1
|
Ramesh C, Anwesh M, Alessia T, Giuffrida D, La Tella R, Chiaia V, Mondello L, Anil K, Le Loarer A, Gauvin-Bialecki A, Fouillaud M, Dufossé L. Genome and Compound Analysis of Sioxanthin-Producing Marine Actinobacterium Micromonospora sp. nov. Strain SH-82 Isolated from Sponge Scopalina hapalia. Curr Microbiol 2024; 81:298. [PMID: 39107520 DOI: 10.1007/s00284-024-03812-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Accepted: 07/19/2024] [Indexed: 08/15/2024]
Abstract
Pigments and other secondary metabolites originating from marine microbes have been a promising natural colorants and drugs for multifaceted applications. However, marine actinobacteria producing such natural molecules are least investigated in terms of their taxonomy, chemical diversity and applications in biomedical, textile, and food industries. In this study, sioxanthin pigment-producing Gram-positive actinobacteria, Micromonospora sp. strain SH-82 was isolated from a marine sponge, Scopalina hapalia, and its whole genome was analyzed. Strain SH-82is a prolific producer of diverse chemical molecules as it produced more compounds on A1 medium with different culture conditions. The genome size of SH-82 is 6.24 Mb (6,246,890 bp) carrying 23 identified biosynthetic gene clusters. A total of 5415 CDS, 60 tRNA, 9 rRNA, and 1 tmRNA are identified from SH-82 genome. The GC content (%) of whole genome was 71.6%. Strain SH-82 harbors genes encoding type I, type II, and type III polyketide synthases. Based on the multi-locus sequence analysis and fatty acid methyl ester (FAME) composition, strain SH-82 is confirmed as a novel species. The genetic information of Micromonospora sp. SH-82 has been deposited to NCBI under the BioProject ID PRJNA1087320, with corresponding identifiers in the Sequence Read Archive (SRA) as SAMN40439676 and the Genome accession as CP148049.
Collapse
Affiliation(s)
- Chatragadda Ramesh
- Biological Oceanography Division (BOD), National Institute of Oceanography (CSIR-NIO), Dona Paula, Panaji, Goa, 403004, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India.
| | - Maile Anwesh
- DBT-Centre for Microbial Informatics, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad, Telangana, 500046, India.
| | - Tropea Alessia
- Messina Institute of Technology c/o Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, Former Veterinary School, University of Messina, Viale G. Palatucci snc, 98168, Messina, Italy.
| | - Daniele Giuffrida
- Department of Biomedical, Dental, Morphological and Functional Imaging Sciences, University of Messina, Via Consolare Valeria, 98125, Messina, Italy
| | - Roberta La Tella
- Messina Institute of Technology c/o Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, Former Veterinary School, University of Messina, Viale G. Palatucci snc, 98168, Messina, Italy
| | - Valentina Chiaia
- Messina Institute of Technology c/o Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, Former Veterinary School, University of Messina, Viale G. Palatucci snc, 98168, Messina, Italy
| | - Luigi Mondello
- Messina Institute of Technology c/o Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, Former Veterinary School, University of Messina, Viale G. Palatucci snc, 98168, Messina, Italy
- Chromaleont S.R.L., Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, Former Veterinary School, University of Messina, Viale G. Palatucci snc, 98168, Messina, Italy
| | - Kanakam Anil
- Biological Oceanography Division (BOD), National Institute of Oceanography (CSIR-NIO), Dona Paula, Panaji, Goa, 403004, India
| | - Alexandre Le Loarer
- Chemistry and Biotechnology of Natural Products, CHEMBIOPRO, Université de La Réunion, Faculté des Sciences et Technologies, 15 Avenue René Cassin, 97744, Saint-Denis CEDEX 9, France
| | - Anne Gauvin-Bialecki
- Chemistry and Biotechnology of Natural Products, CHEMBIOPRO, Université de La Réunion, Faculté des Sciences et Technologies, 15 Avenue René Cassin, 97744, Saint-Denis CEDEX 9, France
| | - Mireille Fouillaud
- Chemistry and Biotechnology of Natural Products, CHEMBIOPRO, Université de La Réunion, Faculté des Sciences et Technologies, 15 Avenue René Cassin, 97744, Saint-Denis CEDEX 9, France
| | - Laurent Dufossé
- Chemistry and Biotechnology of Natural Products, CHEMBIOPRO, Université de La Réunion, Faculté des Sciences et Technologies, 15 Avenue René Cassin, 97744, Saint-Denis CEDEX 9, France.
| |
Collapse
|
2
|
Saati-Santamaría Z, Flores-Félix JD, Igual JM, Velázquez E, García-Fraile P, Martínez-Molina E. Speciation Features of Ferdinandcohnia quinoae sp. nov to Adapt to the Plant Host. J Mol Evol 2024; 92:169-180. [PMID: 38502221 PMCID: PMC10978704 DOI: 10.1007/s00239-024-10164-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 03/08/2024] [Indexed: 03/21/2024]
Abstract
The bacterial strain SECRCQ15T was isolated from seeds of Chenopodium quinoa in Spain. Phylogenetic, chemotaxonomic, and phenotypic analyses, as well as genome similarity indices, support the classification of the strain into a novel species of the genus Ferdinandcohnia, for which we propose the name Ferdinandcohnia quinoae sp. nov. To dig deep into the speciation features of the strain SECRCQ15T, we performed a comparative genomic analysis of the genome of this strain and those of the type strains of species from the genus Ferdinandcohnia. We found several genes related with plant growth-promoting mechanisms within the SECRCQ15T genome. We also found that singletons of F. quinoae SECRCQ15T are mainly related to the use of carbohydrates, which is a common trait of plant-associated bacteria. To further reveal speciation events in this strain, we revealed genes undergoing diversifying selection (e.g., genes encoding ribosomal proteins) and functions likely lost due to pseudogenization. Also, we found that this novel species contains 138 plant-associated gene-cluster functions that are unique within the genus Ferdinandcohnia. These features may explain both the ecological and taxonomical differentiation of this new taxon.
Collapse
Affiliation(s)
- Zaki Saati-Santamaría
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
- Instituto de Investigación en Agrobiotecnología (CIALE), Universidad de Salamanca, Salamanca, Spain
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská, Prague, Czech Republic
| | | | - José M Igual
- Instituto de Recursos Naturales y Agrobiología, IRNASA-CSIC, Salamanca, Spain
- Unidad Asociada Grupo de Interacción Planta-Microorganismo, Universidad de Salamanca-IRNASA-CSIC, Salamanca, Spain
| | - Encarna Velázquez
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
- Instituto de Investigación en Agrobiotecnología (CIALE), Universidad de Salamanca, Salamanca, Spain
- Unidad Asociada Grupo de Interacción Planta-Microorganismo, Universidad de Salamanca-IRNASA-CSIC, Salamanca, Spain
| | - Paula García-Fraile
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain.
- Instituto de Investigación en Agrobiotecnología (CIALE), Universidad de Salamanca, Salamanca, Spain.
- Unidad Asociada Grupo de Interacción Planta-Microorganismo, Universidad de Salamanca-IRNASA-CSIC, Salamanca, Spain.
| | - Eustoquio Martínez-Molina
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
- Instituto de Investigación en Agrobiotecnología (CIALE), Universidad de Salamanca, Salamanca, Spain
- Unidad Asociada Grupo de Interacción Planta-Microorganismo, Universidad de Salamanca-IRNASA-CSIC, Salamanca, Spain
| |
Collapse
|
3
|
Islam MM, Mandal S. Unveiling growth-promoting attributes of peanut root endophyte Micromonospora sp. Arch Microbiol 2024; 206:182. [PMID: 38502250 DOI: 10.1007/s00203-024-03886-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 01/30/2024] [Accepted: 02/05/2024] [Indexed: 03/21/2024]
Abstract
In this study, 20 endophytic actinobacteria were isolated from different parts of peanut plants growing in cropland with low and high salt in West Bengal, India. The endophytes underwent a rigorous morphological, biochemical, and genetic screening process to evaluate their effectiveness in enhancing plant growth. About 20% of these isolates were identified as potential plant growth-promoting endophytic actinobacteria, which showed high 16S rRNA gene sequence similarity (up to 99-100%) with different species of Micromonospora. Among these isolates, Micromonospora sp. ASENR15 produced the highest levels of indole acetic acid (IAA) and gibberellic acid (GA), while Micromonospora sp. ASENL2, Micromonospora sp. ANENR4, and Micromonospora sp. ASENR12 produced the highest level of siderophore. Among these leaf and root endophytic Micromonospora, strain ANENR4 was tested for its plant growth-promoting attributes. ANENR4 can be transmitted into the roots of a healthy peanut plant, enhances growth, and colonize the roots in abundance, suggesting the potential agricultural significance of the strain. Moreover, the study is the first report of endophytic Micromonospora in peanuts with PGP effects. The outcomes of this study open avenues for further research on harnessing the benefits of this endophytic Micromonospora for optimizing plant growth in agriculture.
