Modeled Pathways and Fluxes of PCB Dechlorination by Redox Potentials

Dechlorination is one of the main processes for the natural degradation of polychlorinated biphenyls (PCBs) in an anaerobic environment. However, PCB dechlorination pathways and products vary with PCB congeners, types of functional dechlorinating bacteria, and environmental conditions. The present study develops a novel model for determining dechlorination pathways and fluxes by tracking redox potential variability, transforming the complex dechlorination process into a stepwise sequence. The redox potential is calculated via the Gibbs free energy of formation, PCB concentrations in reactants and products, and environmental conditions. Thus, the continuous change in the PCB congener composition can be tracked during dechlorination processes. The new model is assessed against four measurements from several published studies on PCB dechlorination. The simulation errors in all four measurements are calculated between 2.67 and 35.1% under minimum (n = 0) and maximum (n = 34) numbers of co-eluters, respectively. The dechlorination fluxes for para-dechlorination pathways dominate PCB dechlorination in all measurements. Furthermore, the model also considers multiple-step dechlorination pathways containing intermediate PCB congeners absent in both the reactants and the products. The present study indicates that redox potential might be an appropriate indicator for predicting PCB dechlorination pathways and fluxes even without prior knowledge of the functional dechlorinating bacteria.

Characterization of chlorinated paraffin-degrading bacteria from marine estuarine sediments

This study explored chlorinated paraffin (CP)-degrading bacteria from the marine environment. Aequorivita, Denitromonas, Parvibaculum, Pseudomonas and Ignavibacterium were selected as the dominant genera after enrichment with chlorinated paraffin 52 (CP52) as the sole carbon source. Eight strains were identified as CP degraders, including Pseudomonas sp. NG6 and NF2, Erythrobacter sp. NG3, Castellaniella sp. NF6, Kordiimonas sp. NE3, Zunongwangia sp. NF12, Zunongwangia sp. NH1 and Chryseoglobus sp. NF13, and their degradation efficiencies ranged from 6.4% to 19.0%. In addition to Pseudomonas, the other six genera of bacteria were first reported to have the degradation ability of CPs. Bacterial categories, carbon-chain lengths and chlorination degrees were three crucial factors affecting the degradation efficiencies of CPs, with their influential ability of chlorinated degrees > bacterial categories > carbon-chain lengths. CP degradation can be performed by producing chlorinated alcohols, chlorinated olefins, dechlorinated alcohols and lower chlorinated CPs. This study will provide valuable information on CP biotransformation and targeted bacterial resources for studying the transformation processes of specific CPs in marine environments.

Seed inoculation with antagonistic bacteria limits occurrence of E. coli O157:H7gfp + on baby spinach leaves

Backround

During the last decades, outbreaks of foodborne illnesses have increasingly been linked to fresh and/or minimally processed fruit and vegetables. Enterohemorrhagic Escherichia coli was the causal agent for major outbreaks in Europe with leafy green vegetables and sprouts. To improve food safety, microbial antagonism has received attention during recent years and could be one of the solution to prevent contamination of food borne pathogens on fresh produce. Here we investigate the antagonistic effect of three bacterial strains (Pseudomonas orientalis, P. flavescens and Rhodococcus sp.) isolated from spinach leaves against E. coli O157:H7gfp + under laboratory and greenhouse conditions.

Results

Our results shows that significantly less culturable E.coli O157:H7gfp + were retrieved from the spinach canopy subjected to antagonist seed treatment than canopy inoculation. Seeds inoculated with Rhodococcus sp. significantly reduced growth of E. coli O157:H7gfp + compared with the other antagonists. The result from the in vitro study shows a significant reduction of growth of E. coli O157:H7gfp+, but only after 44 h when E. coli O157:H7gfp + was propagated in a mixture of spent media from all three antagonists.

Conclusions

The antagonistic effect on phyllospheric E.coli O157:H7gfp + observed after seed inoculation with Rhodococcus sp. might be an indication of induced resistance mechanism in the crop. In addition, there was a small reduction of culturable E.coli O157:H7gfp + when propagated in spent media from all three antagonists. Nutritional conditions rather than metabolites formed by the three chosen organisms appear to be critical for controlling E. coli O157:H7gfp+.

Distinct methane-dependent biogeochemical states in Arctic seafloor gas hydrate mounds

Archaea mediating anaerobic methane oxidation are key in preventing methane produced in marine sediments from reaching the hydrosphere; however, a complete understanding of how microbial communities in natural settings respond to changes in the flux of methane remains largely uncharacterized. We investigate microbial communities in gas hydrate-bearing seafloor mounds at Storfjordrenna, offshore Svalbard in the high Arctic, where we identify distinct methane concentration profiles that include steady-state, recently-increasing subsurface diffusive flux, and active gas seepage. Populations of anaerobic methanotrophs and sulfate-reducing bacteria were highest at the seep site, while decreased community diversity was associated with a recent increase in methane influx. Despite high methane fluxes and methanotroph doubling times estimated at 5-9 months, microbial community responses were largely synchronous with the advancement of methane into shallower sediment horizons. Together, these provide a framework for interpreting subseafloor microbial responses to methane escape in a warming Arctic Ocean.

Response of soil enzyme activity and soil bacterial community to PCB dissipation across different soils

Soils are a repository for polychlorinated biphenyls (PCBs). A pot incubation experiment was performed with four soils (black soil, paddy soil, oasis soil, and fluvo-aquic soil) treated with Aroclor 1242 to achieve PCB concentrations of 5 mg kg^-1. The soil enzyme activities of protease, phosphatase, catalase, dehydrogenase, and laccase were determined by spectrophotometry. The soil bacterial communities were investigated using Illumina sequencing analysis. The results showed that the characteristics of the test soils varied among the soil types. The fluvo-aquic soil had the greatest PCB dissipation rate (86.41%), followed by the oasis (79.31%), paddy (56.09%), and black (50.65%) soils. The soil pH, cation exchange capacity, soil organic matter content, and particle diameter played significant roles in PCB dissipation from soils. The soil type had a greater influence than PCB contamination on the soil enzyme activities and bacterial communities (alpha diversity, community structure, and composition). Among the four soils, the bacterial communities of the fluvo-aquic soil were the most susceptible to PCB contamination. However, the bacterial communities of the black soil were not changed by PCB contamination.

Biotreatment potential of co-contaminants hexavalent chromium and polychlorinated biphenyls in industrial wastewater: Individual and simultaneous prospects

Co-existence of polychlorinated biphenyls (PCBs) and hexavalent chromium (Cr(VI)) in the environment due to effluent from industries has aggravated the pollution problem. Both contaminants can alter chemical interactions, processes and impair enzymatic activities in the ecosystem that results in negative impacts on aquatic and terrestrial life. Previously, research has been performed for the fate and transfer of these contaminants individually, but simultaneous removal approaches have not received much attention. Cr(VI) exists in a highly toxic form in the environment once released, whereas location of chlorine atoms in the ring determines PCBs toxicity. Lower chlorinated compounds are easily degradable whereas as high chlorinated compounds require sequential strategy for transformation. Microorganisms can develop different mechanism to detoxify both pollutants. However, occurrence of multiple contaminants in single system can alter the bioremediation efficiency of bacteria. Use of metal resistance bacterial for the degradation of organic compounds has been widely used bioaugmentation strategy. Along with that use of sorbents/bio sorbents, biosurfactants and phytoremediation approaches have already been well reported. Bioremediation strategy with dual potential to detoxify the Cr(VI) and PCBs would be a probable option for simultaneous biotreatment. Application of bioreactors and biofilms covered organic particles can be utilized as efficient bioaugmentation approach. In this review, biotreatment systems and bacterial oxidative and reductive enzymes/processes are explained and possible biotransformation pathway has been purposed for bioremediation of co-contaminated waters.

