Offshore Marine Sediment Microbiota Respire Structurally Distinct Organohalide Pollutants

Underexplored Organohalide-Respiring Bacteria in Sewage Sludge Debrominating Polybrominated Diphenyl Ethers

Polybrominated diphenyl ethers (PBDEs) are persistent organic pollutants prevalent in the environment. Organohalide-respiring bacteria (OHRB) can attenuate PBDEs via reductive debromination, but often producing toxic end-products. Debromination of PBDEs to diphenyl ether remains a rare phenomenon and is so far specifically associated with Dehalococcoides isolated from e-waste polluted sites. The occurrence of PBDE debromination in other ecosystems and underpinning OHRB are underexplored. Here we found that debromination of PBDEs is a common trait of sewage sludge microbiota, and diphenyl ether was produced as the end-product at varying quantities (0.6-52.9% mol of the parent PBDEs) in 76 of 84 cultures established with bioreactor sludge. Diverse debromination pathways converting PBDEs to diphenyl ether, including several new routes, were identified. Although Dehalococcoides contributed to PBDE debromination, Dehalogenimonas, Dehalobacter, and uncultivated Dehalococcoidia likely played more important roles than previously recognized. Multiple reductive dehalogenase genes (including bdeA, pcbA4, pteA, and tceA) were also prevalent and coexisted in bioreactor sludge. Collectively, these findings contribute to enhancing our comprehension of the environmental fate of PBDEs, expanding the diversity of microorganisms catalyzing PBDE debromination, and developing consortia for bioremediation application.

Complete 2,4,6-trichlorophenol degradation by anaerobic sludge acclimated with 4-chlorophenol: Synergetic effect of nZVI@BMPC and sodium lactate as an external nutrient

Ball-milled plastic char supported nano zero-valent iron (nZVI@BMPC) and their application combined with anaerobic sludge for microbial dechlorination of 2,4,6-trichlorophenol (2,4,6-TCP) were investigated. The XRD and FTIR analysis proved composition of zero valent states of iron, and the BET and SEM analysis showed that nZVI was uniformly distributed on the surface of BMPC. Successive addition of 1000 mg/L sodium lactate and nZVI@BMPC enhanced the acclamation of anaerobic sludge and resulted in the degradation of 4-CP within 80 days. The acclimated consortium with nZVI@BMPC completely degraded 2,4,6-TCP into CH4 and CO2, and the key dechlorination route was through 4-CP dechlorinaion and mineralization. The degradation rate of 2,4,6-TCP with nZVI@BMPC was 0.22/d, greater than that without nZVI@BMPC. The dechlorination efficiency was enhanced in the Fe2+/Fe3+ system controlled by nZVI@BMPC and iron-reducing bacteria. Metagenomic analysis result showed that the dominant de-chlorinators were Chloroflexi sp., Desulfovibrio, and Pseudomonas, which could directly degrade 2,4,6-TCP to 4-CP, especially, Chloroflexi bacterium could concurrently be used to mineralize 4-CP. The relative abundance of the functional genes cprA, acoA, acoB, and tfdB increased significantly in the presence of the nZVI@BMPC. This study provides a new strategy can be a good alternative for possible application in groundwater remediation.

Combatting multiple aromatic organohalide pollutants in sediments by bioaugmentation with a single Dehalococcoides

Dehalococcoides are capable of dehalogenating various organohalide pollutants under anaerobic conditions, and they have been applied in bioremediation. However, the presence of multiple aromatic organohalides, including polychlorinated biphenyls (PCBs), polybrominated diphenyl ethers (PBDEs), and tetrabromobisphenol A (TBBPA), at contaminated sites may pose challenges to Dehalococcoides-mediated bioremediation due to the lack of knowledge about the influence of co-contamination on bioremediation. In this study, we investigated the bioremediation of aromatic organohalides present as individual and co-contaminants in sediments by bioaugmentation with a single population of Dehalococcoides. Bioaugmentation with Dehalococcoides significantly increased the dehalogenation rate of PCBs, PBDEs, and TBBPA in sediments contaminated with individual pollutants, being up to 19.7, 27.4 and 2.1 times as that in the controls not receiving bioinoculants. For sediments containing all the three classes of pollutants, bioaugmentation with Dehalococcoides also effectively enhanced dehalogenation, and the extent of enhancement depended on the bioinoculants and types of pollutants. Interestingly, in many cases co-contaminated sediments bioaugmented with Dehalococcoides mccartyi strain CG1 displayed a greater enhancement in dehalogenation rates compared to the sediments polluted with individual pollutant. For instance, when augmented with a low quantity of strain CG1, the dehalogenation rates of Aroclor1260 and PBDEs in co-contaminated sediments were approximately two times as that in sediments containing individual pollutants (0.428 and 9.03 vs. 0.195 and 4.20 × 10-3d-1). Additionally, D. mccartyi CG1 grew to higher abundances in co-contaminated sediments. These findings demonstrate that a single Dehalococcoides population can sustain dehalogenation of multiple aromatic organohalides in contaminated sediments, suggesting that co-contamination does not necessarily impede the use of Dehalococcoides for bioremediation. The study also underscores the significance of anaerobic organohalide respiration for effective bioremediation.

