Exploiting the intrinsic microbial degradative potential for field-based in situ dechlorination of trichloroethene contaminated groundwater

An innovative permeable reactive bio-barrier to remediate trichloroethene-contaminated groundwater: A field study

Permeable reactive bio-barrier (PRBB), an innovative technology, could treat many contaminants via the natural gradient flow of groundwater based on immobilization or transformation of pollutants into less toxic and harmful forms. In this field study, we developed an innovative PRBB system comprising immobilized Dehalococcoides mccartyi (Dhc) and Clostridium butyricum embedded into the silica gel for long-term treatment of trichloroethene (TCE) polluted groundwater. Four injection wells and two monitoring wells were installed at the downstream of the TCE plume. Without PRBB, results showed that the TCE (6.23 ± 0.43 μmole/L) was converted to cis-dichloroethene (0.52 ± 0.63 μmole/L), and ethene was not detected, whereas TCE was completely converted to ethene (3.31 μmole/L) with PRBB treatment, indicating that PRBB could promote complete dechlorination of TCE. Noticeably, PRBB showed the long-term capability to maintain a high dechlorinating efficiency for TCE removal during the 300-day operational period. Furthermore, with qPCR analysis, the PRBB application could stably maintain the populations of Dhc and functional genes (bvcA, tceA, and vcrA) at >108 copies/L within the remediation course and change the bacterial communities in the contaminated groundwater. We concluded that our PRBB was first set up for cleaning up TCE-contaminated groundwater in a field trial.

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.

Underpinning the ecological response of mixed chlorinated volatile organic compounds (CVOCs) associated with contaminated and bioremediated groundwaters: A potential nexus of microbial community structure and function for strategizing efficient bioremediation

Understanding the structure, dynamics, and functionality of microbial communities is essential for developing sustainable and effective bioremediation strategies, particularly for sites contaminated with mixed chlorinated volatile organic compounds (CVOCs), which can make the biodegradation process more complex and challenging. In this study, 16S rRNA amplicon sequencing revealed a significant change in microbial distribution in response to CVOCs contamination. The loss of sensitive taxa such as Proteobacteria and Acidobacteriota was observed, while CVOCs-resistant taxa such as Campilobacterota were found significantly enriched in contaminated sites. Additionally, varying abundances of crucial enzymes involved in the sequential biodegradation of CVOCs were expressed depending on the contamination level. Association analysis revealed that specific genera such as Sulfurospirillum, Azospira, Trichlorobacter, Acidiphilium, and Magnetospririllum could relatively survive under higher levels of CVOC contamination, whereas pH, ORP and temperature had a negative influence in their abundance and distribution. However, Dechloromonas, Thiobacillus, Pseudarcicella, Hydrogenophaga, and Sulfuritalea showed a negative relationship with CVOC contamination, highlighting their sensitivity towards CVOC contamination. These findings provide valuable insights into the relationship among ecological responses, the groundwater bacterial community, and their functionality in response to mixed CVOC contamination, offering a fundamental basis for developing effective and sustainable bioremediation strategies for CVOC-contaminated groundwater systems.

Ecological landscape explains aquifers microbial structure

Aquifers have significant social, economic, and ecological importance. They supply 30 % of the freshwater for human consumption worldwide, including agricultural and industrial use. Despite aquifers' importance, the relationships between aquifer categories and their inhabiting microbial communities are still unknown. Characterizing variations within microbial communities' function and taxonomy structure at different aquifers could give a panoramic view of patterns that may enable the detection and prediction of environmental impact caused by multiple sources. Using publicly available shotgun metagenomic datasets, we examined whether soil properties, land use, and climate variables would have a more significant influence on the taxonomy and functional structure of the microbial communities than the ecological landscapes of the aquifer (i.e., Karst, Porous, Saline, Geyser, and Porous Contaminated). We found that these categories are stronger predictors of microbial communities' structure than geographical localization. In addition, our results show that microbial richness and dominance patterns are the opposite of those found in multicellular life, where extreme habitats harbour richer functional and taxonomic microbial communities. We found that low-abundant and recently described candidate taxa, such as the chemolithoautotrophic genus Candidatus Altiarcheum and the Candidate phylum Parcubacteria, are the main contributors to aquifer microbial communities' dissimilarities. Genes related to gram-negative bacteria proteins, cell wall structures, and phage activity were the primary contributors to aquifer microbial communities' dissimilarities among the aquifers' ecological landscapes. The results reported in the present study highlight the utility of using ecological landscapes for investigating aquifer microbial communities. In addition, we suggest that functions played by recently described and low abundant bacterial groups need further investigation once they might affect water quality, geochemical cycles, and the effects of anthropogenic disturbances such as pollution and climatic events on aquifers.

