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Riesco R, Ortúzar M, Román-Ponce B, Sánchez-Juanes F, Igual JM, Trujillo ME. Six novel Micromonospora species associated with the phyllosphere and roots of leguminous plants: Micromonospora alfalfae sp. nov., Micromonospora cabrerizensis sp. nov., Micromonospora foliorum sp. nov., Micromonospora hortensis sp. nov., Micromonospora salmantinae sp. nov., and Micromonospora trifolii sp. nov. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Six actinobacterial strains isolated from diverse legume tissues collected in various locations in Spain were characterized to determine their taxonomic status. Using 16S rRNA gene sequencing, the strains were primarily identified as members of the genus
Micromonospora
with more than 99 % similarity. Digital DNA–DNA hybridization values and average nucleotide identities between the six strains and the nearest type strains confirmed that each strain represented a novel species. Genome sequences were analysed to infer their metabolic profiles, their potential to produce secondary metabolites and plant growth promoting features. Chemotaxonomic and physiological studies were carried out to complete the phenotypic characterization and to distinguish the new
Micromonospora
species. The genomic and phenotypic characterization of the
Micromonospora
strains strongly support their classification as representatives of new species with the following names: Micromonospora alfalfae sp. nov., Micromonospora cabrerizensis sp. nov., Micromonospora foliorum sp. nov., Micromonospora hortensis sp. nov., Micromonospora salmantinae sp. nov. and Micromonospora trifolii sp. nov., with the type strains MED01T, LAH09T, PSH25T, NIE111T, PSH03T and NIE79T, respectively.
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Affiliation(s)
- Raúl Riesco
- Departamento de Microbiología y Genética, Campus Miguel de Unamuno, University of Salamanca, 37007 Salamanca, Spain
| | - Maite Ortúzar
- Departamento de Microbiología y Genética, Campus Miguel de Unamuno, University of Salamanca, 37007 Salamanca, Spain
| | - Brenda Román-Ponce
- Present address: Universidad Politécnica del Estado de Morelos, Morelos, Boulevard Cuauhnáhuac 556, Lomas del Texcal, 62550, Jiutepec, Mexico
- Departamento de Microbiología y Genética, Campus Miguel de Unamuno, University of Salamanca, 37007 Salamanca, Spain
| | - Fernando Sánchez-Juanes
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Complejo Asistencial Universitario de Salamanca, CSIC, Salamanca, Spain
- Department of Biochemistry and Molecular Biology, University of Salamanca, Salamanca, Spain
| | - José Mariano Igual
- Instituto de Recursos Naturales y Agrobiología de Salamanca (CSIC), Cordel de Merinas 40-52, 37008, Salamanca, Spain
| | - Martha E. Trujillo
- Departamento de Microbiología y Genética, Campus Miguel de Unamuno, University of Salamanca, 37007 Salamanca, Spain
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2
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Guzman J, Ortúzar M, Poehlein A, Daniel R, Trujillo ME, Vilcinskas A. Agromyces archimandritae sp. nov., isolated from the cockroach Archimandrita tessellata. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005283] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-positive bacterial strain, designated G127ATT, was isolated as soft small white colonies from the hindgut of the cockroach Archimandrita tesselata. Examination of the complete 16S rRNA sequence mapped the strain to the genus
Agromyces
. The type strain with the highest pairwise similarity was
Agromyces marinus
H23-8T (97.3%). The genome of G127ATT was sequenced by a combination of Illumina and Nanopore methods and consisted of a single circular DNA molecule with a size of 3.45 Mb. The DNA G+C content was 71.3 mol%. A phylogenomic tree based on conserved single copy housekeeping genes, placed G127ATT among the ancestral species of the genus
Agromyces
, and only
Agromyces atrinae
P27T was found to diverge earlier than G127ATT. Genome distance metrics average nucleotide identity (ANI) (76–78 %) and digital DNA–DNA hybridization (dDDH) (20.2–21.5 %) of the isolate against available genomes of several type strains of species of the genus
Agromyces
indicated that G127ATT represented a previously undescribed species of the genus
Agromyces
. Morphological, physiological and biochemical characteristics, including lipid profile, cellular fatty acids and peptidoglycan type were in accordance with usual attributes of members of the genus
Agromyces
. The novel isolate could be differentiated from the most closely related species by extracellular expression of acid and alkaline phosphatases, trypsin and α-chymotrypsin, and utilization of l-arabinose and salicin as sole carbon sources. On the basis of the combined genomic and phenotypic features, isolate G127ATT (=DSM 111850T=LMG 32099T) is considered to represent a novel species of the genus
Agromyces
, for which we propose the name Agromyces archimandritae sp. nov.
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Affiliation(s)
- Juan Guzman
- Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Giessen, Germany
- Institute for Insect Biotechnology, Justus-Liebig-University of Giessen, Giessen, Germany
| | - Maite Ortúzar
- Department of Microbiology and Genetics, University of Salamanca, Salamanca, Spain
| | - Anja Poehlein
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany
| | - Rolf Daniel
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany
| | - Martha E. Trujillo
- Department of Microbiology and Genetics, University of Salamanca, Salamanca, Spain
| | - Andreas Vilcinskas
- Institute for Insect Biotechnology, Justus-Liebig-University of Giessen, Giessen, Germany
- Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Giessen, Germany
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3
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Zhao S, Cheng M, Lin C, Liu H, Wang Z, Zhang K, Song S, Yang Q. Streptomyces luteolifulvus sp. nov., a novel actinomycete isolated from soil in Nanjing, China. Antonie van Leeuwenhoek 2021; 114:1829-1839. [PMID: 34460021 DOI: 10.1007/s10482-021-01643-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 08/13/2021] [Indexed: 10/20/2022]
Abstract
During the investigation of exploring potential sources of novel species and natural bioactives, a novel actinomycete, designated strain HIT-DPA4T, was isolated from a soil sample, which was collected from Nanjing, Jiangsu Province, PR China and characterized using a polyphasic approach. On the basis of 16S rRNA gene sequence similarities and the result of phylogenetic analysis, strain HIT-DPA4T was most closely related to Streptomyces cyaneus CGMCC 4.1671 T, and shared the highest sequence similarity of 98.76%. In addition, the cell walls of the species HIT-DPA4T contained LL-diaminopimelic acid as the diagnostic diamino acid and the whole-cell hydrolysates were identified as glucose and ribose, and the principal phospholipids were found to be diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol mannoside and phosphatidylmonomethylethanolamine. MK-9(H6) and MK-9(H4) were predominant menaquinones; and C16:0, anteiso-C15:0 and C15:0 as major cellular fatty acids of the organism HIT-DPA4T. Gene Ontology database analysis and antiSMASH server predicted results displayed that strain HIT-DPA4T was a promising classification units, which has various types of functions and contains multiple biosynthetic gene clusters with the similarity more than 80%. Multilocus sequence analysis (MLSA) of five housekeeping genes (atpD, gyrB, recA, rpoB and trpB) illustrated that Streptomyces luteolifulvus formed a separate branch in the genus Streptomyces. However, a combination of low level of DNA-DNA relatedness and physiological properties indicated that strain HIT-DPA4T can be distinguished from its phylogenetically related species Streptomyces cyaneus CGMCC 4.1671 T. Moreover, gene synteny research could be further differed organism HIT-DPA4T from similarity species. Therefore, the strain is concluded to represent a novel species of the genus Streptomyces, for which the name Streptomyces luteolifulvus sp. nov. is proposed. The type strain is HIT-DPA4T (= CGMCC 4.7558 T = TISTR 2751 T).
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Affiliation(s)
- Shanshan Zhao
- School of Life Science and Technology, Harbin Institute of Technology, No. 2 Yikuang Street, Nangang District, Harbin, 150080, People's Republic of China
| | - Ming Cheng
- School of Life Science and Technology, Harbin Institute of Technology, No. 2 Yikuang Street, Nangang District, Harbin, 150080, People's Republic of China
| | - Congyu Lin
- School of Life Science and Technology, Harbin Institute of Technology, No. 2 Yikuang Street, Nangang District, Harbin, 150080, People's Republic of China
| | - He Liu
- School of Life Science and Technology, Harbin Institute of Technology, No. 2 Yikuang Street, Nangang District, Harbin, 150080, People's Republic of China
| | - Zhengran Wang
- School of Life Science and Technology, Harbin Institute of Technology, No. 2 Yikuang Street, Nangang District, Harbin, 150080, People's Republic of China
| | - Kai Zhang
- School of Life Science and Technology, Harbin Institute of Technology, No. 2 Yikuang Street, Nangang District, Harbin, 150080, People's Republic of China
| | - Simin Song
- School of Life Science and Technology, Harbin Institute of Technology, No. 2 Yikuang Street, Nangang District, Harbin, 150080, People's Republic of China
| | - Qian Yang
- School of Life Science and Technology, Harbin Institute of Technology, No. 2 Yikuang Street, Nangang District, Harbin, 150080, People's Republic of China.
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Román-Ponce B, Millán-Aguiñaga N, Guillen-Matus D, Chase AB, Ginigini JGM, Soapi K, Feussner KD, Jensen PR, Trujillo ME. Six novel species of the obligate marine actinobacterium Salinispora, Salinispora cortesiana sp. nov., Salinispora fenicalii sp. nov., Salinispora goodfellowii sp. nov., Salinispora mooreana sp. nov., Salinispora oceanensis sp. nov. and Salinispora vitiensis sp. nov., and emended description of the genus Salinispora. Int J Syst Evol Microbiol 2020; 70:4668-4682. [PMID: 32701422 DOI: 10.1099/ijsem.0.004330] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Ten representative actinobacterial strains isolated from marine sediments collected worldwide were studied to determine their taxonomic status. The strains were previously identified as members of the genus Salinispora and shared >99 % 16S rRNA gene sequence similarity to the three currently recognized Salinispora species. Comparative genomic analyses resulted in the delineation of six new species based on average nucleotide identity and digital DNA-DNA hybridization values below 95 and 70 %, respectively. The species status of the six new groups was supported by a core-genome phylogeny reconstructed from 2106 orthologs detected in 118 publicly available Salinispora genomes. Chemotaxonomic and physiological studies were used to complete the phenotypic characterization of the strains. The fatty acid profiles contained the major components iso-C16 : 0, C15 : 0, iso-17 : 0 and anteiso C17 : 0. Galactose and xylose were common in all whole-sugar patterns but differences were found between the six groups of strains. Polar lipid compositions were also unique for each species. Distinguishable physiological and biochemical characteristics were also recorded. The names proposed are Salinispora cortesiana sp. nov., CNY-202T (=DSM 108615T=CECT 9739T); Salinispora fenicalii sp. nov., CNT-569T (=DSM 108614T=CECT 9740T); Salinispora goodfellowii sp. nov., CNY-666T (=DSM 108616T=CECT 9738T); Salinispora mooreana sp. nov., CNT-150T (=DSM 45549T=CECT 9741T); Salinispora oceanensis sp. nov., CNT-138T (=DSM 45547T=CECT 9742T); and Salinispora vitiensis sp. nov., CNT-148T (=DSM 45548T=CECT 9743T).
