Genomic insights into organohalide respiration

Understanding the sources, function, and irreplaceable role of cobamides in organohalide-respiring bacteria

Halogenated organic compounds are persistent pollutants that pose a serious threat to human health and the safety of ecosystems. Cobamides are essential cofactors for reductive dehalogenases (RDase) in organohalide-respiring bacteria (OHRB), which catalyze the dehalogenation process. This review systematically summarizes the impact of cobamides on organohalide respiration. The catalytic processes of cobamide in dehalogenation processes are also discussed. Additionally, we examine OHRB, which cannot synthesize cobamide and must obtain it from the environment through a salvage pathway; the co-culture with cobamide producer is more beneficial and possible. This review aims to help readers better understand the importance and function of cobamides in reductive dehalogenation. The presented information can aid in the development of bioremediation strategies.

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

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

Quantitative analysis of TCE biodegradation pathway in landfill cover utilizing continuous monitoring, droplet digital PCR and multi-omics sequencing technology

The remediation of volatile chlorinated hydrocarbons in the quasi-vadose zone has become a significant challenge. We applied an integrated approach to assess the biodegradability of trichloroethylene to identify the biotransformation mechanism. The formation of the functional zone biochemical layer was assessed by analyzing the distribution of landfill gas, physical and chemical properties of cover soil, spatial-temporal variations of micro-ecology, biodegradability of landfill cover soil and distributional difference metabolic pathway. Real-time online monitoring showed that trichloroethylene continuously undergoes anaerobic dichlorination and simultaneous aerobic/anaerobic conversion-aerobic co-metabolic degradation on the vertical gradient of the landfill cover system and reduction in trans-1,2-dichloroethylene in the anoxic zone but not 1,1-dichloroethylene. PCR and diversity sequencing revealed the abundance and spatial distribution of known dichlorination-related genes within the landfill cover, with 6.61 ± 0.25 × 104-6.78 ± 0.09 × 106 and 1.17 ± 0.78 × 103-7.82 ± 0.07 × 105 copies per g/soil of pmoA and tceA, respectively. In addition, dominant bacteria and diversity were significantly linked with physicochemical factors, and Mesorhizobium, Pseudoxanthomonas and Gemmatimonas were responsible for biodegradation in the aerobic, anoxic and anaerobic zones. Metagenome sequencing identified 6 degradation pathways of trichloroethylene that may occur in the landfill cover; the main pathway was incomplete dechlorination accompanied by cometabolic degradation. These results indicate that the anoxic zone is important for trichloroethylene degradation.

Intermittent Oxygen Supply Facilitates Codegradation of Trichloroethene and Toluene by Anaerobic Consortia

Biodegradation is commonly employed for remediating trichloroethene- or toluene-contaminated sites. However, remediation methods using either anaerobic or aerobic degradation are inefficient for dual pollutants. We developed an anaerobic sequencing batch reactor system with intermittent oxygen supply for the codegradation of trichloroethylene and toluene. Our results showed that oxygen inhibited anaerobic dechlorination of trichloroethene, but dechlorination rates remained comparable to that at dissolved oxygen levels of 0.2 mg/L. Intermittent oxygenation engendered reactor redox fluctuations (-146 to -475 mV) and facilitated rapid codegradation of targeting dual pollutants, with trichloroethene degradation constituting only 27.5% of the noninhibited dechlorination. Amplicon sequencing analysis revealed the predominance of Dehalogenimonas (16.0% ± 3.5%) over Dehalococcoides (0.3% ± 0.2%), with ten times higher transcriptomic activity in Dehalogenimonas. Shotgun metagenomics revealed numerous genes related to reductive dehalogenases and oxidative stress resistance in Dehalogenimonas and Dehalococcoides, as well as the enrichment of diversified facultative populations with functional genes related to trichloroethylene cometabolism and aerobic and anaerobic toluene degradation. These findings suggested that the codegradation of trichloroethylene and toluene may involve multiple biodegradation mechanisms. Overall results of this study demonstrate the effectiveness of intermittent micro-oxygenation in aiding trichloroethene-toluene degradation, suggesting the potential for the bioremediation of sites with similar organic pollutants.

In situ reductive dehalogenation of groundwater driven by innovative organic carbon source materials: Insights into the organohalide-respiratory electron transport chain

In situ bioremediation using organohalide-respiring bacteria (OHRB) is a prospective method for the removal of persistent halogenated organic pollutants from groundwater, as OHRB can utilize H₂ or organic compounds produced by carbon source materials as electron donors for cell growth through organohalide respiration. However, few previous studies have determined the suitability of different carbon source materials to the metabolic mechanism of reductive dehalogenation from the perspective of electron transfer. The focus of this critical review was to reveal the interactions and relationships between carbon source materials and functional microbes, in terms of the electron transfer mechanism. Furthermore, this review illustrates some innovative strategies that have used the physiological characteristics of OHRB to guide the optimization of carbon source materials, improving the abundance of indigenous dehalogenated bacteria and enhancing electron transfer efficiency. Finally, it is proposed that future research should combine multi-omics analysis with machine learning (ML) to guide the design of effective carbon source materials and optimize current dehalogenation bioremediation strategies to reduce the cost and footprint of practical groundwater bioremediation applications.

Sustained detoxification of 1,2-dichloroethane to ethylene by a symbiotic consortium containing Dehalococcoides species

1,2-Dichloroethane (1,2-DCA) is a ubiquitous volatile halogenated organic pollutant in groundwater and soil, which poses a serious threat to the ecosystem and human health. Microbial reductive dechlorination has been recognized as an environmentally-friendly strategy for the remediation of sites contaminated with 1,2-DCA. In this study, we obtained an anaerobic microbiota derived from 1,2-DCA contaminated groundwater, which was able to sustainably convert 1,2-DCA into non-toxic ethylene with an average dechlorination rate of 30.70 ± 11.06 μM d^-1 (N = 6). The microbial community profile demonstrated that the relative abundance of Dehalococcoides species increased from 0.53 ± 0.08% to 44.68 ± 3.61% in parallel with the dechlorination of 1,2-DCA. Quantitative PCR results showed that the Dehalococcoides species 16S rRNA gene increased from 2.40 ± 1.71 × 10⁸ copies∙mL^-1 culture to 4.07 ± 2.45 × 10⁸ copies∙mL^-1 culture after dechlorinating 110.69 ± 30.61 μmol of 1,2-DCA with a growth yield of 1.55 ± 0.93 × 10⁸ cells per μmol Cl^- released (N = 6), suggesting that Dehalococcoides species used 1,2-DCA for organohalide respiration to maintain cell growth. Notably, the relative abundances of Methanobacterium sp. (p = 0.0618) and Desulfovibrio sp. (p = 0.0001995) also increased significantly during the dechlorination of 1,2-DCA and were clustered in the same module with Dehalococcoides species in the co-occurrence network. These results hinted that Dehalococcoides species, the obligate organohalide-respiring bacterium, exhibited potential symbiotic relationships with Methanobacterium and Desulfovibrio species. This study illustrates the importance of microbial interactions within functional microbiota and provides a promising microbial resource for in situ bioremediation in sites contaminated with 1,2-DCA.