Chemical-physical parameters and microbial community changes induced by electrodes polarization inhibit PCB dechlorination in a marine sediment

Microbial reductive dechlorination of organohalogenated pollutants is often limited by the scarcity of electron donors, that can be overcome with microbial electrochemical technologies (METs). In this study, polarized electrodes buried in marine sediment microcosms were investigated to stimulate PCB reductive dechlorination under potentiostatic (-0.7 V vs Ag/AgCl) and galvanostatic conditions (0.025 mA·cm-2-0.05 mA·cm-2), using graphite rod as cathode and iron plate as sacrificial anode. A single circuit and a novel two antiparallel circuits configuration (2AP) were investigated. Single circuit polarization impacted the sediment pH and redox potential (ORP) proportionally to the intensity of the electrical input and inhibited PCB reductive dechlorination. The effects on the sediment's pH and ORP, along with the inhibition of PCB reductive dechlorination, were mitigated in the 2AP system. Electrodes polarization stimulated sulfate-reduction and promoted the enrichment of bacterial clades potentially involved in sulfate-reduction as well as in sulfur oxidation. This suggested the electrons provided were consumed by competitors of organohalide respiring bacteria and specifically sequestered by sulfur cycling, which may represent the main factor limiting the applicability of METs for stimulating PCB reductive dechlorination in marine sediments.

Biodegradation of phenolic pollutants and bioaugmentation strategies: A review of current knowledge and future perspectives

The widespread use of phenolic compounds renders their occurrence in various environmental matrices, posing ecological risks especially the endocrine disruption effects. Biodegradation-based techniques are efficient and cost-effective in degrading phenolic pollutants with less production of secondary pollution. This review focuses on phenol, 4-nonylphenol, 4-nitrophenol, bisphenol A and tetrabromobisphenol A as the representatives, and summarizes the current knowledge and future perspectives of their biodegradation and the enhancement strategy of bioaugmentation. Biodegradation and isolation of degrading microorganisms were mainly investigated under oxic conditions, where phenolic pollutants are typically hydroxylated to 4-hydroxybenzoate or hydroquinone prior to ring opening. Bioaugmentation efficiencies of phenolic pollutants significantly vary under different application conditions (e.g., increased degradation by 10-95% in soil and sediment). To optimize degradation of phenolic pollutants in different matrices, the factors that influence biodegradation capacity of microorganisms and performance of bioaugmentation are discussed. The use of immobilization strategy, indigenous degrading bacteria, and highly competent exogenous bacteria are proposed to facilitate the bioaugmentation process. Further studies are suggested to illustrate 1) biodegradation of phenolic pollutants under anoxic conditions, 2) application of microbial consortia with synergistic effects for phenolic pollutant degradation, and 3) assessment on the uncertain ecological risks associated with bioaugmentation, resulting from changes in degradation pathway of phenolic pollutants and alterations in structure and function of indigenous microbial community.

Efficient biostimulation of microbial dechlorination of polychlorinated biphenyls by acetate and lactate under nitrate reducing conditions: Insights into dechlorination pathways and functional genes

Microbial-catalyzed reductive dechlorination of polychlorinated biphenyls (PCBs) is largely affected by the indigenous sediment geochemical properties. In this study, the effects of nitrate on PCB dechlorination and microbial community structures were first investigated in Taihu Lake sediment microcosms. And biostimulation study was attempted supplementing acetate/lactate. PCB dechlorination was apparently inhibited under nitrate-reducing conditions. Lower PCB dechlorination rate and less PCB dechlorination extent were observed in nitrate amended sediment microcosms (T-N) than those in non-nitrate amended microcosms (T-1) during 66 weeks of incubation. The total PCB mass reduction in T-N was 17.6% lower than that in T-1. The flanked-para dechlorination was completely inhibited, while the ortho-flanked meta dechlorination was only partially inhibited in T-N. The 7.5 mM of acetate/lactate supplementation recovered PCB dechlorination by resuming ortho-flanked meta dechlorination. Repeated additions of lactate showed more effective biostimulation than acetate. Phylum Chloroflexi, containing most known PCB dechlorinators, was found to play a vital role on stability of the network structures. In T-N, putative dechlorinating Chloroflexi, Dehalococcoides and RDase genes rdh12, pcbA4, pcbA5 all declined. With acetate/lactate supplementation, Dehalococcoides grew by 1-2 orders of magnitude and rdh12, pcbA4, pcbA5 increased by 1-3 orders of magnitude. At Week 66, parent PCBs declined by 86.4% and 80.9% respectively in T-N-LA and T-N-AC compared to 69.9% in T-N. These findings provide insights into acetate/lactate biostimulation as a cost-effective approach for treating PCB contaminated sediments undergoing nitrate inhibition.

Global prevalence of organohalide-respiring bacteria dechlorinating polychlorinated biphenyls in sewage sludge

BACKGROUND

Massive amounts of sewage sludge are generated during biological sewage treatment and are commonly subjected to anaerobic digestion, land application, and landfill disposal. Concurrently, persistent organic pollutants (POPs) are frequently found in sludge treatment and disposal systems, posing significant risks to both human health and wildlife. Metabolically versatile microorganisms originating from sewage sludge are inevitably introduced to sludge treatment and disposal systems, potentially affecting the fate of POPs. However, there is currently a dearth of comprehensive assessments regarding the capability of sewage sludge microbiota from geographically disparate regions to attenuate POPs and the underpinning microbiomes.

