Introduction of anaerobic dechlorinating bacteria into soil slurry microcosms and nested-PCR monitoring

Preparation and characterization of site-specific dechlorinating microbial inocula capable of complete dechlorination enriched in anaerobic microcosms amended with clay mineral

Abstract

Short-chain halogenated aliphatic hydrocarbons (e.g. perchloroethene, trichloroethene) are among the most toxic environmental pollutants. Perchloroethene and trichloroethene can be dechlorinated to non-toxic ethene through reductive dechlorination by Dehalococcoides sp. Bioaugmentation, applying cultures containing organohalide-respiring microorganisms, is a possible technique to remediate sites contaminated with chlorinated ethenes. Application of site specific inocula is an efficient alternative solution. Our aim was to develop site specific dechlorinating microbial inocula by enriching microbial consortia from groundwater contaminated with trichloroethene using microcosm experiments containing clay mineral as solid phase. Our main goal was to develop fast and reliable method to produce large amount (100 L) of bioactive agent with anaerobic fermentation technology. Polyphasic approach has been applied to monitor the effectiveness of dechlorination during the transfer process from bench-scale (500 mL) to industrial-scale (100 L). Gas chromatography measurement and T-RFLP (Terminal Restriction Fragment Length Polymorphism) revealed that the serial subculture of the enrichments shortened the time-course of the complete dechlorination of trichloroethene to ethene and altered the composition of bacterial communities. Complete dechlorination was observed in enrichments with significant abundance of Dehalococcoides sp. cultivated at 8 °C. Consortia incubated in fermenters at 18 °C accelerated the conversion of TCE to ethene by 7–14 days. Members of the enrichments belong to the phyla Bacteroidetes, Chloroflexi, Proteobacteria and Firmicutes. According to the operational taxonomic units, main differences between the composition of the enrichment incubated at 8 °C and 18 °C occurred with relative abundance of acetogenic and fermentative species. In addition to the temperature, the site-specific origin of the microbial communities and the solid phase applied during the fermentation technique contributed to the development of a unique microbial composition.

Graphic abstract

Electronic supplementary material

The online version of this article (10.1007/s11274-020-2806-7) contains supplementary material, which is available to authorized users.

Presence, Diversity, and Enrichment of Respiratory Reductive Dehalogenase and Non-respiratory Hydrolytic and Oxidative Dehalogenase Genes in Terrestrial Environments

Organohalide-respiring bacteria have been linked to the cycling and possible respiration of chlorinated natural organic matter (Cl-NOM) in uncontaminated soils and sediments. The importance of non-respiratory hydrolytic/oxidative dechlorination processes in the cycling of Cl-NOM in terrestrial soil and sediment, however, is still not understood. This research analyzes the dechlorination potential of terrestrial systems through analysis of the metagenomes of urban lake sediments and cultures enriched with Cl-NOM. Even with the variability in sample type and enrichment conditions, the potential to dechlorinate was universal, with reductive dehalogenase genes and hydrolytic or oxidative dehalogenase genes found in all samples analyzed. The reductive dehalogenase genes detected grouped taxonomically with those from organohalide-respiring bacteria with broad metabolic capabilities, as opposed to those that obligately respire organohalides. Furthermore, reductive dehalogenase genes and two haloacid dehalogenase genes increased in abundance when sediment was enriched with high concentrations of Cl-NOM. Our data suggests that both respiratory and non-respiratory dechlorination processes are important for Cl-NOM cycling, and that non-obligate organohalide-respiring bacteria are most likely involved in these processes.

Influence of food waste addition over microbial communities in an Anaerobic Membrane Bioreactor plant treating urban wastewater

Notorious changes in microbial communities were observed during and after the joint treatment of wastewater with Food Waste (FW) in an Anaerobic Membrane Bioreactor (AnMBR) plant. The microbial population was analysed by high-throughput sequencing of the 16S rRNA gene and dominance of Chloroflexi, Firmicutes, Synergistetes and Proteobacteria phyla was found. The relative abundance of these potential hydrolytic phyla increased as a higher fraction of FW was jointly treated. Moreover, whereas Specific Methanogenic Activity (SMA) rose from 10 to 51 mL CH₄ g^-1 VS, Methanosarcinales order increased from 34.0% over 80.0% of total Archaea, being Methanosaeta the dominant genus. The effect of FW over AnMBR biomass was observed during the whole experience, as methane production rose from 49.2 to 144.5 L CH₄ · kg^-1 influent COD. Furthermore, biomethanization potential was increased over 82% after the experience. AnMBR technology allows the established microbial community to remain in the bioreactor even after the addition of FW, improving the anaerobic digestion of urban wastewater.

