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Ge X, Yang S, Zhen C, Liu W. Actinophytocola gossypii sp. nov. and Streptomyces gossypii sp. nov., two novel actinomycetes isolated from rhizosphere soil of cotton. Int J Syst Evol Microbiol 2023; 73. [PMID: 37068120 DOI: 10.1099/ijsem.0.005832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/18/2023] Open
Abstract
Two Gram-positive, aerobic and non-motile actinomycetes, designated S1-96T and N2-109T, were isolated from soils collected from a cotton field. They are described as representing two novel species of genera Actinophytocola and Streptomyces through a polyphasic approach. Analysis of 16S rRNA gene sequences revealed that strains S1-96T and N2-109T showed highest similarity to Actinophytocola xinjiangensis CGMCC 4.4663T (99.10 %) and Streptomyces iconiensis BNT558T (98.21 %), respectively. Phylogenetic analyses based on 16S rRNA and core genes confirmed the close relationships of these strains. Genomic analyses further supported the novel taxonomic delimitation of these two species based on digital DNA-DNA hybridization and average nucleotide identity. Strains S1-96T and N2-109T contained MK-9(H4) and MK-9(H6) as the most abundant menaquinone, respectively. High abundances of iso-fatty acids were detected in both strains, which was similar to their close relatives. Physiological and polar lipid analyses also revealed differences between these strains and their phylogenetic neighbours, supporting their taxonomic delimitation as novel species. The names Actinophytocola gossypii sp. nov. (type strain S1-96T=JCM 34412T=CGMCC 4.7707T) and Streptomyces gossypii sp. nov. (type strain N2-109T=JCM 34628T=CGMCC 4.7717T) are proposed.
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Affiliation(s)
- Xianfeng Ge
- School of Food and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, PR China
| | - Shenrong Yang
- School of Food and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, PR China
| | - Cheng Zhen
- School of Food and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, PR China
| | - Wenzheng Liu
- School of Food and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, PR China
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Jin CZ, Jin L, Liu MJ, Lee JM, Park DJ, Kim CJ. Solihabitans fulvus gen. nov., sp. nov., a member of the family Pseudonocardiaceae isolated from soil. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005110] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A polyphasic taxonomic study was carried out on an actinobacterial strain (AN110305T) isolated from soil sampled in the Republic of Korea. Cells of the strain were Gram-stain-positive, aerobic, non-motile and rod-shaped. Comparative 16S rRNA gene sequence studies showed a clear affiliation of strain AN110305T with
Actinomycetia
, with highest pairwise sequence similarities to
Goodfellowiella coeruleoviolacea
DSM 43935T (97.6%),
Umezawaea tangerina
MK27-91F2T (97.0%),
Kutzneria chonburiensis
NBRC 110610T (96.9%),
Kutzneria buriramensis
A-T 1846T (96.8%),
Umezawaea endophytica
YIM 2047XT (96.8%),
Kutzneria albida
NRRL B-24060T (96.7%) and
Saccharothrix coeruleofusca
NRRL B-16115T (96.6%). Cells of strain AN110305T formed pale-yellow colonies on Reasoner's 2A agar. MK-9 (H4) (68%) and MK-10 (H4) (32%) were the predominant menaquinones. Diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmethyl ethanolamine, hydroxy-phosphatidylethanolamine, an unidentified aminolipid and an unidentified aminophospholipid were major polar lipids. Iso-C16:0 (24.5%), anteiso-C15:0 (19.3%), anteiso-C17:0 (15.7%) and iso-C15:0 (15.2%) were the major fatty acids and meso-diaminopimelic acid was the pepdidoglycan. The cell-wall sugars were composed of galactose, glucose, mannose and ribose. The genomic DNA G+C content was 70.7 mol%. Based on genotypic and phenotypic data, strain AN110305T could be distinguished from all genera within the family
Pseudonocardiaceae
and represents a novel genus and species named Solihabitans fulvus gen. nov., sp nov. The type strain is AN110305T (=KCTC 39307T =DSM 103572T).
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Affiliation(s)
- Chun-Zhi Jin
- Industrial Biomaterial Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Republic of Korea
- College of Biology and the Environment, Co-Innovation Centre for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210-037, PR China
| | - Long Jin
- College of Biology and the Environment, Co-Innovation Centre for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210-037, PR China
| | - Min-Jiao Liu
- Industrial Biomaterial Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Republic of Korea
| | - Jong-Min Lee
- Industrial Biomaterial Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Republic of Korea
| | - Dong-Jin Park
- Industrial Biomaterial Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Republic of Korea
| | - Chang-Jin Kim
- Industrial Biomaterial Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Republic of Korea
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Qaidamihabitans albus gen. nov., sp. nov., a new member of the family Pseudonocardiaceae, and transfer of Prauserella shujinwangii to Qaidamihabitans gen. nov. as Qaidamihabitans shujinwangii comb. nov. Arch Microbiol 2021; 203:5363-5371. [PMID: 34386827 DOI: 10.1007/s00203-021-02512-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 08/02/2021] [Accepted: 08/04/2021] [Indexed: 12/29/2022]
Abstract
A novel mycelium-forming actinomycete strain, designated YIM S01255T were isolated from a salt lake. Optimal growth occurred in the presence of 0-5.0% (w/v) NaCl, at pH 7.0-8.0, and at 37 °C. Strain YIM S01255T contained meso-diaminopimelic acid as the diagnostic diamino acid, and glucose, galactose and arabinose as the whole-cell sugars. The major fatty acid (> 5.0%) were iso-C16:0, iso-C16:1H and iso-C15:0. The major menaquinone were MK-9(H4) and MK-8(H4). The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylinositolmannoside and phosphatidylinositol. The DNA G + C content was 70.7 mol%. The 16S rRNA gene sequence of the strain showed high similarity to members of genera in the family Pseudonocardiaceae with values less than 95.8%, and most closely related to the genus Amycolatopsis. Both of phylogenetic analysis based on 16S rRNA gene sequences and the up-to-date bacterial genome sequences analysis revealed that strains YIM S01255T and Prauserella shujinwangii XJ46T formed a distinct monophyletic clade and was separated from the other members within the family Pseudonocardiaceae. The average nucleotide identity (ANI) values and digital DNA-DNA hybridization (dDDH) between the two strains were 81.0% and 40.6%, respectively. The distinctive polyphasic evidences differentiated YIM S01255T from members of the family Pseudonocardiaceae, so strain YIM S01255T is considered to represent a novel species of a novel genus of the family Pseudonocardiaceae, for which the name Qaidamihabitans albus gen. nov., sp. nov. is proposed. The type strain of genus Qaidamihabitans is YIM S01255T (= KCTC 49476T = CGMCC 4.7684T). Moreover, Prauserella shujinwangii is also proposed to being transferred into the genus Qaidamihabitans as Qaidamihabitans shujinwangii comb. nov. (type strain XJ46T = CGMCC 4.7125T = JCM 19736T).
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Teo WFA, Tan GYA, Li WJ. Taxonomic note on the family Pseudonocardiaceae based on phylogenomic analysis and descriptions of Allosaccharopolyspora gen. nov. and Halosaccharopolyspora gen. nov. Int J Syst Evol Microbiol 2021; 71. [PMID: 34714227 DOI: 10.1099/ijsem.0.005075] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The taxonomic positions of members within the family Pseudonocardiaceae were assessed based on phylogenomic trees reconstructed using core-proteome and genome blast distance phylogeny approaches. The closely clustered genome sequences from the type strains of validly published names within the family Pseudonocardiaceae were analysed using overall genome-related indices based on average nucleotide identity, average amino acid identity and digital DNA-DNA hybridization values. The family Pseudonocardiaceae consists of the type genus Pseudonocardia, as well as the genera Actinoalloteichus, Actinocrispum, Actinokineospora, Actinomycetospora, Actinophytocola, Actinopolyspora, Actinorectispora, Actinosynnema, Allokutzneria, Allosaccharopolyspora gen. nov., Amycolatopsis, Bounagaea, Crossiella, Gandjariella, Goodfellowiella, Haloactinomyces, Haloechinothrix, Halopolyspora, Halosaccharopolyspora gen. nov., Herbihabitans, Kibdelosporangium, Kutzneria, Labedaea, Lentzea, Longimycelium, Prauserella, Saccharomonospora, Saccharopolyspora, Saccharothrix, Salinifilum, Sciscionella, Streptoalloteichus, Tamaricihabitans, Thermocrispum, Thermotunica and Umezawaea. The G+C contents of the Pseudonocardiaceae genomes ranged from 66.2 to 74.6 mol% and genome sizes ranged from 3.69 to 12.28 Mbp. Based on the results of phylogenomic analysis, the names Allosaccharopolyspora coralli comb. nov., Halosaccharopolyspora lacisalsi comb. nov. and Actinoalloteichus caeruleus comb. nov. are proposed. This study revealed that Actinokineospora mzabensis is a heterotypic synonym of Actinokineospora spheciospongiae, Lentzea deserti is a heterotypic synonym of Lentzea atacamensis, Prauserella endophytica is a heterotypic synonym of Prauserella coralliicola, and Prauserella flava and Prauserella sediminis are heterotypic synonyms of Prauserella salsuginis. This study addresses the nomenclature conundrums of Actinoalloteichus cyanogriseus and Streptomyces caeruleus as well as Micropolyspora internatus and Saccharomonospora viridis.
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Affiliation(s)
- Wee Fei Aaron Teo
- Department of Microbiology, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, Thailand
- Center for Research in Biotechnology for Agriculture (CEBAR), Universiti Malaya, Kuala, Lumpur, Malaysia
| | - Geok Yuan Annie Tan
- Center for Research in Biotechnology for Agriculture (CEBAR), Universiti Malaya, Kuala, Lumpur, Malaysia
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, Kuala, Lumpur, Malaysia
| | - Wen-Jun Li
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, PR China
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Science, Sun Yat-Sen University, Guangzhou, PR China
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Huang J, Huang Y. Lentzea tibetensis sp. nov., a novel Actinobacterium with antimicrobial activity isolated from soil of the Qinghai-Tibet Plateau. Int J Syst Evol Microbiol 2021; 71. [PMID: 34427551 DOI: 10.1099/ijsem.0.004976] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel filamentous Actinobacterium, designated strain FXJ1.1311T, was isolated from soil collected in Ngari (Ali) Prefecture, Qinghai-Tibet Plateau, western PR China. The strain showed antimicrobial activity against Gram-positive bacteria and Fusarium oxysporum. Results of phylogenetic analysis based on 16S rRNA gene sequences indicated that strain FXJ1.1311T belonged to the genus Lentzea and showed the highest sequence similarity to Lentzea guizhouensis DHS C013T (98.04%). Morphological and chemotaxonomic characteristics supported its assignment to the genus Lentzea. The genome-wide average nucleotide identity between strain FXJ1.1311T and L. guizhouensis DHS C013T as well as other Lentzea type strains was <82.2 %. Strain FXJ1.1311T also formed a monophyletic line distinct from the known Lentzea species in the phylogenomic tree. In addition, physiological and chemotaxonomic characteristics allowed phenotypic differentiation of the novel strain from L. guizhouensis. Based on the evidence presented here, strain FXJ1.1311T represents a novel species of the genus Lentzea, for which the name Lentzea tibetensis sp. nov. is proposed. The type strain is FXJ1.1311T (=CGMCC 4.7383T=DSM 104975T).
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Affiliation(s)
- Jiao Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Ying Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, PR China
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Sun X, Zhao J, Luo X, Hou W, Xiang W, Song J, Wang X. Lentzea alba sp. nov. , a novel actinobacterium isolated from soil. Int J Syst Evol Microbiol 2021; 71. [PMID: 33502301 DOI: 10.1099/ijsem.0.004661] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel actinobacterium, designated strain NEAU-D13T, was isolated from soil collected from Aohan Banner, Chifeng, Inner Mongolia Autonomous Region, China and characterized using a polyphasic approach. On the basis of 16S rRNA gene sequence analysis, strain NEAU-D13T belonged to the genus Lentzea and shared the highest sequence similarity with Lentzea kentuckyensisJCM 14913T (99.17 %). Morphological and chemotaxonomic characteristics of the strain also supported its assignment to the genus Lentzea. Cell walls contained meso-diaminopimelic acid as the diagnostic diamino acid and the whole-cell sugars were ribose and mannose. The phospholipid profile contained diphosphatidylglycerol, phosphatidylethanolamine, hydroxyphosphatidylethanolamine and phosphatidylinositol. The menaquinone was only MK-9(H4). The major fatty acids were iso-C16:0, C16:0, anteiso-C17:0, iso-C15:0 and anteiso-C15:0. DNA G+C content was 68.71 mol%. Phylogenetic analysis using the 16S rRNA gene sequences showed that the strain formed a stable clade with L. kentuckyensisJCM 14913T in the genus Lentzea. Meanwhile, a combination of digital DNA-DNA hybridization results and some phenotypic characteristics demonstrated that strain NEAU-D13T could be distinguished from its closely related strain. Therefore, it is concluded that strain NEAU-D13T represents a novel species of the genus Lentzea, for which the name Lentzea alba sp. nov. is proposed, with NEAU-D13T (=CCTCC AA 2019089T=JCM 33970T) as the type strain.
