Microbial respiration with chlorine oxyanions: diversity and physiological and biochemical properties of chlorate- and perchlorate-reducing microorganisms

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.

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.

Isolation and identification of chlorate-reducing Hafnia sp. from milk

Chlorate has become a concern in the food and beverage sector, related to chlorine sanitizers in industrial food production and water treatment. It is of particular concern to regulatory bodies due to the negative health effects of chlorate exposure. This study investigated the fate of chlorate in raw milk and isolated bacterial strains of interest responsible for chlorate breakdown. Unpasteurized milk was demonstrated to have a chlorate-reducing capacity, breaking down enriched chlorate to undetectable levels in 11 days. Further enrichment and isolation using conditions specific to chlorate-reducing bacteria successfully isolated three distinct strains of Hafnia paralvei. Chlorate-reducing bacteria were observed to grow in a chlorate-enriched medium with lactate as an electron donor. All isolated strains were demonstrated to reduce chlorate in liquid medium; however, the exact mechanism of chlorate degradation was not definitively identified in this study.

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.

Health risk assessment of perchlorate and chlorate in red swamp crayfish (Procambarus clarkii) in China

Perchlorate and chlorate are both strong oxidants and thyroid toxicants that are widely distributed in soil, water and human foods. The red swamp crayfish (Procambarus clarkii) is a common aquatic organism that is popular in Chinese culinary dishes. Dietary intake is the main route of human exposure to perchlorate and chlorate, though the health risks of crayfish consumption are unknown. Thus, this study investigated the quantities of perchlorate and chlorate in red swap crayfish from sampling sites in five provinces located near the Yangtze River in China, along with the associated health risks of consuming this species. Perchlorate was detected in 55.6-100 % of crayfish samples in each sampling location, and chlorate was found in 100 % of samples cross all sites. Concentrations of perchlorate in crayfish from upstream provinces (Hubei, Hunan and Jiangxi) were higher than those from downstream provinces (Anhui and Jiangsu). Perchlorate and chlorate concentrations were positively correlated in crayfish, suggesting that chlorate may be a degradation byproduct of perchlorate. The quantities of both pollutants in hepatopancreas tissue were higher than in muscle tissues (p < 0.05), such that we do not recommend ingesting crayfish hepatopancreas. Hazard quotient (HQ) values for chlorate in crayfish were <1 across all provinces, suggesting no potential health risk of chlorate exposure through crayfish consumption. However, perchlorate concentrations in crayfish from the Jiangxi province had an associated HQ value >1, suggesting potential risks for human health. These results will be useful in informing mitigation measures aimed at reducing perchlorate exposure associated with crayfish consumption.

Impact of Acetate in Reduction of Perchlorate by Mixed Microbial Culture under the Influence of Nitrate and Sulfate

The biological reduction of slow degradation contaminants such as perchlorate (ClO4−) is considered to be a promising water treatment technology. The process is based on the ability of a specific mixed microbial culture to use perchlorate as an electron acceptor in the absence of oxygen. In this study, batch experiments were conducted to investigate the effect of nitrate on perchlorate reduction, the kinetic parameters of the Monod equation and the optimal ratio of acetate to perchlorate for the perchlorate reducing bacterial consortium. The results of this study suggest that acclimated microbial cultures can be applied to treat wastewater containing high concentrations of perchlorate. Reactor experiments were carried out with different hydraulic retention times (HRTs) to determine the optimal operating conditions. A fixed optimal HRT and the effect of nitrate on perchlorate reduction were investigated with various concentrations of the electron donor. The results showed that perchlorate reduction occurred after nitrate removal. Moreover, the presence of sulfate in wastewater had no effect on the perchlorate reduction. However, it had little effect on biomass concentration in the presence of nitrate during exposure to a mixed microbial culture, considering the nitrate as the inhibitor of perchlorate reduction by reducing the degradation rate. The batch scale experiment results illustrated that for efficient operation of perchlorate reduction, the optimal acetate to perchlorate ratio of 1.4:1.0 would be enough. Moreover, these experiments found the following results: the kinetic parameters equivalent to Y = 0.281 mg biomass/mg perchlorate, Ks = 37.619 mg/L and qmax = 0.042 mg perchlorate/mg biomass/h. In addition, anoxic–aerobic experimental reactor results verify the optimal HRT of 6 h for continuous application. Furthermore, it also illustrated that using 600 mg/L of acetate as a carbon source is responsible for 100% of nitrate reduction with less than 50% of the perchlorate reduction, whereas at 1000 mg/L acetate, approximately 100% reduction was recorded.

