, Kunming, PR China
| | - Kun Zhang
- Yunnan Institute of Microbiology, Key Laboratory for Conservation and Utilization of Bio-resource, School of Life Sciences, Yunnan University, Kunming, PR China
| | - Gui-Ding Li
- Institute of Microbial Pharmaceuticals, Northeastern University, Shenyang 110819, PR China.,Yunnan Institute of Microbiology, Key Laboratory for Conservation and Utilization of Bio-resource, School of Life Sciences, Yunnan University, Kunming, PR China
| | - Xin-Yu Wang
- Key Lab for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, PR China
| | - Song-Biao Shi
- School of Chemistry and Chemical Engineering, Guangxi Key Laboratory of Chemistry and Engineering of Forest Products, Guangxi University for Nationalities, Nanning 530008, PR China
| | - Qin-Yuan Li
- Yunnan Institute of Microbiology, Key Laboratory for Conservation and Utilization of Bio-resource, School of Life Sciences, Yunnan University, Kunming, PR China
| | - De-Feng An
- Yunnan Institute of Microbiology, Key Laboratory for Conservation and Utilization of Bio-resource, School of Life Sciences, Yunnan University, Kunming, PR China
| | - Lei Lang
- Yunnan Institute of Microbiology, Key Laboratory for Conservation and Utilization of Bio-resource, School of Life Sciences, Yunnan University, Kunming, PR China
| | - Li-Song Wang
- Key Lab for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, PR China
| | - Cheng-Lin Jiang
- Yunnan Institute of Microbiology, Key Laboratory for Conservation and Utilization of Bio-resource, School of Life Sciences, Yunnan University, Kunming, PR China
| | - Yi Jiang
- Yunnan Institute of Microbiology, Key Laboratory for Conservation and Utilization of Bio-resource, School of Life Sciences, Yunnan University, Kunming, PR China
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Zhuo Y, Jin CZ, Jin FJ, Li T, Kang DH, Oh HM, Lee HG, Jin L. Lacisediminihabitans profunda gen. nov., sp. nov., a member of the family Microbacteriaceae isolated from freshwater sediment. Antonie van Leeuwenhoek 2019; 113:365-375. [PMID: 31691050 PMCID: PMC7033078 DOI: 10.1007/s10482-019-01347-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 10/02/2019] [Indexed: 11/28/2022]
Abstract
A novel Gram-stain-positive bacterial strain, CHu50b-6-2T, was isolated from a 67-cm-long sediment core collected from the Daechung Reservoir at a water depth of 17 m, Daejeon, Republic of Korea. The cells of strain CHu50b-6-2T were aerobic non-motile and formed yellow colonies on R2A agar. The phylogenetic analysis based on 16S rRNA gene sequencing indicated that the strain formed a separate lineage within the family Microbacteriaceae, exhibiting 98.0%, 97.7% and 97.6% 16S rRNA gene sequence similarities to Glaciihabitans tibetensis KCTC 29148T, Frigoribacterium faeni KACC 20509T and Lysinibacter cavernae DSM 27960T, respectively. The phylogenetic trees revealed that strain CHu50b-6-2T did not show a clear affiliation to any genus within the family Microbacteriaceae. The chemotaxonomic results showed B1α type peptidoglacan containg 2, 4-diaminobutyric acid (DAB) as the diagnostic diamino acid, MK-10 as the predominant respiratory menaquinone, diphosphatidylglycerol, phosphatidylglycerol, and an unidentified glycolipid as the major polar lipids, anteiso-C15:0, iso-C16:0, and anteiso-C17:0 as the major fatty acids, and a DNA G + C content of 67.3 mol%. The combined genotypic and phenotypic data showed that strain CHu50b-6-2T could be distinguished from all genera within the family Microbacteriaceae and represents a novel genus, Lacisediminihabitans gen. nov., with the name Lacisediminihabitans profunda sp. nov., in the family Microbacteriaceae. The type strain is CHu50b-6-2T (= KCTC 49081T = JCM 32673T).
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Affiliation(s)
- Ye Zhuo
- College of Biology and the Environment, Co-Innovation Centre for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Chun-Zhi Jin
- Department of Bio-Molecular Science, KRIBB School of Bioscience, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, Republic of Korea
- Industrial Biomaterial Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Feng-Jie Jin
- College of Biology and the Environment, Co-Innovation Centre for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Taihua Li
- College of Biology and the Environment, Co-Innovation Centre for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Dong Hyo Kang
- Department of Bio-Molecular Science, KRIBB School of Bioscience, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, Republic of Korea
- Industrial Biomaterial Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Hee-Mock Oh
- Cell Factory Research Centre, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Hyung-Gwan Lee
- Cell Factory Research Centre, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea.
| | - Long Jin
- College of Biology and the Environment, Co-Innovation Centre for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China.
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Kim I, Chhetri G, Kim J, Seo T. Amnibacterium setariae sp. nov., an endophytic actinobacterium isolated from dried foxtail. Antonie van Leeuwenhoek 2019; 112:1731-1738. [PMID: 31332634 DOI: 10.1007/s10482-019-01302-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 07/16/2019] [Indexed: 11/30/2022]
Abstract
A Gram-stain positive, short rod-shaped, aerobic, motile by means of gliding, yellow-pigmented actinobacterium, designated strain DD4aT, was isolated from dry yellow foxtail. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain DD4aT is closely related to Amnibacterium soli MB78T (98.4% similarity), Amnibacterium kyonggiense KSL51201-037T (98.2%) and Amnibacterium endophyticum 1T4Z-3T (97.43%). Strain DD4aT forms yellow colonies on R2A agar medium. The peptidoglycan was found to contains diaminopimelic acid (which is a diagnostic cell wall diamino acid), alanine, glutamic acid and lysine. The polar lipids diphosphatidylglycerol, phosphatidylglycerol, six unidentified glycolipids and an unidentified polar lipid were found to be present in strain DD4aT. The major cellular fatty acids anteiso-C15:0 (42.9%) and iso-C16:0 (34.6%) were found in strain DD4aT. The predominant respiratory quinones were found to be MK-11 and MK-12. The DNA G+C content of strain DD4aT is 73.9 mol%. DNA-DNA relatedness of strain DD4aT with A. soli MB78T, A. kyonggiense KSL51201-037T, and A. endophyticum 1T4Z-3T were 53.3% (± 1.1%), 47.0% (± 0.5%), and 47.9% (± 0.9%), respectively. The digital DNA-DNA hybridisation and average nucleotide identity values between strain DD4aT and A. kyonggiense KSL51201-037T were determined to be 26.1% and 82.7%. On the basis of phenotypic, genotypic, chemotaxonomic and phylogenetic analysis, DD4aT represents a novel member of the genus Amnibacterium, for which the name Amnibacterium setariae sp. nov., is proposed. The type strain of Amnibacterium setariae is DD4aT (= KACC 19817T = JCM 32878T).
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Affiliation(s)
- Inhyup Kim
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, South Korea
| | - Geeta Chhetri
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, South Korea
| | - Jiyoun Kim
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, South Korea
| | - Taegun Seo
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, South Korea.