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Affiliation(s)
- Xiujun Sun
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin 150030, PR China
| | - Junwei Zhao
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin 150030, PR China
| | - Xianxian Luo
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin 150030, PR China
| | - Wenyu Hou
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin 150030, PR China
| | - Wensheng Xiang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, PR China.,Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin 150030, PR China
| | - Jia Song
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin 150030, PR China
| | - Xiangjing Wang
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin 150030, PR China
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Maiti PK, Mandal S. Lentzea indica sp. nov., a novel actinobacteria isolated from Indian Himalayan-soil. Antonie van Leeuwenhoek 2020; 113:1411-1423. [PMID: 32699968 DOI: 10.1007/s10482-020-01449-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 07/11/2020] [Indexed: 12/26/2022]
Abstract
A novel actinobacterium, strain PSKA42T was isolated from a soil sample of Kashmir Himalaya, India (latitude: 34°-01' N; longitude: 74°-47' E; altitude: 5328 ft). The morphological, biochemical and molecular characteristics predicted that PSKA42T belongs to the genera Lentzea. Using the Ezbiocloud server it has also been manifested that the 16S rRNA gene sequence of PSKA42 was 98.4% similar with Lentzea guizhouensis DHSC013T, Lentzea albidocapillata subsp. violacea IMSNU50388T; 98.26% similar with Lentzea aerocolonigenes NRRLB-3298T, Lentzea albidocapillata subsp. albidocapillata NRRLB-24057T and 98.19% similar with Lentzea californiensis DSM43393T. Whole-genome average nucleotide identity values between PSKA42T and L. guizhouensis DHSC013T, L. albidocapillata subsp. violaera IMSNU50388T, L. aerocolonigenes NRRLB-3298T, L. albidocapillata subsp. albidocapillata NRRLB-24057T, L. californiensis DSM43393T, L. flaviverucosa As40578T were 84.94%, 85.8%, 87.15%, 87.71%, 79.29, and 87.22%, respectively, suggesting that PSKA42T represented a new species. In-silco genome-to-genome distances analysis and MLSA with selected housekeeping genes also indicated that the isolate should be assigned to a new species under the genus Lentzea. Analysis of the whole-cell hydrolysate found mannose and ribose as major sugar while cell wall amino acid was identified as meso-diaminopimelic acid. Major fatty acids (> 5%) were observed as 15:0 iso (23.81%), and 16:0 iso (26.11%). PSKA42 contains polyketide synthase type-I genes but unable to show antimicrobial activity in laboratory conditions. The average GC content in its genome is 68.3%. Further, based on physicochemical, chemotaxonomic markers and molecular analysis, PSKA42T can be assigned as novel species of Lentzea, we proposed Lentzea indica sp nov. The type strain is PSKA42T (JCM 33729T, MTCC 12936T, MCC 4127T).
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Affiliation(s)
- Pulak Kumar Maiti
- Laboratory of Molecular Bacteriology, Department of Microbiology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, 700019, India
| | - Sukhendu Mandal
- Laboratory of Molecular Bacteriology, Department of Microbiology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, 700019, India.
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Liu J, Sun Y, Liu J, Wu Y, Cao C, Li R, Jiang J. Saccharothrix deserti sp. nov., an actinomycete isolated from desert soil. Int J Syst Evol Microbiol 2020; 70:1882-1887. [PMID: 31967951 DOI: 10.1099/ijsem.0.003989] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [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 actinomycete, designated strain BMP B8144T, was isolated from desert soil, in Xinjiang province, northwest China. The isolate produced scanty aerial mycelium and fragmented substrate mycelium on most tested media. Cell-wall hydrolysates contained meso-diaminopimelic acid, galactose and mannose. The diagnostic phospholipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylhydroxylethanolamine, phosphatidylinositol, and phosphatidylinositol mannosides. The major fatty acids included iso-C16 : 0, C17 : 1 ω8c and iso-C15 : 0. The predominant menaquinones were MK-9(H4) and MK-10(H4). The DNA G+C content was 70.4 mol% (genome). Based on the 16S rRNA gene sequence analysis on EzBioCloud server, strain BMP B8144T showed the closest similarities to Saccharothrix lopnurensis YIM LPA2hT (98.9 %) and 'Saccharothrix yanglingensis' Hhs.015 (98.6 %). However, it can be distinguished from the closest strains based on the low levels of DNA-DNA relatedness (59.3±1.8 and 47.9±2.3 %, respectively). A combination of morphological, chemotaxonomic and phylogenetic characteristics, strain BMP B8144T represents a novel species of the genus Saccharothrix, for which the name Saccharothrix deserti sp. nov. is proposed. The type strain is BMP B8144T (=CGMCC 4.7490T=KCTC 49001T).
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Affiliation(s)
- Jinjuan Liu
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu, PR China
| | - Yong Sun
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu, PR China
| | - Jinrong Liu
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu, PR China
| | - Yunjian Wu
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu, PR China
| | - Chengliang Cao
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu, PR China.,Jiangsu Yuanyuan Bioengineering Co. Ltd, Xuzhou, Jiangsu, PR China
| | - Rongpeng Li
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu, PR China
| | - Jihong Jiang
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu, PR China
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Niu MM, Ming H, Cheng LJ, Zhao ZL, Ji WL, Li M, Yi BF, Xia TT, Nie GX. Amycolatopsis nivea sp. nov., isolated from a Yellow River sample. Int J Syst Evol Microbiol 2020; 70:3084-3090. [PMID: 32250240 DOI: 10.1099/ijsem.0.004134] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel actinobacterium, designated strain CFH S0261T, was isolated from a sediment sample of the Yellow River. The taxonomic position of the strain was investigated by using a polyphasic approach. Cells of strain CFH S0261T were Gram-reaction-positive, aerobic, non-motile. Growth occurs at 15-37 °C, pH 6.0-8.0 and with 0-9.0 % (w/v) NaCl. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that strain CFH S0261T was a member of the genus Amycolatopsis. The 16S rRNA gene sequence similarity indicated that strain CFH S0261T is most closely related to the type strains of Amycolatopsis niigatensis LC11T (98.95 %), Amycolatopsis echigonensis LC2T (98.81 %) and Amycolatopsis albidoflavus IMSNU 22139T (98.73 %). The whole-genome of CFH S0261T showed a G+C content of 69.5 mol%. The ANI values and in silico DDH values between CFH S0261T and the other species of the genus Amycolatopsis were found to be low (ANIb <90.61 % and DDH <53.40 %). The cell wall diamino acid in the peptidoglycan of strain CFH S0261T was meso-diaminopimelic acid and the whole-cell hydrolysate comprised arabinose, galactose, glucose, rhamnose and ribose. The predominant menaquinone was MK-9(H4). The major cellular fatty acids were C16 : 0, iso-C15 : 0 and iso-C16 : 0. The polar lipid profile contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannosides and four unidentified glycolipids. On the basis of phenotypic, genotypic and phylogenetic data, strain CFH S0261T represents a novel species of the genus Amycolatopsis, for which the name Amycolatopsis nivea sp. nov. is proposed. The type strain is CFH S0261T (=KCTC 39515T =CCTCC AA 2014028T).
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Affiliation(s)
- Ming-Ming Niu
- College of Fisheries, Henan Normal University, Xinxiang 453007, PR China
| | - Hong Ming
- Synthetic Biology Engineering Lab of Henan Province, College of Life Sciences and Technology, Xinxiang Medical University, Xinxiang 453003, PR China
| | - Li-Jiao Cheng
- College of Fisheries, Henan Normal University, Xinxiang 453007, PR China
| | - Zhuo-Li Zhao
- College of Fisheries, Henan Normal University, Xinxiang 453007, PR China
| | - Wei-Li Ji
- Synthetic Biology Engineering Lab of Henan Province, College of Life Sciences and Technology, Xinxiang Medical University, Xinxiang 453003, PR China
| | - Meng Li
- Synthetic Biology Engineering Lab of Henan Province, College of Life Sciences and Technology, Xinxiang Medical University, Xinxiang 453003, PR China
| | - Bing-Fang Yi
- College of Fisheries, Henan Normal University, Xinxiang 453007, PR China
| | - Ting-Ting Xia
- Synthetic Biology Engineering Lab of Henan Province, College of Life Sciences and Technology, Xinxiang Medical University, Xinxiang 453003, PR China
| | - Guo-Xing Nie
- College of Fisheries, Henan Normal University, Xinxiang 453007, PR China
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Teo WFA, Srisuk N, Duangmal K. Amycolatopsis acidicola sp. nov., isolated from peat swamp forest soil. Int J Syst Evol Microbiol 2019; 70:1547-1554. [PMID: 31851605 DOI: 10.1099/ijsem.0.003933] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel actinobacterial strain, designated K81G1T, was isolated from a soil sample collected in Kantulee peat swamp forest, Surat Thani Province, Thailand, and its taxonomic position was determined using a polyphasic approach. Optimal growth of strain K81G1T occurred at 28-30 °C, at pH 5.0-6.0 and without NaCl. Strain K81G1T had cell-wall chemotype IV (meso-diaminopimelic acid as the diagnostic diamino acid, and arabinose and galactose as diagnostic sugars) and phospholipid pattern type II, characteristic of the genus Amycolatopsis. It contained MK-9(H4) as the predominant menaquinone, iso-C16 : 0, C17 : 0 cyclo and C16 : 0 as the major cellular fatty acids, and phospholipids consisting of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, hydroxyphosphatidylethanolamine, phosphatidylinositol and two unidentified phospholipids. Based on 16S rRNA gene sequence similarity and phylogenetic analyses, strain K81G1T was most closely related to Amycolatopsis rhizosphaerae TBRC 6029T (97.8 % similarity), Amycolatopsis acidiphila JCM 30562T (97.8 %) and Amycolatopsis bartoniae DSM 45807T (97.6 %). Strain K81G1T exhibited low average nucleotide identity and digital DNA-DNA hybridization values with A. rhizosphaerae TBRC 6029T (76.4 %, 23.0 %), A. acidiphila JCM 30562T (77.9 %, 24.6 %) and A. bartoniae DSM 45807T (77.8 %, 24.3 %). The DNA G+C content of strain K81G1T was 69.7 mol%. Based on data from this polyphasic study, strain K81G1T represents a novel species of the genus Amycolatopsis, for which the name Amycolatopsis acidicola sp. nov. is proposed. The type strain is K81G1T (=TBRC 10047T=NBRC 113896T).
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Affiliation(s)
- Wee Fei Aaron Teo
- Department of Microbiology, Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
| | - Nantana Srisuk
- Department of Microbiology, Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
| | - Kannika Duangmal
- Department of Microbiology, Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
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Ningsih F, Yokota A, Sakai Y, Nanatani K, Yabe S, Oetari A, Sjamsuridzal W. Gandjariella thermophila gen. nov., sp. nov., a new member of the family Pseudonocardiaceae, isolated from forest soil in a geothermal area. Int J Syst Evol Microbiol 2019; 69:3080-3086. [DOI: 10.1099/ijsem.0.003594] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Fitria Ningsih
- Center of Excellence for Indigenous Biological Resources-Genome Studies, Faculty of Mathematics and Natural Sciences, Universitas Indonesia, Kampus UI Depok, 16424, Indonesia
- Department of Biology, Faculty of Mathematics and Natural Sciences, Universitas Indonesia, Kampus UI Depok, 16424, Indonesia
| | - Akira Yokota
- Department of Microbial Resources, Graduate School of Agricultural Science, Faculty of Agriculture, Tohoku University, Tohoku University, 468-1 Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-0845, Japan
| | - Yasuteru Sakai
- Hazaka Plant Research Center, Kennan Eisei Kogyo Co., Ltd, 44 Aza-Inariyama, Oaza-Ashitate, Murata-cho, Shibata-gun, Miyagi 989-1311, Japan
- Department of Microbial Resources, Graduate School of Agricultural Science, Faculty of Agriculture, Tohoku University, Tohoku University, 468-1 Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-0845, Japan
| | - Kei Nanatani
- Department of Microbial Resources, Graduate School of Agricultural Science, Faculty of Agriculture, Tohoku University, Tohoku University, 468-1 Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-0845, Japan
| | - Shuhei Yabe
- Hazaka Plant Research Center, Kennan Eisei Kogyo Co., Ltd, 44 Aza-Inariyama, Oaza-Ashitate, Murata-cho, Shibata-gun, Miyagi 989-1311, Japan
- Department of Microbial Resources, Graduate School of Agricultural Science, Faculty of Agriculture, Tohoku University, Tohoku University, 468-1 Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-0845, Japan
| | - Ariyanti Oetari
- Center of Excellence for Indigenous Biological Resources-Genome Studies, Faculty of Mathematics and Natural Sciences, Universitas Indonesia, Kampus UI Depok, 16424, Indonesia
- Department of Biology, Faculty of Mathematics and Natural Sciences, Universitas Indonesia, Kampus UI Depok, 16424, Indonesia
| | - Wellyzar Sjamsuridzal
- Department of Biology, Faculty of Mathematics and Natural Sciences, Universitas Indonesia, Kampus UI Depok, 16424, Indonesia
- Center of Excellence for Indigenous Biological Resources-Genome Studies, Faculty of Mathematics and Natural Sciences, Universitas Indonesia, Kampus UI Depok, 16424, Indonesia
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Li D, Jiang H, Han L, Li Y, Zhao J, Jiang S, Wang X, Xiang W. Lentzea terrae sp. nov., isolated from soil and an emended description of Lentzea soli. Int J Syst Evol Microbiol 2018; 68:3528-3533. [PMID: 30231959 DOI: 10.1099/ijsem.0.003024] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
A novel actinobacterium, designated strain NEAU-LZS 42T, was isolated from soil collected from Mount Song, Henan Province, China, and characterized using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the organism should be assigned to the genus Lentzea and had the closest relationship with Lentzea soli NEAU-LZC 7T (99.1 % similarity) and Lentzea cavernae SYSU K10001T (98.2 %). The major menaquinones were identified as MK-9(H4) and MK-9(H2). The phospholipid profile was found to contain diphosphatidylglycerol, phosphatidylethanolamine, hydroxy-phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannoside, glycophospholipid and three unidentified lipids. The major fatty acids were iso-C16 : 0, C16 : 1ω7c and C16 : 0. DNA-DNA hybridization results and some phenotypic characteristics indicated that strain NEAU-LZS 42T could be clearly differentiated from L. soli NEAU-LZC 7T and L. cavernae SYSU K10001T. Therefore, it is concluded that strain NEAU-LZS 42T represents a novel species of the genus Lentzea, for which the name Lentzea terrae sp. nov. is proposed. The type stain is NEAU-LZS 42T (=CGMCC 4.7428T=DSM 105696T).