RESULTS

Here we report the global prevalence of organohalide-respiring bacteria (OHRB) known for their capacity to attenuate POPs in sewage sludge, with an occurrence frequency of ~50% in the investigated samples (605 of 1186). Subsequent laboratory tests revealed microbial reductive dechlorination of polychlorinated biphenyls (PCBs), one of the most notorious categories of POPs, in 80 out of 84 sludge microcosms via various pathways. Most chlorines were removed from the para- and meta-positions of PCBs; nevertheless, ortho-dechlorination of PCBs also occurred widely, although to lower extents. Abundances of several well-characterized OHRB genera (Dehalococcoides, Dehalogenimonas, and Dehalobacter) and uncultivated Dehalococcoidia lineages increased during incubation and were positively correlated with PCB dechlorination, suggesting their involvement in dechlorinating PCBs. The previously identified PCB reductive dehalogenase (RDase) genes pcbA4 and pcbA5 tended to coexist in most sludge microcosms, but the low ratios of these RDase genes to OHRB abundance also indicated the existence of currently undescribed RDases in sewage sludge. Microbial community analyses revealed a positive correlation between biodiversity and PCB dechlorination activity although there was an apparent threshold of community co-occurrence network complexity beyond which dechlorination activity decreased.

CONCLUSIONS

Our findings that sludge microbiota exhibited nearly ubiquitous dechlorination of PCBs indicate widespread and nonnegligible impacts of sludge microbiota on the fate of POPs in sludge treatment and disposal systems. The existence of diverse OHRB also suggests sewage sludge as an alternative source to obtain POP-attenuating consortia and calls for further exploration of OHRB populations in sewage sludge. Video Abstract.

Residual effects of chlorinated organic pollutants on microbial community and natural redox processes in coastal wetlands

Chlorinated organic pollutants (COPs) are common in flooded environments. To examine the residual status and effects of COPs on flooded environments, a survey of 7 coastal wetlands in Zhejiang, East China was conducted. Total COP concentrations detected from 95.69 to 412.76 ng g-1 dw. Gamma-HCH and o,p'-DDT posed the greatest risk with exceedance rates of 100% according to sediment quality guidelines. Samples with higher COP pollution had higher microbial diversity, more complex microbial networks, more deterministic community assembly processes and lower microbiome stability, indicating an improved soil function for balance cycle of substances, especially for COP degradation. Further analysis using quantitative real-time PCR suggested COP-dechlorination interacted with natural redox processes, especially sulfate reduction and methanogenesis. The positive correlation between CH4 and pentachlorobenzene indicated a potential increase in greenhouse gas emissions caused by COP pollution. Correlation between dsr gene and COPs demonstrated the ability of sulfate-reducing bacteria to degrade COPs. Particularly, facultative OHRB such as sulfate-reducing bacteria hold significant importance in the process of COP-dechlorination. This finding provides a reference for COP pollution remediation. Collectively, our study offers new insight into the residual effect of COPs in coastal wetlands and contributes to an improved understanding of bioremediation strategies for COP pollution.

Kelp as a biomonitor of persistent organic pollutants in coastal areas of China: Contamination levels and human health risk

Kelp, the brown alga distributed in coastal areas all over the world, is also an important medicine food homology product in China. However, the levels and profiles of persistent organic pollutants (POPs) in kelp have not been thoroughly investigated to date. Polychlorinated biphenyls (PCBs), polybrominated diphenyl ethers (PBDEs) and emerging bromine flame retardants (eBFRs) were evaluated in 41 kelp samples from the main kelp producing areas in China. The concentrations of total PCBs, PBDEs and eBFRs were in the range of 0.321-4.24 ng/g dry weight (dw), 0.255-25.5 ng/g dw and 3.00 × 10-3-47.2 ng/g dw in kelp, respectively. The pollutant pattern was dominated by decabromodiphenyl ethane (DBDPE, 13.0 ± 11.7 ng/g dw) followed in decreasing order by BDE-209 (2.74 ± 4.09 ng/g dw), CB-11 (1.32 ± 1.06 ng/g dw). The tested results showed that kelp could reflect the pollution status of PCBs, PBDEs and eBFRs, indicating the suitability of kelp as a biomonitor of these harmful substances. Finally, the data obtained was used to evaluate human non-cancer and cancer risks of PCBs and PBDEs via kelp consumption for Chinese. Though the calculated risk indices were considered acceptable according to the international standards even in the worst scenarios, the POPs levels in kelp should be monitored continuously as a good environmental indicator.

Coupling between 2, 2', 4, 4'-tetrabromodiphenyl ether (BDE-47) debromination and methanogenesis in anaerobic soil microcosms

