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Liu C, Wang L, Chen X, Li J, Wang X, Chu Y. Pseudonocardia lacus sp. nov., An Actinomycete Isolated from a Lake Sediment Sample. Curr Microbiol 2023; 81:7. [PMID: 37962701 DOI: 10.1007/s00284-023-03520-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 10/11/2023] [Indexed: 11/15/2023]
Abstract
A novel actinomycete strain, designated H11425T, was isolated from a sediment sample collected from Baihua Lake, Guizhou Province, PR China, and a polyphasic approach was employed to determine its taxonomic position. 16S rRNA gene sequence comparisons showed that strain H11425T is most closely related to Pseudonocardia sulfidoxydans JCM 10411T (97.9%) and Pseudonocardia kunmingensis JCM 32122T (97.8%). Both of phylogenetic analysis based on 16S rRNA gene sequence and phylogenomic analysis based on whole-genome sequence showed that strain H11425T formed a separate clade within the genus Pseudonocardia. The draft genome had a length of 8,059,576 bp with a G + C content of 74.5%. The average nucleotide identity, average amino acid identity, and digital DNA-DNA hybridization values between strain H11425T and its closely related Pseudonocardia species were 76.8-79.0%, 64.8-69.9% and 21.7-23.3%, respectively, which were significantly lower than the widely accepted species-defined threshold. Strain H11425T contained meso-diaminopimelic acid, arabinose, galactose, glucose and ribose in its whole-cell hydrolysates. Mycolic acids were absent. The menaquinone was identifed as MK-8(H4). The phospholipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, hydroxy-phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, phosphatidylcholine, an unknown phospholipid and four unidentified aminophospholipids. The major fatty acids were iso-C16:0, iso-C14:0, iso H-C16:1 and iso-C16:0 2OH. On the basis of the taxonomic evidence, strain H11425T represents a novel species of the genus Pseudonocardia, for which the name Pseudonocardia lacus sp. nov. is proposed. The type strain is H11425T (= JCM 34851T = CICC 25118T).
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Affiliation(s)
- Chaolan Liu
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, School of Pharmacy, Chengdu University, Chengdu, 610106, People's Republic of China
| | - Limei Wang
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, School of Pharmacy, Chengdu University, Chengdu, 610106, People's Republic of China
| | - Xue Chen
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, School of Pharmacy, Chengdu University, Chengdu, 610106, People's Republic of China
| | - Jianghua Li
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, School of Pharmacy, Chengdu University, Chengdu, 610106, People's Republic of China
| | - Xingrong Wang
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, School of Pharmacy, Chengdu University, Chengdu, 610106, People's Republic of China
| | - Yiwen Chu
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, School of Pharmacy, Chengdu University, Chengdu, 610106, People's Republic of China.
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Koutsoumanis K, Allende A, Alvarez‐Ordóñez A, Bolton D, Bover‐Cid S, Chemaly M, Davies R, De Cesare A, Hilbert F, Lindqvist R, Nauta M, Peixe L, Ru G, Simmons M, Skandamis P, Suffredini E, Cocconcelli PS, Fernández Escámez PS, Maradona MP, Querol A, Sijtsma L, Suarez JE, Sundh I, Vlak J, Barizzone F, Hempen M, Correia S, Herman L. Update of the list of QPS-recommended microbiological agents intentionally added to food or feed as notified to EFSA 16: suitability of taxonomic units notified to EFSA until March 2022. EFSA J 2022; 20:e07408. [PMID: 35898292 PMCID: PMC9310698 DOI: 10.2903/j.efsa.2022.7408] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
The qualified presumption of safety (QPS) approach was developed to provide a regularly updated generic pre-evaluation of the safety of microorganisms, intended for use in the food or feed chains, to support the work of EFSA's Scientific Panels. The QPS approach is based on an assessment of published data for each agent, with respect to its taxonomic identity, the body of relevant knowledge, safety concerns and occurrence of antimicrobial resistance. Safety concerns identified for a taxonomic unit (TU) are, where possible, confirmed at the species/strain or product level and reflected by 'qualifications'. In the period covered by this statement, no new information was found that would change the status of previously recommended QPS TUs. Of the 50 microorganisms notified to EFSA in October 2021 to March 2022 (inclusive), 41 were not evaluated: 10 filamentous fungi, 1 Enterococcus faecium, 1 Clostridium butyricum, 3 Escherichia coli and 1 Streptomyces spp. because are excluded from QPS evaluation, and 25 TUs that have already a QPS status. Nine notifications, corresponding to seven TUs were evaluated: four of these, Streptococcus salivarius, Companilactobacillus formosensis, Pseudonocardia autotrophica and Papiliotrema terrestris, being evaluated for the first time. The other three, Microbacterium foliorum, Pseudomonas fluorescens and Ensifer adhaerens were re-assessed. None of these TUs were recommended for QPS status: Ensifer adhaerens, Microbacterium foliorum, Companilactobacillus formosensis and Papiliotrema terrestris due to a limited body of knowledge, Streptococcus salivarius due to its ability to cause bacteraemia and systemic infection that results in a variety of morbidities, Pseudonocardia autotrophica due to lack of body of knowledge and uncertainty on the safety of biologically active compounds which can be produced, and Pseudomonas fluorescens due to possible safety concerns.
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Zan ZY, Ge XF, Huang RR, Liu WZ. Pseudonocardia humida sp. nov., an Actinomycete Isolated from Mangrove Soil Showing Distinct Distribution Pattern of Biosynthetic Gene Clusters. Curr Microbiol 2022; 79:87. [PMID: 35129703 DOI: 10.1007/s00284-022-02784-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 01/24/2022] [Indexed: 11/03/2022]
Abstract
A novel actinomycete strain, designated S2-4T, was isolated from a mangrove soil sample, and a polyphasic approach was employed to determine its taxonomic position. Phylogenetic analysis based on 16S rRNA gene indicated that strain S2-4T formed a unique clade next to that harboring Pseudonocardia dioxanivorans CB1190T, which shared the highest sequence similarity (98.20%) with the new isolate. Phylogenetic analysis based on core genes of genomic sequences displayed a different scenario, exhibiting closer phylogenetic relationship of strain S2-4T with several species with 16S rRNA gene sequence similarities ranging from 96.95 to 98.06%, which was confirmed by the phylogenetic tree reconstructed based on genomic sequences. Further, substantial differences between the genotypic properties of strain S2-4T and its closest neighbors, including digital DNA-DNA hybridization, average nucleotide identity, and distribution patterns of biosynthetic gene clusters (BGC), indicated the taxonomic position of strain S2-4T as a novel species of the genus Pseudonocardia. Accordingly, strain S2-4T was observed to show a different distribution pattern of a predicted BGC encoding ectoine by comparative genomic analysis, which could be strongly linked to its unique habitat distinct from where its close neighbors were isolated. The major cellular fatty acids were iso-C15:0, C21:0, and iso-C16:0. The predominant menaquinone was MK-8(H4). The polar lipids were composed of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidyl-N-monomethylethanolamine, phosphatidylcholine, phosphatidylinositol, phosphatidylinositol mannosides, and two unidentified glycolipids. Here, we propose a novel species of the genus Pseudonocardia: Pseudonocardia humida sp. nov. with the type strain S2-4T (= JCM 34291T = CGMCC 4.7706T).
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Affiliation(s)
- Zhen-Yu Zan
- School of Food and Pharmaceutical Engineering, Nanjing Normal University, Xuelin Road No. 2, Nanjing, 210023, People's Republic of China
| | - Xian-Feng Ge
- School of Food and Pharmaceutical Engineering, Nanjing Normal University, Xuelin Road No. 2, Nanjing, 210023, People's Republic of China
| | - Rui-Rui Huang
- School of Food and Pharmaceutical Engineering, Nanjing Normal University, Xuelin Road No. 2, Nanjing, 210023, People's Republic of China
| | - Wen-Zheng Liu
- School of Food and Pharmaceutical Engineering, Nanjing Normal University, Xuelin Road No. 2, Nanjing, 210023, People's Republic of China.
