Identification of novel perchloroethene-respiring microorganisms in anoxic river sediment by RNA-based stable isotope probing

Identification of Antimonate Reducing Bacteria and Their Potential Metabolic Traits by the Combination of Stable Isotope Probing and Metagenomic-Pangenomic Analysis

Microorganisms play an important role in altering antimony (Sb) speciation, mobility, and bioavailability, but the understanding of the microorganisms responsible for Sb(V) reduction has been limited. In this study, DNA-stable isotope probing (DNA-SIP) and metagenomics analysis were combined to identify potential Sb(V)-reducing bacteria (SbRB) and predict their metabolic pathways for Sb(V) reduction. Soil slurry cultures inoculated with Sb-contaminated paddy soils from two Sb-contaminated sites demonstrated the capability to reduce Sb(V). DNA-SIP identified bacteria belonging to the genera Pseudomonas and Geobacter as putative SbRB in these two Sb-contaminated sites. In addition, bacteria such as Lysinibacillus and Dechloromonas may potentially participate in Sb(V) reduction. Nearly complete draft genomes of putative SbRB (i.e., Pseudomonas and Geobacter) were obtained, and the genes potentially responsible for arsenic (As) and Sb reduction (i.e., respiratory arsenate reductase (arrA) and antimonate reductase (anrA)) were examined. Notably, bins affiliated with Geobacter contained arrA and anrA genes, supporting our hypothesis that they are putative SbRB. Further, pangenomic analysis indicated that various Geobacter-associated genomes obtained from diverse habitats also contained arrA and anrA genes. In contrast, Pseudomonas may use a predicted DMSO reductase closely related to sbrA (Sb(V) reductase gene) clade II to reduce Sb(V), which may need further experiments to verify. This current work represents a demonstration of using DNA-SIP and metagenomic-binning to identify SbRB and their key genes involved in Sb(V) reduction and provides valuable data sets to link bacterial identities with Sb(V) reduction.

Characterization and Performance of Lactate-Feeding Consortia for Reductive Dechlorination of Trichloroethene

Understanding the underlying mechanism that drives the microbial community mediated by substrates is crucial to enhance the biostimulation in trichloroethene (TCE)-contaminated sites. Here, we investigated the performance of stable TCE-dechlorinating consortia by monitoring the variations in TCE-related metabolites and explored their underlying assembly mechanisms using 16S rDNA amplicon sequencing and bioinformatics analyses. The monitoring results indicated that three stable TCE-dechlorinating consortia were successfully enriched by lactate-containing anaerobic media. The statistical analysis results demonstrated that the microbial communities of the enrichment cultures changed along with time and were distinguished by their sample sources. The deterministic and stochastic processes were simultaneously responsible for shaping the TCE-dechlorinating community assembly. The indicator patterns shifted with the exhaustion of the carbon source and the pollutants, and the tceA-carrying Dehalococcoides, as an indicator for the final stage samples, responded positively to TCE removal during the incubation period. Pseudomonas, Desulforhabdus, Desulfovibrio and Methanofollis were identified as keystone populations in the TCE-dechlorinating process by co-occurrence network analysis. The results of this study indicate that lactate can be an effective substrate for stimulated bioremediation of TCE-contaminated sites, and the reduction of the stochastic forces or enhancement of the deterministic interventions may promote more effective biostimulation.

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.

Identification of a Chlorodibenzo-p-dioxin Dechlorinating Dehalococcoides mccartyi by Stable Isotope Probing

Polychlorinated dibenzo-p-dioxins (PCDDs) are released into the environment from a variety of both anthropogenic and natural sources. While highly chlorinated dibenzo-p-dioxins are persistent under oxic conditions, in anoxic environments, these organohalogens can be reductively dechlorinated to less chlorinated compounds that are then more amenable to subsequent aerobic degradation. Identifying the microorganisms responsible for dechlorination is an important step in developing bioremediation approaches. In this study, we demonstrated the use of a DNA-stable isotope probing (SIP) approach to identify the bacteria active in dechlorination of PCDDs in river sediments, with 1,2,3,4-tetrachlorodibenzo-p-dioxin (1,2,3,4-TeCDD) as a model. In addition, pyrosequencing of reverse transcribed 16S rRNA of TeCDD dechlorinating enrichment cultures was used to reveal active members of the bacterial community. A set of operational taxonomic units (OTUs) responded positively to the addition of 1,2,3,4-TeCDD in SIP microcosms assimilating ¹³C-acetate as the carbon source. Analysis of bacterial community profiles of the ¹³C labeled heavy DNA fraction revealed that an OTU corresponding to Dehalococcoides mccartyi accounted for a significantly greater abundance in cultures amended with 1,2,3,4-TeCDD than in cultures without 1,2,3,4-TeCDD. This implies the involvement of this Dehalococcoides mccartyi strain in the reductive dechlorination of 1,2,3,4-TeCDD and suggests the applicability of SIP for a robust assessment of the bioremediation potential of organohalogen contaminated sites.