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Affiliation(s)
- Brenda Román-Ponce
- Departamento de Microbiología y Genética, Campus Miguel de Unamuno, Universidad de Salamanca, 37007 Salamanca, Spain
| | - Natalie Millán-Aguiñaga
- Universidad Autónoma de Baja California, Facultad de Ciencias Marinas, Ensenada, Baja California, Mexico
| | - Dulce Guillen-Matus
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Alexander B Chase
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Joape G M Ginigini
- The University of South Pacific, Faculty of Science, Technology and Environment, Institute of Applied Sciences, Suva, Fiji
| | - Katy Soapi
- The University of South Pacific, Faculty of Science, Technology and Environment, Institute of Applied Sciences, Suva, Fiji
| | - Klaus D Feussner
- The University of South Pacific, Faculty of Science, Technology and Environment, Institute of Applied Sciences, Suva, Fiji
| | - Paul R Jensen
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Martha E Trujillo
- Departamento de Microbiología y Genética, Campus Miguel de Unamuno, Universidad de Salamanca, 37007 Salamanca, Spain
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5
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Fu G, Wang R, Ding J, Qi H, Zhao Z, Chen C, Zhang H, Xue Z, Wang J, Wu M. Micromonospora zhangzhouensis sp. nov., a Novel Actinobacterium Isolated from Mangrove Soil, Exerts a Cytotoxic Activity in vitro. Sci Rep 2020; 10:3889. [PMID: 32127574 PMCID: PMC7054543 DOI: 10.1038/s41598-020-60677-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 02/13/2020] [Indexed: 11/21/2022] Open
Abstract
A new bacterial strain, designated HM134T, was isolated from a sample of soil collected from a Chinese mangrove Avicennia marina forest. Assessed by a polyphasic approach, the taxonomy of strain HM134T was found to be associated with a range of phylogenetic and chemotaxonomic properties consistent with the genus Micromonospora. Phylogenetic analysis based on the 16s rRNA gene sequence indicated that strain HM134T formed a distinct lineage with the most closely related species, including M. rifamycinica AM105T, M. wenchangensis CCTCC AA 2012002T and M. mangrovi 2803GPT1-18T. The ANI values between strain HM134T and the reference strains ranged from 82.6% to 95.2%, which was below the standard criteria for classifying strains as the same species (96.5%). Strain HM134T and related species shared in silico dDDH similarities values below the recommended 70% cut-off for the delineation of species (range from 25.7–62.6%). The DNA G+C content of strain HM134T was 73.2 mol%. Analysis of phylogenetic, genomic, phenotypic and chemotaxonomic characteristics revealed that strain HM134T is considered to represent a novel species of the genus Micromonospora, for which the name M. zhangzhouensis sp. nov. is proposed. The extract of strain HM134T was demonstrated to exhibit cytotoxic activity against the human cancer cell lines HepG2, HCT-116 and A549. Active substance presented in the fermentation broth of strain HM134T was isolated by bioassay-guided analysis and purified afterwards. A new derivative of diterpenoid was identified through electrospray ionizing mass spectrometry (MS) and nuclear magnetic resonance (NMR). The compound showed different cytotoxic activities against cancer cells, with the highest cytotoxicity against HCT-116, corresponding to IC50 value of 38.4 μg/mL.
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Affiliation(s)
- Geyi Fu
- Ocean College, Zhejiang University, Zhoushan, China
| | - Ruijun Wang
- Ocean College, Zhejiang University, Zhoushan, China
| | - Jinglin Ding
- Zhoushan Tourism & Health College, Zhoushan, China
| | - Huan Qi
- Zhejiang Key Laboratory of Antifungal Drugs, Zhejiang Hisun Pharmaceutical Co., Ltd., Taizhou, China
| | - Zhe Zhao
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Can Chen
- Ocean College, Zhejiang University, Zhoushan, China
| | - Hui Zhang
- Zhejiang Key Laboratory of Antifungal Drugs, Zhejiang Hisun Pharmaceutical Co., Ltd., Taizhou, China.,College of Biochemical Engineering, Anhui Polytechnic University, Wuhu, China
| | - Zhenglian Xue
- College of Biochemical Engineering, Anhui Polytechnic University, Wuhu, China
| | - Jidong Wang
- Zhejiang Key Laboratory of Antifungal Drugs, Zhejiang Hisun Pharmaceutical Co., Ltd., Taizhou, China. .,College of Biochemical Engineering, Anhui Polytechnic University, Wuhu, China.
| | - Min Wu
- Ocean College, Zhejiang University, Zhoushan, China. .,College of Life Sciences, Zhejiang University, Hangzhou, China.
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6
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Carro L, Golinska P, Nouioui I, Bull AT, Igual JM, Andrews BA, Klenk HP, Goodfellow M. Micromonospora acroterricola sp. nov., a novel actinobacterium isolated from a high altitude Atacama Desert soil. Int J Syst Evol Microbiol 2019; 69:3426-3436. [PMID: 31395106 DOI: 10.1099/ijsem.0.003634] [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 Micromonospora strain, designated 5R2A7T, isolated from a high altitude Atacama Desert soil was examined by using a polyphasic approach. Strain 5R2A7T was found to have morphological, chemotaxonomic and cultural characteristics typical of members of the genus Micromonospora. The cell wall contains meso- and hydroxy-diaminopimelic acid, the major whole-cell sugars are glucose, ribose and xylose, the predominant menaquinones MK-10(H4), MK-10(H6), MK-10(H8) and MK-9(H6), the major polar lipids diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and an unknown glycolipid, and the predominant cellular fatty acids iso-C16 : 0, iso-C15 : 0 and 10-methyl C17 : 0. The digital genomic DNA G+C content is 72.3 mol%. Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain 5R2A7T was closely related to Micromonospora coriariae DSM 44875T (99.8 %) and Micromonospora cremea CR30T (99.7 %), and was separated readily from the latter, its closest phylogenetic neighbour, based on gyrB and multilocus sequence data, by low average nucleotide identity (92.59 %) and in silico DNA-DNA relatedness (51.7 %) values calculated from draft genome assemblies and by a range of chemotaxonomic and phenotypic properties. Consequently, strain 5R2A7T is considered to represent a novel species of Micromonospora for which the name Micromonospora acroterricola sp. nov. is proposed. The type strain is 5R2A7T (=LMG 30755T=CECT 9656T).
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Affiliation(s)
- Lorena Carro
- School of Natural and Environmental Sciences, Ridley Building 2, Newcastle University, Newcastle upon Tyne NE1 7RU, UK.,Departamento de Microbiología y Genética, Edificio Departamental, Lab. 214, Campus Miguel de Unamuno, Universidad de Salamanca, 37007 Salamanca, Spain
| | - Patrycja Golinska
- Department of Microbiology, Faculty of Biology and Environmental Protection, Nicolaus Copernicus University, Lwowska 1, 87 100 Torun, Poland
| | - Imen Nouioui
- School of Natural and Environmental Sciences, Ridley Building 2, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Alan T Bull
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK
| | - Jose Mariano Igual
- Instituto de Recursos Naturales y Agrobiología de Salamanca, Consejo Superior de Investigaciones Científicas (IRNASA-CSIC), c/Cordel de Merinas 40-52, 37008 Salamanca, Spain
| | - Barbara A Andrews
- Department of Chemical Engineering and Biotechnology, Centre for Biotechnology and Bioengineering (CeBiB) University of Chile, Santiago, Chile
| | - Hans-Peter Klenk
- School of Natural and Environmental Sciences, Ridley Building 2, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Michael Goodfellow
- School of Natural and Environmental Sciences, Ridley Building 2, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
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Nouioui I, Carro L, García-López M, Meier-Kolthoff JP, Woyke T, Kyrpides NC, Pukall R, Klenk HP, Goodfellow M, Göker M. Genome-Based Taxonomic Classification of the Phylum Actinobacteria. Front Microbiol 2018; 9:2007. [PMID: 30186281 PMCID: PMC6113628 DOI: 10.3389/fmicb.2018.02007] [Citation(s) in RCA: 414] [Impact Index Per Article: 69.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 08/09/2018] [Indexed: 11/29/2022] Open
Abstract
The application of phylogenetic taxonomic procedures led to improvements in the classification of bacteria assigned to the phylum Actinobacteria but even so there remains a need to further clarify relationships within a taxon that encompasses organisms of agricultural, biotechnological, clinical, and ecological importance. Classification of the morphologically diverse bacteria belonging to this large phylum based on a limited number of features has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees. Here, draft genome sequences of a large collection of actinobacterial type strains were used to infer phylogenetic trees from genome-scale data using principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families, and genera, as well as many species and a few subspecies were shown to be in need of revision leading to proposals for the recognition of 2 orders, 10 families, and 17 genera, as well as the transfer of over 100 species to other genera. In addition, emended descriptions are given for many species mainly involving the addition of data on genome size and DNA G+C content, the former can be considered to be a valuable taxonomic marker in actinobacterial systematics. Many of the incongruities detected when the results of the present study were compared with existing classifications had been recognized from 16S rRNA gene trees though whole-genome phylogenies proved to be much better resolved. The few significant incongruities found between 16S/23S rRNA and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences. Similarly good congruence was found between the discontinuous distribution of phenotypic properties and taxa delineated in the phylogenetic trees though diverse non-monophyletic taxa appeared to be based on the use of plesiomorphic character states as diagnostic features.
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Affiliation(s)
- Imen Nouioui
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Lorena Carro
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Marina García-López
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Jan P. Meier-Kolthoff
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Tanja Woyke
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, United States
| | - Nikos C. Kyrpides
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, United States
| | - Rüdiger Pukall
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Hans-Peter Klenk
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Michael Goodfellow
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Markus Göker
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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8
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Riesco R, Carro L, Román-Ponce B, Prieto C, Blom J, Klenk HP, Normand P, Trujillo ME. Defining the Species Micromonospora saelicesensis and Micromonospora noduli Under the Framework of Genomics. Front Microbiol 2018; 9:1360. [PMID: 29988535 PMCID: PMC6026663 DOI: 10.3389/fmicb.2018.01360] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 06/05/2018] [Indexed: 11/13/2022] Open
Abstract
The type isolates of species Micromonospora saelicesensis and Micromonospora noduli are Gram-stain positive actinobacteria that were originally isolated from nitrogen fixing nodules of the legumes Lupinus angustifolius and Pisum sativum, respectively. These two species are very closely related and questions arise as to whether they should be merged into a single species. To better delineate the relationship of M. saelicesensis and M. noduli, 10 strains isolated from plant tissue (nodules and leaves) and identified by their 16S rRNA gene sequences as either M. saelicensesis or M. noduli, based on a cut-off value of ≥99.5% were selected for whole-genome sequencing and compared with the type strains of M. saelicesensis Lupac 09T and M. noduli GUI43T using overall genome relatedness indices (OGRI) which included ANI, OrthoANI and digital DNA-DNA hybridization. Whole- and core-genome phylogenomic analyses were also carried out. These results were compared with the topologies of the 16S rRNA and gyrB gene phylogenies. Good correlation was found between all trees except for the 16S rRNA gene. Overall results also supported the current classification of M. saelicesensis and M. noduli as separate species. Especially useful was the core-genome phylogenetic analyses based on 92 genes and the dDDH results which were highly correlated. The importance of using more than one strain for a better definition of a species was also shown. A series of in vitro phenotypic assays performed at different times were compared with in silico predictions based on genomic data. In vitro phenotypic tests showed discrepancies among the independent studies, confirming the lack of reproducibility even when tests were performed in the same laboratory. On the other hand, the use of in silico predictions proved useful for defining a stable phenotype profile among the strains analyzed. These results provide a working framework for defining Micromonospora species at the genomic and phenotypic level.
