(Per)chlorate in Biology on Earth and Beyond

Molecular adaptations specific to extreme halophilic archaea could promote high perchlorate tolerance

Perchlorate is a strong chaotropic agent that causes macromolecule denaturation, DNA damage, and oxidative stress. However, perchlorate deliquescence is thought to promote the formation of liquid salt brines, even at hyper-arid and cold environments, such as the Martian regolith. For that reason, the detection of high levels of perchlorate at different locations on the Martian surface led to hypotheses about the existence of Martian microenvironments compatible with life, especially with those organisms tolerant to hyper-salinity and perchlorate. Extreme halophilic archaea have been proposed as the best candidates to inhabit those environments not only due to their high tolerance to salinity and perchlorate, but also because of their resistance to a wide variety of stress conditions. Since specific perchlorate responses remain largely unknown, in this work, we have analyzed the molecular mechanisms of perchlorate tolerance exhibited by the model extreme halophilic archaeon Haloferax volcanii using a transcriptomic approach. We report that perchlorate produced transcriptional effects opposite to those of salinity, and we propose that the "salt-in" strategy could promote high perchlorate tolerance in extreme halophilic archaea due to the intracellular accumulation of KCl, which may shield the chaotropic activity of perchlorate. This natural adaptation would be enhanced by changes in other stress responses like DNA repair, refolding and turnover of damaged proteins, removal of oxidative species, and tRNA modifications, among others. These results may help to understand how life could survive on Mars, now or in the past, and highlight the importance of extreme halophiles in the development of in situ resource utilization systems.IMPORTANCEPerchlorate is a toxic chlorinated compound that promotes the formation of liquid salt brines, even at hyper-arid and cold environments. For the past two decades, different probes have reported high levels of perchlorate salts at multiple locations on the Martian surface, which could facilitate the presence of potentially habitable environments by specific microorganisms capable of tolerating both hyper-salinity and high perchlorate concentrations. Therefore, the significance of this research was to investigate the molecular mechanisms for perchlorate tolerance using the extreme haloarchaeon Haloferax volcanii as a model organism. This analysis leads to the identification of critical genes and pathways involved in perchlorate tolerance and supports that certain molecular adaptations specific to extreme haloarchaea may be responsible for the high levels of perchlorate tolerance exhibited by these microorganisms, serving as a valuable resource for Mars exploration.

The horizontal gene transfer of perchlorate reduction genomic island in three bacteria from an ecological niche

Three new strains of dissimilatory perchlorate-reducing bacteria (DPRB), QD19-16, QD1-5, and P3-1, were isolated from an active sludge. Phylogenetic trees based on 16S rRNA genes indicated that QD19-16, QD1-5, and P3-1 belonged to Brucella, Acidovorax, and Citrobacter, respectively, expanding the distribution of DPRB in the Proteobacteria. The three strains were gram-negative and facultative anaerobes with rod-shaped cells without flagella, which were 1.0-1.6 μm long and 0.5-0.6 μm wide. The three DPRB strains utilized similar broad spectrum of electron donors and acceptors and demonstrated a similar capability to reduce perchlorate within 6 days. The enzyme activity of perchlorate reductase in QD19-16 toward chlorate was higher than that toward perchlorate. The high sequence similarity of the perchlorate reductase operon and chlorite dismutase genes in the perchlorate reduction genomic islands (PRI) of the three strains implied that they were monophyletic origin from a common ancestral PRI. Two transposase genes (tnp1 and tnp2) were found in the PRIs of strain QD19-16 and QD1-5, but were absent in the strain P3-1 PRI. The presence of fragments of IR sequences in the P3-1 PRI suggested that P3-1 PRI had previously contained these two tnp genes. Therefore, it is plausible to suggest that a common ancestral PRI transferred across the strains Brucella sp. QD19-16, Acidovorax sp. QD1-5, and Citrobacter sp. P3-1 through horizontal gene transfer, facilitated by transposases. These results provided a direct evidence of horizontal gene transfer of PRI that could jump across phylogenetically unrelated bacteria through transposase. KEY POINTS: • Three new DPRB strains can effectively remove high concentration of perchlorate. • The PRIs of three DPRB strains are acquired from a single ancestral PRI. • PRIs are incorporated into different bacteria genome through HGT by transposase.

Metagenomic profiling of halites from the Atacama Desert: an extreme environment with natural perchlorate does not promote high diversity of perchlorate reducing microorganisms

We surveyed the presence of perchlorate-reducing microorganisms in available metagenomic data of halite environments from the Atacama Desert, an extreme environment characterized by high perchlorate concentrations, intense ultraviolet radiation, saline and oxidizing soils, and severe desiccation. While the presence of perchlorate might suggest a broad community of perchlorate reducers or a high abundance of a dominant taxa, our search reveals a scarce presence. In fact, we identified only one halophilic species, Salinibacter sp003022435, carrying the pcrA and pcrC genes, represented in low abundance. Moreover, we also discovered some napA genes and organisms carrying the nitrate reductase nasB gene, which hints at the possibility of cryptic perchlorate reduction occurring in these ecosystems. Our findings contribute with the knowledge of perchlorate reduction metabolism potentially occurring in halites from Atacama Desert and point towards promising future research into the perchlorate-reducing mechanism in Salinibacter, a common halophilic bacterium found in hypersaline ecosystems, whose metabolic potential remains largely unknown.

Iron-Catalyzed C-H Oxygenation Using Perchlorate Enabled by Secondary Sphere Hydrogen Bonds

Perchlorate (ClO4-) is a groundwater pollutant that is challenging to remediate. We report a strategy to use Fe(II) tris(2-pyridylmethyl)amine (TPA) complexes featuring appended aniline hydrogen bonds (H-bonds) to promote ClO4- reduction. These complexes facilitate oxygen atom transfer from ClO4- to PPh3 and C-H oxygenation reactions of organic substrates. Catalytic reactions using 15 mol % afforded excellent yields for oxygenation of anthracene and cyclic alkyl aromatics, and this methodology tolerates aryl halides as well as heterocycles containing either O, S, or N.

Integration of molecular and computational approaches paints a holistic portrait of obscure metabolisms

Microorganisms are essential drivers of earth's geochemical cycles. However, the significance of elemental redox cycling mediated by microorganisms is often underestimated beyond the most well-studied nutrient cycles. Phosphite, (per)chlorate, and iodate are each considered esoteric substrates metabolized by microorganisms. However, recent investigations have indicated that these metabolisms are widespread and ubiquitous, affirming a need to continue studying the underlying microbiology to understand their biogeochemical effects and their interface with each other and our biosphere. This review focuses on combining canonical techniques of culturing microorganisms with modern omic approaches to further our understanding of obscure metabolic pathways and elucidate their importance in global biogeochemical cycles. Using these approaches, marker genes of interest have already been identified for phosphite, (per)chlorate, and iodate using traditional microbial physiology and genetics. Subsequently, their presence was queried to reveal the distribution of metabolic pathways in the environment using publicly available databases. In conjunction with each other, computational and experimental techniques provide a more comprehensive understanding of the location of these microorganisms, their underlying biochemistry and genetics, and how they tie into our planet's geochemical cycles.

