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

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

Dynamics of an Oligotrophic Bacterial Aquifer Community during Contact with a Groundwater Plume Contaminated with Benzene, Toluene, Ethylbenzene, and Xylenes: an In Situ Mesocosm Study{dagger}

An in situ mesocosm system was designed to monitor the in situ dynamics of the microbial community in polluted aquifers. The mesocosm system consists of a permeable membrane pocket filled with aquifer material and placed within a polypropylene holder, which is inserted below groundwater level in a monitoring well. After a specific time period, the microcosm is recovered from the well and its bacterial community is analyzed. Using this system, we examined the effect of benzene, toluene, ethylbenzene, and xylene (BTEX) contamination on the response of an aquifer bacterial community by denaturing gradient gel electrophoresis analysis of PCR-amplified 16S rRNA genes and PCR detection of BTEX degradation genes. Mesocosms were filled with nonsterile or sterile aquifer material derived from an uncontaminated area and positioned in a well located in either the uncontaminated area or a nearby contaminated area. In the contaminated area, the bacterial community in the microcosms rapidly evolved into a stable community identical to that in the adjacent aquifer but different from that in the uncontaminated area. At the contaminated location, bacteria with tmoA- and xylM/xylE1-like BTEX catabolic genotypes colonized the aquifer, while at the uncontaminated location only tmoA-like genotypes were detected. The communities in the mesocosms and in the aquifer adjacent to the wells in the contaminated area consisted mainly of Proteobacteria. At the uncontaminated location, Actinobacteria and Proteobacteria were found. Our results indicate that communities with long-term stability in their structures follow the contamination plume and rapidly colonize downstream areas upon contaminatio

The great screen anomaly—a new frontier in product discovery through functional metagenomics

Functional metagenomics, the study of the collective genome of a microbial community by expressing it in a foreign host, is an emerging field in biotechnology. Over the past years, the possibility of novel product discovery through metagenomics has developed rapidly. Thus, metagenomics has been heralded as a promising mining strategy of resources for the biotechnological and pharmaceutical industry. However, in spite of innovative work in the field of functional genomics in recent years, yields from function-based metagenomics studies still fall short of producing significant amounts of new products that are valuable for biotechnological processes. Thus, a new set of strategies is required with respect to fostering gene expression in comparison to the traditional work. These new strategies should address a major issue, that is, how to successfully express a set of unknown genes of unknown origin in a foreign host in high throughput. This article is an opinionating review of functional metagenomic screening of natural microbial communities, with a focus on the optimization of new product discovery. It first summarizes current major bottlenecks in functional metagenomics and then provides an overview of the general metagenomic assessment strategies, with a focus on the challenges that are met in the screening for, and selection of, target genes in metagenomic libraries. To identify possible screening limitations, strategies to achieve optimal gene expression are reviewed, examining the molecular events all the way from the transcription level through to the secretion of the target gene product

Assessment of bioremediation potential and monitoring of biological reductive dechlorination in sites contaminated with chlorinated ethenes

Chlorinated ethenes (CEs), such as perchloroethene (PCE) and trichloroethene, are one of the most common classes of groundwater contaminants. In this project, the contaminant biodegradation capacities of two aquifers, presenting both dichloroethene (DCE) and vinyl chloride (VC) accumulation, was carried out. Aquifers are considered nowadays as dynamic ecosystems, showing multiple interactions between the physical, chemical and biotic components. In this sense, an integrative methodology using multivariate statistics and combining together bacterial community structures, detection of dechlorinating bacteria and genes and water geochemical data were used to investigate these aquifers. Results from multifactorial analysis of data collected from a PCE-contaminated site in Switzerland (25 groundwater samples) showed that manganese reduction (MR) was a key terminal electron accepting process, suggesting a potential competition between MR and DCE degradation to VC. Dehalococcoides sp. and VC reductive dehalogenase genes were detected but ethene concentration was below 0.007mg/L. Potential for a complete natural biodegradation of PCE was present in this aquifer. However, DCE reduction will be strongly inhibited under local conditions as long as oxidized manganese resources are present. The second site located in Czech Republic (Velamos) and sampled at 7 different dates (35 groundwater samples) was under active biostimulation process. Multifactorial analysis showed that successive cheese whey injections modified the aquifer habitat that became favourable not only for a complete dechlorination, but also for sulfate reduction (SR) and methanogenesis. DCE and VC accumulated along with the production of ethene, methane and hydrogen sulphide, indicating a competition between CEs dechlorination and SR and methanogenesis. This possibly explained the transitional slower reaction of CEs dechlorination observed during the remediation process. In conclusion, the used methodology allows evaluation of the bioremediation potential present in contaminated aquifers and monitoring biostimulation processes. This study was funded by grant No. TA02020534 - TECHTOOL of the Technology Agency of the CR, and the Swiss Federal Office for the Environment FOEN