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Affiliation(s)
- Raúl Riesco
- Departament of Microbiology and Genetics, Edificio Departamental, University of Salamanca, Salamanca, Spain
| | - Lorena Carro
- Departament of Microbiology and Genetics, Edificio Departamental, University of Salamanca, Salamanca, Spain
| | - Brenda Román-Ponce
- Departament of Microbiology and Genetics, Edificio Departamental, University of Salamanca, Salamanca, Spain
| | - Carlos Prieto
- Servicio de Bioinformática, NUCLEUS, Edificio I+D+i, University of Salamanca, Salamanca, Spain
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Hans-Peter Klenk
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Philippe Normand
- Centre National de la Recherche Scientifique-UMR5557 Ecologie Microbienne, Université de Lyon, Université Lyon1, Villeurbanne, France
| | - Martha E Trujillo
- Departament of Microbiology and Genetics, Edificio Departamental, University of Salamanca, Salamanca, Spain
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9
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Carro L, Nouioui I, Sangal V, Meier-Kolthoff JP, Trujillo ME, Montero-Calasanz MDC, Sahin N, Smith DL, Kim KE, Peluso P, Deshpande S, Woyke T, Shapiro N, Kyrpides NC, Klenk HP, Göker M, Goodfellow M. Genome-based classification of micromonosporae with a focus on their biotechnological and ecological potential. Sci Rep 2018; 8:525. [PMID: 29323202 PMCID: PMC5765111 DOI: 10.1038/s41598-017-17392-0] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 11/08/2017] [Indexed: 12/14/2022] Open
Abstract
There is a need to clarify relationships within the actinobacterial genus Micromonospora, the type genus of the family Micromonosporaceae, given its biotechnological and ecological importance. Here, draft genomes of 40 Micromonospora type strains and two non-type strains are made available through the Genomic Encyclopedia of Bacteria and Archaea project and used to generate a phylogenomic tree which showed they could be assigned to well supported phyletic lines that were not evident in corresponding trees based on single and concatenated sequences of conserved genes. DNA G+C ratios derived from genome sequences showed that corresponding data from species descriptions were imprecise. Emended descriptions include precise base composition data and approximate genome sizes of the type strains. antiSMASH analyses of the draft genomes show that micromonosporae have a previously unrealised potential to synthesize novel specialized metabolites. Close to one thousand biosynthetic gene clusters were detected, including NRPS, PKS, terpenes and siderophores clusters that were discontinuously distributed thereby opening up the prospect of prioritising gifted strains for natural product discovery. The distribution of key stress related genes provide an insight into how micromonosporae adapt to key environmental variables. Genes associated with plant interactions highlight the potential use of micromonosporae in agriculture and biotechnology.
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Affiliation(s)
- Lorena Carro
- School of Biology, Newcastle University, Newcastle upon Tyne, UK.
| | - Imen Nouioui
- School of Biology, Newcastle University, Newcastle upon Tyne, UK
| | - Vartul Sangal
- Department of Biomedical Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - Jan P Meier-Kolthoff
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, Braunschweig, Germany
| | - Martha E Trujillo
- Departamento de Microbiologia y Genetica, Lab 214, Universidad de Salamanca, Salamanca, Spain
| | | | - Nevzat Sahin
- Department of Biology, Faculty of Art and Science, Ondokuz Mayis University, Kurupelit-Samsun, Turkey
| | - Darren Lee Smith
- Department of Biomedical Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - Kristi E Kim
- Pacific Biosciences, 1380 Willow Rd, Menlo Park, California, USA
| | - Paul Peluso
- Pacific Biosciences, 1380 Willow Rd, Menlo Park, California, USA
| | | | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Nicole Shapiro
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | | | - Hans-Peter Klenk
- School of Biology, Newcastle University, Newcastle upon Tyne, UK.
| | - Markus Göker
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, Braunschweig, Germany
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10
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Qu Z, Bao XD, Xie QY, Zhao YX, Yan B, Dai HF, Chen HQ. Actinoplanes sediminis sp. nov., isolated from marine sediment. Int J Syst Evol Microbiol 2018; 68:71-75. [DOI: 10.1099/ijsem.0.002451] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Zhi Qu
- Guangxi Mangrove Research Center, Guangxi Key Lab of Mangrove Conservation and Utilization, Beihai 536000, PR China
- Key Laboratory of Tropical Microbial Resources, Hainan Province, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, PR China
| | - Xiao-dong Bao
- Key Laboratory of Tropical Microbial Resources, Hainan Province, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, PR China
| | - Qing-yi Xie
- Guangxi Mangrove Research Center, Guangxi Key Lab of Mangrove Conservation and Utilization, Beihai 536000, PR China
- Key Laboratory of Tropical Microbial Resources, Hainan Province, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, PR China
| | - You-xing Zhao
- Key Laboratory of Tropical Microbial Resources, Hainan Province, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, PR China
| | - Bing Yan
- Guangxi Mangrove Research Center, Guangxi Key Lab of Mangrove Conservation and Utilization, Beihai 536000, PR China
| | - Hao-fu Dai
- Key Laboratory of Tropical Microbial Resources, Hainan Province, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, PR China
| | - Hui-Qin Chen
- Key Laboratory of Tropical Microbial Resources, Hainan Province, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, PR China
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11
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Carro L, Veyisoglu A, Riesco R, Spröer C, Klenk HP, Sahin N, Trujillo ME. Micromonospora phytophila sp. nov. and Micromonospora luteiviridis sp. nov., isolated as natural inhabitants of plant nodules. Int J Syst Evol Microbiol 2018; 68:248-253. [PMID: 29148367 DOI: 10.1099/ijsem.0.002490] [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] [Indexed: 11/18/2022] Open
Abstract
Two actinobacterial isolates, strains SG15T and SGB14T, were recovered through a microbial diversity study of nitrogen fixing nodules from Pisum sativum plants collected in Salamanca (Spain). The taxonomic status of these isolates was determined using a polyphasic approach and both presented chemotaxonomic and morphological properties consistent with their classification in the genus Micromonospora. For strains SG15T and SGB14T, the highest 16S rRNA gene sequence similarities were observed with Micromonospora coxensis JCM 13248T (99.2 %) and Micromonospora purpureochromogenes DSM 43821T (99.4 %), respectively. However, strains SG15T and SGB14T were readily distinguished from their phylogenetic neighbours both genetically and phenotypically indicating that they represent two new Micromonospora species. The following names are proposed for these species: Micromonosporaphytophila sp. nov. type strain SG15T (=CECT 9369T; =DSM 105363T), and Micromonosporaluteiviridis sp. nov. type strain SGB14T (=CECT 9370T; =DSM 105362T).
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Affiliation(s)
- Lorena Carro
- School of Biology, Ridley and Devonshire Building, Newcastle University, NE1 7RU Newcastle upon Tyne, UK
- Departamento de Microbiología y Genética, Edificio Departamental, Lab. 214, Campus Miguel de Unamuno, Universidad de Salamanca, 37007 Salamanca, Spain
| | - Aysel Veyisoglu
- Department of Bioengineering, Faculty of Engineering and Architecture, Sinop University, 57000 Sinop, Turkey
| | - Raúl Riesco
- Departamento de Microbiología y Genética, Edificio Departamental, Lab. 214, Campus Miguel de Unamuno, Universidad de Salamanca, 37007 Salamanca, Spain
| | - Cathrin Spröer
- Leibniz-Institute DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Inhoffenstrasse 7B, 38124 Braunschweig, Germany
| | - Hans-Peter Klenk
- School of Biology, Ridley and Devonshire Building, Newcastle University, NE1 7RU Newcastle upon Tyne, UK
| | - Nevzat Sahin
- Department of Biology, Faculty of Art and Science, Ondokuz Mayis University, 55139 Kurupelit-Samsun, Turkey
| | - Martha E Trujillo
- Departamento de Microbiología y Genética, Edificio Departamental, Lab. 214, Campus Miguel de Unamuno, Universidad de Salamanca, 37007 Salamanca, Spain
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12
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Benito P, Alonso-Vega P, Aguado C, Luján R, Anzai Y, Hirsch AM, Trujillo ME. Monitoring the colonization and infection of legume nodules by Micromonospora in co-inoculation experiments with rhizobia. Sci Rep 2017; 7:11051. [PMID: 28887555 PMCID: PMC5591303 DOI: 10.1038/s41598-017-11428-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 08/23/2017] [Indexed: 11/11/2022] Open
Abstract
The discovery that the actinobacterium Micromonospora inhabits nitrogen-fixing nodules raised questions as to its potential ecological role. The capacity of two Micromonospora strains to infect legumes other than their original host, Lupinus angustifolius, was investigated using Medicago and Trifolium as test plants. Compatible rhizobial strains were used for coinoculation of the plants because Micromonospora itself does not induce nodulation. Over 50% of nodules from each legume housed Micromonospora, and using 16S rRNA gene sequence identification, we verified that the reisolated strains corresponded to the microorganisms inoculated. Entry of the bacteria and colonization of the plant hosts were monitored using a GFP-tagged Lupac 08 mutant together with rhizobia, and by using immunogold labeling. Strain Lupac 08 was localized in plant tissues, confirming its capacity to enter and colonize all hosts. Based on studying three different plants, our results support a non-specific relationship between Micromonospora and legumes. Micromonospora Lupac 08, originally isolated from Lupinus re-enters root tissue, but only when coinoculated with the corresponding rhizobia. The ability of Micromonospora to infect and colonize different legume species and function as a potential plant-growth promoting bacterium is relevant because this microbe enhances the symbiosis without interfering with the host and its nodulating and nitrogen-fixing microbes.
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Affiliation(s)
- Patricia Benito
- Departamento de Microbiología y Genética, Edificio Departamental, Campus Miguel de Unamuno, Universidad de Salamanca, Salamanca, Spain
| | - Pablo Alonso-Vega
- Departamento de Microbiología y Genética, Edificio Departamental, Campus Miguel de Unamuno, Universidad de Salamanca, Salamanca, Spain
| | - Carolina Aguado
- Synaptic Structure Laboratory, Instituto de Investigación en Discapacidades Neurológicas (IDINE), Departamento Ciencias Médicas, Facultad de Medicina, Universidad Castilla-La Mancha Albacete, Ciudad Real, Spain
| | - Rafael Luján
- Synaptic Structure Laboratory, Instituto de Investigación en Discapacidades Neurológicas (IDINE), Departamento Ciencias Médicas, Facultad de Medicina, Universidad Castilla-La Mancha Albacete, Ciudad Real, Spain
| | - Yojiro Anzai
- Department of Microbiology, Faculty of Pharmaceutical Sciences, Toho University, Funabashi, Chiba, Japan
| | - Ann M Hirsch
- Department of Molecular, Cell and Developmental Biology and Molecular Biology Institute, University of California-Los Angeles, Los Angeles, CA, USA
| | - Martha E Trujillo
- Departamento de Microbiología y Genética, Edificio Departamental, Campus Miguel de Unamuno, Universidad de Salamanca, Salamanca, Spain.