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Affiliation(s)
- Dongmei Li
- 1Key Laboratory of Agriculture Biological Functional Gene of Heilongjiang Provincial Education Committee, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin 150030, PR China
| | - Hao Jiang
- 1Key Laboratory of Agriculture Biological Functional Gene of Heilongjiang Provincial Education Committee, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin 150030, PR China
| | - Liyuan Han
- 1Key Laboratory of Agriculture Biological Functional Gene of Heilongjiang Provincial Education Committee, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin 150030, PR China
| | - Yuanyuan Li
- 1Key Laboratory of Agriculture Biological Functional Gene of Heilongjiang Provincial Education Committee, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin 150030, PR China
| | - Junwei Zhao
- 1Key Laboratory of Agriculture Biological Functional Gene of Heilongjiang Provincial Education Committee, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin 150030, PR China
| | - Shanwen Jiang
- 1Key Laboratory of Agriculture Biological Functional Gene of Heilongjiang Provincial Education Committee, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin 150030, PR China
| | - Xiangjing Wang
- 1Key Laboratory of Agriculture Biological Functional Gene of Heilongjiang Provincial Education Committee, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin 150030, PR China
| | - Wensheng Xiang
- 2State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, PR China
- 1Key Laboratory of Agriculture Biological Functional Gene of Heilongjiang Provincial Education Committee, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin 150030, PR China
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Nouioui I, Carro L, García-López M, Meier-Kolthoff JP, Woyke T, Kyrpides NC, Pukall R, Klenk HP, Goodfellow M, Göker M. Genome-Based Taxonomic Classification of the Phylum Actinobacteria. Front Microbiol 2018; 9:2007. [PMID: 30186281 PMCID: PMC6113628 DOI: 10.3389/fmicb.2018.02007] [Citation(s) in RCA: 404] [Impact Index Per Article: 67.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 08/09/2018] [Indexed: 11/29/2022] Open
Abstract
The application of phylogenetic taxonomic procedures led to improvements in the classification of bacteria assigned to the phylum Actinobacteria but even so there remains a need to further clarify relationships within a taxon that encompasses organisms of agricultural, biotechnological, clinical, and ecological importance. Classification of the morphologically diverse bacteria belonging to this large phylum based on a limited number of features has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees. Here, draft genome sequences of a large collection of actinobacterial type strains were used to infer phylogenetic trees from genome-scale data using principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families, and genera, as well as many species and a few subspecies were shown to be in need of revision leading to proposals for the recognition of 2 orders, 10 families, and 17 genera, as well as the transfer of over 100 species to other genera. In addition, emended descriptions are given for many species mainly involving the addition of data on genome size and DNA G+C content, the former can be considered to be a valuable taxonomic marker in actinobacterial systematics. Many of the incongruities detected when the results of the present study were compared with existing classifications had been recognized from 16S rRNA gene trees though whole-genome phylogenies proved to be much better resolved. The few significant incongruities found between 16S/23S rRNA and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences. Similarly good congruence was found between the discontinuous distribution of phenotypic properties and taxa delineated in the phylogenetic trees though diverse non-monophyletic taxa appeared to be based on the use of plesiomorphic character states as diagnostic features.
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Affiliation(s)
- Imen Nouioui
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Lorena Carro
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Marina García-López
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Jan P. Meier-Kolthoff
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Tanja Woyke
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, United States
| | - Nikos C. Kyrpides
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, United States
| | - Rüdiger Pukall
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Hans-Peter Klenk
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Michael Goodfellow
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Markus Göker
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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Chanama S, Janphen S, Suriyachadkun C, Chanama M. Pseudonocardia mangrovi sp. nov., isolated from soil. Int J Syst Evol Microbiol 2018; 68:2949-2955. [PMID: 30040061 DOI: 10.1099/ijsem.0.002927] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-stain-positive, aerobic actinomycete, designated strain SMC 195T, was isolated from soil collected from a mangrove forest in Thailand. The strain produced extensively branched substrate and aerial mycelia. The substrate mycelium was fragmented into rod-shaped elements, and spore chains consisting of smooth and rod-shaped spores were formed on the aerial mycelium. The results of phylogenetic analysis based on 16S rRNA gene sequences indicated that SMC 195T represented a member of the genus Pseudonocardia, and the most closely phylogenetically related species were Pseudonocardia yuanmonensisJCM 18055T (99.2 % 16S rRNA gene sequence similarity), Pseudonocardia halophobicaNRRL B-16514T (98.9 %) and Pseudonocardia kujensisNRRL B-24890T (98.7 %). However, the DNA-DNA relatedness values between SMC 195Tand the closest phylogenetically related species were significantly below 70 %. The G+C content of the genomic DNA was 74±0.8 mol%. The cell wall peptidoglycan contained meso-diaminopimelic acid. The whole-cell sugars consisted of arabinose, galactose, glucose, rhamnose and ribose. The menaquinone was MK-8(H4) only. The major cellular fatty acid was the branched fatty acid iso-C16 : 0 (33.6 %). The polar lipids detected were phosphatidylethanolamine, phosphatidylmethylethanolamine, hydroxyphosphatidylethanolamine, diphosphatidylglycerol, phosphatidylinositol and unidentified glycolipids. On the basis of the results from phenotypic, chemotaxonomic and genotypic studies, it is concluded that SMC 195T represents a novel species of the genus Pseudonocardia, for which the name Pseudonocardia mangrovi sp. nov. is proposed. The type strain is SMC 195T (=TBRC 7778T=NBRC 113150T).
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Affiliation(s)
- Suchart Chanama
- 1Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Suphansa Janphen
- 2Department of Microbiology, Faculty of Public Health, Mahidol University, Bangkok 10400, Thailand
| | - Chanwit Suriyachadkun
- 3BIOTEC Culture Collection, Bioresources Technology Unit, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Thanon Phahonyothin, Tambon Khlong Nueng, Amphoe Khlong Luang, Pathum Thani 12120, Thailand
| | - Manee Chanama
- 2Department of Microbiology, Faculty of Public Health, Mahidol University, Bangkok 10400, Thailand
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Wang J, Leiva S, Huang J, Huang Y. Amycolatopsis antarctica sp. nov., isolated from the surface of an Antarctic brown macroalga. Int J Syst Evol Microbiol 2018; 68:2348-2356. [PMID: 29869978 DOI: 10.1099/ijsem.0.002844] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two moderately psychrophilic actinobacterial strains, designated AU-G6T and AU-A3.2, isolated from the surface of an Antarctic macroalga, Adenocystis utricularis (Bory) Skottsberg, was taxonomically characterized based on a polyphasic investigation. The two strains had nearly identical 16S rRNA gene sequences and formed a distinct phyletic line within the genus Amycolatopsis of the family Pseudonocardiaceae. They were phylogenetically close to Amycolatopsis nigrescens JCM 14717T, Amycolatopsis minnesotensis JCM 14545T and Amycolatopsis magusensis DSM 45510T, with 16S rRNA gene sequence similarities of 97.77, 97.20 and 97.19 %, respectively. Phylogenomic analysis based on the whole genome data supported that strain AU-G6T was distantly related to the Amycolatopsis species. The isolates shared a range of phenotypic markers typical of members of the genus Amycolatopsis, but also had a range of cultural, physiological and biochemical characteristics that separated them from related Amycolatopsis species. The isolates showed growth only in media supplemented with salt, indicating their marine origin. The cell wall of the isolates contained meso-diaminopimelic acid, and arabinose and galactose were detected as diagnostic sugars (type IV). The main menaquinone was MK-9(H4). The main polar lipids were phosphatidylethanolamine, hydroxy-phosphotidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol (type II). The fatty acid type was 3c. The combined genotypic and phenotypic data indicated that the two isolates represent a novel species of the genus Amycolatopsis. The name proposed for this species is Amycolatopsis antarctica sp. nov., with type strain AU-G6T (=CGMCC 4.7351T=NBRC 112404T).
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Affiliation(s)
- Jian Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Sergio Leiva
- Instituto de Bioquímica & Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Casilla 567, Valdivia, Chile
| | - Jiao Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Ying Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
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Cao C, Sun Y, Wu B, Zhao S, Yuan B, Qin S, Jiang J, Huang Y. Actinophytocola glycyrrhizae sp. nov. isolated from the rhizosphere of Glycyrrhiza inflata. Int J Syst Evol Microbiol 2018; 68:2504-2508. [PMID: 29939121 DOI: 10.1099/ijsem.0.002864] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-positive, aerobic actinomycete, designated strain BMP B8152T, was isolated from the rhizosphere of Glycyrrhiza inflata collected ashore, in Kashi, Xinjiang province, northwest PR China. A polyphasic approach was used to establish the taxonomic position of this strain. BMP B8152T was observed to form non-fragmented substrate mycelium, and relatively scanty aerial mycelium with rod-shaped spores. Cell-wall hydrolysates contained meso-diaminopimelic acid, galactose, arabinose, glucose and rhamnose (trace). Mycolic acids were not detected. The diagnostic phospholipids were identified as diphosphatidylglycerol, phosphatidylethanolamine, hydroxyphosphatidylethanolamine, ninhydrin-positive phosphoglycolipid and phosphatidylinositol. The predominant menaquinone and fatty acid were MK-9(H4) and iso-branched hexadecanoate (iso-C16 : 0), respectively. The phylogenetic analyses based on the 16S rRNA gene sequences indicated that BMP B8152T formed a distinct monophyletic clade clustered with Actinophytocola timorensisID05-A0653T (98.8 % 16S rRNA gene sequence similarity), Actinophytocola oryzaeGMKU 367T (98.6 %), Actinophytocola corallinaID06-A0464T (98.2 %) and Actinophytocola burenkhanensisMN08-A0203T (97.5 %). In addition, DNA-DNA hybridization values between BMP B8152T and A. timorensisID05-A0653T(44.2±3.6 %) and A. oryzaeGMKU 367T(36.7±2.3 %) were well below the 70 % limit for species identification. The combined phenotypic and genotypic data indicate that the isolate represents a novel species of the genus Actinophytocola, for which the name Actinophytocola glycyrrhizae sp. nov., is proposed, with the type strain BMP B8152T (=KCTC 49002T=CGMCC 4.7433T).
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Affiliation(s)
- Chengliang Cao
- 1The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu, PR China.,2Jiangsu Yuanyuan Bioengineering Co. Ltd, Xuzhou, Jiangsu, PR China
| | - Yong Sun
- 1The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu, PR China
| | - Bo Wu
- 1The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu, PR China
| | - Shuai Zhao
- 1The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu, PR China
| | - Bo Yuan
- 1The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu, PR China
| | - Sheng Qin
- 1The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu, PR China
| | - Jihong Jiang
- 1The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu, PR China
| | - Ying Huang
- 3State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, PR China
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Li D, Zheng W, Zhao J, Han L, Zhao X, Jiang H, Wang X, Xiang W. Lentzea soli sp. nov., an actinomycete isolated from soil. Int J Syst Evol Microbiol 2018. [PMID: 29537362 DOI: 10.1099/ijsem.0.002698] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel actinobacterium, designated strain NEAU-LZC 7T, was isolated from soil collected from Mount Song and characterized using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequence indicated that strain NEAU-LZC 7T belonged to the genus Lentzea, with highest sequence similarity to Lentzea violacea JCM 10975T (98.1 %). Morphological and chemotaxonomic characteristics of the strain also supported its assignment to the genus Lentzea. However, DNA-DNA relatedness, physiological and biochemical data showed that strain NEAU-LZC 7T could be distinguished from its closest relative. Therefore, strain NEAU-LZC 7T represents a novel species of the genus Lentzea, for which the name Lentzea soli sp. nov. is proposed, with NEAU-LZC 7T (=CCTCC AA 2017027T=JCM 32384T) as the type strain.
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Affiliation(s)
- Dongmei Li
- Key Laboratory of Agriculture Biological Functional Gene of Heilongjiang Provincial Education Committee, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin 150030, PR China
| | - Weiwei Zheng
- Key Laboratory of Agriculture Biological Functional Gene of Heilongjiang Provincial Education Committee, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin 150030, PR China
| | - Junwei Zhao
- Key Laboratory of Agriculture Biological Functional Gene of Heilongjiang Provincial Education Committee, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin 150030, PR China
| | - Liyuan Han
- Key Laboratory of Agriculture Biological Functional Gene of Heilongjiang Provincial Education Committee, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin 150030, PR China
| | - Xueli Zhao
- Key Laboratory of Agriculture Biological Functional Gene of Heilongjiang Provincial Education Committee, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin 150030, PR China
| | - Hao Jiang
- Key Laboratory of Agriculture Biological Functional Gene of Heilongjiang Provincial Education Committee, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin 150030, PR China
| | - Xiangjing Wang
- Key Laboratory of Agriculture Biological Functional Gene of Heilongjiang Provincial Education Committee, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin 150030, PR China
| | - Wensheng Xiang
- Key Laboratory of Agriculture Biological Functional Gene of Heilongjiang Provincial Education Committee, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin 150030, PR China.,State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, PR China
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Zhao J, Li W, Shi L, Wang H, Wang Y, Zhao Y, Xiang W, Wang X. Lechevalieria rhizosphaerae sp. nov., a novel actinomycete isolated from rhizosphere soil of wheat (Triticum aestivum L.) and emended description of the genus Lechevalieria. Int J Syst Evol Microbiol 2017; 67:4655-4659. [PMID: 28950934 DOI: 10.1099/ijsem.0.002351] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel actinomycete, designated strain NEAU-A2T, was isolated from rhizosphere soil of wheat (Triticum aestivum L.) and characterized using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain NEAU-A2T should be assigned to the genus Lechevalieria and forms a distinct branch with its closest neighbour Lechevalieria aerocolonigenes DSM 40034T (99.0 %). Moreover, key morphological and chemotaxonomic properties also confirmed the affiliation of strain NEAU-A2T to the genus Lechevalieria. The cell wall contained meso-diaminopimelic acid and the whole-cell hydrolysates were galactose, mannose, rhamnose, glucose and ribose. The polar lipids were diphosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylethanolamine, phosphatidylinositolmannoside and two glycolipids. The predominant menaquinones were MK-9(H4) and MK-9(H6). The major fatty acids were iso-C16 : 0, anteiso-C15 : 0, C16 : 1ω7c and anteiso-C17 : 0. The DNA G+C content was 68.2 mol%. The combination of the DNA-DNA hybridization result and some phenotypic characteristics demonstrated that strain NEAU-A2T could be distinguished from its closest relative. Therefore, it is proposed that strain NEAU-A2T represents a novel species of the genus Lechevalieria, for which the name Lechevalieriarhizosphaerae sp. nov. is proposed. The type strain is NEAU-A2T (=CGMCC 4.7405T=DSM 104541T).