Critical review on phytoremediation of polyfluoroalkyl substances from environmental matrices: Need for global concern

Poly- and perfluoroalkyl substances (PFAS) are a class of emerging organic contaminants that are impervious to standard physicochemical treatments. The widespread use of PFAS poses serious environmental issues. PFAS pollution of soils and water has become a significant issue due to the harmful effects of these chemicals both on the environment and public health. Owing to their complex chemical structures and interaction with soil and water, PFAS are difficult to remove from the environment. Traditional soil remediation procedures have not been successful in reducing or removing them from the environment. Therefore, this review focuses on new phytoremediation techniques for PFAS contamination of soils and water. The bioaccumulation and dispersion of PFAS inside plant compartments has shown great potential for phytoremediation, which is a promising and unique technology that is realistic, cost-effective, and may be employed as a wide scale in situ remediation strategy.

Remediation of groundwater contaminated with dye using carbon dots technology: Ecotoxicological and microbial community responses

Groundwater pollution poses a serious threat to the main source of clean water globally. Nanoparticles have the potential for remediation of polluted aquifers; however, environmental safety concerns associated with in situ deployments of such technology include potential detrimental effects on microorganisms in terms of toxicity and functional disruptions. In this work, we evaluated a new and ecofriendly approach using carbon dots (CDs) as Fenton-like catalysts to catalyse the degradation of dye-containing groundwater samples. This investigation aimed at evaluating the efficacy of a novel remediation technology in terms of dye degradation and toxicity reduction while assessing its impacts on aquatic microorganisms. Uncontaminated Australian groundwater samples were spiked with methylene blue and incubated in the dark, at 18 °C, under slow agitation, using CDs at 0.5 mg mL^-1 and H₂O₂ at 73.5 mM for 25 h. The dye degradation rate was determined as well as the toxicity of the treated solutions using the Microtox® bioassay. Further, to determine the changes in the groundwater microbial community, 16 S rRNA sequencing was used and evenness and diversity indices were analysed using Pielou's evenness and Simpson index, respectively. This study revealed that dye-containing groundwater were effectively treated by CDs showing a degradation rate of 78-82% and a significant 4-fold reduction in the toxicity. Characterisation of the groundwater microbiota revealed a predominance of at least 60% Proteobacteria phylum in all samples where diversity and evenness were maintained throughout the remediation process. The results showed that CDs could be an efficient approach to treat polluted groundwater and potentially have minimum impact on the environmental microbiome.

Can polymer-degrading microorganisms solve the bottleneck of plastics' environmental challenges?

Increasing world population and industrial activities have enhanced anthropogenic pollution, plastic pollution being especially alarming. So, plastics should be recycled and/or make them biodegradable. Chemical and physical remediating methods are usually energy consuming and costly. In addition, they are not ecofriendly and usually produce toxic byproducts. Bioremediation is a proper option as it is cost-efficient and environmentally friendly. Plastic production and consumption are increasing daily, and, as a consequence, more microorganisms are exposed to these nonbiodegradable polymers. Therefore, investigating new efficient microorganisms and increasing the knowledge about their biology can pave the way for efficient and feasible plastic bioremediation processes. In this sense, omics, systems biology and bioinformatics are three important fields to analyze the biodegradation pathways in microorganisms. Based on the above-mentioned technologies, researchers can engineer microorganisms with specific desired properties to make bioremediation more efficient.

Cleanup chlorinated ethene-polluted groundwater using an innovative immobilized Clostridium butyricum column scheme: A pilot-scale study

In this study, the developed innovative immobilized Clostridium butyricum (ICB) (hydrogen-producing bacteria) column scheme was applied to cleanup chlorinated-ethene [mainly cis-1,2-dichloroethene (cis-DCE)] polluted groundwater in situ via the anaerobic reductive dechlorinating processes. The objectives were to assess the effectiveness of the field application of ICB scheme on the cleanup of cis-DCE polluted groundwater, and characterize changes of microbial communities after ICB application. Three remediation wells and two monitor wells were installed within the cis-DCE plume. In the remediation well, a 1.2-m PVC column (radius = 2.5 cm) (filled with ICB beads) and 20 L of slow polycolloid-releasing substrate (SPRS) were supplied for hydrogen production enhancement and primary carbon supply, respectively. Groundwater samples from remediation and monitor wells were analyzed periodically for cis-DCE and its degradation byproducts, microbial diversity, reductive dehalogenase, and geochemical indicators. Results reveal that cis-DCE was significantly decreased within the ICB and SPRS influence zone. In a remediation well with ICB injection, approximately 98.4% of cis-DCE removal (initial concentration = 1.46 mg/L) was observed with the production of ethene (end-product of cis-DCE dechlorination) after 56 days of system operation. Up to 0.72 mg/L of hydrogen was observed in remediation wells after 14 days of ICB and SPRS introduction, which corresponded with the increased population of Dehalococcoides spp. (Dhc) (increased from 3.76 × 103 to 5.08 × 105 gene copies/L). Results of metagenomics analyses show that the SPRS and ICB introduction caused significant impacts on the bacterial communities, and increased Bacteroides, Citrobacter, and Desulfovibrio populations were observed, which had significant contributions to the reductive dechlorination of cis-DCE. Application of ICB could effectively result in increased populations of Dhc and RDase genes, which corresponded with improved dechlorination of cis-DCE and vinyl chloride. Introduction of ICB and SPRS could be applied as a potential in situ remedial option to enhance anaerobic dechlorination efficiencies of chlorinated ethenes.