Role of Microorganisms in the Remediation of Wastewater in Floating Treatment Wetlands: A Review

This article provides useful information for understanding the specific role of microbes in the pollutant removal process in floating treatment wetlands (FTWs). The current literature is collected and organized to provide an insight into the specific role of microbes toward plants and pollutants. Several aspects are discussed, such as important components of FTWs, common bacterial species, rhizospheric and endophytes bacteria, and their specific role in the pollutant removal process. The roots of plants release oxygen and exudates, which act as a substrate for microbial growth. The bacteria attach themselves to the roots and form biofilms to get nutrients from the plants. Along the plants, the microbial community also influences the performance of FTWs. The bacterial community contributes to the removal of nitrogen, phosphorus, toxic metals, hydrocarbon, and organic compounds. Plant–microbe interaction breaks down complex compounds into simple nutrients, mobilizes metal ions, and increases the uptake of pollutants by plants. The inoculation of the roots of plants with acclimatized microbes may improve the phytoremediation potential of FTWs. The bacteria also encourage plant growth and the bioavailability of toxic pollutants and can alleviate metal toxicity.

Aided Phytoremediation to Clean Up Dioxins/Furans-Aged Contaminated Soil: correlation between microbial communities and pollutant dissipation

To restore and clean up polluted soils, aided phytoremediation was found to be an effective, eco-friendly, and feasible approach in the case of many organic pollutants. However, little is known about its potential efficiency regarding polychlorinated dibenzo-p-dioxins and furans-contaminated soils. Thus, phytoremediation of aged dioxins/furans-contaminated soil was carried out through microcosm experiments vegetated with alfalfa combined with different amendments: an arbuscular mycorrhizal fungal inoculum (Funneliformis mosseae), a biosurfactant (rhamnolipids), a dioxins/furans degrading-bacterium (Sphingomonas wittichii RW1), and native microbiota. The total dioxins/furans dissipation was estimated to 23%, which corresponds to 48 ng.kg-1 of soil, after six months of culture in the vegetated soil combined with the four amendments compared to the non-vegetated soil. Our findings showed that the dioxins/furans dissipation resulted from the stimulation of soil microbial enzyme activities (fluorescein diacetate hydrolase and dehydrogenase) and the increase of bacterial abundance, richness, and diversity, as well as fungal diversity. Amplicon sequencing using Illumina MiSeq analysis led to identification of several bacterial (Bacillaceae, Sphingomonadaceae) and fungal (Chaetomium) groups known to be involved in dioxins/furans degradation. Furthermore, concomitant cytotoxicity and dioxins/furans concentration decreases were pointed out in the phytoremediated soil. The current study demonstrated the usefulness of combining different types of amendments to improve phytoremediation efficacy of aged dioxins/furans-contaminated soils.

Kinetics of PCB Microbial Dechlorination Explained by Freely Dissolved Concentration in Sediment Microcosms

While microbial dechlorination of polychlorinated biphenyls (PCBs) has been observed in sediments over the last 3 decades, translation to the field has been difficult due to a lack of a clear understanding of the kinetic limitations. To address this issue, the present study used passive dosing/sampling to accurately measure the biological rate of dechlorination of 2,3,4,5-tetrachlorobiphenyl (PCB 61) to 2,3,5-trichlorobiphenyl (PCB 23) by an organohalide-respiring bacterium, Dehalobium chlorocoercia (DF-1). The biological rates were measured over an environmentally relevant concentration range of 1-50 ng/L of freely dissolved concentrations with and without the presence of sediment in bench-scale microcosm studies. The rate of dechlorination was found to be linearly dependent on the freely dissolved concentration of PCB 61 both in sediment and in sediment-free microcosms. The observed rate of dechlorination in sediment microcosms could be predicted within a factor of 2 based on the kinetics measured in sediment-free microcosms. A threshold for dechlorination was not observed down to an aqueous concentration of about 1 ng/L PCB 61. We demonstrate that with the combination of an accurate measurement of the aqueous-phase dechlorination kinetics and an understanding of the site-specific partitioning characteristics, it is possible to predict PCB microbial dechlorination in sediments.

Bioremediation of chlorophenol-contaminated sawmill soil using pilot-scale bioreactors under consecutive anaerobic-aerobic conditions

Chlorophenols (CPs), including pentachlorophenol (PCP), are chemicals of concern due to their toxicity and persistence. Here we describe a successful reactor-based remediation of CP-contaminated soil and assess changes in the toxicity patterns and bacterial communities during the remediation. The remediation consisted of separating half of the contaminated soil to be ground (samples M) in order to test whether the grinding expedited the remediation, the other half was left unground (samples P). Both soils were mixed with wastewater treatment sludge to increase their bacterial diversity and facilitate the degradation of CPs, and the resultant mixtures were placed in 2 bioreactors, M and P, operated for 16 months under anaerobic conditions to favor dehalogenation and for an additional 16 months under aerobic conditions to achieve complete mineralization. Samples were taken every 4 months for toxicity and microbial analyses. The results showed a 64% removal of total CPs (ΣCPs) in reactor P after just 18 months of remediation, whereas similar depletion in reactor M occurred after ∼25 months, indicating that the grinding decelerated the remediation. By the end of the experiment, both reactors achieved 93.5-95% removal. The toxicity tests showed a decrease in toxicity as the remediation progressed. The succession of bacterial communities over time was significantly associated with pH, anaerobic/aerobic phase and the concentration of the majority of CP congeners. Our data indicate that the supplementation of contaminated soil with sludge and further incubation in pilot-scale bioreactors under consecutive anaerobic-aerobic conditions proved to be effective at the remediation of CP-contaminated soil.

Redox fluctuations shape the soil microbiome in the hypoxic bioremediation of octachlorinated dibenzodioxin- and dibenzofuran-contaminated soil

The biodegradation of polychlorinated-p-dioxins and dibenzofurans (PCDD/Fs) has been recently demonstrated in a single reactor under hypoxic conditions. Maintaining hypoxic conditions through periodic aerations results in a marked fluctuation of reduction-oxidation (redox) potential. To further assess the effects of redox fluctuations, we operated two fed-batch continuously stirred tank reactors (CSTRs) with sophisticated redox controls at different anoxic/oxic fluctuations to reduce PCDD/Fs in contaminated soil. The results of long-term reactor operation showed that the CSTR with redox fluctuations at a narrow range (-63 ± 68 mV) (CSTR_A) revealed a higher substrate hydrolysis level and PCDD/F degradation rate than did the CSTR with a redox potential that fluctuated at a broad range (-13 ± 118 mV) (CSTR_B). In accordance with analyses of bacterial 16S rRNA genes, the designated hypoxic conditions with added compost supported survival of bacterial populations at a density of approximately 10⁹ copies/g slurry. The evolved core microbiome was dominated by anoxic/oxic fluctuation-adapted Bacteroidetes, Alphaproteobacteria, and Actinobacteria, with higher species diversity and functionality, including hydrolysis and degradation of dioxin-like compounds in CSTR_A than in CSTR_B. Taken together, the overall results of this study expand the understanding of redox fluctuations in association with the degradation of recalcitrant substrates in soil and the corresponding microbiome.

The effect of chlorination degree and substitution pattern on the interactions of polychlorinated biphenyls with model bacterial membranes

Polychlorinated biphenyls (PCB) are persistent organic pollutants that due to their chemical resistivity and inflammability found multiple applications. In spite of the global ban for PCB production, due to their long half-lives periods, PCB accumulate in the soils, so effective bioremediation of the polluted lands is of crucial importance. Some of the 209 PCB congeners exhibit increased toxicity to soil bacteria and their presence impoverish the soil decomposer community and slows down the degradation of environmental pollutants in the soils. The exact mechanism of PCB antimicrobial activity is unknown, but it is strictly related with the membrane activity of PCB. Therefore, to shed light on these interactions we applied Langmuir monolayers formed by selected phospholipids as model bacterial membranes. In our studies we tested 5 PCB congeners differing in the degree of chlorination and the distribution of the chlorine substituents around the biphenyl frame. Special attention was paid to tetra-substituted PCB because of their increased presence in the environment and disubstituted PCB being their degradation products. To characterize the model membranes as Langmuir monolayers, we used surface pressure measurements, Brewster angle microscopy and Grazing Incidence X-ray Diffraction. It turned out that among the tetra-substituted PCB the ortho-substituted non-dioxin like compound was much more membrane destructive than the flat dioxin-like congener. On the contrary, among the di-substituted PCB the flat para-substituted 2,2'-dichlorobiphenyl turned out to exhibit high membrane activity.