Extremophilic microbial metabolism and radioactive waste disposal

Decades of nuclear activities have left a legacy of hazardous radioactive waste, which must be isolated from the biosphere for over 100,000 years. The preferred option for safe waste disposal is a deep subsurface geological disposal facility (GDF). Due to the very long geological timescales required, and the complexity of materials to be disposed of (including a wide range of nutrients and electron donors/acceptors) microbial activity will likely play a pivotal role in the safe operation of these mega-facilities. A GDF environment provides many metabolic challenges to microbes that may inhabit the facility, including high temperature, pressure, radiation, alkalinity, and salinity, depending on the specific disposal concept employed. However, as our understanding of the boundaries of life is continuously challenged and expanded by the discovery of novel extremophiles in Earth's most inhospitable environments, it is becoming clear that microorganisms must be considered in GDF safety cases to ensure accurate predictions of long-term performance. This review explores extremophilic adaptations and how this knowledge can be applied to challenge our current assumptions on microbial activity in GDF environments. We conclude that regardless of concept, a GDF will consist of multiple extremes and it is of high importance to understand the limits of polyextremophiles under realistic environmental conditions.

Perchlorate and chlorate assessment in drinking water in northern Chilean cities

Perchlorate and chlorate are endocrine disruptors considered emerging contaminants (ECs). Both oxyanions are commonly associated with anthropogenic contamination from fertilizers, pesticides, explosives, and disinfection byproducts. However, the soils of the Atacama Desert are the most extensive natural reservoirs of perchlorate in the world, compromising drinking water sources in northern Chile. Field campaigns were carried (2014-2018) to assess the presence of these ECs in the water supply networks of twelve Chilean cities. Additionally, the occurrence of perchlorate, chlorate and other anions typically observed in drinking water matrices of the Atacama Desert (i.e., nitrate, chloride, sulfate) was evaluated using a Spearman correlation analysis to determine predictors for perchlorate and chlorate. High concentrations of perchlorate (up to 114.48 μg L-1) and chlorate (up to 9650 μg L-1) were found in three northern cities. Spatial heterogeneities were observed in the physicochemical properties and anion concentrations of the water supply network. Spearman correlation analysis indicated that nitrate, chloride, and sulfate were not useful predictors for the presence of perchlorate and chlorate in drinking water in Chile. Hence, this study highlights the need to establish systematic monitoring, regulation, and treatment for these EC of drinking water sources in northern Chilean cities for public health protection.

Synergistic effect of electrotrophic perchlorate reducing microorganisms and chemically modified electrodes for enhancing bioelectrochemical perchlorate removal

Perchlorate has been described as an emerging pollutant that compromises water sources and human health. In this study, a new electrotrophic perchlorate reducing microorganism (EPRM) isolated from the Atacama Desert, Dechloromonas sp. CS-1, was evaluated for perchlorate removal in water in a bioelectrochemical reactor (BER) with a chemically modified electrode. BERs were operated for 17 days under batch mode conditions with an applied potential of -500 mV vs. Ag/AgCl. Surface analysis (i.e., SEM, XPS, FT-IR, RAMAN spectroscopy) on the modified electrode demonstrated heterogeneous transformation of the carbon fibers with the incorporation of nitrogen functional groups and the oxidation of the carbonaceous material. The BERs with the modified electrode and the presence of the EAM reached high cathodic efficiency (90.79 ± 9.157%) and removal rate (0.34 ± 0.007 mol m-3-day) compared with both control conditions. The observed catalytic enhancement of CS-1 was confirmed by a reduction in the charge transfer resistance obtained by electrochemical impedance spectroscopy (EIS). Finally, an electrochemical kinetic study revealed an eight-electron perchlorate bioreduction reaction at -638.33 ± 24.132 mV vs. Ag/AgCl. Therefore, our results show the synergistic effect of EPRM and chemically modified electrodes on perchlorate removal in a BER.

Impacts of co-contaminants and dilution on perchlorate biodegradation using various carbon sources

This research investigates the biodegradation of perchlorate in the presence of the co-contaminants nitrate and chlorate using soluble and slow-release carbon sources. In addition, the impact of bio-augmentation and dilution, which results in lower total dissolved salts (TDS) and contaminant levels, is examined. Laboratory microcosms were conducted using actual groundwater and soils from a contaminated aquifer. The results revealed that both soluble and slow-release carbon sources support biodegradation of contaminants in the sequence nitrate > chlorate > perchlorate. Degradation rates, including and excluding lag times, revealed that the overall impact of the presence of co-contaminants depends on degradation kinetics and the relative concentrations of the contaminants. When the lag time caused by the presence of the co-contaminants is considered, the degradation rates for chlorate and perchlorate were two to three times slower. The results also show that dilution causes lower initial contaminant concentrations, and consequently, slower degradation rates, which is not desirable. On the other hand, the dilution resulting from the injection of amendments to support remediation promotes desirably lower salinity levels. However, the salinity associated with the presence of sulfate does not inhibit biodegradation. The naturally occurring bacteria were able to support the degradation of all contaminants. Bio-augmentation was effective only in diluted microcosms. Proteobacteria and Firmicutes were the dominant phyla identified in the microcosms.

Hydrogen and dark oxygen drive microbial productivity in diverse groundwater ecosystems

Around 50% of humankind relies on groundwater as a source of drinking water. Here we investigate the age, geochemistry, and microbiology of 138 groundwater samples from 95 monitoring wells (<250 m depth) located in 14 aquifers in Canada. The geochemistry and microbiology show consistent trends suggesting large-scale aerobic and anaerobic hydrogen, methane, nitrogen, and sulfur cycling carried out by diverse microbial communities. Older groundwaters, especially in aquifers with organic carbon-rich strata, contain on average more cells (up to 1.4 × 10⁷ mL^-1) than younger groundwaters, challenging current estimates of subsurface cell abundances. We observe substantial concentrations of dissolved oxygen (0.52 ± 0.12 mg L^-1 [mean ± SE]; n = 57) in older groundwaters that seem to support aerobic metabolisms in subsurface ecosystems at an unprecedented scale. Metagenomics, oxygen isotope analyses and mixing models indicate that dark oxygen is produced in situ via microbial dismutation. We show that ancient groundwaters sustain productive communities and highlight an overlooked oxygen source in present and past subsurface ecosystems of Earth.

Engineering of a Bacterial Biosensor for the Detection of Chlorate in Food

Chlorate can contaminate food due to the use of chlorinated water for processing or equipment disinfection. Chronic exposure to chlorate in food and drinking water is a potential health concern. The current methods for detecting chlorate in liquids and foods are expensive and not easily accessible to all laboratories, highlighting an urgent need for a simple and cost-effective method. The discovery of the adaptation mechanism of Escherichia coli to chlorate stress, which involves the production of the periplasmic Methionine Sulfoxide Reductase (MsrP), prompted us to use an E. coli strain with an msrP-lacZ fusion as a biosensor for detecting chlorate. Our study aimed to optimize the bacterial biosensor's sensitivity and efficiency to detect chlorate in various food samples using synthetic biology and adapted growth conditions. Our results demonstrate successful biosensor enhancement and provide proof of concept for detecting chlorate in food samples.

Electrotrophic perchlorate reduction by a psychrotolerant acidophile isolated from an acid rock drainage in Antarctica

A new extremophilic isolate (USS-CCA7) was obtained from an acidic environment (pH ∼ 3.2) in Antarctica phylogenetically related to Acidithiobacillus ferrivorans; its electrotrophic capacities were evaluated in a three-electrode electrochemical cell. Cyclic voltammetry showed cathodic peaks of -428 mV, -536 mV, and -634 mV (vs. Ag/AgCl; pH = 1.7; 3 M KCl) for nitrate, oxygen, and perchlorate, respectively. The catalytic role of this microorganism was also observed by a decrease in the charge transfer resistance registered via electrochemical impedance spectroscopy. Five-day chronoamperometry of culture at pH = 1.7, USS-CCA7 showed a perchlorate removal rate of 19.106 ± 1.689 mgL^-1 day^-1 and a cathodic efficiency of 112 ± 5.2  %. Growth on electrodes was observed by epifluorescence and scanning electron microscopy. Interestingly, the results showed that toward higher pH, the cathodic peak of perchlorate is reduced in the voltammetric profiles. This study highlights the use of this psychrotolerant acidophile for the bioremediation of harsh perchlorate-pressured terrestrial under acidic conditions.