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Heo J, Cho H, Kim MA, Hamada M, Tamura T, Saitou S, Kim SJ, Kwon SW. Protaetiibacter intestinalis gen. nov., of the family Microbacteriaceae, isolated from gut of Protaetia brevitarsis seulensis, reclassification of Lysinimonas kribbensis Jang et al. 2013 as Pseudolysinimonas kribbensis gen. nov., comb. nov. and emended description of the genus Lysinimonas Jang et al. 2013. Int J Syst Evol Microbiol 2019; 69:2101-2107. [DOI: 10.1099/ijsem.0.003444] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Jun Heo
- 1Agricultural Microbiology Division, National Institute of Agricultural Science, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Hayoung Cho
- 1Agricultural Microbiology Division, National Institute of Agricultural Science, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Mi Ae Kim
- 2Industrial Insect Division, National Institute of Agricultural Science, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Moriyuki Hamada
- 3NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation, 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Tomohiko Tamura
- 3NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation, 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Satomi Saitou
- 3NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation, 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Soo-Jin Kim
- 1Agricultural Microbiology Division, National Institute of Agricultural Science, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Soon-Wo Kwon
- 1Agricultural Microbiology Division, National Institute of Agricultural Science, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
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6
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Tuo L, Yan XR, Li FN, Yang C, An MB, Sun CH. Amnibacterium flavum sp. nov., a novel endophytic actinobacterium isolated from bark of Nerium indicum Mill. Int J Syst Evol Microbiol 2018; 69:285-290. [PMID: 30511915 DOI: 10.1099/ijsem.0.003156] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
A Gram-stain-positive, aerobic, short-rod-shaped, non-spore-forming actinobacterial strain, designated M8JJ-5T, was isolated from a surface-sterilized bark of Neriumindicum Mill. collected from Guizhou, China, and investigated by a polyphasic approach to determine its taxonomic position. Strain M8JJ-5T grew optimally without NaCl at 28 °C and at pH 7.0-8.0. Substrate mycelia and aerial mycelia were not formed, and no diffusible pigments were observed on the media tested. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain M8JJ-5T was most closely related to the type strains of genus Amnibacterium, and shared highest 16S rRNA gene sequence similarity of 97.29 % to Amnibacterium kyonggiense KSL51201-037T. The DNA G+C content of strain M8JJ-5T was 68.6 mol%. The cell-wall peptidoglycan contained l-2,4-diaminobutyric acid and MK-12, MK-11 were the major menaquinones. The predominant polar lipids were diphosphatidylglycerol, phosphatidylglycerol, an unidentified glycolipid, an unidentified phospholipid and an unidentified lipid, while the major fatty acids were iso-C16 : 0, anteiso-C15 : 0 and anteiso-C17 : 0. On the basis of phylogenetic, chemotaxonomic and phenotypic data, strain M8JJ-5T can be characterized to represent a novel species of the genus Amnibacterium, for which the name Amnibacteriumflavum sp. nov. is proposed. The type strain is M8JJ-5T (=KCTC 49089T=CGMCC 1.16390T).
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Affiliation(s)
- Li Tuo
- 1Research Center for Medicine and Biology, Zunyi Medical University, Zunyi 563006, PR China
| | - Xiao-Rui Yan
- 1Research Center for Medicine and Biology, Zunyi Medical University, Zunyi 563006, PR China
| | - Fei-Na Li
- 2Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, PR China
| | - Chao Yang
- 1Research Center for Medicine and Biology, Zunyi Medical University, Zunyi 563006, PR China
| | - Ming-Biao An
- 1Research Center for Medicine and Biology, Zunyi Medical University, Zunyi 563006, PR China
| | - Cheng-Hang Sun
- 2Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, PR China
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Jiang ZK, Tuo L, Huang DL, Osterman IA, Tyurin AP, Liu SW, Lukyanov DA, Sergiev PV, Dontsova OA, Korshun VA, Li FN, Sun CH. Diversity, Novelty, and Antimicrobial Activity of Endophytic Actinobacteria From Mangrove Plants in Beilun Estuary National Nature Reserve of Guangxi, China. Front Microbiol 2018; 9:868. [PMID: 29780376 PMCID: PMC5945994 DOI: 10.3389/fmicb.2018.00868] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Accepted: 04/16/2018] [Indexed: 11/13/2022] Open
Abstract
Endophytic actinobacteria are one of the important pharmaceutical resources and well known for producing different types of bioactive substances. Nevertheless, detection of the novelty, diversity, and bioactivity on endophytic actinobacteria isolated from mangrove plants are scarce. In this study, five different mangrove plants, Avicennia marina, Aegiceras corniculatum, Kandelia obovota, Bruguiera gymnorrhiza, and Thespesia populnea, were collected from Beilun Estuary National Nature Reserve in Guangxi Zhuang Autonomous Region, China. A total of 101 endophytic actinobacteria strains were recovered by culture-based approaches. They distributed in 7 orders, 15 families, and 28 genera including Streptomyces, Curtobacterium, Mycobacterium, Micrococcus, Brevibacterium, Kocuria, Nocardioides, Kineococcus, Kytococcus, Marmoricola, Microbacterium, Micromonospora, Actinoplanes, Agrococcus, Amnibacterium, Brachybacterium, Citricoccus, Dermacoccus, Glutamicibacter, Gordonia, Isoptericola, Janibacter, Leucobacter, Nocardia, Nocardiopsis, Pseudokineococcus, Sanguibacter, and Verrucosispora. Among them, seven strains were potentially new species of genera Nocardioides, Streptomyces, Amnibacterium, Marmoricola, and Mycobacterium. Above all, strain 8BXZ-J1 has already been characterized as a new species of the genus Marmoricola. A total of 63 out of 101 strains were chosen to screen antibacterial activities by paper-disk diffusion method and inhibitors of ribosome and DNA biosynthesis by means of a double fluorescent protein reporter. A total of 31 strains exhibited positive results in at least one antibacterial assay. Notably, strain 8BXZ-J1 and three other potential novel species, 7BMP-1, 5BQP-J3, and 1BXZ-J1, all showed antibacterial bioactivity. In addition, 21 strains showed inhibitory activities against at least one "ESKAPE" resistant pathogens. We also found that Streptomyces strains 2BBP-J2 and 1BBP-1 produce bioactive compound with inhibitory activity on protein biosynthesis as result of translation stalling. Meanwhile, Streptomyces strain 3BQP-1 produces bioactive compound inducing SOS-response due to DNA damage. In conclusion, this study proved mangrove plants harbored a high diversity of cultivable endophytic actinobacteria, which can be a promising source for discovery of novel species and bioactive compounds.
