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.

In vitro demetalation of central magnesium in various chlorophyll derivatives using Mg-dechelatase homolog from the chloroflexi Anaerolineae

In the metabolic pathway of chlorophylls (Chls), an enzyme called STAY-GREEN or SGR catalyzes the removal of the central magnesium ion of Chls and their derivatives to their corresponding free bases, including pheophytins. The substrate specificity of SGR has been investigated through in vitro reactions using Chl-related molecules. However, information about the biochemical properties and reaction mechanisms of SGR and its substrate specificity remains elusive. In this study, we synthesized various Chl derivatives and investigated their in vitro dechelations using an SGR enzyme. Chl-a derivatives with the C3-vinyl group on the A-ring, which is commonly found as a substituent in natural substrates, and their analogs with ethyl, hydroxymethyl, formyl, and styryl groups at the C3-position were prepared as substrates. In vitro dechelatase reactions of these substrates were performed using an SGR enzyme derived from an Anaerolineae bacterium, allowing us to investigate their specificity. Reactivity was reduced for substrates with an electron-withdrawing formyl or sterically demanding styryl group at the C3-position. Furthermore, the Chl derivative with the C8-styryl group on the B-ring was less reactive for SGR dechelation than the C3-styryl substrate. These results indicate that the SGR enzyme recognizes substituents on the B-ring of substrates more than those on the A-ring.

Comprehensive exploration of the anaerobic biotransformation of polychlorinated biphenyls in Dehalococcoides mccartyi CG1: Kinetics, enantioselectivity, and isotope fractionation

Anaerobic microbial transformation is a key pathway in the natural attenuation of polychlorinated biphenyls (PCBs). Much less is known about the transformation behaviors induced by pure organohalide-respiring bacteria, especially kinetic isotope effects. Therefore, the kinetics, pathways, enantioselectivity, and carbon and chlorine isotope fractionation of PCBs transformation by Dehalococcoides mccartyi CG1 were comprehensively explored. The results indicated that the PCBs were mainly dechlorinated via removing their double-flanked meta-chlorine, with their first-order kinetic constants following the order of PCB132 > PCB174 > PCB85 > PCB183 > PCB138. However, PCBs occurred great loss of stoichiometric mass balance during microbial transformation, suggesting the generation of other non-dehalogenation products and/or stable intermediates. The preferential transformation of (-)-atropisomers and generation of (+)-atropisomers were observed during PCB132 and PCB174 biotransformation with the enantiomeric enrichment factors of -0.8609 ± 0.1077 and -0.4503 ± 0.1334 (first half incubation times)/-0.1888 ± 0.1354 (second half incubation times), respectively, whereas no enantioselectivity occurred during PCB183 biotransformation. More importantly, although there was no carbon and chlorine isotope fractionation occurring for studied substrates, the δ13C values of dechlorination products, including PCB47 (-28.15 ± 0.35‰ ∼ -27.77 ± 0.20‰), PCB91 (-36.36 ± 0.09‰ ∼ -34.71 ± 0.49‰), and PCB149 (-28.08 ± 0.26‰ ∼ -26.83 ± 0.10‰), were all significantly different from those of their corresponding substrates (PCB85: -30.81 ± 0.02‰ ∼ -30.22 ± 0.21‰, PCB132: -33.57 ± 0.15‰ ∼ -33.13 ± 0.14‰, and PCB174: -26.30 ± 0.09‰ ∼ -26.01 ± 0.07‰), which further supported the generation of other non-dehalogenation products and/or stable intermediates with enrichment or depletion of 13C. These findings provide deeper insights into the anaerobic microbial transformation behaviors of PCBs.

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.

Integrated Advanced Molecular Tools Predict In Situ cVOC Degradation Rates: Field Demonstration

Chlorinated volatile organic compound (cVOC) degradation rate constants are crucial information for site management. Conventional approaches generate rate estimates from the monitoring and modeling of cVOC concentrations. This requires time series data collected along the flow path of the plume. The estimates of rate constants are often plagued by confounding issues, making predictions cumbersome and unreliable. Laboratory data suggest that targeted quantitative analysis of Dehalococcoides mccartyi (Dhc) biomarker genes (qPCR) and proteins (qProt) can be directly correlated with reductive dechlorination activity. To assess the potential of qPCR and qProt measurements to predict rates, we collected data from cVOC-contaminated aquifers. At the benchmark study site, the rate constant for degradation of cis-dichloroethene (cDCE) extracted from monitoring data was 11.0 ± 3.4 yr-1, and the rate constant predicted from the abundance of TceA peptides was 6.9 yr-1. The rate constant for degradation of vinyl chloride (VC) from monitoring data was 8.4 ± 5.7 yr-1, and the rate constant predicted from the abundance of TceA peptides was 5.2 yr-1. At the other study sites, the rate constants for cDCE degradation predicted from qPCR and qProt measurements agreed within a factor of 4. Under the right circumstances, qPCR and qProt measurements can be useful to rapidly predict rates of cDCE and VC biodegradation, providing a major advance in effective site management.

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.

The effects of arsenic on dechlorination of trichloroethene by consortium DH: Microbial response and resistance

Inorganic arsenic and organochlorines are frequently co-occurring contaminants in anoxic groundwater environments, and the bioremediation of their composite pollution has long been a rigorous predicament. Currently, the dechlorination behaviors and stress responses of microbial dechlorination consortia to arsenic are not yet fully understood. This study assessed the reductive dechlorination performance of a Dehalococcoides-bearing microcosm DH under gradient concentrations of arsenate [As(V)] or arsenite [As(III)] and investigated the response patterns of different functional microorganisms. Our results demonstrated that although the dechlorination rates declined with increasing arsenic concentrations in both As(III/V) scenarios, the inhibitory impact was more pronounced in As(III)-amended groups compared to As(V)-amended groups. Moreover, the vinyl chloride (VC)-to-ethene step was more susceptible to arsenic exposure compared to the trichloroethene (TCE)-to-dichloroethane (DCE) step, while high levels of arsenic exposure [e.g. As(III) > 75 μM] can induce significant accumulation of VC. Functional gene variations and microbial community analyses revealed that As(III/V) affected reductive dechlorination by directly inhibiting organohalide-respiring bacteria (OHRB) and indirectly inhibiting synergistic populations such as acetogens. Metagenomic results indicated that arsenic metabolic and efflux mechanisms were identical among different Dhc strains, and variations in arsenic uptake pathways were possibly responsible for their differential responses to arsenic exposures. By comparison, fermentative bacteria showed high potential for arsenic resistance due to their inherent advantages in arsenic detoxification and efflux mechanisms. Collectively, our findings expanded the understanding of the response patterns of different functional populations to arsenic stress in the dechlorinating consortium and provided insights into modifying bioremediation strategies at co-contaminated sites for furtherance.

Redox gradient shapes the abundance and diversity of mercury-methylating microorganisms along the water column of the Black Sea

In the global context of seawater deoxygenation triggered by climate change and anthropogenic activities, changes in redox gradients impacting biogeochemical transformations of pollutants, such as mercury, become more likely. Being the largest anoxic basin worldwide, with high concentrations of the potent neurotoxic methylmercury (MeHg), the Black Sea is an ideal natural laboratory to provide new insights about the link between dissolved oxygen concentration and hgcAB gene-carrying (hgc+) microorganisms involved in the formation of MeHg. We combined geochemical and microbial approaches to assess the effect of vertical redox gradients on abundance, diversity, and metabolic potential of hgc+ microorganisms in the Black Sea water column. The abundance of hgcA genes [congruently estimated by quantitative PCR (qPCR) and metagenomics] correlated with MeHg concentration, both maximal in the upper part of the anoxic water. Besides the predominant Desulfobacterales, hgc+ microorganisms belonged to a unique assemblage of diverse-previously underappreciated-anaerobic fermenters from Anaerolineales, Phycisphaerae (characteristic of the anoxic and sulfidic zone), Kiritimatiellales, and Bacteroidales (characteristic of the suboxic zone). The metabolic versatility of Desulfobacterota differed from strict sulfate reduction in the anoxic water to reduction of various electron acceptors in the suboxic water. Linking microbial activity and contaminant concentration in environmental studies is rare due to the complexity of biological pathways. In this study, we disentangle the role of oxygen in shaping the distribution of Hg-methylating microorganisms consistently with MeHg concentration, and we highlight their taxonomic and metabolic niche partitioning across redox gradients, improving the prediction of the response of marine communities to the expansion of oxygen-deficient zones. IMPORTANCE Methylmercury (MeHg) is a neurotoxin detected at high concentrations in certain marine ecosystems, posing a threat to human health. MeHg production is mainly mediated by hgcAB gene-carrying (hgc+) microorganisms. Oxygen is one of the main factors controlling Hg methylation; however, its effect on the diversity and ecology of hgc+ microorganisms remains unknown. Under the current context of seawater deoxygenation, mercury cycling is expected to be disturbed. Here, we show the strong effect of oxygen gradients on the distribution of potential Hg methylators. In addition, we show for the first time the significant contribution of a unique assemblage of potential fermenters from Anaerolineales, Phycisphaerae, and Kiritimatiellales to Hg methylation, stratified in different redox niches along the Black Sea gradient. Our results considerably expand the known taxonomic diversity and ecological niches prone to the formation of MeHg and contribute to better apprehend the consequences of oxygen depletion in seawater.