Chlorine redox chemistry is widespread in microbiology

Chlorine is abundant in cells and biomolecules, yet the biology of chlorine oxidation and reduction is poorly understood. Some bacteria encode the enzyme chlorite dismutase (Cld), which detoxifies chlorite (ClO2-) by converting it to chloride (Cl-) and molecular oxygen (O2). Cld is highly specific for chlorite and aside from low hydrogen peroxide activity has no known alternative substrate. Here, we reasoned that because chlorite is an intermediate oxidation state of chlorine, Cld can be used as a biomarker for oxidized chlorine species. Cld was abundant in metagenomes from various terrestrial habitats. About 5% of bacterial and archaeal genera contain a microorganism encoding Cld in its genome, and within some genera Cld is highly conserved. Cld has been subjected to extensive horizontal gene transfer. Genes found to have a genetic association with Cld include known genes for responding to reactive chlorine species and uncharacterized genes for transporters, regulatory elements, and putative oxidoreductases that present targets for future research. Cld was repeatedly co-located in genomes with genes for enzymes that can inadvertently reduce perchlorate (ClO4-) or chlorate (ClO3-), indicating that in situ (per)chlorate reduction does not only occur through specialized anaerobic respiratory metabolisms. The presence of Cld in genomes of obligate aerobes without such enzymes suggested that chlorite, like hypochlorous acid (HOCl), might be formed by oxidative processes within natural habitats. In summary, the comparative genomics of Cld has provided an atlas for a deeper understanding of chlorine oxidation and reduction reactions that are an underrecognized feature of biology.

Perchlorate reduction kinetics and genome-resolved metagenomics identify metabolic interactions in acclimated saline lake perchlorate-reducing consortia

Perchlorate is a widely detected environmental contaminant in surface and underground water, that seriously impacts human health by inhibiting the uptake of thyroidal radioiodine. Perchlorate reduction due to saline lake microorganisms is not as well understood as that in marine environments. In this study, we enriched a perchlorate-reducing microbial consortium collected from saline lake sediments and found that the perchlorate reduction kinetics of the enriched consortium fit the Michaelis-Menten kinetics well, with a maximum specific substrate reduction rate (q_max) of 0.596 ± 0.001 mg ClO₄^-/mg DW/h and half-saturation constant (K_s) of 16.549 ± 0.488 mg ClO₄^-/L. Furthermore, we used improved metagenome binning to reconstruct high-quality metagenome-assembled genomes from the metagenomes of the microbial consortia, including the perchlorate-reducing bacteria (PRB) Dechloromonas agitata and Wolinella succinogenes, with the genome of W. succinogenes harboring complete functional genes for perchlorate reduction being the first recovered. Given that the electrons were directly transferred to the electronic carrier cytochrome c-553 from the quinone pool, the electron transfer pathway of W. succinogenes was shorter and more efficient than the canonical pattern. This finding provides a theoretical basis for microbial remediation of sites contaminated by high concentrations of perchlorate. Metagenomic binning and metatranscriptomic analyses revealed the gene transcription variation of perchlorate reductase pcr and chlorite dismutase cld by PRB and the synergistic metabolic mechanism.

Mechanisms of chlorate toxicity and resistance in Pseudomonas aeruginosa

Pseudomonas aeruginosa is an opportunistic bacterial pathogen that often encounters hypoxic/anoxic environments within the host, which increases its tolerance to many conventional antibiotics. Toward identifying novel treatments, we explored the therapeutic potential of chlorate, a pro-drug that kills hypoxic/anoxic, antibiotic-tolerant P. aeruginosa populations. While chlorate itself is relatively nontoxic, it is enzymatically reduced to the toxic oxidizing agent, chlorite, by hypoxically induced nitrate reductase. To better assess chlorate's therapeutic potential, we investigated mechanisms of chlorate toxicity and resistance in P. aeruginosa. We used transposon mutagenesis to identify genes that alter P. aeruginosa fitness during chlorate treatment, finding that methionine sulfoxide reductases (Msr), which repair oxidized methionine residues, support survival during chlorate stress. Chlorate treatment leads to proteome-wide methionine oxidation, which is exacerbated in a ∆msrA∆msrB strain. In response to chlorate, P. aeruginosa upregulates proteins involved in a wide range of functions, including metabolism, DNA replication/repair, protein repair, transcription, and translation, and these newly synthesized proteins are particularly vulnerable to methionine oxidation. The addition of exogenous methionine partially rescues P. aeruginosa survival during chlorate treatment, suggesting that widespread methionine oxidation contributes to death. Finally, we found that mutations that decrease nitrate reductase activity are a common mechanism of chlorate resistance.

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.

Genome-Based Taxonomy of the Genus Stutzerimonas and Proposal of S. frequens sp. nov. and S. degradans sp. nov. and Emended Descriptions of S. perfectomarina and S. chloritidismutans

Stutzerimonas is a recently proposed genus within the Pseudomonadaceae comprising strains in the formerly phylogenetic group of Pseudomonas stutzeri. At least sixteen named species have to be included in the genus, together with 22 genomovars of Stutzerimonas stutzeri. To clarify the taxonomy of Stutzerimonas, a core-genome phylogeny of 200 strains in the genus was inferred and monophyletic strains with average nucleotide identities (ANIb) with values equal to or higher than 95 were grouped in the same phylogenomic species. A total of 45 phylogenomic species within the genus Stutzerimonas were detected in the present study. Sixteen phylogenomic species correspond to already named species, although three of them are not yet validated and two are proposed in the present study. A synonymy was detected between P. kunmingensis and S. chloritidismutans, both members of phylogenomic species 3, with a prevalence of the S. chloritidismutans name. The correspondence of the phylogenomic species to the genome taxonomy database classification (GTDB taxonomy) is discussed. Combining phylogenomic and phenotypic data, two novel species are described (Stutzerimonas frequens and Stutzerimonas degradans) and two species descriptions are emended (Stutzerimonas perfectomarina and Stutzerimonas chloritidismutans).

Chlorate addition enhances perchlorate reduction in denitrifying membrane-biofilm reactors

Perchlorate is a widespread drinking water contaminant with regulatory standards ranging from 2 to 18 μg/L. The hydrogen-based membrane-biofilm reactor (MBfR) can effectively reduce perchlorate, but it is challenging to achieve low-µg/L levels. We explored chlorate addition to increase the abundance of perchlorate-reducing bacteria (PRB) and improve removals. MBfR reactors were operated with and without chlorate addition. Results show that chlorate doubled the abundance of putative PRB (e.g., Rhodocyclales) and improved perchlorate reduction to 23 ± 17 µg/L, compared to 53 ± 37 µg/L in the control. Sulfate reduction was substantially inhibited during chlorate addition, but quickly recovered once suspended. Our results suggest that chlorate addition can enhance perchlorate reduction by providing a selective pressure for PRB. It also decreases net sulfate reduction. KEY POINTS: • Chlorate increased the abundance of perchlorate-reducing bacteria • Chlorate addition improved perchlorate removal • Chlorate appeared to suppress sulfate reduction.