Approach to determine the diversity of Legionella species by nested PCR-DGGE in aquatic environments

In this study, we describe a nested PCR-DGGE strategy to detect Legionella communities from river water samples. The nearly full-length 16S rRNA gene was amplified using bacterial primer in the first step. After, the amplicons were employed as DNA templates in the second PCR using Legionella specific primer. The third round of gene amplification was conducted to gain PCR fragments apposite for DGGE analysis. Then the total numbers of amplified genes were observed in DGGE bands of products gained with primers specific for the diversity of Legionella species. The DGGE patterns are thus potential for a high-throughput preliminary determination of aquatic environmental Legionella species before sequencing. Comparative DNA sequence analysis of excised DGGE unique band patterns showed the identity of the Legionella community members, including a reference profile with two pathogenic species of Legionella strains. In addition, only members of Legionella pneumophila and uncultured Legionella sp. were detected. Development of three step nested PCR-DGGE tactic is seen as a useful method for studying the diversity of Legionella community. The method is rapid and provided sequence information for phylogenetic analysis.

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.

Novel Firmicutes group implicated in the dechlorination of two chlorinated xanthones, analogues of natural organochlorines

Although the abundance and diversity of natural organochlorines are well established, much is still unknown about the degradation of these compounds. Triplicate microcosms were used to determine whether, and which, bacterial communities could dechlorinate two chlorinated xanthones (2,7-dichloroxanthone and 5,7-dichloro-1,3-dihydroxylxanthone), analogues of a diverse class of natural organochlorines. According to quantitative-PCR (qPCR) results, several known dechlorinating genera were either not present or not enriched during dechlorination of the xanthones. Denaturing gradient gel electrophoresis, however, indicated that several Firmicutes were enriched in the dechlorinating cultures compared to triplicate controls amended with nonchlorinated xanthones. One such group, herein referred to as the Gopher group, was further studied with a novel qPCR method that confirmed enrichment of Gopher group 16S rRNA genes in the dechlorinating cultures. The enrichment of the Gopher group was again tested with two new sets of triplicate microcosms. Enrichment was observed during chlorinated xanthone dechlorination in one set of these triplicate microcosms. In the other set, two microcosms showed clear enrichment while a third did not. The Gopher group is a previously unidentified group of Firmicutes, distinct from but related to the Dehalobacter and Desulfitobacterium genera; this group also contains clones from at least four unique cultures capable of dechlorinating anthropogenic organochlorines that have been previously described in the literature. This study suggests that natural chlorinated xanthones may be effective biostimulants to enhance the remediation of pollutants and highlights the idea that novel genera of dechlorinators likely exist and may be active in bioremediation and the natural cycling of chlorine.

Dechlorination and organohalide-respiring bacteria dynamics in sediment samples of the Yangtze Three Gorges Reservoir

Several groups of bacteria such as Dehalococcoides spp., Dehalobacter spp., Desulfomonile spp., Desulfuromonas spp., or Desulfitobacterium spp. are able to dehalogenate chlorinated pollutants such as chloroethenes, chlorobenzenes, or polychlorinated biphenyls under anaerobic conditions. In order to assess the dechlorination potential in Yangtze sediment samples, the presence and activity of the reductively dechlorinating bacteria were studied in anaerobic batch tests. Eighteen sediment samples were taken in the Three Gorges Reservoir catchment area of the Yangtze River, including the tributaries Jialing River, Daning River, and Xiangxi River. Polymerase chain reaction analysis indicated the presence of dechlorinating bacteria in most samples, with varying dechlorinating microbial community compositions at different sampling locations. Subsequently, anaerobic reductive dechlorination of tetrachloroethene (PCE) was tested after the addition of electron donors. Most cultures dechlorinated PCE completely to ethene via cis-dichloroethene (cis-DCE) or trans-dichloroethene. Dehalogenating activity corresponded to increasing numbers of Dehalobacter spp., Desulfomonile spp., Desulfitobacterium spp., or Dehalococcoides spp. If no bacteria of the genus Dehalococcoides spp. were present in the sediment, reductive dechlorination stopped at cis-DCE. Our results demonstrate the presence of viable dechlorinating bacteria in Yangtze samples, indicating their relevance for pollutant turnover.

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.