Electrokinetically-enhanced emplacement of lactate in a chlorinated solvent contaminated clay site to promote bioremediation

Bioremediation through the injection of electron donors and bacterial cultures is effective at treating chlorinated solvent contamination. However, it has had limited application in low permeability zones where amendments cannot be delivered successfully. This field-scale study investigated the application of electrokinetics to enhance the delivery of lactate at a clay site contaminated with chlorinated solvents. Groundwater and soil samples were collected before, during and for 1 year after the 71-day field test and analyzed for a wide suite of chemical and biological parameters. Lactate was successfully delivered to all monitoring locations. Lactate emplacement resulted in the stimulation of bacterial populations, specifically within the phylum Firmicutes, which contains fermenters and strict anaerobes. This likely led to biodegradation, as the field trial resulted in significant decreases in both soil and aqueous phase chlorinated solvent concentrations. Contaminant decreases were also partially attributable to dilution, given evidence of some advective lactate flux. This research provides evidence that electrokinetically-enhanced bioremediation has potential as a treatment strategy for contaminated low permeability strata.

Bioremediation of lignin derivatives and phenolics in wastewater with lignin modifying enzymes: Status, opportunities and challenges

Lignin modifying enzymes from fungi and bacteria are potential biocatalysts for sustainable mitigation of different potentially toxic pollutants in wastewater. Notably, the paper and pulp industry generates enormous amounts of wastewater containing high amounts of complex lignin-derived chlorinated phenolics and sulfonated pollutants. The presence of these compounds in wastewater is a critical issue from environmental and toxicological perspectives. Some chloro-phenols are harmful to the environment and human health, as they exert carcinogenic, mutagenic, cytotoxic, and endocrine-disrupting effects. In order to address these most urgent concerns, the use of oxidative lignin modifying enzymes for bioremediation has come into focus. These enzymes catalyze modification of phenolic and non-phenolic lignin-derived substances, and include laccase and a range of peroxidases, specifically lignin peroxidase (LiP), manganese peroxidase (MnP), versatile peroxidase (VP), and dye-decolorizing peroxidase (DyP). In this review, we explore the key pollutant-generating steps in paper and pulp processing, summarize the most recently reported toxicological effects of industrial lignin-derived phenolic compounds, especially chlorinated phenolic pollutants, and outline bioremediation approaches for pollutant mitigation in wastewater from this industry, emphasizing the oxidative catalytic potential of oxidative lignin modifying enzymes in this regard. We highlight other emerging biotechnical approaches, including phytobioremediation, bioaugmentation, Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-based technology, protein engineering, and degradation pathways prediction, that are currently gathering momentum for the mitigation of wastewater pollutants. Finally, we address current research needs and options for maximizing sustainable biobased and biocatalytic degradation of toxic industrial wastewater pollutants.

Increasing electron donor concentration does not accelerate complete microbial reductive dechlorination in contaminated sediment with native organic carbon

Experiments with Fe(III)-rich, chloroethene-contaminated sediment demonstrated that trichloroethylene (TCE) and vinyl chloride (VC) were completely reduced to ethene regardless of whether electron donor(s) were added at 1 × stoichiometry or 10 × stoichiometry relative to all-electron acceptors. Unamended controls uniformly reduced TCE to ethene with a mean time to complete dechlorination (operationally defined as the presence of stoichiometric ethene production) of 79 days. Adding 1 × and 10 × acetate hindered the rate and extent of TCE and VC reduction relative to unamended controls, with several only partially reduced when the experiments were terminated. Adding high molecular mass (soybean oil derivative) substrates did not increase microbial reductive dechlorination relative to unamended incubations, and in many cases, hindered microbial dechlorination in favor of methanogenesis. The mean time to complete dechlorination was comparable between low (× 1) and high (× 10) electron donor concentration for all lipid-based electron donors tested. Those tested included Newman Zone® Standard without sodium lactate (96 vs. 75 days, respectively), CAP 18 ME (85 vs. 94 days, respectively), EOS 598B42 (68 vs. 72 days, respectively), and acetate (134 vs. 125 days, respectively). These data suggest that the addition of an electron donor does not always increase the rate and extent of reductive dechlorination but will increase costs. In particular, increasing the concentration of electron donors higher than the stoichiometric demand only decreased complete microbial reductive dechlorination, which is the opposite of most standard "more time and more electrons" approaches. These data argue that site-specific electron donor demands must be evaluated, and in some cases, a monitored natural attenuation (MNA) approach is most favorable.