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Affiliation(s)
- Junwei Zhao
- Key Laboratory of Agriculture Biological Functional Gene of Heilongjiang Provincial Education Committee, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin 150030, PR China
| | - Wenchao Li
- Key Laboratory of Agriculture Biological Functional Gene of Heilongjiang Provincial Education Committee, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin 150030, PR China
| | - Linlin Shi
- Key Laboratory of Agriculture Biological Functional Gene of Heilongjiang Provincial Education Committee, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin 150030, PR China
| | - Han Wang
- Key Laboratory of Agriculture Biological Functional Gene of Heilongjiang Provincial Education Committee, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin 150030, PR China
| | - Ying Wang
- Key Laboratory of Agriculture Biological Functional Gene of Heilongjiang Provincial Education Committee, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin 150030, PR China
| | - Yue Zhao
- Key Laboratory of Agriculture Biological Functional Gene of Heilongjiang Provincial Education Committee, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin 150030, PR China
| | - Wensheng Xiang
- Key Laboratory of Agriculture Biological Functional Gene of Heilongjiang Provincial Education Committee, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin 150030, PR China.,State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, PR China
| | - Xiangjing Wang
- Key Laboratory of Agriculture Biological Functional Gene of Heilongjiang Provincial Education Committee, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin 150030, PR China
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Actinoalloteichus fjordicus sp. nov. isolated from marine sponges: phenotypic, chemotaxonomic and genomic characterisation. Antonie van Leeuwenhoek 2017; 110:1705-1717. [PMID: 28770445 PMCID: PMC5676828 DOI: 10.1007/s10482-017-0920-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 07/25/2017] [Indexed: 12/04/2022]
Abstract
Two actinobacterial strains, ADI 127-17T and GBA 129-24, isolated from marine sponges Antho dichotoma and Geodia barretti, respectively, collected at the Trondheim fjord in Norway, were the subjects of a polyphasic study. According to their 16S rRNA gene sequences, the new isolates were preliminarily classified as belonging to the genus Actinoalloteichus. Both strains formed a distinct branch, closely related to the type strains of Actinoalloteichus hoggarensis and Actinoalloteichus hymeniacidonis, within the evolutionary radiation of the genus Actinoalloteichus in the 16S rRNA gene-based phylogenetic tree. Isolates ADI 127-17T and GBA 129-24 exhibited morphological, chemotaxonomic and genotypic features distinguishable from their close phylogenetic neighbours. Digital DNA: DNA hybridization and ANI values between strains ADI 127-17T and GBA 129-24 were 97.6 and 99.7%, respectively, whereas the corresponding values between both tested strains and type strains of their closely related phylogenetic neighbours, A. hoggarensis and A. hymeniacidonis, were well below the threshold for delineation of prokaryotic species. Therefore, strains ADI 127-17T (= DSM 46855T) and GBA 129-24 (= DSM 46856) are concluded to represent a novel species of the genus Actinoalloteichus for which the name of Actinoalloteichus fjordicus sp. nov. (type strain ADI 127-17T = DSM 46855T = CECT 9355T) is proposed. The complete genome sequences of the new strains were obtained and compared to that of A. hymeniacidonis DSM 45092T and A. hoggarensis DSM 45943T to unravel unique genome features and biosynthetic potential of the new isolates.
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Sujarit K, Sujada N, Kudo T, Ohkuma M, Pathom-Aree W, Lumyong S. Pseudonocardia thailandensis sp. nov., an actinomycete isolated from a subterranean termite nest. Int J Syst Evol Microbiol 2017; 67:2773-2778. [DOI: 10.1099/ijsem.0.002017] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Kanaporn Sujarit
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Nikhom Sujada
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Takuji Kudo
- Japan Collection of Microorganisms, RIKEN BioResource Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Moriya Ohkuma
- Japan Collection of Microorganisms, RIKEN BioResource Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Wasu Pathom-Aree
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Saisamorn Lumyong
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
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Fang BZ, Han MX, Liu L, Zhang ZT, Liu WL, Shen JT, Wang Y, Zhang WQ, Wei DQ, Li WJ. Lentzea cavernae sp. nov., an actinobacterium isolated from a karst cave sample, and emended description of the genus Lentzea. Int J Syst Evol Microbiol 2017; 67:2357-2362. [PMID: 28699862 DOI: 10.1099/ijsem.0.001958] [Citation(s) in RCA: 13] [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 novel actinobacterial strain, designated SYSU K10001T, was isolated from a limestone sample collected from a karst cave in Xingyi county, Guizhou province, south-western China. The taxonomic position of the strain was investigated using a polyphasic approach. Cells of the strain were aerobic and Gram-stain-positive. On the basis of 16S rRNA gene sequence analysis, strain SYSU K10001T was most closely related to the type strains of the genus Lentzea, Lentzea albida NBRC 16102T (98.8 % similarity) and Lentzea waywayandensis NRRL B-16159T (98.6 %), and is therefore considered to represent a member of the genus Lentzea. DNA-DNA hybridization values between strain SYSU K10001T and related type strains of the genus Lentzea were less than 70 %. In addition, meso-diaminopimelic acid was the diagnostic diamino acid in the cell-wall peptidoglycan. The whole-cell sugars were arabinose, fructose, mannose and xylose. The major isoprenoid quinone was MK-9(H4), while the major fatty acids (>10 %) were iso-C16 : 0 and C14 : 0. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, hydroxy-phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannoside, one unidentified phospholipid and one unidentified lipid. The genomic DNA G+C content of strain SYSU K10001T was 69.4 mol%. On the basis of phenotypic, genotypic and phylogenetic data, strain SYSU K10001T represents a novel species of the genus Lentzea, for which the name Lentzea cavernae sp. nov. is proposed. The type strain is SYSU K10001T (=KCTC 39804T=CGMCC 4.7367T=NBRC 112394T).
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Affiliation(s)
- Bao-Zhu Fang
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Ming-Xian Han
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China.,Medical Faculty of Kunming University of Science and Technology, Kunming University of Science and Technology, Kunming, PR China
| | - Lan Liu
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Zi-Tong Zhang
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Wei-Liang Liu
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Jing-Ting Shen
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Yan Wang
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Wan-Qin Zhang
- College of Biology and Chemistry, Xingyi Normal University for Nationalities, Xingyi, 562400, PR China
| | - Da-Qiao Wei
- Medical Faculty of Kunming University of Science and Technology, Kunming University of Science and Technology, Kunming, PR China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
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Polysaccharide Degradation Capability of Actinomycetales Soil Isolates from a Semiarid Grassland of the Colorado Plateau. Appl Environ Microbiol 2017; 83:AEM.03020-16. [PMID: 28087533 DOI: 10.1128/aem.03020-16] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 01/10/2017] [Indexed: 02/03/2023] Open
Abstract
Among the bacteria, members of the order Actinomycetales are considered quintessential degraders of complex polysaccharides in soils. However, studies examining complex polysaccharide degradation by Actinomycetales (other than Streptomyces spp.) in soils are limited. Here, we examine the lignocellulolytic and chitinolytic potential of 112 Actinomycetales strains, encompassing 13 families, isolated from a semiarid grassland of the Colorado Plateau in Utah. Members of the Streptomycetaceae, Pseudonocardiaceae, Micromonosporaceae, and Promicromonosporaceae families exhibited robust activity against carboxymethyl cellulose, xylan, chitin, and pectin substrates (except for low/no pectinase activity by the Micromonosporaceae). When incubated in a hydrated mixture of blended Stipa and Hilaria grass biomass over a 5-week period, Streptomyces and Saccharothrix (a member of the Pseudonocardiaceae) isolates produced high levels of extracellular enzyme activity, such as endo- and exocellulase, glucosidase, endo- and exoxylosidase, and arabinofuranosidase. These characteristics make them well suited to degrade the cellulose and hemicellulose components of grass cell walls. On the basis of the polysaccharide degradation profiles of the isolates, relative abundance of Actinomycetales sequences in 16S rRNA gene surveys of Colorado Plateau soils, and analysis of genes coding for polysaccharide-degrading enzymes among 237 Actinomycetales genomes in the CAZy database and 5 genomes from our isolates, we posit that Streptomyces spp. and select members of the Pseudonocardiaceae and Micromonosporaceae likely play an important role in the degradation of hemicellulose, cellulose, and chitin substances in dryland soils.IMPORTANCE Shifts in the relative abundance of Actinomycetales taxa have been observed in soil microbial community surveys during large, manipulated climate change field studies. However, our limited understanding of the ecophysiology of diverse Actinomycetales taxa in soil systems undermines attempts to determine the underlying causes of the population shifts or their impact on carbon cycling in soil. This study combines a systematic analysis of the polysaccharide degradation potential of a diverse collection of Actinomycetales isolates from surface soils of a semiarid grassland with analysis of genomes from five of these isolates and publicly available Actinomycetales genomes for genes encoding polysaccharide-active enzymes. The results address an important gap in knowledge of Actinomycetales ecophysiology-identification of key taxa capable of facilitating lignocellulose degradation in dryland soils. Information from this study will benefit future metagenomic studies related to carbon cycling in dryland soils by providing a baseline linkage of Actinomycetales phylogeny with lignocellulolytic functional potential.
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Schaffert L, Albersmeier A, Winkler A, Kalinowski J, Zotchev SB, Rückert C. Complete genome sequence of the actinomycete Actinoalloteichus hymeniacidonis type strain HPA 177 T isolated from a marine sponge. Stand Genomic Sci 2016; 11:91. [PMID: 28031775 PMCID: PMC5168871 DOI: 10.1186/s40793-016-0213-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 11/26/2016] [Indexed: 11/10/2022] Open
Abstract
Actinoalloteichus hymeniacidonis HPA 177T is a Gram-positive, strictly aerobic, black pigment producing and spore-forming actinomycete, which forms branching vegetative hyphae and was isolated from the marine sponge Hymeniacidon perlevis. Actinomycete bacteria are prolific producers of secondary metabolites, some of which have been developed into anti-microbial, anti-tumor and immunosuppressive drugs currently used in human therapy. Considering this and the growing interest in natural products as sources of new drugs, actinomycete bacteria from the hitherto poorly explored marine environments may represent promising sources for drug discovery. As A. hymeniacidonis, isolated from the marine sponge, is a type strain of the recently described and rare genus Actinoalloteichus, knowledge of the complete genome sequence enables genome analyses to identify genetic loci for novel bioactive compounds. This project, describing the 6.31 Mbp long chromosome, with its 5346 protein-coding and 73 RNA genes, will aid the Genomic Encyclopedia of Bacteria and Archaea project.
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Affiliation(s)
- Lena Schaffert
- Technology Platform Genomics, CeBiTec, Bielefeld University, Bielefeld, Germany
| | - Andreas Albersmeier
- Technology Platform Genomics, CeBiTec, Bielefeld University, Bielefeld, Germany
| | - Anika Winkler
- Technology Platform Genomics, CeBiTec, Bielefeld University, Bielefeld, Germany
| | - Jörn Kalinowski
- Technology Platform Genomics, CeBiTec, Bielefeld University, Bielefeld, Germany
| | - Sergey B. Zotchev
- Department of Pharmacognosy, University of Vienna, 1090 Vienna, Austria
| | - Christian Rückert
- Technology Platform Genomics, CeBiTec, Bielefeld University, Bielefeld, Germany
- Sinkey Lab, Department of Biology, Massachusetts Institute of Technology, Cambridge, USA
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24
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Bouznada K, Bouras N, Mokrane S, Chaabane Chaouch F, Zitouni A, Pötter G, Spröer C, Klenk HP, Sabaou N. Saccharothrix ghardaiensis sp. nov., an actinobacterium isolated from Saharan soil. Antonie van Leeuwenhoek 2016; 110:399-405. [PMID: 27915411 DOI: 10.1007/s10482-016-0812-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 11/24/2016] [Indexed: 11/26/2022]
Abstract
The taxonomic position of a new Saccharothrix strain, designated MB46T, isolated from a Saharan soil sample collected in Mzab region (Ghardaïa province, South Algeria) was established following a polyphasic approach. The novel microorganism has morphological and chemical characteristics typical of the members of the genus Saccharothrix and formed a phyletic line at the periphery of the Saccharothrix espanaensis subcluster in the 16S rRNA gene dendrograms. Results of the 16S rRNA gene sequence comparisons revealed that strain MB46T shares high degrees of similarity with S. espanaensis DSM 44229T (99.2%), Saccharothrix variisporea DSM 43911T (98.7%) and Saccharothrix texasensis NRRL B-16134T (98.6%). However, the new strain exhibited only 12.5-17.5% DNA relatedness to the neighbouring Saccharothrix spp. On the basis of phenotypic characteristics, 16S rRNA gene sequence comparisons and DNA-DNA hybridizations, strain MB46T is concluded to represent a novel species of the genus Saccharothrix, for which the name Saccharothrix ghardaiensis sp. nov. (type strain MB46T = DSM 46886T = CECT 9046T) is proposed.
