Environmentally relevant microorganisms

An Environmental Friendly Perspective of Microbial Degradation

In the recent years attempt to find cost-effective and ecological ways to deal with noxious waste led mankind to focus on the use of microbes for the degradation of pollutants. These environmental friendly remediation methods employs the microbial naturally occurring catabolic capabilities to alter, vitiate or accrue a large number of pollutants including poly aromatic hydrocarbons, polychlorinated biphenyls, radio nuclides ,heavy metals etc. High-through put analyses of environmentally relevant microbes provides an insight of their major degradative pathways as well as their competence to acclimate to altering environmental conditions.

The role of operating parameters and oxidative damage mechanisms of advanced chemical oxidation processes in the combat against antibiotic-resistant bacteria and resistance genes present in urban wastewater

An upsurge in the study of antibiotic resistance in the environment has been observed in the last decade. Nowadays, it is becoming increasingly clear that urban wastewater is a key source of antibiotic resistance determinants, i.e. antibiotic-resistant bacteria and antibiotic resistance genes (ARB&ARGs). Urban wastewater reuse has arisen as an important component of water resources management in the European Union and worldwide to address prolonged water scarcity issues. Especially, biological wastewater treatment processes (i.e. conventional activated sludge), which are widely applied in urban wastewater treatment plants, have been shown to provide an ideal environment for the evolution and spread of antibiotic resistance. The ability of advanced chemical oxidation processes (AOPs), e.g. light-driven oxidation in the presence of H₂O₂, ozonation, homogeneous and heterogeneous photocatalysis, to inactivate ARB and remove ARGs in wastewater effluents has not been yet evaluated through a systematic and integrated approach. Consequently, this review seeks to provide an extensive and critical appraisal on the assessment of the efficiency of these processes in inactivating ARB and removing ARGs in wastewater effluents, based on recent available scientific literature. It tries to elucidate how the key operating conditions may affect the process efficiency, while pinpointing potential areas for further research and major knowledge gaps which need to be addressed. Also, this review aims at shedding light on the main oxidative damage pathways involved in the inactivation of ARB and removal of ARGs by these processes. In general, the lack and/or heterogeneity of the available scientific data, as well as the different methodological approaches applied in the various studies, make difficult the accurate evaluation of the efficiency of the processes applied. Besides the operating conditions, the variable behavior observed by the various examined genetic constituents of the microbial community, may be directed by the process distinct oxidative damage mechanisms in place during the application of each treatment technology. For example, it was shown in various studies that the majority of cellular damage by advanced chemical oxidation may be on cell wall and membrane structures of the targeted bacteria, leaving the internal components of the cells relatively intact/able to repair damage. As a result, further in-depth mechanistic studies are required, to establish the optimum operating conditions under which oxidative mechanisms target internal cell components such as genetic material and ribosomal structures more intensively, thus conferring permanent damage and/or death and preventing potential post-treatment re-growth.

Potential of plant growth promoting traits by bacteria isolated from heavy metal contaminated soils

Rhizobacteria can enhance biomass production and heavy metal tolerance of plants under the stress environment. The aim of this study was to collect soil samples from different industrial sites followed by their heavy metal analysis. After performing the ICP-AES analysis of soil samples from seven different sites, bacterial strains were isolated from the soil samples of most polluted (heavy metal) site. Phylogenetic analysis of isolates based on 16S rDNA sequences showed that the isolates belonged to four species: Bacillus thuringiensis, Azotobacter chroococcum, Paenibacillus ehimensis and Pseudomonas pseudoalcaligenes. Plant growth promoting activities; siderophore production, indole acetic acid production, HCN production, and phosphate solubilisation were assayed in vitro, and statistically analysis done by using ANOVA analysis and Tukey's Honestly Significant Difference test (p ≤ 0.05). Plant growth-promoting characteristics of isolated strains were higher compared to the control Pseudomonas fluorescens (NICM 5096). In vitro study was performed to check resistance against two heavy metals of isolates. It was observed that isolated bacterial strains have higher heavy metal resistance as compared to control E. coli (NICM 2563). These isolates may cause pathogenic effects, so to avoid this risk, their antibacterial susceptibility was checked against eight antibiotics. Among the eight antibiotics, Ciprofloxacin-1 has shown higher inhibition against all the isolated bacterial strains.