Structural basis of a bi-functional malonyl-CoA reductase (MCR) from the photosynthetic green non-sulfur bacterium Roseiflexus castenholzii

Malonyl-CoA reductase (MCR) is a NADPH-dependent bi-functional enzyme that performs alcohol dehydrogenase and aldehyde dehydrogenase (CoA-acylating) activities in the N- and C-terminal fragments, respectively. It catalyzes the two-step reduction of malonyl-CoA to 3-hydroxypropionate (3-HP), a key reaction in the autotrophic CO2 fixation cycles of Chloroflexaceae green non-sulfur bacteria and the archaea Crenarchaeota. However, the structural basis underlying substrate selection, coordination, and the subsequent catalytic reactions of full-length MCR is largely unknown. For the first time, we here determined the structure of full-length MCR from the photosynthetic green non-sulfur bacterium Roseiflexus castenholzii (RfxMCR) at 3.35 Å resolution. Furthermore, we determined the crystal structures of the N- and C-terminal fragments bound with reaction intermediates NADP+ and malonate semialdehyde (MSA) at 2.0 Å and 2.3 Å, respectively, and elucidated the catalytic mechanisms using a combination of molecular dynamics simulations and enzymatic analyses. Full-length RfxMCR was a homodimer of two cross-interlocked subunits, each containing four tandemly arranged short-chain dehydrogenase/reductase (SDR) domains. Only the catalytic domains SDR1 and SDR3 incorporated additional secondary structures that changed with NADP+-MSA binding. The substrate, malonyl-CoA, was immobilized in the substrate-binding pocket of SDR3 through coordination with Arg1164 and Arg799 of SDR4 and the extra domain, respectively. Malonyl-CoA was successively reduced through protonation by the Tyr743-Arg746 pair in SDR3 and the catalytic triad (Thr165-Tyr178-Lys182) in SDR1 after nucleophilic attack from NADPH hydrides. IMPORTANCE The bi-functional MCR catalyzes NADPH-dependent reduction of malonyl-CoA to 3-HP, an important metabolic intermediate and platform chemical, from biomass. The individual MCR-N and MCR-C fragments, which contain the alcohol dehydrogenase and aldehyde dehydrogenase (CoA-acylating) activities, respectively, have previously been structurally investigated and reconstructed into a malonyl-CoA pathway for the biosynthetic production of 3-HP. However, no structural information for full-length MCR has been available to illustrate the catalytic mechanism of this enzyme, which greatly limits our capacity to increase the 3-HP yield of recombinant strains. Here, we report the cryo-electron microscopy structure of full-length MCR for the first time and elucidate the mechanisms underlying substrate selection, coordination, and catalysis in the bi-functional MCR. These findings provide a structural and mechanistic basis for enzyme engineering and biosynthetic applications of the 3-HP carbon fixation pathways.

New insights on the photocomplex of Roseiflexus castenholzii revealed from comparisons of native and carotenoid-depleted complexes

In wild-type phototrophic organisms, carotenoids (Crts) are primarily packed into specific pigment-protein complexes along with (Bacterio)chlorophylls and play important roles in the photosynthesis. Diphenylamine (DPA) inhibits carotenogenesis but not phototrophic growth of anoxygenic phototrophs and eliminates virtually all Crts from photocomplexes. To investigate the effect of Crts on assembly of the reaction center-light-harvesting (RC-LH) complex from the filamentous anoxygenic phototroph Roseiflexus (Rfl.) castenholzii, we generated carotenoidless (Crt-less) RC-LH complexes by growing cells in the presence of DPA. Here, we present cryo-EM structures of the Rfl. castenholzii native and Crt-less RC-LH complexes with resolutions of 2.86 Å and 2.85 Å, respectively. From the high-quality map obtained, several important but previously unresolved details in the Rfl. castenholzii RC-LH structure were determined unambiguously including the assignment and likely function of three small polypeptides, and the content and spatial arrangement of Crts with bacteriochlorophyll molecules. The overall structures of Crt-containing and Crt-less complexes are similar. However, structural comparisons showed that only five Crts remain in complexes from DPA-treated cells and that the subunit X (TMx) flanked on the N-terminal helix of the Cyt-subunit is missing. Based on these results, the function of Crts in the assembly of the Rfl. castenholzii RC-LH complex and the molecular mechanism of quinone exchange is discussed. These structural details provide a fresh look at the photosynthetic apparatus of an evolutionary ancient phototroph as well as new insights into the importance of Crts for proper assembly and functioning of the RC-LH complex.

Field application of glycerol to enhance reductive dechlorination of chlorinated ethenes and its impact on microbial community

Chlorinated ethenes (CEs) are common and persistent contaminants of soil and groundwater. Their degradation is mostly driven by a process of bacterial reductive dechlorination (also called organohalide respiration) in anaerobic conditions. This study summarizes the outcomes of the long-term in-situ application of glycerol for the enhanced reductive dechlorination of CEs on a highly contaminated site. Glycerol injection resulted in an almost immediate increase in the abundance of fermentative Firmicutes, which produce essential sources of carbon (acetate) and electrons (H₂) for organohalide-respiring bacteria (OHRB) and change groundwater conditions to be suitable for OHRB growth. The decreased redox potential of groundwater promoted also the proliferation of sulfate-reducing bacteria, which compete for electron donors with OHRB but at the same time support their growth by producing essential corrinoids and acetate. A considerable increase in the abundance of OHRB Dehalococcoides, concurrently with vinyl chloride (VC) reductase gene levels, was revealed by real time polymerase chain reaction (qPCR) method. Consistent with the shifts in bacterial populations, the concentrations of pollutants tetrachloroethylene and trichloroethylene decreased during the monitoring period, with rising levels of cis-1,2-dichloroethylene, VC, and most importantly, the final CE degradation products: ethene and ethane. Our study implies the importance of syntrophic bacterial interactions for successful and complete CE degradation and evaluates glycerol as convenient substrate to enhance reductive dechlorination and as an effective source of electrons for OHRB.

Formate: A promising electron donor to enhance trichloroethene-to-ethene dechlorination in Dehalococcoides-augmented groundwater ecosystems with minimal bacterial growth

Various substrates have been used to stimulate habitat microbes in chloroethene-contaminated groundwater, however, the specific efficiency and minimum growth of microbes have rarely been studied. This study investigated the effects of seven substrates on trichloroethene (TCE) dechlorination by augmentation of groundwater with Dehalococcoides mccartyi NIT01 and its contribution to the microbial community. Three out of eight test groups completed dechlorination of 1 mM TCE-to-ethene in varying durations; groundwater supplemented with formate (FOR) required 78 days, whereas the microcosms with lactate (LAC) and citrate (CIT) required approximately twice as long (143 days). The calculated efficiency of how much produced H₂ was used in dechlorination indicated a higher efficiency in FOR (36%) compared with LAC (1.9%) or CIT (2.9%). FOR showed lower microbial growth (3.4 × 10⁵ copies/mL) than LAC (1.5 × 10⁶) or CIT (4.4 × 10⁶), and maintained a higher Shannon diversity index (5.65) than LAC (4.97) and CIT (4.30). The rapid and higher H₂ transfer efficiency with lower bacterial growth by using formate was attributed to the slightly positive Gibbs free energy identified in H₂ production requiring a H₂-utilizer, lower carbon in the molecule, and adaptation to metabolic potential of the original groundwater microbiome. Formate is, therefore, a promising electron donor for rapid Dehalococcoides-augmented remediation with minimum bacterial growth. Sequential transferring of the FOR culture successfully maintained TCE-to-ethene dechlorination activity and enriched the members of genera Dehalococcoides (33%), Methanosphaerula (23%), Rectinema (13%), and Desulfitobacterium (5.6%). This suggests that formate is transferred to H₂ and acetate, and provided to Dehalococcoides.

Crystal structure and reaction mechanism of a bacterial Mg-dechelatase homolog from the Chloroflexi Anaerolineae

Chlorophyll degradation plays a myriad of physiological roles in photosynthetic organisms, including acclimation to light environment and nutrient remobilization during senescence. Mg extraction from chlorophyll a is the first and committed step of the chlorophyll degradation pathway. This reaction is catalyzed by the Mg-dechelatase enzyme encoded by Stay-Green (SGR). The reaction mechanism of SGR protein remains elusive since metal ion extraction from organic molecules is not a common enzymatic reaction. Additionally, experimentally derived structural information about SGR or its homologs has not yet been reported. In this study, the crystal structure of the SGR homolog from Anaerolineae bacterium was determined using the molecular replacement method at 1.85 Å resolution. Our previous study showed that three residues-H32, D34, and D62 are essential for the catalytic activity of the enzyme. Biochemical analysis involving mutants of D34 residue further strengthened its importance in the functioning of the dechelatase. Docking simulation also revealed the interaction between the D34 side chain and central Mg ion of chlorophyll a. Structural analysis showed the arrangement of D34/H32/D62 in the form of a catalytic triad that is generally found in hydrolases. The probable reaction mechanism suggests that deprotonated D34 side chain coordinates and destabilizes Mg, resulting in Mg extraction. Besides, H32 possibly acts as a general base catalyst and D62 facilitates H32 to be a better proton acceptor. Taken together, the reaction mechanism of SGR partially mirrors the one observed in hydrolases.

