Phylogenomic Reconstruction and Metabolic Potential of the Genus <i>Aminobacter</i>
Bacteria belonging to the genus <i>Aminobacter</i> are metabolically versatile organisms thriving in both natural and anthropized terrestrial environments. To date, the taxonomy of this genus is poorly defined due to the unavailability of the genomic sequence of <i>A. anthyllidis&l...
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MDPI AG
2021-06-01
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| Series: | Microorganisms |
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| Online Access: | https://www.mdpi.com/2076-2607/9/6/1332 |
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| author | Irene Artuso Paolo Turrini Mattia Pirolo Gabriele Andrea Lugli Marco Ventura Paolo Visca |
| author_facet | Irene Artuso Paolo Turrini Mattia Pirolo Gabriele Andrea Lugli Marco Ventura Paolo Visca |
| author_sort | Irene Artuso |
| collection | DOAJ |
| description | Bacteria belonging to the genus <i>Aminobacter</i> are metabolically versatile organisms thriving in both natural and anthropized terrestrial environments. To date, the taxonomy of this genus is poorly defined due to the unavailability of the genomic sequence of <i>A. anthyllidis</i> LMG 26462<sup>T</sup> and the presence of unclassified <i>Aminobacter</i> strains. Here, we determined the genome sequence of <i>A. anthyllidis</i> LMG 26462<sup>T</sup> and performed phylogenomic, average nucleotide identity and digital DNA-DNA hybridization analyses of 17 members of genus <i>Aminobacter</i>. Our results indicate that 16S rRNA-based phylogeny does not provide sufficient species-level discrimination, since most of the unclassified <i>Aminobacter</i> strains belong to valid <i>Aminobacter</i> species or are putative new species. Since some members of the genus <i>Aminobacter</i> can utilize certain C1 compounds, such as methylamines and methyl halides, a comparative genomic analysis was performed to characterize the genetic basis of some degradative/assimilative pathways in the whole genus. Our findings suggest that all <i>Aminobacter</i> species are heterotrophic methylotrophs able to generate the methylene tetrahydrofolate intermediate through multiple oxidative pathways of C1 compounds and convey it in the serine cycle. Moreover, all <i>Aminobacter</i> species carry genes implicated in the degradation of phosphonates via the C-P lyase pathway, whereas only <i>A. anthyllidis</i> LMG 26462<sup>T</sup> contains a symbiosis island implicated in nodulation and nitrogen fixation. |
| first_indexed | 2024-03-10T10:15:40Z |
| format | Article |
| id | doaj.art-7a5379d0893940f380b1cfe64d4e9c14 |
| institution | Directory Open Access Journal |
| issn | 2076-2607 |
| language | English |
| last_indexed | 2024-03-10T10:15:40Z |
| publishDate | 2021-06-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Microorganisms |
| spelling | doaj.art-7a5379d0893940f380b1cfe64d4e9c142023-11-22T00:51:24ZengMDPI AGMicroorganisms2076-26072021-06-0196133210.3390/microorganisms9061332Phylogenomic Reconstruction and Metabolic Potential of the Genus <i>Aminobacter</i>Irene Artuso0Paolo Turrini1Mattia Pirolo2Gabriele Andrea Lugli3Marco Ventura4Paolo Visca5Department of Science, Roma Tre University, Viale G. Marconi 446, 00146 Rome, ItalyDepartment of Science, Roma Tre University, Viale G. Marconi 446, 00146 Rome, ItalyDepartment of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, 1870 Frederiksberg C, DenmarkLaboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124 Parma, ItalyLaboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124 Parma, ItalyDepartment of Science, Roma Tre University, Viale G. Marconi 446, 00146 Rome, ItalyBacteria belonging to the genus <i>Aminobacter</i> are metabolically versatile organisms thriving in both natural and anthropized terrestrial environments. To date, the taxonomy of this genus is poorly defined due to the unavailability of the genomic sequence of <i>A. anthyllidis</i> LMG 26462<sup>T</sup> and the presence of unclassified <i>Aminobacter</i> strains. Here, we determined the genome sequence of <i>A. anthyllidis</i> LMG 26462<sup>T</sup> and performed phylogenomic, average nucleotide identity and digital DNA-DNA hybridization analyses of 17 members of genus <i>Aminobacter</i>. Our results indicate that 16S rRNA-based phylogeny does not provide sufficient species-level discrimination, since most of the unclassified <i>Aminobacter</i> strains belong to valid <i>Aminobacter</i> species or are putative new species. Since some members of the genus <i>Aminobacter</i> can utilize certain C1 compounds, such as methylamines and methyl halides, a comparative genomic analysis was performed to characterize the genetic basis of some degradative/assimilative pathways in the whole genus. Our findings suggest that all <i>Aminobacter</i> species are heterotrophic methylotrophs able to generate the methylene tetrahydrofolate intermediate through multiple oxidative pathways of C1 compounds and convey it in the serine cycle. Moreover, all <i>Aminobacter</i> species carry genes implicated in the degradation of phosphonates via the C-P lyase pathway, whereas only <i>A. anthyllidis</i> LMG 26462<sup>T</sup> contains a symbiosis island implicated in nodulation and nitrogen fixation.https://www.mdpi.com/2076-2607/9/6/1332<i>Aminobacter anthyllidis</i>glyphosatemethylamine degradationmethylotrophymethyl halidenitrogen fixation |
| spellingShingle | Irene Artuso Paolo Turrini Mattia Pirolo Gabriele Andrea Lugli Marco Ventura Paolo Visca Phylogenomic Reconstruction and Metabolic Potential of the Genus <i>Aminobacter</i> Microorganisms <i>Aminobacter anthyllidis</i> glyphosate methylamine degradation methylotrophy methyl halide nitrogen fixation |
| title | Phylogenomic Reconstruction and Metabolic Potential of the Genus <i>Aminobacter</i> |
| title_full | Phylogenomic Reconstruction and Metabolic Potential of the Genus <i>Aminobacter</i> |
| title_fullStr | Phylogenomic Reconstruction and Metabolic Potential of the Genus <i>Aminobacter</i> |
| title_full_unstemmed | Phylogenomic Reconstruction and Metabolic Potential of the Genus <i>Aminobacter</i> |
| title_short | Phylogenomic Reconstruction and Metabolic Potential of the Genus <i>Aminobacter</i> |
| title_sort | phylogenomic reconstruction and metabolic potential of the genus i aminobacter i |
| topic | <i>Aminobacter anthyllidis</i> glyphosate methylamine degradation methylotrophy methyl halide nitrogen fixation |
| url | https://www.mdpi.com/2076-2607/9/6/1332 |
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