Microbial interspecies interactions: recent findings in syntrophic consortia

Microbes are ubiquitous in our biosphere, and inevitably live in communities. They excrete a variety of metabolites and support the growth of other microbes in a community. According to the law of chemical equilibrium, the consumption of excreted metabolites by recipient microbes can accelerate the metabolism of donor microbes. This is the concept of syntrophy, which is a type of mutualism and governs the metabolism and growth of diverse microbes in natural and engineered ecosystems. A representative example of syntrophy is found in methanogenic communities, where reducing equivalents, e.g., hydrogen and formate, transfer between syntrophic partners. Studies have revealed that microbes involved in syntrophy have evolved molecular mechanisms to establish specific partnerships and interspecies communication, resulting in efficient metabolic cooperation. In addition, recent studies have provided evidence suggesting that microbial interspecies transfer of reducing equivalents also occurs as electric current via biotic (e.g., pili) and abiotic (e.g., conductive mineral and carbon particles) electric conduits. In this review, we describe these findings as examples of sophisticated cooperative behavior between different microbial species. We suggest that these interactions have fundamental roles in shaping the structure and activity of microbial communities.

Biosorption of arsenic (III) from aqueous solution by living cells of Bacillus cereus

In this work, removal of arsenic (III) from aqueous solution by living cells (Bacillus cereus), biosorption mechanism, and characterization studies have been reported. B. cereus cell surface was characterized using SEM-EDX and FTIR. Dependence of biosorption on pH of the solution, biosorbent dose, initial arsenic (III) concentration, contact time, and temperature had been studied to achieve optimum condition. The maximum biosorption capacity of living cells of B. cereus for arsenic (III) was found to be 32.42 mg/g at pH 7.5, at optimum conditions of contact time of 30 min, biomass dosage of 6 g/L, and temperature of 30 ± 2 °C. Biosorption data of arsenic (III) are fitted to linearly transformed Langmuir isotherm with R (2) (correlation coefficient) >0.99. The pseudo-second-order model description of the kinetics of arsenic (III) is successfully applied to predict the rate constant of biosorption. Thermodynamic parameters reveal the endothermic, spontaneous, and feasible nature of sorption process of arsenic (III) onto B. cereus biomass. The arsenic (III) ions are desorbed from B. cereus using both 1 M HCl and 1 M HNO(3).

Decolorization of adsorbed textile dyes by developed consortium of Pseudomonas sp. SUK1 and Aspergillus ochraceus NCIM-1146 under solid state fermentation

The objective of this study was to develop consortium using Pseudomonas sp. SUK1 and Aspergillus ochraceus NCIM-1146 to decolorize adsorbed dyes from textile effluent wastewater under solid state fermentation. Among various agricultural wastes rice bran showed dye adsorption up to 90, 62 and 80% from textile dye reactive navy blue HE2R (RNB HE2R) solution, mixture of textile dyes and textile industry wastewater, respectively. Pseudomonas sp. SUK1 and A. ochraceus NCIM-1146 showed 62 and 38% decolorization of RNB HE2R adsorbed on rice bran in 24h under solid state fermentation. However, the consortium of Pseudomonas sp. SUK1 and A. ochraceus NCIM-1146 (consortium-PA) showed 80% decolorization in 24h. The consortium-PA showed effective ADMI removal ratio of adsorbed dyes from textile industry wastewater (77%), mixture of textile dyes (82%) and chemical precipitate of textile dye effluent (CPTDE) (86%). Secretion of extracellular enzymes such as laccase, azoreductase, tyrosinase and NADH-DCIP reductase and their significant induction in the presence of adsorbed dye suggests their role in the decolorization of RNB HE2R. GCMS and HPLC analysis of product suggests the different fates of biodegradation of RNB HE2R when used Pseudomonas sp. SUK1, A. ochraceus NCIM-1146 and consortium PA.