Combining nanoscale zero-valent iron and anaerobic dechlorinating bacteria to degrade chlorinated methanes and 1,2-dichloroethane

Nanoscale zero-valent iron (nZVI) has the potential to degrade a diversity of chlorinated compounds, and it is widely used for remediation of contaminated groundwaters. However, some frequently detected contaminants such as dichloromethane (DCM) and 1,2-dichloroethane (1,2-DCA) have shown nearly no reactivity with nZVI. Here, we tested the feasibility of combining anaerobic dechlorinating bacteria, Dehalobacterium and Dehalogenimonas, and nZVI as a treatment train to detoxify chlorinated methanes (i.e., chloroform-CF- and DCM), and 1,2-DCA. First, we showed that CF (500 μM) was fully degraded by 1 g/L nZVI to DCM as a major by-product, which was susceptible to fermentation by Dehalobacterium to innocuous products. Our results indicate that soluble compounds released by nZVI might cause an inhibitory impact on Dehalobacterium activity, avoiding DCM depletion. The DCM dechlorination activity was recovered when transferred to a fresh medium without nZVI. The increase in H2 production and pH was discarded as potential inhibitors. Similarly, a Dehalogenimonas-containing culture was unable to dichloroeliminate 1,2-DCA when exposed to 1 g/L nZVI, but dechlorinating activity was also recovered when transferred to nZVI-free media. The recovery of the dechlorinating activity of Dehalobacterium and Dehalogenimonas suggests that combination of nZVI and bioremediation techniques can be feasible under field conditions where dilution processes can alleviate the impact of the potential inhibitory soluble compounds.

Efficient biodegradation of tetrabromobisphenol A by the novel strain Enterobacter sp. T2 with good environmental adaptation: Kinetics, pathways and genomic characteristics

T2, a gram-positive bacterium capable of rapidly degrading tetrabromobisphenol A (TBBPA), and affiliated with the genus Enterobacter, was isolated for the first time from sludge that had been contaminated for several years. The TBBPA degradation data fitted the first-order model well. Under optimal conditions (pH of 7, temperature of 31 °C, TBBPA concentration of 5 mg L^-1, and inoculum size of 5%), 99.4% of the initially added TBBPA was degraded after 48 h. TBBPA degradation fitted the first-order model with the half-life of 3.3 h. These results illustrated that the TBBPA degradation capability of strain T2 was significantly better than that of previously reported bacteria. A total of 17 intermediates were detected, among which five were reported for the first time. Whole-genome sequencing revealed that strain T2 had a chromosome with the total length of 4 854 376 bp and a plasmid with the total length of 21 444 bp. It harbored essential genes responsible for debromination, such as cyp450, gstB, gstA, and HADH, and genes responsible for subsequent complete mineralization, such as bioC, yrrM, Tam, and Ubil. A key protein of haloacid dehalogenases responsible for the biodegradation of TBBPA may also be involved in the regulation of TBBPA degradation in natural environment. In soil bioremediation experiments, strain T2 showed excellent environmental adaptation. It was able to biodegrade TBBPA and its typical intermediate bisphenol A efficiently. Therefore, it could potentially be applied to treat TBBPA-contaminated sites.

Direct aerobic oxidation (DAO) of chlorinated aliphatic hydrocarbons: A review of key DAO bacteria, biometabolic pathways and in-situ bioremediation potential

Contamination of aquifers and vadose zones with chlorinated aliphatic hydrocarbons (CAH) is a world-wide issue. Unlike other reactions, direct aerobic oxidation (DAO) of CAHs does not require growth substrates and avoids the generation of toxic by-products. Here, we critically review the current understanding of chlorinated aliphatic hydrocarbons-DAO and its application in bioreactors and at the field scale. According to reports on chlorinated aliphatic hydrocarbons-DAO bacteria, isolates mainly consisted of Methylobacterium and Proteobacterium. Chlorinated aliphatic hydrocarbons-DAO bacteria are characterized by tolerance to a high concentration of CAHs and highly efficient removal of CAHs. Trans-1,2-dichloroethylene (t-DCE) is easily transformed biomass for bacteria, followed by 1,2-dichloroethane (1,2-DCA), dichloromethane (DCM), vinyl chloride (VC) and cis-1,2-dichloroethylene (c-DCE). Significant differences in the maximum specific growth rates were observed with different CAHs and biometabolic pathways for DCM, 1,2-DCA, VC and c-DCE degradation have been successfully parsed. Detection of the functional genes etnC and etnE is useful for the determination of active VC DAO bacteria. Additionally, DAO bacteria have been successfully applied to CAHs in new types of bioreactors with satisfactory results. To the best of the authors' knowledge, only one study on DAO-CAHs was conducted in-situ and resulted in 99% CAH removal. Lastly, we put forward future development prospect of chlorinated aliphatic hydrocarbons-DAO.

Nothing lasts forever: understanding microbial biodegradation of polyfluorinated compounds and perfluorinated alkyl substances

Poly- and perfluorinated chemicals, including perfluorinated alkyl substances (PFAS), are pervasive in today's society, with a negative impact on human and ecosystem health continually emerging. These chemicals are now subject to strict government regulations, leading to costly environmental remediation efforts. Commercial polyfluorinated compounds have been called 'forever chemicals' due to their strong resistance to biological and chemical degradation. Environmental cleanup by bioremediation is not considered practical currently. Implementation of bioremediation will require uncovering and understanding the rare microbial successes in degrading these compounds. This review discusses the underlying reasons why microbial degradation of heavily fluorinated compounds is rare. Fluorinated and chlorinated compounds are very different with respect to chemistry and microbial physiology. Moreover, the end product of biodegradation, fluoride, is much more toxic than chloride. It is imperative to understand these limitations, and elucidate physiological mechanisms of defluorination, in order to better discover, study, and engineer bacteria that can efficiently degrade polyfluorinated compounds.