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Parra J, Soldatou S, Rooney LM, Duncan KR. Pseudonocardia abyssalis sp. nov. and Pseudonocardia oceani sp. nov., two novel actinomycetes isolated from the deep Southern Ocean. Int J Syst Evol Microbiol 2021; 71:005032. [PMID: 34582326 PMCID: PMC8549268 DOI: 10.1099/ijsem.0.005032] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 08/20/2021] [Indexed: 01/25/2023] Open
Abstract
The actinomycetes strains KRD168T and KRD185T were isolated from sediments collected from the deep Southern Ocean and, in this work, they are described as representing two novel species of the genus Pseudonocardia through a polyphasic approach. Despite sharing >99 % 16S rRNA gene sequence similarity with other members of the genus, comparative genomic analysis allowed species delimitation based on average nucleotide identity and digital DNA-DNA hybridization. The KRD168T genome is characterized by a size of 6.31 Mbp and a G+C content of 73.44 mol%, while the KRD185T genome has a size of 6.82 Mbp and a G+C content of 73.98 mol%. Both strains contain meso-diaminopimelic acid as the diagnostic diamino acid, glucose as the major whole-cell sugar, MK-8(H4) as a major menaquinone and iso-branched hexadecanoic acid as a major fatty acid. Biochemical and fatty acid analyses also revealed differences between these strains and their phylogenetic neighbours, supporting their status as distinct species. The names Pseudonocardia abyssalis sp. nov. (type strain KRD168T=DSM 111918T=NCIMB 15270T) and Pseudonocardia oceani (type strain KRD185T=DSM 111919T=NCIMB 15269T) are proposed.
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Affiliation(s)
- Jonathan Parra
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde,, Glasgow G4 0RE, UK
| | - Sylvia Soldatou
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde,, Glasgow G4 0RE, UK
- Present address: School of Pharmacy and Life Sciences, Robert Gordon University, Aberdeen AB10 7GJ, UK
| | - Liam M. Rooney
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde,, Glasgow G4 0RE, UK
- Present address: Institute of Biological Chemistry, Biophysics and Bioengineering, School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh EH14 4AS, UK
| | - Katherine R. Duncan
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde,, Glasgow G4 0RE, UK
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Pseudonocardia pini sp. nov., an endophytic actinobacterium isolated from roots of the pine tree Callitris preissii. Arch Microbiol 2021; 203:3407-3413. [PMID: 33890128 DOI: 10.1007/s00203-021-02309-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Revised: 03/10/2021] [Accepted: 03/26/2021] [Indexed: 10/21/2022]
Abstract
A Gram-positive, aerobic, actinobacterial strain with rod-shaped spores, CAP47RT, which was isolated from the surface-sterilized root of a native pine tree (Callitris preissii), grown in South Australia is described. The major cellular fatty acid of this strain was iso-H-C16:1 and major menaquinone was MK-8(H4). The diagnostic diamino acid in the cell-wall peptidoglycan was identified as meso-diaminopimelic acid. These chemotaxonomic data confirmed the affiliation of strain CAP47RT to the genus Pseudonocardia. Phylogenetic evaluation based on 16S rRNA gene sequence analysis placed this strain in the family Pseudonocardiaceae, being most closely related to Pseudonocardia xishanensis JCM 17906T (98.8%), Pseudonocardia oroxyli DSM 44984T (98.7%), Pseudonocardia thailandensis CMU-NKS-70T (98.7%), and Pseudonocardia ailaonensis DSM 44979T (97.9%). The results of the polyphasic study which contain genome comparisons of ANIb, ANIm, and digital DNA-DNA hybridization revealed the differentiation of strain CAP47RT from the closest species with validated names. This strain represents a novel species and the name proposed for this microorganism is Pseudonocardia pini sp. nov., indicating the source of this actinobacterium from a pine tree. The type strain is CAP47RT (= DSM 108967T = NRRL B-65534T). Genome mining revealed that this strain contained a variety of genes encoding enzymes that can degrade hazardous chemicals.
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Farrer AG, Wright SL, Skelly E, Eisenhofer R, Dobney K, Weyrich LS. Effectiveness of decontamination protocols when analyzing ancient DNA preserved in dental calculus. Sci Rep 2021; 11:7456. [PMID: 33811235 PMCID: PMC8018977 DOI: 10.1038/s41598-021-86100-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Accepted: 02/26/2021] [Indexed: 02/01/2023] Open
Abstract
Ancient DNA analysis of human oral microbial communities within calcified dental plaque (calculus) has revealed key insights into human health, paleodemography, and cultural behaviors. However, contamination imposes a major concern for paleomicrobiological samples due to their low endogenous DNA content and exposure to environmental sources, calling into question some published results. Decontamination protocols (e.g. an ethylenediaminetetraacetic acid (EDTA) pre-digestion or ultraviolet radiation (UV) and 5% sodium hypochlorite immersion treatments) aim to minimize the exogenous content of the outer surface of ancient calculus samples prior to DNA extraction. While these protocols are widely used, no one has systematically compared them in ancient dental calculus. Here, we compare untreated dental calculus samples to samples from the same site treated with four previously published decontamination protocols: a UV only treatment; a 5% sodium hypochlorite immersion treatment; a pre-digestion in EDTA treatment; and a combined UV irradiation and 5% sodium hypochlorite immersion treatment. We examine their efficacy in ancient oral microbiota recovery by applying 16S rRNA gene amplicon and shotgun sequencing, identifying ancient oral microbiota, as well as soil and skin contaminant species. Overall, the EDTA pre-digestion and a combined UV irradiation and 5% sodium hypochlorite immersion treatment were both effective at reducing the proportion of environmental taxa and increasing oral taxa in comparison to untreated samples. This research highlights the importance of using decontamination procedures during ancient DNA analysis of dental calculus to reduce contaminant DNA.
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Affiliation(s)
- Andrew G. Farrer
- grid.1010.00000 0004 1936 7304Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, South Australia Australia
| | - Sterling L. Wright
- grid.29857.310000 0001 2097 4281The Department of Anthropology, The Pennsylvania State University, University Park, PA USA
| | - Emily Skelly
- grid.1010.00000 0004 1936 7304Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, South Australia Australia
| | - Raphael Eisenhofer
- grid.1010.00000 0004 1936 7304Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, South Australia Australia ,grid.1010.00000 0004 1936 7304Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, University of Adelaide, Adelaide, South Australia Australia
| | - Keith Dobney
- grid.1013.30000 0004 1936 834XDepartment of Archaeology, University of Sydney, Sydney, NSW Australia
| | - Laura S. Weyrich
- grid.1010.00000 0004 1936 7304Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, South Australia Australia ,grid.29857.310000 0001 2097 4281The Department of Anthropology, The Pennsylvania State University, University Park, PA USA ,grid.1010.00000 0004 1936 7304Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, University of Adelaide, Adelaide, South Australia Australia ,grid.29857.310000 0001 2097 4281The Huck Institute of Life Sciences, The Pennsylvania State University, University Park, PA USA
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Mo P, Zhao Y, Liu J, Xu Z, Gao J. Pseudonocardia broussonetiae sp. nov., an endophytic actinomycete isolated from the roots of Broussonetia papyrifera. Int J Syst Evol Microbiol 2021; 71. [PMID: 33528351 DOI: 10.1099/ijsem.0.004680] [Citation(s) in RCA: 7] [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 novel endophytic actinomycete, designated strain Gen 01T, was isolated from the roots of Broussonetia papyrifera and characterized by using a polyphasic approach. The predominant cellular fatty acids were iso-C16 : 0, summed feature 3, iso H-C16 : 1, C16 : 0 and iso-C14 : 0. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol mannosides, phospholipids of unknown structure containing glucosamine inositol, phosphatidylinositol and unidentified phospholipids. The major menaquinone was MK-8 (H4). The DNA G+C content of the genome sequence, consisting of 7 177 725 bp, was 74.5 mol%. Phylogenetic analysis of the full-length 16S rRNA gene sequences showed that strain Gen 01T belongs to the genus Pseudonocardia with the highest sequence similarity to Pseudonocardia petroleophila CGMCC 4.1532T (98.9 %) and lower than 98.7 % similarity to other species of the genus Pseudonocardia with validly published names. The average nucleotide identity and digital DNA-DNAhybridization values between strain Gen 01T and P. petroleophila CGMCC 4.1532T were 84.6 and 30.9 %, respectively. Furthermore, the morphological, physiological and biochemical characteristics were sufficient to categorize strain Gen 01T as being distinct from P. petroleophila CGMCC 4.1532T. Consequently, based on phenotypic and genotypic characteristics, strain Gen 01T represents a novel species of the genus Pseudonocardia, for which the name Pseudonocardia broussonetiae sp. nov. is proposed. The type strain is Gen 01T (=CICC 24820T=JCM 33840T).