Communal action of microbial cultures for Red HE3B degradation

The consortium PMB11 consisting of three bacterial species, originally isolated from dye contaminated soil was identified as Bacillus odysseyi SUK3, Morganella morganii SUK5 and Proteus sp. SUK7. The consortium possessed the ability to decolorize various textile dyes as well as mixtures of dyes. PMB11 could decolorize Red HE3B (50 mg l(-1)) with 99% of decolorization within 12 h in nutrient broth, while in mineral medium it could decolorize up to 97% within 24h. Induction in the activities of various oxidative and reductive enzymes indicates the involvement of these enzymes in decolorization. Biodegradation of the dye was monitored using UV-vis spectroscopy, HPLC and FTIR analysis. The Red HE3B degradation pathway was proposed by GC-MS analysis. Various metabolites formed after the degradation were identified as 2,5-diaminobenzene 6-aminotriazine, aniline 2-sulfate, aniline 3-sulfate, 2-amino 5-chlorotriazine and naphthalene. Phytotoxicity studies revealed that metabolites formed after degradation were significantly less toxic in nature.

Bacterial community structure in soils contaminated by polycyclic aromatic hydrocarbons

Bacterial community structure was examined in polycyclic aromatic hydrocarbon (PAH) contaminated soil taken from a timber treatment facility in southern Ireland. Profiles of soil bacterial communities were generated using a molecular fingerprinting technique, terminal restriction fragment length polymorphism (TRFLP), and results were interpreted using sophisticated multivariate statistical analysis. Findings suggested that there was a correlation between PAH structure and bacterial community composition. Initial characterisation of soil from the timber treatment facility indicated that PAH contamination was unevenly distributed across the site. Bacterial community composition was correlated with the type of PAH present, with microbial community structure associated with soil contaminated with two-ringed PAHs only being distinctly different to communities in soils contaminated with multi-component PAH mixtures. Typically the number of bacterial ribotypes detected in samples did not appear to be adversely affected by the level of contamination.

Bioremediation of zinc using Desulfotomaculum nigrificans: bioprecipitation and characterization studies

Desulfotomaculum nigrificans, a typical sulfate reducing bacterium (SRB) was successfully grown in the presence of 12-210 mg/L of zinc. Complete bioremoval of zinc was achieved in 2 days for 12 mg/L while the bioremoval efficiency was about 70% in 40 days in the presence of 210 mg/L initial concentration of zinc, attesting to the inhibition of bacterial cell growth at higher zinc concentrations. The bioremoval mechanism was predominantly governed by bioprecipitation with biosorption contributing to a minor extent. The amount of protein present in the extracellular secretions obtained by growth of SRB in modified Baars' medium devoid of iron was the highest followed by those obtained in the presence of zinc or iron, in that order. Bioremediation studies carried out using a specially designed set-up, facilitating the transfer of biogenically produced hydrogen sulfide gas to a separate precipitation assembly, confirmed that zinc could be successfully precipitated from its corresponding sulfate solution, varying in concentration from 10 to 20,000 mg/L. Detailed characterization of the various zinc sulfide precipitates by EDAX and X-ray diffraction analysis conformed to wurtzite structure. The isoelectric points of high purity zinc sulfide and that of chemically synthesized, biogenically produced and zinc sulfide precipitated using bacterially produced hydrogen sulfide gas (BPH-ZnS) were located at pH 3, 7.8, 2.8 and 8, respectively.