Correlations between maximum reductive dechlorination rates and specific biomass parameters in Dehalococcoides mccartyi consortia enriched on chloroethenes PCE, TCE and cis-1,2-DCE

One of the challenges to implementing the modeling of the biological reductive dechlorination (RD) process is the evaluation of biological parameters that represent the abundance/activity levels of the microorganisms involved in the biodegradation of chloroethenes. Here we report a combined analysis of kinetic and specific biomass parameters conducted on three dechlorinating consortia enriched on PCE, TCE and cis-1,2-DCE. In these consortia, Dehalococcoides mccartyi (Dhc) represented ≥70% of the bacterial population identified via 16S rRNA gene amplicon sequencing. Quantitative biomolecular methods were used to generate specific biomass parameters targeting either the Dhc population (16S rRNA genes or cells) or specific genes encoding RD process-involved reductive dehalogenases. The correlation factor between the abundance of active Dhc cells or tceA gene copies and maximum RD rates allowed to predict an increment of 7E+09 of active Dhc cells or 5E+09 tceA gene copies/L under controlled conditions. Diversely, the utilization of gene transcripts as biomass parameters for RD modeling did not provide reliable correlations with kinetic performances. This study provides valuable insights for further modeling of the RD process through the utilization of specific biomass parameters.

Dehalococcoides mccartyi Strain GEO12 Has a Natural Tolerance to Chloroform Inhibition

Cocontamination by chloroform and chloroethenes often confounds bioremediation efforts. Here, we describe Dehalococcoides mccartyi strain GEO12 that dechlorinates trichloroethene to ethene in 14 μM (1.6 mg·L^-1) chloroform. The same chloroform concentration effectively inhibited dechlorination in Dehalococcoides strains ANAS2, 11a, and BAV1. Successive transfers of strain GEO12 in increasing concentrations of chloroform led to culture GEO12CF that tolerated 83 μM (10 mg·L^-1) chloroform. The genome of strain GEO12 revealed seven reductive dehalogenase homologous (rdh) genes, including tceA and vcrA. Transcriptional analyses showed that chloroform (45 μM; 5.3 mg·L^-1) in culture GEO12CF enhanced the transcription of tceA to a statistically significant degree (the median increase was 55.4 transcripts per 10⁴ 16S rRNA, CI_95% = [12.9, 125]). The increase of vcrA transcripts in the presence of chloroform (45 μM; 5.3 mg·L^-1) in culture GEO12CF was not statistically significant because the CI_95% range spanned 0 (the median increase was 109 transcripts per 10⁴ 16S rRNA, CI_95% = [-13.6, 246]). Inhibition of dehalogenation by chloroform is often seen in Dehalococcoides, but the mechanism remains unknown. Our results suggest that culture GEO12CF may overcome chloroform inhibition by rdh upregulation. The chloroform-adapted culture GEO12CF provides insights into the metabolic flexibility of Dehalococcoides and could be used to fight chloroethene contamination where chloroform is a cocontaminant.

Microbial community composition in alpine lake sediments from the Hengduan Mountains

Microbial communities in sediments play an important role in alpine lake ecosystems. However, the microbial diversity and community composition of alpine lake sediments from the Hengduan Mountains remain largely unknown. Therefore, based on the Illumina MiSeq platform, high‐throughput sequencing analysis of the 16S rRNA gene was performed on 15 alpine lake sediments collected at different locations in the Hengduan Mountains. The abundance‐based coverage estimate (ACE), Chao1, and Shannon indices indicated that the microbial abundance and diversity of these sediments were high. There are some differences in the composition of microbial communities among sediments. However, in general, Proteobacteria accounted for the largest proportion of all sediments (22.3%–67.6%) and was the dominant phylum. Followed by Bacteroidetes, Acidobacteria, Chloroflexi, and Planctomycetes. In addition, the operational taxonomic unit (OTU) interactions network had modular structures and suggested more cooperation than competition in the microbial community. Besides, we also found that temperature has a significant contribution to the sample–environment relationship. This study revealed the diversity and composition of microbial communities in alpine lake sediments from the Hengduan Mountains, and describe the correlation between microbial community structure and different environmental variables.

An integrative overview of genomic, transcriptomic and proteomic analyses in organohalide respiration research

Organohalide respiration (OHR) is a crucial process in the global halogen cycle and of interest for bioremediation. However, investigations on OHR are hampered by the restricted genetic accessibility and the poor growth yields of many organohalide-respiring bacteria (OHRB). Therefore, genomics, transcriptomics and proteomics are often used to investigate OHRB. In general, these gene expression studies are more useful when the data of the different 'omics' approaches are integrated and compared among a wide range of cultivation conditions and ideally involve several closely related OHRB. Despite the availability of a couple of proteomic and transcriptomic datasets dealing with OHRB, such approaches are currently not covered in reviews. Therefore, we here present an integrative and comparative overview of omics studies performed with the OHRB Sulfurospirillum multivorans, Dehalococcoides mccartyi, Desulfitobacterium spp. and Dehalobacter restrictus. Genes, transcripts, proteins and the regulatory and biochemical processes involved in OHR are discussed, and a comprehensive view on the unusual metabolism of D. mccartyi, which is one of the few bacteria possibly using a quinone-independent respiratory chain, is provided. Several 'omics'-derived theories on OHRB, e.g. the organohalide-respiratory chain, hydrogen metabolism, corrinoid biosynthesis or one-carbon metabolism are critically discussed on the basis of this integrative approach.

