1
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Wagh VS, Ram H, Dastager SG. Priestia veravalensis sp. nov., isolated from coastal sample. Arch Microbiol 2021; 203:4839-4845. [PMID: 34226954 DOI: 10.1007/s00203-021-02418-z] [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: 04/02/2021] [Revised: 05/28/2021] [Accepted: 05/31/2021] [Indexed: 11/28/2022]
Abstract
The taxonomic position of two isolates, SGD-V-76T and SGD-M-37, isolated from sediment sample of Veraval coast, India, was examined using the polyphasic taxonomic approach. The morphological and chemotaxonomic characteristics of these two organisms are typical of the genus Priestia. The phylogenetic analyses performed using almost complete 16S rRNA gene sequences demonstrated that the isolate belongs to the Bacillaceae family, and forms a clade within the cluster containing Priestia flexus MTCC 2909T, Priestia aryabhattai B8W22T and Priestia megaterium KCTC 3007T and both strains showed highest similarity of > 98% with 3-29 nucleotide differences. The cell wall contained meso-diaminopimelic acid as the diagnostic diamino acid. The predominant isoprenoid quinone was MK-7 and the G + C content of strains was 37.5-37.7 mol%. However, the DNA-DNA hybridization and the phenotypic characteristics revealed that, the strain SGD-V-76T and strain SGD-M-37 are similar species but different from any known Priestia species with ANI values of 79.2, 79.3 and 79.2 and the dDDH values of 17.7, 17.8 and 18.0% respectively. On the basis of phenotypic characteristics, phylogenetic analysis and the results of biochemical and physiological tests, and genomic data strain SGD-V-76T was clearly distinguished from closely related members of the Priestia genus. Based on the above data analysis strain SGD-V-76T (= DSM28242T = KCTC33802T = CIP111056T = NCIM5510T) represents a novel species of the genus Priestia, and we propose the name Priestia veravalensis sp. nov.
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Affiliation(s)
- Vasudev S Wagh
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.,National Collection of Industrial Microorganisms (NCIM), CSIR National Chemical Laboratory, Pune, 411008, India
| | - Hari Ram
- National Collection of Industrial Microorganisms (NCIM), CSIR National Chemical Laboratory, Pune, 411008, India
| | - Syed G Dastager
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India. .,National Collection of Industrial Microorganisms (NCIM), CSIR National Chemical Laboratory, Pune, 411008, India.
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2
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Asha K, Bhadury P. Myceligenerans indicum sp. nov., an actinobacterium isolated from mangrove sediment of Sundarbans, India. Arch Microbiol 2021; 203:1577-1585. [PMID: 33399896 DOI: 10.1007/s00203-020-02150-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 11/15/2020] [Accepted: 12/03/2020] [Indexed: 11/28/2022]
Abstract
A new actinobacterial species of the genus Myceligenerans has been isolated from the intertidal sediment of Indian Sundarbans mangrove ecosystem. The isolate has been characterized based on polyphasic approaches. The isolate exhibit well-developed substrate mycelia along with the presence of cocci- and rod-shaped elements. The organism can grow across a wide range of temperature, salinity, and pH as well as on different carbon sources. Phylogenetic analyses based on 16S rRNA showed that this isolate is closely related to Myceligenerans salitolerans XHU 5031 (99% identity; 100% coverage). Presence of ketosynthase domain representing polyketide synthases in the isolate provides evidence of its potential ability to produce secondary metabolites. Multigene phylogeny based on atpD and rpoB gene sequences confirmed it as a new species within the family Promicromonosporaceae (Phylum Actinobacteria). The DNA G + C content of the isolate has been determined as 72 mol%. The peptidoglycan type was A4α and the whole-cell hydrolysates contained glucose, galactose, and mannose. The polar lipids were represented by diphosphatidylglycerol, one unknown phospholipid and one unknown glycolipid. Major fatty acids present in the isolate are anteiso-C15, iso-C15, iso-C16, and anteiso-C17. Whole-genome sequence indicates the size of genome is ~ 5 Mbp. GGDC (%), orthoANIu (%), and AAI of I2 genome indicated 28.9%, 77.44% and 0.859 identity with the genome of Myceligenerans xiligouense strain DSM 15,700. The isolate I2 has been proposed as a new species, Myceligenerans indicum sp. nov. The genome sequence has been deposited to GenBank/ENA/DDBJ under the accession number JABBYC000000000.
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Affiliation(s)
- Kannan Asha
- Integrative Taxonomy and Microbial Ecology Research Group, Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur-741246, Nadia, West Bengal, India
| | - Punyasloke Bhadury
- Integrative Taxonomy and Microbial Ecology Research Group, Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur-741246, Nadia, West Bengal, India. .,Centre for Climate and Environmental Studies, Indian Institute of Science Education and Research Kolkata, Mohanpur-741246, Nadia, West Bengal, India.
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3
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Del Mondo A, De Natale A, Pinto G, Pollio A. Survey of relevant taxonomic groups for the design of qPCR primers and internal fluorescent probes for whole characterization of subaerial biofilm. ANN MICROBIOL 2019. [DOI: 10.1007/s13213-019-01461-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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4
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Vargas Hoyos HA, Nobre Santos S, Da Silva LJ, Paulino Silva FS, Bonaldo Genuário D, Domingues Zucchi T, Melo IS. Streptomyces rhizosphaericola sp. nov., an actinobacterium isolated from the wheat rhizosphere. Int J Syst Evol Microbiol 2019; 69:2431-2439. [PMID: 31188092 DOI: 10.1099/ijsem.0.003498] [Citation(s) in RCA: 9] [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 1AS2cT, was isolated from the wheat rhizosphere collected from the Brazilian Cerrado biome. A polyphasic approach, including phenotypic characterization and phylogenetic multilocus sequence analysis (MLSA), was used to determine the taxonomic position of this strain. Analysis of the 16S rRNA gene sequence indicated that the novel strain is closely related to Streptomyces cavourensis NBRC 13026T, Streptomyces albolongus NBRC 13465T and Streptomyces araujoniae ASBV-1T, sharing a similarity value of 98.2, 98.1 and 97.9 %, respectively. Additionally, MLSA of five housekeeping genes (atpD, gyrB, recA, rpoB and trpB) showed evolutionary distances beyond the 0.007 threshold, as well as low DNA-DNA relatedness between strain 1AS2cT and its closest phylogenetic neighbours (S. cavourensis NBRC 13026T, S. albolongus NBRC 13465T and S. araujoniae ASBV-1T: 56, 62.5 and 63.0 %, respectively), indicating a new phylogenetic lineage. The phylogenetic, chemotaxonomic and phenotypic characteristics support the assignment of strain 1AS2cT to the genus Streptomyces, representing a novel species. It is concluded that strain 1AS2cT (=CMAA 1679T=NRRL B-65479T=DSM 105299T) can be classified as the type strain of a novel species of the genus Streptomyces, for which the name Streptomyces rhizosphaericola sp. nov. is proposed.
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Affiliation(s)
- Harold Alexander Vargas Hoyos
- Laboratory of Environmental Microbiology, Embrapa Environment, Rod SP 340, KM 127,5 CEP 13820-000, Jaguariúna - SP, Brazil
| | - Suikinai Nobre Santos
- Laboratory of Environmental Microbiology, Embrapa Environment, Rod SP 340, KM 127,5 CEP 13820-000, Jaguariúna - SP, Brazil
| | - Leonardo Jose Da Silva
- Laboratory of Environmental Microbiology, Embrapa Environment, Rod SP 340, KM 127,5 CEP 13820-000, Jaguariúna - SP, Brazil
| | - Fábio Sérgio Paulino Silva
- Laboratory of Environmental Microbiology, Embrapa Environment, Rod SP 340, KM 127,5 CEP 13820-000, Jaguariúna - SP, Brazil
| | - Diego Bonaldo Genuário
- Laboratory of Environmental Microbiology, Embrapa Environment, Rod SP 340, KM 127,5 CEP 13820-000, Jaguariúna - SP, Brazil
| | - Tiago Domingues Zucchi
- Hinove Agrociência, R. Lilia Elisa Eberle Lupo, 200B, CEP 14803-886, Araraquara - SP, Brazil
| | - Itamar Soares Melo
- Laboratory of Environmental Microbiology, Embrapa Environment, Rod SP 340, KM 127,5 CEP 13820-000, Jaguariúna - SP, Brazil
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5
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Correction to: Novel qPCR probe systems for the characterization of subaerial biofilms on stone monuments. ANN MICROBIOL 2019. [DOI: 10.1007/s13213-019-01480-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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6
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Karami K, Ramezanpour A, Zakariazadeh M, Shahpiri A, Kharaziha M, Kazeminasab A. Luminescent Palladacycles Containing a Pyrene Chromophor; Synthesis, Biological and Computational Studies of the Interaction with DNA and BSA. ChemistrySelect 2019. [DOI: 10.1002/slct.201900707] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Kazem Karami
- Department of ChemistryIsfahan University of Technology Isfahan 84156/83111 Iran
| | - Azar Ramezanpour
- Department of ChemistryIsfahan University of Technology Isfahan 84156/83111 Iran
| | - Mostafa Zakariazadeh
- Research Institute for Fundamental Sciences (RIFS) University of Tabriz Tabriz Iran
| | - Azar Shahpiri
- Department of BiotechnologyCollege of AgricultureIsfahan University of Technology Isfahan Iran
| | - Mahshid Kharaziha
- Department of Materials EngineeringIsfahan Univezrsity of Technology Isfahan Iran
| | - Akram Kazeminasab
- Department of BiotechnologyCollege of AgricultureIsfahan University of Technology Isfahan Iran
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7
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de Menezes CBA, Afonso RS, de Souza WR, Parma MM, de Melo IS, Fugita FLS, Moraes LAB, Zucchi TD, Fantinatti-Garboggini F. Williamsia aurantiacus sp. nov. a novel actinobacterium producer of antimicrobial compounds isolated from the marine sponge. Arch Microbiol 2019; 201:691-698. [PMID: 30799528 DOI: 10.1007/s00203-019-01633-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 01/04/2019] [Accepted: 02/14/2019] [Indexed: 01/15/2023]
Abstract
An antibiotic-producing actinobacterium, designated isolate B375T, was isolated from marine sponge Glodia corticostylifera collected from Praia Guaecá, São Paulo, Brazil (23°49S; 45°25W), and its taxonomic position established using data from a polyphasic study. The organism showed a combination of morphological, physiological, biochemical and chemotaxonomic characteristics consistent with its classification in the genus Williamsia. Comparative 16S rRNA gene sequence analysis indicated that the strain B375T was most closely related to Williamsia serinedens DSM 45037T and Williamsia spongiae DSM 46676T and having 99.43% and 98.65% similarities, respectively, but was distinguished from these strains by a low level of DNA-DNA relatedness (53.2-63.2%) and discriminatory phenotypic properties. Chemotaxonomic investigations revealed the presence of cell-wall chemotype IV and N-glycolated muramic acid residues present in the wall cells. The cells contained C16:0 (23.3%), C18:0 10-methyl (23.2%) and C18:1 ω9c (21.6%) as the major cellular fatty acids. The strain B375T inhibited growing of Staphylococcus aureus and Colletotrichum gloeosporioides strains and was considered a producer of antimicrobial compounds. Based on the data obtained, the isolate B375T (= CBMAI 1090T = DSM 46677T) should, therefore, be classified as the type strain of a novel species of the genus Williamsia, for which the name Williamsia aurantiacus sp. nov. is proposed.
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Affiliation(s)
- Cláudia Beatriz Afonso de Menezes
- Centro Pluridisciplinar de Pesquisas Químicas Biológicas e Agrícolas, UNICAMP, Av. Alexandre Cazelatto 999, Paulínia, SP, CEP 13148-218, Brazil.,Programa de Pós-Graduação em Genética e Biologia Molecular, UNICAMP, CP 6109, Campinas, SP, 13083-970, Brazil
| | - Rafael Sanches Afonso
- Centro Pluridisciplinar de Pesquisas Químicas Biológicas e Agrícolas, UNICAMP, Av. Alexandre Cazelatto 999, Paulínia, SP, CEP 13148-218, Brazil
| | - Wallace Rafael de Souza
- Embrapa Meio Ambiente, Rodovia SP 340 Km 127.5, CP 69, Jaguariúna, SP, CEP 13820-000, Brazil
| | - Márcia Maria Parma
- Embrapa Meio Ambiente, Rodovia SP 340 Km 127.5, CP 69, Jaguariúna, SP, CEP 13820-000, Brazil
| | - Itamar Soares de Melo
- Embrapa Meio Ambiente, Rodovia SP 340 Km 127.5, CP 69, Jaguariúna, SP, CEP 13820-000, Brazil
| | - Fernando Lucas Satoru Fugita
- Departamento de Química, Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, Av. Bandeirantes,3900, Monte Alegre, Ribeirão Preto, São Paulo, 12040-901, Brazil
| | - Luiz Alberto Beraldo Moraes
- Departamento de Química, Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, Av. Bandeirantes,3900, Monte Alegre, Ribeirão Preto, São Paulo, 12040-901, Brazil
| | | | - Fabiana Fantinatti-Garboggini
- Centro Pluridisciplinar de Pesquisas Químicas Biológicas e Agrícolas, UNICAMP, Av. Alexandre Cazelatto 999, Paulínia, SP, CEP 13148-218, Brazil. .,Programa de Pós-Graduação em Genética e Biologia Molecular, UNICAMP, CP 6109, Campinas, SP, 13083-970, Brazil.