Decolorization potential of mixed microbial consortia for reactive and disperse textile dyestuffs

Four different aerobic mixed consortia collected from basins of wastewater streams coming out of dying plants of Crescent Textile (CT), Sitara Textile (ST), Chenab Fabrics (CF) and Noor Fatima Textile (NF), Faisalabad, Pakistan were applied for decolorization of Drimarene Orange K-GL, Drimarene Brilliant Red K-4BL, Foron Yellow SE4G and Foron Blue RDGLN for 10 days using the shake flask technique. CT culture showed the best decolorization potential on all dyestuffs followed by ST, NF and CF, respectively. CT could completely decolorize all dyes within 3-5 days. ST cultures showed effective decolorization potential on Foron Yellow SE4G and Drimarene Brilliant Red K-4BL but complete color removal was achieved after 4 and 7 days, respectively. NF culture showed 100% decolorization efficiencies on Foron Yellow SE4G and Foron Blue RDGLN but it took comparatively longer time periods (5-7 days). Where as, the NF culture had decolorized only 40% and 50% of Drimarene orange and red, respectively, after 10 days. CF caused complete decolorization of Foron Blue RDGLN and Drimarene Brilliant Red K-4BL after 4 and 8 days, respectively but it showed poor performance on other two dyes.

Isolation of novel bacteria able to degrade alpha-halocarboxylic acids by enrichment from environmental samples

In order to isolate novel bacteria able to degrade alpha-halocarboxylic acids a variety of culturing strategies were implemented. Eight pure cultures were obtained and were found to be associated with the Gram negative Proteobacteria and the Gram positive Bacillus and Enterococcus genera. Furthermore, several strains were obtained which were able to degrade the DL-halocarboxylic acids anaerobically. Molecular analysis of the pure cultures led us to conclude that they may possess novel enzymes involved in the biodegradation of the alpha-halocarboxylic acids. These results are the first for nearly 40 years to describe the isolation of Gram positive isolates on an alpha-halocarboxylic acid as the sole source of carbon and energy, which also show the ability to de-toxify the test substrate by releasing chloride.

Effect of petrochemical sludge concentrations on microbial communities during soil bioremediation

Qualitative and quantitative changes of microbial communities in soil microcosms during bioremediation were determined throughout one year. The soil was contaminated with 0%, 2.5%, 5%, 10% (wt/wt) of petrochemical sludge containing polynuclear aromatic hydrocarbons. We analyzed the hydrocarbon concentration in the microcosms, the number of cultivable bacteria using CFU and most probable number assays, the community structure using denaturing gradient gel electrophoresis, and the metabolic activity of soil using dehydrogenase activity and substrate-induced respiration assays. After one year of treatment, the chemical analysis suggested that the hydrocarbon elimination process was over. The biological analysis, however, showed that the contaminated microcosms suffered under long-term disturbance. The number of heterotrophic bacteria that increased after sludge addition (up to 10(8)-10(9) cells ml(-1)) has not returned to the level of the control soil (2-6 x 10(7) cells ml(-1)). The community structure in the contaminated soils differed considerably from that in the control. The substrate-induced respiration of the contaminated soils was significantly lower (approximately 10-fold) and the dehydrogenase activity was significantly higher (20-40-fold) compared to the control. Changes in the community structure of soils depended on the amount of added sludge. The species, which were predominant in the sludge community, could not be detected in the contaminated soils.

Use of DNA-stable isotope probing and functional gene probes to investigate the diversity of methyl chloride-utilizing bacteria in soil

Enrichment and isolation of methyl chloride-utilizing bacteria from various terrestrial environments, including woodland and forest soils, resulted in the identification of seven methyl chloride-utilizing strains belonging to the genus Hyphomicrobium, an Aminobacter strain TW23 and strain WG1, which grouped closely with the genus Mesorhizobium. Methyl chloride enrichment cultures were dominated by Hyphomicrobium species, indicating that these bacteria were most suited to growth under the enrichment and isolation conditions used. However, the application of culture-independent techniques such as DNA-stable isotope probing and the use of a functional gene probe targeting cmuA, which encodes the methyltransferase catalysing the first step in bacterial methyl chloride metabolism, indicated a greater diversity of methyl chloride-utilizing bacteria in the terrestrial environment, compared with the diversity of soil isolates obtained via the enrichment and isolation procedure. It also revealed the presence of as yet uncultured and potentially novel methyl chloride-degrading bacteria in soil.