Perchlorate-reducing bacteria from Antarctic marine sediments

Perchlorate is a contaminant that can persist in groundwater and soil, and is frequently detected in different ecosystems at concentrations relevant to human health. This study isolated and characterised halotolerant bacteria that can potentially perform perchlorate reduction. Bacterial microorganisms were isolated from marine sediments on Deception, Horseshoe and Half Moon Islands of Antarctica. The results of the 16S ribosomal RNA (rRNA) gene sequence analysis indicated that the isolates were phylogenetically related to Psychrobacter cryohalolentis, Psychrobacter urativorans, Idiomarina loihiensis, Psychrobacter nivimaris, Sporosarcina aquimarina and Pseudomonas lactis. The isolates grew at a sodium chloride concentration of up to 30% and a perchlorate concentration of up to 10,000 mg/L, which showed their ability to survive in saline conditions and high perchlorate concentrations. Between 21.6 and 40% of perchlorate was degraded by the isolated bacteria. P. cryohalolentis and P. urativorans degraded 30.3% and 32.6% of perchlorate, respectively. I. loihiensis degraded 40% of perchlorate, and P. nivimaris, S. aquimarina and P. lactis degraded 22%, 21.8% and 21.6% of perchlorate, respectively. I. loihiensis had the highest reduction in perchlorate, whereas P. lactis had the lowest reduction. This study is significant as it is the first finding of P. cryohalolentis and. P. lactis on the Antarctic continent. In conclusion, these bacteria isolated from marine sediments on Antarctica offer promising resources for the bioremediation of perchlorate contamination due to their ability to degrade perchlorate, showing their potential use as a biological system to reduce perchlorate in high-salinity ecosystems.

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

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.

A Review of Sample Analysis at Mars-Evolved Gas Analysis Laboratory Analog Work Supporting the Presence of Perchlorates and Chlorates in Gale Crater, Mars

The Sample Analysis at Mars (SAM) instrument on the Curiosity rover has detected evidence of oxychlorine compounds (i.e., perchlorates and chlorates) in Gale crater, which has implications for past habitability, diagenesis, aqueous processes, interpretation of in situ organic analyses, understanding the martian chlorine cycle, and hazards and resources for future human exploration. Pure oxychlorines and mixtures of oxychlorines with Mars-analog phases have been analyzed for their oxygen (O2) and hydrogen chloride (HCl) releases on SAM laboratory analog instruments in order to constrain which phases are present in Gale crater. These studies demonstrated that oxychlorines evolve O2 releases with peaks between ~200 and 600 °C, although the thermal decomposition temperatures and the amount of evolved O2 decrease when iron phases are present in the sample. Mg and Fe oxychlorines decompose into oxides and release HCl between ~200 and 542 °C. Ca, Na, and K oxychlorines thermally decompose into chlorides and do not evolve HCl by themselves. However, the chlorides (original or from oxychlorine decomposition) can react with water-evolving phases (e.g., phyllosilicates) in the sample and evolve HCl within the temperature range of SAM (<~870 °C). These laboratory analog studies support that the SAM detection of oxychlorine phases is consistent with the presence of Mg, Ca, Na, and K perchlorate and/or chlorate along with possible contributions from adsorbed oxychlorines in Gale crater samples.

Perchlorate bioreduction by anaerobic granular sludge immobilised with Fe-HA complex: Performance, extracellular polymeric substances and microbial community structure

An iron-humic acid (Fe-HA) complex was used as a redox mediator in perchlorate (ClO₄^-) bioreduction. Bioreduction performance, extracellular polymeric substances (EPS), and microbial community structure were comprehensively explored using different types of anaerobic granular sludge (AnGS) immobilised without the Fe-HA complex (AnGS_CON) and with the Fe-HA complex (AnGS_FH). The ClO₄^- was completely removed by AnGS_CON by day 20, while the ClO₄^- was completely removed by AnGS_FH by day 6. The AnGS immobilised with the Fe-HA complex significantly increased the ClO₄^- bioreduction. The acceleration of ClO₄^- bioreduction was also explained by the mixed liquor volatile suspended solids (MLVSS), MLVSS/mixed liquor suspended solids (MLSS), EPS composition, and microbial community structure. Compared with AnGS_CON, the MLVSS and MLVSS/MLSS of the AnGS_FH increased 1.4- and 1.2-fold, respectively. Humic substances in the EPS were stimulated by the Fe-HA complex. The microbial community structure analysis indicated that perchlorate and quinone reducing bacteria were enriched by the Fe-HA complex. Based on the analysis, the ClO₄^- bioreduction mechanism of the AnGS_FH was revealed because the Fe-HA complex in the AnGS increased the biomass concentration, biological activity, and redox-active mediator and shifted the microbial community structure.