Isolation of a Dissimilatory Iodate-Reducing Aromatoleum sp. From a Freshwater Creek in the San Francisco Bay Area

Recent reports of dissimilatory iodate-reducing microorganisms (DIRM) have arisen from studies of bacteria in marine environments. These studies described the physiology and distribution of DIRM while also demonstrating their presence in iodine-rich marine environments. We posited that despite lower iodine concentrations, terrestrial and freshwater ecosystems should also harbor DIRM. We established numerous enrichments from coastal and freshwater environments that actively remove amended iodate. We describe the physiology and genome of a new DIRM isolate, Aromatoleum toluclasticum sp. TC-10, emerging from a freshwater creek microcosm. Like other DIRM, A. toluclasticum sp. TC-10 couples acetate oxidation to iodate reduction with a concomitant increase in the OD₆₀₀. Our results indicate that A. toluclasticum sp. TC-10 performs dissimilatory iodate reduction (DIR) using the recently described iodate reductase (Idr). We provide further evidence of horizontal gene transfer of the idr genes by demonstrating the lack of Idr in the closely related (99.93% 16S rDNA sequence identity) A. toluclasticum sp. MF63 and describe the heterogeneity of the accessory proteins associated with the iodate reduction island (IRI). These observations provide additional evidence that DIR is a horizontally acquired metabolism with broad environmental distribution beyond exclusively marine environments.

Genetic and phylogenetic analysis of dissimilatory iodate-reducing bacteria identifies potential niches across the world's oceans

Iodine is oxidized and reduced as part of a biogeochemical cycle that is especially pronounced in the oceans, where the element naturally concentrates. The use of oxidized iodine in the form of iodate (IO3-) as an electron acceptor by microorganisms is poorly understood. Here, we outline genetic, physiological, and ecological models for dissimilatory IO3- reduction to iodide (I-) by a novel estuarine bacterium, Denitromonas sp. IR-12. Our results show that dissimilatory iodate reduction (DIR) by strain IR-12 is molybdenum-dependent and requires an IO3- reductase (idrA) and likely other genes in a mobile cluster with a conserved association across known and predicted DIR microorganisms (DIRM). Based on genetic and physiological data, we propose a model where three molecules of IO3- are likely reduced to three molecules of hypoiodous acid (HIO), which rapidly disproportionate into one molecule of IO3- and two molecules of iodide (I-), in a respiratory pathway that provides an energy yield equivalent to that of nitrate or perchlorate respiration. Consistent with the ecological niche expected of such a metabolism, idrA is enriched in the metagenome sequence databases of marine sites with a specific biogeochemical signature (high concentrations of nitrate and phosphate) and diminished oxygen. Taken together, these data suggest that DIRM help explain the disequilibrium of the IO3-:I- concentration ratio above oxygen-minimum zones and support a widespread iodine redox cycle mediated by microbiology.

Mining for Perchlorate Resistance Genes in Microorganisms From Sediments of a Hypersaline Pond in Atacama Desert, Chile

Perchlorate is an oxidative pollutant toxic to most of terrestrial life by promoting denaturation of macromolecules, oxidative stress, and DNA damage. However, several microorganisms, especially hyperhalophiles, are able to tolerate high levels of this compound. Furthermore, relatively high quantities of perchlorate salts were detected on the Martian surface, and due to its strong hygroscopicity and its ability to substantially decrease the freezing point of water, perchlorate is thought to increase the availability of liquid brine water in hyper-arid and cold environments, such as the Martian regolith. Therefore, perchlorate has been proposed as a compound worth studying to better understanding the habitability of the Martian surface. In the present work, to study the molecular mechanisms of perchlorate resistance, a functional metagenomic approach was used, and for that, a small-insert library was constructed with DNA isolated from microorganisms exposed to perchlorate in sediments of a hypersaline pond in the Atacama Desert, Chile (Salar de Maricunga), one of the regions with the highest levels of perchlorate on Earth. The metagenomic library was hosted in Escherichia coli DH10B strain and exposed to sodium perchlorate. This technique allowed the identification of nine perchlorate-resistant clones and their environmental DNA fragments were sequenced. A total of seventeen ORFs were predicted, individually cloned, and nine of them increased perchlorate resistance when expressed in E. coli DH10B cells. These genes encoded hypothetical conserved proteins of unknown functions and proteins similar to other not previously reported to be involved in perchlorate resistance that were related to different cellular processes such as RNA processing, tRNA modification, DNA protection and repair, metabolism, and protein degradation. Furthermore, these genes also conferred resistance to UV-radiation, 4-nitroquinoline-N-oxide (4-NQO) and/or hydrogen peroxide (H2O2), other stress conditions that induce oxidative stress, and damage in proteins and nucleic acids. Therefore, the novel genes identified will help us to better understand the molecular strategies of microorganisms to survive in the presence of perchlorate and may be used in Mars exploration for creating perchlorate-resistance strains interesting for developing Bioregenerative Life Support Systems (BLSS) based on in situ resource utilization (ISRU).

A Bioinspired Molybdenum Catalyst for Aqueous Perchlorate Reduction

Perchlorate (ClO₄^-) is a pervasive, harmful, and inert anion on both Earth and Mars. Current technologies for ClO₄^- reduction entail either harsh conditions or multicomponent enzymatic processes. Herein, we report a heterogeneous (L)Mo-Pd/C catalyst directly prepared from Na₂MoO₄, a bidentate nitrogen ligand (L), and Pd/C to reduce aqueous ClO₄^- into Cl^- with 1 atm of H₂ at room temperature. A suite of instrument characterizations and probing reactions suggest that the Mo^VI precursor and L at the optimal 1:1 ratio are transformed in situ into oligomeric Mo^IV active sites at the carbon-water interface. For each Mo site, the initial turnover frequency (TOF₀) for oxygen atom transfer from ClO_x^- substrates reached 165 h^-1. The turnover number (TON) reached 3840 after a single batch reduction of 100 mM ClO₄^-. This study provides a water-compatible, efficient, and robust catalyst to degrade and utilize ClO₄^- for water purification and space exploration.

Inhibition of perchlorate biodegradation by ferric and ferrous iron

Previous observations from in-situ biological treatments in the subsurface of a perchlorate-contaminated site revealed multiple reduction processes occurring parallel to perchlorate degradation. Iron reduction was accelerated and correlated with a decline in the efficiency of the in-situ perchlorate reduction. In the current study, we examined the influence of iron forms on perchlorate reduction. A series of kinetic laboratory experiments were conducted, using an indigenous mixed perchlorate-reducing culture, enriched from the polluted soil that was undergoing bioremediation. The results show that ferrous iron was a non-competitive inhibitor with a 41% decrease in µ_max for perchlorate reduction. Moreover, chlorate was accumulated in all samples treated with ferrous iron, indicating a disruption to the chlorate reduction step. Ferric iron, however, had less impact on perchlorate degradation with non-competitive inhibition reaching a 23% decrease in µ_max. Scanning electron microscopy (SEM) revealed that the presence of ferrous iron in the perchlorate degradation enrichment culture initiated cell encrustation. We propose that during perchlorate reduction and the emission of oxygen from chlorite dismutation, the chemical oxidation of ferrous iron occurred near the bacteria's surface where the enzyme is located, forming an oxidized iron crust layer that can directly affect the perchlorate reduction enzymatic system.