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Affiliation(s)
- Zhong-ke Jiang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Li Tuo
- Research Center for Medicine and Biology, Zunyi Medical University, Zunyi, China
| | - Da-lin Huang
- College of Basic Medical Sciences, Guilin Medical University, Guilin, China
| | - Ilya A. Osterman
- Department of Chemistry, A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
- Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Anton P. Tyurin
- Gause Institute of New Antibiotics, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Shao-wei Liu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Dmitry A. Lukyanov
- Department of Chemistry, A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Petr V. Sergiev
- Department of Chemistry, A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
- Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Olga A. Dontsova
- Department of Chemistry, A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
- Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Vladimir A. Korshun
- Gause Institute of New Antibiotics, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Fei-na Li
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Cheng-hang Sun
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
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Li FN, Tuo L, Lee SMY, Jin T, Liao S, Li W, Yan X, Sun CH. Amnibacterium endophyticum sp. nov., an endophytic actinobacterium isolated from Aegiceras corniculatum. Int J Syst Evol Microbiol 2018; 68:1327-1332. [PMID: 29498617 DOI: 10.1099/ijsem.0.002676] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-positive, aerobic, non-motile, non-spore-forming and short-rod-shaped actinobacterium, designated strain 1T4Z-3T, was isolated from a piece of surface-sterilized branch of Aegiceras corniculatum collected from the Cotai Ecological Zones in Macao, China. Comparative 16S rRNA gene sequence analysis showed that strain 1T4Z-3T was clearly affiliated to the genus Amnibacterium and exhibited 97.9 % gene sequence similarity to Amnibacterium kyonggiense JCM 16463T, 97.3 % gene sequence similarity to Amnibacterium soli JCM 19015T and less than 96.4 % gene sequence similarities to other genera of the family Microbacteriaceae. Strain 1T4Z-3T had L-2,4-diaminobutyric acid as the diagnostic cell-wall diamino acid. The major fatty acids (>10 % of total fatty acids) were iso-C16 : 0 (46.6 %) and anteiso-C15 : 0 (27.3 %). The predominant menaquinones of strain 1T4Z-3T were MK-11 (81.4 %) and MK-12 (14.1 %). The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, six unidentified glycolipids, four unidentified phospholipids and two unidentified lipids. The DNA G+C content of strain 1T4Z-3T was 71.4 mol%. Based on the phylogenetic, phenotypic and chemotaxonomic features, strain 1T4Z-3T is considered to represent a novel species of the genus Amnibacterium, for which the name Amnibacterium endophyticum sp. nov. is proposed. The type strain of Amnibacterium endophyticum is 1T4Z-3T (=KCTC 39983T=CGMCC 1.16066T).
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Affiliation(s)
- Fei-Na Li
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, PR China
| | - Li Tuo
- Research Center for Medicine and Biology, Zunyi Medical University, Zunyi 563003, PR China
| | - Simon Ming-Yuen Lee
- State Key Laboratory of Quality Research of Chinese Medicine and Institute of Chinese Medical Sciences, University of Macau, Macao, PR China
| | - Tao Jin
- BGI-Shenzhen, Beishan, Industrial Zone, Shenzhen 518083, PR China.,China National GeneBank, BGI-Shenzhen, Jinsha Road, Shenzhen 518120, PR China
| | - Shuilin Liao
- BGI-Shenzhen, Beishan, Industrial Zone, Shenzhen 518083, PR China.,China National GeneBank, BGI-Shenzhen, Jinsha Road, Shenzhen 518120, PR China.,BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, PR China
| | - Wenlian Li
- China Pharmaceutical University, Nanjing 210009, PR China
| | - Xinyu Yan
- China Pharmaceutical University, Nanjing 210009, PR China
| | - Cheng-Hang Sun
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, PR China
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Holman DB, Timsit E, Amat S, Abbott DW, Buret AG, Alexander TW. The nasopharyngeal microbiota of beef cattle before and after transport to a feedlot. BMC Microbiol 2017; 17:70. [PMID: 28330466 PMCID: PMC5361731 DOI: 10.1186/s12866-017-0978-6] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 03/11/2017] [Indexed: 12/17/2022] Open
Abstract
Background The nasopharyngeal (NP) microbiota plays an important role in bovine health, comprising a rich and diverse microbial community. The nasopharynx is also the niche for potentially pathogenic agents which are associated with bovine respiratory disease (BRD), a serious and costly illness in feedlot cattle. We used 14 beef heifers from a closed and disease-free herd to assess the dynamics of the NP microbiota of cattle that are transported to a feedlot. Cattle were sampled prior to transport to the feedlot (day 0) and at days 2, 7, and 14. Results The structure of the NP microbiota changed significantly over the course of the study, with the largest shift occurring between day 0 (prior to transport) and day 2 (P < 0.001). Phylogenetic diversity and richness increased following feedlot placement (day 2; P < 0.05). The genera Pasteurella, Bacillus, and Proteus were enriched at day 0, Streptococcus and Acinetobacter at day 2, Bifidobacterium at day 7, and Mycoplasma at day 14. The functional potential of the NP microbiota was assessed using PICRUSt, revealing that replication and repair, as well as translation pathways, were more relatively abundant in day 14 samples. These differences were driven mostly by Mycoplasma. Although eight cattle were culture-positive for the BRD-associated bacterium Pasteurella multocida at one or more sampling times, none were culture-positive for Mannheimia haemolytica or Histophilus somni. Conclusions This study investigated the effect that feedlot placement has on the NP microbiota of beef cattle over a 14-d period. Within two days of transport to the feedlot, the NP microbiota changed significantly, increasing in both phylogenetic diversity and richness. These results demonstrate that there is an abrupt shift in the NP microbiota of cattle after transportation to a feedlot. This may have importance for understanding why cattle are most susceptible to BRD after feedlot placement. Electronic supplementary material The online version of this article (doi:10.1186/s12866-017-0978-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Devin B Holman
- United States Department of Agriculture, National Animal Disease Center, Agricultural Research Service, Ames, IA, USA
| | - Edouard Timsit
- Department of Production Animal Health, University of Calgary, Calgary, AB, Canada
| | - Samat Amat
- Lethbridge Research Centre, Agriculture and Agri-Food Canada, 5403 1st Avenue South, Lethbridge, AB, T1J 4B1, Canada
| | - D Wade Abbott
- Lethbridge Research Centre, Agriculture and Agri-Food Canada, 5403 1st Avenue South, Lethbridge, AB, T1J 4B1, Canada
| | - Andre G Buret
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Trevor W Alexander
- Lethbridge Research Centre, Agriculture and Agri-Food Canada, 5403 1st Avenue South, Lethbridge, AB, T1J 4B1, Canada.