Collapse
Affiliation(s)
- Md Majharul Islam
- Laboratory of Molecular Bacteriology, Department of Microbiology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, 700019, India
| | - Sukhendu Mandal
- Laboratory of Molecular Bacteriology, Department of Microbiology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, 700019, India.
| |
Collapse
|
4
|
Razmilic V, Nouioui I, Karlyshev A, Jawad R, Trujillo ME, Igual JM, Andrews BA, Asenjo JA, Carro L, Goodfellow M. Micromonospora parastrephiae sp. nov. and Micromonospora tarensis sp. nov., isolated from the rhizosphere of a Parastrephia quadrangularis plant growing in the Salar de Tara region of the Central Andes in Chile. Int J Syst Evol Microbiol 2023; 73. [PMID: 38059605 DOI: 10.1099/ijsem.0.006189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2023] Open
Abstract
Two novel Micromonospora strains, STR1-7T and STR1S-6T, were isolated from the rhizosphere of a Parastrephia quadrangularis plant growing in the Salar de Tara region of the Atacama Desert, Chile. Chemotaxonomic, cultural and phenotypic features confirmed that the isolates belonged to the genus Micromonospora. They grew from 20 to 37 °C, from pH7 to 8 and in the presence of up to 3 %, w/v NaCl. The isolates formed distinct branches in Micromonospora gene trees based on 16S rRNA gene sequences and on a multi-locus sequence analysis of conserved house-keeping genes. A phylogenomic tree generated from the draft genomes of the isolates and their closest phylogenetic neighbours showed that isolate STR1-7T is most closely related to Micromonospora orduensis S2509T, and isolate STR1S-6 T forms a distinct branch that is most closely related to 12 validly named Micromonospora species, including Micromonospora saelicesensis the earliest proposed member of the group. The isolates were separated from one another and from their closest phylogenomic neighbours using a combination of chemotaxonomic, genomic and phenotypic features, and by low average nucleotide index and digital DNA-DNA hybridization values. Consequently, it is proposed that isolates STR1-7T and STR1S-6T be recognized as representing new species in the genus Micromonospora, namely as Micromonospora parastrephiae sp. nov. and Micromonospora tarensis sp. nov.; the type strains are STR1-7T (=CECT 9665T=LMG 30768T) and STR1S-6T (=CECT 9666T=LMG 30770T), respectively. Genome mining showed that the isolates have the capacity to produce novel specialized metabolites, notably antibiotics and compounds that promote plant growth, as well as a broad-range of stress-related genes that provide an insight into how they cope with harsh abiotic conditions that prevail in high-altitude Atacama Desert soils.
Collapse
Affiliation(s)
- Valeria Razmilic
- School of Natural and Environmental Sciences, Newcastle University, Newcastle-upon Tyne, UK
- Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering, Biotechnology and Materials, University of Chile, Beauchef 851, Santiago, Chile
| | - Imen Nouioui
- School of Natural and Environmental Sciences, Newcastle University, Newcastle-upon Tyne, UK
- Department of Microorganisms, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, 38124, Braunschweig, Germany
| | - Andrey Karlyshev
- Department of Biomolecular Sciences, School of Life Sciences, Pharmacy and Chemistry, Faculty of Health, Science, Social Care and Education, Kingston University London, Kingston upon Thames, KT1 2EE, UK
| | - Rana Jawad
- Department of Biomolecular Sciences, School of Life Sciences, Pharmacy and Chemistry, Faculty of Health, Science, Social Care and Education, Kingston University London, Kingston upon Thames, KT1 2EE, UK
| | - Martha E Trujillo
- Microbiology and Genetics Department, University of Salamanca, Salamanca, Spain
| | - Jose M 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
- Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering, Biotechnology and Materials, University of Chile, Beauchef 851, Santiago, Chile
| | - Juan A Asenjo
- Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering, Biotechnology and Materials, University of Chile, Beauchef 851, Santiago, Chile
| | - Lorena Carro
- School of Natural and Environmental Sciences, Newcastle University, Newcastle-upon Tyne, UK
- Microbiology and Genetics Department, University of Salamanca, Salamanca, Spain
| | - Michael Goodfellow
- School of Natural and Environmental Sciences, Newcastle University, Newcastle-upon Tyne, UK
| |
Collapse
|
5
|
Świecimska M, Golinska P, Sangal V, Wachnowicz B, Goodfellow M. Streptantibioticus silvisoli sp. nov., acidotolerant actinomycetes from pine litter, reclassification of Streptomyces cocklensis, Streptomyces ferralitis, Streptomyces parmotrematis and Streptomyces rubrisoli as Actinacidiphila cocklensis comb. nov., Streptantibioticus ferralitis comb. nov., Streptantibioticus parmotrematis comb. nov. and Streptantibioticus rubrisoli comb. nov., and emended descriptions of the genus Streptantibioticus, the family Streptomycetaceae and Streptomyces iconiensis. Int J Syst Evol Microbiol 2023; 73. [PMID: 37486349 DOI: 10.1099/ijsem.0.005978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2023] Open
Abstract
Filamentous actinomycetes, designated SL13 and SL54T, were isolated from pine litter and their taxonomic status resolved using a polyphasic approach. The isolates exhibit chemotaxonomic and morphological properties consistent with their classification in the family Streptomycetaceae. They form extensively branched substrate mycelia bearing aerial hyphae that differentiate into straight chains of cylindrical spores. The whole-organism hydrolysates contain ll-diaminopimelic acid, glucose, mannose and ribose, the predominant isoprenologue is MK-9(H8), the polar lipids are diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylglycerol and glycophospholipids, and the major fatty acids are anteiso-C15 : 0, iso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0. Phylogenetic trees based on 16S rRNA gene sequences and multilocus gene sequences of conserved housekeeping genes show that the isolates form a well-supported lineage that is most closely related to Streptomyces parmotrematis NBRC 115203T. All of these strains form a well-defined clade in the multilocus sequence analysis tree together with Streptantibioticus cattleyicolor DSM 46488T, Streptomyces ferralitis DSM 41836T and Streptomyces rubrisoli DSM 42083T. Draft genomes assemblies of the isolates are rich in biosynthetic gene clusters predicted to produce novel specialized metabolites and stress-related genes which provide an insight into how they have adapted to the harsh conditions that prevail in pine litter. Phylogenomically, both isolates belong to the same lineage as the type strains of S. cattleyicolor, S. ferralitis, S. parmotrematis and S. rubrisoli; these relationships are underpinned by high average amino acid identity, average nucleotide identity and genomic DNA-DNA hybridization values. These metrics confirm that isolates SL13 and SL54T belong to a novel species that is most closely related to S. parmotrematis NBRC 115203T and that these strains together with S. ferralitis DSM 41836T, S. rubrisoli DSM 42083T belong to the genus Streptantibioticus. Consequently, it is proposed that the isolates be recognized as a new Streptantibioticus species, Streptantibioticus silvisoli comb. nov., with isolate SL54T (=DSM 111111T=PCM3044T) as the type strain, and that S. ferralitis, S. parmotrematis and S. rubrisoli be transferred to the genus Streptantibioticus as Streptantibioticus ferralitis comb. nov., Streptantibioticus parmotrematis comb. nov. and Streptantibioticus rubrisoli comb. nov. Emended descriptions are given for the genus Streptantibioticus, the family Streptomycetaceae and for Streptomyces iconiensis which was found to be a close relative of the isolates in the 16S rRNA gene sequence analyses. It is also proposed that Streptomyces cocklensis be transferred to the genus Actinacidiphila as Actinacidiphila cocklensis comb. nov based on its position in the MLSA and phylogenomic trees and associated genomic data.
Collapse
Affiliation(s)
- Magdalena Świecimska
- Department of Microbiology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, Lwowska 1, 87 100 Torun, Poland
| | - Patrycja Golinska
- Department of Microbiology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, Lwowska 1, 87 100 Torun, Poland
| | - Vartul Sangal
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - Bartosz Wachnowicz
- Department of Microbiology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, Lwowska 1, 87 100 Torun, Poland
| | - Michael Goodfellow
- School of Natural and Environmental Sciences, Ridley Building 2, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| |
Collapse
|
6
|
Roca-Couso R, Flores-Felix JD, Igual JM, García-Fraile P, Velázquez E, Rivas R. Ferranicluibacter rubi gen. nov., sp. nov., a new member of family Rhizobiaceae isolated from stems of elmleaf blackberry ( Rubus ulmifolius Schott) in Northwest Spain. Int J Syst Evol Microbiol 2023; 73. [PMID: 37093735 DOI: 10.1099/ijsem.0.005789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2023] Open
Abstract
Strain CRRU44T was isolated from the stems of Rubus ulmifolius plants growing in Salamanca (Spain). The phylogenetic analysis of the 16S rRNA gene sequence places this strain within the family Rhizobiaceae showing that it is equidistant to the type species of several genera from this family with similarity values ranging from 91.0 to 96.3 %. Strain CRRU44T formed a divergent lineage which clustered with Endobacterium cereale RZME27T, Neorhizobium galegae HAMBI540T and Pseudorhizobium pelagicum R1-200B4T. The phylogenomic analysis showed that strain CRRU44T was equal to or more distant from the remaining genera of the family Rhizobiaceae than other genera among them. The calculated average nucleotide identity based on blast and average amino acid identity values with respect to the type species of all genera from the family Rhizobiaceae were lower than 78.5 and 76.5 %, respectively, which are the currently cut-off values proposed to differentiate genera within this family. All these results together with those from phenotypic and chemotaxonomic analyses support that strain CRRU44T represents a novel species of a novel genus within the family Rhizobiaceae, for which the name Ferranicluibacter rubi gen. nov., sp. nov. is proposed (type strain CRRU44T=CECT 30117T=LMG 31822T).
