Comparative Analysis of Three Bradyrhizobium diazoefficiens Genomes Show Specific Mutations Acquired during Selection for a Higher Motility Phenotype and Adaption to Laboratory Conditions
ABSTRACT Microbial genomes are being extensively studied using next-generation sequencing technologies in order to understand the changes that occur under different selection regimes. In this work, the number and type of mutations that have occurred in three Bradyrhizobium diazoefficiens USDA 110T s...
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| Language: | English |
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American Society for Microbiology
2021-12-01
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| Series: | Microbiology Spectrum |
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| Online Access: | https://journals.asm.org/doi/10.1128/Spectrum.00569-21 |
| _version_ | 1818744540012478464 |
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| author | Mauricio J. Lozano Miguel Redondo-Nieto Daniel Garrido-Sanz Elías Mongiardini J. Ignacio Quelas Florencia Mengucci Carolina Dardis Aníbal Lodeiro M. Julia Althabegoiti |
| author_facet | Mauricio J. Lozano Miguel Redondo-Nieto Daniel Garrido-Sanz Elías Mongiardini J. Ignacio Quelas Florencia Mengucci Carolina Dardis Aníbal Lodeiro M. Julia Althabegoiti |
| author_sort | Mauricio J. Lozano |
| collection | DOAJ |
| description | ABSTRACT Microbial genomes are being extensively studied using next-generation sequencing technologies in order to understand the changes that occur under different selection regimes. In this work, the number and type of mutations that have occurred in three Bradyrhizobium diazoefficiens USDA 110T strains under laboratory conditions and during selection for a more motile phenotypic variant were analyzed. Most of the mutations found in both processes consisted of single nucleotide polymorphisms, single nucleotide deletions or insertions. In the case of adaptation to laboratory conditions, half of the changes occurred within intergenic regions, and around 80% were insertions. When the more motile phenotypic variant was evaluated, eight single nucleotide polymorphisms and an 11-bp deletion were found, although none of them was directly related to known motility or chemotaxis genes. Two mutants were constructed to evaluate the 11-bp deletion affecting the alpha subunit of 2-oxoacid:acceptor oxidoreductase (AAV28_RS30705-blr6743). The results showed that this single deletion was not responsible for the enhanced motility phenotype. IMPORTANCE The genetic and genomic changes that occur under laboratory conditions in Bradyrhizobium diazoefficiens genomes remain poorly studied. Only a few genome sequences of this important nitrogen-fixing species are available, and there are no genome-wide comparative analyses of related strains. In the present work, we sequenced and compared the genomes of strains derived from a parent strain, B. diazoefficiens USDA 110, that has undergone processes of repeated culture in the laboratory environment, or phenotypic selection toward antibiotic resistance and enhanced motility. Our results represent the first analysis in B. diazoefficiens that provides insights into the specific mutations that are acquired during these processes. |
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| institution | Directory Open Access Journal |
| issn | 2165-0497 |
| language | English |
| last_indexed | 2024-12-18T02:45:55Z |
| publishDate | 2021-12-01 |
| publisher | American Society for Microbiology |
| record_format | Article |
| series | Microbiology Spectrum |
| spelling | doaj.art-3bafa7c2b4ad43fabd12c0ce1a1968172022-12-21T21:23:33ZengAmerican Society for MicrobiologyMicrobiology Spectrum2165-04972021-12-019310.1128/Spectrum.00569-21Comparative Analysis of Three Bradyrhizobium diazoefficiens Genomes Show Specific Mutations Acquired during Selection for a Higher Motility Phenotype and Adaption to Laboratory ConditionsMauricio J. Lozano0Miguel Redondo-Nieto1Daniel Garrido-Sanz2Elías Mongiardini3J. Ignacio Quelas4Florencia Mengucci5Carolina Dardis6Aníbal Lodeiro7M. Julia Althabegoiti8Instituto de Biotecnología y Biología Molecular (IBBM), Facultad de Ciencias Exactas, UNLP-CONICET, La Plata, ArgentinaDepartamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, SpainDepartamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, SpainInstituto de Biotecnología y Biología Molecular (IBBM), Facultad de Ciencias Exactas, UNLP-CONICET, La Plata, ArgentinaInstituto de