Validation of an Integrative Methodology to Assess and Monitor Reductive Dechlorination of Chlorinated Ethenes in Contaminated Aquifers

Bioremediation of tetra-and trichloroethene-contaminated aquifers is frequently hampered due to incomplete dechlorination to the more toxic dichloroethene (DCE) and vinyl chloride (VC), indicating insufficient knowledge about the biological mechanisms related to aquifer functioning. A methodology based on the joint analysis of geochemical and microbiological datasets was developed to assess the presence of the biochemical potential for complete reductive dechlorination to harmless ethene and to explain the reasons for which degradation often stalls at the more toxic intermediates. This methodology is composed of three successive steps, with i) the acquisition of geochemical data including chlorinated ethenes, ii) the detailed analysis of the bacterial community structures as well as the biochemical potential for complete dechlorination using microcosms and molecular detection of organohalide-respiring bacteria and key reductive dehalogenases, and iii) a statistical Multiple Factor Analysis combining the above mentioned abiotic and biotic variables in a functional modelling of the contaminated aquifer. The methodology was validated by analyzing two chlorinated ethenes-contaminated sites. Results from the first site showed that the full biochemical potential for ethene production was present in situ. However, redox potential was overall too high and locally manganese reduction out-competed chlorinated ethenes reduction, explaining the reasons for the local accumulation of DCE and VC to a lesser extent. The second contaminated aquifer was under bioremediation by successive cheese whey injections. Analysis demonstrated that cheese whey additions led to increasingly reduced redox conditions and that hampered reductive dechlorination was not due to competition with other anaerobic respiration processes. Complete reductive dechlorination to ethene was preferentially occurring under methanogenic conditions. DCE and VC accumulation was probably induced first by low pH resulting from whey fermentation and at a later stage by phosphate limitation. In conclusions, the proposed methodology successfully allowed the identification of biogeochemical processes limiting or supporting complete dechlorination in both aquifers. The integrative approach provided fundamental information about the functional heterogeneity of the contaminated aquifers in time and space, and can be used as a reliable tool to support corrective decision-making in the development of remediation strategies based on natural attenuation of chlorinated ethenes

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

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

Alternative primer sets for PCR detection of genotypes involved in bacterial aerobic BTEX degradation: distribution of the genes in BTEX degrading isolates and in subsurface soils of a BTEX contaminated industrial site

Eight new primer sets were designed for PCR detection of (i) mono-oxygenase and dioxygenase gene sequences involved in initial attack of bacterial aerobic BTEX degradation and of (ii) catechol 2,3-dioxygenase gene sequences responsible for meta-cleavage of the aromatic ring. The new primer sets allowed detection of the corresponding genotypes in soil with a detection limit of 10(3)-10(4) or 10(5)-10(6) gene copies g(-1) soil, assuming one copy of the gene per cell. The primer sets were used in PCR to assess the distribution of the catabolic genes in BTEX degrading bacterial strains and DNA extracts isolated from soils sampled from different locations and depths (vadose, capillary fringe and saturated zone) within a BTEX contaminated site. In both soil DNA and the isolates, tmoA-, xylM- and xylE1-like genes were the most frequently recovered BTEX catabolic genes. xylM and xylE1 were only recovered from material from the contaminated samples while tmoA was detected in material from both the contaminated and non-contaminated samples. The isolates, mainly obtained from the contaminated locations, belonged to the Actinobacteria or Proteobacteria (mainly Pseudomonas). The ability to degrade benzene was the most common BTEX degradation phenotype among them and its distribution was largely congruent with the distribution of the tmoA-like genotype. The presence of tmoA and xylM genes in phylogenetically distant strains indicated the occurrence of horizontal transfer of BTEX catabolic genes in the aquifer. Overall, these results show spatial variation in the composition of the BTEX degradation genes and hence in the type of BTEX degradation activity and pathway, at the examined site. They indicate that bacteria carrying specific pathways and primarily carrying tmoA/xylM/xylE1 genotypes, are being selected upon BTEX contamination