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8
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Karami K, Jamshidian N, Zakariazadeh M. Synthesis, characterization and molecular docking of newC,N-palladacycles containing pyridinium-derived ligands: DNA and BSA interaction studies and evaluation as anti-tumor agents. Appl Organomet Chem 2019. [DOI: 10.1002/aoc.4728] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Kazem Karami
- Department of Chemistry; Isfahan University of Technology; Isfahan 84156/83111 Iran
| | - Nasrin Jamshidian
- Department of Chemistry; Isfahan University of Technology; Isfahan 84156/83111 Iran
| | - Mostafa Zakariazadeh
- Research Institute for Fundamental Sciences (RIFS); University of Tabriz; Tabriz Iran
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9
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Damodharan K, Palaniyandi SA, Le B, Suh JW, Yang SH. Streptomyces sp. strain SK68, isolated from peanut rhizosphere, promotes growth and alleviates salt stress in tomato (Solanum lycopersicum cv. Micro-Tom). J Microbiol 2018; 56:753-759. [PMID: 30267318 DOI: 10.1007/s12275-018-8120-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 05/29/2018] [Accepted: 06/28/2018] [Indexed: 11/25/2022]
Abstract
A novel actinobacterium, strain SK68, was isolated from the rhizosphere of peanut plant and its salinity stress alleviation ability was studied using tomato (Solanum lycopersicum cv. Micro-Tom) plants. Based on 16S rDNA based phylogenetic analysis, strain SK68 has been identified as a Streptomyces sp. Strain SK68 had branched substrate mycelium bearing smooth surfaced spores and the spore colour is brownish grey on ISP4 medium. It exhibited enzyme activities such as xylanase, cellulase, amylase, and pectinase and degraded hypoxanthine, casein, and L-tyrosine. The strain SK68 differed in its banding pattern in BOX-PCR and RAPD fingerprinting compared to the closely matching type strains Streptomyces erythrochromogenes NBRC 3304T (AB184746), S. flavotricini NBRC 12770T (AB184132), S. racemochromogenes NBRC 12906T (AB184235), and S. polychromogenes NBRC 13072T (NR041109). Strain SK68 was evaluated for its salinity stress-alleviating activity in tomato plants with 180 mmol/L NaCl under gnotobiotic condition. A significant increase in plant biomass was observed in strain SK68-inoculated tomato plants under salt stress compared to control and salt-stressed non-inoculated plants.
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Affiliation(s)
- Karthiyaini Damodharan
- Center for Nutraceutical and Pharmaceutical Materials, College of Natural Science, Myongji University, Yongin, 17058, Republic of Korea
| | - Sasikumar Arunachalam Palaniyandi
- Department of Biotechnology, Mepco Schlenk Engineering College, Mepco Nagar, Mepco Engineering College, Post-626005, Sivakasi, Tamilnadu, India
| | - Bao Le
- Department of Biotechnology, Chonnam National University, Yeosu, 59626, Republic of Korea
| | - Joo-Won Suh
- Center for Nutraceutical and Pharmaceutical Materials, College of Natural Science, Myongji University, Yongin, 17058, Republic of Korea.
| | - Seung Hwan Yang
- Department of Biotechnology, Chonnam National University, Yeosu, 59626, Republic of Korea.
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10
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Mohapatra B, Satyanarayana T, Sar P. Molecular and eco-physiological characterization of arsenic (As)-transforming Achromobacter sp. KAs 3-5 T from As-contaminated groundwater of West Bengal, India. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART A, TOXIC/HAZARDOUS SUBSTANCES & ENVIRONMENTAL ENGINEERING 2018; 53:915-924. [PMID: 29719162 DOI: 10.1080/10934529.2018.1462897] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Molecular and eco-physiological characterization of arsenic (As)-transforming and hydrocarbon-utilizing Achromobacter type strain KAs 3-5T has been investigated in order to gain an insight into As-geomicrobiology in the contaminated groundwater. The bacterium is isolated from As-rich groundwater of West Bengal, India. Comparative 16S rRNA gene sequence phylogenetic analysis confirmed that the strain KAs 3-5T is closely related to Achromobacter mucicolens LMG 26685T (99.17%) and Achromobacter animicus LMG 26690T (99.17%), thus affiliated to the genus Achromobacter. Strain KAs 3-5T is nonflagellated, mesophilic, facultative anaerobe, having a broad metabolic repertoire of using various sugars, sugar-/fatty acids, hydrocarbons as principal carbon substrates, and O2, NO3-, NO2-, and Fe3+ as terminal electron acceptors. Growth with hydrocarbons led to cellular aggregation and adherence of the cells to the hydrocarbon particles confirmed through electron microscopic observations. The strain KAs 3-5T showed high As resistance (MIC of 5 mM for As3+, 25 mM for As5+) and reductive transformation of As5+ under aerobic conditions while utilizing both sugars and hydrocarbons. Molecular taxonomy specified a high genomic GC content (65.5 mol %), ubiquinone 8 (UQ-8) as respiratory quinone, spermidine as predominant polyamine in the bacterium. The differential presence of C12:0, C14:0 2-OH, C18:1 ω7c, and C 14:0 iso 3-OH/ C16:1 iso fatty acids, phosphatidylglycerol (PG), phosphatidylcholine (PC), two unknown phospholipid (PL1, PL2) as polar lipids, low DNA-DNA relatedness (33.0-41.0%) with the Achromobacter members, and unique metabolic capacities clearly indicated the distinct genomic and physiological properties of strain KAs 3-5T among known species of the genus Achromobacter. These findings lead to improve our understanding on metabolic flexibility of bacteria residing in As-contaminated groundwater and As-bacteria interactions within oligotrophic aquifer system.
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Affiliation(s)
- Balaram Mohapatra
- a Department of Biotechnology , Indian Institute of Technology Kharagpur , Kharagpur , West Bengal , India
| | - Tulasi Satyanarayana
- b Department of Microbiology , University of Delhi South Campus (UDSC) , New Delhi , India
| | - Pinaki Sar
- a Department of Biotechnology , Indian Institute of Technology Kharagpur , Kharagpur , West Bengal , India
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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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12
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Mohapatra B, Sar P, Kazy SK, Maiti MK, Satyanarayana T. Taxonomy and physiology of Pseudoxanthomonas arseniciresistens sp. nov., an arsenate and nitrate-reducing novel gammaproteobacterium from arsenic contaminated groundwater, India. PLoS One 2018; 13:e0193718. [PMID: 29558470 PMCID: PMC5860741 DOI: 10.1371/journal.pone.0193718] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 02/16/2018] [Indexed: 11/23/2022] Open
Abstract
Reductive transformation of toxic arsenic (As) species by As reducing bacteria (AsRB) is a key process in As-biogeochemical-cycling within the subsurface aquifer environment. In this study, we have characterized a Gram-stain-negative, non-spore-forming, rod-shaped As reducing bacterium designated KAs 5-3T, isolated from highly As-contaminated groundwater of India. Strain KAs 5-3T displayed high 16S rRNA gene sequence similarity to the members of the genus Pseudoxanthomonas, with P. mexicana AMX 26BT (99.25% similarity), P. japonensis 12-3T (98.9 0%), P. putridarboris WD-12T (98.02%), and P. indica P15T (97.27%) as closest phylogenetic neighbours. DNA-DNA hybridization study unambiguously indicated that strain KAs 5-3T represented a novel species that was separate from reference strains of P. mexicana AMX 26BT (35.7%), P. japonensis 12-3T (35.5%), P. suwonensis 4M1T (35.5%), P. wuyuanensis XC21-2T (35.0%), P. indica P15T (32.5%), P. daejeonensis TR6-08T (32.0%), and P. putridarboris WD12T (22.1%). The DNA G+C content of strain KAs 5-3T was 64.9 mol %. The predominant fatty acids were C15:0 (37.4%), C16:0 iso (12.6%), C17:1 iso ω9c (10.5%), C15:0 anteiso (9.5%), C11:0 iso 3-OH (8.5%), and C16:1 ω7c/ C16:1 ω6c (7.5%). The major polar lipids were diphosphatidylglycerol, phosphatidyldimethylethanolamine, phosphatidylcholine, and two unknown phospholipids (PL1, PL2). Ubiquinone 8 (Q8) was the predominant respiratory quinone and spermidine was the major polyamine of the strain KAs 5-3T. Cells of strain KAs 5-3T showed the ability to use O2, As5+, NO3-, NO2-, and Fe3+ as terminal electron acceptors as well as to reduce As5+ through the cytosolic process under aerobic incubations. Genes encoding arsenate reductase (arsC) for As-detoxification, nitrate- and nitrite reductase (narG and nirS) for denitrification were detected in the strain KAs 5-3T. Based on taxonomic and physiological data, strain KAs 5-3T is described as a new representative member of the genus Pseudoxanthomonas, for which the name Pseudoxanthomonas arseniciresistens sp. nov. is proposed. The type strain is KAs 5-3T (= LMG 29169T = MTCC 12116T = MCC 3121T).
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Affiliation(s)
- Balaram Mohapatra
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, India
| | - Pinaki Sar
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, India
- * E-mail:
| | - Sufia Khannam Kazy
- Department of Biotechnology, National Institute of Technology Durgapur, Durgapur, West Bengal, India
| | - Mrinal Kumar Maiti
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, India
| | - Tulasi Satyanarayana
- Department of Microbiology, University of Delhi South Campus (UDSC), New Delhi, Delhi, India
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Kim MK, Kim ET, Kim SB, Jeong HY, Park BY, Srinivasan S. Kurthia ruminicola sp. nov., isolated from the rumen contents of a Holstein cow. J Microbiol 2018; 56:36-41. [PMID: 29299848 DOI: 10.1007/s12275-018-7285-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2017] [Revised: 11/23/2017] [Accepted: 11/23/2017] [Indexed: 11/28/2022]
Abstract
Gram-staining-positive, motile, rod-shaped bacteria, designated as H31022T and H31024 was isolated from rumen contents of a Holstein cow. Optimum growth occurred at 25°C and pH 7.0 on R2A agar medium. Oxidase and catalase activities are positive. The 16S rRNA gene sequence (1,452 bp) of the new isolates revealed they belong to the genus Kurthia of the phylum Firmicutes. Highest gene sequence similarities were assessed to be with Kurthia massiliensis JC30T (98.4%), Kurthia senegalensis JC8ET (97.5%), and Kurthia populi 10y-14T (97.4%). Kurthia sibirica DSM 4747T (97.3%), Kurthia zopfii NBRC 101529T (97.0%), and Kurthia gibsonii NCIMB 9758T (96.7%). DNA G + C content of strains H31022T and H31024 were 34.4% and 39.7%. Strains H31022T and H31024 has the following chemotaxonomic characteristics; the major fatty acids are iso-C15:0, iso-C14:0 and anteiso-C15; polar lipid profile contained diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), unknown aminophospholipids (APL), unknown glycolipids (GL), unknown phospholipids (PL), and unknown polar lipids (L); the major quinone is MK-7. Based on polyphasic taxonomic analysis, strains H31022T (= KCTC 33923T = JCM 19640T) and H31024 (= KCTC 33924T = JCM 19641T) identified a novel species in the genus Kurthia for which the name Kurthia ruminicola sp. nov. is proposed.
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Affiliation(s)
- Myung Kyum Kim
- Department of Bio & Environmental Technology, College of Natural Science, Seoul Women's University, Seoul, 01797, Republic of Korea
| | - Eun Tae Kim
- National Institute of Animal Science, RDA, Cheonan, 31000, Republic of Korea.
| | - Sang Bum Kim
- National Institute of Animal Science, RDA, Cheonan, 31000, Republic of Korea
| | - Ha Yeon Jeong
- National Institute of Animal Science, RDA, Cheonan, 31000, Republic of Korea
| | - Beom Young Park
- National Institute of Animal Science, RDA, Cheonan, 31000, Republic of Korea
| | - Sathiyaraj Srinivasan
- Department of Bio & Environmental Technology, College of Natural Science, Seoul Women's University, Seoul, 01797, Republic of Korea.