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Affiliation(s)
- Ping Mo
- Hunan Research Center of Engineering Technology for Utilization of Environmental and Resources Plant, Central South University of Forestry and Technology, Changsha 410004 Hunan, PR China
| | - Yunlin Zhao
- Hunan Research Center of Engineering Technology for Utilization of Environmental and Resources Plant, Central South University of Forestry and Technology, Changsha 410004 Hunan, PR China
| | - Jun Liu
- College of Forestry, Northwest A & F University, Yangling 712100 Shaanxi, PR China
- Hunan Research Center of Engineering Technology for Utilization of Environmental and Resources Plant, Central South University of Forestry and Technology, Changsha 410004 Hunan, PR China
| | - Zhenggang Xu
- College of Forestry, Northwest A & F University, Yangling 712100 Shaanxi, PR China
- Hunan Research Center of Engineering Technology for Utilization of Environmental and Resources Plant, Central South University of Forestry and Technology, Changsha 410004 Hunan, PR China
| | - Jian Gao
- School of Life Science, Hunan University of Science and Technology, Xiangtan 411201 Hunan, 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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Amycolatopsis pithecelloba sp. nov., a novel actinomycete isolated from roots of Pithecellobium dulce in Thailand. J Antibiot (Tokyo) 2020; 73:230-235. [PMID: 31913343 DOI: 10.1038/s41429-019-0271-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 12/01/2019] [Accepted: 12/16/2019] [Indexed: 11/08/2022]
Abstract
An actinomycete strain RM579T isolated from roots of Pithecellobium dulce in Thailand was studied using the polyphasic taxonomic approach. The results of comparative 16S rRNA gene sequence and phylogenetic analysis showed that strain RM579T belonged to the family Pseudonocardiaceae and it was most closely related to members of the genera Amycolatopsis (≤94.5% sequence similarity) and Haloechinothrix (≤93.4% sequence similarity). A phylogenetic tree constructed by neighbor-joining method indicated that strain RM579T was positioned within the clade of the genus Amycolatopsis and formed a monophyletic cluster with Amycolatopsis taiwanensis 0345M-7T, Amycolatopsis pigmentata TT00-43T and Amycolatopsis helveola TT99-32T. Strain RM579T formed white aerial mycelium and yellowish-brown substrate mycelium that fragments into rod-shaped elements. Morphological features and chemotaxonomic characteristics of strain RM579T were consistent with those of the genus Amycolatopsis. The cell wall of strain RM579T contained meso-diaminopimelic acid. Arabinose, galactose, mannose, and ribose were detected as whole-cell sugars. Mycolic acids were absent. The acyl type of the muramic acid in the cell wall was N-acetyl. Diphosphatidylglycerol, hydroxyl-phosphatidylethanolamine, phosphatidylinositol, and an unidentified phospholipid were detected as polar lipids. The major cellular fatty acids (>10%) were iso-C16:0, iso-C16:0 2-OH, and C16:1 cis9. The resultant data indicated that strain RM579T should be classified as representative of a novel species in the genus Amycolatopsis, for which the name Amycolatopsis pithecelloba sp. nov. is proposed. The type strain is RM579T (=TBRC 1849T =NBRC 106096T).
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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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Jiang Y, Lai H, Meng C, Zheng Z, Guo Q, Xue Q, Wei X. Saccharopolyspora qinghaiensis sp. nov., a novel actinobacterium isolated from a salt lake. Antonie van Leeuwenhoek 2019; 112:1039-1046. [DOI: 10.1007/s10482-019-01237-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 01/19/2019] [Indexed: 10/27/2022]
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Song J, Qiu S, Zhao J, Han C, Wang Y, Sun X, Jiang S, Wang X, Xiang W. Pseudonocardia tritici sp. nov., a novel actinomycete isolated from rhizosphere soil of wheat (Triticum aestivum L.). Antonie van Leeuwenhoek 2018; 112:765-773. [PMID: 30536164 DOI: 10.1007/s10482-018-01210-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 12/01/2018] [Indexed: 11/29/2022]
Abstract
An aerobic, non-motile, Gram-stain positive actinomycete, designated strain NEAU-YY211T, was isolated from the rhizosphere soil of wheat (Triticum aestivum L.) collected from Zhumadian, Henan Province, mid-eastern China, and characterised taxonomically using a polyphasic approach. Comparative analysis of the 16S rRNA gene sequence indicated that strain NEAU-YY211T belongs to the genus Pseudonocardia, showing high similarities with respect to Pseudonocardia ammonioxydans H9T (99.1%) and Pseudonocardia antitumoralis SCSIO 01299T (99.0%), respectively. The cell wall was found to contain meso-diaminopimelic acid and the whole cell sugars were identified as arabinose and galactose. The predominant menaquinone of strain NEAU-YY211T was identified as MK-8(H4) and the major fatty acids were identified as iso-C16:0, C17:1ω8c and iso-C16:1. The phospholipid profile was found to consist of diphosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, phosphatidylinositol and an unidentified phospholipid. The G+C content of the genomic DNA was determined to be 72.6 mol%. Levels of DNA-DNA relatedness with P. ammonioxydans JCM 12462T and P. antitumoralis DSM 45322T were 54.5 ± 3.5% and 49.8 ± 2.5% (mean ± SD), respectively. Based on phylogenetic analysis, phenotypic and genotypic data, it is concluded that the isolate can be distinguished from closely related type strains and thus represents a novel species of the genus Pseudonocardia, for which the name Pseudonocardia tritici sp. nov. is proposed. The type strain is NEAU-YY211T (= DSM 106068T = CGMCC 4.7474T).
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Affiliation(s)
- Jia Song
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin, 150030, People's Republic of China
| | - Shiwen Qiu
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin, 150030, People's Republic of China
| | - Junwei Zhao
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin, 150030, People's Republic of China
| | - Chuanyu Han
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin, 150030, People's Republic of China
| | - Ying Wang
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin, 150030, People's Republic of China
| | - Xiujun Sun
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin, 150030, People's Republic of China
| | - Shanwen Jiang
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin, 150030, People's Republic of China
| | - Xiangjing Wang
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin, 150030, People's Republic of China.
| | - Wensheng Xiang
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin, 150030, People's Republic of China. .,State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, People's Republic of China.
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Suksaard P, Srisuk N, Duangmal K. Saccharopolyspora maritima sp. nov., an actinomycete isolated from mangrove sediment. Int J Syst Evol Microbiol 2018; 68:3022-3027. [DOI: 10.1099/ijsem.0.002941] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Paweena Suksaard
- 1Department of Science, Faculty of Science and Technology, Rajamangala University of Technology Suvarnabhumi, Phranakhon Si Ayutthaya 13000, Thailand
| | - Nantana Srisuk
- 2Department of Microbiology, Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
- 3Center for Advanced Studies in Tropical Natural Resources, NRU-KU, Kasetsart Univesity, Chatuchak, Bangkok 10900, Thailand
| | - Kannika Duangmal
- 2Department of Microbiology, Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
- 3Center for Advanced Studies in Tropical Natural Resources, NRU-KU, Kasetsart Univesity, Chatuchak, Bangkok 10900, Thailand
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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: 414] [Impact Index Per Article: 69.0] [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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15
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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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16
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Gao Y, Piao C, Wang H, Shi L, Guo X, Song J, Xiang W, Zhao J, Wang X. Pseudonocardia lutea sp. nov., a novel actinobacterium isolated from soil in Chad. Int J Syst Evol Microbiol 2018; 68:1992-1997. [DOI: 10.1099/ijsem.0.002780] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Yuhang Gao
- 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
| | - Chenyu Piao
- 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
| | - 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
| | - Xiaowei Guo
- 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
| | - Jia Song
- 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
| | - 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
| | - 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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17
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Yang ZW, Salam N, Asem MD, Fang BZ, Lan L, Xiao M, Wadaan MAM, Hozzein WN, Li WJ. Saccharopolyspora deserti sp. nov., a novel halotolerant actinobacterium isolated from a desert. Int J Syst Evol Microbiol 2018; 68:860-864. [PMID: 29458666 DOI: 10.1099/ijsem.0.002598] [Citation(s) in RCA: 10] [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
Strain SYSU D8010T was isolated from a desert sand sample collected in Saudi Arabia. The taxonomic position of the isolate was investigated by the polyphasic taxonomic approach. The isolate was found to be Gram-positive and aerobic. The strain was able to grow at 14-40 °C, pH 5.0-9.0 and in the presence of up to 22 % (w/v) NaCl. Strain SYSU D8010T contained meso-diaminopimelic acid as cell-wall diamino acid, and arabinose, fucose, galactose, glucose and rhamnose as the whole-cell sugars. The primary polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol, phosphatidylinositol and phosphatidylinositolmannosides. Menaquinone MK-9(H4) was detected as the respiratory quinone; and anteiso-C17 : 0, iso-C16 : 0, iso-C15 : 0 and iso-C17 : 0 as the predominant fatty acids. Pairwise comparison of the 16S rRNA gene sequences indicated that strain SYSU D8010T had a sequence similarity of 97.8 % to Saccharopolyspora halophila YIM 90500T. The genomic DNA G+C content of strain SYSU D8010T was determined to be 69.9 mol%. Based on the analyses of the phenotypic, genotypic and phylogenetic characteristics, strain SYSU D8010T was determined to represent a novel species of the genus Saccharopolyspora, for which the name Saccharopolyspora deserti sp. nov. is proposed. The type strain of the species is SYSU D8010T (=KCTC 39989T=CPCC 204620T).