Collapse
Affiliation(s)
- Rocio Roca-Couso
- Department of Microbiology and Genetics, University of Salamanca, Salamanca, Spain
- Institute of Investigation in Agrobiotechnology (CIALE), Salamanca, Spain
| | - Jose David Flores-Felix
- Department of Microbiology and Genetics, University of Salamanca, Salamanca, Spain
- Institute of Investigation in Agrobiotechnology (CIALE), Salamanca, Spain
| | - Jose M Igual
- Institute of Natural Resources and Agrobiology of Salamanca (IRNASA-CSIC), Salamanca, Spain
- Associated Unit USAL-CSIC (IRNASA), Salamanca, Spain
| | - Paula García-Fraile
- Department of Microbiology and Genetics, University of Salamanca, Salamanca, Spain
- Institute of Investigation in Agrobiotechnology (CIALE), Salamanca, Spain
- Associated Unit USAL-CSIC (IRNASA), Salamanca, Spain
| | - Encarna Velázquez
- Department of Microbiology and Genetics, University of Salamanca, Salamanca, Spain
- Institute of Investigation in Agrobiotechnology (CIALE), Salamanca, Spain
- Associated Unit USAL-CSIC (IRNASA), Salamanca, Spain
| | - Raúl Rivas
- Department of Microbiology and Genetics, University of Salamanca, Salamanca, Spain
- Institute of Investigation in Agrobiotechnology (CIALE), Salamanca, Spain
- Associated Unit USAL-CSIC (IRNASA), Salamanca, Spain
| |
Collapse
|
7
|
Definition of the symbiovar viciae in the species Rhizobium azibense and biogeographic implications. Arch Microbiol 2023; 205:18. [PMID: 36480106 PMCID: PMC9732059 DOI: 10.1007/s00203-022-03330-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 11/06/2022] [Accepted: 11/10/2022] [Indexed: 12/13/2022]
Abstract
Vicia faba L. (faba bean) is a legume cultivated worldwide which commonly establishes effective symbiosis with the symbiovar viciae of species from the Rhizobium leguminosarum phylogenetic group. However, on the basis of the rrs, recA, and atpD gene phylogenies, in this work we identified a strain named EFBRI 42 nodulating V. faba as Rhizobium azibense. This is the first report on the nodulation of Vicia by R. azibense which commonly nodulates P. vulgaris and to date encompasses strains harboring the nodC genes typical of the symbiovars gallicum and phaseoli. However, the strain EFBRI 42 carries a nodC gene typical of the symbiovar viciae for which we report here by the first time this symbiovar in R. azibense. This finding showed the existence of symbiotic genes horizontal transfer events during the coevolution of R. azibense with P. vulgaris and V. faba in their respective distribution centers of Mesoamerica and the Middle East.
Collapse
|
8
|
Świecimska M, Golińska P, Goodfellow M. Genome-based classification of Streptomyces pinistramenti sp. nov., a novel actinomycete isolated from a pine forest soil in Poland with a focus on its biotechnological and ecological properties. Antonie van Leeuwenhoek 2022; 115:783-800. [DOI: 10.1007/s10482-022-01734-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 03/19/2022] [Indexed: 10/18/2022]
|
9
|
Riesco R, Ortúzar M, Fernández-Ábalos JM, Trujillo ME. Deciphering Genomes: Genetic Signatures of Plant-Associated Micromonospora. FRONTIERS IN PLANT SCIENCE 2022; 13:872356. [PMID: 35401599 PMCID: PMC8990736 DOI: 10.3389/fpls.2022.872356] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 02/28/2022] [Indexed: 05/13/2023]
Abstract
Understanding plant-microbe interactions with the possibility to modulate the plant's microbiome is essential to design new strategies for a more productive and sustainable agriculture and to maintain natural ecosystems. Therefore, a key question is how to design bacterial consortia that will yield the desired host phenotype. This work was designed to identify the potential genomic features involved in the interaction between Micromonospora and known host plants. Seventy-four Micromonospora genomes representing diverse environments were used to generate a database of all potentially plant-related genes using a novel bioinformatic pipeline that combined screening for microbial-plant related features and comparison with available plant host proteomes. The strains were recovered in three clusters, highly correlated with several environments: plant-associated, soil/rhizosphere, and marine/mangrove. Irrespective of their isolation source, most strains shared genes coding for commonly screened plant growth promotion features, while differences in plant colonization related traits were observed. When Arabidopsis thaliana plants were inoculated with representative Micromonospora strains selected from the three environments, significant differences were in found in the corresponding plant phenotypes. Our results indicate that the identified genomic signatures help select those strains with the highest probability to successfully colonize the plant and contribute to its wellbeing. These results also suggest that plant growth promotion markers alone are not good indicators for the selection of beneficial bacteria to improve crop production and the recovery of ecosystems.
Collapse
|
10
|
Lactic Acid Bacteria Isolated from Fermented Doughs in Spain Produce Dextrans and Riboflavin. Foods 2021; 10:foods10092004. [PMID: 34574114 PMCID: PMC8470351 DOI: 10.3390/foods10092004] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 08/14/2021] [Accepted: 08/24/2021] [Indexed: 12/15/2022] Open
Abstract
Many lactic acid bacteria (LAB) produce metabolites with applications in the food industry, such as dextran-type exopolysaccharides (EPS) and riboflavin (vitamin B2). Here, 72 bacteria were isolated from sourdoughs made by Spanish bread-makers. In the presence of sucrose, colonies of 22 isolates showed a ropy phenotype, and NMR analysis of their EPS supported that 21 of them were dextran producers. These isolates were identified by their random amplified polymorphic DNA (RAPD) patterns and their rrs and pheS gene sequences as LAB belonging to four species (Weissella cibaria, Leuconostoc citreum, Leuconostoc falkenbergense and Leuconostoc mesenteroides). Six selected strains from the Leuconostoc (3) and Weissella (3) genera grew in the absence of riboflavin and synthesized vitamin B2. The EPS produced by these strains were characterized as dextrans by physicochemical analysis, and the L. citreum polymer showed an unusually high degree of branching. Quantification of the riboflavin and the EPS productions showed that the W. cibaria strains produce the highest levels (585–685 μg/and 6.5–7.4 g/L, respectively). Therefore, these new LAB strains would be good candidates for the development of fermented foods bio-fortified with both dextrans and riboflavin. Moreover, this is the first report of riboflavin and dextran production by L. falkenbergense.
Collapse
|
11
|
Analysis of the Interaction between Pisum sativum L. and Rhizobium laguerreae Strains Nodulating This Legume in Northwest Spain. PLANTS 2020; 9:plants9121755. [PMID: 33322342 PMCID: PMC7763339 DOI: 10.3390/plants9121755] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 12/08/2020] [Accepted: 12/09/2020] [Indexed: 01/01/2023]
Abstract
Pisum sativum L. (pea) is one of the most cultivated grain legumes in European countries due to the high protein content of its seeds. Nevertheless, the rhizobial microsymbionts of this legume have been scarcely studied in these countries. In this work, we analyzed the rhizobial strains nodulating the pea in a region from Northwestern Spain, where this legume is widely cultivated. The isolated strains were genetically diverse, and the phylogenetic analysis of core and symbiotic genes showed that these strains belong to different clusters related to R. laguerreae sv. viciae. Representative strains of these clusters were able to produce cellulose and cellulases, which are two key molecules in the legume infection process. They formed biofilms and produced acyl-homoserine lactones (AHLs), which are involved in the quorum sensing regulation process. They also exhibited several plant growth promotion mechanisms, including phosphate solubilization, siderophore, and indole acetic acid production and symbiotic atmospheric nitrogen fixation. All strains showed high symbiotic efficiency on pea plants, indicating that strains of R. laguerreae sv. viciae are promising candidates for the biofertilization of this legume worldwide.