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14
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Silva LJ, Souza DT, Genuario DB, Hoyos HAV, Santos SN, Rosa LH, Zucchi TD, Melo IS. Rhodococcus psychrotolerans sp. nov., isolated from rhizosphere of Deschampsia antarctica. Antonie Van Leeuwenhoek 2017; 111:629-636. [PMID: 29143212 DOI: 10.1007/s10482-017-0983-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 11/10/2017] [Indexed: 12/01/2022]
Abstract
A novel actinobacterium, designated strain CMAA 1533T, was isolated from the rhizosphere of Deschampsia antarctica collected at King George Island, Antarctic Peninsula. Strain CMAA 1533T was found to grow over a wide range of temperatures (4-28 °C) and pH (4-10). Macroscopically, the colonies were observed to be circular shaped, smooth, brittle and opaque-cream on most of the culture media tested. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain CMAA 1533T belongs to the family Nocardiaceae and forms a distinct phyletic line within the genus Rhodococcus. Sequence similarity calculations indicated that the novel strain is closely related to Rhodococcus degradans CCM 4446T, Rhodococcus erythropolis NBRC 15567T and Rhodococcus triatomae DSM 44892T (≤ 96.9%). The organism was found to contain meso-diaminopimelic acid, galactose and arabinose in whole cell hydrolysates. Its predominant isoprenologue was identified as MK-8(H2) and the polar lipids as diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannosides. The major fatty acids were identified as Summed feature (C16:1 ω6c and/or C16:1 ω7c), C16:0, C18:1 ω9c and 10-methyl C18:0. The G+C content of genomic DNA was determined to be 65.5 mol%. Unlike the closely related type strains, CMAA 1533T can grow at 4 °C but not at 37 °C and was able to utilise adonitol and galactose as sole carbon sources. Based on phylogenetic, chemotaxonomic and physiological data, it is concluded that strain CMAA 1533T (= NRRL B-65465T = DSM 104532T) represents a new species of the genus Rhodococcus, for which the name Rhodococcus psychrotolerans sp. nov. is proposed.
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Affiliation(s)
- Leonardo Jose Silva
- College of Agriculture "Luiz de Queiroz", University of São Paulo, Pádua Dias Avenue, 11, Piracicaba, São Paulo, 13418-900, Brazil.,Laboratory of Environmental Microbiology, Brazilian Agricultural Research Corporation, EMBRAPA Environment, SP 340 Highway, Km 127.5, Jaguariúna, São Paulo, 13820-000, Brazil
| | - Danilo Tosta Souza
- Laboratory of Environmental Microbiology, Brazilian Agricultural Research Corporation, EMBRAPA Environment, SP 340 Highway, Km 127.5, Jaguariúna, São Paulo, 13820-000, Brazil
| | - Diego Bonaldo Genuario
- Laboratory of Environmental Microbiology, Brazilian Agricultural Research Corporation, EMBRAPA Environment, SP 340 Highway, Km 127.5, Jaguariúna, São Paulo, 13820-000, Brazil
| | - Harold Alexander Vargas Hoyos
- College of Agriculture "Luiz de Queiroz", University of São Paulo, Pádua Dias Avenue, 11, Piracicaba, São Paulo, 13418-900, Brazil.,Laboratory of Environmental Microbiology, Brazilian Agricultural Research Corporation, EMBRAPA Environment, SP 340 Highway, Km 127.5, Jaguariúna, São Paulo, 13820-000, Brazil
| | - Suikinai Nobre Santos
- Laboratory of Environmental Microbiology, Brazilian Agricultural Research Corporation, EMBRAPA Environment, SP 340 Highway, Km 127.5, Jaguariúna, São Paulo, 13820-000, Brazil
| | - Luiz Henrique Rosa
- Department of Microbiology, Institute of Biological Sciences, Federal University of Minas Gerais, Presidente Antônio Carlos Avenue, 6627, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Tiago Domingues Zucchi
- Agrivalle, Agricultural Biotechnology, Tranquillo Giannini Avenue, 1090, Salto, São Paulo, 13329-600, Brazil
| | - Itamar Soares Melo
- Laboratory of Environmental Microbiology, Brazilian Agricultural Research Corporation, EMBRAPA Environment, SP 340 Highway, Km 127.5, Jaguariúna, São Paulo, 13820-000, Brazil.
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15
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Karami K, Mehri Lighvan Z, Farrokhpour H, Dehdashti Jahromi M, Momtazi-Borojeni AA. Synthesis and spectroscopic characterization study of new palladium complexes containing bioactive O,O-chelated ligands: evaluation of the DNA/protein BSA interaction, in vitro antitumoural activity and molecular docking. J Biomol Struct Dyn 2017; 36:3324-3340. [PMID: 29019431 DOI: 10.1080/07391102.2017.1391125] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
[Pd{(C,N)-C6H4CH2NH(Et) (Qu)] (2) and [Pd{(C,N)-C6H4CH2NH(Et) (Nar)] (3) (Qu = Quercetin, Nar = Naringin) mononuclear palladium (II) complexes have been synthesized and characterized using elemental analysis, IR and electronic spectroscopy. The interaction of the prepared complexes with calf thymus DNA and bovine serum albumin (BSA), monitored by UV-visible and fluorescence titrations, respectively, have been carried out to better understand the mode of their action under biological conditions. Intercalative binding mode between the complexes and DNA is suggested by the binding constant (Kb) values of 2.5 × 106 and 3.2 × 106 for complexes 2 and 3, respectively. In particular, the in vitro cytotoxicity of the complexes on two cancer cells lines (bladder carcinoma TCC and breast cancer MCF7) showed that the compounds had broad spectrum, anti-cancer activity with low IC50 values and the order of in vitro anticancer activities is consistent with the DNA-binding affinities. In the meantime, the quenching of tryptophan emission with the addition of complexes using BSA as a model protein indicated the protein binding ability. The quenching mechanisms of BSA by the complexes were static processes, according to the results obtained. The competitive binding using Warfarin, Digoxin and Ibuprofen site markers, which contain definite biding sites, demonstrated that the complexes bind to site I on BSA. Ultimately, the binding sites of DNA and BSA with the complexes have been determined by molecular modelling studies.
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Affiliation(s)
- Kazem Karami
- a Department of Chemistry , Isfahan University of Technology , Isfahan 84156/83111 , Iran
| | - Zohreh Mehri Lighvan
- a Department of Chemistry , Isfahan University of Technology , Isfahan 84156/83111 , Iran
| | - Hossein Farrokhpour
- a Department of Chemistry , Isfahan University of Technology , Isfahan 84156/83111 , Iran
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16
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Suarez C, Ratering S, Schäfer J, Schnell S. Ancylobacter pratisalsi sp. nov. with plant growth promotion abilities from the rhizosphere of Plantago winteri Wirtg. Int J Syst Evol Microbiol 2017; 67:4500-4506. [PMID: 28945527 DOI: 10.1099/ijsem.0.002320] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-negative bacterium, designated E130T, was isolated from rhizospheric soil of Plantago winteri Wirtg. from a natural salt meadow as part of an investigation on rhizospheric bacteria from salt-resistant plant species and evaluation of their plant growth-promoting abilities. Cells were rods, non-motile, aerobic, and oxidase and catalase positive, grew in a temperature range of between 4 and 37 °C, and in the presence of 0.5-5 % NaCl (w/v). Based on 16S rRNA gene sequence analysis, strain E130T is affiliated within the genus Ancylobacter, sharing the highest similarity with Ancylobacter rudongensis DSM 17131T (97.6 %), Ancylobacter defluvii CCUG 63806T (97.5 %) and Ancylobacter dichloromethanicus DSM 21507T (97.4 %). The DNA G+C content of strain E130T was 65.1 mol%. Its respiratory quinones were Q-9 and Q-10 and its major polar lipids comprised phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine and unidentified phospholipid. Major fatty acids of the strains E130T were C12 : 0, C16 : 0, C18 : 1ω7c and C19 : 0cycloω8c. The DNA-DNA relatedness of E130T to A. rudongensis DSM 17131T, A. defluvii CCUG 63806T and A. dichloromethanicus DSM 21507T was 29.2, 21.2 and 32.2 % respectively. On the basis of our polyphasic taxonomic study the new isolate represents a novel species, for which the name Ancylobacter pratisalsi sp. nov. is proposed. The type strain is E130T (LMG 29367T=DSM 102029T).
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Affiliation(s)
- Christian Suarez
- Institute of Applied Microbiology, Justus-Liebig University Giessen, 35392 Giessen, Germany
| | - Stefan Ratering
- Institute of Applied Microbiology, Justus-Liebig University Giessen, 35392 Giessen, Germany
| | - Johanna Schäfer
- Institute of Applied Microbiology, Justus-Liebig University Giessen, 35392 Giessen, Germany
| | - Sylvia Schnell
- Institute of Applied Microbiology, Justus-Liebig University Giessen, 35392 Giessen, Germany
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17
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Mahato NK, Gupta V, Singh P, Kumari R, Verma H, Tripathi C, Rani P, Sharma A, Singhvi N, Sood U, Hira P, Kohli P, Nayyar N, Puri A, Bajaj A, Kumar R, Negi V, Talwar C, Khurana H, Nagar S, Sharma M, Mishra H, Singh AK, Dhingra G, Negi RK, Shakarad M, Singh Y, Lal R. Microbial taxonomy in the era of OMICS: application of DNA sequences, computational tools and techniques. Antonie van Leeuwenhoek 2017; 110:1357-1371. [PMID: 28831610 DOI: 10.1007/s10482-017-0928-1] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 08/10/2017] [Indexed: 02/06/2023]
Abstract
The current prokaryotic taxonomy classifies phenotypically and genotypically diverse microorganisms using a polyphasic approach. With advances in the next-generation sequencing technologies and computational tools for analysis of genomes, the traditional polyphasic method is complemented with genomic data to delineate and classify bacterial genera and species as an alternative to cumbersome and error-prone laboratory tests. This review discusses the applications of sequence-based tools and techniques for bacterial classification and provides a scheme for more robust and reproducible bacterial classification based on genomic data. The present review highlights promising tools and techniques such as ortho-Average Nucleotide Identity, Genome to Genome Distance Calculator and Multi Locus Sequence Analysis, which can be validly employed for characterizing novel microorganisms and assessing phylogenetic relationships. In addition, the review discusses the possibility of employing metagenomic data to assess the phylogenetic associations of uncultured microorganisms. Through this article, we present a review of genomic approaches that can be included in the scheme of taxonomy of bacteria and archaea based on computational and in silico advances to boost the credibility of taxonomic classification in this genomic era.
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Affiliation(s)
| | - Vipin Gupta
- Department of Zoology, University of Delhi, Delhi, 110007, India
| | - Priya Singh
- Department of Zoology, University of Delhi, Delhi, 110007, India
| | - Rashmi Kumari
- Department of Zoology, University of Delhi, Delhi, 110007, India
| | | | - Charu Tripathi
- Department of Zoology, University of Delhi, Delhi, 110007, India
| | - Pooja Rani
- Department of Zoology, University of Delhi, Delhi, 110007, India
| | - Anukriti Sharma
- Department of Zoology, University of Delhi, Delhi, 110007, India
| | - Nirjara Singhvi
- Department of Zoology, University of Delhi, Delhi, 110007, India
| | - Utkarsh Sood
- Department of Zoology, University of Delhi, Delhi, 110007, India
| | - Princy Hira
- Department of Zoology, University of Delhi, Delhi, 110007, India
| | - Puneet Kohli
- Department of Zoology, University of Delhi, Delhi, 110007, India
| | - Namita Nayyar
- Department of Zoology, University of Delhi, Delhi, 110007, India
| | - Akshita Puri
- Department of Zoology, University of Delhi, Delhi, 110007, India
| | - Abhay Bajaj
- Department of Zoology, University of Delhi, Delhi, 110007, India
| | - Roshan Kumar
- Department of Zoology, University of Delhi, Delhi, 110007, India
| | - Vivek Negi
- Department of Zoology, University of Delhi, Delhi, 110007, India
| | - Chandni Talwar
- Department of Zoology, University of Delhi, Delhi, 110007, India
| | - Himani Khurana
- Department of Zoology, University of Delhi, Delhi, 110007, India
| | - Shekhar Nagar
- Department of Zoology, University of Delhi, Delhi, 110007, India
| | - Monika Sharma
- Department of Zoology, University of Delhi, Delhi, 110007, India
| | - Harshita Mishra
- Department of Zoology, University of Delhi, Delhi, 110007, India
| | - Amit Kumar Singh
- Department of Zoology, University of Delhi, Delhi, 110007, India
| | - Gauri Dhingra
- Department of Zoology, University of Delhi, Delhi, 110007, India
| | - Ram Krishan Negi
- Department of Zoology, University of Delhi, Delhi, 110007, India
| | | | - Yogendra Singh
- Department of Zoology, University of Delhi, Delhi, 110007, India
| | - Rup Lal
- Department of Zoology, University of Delhi, Delhi, 110007, India.