Application of a novel gene encoding bromophenol dehalogenase from Ochrobactrum sp. T in TBBPA degradation

Tetrabromobisphenol-A (TBBPA), a typical brominated flame retardant, leaked from commercial products into the environments has attracted people's attention around the world. Ochrobactrum sp. T capable of degradation and mineralization of TBBPA was isolated in our early work. In this study, the identification of TBBPA-degrading gene from the strain was further carried out by combining whole-genome sequencing with gene cloning and expression procedures. In total, 3877 open reading frames were found within 3.9 Mb genome and seven of them were identified as dehalogenating-relating genes. One gene with a significant ability to degrade TBBPA was designated as tbbpaA. Sequence alignments analysis showed that it shared 100% identity with haloacid dehalogenases. Furthermore, tbbpaA gene was cloned and expressed into E. coli to achieve a constructed strain. Like the original strain, the constructed strain could degrade TBBPA (6 mg L^-1) with 78% of debromination efficiency and 37.8% mineralization efficiency within 96 h. Gene expression study revealed that tbbpaA was up-regulated in the presence of TBBPA. Overall, we report the identification of a functional TBBPA-degrading gene in an aerobe, which can deepen the knowledge of enhancing TBBPA removal by Strain T at the genetic level and facilitate in situ TBBPA bioremediation.

Regulation of organohalide respiration

Organohalide respiration (OHR) is an anaerobic metabolism by which bacteria conserve energy with the use of halogenated compounds as terminal electron acceptors. Genes involved in OHR are organized in reductive dehalogenase (rdh) gene clusters and can be found in relatively high copy numbers in the genomes of organohalide-respiring bacteria (OHRB). The minimal rdh gene set is composed by rdhA and rdhB, encoding the catalytic enzyme involved in reductive dehalogenation and its putative membrane anchor, respectively. In this chapter, we present the major findings concerning the regulatory strategies developed by OHRB to control the expression of the rdh gene clusters. The first section focuses on the description of regulation patterns obtained from targeted transcriptional analyses, and from transcriptomic and proteomic studies, while the second section offers a detailed overview of the biochemically characterized OHR regulatory proteins identified so far. Depending on OHRB, transcriptional regulators belonging to three different protein families are found in the direct vicinity of rdh gene clusters, suggesting that they activate the transcription of their cognate gene cluster. In this chapter, strong emphasis was laid on the family of CRP/FNR-type RdhK regulators which belong to members of the genera Dehalobacter and Desulfitobacterium. Whereas only chlorophenols have been identified as effectors for RdhK regulators, the protein sequence diversity suggests a broader organohalide spectrum. Thus, effector identification of new regulators offers a promising alternative to elucidate the substrates of yet uncharacterized reductive dehalogenases. Future work investigating the possible cross-talk between OHR regulators and their possible use as biosensors is discussed.

Enantioselective Dechlorination of Polychlorinated Biphenyls in Dehalococcoides mccartyi CG1

Reductive dehalogenation mediated by organohalide-respiring bacteria plays a critical role in the global cycling of organohalides. Nonetheless, information on the dehalogenation enantioselectivity of organohalide-respiring bacteria remains limited. In this study, we report the enantioselective dechlorination of chiral polychlorinated biphenyls (PCBs) by Dehalococcoides mccartyi CG1. CG1 preferentially removed halogens from the (-)-enantiomers of the three major environmentally relevant chiral PCBs (PCB174, PCB149, and PCB132), and the enantiomer compositions of the dechlorination products depended on their parent organohalides. The in vitro assays with crude cell extracts or concentrated whole cells and the in vivo experiments with living cells showed similar enantioselectivities, in contrast with the distinct enantiomeric enrichment factors (ε_ER) of the substrate chiral PCBs. Additionally, these results suggest that concentrated whole cells might be an alternative to crude cell extracts in in vitro tests of reductive dehalogenation activities. The enantioselective dechlorination of other chiral PCBs that we resolved via gas chromatography further confirmed the preference of CG1 for the (-)-enantiomers.IMPORTANCE A variety of agrochemicals and pharmaceuticals are chiral. Due to the enantioselectivity in biological processes, enantiomers of chiral compounds may have different environmental occurrences, fates, and ecotoxicologies. Many chiral organohalides exist in anaerobic or anoxic soils and sediments, and organohalide-respiring bacteria play a major role in the environmental attenuation and global cycling of these chiral organohalides. Therefore, it is important to investigate the dehalogenation enantioselectivity of organohalide-respiring bacteria. This study reports the discovery of enantioselective dechlorination of chiral PCBs by Dehalococcoides mccartyi CG1, which provides insights into the dehalogenation enantioselectivity of Dehalococcoides and may shed light on future PCB bioremediation efforts to prevent enantioselective biological side effects.

Microbial Community Changes in a Chlorinated Solvents Polluted Aquifer Over the Field Scale Treatment With Poly-3-Hydroxybutyrate as Amendment

This study investigated the organohalide-respiring bacteria (OHRB) and the supporting microbial populations operating in a pilot scale plant employing poly-3-hydroxybutyrate (PHB), a biodegradable polymer produced by bacteria from waste streams, for the in situ bioremediation of groundwater contaminated by chlorinated solvents. The bioremediation was performed in ground treatment units, including PHB reactors as slow release source of electron donors, where groundwater extracted from the wells flows through before the re-infiltration to the low permeability zones of the aquifer. The coupling of the biological treatment with groundwater recirculation allowed to drastically reducing the contamination level and the remediation time by efficiently stimulating the growth of autochthonous OHRB and enhancing the mobilization of the pollutants. Quantitative PCR performed along the external treatment unit showed that the PHB reactor may efficiently act as an external incubator to growing Dehalococcoides mccartyi, known to be capable of fully converting chlorinated ethenes to innocuous end-products. The slow release source of electron donors for the bioremediation process allowed the establishment of a stable population of D. mccartyi, mainly carrying bvcA and vcrA genes which are implicated in the metabolic conversion of vinyl chloride to harmless ethene. Next generation sequencing was performed to analyze the phylogenetic diversity of the groundwater microbiome before and after the bioremediation treatment and allowed the identification of the microorganisms working closely with organohalide-respiring bacteria.