Photodegradative fate and potential phototoxic products of bromocarbazoles and chlorocarbazoles in water

Bromocarbazoles and chlorocarbazoles are emerging environmental contaminants that have been reported to be persistent and possessing dioxin-like toxicity; however, their photodegradative fate in water is unknown. The photodegradation of 3-bromocarbazole, 3-chlorocarbazole, and 3,6-dichlorocarbazole was determined in ultrapure water. They proceeded by direct photolysis and followed first-order kinetics. The rate constants (k) were 0.4838, 0.3454, and 0.4422 h^-1 corresponding to half-lives (t _1/2) 1.81, 2.01, and 1.62, while the quantum yields (Ф) were 0.232, 0.180, and 0.295 respectively. The maximum wavelengths of absorption (λ _max) were in the near ultraviolet region (295, 296, 299, and 301 nm) implying these compounds are likely to degrade slowly under sunlight in natural aquatic environment. The molar extinction coefficients (ε) determined in acetonitrile were 18,573, 17,028, 13,385, and 14,010 L mol^-1 cm^-1, respectively, the latter being 3,6-dibromocarbazole. A bathochromic shift was observed with halogen addition on their respective mono-substituted congeners. Bromocarbazoles were observed to degrade faster in water than chlorocarbazoles. In addition, photodegradation was estimated to proceed faster in summer than in winter, in natural water system at 50° N latitude. In the absence of light, hydrolytic degradation occurred but proceeded very slowly. Hexahydroxybenzene and trihydroxycarbazole were positively identified as the likely photoproducts with the former being a known toxic compound. Dehalogenation, oxidative cleavage, hydroxylation, and hydrolysis are suggested as the major photodegradation mechanisms in water, yielding phototoxic products that may be of enhanced toxicity than the parent compounds.

Polychlorinated biphenyl and polybrominated diphenyl ether profiles in serum from cattle, sheep, and goats across California

It has been previously been shown by our lab and others that persistent organic pollutants, such as polychlorinated biphenyls (PCBs) and polybrominated diphenyl ethers (PBDEs), are contaminants in milk produced for human consumption. To further this research we determined the concentration of 21 PCB and 14 PBDE congeners in livestock serum, mainly bovine, across California. Congeners were extracted from serum using solid phase extraction (SPE), cleaned up by silica cartridge and quantified using gas chromatography-triple quadruple mass spectrometry. We detected significant differences among species and the production class of cattle (beef or dairy). The sum of all 21 PCB congeners (ΣPCBs) in caprine and ovine sera had a mean value of 9.26 and 9.13 ng/mL, respectively, compared to 3.98 ng/mL in bovine sera. The mean value for the sum of all 14 PBDE congeners (ΣPBDEs) in caprine and ovine sera was 2.82 and 2.39 ng/mL, respectively, compared to 0.91 ng/mL in bovine sera. Mean ΣPCBs in dairy cattle was 5.92 ng/mL compared to 2.70 ng/mL in beef cattle. Mean ΣPBDEs in dairy cattle was 1.33 ng/mL compared to 0.70 ng/mL in beef cattle. There were no regional differences in the ΣPCBs or ΣPBDEs in cattle distributed across California. These results highlight the fact that livestock are still being exposed to these pollutants yet little is known about where this exposure may be coming from.

Anaerobic biodegradation of (emerging) organic contaminants in the aquatic environment

Although strictly anaerobic conditions prevail in several environmental compartments, up to now, biodegradation studies with emerging organic contaminants (EOCs), such as pharmaceuticals and personal care products, have mainly focused on aerobic conditions. One of the reasons probably is the assumption that the aerobic degradation is more energetically favorable than degradation under strictly anaerobic conditions. Certain aerobically recalcitrant contaminants, however, are biodegraded under strictly anaerobic conditions and little is known about the organisms and enzymatic processes involved in their degradation. This review provides a comprehensive survey of characteristic anaerobic biotransformation reactions for a variety of well-studied, structurally rather simple contaminants (SMOCs) bearing one or a few different functional groups/structural moieties. Furthermore it summarizes anaerobic degradation studies of more complex contaminants with several functional groups (CMCs), in soil, sediment and wastewater treatment. While strictly anaerobic conditions are able to promote the transformation of several aerobically persistent contaminants, the variety of observed reactions is limited, with reductive dehalogenations and the cleavage of ether bonds being the most prevalent. Thus, it becomes clear that the transferability of degradation mechanisms deduced from culture studies of SMOCs to predict the degradation of CMCs, such as EOCs, in environmental matrices is hampered due the more complex chemical structure bearing different functional groups, different environmental conditions (e.g. matrix, redox, pH), the microbial community (e.g. adaptation, competition) and the low concentrations typical for EOCs.

Shifts among Eukaryota, Bacteria, and Archaea define the vertical organization of a lake sediment

BACKGROUND

Lake sediments harbor diverse microbial communities that cycle carbon and nutrients while being constantly colonized and potentially buried by organic matter sinking from the water column. The interaction of activity and burial remained largely unexplored in aquatic sediments. We aimed to relate taxonomic composition to sediment biogeochemical parameters, test whether community turnover with depth resulted from taxonomic replacement or from richness effects, and to provide a basic model for the vertical community structure in sediments.

METHODS

We analyzed four replicate sediment cores taken from 30-m depth in oligo-mesotrophic Lake Stechlin in northern Germany. Each 30-cm core spanned ca. 170 years of sediment accumulation according to ¹³⁷Cs dating and was sectioned into layers 1-4 cm thick. We examined a full suite of biogeochemical parameters and used DNA metabarcoding to examine community composition of microbial Archaea, Bacteria, and Eukaryota.

RESULTS

Community β-diversity indicated nearly complete turnover within the uppermost 30 cm. We observed a pronounced shift from Eukaryota- and Bacteria-dominated upper layers (<5 cm) to Bacteria-dominated intermediate layers (5-14 cm) and to deep layers (>14 cm) dominated by enigmatic Archaea that typically occur in deep-sea sediments. Taxonomic replacement was the prevalent mechanism in structuring the community composition and was linked to parameters indicative of microbial activity (e.g., CO₂ and CH₄ concentration, bacterial protein production). Richness loss played a lesser role but was linked to conservative parameters (e.g., C, N, P) indicative of past conditions.

CONCLUSIONS

By including all three domains, we were able to directly link the exponential decay of eukaryotes with the active sediment microbial community. The dominance of Archaea in deeper layers confirms earlier findings from marine systems and establishes freshwater sediments as a potential low-energy environment, similar to deep sea sediments. We propose a general model of sediment structure and function based on microbial characteristics and burial processes. An upper "replacement horizon" is dominated by rapid taxonomic turnover with depth, high microbial activity, and biotic interactions. A lower "depauperate horizon" is characterized by low taxonomic richness, more stable "low-energy" conditions, and a dominance of enigmatic Archaea.