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18
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Kribbella sindirgiensis sp. nov. isolated from soil. Arch Microbiol 2017; 199:1399-1407. [DOI: 10.1007/s00203-017-1414-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 07/19/2017] [Accepted: 07/20/2017] [Indexed: 10/19/2022]
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19
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Pseudomonas aestus sp. nov., a plant growth-promoting bacterium isolated from mangrove sediments. Arch Microbiol 2017; 199:1223-1229. [PMID: 28702688 DOI: 10.1007/s00203-017-1410-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 06/13/2017] [Accepted: 07/04/2017] [Indexed: 10/19/2022]
Abstract
Strain CMAA 1215T, a Gram-reaction-negative, aerobic, catalase positive, polarly flagellated, motile, rod-shaped (0.5-0.8 × 1.3-1.9 µm) bacterium, was isolated from mangrove sediments, Cananéia Island, Brazil. Analysis of the 16S rRNA gene sequences showed that strain CMAA 1215T forms a distinct phyletic line within the Pseudomonas putida subclade, being closely related to P. plecoglossicida ATCC 700383T, P. monteilii NBRC 103158T, and P. taiwanensis BCRC 17751T of sequence similarity of 98.86, 98.73, and 98.71%, respectively. Genomic comparisons of the strain CMAA 1215T with its closest phylogenetic type strains using average nucleotide index (ANI) and DNA:DNA relatedness approaches revealed 84.3-85.3% and 56.0-63.0%, respectively. A multilocus sequence analysis (MLSA) performed concatenating 16S rRNA, gyrB and rpoB gene sequences from the novel species was related with Pseudomonas putida subcluster and formed a new phylogenetic lineage. The phenotypic, physiological, biochemical, and genetic characteristics support the assignment of CMAA 1215T to the genus Pseudomonas, representing a novel species. The name Pseudomonas aestus sp.nov. is proposed, with CMAA 1215T (=NRRL B-653100T = CBMAI 1962T) as the type strain.
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20
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Prathyash Ushus MJ, Divyasree B, Lakshmi KVNS, Dave BP, Sasikala C, Ramana CV. Description of a phototrophic bacterium, Thiorhodococcus alkaliphilus sp. nov. Int J Syst Evol Microbiol 2017; 67:2323-2327. [PMID: 28693683 DOI: 10.1099/ijsem.0.001947] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strain JA878T was purified from a photoheterotrophic enrichment obtained from a sediment sample of a brown pond near Nari Salt Pan, Bhavnagar, Gujarat, India. Cells of the isolate were coccoid, motile by means of single polar flagellum and Gram-stain-negative. The internal photosynthetic membrane architecture was vesicular. Strain JA878T contained bacteriochlorophyll a and spirilloxanthin series of carotenoids with rhodopin (>85 %) as the major component. Strain JA878T grew optimally at pH 10-11, and had no requirement for NaCl (tolerated up to 6 %, w/v) or vitamins for growth. C16 : 1ω7c/C16 : 1ω6c, C18 : 1ω7c/C18 : 1ω6c and C16 : 0 were identified as the major fatty acids (>10 %). Phosphatidylglycerol, phosphatidylethanolamine, aminophospholipid and an unknown polar lipid were identified. Q8 was the predominant quinone system in strain JA878T. The DNA G+C content was 62.4 mol%. Highest 16S rRNA gene sequence similarity through EzTaxon-based blast analysis of strain JA878T was found with the type strains of Thiorhodococcus fuscus (99 %), Thiorhodococcus kakinadensis (98.6 %), Thiohalobacter thiocyanaticus (98.4 %), Thiophaeococcus fuscus (97.3 %) and other members of the class Gammaproteobacteria (<97.3 %), revealing a close affiliation to the genera Thiorhodococcus, Thiohalobacter and Thiophaeococcus. However, the phylogenetic treeing firmly placed the strain in the genus Thiorhodococcus. Phenotypic and chemotaxonomic evidence supported the affiliation of strain JA878T to the genus Thiorhodococcus and not to Thiohalobacter, Thiophaeococcus or other known genera of Chromatiaceae. Distinct physiological, genotypic and chemotaxonomic differences indicate that strain JA878T represents a novel species of the genus Thiorhodococcus, for which the name Thiorhodococcus alkaliphilus sp. nov. is proposed. The type strain is JA878T (=KCTC 15531T=JCM 31245T).
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Affiliation(s)
- M J Prathyash Ushus
- Bacterial Discovery Laboratory, Centre for Environment, Institute of Science and Technology, J. N. T. University Hyderabad, Kukatpally, Hyderabad 500085, India
| | - B Divyasree
- Bacterial Discovery Laboratory, Centre for Environment, Institute of Science and Technology, J. N. T. University Hyderabad, Kukatpally, Hyderabad 500085, India
| | - K V N S Lakshmi
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500046, India
| | - Bharti P Dave
- Department of Life Sciences, M K Bhavnagar University, Bhavnagar, Gujarat 364002, India
| | - Ch Sasikala
- Bacterial Discovery Laboratory, Centre for Environment, Institute of Science and Technology, J. N. T. University Hyderabad, Kukatpally, Hyderabad 500085, India
| | - Ch V Ramana
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500046, India
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21
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Afonso de Menezes CB, Afonso RS, Souza WRD, Parma M, Melo ISD, Zucchi TD, Fantinatti-Garboggini F. Williamsia spongiae sp. nov., an actinomycete isolated from the marine sponge Amphimedon viridis. Int J Syst Evol Microbiol 2017; 67:1260-1265. [PMID: 28100308 DOI: 10.1099/ijsem.0.001796] [Citation(s) in RCA: 14] [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 actinobacterium, designated isolate B138T, was isolated from the marine sponge, Amphimedon viridis, which was collected from Praia Guaecá (São Paulo, Brazil), and its taxonomic position was established using data from a polyphasic study. The organism showed a combination of chemotaxonomic and morphological characteristics consistent with its classification in the genus Williamsia and it formed a distinct phyletic line in the Williamsia 16S rRNA gene tree. It was most closely related to Williamsia serinedens DSM 45037T and Williamsia deligens DSM 44902T (99.0 % 16S rRNA gene sequence similarity) and Williamsia maris DSM 44693T (97.5 % 16S rRNA gene sequence similarity), but was distinguished readily from these strains by the low DNA-DNA relatedness values (62.3-64.4 %) and by the discriminatory phenotypic properties. Based on the data obtained, the isolate B138T (=CBMAI 1094T=DSM 46676T) should be classified as the type strain of a novel species of the genus Williamsia, for which the name Williamsia spongiae sp. nov. is proposed.
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Affiliation(s)
- Cláudia Beatriz Afonso de Menezes
- Centro Pluridisciplinar de Pesquisas Químicas Biológicas e Agrícolas, UNICAMP, Av. Alexandre Cazelatto 999, CEP 13148-218, Paulínia, SP, Brazil.,Programa de Pós-Graduação em Genética e Biologia Molecular, UNICAMP, CP 6109, 13083-970, Campinas, SP, Brazil
| | - Rafael Sanches Afonso
- Centro Pluridisciplinar de Pesquisas Químicas Biológicas e Agrícolas, UNICAMP, Av. Alexandre Cazelatto 999, CEP 13148-218, Paulínia, SP, Brazil
| | - Wallace Rafael de Souza
- Embrapa Meio Ambiente, Rodovia SP 340 Km 127.5, CP 69, CEP 13820-000, Jaguariúna, SP, Brazil
| | - Márcia Parma
- Embrapa Meio Ambiente, Rodovia SP 340 Km 127.5, CP 69, CEP 13820-000, Jaguariúna, SP, Brazil
| | - Itamar Soares de Melo
- Embrapa Meio Ambiente, Rodovia SP 340 Km 127.5, CP 69, CEP 13820-000, Jaguariúna, SP, Brazil
| | - Tiago Domingues Zucchi
- Embrapa Meio Ambiente, Rodovia SP 340 Km 127.5, CP 69, CEP 13820-000, Jaguariúna, SP, Brazil.,Agrivalle - Biotecnologia Agrícola, Rua Moisés Lopes Silva 50, CEP 37550-000, Pouso Alegre, MG, Brazil
| | - Fabiana Fantinatti-Garboggini
- Programa de Pós-Graduação em Genética e Biologia Molecular, UNICAMP, CP 6109, 13083-970, Campinas, SP, Brazil.,Centro Pluridisciplinar de Pesquisas Químicas Biológicas e Agrícolas, UNICAMP, Av. Alexandre Cazelatto 999, CEP 13148-218, Paulínia, SP, Brazil
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22
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Boudjeko T, Tchinda RAM, Zitouni M, Nana JAVT, Lerat S, Beaulieu C. Streptomyces cameroonensis sp. nov., a Geldanamycin Producer That Promotes Theobroma cacao Growth. Microbes Environ 2017; 32:24-31. [PMID: 28260703 PMCID: PMC5371071 DOI: 10.1264/jsme2.me16095] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The taxonomy of an actinobacterial strain, designated JJY4T, was established using a polyphasic approach. JJY4T was isolated from the rhizosphere of Chromolaena odorata in Yaoundé (Cameroon) during a project for the selection of biological control agents. Strain JJY4T exhibited antimicrobial activities against bacteria, fungi, and oomycetes. Strain JJY4T also exhibited the traits of plant growth-promoting rhizobacteria such as the solubilization of inorganic phosphate, production of siderophores and indole-3-acetic acid, and 1-aminocyclopropane-1-carboxylate deaminase activity. In planta assays performed on cocoa plantlets confirmed that strain JJY4T exhibited strong abilities to promote plant growth and protect against Phytophthora megakarya, the main causal agent of cocoa pod rot. The formation of rugose-ornamented spores in spiral spore chains by strain JJY4T is a typical feature of members found in the Streptomyces violaceusniger clade and, similar to some members of the clade, strain JJY4T produces geldanamycin. A phylogenetic analysis based on 16S rRNA gene sequences confirmed this classification and suggests that strain JJY4T be added to the subclade constituted of the type strains Streptomyces malaysiensis DSM 41697T and Streptomyces samsunensis DSM 42010T. However, DNA-DNA relatedness and physiological characteristics allowed for the differentiation of strain JJY4T from its closest phylogenetic relatives. Based on these results, strain JJY4T (=NRRL B-65369, =NBRC 112705) appears to represent a novel species in the S. violaceusniger clade for which the proposed name is Streptomyces cameroonensis sp. nov.
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Affiliation(s)
- Thaddée Boudjeko
- Laboratory of Phytoprotection and Valorization of Plants Resources, Biotechnology Centre-Nkolbisson
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23
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Leite J, Passos SR, Simões-Araújo JL, Rumjanek NG, Xavier GR, Zilli JÉ. Genomic identification and characterization of the elite strains Bradyrhizobium yuanmingense BR 3267 and Bradyrhizobium pachyrhizi BR 3262 recommended for cowpea inoculation in Brazil. Braz J Microbiol 2017; 49:703-713. [PMID: 28410799 PMCID: PMC6175698 DOI: 10.1016/j.bjm.2017.01.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Revised: 01/03/2017] [Accepted: 01/12/2017] [Indexed: 11/21/2022] Open
Abstract
The leguminous inoculation with nodule-inducing bacteria that perform biological nitrogen fixation is a good example of an “eco-friendly agricultural practice”. Bradyrhizobium strains BR 3267 and BR 3262 are recommended for cowpea (Vigna unguiculata) inoculation in Brazil and showed remarkable responses; nevertheless neither strain was characterized at species level, which is our goal in the present work using a polyphasic approach. The strains presented the typical phenotype of Bradyrhizobium with a slow growth and a white colony on yeast extract-mannitol medium. Strain BR 3267 was more versatile in its use of carbon sources compared to BR 3262. The fatty acid composition of BR 3267 was similar to the type strain of Bradyrhizobium yuanmingense; while BR 3262 was similar to Bradyrhizobium elkanii and Bradyrhizobium pachyrhizi. Phylogenetic analyses based on 16S rRNA and three housekeeping genes placed both strains within the genus Bradyrhizobium: strain BR 3267 was closest to B. yuanmingense and BR 3262 to B. pachyrhizi. Genome average nucleotide identity and DNA–DNA reassociation confirmed the genomic identification of B. yuanmingense BR 3267 and B. pachyrhizi BR 3262. The nodC and nifH gene analyses showed that strains BR 3267 and BR 3262 hold divergent symbiotic genes. In summary, the results indicate that cowpea can establish effective symbiosis with divergent bradyrhizobia isolated from Brazilian soils.