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13
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Zhao S, Liu C, Zheng W, Ma Z, Cao T, Zhao J, Yan K, Xiang W, Wang X. Micromonospora parathelypteridis sp. nov., an endophytic actinomycete with antifungal activity isolated from the root of Parathelypteris beddomei (Bak.) Ching. Int J Syst Evol Microbiol 2017; 67:268-274. [PMID: 27902235 DOI: 10.1099/ijsem.0.001614] [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 endophytic actinomycete with antifungal activity, designated strain NEAU-JXY5T, was isolated from the root of Parathelypteris beddomei (Bak.) Ching. Strain NEAU-JXY5T showed closest 16S rRNA gene sequence similarity to Micromonospora luteifusca GUI2T (99.31 %), and phylogenetically clustered with Micromonospora noduli GUI43T (99.24 %), 'Micromonospora lycii' NEAU-gq11 (99.19 %), 'Micromonospora zeae' NEAU-gq9 (99.12 %), Micromonospora saelicesensis Lupac 09T (98.97 %), Micromonospora vinacea GUI63T (98.96 %), 'Micromonospora jinlongensis' NEAU-GRX11 (98.91 %), Micromonospora profundi DS3010T (98.77 %), Micromonospora zamorensis CR38T (98.76 %), Micromonospora chokoriensis 2-19(6)T (98.71 %), Micromonospora lupini Lupac 14NT (98.69 %), Micromonospora ureilytica GUI23T (98.69 %), Micromonospora violae NEAU-zh8T (98.57 %) and Micromonospora taraxaci NEAU-P5T (98.37 %). Phylogenetic analysis based on gyrB gene sequences also indicated that the isolate clustered with the above strains except M. violae NEAU-zh8T. A combination of DNA-DNA hybridization results and some phenotypic characteristics indicated that the strain could be readily distinguished from these closest phylogenetic relatives. Therefore, it is concluded that strain NEAU-JXY5T represents a novel species of the genus Micromonospora, for which the name Micromonospora parathelypteridis sp. nov. is proposed. The type strain is NEAU-JXY5T (=CGMCC 4.7347T=DSM 103125T).
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Affiliation(s)
- Shanshan Zhao
- Key Laboratory of Agriculture Biological Functional Gene of Heilongjiang Provincial Education Committee, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin 150030, PR China
| | - Chongxi Liu
- Key Laboratory of Agriculture Biological Functional Gene of Heilongjiang Provincial Education Committee, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin 150030, PR China
| | - Weiwei Zheng
- Key Laboratory of Agriculture Biological Functional Gene of Heilongjiang Provincial Education Committee, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin 150030, PR China
| | - Zhaoxu Ma
- Key Laboratory of Agriculture Biological Functional Gene of Heilongjiang Provincial Education Committee, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin 150030, PR China
| | - Tingting Cao
- Key Laboratory of Agriculture Biological Functional Gene of Heilongjiang Provincial Education Committee, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin 150030, PR China
| | - Junwei Zhao
- Key Laboratory of Agriculture Biological Functional Gene of Heilongjiang Provincial Education Committee, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin 150030, PR China
| | - Kai Yan
- Key Laboratory of Agriculture Biological Functional Gene of Heilongjiang Provincial Education Committee, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin 150030, PR China
| | - Wensheng Xiang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, PR China.,Key Laboratory of Agriculture Biological Functional Gene of Heilongjiang Provincial Education Committee, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin 150030, PR China
| | - Xiangjing Wang
- Key Laboratory of Agriculture Biological Functional Gene of Heilongjiang Provincial Education Committee, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin 150030, PR China
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14
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Carro L, Riesco R, Spröer C, Trujillo ME. Micromonospora ureilytica sp. nov., Micromonospora noduli sp. nov. and Micromonospora vinacea sp. nov., isolated from Pisum sativum nodules. Int J Syst Evol Microbiol 2016; 66:3509-3514. [PMID: 27282917 DOI: 10.1099/ijsem.0.001231] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2023] Open
Abstract
A diversity study on the presence of strains representing the genus Micromonospora in Pisum sativum nodules collected from Cañizal (Spain) has provided evidence of the high number of isolates that might represent novel species. In the present work, we have characterized three of these isolates: GUI23T, GUI43T and GUI63T. Phenotypic and genotypic analyses confirmed that all strains represent novel species of the genus Micromonospora with the following proposed names: Micromonospora ureilytica sp. nov., type strain GUI23T (=CECT 9022T=DSM 101692T), Micromonospora noduli sp. nov., type strain GUI43T (=CECT 9020T=DSM 101694T), and Micromonospora vinacea sp. nov., type strain GUI63T (=CECT 9019T=DSM 101695T).
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Affiliation(s)
- Lorena Carro
- Departamento de Microbiología y Genética, Edificio Departamental, Lab. 214, Campus Miguel de Unamuno, Universidad de Salamanca, 37007 Salamanca, Spain
- School of Biology, Devonshire building, Newcastle University, NE1 7RU Newcastle upon Tyne, UK
| | - Raúl Riesco
- Departamento de Microbiología y Genética, Edificio Departamental, Lab. 214, Campus Miguel de Unamuno, Universidad de Salamanca, 37007 Salamanca, Spain
| | - Cathrin Spröer
- Leibniz-Institute, DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Inhoffenstrasse 7B, 38124 Braunschweig, Germany
| | - Martha E Trujillo
- Departamento de Microbiología y Genética, Edificio Departamental, Lab. 214, Campus Miguel de Unamuno, Universidad de Salamanca, 37007 Salamanca, Spain
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15
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Carro L, Riesco R, Spröer C, Trujillo ME. Micromonospora luteifusca sp. nov. isolated from cultivated Pisum sativum. Syst Appl Microbiol 2016; 39:237-242. [PMID: 27220477 DOI: 10.1016/j.syapm.2016.04.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Revised: 04/22/2016] [Accepted: 04/25/2016] [Indexed: 10/21/2022]
Abstract
Three novel actinobacterial strains, GUI2(T), GUI42 and CR21 isolated from nodular tissues and the rhizosphere of a sweet pea plant collected in Cañizal, Spain were identified according to their 16S rRNA gene sequences as new members of the genus Micromonospora. The closest phylogenetic members were found to be Micromonospora saelicesensis (99.2%) "Micromonospora zeae" (99.1%), "Micromonospora jinlongensis" (99%), Micromonospora lupini (98.9%) and Micromonospora zamorensis (98.8%). To resolve their full taxonomic position, four additional genes (atpD, gyrB, recA, rpoB) were partially sequenced and compared to available Micromonospora type strain sequences. DNA-DNA hybridization, BOX-PCR and ARDRA profiles confirmed that these strains represent a novel genomic species. All strains contained meso-diaminopimelic and hydroxy-diaminopimelic acids in their cell wall. Their fatty acid profiles comprised iso-C15:0, iso-C16:0 and anteiso-C15:0 as major components. The polar lipids diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol were found in the type strain GUI2(T) which also contained MK-10(H4) as the major menaquinone. Physiological and biochemical characteristics also differentiated the new isolates. Based on the integration of the above studies, strains GUI2(T), GUI42 and CR21 represent a novel Micromonospora species and we propose the name Micromonospora luteifusca sp. nov. The type strain is GUI2(T) (=CECT 8846(T); =DSM 100204(T)).
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Affiliation(s)
- Lorena Carro
- Departamento de Microbiología y Genética, Edificio Departamental, Campus Miguel de Unamuno, Universidad de Salamanca, 37007 Salamanca, Spain
| | - Raúl Riesco
- Departamento de Microbiología y Genética, Edificio Departamental, Campus Miguel de Unamuno, Universidad de Salamanca, 37007 Salamanca, Spain
| | - Cathrin Spröer
- Leibniz-Insitut DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Martha E Trujillo
- Departamento de Microbiología y Genética, Edificio Departamental, Campus Miguel de Unamuno, Universidad de Salamanca, 37007 Salamanca, Spain.
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16
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Xie QY, Ren J, Li L, Li Y, Deng ZX, Hong K. Micromonospora mangrovi sp. nov., isolated from mangrove soil. Antonie van Leeuwenhoek 2016; 109:483-91. [PMID: 26942919 DOI: 10.1007/s10482-015-0641-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 12/21/2015] [Indexed: 01/10/2023]
Abstract
A novel actinomycete strain 2803GPT1-18(T) was isolated from a composite mangrove soil sample collected from Beihai, Guangxi province, China. Phylogenetic analysis of the 16S rRNA gene sequence of strain 2803GPT1-18(T) indicated high similarity with 'Micromonospora harpali' NEAU-JC6(T) (99.2 %), Micromonospora haikouensis 232617(T) (99.1 %), Micromonospora wenchangensis 2602GPT1-05(T) (99.1 %), Micromonospora schwarzwaldensis HKI0641(T) (99.1 %). The gyrB gene sequence analysis also indicated that strain 2803GPT1-18(T) should be assigned to the genus Micromonospora but different from any established Micromonospora species. The strain harbored meso-DAP and glycine as major cell wall amino acids, MK-10(H6) (53.5 %), MK-9(H6) (25.1 %) and MK-9(H4) (13.4 %) as predominant menaquinones. The characteristic whole cell sugars are arabinose, xylose, glucose, galactose and mannose. The polar lipid profile comprises phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylinositol and unidentified polar lipids. The major cellular fatty acids present are iso-C16:0 (44.2 %) and iso-C15:0 (12.4 %). The DNA G+C content is 71.2 mol%. Furthermore, a combination of DNA-DNA relatedness and some physiological and biochemical properties indicated that the novel strain could be readily distinguished from the closely related species. On the basis of these phenotypic and genotypic data, strain 2803GPT1-18(T) represents a novel species of the genus Micromonospora, for which the name Micromonospora mangrovi sp. nov. is proposed. The type strain is 2803GPT1-18(T) (=CCTCC AA2012012(T) = DSM45761(T)).
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Affiliation(s)
- Qing-Yi Xie
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, People's Republic of China.,Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou, 571101, People's Republic of China
| | - Jian Ren
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, People's Republic of China
| | - Lei Li
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, People's Republic of China
| | - Yu Li
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou, 571101, People's Republic of China
| | - Zi-Xin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, People's Republic of China
| | - Kui Hong
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, People's Republic of China.
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17
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Zhang L, Li L, Deng Z, Hong K. Micromonospora zhanjiangensis sp. nov., isolated from mangrove forest soil. Int J Syst Evol Microbiol 2015; 65:4880-4885. [DOI: 10.1099/ijsem.0.000667] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel actinomycete, designated strain 2902at01T was isolated from soil collected at a mangrove forest in Zhanjiang, Guangdong province, China. The strain was identified using a polyphasic classification method. The 16S rRNA gene sequence of strain 2902at01T showed the highest similarity to Micromonospora equina Y22T (98.3 %) and Micromonospora pattaloongensis TJ2-2T (98.1 %). Phylogenetic analysis based on the gyrB gene sequence also clearly showed that the strain was different from any previously discovered species of the genus Micromonospora. The characteristic whole-cell sugars were ribose and xylose. The cell-wall hydrolysates contained alanine, asparagine, glycine and meso-diaminopimelic acid. MK-10(H6) and MK-10(H8) were the major menaquinones of the novel strain. The predominant fatty acids were iso-C15 : 0, anteiso-C15 : 0 and iso-C16 : 0. The characteristic polar lipids of strain 2902at01T were phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannoside and diphosphatidylglycerol. The DNA G+C content was 70.2 mol%. DNA–DNA hybridization data combined with other physiological and biochemical features could distinguish strain 2902at01T from the reference strains M. equina Y22T and M. pattaloongensis TJ2-2 T. On the basis of these phenotypic and genotypic data, strain 2902at01T represents a novel species of the genus Micromonospora, for which the name Micromonospora zhanjiangensis sp. nov. is proposed. The type strain is 2902at01T ( = CCTCC AA2014018T = DSM 45902T).