Organohalide respiration in pristine environments: implications for the natural halogen cycle

Halogenated organic compounds, also termed organohalogens, were initially considered to be of almost exclusively anthropogenic origin. However, over 5000 naturally synthesized organohalogens are known today. This has also fuelled the hypothesis that the natural and ancient origin of organohalogens could have primed development of metabolic machineries for their degradation, especially in microorganisms. Among these, a special group of anaerobic microorganisms was discovered that could conserve energy by reducing organohalogens as terminal electron acceptor in a process termed organohalide respiration. Originally discovered in a quest for biodegradation of anthropogenic organohalogens, these organohalide-respiring bacteria (OHRB) were soon found to reside in pristine environments, such as the deep subseafloor and Arctic tundra soil with limited/no connections to anthropogenic activities. As such, accumulating evidence suggests an important role of OHRB in local natural halogen cycles, presumably taking advantage of natural organohalogens. In this minireview, we integrate current knowledge regarding the natural origin and occurrence of industrially important organohalogens and the evolution and spread of OHRB, and describe potential implications for natural halogen and carbon cycles.

Biodegradation of Volatile Organic Compounds and Their Effects on Biodegradability under Co-Existing Conditions

Volatile organic compounds (VOCs) are major pollutants that are found in contaminated sites, particularly in developed countries such as Japan. Various microorganisms that degrade individual VOCs have been reported, and genomic information related to their phylogenetic classification and VOC-degrading enzymes is available. However, the biodegradation of multiple VOCs remains a challenging issue. Practical sites, such as chemical factories, research facilities, and illegal dumping sites, are often contaminated with multiple VOCs. In order to investigate the potential of biodegrading multiple VOCs, we initially reviewed the biodegradation of individual VOCs. VOCs include chlorinated ethenes (tetrachloroethene, trichloroethene, dichloroethene, and vinyl chloride), BTEX (benzene, toluene, ethylbenzene, and xylene), and chlorinated methanes (carbon tetrachloride, chloroform, and dichloromethane). We also summarized essential information on the biodegradation of each kind of VOC under aerobic and anaerobic conditions, together with the microorganisms that are involved in VOC-degrading pathways. Interactions among multiple VOCs were then discussed based on concrete examples. Under conditions in which multiple VOCs co-exist, the biodegradation of a VOC may be constrained, enhanced, and/or unaffected by other compounds. Co-metabolism may enhance the degradation of other VOCs. In contrast, constraints are imposed by the toxicity of co-existing VOCs and their by-products, catabolite repression, or competition between VOC-degrading enzymes. This review provides fundamental, but systematic information for designing strategies for the bioremediation of multiple VOCs, as well as information on the role of key microorganisms that degrade VOCs.

Effects of 1,1,1-Trichloroethane and Triclocarban on Reductive Dechlorination of Trichloroethene in a TCE-Reducing Culture

Chlorinated compounds were generally present in the environment due to widespread use in the industry. A short-term study was performed to evaluate the effects of 1,1,1- trichloroethane (TCA) and triclocarban (TCC) on trichloroethene (TCE) removal in a reactor fed with lactate as the sole electron donor. Both TCA and TCC inhibited TCE reduction, but the TCC had a more pronounced effect compared to TCA. The TCE-reducing culture, which had never been exposed to TCA before, reductively dechlorinated TCA to 1,1-dichloroethane (DCA). Below 15 μM, TCA had little effect on the transformation of TCE to cis-dichloroethene (DCE); however, the reduction of cis-DCE and vinyl chloride (VC) were more sensitive to TCA, and ethene production was completely inhibited when the concentration of TCA was above 15 μM. In cultures amended with TCC, the reduction of TCE was severely affected, even at concentrations as low as 0.3 μM; all the cultures stalled at VC, and no ethene was detected. The cultures that fully transformed TCE to ethene contained 5.2–8.1% Dehalococcoides. Geobacter and Desulfovibrio, the bacteria capable of partially reducing TCE to DCE, were detected in all cultures, but both represented a larger proportion of the community in TCC-amended cultures. All cultures were dominated by Clostridium_sensu_stricto_7, a genus that belongs to Firmicutes with proportions ranging from 40.9% (in a high TCC (15 μM) culture) to 88.2%. Methanobacteria was detected at levels of 1.1–12.7%, except in cultures added with 15 and 30 μM TCA, in which they only accounted for ∼0.4%. This study implies further environmental factors needed to be considered in the successful bioremediation of TCE in contaminated sites.