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Affiliation(s)
- Jakson Leite
- Departamento de Solos, Universidade Federal Rural do Rio de Janeiro, 23851-970 Seropédica, RJ, Brazil
| | - Samuel Ribeiro Passos
- Departamento de Ciências Ambientais, Universidade Federal Rural do Rio de Janeiro, 23851-970 Seropédica, RJ, Brazil
| | - Jean Luiz Simões-Araújo
- Laboratório de Genética e Bioquímica, Embrapa Agrobiologia, 23851-970 Seropédica, RJ, Brazil
| | - Norma Gouvêa Rumjanek
- Laboratório de Ecologia Microbiana, Embrapa Agrobiologia, 23851-970 Seropédica, RJ, Brazil
| | - Gustavo Ribeiro Xavier
- Laboratório de Ecologia Microbiana, Embrapa Agrobiologia, 23851-970 Seropédica, RJ, Brazil
| | - Jerri Édson Zilli
- Laboratório de Ecologia Microbiana, Embrapa Agrobiologia, 23851-970 Seropédica, RJ, Brazil.
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Kribbella soli sp. nov., isolated from soil. Antonie van Leeuwenhoek 2017; 110:641-649. [DOI: 10.1007/s10482-017-0830-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 01/16/2017] [Indexed: 10/20/2022]
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Description of Alteribacillus alkaliphilus sp. nov., reassignment of Bacillus iranensis (Bagheri et al. 2012) as Alteribacillus iranensis comb. nov. and emended description of the genus Alteribacillus. Int J Syst Evol Microbiol 2016; 66:4772-4778. [DOI: 10.1099/ijsem.0.001428] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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An arsenate-reducing and alkane-metabolizing novel bacterium, Rhizobium arsenicireducens sp. nov., isolated from arsenic-rich groundwater. Arch Microbiol 2016; 199:191-201. [PMID: 27663709 DOI: 10.1007/s00203-016-1286-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 08/31/2016] [Accepted: 09/01/2016] [Indexed: 01/09/2023]
Abstract
A novel arsenic (As)-resistant, arsenate-respiring, alkane-metabolizing bacterium KAs 5-22T, isolated from As-rich groundwater of West Bengal was characterized by physiological and genomic properties. Cells of strain KAs 5-22T were Gram-stain-negative, rod-shaped, motile, and facultative anaerobic. Growth occurred at optimum of pH 6.0-7.0, temperature 30 °C. 16S rRNA gene affiliated the strain KAs 5-22T to the genus Rhizobium showing maximum similarity (98.4 %) with the type strain of Rhizobium naphthalenivorans TSY03bT followed by (98.0 % similarity) Rhizobium selenitireducens B1T. The genomic G + C content was 59.4 mol%, and DNA-DNA relatedness with its closest phylogenetic neighbors was 50.2 %. Chemotaxonomy indicated UQ-10 as the major quinone; phosphatidylethanolamine, phosphatidylglycerol, and diphosphatidylglycerol as major polar lipids; C16:0, C17:0, 2-OH C10:0, 3-OH C16:0, and unresolved C18:1 ɷ7C/ɷ9C as predominant fatty acids. The cells were found to reduce O2, As5+, NO3-, SO42- and Fe3+ as alternate electron acceptors. The strain's ability to metabolize dodecane or other alkanes as sole carbon source using As5+ as terminal electron acceptor was supported by the presence of genes encoding benzyl succinate synthase (bssA like) and molybdopterin-binding site (mopB) of As5+ respiratory reductase (arrA). Differential phenotypic, chemotaxonomic, genotypic as well as physiological properties revealed that the strain KAs 5-22T is separated from its nearest recognized Rhizobium species. On the basis of the data presented, strain KAs 5-22T is considered to represent a novel species of the genus Rhizobium, for which the name Rhizobium arsenicireducens sp. nov. is proposed as type strain (=LMG 28795T=MTCC 12115T).
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Veyisoglu A, Cetin D, Inan Bektas K, Guven K, Sahin N. Streptomyces ovatisporus sp. nov., isolated from deep marine sediment. Int J Syst Evol Microbiol 2016; 66:4856-4863. [PMID: 27553490 DOI: 10.1099/ijsem.0.001442] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The taxonomic position of a Gram-staining-positive strain, designated strain S4702T was isolated from a marine sediment collected from the southern Black Sea coast, Turkey, determined using a polyphasic approach. The isolate was found to have chemotaxonomic, morphological and phylogenetic properties consistent with its classification as representing a member of the genus Streptomyces and formed a distinct phyletic line in the 16S rRNA gene tree. S4702T was found to be most closely related to the type strains of Streptomyces marinus(DSM 41968T; 97.8 % sequence similarity) and Streptomyces abyssalis (YIM M 10400T; 97.6 %). 16S rRNA gene sequence similarities with other members of the genus Streptomyces were lower than 97.5 %. DNA-DNA relatedness of S4702T and the most closely related strain S. marinus DSM 41968T was 21.0 %. The G+C content of the genomic DNA was 72.5 mol%. The cell wall of the strain contained l,l-diaminopimelic acid and the cell-wall sugars were glucose and ribose. The major cellular fatty acids were identified as anteiso-C15 : 0, iso-C16 : 0, anteiso-C17 : 0 and iso-C15 : 0. The predominant menaquinone was MK-9(H8). The polar lipid profile of S4702T consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol and phosphatidylinositol mannoside. S4702T could be distinguished from its closest phylogenetic neighbours using a combination of chemotaxonomic, morphological and physiological properties. Consequently, it is proposed that S4702T represents a novel species of the genus Streptomyces, for which the name Streptomyces ovatisporus sp. nov. is proposed. The type strain is S4702T (DSM 42103T=KCTC 29206T=CGMCC 4.7357T).
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Affiliation(s)
- Aysel Veyisoglu
- Department of Bioengineering, Faculty of Engineering and Architecture, Sinop University, Sinop 57000, Turkey
| | - Demet Cetin
- Science Teaching Programme, Gazi Faculty of Education, Gazi University, Ankara 06500, Turkey
| | - Kadriye Inan Bektas
- Department of Molecular Biology and Genetics, Faculty of Sciences, Karadeniz Technical University, Trabzon 61080, Turkey
| | - Kiymet Guven
- Faculty of Science, Biology Department, Anadolu University, Eskişehir 26470, Turkey
| | - Nevzat Sahin
- Department of Biology, Faculty of Art and Science, Ondokuz Mayis University, Samsun 55139, Turkey
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Delamuta JRM, Ribeiro RA, Araújo JLS, Rouws LFM, Zilli JÉ, Parma MM, Melo IS, Hungria M. Bradyrhizobium stylosanthis sp. nov., comprising nitrogen-fixing symbionts isolated from nodules of the tropical forage legume Stylosanthes spp. Int J Syst Evol Microbiol 2016; 66:3078-3087. [DOI: 10.1099/ijsem.0.001148] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Jakeline Renata Marçon Delamuta
- Embrapa Soja, C.P. 231, 86001-970 Londrina, Paraná, Brazil
- Coordenação de Aperfeiçoamento de Pessoal de Nível Superior, SBN, Quadra 2, BlocoL, Lote 06, Edifício Capes, 70.040-020 Brasília, Distrito Federal, Brazil
| | - Renan Augusto Ribeiro
- Conselho Nacional de Desenvolvimento Científico e Tecnológico, SHIS QI 1 Conjunto B, Blocos A, B, C e D, Lago Sul, 71605-001 Brasília, Distrito Federal, Brazil
| | | | | | - Jerri Édson Zilli
- Embrapa Agrobiologia, C.P. 74.505, 23891-000 Seropédica, Rio de Janeiro, Brazil
| | | | | | - Mariangela Hungria
- Embrapa Soja, C.P. 231, 86001-970 Londrina, Paraná, Brazil
- Conselho Nacional de Desenvolvimento Científico e Tecnológico, SHIS QI 1 Conjunto B, Blocos A, B, C e D, Lago Sul, 71605-001 Brasília, Distrito Federal, Brazil
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Srinivas A, Divyasree B, Tushar L, Suresh G, Sasikala C, Ramana CV. Salinicoccus amylolyticus sp. nov., isolated from a saltern. Int J Syst Evol Microbiol 2016; 66:3814-3820. [PMID: 27381021 DOI: 10.1099/ijsem.0.001270] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-positive coccus, strain JC304T, was isolated from a saltern of Nari along the Bhavnagar Coast, Gujarat, India. The 16S rRNA gene sequence analysis and sequence comparison data indicated that JC304T represented a member of the genus Salinicoccus and was most closely related to Salinicoccus roseus 9T (99.6 %), Salinicoccus luteus YIM 70202T (97.0 %), Salinicoccus hispanicus J-82T (97.0 %) and the remaining species of the genus Salinicoccus (<97 %). Genome relatedness based on DNA-DNA hybridization of JC304T with the type strains of the most closely related species was less than 46 % and the ΔTmwas >5 °C indicating that the strain represents a novel species of the genus Salinicoccus. Independent and concatenated phylogenetic analysis of recA/fusA gene translated product showed a clear distinction of JC304T from its phylogenetic neighbors. Diphosphotidylglycerol, phosphatidylglycerol, an unidentified glycolipid and three unidentified lipids (L1, L2 and L3) were the polar lipids of JC304T. Iso-C15 : 0 and anteiso-C15 : 0 were the major (>10 %) fatty acids in strain JC304T. The cell-wall amino acids were l-lysine and d-glycine. Hopanoids were not detected. The major isoprenoid quinone was menaquinone (MK-6). The DNA G+C content of JC304T was 48 mol%. On the basis of physiological, genotypic, phylogenetic and chemotaxonomic analyses, strain JC304T is considered to represent a novel species of the genus Salinicoccus, for which the name Salinicoccusamylolyticus sp. nov. is proposed. The type strain is JC304T (=KCTC 33661T=LMG 28757T).
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Affiliation(s)
- A Srinivas
- Bacterial Discovery Laboratory, Center for Environment, Institute of Science and Technology, J. N. T. University Hyderabad, Kukatpally, Hyderabad 500085, India
| | - B Divyasree
- Bacterial Discovery Laboratory, Center for Environment, Institute of Science and Technology, J. N. T. University Hyderabad, Kukatpally, Hyderabad 500085, India
| | - L Tushar
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P. O. Central University, Hyderabad 500046, India
| | - G Suresh
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P. O. Central University, Hyderabad 500046, India
| | - Ch Sasikala
- Bacterial Discovery Laboratory, Center for Environment, Institute of Science and Technology, J. N. T. University Hyderabad, Kukatpally, Hyderabad 500085, India
| | - Ch V Ramana
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P. O. Central University, Hyderabad 500046, India
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30
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Thalassospira australica sp. nov. isolated from sea water. Antonie van Leeuwenhoek 2016; 109:1091-100. [DOI: 10.1007/s10482-016-0710-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 05/03/2016] [Indexed: 10/21/2022]
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31
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Zhang W, Yang R, Fang W, Yan L, Lu J, Sheng J, Lv J. Characterization of thermophilic fungal community associated with pile fermentation of Pu-erh tea. Int J Food Microbiol 2016; 227:29-33. [PMID: 27046629 DOI: 10.1016/j.ijfoodmicro.2016.03.025] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2016] [Revised: 03/02/2016] [Accepted: 03/22/2016] [Indexed: 11/17/2022]
Abstract
This study aimed to characterize the thermophilic fungi in pile-fermentation process of Pu-erh tea. Physicochemical analyses showed that the high temperature and low pH provided optimal conditions for propagation of fungi. A number of fungi, including Blastobotrys adeninivorans, Thermomyces lanuginosus, Rasamsonia emersonii, Aspergillus fumigatus, Rhizomucor pusillus, Rasamsonia byssochlamydoides, Rasamsonia cylindrospora, Aspergillus tubingensis, Aspergillus niger, Candida tropicalis and Fusarium graminearum were isolated as thermophilic fungi under combination of high temperature and acid culture conditions from Pu-erh tea pile-fermentation. The fungal communities were analyzed by PCR-DGGE. Results revealed that those fungi are closely related to Debaryomyces hansenii, Cladosporium cladosporioides, A. tubingensis, R. emersonii, R. pusillus, A. fumigatus and A. niger, and the last four presented as dominant species in the pile process. These four preponderant thermophilic fungi reached the order of magnitude of 10(7), 10(7), 10(7) and 10(6)copies/g dry tea, respectively, measured by real-time quantitative PCR (q-PCR). The results indicate that the thermophilic fungi play an important role in Pu-erh tea pile fermentation.