Dehalococcoides and general bacterial ecology of differentially trichloroethene dechlorinating flow-through columns

The diversity of Dehalococcoides mccartyi (Dhc) and/or other organohalide respiring or associated microorganisms in parallel, partial, or complete trichloroethene (TCE) dehalogenating systems has not been well described. The composition of Dhc populations and the associated bacterial community that developed over 7.5 years in the top layer (0-10 cm) of eight TCE-fed columns were examined using pyrosequencing. Columns biostimulated with one of three carbon sources, along with non-stimulated controls, developed into complete (ethene production, whey amended), partial (cis-dichloroethene (DCE) and VC, an emulsified oil with nonionic surfactant), limited (<5 % cis-DCE and 95 % TCE, an emulsified oil), and non- (controls) TCE dehalogenating systems. Bioaugmentation of one column of each treatment with Bachman Road enrichment culture did not change Dhc populations nor the eventual degree of TCE dehalogenation. Pyrosequencing revealed high diversity among Dhc strains. There were 13 OTUs that were represented by more than 1000 sequences each. Cornell group-related populations dominated in complete TCE dehalogenating columns, while Pinellas group related Dhc dominated in all other treatments. General microbial communities varied with biostimulation, and three distinct microbial communities were established: one each for whey, oils, and control treatments. Bacterial genera, including Dehalobacter, Desulfitobacterium, Sulfurospirillum, Desulfuromonas, and Geobacter, all capable of partial TCE dehalogenation, were abundant in the limited and partial TCE dehalogenating systems. Dhc strain diversity was wider than previously reported and their composition within the community varied significantly depending on the nature of the carbon source applied and/or changes in the Dhc associated partners that fostered different biogeochemical conditions across the columns.

Widespread Distribution of Dehalococcoides mccartyi in the Houston Ship Channel and Galveston Bay, Texas, Sediments and the Potential for Reductive Dechlorination of PCDD/F in an Estuarine Environment

Sediments in the Houston Ship Channel and upper Galveston Bay, Texas, USA, are polluted with polychlorinated dibenzo-p-dioxins/furans (PCDD/F; ≤46,000 ng/kg dry weight (wt.)) with 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), the most toxic congener, contributing >50 % of the total toxic equivalents (TEQ) at most locations. We measured PCDD/F concentrations in sediments and evaluated the potential for enhanced in situ biodegradation by surveying for Dehalococcoides mccartyi, an obligate organohalide respiring bacterium. Dehalococcoides spp. (98 % similar to D. mccartyi) and 22 other members of the class Dehalococcoidia were predominant 16S ribosomal RNA (rRNA) phylotypes. Dehalococcoides spp. were also present in the active fraction of the bacterial community. Presence/absence PCR screening detected D. mccartyi in sediment cores and sediment grab samples having at least 1 ng/kg dry wt. TEQ at salinities ranging from 0.6 to 19.5 PSU, indicating that they are widespread in the estuarine environment. Organic carbon-only and organic carbon + sulfate-amended sediment microcosm experiments resulted in ∼60 % reduction of ambient 2,3,7,8-TCDD in just 24 months leading to reductions in total TEQs by 38.4 and 45.0 %, respectively, indicating that 2,3,7,8-TCDD degradation is occurring at appreciable rates.

Bacterial Biotransformation of Pentachlorophenol and Micropollutants Formed during Its Production Process

Pentachlorophenol (PCP) is a toxic and persistent wood and cellulose preservative extensively used in the past decades. The production process of PCP generates polychlorinated dibenzo-p-dioxins and polychlorinated dibenzofurans (PCDD/Fs) as micropollutants. PCDD/Fs are also known to be very persistent and dangerous for human health and ecosystem functioning. Several physico-chemical and biological technologies have been used to remove PCP and PCDD/Fs from the environment. Bacterial degradation appears to be a cost-effective way of removing these contaminants from soil while causing little impact on the environment. Several bacteria that cometabolize or use these pollutants as their sole source of carbon have been isolated and characterized. This review summarizes current knowledge on the metabolic pathways of bacterial degradation of PCP and PCDD/Fs. PCP can be successfully degraded aerobically or anaerobically by bacteria. Highly chlorinated PCDD/Fs are more likely to be reductively dechlorinated, while less chlorinated PCDD/Fs are more prone to aerobic degradation. The biochemical and genetic basis of these pollutants’ degradation is also described. There are several documented studies of effective applications of bioremediation techniques for the removal of PCP and PCDD/Fs from soil and sediments. These findings suggest that biodegradation can occur and be applied to treat these contaminants.

Bioremediation of polychlorinated-p-dioxins/dibenzofurans contaminated soil using simulated compost-amended landfill reactors under hypoxic conditions

Compost-amended landfill reactors were developed to reduce polychlorinated-p-dioxins and dibenzofurans (PCDD/Fs) in contaminated soils. By periodically recirculating leachate and suppling oxygen, the online monitoring of the oxidation reduction potential confirmed that the reactors were maintained under hypoxic conditions, with redox levels constantly fluctuating between -400 and +80mV. The subsequent reactor operation demonstrated that PCDD/F degradation in soil could be facilitated by amending compost originating from the cow manure and waste sludge and that the degradation might be affected by the availability of easily degradable substrates in the soil and compost. The pyrosequencing analysis of V4/V5 regions of bacterial 16S rRNA genes suggested that species richness of the soil microbial community was increased by a factor of 1.37-1.61. Although the bacterial community varied with the compost origin and changed markedly during reactor operation, it was dominated by Alphaproteobacteria, Gammaproteobacteria, Actinobacteria, and Firmicutes. The aerotolerant anaerobic Sedimentibacter and Propionibacterium spp., and the uncultured Chloroflexi group could be temporarily induced to a high abundance by amending the cow manure compost; the bacterial growths were associated with the rapid degradation of PCDD/Fs. Overall, the novel bioremediation method for PCDD/F-contaminated soils using hypoxic conditions was effective, simple, energy saving, and thus easily practicable.

Indirect Evidence Link PCB Dehalogenation with Geobacteraceae in Anaerobic Sediment-Free Microcosms

Although polychlorinated biphenyls (PCBs) production was brought to a halt 30 years ago, recalcitrance to degradation makes them a major environmental pollutant at a global scale. Previous studies confirmed that organohalide-respiring bacteria (OHRB) were capable of utilizing chlorinated congeners as electron acceptor. OHRB belonging to the Phyla Chloroflexi and Firmicutes are nowadays considered as the main PCB-dechlorinating organisms. In this study, we aimed at exploring the involvement of other taxa in PCB dechlorination using sediment-free microcosms (SFMs) and the Delor PCB mixture. High rates of congener dehalogenation (up to 96%) were attained in long-term incubations of up to 692 days. Bacterial communities were dominated by Chloroflexi, Proteobacteria, and Firmicutes, among strictly simplified community structures composed of 12 major phyla only. In a first batch of SFMs, Dehalococcoides mccartyi closely affiliated with strains CG4 and CBDB1 was considered as the main actor associated with congener dehalogenation. Addition of 2-bromoethanesulfonate (BES), a known inhibitor of methanogenic activity in a second batch of SFMs had an adverse effect on the abundance of Dehalococcoides sp. Only two sequences affiliated to this Genus could be detected in two (out of six) BES-treated SFMs, contributing to a mere 0.04% of the communities. BES-treated SFMs showed very different community structures, especially in the contributions of organisms involved in fermentation and syntrophic activities. Indirect evidence provided by both statistical and phylogenetic analysis validated the implication of a new cluster of actors, distantly affiliated with the Family Geobacteraceae (Phylum δ-Proteobacteria), in the dehalogenation of low chlorinated PCB congeners. Members of this Family are known already for their dehalogenation capacity of chlorinated solvents. As a result, the present study widens the knowledge for the phylogenetic reservoir of indigenous PCB dechlorinating taxa.