Collapse
|
12
|
Insuk C, Kuncharoen N, Cheeptham N, Tanasupawat S, Pathom-Aree W. Bryophytes Harbor Cultivable Actinobacteria With Plant Growth Promoting Potential. Front Microbiol 2020; 11:563047. [PMID: 33133038 PMCID: PMC7550540 DOI: 10.3389/fmicb.2020.563047] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 08/24/2020] [Indexed: 11/23/2022] Open
Abstract
This study was designed to investigate the cultivable actinobacteria associated with bryophytes and their plant growth promoting ability. Thirteen actinobacteria were isolated and tested for their ability to promote growth of plant in vitro and in planta. All isolates were able to produce IAA and siderophores. Six isolates were identified as members of the genus Micromonospora. Five isolates belonged to the genus Streptomyces and one each of Microbispora and Mycobacterium. Micromonospora sp. CMU55-4 was inoculated to rare moss [Physcomitrium sphaericum (C. Ludw.) Fürnr.] and could increase the amount of carotenoid, fresh weight, and dry weight of this moss. In addition, this strain promoted capsule production, and rescued P. sphaericum’s gametophytes during acclimatization to land. Strain CMU55-4 was identified as Micromonospora chalcea based on whole genome sequence analysis. Its plant growth promoting potential was further characterized through genome mining. The draft genome size was 6.6 Mb (73% GC). The genome contained 5,933 coding sequences. Functional annotation predicted encoded genes essential for siderophore production, phosphate solubilization that enable bacteria to survive under nutrient limited environment. Glycine-betaine accumulation and trehalose biosynthesis also aid plants under drought stress. M. chalcea CMU55-4 also exhibited genes for various carbohydrate metabolic pathways indicating those for efficient utilization of carbohydrates inside plant cells. Additionally, predictive genes for heat shock proteins, cold shock proteins, and oxidative stress such as glutathione biosynthesis were identified. In conclusion, our results demonstrate that bryophytes harbor plant growth promoting actinobacteria. A representative isolate, M. chalcea CMU55-4 promotes the growth of P. sphaericum moss and contains protein coding sequences related to plant growth promoting activities in its genome.
Collapse
Affiliation(s)
- Chadabhorn Insuk
- Master of Science Program in Applied Microbiology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand.,Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | - Nattakorn Kuncharoen
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Naowarat Cheeptham
- Department of Biological Sciences, Faculty of Science, Thompson Rivers University, Kamloops, BC, Canada
| | - Somboon Tanasupawat
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Wasu Pathom-Aree
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand.,Research Center of Microbial Diversity and Sustainable Utilization, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| |
Collapse
|
13
|
Hu D, Sun C, Jin T, Fan G, Mok KM, Li K, Lee SMY. Exploring the Potential of Antibiotic Production From Rare Actinobacteria by Whole-Genome Sequencing and Guided MS/MS Analysis. Front Microbiol 2020; 11:1540. [PMID: 32922368 PMCID: PMC7375171 DOI: 10.3389/fmicb.2020.01540] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 06/12/2020] [Indexed: 11/26/2022] Open
Abstract
Actinobacteria are well recognized for their production of structurally diverse bioactive secondary metabolites, but the rare actinobacterial genera have been underexploited for such potential. To search for new sources of active compounds, an experiment combining genomic analysis and tandem mass spectrometry (MS/MS) screening was designed to isolate and characterize actinobacterial strains from a mangrove environment in Macau. Fourteen actinobacterial strains were isolated from the collected samples. Partial 16S sequences indicated that they were from six genera, including Brevibacterium, Curtobacterium, Kineococcus, Micromonospora, Mycobacterium, and Streptomyces. The isolate sp.01 showing 99.28% sequence similarity with a reference rare actinobacterial species Micromonospora aurantiaca ATCC 27029T was selected for whole genome sequencing. Organization of its gene clusters for secondary metabolite biosynthesis revealed 21 clusters encoded to antibiotic production, which is higher than other Micromonospora species. Of the genome-predicted antibiotics, kanamycin was found through guided MS/MS analysis producible by the M. aurantiaca strain for the first time. The present study highlighted that genomic analysis combined with MS/MS screening is a promising method to discover potential of antibiotic production from rare actinobacteria.
Collapse
Affiliation(s)
- Dini Hu
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
- Department of Civil and Environmental Engineering, Faculty of Science and Technology, University of Macau, Macau, China
| | - Chenghang Sun
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Tao Jin
- Beijing Genomics Institute, Shenzhen, China
| | | | - Kai Meng Mok
- Department of Civil and Environmental Engineering, Faculty of Science and Technology, University of Macau, Macau, China
| | - Kai Li
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Simon Ming-Yuen Lee
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macau, China
| |
Collapse
|
14
|
Saha J, Saha BK, Pal Sarkar M, Roy V, Mandal P, Pal A. Comparative Genomic Analysis of Soil Dwelling Bacteria Utilizing a Combinational Codon Usage and Molecular Phylogenetic Approach Accentuating on Key Housekeeping Genes. Front Microbiol 2019; 10:2896. [PMID: 31921071 PMCID: PMC6928123 DOI: 10.3389/fmicb.2019.02896] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 12/02/2019] [Indexed: 01/02/2023] Open
Abstract
Soil is a diversified and complex ecological niche, home to a myriad of microorganisms particularly bacteria. The physico-chemical complexities of soil results in a plethora of physiological variations to exist within the different types of soil dwelling bacteria, giving rise to a wide variation in genome structure and complexity. This serves as an attractive proposition to analyze and compare the genome of a large number soil bacteria to comprehend their genome complexity and evolution. In this study a combination of codon usage and molecular phylogenetics of the whole genome and key housekeeping genes like infB (translation initiation factor 2), trpB (tryptophan synthase, beta subunit), atpD (ATP synthase, beta subunit), and rpoB (RNA polymerase, beta subunit) of 92 soil bacterial species spread across the entire eubacterial domain and residing in different soil types was performed. The results indicated the direct relationship of genome size with codon bias and coding frequency in the studied bacteria. The codon usage profile demonstrated by the gene trpB was found to be relatively different from the rest of the housekeeping genes with a large number of bacteria having a greater percentage of genes with Nc values less than the Nc of trpB. The results from the overall codon usage bias profile also depicted that the codon usage bias in the key housekeeping genes of soil bacteria was majorly due to selectional pressure and not mutation. The analysis of hydrophobicity of the gene product encoded by the rpoB coding sequences demonstrated tight clustering across all the soil bacteria suggesting conservation of protein structure for maintenance of form and function. The phylogenetic affinities inferred using 16S rRNA gene and the housekeeping genes demonstrated conflicting signals with trpB gene being the noisiest one. The housekeeping gene atpD was found to depict the least amount of evolutionary change in the soil bacteria considered in this study except in two Clostridium species. The phylogenetic and codon usage analysis of the soil bacteria consistently demonstrated the relatedness of Azotobacter chroococcum with different species of the genus Pseudomonas.
Collapse
Affiliation(s)
- Jayanti Saha
- Microbiology & Computational Biology Laboratory, Department of Botany, Raiganj University, Raiganj, India
| | - Barnan K. Saha
- Microbiology & Computational Biology Laboratory, Department of Botany, Raiganj University, Raiganj, India
| | - Monalisha Pal Sarkar
- Mycology & Plant Pathology Laboratory, Department of Botany, Raiganj University, Raiganj, India
| | - Vivek Roy
- Microbiology & Computational Biology Laboratory, Department of Botany, Raiganj University, Raiganj, India
| | - Parimal Mandal
- Mycology & Plant Pathology Laboratory, Department of Botany, Raiganj University, Raiganj, India
| | - Ayon Pal
- Microbiology & Computational Biology Laboratory, Department of Botany, Raiganj University, Raiganj, India
| |
Collapse
|
15
|
Martínez-Hidalgo P, Flores-Félix JD, Velázquez E, Brau L, Trujillo ME, Martínez-Molina E. High taxonomic diversity of Micromonospora strains isolated from Medicago sativa nodules in Western Spain and Australia. Syst Appl Microbiol 2019; 43:126043. [PMID: 31796230 DOI: 10.1016/j.syapm.2019.126043] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 11/08/2019] [Accepted: 11/15/2019] [Indexed: 10/25/2022]
Abstract
The genus Micromonospora has been found in nodules of several legumes and some new species of this genus were isolated from these plant organs. In this study we analysed the taxonomic diversity of Micromonospora strains isolated from alfalfa nodules in Spain and Australia on the basis of three phylogenetic markers, the rrs and gyrB genes and 16S-23S intergenic spacer (ITS). The genome analysis of selected strains representative of different clusters or lineages found after rrs, gyrB and ITS analyses confirmed the results obtained with these phylogenetic markers. They showed that the analysed strains belong to at least 18 Micromonospora species including previously described ones, such as Micromonospora noduli, Micromonospora ureilytica, Micromonospora taraxaci, Micromonospora zamorensis, Micromonospora aurantiaca and Micromonospora tulbaghiae. Most of these strains belong to undescribed species of Micromonospora showing the high taxonomic diversity of strains from this genus inhabiting alfalfa nodules. Although Micromonospora strains are not able to induce the formation of these nodules, and it seems that they do not contribute to fix atmospheric nitrogen, they could play a role related with the mechanisms of plant growth promotion and pathogen protection presented by Micromonospora strains isolated from legume nodules.