Monitoring of accelerated naphthalene-biodegradation in a bioaugmented soil slurry

The effect of microbial inoculation on the mineralization of naphthalene in a bioslurry treatment was evaluated in soil slurry microcosms. Inoculation by Pseudomonas putida G7 carrying the naphthalene dioxygenase (nahA) gene resulted in rapid mineralization of naphthalene, whereas indigenous microorganisms in the PAH-contaminated soil required a 28 h adaptation period before significant mineralization occurred. The number of nahA-like gene copies increased in both the inoculated and non-inoculated soil as mineralization proceeded, indicating selection towards naphthalene dioxygenase producing bacteria in the microbial community. In addition, 16S rRNA analysis by denaturing gradient gel electrophoresis (DGGE) analysis showed that significant selection occurred in the microbial community as a result of biodegradation. However, the indigenous soil bacteria were not able to compete with the P. putida G7 inoculum adapted to naphthalene biodegradation, even though the soil microbial community slightly suppressed naphthalene mineralization by P. putida G7.

Abundance of dioxygenase genes similar to Ralstonia sp. strain U2 nagAc is correlated with naphthalene concentrations in coal tar-contaminated freshwater sediments

We designed a real-time PCR assay able to recognize dioxygenase large-subunit gene sequences with more than 90% similarity to the Ralstonia sp. strain U2 nagAc gene (nagAc-like gene sequences) in order to study the importance of organisms carrying these genes in the biodegradation of naphthalene. Sequencing of PCR products indicated that this real-time PCR assay was specific and able to detect a variety of nagAc-like gene sequences. One to 100 ng of contaminated-sediment total DNA in 25-microl reaction mixtures produced an amplification efficiency of 0.97 without evident PCR inhibition. The assay was applied to surficial freshwater sediment samples obtained in or in close proximity to a coal tar-contaminated Superfund site. Naphthalene concentrations in the analyzed samples varied between 0.18 and 106 mg/kg of dry weight sediment. The assay for nagAc-like sequences indicated the presence of (4.1 +/- 0.7) x 10(3) to (2.9 +/- 0.3) x 10(5) copies of nagAc-like dioxygenase genes per microg of DNA extracted from sediment samples. These values corresponded to (1.2 +/- 0.6) x 10(5) to (5.4 +/- 0.4) x 10(7) copies of this target per g of dry weight sediment when losses of DNA during extraction were taken into account. There was a positive correlation between naphthalene concentrations and nagAc-like gene copies per microgram of DNA (r = 0.89) and per gram of dry weight sediment (r = 0.77). These results provide evidence of the ecological significance of organisms carrying nagAc-like genes in the biodegradation of naphthalene.

Cleaning up with genomics: applying molecular biology to bioremediation

Bioremediation has the potential to restore contaminated environments inexpensively yet effectively, but a lack of information about the factors controlling the growth and metabolism of microorganisms in polluted environments often limits its implementation. However, rapid advances in the understanding of bioremediation are on the horizon. Researchers now have the ability to culture microorganisms that are important in bioremediation and can evaluate their physiology using a combination of genome-enabled experimental and modelling techniques. In addition, new environmental genomic techniques offer the possibility for similar studies on as-yet-uncultured organisms. Combining models that can predict the activity of microorganisms that are involved in bioremediation with existing geochemical and hydrological models should transform bioremediation from a largely empirical practice into a science.