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

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

Genome sequencing of a single cell of the widely distributed marine subsurface Dehalococcoidia, phylum Chloroflexi

Bacteria of the class Dehalococcoidia (DEH), phylum Chloroflexi, are widely distributed in the marine subsurface, yet metabolic properties of the many uncultivated lineages are completely unknown. This study therefore analysed genomic content from a single DEH cell designated 'DEH-J10' obtained from the sediments of Aarhus Bay, Denmark. Real-time PCR showed the DEH-J10 phylotype was abundant in upper sediments but was absent below 160 cm below sea floor. A 1.44 Mbp assembly was obtained and was estimated to represent up to 60.8% of the full genome. The predicted genome is much larger than genomes of cultivated DEH and appears to confer metabolic versatility. Numerous genes encoding enzymes of core and auxiliary beta-oxidation pathways were identified, suggesting that this organism is capable of oxidising various fatty acids and/or structurally related substrates. Additional substrate versatility was indicated by genes, which may enable the bacterium to oxidise aromatic compounds. Genes encoding enzymes of the reductive acetyl-CoA pathway were identified, which may also enable the fixation of CO2 or oxidation of organics completely to CO2. Genes encoding a putative dimethylsulphoxide reductase were the only evidence for a respiratory terminal reductase. No evidence for reductive dehalogenase genes was found. Genetic evidence also suggests that the organism could synthesise ATP by converting acetyl-CoA to acetate by substrate-level phosphorylation. Other encoded enzymes putatively conferring marine adaptations such as salt tolerance and organo-sulphate sulfohydrolysis were identified. Together, these analyses provide the first insights into the potential metabolic traits that may enable members of the DEH to occupy an ecological niche in marine sediments.

Metagenomic insights into anaerobic metabolism along an Arctic peat soil profile

A metagenomic analysis was performed on a soil profile from a wet tundra site in northern Alaska. The goal was to link existing biogeochemical knowledge of the system with the organisms and genes responsible for the relevant metabolic pathways. We specifically investigated how the importance of iron (Fe) oxides and humic substances (HS) as terminal electron acceptors in this ecosystem is expressed genetically, and how respiratory and fermentative processes varied with soil depth into the active layer and into the upper permafrost. Overall, the metagenomes reflected a microbial community enriched in a diverse range of anaerobic pathways, with a preponderance of known Fe reducing species at all depths in the profile. The abundance of sequences associated with anaerobic metabolic processes generally increased with depth, while aerobic cytochrome c oxidases decreased. Methanogenesis genes and methanogen genomes followed the pattern of CH₄ fluxes : they increased steeply with depth into the active layer, but declined somewhat over the transition zone between the lower active layer and the upper permafrost. The latter was relatively enriched in fermentative and anaerobic respiratory pathways. A survey of decaheme cytochromes (MtrA, MtrC and their homologs) revealed that this is a promising approach to identifying potential reducers of Fe(III) or HS, and indicated a possible role for Acidobacteria as Fe reducers in these soils. Methanogens appear to coexist in the same layers, though in lower abundance, with Fe reducing bacteria and other potential competitors, including acetogens. These observations provide a rich set of hypotheses for further targeted study.

Molecular techniques in the biotechnological fight against halogenated compounds in anoxic environments

Microbial treatment of environmental contamination by anthropogenic halogenated organic compounds has become popular in recent decades, especially in the subsurface environments. Molecular techniques such as polymerase chain reaction-based fingerprinting methods have been extensively used to closely monitor the presence and activities of dehalogenating microbes, which also lead to the discovery of new dehalogenating bacteria and novel functional genes. Nowadays, traditional molecular techniques are being further developed and optimized for higher sensitivity, specificity, and accuracy to better fit the contexts of dehalogenation. On the other hand, newly developed high throughput techniques, such as microarray and next-generation sequencing, provide unsurpassed detection ability, which has enabled large-scale comparative genomic and whole-genome transcriptomic analysis. The aim of this review is to summarize applications of various molecular tools in the field of microbially mediated dehalogenation of various halogenated organic compounds. It is expected that traditional molecular techniques and nucleic-acid-based biomarkers will still be favoured in the foreseeable future because of relative low costs and high flexibility. Collective analyses of metagenomic sequencing data are still in need of information from individual dehalogenating strains and functional reductive dehalogenase genes in order to draw reliable conclusions.