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Affiliation(s)
- Zi-Wen Yang
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Nimaichand Salam
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Mipeshwaree Devi Asem
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Bao-Zhu Fang
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Liu Lan
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Min Xiao
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Mohammed A M Wadaan
- Bioproducts Research Chair, Zoology Department, College of Science, King Saud University, Riyadh 11451, Kingdom of Saudi Arabia
| | - Wael N Hozzein
- Bioproducts Research Chair, Zoology Department, College of Science, King Saud University, Riyadh 11451, Kingdom of Saudi Arabia.,Botany and Microbiology Department, Faculty of Science, Beni-Suef University, Beni-Suef, Egypt
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China.,Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürümqi 830011, PR China
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18
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Saccharopolyspora hattusasensis sp. nov., isolated from soil. Antonie Van Leeuwenhoek 2017; 110:1719-1727. [DOI: 10.1007/s10482-017-0921-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 07/29/2017] [Indexed: 10/19/2022]
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19
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Zhang G, Wang L, Li J, Zhou Y. Pseudonocardia profundimaris sp. nov., isolated from marine sediment. Int J Syst Evol Microbiol 2017; 67:1693-1697. [DOI: 10.1099/ijsem.0.001849] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Gaiyun Zhang
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen 361005, Fujian, PR China
| | - Lina Wang
- School of Biological Engineering, Qilu University of Technology, Jinana 250353, Shandong, PR China
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen 361005, Fujian, PR China
| | - Jinglong Li
- School of Biological Engineering, Qilu University of Technology, Jinana 250353, Shandong, PR China
| | - Yuan Zhou
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen 361005, Fujian, PR China
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Saccharopolyspora griseoalba sp. nov., a novel actinomycete isolated from the Dead Sea. Antonie van Leeuwenhoek 2016; 109:1635-1641. [PMID: 27604103 DOI: 10.1007/s10482-016-0763-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2016] [Accepted: 08/29/2016] [Indexed: 10/21/2022]
Abstract
A novel halotolerant actinomycete, designated strain AFM 10238T, was isolated from a sediment sample collected from the Dead Sea of Israel. The isolate grew at 15-45 °C, pH 6-12 and with 0-15 % (w/v) NaCl. Strain AFM 10238T contains meso-diaminopimelic acid as cell wall diamino acid, and galactose and arabinose as the whole cell sugars. The major polar lipids are phosphatidylcholine, phosphatidylglycerol, and diphosphatidylglycerol. Major fatty acids are iso-C16:0, iso-C17:0, iso-C15:0, anteiso-C17:0 and C17:1 ω8c. MK-9(H4) is the predominant menaquinone and the DNA G + C content is 72.7 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain AFM10238T belongs to the genus Saccharopolyspora. The 16S rRNA gene sequence similarity between strain AFM 10238T and its close neighbours, Saccharopolyspora halophila YIM 90500T , Saccharopolyspora spinosa DSM 44228T, Saccharopolyspora dendranthemae KLBMP 1305T and Saccharopolyspora cebuensis DSM 45019T were 98.2, 97.2, 97.1 and 97.0 %, respectively. Sequence similarities to other type strains of this genus were below 97 %. DNA-DNA relatedness data, together with phenotypic and chemotaxonomic differences, clearly distinguished the isolate from its close neighbours. On the basis of the data from this polyphasic analysis, a novel species Saccharopolyspora griseoalba sp. nov. is proposed. The type strain is AFM 10238T (= DSM 46,663 = CGMCC 4.7124).
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Amycolatopsis xuchangensis sp. nov. and Amycolatopsis jiguanensis sp. nov., isolated from soil. Antonie van Leeuwenhoek 2016; 109:1423-1431. [PMID: 27449024 DOI: 10.1007/s10482-016-0742-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Accepted: 07/18/2016] [Indexed: 10/21/2022]
Abstract
Two novel actinomycetes, designated strains CFH S0322T and CFH S01580T, were isolated from soil samples collected from Xuchang city and Ji Guan cave in Henan province, China, respectively. Their taxonomic positions were investigated by a polyphasic approach. The two isolates were Gram-reaction positive, non-motile, aerobic and catalase-positive actinomycetes. Phylogenetic analysis based on 16S rRNA gene sequence comparisons showed that the two isolates are closely related to the members of the genus Amycolatopsis, sharing high similarities with Amycolatopsis magusensis KCTC 29056T (99.1 %, CFH S0322T) and Amycolatopsis nigrescens DSM 44992T (98.1 %, CFH S01580T), respectively. The major whole cell sugars of strains CFH S0322T and CFH S01580T were arabinose and galactose and the predominant menaquinone was MK-9(H4). The genomic DNA G+C contents of strains CFH S0322T and CFH S01580T were 70.6 and 68.6 mol%, respectively. Morphological, phylogenetic and chemotaxonomic results suggest that strains CFH S0322T and CFH S01580T are representatives of two new species, for which the names Amycolatopsis xuchangensis sp. nov. and Amycolatopsis jiguanensis sp. nov. are proposed. The type strains are CFH S0322T (=NBRC 110769T =KCTC 39516T) and CFH S01580T (=DSM 101526T =CCTCC AA 2015032T).
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22
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Wu H, Liu B, Pan S. Saccharopolyspora subtropica sp. nov., a thermophilic actinomycete isolated from soil of a sugar cane field. Int J Syst Evol Microbiol 2016; 66:1990-1995. [DOI: 10.1099/ijsem.0.000976] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Hao Wu
- Institute of Applied Microbiology, College of Agriculture, Guangxi University, Nanning, PR China
- College of Life Science and Technology, Guangxi University, Nanning, PR China
| | - Bin Liu
- Institute of Applied Microbiology, College of Agriculture, Guangxi University, Nanning, PR China
| | - Shangli Pan
- Institute of Applied Microbiology, College of Agriculture, Guangxi University, Nanning, PR China
- College of Life Science and Technology, Guangxi University, Nanning, PR China
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23
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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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24
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Wei X, Jiang Y, Chen X, Jiang Y, Lai H. Amycolatopsis flava sp. nov., a halophilic actinomycete isolated from Dead Sea. Antonie van Leeuwenhoek 2015; 108:879-85. [DOI: 10.1007/s10482-015-0542-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Accepted: 07/19/2015] [Indexed: 10/23/2022]
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Hamedi J, Mohammadipanah F, Panahi HKS. Biotechnological Exploitation of Actinobacterial Members. SUSTAINABLE DEVELOPMENT AND BIODIVERSITY 2015. [DOI: 10.1007/978-3-319-14595-2_3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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Lv LL, Zhang YF, Xia ZF, Zhang JJ, Zhang LL. Saccharopolyspora halotolerans sp. nov., a halophilic actinomycete isolated from a hypersaline lake. Int J Syst Evol Microbiol 2014; 64:3532-3537. [DOI: 10.1099/ijs.0.063792-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel actinomycete strain, designated TRM 45123T, was isolated from a hypersaline habitat in Xinjiang Province (40° 20′ N 90° 49′ E), north-west China. The isolate was characterized using a polyphasic approach. 16S rRNA gene sequence analysis indicated that strain TRM 45123T belonged to the genus
Saccharopolyspora
and was closely related to
Saccharopolyspora gloriosae
(96.7 % similarity). The G+C content of the DNA was 69.07 mol%. The isolate contained meso-diaminopimelic acid as the diagnostic diamino acid, and arabinose and ribose as the major whole-cell sugars. The diagnostic phospholipids were phosphatidylethanolamine, phosphatidylcholine and phosphatidylglycerol. The predominant menaquinone was MK-9(H4). The major fatty acids were iso-C16 : 0, anteiso-C17 : 0, iso-C15 : 0 and anteiso-C15 : 0. On the basis of the evidence from this polyphasic study, a novel species, Saccharopolyspora
halotolerans sp. nov., is proposed. The type strain of Saccharopolyspora
halotolerans is TRM 45123T ( = CCTCC AA 2013006T = DSM 45990T).