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Affiliation(s)
- Khaoula Bouznada
- Laboratoire de Biologie des Systèmes Microbiens (LBSM), Ecole Normale Supérieure de Kouba, Algiers, Algeria
| | - Noureddine Bouras
- Laboratoire de Biologie des Systèmes Microbiens (LBSM), Ecole Normale Supérieure de Kouba, Algiers, Algeria
- Département de Biologie, Faculté des Sciences de la Nature et de la Vie et Sciences de la Terre, Université de Ghardaïa, BP 455, 47000, Ghardaïa, Algeria
| | - Salim Mokrane
- Laboratoire de Biologie des Systèmes Microbiens (LBSM), Ecole Normale Supérieure de Kouba, Algiers, Algeria
| | - Fawzia Chaabane Chaouch
- Laboratoire de Biologie des Systèmes Microbiens (LBSM), Ecole Normale Supérieure de Kouba, Algiers, Algeria
| | - Abdelghani Zitouni
- Laboratoire de Biologie des Systèmes Microbiens (LBSM), Ecole Normale Supérieure de Kouba, Algiers, Algeria
| | - Gabriele Pötter
- DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124, Brunswick, Germany
| | - Cathrin Spröer
- DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124, Brunswick, Germany
| | - Hans-Peter Klenk
- School of Biology, Newcastle University, Ridley Building, Newcastle upon Tyne, NE1 7RU, UK.
| | - Nasserdine Sabaou
- Laboratoire de Biologie des Systèmes Microbiens (LBSM), Ecole Normale Supérieure de Kouba, Algiers, Algeria.
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25
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Tang B, Xie F, Zhao W, Wang J, Dai S, Zheng H, Ding X, Cen X, Liu H, Yu Y, Zhou H, Zhou Y, Zhang L, Goodfellow M, Zhao GP. A systematic study of the whole genome sequence of Amycolatopsis methanolica strain 239 T provides an insight into its physiological and taxonomic properties which correlate with its position in the genus. Synth Syst Biotechnol 2016; 1:169-186. [PMID: 29062941 PMCID: PMC5640789 DOI: 10.1016/j.synbio.2016.05.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Revised: 04/01/2016] [Accepted: 05/18/2016] [Indexed: 12/31/2022] Open
Abstract
The complete genome of methanol-utilizing Amycolatopsis methanolica strain 239T was generated, revealing a single 7,237,391 nucleotide circular chromosome with 7074 annotated protein-coding sequences (CDSs). Comparative analyses against the complete genome sequences of Amycolatopsis japonica strain MG417-CF17T, Amycolatopsis mediterranei strain U32 and Amycolatopsis orientalis strain HCCB10007 revealed a broad spectrum of genomic structures, including various genome sizes, core/quasi-core/non-core configurations and different kinds of episomes. Although polyketide synthase gene clusters were absent from the A. methanolica genome, 12 gene clusters related to the biosynthesis of other specialized (secondary) metabolites were identified. Complete pathways attributable to the facultative methylotrophic physiology of A. methanolica strain 239T, including both the mdo/mscR encoded methanol oxidation and the hps/hpi encoded formaldehyde assimilation via the ribulose monophosphate cycle, were identified together with evidence that the latter might be the result of horizontal gene transfer. Phylogenetic analyses based on 16S rDNA or orthologues of AMETH_3452, a novel actinobacterial class-specific conserved gene against 62 or 18 Amycolatopsis type strains, respectively, revealed three major phyletic lineages, namely the mesophilic or moderately thermophilic A. orientalis subclade (AOS), the mesophilic Amycolatopsis taiwanensis subclade (ATS) and the thermophilic A. methanolica subclade (AMS). The distinct growth temperatures of members of the subclades correlated with corresponding genetic variations in their encoded compatible solutes. This study shows the value of integrating conventional taxonomic with whole genome sequence data.
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Affiliation(s)
- Biao Tang
- State Key Laboratory of Genetic Engineering, Department of Microbiology, School of Life Sciences and Institute of Biomedical Sciences, Fudan University, Shanghai, 200438, China.,CAS-Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Feng Xie
- CAS-Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, No. 1 Beichen West Road, Chaoyang District, Beijing, 100101, China
| | - Wei Zhao
- CAS-Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Jian Wang
- CAS-Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, No. 1 Beichen West Road, Chaoyang District, Beijing, 100101, China
| | - Shengwang Dai
- CAS-Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, No. 1 Beichen West Road, Chaoyang District, Beijing, 100101, China
| | - Huajun Zheng
- Shanghai-MOST Key Laboratory of Disease and Health Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, 201203, China
| | - Xiaoming Ding
- State Key Laboratory of Genetic Engineering, Department of Microbiology, School of Life Sciences and Institute of Biomedical Sciences, Fudan University, Shanghai, 200438, China
| | - Xufeng Cen
- CAS-Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Haican Liu
- State Key Laboratory for Infectious Diseases Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yucong Yu
- State Key Laboratory of Genetic Engineering, Department of Microbiology, School of Life Sciences and Institute of Biomedical Sciences, Fudan University, Shanghai, 200438, China
| | - Haokui Zhou
- Department of Microbiology and Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Yan Zhou
- State Key Laboratory of Genetic Engineering, Department of Microbiology, School of Life Sciences and Institute of Biomedical Sciences, Fudan University, Shanghai, 200438, China.,Shanghai-MOST Key Laboratory of Disease and Health Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, 201203, China
| | - Lixin Zhang
- CAS-Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, No. 1 Beichen West Road, Chaoyang District, Beijing, 100101, China
| | - Michael Goodfellow
- School of Biology, University of Newcastle, Newcastle upon Tyne, NE1 7RU, UK
| | - Guo-Ping Zhao
- State Key Laboratory of Genetic Engineering, Department of Microbiology, School of Life Sciences and Institute of Biomedical Sciences, Fudan University, Shanghai, 200438, China.,CAS-Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.,Shanghai-MOST Key Laboratory of Disease and Health Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, 201203, China.,Department of Microbiology and Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
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26
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Bouznada K, Bouras N, Mokrane S, Chaabane Chaouch F, Zitouni A, Pötter G, Spröer C, Klenk HP, Sabaou N. Saccharothrix isguenensis sp. nov., an actinobacterium isolated from desert soil. Int J Syst Evol Microbiol 2016; 66:4785-4790. [PMID: 27535702 DOI: 10.1099/ijsem.0.001430] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel actinobacterial strain, designated MB27T, was isolated from a Saharan soil sample collected in Mzab region (Ghardaïa province, South Algeria). Strain MB27T was characterized following a polyphasic taxonomic approach. This strain produced a branched and fragmented substrate mycelium, which was found to have a yellowish orange colour. A white scanty aerial mycelium was produced on most media tested. Chemotaxonomic and phylogenetic studies clearly demonstrated that strain MB27T belongs to the family Pseudonocardiaceae and is closely related to the genus Saccharothrix. Cell-wall hydrolysates contained meso-diaminopimelic acid but not glycine, and whole-cell hydrolysates contained galactose, glucose, ribose and small amounts of mannose and rhamnose. The detected phospholipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannosides. Mycolic acids were not detected while the predominant fatty acid was iso-branched hexadecanoate (iso-C16 : 0). The major menaquinone was MK-9(H4). Results of 16S rRNA gene sequence comparisons revealed that strain MB27T shairs the highest degree of similarity with Saccharothrix ecbatanensis DSM 45486T (99.8%), Saccharothrix hoggarensis DSM 45457T (99.3 %), Saccharothrix longispora DSM 43749T (98.6 %) and Saccharothrix yanglingensis DSM 45665T (98.6 %). However, it exhibited only 11-42 % DNA-DNA relatedness to the neighbouring Saccharothrixspecies. On the basis of phenotypic characteristics, 16S rRNA gene sequence comparisons and DNA-DNA hybridization, strain MB27T is shown to represent a novel species of the genus Saccharothrix, for which the name Saccharothrix isguenensis sp. nov. (type strain MB27T=DSM 46885T=CECT 9045T) is proposed.
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Affiliation(s)
- Khaoula Bouznada
- Laboratoire de Biologie des Systèmes Microbiens (LBSM), Ecole Normale Supérieure de Kouba, Algiers, Algeria
| | - Noureddine Bouras
- Laboratoire de Biologie des Systèmes Microbiens (LBSM), Ecole Normale Supérieure de Kouba, Algiers, Algeria.,Département de Biologie, Faculté des Sciences de la Nature et de la Vie et Sciences de la Terre, Université de Ghardaïa, BP 455, Ghardaïa 47000, Algeria
| | - Salim Mokrane
- Laboratoire de Biologie des Systèmes Microbiens (LBSM), Ecole Normale Supérieure de Kouba, Algiers, Algeria
| | - Fawzia Chaabane Chaouch
- Laboratoire de Biologie des Systèmes Microbiens (LBSM), Ecole Normale Supérieure de Kouba, Algiers, Algeria
| | - Abdelghani Zitouni
- Laboratoire de Biologie des Systèmes Microbiens (LBSM), Ecole Normale Supérieure de Kouba, Algiers, Algeria
| | - Gabriele Pötter
- DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Cathrin Spröer
- DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Hans-Peter Klenk
- School of Biology, Newcastle University, Ridley Building, Newcastle upon Tyne NE1 7RU, UK
| | - Nasserdine Sabaou
- Laboratoire de Biologie des Systèmes Microbiens (LBSM), Ecole Normale Supérieure de Kouba, Algiers, Algeria
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Zhang CF, Ai MJ, Wang JX, Liu SW, Zhao LL, Su J, Sun CH, Yu LY, Zhang YQ. Herbihabitans rhizosphaerae gen. nov., sp. nov., a member of the family Pseudonocardiaceae isolated from rhizosphere soil of the herb Limonium sinense (Girard). Int J Syst Evol Microbiol 2016; 66:4156-4161. [PMID: 27470940 DOI: 10.1099/ijsem.0.001325] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The taxonomic position of an actinobacterium, designated CPCC 204279T, which was isolated from a rhizosphere soil sample of the herb Limonium sinense collected from Xinjiang Province, China, was established using a polyphasic approach. Whole-cell hydrolysates of strain CPCC 204279T contained galactose and arabinose as diagnostic sugars and meso-diaminopimelic acid as the diamino acid. The muramic acid residues in the peptidoglycan were N-acetylated. The predominant menaquinone was MK-9(H4). The phospholipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannosides. The major fatty acids were iso-C16 : 0, iso-C16 : 0 2-OH, C16 : 1ω9c, iso-C16 : 1 and C16 : 0. The genomic DNA G+C content was 73.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain CPCC 204279T should be placed in the family Pseudonocardiaceae, in which the strain formed a distinct lineage next to the genus Actinophytocola. Signature nucleotides in the 16S rRNA gene sequence showed that the strain contained the Pseudonocardiaceae family-specific 16S rRNA signature nucleotides and a genus-specific diagnostic nucleotide signature pattern. The combination of phylogenetic analysis and phenotypic characteristics supported the conclusion that strain CPCC 204279T represents a novel species of a new genus in the family Pseudonocardiaceae, for which the name Herbihabitans rhizosphaerae gen. nov., sp. nov. is proposed. Strain CPCC 204279T (=NBRC 111774T=DSM 101727T) is the type strain of the type species.
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Affiliation(s)
- Chang-Feng Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, PR China
| | - Meng-Jie Ai
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, PR China
| | - Ju-Xian Wang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, PR China
| | - Shao-Wei Liu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, PR China
| | - Li-Li Zhao
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, PR China
| | - Jing Su
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, PR China
| | - Cheng-Hang Sun
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, PR China
| | - Li-Yan Yu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, PR China
| | - Yu-Qin Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, PR China
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Busarakam K, Brown R, Bull AT, Tan GYA, Zucchi TD, da Silva LJ, de Souza WR, Goodfellow M. Classification of thermophilic actinobacteria isolated from arid desert soils, including the description of Amycolatopsis deserti sp. nov. Antonie van Leeuwenhoek 2016; 109:319-34. [PMID: 26809280 DOI: 10.1007/s10482-015-0635-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 12/09/2015] [Indexed: 11/25/2022]
Abstract
The taxonomic position of 26 filamentous actinobacteria isolated from a hyper-arid Atacama Desert soil and 2 from an arid Australian composite soil was established using a polyphasic approach. All of the isolates gave the diagnostic amplification product using 16S rRNA oligonucleotide primers specific for the genus Amycolatopsis. Representative isolates had chemotaxonomic and morphological properties typical of members of the genus Amycolatopsis. 16S rRNA gene analyses showed that all of the isolates belong to the Amycolatopsis methanolica 16S rRNA gene clade. The Atacama Desert isolates were assigned to one or other of two recognised species, namely Amycolatopsis ruanii and Amycolatopsis thermalba, based on 16S rRNA gene sequence, DNA:DNA relatedness and phenotypic data; emended descriptions are given for these species. In contrast, the two strains from the arid Australian composite soil, isolates GY024(T) and GY142, formed a distinct branch at the periphery of the A. methanolica 16S rRNA phyletic line, a taxon that was supported by all of the tree-making algorithms and by a 100 % bootstrap value. These strains shared a high degree of DNA:DNA relatedness and have many phenotypic properties in common, some of which distinguished them from all of the constituent species classified in the A. methanolica 16S rRNA clade. Isolates GY024(T) and GY142 merit recognition as a new species within the A. methanolica group of thermophilic strains. The name proposed for the new species is Amycolatopsis deserti sp. nov.; the type strain is GY024(T) (=NCIMB 14972(T) = NRRL B-65266(T)).