Distribution of Dehalococcoidia in the Anaerobic Deep Water of a Remote Meromictic Crater Lake and Detection of Dehalococcoidia-Derived Reductive Dehalogenase Homologous Genes

Here we describe the natural occurrence of bacteria of the class Dehalococcoidia (DEH) and their diversity at different depths in anoxic waters of a remote meromictic lake (Lake Pavin) using 16S rRNA gene amplicon sequencing and quantitative PCR. Detected DEH are phylogenetically diverse and the majority of 16S rRNA sequences have less than 91% similarity to previously isolated DEH 16S rRNA sequences. To predict the metabolic potential of detected DEH subgroups and to assess if they encode genes to transform halogenated compounds, we enriched DEH-affiliated genomic DNA by using a specific-gene capture method and probes against DEH-derived 16S rRNA genes, reductive dehalogenase genes and known insertion sequences. Two reductive dehalogenase homologous sequences were identified from DEH-enriched genomic DNA, and marker genes in the direct vicinity confirm that gene fragments were derived from DEH. The low sequence similarity with known reductive dehalogenase genes suggests yet-unknown catabolic potential in the anoxic zone of Lake Pavin.

Sequential anaerobic-aerobic biodegradation of 2,3,7,8-TCDD contaminated soil in the presence of CMC-coated nZVI and surfactant

Enriched microorganisms in sediment collected from a dioxin-contaminated site in Vietnam (Bien Hoa airbase) were used for examining the effectiveness in biological treatment of 2,3,7,8-Tetrachlorodibenzo-p-dioxin in soil. Four bio-treatments were investigated using a sequential anaerobic (17 weeks) followed by an aerobic (6 weeks) incubation. The maximum removal efficiency was approximately 60% even at an extremely low pH (approx. 3.6) condition. Surfactant Tween-80 was added to enhance the bioavailability of dioxin in two treatments, but it appeared to biostimulate methanogens rather than dechlorinators. As a result, methane production was the highest while the dioxin removal efficiency was the lowest, as compared with the other bio-treatments. Carboxymethylcellulose (CMC) coated on nanoscale zero valent iron (nZVI) surface used in two treatments could prevent the direct contact between bacterial cell surface and nZVI which prevented cell death and lysis, hence enhancing dioxin removal. The presence of CMC--_nZVI in bio-treatments gradually released H2 required for microbiological processes, but the amount used in the experiments were likely too high to maintain optimum H2 levels for biostimulating dechlorinators rather than methanogens.

Enhancing tetrabromobisphenol A biodegradation in river sediment microcosms and understanding the corresponding microbial community

In situ remediation of contaminated sediment using microbes is a promising environmental treatment method. This study used bioaugmentation to investigate the biodegradation of tetrabromobisphenol A (TBBPA) in sediment microcosms collected from an electronic-waste recycling site. Treatments included adding possible biodegradation intermediates of TBBPA, including 2,4-dibromophenol (2,4-DBP), 2,4,6-tribromophenol (TBP), and bisphenol A (BPA) as co-substrates. Bioaugmentation was done with Ochrobactrum sp. T (TBBPA-degrader) and a mixed culture of Ochrobactrum sp. T, Bacillus sp. GZT (TBP-degrader) and Bacillus sp. GZB (BPA-degrader). Results showed that bioaugmentation with Ochrobactrum sp. T significantly improved TBBPA degradation efficiencies in sediment microcosms (P < 0.01); aerobic conditions increased the microbes' degradation activities. Co-substrates 2,4-DBP, TBP and BPA inhibited biodegradation of TBBPA. A metagenomic analysis of total 16S rRNA genes from the treated sediment microcosms showed that the following dominant genera: Ochrobactrum, Parasegetibacter, Thermithiobacillus, Phenylobacterium and Sphingomonas. The genus level of Ochrobactrum increased with increased degradation time, within 10-week of incubation. Microbes from genus Ochrobactrum are mainly linked to enhance the TBBPA biodegradation.

The key microorganisms for anaerobic degradation of pentachlorophenol in paddy soil as revealed by stable isotope probing

Pentachlorophenol (PCP) is a common residual persistent pesticide in paddy soil and has resulted in harmful effect on soil ecosystem. The anaerobic microbial transformation of PCP, therefore, has been received much attentions, especially the functional microbial communities for the reductive transformation. However, the key functional microorganisms for PCP mineralization in the paddy soil still remain unknown. In this work, DNA-based stable isotope probing (SIP) was applied to explore the key microorganisms responsible for PCP mineralization in paddy soil. The SIP results indicated that the dominant bacteria responsible for PCP biodegradation belonged to the genus Dechloromonas of the class β-Proteobacteria. In addition, the increased production of (13)CH4 and (13)CO2 indicated that the addition of lactate enhanced the rate of biodegradation and mineralization of PCP. Two archaea classified as the genera of Methanosaeta and Methanocella of class Methanobacteria were enriched in the heavy fraction when with lactate, whereas no archaea was detected in the absence of lactate. These findings provide direct evidence for the species of bacteria and archaea responsible for anaerobic PCP or its breakdown products mineralization and reveal a new insight into the microorganisms linked with PCP degradation in paddy soil.

Novel Strategy for Tracking the Microbial Degradation of Azo Dyes with Different Polarities in Living Cells

Direct visualization evidence is important for understanding the microbial degradation mechanisms. To track the microbial degradation pathways of azo dyes with different polar characterizations, sensors based on the fluorescence resonance energy transfer (FRET) from 1,8-naphthalimide to azo dyes were synthesized, in which the quenched fluorescence will recover when the azo bond was cleaved. In living cells, the sensor-tracking experiment showed that the low polarity and hydrophobic azo dye can be taken up into the cells and reduced inside the cells, whereas the high polarity and hydrophilic azo dye can be reduced only outside the cells because of the selective permeability of the cell membranes. These results indicated that there were two different bacterial degradation pathways available for different polarity azo dyes. To our knowledge, no fluorescent sensor has yet been designed for illuminating the microbial degradation mechanisms of organic pollutants with different characteristics.

Divergent PCB organohalide-respiring consortia enriched from the efflux channel of a former Delor manufacturer in Eastern Europe

Polychlorinated biphenyl (PCB) organohalide-respiring communities from the efflux channel of a former Delor manufacturer in Eastern Slovakia were assessed using metagenomic, statistical and cultivation-adapted approaches. Multivariate analysis of environmental factors together with terminal restriction fragment length polymorphisms of the bacterial communities in the primary sediments revealed both temporal and spatial heterogeneity in the distribution of microbial populations, which reflects the dynamic pattern of contamination and altered conditions for biodegradation activity along the channel. Anaerobic microcosms were developed from eight sediments sampled along the channel, where high concentrations of PCBs - from 6.6 to 136mg/kg dry weight, were measured. PCB dehalorespiring activity, congruent with changes in the microbial composition in all microcosms, was detected. After 10 months of cultivation, the divergently evolved consortia achieved up to 35.9 percent reduction of the total PCB concentration. Phylogenetic-analysis of the active Chloroflexi-related organohalide-respiring bacteria by partial sequencing of 16S rRNA genes in cDNA from microcosms with the highest PCB dechlorination activity revealed diverse and unique complexity of the populations. The predominant organohalide respirers were either affiliated with Dehalococcoides sp. and Dehalococcoides-like group (DLG) organisms or were composed of currently unknown distant clades of DLG bacteria. The present study should encourage researchers to explore the full potential of the indigenous PCB dechlorinating populations to develop effective bioremediation approaches that can perform the complete mineralization of PCBs in polluted environments.

Impacts of PCB analytical interpretation uncertainties on dechlorination assessment and remedial decisions

Laboratory analyses of polychlorinated biphenyls (PCBs) often do not quantitate the 209 individual PCB congeners, thereby requiring analyst interpretation to determine individual congener concentrations. Error introduced during this interpretation is subsequently propagated to calculated surrogate variables, such as the number of chlorines per biphenyl (CPB), and the molar dechlorination product ratio (MDPR), which are used to assess the extent of dechlorination and inform remedial decisions. The present work applies a Monte Carlo (MC) analysis to assess current methods for quantitating co-eluting congeners and the errors that could occur in individual congeners and derived CPB and MDPR estimates. Synthetic chromatograms, which were created using two alternative methods (random assignment and assignment based on relative proportions in Aroclors) for assigning mass to co-eluting congeners, were compared to their fully-quantitated counterparts. The percent error introduced in total PCB (∑PCB) concentration ranges from approximately -60% to +50%. Similarly, the errors associated with CPB and MDPR estimates range from approximately -20% to +20% and -120% to +30%, respectively. Uncertainties introduced during congener analysis and propagated to surrogate variables can thus be substantial, and should be considered in assessments of the extent of dechlorination and associated remedial decisions.