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Affiliation(s)
- Li Zhang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, and Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, PR China
| | - Lei Li
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, and Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, PR China
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, and Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, PR China
| | - Kui Hong
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, and Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, PR China
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Zhao J, Guo L, Liu C, Zhang Y, Guan X, Li J, Xu S, Xiang W, Wang X. Micromonospora lycii sp. nov., a novel endophytic actinomycete isolated from wolfberry root (Lycium chinense Mill). J Antibiot (Tokyo) 2015; 69:153-8. [DOI: 10.1038/ja.2015.109] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Revised: 07/21/2015] [Accepted: 09/29/2015] [Indexed: 01/02/2023]
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19
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Martínez-Hidalgo P, García JM, Pozo MJ. Induced systemic resistance against Botrytis cinerea by Micromonospora strains isolated from root nodules. Front Microbiol 2015; 6:922. [PMID: 26388861 PMCID: PMC4556977 DOI: 10.3389/fmicb.2015.00922] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 08/21/2015] [Indexed: 12/21/2022] Open
Abstract
Micromonospora is a Gram positive bacterium that can be isolated from nitrogen fixing nodules from healthy leguminous plants, where they could be beneficial to the plant. Their plant growth promoting activity in legume and non-legume plants has been previously demonstrated. The present study explores the ability of Micromonospora strains to control fungal pathogens and to stimulate plant immunity. Micromonospora strains isolated from surface sterilized nodules of alfalfa showed in vitro antifungal activity against several pathogenic fungi. Moreover, root inoculation of tomato plants with these Micromonospora strains effectively reduced leaf infection by the fungal pathogen Botrytis cinerea, despite spatial separation between both microorganisms. This induced systemic resistance, confirmed in different tomato cultivars, is long lasting. Gene expression analyses evidenced that Micromonospora stimulates the plant capacity to activate defense mechanisms upon pathogen attack. The defensive response of tomato plants inoculated with Micromonospora spp. differs from that of non-inoculated plants, showing a stronger induction of jasmonate-regulated defenses when the plant is challenged with a pathogen. The hypothesis of jasmonates playing a key role in this defense priming effect was confirmed using defense-impaired tomato mutants, since the JA-deficient line def1 was unable to display a long term induced resistance upon Micromonospora spp. inoculation. In conclusion, nodule isolated Micromonospora strains should be considered excellent candidates as biocontrol agents as they combine both direct antifungal activity against plant pathogens and the ability to prime plant immunity.
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Affiliation(s)
- Pilar Martínez-Hidalgo
- Department of Microbiology and Genetics, University of SalamancaSalamanca, Spain
- Unidad Asociada USAL-CSIC “Interacción Planta-Microorganismo”Salamanca, Spain
| | - Juan M. García
- Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones CientíficasGranada, Spain
| | - María J. Pozo
- Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones CientíficasGranada, Spain
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Zhao J, Guo L, He H, Liu C, Zhang Y, Li C, Wang X, Xiang W. Micromonospora taraxaci sp. nov., a novel endophytic actinomycete isolated from dandelion root (Taraxacum mongolicum Hand.-Mazz.). Antonie van Leeuwenhoek 2014; 106:667-74. [DOI: 10.1007/s10482-014-0237-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Accepted: 07/14/2014] [Indexed: 11/29/2022]
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21
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Shen Y, Zhang Y, Liu C, Wang X, Zhao J, Jia F, Yang L, Yang D, Xiang W. Micromonospora zeae sp. nov., a novel endophytic actinomycete isolated from corn root (Zea mays L.). J Antibiot (Tokyo) 2014; 67:739-43. [DOI: 10.1038/ja.2014.54] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Revised: 04/02/2014] [Accepted: 04/07/2014] [Indexed: 11/09/2022]
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22
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Zhang Y, Liu H, Zhang X, Wang S, Liu C, Yu C, Wang X, Xiang W. Micromonospora violae sp. nov., isolated from a root of Viola philippica Car. Antonie van Leeuwenhoek 2014; 106:219-25. [DOI: 10.1007/s10482-014-0184-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Accepted: 04/21/2014] [Indexed: 10/25/2022]
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Carro L, Pukall R, Spröer C, Kroppenstedt RM, Trujillo ME. Micromonospora halotolerans sp. nov., isolated from the rhizosphere of a Pisum sativum plant. Antonie Van Leeuwenhoek 2013; 103:1245-54. [PMID: 23494330 DOI: 10.1007/s10482-013-9903-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2013] [Accepted: 03/07/2013] [Indexed: 10/27/2022]
Abstract
A filamentous actinomycete strain designated CR18(T) was isolated on humic acid agar from the rhizosphere of a Pisum sativum plant collected in Spain. This isolate was observed to grow optimally at 28 °C, pH 7.0 and in the presence of 5 % NaCl. Phylogenetic analyses based on the 16S rRNA gene sequence indicated a close relationship with the type strains of Micromonospora chersina and Micromonospora endolithica. A further analysis based on a concatenated DNA sequence stretch of 4,523 bp that included partial sequences of the atpD, gyrB, recA, rpoB and 16S rRNA genes clearly differentiated the new strain from recognized Micromonospora species compared. DNA-DNA hybridization studies further supported the taxonomic position of strain CR18(T) as a novel genomic species. Chemotaxonomic analyses which included whole cell sugars, polar lipids, fatty acid profiles and menaquinone composition confirmed the affiliation of the new strain to the genus Micromonospora and also highlighted differences at the species level. These studies were finally complemented with an array of physiological tests to help differentiate between the new strain and its phylogenetic neighbours. Consequently, strain CR18(T) (= CECT 7890(T) = DSM 45598(T)) is proposed as the type strain of a novel species, Micromonospora halotolerans sp. nov.
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Affiliation(s)
- Lorena Carro
- Departamento de Microbiología y Genética, Edificio Departamental, Lab. 214, Campus Miguel de Unamuno, Universidad de Salamanca, Salamanca, Spain
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Everest GJ, Meyers PR. Micromonospora equina sp. nov., isolated from soil from a racecourse. Int J Syst Evol Microbiol 2013; 63:879-885. [DOI: 10.1099/ijs.0.042929-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two actinomycete strains were isolated from within the fynbos-rich area surrounded by the horseracing track at Kenilworth Racecourse in Cape Town, South Africa. Rapid molecular identification indicated that the isolates belonged to the family
Micromonosporaceae
. Based on 16S rRNA gene sequence blast analysis, the isolates were identified as members of the genus
Micromonospora
. Phylogenetic analysis showed that the isolates clustered with each other and were most closely related to
Micromonospora viridifaciens
DSM 43909T. Further 16S rRNA gene sequence analysis using EzTaxon revealed that the isolates are closely related to
Micromonospora auratinigra
TT1-11T,
Micromonospora chaiyaphumensis
MC5-1T,
Micromonospora eburnea
LK2-10T,
Micromonospora nigra
DSM 43818T and
Micromonospora olivasterospora
DSM 43868T. DNA–DNA hybridization and physiological tests allowed genotypic and phenotypic differentiation of both isolates from related species; however, their high DNA–DNA relatedness showed that they belong to the same genomic species. Strain Y22T ( = DSM 45644T = NRRL B-24859T) was selected as the type strain to represent this novel species, for which the name Micromonospora equina sp. nov. is proposed.
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Affiliation(s)
- Gareth J. Everest
- Department of Molecular and Cell Biology, University of Cape Town, Private Bag X3, Rondebosch 7701, Cape Town, South Africa
| | - Paul R. Meyers
- Department of Molecular and Cell Biology, University of Cape Town, Private Bag X3, Rondebosch 7701, Cape Town, South Africa
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Carro L, Pukall R, Spröer C, Kroppenstedt RM, Trujillo ME. Micromonospora cremea sp. nov. and Micromonospora zamorensis sp. nov., isolated from the rhizosphere of Pisum sativum. Int J Syst Evol Microbiol 2012; 62:2971-2977. [PMID: 22286910 DOI: 10.1099/ijs.0.038695-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Three actinobacterial strains, CR30(T), CR36 and CR38(T), were isolated from rhizosphere soil of Pisum sativum plants collected in Spain. The strains were filamentous, Gram-stain-positive and produced single spores. Phylogenetic, chemotaxonomic and morphological analyses confirmed that the three strains belonged to the genus Micromonospora. 16S rRNA gene sequence analysis of strains CR30(T) and CR36 showed a close relationship to Micromonospora coriariae NAR01(T) (99.3% similarity) while strain CR38(T) had a similarity of 99.0% with Micromonospora saelicesensis Lupac 09(T). In addition, gyrB gene phylogeny clearly differentiated the novel isolates from recognized Micromonospora species. DNA-DNA hybridization, BOX-PCR and ARDRA profiles confirmed that these strains represent novel genomic species. The cell-wall peptidoglycan of strains CR30(T) and CR38(T) contained meso-diaminopimelic acid. Both strains had MK-10(H(4)) as the main menaquinone and a phospholipid type II pattern. An array of physiological tests also differentiated the isolates from their closest neighbours. Considering all the data obtained, it is proposed that strains CR30(T) and CR36 represent a novel species under the name Micromonospora cremea sp. nov. (type strain CR30(T) = CECT 7891(T) = DSM 45599(T)), whereas CR38(T) represents a second novel species, for which the name Micromonospora zamorensis sp. nov. is proposed, with CR38(T) ( = CECT 7892(T) = DSM 45600(T)) as the type strain.
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Affiliation(s)
- Lorena Carro
- Departamento de Microbiología y Genética, Edificio Departamental, Lab. 205, Campus Miguel de Unamuno, Universidad de Salamanca, 37007 Salamanca, Spain
| | - Rüdiger Pukall
- DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Inhoffenstrasse 7B, 38124 Braunschweig, Germany
| | - Cathrin Spröer
- DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Inhoffenstrasse 7B, 38124 Braunschweig, Germany
| | - Reiner M Kroppenstedt
- DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Inhoffenstrasse 7B, 38124 Braunschweig, Germany
| | - Martha E Trujillo
- Departamento de Microbiología y Genética, Edificio Departamental, Lab. 205, Campus Miguel de Unamuno, Universidad de Salamanca, 37007 Salamanca, Spain
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Ren J, Li L, Wei B, Tang YL, Deng ZX, Sun M, Hong K. Micromonospora wenchangensis sp. nov., isolated from mangrove soil. Int J Syst Evol Microbiol 2012. [PMID: 23178730 DOI: 10.1099/ijs.0.045476-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An actinomycete, strain 2602GPT1-05(T), was isolated from a composite mangrove soil sample collected from Wenchang, Hainan province, China. Strain 2602GPT1-05(T) showed closest 16S rRNA gene sequence similarity to Micromonospora haikouensis 232617(T) (99.05 %), and phylogenetically clustered with Micromonospora haikouensis 232617(T), Micromonospora matsumotoense IMSNU 22003(T) (98.7 %) and Micromonospora rifamycinica AM105(T) (98.6 %) based on the 16S rRNA and gyrB gene sequence phylogenetic analysis. The strain harboured meso-DAP and glycine as major cell-wall amino acids, and MK-10(H6) and MK-9(H6) as predominant menaquinones. The characteristic whole-cell sugars were xylose, arabinose, glucose and galactose. The polar lipid profile comprised phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylinositol, phosphatidylglycerol, phosphatidylinositol mannosides, unknown phospholipid and an unknown phosphoglycolipid. The major cellular fatty acids were C18 : 1ω9c, iso-C15 : 0, 10-methyl C18 : 0 (tuberculostearic acid), C16 : 0, C18 : 0 and iso-C16 : 0. The DNA G+C content was 71.7 mol%. Furthermore, some physiological and biochemical properties and low DNA-DNA relatedness values enabled the strain to be differentiated from members of closely related species. On the basis of these phenotypic, genotypic and chemotaxonomic data, strain 2602GPT1-05(T) represents a novel species of the genus Micromonospora, for which the name Micromonospora wenchangensis sp. nov. is proposed. The type strain is 2602GPT1-05(T) ( = CCTCC AA 2012002(T) = DSM 45709(T)).