Inhibition of biological TCE and sulphate reduction in the presence of iron nanoparticles

Iron (Fe) nanoparticles are increasingly being employed for the remediation of Chlorinated Aliphatic Hydrocarbon (CAH) contaminated sites. However, these particles have recently been reported to be cytotoxic to bacterial cells, and may therefore have a negative impact on exposed microbial communities. The overall objective of this study was to investigate the impact of Fe nanoparticles on the biodegradation of CAHs by an indigenous dechlorinating bacterial community. Also, to determine the most appropriate combination and/or application of bimetallic (Ni/Fe) nanoparticles and dechlorinating bacteria for the remediation of CAH contaminated sites. Addition of Fe nanoparticles to groundwater collected from a CAH contaminated site in Derby, UK, led to a decrease in the oxidation-reduction potential (ORP) and an increase in pH. The biological degradation rate of TCE was observed to progressively decrease in the presence of increasing Fe nanoparticle concentrations; which ranged from 0.01 to 0.1 gL(-1), and cease completely at concentrations of 0.3 gL(-1) or above. Concentrations greater than 0.3 gL(-1) led to a decline in viable bacterial counts and the inhibition of biological sulphate reduction. The most appropriate means of combining bimetallic (Ni/Fe) nanoparticles and indigenous dechlorinating bacteria was to employ a two step process: initially stimulating the biodegradation of TCE using acetate, followed by the addition of bimetallic nanoparticles to degrade the remaining cis-1,2-DCE and VC.

Addressing PCR biases in environmental microbiology studies

Each step of a molecular environmental microbiology study is prone to errors, though the qualitative and quantitative biases of PCR amplification could result in the most serious biases. One has to be aware of this fact, and well-characterized PCR biases have to be avoided by using target-optimized PCR protocols. The most important tasks are primer and thermal profile optimization. We have shown that primer mismatches, even in the case of universal primers, can cause almost complete missing of common taxa from clone libraries, for example. Similarly high annealing temperatures can drastically distort community composition of the sample in the PCR product. Strategies of primer selection and PCR thermal profile design are discussed in detail.

A review on slurry bioreactors for bioremediation of soils and sediments

The aim of this work is to present a critical review on slurry bioreactors (SB) and their application to bioremediation of soils and sediments polluted with recalcitrant and toxic compounds. The scope of the review encompasses the following subjects: (i) process fundamentals of SB and analysis of advantages and disadvantages; (ii) the most recent applications of SB to laboratory scale and commercial scale soil bioremediation, with a focus on pesticides, explosives, polynuclear aromatic hydrocarbons, and chlorinated organic pollutants; (iii) trends on the use of surfactants to improve availability of contaminants and supplementation with degradable carbon sources to enhance cometabolism of pollutants; (iv) recent findings on the utilization of electron acceptors other than oxygen; (v) bioaugmentation and advances made on characterization of microbial communities of SB; (vi) developments on ecotoxicity assays aimed at evaluating bioremediation efficiency of the process.From this review it can be concluded that SB is an effective ad situ and ex situ technology that can be used for bioremediation of problematic sites, such as those characterized by soils with high contents of clay and organic matter, by pollutants that are recalcitrant, toxic, and display hysteretic behavior, or when bioremediation should be accomplished in short times under the pressure and monitoring of environmental agencies and regulators. SB technology allows for the convenient manipulation and control of several environmental parameters that could lead to enhanced and faster treatment of polluted soils: nutrient N, P and organic carbon source (biostimulation), inocula (bioaugmentation), increased availability of pollutants by use of surfactants or inducing biosurfactant production inside the SB, etc. An interesting emerging area is the use of SB with simultaneous electron acceptors, which has demonstrated its usefulness for the bioremediation of soils polluted with hydrocarbons and some organochlorinated compounds. Characterization studies of microbial communities of SB are still in the early stages, in spite of their significance for improving reactor operation and design optimization.We have identified the following niches of research needs for SB in the near and mid term future, inter alia: (i) application of SB with sequential and simultaneous electron acceptors to soils polluted with contaminants other than hydrocarbons (i.e., pesticides, explosives, etc.), (ii) evaluation of the technical feasibility of triphasic SB that use innocuous solvents to help desorbing pollutants strongly attached to soils, and in turn, to enhance their biodegradation, (iii) gaining deeper insight of microbial communities present in SB with the intensified application of molecular biology tools such as PCR-DGGE, PCR-TGGE, ARDRA, etc., (iv) development of more representative ecotoxicological assays to better assess the effectiveness of a given bioremediation process.

Comparative analysis of three tetrachloroethene to ethene halorespiring consortia suggests functional redundancy

Three anaerobic, dechlorinating consortia were enriched from different sites using methanol and tetrachloroethene (PCE) and maintained for approximately 3 years. These consortia were evaluated using chemical species analysis including distribution of dechlorination products, production of organic acids and methane, and using qualitative and quantitative PCR (qPCR), terminal restriction fragment length polymorphism (TRFLP), and denaturing gradient gel electrophoresis (DGGE) with primers specific to Dehalococcoides 16S rRNA gene sequences. TRFLP and analysis of organic acids revealed differing fermentative populations in each consortium, which were dominated by acetogens. Monitoring methane production combined with qPCR for archaea showed that complete dechlorination of PCE-to-ethene occurred in the presence and absence of methanogens. The 16S rRNA gene-based analyses demonstrated that enrichment with PCE resulted in dechlorinating communities dominated by Dehalococcoides and Dehalobacter, and that up to four different PCE-dechlorinating organisms coexisted in one consortium. Further, the DGGE analysis suggested that at least one consortium contained multiple Dehalococcoides strains. The combined analysis of 16S rRNA and reductive dehalogenase genes suggested that one consortium contained a member of the Dehalococcoides "Cornell" group with the ability to respire VC.