Simultaneous adsorption and biodegradation of trichloroethylene occurs in a biochar packed column treating contaminated landfill leachate

Trichloroethylene (TCE) is a human carcinogen that is commonly found in landfill leachate. Contaminated leachate plumes may be intercepted prior to reaching groundwater and treated in situ using permeable reactive barriers (PRB). This study used a packed column system containing herbal pomace and spruce biochar, previously shown to have TCE adsorptive capabilities. Influent containing raw or autoclaved landfill leachate was used to investigate the potential for environmental micro-organisms to establish a TCE-dechlorinating biofilm on the biochar, in order to prolong the operational life span of the system. TCE removal ≥ 99.7 % was observed by both biochars. No dichloroethylene (DCE) isomers were present in the column effluents, but cis-1,2 DCE was adsorbed to the biochar treating raw landfill leachate, indicating that dechlorination was occurring biologically in these columns. Known microbial species that are individually capable of complete dechlorination of TCE to ethene were not detected by 16S rRNA gene sequencing, but several species capable of partial TCE dechlorination (Desulfitobacterium spp., Sulfurospirillium spp. and Desulfuromonas spp) were present in the biofilms of the columns treating raw landfill leachate. These data demonstrate that biochar from waste material may be capable of supporting a dechlorinating biofilm to promote bioremediation of TCE.

Challenges and Current Status of the Biological Treatment of PFAS-Contaminated Soils

Per- and polyfluoroalkyl substances (PFAS) are Synthetic Organic Compounds (SOCs) which are of current concern as they are linked to a myriad of adverse health effects in mammals. They can be found in drinking water, rivers, groundwater, wastewater, household dust, and soils. In this review, the current challenge and status of bioremediation of PFAs in soils was examined. While several technologies to remove PFAS from soil have been developed, including adsorption, filtration, thermal treatment, chemical oxidation/reduction and soil washing, these methods are expensive, impractical for in situ treatment, use high pressures and temperatures, with most resulting in toxic waste. Biodegradation has the potential to form the basis of a cost-effective, large scale in situ remediation strategy for PFAS removal from soils. Both fungal and bacterial strains have been isolated that are capable of degrading PFAS; however, to date, information regarding the mechanisms of degradation of PFAS is limited. Through the application of new technologies in microbial ecology, such as stable isotope probing, metagenomics, transcriptomics, and metabolomics there is the potential to examine and identify the biodegradation of PFAS, a process which will underpin the development of any robust PFAS bioremediation technology.

Bioremediation of typical chlorinated hydrocarbons by microbial reductive dechlorination and its key players: A review

Chlorinated hydrocarbon contamination in soils and groundwater has a severe negative impact on the human health. Microbial reductive dechlorination is a major degradation pathway of chlorinated hydrocarbon in anaerobic subsurface environments, has been extensively studied. Recent progress on the diversity of the reductive dechlorinators and the key enzymes of chlororespiration has been well reviewed. Here, we present a thorough overview of the studies related to bioremediation of chloroethenes and polychlorinated biphenyls based on enhanced in situ reductive dechlorination. The major part of this review is to provide an up-to-date summary of functional microorganisms which are either detected during in situ biostimulation or applied in bioaugmentation strategies. The applied biostimulants and corresponding reductive dechlorination products are also summarized and the future research needs are finally discussed.

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.