Complete Reductive Dechlorination of 4-Hydroxy-chlorothalonil by Dehalogenimonas Populations

Chlorothalonil (2,4,5,6-tetrachloroisophthalonitrile, TePN) is one of the most widely used fungicides all over the world. Its major environmental transformation product 4-hydroxy-chlorothalonil (4-hydroxy-2,5,6-trichloroisophthalonitrile, 4-OH-TPN) is more persistent, mobile, and toxic and is frequently detected at a higher concentration in various habitats compared to its parent compound TePN. Further microbial transformation of 4-OH-TPN has never been reported. In this study, we demonstrated that 4-OH-TPN underwent complete microbial reductive dehalogenation to 4-hydroxy-isophthalonitrile via 4-hydroxy-dichloroisophthalonitrile and 4-hydroxy-monochloroisophthalonitrile. 16S rRNA gene amplicon sequencing demonstrated that Dehalogenimonas species was enriched from 6% to 17-22% after reductive dechlorination of 77.24 μmol of 4-OH-TPN. Meanwhile, Dehalogenimonas copies increased by one order of magnitude and obtained a yield of 1.78 ± 1.47 × 10⁸ cells per μmol Cl^- released (N = 6), indicating that 4-OH-TPN served as the terminal electron acceptor for organohalide respiration of Dehalogenimonas species. A draft genome of Dehalogenimonas species was assembled through metagenomic sequencing, which harbors 30 putative reductive dehalogenase genes. Syntrophobacter, Acetobacterium, and Methanosarcina spp. were found to be the major non-dechlorinating populations in the microbial community, who might play important roles in the reductive dechlorination of 4-OH-TPN by the Dehalogenimonas species. This study first reports that Dehalogenimonas sp. can also respire on the seemingly dead-end product of TePN, paving the way to complete biotransformation of the widely present TePN and broadening the substrate spectrum of Dehalogenimonas sp. to polychlorinated hydroxy-benzonitrile.

Organohalide Respiration with Diclofenac by Dehalogenimonas

Diclofenac (DCF) is a pharmaceutically active contaminant frequently found in aquatic ecosystems. The transformation pathways and microbiology involved in the biodegradation of DCF, particularly under anoxic conditions, remain poorly understood. Here, we demonstrated microbially mediated reductive dechlorination of DCF in anaerobic enrichment culture derived from contaminated river sediment. Over 90% of the initial 76.7 ± 3.6 μM DCF was dechlorinated at a maximum rate of 1.8 ± 0.3 μM day^-1 during a 160 days' incubation. Mass spectrometric analysis confirmed that 2-(2-((2-chlorophenyl)amino)phenyl)acetic acid (2-CPA) and 2-anilinophenylacetic acid (2-APA) were formed as the monochlorinated and nonchlorinated DCF transformation products, respectively. A survey of microbial composition and Sanger sequencing revealed the enrichment and dominance of a new Dehalogenimonas population, designated as Dehalogenimonas sp. strain DCF, in the DCF-dechlorinating community. Following the stoichiometric conversion of DCF to 2-CPA (76.0 ± 2.1 μM) and 2-APA (3.7 ± 0.8 μM), strain DCF cell densities increased by 24.4 ± 4.4-fold with a growth yield of 9.0 ± 0.1 × 10⁸ cells per μmol chloride released. Our findings expand the metabolic capability in the genus Dehalogenimonas and highlight the relevant roles of organohalide-respiring bacteria for the natural attenuation of halogenated contaminants of emerging concerns (e.g., DCF).

Effect of microplastics on microbial dechlorination of a polychlorinated biphenyl mixture (Aroclor 1260)

Microplastics (MPs) and polychlorinated biphenyls (PCBs) generally coexist in the environment, posing risks to public health and the environment. This study investigated the effect of different MPs on the microbial anaerobic reductive dechlorination of Aroclor 1260, a commercial PCB mixture. MP exposure inhibited microbial reductive dechlorination of PCBs, with inhibition rates of 39.43%, 23.97%, and 17.53% by polyethylene (PE), polypropylene (PP), and polystyrene (PS), respectively. The dechlorination rate decreased from 1.63 μM Cl^- d^-1 to 0.99-1.34 μM Cl^- d^-1 after MP amendment. Chlorine removal in the meta-position of PCBs was primarily inhibited by MPs, with no changes in the final PCB dechlorination metabolites. The microbial community compositions in MP biofilms were not significantly different (P > 0.05) from those in suspension culture, although possessing greater Dehalococcoides abundance (0.52-0.81% in MP biofilms; 0.03-0.12% in suspension culture). The co-occurrence network analysis revealed that the presence of MPs attenuated microbial synergistic interactions in the dechlorinating culture systems, which may contribute to the inhibitory effect on microbial PCB dechlorination. These findings are important for comprehensively understanding microbial dechlorination behavior and the environmental fate of PCBs in environments with co-existing PCBs and MPs and for guiding the application of in situ PCB bioremediation.

Mechanistic insight into co-metabolic dechlorination of hexachloro-1,3-butadiene in Dehalococcoides

Hexachloro-1,3-butadiene (HCBD) as one of emerging persistent organic pollutants (POPs) poses potential risk to human health and ecosystems. Organohalide-respiring bacteria (OHRB)-mediated reductive dehalogenation represents a promising strategy to remediate HCBD-contaminated sites. Nonetheless, information on the HCBD-dechlorinating OHRB and their dechlorination pathways remain unknown. In this study, both in vivo and in vitro experiments, as well as quantum chemical calculation, were employed to successfully identify and characterize the reductive dechlorination of HCBD by Dehalococcoides. Results showed that some Dehalococcoides extensively dechlorinated HCBD to (E)-1,2,3-tri-CBD via (E)-1,1,2,3,4-penta-CBD and (Z,E)-1,2,3,4-tetra-CBD in a co-metabolic way. Both qPCR and 16S rRNA gene amplicon sequencing analyses suggested that the HCBD-dechlorinating Dehalococcoides coupled their cell growth with dechlorination of perchloroethene (PCE), rather than HCBD. The in vivo and in vitro ATPase assays indicated ≥78.89% decrease in ATPase activity upon HCBD addition, which suggested HCBD inhibition on ATPase-mediated energy harvest and provided rationality on the Dehalococcoides-mediated co-metabolic dechlorination of HCBD. Interestingly, dehalogenation screening of organohalides with the HCBD-dechlorinating enrichment cultures showed that debromination of bromodichloromethane (BDCM) was active in the in vitro RDase assays but non-active in the in vivo experiments. Further in vitro assays of hydrogenase activity suggested that significant inhibition of BDCM on the hydrogenase activity could block electron derivation from H₂ for consequent reduction of organohalides in the in vivo experiments. Therefore, our results provided unprecedented insight into metabolic, co-metabolic and RDase-active-only dehalogenation of varied organohalides by specific OHRB, which could guide future screening of OHRB for remediation of sites contaminated by HCBD and other POPs.

Metagenomic analysis further extends the role of Chloroflexi in fundamental biogeochemical cycles

Chloroflexi members are ubiquitous and have been extensively studied; however, the evolution and metabolic pathways of Chloroflexi members have long been debated. In the present study, the evolution and the metabolic potentials of 17 newly obtained Chloroflexi metagenome-assembled genomes (MAGs) were evaluated using genome and horizontal gene transfer (HGT) analysis. Taxonomic analysis suggests that the MAGs of the present study might be novel. One MAG encodes genes for anoxygenic phototrophy. The HGT analysis suggest that genes responsible for anoxygenic phototrophy in the MAG might have been transferred from Proteobacteria/Chlorobi. The evolution of anaerobic photosynthesis, which has long been questioned, has now been shown to be the result of HGT events. An incomplete Wood-Ljungdahl pathway (with missing genes metF, acsE, fdh, and acsA) was reported in Dehalococcoidetes members. In the present study, MAGs that were not the Dehalococcoidetes members encode genes acsA, acsB, metF and acsE. The genes responsible for sulfate reduction (sat, cysC and sir), dissimilatory sulfite reductase (dsrA and dsrB), and aerobic and anaerobic carbon monoxide oxidation (coxSML and cooSF) were detected in the present study MAGs. The present study expands our knowledge of the possible metabolic potentials of the phylum Chloroflexi and clarifies the evolution of anaerobic photosynthesis.