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Affiliation(s)
- Jian Ren
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China.,Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, and Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, PR China
| | - Lei Li
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, and Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, PR China
| | - Bin Wei
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, and Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, PR China
| | - Yi-Li Tang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, and Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, PR China
| | - Zi-Xin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, and Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, PR China
| | - Ming Sun
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Kui Hong
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, and Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, PR China
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Carro L, Rivas R, León-Barrios M, González-Tirante M, Velázquez E, Valverde A. Herbaspirillum
canariense sp. nov., Herbaspirillum
aurantiacum sp. nov. and Herbaspirillum
soli sp. nov., isolated from volcanic mountain soil, and emended description of the genus
Herbaspirillum. Int J Syst Evol Microbiol 2012; 62:1300-1306. [DOI: 10.1099/ijs.0.031336-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Three Gram-negative, motile and slightly curved rod-shaped bacteria, strains SUEMI03T, SUEMI08T and SUEMI10T, were isolated from an old volcanic mountain soil on Tenerife (Canary Islands). The three strains were related phylogenetically to
Herbaspirillum seropedicae
. 16S rRNA gene sequence similarity was 99.2–99.6 % among strains SUEMI03T, SUEMI08T and SUEMI10T, which presented 97.5, 97.8 and 97.7 % identity, respectively, with respect to
H. seropedicae
DSM 6445T. The three strains grew optimally in TSB at 28 °C and contained summed features 3 (C16 : 1ω6c and/or C16 : 1ω7c) and 8 (C18 : 1ω6c and/or C18 : 1ω7c) and C16 : 0 as major cellular fatty acids. The DNA G+C contents of strains SUEMI03T, SUEMI08T and SUEMI10T were 61.6, 60.4 and 61.9 mol%, respectively. Strains SUEMI03T, SUEMI08T and SUEMI10T presented less than 60 % interstrain DNA relatedness and less than 30 % relatedness with respect to
H. seropedicae
DSM 6445T. In spite of their common geographical origin, the three strains isolated in this study presented several phenotypic differences, presenting phenotypic profiles highly divergent from that of
H. seropedicae
. Therefore, we propose that the strains isolated in this study represent three novel species of the genus
Herbaspirillum
, named Herbaspirillum canariense sp. nov. (type strain SUEMI03T = LMG 26151T = CECT 7838T), Herbaspirillum aurantiacum sp. nov. (type strain SUEMI08T = LMG 26150T = CECT 7839T) and Herbaspirillum soli sp. nov. (type strain SUEMI10T = LMG 26149T = CECT 7840T).
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Affiliation(s)
- Lorena Carro
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
| | - Raúl Rivas
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
| | - Milagros León-Barrios
- Departamento de Microbiología y Biología Celular, Universidad de la Laguna, Tenerife, Spain
| | | | - Encarna Velázquez
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
| | - Angel Valverde
- Instituto de Recursos Naturales y Agrobiología, CSIC, Salamanca, Spain
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Supong K, Suriyachadkun C, Tanasupawat S, Suwanborirux K, Pittayakhajonwut P, Kudo T, Thawai C. Micromonospora sediminicola sp. nov., isolated from marine sediment. Int J Syst Evol Microbiol 2012; 63:570-575. [PMID: 22523170 DOI: 10.1099/ijs.0.041103-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An actinomycete strain, designated strain SH2-13(T), was isolated from a marine sediment sample collected from the Andaman Sea of Thailand. Applying a polyphasic approach, the isolate was identified as a member of the genus Micromonospora using morphological and chemotaxonomic characteristics, including the presence of meso-diaminopimelic acid in the peptidoglycan. Whole-cell sugars were arabinose, galactose, glucose, rhamnose, ribose and xylose. Diagnostic polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannosides and phosphoglycolipids. The major menaquinones were MK-10(H(2)), MK-10(H(4)) and MK-10(H(6)). 16S rRNA gene sequence analysis revealed similarity to Micromonospora marina JSM1-1(T) (99.1 %), Micromonospora coxensis 2-30-b(28)(T) (99.1 %), Micromonospora aurantiaca DSM 43813(T) (98.8 %) and Micromonospora chalcea DSM 43026(T) (98.7 %). However, a combination of DNA-DNA hybridization results and phenotypic properties indicated that strain SH2-13(T) ( = NBRC 107934(T) = BCC 45601(T)) should be classified as the type strain of a novel species, with the proposed name Micromonospora sediminicola sp. nov.
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Affiliation(s)
- Khomsan Supong
- Department of Biology, Faculty of Science, King Mongkut's Institute of Technology Ladkrabang, Bangkok 10520, Thailand
| | - Chanwit Suriyachadkun
- Biotec Culture Collection (BCC), BIOTEC Central Research Unit, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, 113 Thailand Science Park, Phaholyothin Road, Klong 1, Klong Luang, Pathumthani 12120, Thailand
| | - Somboon Tanasupawat
- Department of Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - Khanit Suwanborirux
- Department of Pharmacognosy and Pharmaceutical Botany, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
- Center for Bioactive Natural Products from Marine Organisms and Endophytic Fungi (BNPME), Bangkok 10330, Thailand
| | - Pattama Pittayakhajonwut
- National Center for Genetic Engineering and Biotechnology (BIOTEC), Thailand Science Park, Phaholyothin Road, Klong 1, Klong Luang, Pathumthani 12120, Thailand
| | - Takuji Kudo
- Japan Collection of Microorganisms, RIKEN BioResource Center, Wako, Saitama 351-0198, Japan
| | - Chitti Thawai
- Actinobacterial Research Unit and Microbial Resource Management Unit, Scientific Instrument Center, Faculty of Science, King Mongkut's Institute of Technology Ladkrabang, Bangkok 10520, Thailand
- Department of Biology, Faculty of Science, King Mongkut's Institute of Technology Ladkrabang, Bangkok 10520, Thailand
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Zhang L, Xi L, Ruan J, Huang Y. Micromonospora yangpuensis sp. nov., isolated from a sponge. Int J Syst Evol Microbiol 2012; 62:272-278. [DOI: 10.1099/ijs.0.029439-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An actinomycete, strain FXJ6.011T, was isolated from a cup-shaped sponge collected at Dachan reef, Yangpu in the South China Sea. The strain had morphological characteristics of members of the family Micromonosporaceae. Phylogenetic analysis of the 16S rRNA gene sequence of strain FXJ6.011T indicated the highest similarity (98.7 %) to Micromonospora auratinigra JCM 12357T, Micromonospora chaiyaphumensis JCM 12873T and Micromonospora echinofusca JCM 3327T. Analysis of the gyrB gene sequence also showed that strain FXJ6.011T should be assigned to the genus Micromonospora. It contained dd-diaminopimelic acid as the major cell-wall diamino acid and MK-10(H2) as predominant menaquinone. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidyl mannosides and phosphatidylinositol dimannoside. The major cellular fatty acids were iso-C16 : 0, C17 : 1ω8c and C16 : 0. Physiological and biochemical data and low DNA–DNA relatedness values enabled the strain to be differentiated from members of closely related species. Based on phenotypic and genotypic data, strain FXJ6.011T represents a novel Micromonospora species, for which the name Micromonospora yangpuensis sp. nov. is proposed; the type strain is FXJ6.011T ( = CGMCC 4.5736T = NBRC 107727T).
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Affiliation(s)
- Limin Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Lijun Xi
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Jisheng Ruan
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Ying Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
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Barona-Gómez F, Cruz-Morales P, Noda-García L. What can genome-scale metabolic network reconstructions do for prokaryotic systematics? Antonie van Leeuwenhoek 2011; 101:35-43. [PMID: 22016333 DOI: 10.1007/s10482-011-9655-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Accepted: 10/07/2011] [Indexed: 11/24/2022]
Abstract
It has recently been proposed that in addition to Nomenclature, Classification and Identification, Comprehending Microbial Diversity may be considered as the fourth tenet of microbial systematics [Staley JT (2010) The Bulletin of BISMiS, 1(1): 1-5]. As this fourth goal implies a fundamental understanding of microbial speciation, this perspective article argues that translation of bacterial genome sequences into metabolic features may contribute to the development of modern polyphasic taxonomic approaches. Genome-scale metabolic network reconstructions (GSMRs), which are the result of computationally predicted and experimentally confirmed stoichiometric matrices incorporating all enzyme and metabolite components encoded by a genome sequence, provide a platform that can illustrate bacterial speciation. As the topology and the composition of GSMRs are expected to be the result of adaptive evolution, the features of these networks may provide the prokaryotic taxonomist with novel tools for reaching the fourth tenet of microbial systematics. Through selected examples from the Actinobacteria, which have been inferred from GSMRs and experimentally confirmed after phenotypic characterisation, it will be shown that this level of information can be incorporated into modern polyphasic taxonomic approaches. In conclusion, three specific examples are illustrated to show how GSMRs will revolutionize prokaryotic systematics, as has previously occurred in many other fields of microbiology.
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Affiliation(s)
- Francisco Barona-Gómez
- Evolution of Metabolic Diversity Laboratory, Laboratorio Nacional de Genómica para la Biodiversidad (Langebio), CINVESTAV-IPN, Km 9.6 Libramiento Norte, Carretera Irapuato-León, Irapuato, Mexico.
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31
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Carro L, Zúñiga P, de la Calle F, Trujillo ME. Streptomyces pharmamarensis sp. nov. isolated from a marine sediment. Int J Syst Evol Microbiol 2011; 62:1165-1170. [PMID: 21724951 DOI: 10.1099/ijs.0.034066-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-positive actinobacterium, strain PM267(T), was isolated from a marine sediment sample in the Mediterranean Sea. The novel strain produced extensively branched substrate and aerial hyphae that carried spiral spore chains. Substrate and aerial mycelia were cream-white and white, respectively. Diffusible pigments were not observed. 16S rRNA gene sequence analysis revealed that strain PM267(T) belonged to the genus Streptomyces and shared a gene sequence similarity of 97.1 % with Streptomyces artemisiae YIM 63135(T) and Streptomyces armeniacus JCM 3070(T). Values <97 % were obtained with other sequences representing members of the genus Streptomyces. The cell wall peptidoglycan contained ll-diaminopimelic acid. MK-9(H(8)) was the major menaquinone. The phospholipid pattern included phosphatidylethanolamine as diagnostic lipid (type II). Major fatty acids found were iso- and anteiso- fatty acids. The G+C content of the DNA was 71.2 mol%. The strain was halotolerant and was able to grow in the presence of 9 % (w/v) NaCl (with an optimum of 2 %). On the basis of these results and additional physiological data obtained in the present study, strain PM267(T) represents a novel species within the genus Streptomyces for which the name Streptomyces pharmamarensis sp. nov. is proposed (type strain PM267(T) = CECT 7841(T) = DSM 42032(T)).