Polybrominated diphenyl ethers (PBDEs) are persistent pollutants that may undergo microbial-mediated debromination in anoxic environments, where diverse anaerobic microbes such as methanogenic archaea co-exist. However, current understanding of the relations between PBDE pollution and methanogenic process is far from complete. To address this knowledge gap, a series of anaerobic soil microcosms were established. BDE-47 (2, 2', 4, 4'-tetrabromodiphenyl ether) was selected as a model pollutant, and electron donors were supplied to stimulate the activity of anaerobes. Debromination and methane production were monitored during the 12 weeks incubation, while obligate organohalide-respiring bacteria (OHRBs), methanogenic, and the total bacterial communities were examined at week 7 and 12. The results demonstrated slow debromination of BDE-47 in all microcosms, with considerable growth of Dehalococcoides and Dehalogenimonas over the incubation observed in most BDE-47 spiked treatments. In addition, the accumulation of intermediate metabolites positively correlated with the abundance of Dehalogenimonas at week 7, suggesting potential role of these OHRBs in debromination. Methanosarcinaceae were identified as the primary methanogenic archaea, and their abundance were correlated with the production of debrominated metabolites at week 7. Furthermore, it was observed for the first time that BDE-47 considerably enhanced methane production and increased the abundance of mcrA genes, highlighting the potential effects of PBDE pollution on climate change. This might be related to the inhibition of reductive N- and S-transforming microbes, as revealed by the quantitative microbial element cycling (QMEC) analysis. Overall, our findings shed light on the intricate interactions between PBDE and methanogenic processes, and contribute to a better understanding of the environmental fate and ecological implication of PBDE under anaerobic settings.

Metabolic Synergy of Dehalococcoides Populations Leading to Greater Reductive Dechlorination of Polychlorinated Biphenyls

Polychlorinated biphenyls (PCBs) are dioxin-like pollutants that cause persistent harm to life. Organohalide-respiring bacteria (OHRB) can detoxify PCBs via reductive dechlorination, but individual OHRB are potent in dechlorinating only specific PCB congeners, restricting the extent of PCB dechlorination. Moreover, the low biomass of OHRB frequently leads to the slow natural attenuation of PCBs at contaminated sites. Here we constructed defined microbial consortia comprising various combinations of PCB-dechlorinating Dehalococcoides strains (CG1, CG4, and CG5) to successfully enhance PCB dechlorination. Specifically, the defined consortia consisting of strains CG1 and CG4 removed 0.28-0.44 and 0.23-0.25 more chlorine per PCB from Aroclor1260 and Aroclor1254, respectively, compared to individual strains, which was attributed to the emergence of new PCB dechlorination pathways in defined consortia. Notably, different Dehalococcoides populations exhibited similar growth when cocultivated, but temporal differences in the expression of PCB reductive dehalogenase genes indicated their metabolic synergy. Bioaugmentation with individual strains (CG1, CG4, and CG5) or defined consortia led to greater PCB dechlorination in wetland sediments, and augmentation with the consortium comprising strains CG1 and CG4 resulted in the greatest PCB dechlorination. These findings collectively suggest that simultaneous application of multiple Dehalococcoides strains, which catalyze complementary dechlorination pathways, is an effective strategy to accelerate PCB dechlorination.

Unlocking the potential of resuscitation-promoting factor for enhancing anaerobic microbial dechlorination of polychlorinated biphenyls

Microbial dechlorination of polychlorinated biphenyls (PCBs) is limited by the slow growth rate and low activity of dechlorinators. Resuscitation promoting factor (Rpf) of Micrococcus luteus, has been demonstrated to accelerate the enrichment of highly active PCB-dechlorinating cultures. However, it remains unclear whether the addition of Rpf can further improve the dechlorination performance of anaerobic dechlorination cultures. In this study, the effect of Rpf on the performance of TG4, an enriched PCB-dechlorinating culture obtained by Rpf amendment, for reductive dechlorination of four typical PCB congeners (PCBs 101, 118, 138, 180) was evaluated. The results indicated that Rpf significantly enhanced the dechlorination of the four PCB congeners, with residual mole percentages of PCBs 101, 118, 138 and 180 in Rpf-amended cultures being 16.2-29.31 %, 13.3-20.1 %, 11.9-14.4 % and 9.4-17.3 % lower than those in the corresponding cultures without Rpf amendment after 18 days of incubation. Different models were identified as appropriate for elucidating the dechlorination kinetics of distinct PCB congeners, and it was observed that the dechlorination rate constant is significantly influenced by the PCB concentration. The supplementing Rpf did not obviously change dechlorination metabolites, and the removal of chlorines occurred mainly at para- and meta- positions. Analysis of microbial community and functional gene abundance suggested that Rpf-amended cultures exhibited a significant enrichment of Dehalococcoides, Dehalogenimonas and Desulfitobacterium, as well as non-dechlorinators belonging to Desulfobacterota and Bacteroidetes. These findings highlight the potential of Rpf as an effective additive for enhancing PCB dechlorination, providing new insights into the survival of functional microorganisms involved in anaerobic reductive dechlorination.

Short-chain fatty acids facilitated long-term dechlorination of PCBs in Taihu Lake sediment microcosms: Evidence from PCB congener and microbial community analyses

Microbial reductive dechlorination hosts great promise as an in situ bioremediation strategy for polychlorinated biphenyls (PCBs) contamination. However, the slow dechlorination in sediments limits natural attenuation. Short-chain fatty acids, as preferred carbon sources and electron donors for dechlorinating microorganisms, might stimulate PCB dechlorination. Herein, two sets of short-chain fatty acids, sole acetate and a fatty acid mixture (acetate, propionate, and butyrate), were amended periodically into Taihu Lake (China) sediment microcosms containing nine PCB congeners (PCB5, 12, 64, 71, 105, 114, 149, 153, and 170) after 24 weeks of incubation. Short-chain fatty acids facilitated the long-term PCB dechlorination and the promoting effect of the fatty acid mixture compared favorably with that of sole acetate. By the end of 108 weeks, the total PCB mass concentrations in acetate amended and fatty acid mixture amended microcosms significantly declined by 7.6% and 10.3% compared with non-amended microcosms (P < 0.05), respectively. Short-chain fatty acids selectively favored the removal of flanked meta and single-flanked para chlorines. Notably, a rare ortho dechlorination pathway, PCB25 (24-3-CB) to PCB13 (3-4-CB), was enhanced. Supplementary fatty acids significantly increased reductive dehalogenases (RDase) gene pcbA5 instead of improving the growth of Dehalococcoides. These findings highlight the merits of low cost short-chain fatty acids on in situ biostimulation in treating PCBs contamination.