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Affiliation(s)
- Kanungnid Busarakam
- School of Biology, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
- Department of Agricultural Technology, Thailand Institute of Scientific and Technological Research, Pathum Thani, 12120, Thailand
| | - Ros Brown
- School of Biology, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Alan T Bull
- School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK
| | - Geok Yuan Annie Tan
- Institute of Biological Sciences, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Tiago D Zucchi
- Laboratório de Microbiologia, EMBRAPA Meio Ambiente, Rod SP 340-Km 127, PO Box 69, Jaguariúna, 13820-000, Brazil
- Agrivalle, Av. Tranquillo Giannini, 1050, Salto, 13329-600, Brazil
| | - Leonardo José da Silva
- Laboratório de Microbiologia, EMBRAPA Meio Ambiente, Rod SP 340-Km 127, PO Box 69, Jaguariúna, 13820-000, Brazil
| | - Wallace Rafael de Souza
- Laboratório de Microbiologia, EMBRAPA Meio Ambiente, Rod SP 340-Km 127, PO Box 69, Jaguariúna, 13820-000, Brazil
| | - Michael Goodfellow
- School of Biology, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK.
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Quadri SR, Tian XP, Zhang J, Ruwaili JA, Hozzein WN, Agsar D, Li WJ, Dastager SG. Actinorectispora indica gen. nov., sp. nov. isolated from soil, a member of the family Pseudonocardiaceae. Int J Syst Evol Microbiol 2015; 66:939-945. [PMID: 26637823 DOI: 10.1099/ijsem.0.000814] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The taxonomic positions of three Gram-stain-positive, aerobic strains, designated YIM 75722, 75726 and 75728T, and isolated from a soil sample collected from Kurnool of Andhra Pradesh province, India, were assessed using a polyphasic approach. Growth was observed at pH 7.0-10.0 (optimum pH 7.0), 15-28 °C (optimum 28 °C) and 0-8 % (w/v) NaCl (grew without NaCl). Strains showed cylindrical spores with straight-chain morphology on aerial mycelium, but did not reveal sporangium-like structures or fragmentation of the substrate mycelium. Whole-cell hydrolysates of all strains contained galactose and ribose as the diagnostic sugars and meso-diaminopimelic acid as the diamino acid. The predominant menaquinone was MK-9(H4); MK-9 (H6) and MK-10 (H4) were present in smaller amounts. The phospholipid pattern consisted mainly of diphosphatidylglycerol, phosphatidylglycerol and phosphatidylcholine. The major fatty acids were i-C15 : 0, ai-C15 : 0, i-C17 : 0 and ai-C17 : 0. The genomic DNA G+C content was 68.0 mol%. Phylogenetic analysis, based on 16S rRNA gene sequences, revealed that strain YIM 75728T should be placed within the family Pseudonocardiaceae, in which the strain formed a distinct lineage. The combination of phylogenetic analysis, phenotypic characteristics and chemotaxonomic data support the conclusion that strain YIM 75728T represents a novel species of a novel genus of the family Pseudonocardiaceae for which the name Actinorectispora indica gen. nov., sp. nov., is proposed. Strain YIM 75728T ( = DSM 45410T = CCTCC AA 209065T) is the type strain of Actinorectispora indica. Strain YIM 75728T was considered as the type strain over the other two strains based on the highest sequence read length of the strain.
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Affiliation(s)
- Syed Raziuddin Quadri
- Department of Medical Laboratory Technology,Faculty of Applied Medical Sciences, Northern Border University, Arar-91431, Northern Borders,Kingdom of Saudi Arabia.,Yunnan Institute of Microbiology,Yunnan University, Kunming- 650091, Yunnan, PRChina.,Department of Microbiology,Gulbarga University, Gulbarga- 585106, Karnataka,India
| | - Xin-Peng Tian
- Key Laboratory of Marine Bio-resources Sustainable Utilization CAS,RNAM Center for Marine Microbiology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou- 510301, PRChina
| | - Jing Zhang
- Key Laboratory of Marine Bio-resources Sustainable Utilization CAS,RNAM Center for Marine Microbiology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou- 510301, PRChina
| | - Jamal Al Ruwaili
- Department of Medical Laboratory Technology,Faculty of Applied Medical Sciences, Northern Border University, Arar-91431, Northern Borders,Kingdom of Saudi Arabia
| | - Wael N Hozzein
- Bioproducts Research Chair (BRC),College of Science, King Saud University, Riyadh 11451,Kingdom of Saudi Arabia
| | - Dayanand Agsar
- Department of Microbiology,Gulbarga University, Gulbarga- 585106, Karnataka,India
| | - Wen-Jun Li
- Yunnan Institute of Microbiology,Yunnan University, Kunming- 650091, Yunnan, PRChina.,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, PRChina
| | - Syed G Dastager
- NCIM-Resource Center,CSIR-National Chemical Laboratory, Pune- 411008,India
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30
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Qin S, Bai JL, Wang Y, Feng WW, Yuan B, Sun Y, Cao CL, Ju XY, Huang Y, Jiang JH. Tamaricihabitans halophyticus gen. nov., sp. nov., an endophytic actinomycete of the family Pseudonocardiaceae. Int J Syst Evol Microbiol 2015; 65:4662-4668. [DOI: 10.1099/ijsem.0.000628] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel actinomycete strain, designated KLBMP 1356T, was isolated from the root of halophyte Tamarix chinensis Lour. collected from the coastal area of Jiangsu province, PR China. The isolate was characterized using a polyphasic approach. Comparative analysis of the 16S rRNA gene sequence indicated that strain KLBMP 1356T was phylogenetically related to members of the family Pseudonocardiaceae and formed a distinct monophyletic clade between the genera Amycolatopsis (93.1–94.7 % 16S rRNA gene sequence similarity), Prauserella (93.6–95.1 %) and Saccharomonospora (93.2–94.3 %). The isolate displayed long spore chains containing rod-shaped and smooth-surfaced spores. Strain KLBMP 1356T contained meso-diaminopimelic acid as the diagnostic diamino acid, and galactose, arabinose and glucose as the whole-cell sugars. The major menaquinone was MK-9(H4) and the fatty acid profile was characterized by the predominance of iso-C16 : 0, C17 : 1ω8c, C17 : 1ω6c and C17 : 0. The polar lipids comprised diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, unknown aminophospholipids and an unknown glycolipid. Mycolic acids were not present. The G+C content of the genomic DNA was 67.2 mol%. On the basis of the evidence from this polyphasic study, strain KLBMP 1356T is considered to represent a novel species of a new genus in the family Pseudonocardiaceae, for which the name Tamaricihabitans halophyticus gen. nov., sp. nov. is proposed. The type strain of the type species is KLBMP 1356T ( = DSM 45765T = NBRC 109361T).
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Affiliation(s)
- Sheng Qin
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, Jiangsu Normal University, Xuzhou, Jiangsu, 221116, PR China
| | - Juan-Luan Bai
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, Jiangsu Normal University, Xuzhou, Jiangsu, 221116, PR China
| | - Yu Wang
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, Jiangsu Normal University, Xuzhou, Jiangsu, 221116, PR China
| | - Wei-Wei Feng
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, Jiangsu Normal University, Xuzhou, Jiangsu, 221116, PR China
| | - Bo Yuan
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, Jiangsu Normal University, Xuzhou, Jiangsu, 221116, PR China
| | - Yong Sun
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, Jiangsu Normal University, Xuzhou, Jiangsu, 221116, PR China
| | - Cheng Liang Cao
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, Jiangsu Normal University, Xuzhou, Jiangsu, 221116, PR China
| | - Xiu-Yun Ju
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, Jiangsu Normal University, Xuzhou, Jiangsu, 221116, PR China
| | - Ying Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Ji-Hong Jiang
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, Jiangsu Normal University, Xuzhou, Jiangsu, 221116, PR China
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31
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Cao CL, Zhou XQ, Qin S, Tao FX, Jiang JH, Lian B. Lentzea guizhouensis sp. nov., a novel lithophilous actinobacterium isolated from limestone from the Karst area, Guizhou, China. Antonie van Leeuwenhoek 2015; 108:1365-1372. [PMID: 26377575 DOI: 10.1007/s10482-015-0589-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 09/08/2015] [Indexed: 11/28/2022]
Abstract
A novel filamentous actinobacterium, designated strain DHS C013(T), was isolated from limestone collected in Guizhou Province, South-west China. Morphological and chemotaxonomic characteristics of the strain support its assignment to the genus Lentzea. Phylogenetic analyses showed that strain DHS C013(T) is closely related to Lentzea jiangxiensis FXJ1.034(T) (98.7 % 16S rRNA gene similarity) and Lentzea flaviverrucosa 4.0578(T) (98.0 % 16S rRNA gene similarity), but it can be distinguished from these strains based on low levels of DNA:DNA relatedness (~44 and ~37 %, respectively). Physiological and biochemical tests also allowed phenotypic differentiation of the novel strain from these closely related species. On the basis of the evidence presented here, strain DHS C013(T) is concluded to represent a novel species of the genus Lentzea, for which the name Lentzea guizhouensis sp. nov. is proposed. The type strain is DHS C013(T) (=KCTC 29677(T) = CGMCC 4.7203(T)).
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Affiliation(s)
- Cheng-Liang Cao
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang, Guizhou, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, People's Republic of China.,The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu, People's Republic of China
| | - Xiao-Qi Zhou
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu, People's Republic of China
| | - Sheng Qin
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu, People's Republic of China
| | - Fa-Xiang Tao
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang, Guizhou, People's Republic of China
| | - Ji-Hong Jiang
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu, People's Republic of China
| | - Bin Lian
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang, Guizhou, People's Republic of China. .,College of Life Science, Nanjing Normal University, Nanjing, Jiangsu, People's Republic of China.
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32
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Biodiversity of Halophilic and Halotolerant Actinobacteria. SUSTAINABLE DEVELOPMENT AND BIODIVERSITY 2015. [DOI: 10.1007/978-3-319-14595-2_1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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33
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Wu H, Lian Y, Liu B, Ren Y, Qin P, Huang F. Thermotunica guangxiensis gen. nov., sp. nov., isolated from mushroom residue compost. Int J Syst Evol Microbiol 2014; 64:1593-1599. [DOI: 10.1099/ijs.0.057562-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel thermophilic actinomycete, designated AG2-7T, was isolated from mushroom residue compost in Guangxi University, Nanning, China. The strain grew optimally at 45–60 °C, at pH 7.0 and with 0–3.0 % (w/v) NaCl. Vegetative mycelia were branched and whitish to pale yellow without fragmentation. Aerial mycelium was abundant, whitish and differentiated into long chains of spores, with a membranous structure or tunica partially covering the surface of aerial hyphae. The non-motile spores were oval in shape with a ridged surface. Strain AG-27T contained meso-diaminopimelic acid as the diagnostic diamino acid, and the whole-cell sugars were galactose and ribose. Major fatty acids were iso-C16 : 0 (27.51 %), iso-C17 : 0 (10.47 %) and anteiso-C17 : 0 (12.01 %). MK-9(H4) was the predominant menaquinone. The polar phospholipids were diphosphatidylglycerol, ninhydrin-positive glycophospholipid, phosphatidylinositol, phosphatidylinositol mannoside, phosphatidylethanolamine, phosphatidylmethylethanolamine, an unknown phospholipid and unknown glucosamine-containing phospholipids. The G+C content of the genomic DNA was 63.6 mol%. 16S rRNA gene sequence analysis showed that the organism belonged to the family
Pseudonocardiaceae
, suborder
Pseudonocardineae
and showed more than 5 % divergence from other members of the family. Based on the phenotypic and phylogenetic data, strain AG2-7T represents a novel species of a new genus in the family
Pseudonocardiaceae
, for which the name Thermotunica guangxiensis gen. nov., sp. nov. is proposed. The type strain of the type species is AG2-7T ( = ATCC BAA-2499T = CGMCC 4.7099T).
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Affiliation(s)
- Hao Wu
- Institute of Applied Microbiology, Guangxi University, Nanning 530005, PR China
| | - Yunpeng Lian
- Institute of Applied Microbiology, Guangxi University, Nanning 530005, PR China
| | - Bin Liu
- Institute of Applied Microbiology, Guangxi University, Nanning 530005, PR China
| | - Yanling Ren
- Institute of Applied Microbiology, Guangxi University, Nanning 530005, PR China
| | - Peisheng Qin
- Institute of Applied Microbiology, Guangxi University, Nanning 530005, PR China
| | - Fuchang Huang
- Institute of Applied Microbiology, Guangxi University, Nanning 530005, PR China
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34
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Sahin N, Veyisoglu A, Tatar D, Spröer C, Cetin D, Guven K, Klenk HP. Pseudonocardia cypriaca sp. nov., Pseudonocardia salamisensis sp. nov., Pseudonocardia hierapolitana sp. nov. and Pseudonocardia kujensis sp. nov., isolated from soil. Int J Syst Evol Microbiol 2014; 64:1703-1711. [PMID: 24523445 DOI: 10.1099/ijs.0.059824-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The taxonomic positions of four novel actinomycetes isolated from soil samples, designated KT2142T, PM2084T, K236T and A4038T, were established by using a polyphasic approach. The organisms had chemical and morphological features that were consistent with their classification in the genus Pseudonocardia. Whole-cell hydrolysates of the four strains contained meso-diaminopimelic acid and arabinose and galactose as the diagnostic sugars (cell-wall type IV). Their predominant menaquinone was found to be MK-8(H4). The major fatty acid was iso-C16:0. 16S rRNA gene sequence data supported the classification of the isolates in the genus Pseudonocardia and showed that they formed four distinct branches within the genus. DNA-DNA relatedness studies between the isolates and their phylogenetic neighbours showed that they belonged to distinct genomic species. The four isolates were readily distinguished from one another and from the type strains of species classified in the genus Pseudonocardia based on a combination of phenotypic and genotypic properties. In conclusion, it is proposed that the four isolates be classified in four novel species of the genus Pseudonocardia, for which the names Pseudonocardia cypriaca sp. nov. (type strain KT2142T=KCTC 29067T=DSM 45511T=NRRL B-24882T), Pseudonocardia hierapolitana sp. nov. (type strain PM2084T=KCTC 29068T=DSM 45671T=NRRL B-24879T), Pseudonocardia salamisensis sp. nov. (type strain K236T=KCTC 29100T=DSM 45717T) and Pseudonocardia kujensis sp. nov. (type strain A4038T=KCTC 29062T=DSM 45670T=NRRL B-24890T) are proposed.