Vertical profiles of abundance and potential activity of methane-oxidizing bacteria in sediment of Lake Biwa, Japan

Vertical profiles of the abundance, community composition, and potential activity of methane-oxidizing bacteria (MOB) were investigated in the sediment of Lake Biwa. Sediment samples were obtained from two sites at different water depths. The abundance of MOB was assessed as the copy number of the pmoA gene (encoding the alpha subunit of particulate methane monooxygenase), measured with quantitative real-time PCR. Abundance of the pmoA gene peaked in the 5–8 cm layer of the sediment from both sites. MOB community composition was investigated by denaturing gradient gel electrophoresis (DGGE) analysis of pmoA and 16S rRNA genes. The band patterns observed in DGGE did not significantly differ with sediment depths or sampling sites. Sequence analysis of the DGGE bands indicated the dominance of the genus Methylobacter. Potential activity, which was measured in the presence of sufficient amounts of methane and oxygen, decreased linearly from the sediment surface to deeper layers. These results suggest that the pmoA gene copy number cannot be regarded as an indicator of aerobic MOB that retain potential activity in sediments.

Natural niche for organohalide-respiring Chloroflexi

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

Role of "Dehalococcoides" spp. in the anaerobic transformation of hexachlorobenzene in European rivers

The diffuse pollution by chlorinated organic compounds in river basins is a concern, due to their potential adverse effects on human health and the environment. Organohalides, like hexachlorobenzene (HCB), are recalcitrant to aerobic microbial degradation, and "Dehalococcoides" spp. are the only known microorganisms capable of anaerobic transformation of these compounds coupled to their growth. In this study, sediments from four European rivers were studied in order to determine their HCB dechlorination capacities and the role of Dehalococcoides spp. in this process. Only a weak correlation was observed between Dehalococcoides species abundance and HCB transformation rates from different locations. In one of these locations, in the Ebro River sediment, HCB dechlorination could be linked to Dehalococcoides species growth and activity by 16S rRNA-based molecular methods. Furthermore, HCB dechlorination activity in this sediment was found over the full range of ambient temperatures that this sediment can be exposed to during different seasons throughout the year. The sediment contained several reductive dehalogenase (rdh) genes, and analysis of their transcription revealed the dominance of cbrA, previously shown to encode a trichlorobenzene reductive dehalogenase. This study investigated the role of Dehalococcoides spp. in HCB dechlorination in river sediments and evaluated if the current knowledge of rdh genes could be used to assess HCB bioremediation potential.

The little bacteria that can - diversity, genomics and ecophysiology of 'Dehalococcoides' spp. in contaminated environments

The fate and persistence of chlorinated organics in the environment have been a concern for the past 50 years. Industrialization and extensive agricultural activities have led to the accumulation of these pollutants in the environment, while their adverse impact on various ecosystems and human health also became evident. This review provides an update on the current knowledge of specialized anaerobic bacteria, namely ‘Dehalococcoides’ spp., which are dedicated to the transformation of various chlorinated organic compounds via reductive dechlorination. Advances in microbiology and molecular techniques shed light into the diversity and functioning of Dehalococcoides spp. in several different locations. Recent genome sequencing projects revealed a large number of genes that are potentially involved in reductive dechlorination. Molecular approaches towards analysis of diversity and expression especially of reductive dehalogenase‐encoding genes are providing a growing body of knowledge on biodegradative pathways active in defined pure and mixed cultures as well as directly in the environment. Moreover, several successful field cases of bioremediation strengthen the notion of dedicated degraders such as Dehalococcoides spp. as key players in the restoration of contaminated environments.

Tracking functional guilds: "Dehalococcoides" spp. in European river basins contaminated with hexachlorobenzene

Hexachlorobenzene (HCB) has been widely used in chemical manufacturing processes and as a pesticide. Due to its resistance to biological degradation, HCB has mainly accumulated in freshwater bodies and agricultural soils. "Dehalococcoides" spp., anaerobic dechlorinating bacteria that are capable of degrading HCB, were previously isolated from river sediments. Yet there is limited knowledge about the abundance, diversity, and activity of this genus in the environment. This study focused on the molecular analysis of the composition and abundance of active Dehalococcoides spp. in HCB-contaminated European river basins. 16S rRNA-based real-time quantitative PCR and denaturing gradient gel electrophoresis in combination with multivariate statistics were applied. Moreover, a functional gene array was used to determine reductive dehalogenase (rdh) gene diversity. Spatial and temporal fluctuations were observed not only in the abundance of Dehalococcoides spp. but also in the composition of the populations and rdh gene diversity. Multivariate statistics revealed that Dehalococcoides sp. abundance is primarily affected by spatial differences, whereas species composition is under the influence of several environmental parameters, such as seasonal changes, total organic carbon and/or nitrogen content, and HCB contamination. This study provides new insight into the natural occurrence and dynamics of active Dehalococcoides spp. in HCB-contaminated river basins.