The Genome of BAM-degrading <i>Aminobacter</i> sp. MSH1 with Several Low Copy Plasmids

Nielsen, Tue Kjærgaard; Hylling, Ole; Ellegaard-Jensen, Lea; Aamand, Jens; Lh, Hansen

doi:10.1101/307967

Cited by 5 publications

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“…MSH1 originally isolated and described by Sørensen et al (2007) was applied in the present study. MSH1 showed great potential for BAM degradation of membrane retentate water in batch studies (Hylling et al, 2019) and it was recently characterized by full genome sequencing (Nielsen et al, 2018). The strain was pre-grown in MSNC medium for 5 days at 20 • C on an orbital shaker (100 rpm).…”

Section: Bacterial Strain and Cultivationmentioning

confidence: 99%

“…A novel primer set was designed to verify that bbdA gene presence corresponded to presence of MSH1 cells. This primer set specifically targets a prophage-insertion-region on the genome of MSH1 (Nielsen et al, 2018), following an analogous method used by Gobbi et al (2020). The prophage sequences in the MSH1-genome were identified by using PHASTER (PHAge Search Tool Enhanced Research) from Arndt et al (2016).…”

Section: Quantification Of Bbda Genes Msh1 Cells and Total 16s Genesmentioning

confidence: 99%

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Bioaugmented Sand Filter Columns Provide Stable Removal of Pesticide Residue From Membrane Retentate

et al. 2020

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Drinking water resources, such as groundwater, are threatened by pollution. The pesticide metabolite 2,6-dichlorobenzamide (BAM) is one of the compounds frequently found in groundwater. Studies have attempted to add specific BAM-degrading bacteria to sand filters at drinking water treatment facilities. This biotechnology has shown great potential in removing BAM from contaminated water. However, the degradation potential was formerly lost after ~2–3 weeks due to a decrease of the degrader population over time. The aim of the present study was to overcome the constraints leading to loss of degraders from inoculated filters. Our approach was threefold: (1) Development of a novel inoculation strategy, (2) lowering the flowrate to reduce washout of cells, and (3) increasing the concentration of nutrients hereunder the pollutant in a smaller inlet water stream. The two latter were achieved via modifications of the inlet water by applying membrane treatment which, besides producing an ultra-pure water fraction, produced a residual water stream with nutrients including BAM concentrated in ~ten-fold reduced volume. This was done to alleviate starvation of degrader bacteria in the otherwise oligotrophic sand filters and to enable a decreased flowrate. By this approach, we achieved 100% BAM removal over a period of 40 days in sand filter columns inoculated with the BAM-degrader Aminobacter sp. MSH1. Molecular targeting of the degrader strain showed that the population of degrader bacteria persisted at high numbers throughout the sand filter columns and over the entire timespan of the experiment. 16S rRNA gene amplicon sequencing confirmed that MSH1 dominated the bacterial communities of the inoculated sand filter columns at experimental termination. The community composition of the indigenous prokaryotes, based on beta diversity, in the sand filter columns was governed by the feed water type i.e., membrane retentate or untreated water.

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Section: Bacterial Strain and Cultivationmentioning

confidence: 99%

Section: Quantification Of Bbda Genes Msh1 Cells and Total 16s Genesmentioning

confidence: 99%

Bioaugmented Sand Filter Columns Provide Stable Removal of Pesticide Residue From Membrane Retentate

et al. 2020

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“…Previous studies on Aminobacter sp. MSH1 reported that 2,6-dichlorobenzamide (BAM) degradation genes map on distinct plasmids: pBAM1 carries the BbdA amidase, responsible for the initial transformation of BAM into 2,6-DCBA [ 65 ], whereas pBAM2 harbors a large region for the complete degradation of 2,6-DCBA, encompassing two major gene clusters: bbdR1B1B2B3CDE and bbdR2FGHIJ [ 30 , 66 ] ( Supplementary Table S5 ). Genome inspection of all Aminobacter members detected BAM degradation genes only in Aminobacter sp.…”

Section: Resultsmentioning

confidence: 99%

Phylogenomic Reconstruction and Metabolic Potential of the Genus Aminobacter

et al. 2021

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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.

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“…The Aminobacter genus of the Phyllobacteriaceae family is present in the microbial consortia MG Kraft 37°C and BY Kraft 37°C in the sixth passage (Figs 2 , 3 and 4 ). Although no previous studies of enriched microbial consortia for lignin degradation have identified species of the genus Aminobacter , sequencing of the genome from a member of this genus indicates the presence of a ligninolytic enzyme, a laccase [ 63 ]. This representative of the genus in our experiments may have a role on the degradation of lignin, indicating the need for further characterization of the activities by bacteria of this genus.…”

Section: Discussionmentioning

confidence: 99%

Bacterial diversity dynamics in microbial consortia selected for lignin utilization

et al. 2021

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Lignin is nature’s largest source of phenolic compounds. Its recalcitrance to enzymatic conversion is still a limiting step to increase the value of lignin. Although bacteria are able to degrade lignin in nature, most studies have focused on lignin degradation by fungi. To understand which bacteria are able to use lignin as the sole carbon source, natural selection over time was used to obtain enriched microbial consortia over a 12-week period. The source of microorganisms to establish these microbial consortia were commercial and backyard compost soils. Cultivation occurred at two different temperatures, 30°C and 37°C, in defined culture media containing either Kraft lignin or alkaline-extracted lignin as carbon source. iTag DNA sequencing of bacterial 16S rDNA gene was performed for each of the consortia at six timepoints (passages). The initial bacterial richness and diversity of backyard compost soil consortia was greater than that of commercial soil consortia, and both parameters decreased after the enrichment protocol, corroborating that selection was occurring. Bacterial consortia composition tended to stabilize from the fourth passage on. After the enrichment protocol, Firmicutes phylum bacteria were predominant when lignin extracted by alkaline method was used as a carbon source, whereas Proteobacteria were predominant when Kraft lignin was used. Bray-Curtis dissimilarity calculations at genus level, visualized using NMDS plots, showed that the type of lignin used as a carbon source contributed more to differentiate the bacterial consortia than the variable temperature. The main known bacterial genera selected to use lignin as a carbon source were Altererythrobacter, Aminobacter, Bacillus, Burkholderia, Lysinibacillus, Microvirga, Mycobacterium, Ochrobactrum, Paenibacillus, Pseudomonas, Pseudoxanthomonas, Rhizobiales and Sphingobium. These selected bacterial genera can be of particular interest for studying lignin degradation and utilization, as well as for lignin-related biotechnology applications.

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The Genome of BAM-degrading Aminobacter sp. MSH1 with Several Low Copy Plasmids

Cited by 5 publications

References 26 publications

Bioaugmented Sand Filter Columns Provide Stable Removal of Pesticide Residue From Membrane Retentate

Bioaugmented Sand Filter Columns Provide Stable Removal of Pesticide Residue From Membrane Retentate

Phylogenomic Reconstruction and Metabolic Potential of the Genus Aminobacter

Bacterial diversity dynamics in microbial consortia selected for lignin utilization

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