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Affiliation(s)
- Wei Zhang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Ruijuan Yang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China; Pu'er Institute of Pu-erh Tea, Pu'er, Yunnan 665000, China
| | - Wenjun Fang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Liang Yan
- Pu'er Institute of Pu-erh Tea, Pu'er, Yunnan 665000, China
| | - Jun Lu
- Institute for Applied Ecology New Zealand, School of Applied Sciences, Faculty of Health and Environmental Sciences, Auckland University of Technology, Auckland 1142, New Zealand; School of Interprofessional Health Studies, Faculty of Health and Environmental Sciences, Auckland University of Technology, Auckland 0627, New Zealand; Institute of Biomedical Technology, Auckland University of Technology, Auckland 1142, New Zealand
| | - Jun Sheng
- Faculty of Food Science and Technology, Yunnan Agricultural University, Kunming, Yunnan 650201, China.
| | - Jie Lv
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China.
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Joshi A, Thite S, Kulkarni G, Dhotre D, Joseph N, Venkata Ramana V, Polkade A, Shouche Y. Nitrincola alkalisediminis sp. nov., an alkaliphilic bacterium isolated from an alkaline lake. Int J Syst Evol Microbiol 2016; 66:1254-1259. [DOI: 10.1099/ijsem.0.000868] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Amaraja Joshi
- Microbial Culture Collection, National Centre for Cell Science, Sai Trinity Complex, Sus Road, Pashan, Pune- 411021, India
| | - Sonia Thite
- Microbial Culture Collection, National Centre for Cell Science, Sai Trinity Complex, Sus Road, Pashan, Pune- 411021, India
| | - Girish Kulkarni
- Microbial Culture Collection, National Centre for Cell Science, Sai Trinity Complex, Sus Road, Pashan, Pune- 411021, India
| | - Dhiraj Dhotre
- Microbial Culture Collection, National Centre for Cell Science, Sai Trinity Complex, Sus Road, Pashan, Pune- 411021, India
| | - Neetha Joseph
- Microbial Culture Collection, National Centre for Cell Science, Sai Trinity Complex, Sus Road, Pashan, Pune- 411021, India
| | - V. Venkata Ramana
- Microbial Culture Collection, National Centre for Cell Science, Sai Trinity Complex, Sus Road, Pashan, Pune- 411021, India
| | - Ashish Polkade
- Microbial Culture Collection, National Centre for Cell Science, Sai Trinity Complex, Sus Road, Pashan, Pune- 411021, India
| | - Yogesh Shouche
- Microbial Culture Collection, National Centre for Cell Science, Sai Trinity Complex, Sus Road, Pashan, Pune- 411021, India
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Busarakam K, Brown R, Bull AT, Tan GYA, Zucchi TD, da Silva LJ, de Souza WR, Goodfellow M. Classification of thermophilic actinobacteria isolated from arid desert soils, including the description of Amycolatopsis deserti sp. nov. Antonie van Leeuwenhoek 2016; 109:319-34. [PMID: 26809280 DOI: 10.1007/s10482-015-0635-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 12/09/2015] [Indexed: 11/25/2022]
Abstract
The taxonomic position of 26 filamentous actinobacteria isolated from a hyper-arid Atacama Desert soil and 2 from an arid Australian composite soil was established using a polyphasic approach. All of the isolates gave the diagnostic amplification product using 16S rRNA oligonucleotide primers specific for the genus Amycolatopsis. Representative isolates had chemotaxonomic and morphological properties typical of members of the genus Amycolatopsis. 16S rRNA gene analyses showed that all of the isolates belong to the Amycolatopsis methanolica 16S rRNA gene clade. The Atacama Desert isolates were assigned to one or other of two recognised species, namely Amycolatopsis ruanii and Amycolatopsis thermalba, based on 16S rRNA gene sequence, DNA:DNA relatedness and phenotypic data; emended descriptions are given for these species. In contrast, the two strains from the arid Australian composite soil, isolates GY024(T) and GY142, formed a distinct branch at the periphery of the A. methanolica 16S rRNA phyletic line, a taxon that was supported by all of the tree-making algorithms and by a 100 % bootstrap value. These strains shared a high degree of DNA:DNA relatedness and have many phenotypic properties in common, some of which distinguished them from all of the constituent species classified in the A. methanolica 16S rRNA clade. Isolates GY024(T) and GY142 merit recognition as a new species within the A. methanolica group of thermophilic strains. The name proposed for the new species is Amycolatopsis deserti sp. nov.; the type strain is GY024(T) (=NCIMB 14972(T) = NRRL B-65266(T)).
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Affiliation(s)
- Kanungnid Busarakam
- School of Biology, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
- Department of Agricultural Technology, Thailand Institute of Scientific and Technological Research, Pathum Thani, 12120, Thailand
| | - Ros Brown
- School of Biology, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Alan T Bull
- School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK
| | - Geok Yuan Annie Tan
- Institute of Biological Sciences, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Tiago D Zucchi
- Laboratório de Microbiologia, EMBRAPA Meio Ambiente, Rod SP 340-Km 127, PO Box 69, Jaguariúna, 13820-000, Brazil
- Agrivalle, Av. Tranquillo Giannini, 1050, Salto, 13329-600, Brazil
| | - Leonardo José da Silva
- Laboratório de Microbiologia, EMBRAPA Meio Ambiente, Rod SP 340-Km 127, PO Box 69, Jaguariúna, 13820-000, Brazil
| | - Wallace Rafael de Souza
- Laboratório de Microbiologia, EMBRAPA Meio Ambiente, Rod SP 340-Km 127, PO Box 69, Jaguariúna, 13820-000, Brazil
| | - Michael Goodfellow
- School of Biology, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK.
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Divyasree B, Lakshmi KVNS, Bharti D, Sasikala C, Ramana CV. Rhodovulum aestuarii sp. nov., isolated from a brackish water body. Int J Syst Evol Microbiol 2016; 66:165-171. [DOI: 10.1099/ijsem.0.000691] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- B. Divyasree
- Bacterial Discovery Laboratory, Centre for Environment, IST, JNT University Hyderabad, Kukatpally, Hyderabad 500085, India
| | - K. V. N. S. Lakshmi
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500046, India
| | - Dave Bharti
- Department of Life Sciences, Majaraja Krishnakunarsinhji Bhavnagar University, Bhavnagar, Gujarat 364002, India
| | - Ch. Sasikala
- Bacterial Discovery Laboratory, Centre for Environment, IST, JNT University Hyderabad, Kukatpally, Hyderabad 500085, India
| | - Ch. V. Ramana
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500046, India
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Veyisoglu A, Tatar D, Saygin H, Inan K, Cetin D, Guven K, Tuncer M, Sahin N. Microvirga makkahensis sp. nov., and Microvirga arabica sp. nov., isolated from sandy arid soil. Antonie van Leeuwenhoek 2015; 109:287-96. [PMID: 26671415 DOI: 10.1007/s10482-015-0631-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 12/08/2015] [Indexed: 10/22/2022]
Abstract
The taxonomic positions of two Gram-negative strains, SV1470(T) and SV2184P(T), isolated from arid soil samples, were determined using a polyphasic approach. Analysis of the 16S rRNA gene and the concatenated sequences of three housekeeping gene loci (dnaK, rpoB and gyrB) confirmed that the strains belong to the genus Microvirga. Strain SV1470(T) was found to be closely related to Microvirga vignae BR3299(T) (98.8 %), Microvirga flocculans TFB(T) (98.3 %) and Microvirga lupini Lut6(T) (98.2 %), whilst similarity to other type strains of the genus ranged from 97.8 to 96.3 %; strain SV2184P(T) was found to be closely related to Microvirga aerilata 5420S-16(T) (98.0 %), Microvirga zambiensis WSM3693(T) (97.8 %) and M. flocculans ATCC BAA-817(T) (97.4 %), whilst similarity to other type strains of the genus ranged from 97.2 to 95.9 %. The G + C content of the genomic DNA was determined to be 61.5 mol % for strain SV1470(T) and 62.1 mol % for strain SV2184P(T). Both strains were found to have the same quinone system, with Q-10 as the major ubiquinone. The polar lipid profile of strain SV1470(T) was found to consist of phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, one unidentified phospholipid and one unidentified aminolipid, while that of strain SV2184P(T) consisted of phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmethylethanolamine, one unidentified aminolipid, one unidentified aminophospholipid and two unidentified phospholipids. DNA-DNA relatedness studies showed that the two strains belong to different genomic species. The strains were also distinguished using a combination of phenotypic properties. Based on the genotypic and phenotypic data, the novel species Microvirga makkahensis sp. nov. (type strain SV1470(T) = DSM 25394(T) = KCTC 23863(T) = NRRL-B 24875(T)) and Microvirga arabica sp. nov. (type strain SV2184P(T) = DSM 25393(T) = KCTC 23864(T) = NRRL-B 24874(T)) are proposed.
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Affiliation(s)
- Aysel Veyisoglu
- Department of Biology, Faculty of Art and Science, Ondokuz Mayis University, 55139, Atakum-Samsun, Turkey.,Department of Bioengineering, Faculty of Engineering and Architecture, Sinop University, 57000, Nasuhbasoglu-Sinop, Turkey
| | - Demet Tatar
- Department of Biology, Faculty of Art and Science, Ondokuz Mayis University, 55139, Atakum-Samsun, Turkey
| | - Hayrettin Saygin
- Department of Biology, Faculty of Art and Science, Ondokuz Mayis University, 55139, Atakum-Samsun, Turkey
| | - Kadriye Inan
- Molecular Biology and Genetics Department, Faculty of Science, Karadeniz Technical University, 61080, Trabzon, Turkey
| | - Demet Cetin
- Science Teaching Programme, Gazi Faculty of Education, Gazi University, 06500, Ankara, Turkey
| | - Kiymet Guven
- Department of Biology, Faculty of Science, Anadolu University, 26470, Eskisehir, Turkey
| | - Munir Tuncer
- Department of Biology, Faculty of Art and Science, Mersin University, 33342, Ciftlikköy-Mersin, Turkey
| | - Nevzat Sahin
- Department of Biology, Faculty of Art and Science, Ondokuz Mayis University, 55139, Atakum-Samsun, Turkey.
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Nocardia zapadnayensis sp. nov., isolated from soil. Antonie van Leeuwenhoek 2015; 109:95-103. [DOI: 10.1007/s10482-015-0612-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 10/24/2015] [Indexed: 10/22/2022]
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Sahin N, Veyisoglu A, Tatar D, Saygin H, Cetin D, Guven K, Klenk HP, Goodfellow M. Phytomonospora cypria sp. nov., isolated from soil. Antonie van Leeuwenhoek 2015; 108:1425-1432. [PMID: 26427856 DOI: 10.1007/s10482-015-0596-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Accepted: 09/21/2015] [Indexed: 10/23/2022]
Abstract
A Gram-stain positive actinobacterial strain, designated KT1403(T), was isolated from a soil sample, collected from Karpaz, Magusa, Northern Cyprus, and characterised using a polyphasic approach. Morphological characteristics and chemotaxonomic data indicated that the strain belongs to the genus Phytomonospora. The cell wall of the novel strain contained meso-diaminopimelic acid and galactose, glucose and mannose as the major sugars in whole cell hydrolysates. The polar lipids in the cell membrane were identified as diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, an unidentified aminophospholipid and three unidentified glycolipids. The predominant menaquinones were MK-10(H6) and MK-10(H4). The major fatty acids were found to be iso C15:0 , anteiso C15:0 and anteiso C17:0. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain KT1403(T) belongs to the genus Phytomonospora with a sequence similarity of 99.73 % with Phytomonospora endophytica, the type species of the genus. DNA-DNA hybridization further differentiated strain KT1403(T) from its near phylogenetic neighbour, P. endophytica DSM 45386(T) (29.0 ± 2.2 % DNA relatedness). Therefore, it is proposed that strain KT1403(T) represents a novel species of the genus Phytomonospora, for which the name Phytomonospora cypria sp. nov. is proposed. The type strain is KT1403(T) (=KCTC 29479(T) = DSM 46767(T)).