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Affiliation(s)
- Ling-Ling Lv
- Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin of Xinjiang Production & Construction Corps, Tarim University, Alar 843300, PR China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Yue-Feng Zhang
- College of Life Science, Tarim University, Alar 843300, PR China
- Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin of Xinjiang Production & Construction Corps, Tarim University, Alar 843300, PR China
| | - Zhan-Feng Xia
- College of Life Science, Tarim University, Alar 843300, PR China
- Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin of Xinjiang Production & Construction Corps, Tarim University, Alar 843300, PR China
| | - Jing-Jing Zhang
- College of Life Science, Tarim University, Alar 843300, PR China
| | - Li-Li Zhang
- College of Life Science, Tarim University, Alar 843300, PR China
- Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin of Xinjiang Production & Construction Corps, Tarim University, Alar 843300, PR China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
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Vaddavalli R, Peddi S, Kothagauni SY, Begum Z, Gaddam B, Periketi M, Linga VR. Saccharopolyspora indica sp. nov., an actinomycete isolated from the rhizosphere of Callistemon citrinus (Curtis). Int J Syst Evol Microbiol 2014; 64:1559-1565. [DOI: 10.1099/ijs.0.057539-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel actinomycete strain, designated VRC122T, was isolated from a Callistemon citrinus rhizosphere sample collected from New Delhi, India, and its taxonomic status was determined by using a polyphasic approach. Strain VRC122T was a Gram-stain-positive, aerobic, non-motile, non-acid–alcohol-fast strain. Phylogenetic analysis based on 16S rRNA gene sequences showed the strain was placed in a well-separated sub-branch within the genus
Saccharopolyspora
. The highest levels of 16S rRNA gene sequence similarity were found with
Saccharopolyspora hirsuta subsp. kobensis
JCM 9109T (98.71 %),
Saccharopolyspora antimicrobica
I05-00074T (98.69 %) and
Saccharopolyspora jiangxiensis
W12T (98.66 %); 16S rRNA gene sequence similarities with type strains of all other species of the genus
Saccharopolyspora
were below 98 %. Chemosystematic studies revealed that it contained meso-diaminopimelic acid. Arabinose and galactose were the predominant whole-cell sugars. Diagnostic polar lipids were diphosphatidylglycerol, phosphatidylinositol and phosphatidylcholine. MK-9(H6) was the predominant menaquinone. C14 : 0, C16 : 0, iso-C15 : 0, iso-C16 : 0, iso-C17 : 0, anteiso-C15 : 0, anteiso-C17 : 0, C17 : 0 cyclo and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) were the major cellular fatty acids. The G+C content of the genomic DNA was 69.5 mol%. The results of DNA–DNA hybridization (30 %, 22 % and 25 %, respectively) with type strains of the above-mentioned species, in combination with differences in physiological and biochemical data supported that strain VRC122T represents a novel species of the genus
Saccharopolyspora
, for which the name Saccharopolyspora indica sp. nov., is proposed. The type strain is VRC122T ( = KCTC 29208T = MTCC 11564T = MCC 2206T = ATCC BAA-2551T).
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Affiliation(s)
- Radha Vaddavalli
- Department of Botany, Osmania University, Hyderabad-500007, Andhra Pradesh, India
| | - Sneha Peddi
- Department of pharmacy, Aditya Pharmaceutical College, Kakinada-533437, India
| | | | - Zareena Begum
- Center for Cellular and Molecular Biology, Uppal Road, Hyderabad-500007, Andhra Pradesh, India
| | | | | | - Venkateswar Rao Linga
- Department of Microbiology, Osmania University, Hyderabad-500007, Andhra Pradesh, India
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28
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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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Saccharopolyspora ghardaiensis sp. nov., an extremely halophilic actinomycete isolated from Algerian Saharan soil. J Antibiot (Tokyo) 2013; 67:299-303. [PMID: 24346634 DOI: 10.1038/ja.2013.136] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Revised: 10/23/2013] [Accepted: 11/15/2013] [Indexed: 11/08/2022]
Abstract
A novel halophilic actinomycete, strain designated H53(T), was isolated from a Saharan soil sample collected from Chaâbet Ntissa, Béni-isguen, Ghardaïa (South of Algeria) and was characterized taxonomically by means of polyphasic approach. Optimal growth was found to occur at 30-35 °C, pH 6-7 and in the presence of 15-25% (w/v) NaCl. The strain was observed to produce abundant aerial mycelium, which formed long chains of rod-shaped spores at maturity, and well developed and fragmented substrate mycelium. The cell wall was determined to contain meso-diaminopimelic acid; the diagnostic whole-cell sugars were arabinose and galactose. The predominant menaquinones were found to be MK-9(H₄) and MK-9(H₆). The predominant cellular fatty acids were determined to be iso- and anteiso-C17:0, iso-C15:0, and cis9 iso-C17:1. The diagnostic phospholipid detected was phosphatidylcholine. The morphological and chemotaxonomic characteristics of the strain were consistent with those of members of the genus Saccharopolyspora. Phylogenetic analyses on the basis of the 16S ribosomal RNA (rRNA) gene sequence showed that this strain formed a distinct phyletic line within the radiation of the genus Saccharopolyspora. The 16S rRNA sequence similarities between strain H53(T) and other members of the genus Saccharopolyspora ranged from 92.1 to 94.3%. The DNA G+C content of strain H53(T) was 72.6%. The genotypic and phenotypic data showed that the strain H53(T) represents a novel species of the genus Saccharopolyspora, for which the name Saccharopolyspora ghardaiensis sp. nov. is proposed, with the type strain H53(T) (=DSM 45606(T)=CCUG 63370(T)=CECT 8304(T)).
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Tatar D, Sazak A, Guven K, Cetin D, Sahin N. Amycolatopsis
cihanbeyliensis sp. nov., a halotolerant actinomycete isolated from a salt mine. Int J Syst Evol Microbiol 2013; 63:3739-3743. [DOI: 10.1099/ijs.0.050963-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel halotolerant actinomycete, designated strain BNT52T, was isolated from soil collected from Cihanbeyli Salt Mine in the central Anatolia region of Turkey, and examined using a polyphasic taxonomic approach. The isolate was found to have chemical and morphological properties typical of the genus
Amycolatopsis
and formed a distinct phyletic line in the 16S rRNA gene tree. Strain BNT52T was most closely related to
Amycolatopsis nigrescens
CSC17Ta-90T (96.7 %),
Amycolatopsis magusensis
KT2025T (96.6 %),
Amycolatopsis sulphurea
DSM 46092T (96.6 %),
Amycolatopsis dongchuanensis
YIM 75904T (96.5 %),
Amycolatopsis ultiminotia
RP-AC36T (96.4 %) and
Amycolatopsis sacchari
DSM 44468T (96.4 %). Sequence similarities with other strains of species of the genus
Amycolatopsis
were lower than 96.2 %. The isolate grew at 20–37 °C, pH 6–12 and in the presence of 0–10 % (w/v) NaCl. The cell wall of the novel strain contained meso-diaminopimelic acid and arabinose and galactose as the diagnostic sugars. Major fatty acids were iso-C16 : 0 2-OH and iso-C16 : 0. The predominant menaquinone was MK-9(H4). The polar lipids detected were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylmethylethanolamine. The genomic DNA G+C content was 68.8 mol%. On the basis of the data from this polyphasic taxonomic study, strain BNT52T represents a novel species within the genus
Amycolatopsis
for which the name
Amycolatopsis
cihanbeyliensis sp. nov. is proposed (type strain BNT52T = KCTC 29065T = NRRL B-24886T = DSM 45679T).