Substrate-dependent strategies to mitigate sulfate inhibition on microbial reductive dechlorination of polychlorinated biphenyls

Sulfate widely co-exists with polychlorinated biphenyls (PCBs) at various concentrations in the subsurface environment. Previous studies have suggested that sulfate often hampers microbial degradation of aliphatic chlorinated solvents such as chloroethenes. However, the impact of sulfate on microbial reductive dechlorination of aromatic PCBs and the underlying mechanisms have received limited attention. Likewise, strategies to mitigate such inhibition remain scarce. Here we found that the mechanisms and mitigation strategies of sulfate inhibition on PCB dechlorination were substrate-dependent. Under electron donor-limiting conditions, even a low concentration of sulfate (2 mM) resulted in a decreased PCB dechlorination rate by 88.7% in a co-culture comprising Dehalococcoides mccartyi CG1 and the sulfate-reducing bacterium Desulfovibrio desulfuricans F1, an inhibition which was attributed to the competition for electron donor between sulfate reduction and PCB dechlorination. As expected, re-amendment of 5 mM lactate effectively re-initiated PCB dechlorination. However, in the presence of a higher concentration of sulfate (5 mM), the PCB dechlorination rate in the co-culture was 77.7% lower than in the control, even with excessive electron donor supply. This inhibition was linked to high concentration of sulfide (∼5 mM) produced from sulfate reduction, as suggested by high availability of electron donor, recovery of dechlorination activity after removal of sulfide, and negligible influence of sulfate on PCB dechlorination in the axenic culture of D. mccartyi CG1. Indeed, sulfide (>5 mM) was found to directly suppress expression of PCB-dechlorinating reductive dehalogenase gene. The highest transcriptional level of pcbA1 was 2.9 ± 0.3 transcripts·cell-1 in the presence of ∼5 mM sulfide, which was increased to 37.4 ± 5.0 transcripts·cell-1 when sulfide was removed. Under this scenario, introduction of ferrous salts (5 mM) efficiently alleviated sulfide inhibition on PCB dechlorination. Interestingly, the augmentation of methanogens in the co-culture was also effective in mitigating sulfide inhibition on PCB dechlorination, offering a new approach to protect Dehalococcoides under sulfide stress. Collectively, these findings deepen our understanding of the influence of sulfate on microbial reductive dechlorination of PCBs and contribute to developing appropriate strategies based on geochemical conditions to alleviate sulfate inhibition during bioremediation of PCB-contaminated sites.

Genome-Resolved Metagenomics and Metatranscriptomics Reveal Insights into the Ecology and Metabolism of Anaerobic Microbial Communities in PCB-Contaminated Sediments

Growth of organohalide-respiring bacteria such as Dehalococcoides mccartyi on halogenated organics (e.g., polychlorinated biphenyls (PCBs)) at contaminated sites or in enrichment culture requires interaction and support from other microbial community members. To evaluate naturally occurring interactions between Dehalococcoides and key supporting microorganisms (e.g., production of H2, acetate, and corrinoids) in PCB-contaminated sediments, metagenomic and metatranscriptomic sequencing was conducted on DNA and RNA extracted from sediment microcosms, showing evidence of both Dehalococcoides growth and PCB dechlorination. Using a genome-resolved approach, 160 metagenome-assembled genomes (MAGs), including three Dehalococcoides MAGs, were recovered. A novel reductive dehalogenase gene, distantly related to the chlorophenol dehalogenase gene cprA (pairwise amino acid identity: 23.75%), was significantly expressed. Using MAG gene expression data, 112 MAGs were assigned functional roles (e.g., corrinoid producers, acetate/H2 producers, etc.). A network coexpression analysis of all 160 MAGs revealed correlations between 39 MAGs and the Dehalococcoides MAGs. The network analysis also showed that MAGs assigned with functional roles that support Dehalococcoides growth (e.g., corrinoid assembly, and production of intermediates required for corrinoid synthesis) displayed significant coexpression correlations with Dehalococcoides MAGs. This work demonstrates the power of genome-resolved metagenomic and metatranscriptomic analyses, which unify taxonomy and function, in investigating the ecology of dehalogenating microbial communities.