Collapse
Affiliation(s)
- Pilar Martínez-Hidalgo
- Departamento de Biología, Geología, Física y Química inorgánica. Universidad Rey Juan Carlos. Departamental II despacho 248. Av. Tulipán s/n, 28933 Móstoles, Madrid.
| | - José David Flores-Félix
- Departamento de Microbiología y Genética and Instituto Hispanoluso de Investigaciones Agrarias (CIALE). Universidad de Salamanca. Edificio Departamental de Biología. Lab 209. Av. Doctores de la Reina S/N. 37007 Salamanca
| | - Encarna Velázquez
- Departamento de Microbiología y Genética and Instituto Hispanoluso de Investigaciones Agrarias (CIALE). Universidad de Salamanca. Edificio Departamental de Biología. Lab 209. Av. Doctores de la Reina S/N. 37007 Salamanca; Unidad Asociada Grupo de Interacción Planta-Microorganismo Universidad de Salamanca-IRNASA-CSIC, Salamanca, Spain
| | - Lambert Brau
- Deakin University, Geelong, Australia, Centre for Regional and Rural Futures, School of Life and Environmental Sciences
| | - Martha E Trujillo
- Departamento de Microbiología y Genética and Instituto Hispanoluso de Investigaciones Agrarias (CIALE). Universidad de Salamanca. Edificio Departamental de Biología. Lab 209. Av. Doctores de la Reina S/N. 37007 Salamanca
| | - Eustoquio Martínez-Molina
- Departamento de Microbiología y Genética and Instituto Hispanoluso de Investigaciones Agrarias (CIALE). Universidad de Salamanca. Edificio Departamental de Biología. Lab 209. Av. Doctores de la Reina S/N. 37007 Salamanca; Unidad Asociada Grupo de Interacción Planta-Microorganismo Universidad de Salamanca-IRNASA-CSIC, Salamanca, Spain
| |
Collapse
|
16
|
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).
Collapse
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
| |
Collapse
|
17
|
Carro L, Castro JF, Razmilic V, Nouioui I, Pan C, Igual JM, Jaspars M, Goodfellow M, Bull AT, Asenjo JA, Klenk HP. Uncovering the potential of novel micromonosporae isolated from an extreme hyper-arid Atacama Desert soil. Sci Rep 2019; 9:4678. [PMID: 30886188 PMCID: PMC6423291 DOI: 10.1038/s41598-019-38789-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 12/12/2018] [Indexed: 11/29/2022] Open
Abstract
The taxonomic status, biotechnological and ecological potential of several Micromonospora strains isolated from an extreme hyper arid Atacama Desert soil were determined. Initially, a polyphasic study was undertaken to clarify the taxonomic status of five micromonosporae, strains LB4, LB19, LB32T, LB39T and LB41, isolated from an extreme hyper-arid soil collected from one of the driest regions of the Atacama Desert. All of the isolates were found to have chemotaxonomic, cultural and morphological properties consistent with their classification in the genus Micromonospora. Isolates LB32T and LB39T were distinguished from their nearest phylogenetic neighbours and proposed as new species, namely as Micromonospora arida sp. nov. and Micromonospora inaquosa sp. nov., respectively. Eluted methanol extracts of all of the isolates showed activity against a panel of bacterial and fungal indicator strains, notably against multi-drug resistant Klebsiella pneumoniae ATCC 700603 while isolates LB4 and LB41 showed pronounced anti-tumour activity against HepG2 cells. Draft genomes generated for the isolates revealed a rich source of novel biosynthetic gene clusters, some of which were unique to individual strains thereby opening up the prospect of selecting especially gifted micromonosporae for natural product discovery. Key stress-related genes detected in the genomes of all of the isolates provided an insight into how micromonosporae adapt to the harsh environmental conditions that prevail in extreme hyper-arid Atacama Desert soils.
Collapse
Affiliation(s)
- Lorena Carro
- Microbiology and Genetics Department, University of Salamanca, Salamanca, Spain.
- School of Natural and Environmental Sciences, Newcastle University, Newcastle-upon Tyne, UK.
| | - Jean Franco Castro
- School of Natural and Environmental Sciences, Newcastle University, Newcastle-upon Tyne, UK
- Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering, Biotechnology and Materials, Universidad de Chile, Beauchef 851, Santiago, Chile
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Scotland, UK
| | - Valeria Razmilic
- School of Natural and Environmental Sciences, Newcastle University, Newcastle-upon Tyne, UK
- Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering, Biotechnology and Materials, Universidad de Chile, Beauchef 851, Santiago, Chile
| | - Imen Nouioui
- School of Natural and Environmental Sciences, Newcastle University, Newcastle-upon Tyne, UK
| | - Che Pan
- School of Natural and Environmental Sciences, Newcastle University, Newcastle-upon Tyne, UK
| | - José M Igual
- Instituto de Recursos Naturales y Agrobiología de Salamanca, Consejo Superior de Investigaciones Científicas (IRNASA-CSIC), Salamanca, Spain
- Grupo de Interacción Planta-Microorganismo, Universidad de Salamanca, Unidad Asociada al CSIC, Spain
| | - Marcel Jaspars
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Scotland, UK
| | - Michael Goodfellow
- School of Natural and Environmental Sciences, Newcastle University, Newcastle-upon Tyne, UK
| | - Alan T Bull
- School of Biosciences, University of Kent Canterbury, Canterbury, UK
| | - Juan A Asenjo
- Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering, Biotechnology and Materials, Universidad de Chile, Beauchef 851, Santiago, Chile
| | - Hans-Peter Klenk
- School of Natural and Environmental Sciences, Newcastle University, Newcastle-upon Tyne, UK
| |
Collapse
|
18
|
Liu Q, Liu HC, Zhou YG, Xin YH. Genetic diversity of glacier-inhabiting Cryobacterium bacteria in China and description of Cryobacterium zongtaii sp. nov. and Arthrobacter glacialis sp. nov. Syst Appl Microbiol 2019; 42:168-177. [DOI: 10.1016/j.syapm.2018.10.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Revised: 09/20/2018] [Accepted: 10/08/2018] [Indexed: 10/28/2022]
|
19
|
Chitinolytic actinobacteria isolated from an Algerian semi-arid soil: development of an antifungal chitinase-dependent assay and GH18 chitinase gene identification. ANN MICROBIOL 2019. [DOI: 10.1007/s13213-018-1426-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
|
20
|
A study of three bacteria isolated from marine sediment and description of Micromonospora globispora sp. nov. Syst Appl Microbiol 2018; 42:190-197. [PMID: 30528275 DOI: 10.1016/j.syapm.2018.11.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 11/05/2018] [Accepted: 11/09/2018] [Indexed: 11/23/2022]
Abstract
During a study looking for the isolation of new actinobacteria strains with potential for antibiotic production from deep marine sediment, three strains were collected with a morphology similar to the one described for the Micromonospora genus. A polyphasic study was designed to determine the taxonomic affiliation of the strains S2901T, S2903, and S2904. All the strains showed chemotaxonomic properties in line with their classification in the genus Micromonospora, meso-diaminopimelic acid in the wall peptidoglycan, a tetrahydrogenated menaquinone with nine isoprene units as major respiratory quinone, iso-C15:0 and iso-C16:0 as major fatty acids and diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol as major polar lipids. The 16S rRNA gene sequences of strain S2901T, S2903, and S2904 showed the highest similarity (99.2%) with the type strain of Micromonospora halophytica DSM 43171T, forming an independent branch in the phylogenetic gene tree. Their independent position was confirmed with gyrB gene and MLSA phylogenies. Whole genome sequences confirmed by digital DNA-DNA hybridization analysis that the isolates should be assigned to a new species within the genus Micromonospora for which the name Micromonospora globispora sp. nov. (S2901T, S2903 and S2904) is proposed.
Collapse
|
21
|
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.
Collapse
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
| |
Collapse
|
22
|
Carro L, Razmilic V, Nouioui I, Richardson L, Pan C, Golinska P, Asenjo JA, Bull AT, Klenk HP, Goodfellow M. Hunting for cultivable Micromonospora strains in soils of the Atacama Desert. Antonie van Leeuwenhoek 2018; 111:1375-1387. [PMID: 29480426 DOI: 10.1007/s10482-018-1049-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 02/16/2018] [Indexed: 02/01/2023]
Abstract
Innovative procedures were used to selectively isolate small numbers of Micromonospora strains from extreme hyper-arid and high altitude Atacama Desert soils. Micromonosporae were recognised on isolation plates by their ability to produce filamentous microcolonies that were strongly attached to the agar. Most of the isolates formed characteristic orange colonies that lacked aerial hyphae and turned black on spore formation, whereas those from the high altitude soil were dry, blue-green and covered by white aerial hyphae. The isolates were assigned to seven multi- and eleven single-membered groups based on BOX-PCR profiles. Representatives of the groups were assigned to either multi-membered clades that also contained marker strains or formed distinct phyletic lines in the Micromonospora 16S rRNA gene tree; many of the isolates were considered to be putatively novel species of Micromonospora. Most of the isolates from the high altitude soils showed activity against wild type strains of Bacillus subtilis and Pseudomonas fluorescens while those from the rhizosphere of Parastrephia quadrangulares and from the Lomas Bayas hyper-arid soil showed resistance to UV radiation.
Collapse
Affiliation(s)
- Lorena Carro
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK.
| | - Valeria Razmilic
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK.,Department of Chemical Engineering and Biotechnology, Centre for Biotechnology and Bioengineering (CeBiB), Universidad de Chile, Beauchef 850, Santiago, Chile
| | - Imen Nouioui
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Lee Richardson
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Che Pan
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Patrycja Golinska
- Department of Microbiology, Nicolaus Copernicus University, Torun, Poland
| | - Juan A Asenjo
- Department of Chemical Engineering and Biotechnology, Centre for Biotechnology and Bioengineering (CeBiB), Universidad de Chile, Beauchef 850, Santiago, Chile
| | - Alan T Bull
- School of Biosciences, University of Kent, Canterbury, Kent, CT2 7NJ, UK
| | - Hans-Peter Klenk
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Michael Goodfellow
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
| |
Collapse
|
23
|
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.