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Affiliation(s)
- Demet Tatar
- 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
| | - Kiymet Guven
- Anadolu University, Faculty of Science, Biology Department, 26470 Eskişehir, Turkey
| | - Demet Cetin
- Science Teaching Programme, Gazi Faculty of Education, Gazi University, Ankara, Turkey
| | - Nevzat Sahin
- Department of Biology, Faculty of Art and Science, Ondokuz Mayis University, 55139 Kurupelit-Samsun, Turkey
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Saccharopolyspora cavernae sp. nov., a novel actinomycete isolated from the Swallow Cave in Yunnan, south-west China. Antonie van Leeuwenhoek 2013; 104:837-43. [DOI: 10.1007/s10482-013-9996-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Accepted: 08/05/2013] [Indexed: 11/28/2022]
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Pseudonocardia antitumoralis sp. nov., a deoxynyboquinone-producing actinomycete isolated from a deep-sea sediment. Int J Syst Evol Microbiol 2013; 63:893-899. [DOI: 10.1099/ijs.0.037135-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An aerobic actinomycete, designated SCSIO 01299T, was isolated from a deep-sea sediment collected from the northern South China Sea at a depth of 3258 m. The isolate was found to be a natural producer of the synthesized antitumour agent deoxynyboquinone and its three new derivatives, pseudonocardians A, B and C. A blast search based on almost-complete 16S rRNA gene sequences showed that strain SCSIO 01299T had high sequence similarities with members of the genus
Pseudonocardia
. The 16S rRNA gene sequence phylogenetic tree revealed that strain SCSIO 01299T was a member of the genus
Pseudonocardia
. Phenotypic analysis, chemotaxonomy and DNA–DNA relatedness could readily distinguish the isolate from established members in this genus. It was concluded that strain SCSIO 01299T represents a novel species, for which the name Pseudonocardia antitumoralis sp. nov. is proposed. The type strain is SCSIO 01299T ( = DSM 45322T = CCTCC M 2011255T).
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Kaewkla O, Franco CMM. Rational approaches to improving the isolation of endophytic actinobacteria from Australian native trees. MICROBIAL ECOLOGY 2013; 65:384-393. [PMID: 22976339 DOI: 10.1007/s00248-012-0113-z] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2012] [Accepted: 08/14/2012] [Indexed: 06/01/2023]
Abstract
In recent years, new actinobacterial species have been isolated as endophytes of plants and shrubs and are sought after both for their role as potential producers of new drug candidates for the pharmaceutical industry and as biocontrol inoculants for sustainable agriculture. Molecular-based approaches to the study of microbial ecology generally reveal a broader microbial diversity than can be obtained by cultivation methods. This study aimed to improve the success of isolating individual members of the actinobacterial population as pure cultures as well as improving the ability to characterise the large numbers obtained in pure culture. To achieve this objective, our study successfully employed rational and holistic approaches including the use of isolation media with low concentrations of nutrients normally available to the microorganism in the plant, plating larger quantities of plant sample, incubating isolation plates for up to 16 weeks, excising colonies when they are visible and choosing Australian endemic trees as the source of the actinobacteria. A hierarchy of polyphasic methods based on culture morphology, amplified 16S rRNA gene restriction analysis and limited sequencing was used to classify all 576 actinobacterial isolates from leaf, stem and root samples of two eucalypts: a Grey Box and Red Gum, a native apricot tree and a native pine tree. The classification revealed that, in addition to 413 Streptomyces spp., isolates belonged to 16 other actinobacterial genera: Actinomadura (two strains), Actinomycetospora (six), Actinopolymorpha (two), Amycolatopsis (six), Gordonia (one), Kribbella (25), Micromonospora (six), Nocardia (ten), Nocardioides (11), Nocardiopsis (one), Nonomuraea (one), Polymorphospora (two), Promicromonospora (51), Pseudonocardia (36), Williamsia (two) and a novel genus Flindersiella (one). In order to prove novelty, 12 strains were characterised fully to the species level based on polyphasic taxonomy. One strain represented a novel genus in the family Nocardioides, and the other 11 strains were accepted as novel species. In summary, the holistic isolation strategies were successful in obtaining significant culturable actinobacterial diversity within Australian native trees that includes rare and novel species.
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Affiliation(s)
- Onuma Kaewkla
- Department of Medical Biotechnology, School of Medicine, Flinders University, Bedford Park, Adelaide, South Australia, Australia
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34
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Nie GX, Ming H, Li S, Zhou EM, Cheng J, Tang X, Feng HG, Tang SK, Li WJ. Amycolatopsis dongchuanensis sp. nov., an actinobacterium isolated from soil. Int J Syst Evol Microbiol 2012; 62:2650-2656. [DOI: 10.1099/ijs.0.038125-0] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel actinomycete strain, designated YIM 75904T, was isolated from a soil sample that had been collected from a dry and hot river valley in Dongchuan county, Yunnan province, south-western China. The taxonomic position of the novel strain was investigated by a polyphasic approach. In phylogenetic analyses based on 16S rRNA gene sequences, strain YIM 75904T formed a distinct clade within the genus
Amycolatopsis
and appeared to be closely related to
Amycolatopsis sacchari
K24T (99.3 % sequence similarity). Strain YIM 75904T had a type-IV cell wall, with no detectable mycolic acids, and had MK-9(H4) as its predominant menaquonine. Its cell wall contained meso-diaminopimelic acid, galactose, glucose and arabinose, and its major cellular fatty acids were iso-C16 : 0, iso-C15 : 0, anteiso-C17 : 0 and anteiso-C15 : 0. The genomic DNA G+C content of the novel strain was 68.5 mol%. Based on the results of physiological and biochemical tests and DNA–DNA hybridizations, strain YIM 75904T represents a novel species of the genus
Amycolatopsis
for which the name Amycolatopsis dongchuanensis sp. nov. is proposed. The type strain is YIM 75904T ( = CCTCC AA 2011016T = JCM 18054T).
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Affiliation(s)
- Guo-Xing Nie
- College of Life Sciences, Henan Normal University, Xinxiang 453007, PR China
| | - Hong Ming
- Department of Life Sciences and Technology, Xinxiang Medical University, Xinxiang 453003, PR China
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education and Laboratory for Conservation and Utilization of Bio-resources, Yunnan Institute of Microbiology, Yunnan University, Kunming 650091, PR China
| | - Shuai Li
- College of Life Sciences, Henan Normal University, Xinxiang 453007, PR China
| | - En-Min Zhou
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education and Laboratory for Conservation and Utilization of Bio-resources, Yunnan Institute of Microbiology, Yunnan University, Kunming 650091, PR China
| | - Juan Cheng
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education and Laboratory for Conservation and Utilization of Bio-resources, Yunnan Institute of Microbiology, Yunnan University, Kunming 650091, PR China
| | - Xia Tang
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education and Laboratory for Conservation and Utilization of Bio-resources, Yunnan Institute of Microbiology, Yunnan University, Kunming 650091, PR China
| | - Hui-Gen Feng
- Department of Life Sciences and Technology, Xinxiang Medical University, Xinxiang 453003, PR China
| | - Shu-Kun Tang
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education and Laboratory for Conservation and Utilization of Bio-resources, Yunnan Institute of Microbiology, Yunnan University, Kunming 650091, PR China
| | - Wen-Jun Li
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education and Laboratory for Conservation and Utilization of Bio-resources, Yunnan Institute of Microbiology, Yunnan University, Kunming 650091, PR China
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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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36
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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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Pseudonocardia antimicrobica sp. nov., a novel endophytic actinomycete associated with Artemisia annua L. (sweet wormwood). J Antibiot (Tokyo) 2012; 65:469-72. [DOI: 10.1038/ja.2012.56] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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38
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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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Xing K, Qin S, Bian GK, Zhang YJ, Zhang WD, Dai CC, Liu CH, Li WJ, Jiang JH. Pseudonocardia nantongensis sp. nov., a novel endophytic actinomycete isolated from the coastal halophyte Tamarix chinensis Lour. Antonie van Leeuwenhoek 2012; 102:659-67. [DOI: 10.1007/s10482-012-9764-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Accepted: 06/13/2012] [Indexed: 11/30/2022]
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Nie GX, Ming H, Wei DQ, Zhou EM, Tang X, Cheng J, Tang SK, Li WJ. Pseudonocardia yuanmoensis sp. nov., a novel actinobacterium isolated from soil in Yunnan, south-west China. Antonie van Leeuwenhoek 2011; 101:753-60. [DOI: 10.1007/s10482-011-9689-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2011] [Accepted: 12/13/2011] [Indexed: 10/14/2022]
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Zhao GZ, Li J, Zhu WY, Wei DQ, Zhang JL, Xu LH, Li WJ. Pseudonocardia xishanensis sp. nov., an endophytic actinomycete isolated from the roots of Artemisia annua L. Int J Syst Evol Microbiol 2011; 62:2395-2399. [PMID: 22140165 DOI: 10.1099/ijs.0.037028-0] [Citation(s) in RCA: 20] [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 Gram-positive, non-motile, endophytic actinomycete, designated strain YIM 63638(T), was isolated from the surface-sterilized roots of Artemisia annua L. The isolate grew optimally with 1-3 % (w/v) NaCl, at pH 6.0-7.0 and at 20-37 °C. Comparative analysis of the 16S rRNA gene sequence showed that the isolate belonged to the genus Pseudonocardia and showed highest sequence similarity with Pseudonocardia oroxyli D10(T) (98.9 %), Pseudonocardia ailaonensis YIM 45505(T) (98.3 %) and Pseudonocardia halophobica IMSNU 21327(T) (98.0 %). Phylogenetic distance from other type strains of species with validly published names within the genus Pseudonocardia was greater than 2.3 %. Strain YIM 63638(T) had a genomic DNA G+C content of 72.1 mol% and MK-8(H(4)) as the predominant respiratory quinone. The major fatty acids were iso-C(16 : 0) (36.32 %) and 10-methyl-C(16 : 0) (19.78 %). On the basis of phenotypic properties and phylogenetic distinctiveness, strain YIM 63638(T) represents a novel species of the genus Pseudonocardia, for which the name Pseudonocardia xishanensis sp. nov. is proposed. The type strain is YIM 63638(T) ( = JCM 17906(T) = KCTC 29005(T)).