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10
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Bae KS, Kim MS, Lee JH, Kang JW, Kim DI, Lee JH, Seong CN. Korean indigenous bacterial species with valid names belonging to the phylum Actinobacteria. J Microbiol 2016; 54:789-795. [PMID: 27888457 DOI: 10.1007/s12275-016-6446-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 11/02/2016] [Indexed: 11/26/2022]
Abstract
To understand the isolation and classification state of actinobacterial species with valid names for Korean indigenous isolates, isolation source, regional origin, and taxonomic affiliation of the isolates were studied. At the time of this writing, the phylum Actinobacteria consisted of only one class, Actinobacteria, including five subclasses, 10 orders, 56 families, and 330 genera. Moreover, new taxa of this phylum continue to be discovered. Korean actinobacterial species with a valid name has been reported from 1995 as Tsukamurella inchonensis isolated from a clinical specimen. In 1997, Streptomyces seoulensis was validated with the isolate from the natural Korean environment. Until Feb. 2016, 256 actinobacterial species with valid names originated from Korean territory were listed on LPSN. The species were affiliated with three subclasses (Acidimicrobidae, Actinobacteridae, and Rubrobacteridae), four orders (Acidimicrobiales, Actinomycetales, Bifidobacteriales, and Solirubrobacterales), 12 suborders, 36 families, and 93 genera. Most of the species belonged to the subclass Actinobacteridae, and almost of the members of this subclass were affiliated with the order Actinomycetales. A number of novel isolates belonged to the families Nocardioidaceae, Microbacteriaceae, Intrasporangiaceae, and Streptomycetaceae as well as the genera Nocardioides, Streptomyces, and Microbacterium. Twenty-six novel genera and one novel family, Motilibacteraceae, were created first with Korean indigenous isolates. Most of the Korean indigenous actionobacterial species were isolated from natural environments such as soil, seawater, tidal flat sediment, and fresh-water. A considerable number of species were isolated from artificial resources such as fermented foods, wastewater, compost, biofilm, and water-cooling systems or clinical specimens. Korean indigenous actinobacterial species were isolated from whole territory of Korea, and especially a large number of species were from Jeju, Gyeonggi, Jeonnam, Daejeon, and Chungnam. A large number of novel actinobacterial species continue to be discovered since the Korean government is encouraging the search for new bacterial species and researchers are endeavoring to find out novel strains from extreme or untapped environments.
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Affiliation(s)
- Kyung Sook Bae
- Biological Resource Center, KRIBB, Jeongeup, 56212, Republic of Korea
| | - Mi Sun Kim
- Department of Biology, College of Life Science and Natural Resources, Sunchon National University, Suncheon, 57922, Republic of Korea
| | - Ji Hee Lee
- Department of Biology, College of Life Science and Natural Resources, Sunchon National University, Suncheon, 57922, Republic of Korea
| | - Joo Won Kang
- Department of Biology, College of Life Science and Natural Resources, Sunchon National University, Suncheon, 57922, Republic of Korea
| | - Dae In Kim
- Department of Biology, College of Life Science and Natural Resources, Sunchon National University, Suncheon, 57922, Republic of Korea
| | - Ji Hee Lee
- Department of Biology, College of Life Science and Natural Resources, Sunchon National University, Suncheon, 57922, Republic of Korea
| | - Chi Nam Seong
- Department of Biology, College of Life Science and Natural Resources, Sunchon National University, Suncheon, 57922, Republic of Korea.
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11
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Hu QW, Chu X, Xiao M, Li CT, Yan ZF, Hozzein WN, Kim CJ, Zhi XY, Li WJ. Arthrobacter deserti sp. nov., isolated from a desert soil sample. Int J Syst Evol Microbiol 2016; 66:2035-2040. [PMID: 26908080 DOI: 10.1099/ijsem.0.000986] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-positive, non-motile, rod-shaped, catalase-positive and oxidase-negative bacterium, designated YIM CS25T, was isolated from a soil sample collected from Turpan desert in Xinjiang Uyghur Autonomous Region, north-western China. The isolate grew at 15-40 °C, at pH 6.0-8.0 and with 0-6 % (w/v) NaCl. The phylogenetic trees based on 16S rRNA gene sequences revealed that strain YIM CS25T belonged to the genus Arthrobacter and was closely related to Arthrobacter halodurans JSM 078085T (95.89 % similarity). The peptidoglycan type contained lysine, alanine and glutamic acid. The major whole-cell sugars were galactose, glucose and ribose. The isolate contained diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol as the major polar lipids and MK-9 (H2) as the predominant menaquinone. The major cellular fatty acids were anteiso-C15 : 0, iso-C15 : 0, anteiso-C17 : 0, iso-C16 : 0 and anteiso-C17 : 1ω9c. The genomic DNA G+C content was 68.3 mol%. On the basis of phylogenetic, phenotypic and chemotaxonomic analysis, strain YIM CS25T is considered to represent a novel species of the genus Arthrobacter, for which the name Arthrobacter deserti sp. nov. is proposed. The type strain is YIM CS25T ( = KCTC 39544T = CGMCC 1.15091T).
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Affiliation(s)
- Qing-Wen Hu
- Yunnan Institute of Microbiology, Yunnan University,Kunming, 650091, PRChina
| | - Xiao Chu
- Yunnan Institute of Microbiology, Yunnan University,Kunming, 650091, PRChina
| | - Min Xiao
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University,Guangzhou, 510275, PRChina
| | - Chang-Tian Li
- College of Chinese Medicinal Materials, Jilin Agricultural University,Changchun, 130118, PRChina
| | - Zheng-Fei Yan
- College of Chinese Medicinal Materials, Jilin Agricultural University,Changchun, 130118, PRChina
| | - Wael N Hozzein
- Bioproducts Research Chair (BRC), College of Science, King Saud University,Riyadh 11451,Kingdom of Saudi Arabia.,Botany and Microbiology Department, Faculty of Science, Beni-Suef University,Beni-Suef, 62511,Egypt
| | - Chang-Jin Kim
- Microbial Resource Center, Korea Research Institute of Bioscience & Biotechnology,Daejeon 305-806,Republic of Korea
| | - Xiao-Yang Zhi
- Yunnan Institute of Microbiology, Yunnan University,Kunming, 650091, PRChina
| | - Wen-Jun Li
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences,Ürümqi 830011, PRChina.,State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University,Guangzhou, 510275, PRChina.,Yunnan Institute of Microbiology, Yunnan University,Kunming, 650091, PRChina
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12
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Nakai R, Baba T, Niki H, Nishijima M, Naganuma T. Aurantimicrobium minutum gen. nov., sp. nov., a novel ultramicrobacterium of the family Microbacteriaceae, isolated from river water. Int J Syst Evol Microbiol 2015; 65:4072-4079. [PMID: 26294911 DOI: 10.1099/ijsem.0.000541] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-positive, aerobic, non-motile, curved (selenoid), rod-shaped actinobacterium, designated KNCT, was isolated from the 0.2 μm-filtrate of river water in western Japan. Cells of strain KNCT were ultramicrosized (0.04-0.05 μm3). The strain grew at 15-37 °C, with no observable growth at 10 °C or 40 °C. The pH range for growth was 7-9, with weaker growth at pH 10. Growth was impeded by the presence of NaCl at concentrations greater than 1 %. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain KNCT showed relatively high sequence similarity (97.2 %) to Alpinimonas psychrophila Cr8-25T in the family Microbacteriaceae. However, strain KNCT formed an independent cluster with cultured, but as-yet-unidentified, species and environmental clones on the phylogenetic tree. The major cellular fatty acids were anteiso-C15 : 0 (41.0 %), iso-C16 : 0 (21.8 %), C16 : 0 (18.0 %) and anteiso-C17 : 0 (12.9 %), and the major menaquinones were MK-11 (71.3 %) and MK-12 (13.6 %). The major polar lipids were phosphatidylglycerol and two unknown glycolipids. The cell-wall muramic acid acyl type was acetyl. The peptidoglycan was B-type, and contained 3-hydroxyglutamic acid, glutamic acid, aspartic acid, glycine, alanine and lysine, with the latter being the diagnostic diamino acid. The G+C content of the genome was unusually low for actinobacteria (52.1 mol%), compared with other genera in the family Microbacteriaceae. Based on the phenotypic characteristics and phylogenetic evidence, strain KNCT represents a novel species of a new genus within the family Microbacteriaceae, for which the name Aurantimicrobium minutum gen. nov., sp. nov. is proposed. The type strain of the type species is KNCT ( = NBRC 105389T = NCIMB 14875T).