Alleviating Chlorinated Alkane Inhibition on Dehalococcoides to Achieve Detoxification of Chlorinated Aliphatic Cocontaminants

Cocontamination by multiple chlorinated solvents is a prevalent issue in groundwater, presenting a formidable challenge for effective remediation. Despite the recognition of this issue, a comprehensive assessment of microbial detoxification processes involving chloroethenes and associated cocontaminants, along with the underpinning microbiome, remains absent. Moreover, strategies to mitigate the inhibitory effects of cocontaminants have not been reported. Here, we revealed that chloroform exhibited the most potent inhibitory effects, followed by 1,1,1-trichloroethane and 1,1,2-trichloroethane, on dechlorination of dichloroethenes (DCEs) in Dehalococcoides-containing consortia. The observed inhibition could be attributed to suppression of biosynthesis and enzymatic activity of reductive dehalogenases and growth of Dehalococcoides. Notably, cocontaminants more profoundly inhibited Dehalococcoides populations harboring the vcrA gene than those possessing the tceA gene, thereby explaining the accumulation of vinyl chloride under cocontaminant stress. Nonetheless, we successfully ameliorated cocontaminant inhibition by augmentation with Desulfitobacterium sp. strain PR owing to its ability to attenuate cocontaminants, resulting in concurrent detoxification of DCEs, trichloroethanes, and chloroform. Microbial community analyses demonstrated obvious alterations in taxonomic composition, structure, and assembly of the dechlorinating microbiome in the presence of cocontaminants, and introduction of strain PR reshaped the dechlorinating microbiome to be similar to its original state in the absence of cocontaminants. Altogether, these findings contribute to developing bioremediation technologies to clean up challenging sites polluted with multiple chlorinated solvents.

Impact of different zero valent iron-based particles on anaerobic microbial dechlorination of 2,4-dichlorophenol: Comparison of dechlorination performance and the underlying mechanism

The integration of iron-based materials and anaerobic microbial consortia has been extensively studied owing to its potential to enhance pollutant degradation. However, few studies have compared how different iron materials enhance the dechlorination of chlorophenols in coupled microbial systems. This study systematically compared the combined performances of microbial community (MC) and iron materials (Fe0/FeS2 +MC, S-nZVI+MC, n-ZVI+MC, and nFe/Ni+MC) for the dechlorination of 2,4-dichlorophenol (DCP) as one representative of chlorophenols. DCP dechlorination rate was significantly higher in Fe0/FeS2 +MC and S-nZVI+MC (1.92 and 1.67 times, with no significant difference between two groups) than in nZVI+MC and nFe/Ni+MC (1.29 and 1.25 times, with no significant difference between two groups). Fe0/FeS2 had better performance for the reductive dechlorination process as compared with other three iron-based materials via the consumption of any trace amount of oxygen in anoxic condition and accelerated electron transfer. On the other hand, nFe/Ni could induce different dechlorinating bacteria as compared to other iron materials. The enhanced microbial dechlorination was mainly due to some putative dechlorinating bacteria (Pseudomonas, Azotobacter, Propionibacterium), and due to improved electron transfer of sulfidated iron particles. Therefore, Fe0/FeS2 as a biocompatible as well as low-cost sulfidated material can be a good alternative for possible engineering applications in groundwater remediation.

Marine Dehalogenator and Its Chaperones: Microbial Duties and Responses in 2,4,6-Trichlorophenol Dechlorination

Marine environments contain diverse halogenated organic compounds (HOCs), both anthropogenic and natural, nourishing a group of versatile organohalide-respiring bacteria (OHRB). Here, we identified a novel OHRB (Peptococcaceae DCH) with conserved motifs but phylogenetically diverse reductive dehalogenase catalytic subunit (RdhAs) from marine enrichment culture. Further analyses clearly demonstrate the horizontal gene transfer of rdhAs among marine OHRB. Moreover, 2,4,6-trichlorophenol (TCP) was dechlorinated to 2,4-dichlorophenol and terminated at 4-chlorophenol in culture. Dendrosporobacter and Methanosarcina were the two dominant genera, and the constructed and verified metabolic pathways clearly demonstrated that the former provided various substrates for other microbes, while the latter drew nutrients, but might provide little benefit to microbial dehalogenation. Furthermore, Dendrosporobacter could readily adapt to TCP, and sporulation-related proteins of Dendrosporobacter were significantly upregulated in TCP-free controls, whereas other microbes (e.g., Methanosarcina and Aminivibrio) became more active, providing insights into how HOCs shape microbial communities. Additionally, sulfate could affect the dechlorination of Peptococcaceae DCH, but not debromination. Considering their electron accessibility and energy generation, the results clearly demonstrate that bromophenols are more suitable than chlorophenols for the enrichment of OHRB in marine environments. This study will greatly enhance our understanding of marine OHRB (rdhAs), auxiliary microbes, and microbial HOC adaptive mechanisms.

Organic matter degradation determines the concentrations of polybrominated diphenyl ethers in sediments. Multivariate learning on environmental and experimental models

Sediment organic matter (SOM) plays an important role in capturing polybrominated diphenyl ethers (PBDEs) due to its affinity to hydrophobic and lipophilic compounds. Previous publications about correlations between PBDE concentrations and SOM content showed discrepancies among the results, reporting either significant positive correlations or no correlations at all. This work aimed to provide a deeper insight into SOM characteristics that might determine the concentrations of PBDEs in sediments. Sediment samples from Mendoza province, Argentina, were analyzed to contrast two models, environmental and experimental, using multivariate learning methods. Mendoza has been going through increasing events of drought and water scarcity, hence the occurrence, transport, and fate of contaminants as PBDEs in aquatic environments is of superlative importance. Principal component analysis (PCA) and partial least squares regression (PLS) were used to evaluate the correlations between physicochemical properties of sediments, semi-quantitative Fourier transform infrared (FTIR) area ratios obtained from SOM spectra, and PBDE concentrations in sediments. Moreover, a linear model was proposed to determine SOM density using FTIR area ratios and it was used as an additional variable in multivariate analyses. The results obtained from PCA and PLS were consistent and revealed that PBDE concentrations in sediments were correlated with a more degraded SOM, characterized by shorter and more branched hydrocarbon chains. PBDE concentrations were also correlated with higher SOM density values, which in turn were correlated with SOM degradation. These findings extend previous understanding and emphasize that not only is the organic matter content a factor in determining PBDE concentrations in sediments, but also and more significantly, its degree of degradation.

