Evolutionary, genomic, and biogeographic characterization of two novel xenobiotics-degrading strains affiliated with Dechloromonas

Abstract

Xenobiotics are generally known as man-made refractory organic pollutants widely distributed in various environments. For exploring the bioremediation possibility of xenobiotics, two novel xenobiotics-degrading strains affiliated with Azonexaceae were isolated. We report here the phylogenetics, genome, and geo-distribution of a novel and ubiquitous Azonexaceae species that primarily joins in the cometabolic process of some xenobiotics in natural communities. Strains s22 and t15 could be proposed as a novel species within Dechloromonas based on genomic and multi-phylogenetic analysis. Pan-genome analysis showed that the 63 core genes in Dechloromonas include genes for dozens of metabolisms such as nitrogen fixation protein ( nifU ), nitrogen regulatory protein ( glnK ), dCTP deaminase, C4-dicarboxylate transporter, and fructose-bisphosphate aldolase. Strains s22 and t15 have the ability to metabolize nitrogen, including nitrogen fixation, NirS -dependent denitrification, and dissimilatory nitrate reduction. Moreover, the novel species possesses the EnvZ-OmpR two-component system for controlling osmotic stress and QseC-QseB system for quorum sensing to rapidly sense environmental changes. It is intriguing that this new species has a series of genes for the biodegradation of some xenobiotics such as azathioprine, 6-Mercaptopurine, trinitrotoluene, chloroalkane, and chloroalkene. Specifically, glutathione S-transferase ( GST ) and 4-oxalocrotonate tautomerase ( praC ) in this novel species play important roles in the detoxification metabolism of some xenobiotics like dioxin, trichloroethene, chloroacetyl chloride, benzo[a]pyrene, and aflatoxin B1. Using data from GenBank, DDBJ and EMBL databases, we also demonstrated that members of this novel species were found globally in plants (e.g. rice), guts (e.g. insect), pristine and contaminated regions. Given these data, Dechloromonas sp. strains s22 and t15 take part in the biodegradation of some xenobiotics through key enzymes.

Water Hyacinth microbiome: metagenomic cues from environment and functionality in urban aquatic bodies

“…Along with freshwater bacterial groups such as Flavobacteraceae , we observed a significantly higher abundance of gut-related and pathogen-containing groups such as Campylobacteraceae, Burkholderiaceae , and Prevotellaceae in water samples than in water hyacinth (Bernardet and Nakagawa et al, 2006; Magana-Arachchi & Wanigatunge, 2020) (Supplementary Figure 12). Further, the organisms reported for bioremediation (Loredanan et al, 2017; Zhang et al, 2021; Yadav et al, 2020), such as Rhodobacteriaceae, Azonexaceae, Xanthomonadaceae, Rhodobacteraceae, Azonexaceae , and few others were numerically more abundant in the WH than water (Supplementary Figure 12). Also, significantly higher occurrences of methanogens and methanotrophs such as Methylococcaceae, Methanotrichaceae , and Methanocellaceae were observed in WH than in water (Supplementary Figure 12).…”

“…Further, the organisms reported for bioremediation (Loredanan et al, 2017;Zhang et al, 2021;Yadav et al, 2020), such as Rhodobacteriaceae, Azonexaceae, Xanthomonadaceae, Rhodobacteraceae, Azonexaceae, and few others were numerically more abundant in the WH than water (Supplementary Figure 12). Also, significantly higher occurrences of methanogens and methanotrophs such as Methylococcaceae, Methanotrichaceae, and Methanocellaceae were observed in WH than in water (Supplementary Figure 12).…”

Investigating Biodegradation of 1,4-Dioxane by Groundwater and Soil Microbiomes: Insights into Microbial Ecology and Process Prediction

“…The decreased bioaugmented CB1190 overtime could be a result of insufficient carbon and energy sources, as well as the competition with indigenous microorganisms. , The evolution within Pseudomonas demonstrated the selective impact of chlorinated solvents and 1,4-dioxane, and that the resilient P. monteilii has the capability to degrade hydrocarbons in both water and soil environments . Similarly, the potential CVOCs degrader Dechloromonas played an important role in the biodegradation of xenobiotics through key enzymes like glutathione S-transferase, and could survive in a polluted environment . The increased functions related to the metabolism pathway after bioaugmentation indicated the boosted activity of the microbial community, corresponding to contaminant removals.…”

Rhizosphere melatonin application reprograms nitrogen-cycling related microorganisms to modulate low temperature response in barley

“…The genus Azoarcus can secrete auxin ( Rasul et al., 1998 ) and promote plant growth ( Mehnaz et al., 1998 ; Raittz et al., 2021 ). Dechloromonas includes genes for dozens of metabolisms, such as nitrogen fixation protein, nitrogen regulatory protein, has the ability to metabolize nitrogen, including nitrogen fixation, denitrification and dissimilatory nitrate reduction ( Zhang et al., 2021 ). The significantly increased in the relative abundance of Azotobacter , Azoarcus and Dechloromonas in MT treatment further proved that melatonin induced changes in microorganism under low temperature were closely related to the nitrogen metabolism, which was beneficial to the plant growth.…”