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Affiliation(s)
- Nevzat Sahin
- Department of Biology, Faculty of Art and Science, Ondokuz Mayis University, 55139 Kurupelit-Samsun, Turkey
| | - Aysel Veyisoglu
- Department of Molecular Biology and Genetics, Faculty of Sciences, Canik Basari University, 55080 Samsun, Turkey.,Department of Biology, Faculty of Art and Science, Ondokuz Mayis University, 55139 Kurupelit-Samsun, Turkey
| | - Demet Tatar
- Department of Biology, Faculty of Art and Science, Ondokuz Mayis University, 55139 Kurupelit-Samsun, Turkey
| | - Cathrin Spröer
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, 38124 Braunschweig, Germany
| | - Demet Cetin
- Science Teaching Programme, Gazi Faculty of Education, Gazi University, Ankara, Turkey
| | - Kiymet Guven
- Anadolu University, Faculty of Science, Biology Department, 26470 Eskisehir, Turkey
| | - Hans-Peter Klenk
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, 38124 Braunschweig, Germany
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35
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Meier-Kolthoff JP, Lu M, Huntemann M, Lucas S, Lapidus A, Copeland A, Pitluck S, Goodwin LA, Han C, Tapia R, Pötter G, Land M, Ivanova N, Rohde M, Göker M, Detter JC, Woyke T, Kyrpides NC, Klenk HP. Genome sequence of the chemoheterotrophic soil bacterium Saccharomonospora cyanea type strain (NA-134(T)). Stand Genomic Sci 2013; 9:28-41. [PMID: 24501643 PMCID: PMC3910552 DOI: 10.4056/sigs.4207886] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Saccharomonospora cyanea Runmao et al. 1988 is a member of the genus Saccharomonospora in the family Pseudonocardiaceae that is moderately well characterized at the genome level thus far. Members of the genus Saccharomonospora are of interest because they originate from diverse habitats, such as soil, leaf litter, manure, compost, surface of peat, moist, over-heated grain, and ocean sediment, where they probably play a role in the primary degradation of plant material by attacking hemicellulose. Species of the genus Saccharomonospora are usually Gram-positive, non-acid fast, and are classified among the actinomycetes. S. cyanea is characterized by a dark blue (= cyan blue) aerial mycelium. After S. viridis, S. azurea, and S. marina, S. cyanea is only the fourth member in the genus for which a completely sequenced (non-contiguous finished draft status) type strain genome will be published. Here we describe the features of this organism, together with the draft genome sequence, and annotation. The 5,408,301 bp long chromosome with its 5,139 protein-coding and 57 RNA genes was sequenced as part of the DOE funded Community Sequencing Program (CSP) 2010 at the Joint Genome Institute (JGI).
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Affiliation(s)
- Jan P Meier-Kolthoff
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Megan Lu
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | | | - Susan Lucas
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Alla Lapidus
- Theodosius Dobzhansky Center for Genome Bionformatics, St. Petersburg State University, St. Petersburg, Russia ; Algorithmic Biology Lab, St. Petersburg Academic University, St.Petersburg, Russia
| | - Alex Copeland
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Sam Pitluck
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Lynne A Goodwin
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA ; DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Cliff Han
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA ; DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Roxanne Tapia
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA ; DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Gabriele Pötter
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Miriam Land
- DOE Joint Genome Institute, Walnut Creek, California, USA ; Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | | | - Manfred Rohde
- HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Markus Göker
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - John C Detter
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA ; DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | | | - Hans-Peter Klenk
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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36
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Xia ZF, Guan TW, Ruan JS, Huang Y, Zhang LL. Longimycelium tulufanense gen. nov., sp. nov., a filamentous actinomycete of the family
Pseudonocardiaceae. Int J Syst Evol Microbiol 2013; 63:2813-2818. [DOI: 10.1099/ijs.0.044222-0] [Citation(s) in RCA: 15] [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 novel filamentous actinomycete strain, designated TRM 46004T, was isolated from sediment of Aiding Lake in Tulufan Basin (42° 64′ N 89° 26′ E), north-west China. The isolate was characterized using a polyphasic approach. The isolate formed abundant aerial mycelium with few branches and vegetative mycelium, occasionally twisted and coiled; spherical sporangia containing one to several spherical spores developed at the ends of short sporangiophores on aerial mycelium. The G+C content of the DNA was 65.2 mol%. The isolate contained meso-diaminopimelic acid as the diagnostic diamino acid and xylose, galactose and ribose as the major whole-cell sugars. The diagnostic phospholipids were phosphatidylethanolamine, phosphatidylcholine and phosphatidylglycerol. The predominant menaquinones were MK-9(H4), MK-9(H6) and MK-9(H10). The major fatty acids were iso-C16 : 0 and anteiso-C17 : 0. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain TRM 46004T formed a distinct lineage within the family
Pseudonocardiaceae
and showed 91.7–96.1 % 16S rRNA gene sequence similarity with members of the family
Pseudonocardiaceae
. On the basis of the evidence from this polyphasic study, a novel genus and species, Longimycelium tulufanense gen. nov., sp. nov., are proposed. The type strain of Longimycelium tulufanense is TRM 46004T ( = CGMCC 4.5737T = NBRC 107726T).
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Affiliation(s)
- Zhan-Feng Xia
- Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin of Xinjiang Production &Construction Corps; Tarim University, Alar 843300, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Tong-Wei Guan
- College of Life Science, Tarim University, Alar 843300, China
- Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin of Xinjiang Production &Construction Corps; Tarim University, Alar 843300, China
| | - Ji-Sheng Ruan
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Ying Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Li-Li Zhang
- College of Life Science, Tarim University, Alar 843300, China
- Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin of Xinjiang Production &Construction Corps; Tarim University, Alar 843300, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
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37
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Strobel T, Al-Dilaimi A, Blom J, Gessner A, Kalinowski J, Luzhetska M, Pühler A, Szczepanowski R, Bechthold A, Rückert C. Complete genome sequence of Saccharothrix espanaensis DSM 44229(T) and comparison to the other completely sequenced Pseudonocardiaceae. BMC Genomics 2012; 13:465. [PMID: 22958348 PMCID: PMC3469384 DOI: 10.1186/1471-2164-13-465] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2012] [Accepted: 08/30/2012] [Indexed: 12/04/2022] Open
Abstract
Background The genus Saccharothrix is a representative of the family Pseudonocardiaceae, known to include producer strains of a wide variety of potent antibiotics. Saccharothrix espanaensis produces both saccharomicins A and B of the promising new class of heptadecaglycoside antibiotics, active against both bacteria and yeast. Results To better assess its capabilities, the complete genome sequence of S. espanaensis was established. With a size of 9,360,653 bp, coding for 8,501 genes, it stands alongside other Pseudonocardiaceae with large genomes. Besides a predicted core genome of 810 genes shared in the family, S. espanaensis has a large number of accessory genes: 2,967 singletons when compared to the family, of which 1,292 have no clear orthologs in the RefSeq database. The genome analysis revealed the presence of 26 biosynthetic gene clusters potentially encoding secondary metabolites. Among them, the cluster coding for the saccharomicins could be identified. Conclusion S. espanaensis is the first completely sequenced species of the genus Saccharothrix. The genome discloses the cluster responsible for the biosynthesis of the saccharomicins, the largest oligosaccharide antibiotic currently identified. Moreover, the genome revealed 25 additional putative secondary metabolite gene clusters further suggesting the strain’s potential for natural product synthesis.
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Affiliation(s)
- Tina Strobel
- Department of Pharmaceutical Biology and Biotechnology, Institute of Pharmaceutical Sciences, Albert-Ludwigs-University, Freiburg 79104, Germany
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Cuesta G, Soler A, Alonso JL, Ruvira MA, Lucena T, Arahal DR, Goodfellow M. Pseudonocardia hispaniensis sp. nov., a novel actinomycete isolated from industrial wastewater activated sludge. Antonie van Leeuwenhoek 2012; 103:135-42. [PMID: 22899021 DOI: 10.1007/s10482-012-9792-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2012] [Accepted: 08/06/2012] [Indexed: 10/28/2022]
Abstract
A novel actinomycete, designated PA3(T), was isolated from an oil refinery wastewater treatment plant, located in Palos de la Frontera, Huelva, Spain, and characterized taxonomically by using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences showed that the isolate formed a distinct subclade in the Pseudonocardia tree together with Pseudonocardia asaccharolytica DSM 44247(T). The chemotaxonomic properties of the isolate, for example, the presence of MK-8 (H(4)) as the predominant menaquinone and iso-C(16:0) as the major fatty acid, are consistent with its classification in the genus Pseudonocardia. DNA:DNA pairing experiments between the isolate and the type strain of P. asaccharolytica DSM 44247(T) showed that they belonged to separate genomic species. The two strains were readily distinguished using a combination of phenotypic properties. Consequently, it is proposed that isolate PA3(T) represents a novel species for which the name Pseudonocardia hispaniensis sp. nov. is proposed. The type strain is PA3(T) (= CCM 8391(T) = CECT 8030(T)).
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Affiliation(s)
- G Cuesta
- Área de Microbiología, Departamento de Biotecnología, E.T.S.I. Agronómica y Medio Natural, Universitat Politècnica de València, Camino de Vera 14, 46022, Valencia, Spain.
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Lee SD. Labedaea rhizosphaerae gen. nov., sp. nov., isolated from rhizosphere soil. Int J Syst Evol Microbiol 2012; 62:1772-1778. [DOI: 10.1099/ijs.0.034355-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel actinomycete, designated strain RS-49T, was isolated from the rhizosphere soil of a cliff-associated plant (Peucedanum japonicum Thunb.) in the Republic of Korea and subjected to a polyphasic taxonomic study. The results of comparative 16S rRNA gene sequence analyses showed that the organism belonged to the family
Pseudonocardiaceae
, suborder
Pseudonocardineae
and that it was most closely related to members of the genera
Kibdelosporangium
(96.6–97.0 % sequence similarity),
Actinokineospora
(96.3–96.7 %),
Streptoalloteichus
(96.2 %) and
Actinophytocola
(96.2 %). Substrate mycelia were well-developed and whitish or pale yellow to strong yellow. Aerial mycelia were branched and fragmented into rod-shaped elements. Single spherical spores were produced directly on the substrate mycelium. Sporangium-like structures and fragmentation of the substrate mycelium were absent. The diagnostic diamino acid in the cell-wall peptidoglycan was meso-diaminopimelic acid. The acyl type of the muramic acid residues in the peptidoglycan was N-acetylated. Whole-cell sugars were glucose, rhamnose, galactose, ribose, mannose, arabinose and xylose. The major menaquinone was MK-9(H4). Small amounts of MK-8 and MK-9(H2) were also detected. The polar lipids contained diphosphatidylglycerol, phosphatidyldimethylethanolamine, phosphatidylglycerol, phosphatidylinositol, an unknown phospholipid and an unknown lipid. The predominant fatty acids were iso-C15 : 0 and iso-C16 : 0. The DNA G+C content was 64.2 mol%. The phenotypic and phylogenetic characteristics show that strain RS-49T can be differentiated from members of all genera in the suborder
Pseudonocardineae
and thus represents a novel species in a new genus for which the name Labedaea rhizosphaerae gen. nov., sp. nov. is proposed; the type strain of the type species is RS-49T ( = KCTC 19662T = DSM 45361T).
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Affiliation(s)
- Soon Dong Lee
- Department of Science Education, Jeju National University, Jeju 690-756, Republic of Korea
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Camas M, Sahin N, Sazak A, Spröer C, Klenk HP. Amycolatopsis magusensis sp. nov., isolated from soil. Int J Syst Evol Microbiol 2012; 63:1254-1260. [PMID: 22771685 DOI: 10.1099/ijs.0.042770-0] [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 novel actinomycete, designated strain KT2025(T), was isolated from arid soil collected from Magusa, northern Cyprus. The taxonomic position of the novel strain was established by using a polyphasic approach. The organism had chemical and morphological features consistent with its classification in the genus Amycolatopsis. Phylogenetic analyses based on 16S rRNA gene sequences supported the classification of the isolate in the genus Amycolatopsis and showed that the organism formed a cluster with Amycolatopsis nigrescens CSC17-Ta-90(T), Amycolatopsis minnesotensis 32U-2(T), Amycolatopsis sacchari DSM 44468(T) and Amycolatopsis dongchuanensis YIM 75904(T). 16S rRNA gene sequence similarity analysis indicated that strain KT2025(T) was most closely related to Amycolatopsis lurida DSM 43134(T) (97.5 %), Amycolatopsis keratiniphila subsp. keratiniphila DSM 44409(T) (97.4 %), Amycolatopsis keratiniphila subsp. nogabecina DSM 44586(T) (97.1 %), Amycolatopsis nigrescens DSM 44992(T) (97.1 %), Amycolatopsis azurea DSM 43854(T) (97.1 %) and Amycolatopsis minnesotensis DSM 44988(T) (96.9 %). The organism was found to have chemical features typical of members of the genus Amycolatopsis such as meso-diaminopimelic acid as the diagnostic diamino acid in the cell-wall peptidoglycan, and arabinose and galactose as diagnostic sugars. The predominant menaquinone was MK-9(H4). The polar lipids detected were phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol and hydroxy-phosphatidylethanolamine. The major fatty acids were iso-C16 : 0, iso-C15 : 0 and iso-C14 : 0. The G+C content of the genomic DNA was 70.8 mol%. Phenotypic data clearly distinguished the isolate from its closest relatives. The combined genotypic and phenotypic data and low levels of DNA-DNA relatedness with its closest relatives indicated that strain KT2025(T) represents a novel species of the genus Amycolatopsis, for which the name Amycolatopsis magusensis sp. nov. is proposed. The type strain is KT2025(T) ( = DSM 45510(T) = KCTC 29056(T)).
