Aminobacter aminovorans
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PROVIDER: PRJNA503019 | ENA |
REPOSITORIES: ENA
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Project description:Aminobacter aminovorans is a Gram-negative, pleomorphic rod-shaped, flagellated, and obligately aerobic bacterium that was isolated from soil. Here, we report the complete genome sequence of A. aminovorans KCTC 2477T, which degrades nitrilotriacetate-metal complexes and iminodiacetate, a metabolic intermediate of nitrilotriacetate.
| S-EPMC5146447 | BioStudies
Project description:Aminobacter aminovorans DSM 7048 genome sequencing
| PRJNA500324 | ENA
Project description:Aminobacter aminovorans BE290 genome sequencing
| PRJNA709310 | ENA
Project description:Aminobacter aminovorans strain:KCTC 2477 Genome sequencing and assembly
| PRJNA316647 | ENA
Project description:Methomyl {bis[1-methylthioacetaldehyde-<i>O</i>-(<i>N</i>-methylcarbamoyl)oximino]sulfide} is a highly toxic oxime carbamate insecticide. Several methomyl-degrading microorganisms have been reported so far, but the role of specific enzymes and genes in this process is still unexplored. In this study, a protein annotated as a carbamate C-N hydrolase was identified in the methomyl-degrading strain <i>Aminobacter aminovorans</i> MDW-2, and the encoding gene was termed <i>ameH</i> A comparative analysis between the mass fingerprints of AmeH and deduced proteins of the strain MDW-2 genome revealed AmeH to be a key enzyme of the detoxification step of methomyl degradation. The results also demonstrated that AmeH was a functional homodimer with a subunit molecular mass of approximately 34 kDa and shared the highest identity (27%) with the putative formamidase from <i>Schizosaccharomyces pombe</i> ATCC 24843. AmeH displayed maximal enzymatic activity at 50°C and pH 8.5. <i>K<sub>m</sub></i> and <i>k</i> <sub>cat</sub> of AmeH for methomyl were 87.5 μM and 345.2 s<sup>-1</sup>, respectively, and catalytic efficiency (<i>k</i> <sub>cat</sub>/<i>K<sub>m</sub></i> ) was 3.9 μM<sup>-1</sup> s<sup>-1</sup> Phylogenetic analysis revealed AmeH to be a member of the FmdA_AmdA superfamily. Additionally, five key amino acid residues (162, 164, 191, 193, and 207) of AmeH were identified by amino acid variations.<b>IMPORTANCE</b> Based on the structural characteristic, carbamate insecticides can be classified into oxime carbamates (methomyl, aldicarb, oxamyl, etc.) and <i>N</i>-methyl carbamates (carbaryl, carbofuran, isoprocarb, etc.). So far, research on the degradation of carbamate pesticides has mainly focused on the detoxification step and hydrolysis of their carbamate bond. Several genes, such as <i>cehA</i>, <i>mcbA</i>, <i>cahA</i>, and <i>mcd</i>, and their encoding enzymes have also been reported to be involved in the detoxification step. However, none of these enzymes can hydrolyze methomyl. In this study, a carbamate C-N hydrolase gene, <i>ameH</i>, responsible for the detoxification step of methomyl in strain MDW-2 was cloned and the key amino acid sites of AmeH were investigated. These findings provide insight into the microbial degradation mechanism of methomyl.
| S-EPMC7755249 | BioStudies
Project 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.
| S-EPMC8235418 | BioStudies
Project description:Taxonomic decisions within the order <i>Rhizobiales</i> have relied heavily on the interpretations of highly conserved 16S rRNA sequences and DNA-DNA hybridizations (DDH). Currently, bacterial species are defined as including strains that present 95-96% of average nucleotide identity (ANI) and 70% of digital DDH (dDDH). Thus, ANI values from 520 genome sequences of type strains from species of <i>Rhizobiales</i> order were computed. From the resulting 270,400 comparisons, a ≥95% cut-off was used to extract high identity genome clusters through enumerating maximal cliques. Coupling this graph-based approach with dDDH from clusters of interest, it was found that: (i) there are synonymy between <i>Aminobacter lissarensis</i> and <i>Aminobacter carboxidus</i>, <i>Aurantimonas manganoxydans</i> and <i>Aurantimonas coralicida</i>, "<i>Bartonella mastomydis</i>," and <i>Bartonella elizabethae</i>, <i>Chelativorans oligotrophicus</i>, and <i>Chelativorans multitrophicus</i>, <i>Rhizobium azibense</i>, and <i>Rhizobium gallicum</i>, <i>Rhizobium fabae</i>, and <i>Rhizobium pisi</i>, and <i>Rhodoplanes piscinae</i> and <i>Rhodoplanes serenus</i>; (ii) <i>Chelatobacter heintzii</i> is not a synonym of <i>Aminobacter aminovorans</i>; (iii) "<i>Bartonella vinsonii</i>" subsp. <i>arupensis</i> and "<i>B. vinsonii</i>" subsp. <i>berkhoffii</i> represent members of different species; (iv) the genome accessions GCF_003024615.1 ("<i>Mesorhizobium loti</i> LMG 6,125<sup>T</sup>"), GCF_003024595.1 ("<i>Mesorhizobium plurifarium</i> LMG 11,892<sup>T</sup>"), GCF_003096615.1 ("<i>Methylobacterium organophilum</i> DSM 760<sup>T</sup>"), and GCF_000373025.1 ("<i>R. gallicum</i> R-602 sp<sup>T</sup>") are not from the genuine type strains used for the respective species descriptions; and v) "<i>Xanthobacter autotrophicus</i>" Py2 and "<i>Aminobacter aminovorans</i>" KCTC 2,477<sup>T</sup> represent cases of misuse of the term "type strain". <i>Aminobacter heintzii</i> comb. nov. and the reclassification of <i>Aminobacter ciceronei</i> as <i>A. heintzii</i> is also proposed. To facilitate the downstream analysis of large ANI matrices, we introduce here ProKlust ("Prokaryotic Clusters"), an R package that uses a graph-based approach to obtain, filter, and visualize clusters on identity/similarity matrices, with settable cut-off points and the possibility of multiple matrices entries.
| S-EPMC8026895 | BioStudies
Project description:BAM (2,6-dichlorobenzamide) is a metabolite of the pesticide dichlobenil. Naturally occurring bacteria that can utilize BAM are rare. Often the compound cannot be degraded before it reaches the groundwater and therefore it poses a serious threat to drinking water supplies. The bacterial strain Aminobacter MSH1 is a BAM degrader and therefore a potential candidate to be amended to sand filters in waterworks to remediate BAM polluted drinking water. A common problem in bioremediation is that bacteria artificially introduced into new diverse environments often thrive poorly, which is even more unfortunate because biologically diverse environments may ensure a more complete decomposition. To test the bioaugmentative potential of MSH1, we used a serial dilution approach to construct microcosms with different biological diversity. Subsequently, we amended Aminobacter MSH1 to the microcosms in two final concentrations; i.e. 10(5) cells mL(-1) and 10(7) cells mL(-1). We anticipated that BAM degradation would be most efficient at "intermediate diversities" as low diversity would counteract decomposition because of incomplete decomposition of metabolites and high diversity would be detrimental because of eradication of Aminobacter MSH1. This hypothesis was only confirmed when Aminobacter MSH1 was amended in concentrations of 10(5) cells mL(-1). Our findings suggest that Aminobacter MSH1 is a very promising bioremediator at several diversity levels.
| S-EPMC4468195 | BioStudies