Comparing the dehalogenase gene pool in cultivated alpha-halocarboxylic acid-degrading bacteria with the environmental metagene pool

Culture-dependent and culture-independent approaches were used to determine the relationship between the dehalogenase gene pool in bacteria enriched and isolated on 2,2-dichloropropionic acid (22DCPA) and the environmental metagene pool (the collective gene pool of both the culturable and uncultured microbes) from which they were isolated. The dehalogenases in the pure-cultures isolates, which were able to degrade 22DCPA, were similar to previously described group I and II dehalogenases. Significantly, the majority of the dehalogenases isolated from activated sludge by degenerate PCR with primers specific for alpha-halocarboxylic acid dehalogenases were not closely related to the dehalogenases in any isolate. Furthermore, the dehalogenases found in the pure cultures predominated in the enrichments but were a minor component of the community used to inoculate the batch cultures. Phylogenetic analysis of the dehalogenase sequences isolated by degenerate PCR showed that the diversity of the group II deh gene was greater than that of the group I deh gene. Direct plating of the activated sludge onto minimal media supplemented with 22DCPA resulted in biomass and DNA from which dehalogenases were amplified. Analysis of the sequences revealed that they were much more closely related to the sequences found in the community used to start the enrichments. However, no pure cultures were obtained with this isolation method, and thus no pure cultures were available for identification. In this study we examined the link between genes found in pure cultures with the metagene pool from which they were isolated. The results show that there is a large bias introduced by culturing, not just in the bacteria isolated but also the degradative genes that they contain. Moreover, our findings serve as a caveat for studies involving the culturing of pure cultures of bacteria and conclusions which are drawn from analysis of these organisms.

Bioremediation of textile azo dyes by an aerobic bacterial consortium using a rotating biological contactor

The degradation of an azo dye mixture by an aerobic bacterial consortium was studied in a rotating biological reactor. Laterite pebbles of particle size 850 microm to 1.44 mm were fixed on gramophone records using an epoxy resin on which the developed consortium was immobilized. Rate of degradation, BOD, biomass determination, enzymes involved, and fish bioassay were studied. The RBC has a high efficiency for dye degradation even at high dye concentrations (100 microg/mL) and high flow rate (36 L/h) at alkaline pH and salinity conditions normally encountered in the textile effluents. Bioassays (LD-50) using Thilapia fish in treated effluent showed that the percentage mortality was zero over a period of 96 h, whereas the mortality was 100% in untreated dye water within 26 h. Fish bioassay confirms that the effluent from RBC can be discharged safely to the environment.

Linking genetics, physiology and ecology: an interdisciplinary approach for advancing bioremediation

Our understanding of microbial catabolic pathways relevant to bioremediation has been shaped by laboratory studies using isolated pollutant-degrading microorganisms. Recent investigations of natural microbial communities have, however, suggested that catabolic populations in the environment are much more diverse than those previously isolated in the laboratory. In addition, most laboratory strains are now thought to constitute minor populations in the environment, sharing only small contributions to bioremediation processes. Currently, attempts to isolate microorganisms that constitute major populations in the environment have been initiated with the aid of molecular ecological techniques. Such studies will provide information more directly relevant to the catabolic reactions occurring in bioremediation processes and are thus expected to help develop new strategies for advancing bioremediation. This article outlines our studies on phenol-degrading bacteria in activated sludge to illustrate a possible scheme of how genetic and physiological information obtained in the laboratory can be applied to advancing bioremediation processes.

Polycyclic aromatic hydrocarbons: environmental pollution and bioremediation

Polycyclic aromatic hydrocarbons (PAHs) are widely distributed and relocated in the environment as a result of the incomplete combustion of organic matter. Many PAHs and their epoxides are highly toxic, mutagenic and/or carcinogenic to microorganisms as well as to higher systems including humans. Although various physicochemical methods have been used to remove these compounds from our environment, they have many limitations. Xenobiotic-degrading microorganisms have tremendous potential for bioremediation but new modifications are required to make such microorganisms effective and efficient in removing these compounds, which were once thought to be recalcitrant. Metabolic engineering might help to improve the efficiency of degradation of toxic compounds by microorganisms. However, efficiency of naturally occurring microorganisms for field bioremediation could be significantly improved by optimizing certain factors such as bioavailability, adsorption and mass transfer. Chemotaxis could also have an important role in enhancing biodegradation of pollutants. Here, we discuss the problems of PAH pollution and PAH degradation, and relevant bioremediation efforts.