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Affiliation(s)
- Lorena Carro
- Departamento de Microbiología y Genética, Edificio Departamental, Lab. 205, Campus Miguel de Unamuno, Universidad de Salamanca, Salamanca, Spain
| | - Paz Zúñiga
- PharmaMar, Avenida de los Reyes 1, 28770 Colmenar, Madrid, Spain
| | | | - Martha E Trujillo
- Departamento de Microbiología y Genética, Edificio Departamental, Lab. 205, Campus Miguel de Unamuno, Universidad de Salamanca, Salamanca, Spain
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32
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Songsumanus A, Tanasupawat S, Thawai C, Suwanborirux K, Kudo T. Micromonospora humi sp. nov., isolated from peat swamp forest soil. Int J Syst Evol Microbiol 2011; 61:1176-1181. [DOI: 10.1099/ijs.0.024281-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel actinomycete, strain P0402T, was isolated from peat swamp forest soil collected in Thailand. Its taxonomic position was determined by using a polyphasic taxonomic approach. The chemotaxonomic characteristics of this strain matched those of the genus Micromonospora, i.e. the presence of meso-diaminopimelic acid and N-glycolyl muramic acid in the peptidoglycan, whole-cell sugar pattern D, phospholipid type II, and cellular fatty acid type 3b. Phylogenetic analysis based on 16S rRNA gene sequences revealed a close relationship between strain P0402T and Micromonospora coxensis JCM 13248T (99.0 % similarity), Micromonospora eburnea JCM 12345T (99.0 %), Micromonospora marina JCM 12870T (98.9 %), Micromonospora halophytica JCM 3125T (98.7 %), Micromonospora chalcea JCM 3031T (98.7 %), Micromonospora purpureochromogenes JCM 3156T (98.6 %) and Micromonospora aurantiaca JCM 10878T (98.5 %). It could be clearly distinguished from these type strains based on low levels of DNA–DNA relatedness and phenotypic differences. On the basis of the data presented, strain P0402T is suggested to represent a novel species of the genus Micromonospora, for which the name Micromonospora humi sp. nov. is proposed. The type strain is P0402T ( = JCM 15292T = PCU 315T = TISTR 1883T).
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Affiliation(s)
- Apakorn Songsumanus
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - Somboon Tanasupawat
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - Chitti Thawai
- Department of Biology and Microbiol Resource Management Unit, Scientific Instrument Center, Faculty of Science, King Mongkut’s Institute of Technology, Ladkrabang, Bangkok 10520, Thailand
| | - Khanit Suwanborirux
- Department of Pharmacognosy and Pharmaceutical Botany, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - Takuji Kudo
- Japan Collection of Microorganisms, RIKEN BioResource Center, Wako, Saitama 351-0198, Japan
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Wang C, Xu XX, Qu Z, Wang HL, Lin HP, Xie QY, Ruan JS, Hong K. Micromonospora rhizosphaerae sp. nov., isolated from mangrove rhizosphere soil. Int J Syst Evol Microbiol 2011; 61:320-324. [DOI: 10.1099/ijs.0.020461-0] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strain 211018T was isolated from mangrove Excocaria agallocha rhizosphere soil. 16S rRNA gene sequence analysis showed the highest similarity to the type strains of Micromonospora olivasterospora DSM 43868T (98.6 %) and Micromonospora pattaloongensis TJ2-2T (98.4 %). gyrB gene sequence analysis also indicated that strain 211018T should be assigned to the genus Micromonospora. The characteristic whole-cell sugars are xylose, mannose and arabinose. The predominant menaquinone is MK-9(H4) and the major fatty acids are iso-C15 : 0 (27.5 %), 10-methyl C17 : 0 (14.2 %), C17 : 1
ω8c (12.8 %), iso-C16 : 0 (12.6 %), anteiso-C15 : 0 (6.1 %), iso-C17 : 0 (4.1 %) and anteiso-C17 : 0 (4.0 %). The phospholipid profile comprises phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol and phosphatidylinositol mannosides. The DNA G+C content is 70.8 mol%. The chemotaxonomic data of the strain coincided with those of the genus Micromonospora. Furthermore, a combination of DNA–DNA hybridization results and some physiological and biochemical properties indicated that the novel strain could be readily distinguished from the closest phylogenetic relatives. On the basis of these phenotypic and genotypic data, strain 211018T represents a novel species of the genus Micromonospora, for which the name Micromonospora rhizosphaerae sp. nov. is proposed. The type strain is 211018T (=CGMCC 4.5599T =DSM 45431T).
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Affiliation(s)
- Cheng Wang
- College of Environment and Plant Protection, Hainan University, Danzhou 571737, PR China
- Laboratory of Tropical Microbial Resources, Hainan Province; Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture; Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou 571101, PR China
| | - Xiao-Xiong Xu
- Laboratory of Tropical Microbial Resources, Hainan Province; Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture; Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou 571101, PR China
| | - Zhi Qu
- Laboratory of Tropical Microbial Resources, Hainan Province; Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture; Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou 571101, PR China
| | - Hai-Long Wang
- Laboratory of Tropical Microbial Resources, Hainan Province; Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture; Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou 571101, PR China
| | - Hai-Peng Lin
- Laboratory of Tropical Microbial Resources, Hainan Province; Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture; Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou 571101, PR China
| | - Qing-Yi Xie
- Laboratory of Tropical Microbial Resources, Hainan Province; Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture; Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou 571101, PR China
| | - Ji-Sheng Ruan
- Laboratory of Tropical Microbial Resources, Hainan Province; Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture; Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou 571101, PR China
| | - Kui Hong
- Laboratory of Tropical Microbial Resources, Hainan Province; Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture; Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou 571101, PR China
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Kirby BM, Meyers PR. Micromonospora tulbaghiae sp. nov., isolated from the leaves of wild garlic, Tulbaghia violacea. Int J Syst Evol Microbiol 2010; 60:1328-1333. [PMID: 19667372 DOI: 10.1099/ijs.0.013243-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel actinomycete, strain TVU1(T), was isolated from leaves of the indigenous South African plant Tulbaghia violacea. Applying a polyphasic approach, the isolate was identified as a member of the genus Micromonospora. Phylogenetic analysis of the 16S rRNA gene sequence showed that strain TVU1(T) was most closely related to Micromonospora echinospora DSM 43816(T). However, phylogenetic analysis based on gyrB gene sequences showed that strain TVU1(T) was most closely related to the type strains of Micromonospora aurantiaca and Micromonospora chalcea. DNA-DNA relatedness values between strain TVU1(T) and the type strains of M. echinospora, M. aurantiaca and M. chalcea were 7.6+/-4.5, 45.9+/-2.0 and 60.9+/-4.5 %, respectively. Strain TVU1(T) could be distinguished from the type strains of all three of these species by several physiological characteristics, such as colony colour, NaCl tolerance, growth temperature range and sole carbon source utilization pattern. Strain TVU1(T) (=DSM 45142(T)=NRRL B-24576(T)) therefore represents a novel species for which the name Micromonospora tulbaghiae sp. nov. is proposed.
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Affiliation(s)
- Bronwyn M Kirby
- Department of Molecular and Cell Biology, University of Cape Town, Private Bag X3, Rondebosch 7701, Cape Town, South Africa
| | - Paul R Meyers
- Department of Molecular and Cell Biology, University of Cape Town, Private Bag X3, Rondebosch 7701, Cape Town, South Africa
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C Garcia L, Martínez-Molina E, Trujillo ME. Micromonospora pisi sp. nov., isolated from root nodules of Pisum sativum. Int J Syst Evol Microbiol 2010; 60:331-337. [PMID: 19651739 DOI: 10.1099/ijs.0.012708-0] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2023] Open
Abstract
A novel actinomycete, designated strain GUI 15(T), isolated from the root nodules of a Pisum sativum plant was characterized taxonomically by using a polyphasic approach. The 16S rRNA gene sequence of strain GUI 15(T) showed highest similarity to Micromonospora pattaloongensis TJ2-2(T) (98.7 %) and Polymorphospora rubra TT 97-42(T) (98.5 %). Phylogenetic analysis based on the gyrase B gene also supported the close relationship of these three strains, but indicated that strain GUI 15(T) should be assigned to the genus Micromonospora. Chemotaxonomic results confirmed the position of the isolate in the genus Micromonospora, but revealed differences at the species level. The novel strain could be distinguished from recognized Micromonospora species by using a combination of physiological and biochemical tests. Based on these observations, strain GUI 15(T) is considered to represent a novel species of the genus Micromonospora, for which the name Micromonospora pisi sp. nov. is proposed. The type strain is GUI 15(T) (=DSM 45175(T)=LMG 24546(T)).
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Affiliation(s)
- Lorena C Garcia
- Departamento de Microbiología y Genética, Edificio Departamental, Lab. 205, Campus Miguel de Unamuno, Universidad de Salamanca, 37007 Salamanca, Spain
| | - Eustoquio Martínez-Molina
- Departamento de Microbiología y Genética, Edificio Departamental, Lab. 205, Campus Miguel de Unamuno, Universidad de Salamanca, 37007 Salamanca, Spain
| | - Martha E Trujillo
- Departamento de Microbiología y Genética, Edificio Departamental, Lab. 205, Campus Miguel de Unamuno, Universidad de Salamanca, 37007 Salamanca, Spain
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Tanasupawat S, Jongrungruangchok S, Kudo T. Micromonospora marina sp. nov., isolated from sea sand. Int J Syst Evol Microbiol 2009; 60:648-652. [PMID: 19656925 DOI: 10.1099/ijs.0.014068-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two actinomycete strains, JSM1-1(T) and JSM1-3, were isolated from sea sand collected in Thailand. Their taxonomic position was determined using a polyphasic approach. The chemotaxonomic characteristics of these strains coincided with those of the genus Micromonospora, i.e. the presence of meso-diaminopimelic acid and N-glycolyl muramic acid in the peptidoglycan, whole cell sugar pattern D, phospholipids type II, and cellular fatty acid type 3b. Phylogenetic analysis of 16S rRNA gene sequences revealed a close relationship between strains JSM1-1(T) and JSM1-3 (99.8 %), and between JSM1-1(T) and Micromonospora aurantiaca JCM 10878(T) (99.3 %), Micromonospora chalcea JCM 3031(T) (99.0 %), and Micromonospora coxensis JCM 13248 (T) (99.0 %). However, strains JSM1-1(T) and JSM1-3 could be clearly distinguished from these type strains by a low DNA-DNA relatedness and by phenotypic differences. On the basis of the data presented, a new species, Micromonospora marina sp. nov., is proposed. The type strain is JSM1-1(T) (=JCM 12870(T) =PCU 269(T) =TISTR 1566(T)).