High-throughput sequencing revealed novel Dehalococcoidia in dechlorinating microbial enrichments from PCB-contaminated marine sediments

In this study, six PCE-to-ethene dechlorinating cultures, fed with a fermentable substrate (lactate) or hydrogen as electron donor, were obtained from PCB and PCE dechlorinating microcosms constructed with PCB-contaminated marine sediments. A novel Chloroflexi member (OTU-DIS1) affiliated to Dehalococcoidales Incertae Sedis, only distantly related to known dechlorinating bacteria, dominated the enrichment cultures (up to 86% of total OTUs). Sulfate-, thiosulfate- and sulfur-reducing bacteria affiliated to genera Desulfobacter, Dethiosulfatibacter and Desulfuromusa were also found to lesser extent. Remarkably, tceA, vcrA and the bifunctional PCE/PCB dehalogenase genes pcbA1, pcbA4 and pcbA5 were found in all dechlorinating microbial enrichments indicating the coexistence of different Dehalococcoides mccartyi strains. The reductive dechlorination rate in each culture remained unvaried over long-term operation (≈ 30 months) and ranged between 0.85 and 0.97 mmol Cl-1 released L-1 d-1 in the lactate-fed microbial enrichments and between 0.66 and 0.85 mmol Cl-1 released L-1 d-1 in the H2-fed microbial enrichments. Overall, this study highlights the presence of yet unexplored biodiversity in PCBs contaminated marine sediments and indicates these environments as promising sources of novel organohalide-respiring bacteria.

Variable dual carbon-bromine stable isotope fractionation during enzyme-catalyzed reductive dehalogenation of brominated ethenes

The potential of compound-specific stable isotope analysis (CSIA) to characterize biotransformation of brominated organic compounds (BOCs) was assessed and compared to chlorinated analogues. Sulfurospirillum multivorans and Desulfitobacterium hafniense PCE-S catalyzed the dehalogenation of tribromoethene (TBE) to either vinyl bromide (VB) or ethene, respectively. Significantly lower isotope fractionation was observed for TBE dehalogenation by S. multivorans (ε_C = -1.3 ± 0.2‰) compared to D. hafniense (ε_C = -7.7 ± 1.5‰). However, higher fractionation was observed for dibromoethene (DBE) dehalogenation by S. multivorans (ε_C = -16.8 ± 1.8‰ and -21.2 ± 1.6‰ for trans- and cis-1,2- (DBE) respectively), compared to D. hafniense PCE-S (ε_C = -9.5 ± 1.2‰ and -14.5 ± 0.7‰ for trans-1,2-DBE and cis-1,2-DBE, respectively). Significant, but similar, bromine fractionation was observed for for S. multivorans (ε_Br = -0.53 ± 0.15‰, -1.03 ± 0.26‰, and -1.18 ± 0.13‰ for trans-1,2-DBE, cis-1,2-DBE and TBE, respectively) and D. hafniense PCE-S (ε_Br = -0.97 ± 0.28‰, -1.16 ± 0.36‰, and -1.34 ± 0.32‰ for cis-1,2-DBE, TBE and trans-1,2-DBE, respectively). Variable CBr dual-element slopes were estimated at Λ (ε_C/ε_Br) = 1.03 ± 0.2, 17.9 ± 5.8, and 29.9 ± 11.0 for S. multivorans debrominating TBE, cis-1,2-DBE and trans-1,2-DBE, respectively, and at 7.14 ± 1.6, 8.27 ± 3.7, and 8.92 ± 2.4 for D. hafniense PCE-S debrominating trans-1,2-DBE, TBE and cis-1,2-DBE, respectively. A high variability in isotope fractionation, which was substrate property related, was observed for S. multivorans but not D. hafniense, similar as observed for chlorinated ethenes, and may be due to rate-limiting steps preceding the bond-cleavage or differences in the reaction mechanism. Overall, significant isotope fractionation was observed and, therefore, CSIA can be applied to monitor the fate of brominated ethenes in the environment. Isotope effects differences, however, are not systematically comparable to chlorinated ethenes.

Isotopic effects of PCE induced by organohalide-respiring bacteria

Reductive dechlorination performed by organohalide-respiring bacteria (OHRB) enables the complete detoxification of certain emerging groundwater pollutants such as perchloroethene (PCE). Environmental samples from a contaminated site incubated in a lab-scale microcosm (MC) study enable documentation of such reductive dechlorination processes. As compound-specific isotope analysis is used to monitor PCE degradation processes, nucleic acid analysis-like 16S-rDNA analysis-can be used to determine the key OHRB that are present. This study applied both methods to laboratory MCs prepared from environmental samples to investigate OHRB-specific isotope enrichment at PCE dechlorination. This method linkage can enhance the understanding of isotope enrichment patterns of distinct OHRB, which further contribute to more accurate evaluation, characterisation and prospection of natural attenuation processes. Results identified three known OHRB genera (Dehalogenimonas, Desulfuromonas, Geobacter) in diverse abundance within MCs. One species of Dehalogenimonas was potentially involved in complete reductive dechlorination of PCE to ethene. Furthermore, the isotopic effects of PCE degradation were clustered and two isotope enrichment factors (ε) (- 11.6‰, - 1.7‰) were obtained. Notably, ε values were independent of degradation rates and kinetics, but did reflect the genera of the dechlorinating OHRB.

Microbial degradation of chloroethenes: a review

Contamination by chloroethenes has a severe negative effect on both the environment and human health. This has prompted intensive remediation activity in recent years, along with research into the efficacy of natural microbial communities for degrading toxic chloroethenes into less harmful compounds. Microbial degradation of chloroethenes can take place either through anaerobic organohalide respiration, where chloroethenes serve as electron acceptors; anaerobic and aerobic metabolic degradation, where chloroethenes are used as electron donors; or anaerobic and aerobic co-metabolic degradation, with chloroethene degradation occurring as a by-product during microbial metabolism of other growth substrates, without energy or carbon benefit. Recent research has focused on optimising these natural processes to serve as effective bioremediation technologies, with particular emphasis on (a) the diversity and role of bacterial groups involved in dechlorination microbial processes, and (b) detection of bacterial enzymes and genes connected with dehalogenation activity. In this review, we summarise the different mechanisms of chloroethene bacterial degradation suitable for bioremediation and provide a list of dechlorinating bacteria. We also provide an up-to-date summary of primers available for detecting functional genes in anaerobic and aerobic bacteria degrading chloroethenes metabolically or co-metabolically.