The Dehalococcoides population in sediment-free mixed cultures metabolically dechlorinates the commercial polychlorinated biphenyl mixture aroclor 1260

Microbial reductive dechlorination of commercial polychlorinated biphenyl (PCB) mixtures (e.g., Aroclors) in aquatic sediments is crucial to achieve detoxification. Despite extensive efforts over nearly two decades, the microorganisms responsible for Aroclor dechlorination remained elusive. Here we demonstrate that anaerobic bacteria of the Dehalococcoides group derived from sediment of the Housatonic River (Lenox, MA) simultaneously dechlorinate 64 PCB congeners carrying four to nine chlorines in Aroclor 1260 in the sediment-free JN cultures. Quantitative real-time PCR showed that the Dehalococcoides cell titer in JN cultures amended with acetate and hydrogen increased from 7.07 x 10(6) +/- 0.42 x 10(6) to 1.67 x 10(8) +/- 0.04 x 10(8) cells/ml, concomitant with a 64.2% decrease of the PCBs with six or more chlorines in Aroclor 1260. No Dehalococcoides growth occurred in parallel cultures without PCBs. Aroclor 1260 dechlorination supported the growth of 9.25 x 10(8) +/- 0.04 x 10(8) Dehalococcoides cells per mumol of chlorine removed. 16S rRNA gene-targeted PCR analysis of known dechlorinators (i.e., Desulfitobacterium, Dehalobacter, Desulfuromonas, Sulfurospirillum, Anaeromyxobacter, Geobacter, and o-17/DF-1-type Chloroflexi organisms) ruled out any involvement of these bacterial groups in the dechlorination. Our results suggest that the Dehalococcoides population present in the JN cultures also catalyzes in situ dechlorination of Aroclor 1260 in the Housatonic River. The identification of Dehalococcoides organisms as catalysts of extensive Aroclor 1260 dechlorination and our ability to propagate the JN cultures under defined conditions offer opportunities to study the organisms' ecophysiology, elucidate nutritional requirements, identify reductive dehalogenase genes involved in PCB dechlorination, and design molecular tools required for bioremediation applications.

The Desulfitobacterium genus

Desulfitobacterium spp. are strictly anaerobic bacteria that were first isolated from environments contaminated by halogenated organic compounds. They are very versatile microorganisms that can use a wide variety of electron acceptors, such as nitrate, sulfite, metals, humic acids, and man-made or naturally occurring halogenated organic compounds. Most of the Desulfitobacterium strains can dehalogenate halogenated organic compounds by mechanisms of reductive dehalogenation, although the substrate spectrum of halogenated organic compounds varies substantially from one strain to another, even with strains belonging to the same species. A number of reductive dehalogenases and their corresponding gene loci have been isolated from these strains. Some of these loci are flanked by transposition sequences, suggesting that they can be transmitted by horizontal transfer via a catabolic transposon. Desulfitobacterium spp. can use H2 as electron donor below the threshold concentration that would allow sulfate reduction and methanogenesis. Furthermore, there is some evidence that syntrophic relationships occur between Desulfitobacterium spp. and sulfate-reducing bacteria, from which the Desulfitobacterium cells acquire their electrons by interspecies hydrogen transfer, and it is believed that this relationship also occurs in a methanogenic consortium. Because of their versatility, desulfitobacteria can be excellent candidates for the development of anaerobic bioremediation processes. The release of the complete genome of Desulfitobacterium hafniense strain Y51 and information from the partial genome sequence of D. hafniense strain DCB-2 will certainly help in predicting how desulfitobacteria interact with their environments and other microorganisms, and the mechanisms of actions related to reductive dehalogenation.