Mechanistic and microbial ecological insights into the impacts of micro- and nano- plastics on microbial reductive dehalogenation of organohalide pollutants

Micro- and nano-plastics are prevalent in diverse ecosystems, but their impacts on biotransformation of organohalide pollutants and underpinning microbial communities remain poorly understood. Here we investigated the influence of micro- and nano-plastics on microbial reductive dehalogenation at strain and community levels. Generally, microplastics including polyethylene (PE), polystyrene (PS), polylactic acid (PLA), and a weathered microplastic mixture increased dehalogenation rate by 10 - 217% in both the Dehalococcoides isolate and enrichment culture, whereas the effects of polyvinyl chloride (PVC) and a defined microplastic mixture depended on their concentrations and cultures. Contrarily, nano-PS (80 nm) consistently inhibited dehalogenation due to increased production of reactive oxygen species. Nevertheless, the enrichment culture showed higher tolerance to nano-PS inhibition, implying crucial roles of non-dehalogenating populations in ameliorating nanoplastic inhibition. The variation in dehalogenation activity was linked to altered organohalide-respiring bacteria (OHRB) growth and reductive dehalogenase (RDase) gene transcription. Moreover, microplastics changed the community structure and benefited the enrichment of OHRB, favoring the proliferation of Dehalogenimonas. More broadly, the assembly of microbial communities on plastic biofilms was more deterministic than that in the planktonic cells, with more complex co-occurrence networks in the former. Collectively, these findings contribute to better understanding the fate of organohalides in changing environments with increasing plastic pollution.

Chlorinated organic pollutants in global flooded soil and sediments: Pollution status and potential risk

Chlorinated organic pollutants (COPs) were widely detected in anaerobic environments while there is limited understanding of their pollution status and potential environmental risks. Here, we applied meta-analysis to identify the occurrence status, pollution sources, and environmental risk of COPs from 246 peer-published literature, including 25 kinds of COPs from 977 sites. The results showed that the median concentrations of COPs were at the ng g^-1 level. By the combination of principal component analysis (PCA) and positive matrix factorization (PMF), we established 7 pollution sources for COPs. Environmental risk assessment found 73.3% of selected sites were at a security level but the rest were not, especially for the wetlands. The environmental risk of COPs was usually underestimated by the existing evaluation methods, such as without the consideration of the non-extractable residues (NER) and the multi-process coupling effect. Especially, the synergetic coupling associations between dechlorination and methanogenesis might increase the risk of methane emission that has barely been previously considered in previous risk assessment approaches. Our results expanded the knowledge for the pollution control and remediation of COPs in anaerobic environments.

Tritium and Carbon-14 Contamination Reshaping the Microbial Community Structure, Metabolic Network, and Element Cycle in the Seawater Environment

The potential ecological risks caused by entering radioactive wastewater containing tritium and carbon-14 into the sea require careful evaluation. This study simulated seawater's tritium and carbon-14 pollution and analyzed the effects on the seawater and sediment microenvironments. Tritium and carbon-14 pollution primarily altered nitrogen and phosphorus metabolism in the seawater environment. Analysis by 16S rRNA sequencing showed changes in the relative abundance of microorganisms involved in carbon, nitrogen, and phosphorus metabolism and organic matter degradation in response to tritium and carbon-14 exposure. Metabonomics and metagenomic analysis showed that tritium and carbon-14 exposure interfered with gene expression involving nucleotide and amino acid metabolites, in agreement with the results seen for microbial community structure. Tritium and carbon-14 exposure also modulated the abundance of functional genes involved in carbohydrate, phosphorus, sulfur, and nitrogen metabolic pathways in sediments. Tritium and carbon-14 pollution in seawater adversely affected microbial diversity, metabolic processes, and the abundance of nutrient-cycling genes. These results provide valuable information for further evaluating the risks of tritium and carbon-14 in marine environments.

Influence of microplastics on microbial anaerobic detoxification of chlorophenols

Microplastics (MPs) can absorb halogenated organic compounds and transport them into marine anaerobic zones. Microbial reductive dehalogenation is a major process that naturally attenuates organohalide pollutants in anaerobic environments. Here, we aimed to determine the mechanisms through which MPs affect the microbe-mediated marine halogen cycle by incubating 2,4,6-trichlorophenol (TCP) dechlorinating cultures with various types of MPs. We found that TCP was dechlorinated to 4-chlorophenol in biotic control and polypropylene (PP) cultures, but essentially terminated at 2,4-dichlorophenol in polyethylene (PE) and polyethylene terephthalate (PET) cultures after incubation for 20 days. Oxygen-containing functional groups such as peroxide and aldehyde were enriched on PE and PET after incubation and corresponded to elevated levels of intracellular reactive oxygen species (ROS) in the microorganisms. Adding PE or PET to the cultures exerted limited effects on hydrogenase and ATPase activities, but delayed the expression of the gene encoding reductive dehalogenase (RDase). Considering the limited changes in the microbial composition of the enriched cultures, these findings suggested that microbial dechlorination is probably affected by MPs through the ROS-induced inhibition of RDase synthesis and/or activity. Overall, our findings showed that extensive MP pollution is unfavorable to environmental xenobiotic detoxification.