Structural dynamics of microbial communities in polycyclic aromatic hydrocarbon-contaminated tropical estuarine sediments undergoing simulated aerobic biotreatment

Coastal sediments contaminated by polycyclic aromatic hydrocarbons (PAHs) can be candidates for remediation via an approach like land farming. Land farming converts naturally anaerobic sediments to aerobic environments, and the response of microbial communities, in terms of community structure alterations and corresponding effects on biodegradative activities, is unknown. A key goal of this study was to determine if different sediments exhibited common patterns in microbial community responses that might serve as indicators of PAH biodegradation. Sediments from three stations in the Lagos Lagoon (Nigeria) were used in microcosms, which were spiked with a mixture of four PAH, then examined for PAH biodegradation and for shifts in microbial community structure by analysis of diversity in PAH degradation genes and Illumina sequencing of 16S rRNA genes. PAH biodegradation was similar in all sediments, yet each exhibited unique microbiological responses and there were no microbial indicators of PAH bioremediation common to all sediments.

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.

First evidence on the occurrence and dynamics of Dehalococcoides mccartyi PCB-dechlorinase genes in marine sediment during Aroclor1254 reductive dechlorination

The present study evaluates the PCB-dehalorespiring capabilities and dynamics of indigenous Dehalococcoides mccartyi population in a PCB contaminated marine sediment. Specialized PCB-dechlorinase genes pcbA1, pcbA4 and pcbA5 previously characterized in pure cultures of D. mccartyi, were here found for the first time in environmental samples. Reductive dechlorination was stimulated by spiking Aroclor1254 to the sediment and by imposing strictly anaerobic conditions both with and without bioaugmentation with a Dehalococcoides mccartyi enrichment culture. In line with the contaminant dechlorination kinetics, Dehalococcoides population increased during the entire incubation period showing growth yields of 4.94E+07 Dehalococcoides per μmolCl^-1 and 7.30E+05 Dehalococcoides per μmolCl^-1 in the marine sediment with and without bioaugmentation respectively. The pcbA4 and pcbA5 dechlorinase genes, and to a lesser extent pcbA1 gene, were enriched during the anaerobic incubation suggesting their role in Aroclor1254 dechlorination under salinity conditions.

Particles and enzymes: Combining nanoscale zero valent iron and organochlorine respiring bacteria for the detoxification of chloroethane mixtures

Nanoscale zero valent iron (nZVI) and organochlorine respiring bacteria (ORB) are two technologies used to detoxify chlorinated aliphatic hydrocarbons (CAHs). nZVI can rapidly detoxify high CAH concentrations, but is quickly oxidised and unable to degrade certain CAHs (e.g., 1,2-dichlorothane). In contrast, ORB can dechlorinate CAHs resistant to nZVI (e.g., 1,2-dichlorothane) but are inhibited by other CAHs of concern degradable by nZVI (e.g., chloroform and carbon tetrachloride). Combining the two was proposed as a unique treatment train to overcome each technology's shortcomings. In this study, this combined remedy was investigated using a mixture of 1,2-dichloroethane, degradable by ORB but not nZVI, and 1,1,2-trichloroethane, susceptible to both. Results indicated that nZVI rapidly dechlorinated 1,1,2-trichloroethane when supplied above 0.5 g/L, however ORB were inhibited and unable to dechlorinate 1,2-dichloroethane. pH increase and ionic species associated with nZVI did not significantly impact ORB, pinpointing Fe(0) particles as responsible for ORB inhibition. Below 0.05 g/L nZVI, ORB activity was stimulated. Results suggest that combining ORB and nZVI at appropriate doses can potentially treat a wider range of CAHs than each individual remedy. At field sites where nZVI was applied, it is likely that in situ nZVI concentrations were below the threshold of negative consequences.

Reductive dechlorination of tetrachloroethene in marine sediments: Biodiversity and dehalorespiring capabilities of the indigenous microbes

Chlorinated compounds pose environmental concerns due to their toxicity and wide distribution in several matrices. Microorganisms specialized in leading anaerobic reductive dechlorination (RD) processes, including Dehalococcoides mccartyi (Dhc), are able to reduce chlorinated compounds to harmless products or to less toxic forms. Here we report the first detailed study dealing with the RD potential of heavy polluted marine sediment by evaluating the biodegradation kinetics together with the composition, dynamics and activity of indigenous microbial population. A microcosm study was conducted under strictly anaerobic conditions on marine sediment collected near the marine coast of Sarno river mouth, one of the most polluted river in Europe. Tetrachloroethene (PCE), used as model pollutant, was completely converted to ethene within 150 days at reductive dechlorination rate equal to 0.016 meq L(-1) d(-1). Consecutive spikes of PCE allowed increasing the degradation kinetics up to 0.1 meq L(-1)d(-1) within 20 days. Strictly anaerobiosis and repeated spikes of PCE stimulated the growth of indigenous Dhc cells (growth yield of ~7.0 E + 07 Dhc cells per μM Cl(-1) released). Dhc strains carrying the reductive dehalogenase genes tceA and vcrA were detected in the original marine sediment and their number increased during the treatment as demonstrated by the high level of tceA expression at the end of the microcosm study (2.41 E + 05 tceA gene transcripts g(-1)). Notably, the structure of the microbial communities was fully described by Catalysed Reporter Deposition Fluorescence In Situ Hybridization (CARD-FISH) as wells as the dynamics of the dechlorinating bacteria during the microcosms operation. Interestingly, a direct role of Dhc cells was ascertained suggesting the existence of strains adapted at salinity conditions. Additionally, non-Dhc Chloroflexi were retrieved in the original sediment and were kept stable over time suggesting their likely flanking role of the RD process.

Organohalide Respiring Bacteria and Reductive Dehalogenases: Key Tools in Organohalide Bioremediation

Organohalides are recalcitrant pollutants that have been responsible for substantial contamination of soils and groundwater. Organohalide-respiring bacteria (ORB) provide a potential solution to remediate contaminated sites, through their ability to use organohalides as terminal electron acceptors to yield energy for growth (i.e., organohalide respiration). Ideally, this process results in non- or lesser-halogenated compounds that are mostly less toxic to the environment or more easily degraded. At the heart of these processes are reductive dehalogenases (RDases), which are membrane bound enzymes coupled with other components that facilitate dehalogenation of organohalides to generate cellular energy. This review focuses on RDases, concentrating on those which have been purified (partially or wholly) and functionally characterized. Further, the paper reviews the major bacteria involved in organohalide breakdown and the evidence for microbial evolution of RDases. Finally, the capacity for using ORB in a bioremediation and bioaugmentation capacity are discussed.