Biotecnología y Biología Molecular (IBBM), Facultad de Ciencias Exactas, UNLP-CONICET, La Plata, ArgentinaInstituto de Biotecnología y Biología Molecular (IBBM), Facultad de Ciencias Exactas, UNLP-CONICET, La Plata, ArgentinaInstituto de Biotecnología y Biología Molecular (IBBM), Facultad de Ciencias Exactas, UNLP-CONICET, La Plata, ArgentinaInstituto de Biotecnología y Biología Molecular (IBBM), Facultad de Ciencias Exactas, UNLP-CONICET, La Plata, ArgentinaInstituto de Biotecnología y Biología Molecular (IBBM), Facultad de Ciencias Exactas, UNLP-CONICET, La Plata, ArgentinaABSTRACT Microbial genomes are being extensively studied using next-generation sequencing technologies in order to understand the changes that occur under different selection regimes. In this work, the number and type of mutations that have occurred in three Bradyrhizobium diazoefficiens USDA 110T strains under laboratory conditions and during selection for a more motile phenotypic variant were analyzed. Most of the mutations found in both processes consisted of single nucleotide polymorphisms, single nucleotide deletions or insertions. In the case of adaptation to laboratory conditions, half of the changes occurred within intergenic regions, and around 80% were insertions. When the more motile phenotypic variant was evaluated, eight single nucleotide polymorphisms and an 11-bp deletion were found, although none of them was directly related to known motility or chemotaxis genes. Two mutants were constructed to evaluate the 11-bp deletion affecting the alpha subunit of 2-oxoacid:acceptor oxidoreductase (AAV28_RS30705-blr6743). The results showed that this single deletion was not responsible for the enhanced motility phenotype. IMPORTANCE The genetic and genomic changes that occur under laboratory conditions in Bradyrhizobium diazoefficiens genomes remain poorly studied. Only a few genome sequences of this important nitrogen-fixing species are available, and there are no genome-wide comparative analyses of related strains. In the present work, we sequenced and compared the genomes of strains derived from a parent strain, B. diazoefficiens USDA 110, that has undergone processes of repeated culture in the laboratory environment, or phenotypic selection toward antibiotic resistance and enhanced motility. Our results represent the first analysis in B. diazoefficiens that provides insights into the specific mutations that are acquired during these processes.https://journals.asm.org/doi/10.1128/Spectrum.00569-21laboratory adaptationsingle nucleotide polymorphismswimming motilitycomparative genomics |
| spellingShingle | Mauricio J. Lozano Miguel Redondo-Nieto Daniel Garrido-Sanz Elías Mongiardini J. Ignacio Quelas Florencia Mengucci Carolina Dardis Aníbal Lodeiro M. Julia Althabegoiti Comparative Analysis of Three Bradyrhizobium diazoefficiens Genomes Show Specific Mutations Acquired during Selection for a Higher Motility Phenotype and Adaption to Laboratory Conditions Microbiology Spectrum laboratory adaptation single nucleotide polymorphism swimming motility comparative genomics |
| title | Comparative Analysis of Three Bradyrhizobium diazoefficiens Genomes Show Specific Mutations Acquired during Selection for a Higher Motility Phenotype and Adaption to Laboratory Conditions |
| title_full | Comparative Analysis of Three Bradyrhizobium diazoefficiens Genomes Show Specific Mutations Acquired during Selection for a Higher Motility Phenotype and Adaption to Laboratory Conditions |
| title_fullStr | Comparative Analysis of Three Bradyrhizobium diazoefficiens Genomes Show Specific Mutations Acquired during Selection for a Higher Motility Phenotype and Adaption to Laboratory Conditions |
| title_full_unstemmed | Comparative Analysis of Three Bradyrhizobium diazoefficiens Genomes Show Specific Mutations Acquired during Selection for a Higher Motility Phenotype and Adaption to Laboratory Conditions |
| title_short | Comparative Analysis of Three Bradyrhizobium diazoefficiens Genomes Show Specific Mutations Acquired during Selection for a Higher Motility Phenotype and Adaption to Laboratory Conditions |
| title_sort | comparative analysis of three bradyrhizobium diazoefficiens genomes show specific mutations acquired during selection for a higher motility phenotype and adaption to laboratory conditions |
| topic | laboratory adaptation single nucleotide polymorphism swimming motility comparative genomics |
| url | https://journals.asm.org/doi/10.1128/Spectrum.00569-21 |
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