Bacterial colonization dynamics of different microplastic types in an anoxic salt marsh sediment and impact of adsorbed polychlorinated biphenyls on the plastisphere

Plastic debris dispersed into the environment provide a substrate for microbial colonization, constituting a new human-made ecosystem called "plastisphere", and altering the microbial species distribution in aquatic, coastal and benthic ecosystems. The study aims at exploring the interaction among microplastics (MPs) made of different polymers, a persistent organic contaminant (polychlorinated biphenyls, PCBs), and the environmental microbial communities, in an anoxic marine sediment. Plastic pellets were incubated in the field in a salt marsh anoxic sediment, to observe the stages of plastisphere formation, by quantitative PCR and 16S rRNA gene sequencing, and PCB dechlorination activity on the MPs surface. Microbes from the sediment rapidly colonized the different microplastics types, with PVC recruiting a peculiar community enriched in sulfate-reducing bacteria. The composition of the plastisphere varied along the 1-year incubation possibly in response either to warmer temperatures in spring-summer or to microhabitat's changes due to the progressive plastic surface weathering. Even if PCB contaminated MPs were able to recruit potentially dehalogenating taxa, actual dechlorination was not detectable after 1 year. This suggests that the concentration of potentially dehalorespiring bacteria in the natural environment could be too low for the onset of the dechlorination process on MP-sorbed contaminants. Our study, which is among very few available longitudinally exploring the plastisphere composition in an anoxic sediment context, is the first exploring the fate and possible biodegradation of persistent organic pollutants sorbed on MPs reaching the seafloor.

Resilience of organohalide-detoxifying microbial community to oxygen stress in sewage sludge

Organohalide pollutants are prevalent in the environment, causing harms to wildlife and human. Organohalide-respiring bacteria (OHRB) could detoxify these pollutants in anaerobic environments, but the most competent OHRB (i.e., Dehalococcoides) is susceptible to oxygen. This study reports exceptional resistance and resilience of sewage sludge microbial communities to oxygen stress for attenuation of structurally distinct organohalide pollutants, including tetrachloroethene, tetrabromobisphenol A, and polybrominated diphenyl ethers. The dehalogenation rate constant of these organohalide pollutants in oxygen-exposed sludge microcosms was maintained as 74-120% as that in the control without oxygen exposure. Subsequent top-down experiments clarified that sludge flocs and non-OHRB contributed to alleviating oxygen stress on OHRB. In the dehalogenating microcosms, multiple OHRB (Dehahlococcoides, Dehalogenimonas, and Sulfurospirillum) harboring distinct reductive dehalogenase genes (pceA, pteA, tceA, vcrA, and bdeA) collaborated to detoxify organohalide pollutants but responded differentially to oxygen stress. Comprehensive microbial community analyses (taxonomy, diversity, and structure) demonstrated certain resilience of the sludge-derived dehalogenating microbial communities to oxygen stress. Additionally, microbial co-occurrence networks were intensified by oxygen stress in most microcosms, as a possible stress mitigation strategy. Altogether the mechanistic and ecological findings in this study contribute to remediation of organohalide-contaminated sites encountering oxygen disturbance.

Efficient and Complete Detoxification of Polybrominated Diphenyl Ethers in Sediments Achieved by Bioaugmentation with Dehalococcoides and Microbial Ecological Insights

Polybrominated diphenyl ethers (PBDEs) are prevalent environmental pollutants, but bioremediation of PBDEs remains to be reported. Here we report accelerated remediation of a penta-BDE mixture in sediments by bioaugmentation with Dehalococcoides mccartyi strains CG1 and TZ50. Bioaugmentation with different amounts of each Dehalococcoides strain enhanced debromination of penta-BDEs compared with the controls. The sediment microcosm spiked with 6.8 × 10⁶ cells/mL strain CG1 showed the highest penta-BDEs removal (89.9 ± 7.3%) to diphenyl ether within 60 days. Interestingly, co-contaminant tetrachloroethene (PCE) improved bioaugmentation performance, resulting in faster and more extensive penta-BDEs debromination using less bioinoculants, which was also completely dechlorinated to ethene by introducing D. mccartyi strain 11a. The better bioaugmentation performance in sediments with PCE could be attributed to the boosted growth of the augmented Dehalococcoides and capability of the PCE-induced reductive dehalogenases to debrominate penta-BDEs. Finally, ecological analyses showed that bioaugmentation resulted in more deterministic microbial communities, where the augmented Dehalococcoides established linkages with indigenous microorganisms but without causing obvious alterations of the overall community diversity and structure. Collectively, this study demonstrates that bioaugmentation with Dehalococcoides is a feasible strategy to completely remove PBDEs in sediments.