Long-term dechlorination of cis-DCE to ethene with co-immobilized Dehalococcoides mccartyi BAV1 and Clostridium butyricum in silica gel system

Chloroethenes are common groundwater pollutants, and have been classified as toxic and carcinogenic to humans. The metabolites of chloroethenes, cis-dichloroethene (cis-DCE) and vinyl chloride (VC) commonly accumulate in groundwater due to their recalcitrant reductive dechlorination under anaerobic conditions. Dehalococcoides mccartyi (Dhc) is the key anaerobic bacteria for complete dechlorination of chloroethene, and Clostridium butyricum (C. butyricum) can provide hydrogen for supporting the growth of Dhc. In this study, we co-immobilized Dhc strain BAV1 and C. butyricum in a silica gel to determine the ability of the complete dechlorination of cis-DCE. Our results showed that our immobilized system could protect BAV1 from a high concentration (8 mM) of cis-DCE to carry out complete dechlorination. After the long-term use of our immobilized system, the activity of complete dechlorination was maintained for more than 180 consecutive days. Furthermore, we applied the immobilized system to remediate contaminated groundwater and uncovered the complete dechlorination of cis-DCE into ethene, a non-toxic product, within 28 days. Therefore, this novel co-immobilized system could serve a solution for bioremediation at chloroethene-contaminated sites.

Dehalococcoides mccartyi NIT01, a novel isolate, dechlorinates high concentrations of chloroethenes by expressing at least six different reductive dehalogenases

This study presents the isolation of a novel strain of Dehalococcoides mccartyi, NIT01, which can completely dechlorinate up to 4.0 mM of trichloroethene to ethene via 1,2-cis-dichroroethene and vinyl chloride within 25 days. Strain NIT01 dechlorinated chloroethenes (CEs) at a temperature range of 25-32 °C and pH range of 6.5-7.8. The activity of the strain was inhibited by salt at more than 1.3% and inactivated by 1 h exposure to 2.0% air or 0.5 ppm hypochlorous acid. The genome of NIT01 was highly similar to that of the Dehalococcoides strains DCMB5, GT, 11a5, CBDB1, and CG5, and all included identical 16S rRNA genes. Moreover, NIT01 had 19 rdhA genes including NIT01-rdhA7 and rdhA13, which are almost identical to vcrA and pceA that encode known dehalogenases for tetrachloroethene and vinyl chloride, respectively. We also extracted RdhAs from the membrane fraction of NIT01 using 0.5% n-dodecyl-β-d-maltoside and separated them by anion exchange chromatography to identify those involved in CE dechlorination. LC/MS identification of the LDS-PAGE bands and RdhA activities in the fractions indicated cellular expression of six RdhAs. NIT01-RdhA7 (VcrA) and NIT01-RdhA15 were highly detected and NIT01-RdhA6 was the third-most detected. Among these three RdhAs, NIT01-RdhA15 and NIT01-RdhA6 had no biochemically identified relatives and were suggested to be novel functional dehalogenases for CEs. The expression of multiple dehalogenases may support bacterial tolerance to high concentrations of CEs.

Dehalogenation of Polybrominated Diphenyl Ethers and Polychlorinated Biphenyls Catalyzed by a Reductive Dehalogenase in Dehalococcoides mccartyi Strain MB

Polybrominated diphenyl ethers (PBDEs) and polychlorinated biphenyls (PCBs) are notorious persistent organic pollutants. However, few organohalide-respiring bacteria that harbor reductive dehalogenases (RDases) capable of dehalogenating these pollutants have been identified. Here, we report reductive dehalogenation of penta-BDEs and PCBs byDehalococcoides mccartyi strain MB. The PCE-pregrown cultures of strain MB debrominated 86.6 ± 7.4% penta-BDEs to di- to tetra-BDEs within 5 days. Similarly, extensive dechlorination of Aroclor1260 and Aroclor1254 was observed in the PCE-pregrown cultures of strain MB, with the average chlorine per PCB decreasing from 6.40 ± 0.02 and 5.40 ± 0.03 to 5.98 ± 0.11 and 5.19 ± 0.07 within 14 days, respectively; para-substituents were preferentially dechlorinated from PCBs. Moreover, strain MB showed distinct enantioselective dechlorination of different chiral PCB congeners. Dehalogenation activity and cell growth were maintained during the successive transfer of cultures when amended with penta-BDEs as the sole electron acceptors but not when amended with only PCBs, suggesting metabolic and co-metabolic dehalogenation of these compounds, respectively. Transcriptional analysis, proteomic profiling, and in vitro activity assays indicated that MbrA was involved in dehalogenating PCE, PCBs, and PBDEs. Interestingly, resequencing of mbrA in strain MB identified three nonsynonymous mutations within the nucleotide sequence, although the consequences of which remain unknown. The substrate versatility of MbrA enabled strain MB to dechlorinate PCBs in the presence of either penta-BDEs or PCE, suggesting that co-metabolic dehalogenation initiated by multifunctional RDases may contribute to PCB attenuation at sites contaminated with multiple organohalide pollutants.

Interspecies transfer of biosynthetic cobalamin for complete dechlorination of trichloroethene by Dehalococcoides mccartyi

Complete dechlorination of trichloroethene (TCE) by Dehalococcoides mccartyi is catalyzed by reductive dehalogenases (RDases), which possess cobalamin as the crucial cofactor. However, virtually all D. mccartyi isolated thus far are corrinoid auxotrophs. The exogenous addition of commercially available cobalamin for TCE-contaminated site decontamination is costly. In this study, TCE reduction by a D. mccartyi-containing microbial consortium utilizing biosynthetic cobalamin generated by interior corrinoid-producing organisms within this microbial consortium was studied. The results confirmed that subcultures without exogenous cobalamin in the medium were apparently unaffected and were able to successively metabolize TCE to nonchlorinated ethene. The 2-bromoethanesulfonate and ampicillin resistance tests results suggested that ampicillin-sensitive bacteria rather than methanogenic archaea within this microbial consortium were responsible for biosynthesizing cobalamin. Moreover, relatively stable carbon isotopic enrichment factor (ɛ-_carbon) values of TCE were obtained regardless of whether exogenous cobalamin or selective inhibitors existed in the medium, indicating that the cobalamin biosynthesized by these organisms was absorbed and utilized by D. mccartyi for RDase synthesis and eventually participated in TCE reduction. Finally, the Illumina MiSeq sequencing analysis indicated that Desulfitobacterium and Acetobacterium in this microbial consortium were responsible for the de novo cobalamin biosynthesis to fulfill the requirements of D. mccartyi for TCE metabolism.

Novel nitrite reductase domain structure suggests a chimeric denitrification repertoire in the phylum Chloroflexi

Denitrification plays a central role in the global nitrogen cycle, reducing and removing nitrogen from marine and terrestrial ecosystems. The flux of nitrogen species through this pathway has a widespread impact, affecting ecological carrying capacity, agriculture, and climate. Nitrite reductase (Nir) and nitric oxide reductase (NOR) are the two central enzymes in this pathway. Here we present a previously unreported Nir domain architecture in members of phylum Chloroflexi. Phylogenetic analyses of protein domains within Nir indicate that an ancestral horizontal transfer and fusion event produced this chimeric domain architecture. We also identify an expanded genomic diversity of a rarely reported NOR subtype, eNOR. Together, these results suggest a greater diversity of denitrification enzyme arrangements exist than have been previously reported.

Anaerobic Microbial Dechlorination of 6:2 Chlorinated Polyfluorooctane Ether Sulfonate and the Underlying Mechanisms

The microbial transformation potential of 6:2 chlorinated polyfluorooctane ether sulfonate (6:2 Cl-PFESA) was explored in anaerobic microbial systems. Microbial communities from anaerobic wastewater sludge, an anaerobic digester, and anaerobic dechlorinating cultures enriched from aquifer materials reductively dechlorinated 6:2 Cl-PFESA to 6:2 hydrogen-substituted polyfluorooctane ether sulfonate (6:2 H-PFESA), which was identified as the sole metabolite by non-target analysis. Rapid and complete reductive dechlorination of 6:2 Cl-PFESA was achieved by the anaerobic dechlorinating cultures. The microbial community of the anaerobic dechlorinating cultures was impacted by 6:2 Cl-PFESA exposure. Organohalide-respiring bacteria originally present in the anaerobic dechlorinating cultures, including Geobacter, Dehalobacter, and Dehalococcoides, decreased in relative abundance over time. As the relative abundance of organohalide-respiring bacteria decreased, the rates of 6:2 Cl-PFESA dechlorination decreased, suggesting that the most likely mechanism for reductive dechlorination of 6:2 Cl-PFESA was co-metabolism rather than organohalide respiration. Reductive defluorination of 6:2 Cl-PFESA was not observed. Furthermore, 6:2 H-PFESA exhibited 5.5 times lower sorption affinity to the suspended biosolids than 6:2 Cl-PFESA, with the prospect of increased mobility in the environment. These results show the susceptibility of 6:2 Cl-PFESA to microbially mediated reductive dechlorination and the likely persistence of the product, 6:2 H-PFESA, in anaerobic environments.