Ecological impact assessment of a bioaugmentation site on remediation of chlorinated ethylenes by multi-omics analysis

Bioremediation may affect the ecological system around bioremediation sites. However, little is known about how microbial community structures change over time after the initial injection of degraders. In this study, we have assessed the ecological impact of bioaugmentation using metagenomic and metatranscriptomic approaches to remove trichlorinated ethylene/cis-dichloroethylene (TCE/cDCE) by Rhodococcus jostii strain RHA1 as an aerobic chemical compound degrader. Metagenomic analysis showed that the number of organisms belonging to the genus Rhodococcus, including strain RHA1, increased from 0.1% to 76.6% of the total microbial community on day 0 at the injection site. Subsequently, the populations of strain RHA1 and other TCE/cDCE-degrading bacteria gradually decreased over time, whereas the populations of the anaerobic dechlorinators Geobacter and Dehalococcoides increased at later stages. Metatranscriptomic analysis revealed a high expression of aromatic compound-degrading genes (bphA1-A4) in strain RHA1 after RHA1 injection. From these results, we concluded that the key dechlorinators of TCE/cDCE were mainly aerobic bacteria, such as RHA1, until day 1, after which the key dechlorinators changed to anaerobic bacteria, such as Geobacter and Dehalococcocides, after day 6 at the injection well. Based on the α-diversity, the richness levels of the microbial community were increased after injection of strain RHA1, and the microbial community composition had not been restored to that of the original composition during the 19 days after treatment. These results provide insights into the assessment of the ecological impact and bioaugmentation process of RHA1 at bioremediation sites.

A hydrocarbon-contaminated aquifer reveals a Piggyback-the-Persistent viral strategy

Subsurface environments hold the largest reservoir of microbes in the biosphere. They play essential roles in transforming nutrients, degrading contaminants and recycling organic matter. Here, we propose a previously unrecognised fundamental microbial process that influences aquifer bioremediation dynamics and that applies to all microbial communities. In contrast to previous models, our proposed Piggyback-the-Persistent (PtP) mechanism occurs when viruses become more dominated by those exhibiting temperate rather than lytic lifestyles driven by persistent chemicals (in our case chlorinated-hydrocarbon pollutants) that provide long-term carbon sources and that refocus the aquifer carbon cycle, thus altering the microbial community. In this ultra-oligotrophic system, the virus:microbial ratio (VMR) ranges from below the detection limit of 0.0001 to 0.6, well below the common aquatic range of 3-10. Shortest-average-path network analysis revealed VMR and trichlorethene (TCE) as nodes through which ecosystem information and biomass most efficiently pass. Novel network rearrangement revealed a hierarchy of Kill-the-Winner (KtW), Piggyback-the-Winner (PtW) and PtP nodes. We propose that KtW, PtW and PtP occur simultaneously as competing strategies, with their relative importance depending on conditions at a particular time and location with unusual nutrient sources, such as TCE, appearing to contribute to a shift in this balance between viral mechanisms.

Dependency of DNA extraction efficiency on cell concentration confounds molecular quantification of microorganisms in groundwater

Quantification of microbes in water systems is essential to industrial practices ranging from drinking water and wastewater treatment to groundwater remediation. While quantification using DNA-based molecular methods is precise, the accuracy is dependent on DNA extraction efficiencies. We show that the DNA yield is strongly impacted by the cell concentration in groundwater samples (r = -0.92, P < 0.0001). This has major implications for industrial applications using quantitative polymerase chain reaction (qPCR) to determine cell concentrations in water, including bioremediation. We propose a simple normalization method using a DNA recovery ratio, calculated with the total cell count and DNA yield. Application of this method to enumeration of bacteria and archaea in groundwater samples targeting phylogenetic markers (16S rRNA) demonstrated an increased goodness of fit after normalization (7.04 vs 0.94 difference in Akaike's information criteria). Furthermore, normalization was applied to qPCR quantification of functional genes and combined with DNA sequencing of archaeal and bacterial 16S rRNA genes to monitor changes in abundance of methanogenic archaea and sulphate-reducing bacteria in groundwater. The integration of qPCR and DNA sequencing with appropriate normalization enables high-throughput quantification of microbial groups using increasingly affordable and accessible techniques. This research has implications for microbial ecology and engineering research as well as industrial practice.

Harnessing Nature's Anaerobes for Biotechnology and Bioprocessing

Industrial biotechnology has the potential to decrease our reliance on petroleum for fuel and bio-based chemical production and also enable valorization of waste streams. Anaerobic microorganisms thrive in resource-limited environments and offer an array of novel bioactivities in this regard that could revolutionize biomanufacturing. However, they have not been adopted for widespread industrial use owing to their strict growth requirements, limited number of available strains, difficulty in scale-up, and genetic intractability. This review provides an overview of current and future uses for anaerobes in biotechnology and bioprocessing in the postgenomic era. We focus on the recently characterized anaerobic fungi (Neocallimastigomycota) native to the digestive tract of large herbivores, which possess a trove of enzymes, pathways, transporters, and other biomolecules that can be harnessed for numerous biotechnological applications. Resolving current genetic intractability, scale-up, and cultivation challenges will unlock the potential of these lignocellulolytic fungi and other nonmodel micro-organisms to accelerate bio-based production.

