Bromate Reduction by Rhodococcus sp. Br-6 in the Presence of Multiple Redox Mediators

A metabologenomics approach reveals the unexplored biosynthetic potential of bacteria isolated from an Amazon Conservation Unit

The Amazon, an important biodiversity hotspot, remains poorly explored in terms of its microbial diversity and biotechnological potential. The present study characterized the metabolic potential of Gram-positive strains of the Actinomycetes and Bacilli classes isolated from soil samples of an Amazon Conservation Unit. The sequencing of the 16S rRNA gene classified the strains ACT015, ACT016, and FIR094 within the genera Streptomyces, Rhodococcus, and Brevibacillus, respectively. Genome mining identified 33, 17, and 14 biosynthetic gene clusters (BGCs) in these strains, including pathways for the biosynthesis of antibiotic and antitumor agents. Additionally, 40 BGCs (62,5% of the total BGCs) were related to unknown metabolites. The OSMAC approach and untargeted metabolomics analysis revealed a plethora of metabolites under laboratory conditions, underscoring the untapped chemical diversity and biotechnological potential of these isolates. Our findings illustrated the efficacy of the metabologenomics approach in elucidating secondary metabolism and selecting BGCs with chemical novelty.IMPORTANCEThe largest rainforest in the world is globally recognized for its biodiversity. However, until now, few studies have been conducted to prospect natural products from the Amazon microbiome. In this work, we isolated three free-living bacterial species from the microbiome of pristine soils and used two high-throughput technologies to reveal the vast unexplored repertoire of secondary metabolites produced by these microorganisms.

Bromate reduction by Shewanella oneidensis MR-1 is mediated by dimethylsulfoxide reductase

Microbial bromate reduction plays an important role in remediating bromate-contaminated waters as well as biogeochemical cycling of bromine. However, little is known about the molecular mechanism of microbial bromate reduction so far. Since the model strain Shewanella oneidensis MR-1 is capable of reducing a variety of oxyanions such as iodate, which has a high similarity to bromate, we hypothesize that S. oneidensis MR-1 can reduce bromate. Here, we conducted an experiment to investigate whether S. oneidensis MR-1 can reduce bromate, and report bromate reduction mediated by a dimethylsulfoxide reductase encoded with dmsA. S. oneidensis MR-1 is not a bromate-respiring bacterium but can reduce bromate to bromide under microaerobic conditions. When exposed to 0.15, 0.2, 0.25, 0.5, and 1 mM bromate, S. oneidensis MR-1 reduced bromate by around 100, 75, 64, 48, and 23%, respectively, within 12 h. In vivo evidence from gene deletion mutants and complemented strains of S. oneidensis MR-1 indicates that MtrB, MtrC, CymA, GspD, and DmsA are involved in bromate reduction, but not NapA, FccA, or SYE4. Based on our results as well as previous findings, a proposed molecular mechanism for bromate reduction is presented in this study. Moreover, a genomic survey indicates that 9 of the other 56 reported Shewanella species encode proteins highly homologous to CymA, GspD, and DmsA of S. oneidensis MR-1 by sequence alignment. The results of this study contribute to understanding a pathway for microbial bromate reduction.

Transcriptome analysis provides new insights into the tolerance and aerobic reduction of Shewanella decolorationis Ni1-3 to bromate

As a possible human carcinogen, bromate is easily formed in drinking water and wastewater treatments using advanced oxidation technology. Microbial reduction is a promising method to remove bromate, but little is known about aerobic bromate reduction as well as the molecular mechanism of tolerance and reduction to bromate in bacteria. Herein, bromate reduction by isolate under aerobic conditions was reported for the first time. Shewanella decolorationis Ni1-3, isolated from an activated sludge recently, was identified to reduce bromate to bromide under both aerobic and anaerobic conditions. RNA-Seq together with differential gene expression analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis was performed to identify that bromate triggered the expression of genes for oxidative stress protection (e.g., ohr, msrQ, dsbC, gpo, gorA, and gst), DNA damage repair (e.g., dprA, parA, and recJ), and sulfur metabolism (e.g., cysH, cysK, and cysP). However, the genes for lactate utilization (e.g., lldF and dld), nitrate reduction (e.g., napA and narG), and dissimilatory metal reduction (e.g., mtrC and omcA) were down-regulated in the presence of bromate. The results contribute to revealing the molecular mechanism of resistance and reduction in S. decolorationis Ni1-3 to bromate under aerobic conditions and clarifying the biogeochemical cycle of bromine. KEY POINTS: • Aerobic bromate reduction by pure culture was observed for the first time • Strain Ni1-3 effectively reduced bromate under both aerobic and anaerobic conditions • ROS and SOS response genes were strongly induced in the presence of bromate.

Isolation of Anaerobic Bromate-Reducing Bacteria Using Different Carbon Sources and Transcriptomic Insights From Klebsiella variicola Glu3

Bromate, a possible human carcinogen, can be reduced to innocuous bromide by microorganisms. To characterize bromate reducers, microbes were enriched anaerobically from activated sludge by using bromate as the sole electron acceptor and different carbon sources as the electron donor. Bacteria that showed significant bromate-reducing activity but not coupled to cell growth were isolated. Two whole genomes of the isolates, namely, Raoultella electrica Lac1 and Klebsiella variicola Glu3, were reconstructed by Illumina and Nanopore sequencing. Transcriptomic analysis suggested that neither the respiratory nitrate reductase, the selenate reductase, nor the dimethylsulfoxide reductase was involved in the bromate reduction process, and strain K. variicola Glu3 reduced bromate via a yet undiscovered enzymatic mechanism. The results provide novel phylogenetic insights into bromate-reducing microorganisms and clues in putative genes encoding enzymes related to bromate reduction.

Microbial reduction of bromate: current status and prospects

Bromate is a disinfection byproduct (DBP) that forms during the ozonation of bromide-containing natural water, which may cause health risks to humans. In this review, we provide an overview of the mechanism of bromate formation, microbial communities and bioreactors that are responsible for bromate reduction. Bromate can be formed through two pathways of bromide oxidation by ozone or by ^·OH, and it can be removed by biological approaches. Members belonging to phyla of Spirochaetes, Proteobacteria, Firmicutes, Actinobacteria, Clostridium, Deinococcus-Thermus and Bacteroidetes have been identified as capable of reducing bromate to bromide. Multiple configurations of biofilm bioreactors have been employed to cultivate microbial communities to perform bromate removal. The rapid development of multiomics has and will continue to accelerate the elucidation of the mechanisms involved in bromate and other DBP conversions, as well as the interaction patterns among different bacterial subdivisions in the bioremoval of DBPs.

Genomic Analysis of Rhodococcus sp. Br-6, a Bromate Reducing Bacterium Isolated From Soil in Chiba, Japan

Bromate is a byproduct of the ozone disinfection of drinking water. It is a genotoxic carcinogen and causes renal cell tumors in rats. Physicochemical removal of bromate is very difficult, making microbial reduction of bromate to bromide a promising approach to eliminate bromate from water. Rhodococcus sp. Br-6, isolated from soil, can efficiently reduce bromate by using acetate as an electron donor. We determined the draft genome sequence of Rhodococcus sp. Br-6 for the potential practical application of the bromate-reducing bacterium. Core genome phylogeny suggests that the Br-6 strain is most closely related to R. equi. The Br-6 genome contains genes encoding multiple isoforms of diaphorase, previously found to be involved in Br-6-mediated bromate reduction. The genes identified in the present study could be effective targets for experimental studies of microbial bromate reduction in the future.