Metagenomic Evidence for a Methylocystis Species Capable of Bioremediation of Diverse Heavy Metals

Abstract

Heavy metal pollution has become an increasingly serious problem worldwide. Co-contamination with toxic mercury (Hg) and arsenic (As) presents a particularly difficult bioremediation trouble. By oxidizing the greenhouse gas methane, methanotrophs have been demonstrated to have high denitrification activity in eutrophic waters, indicating their possible potential for use in bioremediation of Hg(II) and As(V) in polluted water. Using metagenomics, a novel Methylocystis species (HL18), which was one of the most prevalent bacteria (9.9% of the relative abundance) in a CH4-based bio-reactor, is described here. The metagenomic-assembled genome (MAG) HL18 had gene products whose average amino acid identity against other known Methylocystis species varied from 69 to 85%, higher than the genus threshold but lower than the species boundary. Genomic analysis indicated that HL18 possessed all the genes necessary for the reduction of Hg(II) and As(V). Phylogenetic investigation of mercuric reductase (MerA) found that the HL18 protein was most closely affiliated with proteins from two Hg(II)-reducing bacteria, Bradyrhizobium sp. strain CCH5-F6 and Paracoccus halophilus. The genomic organization and phylogeny of the genes in the As(V)-reducing operon (arsRCCB) had significant identity with those from a As(V)-reducing bacterium belonging to the Rhodopseudomonas genus, indicating their reduction capability of As(V). Further analysis found that at least eight genera of methanotrophs possess both Hg(II) and As(V) reductases, illustrating the generally overlooked metabolic potential of methanotrophs. These results suggest that methanotrophs have greater bioremediation potential in heavy metal contaminated water than has been appreciated and could play an important role in the mitigation of heavy metal toxicity of contaminated wastewater.

Methanogens and Their Syntrophic Partners Dominate Zones of Enhanced Magnetic Susceptibility at a Petroleum Contaminated Site

“…This wide distribution is explained by Methylocystis' extended metabolic capability to use acetate or ethanol in the absence of methane and to fix dinitrogen (Han et al, 2018). Methylocystis has also been detected in groundwater contaminated with heavy metals including arsenic, displaying genes for As(III) oxidation and As(V) reduction (Shi et al, 2018;Danczak et al, 2019). High LDA scores for the lower vadose zone were also assigned to the Alphaproteobacteria Devosia and Rhodopseudomonas.…”

Enhanced Adsorptive Bioremediation of Heavy Metals (Cd2+, Cr6+, Pb2+) by Methane-Oxidizing Epipelon

“…Similarly, Methylococcus capsulatus has been found to detoxify lead and zinc at low pH [65] and chromium [17]. The type II methanotrophic strains identified in this study have been widely utilized for the bioremediation of heavy metals [16,66].…”

“…Methylosinus, a type II methanotrophs contributed 11-21% of the total bacterial DNA in the biofilm after addition of chromium (Cr) metal [15]. Additionally, the presence of Hg(II) and As(V) reductases was also confirmed in almost eight genera of methanotrophs, demonstrating that the metabolic potential of methanotrophs is generally overlooked [16]. Methylococcus capsulatus (Bath) was found to effectually bioremediate aquatic pollution caused by a broad range of chromium(VI) concentration (1.4-1000 mg L −1 of Cr +6 ) [17].…”

Molecular Insight Into Key Eco-Physiological Process in Bioremediating and Plant-Growth-Promoting Bacteria

“…Nonetheless, using a metagenomic survey, several groups also reported the presence of potential arsenic reduction (80% metagenomic reads ascribed for this)/methylation/efflux related genes (6-9% metagenomic reads ascribed for this) in wetland environments like paddy soil (Xiao et al, 2016;Imchen et al, 2018). Notably, in a separate study conducted by Shi et al (2019), the As(V) and Hg(II) bioremediation efficiency in methanotrophic bacterial members such as Methylocystis sp. HL18, whose assembled genome encompassed with operons like mer (having genes like merR, merT, merP, merC and merA), arsRCB, and arsRCCB, were reported (Shi et al, 2019).…”

“…Notably, in a separate study conducted by Shi et al (2019), the As(V) and Hg(II) bioremediation efficiency in methanotrophic bacterial members such as Methylocystis sp. HL18, whose assembled genome encompassed with operons like mer (having genes like merR, merT, merP, merC and merA), arsRCB, and arsRCCB, were reported (Shi et al, 2019). In this connection it is noteworthy to mention that functionalprotein-based phylogenetic analysis (MerA, arsRCCB) indicates acquisition of metal-remediating genes in this organism follow a horizontal path of gene transfer, a phenomenon that hints toward the new possibilities for getting bioremediation potency in novel taxonomically diverse bacterial groups that has not been explored till date.…”