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Affiliation(s)
- Guo-Zhen Zhao
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming 650091, PR China
| | - Jie Li
- 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, PR China
| | - Wen-Yong Zhu
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming 650091, PR China
| | - Da-Qiao Wei
- Faculty of Environmental Science and Engineering and Life science and Technology of Kunming University of Science and Technology 650500, Kunming 650224, PR China
| | - Jin-Li Zhang
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming 650091, PR China
| | - Li-Hua Xu
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming 650091, PR China
| | - Wen-Jun Li
- Key Laboratory of Biogeography and Bioresource in Arid Land, Chinese Academy of Science, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürmqui 830011, PR China.,Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming 650091, PR China
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Sinma K, Ishida Y, Tamura T, Kitpreechavanich V, Tokuyama S. Saccharopolyspora pathumthaniensis sp. nov., a novel actinomycetes isolated from termite guts (Speculitermes sp.). J GEN APPL MICROBIOL 2011; 57:93-100. [PMID: 21606610 DOI: 10.2323/jgam.57.93] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Morphological and chemotaxonomic characterization of actinomycete strain S582 isolated from the gut of a termite (Speculitermes sp.) in Pathum Thani Province, Thailand, clearly demonstrated that this strain is a member of the genus Saccharopolyspora. 16S rDNA sequence analysis for the strain supported the assignment of the strain to the genus Saccharopolyspora. The similarity value of sequences between this strain and the closely related species Saccharopolyspora endophytica was 99.5%. The DNA G+C content was 70.2 mol%. DNA-DNA hybridization results (53.3%) and some physiological and biochemical properties indicated that strain S582(T) was distinguished from the phylogenetically closest relatives. Based on these genotypic and phenotypic data, strain S582(T) should be a new species in the genus Saccharopolyspora and the name Saccharopolyspora pathumthaniensis sp. nov. is proposed for the strain. The type strain is S582(T) (=NBRC 104112(T) =BCC 28624(T)).
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Affiliation(s)
- Kanokkorn Sinma
- Department of Applied Biological Chemistry, Faculty of Agriculture, Shizuoka University, Japan
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Pseudonocardia serianimatus sp. nov., a novel actinomycete isolated from the surface-sterilized leaves of Artemisia annua L. Antonie van Leeuwenhoek 2011; 100:521-8. [DOI: 10.1007/s10482-011-9607-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2011] [Accepted: 06/06/2011] [Indexed: 11/26/2022]
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Zhao GZ, Li J, Huang HY, Zhu WY, Zhao LX, Tang SK, Xu LH, Li WJ. Pseudonocardia artemisiae sp. nov., isolated from surface-sterilized Artemisia annua L. Int J Syst Evol Microbiol 2011; 61:1061-1065. [DOI: 10.1099/ijs.0.021931-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel actinomycete strain, designated YIM 63587T, was isolated from surface-sterilized roots of Artemisia annua L. collected from Yunnan province, south-west China. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain YIM 63587T was affiliated to the genus Pseudonocardia. 16S rRNA gene sequence similarities between strain YIM 63587T and type strains of species of the genus Pseudonocardia were 96.6–93.8 %. The diagnostic cell-wall diamino acid in the peptidoglycan layer of strain YIM 63587T was meso-diaminopimelic acid and the whole-cell sugars were arabinose, galactose, mannose and ribose. The predominant menaquinone was MK-8(H4) (97.7 %). The phospholipids were diphosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, phosphatidylinositol mannosides, phosphatidylinositol and an unknown phospholipid. The major cellular fatty acids (>5 %) were iso-C16 : 0 (44.7 %), iso-C14 : 0 (10.3 %), iso-C16 : 1 H (9.8 %) and iso-C15 : 0 (7.7 %). The G+C content of the genomic DNA was 68.2 mol%. On the basis of phylogenetic, physiological and chemotaxonomic data, strain YIM 63587T represents a novel species of the genus Pseudonocardia, for which the name Pseudonocardia artemisiae sp. nov. is proposed. The type strain is YIM 63587T ( = DSM 45313T = CCTCC AA 208081T).
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Affiliation(s)
- Guo-Zhen Zhao
- The Key Laboratory for Microbial Resources of the Ministry of Education and Laboratory for Conservation and Utilization of Bio-resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan, 650091, PR China
| | - Jie Li
- The Key Laboratory for Microbial Resources of the Ministry of Education and Laboratory for Conservation and Utilization of Bio-resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan, 650091, PR China
| | - Hai-Yu Huang
- The Key Laboratory for Microbial Resources of the Ministry of Education and Laboratory for Conservation and Utilization of Bio-resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan, 650091, PR China
| | - Wen-Yong Zhu
- The Key Laboratory for Microbial Resources of the Ministry of Education and Laboratory for Conservation and Utilization of Bio-resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan, 650091, PR China
| | - Li-Xing Zhao
- The Key Laboratory for Microbial Resources of the Ministry of Education and Laboratory for Conservation and Utilization of Bio-resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan, 650091, PR China
| | - Shu-Kun Tang
- The Key Laboratory for Microbial Resources of the Ministry of Education and Laboratory for Conservation and Utilization of Bio-resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan, 650091, PR China
| | - Li-Hua Xu
- The Key Laboratory for Microbial Resources of the Ministry of Education and Laboratory for Conservation and Utilization of Bio-resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan, 650091, PR China
| | - Wen-Jun Li
- The Key Laboratory for Microbial Resources of the Ministry of Education and Laboratory for Conservation and Utilization of Bio-resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan, 650091, PR China
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Guan TW, Wu N, Xia ZF, Ruan JS, Zhang XP, Huang Y, Zhang LL. Saccharopolyspora lacisalsi sp. nov., a novel halophilic actinomycete isolated from a salt lake in Xinjiang, China. Extremophiles 2011; 15:373-8. [DOI: 10.1007/s00792-011-0369-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2011] [Accepted: 03/14/2011] [Indexed: 11/30/2022]
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Pseudonocardia mongoliensis sp. nov. and Pseudonocardia khuvsgulensis sp. nov., isolated from soil. Int J Syst Evol Microbiol 2011; 61:747-756. [DOI: 10.1099/ijs.0.019562-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two actinomycetes, designated MN08-A0270T and MN08-A0297T, were isolated from soil from the area around Khuvsgul Lake, Khuvsgul province, Mongolia, and subjected to phenotypic and genotypic characterization. They produced well-developed, branched substrate hyphae and, similar to closely related species of the genus Pseudonocardia, produced zigzag-shaped aerial hyphae by acropetal budding and blastospores. A comparative analysis of 16S rRNA gene sequences indicated that strains MN08-A0270T and MN08-A0297T formed two distinct clades within the genus Pseudonocardia and were respectively most closely related to Pseudonocardia yunnanensis NBRC 15681T (97.3 % similarity) and Pseudonocardia thermophila IMSNU 20112T (97.1 %). Chemotaxonomic characteristics, including cell-wall diaminopimelic acid, whole-cell sugars, fatty acid components and major menaquinones, suggested that the two organisms belonged to the genus Pseudonocardia. Strains MN08-A0270T and MN08-A0297T could be differentiated from each other and from closely related species of the genus Pseudonocardia by physiological and biochemical characteristics, predominant fatty acids, menaquinones and whole-cell sugar components. Combined with the results of a broad range of phenotypic tests and DNA–DNA hybridization data and phylogenetic analysis, these results support the conclusion that these strains represent two novel species of the genus Pseudonocardia, for which we propose the names Pseudonocardia mongoliensis sp. nov. (type strain MN08-A0270T = NBRC 105885T = VTCC D9-25T) and Pseudonocardia khuvsgulensis sp. nov. (type strain MN08-A0297T = NBRC 105886T = VTCC D9-26T).