Rhizosphere bacteria community and functions under typical natural halophyte communities in North China salinized areas

Soil salinity is a serious environmental issue in arid China. Halophytes show extreme salt tolerance and are grow in saline-alkaline environments. There rhizosphere have complex bacterial communities, which mediate a variety of interactions between plants and soil. High-throughput sequencing was used to investigated rhizosphere bacterial community changes under the typical halophyte species in arid China. Three typical halophytes were Leymus chinensis (LC), Puccinellia tenuiflora (PT), Suaeda glauca (SG). The dominant phyla were Proteobacteria, Actinobacteria, Chloroflexi, Gemmatimonadetes, Acidobacteria and Bacteroidetes, Suaeda glauca rhizosphere has stronger enrichment of Nitrospirae and Cyanobacteria. The Ace, Chao and Shannon indices were significantly higher in soils under LC and SG (P<0.05). Functional predictions, based on 16S rRNA gene by PICRUSt, indicated that Energy metabolism, Amino acid metabolism, Carbohydrate metabolism and Fatty acid metabolism are dominant bacterial functions in three halophytes rhizosphere soil. Carbon metabolism, Oxidative phosphorylation, Methane metabolism, Sulfur metabolism and Nitrogen metabolism in SG were significantly higher than that in LC and PT. Regression analysis revealed that rhizosphere soil bacterial community structure is influenced by soil organic matter (SOM) and soil water content (SWC), while soil bacterial community diversity is affected by soil pH. This study contributes to our understanding of the distribution characteristics and metabolic functions under different halophyte rhizosphere bacterial communities, and will provide references for the use of rhizosphere bacteria to regulate the growth of halophytes and ecological restoration of saline soil.

Metagenomic insights into mixotrophic denitrification facilitated nitrogen removal in a full-scale A2/O wastewater treatment plant

Wastewater treatment plants (WWTPs) are important for pollutant removal from wastewater, elimination of point discharges of nutrients into the environment and water resource protection. The anaerobic/anoxic/oxic (A2/O) process is widely used in WWTPs for nitrogen removal, but the requirement for additional organics to ensure a suitable nitrogen removal efficiency makes this process costly and energy consuming. In this study, we report mixotrophic denitrification at a low COD (chemical oxygen demand)/TN (total nitrogen) ratio in a full-scale A2/O WWTP with relatively high sulfate in the inlet. Nitrogen and sulfur species analysis in different units of this A2/O WWTP showed that the internal sulfur cycle of sulfate reduction and reoxidation occurred and that the reduced sulfur species might contribute to denitrification. Microbial community analysis revealed that Thiobacillus, an autotrophic sulfur-oxidizing denitrifier, dominated the activated sludge bacterial community. Metagenomics data also supported the potential of sulfur-based denitrification when high levels of denitrification occurred, and sulfur oxidation and sulfate reduction genes coexisted in the activated sludge. Although most of the denitrification genes were affiliated with heterotrophic denitrifiers with high abundance, the narG and napA genes were mainly associated with autotrophic sulfur-oxidizing denitrifiers. The functional genes related to nitrogen removal were actively expressed even in the unit containing relatively highly reduced sulfur species, indicating that the mixotrophic denitrification process in A2/O could overcome not only a shortage of carbon sources but also the inhibition by reduced sulfur of nitrification and denitrification. Our results indicate that a mixotrophic denitrification process could be developed in full-scale WWTPs and reduce the requirement for additional carbon sources, which could endow WWTPs with more flexible and adaptable nitrogen removal.

Thermogenic hydrocarbon biodegradation by diverse depth-stratified microbial populations at a Scotian Basin cold seep

At marine cold seeps, gaseous and liquid hydrocarbons migrate from deep subsurface origins to the sediment-water interface. Cold seep sediments are known to host taxonomically diverse microorganisms, but little is known about their metabolic potential and depth distribution in relation to hydrocarbon and electron acceptor availability. Here we combined geophysical, geochemical, metagenomic and metabolomic measurements to profile microbial activities at a newly discovered cold seep in the deep sea. Metagenomic profiling revealed compositional and functional differentiation between near-surface sediments and deeper subsurface layers. In both sulfate-rich and sulfate-depleted depths, various archaeal and bacterial community members are actively oxidizing thermogenic hydrocarbons anaerobically. Depth distributions of hydrocarbon-oxidizing archaea revealed that they are not necessarily associated with sulfate reduction, which is especially surprising for anaerobic ethane and butane oxidizers. Overall, these findings link subseafloor microbiomes to various biochemical mechanisms for the anaerobic degradation of deeply-sourced thermogenic hydrocarbons.

Temperature impacts community structure and function of phototrophic Chloroflexi and Cyanobacteria in two alkaline hot springs in Yellowstone National Park

Photosynthetic bacteria are abundant in alkaline, terrestrial hot springs and there is a long history of research on phototrophs in Yellowstone National Park (YNP). Hot springs provide a framework to examine the ecophysiology of phototrophs in situ because they provide natural gradients of geochemistry, pH and temperature. Phototrophs within the Cyanobacteria and Chloroflexi groups are frequently observed in alkaline hot springs. Decades of research has determined that temperature constrains Cyanobacteria in alkaline hot springs, but factors that constrain the distribution of phototrophic Chloroflexi remain unresolved. Using a combination of 16S rRNA gene sequencing and photoassimilation microcosms, we tested the hypothesis that temperature would constrain the activity and composition of phototrophic Cyanobacteria and Chloroflexi. We expected diversity and rates of photoassimilation to decrease with increasing temperature. We report 16S rRNA amplicon sequencing along with carbon isotope signatures and photoassimilation from 45 to 72°C in two alkaline hot springs. We find that Roseiflexus, Chloroflexus (Chloroflexi) and Leptococcus (Cyanobacteria) operational taxonomic units (OTUs) have distinct distributions with temperature. This distribution suggests that, like phototrophic Cyanobacteria, temperature selects for specific phototrophic Chloroflexi taxa. The richness of phototrophic Cyanobacteria decreased with increasing temperature along with a decrease in oxygenic photosynthesis, whereas Chloroflexi richness and rates of anoxygenic photosynthesis did not decrease with increasing temperature, even at temperatures approaching the upper limit of photosynthesis (~72-73°C). Our carbon isotopic data suggest an increasing prevalence of the 3-hydroxypropionate pathway with decreasing temperature coincident with photoautotrophic Chloroflexi. Together these results indicate temperature plays a role in defining the niche space of phototrophic Chloroflexi (as has been observed for Cyanobacteria), but other factors such as morphology, geochemistry, or metabolic diversity of Chloroflexi, in addition to temperature, could determine the niche space of this highly versatile group.

Bioenhanced back diffusion and population dynamics of Dehalococcoides mccartyi strains in heterogeneous porous media

Diffusion, sorption-desorption, and biodegradation influence chlorinated solvent storage in, and release (mass flux) from, low-permeability media. Although bioenhanced dissolution of non-aqueous phase liquids has been well-documented, less attention has been directed towards biologically-mediated enhanced diffusion from low-permeability media. This process was investigated using a heterogeneous aquifer cell, packed with 20-30 mesh Ottawa sand and lenses of varying permeability (1.0 × 10^-12-1.2 × 10^-11 m²) and organic carbon (OC) content (<0.1%-2%), underlain by trichloroethene (TCE)-saturated clay. Initial contaminant loading was attained by flushing with 0.5 mM TCE. Total chlorinated ethenes removal by hydraulic flushing was then compared for abiotic and bioaugmented systems (KB-1® SIREM; Guelph, ON). A numerical model incorporating coupled diffusion and (de)sorption facilitated quantification of bio-enhanced TCE release from low-permeability lenses, which ranged from 6% to 53%. Although Dehalococcoides mccartyi (Dhc) 16S rRNA genes were uniformly distributed throughout the porous media, strain-specific distribution, as indicated by the reductive dehalogenase (RDase) genes vcrA, bvcA, and tceA, was influenced by physical and chemical heterogeneity. Cells harboring the bvcA gene comprised 44% of the total RDase genes in the lower clay layer and media surrounding high OC lenses, but only 2% of RDase genes at other locations. Conversely, cells harboring the vcrA gene comprised 50% of RDase genes in low-permeability media compared with 85% at other locations. These results demonstrate the influence of microbial processes on back diffusion, which was most evident in regions with pronounced contrasts in permeability and OC content. Bioenhanced mass transfer and changes in the relative abundance of Dhc strains are likely to impact bioremediation performance in heterogeneous systems.

Widespread microbial mercury methylation genes in the global ocean

Methylmercury is a neurotoxin that bioaccumulates from seawater to high concentrations in marine fish, putting human and ecosystem health at risk. High methylmercury levels have been found in the oxic subsurface waters of all oceans, but only anaerobic microorganisms have been shown to efficiently produce methylmercury in anoxic environments. The microaerophilic nitrite-oxidizing bacteria Nitrospina have previously been suggested as possible mercury methylating bacteria in Antarctic sea ice. However, the microorganisms responsible for processing inorganic mercury into methylmercury in oxic seawater remain unknown. Here, we show metagenomic and metatranscriptomic evidence that the genetic potential for microbial methylmercury production is widespread in oxic seawater. We find high abundance and expression of the key mercury methylating genes hgcAB across all ocean basins, corresponding to the taxonomic relatives of known mercury methylating bacteria from Deltaproteobacteria, Firmicutes and Chloroflexi. Our results identify Nitrospina as the predominant and widespread microorganism carrying and actively expressing hgcAB. The highest hgcAB abundance and expression occurs in the oxic subsurface waters of the global ocean where the highest MeHg concentrations are typically observed.