Functional Genes and Bacterial Communities During Organohalide Respiration of Chloroethenes in Microcosms of Multi-Contaminated Groundwater

Microcosm experiments with CE-contaminated groundwater from a former industrial site were set-up to evaluate the relationships between biological CE dissipation, dehalogenase genes abundance and bacterial genera diversity. Impact of high concentrations of PCE on organohalide respiration was also evaluated. Complete or partial dechlorination of PCE, TCE, cis-DCE and VC was observed independently of the addition of a reducing agent (Na₂S) or an electron donor (acetate). The addition of either 10 or 100 μM PCE had no effect on organohalide respiration. qPCR analysis of reductive dehalogenases genes (pceA, tceA, vcrA, and bvcA) indicated that the version of pceA gene found in the genus Dehalococcoides [hereafter named pceA(Dhc)] and vcrA gene increased in abundance by one order of magnitude during the first 10 days of incubation. The version of the pceA gene found, among others, in the genus Dehalobacter, Sulfurospirillum, Desulfuromonas, and Geobacter [hereafter named pceA(Dhb)] and bvcA gene showed very low abundance. The tceA gene was not detected throughout the experiment. The proportion of pceA(Dhc) or vcrA genes relative to the universal 16S ribosomal RNA (16S rRNA) gene increased by up to 6-fold upon completion of cis-DCE dissipation. Sequencing of 16S rRNA amplicons indicated that the abundance of Operational Taxonomic Units (OTUs) affiliated to dehalogenating genera Dehalococcoides, Sulfurospirillum, and Geobacter represented more than 20% sequence abundance in the microcosms. Among organohalide respiration associated genera, only abundance of Dehalococcoides spp. increased up to fourfold upon complete dissipation of PCE and cis-DCE, suggesting a major implication of Dehalococcoides in CEs organohalide respiration. The relative abundance of pceA and vcrA genes correlated with the occurrence of Dehalococcoides and with dissipation extent of PCE, cis-DCE and CV. A new type of dehalogenating Dehalococcoides sp. phylotype affiliated to the Pinellas group, and suggested to contain both pceA(Dhc) and vcrA genes, may be involved in organohalide respiration of CEs in groundwater of the study site. Overall, the results demonstrate in situ dechlorination potential of CE in the plume, and suggest that taxonomic and functional biomarkers in laboratory microcosms of contaminated groundwater following pollutant exposure can help predict bioremediation potential at contaminated industrial sites.

A Case Study of Natural Attenuation of Chlorinated Solvents Under Unstable Groundwater Conditions in Takahata, Japan

The natural attenuation behavior of chlorinated solvents and their risks to human health at a contaminated groundwater site in Takahata, Japan, were investigated. It was found that volatile organic compound (VOC) concentrations gradually decreased via two attenuation mechanisms, namely dilution and biodegradation. It was estimated that the VOC concentrations will be below the Japanese limits within 30 years after stopping the active remediation in 2003, which suggests that there is a high possibility that monitored natural attenuation can be adopted as the clean-up method at this contaminated site. The risk levels of VOCs at the present time are much lower than those at the time when the contamination was discovered. Vinyl chloride still presents a risk in some wells, and there were occasional unexpected increases in the risk levels of tetrachloroethylene, trichloroethylene, and cis-1,2-dichloloethylene, which means that continuous monitoring of the groundwater is necessary for forecasting risk levels.

Abundance of Chlorinated Solvent and 1,4-Dioxane Degrading Microorganisms at Five Chlorinated Solvent Contaminated Sites Determined via Shotgun Sequencing

Shotgun sequencing was used for the quantification of taxonomic and functional biomarkers associated with chlorinated solvent bioremediation in 20 groundwater samples (five sites), following bioaugmentation with SDC-9. The analysis determined the abundance of (1) genera associated with chlorinated solvent degradation, (2) reductive dehalogenase (RDases) genes, (3) genes associated with 1,4-dioxane removal, (4) genes associated with aerobic chlorinated solvent degradation, and (5) D. mccartyi genes associated with hydrogen and corrinoid metabolism. The taxonomic analysis revealed numerous genera previously linked to chlorinated solvent degradation, including Dehalococcoides, Desulfitobacterium, and Dehalogenimonas. The functional gene analysis indicated vcrA and tceA from D. mccartyi were the RDases with the highest relative abundance. Reads aligning with both aerobic and anaerobic biomarkers were observed across all sites. Aerobic solvent degradation genes, etnC or etnE, were detected in at least one sample from each site, as were pmoA and mmoX. The most abundant 1,4-dioxane biomarker detected was Methylosinus trichosporium OB3b mmoX. Reads aligning to thmA or Pseudonocardia were not found. The work illustrates the importance of shotgun sequencing to provide a more complete picture of the functional abilities of microbial communities. The approach is advantageous over current methods because an unlimited number of functional genes can be quantified.