Collapse
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
| | | |
Collapse
|
24
|
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).
Collapse
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
| |
Collapse
|
25
|
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.
Collapse
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.
| |
Collapse
|
26
|
Nie YL, Wu YD, Wang CX, Lin R, Xie Y, Fang DS, Jiang H, Lian YY. Structure elucidation and antitumour activity of a new macrolactam produced by marine-derived actinomycete Micromonospora sp. FIM05328. Nat Prod Res 2017; 32:2133-2138. [DOI: 10.1080/14786419.2017.1366479] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Yi-Lei Nie
- Fujian Provincial Key Laboratory of Screening for Novel Microbial Products, Fujian Institute of Microbiology, Fuzhou, China
| | - Yun-Dan Wu
- Fujian Provincial Key Laboratory of Screening for Novel Microbial Products, Fujian Institute of Microbiology, Fuzhou, China
| | - Chuan-Xi Wang
- Fujian Provincial Key Laboratory of Screening for Novel Microbial Products, Fujian Institute of Microbiology, Fuzhou, China
| | - Ru Lin
- Fujian Provincial Key Laboratory of Screening for Novel Microbial Products, Fujian Institute of Microbiology, Fuzhou, China
| | - Yang Xie
- Fujian Provincial Key Laboratory of Screening for Novel Microbial Products, Fujian Institute of Microbiology, Fuzhou, China
| | - Dong-Sheng Fang
- Fujian Provincial Key Laboratory of Screening for Novel Microbial Products, Fujian Institute of Microbiology, Fuzhou, China
| | - Hong Jiang
- Fujian Provincial Key Laboratory of Screening for Novel Microbial Products, Fujian Institute of Microbiology, Fuzhou, China
| | - Yun-Yang Lian
- Fujian Provincial Key Laboratory of Screening for Novel Microbial Products, Fujian Institute of Microbiology, Fuzhou, China
| |
Collapse
|
27
|
Carro L, Nouioui I. Taxonomy and systematics of plant probiotic bacteria in the genomic era. AIMS Microbiol 2017; 3:383-412. [PMID: 31294168 PMCID: PMC6604993 DOI: 10.3934/microbiol.2017.3.383] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 05/22/2017] [Indexed: 12/20/2022] Open
Abstract
Recent decades have predicted significant changes within our concept of plant endophytes, from only a small number specific microorganisms being able to colonize plant tissues, to whole communities that live and interact with their hosts and each other. Many of these microorganisms are responsible for health status of the plant, and have become known in recent years as plant probiotics. Contrary to human probiotics, they belong to many different phyla and have usually had each genus analysed independently, which has resulted in lack of a complete taxonomic analysis as a group. This review scrutinizes the plant probiotic concept, and the taxonomic status of plant probiotic bacteria, based on both traditional and more recent approaches. Phylogenomic studies and genes with implications in plant-beneficial effects are discussed. This report covers some representative probiotic bacteria of the phylum Proteobacteria, Actinobacteria, Firmicutes and Bacteroidetes, but also includes minor representatives and less studied groups within these phyla which have been identified as plant probiotics.
Collapse
Affiliation(s)
- Lorena Carro
- School of Biology, Newcastle University, Newcastle upon Tyne, UK
| | - Imen Nouioui
- School of Biology, Newcastle University, Newcastle upon Tyne, UK
| |
Collapse
|
28
|
Bacterial Endophytes of Plants: Diversity, Invasion Mechanisms and Effects on the Host. SUSTAINABLE DEVELOPMENT AND BIODIVERSITY 2017. [DOI: 10.1007/978-3-319-66541-2_2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
|
29
|
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).
Collapse
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
| |
Collapse
|
30
|
Veyisoglu A, Carro L, Cetin D, Guven K, Spröer C, Pötter G, Klenk HP, Sahin N, Goodfellow M. Micromonospora profundi sp. nov., isolated from deep marine sediment. Int J Syst Evol Microbiol 2016; 66:4735-4743. [PMID: 27515497 DOI: 10.1099/ijsem.0.001419] [Citation(s) in RCA: 10] [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 actinobacterial strain, designated DS3010T, was isolated from a Black Sea marine sediment and characterized using a polyphasic approach. The strain was shown to have chemotaxonomic, morphological and phylogenetic properties consistent with classification as representing a member of the genus Micromonospora. Comparative 16S rRNA gene sequence studies showed that the strain was most closely related to the type strains of Micromonospora saelicesensis (99.5 %), Micromonospora chokoriensis (99.4 %) and Micromonospora violae (99.3 %). Similarly, a corresponding analysis based on partial gyrB gene sequences showed that it formed a distinct phyletic branch in a subclade that included the type strains of Micromonosporazamorensis, 'Micromonospora zeae', 'Micromonospora jinlongensis', M. saelicesensis and Micromonospora lupini. DS3010T was distinguished from its closest phylogenetic neighbours by low levels of DNA-DNA relatedness and by a combination of chemotaxonomic and phenotypic properties. On the basis of these data, it is proposed that the isolate should be assigned to the genus Micromonospora as Micromonospora profundi sp. nov. with isolate DS3010T (=DSM 45981T=KCTC 29243T) as the type strain.
Collapse
Affiliation(s)
- Aysel Veyisoglu
- Department of Bioengineering, Faculty of Engineering and Architecture, Sinop University, Nasuhbasoglu-Sinop 57000, Turkey
| | - Lorena Carro
- School of Biology, Newcastle University, Ridley Building, Newcastle upon Tyne, NE1 7RU, UK
| | - Demet Cetin
- Science Teaching Programme, Gazi Faculty of Education, Gazi University, Ankara, Turkey
| | - Kiymet Guven
- Anadolu University, Faculty of Science, Biology Department, Eskisehir 26470, Turkey
| | - Cathrin Spröer
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, Braunschweig 38124, Germany
| | - Gabriele Pötter
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, Braunschweig 38124, Germany
| | - Hans-Peter Klenk
- School of Biology, Newcastle University, Ridley Building, Newcastle upon Tyne, NE1 7RU, UK
| | - Nevzat Sahin
- Department of Biology, Faculty of Art and Science, Ondokuz Mayis University, Kurupelit-Samsun 55139, Turkey
| | - Michael Goodfellow
- School of Biology, Newcastle University, Ridley Building, Newcastle upon Tyne, NE1 7RU, UK
| |
Collapse
|
31
|
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)).
Collapse
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.
| |
Collapse
|
32
|
Modestobacter caceresii sp. nov., novel actinobacteria with an insight into their adaptive mechanisms for survival in extreme hyper-arid Atacama Desert soils. Syst Appl Microbiol 2016; 39:243-251. [DOI: 10.1016/j.syapm.2016.03.007] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Revised: 03/16/2016] [Accepted: 03/18/2016] [Indexed: 11/20/2022]
|
33
|
Micromonospora yasonensis sp. nov., isolated from a Black Sea sediment. Antonie Van Leeuwenhoek 2016; 109:1019-28. [PMID: 27154186 DOI: 10.1007/s10482-016-0701-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 04/25/2016] [Indexed: 10/21/2022]
Abstract
A Micromonospora strain, designated DS3186(T), isolated from sediment collected from the Black Sea off the Yason Peninsula, Ordu, Turkey, was examinated using a polyphasic approach. The strain was found to have chemotaxonomic, morphological and phylogenetic properties consistent with its clasification in the genus Micromonospora. A comparative 16S rRNA gene sequence analysis showed that the strain was closely related to the type strains of Micromonospora olivasterospora (99.0 %), Micromonospora equina (98.8 %), Micromonospora rhizosphaerae (98.8 %) and Micromonospora viridifaciens (98.8 %); low levels of DNA-DNA relatednes were found between the isolate and the M. olivasterospora and M. rhizosphaerae strains. Corresponding phylogenetic analysis based on partial gyrB gene sequences showed that strain DS3186(T) formed a subclade with the type strains of Micromonospora eburnea, M. equina, Micromonospora narathiwatensis and M. viridifaciens. Strain DS3186(T) was distinguished from its close phylogenetic neighbours using a combination of chemotaxonomic, morphological and physiological properties. Consequently, it is proposed that strain DS3186(T) represents a novel Micromonospora species for which the name Micromonospora yasonensis sp. nov. is proposed. The type strain is DS3186(T) (=DSM 45980(T) = KCTC 29433(T)).