Diverse bacteria associated with root nodules of spontaneous legumes in Tunisia and first report for nifH-like gene within the genera Microbacterium and Starkeya

We characterized 34 endophytic bacterial isolates associated to root nodules collected from spontaneous legumes in the arid zone of Tunisia by 16S rDNA polymerase chain reaction (PCR)-restriction fragment length polymorphism, whole cell protein sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), 16S rDNA and 16S-23S rDNA internal transcribed spacer sequencing. Phylogenetically, these isolates belong to the branches containing the genera Inquilinus, Bosea, Rhodopseudomonas, Paracraurococcus, Phyllobacterium, Ochrobactrum, Starkeya, Sphingomonas, Pseudomonas, Agromyces, Microbacterium, Ornithinicoccus, Bacillus, and Paenibacillus. These strains did not induce any nodule formation when inoculated on the wide host spectrum legume species M. atropurpureum (Siratro) and no nodA gene could be amplified by PCR. However, nifH sequences, most similar to those of Sinorhizobium meliloti, were detected within strains related to the genera Microbacterium, Agromyces, Starkeya and Phyllobacterium.

1,1-dichloroethene as a predominant intermediate of microbial trichloroethene reduction

A microbial culture derived from a landfill site in Dover, DE consistently reduced trichloroethene (TCE) to ethene through 1,1-dichloroethene (DCE) as a dominant intermediate in the presence of ampicillin. A constant 1,1-DCE-to-cis-DCE ratio of 2.4 +/- 0.3 was observed for more than two years, while trans-DCE was never detected. Without ampicillin, however, TCE was reduced to ethene almost exclusively through cis-DCE, suggesting that the culture contained at leasttwo TCE-dechlorinating populations. Two subcultures, which were established using 1,1-DCE or vinyl chloride as an electron acceptor, exhibited the same 1,1-DCE-to-cis-DCE ratio when TCE was introduced. PCR amplification of 16S rRNA gene followed by sequencing and DGGE analysis indicate that these (sub)cultures contained a Dehalococcoides population(s). TCE dechlorination assays with crude cell extract showed a DCE distribution pattern similar to that with whole cells. The enzyme involved in 1,1-DCE formation was likely a cobalt corrinoid enzyme, as suggested by the inhibitory effect of CH3I and photoreversibility of the inhibition. This study provides a possible biological mechanism forthe occurrence of 1,1-DCE in TCE-contaminated sites.

Diversity of microorganisms in Fe-As-rich acid mine drainage waters of Carnoulès, France

The acid waters (pH 2.7 to 3.4) originating from the Carnoulès mine tailings contain high concentrations of dissolved arsenic (80 to 350 mg.liter(-1)), iron (750 to 2,700 mg.liter(-1)), and sulfate (2,000 to 7,500 mg.liter(-1)). During the first 30 m of downflow in Reigous creek issuing from the mine tailings, 20 to 60% of the dissolved arsenic is removed by coprecipitation with Fe(III). The microbial communities along the creek have been characterized using terminal-restriction fragment length polymorphism (T-RFLP) and 16S rRNA gene library analyses. The results indicate a low bacterial diversity in comparison with unpolluted water. Eighty percent of the sequences obtained are related to sequences from uncultured, newly described organisms or recently associated with acid mine drainage. As expected owing to the water chemistry, the sequences recovered are mainly related to bacteria involved in the geochemical Fe and S cycles. Among them, sequences related to uncultured TrefC4 affiliated with Gallionella ferruginea, a neutrophilic Fe-oxidizing bacterium, are dominant. The description of the bacterial community structure and its dynamics lead to a better understanding of the natural remediation processes occurring at this site.

Effects of endogenous substrates on adaptation of anaerobic microbial communities to 3-chlorobenzoate

Lengthy adaptation periods in laboratory studies evaluating the potential for contaminant biodegradation in natural or engineered environments may indicate that the native microbial communities are not metabolizing the contaminants in situ. In this study, we characterized the adaptation period preceding the biodegradation of 3-chlorobenzoate in anaerobic communities derived from lake sediment and wastewater sludge digesters. The importance of alternative mechanisms of adaptation of the anaerobic communities to 3-chlorobenzoate was evaluated by monitoring the concentrations of metabolic substrates and products as well as the levels of total small subunit (SSU) rRNA and SSU rRNA from populations thought to be important in 3-chlorobenzoate mineralization. The anaerobic environments from which the 3-chlorobenzoate-degrading communities were derived contained different levels of endogenous substrates. Increasing methane levels in the digester and sediment communities and decreasing chemical oxygen demand concentrations in the sediment community during the adaptation periods revealed that endogenous substrates were preferentially utilized relative to 3-chlorobenzoate. Methane and chemical oxygen demand concentrations leveled off concomitantly with the onset of 3-chlorobenzoate biodegradation, suggesting that depletion of the preferentially degraded endogenous substrates stimulated 3-chlorobenzoate metabolism. Consistent with these observations, adaptation to 3-chlorobenzoate occurred more rapidly in digester samples that were depleted of endogenous substrates compared to samples that contained high levels of these biodegradable compounds. Other potential adaptation mechanisms, e.g., genetic change or selective population enrichment, appeared to be less important based on the reproducibility and relative lengths of the adaptation events, trends in the SSU rRNA levels, and/or amplification of SSU rRNA genes from key populations.