Microbial niche differentiation explains nitrite oxidation in marine oxygen minimum zones

Nitrite is a pivotal component of the marine nitrogen cycle. The fate of nitrite determines the loss or retention of fixed nitrogen, an essential nutrient for all organisms. Loss occurs via anaerobic nitrite reduction to gases during denitrification and anammox, while retention occurs via nitrite oxidation to nitrate. Nitrite oxidation is usually represented in biogeochemical models by one kinetic parameter and one oxygen threshold, below which nitrite oxidation is set to zero. Here we find that the responses of nitrite oxidation to nitrite and oxygen concentrations vary along a redox gradient in a Pacific Ocean oxygen minimum zone, indicating niche differentiation of nitrite-oxidizing assemblages. Notably, we observe the full inhibition of nitrite oxidation by oxygen addition and nitrite oxidation coupled with nitrogen loss in the absence of oxygen consumption in samples collected from anoxic waters. Nitrite-oxidizing bacteria, including novel clades with high relative abundance in anoxic depths, were also detected in the same samples. Mechanisms corresponding to niche differentiation of nitrite-oxidizing bacteria across the redox gradient are considered. Implementing these mechanisms in biogeochemical models has a significant effect on the estimated fixed nitrogen budget.

A Multiplex Immunosensor for Detecting Perchlorate-Reducing Bacteria for Environmental Monitoring and Planetary Exploration

Perchlorate anions are produced by chemical industries and are important contaminants in certain natural ecosystems. Perchlorate also occurs in some natural and uncontaminated environments such as the Atacama Desert, the high Arctic or the Antarctic Dry Valleys, and is especially abundant on the surface of Mars. As some bacterial strains are capable of using perchlorate as an electron acceptor under anaerobic conditions, their detection is relevant for environmental monitoring on Earth as well as for the search for life on Mars. We have developed an antibody microarray with 20 polyclonal antibodies to detect perchlorate-reducing bacteria (PRB) strains and two crucial and highly conserved enzymes involved in perchlorate respiration: perchlorate reductase and chlorite dismutase. We determined the cross-reactivity, the working concentration, and the limit of detection of each antibody individually and in a multiplex format by Fluorescent Sandwich Microarray Immunoassay. Although most of them exhibited relatively high sensitivity and specificity, we applied a deconvolution method based on graph theory to discriminate between specific signals and cross-reactions from related microorganisms. We validated the system by analyzing multiple bacterial isolates, crude extracts from contaminated reactors and salt-rich natural samples from the high Arctic. The PRB detecting chip (PRBCHIP) allowed us to detect and classify environmental isolates as well as to detect similar strains by using crude extracts obtained from 0.5 g even from soils with low organic-matter levels (<10³ cells/g of soil). Our results demonstrated that PRBCHIP is a valuable tool for sensitive and reliable detection of perchlorate-reducing bacteria for research purposes, environmental monitoring and planetary exploration.

Bioelectrochemical chlorate reduction by Dechloromonas agitata CKB

Chlorate has been described as an emerging pollutant that compromises water sources. In this study, bioelectrochemical reactors (BERs) using Dechloromonas agitata CKB, were evaluated as a sustainable alternative for chlorate removal. BERs were operated under flow-recirculation and batch modes with an applied cell-voltage of 0.44 V over a resistance of 1 kΩ. Results show chlorate removal up to 607.288 mg/L. After 115 days, scanning electron microscopy showed biofilm development over the electrodes, and electrochemical impedance spectroscopy confirmed the biocatalytic effect of CKB. The theoretical chlorate bioreduction potential (ε° = 0.792 V) was proven, and a kinetic study indicated that 6 electrons were involved in the reduction mechanism. Finally, a hypothetical bioelectrochemical mechanism for chlorate reduction in a BER was proposed. This research expands upon current knowledge of novel electrochemically active microorganisms and widens the scope of BER applications for chlorate removal.

An uncharacterized clade in the DMSO reductase family of molybdenum oxidoreductases is a new type of chlorate reductase

The dimethylsulfoxide (DMSO) reductase family of enzymes has many subfamilies catalysing unique biogeochemical reactions. It also has many uncharacterized subfamilies. Comparative genomics predicted one such subfamily to participate in a key step of the chlorine cycle because of a conserved genetic association with chlorite dismutase, implying they produce chlorite through chlorate or perchlorate reduction. We determined the activity of the uncharacterized enzyme by comparing strains in the phototrophic genus Rhodoplanes that encode either a typical perchlorate reductase or the uncharacterized enzyme. Rpl. piscinae and Rpl. elegans, which encode perchlorate reductase, grew by using perchlorate as an electron acceptor. In contrast, Rpl. roseus, which encodes the uncharacterized enzyme, grew by chlorate reduction but not by perchlorate reduction. This is the first report of perchlorate and chlorate being used as respiratory electron acceptors by phototrophs. When both chlorate and perchlorate were present, Rpl. roseus consumed only chlorate. Highly concentrated Rpl. roseus cells showed some perchlorate consumption, but chlorate consumption occurred at a 10-fold higher rate. Together, these genomic and physiological data define a new group of chlorate reductases. Some organisms encode both this chlorate reductase and a perchlorate reductase, raising new questions about the physiology and evolution of chlorine oxyanion respiration.

Identification of a parasitic symbiosis between respiratory metabolisms in the biogeochemical chlorine cycle

A key step in the chlorine cycle is the reduction of perchlorate (ClO4-) and chlorate (ClO3-) to chloride by microbial respiratory pathways. Perchlorate-reducing bacteria and chlorate-reducing bacteria differ in that the latter cannot use perchlorate, the most oxidized chlorine compound. However, a recent study identified a bacterium with the chlorate reduction pathway dominating a community provided only perchlorate. Here we confirm a metabolic interaction between perchlorate- and chlorate-reducing bacteria and define its mechanism. Perchlorate-reducing bacteria supported the growth of chlorate-reducing bacteria to up to 90% of total cells in communities and co-cultures. Chlorate-reducing bacteria required the gene for chlorate reductase to grow in co-culture with perchlorate-reducing bacteria, demonstrating that chlorate is responsible for the interaction, not the subsequent intermediates chlorite and oxygen. Modeling of the interaction suggested that cells specialized for chlorate reduction have a competitive advantage for consuming chlorate produced from perchlorate, especially at high concentrations of perchlorate, because perchlorate and chlorate compete for a single enzyme in perchlorate-reducing cells. We conclude that perchlorate-reducing bacteria inadvertently support large populations of chlorate-reducing bacteria in a parasitic relationship through the release of the intermediate chlorate. An implication of these findings is that undetected chlorate-reducing bacteria have likely negatively impacted efforts to bioremediate perchlorate pollution for decades.

Uncultured Nitrospina-like species are major nitrite oxidizing bacteria in oxygen minimum zones

Oxygen minimum zones (OMZs) are marine regions where O2 is undetectable at intermediate depths. Within OMZs, the oxygen-depleted zone (ODZ) induces anaerobic microbial processes that lead to fixed nitrogen loss via denitrification and anammox. Surprisingly, nitrite oxidation is also detected in ODZs, although all known marine nitrite oxidizers (mainly Nitrospina) are aerobes. We used metagenomic binning to construct metagenome-assembled genomes (MAGs) of nitrite oxidizers from OMZs. These MAGs represent two novel Nitrospina-like species, both of which differed from all known Nitrospina species, including cultured species and published MAGs. Relative abundances of different Nitrospina genotypes in OMZ and non-OMZ seawaters were estimated by mapping metagenomic reads to newly constructed MAGs and published high-quality genomes of members from the Nitrospinae phylum. The two novel species were present in all major OMZs and were more abundant inside ODZs, which is consistent with the detection of higher nitrite oxidation rates in ODZs than in oxic seawaters and suggests novel adaptations to anoxic environments. The detection of a large number of unclassified nitrite oxidoreductase genes in the dataset implies that the phylogenetic diversity of nitrite oxidizers is greater than previously thought.

