Phylogenomic Reconstruction and Metabolic Potential of the Genus Aminobacter

Abstract

Bacteria belonging to the genus Aminobacter 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 A. anthyllidis LMG 26462T and the presence of unclassified Aminobacter strains. Here, we determined the genome sequence of A. anthyllidis LMG 26462T and performed phylogenomic, average nucleotide identity and digital DNA-DNA hybridization analyses of 17 members of genus Aminobacter. Our results indicate that 16S rRNA-based phylogeny does not provide sufficient species-level discrimination, since most of the unclassified Aminobacter strains belong to valid Aminobacter species or are putative new species. Since some members of the genus Aminobacter 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 Aminobacter 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 Aminobacter species carry genes implicated in the degradation of phosphonates via the C-P lyase pathway, whereas only A. anthyllidis LMG 26462T contains a symbiosis island implicated in nodulation and nitrogen fixation.

Aerobic Degradation of the Antidiabetic Drug Metformin by Aminobacter sp. Strain NyZ550

“…Nitrogen availability is often a growth-limiting factor for bacteria, and strains of Aminobacter are known for their versatile abilities to utilize nitrogenous compounds, thereby conferring them a selective advantage in the environment. , Here, we tested the growth of strain NyZ550 on various nitrogenous compounds (2 mM) analogous to MET or derived from MET. The results showed that strain NyZ550 was able to use trimethylamine, DMA, methylamine, and 1-methylbiguanide as sole carbon, nitrogen, and energy sources for its growth (Figures A and S2).…”

Wastewater bacteria remediating the pharmaceutical metformin: Genomes, plasmids and products

“…Under aerobic conditions, dimethylamine could not be identified (<0.02 mM). Dimethylamine is reported to be oxidized by a monooxygenase in other Aminobacter strains (Artuso et al, 2021) and this could explain the failure to detect it here. In an effort to trap dimethylamine if it were formed, resting cell suspensions were incubated with metformin under anaerobic conditions and then combined with a derivatizing reagent (FMOC-Cl).…”

Glyphosate has a negligible impact on bacterial diversity and dynamics during composting

“…Both glyphosate degradation pathways: the sarcosine pathway through the production of the enzyme C-P lyase and the AMPA pathway through the production of the enzyme GOX were potentially induced during the experiment. Indeed, some members of the genera Streptomyces, Bacillus and Pseudomonas are known to use both pathways to degrade glyphosate (Singh et al, 2019(Singh et al, , 2020, while Geobacillus uses the AMPA pathway (Obojska et al, 2002) and Lysinibacillus and Aminobacter use the sarcosine pathway (Artuso et al, 2021;Gonz alez-Valenzuela & Duss an, 2018). Furthermore, glyphosate degradation is thought to be activated in Aminobacter, Lysinibacillus, Geobacillus, Pseudomonas and Bacillus to obtain inorganic phosphorus molecules, while Streptomyces uses it as a source of both phosphorus and nitrogen.…”