Dehalococcoides mccartyi strain JNA in pure culture extensively dechlorinates Aroclor 1260 according to polychlorinated biphenyl (PCB) dechlorination Process N

We isolated Dehalococcoides mccartyi strain JNA from the JN mixed culture which was enriched and maintained using the highly chlorinated commercial PCB mixture Aroclor 1260 for organohalide respiration. For isolation we grew the culture in minimal liquid medium with 2,2',3,3',6,6'-hexachlorobiphenyl (236-236-CB)(20 μM) as respiratory electron acceptor. We repeatedly carried out serial dilutions to extinction and recovered dechlorination activity from transfers of 10(-7) and 10(-8) dilutions. Fluorescence microscopy, DGGE and RFLP analysis of PCR amplified16S rRNA genes, and multilocus sequence typing of three housekeeping genes confirmed culture purity. No growth occurred on complex media. JNA dechlorinated most hexa- and heptachlorobiphenyls in Aroclor 1260 (50 μg/mL) leading to losses of 51% and 20%, respectively. Dechlorination was predominantly from flanked meta positions of 34-, 234-, 235-, 236-, 245-, 2345-, 2346-, and 2356-chlorophenyl rings, as indicated by the underscores. The major products were 24-24-CB, 24-26-CB, 24-25-CB, and 25-26-CB. We identified 85 distinct PCB dechlorination reactions and 56 different PCB dechlorination pathways catalyzed by JNA. Dechlorination pathways were confirmed by mass balance of substrates and products. This dechlorination pattern matches PCB Dechlorination Process N. JNA is the first pure culture demonstrated to carry out this extensive and environmentally relevant PCB dechlorination pattern.

Enhanced anaerobic biodegradation of OCDD-contaminated soils by Pseudomonas mendocina NSYSU: microcosm, pilot-scale, and gene studies

In this study, microcosm and pilot-scale experiments were performed to investigate the capability and effectiveness of Pseudomonas mendocina NSYSU (P. mendocina NSYSU) on the bioremediation of octachlorodibenzo-p-dioxin (OCDD)-contaminated soils. The objectives were to evaluate the (1) characteristics of P. mendocina NSYSU, (2) feasibility of enhancing OCDD biodegradation with the addition of P. mendocina NSYSU and lecithin, and (3) variation in microbial diversity and genes responsible for the dechlorination of OCDD. P. mendocina NSYSU was inhibited when salinity was higher than 7%, and it could biodegrade OCDD under reductive dechlorinating conditions. Lecithin could serve as the solubilization agent causing the enhanced solubilization and dechlorination of OCDD. Up to 71 and 62% of OCDD could be degraded after 65 days of incubation under anaerobic conditions with and without the addition of lecithin, respectively. Decreased OCDD concentrations caused significant increase in microbial diversity. Results from the pilot-scale study show that up to 75% of OCDD could be degraded after a 2.5-month operational period with lecithin addition. Results from the gene analyses show that two genes encoding the extradiol/intradiol ring-cleavage dioxygenase and five genes encoding the hydrolase in P. mendocina NSYSU were identified and played important roles in OCDD degradation.

Potential for Polychlorinated Biphenyl Biodegradation in Sediments from Indiana Harbor and Ship Canal

Polychlorinated biphenyls (PCBs) are carcinogenic, persistent, and bioaccumulative contaminants that pose risks to human and environmental health. In this study, we evaluated the PCB biodegradation of sediments from Indiana Harbor and Ship Canal (IHSC), a PCB-contaminated site (average PCB concentration = 12,570 ng/g d.w.). PCB congener profiles and bacterial community structure in a core sediment sample (4.57 m long) were characterized. Analysis of vertical PCB congener profile patterns in sediment and pore water strongly suggest that in situ dechlorination occurred in sediments. However, 16S rRNA genes from putative PCB-dechlorinating Chloroflexi were relatively more abundant in upper 2 m sediments, as were genes indicative of aerobic biodegradation potential (i.e. biphenyl dioxygenase (bphA)). Characterization of the bacterial community by terminal restriction fragment length polymorphism and comparison of these with sediment and pore water PCB congener profiles with the Mantel test revealed a statistical correlation (p<0.001). Sequences classified as Acinetobacter and Acidovorax were highly abundant in deep sediments. Overall, our results suggest that PCB dechlorination has already occurred, and that IHSC sediments have the potential for further aerobic and anaerobic PCB biodegradation.

Bioremediation potential of soil contaminated with highly substituted polychlorinated dibenzo-p-dioxins and dibenzofurans: microcosm study and microbial community analysis

Highly chlorinated dibenzo-p-dioxins/dibenzofurans (DD/Fs) are main hazardous dioxins, and ubiquitously distributed in the environment. To study the feasibility of bioremediation for remedying contamination of highly chlorinated dioxins, closed microcosms were constructed with soil from a chronological site under oxygen-stimulated conditions. The results showed that high levels of near-fully and fully chlorinated DD/Fs, particularly octachlorodibenzofuran were effectually reduced without accumulation of less substituted congeners. The clone library analysis of PCR-amplified 16S rRNA gene from the octachlorodibenzofuran-degrading consortia showed that 98.3% of the detected sequences were affiliated with Proteobacteria. The obtained strains with putative aromatic dioxygenase genes and abilities to repetitively grow in octachlorodibenzofuran-containing agars were closely related to members within Actinobacteria, Firmicutes, and Proteobacteria. Among them, certain Rhodococcus, Micrococcus, Mesorhizobium and Bacillus isolates could degrade octachlorodibenzofuran with efficiencies of 26-43% within 21 days. Hierarchical oligonucleotide primer extension analysis further showed that Micrococcus, Rhizobium, Pseudoxanthomonas, and Brevudimonas populations increased largely when high concentrations of octachlorodibenzofuran were reduced. Overall, our results suggest that a distinctive microbial composition and population dynamic could be required for the enhanced degradation of highly chlorinated DD/Fs in the batch microcosm and highlight a potential of bioremediation technologies in remedying polychlorinated dioxins in the polluted sites.

Characterization of Rhizobium naphthalenivorans sp. nov. with special emphasis on aromatic compound degradation and multilocus sequence analysis of housekeeping genes

Three strains of aerobic chemoorganotrophic naphthalene-degrading bacteria (designated TSY03b(T), TSY04, and TSW01) isolated from sediment of a polychlorinated-dioxin-transforming microcosm were characterized. These strains had Gram-negative-stained, rod-shaped cells measuring 0.6‒0.9 μm in width and 1.2‒3.0 μm in length and were motile by means of peritrichous flagella. Naphthalene was utilized as the sole carbon and energy source, and the transcription of a putative aromatic-ring hydroxylating gene was inducible by naphthalene. The major component of cellular fatty acids was summed feature 8 (C18:1ω7c and/or C18:1ω6c), and significant proportions of C18:0 and C19:0 cyclo ω8cis were also found. The major respiratory quinone was ubiquinone-10. The G+C content of the DNA was 60.3‒60.9 mol%. Phylogenetic analyses by studying sequence information on the housekeeping atpD, dnaK, glnII, gyrB, and recA genes as well as on 16S rRNA genes and the 16S-23S rDNA internal transcribed spacer region revealed that the strains grouped with members of the genus Rhizobium, with Rhizobium selenitireducens as their closest relative but formed a distinct lineage at the species level. This was confirmed by genomic DNA-DNA hybridization studies. These phenotypic, genotypic, and phylogenetic data strongly suggest that our isolates should be classified under a novel species of the genus Rhizobium. Thus, we propose the name Rhizobium naphthalenivorans sp. nov. to accommodate the novel isolates. The type strain is TSY03b(T) (= NBRC 107585T = KCTC 23252T).