DMSO Reductase Family: Phylogenetics and Applications of Extremophiles

Dimethyl sulfoxide reductases (DMSO) are molybdoenzymes widespread in all domains of life. They catalyse not only redox reactions, but also hydroxylation/hydration and oxygen transfer processes. Although literature on DMSO is abundant, the biological significance of these enzymes in anaerobic respiration and the molecular mechanisms beyond the expression of genes coding for them are still scarce. In this review, a deep revision of the literature reported on DMSO as well as the use of bioinformatics tools and free software has been developed in order to highlight the relevance of DMSO reductases on anaerobic processes connected to different biogeochemical cycles. Special emphasis has been addressed to DMSO from extremophilic organisms and their role in nitrogen cycle. Besides, an updated overview of phylogeny of DMSOs as well as potential applications of some DMSO reductases on bioremediation approaches are also described.

Combined in-situ bioremediation treatment for perchlorate pollution in the vadose zone and groundwater

Perchlorate is considered a rapidly spreading environmental pollutant. In Israel, it has been found at high concentrations in the vadose zone (up to 30,000 mg/L) and groundwater (up to 800 mg/L) underlying former industrial waste ponds. A perchlorate-reduction method that utilizes the high degradation potential of shallow soil and the high mobility of perchlorate across the deep unsaturated zone has been proposed. The combined treatment method includes recurrent pumping and application of polluted groundwater amended with an electron donor to the shallow soil layers. As a result, perchlorate is biodegraded in the upper soil, and the treated water drains through the unsaturated zone, displacing the pollutant toward the water table, where it is immediately pumped back to the surface for further treatment through a cyclic process. In the current study, the combined treatment approach was tested in a full-scale unsaturated zone (40 m), long-term (1 year) field experiment. Results showed a daily reduction in perchlorate concentration from 800 mg/L to practically zero. A total of ˜330 kg of perchlorate was reduced during the experiment. Nevertheless, competitive reduction (iron and sulfate) and soil acidification were found to be limiting factors. The study demonstrates a potentially efficient way to overcome these limitations by optimizing electron donor concentration.

Evidence for Biotic Perchlorate Reduction in Naturally Perchlorate-Rich Sediments of Pilot Valley Basin, Utah

The presence of perchlorate on Mars suggests a possible energy source for sustaining microbial life. Perchlorate-reducing microbes have been isolated from perchlorate-contaminated soils and sediments on the Earth, but to date, never from an environment that is naturally enriched in perchlorate. The arid Pilot Valley paleolake basin in Utah is a Mars analog environment whose sediments are naturally enriched with up to ∼6.5 μg kg^-1 perchlorate oxyanions. Here, we present results of field and laboratory studies indicating that perchlorate-reducing microorganisms co-occur with this potential electron acceptor. Biogeochemical data suggest ongoing perchlorate reduction; phylogenetic data indicate the presence of diverse microbial communities; and laboratory enrichments using Pilot Valley sediments show that resident microbes can reduce perchlorate. This is the first article of the co-existence of perchlorate-reducing microbes in an environment where perchlorate occurs naturally, arguing for Pilot Valley's utility as an analog for studying biogeochemical processes that may have occurred, and may yet still be occurring, in ancient martian lacustrine sediments.

Rapid of cultivation dissimilatory perchlorate reducing granular sludge and characterization of the granulation process

To remove high-strength perchlorate, dissimilatory perchlorate reducing granular sludge (DPR-GS) was first cultivated. Three identical UASB reactors were set up under different seed sludge and up-flow velocities (R_AS: active sludge (AS) and constant up-flow velocities; R_DGS: denitrifying granular sludge (DGS) and constant up-flow velocities; R_DGS-f: DGS and fluctuating up-flow velocities). The AS in the R_AS was completely granulated by day 117, while the DGS in the R_DGS and R_DGS-f were both shortened the granulation time to 99 days. In addition, the fluctuating up-flow velocity can better ensure rapid cultivation of DPR-GS. Removal of ClO₄^- loading rate with 7.20 kg/(m³·d) occurred in all three reactors. The results of extracellular polymeric substances (EPS) composition analysis indicated the polysaccharose (PS) promoted the formation of bio-aggregates, while the protein (PN) benefited the granulation of sludge. The analyses of the microbial communities indicated that Sulfurospirillum and Acinetobacter were the dominant dissimilatory perchlorate reducing bacteria.

Microbial Synthesis and Transformation of Inorganic and Organic Chlorine Compounds

Organic and inorganic chlorine compounds are formed by a broad range of natural geochemical, photochemical and biological processes. In addition, chlorine compounds are produced in large quantities for industrial, agricultural and pharmaceutical purposes, which has led to widespread environmental pollution. Abiotic transformations and microbial metabolism of inorganic and organic chlorine compounds combined with human activities constitute the chlorine cycle on Earth. Naturally occurring organochlorines compounds are synthesized and transformed by diverse groups of (micro)organisms in the presence or absence of oxygen. In turn, anthropogenic chlorine contaminants may be degraded under natural or stimulated conditions. Here, we review phylogeny, biochemistry and ecology of microorganisms mediating chlorination and dechlorination processes. In addition, the co-occurrence and potential interdependency of catabolic and anabolic transformations of natural and synthetic chlorine compounds are discussed for selected microorganisms and particular ecosystems.

Mitigating Sulfidogenesis With Simultaneous Perchlorate and Nitrate Treatments

Sulfide biogenesis (souring) in oil reservoirs is an extensive and costly problem. Nitrate is currently used as a souring inhibitor but often requires high concentrations and yields inconsistent results. Recently, perchlorate has displayed promise as a more potent inhibitor in lab scale studies. However, combining the two treatments to determine synergy and effectiveness in a dynamic system has never been tested. Nitrate inhibits perchlorate consumption by perchlorate reducing bacteria, suggesting that the combined treatment may allow deeper penetration of the perchlorate into the reservoir matrix. Furthermore, the metabolic intermediates of perchlorate and nitrate reduction (nitrite and chlorite, respectively) are synergistic with the primary electron acceptors for inhibition of sulfate reduction. To assess the possible synergies between nitrate and perchlorate treatments, triplicate glass columns packed with pre-soured marine sediment were flushed with media containing sulfate and an inhibitor treatment [(i) perchlorate; (ii) nitrate; (iii) perchlorate and nitrate; or (iv) none]. Internal geochemistry and microbial community changes were monitored along the length of the columns during six phases of increasing treatment concentrations. In a final phase all treatments were removed. Sulfide production decreased in all treated columns in conjunction with increased inhibitor concentrations relative to the untreated control. Interestingly, the potency of the "mixed" treatment was additive relative to the individual treatments suggesting no interaction. Microbial community analyses indicated community shifts and clustering by treatment. The mixed treatment column community's trajectory closely resembled that of the community found in the perchlorate only treatment, suggesting that perchlorate was the dominant control on the "mixed" community structure. In contrast, the nitrate and untreated column communities had unique trajectories. This study indicates that concurrent nitrate and perchlorate treatment is not more effective than perchlorate treatment alone but is more effective than nitrate treatment. As such, treatment decisions may be based on economic factors.