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Affiliation(s)
- Nevzat Sahin
- Department of Biology, Faculty of Art and Science, Ondokuz Mayis University, 55139, Atakum-Samsun, Turkey.
| | - Aysel Veyisoglu
- Department of Biology, Faculty of Art and Science, Ondokuz Mayis University, 55139, Atakum-Samsun, Turkey.,Department of Bioengineering, Faculty of Engineering and Architecture, Sinop University, 57000, Nasuhbasoglu-Sinop, Turkey
| | - Demet Tatar
- Department of Biology, Faculty of Art and Science, Ondokuz Mayis University, 55139, Atakum-Samsun, Turkey
| | - Hayrettin Saygin
- Department of Biology, Faculty of Art and Science, Ondokuz Mayis University, 55139, Atakum-Samsun, Turkey
| | - Demet Cetin
- Science Teaching Programme, Gazi Faculty of Education, Gazi University, 06500, Ankara, Turkey
| | - Kiymet Guven
- Biology Department, Faculty of Science, Anadolu University, 26470, Eskisehir, Turkey
| | - Hans-Peter Klenk
- Department of Agricultural & Environmental Science, School of Biology, Newcastle University, Ridley Building, Newcastle upon Tyne, NE1 7RU, UK
| | - Michael Goodfellow
- Department of Agricultural & Environmental Science, School of Biology, Newcastle University, Ridley Building, Newcastle upon Tyne, NE1 7RU, UK
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38
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Padakandla SR, Lee GW, Chae JC. Paenibacillus gelatinilyticus sp. nov. a psychrotolerant bacterium isolated from a reclaimed soil and amended description of Paenibacillus shenyangensis. Antonie van Leeuwenhoek 2015; 108:1197-203. [PMID: 26319400 DOI: 10.1007/s10482-015-0574-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 08/21/2015] [Indexed: 11/24/2022]
Abstract
A rod shaped, Gram-stain positive, non-motile, facultative anaerobic and gelatin hydrolysing bacterium, strain PG1(T), was isolated from reclaimed land soil in Kyehwa-do, Republic of Korea. Strain PG1(T) showed highest 16S rRNA gene sequence similarity (97.4 and 96.5%, respectively) to Paenibacillus shenyangensis A9(T) and Paenibacillus hunanensis FeL05(T), and clustered closely with the members of the family Paenibacillaceae. DNA-DNA hybridization studies revealed a genomic relatedness of 47 ± 9% with P. shenyangensis A9(T). The predominant fatty acids of strain PG1(T) were identified to be anteiso-C(15:0) (46.7%) and C(16:0) (22.7%). Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and an unidentified phospholipid were found to be the major polar lipids. The genomic DNA G+C content was found to be 47.7 mol%. This polyphasic characterisation of the newly isolated strain PG1(T) justifies its description as representative of a novel species in the genus Paenibacillus, for which the name Paenibacillus gelatinilyticus sp. nov., (type strain = PG1(T) = KCTC 33642(T) = JCM 30624(T)) is proposed.
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Affiliation(s)
- Shalem Raj Padakandla
- Division of Biotechnology, Chonbuk National University, Iksan, 570-752, Republic of Korea
| | - Gun-Woong Lee
- Division of Biotechnology, Chonbuk National University, Iksan, 570-752, Republic of Korea
| | - Jong-Chan Chae
- Division of Biotechnology, Chonbuk National University, Iksan, 570-752, Republic of Korea.
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39
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Jia L, Feng X, Zheng Z, Han L, Hou X, Lu Z, Lv J. Polymorphobacter fuscus sp. nov., isolated from permafrost soil, and emended description of the genus Polymorphobacter. Int J Syst Evol Microbiol 2015; 65:3920-3925. [PMID: 26246176 DOI: 10.1099/ijsem.0.000514] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strain D40PT, representing a novel Gram-stain-negative, obligately aerobic, bacteriochlorophyll a-containing bacterium of the α-4 subgroup of the phylum Proteobacteria, was isolated from permafrost soil of Kunlun mountains gap, Qinghai-Tibet plateau. Cells were non-motile rod-cocci and formed brown-pigmented colonies. According to the absorption spectrum, carotenoids and two different photosynthetic light-harvesting complexes, an LHI complex and a B800-835-type peripheral LHII complex, were present in the cells. The strain was oxidase-negative and catalase-positive. The predominant fatty acids of strain D40PT were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C17 : 1ω6c and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c). The main polar lipids were phosphatidylethanolamine, phosphatidylglycerol, unidentified phospholipid, two glycolipids and sphingoglycolipid. The major respiratory quinone was ubiquinone-10, whereas ubiquinone-9 was present in smaller amounts. The 16S rRNA gene sequence similarity to the closest phylogenetic relative, Polymorphobacter multimanifer JCM 18140T, was 97.5 %. DNA-DNA relatedness (ΔTm) between strain D40PT and P. multimanifer was 12.4 °C. The G+C content of the genomic DNA of strain D40PT was 67.4 mol%. Accordingly, the strain represents a novel species, for which the name Polymorphobacter fuscus sp. nov. is proposed. The type strain is D40PT ( = CGMCC 1.12714T = JCM 19740T). An emended description of the genus Polymorphobacter is also proposed.
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Affiliation(s)
- Li Jia
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, PR China
| | - Xiaomin Feng
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, PR China
| | - Zhong Zheng
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, PR China
| | - Lu Han
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, PR China.,College of Resources and Environmental Science, East China Normal University, Shanghai 200241, PR China
| | - Xiaocui Hou
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, PR China
| | - Zhenquan Lu
- Oil and Gas Survey, China Geological Survey, Beijing 100029, PR China
| | - Jie Lv
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, PR China
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40
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Wang YX, Huang FQ, Nogi Y, Pang SJ, Wang PK, Lv J. Youhaiella tibetensis gen. nov., sp. nov., isolated from subsurface sediment. Int J Syst Evol Microbiol 2015; 65:2048-2055. [DOI: 10.1099/ijs.0.000219] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-reaction-negative bacterial strain, designated fig4T, was isolated from a subsurface sediment core of Qiangtang Basin permafrost in China. Cells were catalase- and oxidase-positive and rods. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain fig4T was a member of the family Hyphomicrobiaceae and was most closely related to members of the genera Pelagibacterium, Vasilyevaea and Devosia with 93.8–96.2 % sequence similarities. The major cellular fatty acids were C16 : 0, C18 : 0, 11-methyl C18 : 1ω7c, C19 : 0 cyclo ω8c and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c). The major respiratory quinone was Q-10 and the major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and two unknown glycolipids. The DNA G+C content was 60.7 mol%. Based on the phenotypic, phylogenetic and genotypic data, strain fig4T is considered to represent a novel species of a new genus in the family Hyphomicrobiaceae, for which the name Youhaiella tibetensis gen. nov., sp. nov. is proposed. The type strain is fig4T ( = CGMCC 1.12719T = JCM 19854T).
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Affiliation(s)
- Yun-xiang Wang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, PR China
| | - Fa-qi Huang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, PR China
| | - Yuichi Nogi
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Shou-ji Pang
- Oil & Gas Survey, China Geological Survey, Beijing 100029, PR China
| | - Ping-kang Wang
- Oil & Gas Survey, China Geological Survey, Beijing 100029, PR China
| | - Jie Lv
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, PR China
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41
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Souza WR, Silva RE, Goodfellow M, Busarakam K, Figueiro FS, Ferreira D, Rodrigues-Filho E, Moraes LAB, Zucchi TD. Amycolatopsis rhabdoformis sp. nov., an actinomycete isolated from a tropical forest soil. Int J Syst Evol Microbiol 2015; 65:1786-1793. [DOI: 10.1099/ijs.0.000176] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strain SB026T was isolated from Brazilian rainforest soil and its taxonomic position established using data from a polyphasic study. The organism showed a combination of chemotaxonomic and morphological features consistent with its classification in the genus
Amycolatopsis
and formed a branch in the
Amycolatopsis
16S rRNA gene tree together with
Amycolatopsis bullii
NRRL B-24847T,
Amycolatopsis plumensis
NRRL B-24324T,
Amycolatopsis tolypomycina
DSM 44544T and
Amycolatopsis vancoresmycina
NRRL B-24208T. It was related most closely to
A. bullii
NRRL B-24847T (99.0 % 16S rRNA gene sequence similarity), but was distinguished from this strain by a low level of DNA–DNA relatedness (~46 %) and discriminatory phenotypic properties. Based on the combined genotypic and phenotypic data, it is proposed that the isolate should be classified in the genus
Amycolatopsis
as representing a novel species, Amycolatopsis rhabdoformis sp. nov. The type strain is SB026T ( = CBMAI 1694T = CMAA 1285T = NCIMB 14900T).
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Affiliation(s)
- Wallace Rafael Souza
- Laboratório de Microbiologia Ambiental, Rod SP 340-Km 127, 5, Caixa Postal 69, EMBRAPA Meio Ambiente, 13820-000 Jaguariúna, Brazil
| | - Rafael Eduardo Silva
- Laboratório de Microbiologia Ambiental, Rod SP 340-Km 127, 5, Caixa Postal 69, EMBRAPA Meio Ambiente, 13820-000 Jaguariúna, Brazil
| | - Michael Goodfellow
- School of Biology, University of Newcastle, Newcastle upon Tyne NE1 7RU, UK
| | | | - Fernanda Sales Figueiro
- Laboratório de Espectrometria de Massa Aplicado à Química de Produtos Naturais, Faculdade de Filosofia, Ciencias e Letras de Ribeirão Preto, Universidade de São Paulo, Avenida dos Bandeirantes, 3900, 14040-901, Ribeirão Preto, Brazil
| | - Douglas Ferreira
- Laboratório de Bioquímica Micromolecular de Microorganismos, Departamento de Química, Universidade Federal de São Carlos, Rodovia Washington Luiz, Km 235, Caixa Postal 676, 13565-905, São Carlos, Brazil
| | - Edson Rodrigues-Filho
- Laboratório de Bioquímica Micromolecular de Microorganismos, Departamento de Química, Universidade Federal de São Carlos, Rodovia Washington Luiz, Km 235, Caixa Postal 676, 13565-905, São Carlos, Brazil
| | - Luiz Alberto Beraldo Moraes
- Laboratório de Espectrometria de Massa Aplicado à Química de Produtos Naturais, Faculdade de Filosofia, Ciencias e Letras de Ribeirão Preto, Universidade de São Paulo, Avenida dos Bandeirantes, 3900, 14040-901, Ribeirão Preto, Brazil
| | - Tiago Domingues Zucchi
- Laboratório de Microbiologia Ambiental, Rod SP 340-Km 127, 5, Caixa Postal 69, EMBRAPA Meio Ambiente, 13820-000 Jaguariúna, Brazil
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42
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Lucena-Padrós H, González JM, Caballero-Guerrero B, Luis Ruiz-Barba J, Maldonado-Barragán A. Vibrio olivae sp. nov., isolated from Spanish-style green-olive fermentations. Int J Syst Evol Microbiol 2015; 65:1895-1901. [PMID: 25792368 DOI: 10.1099/ijs.0.000196] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Three isolates originating from Spanish-style green-olive fermentations in a manufacturing company in the province of Seville, Spain, were taxonomically characterized by a polyphasic approach. This included a phylogenetic analysis based on 16S rRNA gene sequences and multi-locus sequence analysis (MLSA) based on pyrH, recA, rpoA, gyrB and mreB genes. The isolates shared 98.0 % 16S rRNA gene sequence similarity with Vibrio xiamenensis G21T. Phylogenetic analysis based on 16S rRNA gene sequences using the neighbour-joining and maximum-likelihood methods showed that the isolates fell within the genus Vibrio and formed an independent branch close to V. xiamenensis G21T. The maximum-parsimony method grouped the isolates to V. xiamenensis G21T but forming two clearly separated branches. Phylogenetic trees based on individual pyrH, recA, rpoA, gyrB and mreB gene sequences revealed that strain IGJ1.11T formed a clade alone or with V. xiamenensis G21T. Sequence similarities of the pyrH, recA, rpoA, gyrB and mreB genes between strain IGJ1.11T and V. xiamenensis G21T were 86.7, 85.7, 97.3, 87.6 and 84.8 %, respectively. MLSA of concatenated sequences showed that strain IGJ1.11T and V. xiamenensis G21T are two clearly separated species that form a clade, which we named Clade Xiamenensis, that presented 89.7 % concatenated gene sequence similarity, i.e. less than 92 %. The major cellular fatty acids (>5 %) of strain IGJ1.11T were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c). Enzymic activity profiles, sugar fermentation patterns and DNA G+C content (52.9 mol%) differentiated the novel strains from the closest related members of the genus Vibrio. The name Vibrio olivae sp. nov. is proposed for the novel species. The type strain is IGJ1.11T ( = CECT 8064T = DSM 25438T).