Chemical and toxicological assessment of a full-scale biosolid compost

The impact of a full-scale biosolid composting plant on the fate of a broad range of priority organic pollutants was investigated. Chemical analysis was performed at different steps of the process during two seasons. Simultaneously, the toxicological quality was assessed using estrogen α-, dioxin-, and pregnane X-receptor reporter cell lines. Mass-balance calculation highlighted the removal of easily degradable pollutants during composting. The important variations observed for each compound and for the two seasons might be explained by pollutant-fate dependency on process parameters like temperature. The final compost displayed low pregnane X activity but high estrogenic activity. The dioxin-like activity stayed constant through the process. The chemical and toxicological results highlight the importance of combining both approaches to accurately assess the compost quality. Such compilation of data on full-scale processes may be also very helpful for the environmental risk assessment of new organic waste disposal practices.

Isolation and functional gene analyses of aromatic-hydrocarbon-degrading bacteria from a polychlorinated-dioxin-dechlorinating process

Aerobic aromatic-hydrocarbon-degrading bacteria from a semi-anaerobic microbial microcosm that exhibited apparent complete dechlorination of polychlorinated dibenzo-p-dioxins/dibenzofurans (PCDD/Fs) were isolated through enrichment and plating culture procedures with dibenzofuran as the model substrate. By 16S rRNA gene sequence comparisons, these dibenzofuran-degrading isolates were identified as being members of the phyla Actinobacteria, Firmicutes, and Proteobacteria, among which those of the genera Paenibacillus and Rhizobium were most abundant. All of the isolates utilized naphthalene as the sole carbon and energy source and degraded dibenzofuran metabolically or co-metabolically; however, they hardly attacked monochlorinated dibenzofuran and dibenzo-p-dioxin. By PCR cloning and sequencing, genes predicted to encode aromatic-ring-hydroxylating dioxygenase (AhDO) were detected in all test isolates. Real-time quantitative PCR assays with specific primer sets detected approximately 10⁵ copies of the AhDO large subunit genes g⁻¹ wet wt in the microcosm from which the isolates were obtained. This order of the copy number corresponded to approximately 1% of the 16S rRNA gene copies from "Dehalococcoides" and its relatives present as potent dechlorinators. These results suggest that aerobic AhDO-containing bacteria co-exist and play a role in the oxidative degradation of less chlorinated and completely dechlorinated products in the PCDD/F-dechlorinating process, thereby achieving the apparent complete dechlorination of PCDD/Fs.

Ecogenomics of microbial communities in bioremediation of chlorinated contaminated sites

Organohalide compounds such as chloroethenes, chloroethanes, and polychlorinated benzenes are among the most significant pollutants in the world. These compounds are often found in contamination plumes with other pollutants such as solvents, pesticides, and petroleum derivatives. Microbial bioremediation of contaminated sites, has become commonplace whereby key processes involved in bioremediation include anaerobic degradation and transformation of these organohalides by organohalide respiring bacteria and also via hydrolytic, oxygenic, and reductive mechanisms by aerobic bacteria. Microbial ecogenomics has enabled us to not only study the microbiology involved in these complex processes but also develop tools to better monitor and assess these sites during bioremediation. Microbial ecogenomics have capitalized on recent advances in high-throughput and -output genomics technologies in combination with microbial physiology studies to address these complex bioremediation problems at a system level. Advances in environmental metagenomics, transcriptomics, and proteomics have provided insights into key genes and their regulation in the environment. They have also given us clues into microbial community structures, dynamics, and functions at contaminated sites. These techniques have not only aided us in understanding the lifestyles of common organohalide respirers, for example Dehalococcoides, Dehalobacter, and Desulfitobacterium, but also provided insights into novel and yet uncultured microorganisms found in organohalide respiring consortia. In this paper, we look at how ecogenomic studies have aided us to understand the microbial structures and functions in response to environmental stimuli such as the presence of chlorinated pollutants.

Reductive Dechlorination of Polychlorinated Biphenyls and Dibenzo-p-Dioxins in an Enrichment Culture Containing Dehalobacter Species

The dechlorination of polychlorinated biphenyls (PCBs) and polychlorinated dibenzo-p-dioxins was examined in an enrichment culture (KFL culture) that contained two phylotypes of Dehalobacter, FTH1 and FTH2. The KFL culture dechlorinated 2,3,4,5-tetrachlorobiphenyl, 2,3,4-trichorobiphenyl (2,3,4-TriCB), and 1,2,3-trichlorodibenzo-p-dioxin (1,2,3-TriCDD). Quantitative real-time PCR targeting FTH1 and FTH2 revealed significant increases with the addition of PCBs and 1,2,3-TriCDD, suggesting halorespiring growth of the Dehalobacter species in the KFL culture. This study demonstrated the reductive dechlorination of PCBs and 1,2,3-TriCDD by Dehalobacter species in a sediment-free culture and a novel dechlorination pathway, the conversion of 2,3,4-TriCB to 4-monochlorobiphenyl via 3,4-dichlorobiphenyl.

Phylogenetic and Transcriptional Analyses of a Tetrachloroethene-Dechlorinating "Dehalococcoides" Enrichment Culture TUT2264 and Its Reductive-Dehalogenase Genes

A dechlorinating microbial enrichment culture designated TUT2264 was cultured with tetrachloroethene and then characterized for tetrachloroethene-dechlorination by culture-dependent and -independent methods. The fourth-transferred TUT2264 culture completely dechlorinated tetrachloroethene and trichloroethene, and accumulated more trans-1,2-dichloroethene than cis-1,2-dichloroethene. A real-time PCR analysis revealed that "Dehalococcoides" cells made up only 0.3% of the total. Eight distinct reductive-dehalogenase-homologous genes (rdh) were detected with degenerate primers. Phylogenetic analyses revealed 5 of the 8 RdhAs to be very similar to RdhAs reported previously but not to share 100% identity. Transcriptional levels were quantified as the number of transcripts per rdhA by combining the reverse transcription real-time PCR and exogenous internal reference mRNA methods. TUT2264 responded to all the chloroethenes tested. rdhA4 was transcribed with all chloroethenes except vinyl chloride, whereas rdhA8 was only transcribed on tetrachloroethene. Furthermore, multiple rdhAs were induced to express by a single chloroethene as a growth-supporting or non-supporting substrate. These results suggested that Rdhs are multi-functional and rdhAs are a powerful tool to evaluate the potential of contaminated sites and isolates to dechlorinate chloroethenes.

Cultivation-independent identification of candidate dehalorespiring bacteria in tetrachloroethylene degradation

Tetrachloroethylene (PCE) is one of the major pollutants and is degraded by dissimilation by dehalorespiring bacteria. The dehalorespiring bacteria are anaerobic, and most cannot be cultured by conventional agar plating methods. Therefore, to identify the dehalorespiring bacteria that dissimilatively degrade PCE, a cultivation-independent method is required. To achieve accurate and detailed analysis of the bacteria, we developed a novel stable isotope probing (SIP) method. This technique involves 2 steps, namely, a labeling step, in which a labeled carbon source is incorporated into the sample's DNA, and an analysis step, in which the DNA is isolated, fractionated, and analyzed by polymerase chain reaction denaturing gradient gel electrophoresis (PCR-DGGE). Subsequently, 16S rRNA sequencing and phylogenetic analysis were performed to identify the bacteria. Initially, we examined the effectiveness of this method by using Dehalococcoides ethenogenes 195 consortium as a defined model system. The result indicated the method was able to correctly identify the dehalorespiring bacteria D. ethenogenes 195 from the consortium. Moreover, in an artificially contaminated microcosm experiment, we confirmed that the method was able to identify the indigenous dehalorespiring bacteria Dehalobacter sp. Thus, we concluded that this novel method was a feasible tool to identify dehalorespiring bacteria in natural environments.