Loop-mediated isothermal amplification method for rapid detection of the periodontopathic bacteria Porphyromonas gingivalis, Tannerella forsythia, and Treponema denticola

Loop-mediated isothermal amplification (LAMP), a novel nucleic acid amplification method, was developed for the rapid detection of the major periodontal pathogens Porphyromonas gingivalis, Tannerella forsythia, and Treponema denticola. The LAMP method amplifies DNA with high specificity, efficiency, and rapidity under isothermal conditions using a set of four specially designed primers and a DNA polymerase with strand displacement activity. In this study, we initially designed the primers for LAMP assays to detect these bacteria and evaluated the specificity and sensitivity of these assays. The specificities of the primers for these bacteria were examined using various oral bacteria and various reaction times. The lower detection limits of the 60-min LAMP reaction without loop primers were 1 microg/tube for P. gingivalis, 10 fg/tube for T. forsythia, and 1 ng/tube for T. denticola. Addition of the loop primers for each bacterium improved the detection specificities and sensitivities by several magnitudes. Furthermore, LAMP assays were applied to the rapid detection of these periodontal pathogens in clinical specimens, and the results were compared with those of conventional PCR detection. The results of the LAMP assays corresponded to those of conventional PCR assays. These results indicate that the LAMP assay is an extremely rapid, highly sensitive, specific method. This method is very useful for the rapid detection of periodontopathic bacteria and the diagnosis of periodontal disease.

Nested PCR-denaturing gradient gel electrophoresis approach to determine the diversity of sulfate-reducing bacteria in complex microbial communities

Here, we describe a three-step nested-PCR-denaturing gradient gel electrophoresis (DGGE) strategy to detect sulfate-reducing bacteria (SRB) in complex microbial communities from industrial bioreactors. In the first step, the nearly complete 16S rRNA gene was amplified using bacterial primers. Subsequently, this product was used as a template in a second PCR with group-specific SRB primers. A third round of amplification was conducted to obtain fragments suitable for DGGE. The largest number of bands was observed in DGGE patterns of products obtained with primers specific for the Desulfovibrio-Desulfomicrobium group, indicating a large diversity of these SRBs. In addition, members of other phylogenetic SRB groups, i.e., Desulfotomaculum, Desulfobulbus, and Desulfococcus-Desulfonema-Desulfosarcina, were detected. Bands corresponding to Desulfobacterium and Desulfobacter were not detected in the bioreactor samples. Comparative sequence analysis of excised DGGE bands revealed the identity of the community members. The developed three-step PCR-DGGE strategy is a welcome tool for studying the diversity of sulfate-reducing bacteria.

Enrichment, cultivation, and detection of reductively dechlorinating bacteria

Strategies and procedures for enriching, isolating, and cultivating reductively dechlorinating bacteria that use chloroorganic compounds as metabolic electron acceptors from environmental samples are described. Further, nucleic acid-based approaches used to detect and quantify dechlorinator (i.e., Dehalococcoides)-specific genes are presented.

Populations implicated in anaerobic reductive dechlorination of 1,2-dichloropropane in highly enriched bacterial communities

1,2-Dichloropropane (1,2-D), a widespread groundwater contaminant, can be reductively dechlorinated to propene by anaerobic bacteria. To shed light on the populations involved in the detoxification process, a comprehensive 16S rRNA gene-based bacterial community analysis of two enrichment cultures derived from geographically distinct locations was performed. Analysis of terminal restriction fragments, amplicons obtained with dechlorinator-specific PCR primers, and enumeration with quantitative real-time PCR as well as screening clone libraries all implied that Dehalococcoides populations were involved in 1,2-D dechlorination in both enrichment cultures. Physiological traits (e.g., dechlorination in the presence of ampicillin and a requirement for hydrogen as the electron donor) supported the involvement of Dehalococcoides populations in the dechlorination process. These findings expand the spectrum of chloroorganic compounds used by Dehalococcoides species as growth-supporting electron acceptors. The combined molecular approach allowed a comparison between different 16S rRNA gene-based approaches for the detection of Dehalococcoides populations.