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Affiliation(s)
- Helena Lucena-Padrós
- Departamento de Biotecnología de Alimentos, Instituto de la Grasa, Consejo Superior de Investigaciones Científicas (CSIC), Campus Universitario Pablo de Olavide, Edificio 46; Carretera de Utrera, Km 1 41013 Sevilla, Spain
| | - Juan M González
- Instituto de Recursos Naturales y Agrobiología, Consejo Superior de Investigaciones Científicas (CSIC), P.O. Box 1052, 41080 Sevilla, Spain
| | - Belén Caballero-Guerrero
- Departamento de Biotecnología de Alimentos, Instituto de la Grasa, Consejo Superior de Investigaciones Científicas (CSIC), Campus Universitario Pablo de Olavide, Edificio 46; Carretera de Utrera, Km 1 41013 Sevilla, Spain
| | - José Luis Ruiz-Barba
- Departamento de Biotecnología de Alimentos, Instituto de la Grasa, Consejo Superior de Investigaciones Científicas (CSIC), Campus Universitario Pablo de Olavide, Edificio 46; Carretera de Utrera, Km 1 41013 Sevilla, Spain
| | - Antonio Maldonado-Barragán
- Departamento de Biotecnología de Alimentos, Instituto de la Grasa, Consejo Superior de Investigaciones Científicas (CSIC), Campus Universitario Pablo de Olavide, Edificio 46; Carretera de Utrera, Km 1 41013 Sevilla, Spain
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43
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Patil VS, Salunkhe RC, Patil RH, Husseneder C, Shouche YS, Venkata Ramana V. Enterobacillus tribolii gen. nov., sp. nov., a novel member of the family Enterobacteriaceae, isolated from the gut of a red flour beetle, Tribolium castaneum. Antonie Van Leeuwenhoek 2015; 107:1207-16. [PMID: 25716888 DOI: 10.1007/s10482-015-0412-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 02/20/2015] [Indexed: 10/24/2022]
Abstract
Two novel Gram-stain negative facultative anaerobic, motile, rod-shaped bacterial strains IG-V01(T) and IG-V01b were isolated from the gut of red flour beetles, Tribolium castaneum. The 16S rRNA gene sequences of strains IG-V01(T) and IG-V01b were found to have their highest sequence similarity (96.5% and 96.4%) with Serratia nematodiphila DZ0503SBS1(T) (Enterobacteriaceae family) respectively. Strains IG-V01(T) and IG-V01b share 100% 16S rRNA gene sequence similarity and exhibit very similar phenotypic characteristics. In addition, they show 89.7% genomic relatedness (DNA-DNA hybridisation). Major fatty acids were identified to be C(16:0) (38.3%), C(17:0) cyclo (19.5-20%) and C(14:0) (11.2-11.3%). Cells contain phosphatidylethanolamine and diphosphatidylglycerol as predominant polar lipids. Genomic DNA G+C content (mol%) was determined to be 51.5-51.7. A polyphasic approach employing the study of morphological, physiological, chemotaxonomic, genomic and phylogenetic analysis revealed that the two newly isolated strains cannot be placed in any of the existing genera of the family Enterobacteriaceae. Therefore, it is proposed that strains IG-V01(T) and IG-V01b belong to a novel genus within the family Enterobacteriaceae, and represent a new species Enterobacillus tribolii gen. nov., sp. nov., with the type strain =IG-V01(T) = KCTC 42159(T) = MCC 2532(T).
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Affiliation(s)
- Vikas S Patil
- Microbial Culture Collection, National Centre for Cell Science, Pune, 411007, Maharastra, India
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Streptosporangium terrae sp. nov., a novel actinomycete isolated from the rhizosphere of Callistemon citrinus (Curtis), India. J Antibiot (Tokyo) 2015; 68:425-30. [PMID: 25690360 DOI: 10.1038/ja.2015.5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2014] [Revised: 12/29/2014] [Accepted: 01/12/2015] [Indexed: 11/08/2022]
Abstract
A novel actinomycete strain, designated VRC21(T), was isolated from the rhizosphere of Callistemon citrinus collected from Hyderabad, India. The morphological and chemotaxonomic properties of strain VRC21(T) was consistent with the characteristics of members of the genus Streptosporangium, that is, the formation of sporangia on aerial mycelium, coiled unbranched hyphae within the spore vesicle, the presence of meso-diaminopimelic acid in the cell wall, and madurose and galactose as major whole-cell sugars. Diagnostic polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and phosphatidylinositol-mannosides. The predominant menaquinones were MK-9(H2) and MK-9(H4). The major cellular fatty acids were iso-C14:0, iso-C16:0, C17:0 10-methyl, C18:1w9c and C18:0 10-methyl. 16S rRNA gene sequence analyses revealed that strain VRC21(T) was a member of the genus Streptosporangium. The highest similarity values were observed with S. carneum DSM 44125(T) (98.2%) and S. fragile DSM 43847(T) (98.2%); the values of the remaining type strains were below 98%. The values of DNA-DNA relatedness between the strain VRC21(T) and the type strains of the related species were below 70%. On the basis of the polyphasic evidence, the strain VRC21(T) should be classified as novel species Streptosporangium terrae sp. nov. in the genus Streptosporangium. The type strain is VRC21(T) (=KCTC 29207(T)=MTCC 11724(T)).
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Menezes CBA, Tonin MF, Corrêa DBA, Parma M, de Melo IS, Zucchi TD, Destéfano SAL, Fantinatti-Garboggini F. Chromobacterium amazonense sp. nov. isolated from water samples from the Rio Negro, Amazon, Brazil. Antonie van Leeuwenhoek 2015; 107:1057-63. [PMID: 25663027 DOI: 10.1007/s10482-015-0397-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2014] [Accepted: 01/23/2015] [Indexed: 11/25/2022]
Abstract
The taxonomic position of a bacterium isolated from water samples from the Rio Negro, in Amazon, Brazil, was determined by using a polyphasic approach. The organism formed a distinct phyletic line in the Chromobacterium 16S rRNA gene tree and had chemotaxonomic and morphological properties consistent with its classification in this genus. It was found to be closely related to Chromobacterium vaccinii DSM 25150(T) (98.6 % 16S rRNA gene similarity) and shared 98.5 % 16S rRNA gene similarity with Chromobacterium piscinae LGM 3947(T). DNA-DNA relatedness studies showed that isolate CBMAI 310(T) belongs to distinct genomic species. The isolate was readily distinguished from the type strain of these species using a combination of phenotypic and chemotaxonomic properties. Thus, based on genotypic and phenotypic data, it is proposed that isolate CBMAI 310(T) (=DSM 26508(T)) be classified in the genus Chromobacterium as the type strain of a novel species, namely, Chromobacterium amazonense sp. nov.
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Affiliation(s)
- Claudia Beatriz Afonso Menezes
- Centro Pluridisciplinar de Pesquisas Químicas Biológicas e Agrícolas, UNICAMP, Avenida Alexandre Cazelatto, 999, Campinas, SP, CEP 13083-218, Brazil
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46
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Feng Q, Gao Y, Nogi Y, Tan X, Han L, Zhang Y, Lv J. Flavobacterium maotaiense sp. nov., isolated from freshwater. Int J Syst Evol Microbiol 2015; 65:171-176. [DOI: 10.1099/ijs.0.064139-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two novel strains, T9T and T10, were isolated from water samples collected from Chishui River flowing through Maotai town, Guizhou, south-west China. The isolates were yellow-pigmented, Gram-reaction-negative, rod-shaped, non-motile and aerobic. Phylogenetic analysis based on 16S rRNA gene sequences showed that the isolates belonged to the genus
Flavobacterium
, and showed highest similarities to
Flavobacterium hibernum
DSM 12611T (97.0 %), followed by
Flavobacterium granuli
Kw05T (96.7 %) and
Flavobacterium pectinovorum
DSM 6368T (96.7 %). The novel strains were able to grow at 20–37 °C (optimum 25 °C), pH 7.0–10.0 (optimum pH 7.0–8.0) and with 0–0.5 % (w/v) NaCl (optimum 0.5 %). The predominant fatty acids were iso-C15 : 0, C16 : 1ω7c, anteiso-C15 : 0, C15 : 0, iso-C15 : 0 3-OH and iso-C15 : 1ω10c, and menaquinone-6 (MK-6) was the main respiratory quinone. The major polar lipids were phosphatidylethanolamine, one unknown glycolipid, two unknown aminolipids and two unidentified lipids. The DNA G+C contents of strains T9T and T10 were 37.7 and 36.4 mol%, respectively. According to the phenotypic and genetic data, strains T9T and T10 represent a novel species in the genus
Flavobacterium
, for which the name Flavobacterium maotaiense sp. nov. is proposed. The type strain is T9T ( = CGMCC 1.12712T = JCM 19927T).
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Affiliation(s)
- Qingqing Feng
- College of Life Science and Technology, Beijing University of Chemical Technology, 15 Beisanhuan East Road, Chaoyang District, Beijing 100029, PR China
| | - Yuan Gao
- College of Life Science and Technology, Beijing University of Chemical Technology, 15 Beisanhuan East Road, Chaoyang District, Beijing 100029, PR China
| | - Yuichi Nogi
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Xu Tan
- College of Life Science and Technology, Beijing University of Chemical Technology, 15 Beisanhuan East Road, Chaoyang District, Beijing 100029, PR China
| | - Lu Han
- College of Resources and Environmental Science, East China Normal University, Shanghai, 200241, PR China
- College of Life Science and Technology, Beijing University of Chemical Technology, 15 Beisanhuan East Road, Chaoyang District, Beijing 100029, PR China
| | - Yali Zhang
- College of Life Science and Technology, Beijing University of Chemical Technology, 15 Beisanhuan East Road, Chaoyang District, Beijing 100029, PR China
| | - Jie Lv
- College of Life Science and Technology, Beijing University of Chemical Technology, 15 Beisanhuan East Road, Chaoyang District, Beijing 100029, PR China
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47
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Saricaoglu S, Isik K, Veyisoglu A, Saygin H, Cetin D, Guven K, Spröer C, Klenk HP, Sahin N. Streptomyces burgazadensis sp. nov., isolated from soil. Int J Syst Evol Microbiol 2014; 64:4043-4048. [DOI: 10.1099/ijs.0.065870-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel actinobacterial strain, designated Z1R7T, was isolated from a soil sample collected from Burgazada, in the Marmara Sea (Turkey), and the strain identity was determined using a polyphasic taxonomic approach. The organism had chemotaxonomic and morphological properties consistent with its classification in the genus
Streptomyces
and it formed a distinct phyletic line in the 16S rRNA gene tree, together with the type strains
Streptomyces specialis
GW41-1564T (95.76 %),
Streptomyces mayteni
YIM 60475T (95.64 %),
Streptomyces hainanensis
YIM 47672T (95.53 %),
Streptomyces hoynatensis
S1412T (95.29 %),
Streptomyces avicenniae
MCCC 1A01535T (94.74 %),
Streptomyces sedi
YIM 65188T (94.59 %) and
Streptomyces zhaozhouensis
NEAU-LZS-5T (94.68 %). Chomotaxonomic data revealed that strain Z1R7T possesed MK-9 (H8) as the predominant menaquinone, ll-diaminopimelic acid as the diagnostic diamino acid, and galactose, glucose and ribose as whole cell sugars. Diphosphatidylglycerol, phoshphatidylethanolamine and phosphatidylinositol were the predominant polar lipids; iso-C16 : 0, anteiso-C17 : 0 and anteiso-C15 : 0 were the major fatty acids, and the genomic DNA G+C content was 69.4 mol%. On the basis of these genotypic and phenotypic data, it is proposed that isolate Z1R7T ( = KCTC 29434T = DSM 42126T) should be classified in the genus
Streptomyces
as Streptomyces burgazadensis sp. nov.
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Affiliation(s)
- Salih Saricaoglu
- Department of Biology, Faculty of Art and Science, Ondokuz Mayis University, 55139 Kurupelit-Samsun, Turkey
| | - Kamil Isik
- Department of Biology, Faculty of Art and Science, Ondokuz Mayis University, 55139 Kurupelit-Samsun, Turkey
| | - Aysel Veyisoglu
- Department of Biology, Faculty of Art and Science, Ondokuz Mayis University, 55139 Kurupelit-Samsun, Turkey
| | - Hayrettin Saygin
- Department of Biology, Faculty of Art and Science, Ondokuz Mayis University, 55139 Kurupelit-Samsun, Turkey
| | - Demet Cetin
- Science Teaching Programme, Gazi Faculty of Education, Gazi University, Ankara, Turkey
| | - Kiymet Guven
- Anadolu University, Faculty of Science, Biology Department, 26470, Eskişehir, Turkey
| | - Cathrin Spröer
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, 38124 Braunschweig, Germany
| | - Hans-Peter Klenk
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, 38124 Braunschweig, Germany
| | - Nevzat Sahin
- Department of Biology, Faculty of Art and Science, Ondokuz Mayis University, 55139 Kurupelit-Samsun, Turkey
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Sonalkar VV, Mawlankar R, Venkata Ramana V, Joseph N, Shouche YS, Dastager SG. Bacillus filamentosus sp. nov., isolated from sediment sample. Antonie van Leeuwenhoek 2014; 107:433-41. [DOI: 10.1007/s10482-014-0341-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 11/18/2014] [Indexed: 11/30/2022]
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Tatar D, Sahin N. Streptomyces seymenliensis sp. nov., isolated from soil. Antonie van Leeuwenhoek 2014; 107:411-8. [DOI: 10.1007/s10482-014-0339-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Accepted: 11/15/2014] [Indexed: 10/24/2022]
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Streptomyces klenkii sp. nov., isolated from deep marine sediment. Antonie Van Leeuwenhoek 2014; 107:273-9. [DOI: 10.1007/s10482-014-0325-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Accepted: 10/30/2014] [Indexed: 10/24/2022]
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