Successful microcosm demonstration of a strategy for biodegradation of a mixture of carbon tetrachloride and perchloroethene harnessing sulfate reducing and dehalorespiring bacteria

Carbon tetrachloride (CT) is known to inhibit the transformation of perchloroethene (PCE) to ethene by dehalorespiring bacteria, creating a challenge for the bioremediation of environments contaminated with both compounds. We report on the sequential use of sulfate reduction and dehalorespiration as a microbial strategy for the transformation of a mixture of CT (10 μM) and PCE (14 μM). Sulfide production in Desulfovibrio vulgaris cultures led to complete CT disappearance in as little as 12 days. The addition of amorphous ferric oxide decreased the proportion of chloroform (CF) produced from 65% to 30%. CT conversion rates were enhanced more than 13-fold where vitamin B(12) (5 μM) was added. In vitamin B(12)-containing D. vulgaris cultures, no chlorinated products were detected and carbon disulfide was the major product of CT transformation. PCE concentrations were not impacted upon by D. vulgaris activity. The subsequent inoculation of a PCE-respiring enrichment culture resulted in microbial PCE dechlorination to ethene.

O-Demethylation and successive oxidative dechlorination of methoxychlor by Bradyrhizobium sp. strain 17-4, isolated from river sediment

O-Demethylation of insecticide methoxychlor is well known as a phase I metabolic reaction in various eukaryotic organisms. Regarding prokaryotic organisms, however, no individual species involved in such reaction have been specified and characterized so far. Here we successfully isolated a bacterium that mediates oxidative transformation of methoxychlor, including O-demethylation and dechlorination, from river sediment. The isolate was found to be closely related to Bradyrhizobium elkanii at the 16S rRNA gene sequence level (100% identical). However, based on some differences in the physiological properties of this bacterium, we determined that it was actually a different species, Bradyrhizobium sp. strain 17-4. The isolate mediated O-demethylation of methoxychlor to yield a monophenolic derivative [Mono-OH; 1,1,1-trichloro-2-(4-hydroxyphenyl)-2-(4-methoxyphenyl)ethane] as the primary degradation product. The chiral high-performance liquid chromatography (HPLC) analysis revealed that the isolate possesses high enantioselectivity favoring the formation of (S)-Mono-OH (nearly 100%). Accompanied by the sequential O-demethylation to form the bis-phenolic derivative Bis-OH [1,1,1-trichloro-2,2-bis(4-hydroxyphenyl)ethane], oxidative dechlorination of the side chain proceeded, and monophenolic carboxylic acid accumulated, followed by the formation of multiple unidentified polar degradation products. The breakdown proceeded more rapidly when reductively dechlorinated (dichloro-form) methoxychlor was applied as the initial substrate. The resultant carboxylic acids and polar degradation products are likely further biodegraded by ubiquitous bacteria. The isolate possibly plays an important role for complete degradation (mineralization) of methoxychlor by providing the readily biodegradable substrates.

A Chloroflexi bacterium dechlorinates polychlorinated biphenyls in marine sediments under in situ-like biogeochemical conditions

We investigated the reductive dechlorination of Aroclor 1254 PCBs by a coplanar PCB-dechlorinating microbial community enriched from an actual site contaminated marine sediment of the Venice lagoon in sterile slurry microcosms of the same sediment suspended in its site water, i.e., under biogeochemical conditions that closely mime those occurring in situ. The culture dechlorinated more than 75% of the penta- through hepta-chlorinated biphenyls to tri- and tetra-chlorinated congeners in 30 weeks. The dechlorination rate was reduced by the addition of H(2) and short chain fatty acids, which stimulated sulfate-reduction and methane production, and markedly increased by the presence of vancomycin or ampicillin. DGGE analysis of 16S rRNA genes on PCB-spiked and PCB-free cultures ruled out sulfate-reducing and methanogenic bacteria and revealed the presence of a single Chloroflexi phylotype closely related to the uncultured bacteria m-1 and SF1 associated to PCB dechlorination. These findings suggest that a single dechlorinator is responsible for the observed extensive dechlorination of Aroclor 1254 and that a Chloroflexi species similar to those already detected in freshwater and estuarine contaminated sediments mediates PCB dechlorination in the marine sediment adopted in this study under biogeochemical conditions resembling those occurring in situ in the Brentella Canal of Venice Lagoon.

Reductive dechlorination of methoxychlor by bacterial species of environmental origin: evidence for primary biodegradation of methoxychlor in submerged environments

Methoxychlor [1,1,1-trichloro-2,2-bis(4-methoxyphenyl)ethane] is an organochlorine insecticide that undergoes dechlorination in natural submerged environments. We investigated the ability to dechlorinate this compound in seven environmental bacterial species ( Aeromonas hydrophila , Enterobacter amnigenus , Klebsiella terrigena , Bacillus subtilis , Achromobacter xylosoxidans , Acinetobacter calcoaceticus , and Mycobacterium obuense ) and the enteric bacterium Escherichia coli as a positive control. In R2A broth at 25 °C under aerobic, static culture, all species except Ach. xylosoxidans were observed to convert methoxychlor to dechlorinated methoxychlor [1,1-dichloro-2,2-bis(4-methoxyphenyl)ethane]. The medium was aerobic at first, but bacterial growth resulted in the consumption of oxygen and generated microaerobic and weakly reductive conditions. Replacement of the headspace of the culture tubes with nitrogen gas was found to decrease the dechlorination rate. Our findings suggest that extensive bacterial species ubiquitously inhabiting the subsurface water environment play an important role in the primary dechlorination of methoxychlor.

Natural niche for organohalide-respiring Chloroflexi

The phylum Chloroflexi contains several isolated bacteria that have been found to respire a diverse array of halogenated anthropogenic chemicals. The distribution and role of these Chloroflexi in uncontaminated terrestrial environments, where abundant natural organohalogens could function as potential electron acceptors, have not been studied. Soil samples (116 total, including 6 sectioned cores) from a range of uncontaminated sites were analyzed for the number of Dehalococcoides-like Chloroflexi 16S rRNA genes present. Dehalococcoides-like Chloroflexi populations were detected in all but 13 samples. The concentrations of organochlorine ([organochlorine]), inorganic chloride, and total organic carbon (TOC) were obtained for 67 soil core sections. The number of Dehalococcoides-like Chloroflexi 16S rRNA genes positively correlated with [organochlorine]/TOC while the number of Bacteria 16S rRNA genes did not. Dehalococcoides-like Chloroflexi were also observed to increase in number with a concomitant accumulation of chloride when cultured with an enzymatically produced mixture of organochlorines. This research provides evidence that organohalide-respiring Chloroflexi are widely distributed as part of uncontaminated terrestrial ecosystems, they are correlated with the fraction of TOC present as organochlorines, and they increase in abundance while dechlorinating organochlorines. These findings suggest that organohalide-respiring Chloroflexi may play an integral role in the biogeochemical chlorine cycle.

A great leap forward in microbial ecology

Ribosomal RNA (rRNA) sequence-based molecular techniques emerged in the late 1980s, which completely changed our general view of microbial life. Coincidentally, the Japanese Society of Microbial Ecology (JSME) was founded, and its official journal "Microbes and Environments (M&E)" was launched, in 1985. Thus, the past 25 years have been an exciting and fruitful period for M&E readers and microbiologists as demonstrated by the numerous excellent papers published in M&E. In this minireview, recent progress made in microbial ecology and related fields is summarized, with a special emphasis on 8 landmark areas; the cultivation of uncultured microbes, in situ methods for the assessment of microorganisms and their activities, biofilms, plant microbiology, chemolithotrophic bacteria in early volcanic environments, symbionts of animals and their ecology, wastewater treatment microbiology, and the biodegradation of hazardous organic compounds.