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Affiliation(s)
- Ryosuke Nakai
- Genetic Strains Research Center, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan.,Superlative Postdoctoral Research Fellow of the Japan Society for the Promotion of Science, Chiyoda-ku, Tokyo 102-8471, Japan
| | - Tomoya Baba
- Transdisciplinary Research Integration Center, Research Organization of Information and Systems (ROIS), 1111 Yata, Mishima, Shizuoka 411-8540, Japan
| | - Hironori Niki
- Genetic Strains Research Center, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan.,Department of Genetics, Graduate University for Advanced Studies (SOKENDAI), 1111 Yata, Mishima, Shizuoka 411-8540, Japan
| | - Miyuki Nishijima
- Technical Department, TechnoSuruga Laboratory Co., Ltd, 330 Nagasaki, Shimizu-ku, Shizuoka 424-0065, Japan
| | - Takeshi Naganuma
- Graduate School of Biosphere Science, Hiroshima University, 1-4-4 Kagamiyama, Higashi-hiroshima, Hiroshima 739-8528, Japan
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13
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Wang HF, Li L, Zhang YG, Hozzein WN, Zhou XK, Liu WH, Duan YQ, Li WJ. Arthrobacter endophyticus sp. nov., an endophytic actinobacterium isolated from root of Salsola affinis C. A. Mey. Int J Syst Evol Microbiol 2015; 65:2154-2160. [PMID: 25858247 DOI: 10.1099/ijs.0.000235] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-staining-positive, white-coloured, aerobic, non-motile, catalase-positive and oxidase-negative, endophytic actinobacterium, designated strain EGI 6500322(T), was isolated from the surface-sterilized root of the halophyte Salsola affinis C. A. Mey collected from Urumqi, Xinjiang province, north-west China. Growth occurred at 5-35 °C (optimum 25-30 °C), at pH 5-10 (optimum pH 7-8) and with 0-13% NaCl (w/v) (optimum 0-5%). The predominant menaquinone was MK-9 (93.1%). The major cellular fatty acids were anteiso-C15:0 (49.5%) and iso-C15:0 (15.1%). The cell-wall peptidoglycan contained lysine, alanine and glutamic acid. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, two unknown phospholipids and one unknown glycolipid. The DNA G+C content of strain EGI 6500322(T) was 62.0 mol%. Based on 16S rRNA gene sequence analysis, the nearest phylogenetic neighbours of strain EGI 6500322(T) were identified as Arthrobacter ardleyensis DSM 17432(T) (98.38%) and Arthrobacter bergerei DSM 16367(T (98.37%). The DNA-DNA relatedness between strain EGI 6500322(T) and Arthrobacter ardleyensis DSM 17432(T) and Arthrobacter bergerei DSM 16367(T) was 53.4 ± 4.1% and 30.5 ± 1.7%, respectively. On the basis of the phylogenetic analysis, chemotaxonomic data, physiological characteristics and DNA-DNA hybridization data, strain EGI 6500322(T) should represent a novel species of the genus Arthrobacter, for which the name Arthrobacter endophyticus sp. nov. is proposed. The type strain is EGI 6500322(T) ( = CTC 29490(T) = JCM 30091(T)).
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Affiliation(s)
- Hong-Fei Wang
- State Key Laboratory of Biocontrol, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, College of Ecology and Evolution, Sun Yat-Sen University, Guangzhou 510275, PR China.,Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürümqi 830011, PR China.,University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Li Li
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürümqi 830011, PR China.,State Key Laboratory of Biocontrol, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, College of Ecology and Evolution, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Yong-Guang Zhang
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürümqi 830011, PR China.,Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, Yunnan Institute of Microbiology, Yunnan University, Kunming 650091, PR China
| | - Wael N Hozzein
- Bioproducts Research Chair (BRC), Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Xing-Kui Zhou
- China Tobacco Yunnan Industrial Co., Ltd, Kunming 650231, PR China
| | - Wei-Hong Liu
- Department of Agriculture and Biological Sciences, Dali University, Dali 671003, PR China
| | - Yan-Qing Duan
- Bioproducts Research Chair (BRC), Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Wen-Jun Li
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürümqi 830011, PR China.,State Key Laboratory of Biocontrol, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, College of Ecology and Evolution, Sun Yat-Sen University, Guangzhou 510275, PR China.,Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, Yunnan Institute of Microbiology, Yunnan University, Kunming 650091, PR China
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14
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Wang HF, Zhang YG, Chen JY, Guo JW, Li L, Hozzein WN, Zhang YM, Wadaan MAM, Li WJ. Frigoribacterium endophyticum sp. nov., an endophytic actinobacterium isolated from the root of Anabasis elatior (C. A. Mey.) Schischk. Int J Syst Evol Microbiol 2015; 65:1207-1212. [PMID: 25609679 DOI: 10.1099/ijs.0.000081] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel endophytic actinobacterium, designated EGI 6500707(T), was isolated from the surface-sterilized root of a halophyte Anabasis elatior (C. A. Mey.) Schischk collected from Urumqi, Xinjiang province, north-west China, and characterized using a polyphasic approach. Cells were Gram-stain-positive, non-motile, short rods and produced white colonies. Growth occurred at 10-45 °C (optimum 25-30 °C), at pH 5-10 (optimum pH 8) and in presence of 0-4% (w/v) NaCl (optimum 0-3%). The predominant menaquinone was MK-9. The diagnostic phospholipids were diphosphatidylglycerol and phosphatidylglycerol. The major fatty acids were anteiso-C(15 : 0), anteiso-C(17 : 0) and iso-C(16 : 0). The DNA G+C content of strain EGI 6500707(T) was 69.1 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain EGI 6500707(T) should be placed in the genus Frigoribacterium (family Microbacteriaceae , phylum Actinobacteria ), and that the novel strain exhibited the highest 16S rRNA gene sequence similarity to Frigoribacterium faeni JCM 11265(T) (99.1%) and Frigoribacterium mesophilum MSL-08(T) (96.5%). DNA-DNA relatedness between strain EGI 6500707(T) and F. faeni JCM 11265(T) was 47.2%. On the basis of phenotypic and chemotaxonomic characteristics, phylogenetic analysis and DNA-DNA relatedness data, strain EGI 6500707(T) represents a novel species of the genus Frigoribacterium , for which the name Frigoribacterium endophyticum sp. nov. is proposed. The type strain is EGI 6500707(T) ( = JCM 30093(T) = KCTC 29493(T)).