Functional Redundancy in Perchlorate and Nitrate Electron Transport Chains and Rewiring Respiratory Pathways to Alter Terminal Electron Acceptor Preference

Most dissimilatory perchlorate reducing bacteria (DPRB) are also capable of respiratory nitrate reduction, and preferentially utilize nitrate over perchlorate as a terminal electron acceptor. The similar domain architectures and phylogenetic relatedness of the nitrate and perchlorate respiratory complexes suggests a common evolutionary history and a potential for functionally redundant electron carriers. In this study, we identify key genetic redundancies in the electron transfer pathways from the quinone pool(s) to the terminal nitrate and perchlorate reductases in Azospira suillum PS (hereafter referred to as PS). We show that the putative quinol dehydrogenases, (PcrQ and NapC) and the soluble cytochrome electron carriers (PcrO and NapO) are functionally redundant under anaerobic growth conditions. We demonstrate that, when grown diauxically with both nitrate and perchlorate, the endogenous expression of NapC and NapO during the nitrate reduction phase was sufficient to completely erase any growth defect in the perchlorate reduction phase caused by deletion of pcrQ and/or pcrO. We leveraged our understanding of these genetic redundancies to make PS mutants with altered electron acceptor preferences. Deletion of the periplasmic nitrate reductase catalytic subunit, napA, led to preferential utilization of perchlorate even in the presence of equimolar nitrate, and deletion of the electron carrier proteins napQ and napO, resulted in concurrent reduction of nitrate and perchlorate. Our results demonstrate that nitrate and perchlorate respiratory pathways in PS share key functionally redundant electron transfer proteins and that mutagenesis of these proteins can be utilized as a strategy to alter the preferential usage of nitrate over perchlorate.

Genome-resolved metagenomics identifies genetic mobility, metabolic interactions, and unexpected diversity in perchlorate-reducing communities

Dissimilatory perchlorate reduction is an anaerobic respiratory pathway that in communities might be influenced by metabolic interactions. Because the genes for perchlorate reduction are horizontally transferred, previous studies have been unable to identify uncultivated perchlorate-reducing populations. Here we recovered metagenome-assembled genomes from perchlorate-reducing sediment enrichments and employed a manual scaffolding approach to reconstruct gene clusters for perchlorate reduction found within mobile genetic elements. De novo assembly and binning of four enriched communities yielded 48 total draft genomes. In addition to canonical perchlorate reduction gene clusters and taxa, a new type of gene cluster with an alternative perchlorate reductase was identified. Phylogenetic analysis indicated past exchange between these gene clusters, and the presence of plasmids with either gene cluster shows that the potential for gene transfer via plasmid persisted throughout enrichment. However, a majority of genomes in each community lacked perchlorate reduction genes. Putative chlorate-reducing or sulfur-reducing populations were dominant in most communities, supporting the hypothesis that metabolic interactions might result from perchlorate reduction intermediates and byproducts. Other populations included a novel phylum-level lineage (Ca. Muirbacteria) and epibiotic prokaryotes with no known role in perchlorate reduction. These results reveal unexpected genetic diversity, suggest that perchlorate-reducing communities involve substantial metabolic interactions, and encourage expanded strategies to further understand the evolution and ecology of this metabolism.

Robust Production, Crystallization, Structure Determination, and Analysis of [Fe-S] Proteins: Uncovering Control of Electron Shuttling and Gating in the Respiratory Metabolism of Molybdopterin Guanine Dinucleotide Enzymes

[Fe-S] clusters are essential cofactors in all domains of life. They play many biological roles due to their unique abilities for electron transfer and conformational control. Yet, producing and analyzing Fe-S proteins can be difficult and even misleading if not done anaerobically. Due to unique redox properties of [Fe-S] clusters and their oxygen sensitivity, they pose multiple challenges and can lose enzymatic activity or cause their component proteins to be structurally disordered due to [Fe-S] cluster oxidation and loss in air. Here we highlight tested protocols and strategies enabling efficient and stable [Fe-S] protein production, purification, crystallization, X-ray diffraction data collection, and structure determination. From multiple high-resolution anaerobic crystal structures, we furthermore analyze exemplary data defining [Fe-S] clusters, substrate entry, and product exit for the functional oxidation states of type II molybdo-bis(molybdopterin guanine dinucleotide) (Mo-bisMGD) enzymes. Notably, these enzymes perform electron shuttling between quinone pools and specific substrates to catalyze respiratory metabolism. The identified structure-activity relationships for this enzyme class have broad implications germane to perchlorate environments on Earth and Mars extending to an alternative mechanism underlying metabolic origins for the evolution of the oxygen atmosphere. Integrated structural analyses of type II Mo-bisMGD enzymes unveil novel distinctive shared molecular mechanisms for dynamic control of substrate entry and product release gated by hydrophobic residues. Collective findings support a prototypic model for type II Mo-bisMGD enzymes including insights for a fundamental molecular mechanistic understanding of selectivity and regulation by a conformationally gated channel with general implications for [Fe-S] cluster respiratory enzymes.

Biotechnological Applications of Microbial (Per)chlorate Reduction

While the microbial degradation of a chloroxyanion-based herbicide was first observed nearly ninety years ago, only recently have researchers elucidated the underlying mechanisms of perchlorate and chlorate [collectively, (per)chlorate] respiration. Although the obvious application of these metabolisms lies in the bioremediation and attenuation of (per)chlorate in contaminated environments, a diversity of alternative and innovative biotechnological applications has been proposed based on the unique metabolic abilities of dissimilatory (per)chlorate-reducing bacteria (DPRB). This is fueled in part by the unique ability of these organisms to generate molecular oxygen as a transient intermediate of the central pathway of (per)chlorate respiration. This ability, along with other novel aspects of the metabolism, have resulted in a wide and disparate range of potential biotechnological applications being proposed, including enzymatic perchlorate detection; gas gangrene therapy; enhanced xenobiotic bioremediation; oil reservoir bio-souring control; chemostat hygiene control; aeration enhancement in industrial bioreactors; and, biogenic oxygen production for planetary exploration. While previous reviews focus on the fundamental science of microbial (per)chlorate reduction (for example see Youngblut et al., 2016), here, we provide an overview of the emerging biotechnological applications of (per)chlorate respiration and the underlying organisms and enzymes to environmental and biotechnological industries.

37Cl/35Cl isotope ratio analysis in perchlorate by ion chromatography/multi collector -ICPMS: Analytical performance and implication for biodegradation studies

In the present study we propose a new analytical method for ³⁷Cl/³⁵Cl analysis in perchlorate by Ion Chromatography(IC) coupled to Multicollector Inductively Coupled Plasma Mass Spectrometry (MC-ICPMS). The accuracy of the analytical method was validated by analysis of international perchlorate standard materials USGS-37 and USGS -38; analytical precision better than ±0.4‰ was achieved. ³⁷Cl/³⁵Cl isotope ratio analysis in perchlorate during laboratory biodegradation experiment with microbial cultures enriched from the contaminated soil in Israel resulted in isotope enrichment factor ε³⁷Cl = -13.3 ± 1‰, which falls in the range reported previously for perchlorate biodegradation by pure microbial cultures. The proposed analytical method may significantly simplify the procedure for isotope analysis of perchlorate which is currently applied in environmental studies.