Development of a real-time PCR method for quantification of the three genera Dehalobacter, Dehalococcoides, and Desulfitobacterium in microbial communities

We developed standard curves based on plasmids containing a 16S rRNA gene of a member of one of the three genera Dehalobacter, Desulfitobacterium, and Dehalococcoides. A large difference in amplification efficiency between the standard curves was observed ranging from 1.5 to 2.0. The total eubacterial 16S rRNA gene copy number determined in a sample DNA by using eubacterial primers and the three standard curves led to differences in the estimated copy numbers of a factor up to 73. However, the amplification efficiencies for one specific standard curve were the same independent of the PCR primer pair used. This allowed the determination of the abundance of a population expressed as fractional number, hence, the percentage of genus-specific copy numbers within the total eubacterial 16S rRNA gene copy numbers. Determination of the fractional numbers in DNA mixtures of known composition showed the accuracy of this approach. The average difference in threshold value between two 10-fold dilutions of DNA of pure cultures, mixtures thereof and of environmental samples was -3.45+/-0.34, corresponding to an average almost optimal amplification efficiency of 1.95. This indicated that the low amplification efficiency of certain standard curves seemed to be mainly a problem of the plasmid DNA used and not of the 16S rRNA gene of the target genera.

Development of degenerate and specific PCR primers for the detection and isolation of known and putative chloroethene reductive dehalogenase genes

Degenerate and specific PCR primers were designed for the detection of chloroethene reductive dehalogenases (CE-RDase), the key enzymes of chloroethene dehalorespiration, based on sequence information of three CE-RDases and three chlorophenol (CP) RDases. For the design of the degenerate primers, seven conserved amino-acid blocks identified with different bioinformatic tools were used. For one block degenerate, primers containing a 5'-consensus clamp region specific for CE-RDases and a 3'-end degenerate core region specific for RDases in general were designed using the Consensus-Degenerate Hybrid Oligonucleotide Primer (CDHOP) design method. Applying the degenerate primers to genomic DNA of Sulfurospirillum multivorans strain K, Dehalobacter restrictus strain PER-K23, and Desulfitobacterium sp. strain PCE1 led to the isolation of the known CE-RDase genes and three new genes encoding putative reductive dehalogenases that cluster with CE-RDases and not with CP-RDases. In addition, primers designed to be specific for the three known CE-RDase genes, namely pceA of S. multivorans, pceA of D. restrictus, and tceA of Dehalococcoides ethenogenes were successfully tested on genomic DNA of different chloroethene-dehalorespiring bacteria. Nested PCR using degenerate primers followed by a PCR with specific primers allowed a sensitive detection of only 10(2) copies per reaction.

Geographic distribution of Desulfitobacterium frappieri PCP-1 and Desulfitobacterium spp. in soils from the province of Quebec, Canada

The presence of indigenous Desulfitobacterium species in 44 soil samples taken from various sites in the southern part of the province of Quebec (Canada) and four from locations outside Quebec was investigated. Twenty-four of these soils were sampled from contaminated industrial sites. Indigenous Desulfitobacterium bacteria from soil samples were enriched by cultivation in anaerobic soil slurry culture. Total DNA was then extracted from these slurries and polymerase chain reaction (PCR) amplifications were performed with primers targeting 16S ribosomal RNA gene sequences of Desulfitobacterium spp. and of Desulfitobacterium frappieri PCP-1. A positive PCR signal was obtained in 31 soil slurry cultures. Resolution of single-strand DNAs of some of the PCR products by a single-strand conformational polymorphism protocol suggests that more than one species of Desulfitobacterium were present in the corresponding slurry cultures. These results suggest that Desulfitobacterium are ubiquitous in soils in the province of Quebec, especially in soils from the St. Lawrence valley and the southern part of the province.

Monitoring of Desulfitobacterium frappieri PCP-1 in pentachlorophenol-degrading anaerobic soil slurry reactors

Anaerobic biodegradation of pentachlorophenol (PCP) was studied in rotative bioreactors containing 200 g of PCP-contaminated soil and 250 ml of liquid medium. Reactors were bioaugmented with cells of Desulfitobacterium frappieri strain PCP-1, a bacterium able to dehalogenate PCP to 3-chlorophenol. Cells of strain PCP-1 were detected by quantitative PCR for at least 21 days in reactors containing 500 mg of PCP per kg of soil but disappeared after 21 days in reactors with 750 mg of PCP per kg of soil. Generally, PCP was completely removed in less than 9 days in soils contaminated with 189 mg of PCP per kg of soil. Sorption of PCP to soil organic matter reduced its toxicity and enhanced the survival of strain PCP-1. In some non-inoculated reactors, the indigenous microorganisms of some soils were also able to degrade PCP. These results suggest that anaerobic dechlorination of PCP in soils by indigenous PCP-degrading bacteria, or after augmentation with D. frappieri PCP-1, should be possible in situ and ex situ when the conditions are favourable for the survival of the degrading microorganisms.