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Affiliation(s)
- Somboon Tanasupawat
- Department of Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - Suchada Jongrungruangchok
- Department of Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - Takuji Kudo
- Japan Collection of Microorganisms, RIKEN BioResource Center, Wako, Saitama 351-0198, Japan
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Promicromonospora kroppenstedtii sp. nov., isolated from sandy soil. Int J Syst Evol Microbiol 2008; 58:1476-81. [DOI: 10.1099/ijs.0.65458-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Jongrungruangchok S, Tanasupawat S, Kudo T. Micromonospora chaiyaphumensis sp. nov., isolated from Thai soils. Int J Syst Evol Microbiol 2008; 58:924-8. [DOI: 10.1099/ijs.0.65594-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Jongrungruangchok S, Tanasupawat S, Kudo T. Micromonospora krabiensis sp. nov., isolated from marine soil in Thailand. J GEN APPL MICROBIOL 2008; 54:127-33. [DOI: 10.2323/jgam.54.127] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Micromonospora lupini sp. nov. and Micromonospora saelicesensis sp. nov., isolated from root nodules of Lupinus angustifolius. Int J Syst Evol Microbiol 2007; 57:2799-2804. [DOI: 10.1099/ijs.0.65192-0] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A study was conducted to determine the taxonomic status of six actinomycete strains isolated from root nodules of Lupinus angustifolius. The strains were filamentous, Gram-positive and produced single spores at the tip of the hyphae. Phylogenetic, chemotaxonomic and morphological analyses demonstrated that all six strains belonged to the genus Micromonospora. According to the 16S rRNA gene sequence data, the strains were divided into two clusters that are moderately related to Micromonospora mirobrigensis, Micromonospora matsumotoense and Micromonospora purpureochromogenes. Fatty acid patterns also supported the division of the strains, and significant differences between the two groups were found in the amounts of iso-15 : 0, iso-16 : 0, iso-16 : 1 and iso-17 : 0. Furthermore, the two groups showed physiological differences which included utilization of arabinose, trehalose, alanine and sucrose and xylan hydrolysis. Finally, DNA–DNA hybridization and ribotyping studies confirmed that each group represents a novel species. Based on the genotypic and phenotypic data, the novel species Micromonospora lupini sp. nov. (type strain Lupac 14NT =DSM 44874T =LMG 24055T) and Micromonospora saelicesensis sp. nov. (type strain Lupac 09T =DSM 44871T =LMG 24056T) are proposed.
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Thawai C, Tanasupawat S, Suwanborirux K, Itoh T, Kudo T. Micromonospora narathiwatensis sp. nov., from Thai peat swamp forest soils. J GEN APPL MICROBIOL 2007; 53:287-93. [DOI: 10.2323/jgam.53.287] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Ara I, Kudo T. Two new species of the genus Micromonospora: Micromonospora chokoriensis sp. nov. and Micromonospora coxensis sp. nov., isolated from sandy soil. J GEN APPL MICROBIOL 2007; 53:29-37. [PMID: 17429159 DOI: 10.2323/jgam.53.29] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Two actinomycete strains, 2-19(6)(T) and 2-30-b(28)(T), which produced single, non-motile noduler to warty spore surfaces, were isolated from sandy soil in Chokoria, Cox's Bazar, Bangladesh. A polyphasic study was carried out to establish the taxonomic position of these strains. Morphological and chemotaxonomic characteristics of these strains coincided with those of the genus Micromonospora. Phylogenetic analysis using 16S rDNA sequences indicated that these strains should be classified in the genus Micromonospora. The 16S rDNA sequence of strain 2-19(6)(T )showed closest similarity to the type strains of M. mirobrigensis (98.9%) and M. carbonacea (98.8%), and the strain 2-30-b(28)(T) to the type strains of M. purpureochromogenes (99.4%), M. halophytica (99.3%) and M. aurantiaca (99.2%). Furthermore, a combination of DNA-DNA hybridization results and some differential physiological and biochemical properties indicated that these strains were distinguished from the phylogenetically closest relatives. These strains therefore represent two novel species, for which the name Micromonospora chokoriensis sp. nov. and Micromonospora coxensis sp. nov. are proposed. The type strains are 2-19(6)(T) (=JCM 13247(T) =MTCC 8535(T)) and 2-30-b(28)(T) (=JCM 13248(T)=MTCC 8093(T)).
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Affiliation(s)
- Ismet Ara
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, Wako, Saitama, Japan.
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Trujillo ME, Kroppenstedt RM, Schumann P, Carro L, Martínez-Molina E. Micromonospora coriariae sp. nov., isolated from root nodules of Coriaria myrtifolia. Int J Syst Evol Microbiol 2006; 56:2381-2385. [PMID: 17012566 DOI: 10.1099/ijs.0.64449-0] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An actinomycete strain, NAR01T, was isolated from root nodules of a Coriaria plant. The 16S rRNA gene sequence of strain NAR01T showed most similarity to the type strains of Micromonospora endolithica (98.94 %) and Micromonospora chersina (98.4 %). The chemotaxonomic results obtained confirmed the taxonomic position of the isolate within the genus Micromonospora, and revealed differences at the species level. Physiological and biochemical tests showed that strain NAR01T could be clearly distinguished from its closest phylogenetic neighbours, while DNA–DNA hybridization results indicated that the isolate represents a novel species. On the basis of these results, strain NAR01T (=DSM 44875T=LMG 23557T) is proposed as the type strain of the novel species Micromonospora coriariae sp. nov.
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Affiliation(s)
- Martha E Trujillo
- Departamento de Microbiología y Genética, Edificio Departamental, Lab. 209, Campus Miguel de Unamuno, Universidad de Salamanca, 37007 Salamanca, Spain
| | - Reiner M Kroppenstedt
- DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Mascheroder Weg 1b, 38124 Braunschweig, Germany
| | - Peter Schumann
- DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Mascheroder Weg 1b, 38124 Braunschweig, Germany
| | - Lorena Carro
- Departamento de Microbiología y Genética, Edificio Departamental, Lab. 209, Campus Miguel de Unamuno, Universidad de Salamanca, 37007 Salamanca, Spain
| | - Eustoquio Martínez-Molina
- Departamento de Microbiología y Genética, Edificio Departamental, Lab. 209, Campus Miguel de Unamuno, Universidad de Salamanca, 37007 Salamanca, Spain
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Trujillo ME, Kroppenstedt RM, Schumann P, Martínez-Molina E. Kribbella lupini sp. nov., isolated from the roots of Lupinus angustifolius. Int J Syst Evol Microbiol 2006; 56:407-411. [PMID: 16449448 DOI: 10.1099/ijs.0.63745-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strain LU14T, isolated from the roots of Lupinus angustifolius, was characterized using a polyphasic approach. 16S rRNA gene sequence studies showed a similarity of 98·7 % to the corresponding sequence of Kribbella sandramycini DSM 15626T. Chemotaxonomic data gathered for fatty acids, phospholipids, cell-wall peptidoglycan and menaquinones strongly supported the classification of this strain in the genus Kribbella and DNA–DNA hybridization studies suggested that it may represent a novel species. Many physiological features were found that clearly distinguished isolate LU14T from other Kribbella species. Based on the above data, a novel species of the genus Kribbella, Kribbella lupini sp. nov., is proposed with the type strain LU14T (=DSM 16683T=LMG 22957T).
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Affiliation(s)
- Martha E Trujillo
- Departamento de Microbiología y Genética, Edificio Departamental, Lab. 209, Campus Miguel de Unamuno, Universidad de Salamanca, 37007 Salamanca, Spain
| | - Reiner M Kroppenstedt
- DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Mascheroder Weg 1b, 38124 Braunschweig, Germany
| | - Peter Schumann
- DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Mascheroder Weg 1b, 38124 Braunschweig, Germany
| | - Eustoquio Martínez-Molina
- Departamento de Microbiología y Genética, Edificio Departamental, Lab. 209, Campus Miguel de Unamuno, Universidad de Salamanca, 37007 Salamanca, Spain
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Díaz M, Esteban A, Fernández-Abalos JM, Santamaría RI. The high-affinity phosphate-binding protein PstS is accumulated under high fructose concentrations and mutation of the corresponding gene affects differentiation in Streptomyces lividans. MICROBIOLOGY-SGM 2005; 151:2583-2592. [PMID: 16079337 DOI: 10.1099/mic.0.27983-0] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The secreted protein pattern of Streptomyces lividans depends on the carbon source present in the culture media. One protein that shows the most dramatic change is the high-affinity phosphate-binding protein PstS, which is strongly accumulated in the supernatant of liquid cultures containing high concentrations (>3 %) of certain sugars, such as fructose, galactose and mannose. The promoter region of this gene and that of its Streptomyces coelicolor homologue were used to drive the expression of a xylanase in S. lividans that was accumulated in the culture supernatant when grown in the presence of fructose. PstS accumulation was dramatically increased in a S. lividans polyphosphate kinase null mutant (Deltappk) and was impaired in a deletion mutant lacking phoP, the transcriptional regulator gene of the two-component phoR-phoP system that controls the Pho regulon. Deletion of the pstS genes in S. lividans and S. coelicolor impaired phosphate transport and accelerated differentiation and sporulation on solid media. Complementation with a single copy in a S. lividans pstS null mutant returned phosphate transport and sporulation to levels similar to those of the wild-type strain. The present work demonstrates that carbon and phosphate metabolism are linked in the regulation of genes and that this can trigger the genetic switch towards morphogenesis.
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Affiliation(s)
- Margarita Díaz
- Instituto de Microbiología Bioquímica/Departamento de Microbiología y Genética, Consejo Superior de Investigaciones Científicas (CSIC)/Universidad de Salamanca, Edificio Departamental, Campus Miguel de Unamuno, 37007 Salamanca, Spain
| | - Ana Esteban
- Instituto de Microbiología Bioquímica/Departamento de Microbiología y Genética, Consejo Superior de Investigaciones Científicas (CSIC)/Universidad de Salamanca, Edificio Departamental, Campus Miguel de Unamuno, 37007 Salamanca, Spain
| | - José Manuel Fernández-Abalos
- Instituto de Microbiología Bioquímica/Departamento de Microbiología y Genética, Consejo Superior de Investigaciones Científicas (CSIC)/Universidad de Salamanca, Edificio Departamental, Campus Miguel de Unamuno, 37007 Salamanca, Spain
| | - Ramón I Santamaría
- Instituto de Microbiología Bioquímica/Departamento de Microbiología y Genética, Consejo Superior de Investigaciones Científicas (CSIC)/Universidad de Salamanca, Edificio Departamental, Campus Miguel de Unamuno, 37007 Salamanca, Spain
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Thawai C, Tanasupawat S, Itoh T, Suwanborirux K, Kudo T. Micromonospora siamensis sp. nov., isolated from Thai peat swamp forest. J GEN APPL MICROBIOL 2005; 51:229-34. [PMID: 16205030 DOI: 10.2323/jgam.51.229] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Morphological and chemotaxonomic characterization of actinomycete strain TT2-4T isolated from peat swamp forest soil in Pattaloong Province, Thailand, clearly demonstrated that this strain belongs to the genus Micromonospora. 16S rDNA sequence analysis for the strain supported the assignment of the strain to the genus Micromonospora and the similarity value of sequences between this strain and the closely related species, Micromonospora mirobrigensis was 99.1%, and M. carbonacea and M. matsumotoense were 98.8%. The DNA-DNA hybridization result and some physiological and biochemical properties indicated that strain TT2-4T was distinguished from the phylogenetically closest relatives. Based on these genotypic and phenotypic data, strain TT2-4T merits a new species in the genus Micromonospora and the name Micromonospora siamensis sp. nov. is proposed for the strain. The type strain is strain TT2-4T (=JCM 12769T =PCU 266T =TISTR 1554T).
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Affiliation(s)
- Chitti Thawai
- Department of Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, Thailand
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