Next-generation sequencing showing potential leachate influence on bacterial communities around a landfill in China

The impact of contaminated leachate on groundwater from landfills is well known, but the specific effects on bacterial consortia are less well-studied. Bacterial communities in a landfill and an urban site located in Suzhou, China, were studied using Illumina high-throughput sequencing. A total of 153 944 good-quality reads were produced and sequences assigned to 6388 operational taxonomic units. Bacterial consortia consisted of up to 16 phyla, including Proteobacteria (31.9%-94.9% at landfill, 25.1%-43.3% at urban sites), Actinobacteria (0%-28.7% at landfill, 9.9%-34.3% at urban sites), Bacteroidetes (1.4%-25.6% at landfill, 5.6%-7.8% at urban sites), Chloroflexi (0.4%-26.5% at urban sites only), and unclassified bacteria. Pseudomonas was the dominant (67%-93%) genus in landfill leachate. Arsenic concentrations in landfill raw leachate (RL) (1.11 × 10³ μg/L) and fresh leachate (FL2) (1.78 × 10³ μg/L) and mercury concentrations in RL (10.9 μg/L) and FL2 (7.37 μg/L) exceeded Chinese State Environmental Protection Administration standards for leachate in landfills. The Shannon diversity index and Chao1 richness estimate showed RL and FL2 lacked richness and diversity when compared with other samples. This is consistent with stresses imposed by elevated arsenic and mercury and has implications for ecological site remediation by bioremediation or natural attenuation.

Dechlorinating performance of Dehalococcoides spp. mixed culture enhanced by tourmaline

Dehalococcoides spp. were extensively studied and applied to in-situ trichloroethylene (TCE) remediation since it is the only genus that can reduce TCE to harmless ethene completely. However, this technology was hindered because of the requirement of electron donor (i.e. hydrogen or fermentable organic substrate). Considering the spontaneous electric field and in-situ hydrogen production capacity of tourmaline, this mineral was used as an environmental-friendly bio-promoter for dechlorinating mixed culture containing Dehalococcoides spp. in this work. Research results showed that biodegradation of TCE and the intermediates were both significantly improved by tourmaline. The first-order TCE degradation rate coefficient increased from 0.0125 h^-1 for the tourmaline-free system to 0.0306 h^-1 for the system combined with 5 g L^-1 tourmaline, and ethene production increased by 36%. The outstanding TCE-degrading ability in the tourmaline-bacteria system without the addition of fermentative electron donor (i.e. methanol) indicated that tourmaline could also produce electron donor to support dechlorinating bacteria. Tourmaline could have direct electric biostimulatory effect and indirect enhanced effect associated with water-derived H₂ production in the electric field of tourmaline. Meanwhile, PCR-DGGE analysis exhibited that tourmaline could accelerate the succession of a bacterial, dechlorinating community. The distinctive effects of tourmaline on bacteria were related to its stable electric properties. Therefore, tourmaline could be continuously used in the bioremediation. The present study provided a safe, convenient and persistent alternative to the commonly used enhancement approaches for anaerobic reductive dechlorination process.

Biological Limitations of Dechlorination of cis-Dichloroethene during Transport in Porous Media

We applied a mathematical model to data from experimental column studies to understand the dynamics of successful and unsuccessful reductive dechlorination of chlorinated ethenes in groundwater under different flow conditions. In laboratory column experiments (reported previously), it was observed that complete dechlorination of cis-dichloroethene to ethene was sustained at high flow velocity (0.51 m/d), but that dechlorination failed at medium or low flow velocity (0.080 or 0.036 m/d). The mathematical model applied here accounts for transport of chlorinated ethenes in flowing groundwater, mass transfer of chlorinated ethenes between mobile groundwater and stationary biofilms, and diffusion and biodegradation within the biofilms. Monod kinetics with competitive inhibition are used to describe biodegradation. Nearly all parameters needed to solve the model are estimated independently from batch and nonreactive transport experiments. Comparing the model predictions to the experimental results permits the evaluation of three hypothesized biological limitations: insufficient supply of electron donor, decay of dechlorinators' biomass, and reduction in bacterial metabolism rates. Any of these three limitations are able to adequately describe observed experimental data, but insufficient supply of electron donor is the most plausible explanation for failure of dechlorination. Therefore, an important conclusion of this investigation is that insufficient hydrogen production occurs if groundwater flow is too slow to provide adequate flux of electron donor. Model simulations were in good agreement with experimental results for both successful and unsuccessful dechlorination, suggesting the model is a valid tool for describing transport and reductive dechlorination. An implication of our findings is that in engineered or natural bioremediation of chloroethene-contaminated groundwater, not only must the proper dechlorinating organisms be present, but also proper groundwater flow conditions must be maintained or else dechlorination may fail.