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Affiliation(s)
- Mustafa Camas
- Department of Biology, Faculty of Art and Science, Ondokuz Mayis University, 55139 Kurupelit-Samsun, Turkey
| | - Nevzat Sahin
- Department of Biology, Faculty of Art and Science, Ondokuz Mayis University, 55139 Kurupelit-Samsun, Turkey
| | - Anil Sazak
- Department of Biology, Faculty of Art and Science, Ondokuz Mayis University, 55139 Kurupelit-Samsun, Turkey
| | - Cathrin Spröer
- German Collection of Microorganisms and Cell Cultures GmbH, 38124 Braunschweig, Germany
| | - Hans-Peter Klenk
- German Collection of Microorganisms and Cell Cultures GmbH, 38124 Braunschweig, Germany
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41
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Klenk HP, Held B, Lucas S, Lapidus A, Copeland A, Hammon N, Pitluck S, Goodwin LA, Han C, Tapia R, Brambilla EM, Pötter G, Land M, Ivanova N, Rohde M, Göker M, Detter JC, Kyrpides NC, Woyke T. Genome sequence of the soil bacterium Saccharomonospora azurea type strain (NA-128(T)). Stand Genomic Sci 2012; 6:220-9. [PMID: 22768365 PMCID: PMC3387790 DOI: 10.4056/sigs.2635833] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Saccharomonospora azurea Runmao et al. 1987 is a member of the genus Saccharomonospora, which is in the family Pseudonocardiaceae and thus far poorly characterized genomically. Members of the genus Saccharomonospora are of interest because they originate from diverse habitats, such as leaf litter, manure, compost, the surface of peat, and moist and over-heated grain, and may play a role in the primary degradation of plant material by attacking hemicellulose. Next to S. viridis, S. azurea is only the second member in the genus Saccharomonospora for which a completely sequenced type strain genome will be published. Here we describe the features of this organism, together with the complete genome sequence with project status 'Improved high quality draft', and the annotation. The 4,763,832 bp long chromosome with its 4,472 protein-coding and 58 RNA genes was sequenced as part of the DOE funded Community Sequencing Program (CSP) 2010 at the Joint Genome Institute (JGI).
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Klenk HP, Lu M, Lucas S, Lapidus A, Copeland A, Pitluck S, Goodwin LA, Han C, Tapia R, Brambilla EM, Pötter G, Land M, Ivanova N, Rohde M, Göker M, Detter JC, Li WJ, Kyrpides NC, Woyke T. Genome sequence of the ocean sediment bacterium Saccharomonospora marina type strain (XMU15(T)). Stand Genomic Sci 2012; 6:265-75. [PMID: 22768369 PMCID: PMC3387791 DOI: 10.4056/sigs.2655905] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Saccharomonospora marina Liu et al. 2010 is a member of the genus Saccharomonospora, in the family Pseudonocardiaceae that is poorly characterized at the genome level thus far. Members of the genus Saccharomonospora are of interest because they originate from diverse habitats, such as leaf litter, manure, compost, surface of peat, moist, over-heated grain, and ocean sediment, where they might play a role in the primary degradation of plant material by attacking hemicellulose. Organisms belonging to the genus are usually Gram-positive staining, non-acid fast, and classify among the actinomycetes. Here we describe the features of this organism, together with the complete genome sequence (permanent draft status), and annotation. The 5,965,593 bp long chromosome with its 5,727 protein-coding and 57 RNA genes was sequenced as part of the DOE funded Community Sequencing Program (CSP) 2010 at the Joint Genome Institute (JGI).
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43
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Zucchi TD, Bonda ANV, Frank S, Kim BY, Kshetrimayum JD, Goodfellow M. Amycolatopsis bartoniae sp. nov. and Amycolatopsis bullii sp. nov., mesophilic actinomycetes isolated from arid Australian soils. Antonie van Leeuwenhoek 2012; 102:91-8. [PMID: 22434348 DOI: 10.1007/s10482-012-9716-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2012] [Accepted: 02/27/2012] [Indexed: 10/28/2022]
Abstract
The status of two mesophilic filamentous actinomycetes isolated from an arid Australian soil sample was determined using a polyphasic taxonomic approach. The isolates had chemical and morphological properties consistent with their classification in the genus Amycolatopsis, assignments that were supported by analysis of 16S rRNA gene sequence data. Isolate SF26(T) formed a distinct phyletic line and hence was sharply separated from its nearest phylogenetic neighbour, Amycolatopsis sacchari DSM 44468(T). In contrast, isolate SF27(T) formed a subclade in the Amycolatopsis tree with Amycolatopsis vancoresmycina DSM 44592(T) but was separated readily from the latter by DNA:DNA pairing data. The two isolates were distinguished from one another and from their respective nearest phylogenetic neighbours using a range of phenotypic properties. These data indicate that the two isolates should be recognized as new species in the genus Amycolatopsis. The names proposed for these new taxa are Amycolatopsis bartoniae sp. nov. and Amycolatopsis bullii sp. nov. with isolates SF26(T) (=NCIMB 14706(T) = NRRL B-2846(T)) and SF27(T) (=NCIMB 14707(T) = NRRL B-24847(T)) as the respective type strains.
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44
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Gao B, Gupta RS. Phylogenetic framework and molecular signatures for the main clades of the phylum Actinobacteria. Microbiol Mol Biol Rev 2012; 76:66-112. [PMID: 22390973 PMCID: PMC3294427 DOI: 10.1128/mmbr.05011-11] [Citation(s) in RCA: 160] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The phylum Actinobacteria harbors many important human pathogens and also provides one of the richest sources of natural products, including numerous antibiotics and other compounds of biotechnological interest. Thus, a reliable phylogeny of this large phylum and the means to accurately identify its different constituent groups are of much interest. Detailed phylogenetic and comparative analyses of >150 actinobacterial genomes reported here form the basis for achieving these objectives. In phylogenetic trees based upon 35 conserved proteins, most of the main groups of Actinobacteria as well as a number of their superageneric clades are resolved. We also describe large numbers of molecular markers consisting of conserved signature indels in protein sequences and whole proteins that are specific for either all Actinobacteria or their different clades (viz., orders, families, genera, and subgenera) at various taxonomic levels. These signatures independently support the existence of different phylogenetic clades, and based upon them, it is now possible to delimit the phylum Actinobacteria (excluding Coriobacteriia) and most of its major groups in clear molecular terms. The species distribution patterns of these markers also provide important information regarding the interrelationships among different main orders of Actinobacteria. The identified molecular markers, in addition to enabling the development of a stable and reliable phylogenetic framework for this phylum, also provide novel and powerful means for the identification of different groups of Actinobacteria in diverse environments. Genetic and biochemical studies on these Actinobacteria-specific markers should lead to the discovery of novel biochemical and/or other properties that are unique to different groups of Actinobacteria.
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Affiliation(s)
- Beile Gao
- Department of Biochemistry and Biomedical Science, McMaster University, Hamilton, Ontario, Canada
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45
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Guo X, Qiu D, Ruan J, Huang Y. Actinophytocola xinjiangensis sp. nov., isolated from virgin forest soil. Int J Syst Evol Microbiol 2011; 61:2928-2932. [DOI: 10.1099/ijs.0.027722-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An aerobic, non-motile actinobacterium, strain QAIII60T, was isolated from virgin forest soil of Kanas Nature Reserve, Xinjiang, north-west China. The isolate produced a very scant aerial mycelium that fragmented into cylindrical spores and a non-fragmented substrate mycelium with occasional septa. Whole-cell hydrolysates contained meso-diaminopimelic acid, arabinose, galactose, glucose, ribose and rhamnose (trace). The diagnostic polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, hydroxyphosphatidylethanolamine and ninhydrin-positive phosphoglycolipids. The major cellular fatty acids were iso-C16 : 0, iso-C14 : 0, iso-C16 : 1 H and C17 : 1ω6c. The isoprenoid quinones consisted of MK-9(H4) and MK-10(H2). The G+C content of the genomic DNA was 72.5 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain QAIII60T formed a distinct phyletic line that was most closely, albeit loosely, associated with the genus Actinophytocola. A number of physiological characteristics differentiated the isolate from members of the genus Actinophytocola. On the basis of these data, we propose that strain QAIII60T ( = CGMCC 4.4663T = NBRC 106673T) be assigned as the type strain of a novel species, Actinophytocola xinjiangensis sp. nov.
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Affiliation(s)
- Xiaoxuan Guo
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Danheng Qiu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Jisheng Ruan
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Ying Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
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46
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Li X, Zhang L, Ding Y, Gao Y, Ruan J, Huang Y. Lentzea jiangxiensis sp. nov., isolated from acidic soil. Int J Syst Evol Microbiol 2011; 62:2342-2346. [PMID: 22140164 DOI: 10.1099/ijs.0.033795-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel actinomycete, designated strain FXJ1.034(T), was isolated from acidic soil collected in Jiangxi Province, South-east China. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain FXJ1.034(T) belonged to the genus Lentzea and showed high sequence similarities to Lentzea kentuckyensis NRRL B-24416(T) (98.5%) and Lentzea albida NBRC 16102(T) (98.3%). Morphological and chemotaxonomic characteristics supported its assignment to the genus Lentzea. The results of DNA-DNA hybridization, physiological and biochemical tests allowed genotypic and phenotypic differentiation of the novel strain from closely related species. Based on the evidence presented here, strain FXJ1.034(T) represents a novel species of the genus Lentzea, for which the name Lentzea jiangxiensis sp. nov. is proposed. The type strain is FXJ1.034(T) ( = CGMCC 4.6609(T) = NBRC 106680(T)).
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Affiliation(s)
- Xiaomin Li
- College of Land Resources and Environment, Jiangxi Agricultural University, Nanchang 330045, Jiangxi Province, PR China
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Limin Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Yun Ding
- College of Land Resources and Environment, Jiangxi Agricultural University, Nanchang 330045, Jiangxi Province, PR China
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Yongsheng Gao
- College of Land Resources and Environment, Jiangxi Agricultural University, Nanchang 330045, Jiangxi Province, PR China
| | - Jisheng Ruan
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Ying Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
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Zucchi TD, Tan GYA, Bonda ANV, Frank S, Kshetrimayum JD, Goodfellow M. Amycolatopsis granulosa sp. nov., Amycolatopsis ruanii sp. nov. and Amycolatopsis thermalba sp. nov., thermophilic actinomycetes isolated from arid soils. Int J Syst Evol Microbiol 2011; 62:1245-1251. [PMID: 21764982 DOI: 10.1099/ijs.0.031039-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The taxonomic positions of three thermophilic actinomycetes isolated from arid soil samples were established by using a polyphasic approach. The organisms had chemical and morphological features that were consistent with their classification in the genus Amycolatopsis. 16S rRNA gene sequence data supported the classification of the isolates in the genus Amycolatopsis and showed that they formed distinct branches in the Amycolatopsis methanolica subclade. DNA-DNA relatedness studies between the isolates and their phylogenetic neighbours showed that they belonged to distinct genomic species. The three isolates were readily distinguished from one another and from the type strains of species classified in the A. methanolica subclade based on a combination of phenotypic properties and by genomic fingerprinting. Consequently, it is proposed that the three isolates be classified in the genus Amycolatopsis as representatives of Amycolatopsis granulosa sp. nov. (type strain GY307(T) = NCIMB 14709(T) = NRRL B-24844(T)), Amycolatopsis ruanii sp. nov. (type strain NMG112(T) = NCIMB 14711(T) = NRRL B-24848(T)) and Amycolatopsis thermalba sp. nov. (type strain SF45(T) = NCIMB 14705(T) = NRRL B-24845(T)).
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Affiliation(s)
- Tiago Domingues Zucchi
- Departamento de Entomologia and Acarologia, ESALQ, Universidade de São Paulo, Piracicaba, Brazil
- School of Biology, University of Newcastle, Newcastle upon Tyne NE1 7RU, UK
| | - Geok Yuan Annie Tan
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | | | - Sarah Frank
- School of Biology, University of Newcastle, Newcastle upon Tyne NE1 7RU, UK
| | | | - Michael Goodfellow
- School of Biology, University of Newcastle, Newcastle upon Tyne NE1 7RU, UK
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48
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Zucchi TD, Tan GYA, Goodfellow M. Amycolatopsis thermophila sp. nov. and Amycolatopsis viridis sp. nov., thermophilic actinomycetes isolated from arid soil. Int J Syst Evol Microbiol 2011; 62:168-172. [PMID: 21378137 DOI: 10.1099/ijs.0.029256-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The taxonomic positions of two thermophilic actinomycetes isolated from an arid Australian soil sample were established based on an investigation using a polyphasic taxonomic approach. The organisms had chemical and morphological properties typical of members of the genus Amycolatopsis and formed distinct phyletic lines in the Amycolatopsis methanolica 16S rRNA subclade. The two organisms were distinguished from one another and from the type strains of related species of the genus Amycolatopsis using a range of phenotypic properties. Based on the combined genotypic and phenotypic data, it is proposed that the two isolates be classified in the genus Amycolatopsis as Amycolatopsis thermophila sp. nov. (type strain GY088(T)=NCIMB 14699(T)=NRRL B-24836(T)) and Amycolatopsis viridis sp. nov. (type strain GY115(T)=NCIMB 14700(T)=NRRL B-24837(T)).
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Affiliation(s)
- Tiago Domingues Zucchi
- Departamento de Entomologia & Acarologia, ESALQ, Universidade de São Paulo, Piracicaba, Brazil
- School of Biology, University of Newcastle, Newcastle upon Tyne NE1 7RU, UK
| | - Geok Yuan Annie Tan
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
- School of Biology, University of Newcastle, Newcastle upon Tyne NE1 7RU, UK
| | - Michael Goodfellow
- School of Biology, University of Newcastle, Newcastle upon Tyne NE1 7RU, UK
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