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Kaewkla O, Franco CMM. Pseudonocardia eucalypti sp. nov., an endophytic actinobacterium with a unique knobby spore surface, isolated from roots of a native Australian eucalyptus tree. Int J Syst Evol Microbiol 2011; 61:742-746. [DOI: 10.1099/ijs.0.022327-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel strain, designated EUM 374T, was isolated from the root of a native Australian eucalyptus tree, Eucalyptus microcarpa, and subjected to a range of morphological, phylogenetic and chemotaxonomic analyses. The strain was Gram-reaction-positive with well-developed aerial mycelia, which fragmented into rod-shaped spores that had unique knobby protrusions on the spore surface. Substrate mycelia were not present in the media used. Strain EUM 374T grew as a film on the surface of static liquid culture medium but did not grow under shaking conditions. Phylogenetic evaluation based on 16S rRNA gene sequences identified the new isolate as belonging to the family Pseudonocardiaceae with sequence similarities of 96.1 and 96.3 % to Pseudonocardia acaciae GMKU095T and Pseudonocardia spinosispora LM 141T, respectively, and 93–96 % sequence similarity to other members of the genus Pseudonocardia. The results of comprehensive phylogenetic analyses, including physiological and biochemical tests, differentiated strain EUM 374T from related members of the genus Pseudonocardia. Based on the phenotypic, phylogenetic and chemotaxonomic evidence, strain EUM 374T represents a novel species of the genus Pseudonocardia, for which the name Pseudonocardia eucalypti sp. nov. is proposed. The type strain is EUM 374T ( = DSM 45351T = ACM 5285T).
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Affiliation(s)
- Onuma Kaewkla
- Department of Medical Biotechnology, Flinders University, Bedford Park, Australia
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Pseudonocardia bannaensis sp. nov., a novel actinomycete isolated from the surface-sterilized roots of Artemisia annua L. Antonie van Leeuwenhoek 2011; 100:35-42. [DOI: 10.1007/s10482-011-9562-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2010] [Accepted: 02/04/2011] [Indexed: 10/18/2022]
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Kaewkla O, Franco CMM. Pseudonocardia adelaidensis sp. nov., an endophytic actinobacterium isolated from the surface-sterilized stem of a grey box tree (Eucalyptus microcarpa). Int J Syst Evol Microbiol 2010; 60:2818-2822. [DOI: 10.1099/ijs.0.019208-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An aerobic, actinobacterial strain with rod-shaped spores, EUM 221T, which was isolated from the surface-sterilized stem of a grey box tree (Eucalyptus microcarpa), is described. Phylogenetic evaluation based on 16S rRNA gene sequence similarity showed that this isolate belongs to the family Pseudonocardiaceae, with the closest neighbour being Pseudonocardia zijingensis 6330T (98.7 %). The level of 16S rRNA gene sequence similarity between the isolate and species of the genus Pseudonocardia with validly published names ranged from 95 to 98 %. Chemotaxonomic data (meso-diaminopimelic acid; major menaquinone MK-8(H4); major fatty acid iso-C16 : 0) confirmed the affiliation of strain EUM 221T to the genus Pseudonocardia. The results of the phylogenetic analysis, including physiological and biochemical studies in combination with DNA–DNA hybridization, allowed the genotypic and phenotypic differentiation of strain EUM 221T from the closest described species. Therefore, this strain represented a novel species and the name proposed is Pseudonocardia adelaidensis sp. nov. The type strain is EUM 221T (=DSM 45352T =ACM 5286T).
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Affiliation(s)
- Onuma Kaewkla
- Department of Medical Biotechnology, School of Medicine, Flinders University, Bedford Park, South Australia 5042, Australia
| | - Christopher M. M. Franco
- Department of Medical Biotechnology, School of Medicine, Flinders University, Bedford Park, South Australia 5042, Australia
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Qin S, Zhu WY, Jiang JH, Klenk HP, Li J, Zhao GZ, Xu LH, Li WJ. Pseudonocardia tropica sp. nov., an endophytic actinomycete isolated from the stem of Maytenus austroyunnanensis. Int J Syst Evol Microbiol 2010; 60:2524-2528. [DOI: 10.1099/ijs.0.020099-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel strain, designated YIM 61452T, was isolated from the stem of Maytenus austroyunnanensis collected from the tropical rainforest of Xishuangbanna, Yunnan Province, south-west China. The strain was characterized taxonomically by using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain YIM 61452T belonged to the genus Pseudonocardia and was most closely related to Pseudonocardia alni IMSNU 20049T (99.5 %), Pseudonocardia antarctica DVS 5a1T (99.5 %) and Pseudonocardia carboxydivorans Y8T (99.4 %). The chemotaxonomic properties of strain YIM 61452T, for example MK-8(H4) as the predominant quinone system and iso-C16 : 0 and iso-C16 : 1 H as the major fatty acids, were also consistent with its classification within the genus Pseudonocardia. Strain YIM 61452T could be differentiated from closely related species of the genus Pseudonocardia by phenotypic and genotypic analysis. DNA–DNA hybridization experiments between strain YIM 61452T and closely related reference strains further confirmed that strain YIM 61452T represented a novel taxon of the genus Pseudonocardia. Therefore, strain YIM 61452T represents a novel species, for which the name Pseudonocardia tropica sp. nov. is proposed. The type strain is YIM 61452T (=DSM 45199T=CCTCC AA 208018T).
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Affiliation(s)
- Sheng Qin
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, Xuzhou Normal University, Xuzhou, Jiangsu, 221116, PR China
- The Key Laboratory for Microbial Resources of the Ministry of Education and Laboratory for Conservation and Utilization of Bio-resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan, 650091, PR China
| | - Wen-Yong Zhu
- The Key Laboratory for Microbial Resources of the Ministry of Education and Laboratory for Conservation and Utilization of Bio-resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan, 650091, PR China
| | - Ji-Hong Jiang
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, Xuzhou Normal University, Xuzhou, Jiangsu, 221116, PR China
| | - Hans-Peter Klenk
- DSMZ – Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Inhoffenstraße 7B, D-38124 Braunschweig, Germany
| | - Jie Li
- The Key Laboratory for Microbial Resources of the Ministry of Education and Laboratory for Conservation and Utilization of Bio-resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan, 650091, PR China
| | - Guo-Zhen Zhao
- The Key Laboratory for Microbial Resources of the Ministry of Education and Laboratory for Conservation and Utilization of Bio-resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan, 650091, PR China
| | - Li-Hua Xu
- The Key Laboratory for Microbial Resources of the Ministry of Education and Laboratory for Conservation and Utilization of Bio-resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan, 650091, PR China
| | - Wen-Jun Li
- The Key Laboratory for Microbial Resources of the Ministry of Education and Laboratory for Conservation and Utilization of Bio-resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan, 650091, PR China
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