Collapse
|
34
|
16S-gyrB-rpoB multilocus sequence analysis for species identification in the genus Microbispora. Antonie van Leeuwenhoek 2016; 109:801-15. [DOI: 10.1007/s10482-016-0680-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 03/10/2016] [Indexed: 10/22/2022]
|
35
|
Meyers PR. Analysis of recombinase A (recA/RecA) in the actinobacterial family Streptosporangiaceae and identification of molecular signatures. Syst Appl Microbiol 2015; 38:567-77. [DOI: 10.1016/j.syapm.2015.10.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Revised: 09/28/2015] [Accepted: 10/02/2015] [Indexed: 12/23/2022]
|
36
|
Trujillo ME, Riesco R, Benito P, Carro L. Endophytic Actinobacteria and the Interaction of Micromonospora and Nitrogen Fixing Plants. Front Microbiol 2015; 6:1341. [PMID: 26648923 PMCID: PMC4664631 DOI: 10.3389/fmicb.2015.01341] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 11/16/2015] [Indexed: 01/07/2023] Open
Abstract
For a long time, it was believed that a healthy plant did not harbor any microorganisms within its tissues, as these were often considered detrimental for the plant. In the last three decades, the numbers of studies on plant microbe-interactions has led to a change in our view and we now know that many of these invisible partners are essential for the overall welfare of the plant. The application of Next Generation Sequencing techniques is a powerful tool that has permitted the detection and identification of microbial communities in healthy plants. Among the new plant microbe interactions recently reported several actinobacteria such as Micromonospora are included. Micromonospora is a Gram-positive bacterium with a wide geographical distribution; it can be found in the soil, mangrove sediments, and freshwater and marine ecosistems. In the last years our group has focused on the isolation of Micromonospora strains from nitrogen fixing nodules of both leguminous and actinorhizal plants and reported for the first time its wide distribution in nitrogen fixing nodules of both types of plants. These studies have shown how this microoganism had been largely overlooked in this niche due to its slow growth. Surprisingly, the genetic diversity of Micromonospora strains isolated from nodules is very high and several new species have been described. The current data indicate that Micromonospora saelicesensis is the most frequently isolated species from the nodular tissues of both leguminous and actinorhizal plants. Further studies have also been carried out to confirm the presence of Micromonospora inside the nodule tissues, mainly by specific in situ hybridization. The information derived from the genome of the model strain, Micromonospora lupini, Lupac 08, has provided useful information as to how this bacterium may relate with its host plant. Several strategies potentially necessary for Micromonospora to thrive in the soil, a highly competitive, and rough environment, and as an endophytic bacterium with the capacity to colonize the internal plant tissues which are protected from the invasion of other soil microbes were identified. The genome data also revealed the potential of M. lupini Lupac 08 as a plant growth promoting bacterium. Several loci involved in plant growth promotion features such as the production of siderophores, phytohormones, and the degradation of chitin (biocontrol) were also located on the genome and the functionality of these genes was confirmed in the laboratory. In addition, when several host plants species were inoculated with Micromonospora strains, the plant growth enhancing effect was evident under greenhouse conditions. Unexpectedly, a high number of plant-cell wall degrading enzymes were also detected, a trait usually found only in pathogenic bacteria. Thus, Micromonospora can be added to the list of new plant-microbe interactions. The current data indicate that this microorganism may have an important application in agriculture and other biotechnological processes. The available information is promising but limited, much research is still needed to determine which is the ecological function of Micromonospora in interaction with nitrogen fixing plants.
Collapse
Affiliation(s)
- Martha E Trujillo
- Departamento de Microbiología y Genética, Universidad de Salamanca Salamanca, Spain
| | - Raúl Riesco
- Departamento de Microbiología y Genética, Universidad de Salamanca Salamanca, Spain
| | - Patricia Benito
- Departamento de Microbiología y Genética, Universidad de Salamanca Salamanca, Spain
| | - Lorena Carro
- Departamento de Microbiología y Genética, Universidad de Salamanca Salamanca, Spain
| |
Collapse
|
37
|
Trujillo ME, Goodfellow M, Busarakam K, Riesco R. Modestobacter lapidis sp. nov. and Modestobacter muralis sp. nov., isolated from a deteriorated sandstone historic building in Salamanca, Spain. Antonie van Leeuwenhoek 2015; 108:311-20. [PMID: 25987397 DOI: 10.1007/s10482-015-0482-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2015] [Accepted: 05/15/2015] [Indexed: 11/28/2022]
Abstract
A polyphasic study was undertaken to establish the taxonomic status of two Modestobacter strains isolated from the surface of deteriorated sandstone of a historic building in Salamanca, Spain. The strains, isolates MDVD1(T) and MON 3.1(T), were found to have chemotaxonomic and morphological properties consistent with their classification in the genus Modestobacter and to form distinct phyletic lines in the Modestobacter 16S rRNA gene tree. Isolate MDVD1(T) was found to be closely related to the type strain of Modestobacter versicolor (98.7 % similarity) and isolate MON 3.1(T) to the type strain of Modestobacter multiseptatus (98.6 % similarity). The isolates were distinguished readily from one another and from the Modestobacter type strains by a broad range of phenotypic properties, by qualitative and quantitative differences in fatty acid profiles and by BOX fingerprint patterns. On the basis of these data, it is proposed that the isolates be classified in the genus Modestobacter as Modestobacter lapidis sp. nov. and Modestobacter muralis sp. nov., with isolates MON 3.1(T) (CECT 8844(T) = DSM 100206(T)) and MDVD1(T) (CECT 8845(T) = DSM 100205(T)) as the respective type strains.
Collapse
Affiliation(s)
- Martha E Trujillo
- Departamento de Microbiología y Genética, Universidad de Salamanca, Campus Miguel de Unamuno, 37007, Salamanca, Spain,
| | | | | | | |
Collapse
|
38
|
Trujillo ME, Bacigalupe R, Pujic P, Igarashi Y, Benito P, Riesco R, Médigue C, Normand P. Genome features of the endophytic actinobacterium Micromonospora lupini strain Lupac 08: on the process of adaptation to an endophytic life style? PLoS One 2014; 9:e108522. [PMID: 25268993 PMCID: PMC4182475 DOI: 10.1371/journal.pone.0108522] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Accepted: 08/22/2014] [Indexed: 12/03/2022] Open
Abstract
Endophytic microorganisms live inside plants for at least part of their life cycle. According to their life strategies, bacterial endophytes can be classified as “obligate” or “facultative”. Reports that members of the genus Micromonospora, Gram-positive Actinobacteria, are normal occupants of nitrogen-fixing nodules has opened up a question as to what is the ecological role of these bacteria in interactions with nitrogen-fixing plants and whether it is in a process of adaptation from a terrestrial to a facultative endophytic life. The aim of this work was to analyse the genome sequence of Micromonospora lupini Lupac 08 isolated from a nitrogen fixing nodule of the legume Lupinus angustifolius and to identify genomic traits that provide information on this new plant-microbe interaction. The genome of M. lupini contains a diverse array of genes that may help its survival in soil or in plant tissues, while the high number of putative plant degrading enzyme genes identified is quite surprising since this bacterium is not considered a plant-pathogen. Functionality of several of these genes was demonstrated in vitro, showing that Lupac 08 degraded carboxymethylcellulose, starch and xylan. In addition, the production of chitinases detected in vitro, indicates that strain Lupac 08 may also confer protection to the plant. Micromonospora species appears as new candidates in plant-microbe interactions with an important potential in agriculture and biotechnology. The current data strongly suggests that a beneficial effect is produced on the host-plant.
Collapse
Affiliation(s)
- Martha E. Trujillo
- Departamento de Microbiología y Genética, Edificio Departamental, Campus Miguel de Unamuno, Universidad de Salamanca, Salamanca, Spain
- * E-mail:
| | - Rodrigo Bacigalupe
- Departamento de Microbiología y Genética, Edificio Departamental, Campus Miguel de Unamuno, Universidad de Salamanca, Salamanca, Spain
| | - Petar Pujic
- Université Lyon 1, Université de Lyon, CNRS-UMR5557 Ecologie Microbienne, Villeurbanne, France
| | - Yasuhiro Igarashi
- Biotechnology Research Center, Toyama Prefectural University, Kurokawa, Imizu, Toyama, Japan
| | - Patricia Benito
- Departamento de Microbiología y Genética, Edificio Departamental, Campus Miguel de Unamuno, Universidad de Salamanca, Salamanca, Spain
| | - Raúl Riesco
- Departamento de Microbiología y Genética, Edificio Departamental, Campus Miguel de Unamuno, Universidad de Salamanca, Salamanca, Spain
| | - Claudine Médigue
- Genoscope, CNRS-UMR 8030, Atelier de Génomique Comparative, Evry, France
| | - Philippe Normand
- Université Lyon 1, Université de Lyon, CNRS-UMR5557 Ecologie Microbienne, Villeurbanne, France
| |
Collapse
|
39
|
Carro L, Pujic P, Trujillo ME, Normand P. Micromonospora is a normal occupant of actinorhizal nodules. J Biosci 2014; 38:685-93. [PMID: 24287646 DOI: 10.1007/s12038-013-9359-y] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Actinorhizal plants have been found in eight genera belonging to three orders (Fagales, Rosales and Cucurbitales). These all bear root nodules inhabited by bacteria identified as the nitrogen-fixing actinobacterium Frankia. These nodules all have a peripheral cortex with enlarged cells filled with Frankia hyphae and vesicles. Isolation in pure culture has been notoriously difficult, due in a large part to the growth of fast-growing contaminants where, it was later found, Frankia was slow-growing. Many of these contaminants, which were later found to be Micromonospora, were obtained from Casuarina and Coriaria. Our study was aimed at determining if Micromonospora were also present in other actinorhizal plants. Nodules from Alnus glutinosa, Alnus viridis, Coriaria myrtifolia, Elaeagnus x ebbingei, Hippophae rhamnoides, Myrica gale and Morella pensylvanica were tested and were all found to contain Micromonospora isolates. These were found to belong to mainly three species: Micromonospora lupini, Micromonospora coriariae and Micromonospora saelicesensis. Micromonospora isolates were found to inhibit some Frankia strains and to be innocuous to other strains.