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Affiliation(s)
- Hong-Fei Wang
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürűmqi, 830011, PR China
- State Key Laboratory of Biocontrol, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, College of Ecology and Evolution, Sun Yat-Sen University, Guangzhou, 510275, PR China
- University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Yong-Guang Zhang
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, PR China
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürűmqi, 830011, PR China
| | - Ji-Yue Chen
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürűmqi, 830011, PR China
| | - Jian-Wei Guo
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürűmqi, 830011, PR China
| | - Li Li
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürűmqi, 830011, PR China
| | - Wael N Hozzein
- Bioproducts Research Chair (BRC), College of Science, King Saud University, P.O. Box 2455 Riyadh, 11451, Kingdom of Saudi Arabia
| | - Yuan-Ming Zhang
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürűmqi, 830011, PR China
| | - Mohammed A M Wadaan
- Bioproducts Research Chair (BRC), College of Science, King Saud University, P.O. Box 2455 Riyadh, 11451, Kingdom of Saudi Arabia
| | - Wen-Jun Li
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, PR China
- State Key Laboratory of Biocontrol, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, College of Ecology and Evolution, Sun Yat-Sen University, Guangzhou, 510275, PR China
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürűmqi, 830011, PR China
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15
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Wang HF, Zhang YG, Li L, Liu WH, Hozzein WN, Chen JY, Guo JW, Zhang YM, Li WJ. Okibacterium endophyticum sp. nov., a novel endophytic actinobacterium isolated from roots of Salsola affinis C. A. Mey. Antonie van Leeuwenhoek 2015; 107:835-43. [PMID: 25566956 DOI: 10.1007/s10482-014-0376-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 12/30/2014] [Indexed: 11/26/2022]
Abstract
A white bacterial strain, designated EGI 650022(T), was isolated from the roots of Salsola affinis C. A. Mey, collected from Urumqi City, Xinjiang, north-western China. The strain was found to be aerobic, Gram-stain positive, oxidase-positive and catalase-positive. Cells were non-motile and irregular rods. Growth occurred at NaCl concentrations between 0 and 7 % (w/v), temperatures between 5 and 45 °C, and pH 6.0-9.0. Phylogenetic analysis based on 16S rRNA gene sequence indicated that strain EGI 650022(T) belongs to a clade with the genera Okibacterium and Plantibacter in the family Microbacteriaceae. The novel strain EGI 650022(T) showed highest levels of 16S rRNA gene sequence similarity with members of the genera Okibacterium and Plantibacter (97.2-98.0 %). The cell-wall peptidoglycan contained glutamate, homoserine, glycine, alanine and lysine. The predominant menaquinones (MKs) were MK-11, MK-12 and MK-12 (H4). The polar lipid pattern comprised phosphatidylglycerol, diphosphatidylglycerol, two unknown glycolipids and two unknown phospholipids. The major fatty acids were anteiso-C15:0 and anteiso-C17:0. The DNA G+C content was 66.0 mol%. The DNA-DNA relatedness values of strain EGI 650022(T) with Okibacterium fritillariae DSM 12584(T), Plantibacter flavus DSM 14012(T) and Plantibacter auratus DSM 19586(T) were 39.7, 19.7 and 22.0 %. Based on phylogenetic, phenotypic, chemotaxonomic and DNA-DNA hybridization data, strain EGI 650022(T) is considered to represent a novel species of the genus Okibacterium, for which the name Okibacterium endophyticum sp. nov. is proposed; the type strain is EGI 650022(T) (=JCM 30086(T) = KCTC 29492(T)).
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Affiliation(s)
- Hong-Fei Wang
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürűmqi, 830011, People's Republic of China
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16
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Labedella endophytica sp. nov., a novel endophytic actinobacterium isolated from stem of Anabasis elatior (C. A. Mey.) Schischk. Antonie van Leeuwenhoek 2014; 107:95-102. [DOI: 10.1007/s10482-014-0307-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2014] [Accepted: 10/15/2014] [Indexed: 11/25/2022]
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17
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Glaciihabitans tibetensis gen. nov., sp. nov., a psychrotolerant bacterium of the family Microbacteriaceae, isolated from glacier ice water. Int J Syst Evol Microbiol 2014; 64:579-587. [DOI: 10.1099/ijs.0.052670-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-positive, aerobic, non-spore-forming, short-rod-shaped bacterium, designated strain MP203T, was isolated from ice water of Midui Glacier in Tibet Autonomous Region, China. The strain was psychrotolerant, growing at 0–25 °C. 16S rRNA gene sequence analysis showed that strain MP203T was most similar to
Frigoribacterium faeni
NBRC 103066T,
Compostimonas suwonensis
KACC 13354T,
Frigoribacterium mesophilum
KCTC 19311T,
Marisediminicola antarctica
CCTCC AB 209077T and
Alpinimonas psychrophila
JCM 18951T, with similarities of 97.4, 97.2, 97.2, 97.1 and 97.1 %, respectively. The maximum-likelihood phylogenetic tree indicated that strain MP203T clustered with nine genera of the family
Microbacteriaceae
, namely
Frigoribacterium
,
Compostimonas
,
Marisediminicola
,
Alpinimonas
,
Frondihabitans
,
Clavibacter
,
Subtercola
,
Klugiella
and
Agreia
. However, bootstrap analysis showed that there was no significance in the branching pattern of the linage comprising strain MP203T and any existing generic lineage of the family
Microbacteriaceae
. DNA–DNA hybridization results indicated levels of relatedness between strain MP203T and
Marisediminicola antarctica
CCTCC AB 209077T,
Frigoribacterium faeni
NBRC 103066T,
Frigoribacterium mesophilum
KCTC 19311T,
Compostimonas suwonensis
KACC 13354T and
Alpinimonas psychrophila
JCM 18951T were 25.8±7.3, 29.6±7.6, 19.7±6.7, 16.0±4.2 and 12.4±5.1 % (mean±sd), respectively. The G+C content of the genomic DNA was 64.1 mol%. Analysis of the cell-wall peptidoglycan revealed that the peptidoglycan structure of strain MP203T was B10 type with Gly[l-Hse]–d-Glu–d-DAB, containing 2, 4-diaminobutyric acid (DAB) as a diagnostic amino acid. The cell-wall sugars were rhamnose, ribose, mannose and glucose. The major fatty acids were anteiso-C15 : 0, iso-C16 : 0 and anteiso A-C15 : 1. An unusual compound identified as anteiso-C15 : 0-DMA (1, 1-dimethoxy-anteiso-pentadecane) was also present in strain MP203T. The predominant menaquinone was MK-10. Diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), one unknown glycolipid and four unknown lipids were detected in the polar lipid extracts. As strain MP203T was distinguishable from phylogenetically related genera in the family
Microbacteriaceae
in terms of its physiological and chemotaxonomic characteristics and phylogenetic position, it was considered to represent a novel species of a new genus. Thus, the name Glaciihabitans tibetensis gen. nov., sp. nov. is proposed. The type strain of Glaciihabitans tibetensis is MP203T ( = CGMCC 1.12484T = KCTC 29148T).