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

Bioremediation of trichloroethene (TCE) polluted groundwater is challenging, with limited next generation sequencing (NGS) derived information available on microbial community dynamics associated with dechlorination. Understanding these dynamics is important for designing and improving TCE bioremediation. In this study, biostimulation (BS), biostimulation-bioaugmentation (BS-BA) and monitored natural attenuation (MNA) approaches were applied to contaminated groundwater wells resulted in ≥ 95% dechlorination within 7 months. Vinyl chloride's final concentrations in stimulated wells were between 1.84 and 1.87 μg L(-1), below the US EPA limit of 2.0 μg L(-1), compared to MNA (4.3 μg L(-1)). Assessment of the groundwater microbial community with qPCR showed up to ∼ 50-fold increase in the classical dechlorinators' (Geobacter and Dehalococcoides sp.) population post-treatment. Metagenomic assays revealed shifts from Gammaproteobacteria (pre-treatment) to Epsilonproteobacteria and Deltaproteobacteria (post-treatment) only in stimulated wells. Although stimulated wells were functionally distinct from MNA wells post-treatment, substantial dechlorination in all the wells implied some measure of redundancy. This study, one of the few NGS-based field studies on TCE bioremediation, provides greater insights into dechlorinating microbial community dynamics which should be useful for future field-based studies.

Resiliency of Stable Isotope Fractionation (δ(13)C and δ(37)Cl) of Trichloroethene to Bacterial Growth Physiology and Expression of Key Enzymes

Quantification of in situ (bio)degradation using compound-specific isotope analysis requires a known and constant isotope enrichment factor (ε). Because reported isotope enrichment factors for microbial dehalogenation of chlorinated ethenes vary considerably we studied the potential effects of metabolic adaptation to TCE respiration on isotope fractionation (δ(13)C and δ(37)Cl) using a model organism (Desulfitobacterium hafniesne Y51), which only has one reductive dehalogenase (PceA). Cells grown on TCE for the first time showed exponential growth until 10(9) cells/mL. During exponential growth, the cell-normalized amount of PceA enzyme increased steadily in the presence of TCE (up to 21 pceA transcripts per cell) but not with alternative substrates (<1 pceA transcript per cell). Cultures initially transferred or subcultivated on TCE showed very similar isotope fractionation, both for carbon (εcarbon: -8.6‰ ± 0.3‰ or -8.8‰ ± 0.2‰) and chlorine (εchlorine: -2.7‰ ± 0.3‰) with little variation (0.7‰) for the different experimental conditions. Thus, TCE isotope fractionation by D. hafniense strain Y51 was affected by neither growth phase, pceA transcription, or translation, nor by PceA content per cell, suggesting that transport limitations did not affect isotope fractionation. Previously reported variable ε values for other organohalide-respiring bacteria might thus be attributed to different expression levels of their multiple reductive dehalogenases.

Enumeration of Organohalide Respirers in Municipal Wastewater Anaerobic Digesters

Organohalide contaminants such as triclosan and triclocarban have been well documented in municipal wastewater treatment plants (WWTPs), but the degradation of these contaminants is not well understood. One possible removal mechanism is organohalide respiration by which bacteria reduce the halogenated compound. The purpose of this study was to determine the abundance of organohalide-respiring bacteria in eight WWTP anaerobic digesters. The obligate organohalide respiring Dehalococcoides mccartyi was the most abundant and averaged 3.3 × 10⁷ copies of 16S rRNA genes per gram, while the Dehalobacter was much lower at 2.6 × 10⁴ copies of 16S rRNA genes per gram. The genus Sulfurospirillum spp. was also detected at 1.0 × 10⁷ copies of 16S rRNA genes per gram. No other known or putatively organohalide-respiring strains in the Dehalococcoidaceae family were found to be present nor were the genera Desulfitobacterium or Desulfomonile.

The relationship between microbial community evenness and function in slow sand filters

Two full-scale slow sand filters (SSFs) were sampled periodically from April until November 2011 to study the spatial and temporal structures of the bacterial communities found in the filters. To monitor global changes in the microbial communities, DNA from sand samples taken at different depths and locations within the SSFs and at different filters ages was used for Illumina 16S rRNA gene sequencing. Additionally, 15 water quality parameters were monitored to assess filter performance, with functionally relevant microbial members being identified by using multivariate statistics. The bacterial diversity in the SSFs was found to be much larger than previously documented, with community composition being shaped by the characteristics of the SSFs (filter age and depth) and sampling characteristics (month, side, and distance from the influent and effluent pipes). We found that several key genera (Acidovorax, Halomonas, Sphingobium, and Sphingomonas) were associated with filter performance. In addition, at the whole-community level, a strong positive correlation was found between species evenness and filter performance. This study is the first to comprehensively characterize the microbial community of SSFs and link specific microbes to water quality parameters. In doing so, we reveal key patterns in microbial community structure that relate to overall community function.

IMPORTANCE

The supply of sustainable, energy-efficient, and safe drinking water to an increasing world population is a huge challenge faced by the water industry. SSFs have been used for hundreds of years to provide a safe and reliable source of potable drinking water, with minimal energy requirements. However, a lack of knowledge pertaining to the treatment mechanisms, particularly the biological processes, underpinning SSF operation has meant that SSFs are still operated as "black boxes." Understanding these dynamics alongside performance-induced effects associated with operational differences will promote optimized SSF design, maintenance, and operation, creating more efficient and environmentally sustainable filters. Through a spatial-temporal survey of full-scale SSFs at various points of operation, we present the most detailed characterization to date of the functional microbial communities found in SSFs, linking various taxa and community metrics to optimal water quality production.