Collapse
Affiliation(s)
- Lorena Carro
- Universite Lyon 1, Universite de Lyon, CNRS, Ecologie Microbienne UMR5557, Villeurbanne 69622 Cedex, France
| | | | | | | |
Collapse
|
40
|
|
41
|
Bouizgarne B, Ait Ben Aouamar A. Diversity of Plant Associated Actinobacteria. SUSTAINABLE DEVELOPMENT AND BIODIVERSITY 2014. [DOI: 10.1007/978-3-319-05936-5_3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
42
|
Rong X, Doroghazi JR, Cheng K, Zhang L, Buckley DH, Huang Y. Classification of Streptomyces phylogroup pratensis (Doroghazi and Buckley, 2010) based on genetic and phenotypic evidence, and proposal of Streptomyces pratensis sp. nov. Syst Appl Microbiol 2013; 36:401-7. [PMID: 23769815 DOI: 10.1016/j.syapm.2013.03.010] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Revised: 03/22/2013] [Accepted: 03/25/2013] [Indexed: 11/26/2022]
Abstract
The Streptomyces phylogroup pratensis (Doroghazi and Buckley, 2010) contains isolates obtained from grassy fields, as well as Streptomyces flavogriseus ATCC 33331 and strain CGMCC 4.1868. This latter strain was received as Streptomyces griseoplanus but was subsequently found to be mislabeled, and S. flavogriseus ATCC 33331 (=IAF-45-CD) was shown to be clearly distinct from the type strain S. flavogriseus ATCC 25452(T) (=CGMCC 4.1884(T)). In order to evaluate the taxonomic position of phylogroup pratensis further, sequences of the 16S rRNA gene and five protein-coding housekeeping genes (atpD, gyrB, recA, rpoB and trpB) were determined for six strains of the phylogroup and type strains of 19 related species, which were selected by a BLAST search based on the sequences of the phylogroup. The 16S rRNA gene sequences for the phylogroup were identical to those of eight species belonging to cluster I of the S. griseus clade. However, in all the individual protein-coding gene and MLSA phylogenies, the phylogroup strains without exception formed an obviously distinct cluster that could be equated with a new species status. The phylogenetic evidence for the new species assignment was also supported by corresponding DNA-DNA hybridization values and by phenotypic characteristics. It is therefore proposed that the phylogroup should be classified as Streptomyces pratensis sp. nov., and the type strain is ch24(T) (=CGMCC 4.6829(T)=NRRL B-24916(T)).
Collapse
Affiliation(s)
- Xiaoying Rong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | | | | | | | | | | |
Collapse
|
43
|
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.
Collapse
Affiliation(s)
- Lorena Carro
- Departamento de Microbiología y Genética, Edificio Departamental, Lab. 214, Campus Miguel de Unamuno, Universidad de Salamanca, Salamanca, Spain
| | | | | | | | | |
Collapse
|
44
|
Gurovic MSV, Müller S, Domin N, Seccareccia I, Nietzsche S, Martin K, Nett M. Micromonospora schwarzwaldensis sp. nov., a producer of telomycin, isolated from soil. Int J Syst Evol Microbiol 2013; 63:3812-3817. [PMID: 23667141 DOI: 10.1099/ijs.0.051623-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-positive, spore-forming actinomycete strain (HKI0641(T)) was isolated from a soil sample collected in the Black Forest, Germany. During screening for antimicrobial natural products this bacterium was identified as a producer of the antibiotic telomycin. Morphological characteristics and chemotaxonomic data indicated that the strain belonged to the genus Micromonospora. The peptidoglycan of strain HKI0641(T) contained meso-diaminopimelic acid, and the fatty acid profile consisted predominantly of anteiso-C15 : 0, iso-C15 : 0, iso-C16 : 0 and C16 : 0. MK-10(H4), MK-10(H2) and MK-10 were identified as the major menaquinones. To determine the taxonomic positioning of strain HKI0641(T), we computed a binary tanglegram of two rooted phylogenetic trees that were based upon 16S rRNA and gyrB gene sequences. The comparative analysis of the two common classification methods strongly supported the phylogenetic affiliation with the genus Micromonospora, but it also revealed discrepancies in the assignment at the level of the genomic species. 16S rRNA gene sequence analysis identified Micromonospora coxensis DSM 45161(T) (99.1 % sequence similarity) and Micromonospora marina DSM 45555(T) (99.0 %) as the nearest taxonomic neighbours, whereas the gyrB sequence of strain HKI0641(T) indicated a closer relationship to Micromonospora aurantiaca DSM 43813(T) (95.1 %). By means of DNA-DNA hybridization experiments, it was possible to resolve this issue and to clearly differentiate strain HKI0641(T) from other species of the genus Micromonospora. The type strains of the aforementioned species of the genus Micromonospora could be further distinguished from strain HKI0641(T) by several phenotypic properties, such as colony colour, NaCl tolerance and the utilization of carbon sources. The isolate was therefore assigned to a novel species of the genus Micromonospora, for which the name Micromonospora schwarzwaldensis sp. nov. is proposed. The type strain is HKI0641(T) ( = DSM 45708(T) = CIP 110415(T)).
Collapse
Affiliation(s)
- Maria Soledad Vela Gurovic
- Junior Research Group 'Secondary Metabolism of Predatory Bacteria', Leibniz Institute for Natural Product Research and Infection Biology e. V., Hans-Knöll-Institute, 07745 Jena, Germany
| | - Sebastian Müller
- Systems Biology/Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology e. V., Hans-Knöll-Institute, 07745 Jena, Germany
| | - Nicole Domin
- Junior Research Group 'Secondary Metabolism of Predatory Bacteria', Leibniz Institute for Natural Product Research and Infection Biology e. V., Hans-Knöll-Institute, 07745 Jena, Germany
| | - Ivana Seccareccia
- Junior Research Group 'Secondary Metabolism of Predatory Bacteria', Leibniz Institute for Natural Product Research and Infection Biology e. V., Hans-Knöll-Institute, 07745 Jena, Germany
| | - Sandor Nietzsche
- Centre for Electron Microscopy, University Hospital Jena, 07745 Jena, Germany
| | - Karin Martin
- Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology e. V., Hans-Knöll-Institute, 07745 Jena, Germany
| | - Markus Nett
- Junior Research Group 'Secondary Metabolism of Predatory Bacteria', Leibniz Institute for Natural Product Research and Infection Biology e. V., Hans-Knöll-Institute, 07745 Jena, Germany
| |
Collapse
|
45
|
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.
Collapse
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
| |
Collapse
|
46
|
Genome sequence of Micromonospora lupini Lupac 08, isolated from root nodules of Lupinus angustifolius. J Bacteriol 2012; 194:4135. [PMID: 22815450 DOI: 10.1128/jb.00628-12] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Micromonospora strains have been isolated from diverse niches, including soil, water, and marine sediments and root nodules of diverse symbiotic plants. In this work, we report the genome sequence of Micromonospora lupini Lupac 08 isolated from root nodules of the wild legume Lupinus angustifolious.
Collapse
|
47
|
Curtis SM, Meyers PR. Multilocus sequence analysis of the actinobacterial genus Kribbella. Syst Appl Microbiol 2012; 35:441-6. [PMID: 22981391 DOI: 10.1016/j.syapm.2012.08.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Revised: 08/03/2012] [Accepted: 08/06/2012] [Indexed: 11/19/2022]
Abstract
Multilocus sequence analysis (MLSA) was used to refine the phylogenetic analysis of the genus Kribbella, which currently contains 17 species with validly-published names. Sequences were obtained for the 16S rRNA, gyrB, rpoB, recA, relA and atpD genes for 16 of the 17 type strains of the genus plus seven non-type strains. A five-gene concatenated sequence of 4099 nt was used to examine the phylogenetic relationships between the species of the genus Kribbella. Using the concatenated sequence of the gyrB-rpoB-recA-relA and atpD genes, most Kribbella type strains can be distinguished by a genetic distance of >0.04. Each single-gene tree had an overall topology similar to that of the concatenated sequence tree. The single-gene relA tree, used here for the first time in MLSA of actinobacteria, had good bootstrap support, comparable to the rpoB and atpD gene trees, which had topologies closest to that of the concatenated sequence tree. This illustrates that relA is a useful addition in MLSA studies of the genus Kribbella. We propose that concatenated gyrB-rpoB-recA-relA-atpD gene sequences be used for examining the phylogenetic relationships within the genus Kribbella and for determining the closest phylogenetic relatives to be used for taxonomic comparisons.
Collapse
Affiliation(s)
- Sarah M Curtis
- Department of Molecular and Cell Biology, University of Cape Town, Private Bag X3, Rondebosch, 7701 Cape Town, South Africa
| | | |
Collapse
|