Concurrent Haloalkanoate Degradation and Chlorate Reduction by Pseudomonas chloritidismutans AW-1T

Haloalkanoates are environmental pollutants that can be degraded aerobically by microorganisms producing hydrolytic dehalogenases. However, there is a lack of information about the anaerobic degradation of haloalkanoates. Genome analysis of Pseudomonas chloritidismutans AW-1^T, a facultative anaerobic chlorate-reducing bacterium, showed the presence of two putative haloacid dehalogenase genes, the l-DEX gene and dehI, encoding an l-2-haloacid dehalogenase (l-DEX) and a halocarboxylic acid dehydrogenase (DehI), respectively. Hence, we studied the concurrent degradation of haloalkanoates and chlorate as a yet-unexplored trait of strain AW-1^T The deduced amino acid sequences of l-DEX and DehI revealed 33 to 37% and 26 to 86% identities with biochemically/structurally characterized l-DEX and the d- and dl-2-haloacid dehalogenase enzymes, respectively. Physiological experiments confirmed that strain AW-1^T can grow on chloroacetate, bromoacetate, and both l- and d-α-halogenated propionates with chlorate as an electron acceptor. Interestingly, growth and haloalkanoate degradation were generally faster with chlorate as an electron acceptor than with oxygen as an electron acceptor. In line with this, analyses of l-DEX and DehI dehalogenase activities using cell-free extract (CFE) of strain AW-1^T grown on dl-2-chloropropionate under chlorate-reducing conditions showed up to 3.5-fold higher dehalogenase activity than the CFE obtained from AW-1^T cells grown on dl-2-chloropropionate under aerobic conditions. Reverse transcription-quantitative PCR showed that the l-DEX gene was expressed constitutively independently of the electron donor (haloalkanoates or acetate) or acceptor (chlorate or oxygen), whereas the expression of dehI was induced by haloalkanoates. Concurrent degradation of organic and inorganic halogenated compounds by strain AW-1^T represents a unique metabolic capacity in a single bacterium, providing a new piece of the puzzle of the microbial halogen cycle.IMPORTANCE Halogenated organic and inorganic compounds are important environmental pollutants that have carcinogenic and genotoxic effects on both animals and humans. Previous research studied the degradation of organic and inorganic halogenated compounds separately but not concurrently. This study shows concurrent degradation of halogenated alkanoates and chlorate as an electron donor and acceptor, respectively, coupled to growth in a single bacterium, Pseudomonas chloritidismutans AW-1^T Hence, besides biogenesis of molecular oxygen from chlorate reduction enabling a distinctive placement of strain AW-1^T between aerobic and anaerobic microorganisms, we can now add another unique metabolic potential of this bacterium to the roster. The degradation of different halogenated compounds under anoxic conditions by a single bacterium is also of interest for the natural halogen cycle in different aquatic and terrestrial ecosystems where ample natural production of halogenated compounds has been documented.

Mechanism of H2S Oxidation by the Dissimilatory Perchlorate-Reducing Microorganism Azospira suillum PS

The genetic and biochemical basis of perchlorate-dependent H₂S oxidation (PSOX) was investigated in the dissimilatory perchlorate-reducing microorganism (DPRM) Azospira suillum PS (PS). Previously, it was shown that all known DPRMs innately oxidize H₂S, producing elemental sulfur (S^o). Although the process involving PSOX is thermodynamically favorable (ΔG°' = -206 kJ ⋅ mol^-1 H₂S), the underlying biochemical and genetic mechanisms are currently unknown. Interestingly, H₂S is preferentially utilized over physiological electron donors such as lactate or acetate although no growth benefit is obtained from the metabolism. Here, we determined that PSOX is due to a combination of enzymatic and abiotic interactions involving reactive intermediates of perchlorate respiration. Using various approaches, including barcode analysis by sequencing (Bar-seq), transcriptome sequencing (RNA-seq), and proteomics, along with targeted mutagenesis and biochemical characterization, we identified all facets of PSOX in PS. In support of our proposed model, deletion of identified upregulated PS genes traditionally known to be involved in sulfur redox cycling (e.g., Sox, sulfide:quinone reductase [SQR]) showed no defect in PSOX activity. Proteomic analysis revealed differential abundances of a variety of stress response metal efflux pumps and divalent heavy-metal transporter proteins, suggesting a general toxicity response. Furthermore, in vitro biochemical studies demonstrated direct PSOX mediated by purified perchlorate reductase (PcrAB) in the absence of other electron transfer proteins. The results of these studies support a model in which H₂S oxidation is mediated by electron transport chain short-circuiting in the periplasmic space where the PcrAB directly oxidizes H₂S to S^o The biogenically formed reactive intermediates (ClO₂^- and O₂) subsequently react with additional H₂S, producing polysulfide and S^o as end products.IMPORTANCE Inorganic sulfur compounds are widespread in nature, and microorganisms are central to their transformation, thereby playing a key role in the global sulfur cycle. Sulfur oxidation is mediated by a broad phylogenetic diversity of microorganisms, including anoxygenic phototrophs and either aerobic or anaerobic chemotrophs coupled to oxygen or nitrate respiration, respectively. Recently, perchlorate-respiring microorganisms were demonstrated to be innately capable of sulfur oxidation regardless of their phylogenetic affiliation. As recognition of the prevalence of these organisms intensifies, their role in global geochemical cycles is being queried. This is further highlighted by the recently recognized environmental pervasiveness of perchlorate not only across Earth but also throughout our solar system. The inferred importance of this metabolism not only is that it is a novel and previously unrecognized component of the global sulfur redox cycle but also is because of the recently demonstrated applicability of perchlorate respiration in the control of biogenic sulfide production in engineered environments such as oil reservoirs and wastewater treatment facilities, where excess H₂S represents a significant environmental, process, and health risk, with associated costs approximating $90 billion annually.

Characterization of an anaerobic marine microbial community exposed to combined fluxes of perchlorate and salinity

The recent recognition of the environmental prevalence of perchlorate and its discovery on Mars, Earth's moon, and in meteorites, in addition to its novel application to controlling oil reservoir sulfidogenesis, has resulted in a renewed interest in this exotic ion and its associated microbiology. However, while plentiful data exists on freshwater perchlorate respiring organisms, information on their halophilic counterparts and microbial communities is scarce. Here, we investigated the temporal evolving structure of perchlorate respiring communities under a range of NaCl concentrations (1, 3, 5, 7, and 10 % wt/vol) using marine sediment amended with acetate and perchlorate. In general, perchlorate consumption rates were inversely proportional to NaCl concentration with the most rapid rate observed at 1 % NaCl. At 10 % NaCl, no perchlorate removal was observed. Transcriptional analysis of the 16S rRNA gene indicated that salinity impacted microbial community structure and the most active members were in families Rhodocyclaceae (1 and 3 % NaCl), Pseudomonadaceae (1 NaCl), Campylobacteraceae (1, 5, and 7 % NaCl), Sedimenticolaceae (3 % NaCl), Desulfuromonadaceae (5 and 7 % NaCl), Pelobacteraceae (5 % NaCl), Helicobacteraceae (5 and 7 % NaCl), and V1B07b93 (7 %). Novel isolates of genera Sedimenticola, Marinobacter, Denitromonas, Azoarcus, and Pseudomonas were obtained and their perchlorate respiring capacity confirmed. Although the obligate anaerobic, sulfur-reducing Desulfuromonadaceae species were dominant at 5 and 7 % NaCl, their enrichment may result from biological sulfur cycling, ensuing from the innate ability of DPRB to oxidize sulfide. Additionally, our results demonstrated enrichment of an archaeon of phylum Parvarchaeota at 5 % NaCl. To date, this phylum has only been described in metagenomic experiments of acid mine drainage and is unexpected in a marine community. These studies identify the intrinsic capacity of marine systems to respire perchlorate and significantly expand the known diversity of organisms capable of this novel metabolism.