SPINE: SParse eIgengene NEtwork linking gene expression clusters in Dehalococcoides mccartyi to perturbations in experimental conditions

We present a statistical model designed to identify the effect of experimental perturbations on the aggregate behavior of the transcriptome expressed by the bacterium Dehalococcoides mccartyi strain 195. Strains of Dehalococcoides are used in sub-surface bioremediation applications because they organohalorespire tetrachloroethene and trichloroethene (common chlorinated solvents that contaminate the environment) to non-toxic ethene. However, the biochemical mechanism of this process remains incompletely described. Additionally, the response of Dehalococcoides to stress-inducing conditions that may be encountered at field-sites is not well understood. The constructed statistical model captured the aggregate behavior of gene expression phenotypes by modeling the distinct eigengenes of 100 transcript clusters, determining stable relationships among these clusters of gene transcripts with a sparse network-inference algorithm, and directly modeling the effect of changes in experimental conditions by constructing networks conditioned on the experimental state. Based on the model predictions, we discovered new response mechanisms for DMC, notably when the bacterium is exposed to solvent toxicity. The network identified a cluster containing thirteen gene transcripts directly connected to the solvent toxicity condition. Transcripts in this cluster include an iron-dependent regulator (DET0096-97) and a methylglyoxal synthase (DET0137). To validate these predictions, additional experiments were performed. Continuously fed cultures were exposed to saturating levels of tetrachloethene, thereby causing solvent toxicity, and transcripts that were predicted to be linked to solvent toxicity were monitored by quantitative reverse-transcription polymerase chain reaction. Twelve hours after being shocked with saturating levels of tetrachloroethene, the control transcripts (encoding for a key hydrogenase and the 16S rRNA) did not significantly change. By contrast, transcripts for DET0137 and DET0097 displayed a 46.8±11.5 and 14.6±9.3 fold up-regulation, respectively, supporting the model. This is the first study to identify transcripts in Dehalococcoides that potentially respond to tetrachloroethene solvent-toxicity conditions that may be encountered near contamination source zones in sub-surface environments.

Development of a fluorescence-activated cell sorting method coupled with whole genome amplification to analyze minority and trace Dehalococcoides genomes in microbial communities

Dehalococcoides mccartyi are functionally important bacteria that catalyze the reductive dechlorination of chlorinated ethenes. However, these anaerobic bacteria are fastidious to isolate, making downstream genomic characterization challenging. In order to facilitate genomic analysis, a fluorescence-activated cell sorting (FACS) method was developed in this study to separate D. mccartyi cells from a microbial community, and the DNA of the isolated cells was processed by whole genome amplification (WGA) and hybridized onto a D. mccartyi microarray for comparative genomics against four sequenced strains. First, FACS was successfully applied to a D. mccartyi isolate as positive control, and then microarray results verified that WGA from 10(6) cells or ∼1 ng of genomic DNA yielded high-quality coverage detecting nearly all genes across the genome. As expected, some inter- and intrasample variability in WGA was observed, but these biases were minimized by performing multiple parallel amplifications. Subsequent application of the FACS and WGA protocols to two enrichment cultures containing ∼10% and ∼1% D. mccartyi cells successfully enabled genomic analysis. As proof of concept, this study demonstrates that coupling FACS with WGA and microarrays is a promising tool to expedite genomic characterization of target strains in environmental communities where the relative concentrations are low.

Systematic genomic analysis reveals the complementary aerobic and anaerobic respiration capacities of the human gut microbiota

Because of the specific anatomical and physiological properties of the human intestine, a specific oxygen gradient builds up within this organ that influences the intestinal microbiota. The intestinal microbiome has been intensively studied in recent years, and certain respiratory substrates used by gut inhabiting microbes have been shown to play a crucial role in human health. Unfortunately, a systematic analysis has not been previously performed to determine the respiratory capabilities of human gut microbes (HGM). Here, we analyzed the distribution of aerobic and anaerobic respiratory reductases in 254 HGM genomes. In addition to the annotation of known enzymes, we also predicted a novel microaerobic reductase and novel thiosulfate reductase. Based on this comprehensive assessment of respiratory reductases in the HGM, we proposed a number of exchange pathways among different bacteria involved in the reduction of various nitrogen oxides. The results significantly expanded our knowledge of HGM metabolism and interactions in bacterial communities.

Characterization of new bacterial catabolic genes and mobile genetic elements by high throughput genetic screening of a soil metagenomic library

A mix of oligonucleotide probes was used to hybridize soil metagenomic DNA from a fosmid clone library spotted on high density membranes. The pooled radio-labeled probes were designed to target genes encoding glycoside hydrolases GH18, dehalogenases, bacterial laccases and mobile genetic elements (integrases from integrons and insertion sequences). Positive hybridizing spots were affiliated to the corresponding clones in the library and the metagenomic inserts were sequenced. After assembly and annotation, new coding DNA sequences related to genes of interest were identified with low protein similarity against the closest hits in databases. This work highlights the sensitivity of DNA/DNA hybridization techniques as an effective and complementary way to recover novel genes from large metagenomic clone libraries. This study also supports that some of the identified catabolic genes might be associated with horizontal transfer events.

High frequency of phylogenetically diverse reductive dehalogenase-homologous genes in deep subseafloor sedimentary metagenomes

Marine subsurface sediments on the Pacific margin harbor diverse microbial communities even at depths of several hundreds meters below the seafloor (mbsf) or more. Previous PCR-based molecular analysis showed the presence of diverse reductive dehalogenase gene (rdhA) homologs in marine subsurface sediment, suggesting that anaerobic respiration of organohalides is one of the possible energy-yielding pathways in the organic-rich sedimentary habitat. However, primer-independent molecular characterization of rdhA has remained to be demonstrated. Here, we studied the diversity and frequency of rdhA homologs by metagenomic analysis of five different depth horizons (0.8, 5.1, 18.6, 48.5, and 107.0 mbsf) at Site C9001 off the Shimokita Peninsula of Japan. From all metagenomic pools, remarkably diverse rdhA-homologous sequences, some of which are affiliated with novel clusters, were observed with high frequency. As a comparison, we also examined frequency of dissimilatory sulfite reductase genes (dsrAB), key functional genes for microbial sulfate reduction. The dsrAB were also widely observed in the metagenomic pools whereas the frequency of dsrAB genes was generally smaller than that of rdhA-homologous genes. The phylogenetic composition of rdhA-homologous genes was similar among the five depth horizons. Our metagenomic data revealed that subseafloor rdhA homologs are more diverse than previously identified from PCR-based molecular studies. Spatial distribution of similar rdhA homologs across wide depositional ages indicates that the heterotrophic metabolic processes mediated by the genes can be ecologically important, functioning in the organic-rich subseafloor sedimentary biosphere.