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18
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Jin L, Lee HG, Kim HS, Ahn CY, Oh HM. Amnibacterium soli sp. nov., an actinobacterium isolated from grass soil. Int J Syst Evol Microbiol 2013; 63:4750-4753. [PMID: 23990652 DOI: 10.1099/ijs.0.052506-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Abstract
A Gram-stain-positive, aerobic, non-motile, non-spore-forming, short rod-shaped actinobacterium, designated strain PB243(T), was isolated from grass soil sampled in Daejeon, Republic of Korea. Comparative 16S rRNA gene sequence studies showed the isolate was clearly affiliated with the class Actinobacteria, and most closely related to Amnibacterium kyonggiense KEMC 51201-037(T), showing 98.8 % 16S rRNA gene sequence similarity. Cells of strain PB243(T) formed yellow colonies on R2A agar, contained MK-11 and MK-12 as the predominant menaquinones, l-2,4-diaminobutyric acid as the diagnostic cell-wall diamino acid, and anteiso-C15:0 and iso-C16:0 among the major fatty acids. The acyl type of the muramic acid was acetyl. The G+C content of the genomic DNA of strain PB243(T) was 71.5 mol%. Thus, the combined genotypic and phenotypic data supported the conclusion that strain PB243(T) represents a novel species of the genus Amnibacterium, for which the name Amnibacterium soli sp. nov. is proposed. The type strain is PB243(T) ( = KCTC 33147(T) = JCM 19015(T)).
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Affiliation(s)
- Long Jin
- Environmental Biotechnology Research Centre, Korea Research Institute of Bioscience & Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Republic of Korea
| | - Hyung-Gwan Lee
- Environmental Biotechnology Research Centre, Korea Research Institute of Bioscience & Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Republic of Korea
| | - Hee-Sik Kim
- Environmental Biotechnology Research Centre, Korea Research Institute of Bioscience & Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Republic of Korea
| | - Chi-Yong Ahn
- Environmental Biotechnology Research Centre, Korea Research Institute of Bioscience & Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Republic of Korea
| | - Hee-Mock Oh
- Environmental Biotechnology Research Centre, Korea Research Institute of Bioscience & Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Republic of Korea
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19
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Naasia aerilata gen. nov., sp. nov., a member of the family
Microbacteriaceae
isolated from air. Int J Syst Evol Microbiol 2013. [DOI: 10.1099/ijs.0.046599-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-positive, aerobic, rod-shaped bacterial strain, 5116S-4T, was isolated from an air sample collected in Suwon city, Republic of Korea. Phylogenetic analysis based on 16S rRNA gene sequences indicated that this strain was a new member of the family
Microbacteriaceae
. The sequence similarities of this strain to the members of the family
Microbacteriaceae
were less than 97 %, with the highest values observed with
Cryobacterium mesophilum
MSL-15T (96.3 %),
Cryobacterium roopkundense
RuGl7T (96.2 %),
Labedella gwakjiensis
KSW2-17T (96.2 %),
Cryobacterium luteum
Hh15T (96.2 %),
Cryobacterium psychrophilum
DSM 4854T (96.2 %),
Klugiella xanthotipulae
44C3T (96.0 %) and
Amnibacterium kyonggiense
KSL51201-037T (96.0 %). According to the phylogenetic tree, strain 5116S-4T formed a cluster with
A. kyonggiense
KSL51201-037T,
Labedella gwakjiensis
KSW2-17T and
Lysinimonas soli
SGM3-12T (95.3 % sequence similarity) on the support of high bootstrap values. Cells were motile with single polar flagellum and showed optimum growth at 30 °C and pH 7 without NaCl. Predominant cellular fatty acids were anteiso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0. Polar lipids were diphosphatidylglycerol, dimannosyldiacylglycerol, phosphatidylglycerol, one unknown glycolipid, one unknown phospholipid and one unknown lipid. The acyl type of the cell-wall muramic acid was the acetyl type. Peptidoglycan was supposed to be the type B1 with 2,4-diaminobutyric acid on position 3. Strain 5116S-4T was clearly distinguishable from the phylogenetically related genera in the family
Microbacteriaceae
in terms of chemotaxonomic characteristics. On the basis of the chemotaxonomic and phylogenetic characteristics, a novel genus and species are proposed, Naasia aerilata gen. nov., sp. nov. The type strain of Naasia aerilata is 5116S-4T ( = KACC 15517T = NBRC 108725T).
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Diaminobutyricimonas aerilata gen. nov., sp. nov., a novel member of the family Microbacteriaceae isolated from an air sample in Korea. J Microbiol 2012; 50:1047-52. [DOI: 10.1007/s12275-012-2118-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2012] [Accepted: 07/20/2012] [Indexed: 10/27/2022]
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21
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Jang GI, Cho Y, Cho BC. Pontimonas salivibrio gen. nov., sp. nov., a new member of the family Microbacteriaceae isolated from a seawater reservoir of a solar saltern. Int J Syst Evol Microbiol 2012; 63:2124-2131. [PMID: 23104361 DOI: 10.1099/ijs.0.043661-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-staining-positive, non-motile, strictly aerobic, non-spore-forming, vibrio-shaped bacterial strain, CL-TW6(T), was isolated from a reservoir seawater sample from a solar saltern in Korea. Analysis of the 16S rRNA gene sequence of strain CL-TW6(T) revealed a clear affiliation with the family Microbacteriaceae. Strain CL-TW6(T) showed the closest phylogenetic relationships with the genera Yonghaparkia and Microcella, with 16S rRNA gene sequence similarity of 94.8-95.3%. The strain grew in the presence of 1-9% sea salts, at 15-35 °C and at pH 7.0-9.0. The major cellular fatty acids of strain CL-TW6(T) were anteiso-C15:0 (32.6%), iso-C16:0 (20.4%), iso-C15:0 (13.2%) and iso-C14:0 (11.8%) and the major menaquinones were MK-9 and MK-10. Cell-wall analysis showed that the peptidoglycan of strain CL-TW6(T) contained 2,4-diaminobutyric acid, alanine, glycine and glutamic acid. The major polar lipids were diphosphatidylglycerol and phosphatidylglycerol. The genomic DNA G+C content of strain CL-TW6(T) was 60.0 mol%. The combined phenotypic, chemotaxonomic and phylogenetic data showed clearly that strain CL-TW6(T) could be distinguished from members of the family Microbacteriaceae with validly published names. Thus, strain CL-TW6(T) should be classified as representing a novel genus and species in the family Microbacteriaceae, for which the name Pontimonas salivibrio gen. nov., sp. nov. is proposed. The type strain of Pontimonas salivibrio is CL-TW6(T) (=KCCM 90105(T) =JCM 18206(T)).