Widespread microbial mercury methylation genes in the global ocean

Methylmercury is a neurotoxin that bioaccumulates from seawater to high concentrations in marine fish, putting human and ecosystem health at risk. High methylmercury levels have been found in the oxic subsurface waters of all oceans, but only anaerobic microorganisms have been shown to efficiently produce methylmercury in anoxic environments. The microaerophilic nitrite-oxidizing bacteria Nitrospina have previously been suggested as possible mercury methylating bacteria in Antarctic sea ice. However, the microorganisms responsible for processing inorganic mercury into methylmercury in oxic seawater remain unknown. Here, we show metagenomic and metatranscriptomic evidence that the genetic potential for microbial methylmercury production is widespread in oxic seawater. We find high abundance and expression of the key mercury methylating genes hgcAB across all ocean basins, corresponding to the taxonomic relatives of known mercury methylating bacteria from Deltaproteobacteria, Firmicutes and Chloroflexi. Our results identify Nitrospina as the predominant and widespread microorganism carrying and actively expressing hgcAB. The highest hgcAB abundance and expression occurs in the oxic subsurface waters of the global ocean where the highest MeHg concentrations are typically observed.

Widespread microbial mercury methylation genes in the global ocean

Methylmercury is a neurotoxin that bioaccumulates from seawater to high concentrations in marine fish, putting human and ecosystem health at risk. High methylmercury levels have been found in the oxic subsurface waters of all oceans, but only anaerobic microorganisms have been shown to efficiently produce methylmercury in anoxic environments. The microaerophilic nitrite-oxidizing bacteria Nitrospina have previously been suggested as possible mercury methylating bacteria in Antarctic sea ice. However, the microorganisms responsible for processing inorganic mercury into methylmercury in oxic seawater remain unknown. Here, we show metagenomic and metatranscriptomic evidence that the genetic potential for microbial methylmercury production is widespread in oxic seawater. We find high abundance and expression of the key mercury methylating genes hgcAB across all ocean basins, corresponding to the taxonomic relatives of known mercury methylating bacteria from Deltaproteobacteria, Firmicutes and Chloroflexi. Our results identify Nitrospina as the predominant and widespread microorganism carrying and actively expressing hgcAB. The highest hgcAB abundance and expression occurs in the oxic subsurface waters of the global ocean where the highest MeHg concentrations are typically observed.

Structural basis underlying the electron transfer features of a blue copper protein auracyanin from the photosynthetic bacterium Roseiflexus castenholzii

Auracyanin (Ac) is a blue copper protein that mediates the electron transfer between Alternative Complex III (ACIII) and downstream electron acceptors in both fort chains of filamentous anoxygenic phototrophs. Here, we extracted and purified the air-oxidized RfxAc from the photoheterotrophically grown Roseiflexus castenholzii, and we illustrated the structural basis underlying its electron transferring features. Spectroscopic and enzymatic analyses demonstrated the reduction of air-oxidized RfxAc by the ACIII upon oxidation of menaquinol-4 and menaquinol-7. Crystal structures of the air-oxidized and Na-dithionite-reduced RfxAc at 2.2 and 2.0 Å resolutions, respectively, showed that the copper ions are coordinated by His77, His146, Cys141, and Met151 in minor different geometries. The Cu¹-S^δ bond length increase of Met151, and the electron density Fourier differences at Cu¹ and His77 demonstrated their essential roles in the dithionite-induced reduction. Structural comparisons further revealed that the RfxAc contains a Chloroflexus aurantiacus Ac-A-like copper binding pocket and a hydrophobic patch surrounding the exposed edge of His146 imidazole, as well as an Ac-B-like Ser- and Thr-rich polar patch located at a different site on the surface. These spectroscopic and structural features allow RfxAc to mediate electron transfers between the ACIII and redox partners different from those of Ac-A and Ac-B. These results provide a structural basis for further investigating the electron transfer and energy transformation mechanism of bacterial photosynthesis, and the diversity and evolution of electron transport chains.

Enhanced anaerobic degradation of nitrogen heterocyclic compounds with methanol, sodium citrate, chlorella, spirulina, and carboxymethylcellulose as co-metabolic substances

The aim of the study was to explore the feasibility of methanol, sodium citrate, chlorella, spirulina, and carboxymethylcellulose (CMC) as co-metabolic substances in strengthening the anaerobic degradation of selected nitrogen heterocyclic compounds (NHCs). Chlorella, spirulina, and CMC as co-metabolic substances were first introduced into the enhanced anaerobic treatment of refractory compounds. With the addition of 300 μg/L sodium citrate, chlorella, spirulina, and CMC, reactor 3, reactor 4, reactor 5, and reactor 6 had higher degradation ratios than reactor 2 with methanol as co-metabolic substance. The addition of sodium citrate, chlorella, spirulina, and CMC increased the number of bacterial sequences, promoted the richness and diversity of the bacterial community structure, and enriched the functional genera (Levilinea and Longilinea) responsible for the degradation of quinoline and indole.

Identification and characterization of a bacterial core methionine synthase

Methionine synthases are essential enzymes for amino acid and methyl group metabolism in all domains of life. Here, we describe a putatively anciently derived type of methionine synthase yet unknown in bacteria, here referred to as core-MetE. The enzyme appears to represent a minimal MetE form and transfers methyl groups from methylcobalamin instead of methyl-tetrahydrofolate to homocysteine. Accordingly, it does not possess the tetrahydrofolate binding domain described for canonical bacterial MetE proteins. In Dehalococcoides mccartyi strain CBDB1, an obligate anaerobic, mesophilic, slowly growing organohalide-respiring bacterium, it is encoded by the locus cbdbA481. In line with the observation to not accept methyl groups from methyl-tetrahydrofolate, all known genomes of bacteria of the class Dehalococcoidia lack metF encoding for methylene-tetrahydrofolate reductase synthesizing methyl-tetrahydrofolate, but all contain a core-metE gene. We heterologously expressed core-MetECBDB in E. coli and purified the 38 kDa protein. Core-MetECBDB exhibited Michaelis-Menten kinetics with respect to methylcob(III)alamin (KM ≈ 240 µM) and L-homocysteine (KM ≈ 50 µM). Only methylcob(III)alamin was found to be active as methyl donor with a kcat ≈ 60 s-1. Core-MetECBDB did not functionally complement metE-deficient E. coli strain DH5α (ΔmetE::kan) suggesting that core-MetECBDB and the canonical MetE enzyme from E. coli have different enzymatic specificities also in vivo. Core-MetE appears to be similar to a MetE-ancestor evolved before LUCA (last universal common ancestor) using methylated cobalamins as methyl donor whereas the canonical MetE consists of a tandem repeat and might have evolved by duplication of the core-MetE and diversification of the N-terminal part to a tetrahydrofolate-binding domain.

Deciphering microbiomes in anaerobic reactors with superior trichloroethylene dechlorination performance at low pH conditions

Different pH conditions have been demonstrated to affect the activities of dechlorinating populations participating in the successive dechlorination of trichloroethylene to ethylene. However, the mechanism of the effect of pH conditions on the assembly of dechlorinating populations and their relations to the structure, function, and dynamics of the microbiome are unclear. In this study, we evaluated the effects of pH on microbiomes assembled in anaerobic trichloroethylene-dechlorinating reactors under neutral (pH 7.2), acidic (pH 6.2), and alkaline (pH 8.2) conditions. The results revealed that among the reactors, the acidic reactor had the highest efficiency for dechlorination without accumulation of dechlorinated metabolites, even at high loading rates. The results of high-throughput sequencing of the 16S rRNA gene indicated that the microbiomes in the 3 reactors underwent varied dynamic succession. The acidic reactor harbored a higher degree of complex microbes, dechlorinator diversity, and abundance of the Victoria subgroup of Dehalococcoides (1.2 ± 0.1 × 10⁶ cell/mL), which were approximately 10-10²-fold higher than those at neutral and alkaline conditions. The pH settings altered species-species connectivity and complexity of microbial interaction networks, with more commensal interactions in the dechlorinators of the acidic reactor. As predicted, abundances of several functional gene categories were in strong linearity with pH values, and the microbiome possessed significantly more abundant functions in the acidic reactor (P < 0.001), such as potentially stimulating hydrogen production, cobalamin synthesis, cobalt transport, transport and metabolism of amino acids and secondary metabolites, cell motility, and transcription. All results of microbiomic analyses consistently revealed the observed superior dechlorination process and suggested an association of the reductive dechlorination process with the pH-dependent microbiome. The results of this study provide a new insight into the trichloroethylene dechlorination with regards to pH, and they will be useful for improving bioremediation and management of trichloroethylene-contaminated sites.