Metagenomics: Probing pollutant fate in natural and engineered ecosystems

Polluted environments are a reservoir of microbial species able to degrade or to convert pollutants to harmless compounds. The proper management of microbial resources requires a comprehensive characterization of their genetic pool to assess the fate of contaminants and increase the efficiency of bioremediation processes. Metagenomics offers appropriate tools to describe microbial communities in their whole complexity without lab-based cultivation of individual strains. After a decade of use of metagenomics to study microbiomes, the scientific community has made significant progress in this field. In this review, we survey the main steps of metagenomics applied to environments contaminated with organic compounds or heavy metals. We emphasize technical solutions proposed to overcome encountered obstacles. We then compare two metagenomic approaches, i.e. library-based targeted metagenomics and direct sequencing of metagenomes. In the former, environmental DNA is cloned inside a host, and then clones of interest are selected based on (i) their expression of biodegradative functions or (ii) sequence homology with probes and primers designed from relevant, already known sequences. The highest score for the discovery of novel genes and degradation pathways has been achieved so far by functional screening of large clone libraries. On the other hand, direct sequencing of metagenomes without a cloning step has been more often applied to polluted environments for characterization of the taxonomic and functional composition of microbial communities and their dynamics. In this case, the analysis has focused on 16S rRNA genes and marker genes of biodegradation. Advances in next generation sequencing and in bioinformatic analysis of sequencing data have opened up new opportunities for assessing the potential of biodegradation by microbes, but annotation of collected genes is still hampered by a limited number of available reference sequences in databases. Although metagenomics is still facing technical and computational challenges, our review of the recent literature highlights its value as an aid to efficiently monitor the clean-up of contaminated environments and develop successful strategies to mitigate the impact of pollutants on ecosystems.

Bioremediation techniques-classification based on site of application: principles, advantages, limitations and prospects

Environmental pollution has been on the rise in the past few decades owing to increased human activities on energy reservoirs, unsafe agricultural practices and rapid industrialization. Amongst the pollutants that are of environmental and public health concerns due to their toxicities are: heavy metals, nuclear wastes, pesticides, green house gases, and hydrocarbons. Remediation of polluted sites using microbial process (bioremediation) has proven effective and reliable due to its eco-friendly features. Bioremediation can either be carried out ex situ or in situ, depending on several factors, which include but not limited to cost, site characteristics, type and concentration of pollutants. Generally, ex situ techniques apparently are more expensive compared to in situ techniques as a result of additional cost attributable to excavation. However, cost of on-site installation of equipment, and inability to effectively visualize and control the subsurface of polluted sites are of major concerns when carrying out in situ bioremediation. Therefore, choosing appropriate bioremediation technique, which will effectively reduce pollutant concentrations to an innocuous state, is crucial for a successful bioremediation project. Furthermore, the two major approaches to enhance bioremediation are biostimulation and bioaugmentation provided that environmental factors, which determine the success of bioremediation, are maintained at optimal range. This review provides more insight into the two major bioremediation techniques, their principles, advantages, limitations and prospects.

Dynamics of organohalide-respiring bacteria and their genes following in-situ chemical oxidation of chlorinated ethenes and biostimulation

Application of Fenton's reagent and enhanced reductive dechlorination are currently the most common remediation strategies resulting in removal of chlorinated ethenes. In this study, the influence of such techniques on organohalide-respiring bacteria was assessed at a site contaminated by chlorinated ethenes using a wide spectrum of molecular genetic markers, including 16S rRNA gene of the organohalide-respiring bacteria Dehaloccocoides spp., Desulfitobacterium and Dehalobacter; reductive dehalogenase genes (vcrA, bvcA) responsible for dechlorination of vinyl chloride and sulphate-reducing and denitrifying bacteria. In-situ application of hydrogen peroxide to induce a Fenton-like reaction caused an instantaneous decline in all markers below detection limit. Two weeks after application, the bvcA gene and Desulfitobacterium relative abundance increased to levels significantly higher than those prior to application. No significant decrease in the concentration of a range of chlorinated ethenes was observed due to the low hydrogen peroxide dose used. A clear increase in marker levels was also observed following in-situ application of sodium lactate, which resulted in a seven-fold increase in Desulfitobacterium and a three-fold increase in Dehaloccocoides spp. after 70 days. An increase in the vcrA gene corresponded with increase in Dehaloccocoides spp. Analysis of selected markers clearly revealed a positive response of organohalide-respiring bacteria to biostimulation and unexpectedly fast recovery after the Fenton-like reaction.