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.

Aerobic microbial communities in the sediments of a marine oxygen minimum zone

The ecology of aerobic microorganisms is never explored in marine oxygen minimum zone (OMZ) sediments. Here we reveal aerobic bacterial communities along ∼3 m sediment-horizons of the eastern Arabian Sea OMZ. Sulfide-containing sediment-cores retrieved from 530 mbsl (meters beneath the sea-level) and 580 mbsl were explored at 15–30 cm intervals, using metagenomics, pure-culture-isolation, genomics and metatranscriptomics. Genes for aerobic respiration, and oxidation of methane/ammonia/alcohols/thiosulfate/sulfite/organosulfur-compounds, were detected in the metagenomes from all 25 sediment-samples explored. Most probable numbers for aerobic chemolithoautotrophs and chemoorganoheterotrophs at individual sample-sites were up to 1.1 × 10⁷ (g sediment)^-1. The sediment-sample collected from 275 cmbsf (centimeters beneath the seafloor) of the 530-mbsl-core yielded many such obligately aerobic isolates belonging to Cereibacter, Guyparkeria, Halomonas, Methylophaga, Pseudomonas and Sulfitobacter which died upon anaerobic incubation, despite being provided with all possible electron acceptors and fermentative substrates. High percentages of metatranscriptomic reads from the 275 cmbsf sediment-sample, and metagenomic reads from all 25 sediment-samples, matched the isolates’ genomic sequences including those for aerobic metabolisms, genetic/environmental information processing and cell division, thereby illustrating the bacteria's in-situ activity, and ubiquity across the sediment-horizons, respectively. The findings hold critical implications for organic carbon sequestration/remineralization, and inorganic compounds oxidation, within the sediment realm of global marine OMZs.

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.

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.

Perchlorate-Reducing Bacteria from Hypersaline Soils of the Colombian Caribbean

Perchlorate (ClO₄ ^-) has several industrial applications and is frequently detected in environmental matrices at relevant concentrations to human health. Currently, perchlorate-degrading bacteria are promising strategies for bioremediation in polluted sites. The aim of this study was to isolate and characterize halophilic bacteria with the potential for perchlorate reduction. Ten bacterial strains were isolated from soils of Galerazamba-Bolivar, Manaure-Guajira, and Salamanca Island-Magdalena, Colombia. Isolates grew at concentrations up to 30% sodium chloride. The isolates tolerated pH variations ranging from 6.5 to 12.0 and perchlorate concentrations up to 10000 mg/L. Perchlorate was degraded by these bacteria on percentages between 25 and 10. 16S rRNA gene sequence analysis indicated that the strains were phylogenetically related to Vibrio, Bacillus, Salinovibrio, Staphylococcus, and Nesiotobacter genera. In conclusion, halophilic-isolated bacteria from hypersaline soils of the Colombian Caribbean are promising resources for the bioremediation of perchlorate contamination.

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.

Flux, Impact, and Fate of Halogenated Xenobiotic Compounds in the Gut

Humans and their associated microbiomes are exposed to numerous xenobiotics through drugs, dietary components, personal care products as well as environmental chemicals. Most of the reciprocal interactions between the microbiota and xenobiotics, such as halogenated compounds, occur within the human gut harboring diverse and dense microbial communities. Here, we provide an overview of the flux of halogenated compounds in the environment, and diverse exposure routes of human microbiota to these compounds. Subsequently, we review the impact of halogenated compounds in perturbing the structure and function of gut microbiota and host cells. In turn, cultivation-dependent and metagenomic surveys of dehalogenating genes revealed the potential of the gut microbiota to chemically alter halogenated xenobiotics and impact their fate. Finally, we provide an outlook for future research to draw attention and attract interest to study the bidirectional impact of halogenated and other xenobiotic compounds and the gut microbiota.