Enhanced reductive dechlorination of trichloroethene with immobilized Clostridium butyricum in silica gel

Deteriorated environmental conditions during the bioremediation of trichloroethene (TCE)-polluted groundwater cause decreased treatment efficiencies. This study assessed the effect of applying immobilized Clostridium butyricum (a hydrogen-producing bacterium) in silica gel on enhancing the reductive dechlorination efficiency of TCE with the slow polycolloid-releasing substrate (SPRS) supplement in groundwater. The responses of microbial communities with the immobilized system (immobilized Clostridium butyricum and SPRS amendments) were also characterized by the metagenomics assay. A complete TCE removal in microcosms was obtained within 30 days with the application of this immobilized system via reductive dechlorination processes. An increase in the population of Dehalococcoides spp. was observed using the quantitative polymerase chain reaction (qPCR) analysis. Results of metagenomics assay reveal that the microbial communities in the immobilized system were distinct from those in systems with SPRS only. Bacterial communities associated with TCE biodegradation also increased in microcosms treated with the immobilized system. The immobilized system shows a great potential to promote the TCE dechlorination efficiency, and the metagenomics-based approach provides detailed insights into dechlorinating microbial community dynamics. The results would be helpful in designing an in situ immobilized system to enhance the bioremediation efficiency of TCE-contaminated groundwater.

Engineered in situ biogeochemical transformation as a secondary treatment following ISCO - A field test

ISCO using activated sodium persulphate is a widely used technology for treating chlorinated solvent source zones. In sensitive areas, however, high groundwater sulphate concentrations following treatment may be a drawback. In situ biogeochemical transformation, a technology that degrades contaminants via reduced iron minerals formed by microbial activity, offers a potential solution for such sites, the bioreduction of sulphate and production of iron sulphides that abiotically degrade chlorinated ethenes acting as a secondary technology following ISCO. This study assesses this approach in the field using hydrochemical and molecular tools, solid phase analysis and geochemical modelling. Following a neutralisation and bioaugmentation, favourable conditions for iron- and sulphate-reducers were created, resulting in a remarkable increase in their relative abundance. The abundance of dechlorinating bacteria (Dehalococcoides mccartyi, Dehalobacter sp. and Desulfitobacterium spp.) remained low throughout this process. The activity of iron- and sulphate-reducers was further stimulated through application of magnetite plus starch and microiron plus starch, resulting in an increase in ferrous iron concentration (from <LOQ to 337 mg/l), a decrease in sulphate concentration by 74-95% and production of hydrogen sulphide (from <LOQ to 25.9 mg/l). At the same time, a gradual revival of dechlorinators and an increase in ethene concentration was also observed. Tetrachloroethene and trichloroethene concentrations decreased by 98.5-99.98% and 75.4-98.5%, respectively. A decline in chlorine number indicated that biological dechlorination contributed to CVOC removal. This study brings new insights into biogeochemical processes that, when properly engineered, could provide a viable solution for secondary treatment.

Addition of Shewanella oneidensis MR-1 to the Dehalococcoides-containing culture enhances the trichloroethene dechlorination

Dehalococcoides is able to completely dehalogenate tetrachloroethene (PCE) and trichloroethene (TCE) to ethene (ETH). However, the dechlorination efficiency of Dehalococcoides is low and result in the accumulation of toxic intermediates. In this study, Shewanella oneidensis MR-1 (S. oneidensis MR-1) was added to the Dehalococcoides-containing culture and the complete TCE to ETH dechlorination was shortened from 24 days to 16 days. Dehalococcoides-targeted 16S rRNA gene and two model reductive dehalogenase (RDase) genes (tceA and vcrA), responsible for dechlorinating TCE to vinyl chloride (VC) and VC to ETH respectively, were characterized. Results showed that S. oneidensis MR-1 has no effect on the cell growth while the RDase genes expression was up-regulated and the RDase activity of Dehalococcoides was elevated. The mRNA abundance of vcrA increased approximately tenfold along with the increased concentration of vitamin B₁₂ (cyanocobalamin). Interestingly, the addition of S. oneidensis MR-1 increased the concentration of vitamin B₁₂ by affecting the microbial community structure. Therefore, the addition of S. oneidensis MR-1 might have a positive effect on regulating the activity of RDase of functional microorganisms and uptake of vitamin B₁₂, and further provided a practical vision of chloroethene dechlorination by the Dehalococcoides-containing culture.

Anaerobic degradation of 2,4,5-trichlorophenoxyacetic acid by enrichment cultures from freshwater sediments

The anaerobic biodegradation of 2,4,5-trichlorophenoxyacetic acid (2,4,5-T) was investigated using enrichment cultures from freshwater sediments at two different sites in the region of Halle, central Germany. 2,4,5-T and different organic acids or hydrogen were added as possible electron acceptor and electron donors, respectively. The primary enrichment cultures from Saale river sediment completely degraded 2,4,5-T to 3-chlorophenol (3-CP) (major product) and 3,4-dichlorophenol (3,4-DCP) during a 28-day incubation period. Subcultures showed ether cleavage of 2,4,5-T to 2,4,5-trichlorophenol and its stoichiometric dechlorination to 3-CP only in the presence of butyrate. In contrast, the primary enrichment culture from sediment of Posthorn pond dechlorinated 2,4,5-T to 2,5-dichlorophenoxyacetic acid (2,5-D), which, in the presence of butyrate, was degraded further to products such as 3,4-DCP, 2,5-DCP, and 3CP, indicating ether cleaving activities and subsequent dechlorination steps. Experiments with pure cultures of Dehalococcoides mccartyi and Desulfitobacterium hafniense demonstrated their specific dechlorination steps within the overall 2,4,5-T degradation pathways. The results indicate that the route and efficiency of anaerobic 2,4,5-T degradation in the environment depend heavily on the microorganisms present and the availability of slowly fermentable organic compounds.

Degradation of BDE-47 in mangrove sediments under alternating anaerobic-aerobic conditions

Polybrominated diphenyl ethers (PBDEs) resistant to degradation have significant environmental impacts. Anaerobic reductive debromination and aerobic oxidation of PBDEs by microorganisms are main removal mechanisms during natural attenuation, but previous studies often focused on the process under either aerobic or anaerobic condition leading to unsatisfactory removal. The present study aims to remove PBDEs by employing alternating anaerobic-aerobic condition, which is common in inter-tidal mangrove sediments, and elucidate the degradation pathways. During 40-week experiment, BDE-47 reduced with an accumulation of tri-BDEs and di-BDEs as debromination products in all sediments. However, the removal percentages of BDE-47 and the concentrations of debromination congeners varied among flushing regimes. Sediments under less frequent flushing regime (longer duration of aerobic period) had significantly lower concentration and proportion of debromination products, especially BDE-17, than that under more frequent regime (longer anaerobic period). BDE-17 then went through aerobic degradation pathway, as evidenced by the accumulation of its hydroxylation form. Microbial analyses further revealed that less frequent regime favored accumulation of biphenyl dioxygenase gene for aerobic degradation, while more frequent tidal regime promoted growth of dehalogenating bacteria for reductive debromination. This study first time demonstrated that PBDEs in contaminated sediments could be removed under alternating anaerobic-aerobic conditions.

Application of molecular biological tools for monitoring efficiency of trichloroethylene remediation

Trichloroethylene (TCE) is one of the most ubiquitous halogenated organic compounds of concerns of carcinogens in groundwater in Taiwan. Bioremediation has been recognized as a cost-effective approach in reducing TCE concentration. Five pilot-scale wells were constructed to monitor TCE concentrations in contaminated groundwater. With injection of EOS^®, TCE was effectively degraded to 42%-93% by the end of 175 days. The biostimulation with EOS^® was useful in establishing a micro-site anaerobic but with limited contribution. Dilution of the aquifer movement also caused the TCE reduction among injection and monitoring wells. The degradability was affected by the location and the proximity from the injection well. TCE concentrations found to be negatively correlated with the associated Dehalococcoides spp. and functional genes levels. Dhc concentration of 10⁸ copies L^-1 caused the initial 40% of TCE degradation. The well with the optimal degradation owned tceA of 10⁹ cells L^-1_. T-RFLP results indicate the wells with the superior TCE degradability also performed the highest Shannon index number (means the highest diversity), which occurred on the same day that Dhc levels started to enlarge. Desulfovibrio desulfuricans and Desulfuromonas chloroethenica were predominant species identified in the T-RFLP fingerprint profile. In brief, a variety of different factors including well locations, geochemical indicators, and microbial contribution were useful to explain the site-specific optimal TCE remediation approach. The consistence among TCE degradation, Dhc growing pattern, functional gene levels, and the dynamics of the microbial community structure present the novelty of this study.

Reduction in sulfate inhibition of microbial dechlorination of polychlorinated biphenyls in Hudson and Grasse River sediments through fatty acid supplementation

Microbial dechlorination of polychlorinated biphenyls (PCBs) in aquatic sediments may reduce the need for dredging for remediation. To better understand this biotransformation route under different geochemical conditions, the influence of sulfate on dechlorination in sediments from the Hudson River and the Grasse River spiked with two PCB mixtures (PCB 5/12, 64/71, 105/114 and 149/153/170 in Mixture 1 and PCB 5/12, 64/71, 82/97/99, 144/170 in Mixture 2) was investigated. The results showed that PCB dechlorination was partially inhibited in the sulfate-amended sediment microcosms. The rate, extent and preference of dechlorination were mainly controlled by the indigenous differences (sulfate, carbon content etc.) in sediment, but also affected by the PCB mixture composition. An increase of Dehalococcoides 16S rRNA genes coincided with the resumption of dechlorination. Dechlorination preferences were identified using a modified dechlorination pathway analysis approach. The low carbon content and high background sulfate Hudson sediment exhibited more para dechlorination targeting flanked para chlorines. The high carbon content and low background sulfate Grasse sediment preferentially removed more para-flanked meta chlorines than flanked para chlorines. The supplementation of fatty acids (acetate or a mixture of acetate, propionate and butyrate) dramatically increased PCB dechlorination in the Grasse sediment by resuming ortho-flanked meta dechlorination. Rare ortho removals were found in the Grasse sediment after adding fatty acids. This study suggests that supplementary fatty acids might be used to stimulate PCB dechlorination under sulfate reducing conditions, but the effectiveness largely depends on sediment geochemistry.