Hypergastrinemia in response to gastric inflammation suppresses somatostatin

Hypergastrinemia and a reduction in tissue somatostatin occur in Helicobacter pylori-infected patients. We investigated whether the D cell may be a direct target of gastric inflammation and hypergastrinemia. D cells were quantified by morphometry and flow cytometry in 16-wk-old wild-type (G+/+) and gastrin-deficient (G-/-) mice. Hypochlorhydric G-/- mice were treated with either antibiotics for 20 days or infused with gastrin (G-17) for 14 days. G+/+ mice were made hypochlorhydric by treating them with omeprazole for 2 mo. G-/- mice showed significant inflammation compared with the G+/+ mice, which resolved after 20 days of antibiotic treatment. D cell numbers were not significantly different between G-/- and G+/+ mice. After G-17 was infused, fundic and antral D cell numbers decreased in the G-/- mice. G+/+ animals made hypergastrinemic with omeprazole exhibited decreased D cell numbers. When omeprazole-treated mice were treated with antibiotics alone, elevated plasma gastrin levels returned to baseline and D cell numbers returned to resting levels despite persistent hypochlorhydria. Hypergastrinemia, induced by inflammation, results in decreased D cell numbers. Thus the stomach responds to the presence of inflammation by reducing somatostatin levels, thereby releasing the inhibition on the G and parietal cells to maximize gastric acid output.

Group-specific monitoring of phenol hydroxylase genes for a functional assessment of phenol-stimulated trichloroethylene bioremediation

The sequences of the largest subunit of bacterial multicomponent phenol hydroxylases (LmPHs) were compared. It was found that LmPHs formed three phylogenetic groups, I, II, and III, corresponding to three previously reported kinetic groups, low-K(s) (the half-saturation constant in Haldane's equation for trichloroethylene [TCE]), moderate-K(s), and high-K(s) groups. Consensus sequences and specific amino acid residues for each group of LmPH were found, which facilitated the design of universal and group-specific PCR primers. PCR-mediated approaches using these primers were applied to analyze phenol/TCE-degrading populations in TCE-contaminated aquifer soil. It was found that the aquifer soil harbored diverse genotypes of LmPH, and the group-specific primers successfully amplified LmPH fragments affiliated with each of the three groups. Analyses of phenol-degrading bacteria isolated from the aquifer soil confirmed the correlation between genotype and phenotype. Competitive PCR assays were used to quantify LmPHs belonging to each group during the enrichment of phenol/TCE-degrading bacteria from the aquifer soil. We found that an enrichment culture established by batch phenol feeding expressed low TCE-degrading activity at a TCE concentration relevant to the contaminated aquifer (e.g., 0.5 mg liter(-1)); group II and III LmPHs were predominant in this batch enrichment. In contrast, group I LmPHs overgrew an enrichment culture when phenol was fed continuously. This enrichment expressed unexpectedly high TCE-degrading activity that was comparable to the activity expressed by a pure culture of Methylosinus trichosporium OB3b. These results demonstrate the utility of the group-specific monitoring of LmPH genes in phenol-stimulated TCE bioremediation. It is also suggested that phenol biostimulation could become a powerful TCE bioremediation strategy when bacteria possessing group I LmPHs are selectively stimulated.

Microorganisms relevant to bioremediation

Naturally occurring microbial consortia have been utilized in a variety of bioremediation processes. Recent developments in molecular microbial ecology offer new tools that facilitate molecular analyses of microbial populations at contaminated and bioremediated sites. Information provided by such analyses aids in the evaluation of the effectiveness of bioremediation and the formulation of strategies that might accelerate bioremediation.