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Affiliation(s)
- Gwang Il Jang
- Microbial Oceanography Laboratory, School of Earth and Environmental Sciences and Research Institute of Oceanography, Seoul National University, 599 Gwanak-ro, Gwanak-gu, Seoul 151-742, Republic of Korea
| | - Yirang Cho
- Microbial Oceanography Laboratory, School of Earth and Environmental Sciences and Research Institute of Oceanography, Seoul National University, 599 Gwanak-ro, Gwanak-gu, Seoul 151-742, Republic of Korea
| | - Byung Cheol Cho
- Microbial Oceanography Laboratory, School of Earth and Environmental Sciences and Research Institute of Oceanography, Seoul National University, 599 Gwanak-ro, Gwanak-gu, Seoul 151-742, Republic of Korea
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22
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Kim SJ, Tamura T, Hamada M, Ahn JH, Weon HY, Park IC, Suzuki KI, Kwon SW. Compostimonas suwonensis gen. nov., sp. nov., isolated from spent mushroom compost. Int J Syst Evol Microbiol 2012; 62:2410-2416. [DOI: 10.1099/ijs.0.036343-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-positive, aerobic, non-motile, short rod, designated SMC46T, was isolated from a spent mushroom compost sample collected in the Suwon region, South Korea. 16S rRNA gene sequence analysis revealed that strain SMC46T was a member of the family
Microbacteriaceae
; however, the isolate formed a branch separate from other genera within the family. Sequence similarity between strain SMC46T and other members of the family
Microbacteriaceae
was ≤97 %, the highest sequence similarity being with
Frigoribacterium faeni
801T and
Frondihabitans australicus
E1HC-02T (both 97.0 %). Some chemotaxonomic properties of strain SMC46T were consistent with those of the family
Microbacteriaceae
: MK-11 and MK-12 as the predominant menaquinones, anteiso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0 as the major cellular fatty acids and diphosphatidylglycerol, phosphatidylglycerol and an unidentified glycolipid as the polar lipids. However, strain SMC46T contained a B-type peptidoglycan not previously found in the family
Microbacteriaceae
. The DNA G+C content was 68 mol%. On the basis of phenotypic, chemotaxonomic and phylogenetic distinctiveness, strain SMC46T was considered to represent a novel genus and species in the family
Microbacteriaceae
, for which the name Compostimonas suwonensis gen. nov., sp. nov. is proposed. The type strain of the type species is SMC46T ( = KACC 13354T = NBRC 106304T).
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Affiliation(s)
- Soo-Jin Kim
- Korean Agricultural Culture Collection (KACC), National Academy of Agricultural Science, Rural Development Administration, Suwon, Republic of Korea
| | - Tomohiko Tamura
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation, 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Moriyuki Hamada
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation, 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Jae-Hyung Ahn
- Korean Agricultural Culture Collection (KACC), National Academy of Agricultural Science, Rural Development Administration, Suwon, Republic of Korea
| | - Hang-Yeon Weon
- Korean Agricultural Culture Collection (KACC), National Academy of Agricultural Science, Rural Development Administration, Suwon, Republic of Korea
| | - In-Cheol Park
- Korean Agricultural Culture Collection (KACC), National Academy of Agricultural Science, Rural Development Administration, Suwon, Republic of Korea
| | - Ken-ichiro Suzuki
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation, 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Soon-Wo Kwon
- Korean Agricultural Culture Collection (KACC), National Academy of Agricultural Science, Rural Development Administration, Suwon, Republic of Korea
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23
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Kim SJ, Jang YH, Hamada M, Tamura T, Ahn JH, Weon HY, Suzuki KI, Kwon SW. Homoserinimonas aerilata gen. nov., sp. nov., a novel member of the family Microbacteriaceae isolated from an air sample in Korea. J Microbiol 2012; 50:673-9. [DOI: 10.1007/s12275-012-2096-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2012] [Accepted: 04/23/2012] [Indexed: 11/24/2022]
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24
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Schumann P, Zhang DC, Redzic M, Margesin R. Alpinimonas psychrophila gen. nov., sp. nov., an actinobacterium of the family Microbacteriaceae isolated from alpine glacier cryoconite. Int J Syst Evol Microbiol 2012; 62:2724-2730. [PMID: 22228665 DOI: 10.1099/ijs.0.036160-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-type positive, Gram-reaction variable, non-motile, psychrophilic actinobacterium, designated Cr8-25(T), was isolated from alpine glacier cryoconite and was able to grow well over a temperature range of 1-15 °C. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain Cr8-25(T) belonged to the family Microbacteriaceae and showed highest 16S rRNA gene sequence similarity with Klugiella xanthotipulae 44C3(T) (97.0%). However, strain Cr8-25(T) could be differentiated from the type strain of K. xanthotipulae on the level of genomospecies by a DNA-DNA relatedness value of only 37.2%. Strain Cr8-25(T) contained a cell-wall peptidoglycan that was cross-linked according to the B-type, which is based on 2,4-diaminobutyric acid. The cell wall contained the sugars galactose, fucose and rhamnose. The predominant cellular fatty acids of strain Cr8-25(T) were C(15:0) anteiso (64.6%) and iso-C(16:0) (22.5%) and the major menaquinones were MK-11 and MK-10. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and unknown glycolipids. The G+C content of the genomic DNA was 58.8 mol%. On the basis of the phenotypic characteristics, phylogenetic and chemotaxonomic analyses and DNA-DNA relatedness data, strain Cr8-25(T) represents a novel species of a new genus in the family Microbacteriaceae, for which the name Alpinimonas psychrophila gen. nov., sp. nov. is proposed. The type strain is Cr8-25(T) (=DSM 23737(T)=LMG 26215(T)).
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Affiliation(s)
- Peter Schumann
- DSMZ-Deutsche Sammlung für Mikroorganismen und Zellkulturen GmbH, Inhoffenstrasse 7B, D-38124 Braunschweig, Germany
| | - De-Chao Zhang
- Institute of Microbiology, University of Innsbruck, Technikerstrasse 25, A-6020 Innsbruck, Austria
| | - Mersiha Redzic
- Institute of Microbiology, University of Innsbruck, Technikerstrasse 25, A-6020 Innsbruck, Austria
| | - Rosa Margesin
- Institute of Microbiology, University of Innsbruck, Technikerstrasse 25, A-6020 Innsbruck, Austria
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25
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Taxonomic and ecological studies of actinomycetes from Vietnam: isolation and genus-level diversity. J Antibiot (Tokyo) 2011; 64:599-606. [PMID: 21610715 DOI: 10.1038/ja.2011.40] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Actinomycetes were isolated from 109 soil and 93 leaf-litter samples collected at five sites in Vietnam between 2005 and 2008 using the rehydration-centrifugation (RC) method, sodium dodecyl sulfate-yeast extract dilution method, dry-heating method and oil-separation method in conjunction with humic acid-vitamin agar as an isolation medium. A total of 1882 strains were identified as Vietnamese (VN)-actinomycetes including 1080 (57%) streptomycetes (the genus Streptomyces isolates) and 802 (43%) non-streptomycetes. The 16S ribosomal RNA gene sequences of the VN-actinomycetes were analyzed using BLAST searches. The results showed that these isolates belonged to 53 genera distributed among 21 families. Approximately 90% of these strains were members of three families: Streptomycetaceae (1087 strains, 58%); Micromonosporaceae (516 strains, 27%); and Streptosporangiaceae (89 strains, 5%). Motile actinomycetes of the genera Actinoplanes, Kineosporia and Cryptosporangium, which have quite common morphological characteristics, were frequently isolated from leaf-litter samples using the RC method. It is possible that these three genera acquired common properties during a process of convergent evolution. By contrast, strains belonging to the suborder Streptosporangineae were exclusively isolated from soils. A comparison of the sampling sites revealed no significant difference in taxonomic diversity between these sites. Among the non-streptomycetes, 156 strains (19%) were considered as new taxa distributed into 21 genera belonging to 12 families. Interestingly, the isolation of actinomycetes from leaf-litter samples using the RC method proved to be the most efficient way to isolate new actinomycetes in Vietnam, especially the Micromonosporaceae species.
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