Halorespiring bacteria-molecular characterization and detection

Recently, a rapidly increasing number of bacteria has been isolated that is able to couple the reductive dehalogenation of various halogenated aromatic and aliphatic compounds like chlorophenols and tetrachloroethene to energy conservation by electron-transport-coupled phosphorylation. The potential of these halorespiring bacteria for innovative clean-up strategies of polluted anoxic environments has greatly stimulated efforts to unravel the molecular basis of the novel respiratory chains they possess. The thorough characterization of halorespiratory key components at the physiological, biochemical and molecular genetic level has revealed both structural and functional similarity of chloroaryl- and chloroalkyl-respiratory chains from different phylogenetically distinct microorganisms. The reductive dehalogenases from halorespiring bacteria were found to comprise a novel class of corrinoid-containing Fe/S-proteins. Sensitive molecular methods for monitoring both presence and fate of halorespiring bacteria have been developed, which will be instrumental for the design and maintenance of optimised in situ bioremediation processes.

Influence of different electron donors and acceptors on dehalorespiration of tetrachloroethene by Desulfitobacterium frappieri TCE1

Strain TCE1, a strictly anaerobic bacterium that can grow by reductive dechlorination of tetrachloroethene (PCE) and trichloroethene (TCE), was isolated by selective enrichment from a PCE-dechlorinating chemostat mixed culture. Strain TCE1 is a gram-positive, motile, curved rod-shaped organism that is 2 to 4 by 0.6 to 0.8 microm and has approximately six lateral flagella. The pH and temperature optima for growth are 7.2 and 35 degrees C, respectively. On the basis of a comparative 16S rRNA sequence analysis, this bacterium was identified as a new strain of Desulfitobacterium frappieri, because it exhibited 99.7% relatedness to the D. frappieri type strain, strain PCP-1. Growth with H(2), formate, L-lactate, butyrate, crotonate, or ethanol as the electron donor depends on the availability of an external electron acceptor. Pyruvate and serine can also be used fermentatively. Electron donors (except formate and H(2)) are oxidized to acetate and CO(2). When L-lactate is the growth substrate, strain TCE1 can use the following electron acceptors: PCE and TCE (to produce cis-1,2-dichloroethene), sulfite and thiosulfate (to produce sulfide), nitrate (to produce nitrite), and fumarate (to produce succinate). Strain TCE1 is not able to reductively dechlorinate 3-chloro-4-hydroxyphenylacetate. The growth yields of the newly isolated bacterium when PCE is the electron acceptor are similar to those obtained for other dehalorespiring anaerobes (e.g., Desulfitobacterium sp. strain PCE1 and Desulfitobacterium hafniense) and the maximum specific reductive dechlorination rates are 4 to 16 times higher (up to 1.4 micromol of chloride released. min(-1). mg of protein(-1)). Dechlorination of PCE and TCE is an inducible process. In PCE-limited chemostat cultures of strain TCE1, dechlorination is strongly inhibited by sulfite but not by other alternative electron acceptors, such as fumarate or nitrate.

Analysis of nifH gene pool complexity in soil and litter at a Douglas fir forest site in the Oregon cascade mountain range

Nitrogen-fixing microbial populations in a Douglas fir forest on the western slope of the Oregon Cascade Mountain Range were analyzed. The complexity of the nifH gene pool (nifH is the marker gene which encodes nitrogenase reductase) was assessed by performing nested PCR with bulk DNA extracted from plant litter and soil. The restriction fragment length polymorphisms (RFLPs) of PCR products obtained from litter were reproducibly different than the RFLPs of PCR products obtained from the underlying soil. The characteristic differences were found during the entire sampling period between May and September. RFLP analyses of cloned nifH PCR products also revealed characteristic patterns for each sample type. Among 42 nifH clones obtained from a forest litter library nine different RFLP patterns were found, and among 64 nifH clones obtained from forest soil libraries 13 different patterns were found. Only two of the patterns were found in both the litter and the soil, indicating that there were major differences between the nitrogen-fixing microbial populations. A sequence analysis of clones representing the 20 distinct patterns revealed that 19 of the patterns had a proteobacterial origin. All of the nifH sequences obtained from the Douglas fir forest litter localized in a distinct phylogenetic cluster characterized by the nifH sequences of members of the genera Rhizobium, Sinorhizobium, and Azospirillum. The nifH sequences obtained from soil were found in two additional clusters, one characterized by sequences of members of the genera Bradyrhizobium, Azorhizobium, Herbaspirillum, and Thiobacillus and the other, represented by a single nifH clone, located between the gram-positive bacteria and the cyanobacteria. Our results revealed the distinctness of the nitrogen-fixing microbial populations in litter and soil in a Douglas fir forest; the differences may be related to special requirements for degradation and mineralization processes in the plant litter.