Redox characteristics of humins and their coupling with potential PCB dechlorinators in southern Yellow Sea sediments

Natural attenuation of polychlorinated biphenyls (PCBs) by indigenous bacteria is an effective remediation strategy for polluted marine sediments. This study investigated the relationships between PCB concentrations in sediment pore water, humin electron transfer capacity, and potential PCB dechlorinators at eight sediment sampling sites in the southern Yellow Sea, China, with differential PCB contamination. Station A2 showed the highest PCB concentration (453.16 ng L^-1 for seven indicator PCBs), especially of less chlorinated PCB congeners (≤5 Cl atoms), humin redox activity, and Dehalococcoides abundance (p < 0.05). Statistical analyses revealed a highly positive correlation between Dehalococcoides abundance and PCB concentration (r = 0.836, p < 0.05) and the electron shuttling ability of humins (r = 0.952, p < 0.01), whereas this was not observed for total bacteria and other potential PCB dechlorinators, e.g., Dehalobacter and Dehalogenimonas. Based on these results, Dehalococcoides might play an important role in the in situ reductive dechlorination of PCBs involving humins in marine sediments, and the natural microbial PCB attenuation capacity at station A2 was high. Chemical characterizations, electrochemical properties, and Fourier transform infrared analysis suggested that humins at station A2 had the highest electron transfer capacity. Furthermore, quinones are likely to be the functional groups that shuttle electrons during PCB dechlorination. Overall, this study provides a useful foundation for evaluating the natural microbial attenuation potential and fates of PCBs in marine sediments and for determining the role of humins as redox mediators in in situ PCB dechlorination by putative indigenous dechlorinators.

Influence of application of manganese ore in constructed wetlands on the mechanisms and improvement of nitrogen and phosphorus removal

Vertical up-flow constructed wetlands (CWs) with manganese ore (Mn ore) as media (M-CWs) were developed to treat simulated polluted river water. The results showed that the average removal efficiencies for NH₄-N, NO₃-N, TN and TP were 91.74%, 83.29%, 87.47% and 65.12% in M-CWs, respectively, which were only 79.12%, 72.90%, 75.85% and 43.23% in the CWs without Mn ore (C-CWs). Nutrient mass balance showed that nitrogen (N) removal was improved by enhanced microbial processes, media storage and plant uptake in M-CWs. Moreover, almost 50% of phosphorus (P) was retained by media storage because of the adsorption processes on Mn ore. It was found that addition of Mn ore enhanced denitrification as the relative abundance of denitrifying bacteria increased. The produced Mn(II) and more abundant Gammaproteobacteria confirmed alternative N removal pathways including anoxic nitrification coupled to Mn ore reduction and denitrification using Mn(II) as electron donor. Mn(II) concentration in the effluent of M-CWs was below the drinking water limit of 0.1 mg/L, which makes them environmentally-friendly.

Dual carbon - chlorine isotope fractionation during dichloroelimination of 1,1,2-trichloroethane by an enrichment culture containing Dehalogenimonas sp

Chlorinated ethanes are frequent groundwater contaminants but compound specific isotope analysis (CSIA) has been scarcely applied to investigate their degradation pathways. In this study, dual carbon and chlorine isotope fractionation was used to investigate for the first time the anoxic biodegradation of 1,1,2-trichloroethane (1,1,2-TCA) using a Dehalogenimonas-containing culture. The isotopic fractionation values obtained for the biodegradation of 1,1,2-TCA were ɛ_C = -6.9 ± 0.4‰ and ɛ_Cl = -2.7 ± 0.3‰. The detection of vinyl chloride (VC) as unique byproduct and a closed carbon isotopic mass balance corroborated that dichloroelimination was the degradation pathway used by this strain. Combining the values of δ¹³C and δ³⁷Cl resulted in a dual element C-Cl isotope slope of Λ = 2.5 ± 0.2‰. Investigation of the apparent kinetic isotope effects (AKIEs) expected for cleavage of a CCl bond showed an important masking of the intrinsic isotope fractionation. Theoretical calculation of Λ suggested that dichloroelimination of 1,1,2-TCA was taking place via simultaneous cleavage of two CCl bonds (concerted reaction mechanism). The isotope data obtained in this study can be useful to monitor natural attenuation of 1,1,2-TCA via dichloroelimination and provide insights into the source and fate of VC in contaminated groundwaters.

Estimating bioaugmentation efficacy of TCE dechlorination using long-term field well-to-well tests in a highly recharged and TCE-contaminated aquifer

This study demonstrates a combined field method accurately assessing the extent of trichloroethylene (TCE) reductive dechlorination activity and the mass fraction of its by-products. A combined method of injecting a known concentration of 1,1,2-trichloro-2-fluoroethene (TCFE) as a TCE bio-surrogate and a data processing technique of forced mass balance (FMB), considering the sorption effect on the mass fraction of chloroethene was evaluated by performing soil column and field bioaugmentation tests. In the soil column test, the FMB resulted in the mass fraction of 6% TCE, 48.3% cis-1,2-dichloroethene, 18.5% vinyl chloride and 27.2% ethylene. In the field bioaugmentation test, TCFE showed equivalent dechlorination pathways of TCE. The mass fractions estimated by FMB were very similar to those observed in the soil column bioaugmentation tests: 4.5% TCFE, 57.1% 1,2-dichloro-1-fluoroethene, 12% 1-chloro-1-fluoroethene and 26.4% fluoroethene (FE). The FMB method gave ∼50% higher mass fraction for more chlorinated ethenes (i.e., TCFE) and ∼10% lower mass fraction of less chlorinated ethenes (i.e., FE) than those considering only the aqueous concentrations of chlorofluoroethenes. A combined method of TCFE and FMB that could accurately estimate both the extent of dechlorination activities and mass distribution of TCE reductive dechlorination would be highly useful.

Presence of organohalide-respiring bacteria in and around a permeable reactive barrier at a trichloroethylene-contaminated Superfund site

Trichloroethylene (TCE) is one of the most common groundwater contaminants in the United States; however clean-up efforts are a challenge due to its physical and chemical properties. TCE and several of its degradation products were detected in the groundwater of the Beaver Dam Road Landfill site (Beltsville, MD) at concentrations above accepted maximum contaminant levels. A permeable reactive barrier (i.e., biowall) was installed to remediate the groundwater. Microbial infiltration and colonization of the biowall with native site bacteria was expected to occur. An array of molecular biological tools was applied to survey the microbial community for presence of organohalide-respiring microorganisms at the site. Microorganisms belonging to methanogens, acetogens, sulfate-reducing bacteria, and chlorinated aliphatic hydrocarbon-metabolizing bacteria were identified, thus making way for the application of the microbial populations in the biowall bioaugmentation efforts. In concomitant laboratory studies, molecular approaches were used to monitor continuously-fed column reactors containing saturated biowall material spiked with a commercially-available, Dehalococcoides-containing culture (SDC-9), with or without zero-valent iron (ZVI) shavings. The column without ZVI had the highest abundance of Dehalococcoides spp. (2.7 × 10⁶ cells g^-1 material, S.D. = 3.8 × 10⁵ cells g^-1 material), while the addition of ZVI did not affect the overall population. Although the addition of ZVI and biostimulation did change ratios of the Dehalococcoides strains, the results suggests that if ZVI would be applied as a biowall material amendment, biostimulation would not be required to maintain a Dehalococcoides population. These experimental results will be utilized in future remediation and/or biowall expansion plans to utilize the natural resources most effectively at the biowall site.

The time response of anaerobic digestion microbiome during an organic loading rate shock

Knowledge of connections between operational conditions, process stability, and microbial community dynamics is essential to enhance anaerobic digestion (AD) process efficiency and management. In this study, the detailed temporal effects of a sudden glycerol-based organic overloading on the AD microbial community and process imbalance were investigated in two replicate anaerobic digesters by a time-intensive sampling scheme. The microbial community time response to the overloading event was shorter than the shifts of reactor performance parameters. An increase in bacterial community dynamics and in the abundances of several microbial taxa, mainly within the Firmicutes, Tenericutes, and Chloroflexi phyla and Methanoculleus genera, could be detected prior to any shift on the reactor operational parameters. Reactor acidification already started within the first 24 h of the shock and headed the AD process to total inhibition in 72 h alongside with the largest shifts on microbiome, mostly the increase of Anaerosinus sp. and hydrogenotrophic methanogenic Archaea. In sum, this work proved that AD microbial community reacts very quickly to an organic overloading and some shifts occur prior to alterations on the performance parameters. The latter is very interesting as it can be used to improve AD process management protocols.