The complete genome of 2,6-dichlorobenzamide (BAM) degrader Aminobacter sp. MSH1 suggests a polyploid chromosome, phylogenetic reassignment, and functions of plasmids

Abstract

Aminobacter sp. MSH1 (CIP 110285) can use the pesticide dichlobenil and its recalcitrant transformation product, 2,6-dichlorobenzamide (BAM), as sole source of carbon, nitrogen, and energy. The concentration of BAM in groundwater often exceeds the threshold limit for drinking water, requiring additional treatment in drinking water treatment plants or closure of the affected abstraction wells. Biological treatment with MSH1 is considered a potential sustainable alternative to remediate BAM-contamination in drinking water production. We present the complete genome of MSH1, which was determined independently in two institutes at Aarhus University and KU Leuven. Divergences were observed between the two genomes, i.e. one of them lacked four plasmids compared to the other. Besides the circular chromosome and the two previously described plasmids involved in BAM catabolism, pBAM1 and pBAM2, the genome of MSH1 contained two megaplasmids and three smaller plasmids. The MSH1 substrain from KU Leuven showed a reduced genome lacking a megaplasmid and three smaller plasmids and was designated substrain MK1, whereas the Aarhus variant with all plasmids was designated substrain DK1. A plasmid stability experiment indicate that substrain DK1 may have a polyploid chromosome when growing in R2B medium with more chromosomes than plasmids per cell. Finally, strain MSH1 is reassigned as Aminobacter niigataensis MSH1.

Single-strain mobilome sequencing quantifies bacterial genetic response to stress, including activity of IS elements, prophages, RNAs, and REPINs

“…This study shows that several stressors, especially copper, induces the formation of circular intermediate DNA molecules from several IS elements within only 60 minutes after exposure. These insights can help to explain how MGEs are activate upon stress response and can lead to mobilization of important DNA, such as antibiotic resistance genes 26,27 or xenobiotics catabolic genes 20,[28][29][30] .…”

A Methylotrophic Bacterium Growing with the Antidiabetic Drug Metformin as Its Sole Carbon, Nitrogen and Energy Source

“…Aminobacter strain MD1, A. niigataensis DSM 7050 T , A. aganoensis DSM 7051 T and strain Root100 [35] (obtained from the Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSMZ, Braunschweig, Germany)), and strain MSH1 [36] (obtained from the Pasteur Institute Collection, France), were cultivated aerobically at 30 • C on solid or in liquid M3 mineral medium. Carbon and nitrogen substrates were added from stock solutions sterilized by filtration (0.22 mm, Sarstedt, Nümbrecht, Germany) after autoclaving of the medium.…”

“…Most importantly, Aminobacter type strain A. niigataensis DSM 7050 T , Aminobacter sp. strain MSH1 (recently assigned to the species A. niigataensis [36]), the A. aganoensis type strain DSM 7051 T , and Aminobacter sp. strain Root100 which are all closely related to strain MD1 (Figure S2) did not grow with metformin as the sole carbon source (Figure 3).…”

Dissemination of metaldehyde catabolic pathways is driven by mobile genetic elements in Proteobacteria

“…Third generation long-range sequencing technologies have been used to gain insights into xenobiotic-degrading prokaryotes for compounds such as linuron [16], dibenzofuran [17], 2,6-dichlorobenzamide [18] and organophosphorus insecticide [19]…”

“…Third generation long-range sequencing technologies have been used to gain insights into xenobiotic-degrading prokaryotes for compounds such as linuron [ 16 ], dibenzofuran [ 17 ], 2,6-dichlorobenzamide [ 18 ] and organophosphorus insecticide [ 19 ] degraders, and can also be applied to explore MGEs for metaldehyde. In-depth knowledge of MGEs and HGT mechanisms for this compound can open new possibilities for drinking water bioremediation.…”