Ecological and physiological analyses of Pseudomonad species within a phenol remediation system

Kinetics of Phenol Biodegradation by Heavy Metal Tolerant Rhizobacteria Glutamicibacter nicotianae MSSRFPD35 From Distillery Effluent Contaminated Soils

Biodegradation of phenol using bacteria is recognized as an efficient, environmentally friendly and cost-effective approach for reducing phenol pollutants compared to the current conventional physicochemical processes adopted. A potential phenol degrading bacterial strain Glutamicibacter nicotianae MSSRFPD35 was isolated and identified from Canna indica rhizosphere grown in distillery effluent contaminated sites. It showed high phenol degrading efficiency up to 1117 mg L^–1 within 60 h by the secretion of catechol 1,2-dioxygenase via ortho intradial pathway. The strain MSSRFPD35 possess both the catechol 1,2 dioxygenase and catechol 2,3 dioxygenase coding genes that drive the ortho and meta pathways, but the enzymatic assay revealed that the strain cleaves catechol via ortho pathway. Haldane’s kinetic method was well fit to exponential growth data and the following kinetic parameter was obtained: μ^∗ = 0.574 h^–1, K_i = 268.1, K_s = 20.29 mg L^–1. The true μ_max and S_m were calculated as 0.37 h^–1 and 73.76 mg L^–1, respectively. The Haldane’s constant values were similar to earlier studies and healthy fitness depicted in correlation coefficient value R² of 0.98. Phenol degrading kinetic’s was predicted using Haldane’s model as q_max 0.983, K_i′ 517.5 and K_s′ 9.152. Further, MSSRFPD35 was capable of utilizing different monocyclic and polycyclic aromatic hydrocarbons and to degrade phenol in the presence of different heavy metals. This study for the first time reports high phenol degrading efficiency of G. nicotianae MSSRFPD35 in the presence of toxic heavy metals. Thus, the strain G. nicotianae MSSRFPD35 can be exploited for the bioremediation of phenol and its derivatives polluted environments, co-contaminated with heavy metals.

Isolation, characterization and growth kinetics of phenol hyper-tolerant bacteria from sewage-fed aquaculture system

Pollution of aquatic resources is increasing day-by-day, and phenolic compounds are common pollutants negatively impacting aquatic biodiversity and production. This study aimed at isolation of phenol hyper-tolerant bacteria from polluted aquaculture resource so that they might be useful in aquaculture systems. Four phenol hyper-tolerant bacterial strains were isolated from sewage fed East Kolkata Wetlands, a Ramsar site. By 16S rDNA sequence, cell morphology and biochemical characteristics the strains PDB2, PDB13, PDB16, and PDB26 were identified as Acinetobacter sp., Acinetobacter junii, Pseudomonas citronellolis, and Bacillus cereus, respectively. Pseudomonas citronellolis strain PDB16, described in this study, is possibly the first report of phenol hyper-tolerant strain in this species. All the four strains degraded 600 mg L^-1 phenol within 5 days and expressed catechol 1,2-dioxygenase but lacked catechol 2,3-dioxygenase enzyme suggesting that the bacteria used the ortho-cleavage pathway for phenol degradation. In growth kinetic study Edwards and Aiba model, rather than the most popular Haldane model, gave the best fit indicating behavioral divergence of these strains with those from petroleum contaminated environments. The phenol degrading bacteria isolated from a polluted sewage fed aquaculture system might be useful in degradation and remediation of polluted aquaculture resources as well as inland open waters.

Spatial Patterns of bphA Gene Diversity Reveal Local Adaptation of Microbial Communities to PCB and PAH Contaminants

Biphenyl dioxygenases, encoded by the bphA gene, initiate the oxidation of polychlorinated biphenyls (PCBs) and specify the substrate range of PCB congeners metabolized by bacteria. Increased bphA gene diversity within microbial communities may allow a broader range of PCB congeners to be catabolized, thus resulting in greater PCB degradation. To assess the role of PCBs in modulating bphA gene diversity, 16S ribosomal RNA (rRNA) gene and bphA environmental DNA libraries were generated from bacterial communities in sediments with a steep gradient of PCB contamination. Multiple measures of sequence diversity revealed greater heterogeneity of bphA sequences in polluted compared to unpolluted locations. Codon-based signatures of selection in bphA sequences provided evidence of purifying selection. Unifrac analysis of 16S rRNA sequences revealed independent taxonomic lineages from polluted and unpolluted locations, consistent with the presence of locally adapted bacterial communities. Phylogenetic analysis of bphA sequences indicated that dioxygenases from sediments were closely related to previously characterized dioxygenases that metabolize PCBs and polynuclear aromatic hydrocarbons (PAHs), consistent with high levels of these contaminants within the studied sediments. Structural analyses indicated that the BphA protein of Rhodococcus jostii, capable of metabolizing both PCBs and PAHs, provided a more optimal modeling template for bphA sequences reported in this study than a BphA homologue with more restricted substrate specificity. Results from this study suggest that PCBs and PAHs may drive local adaptation of microbial communities by acting as strong selective agents for biphenyl dioxygenases capable of metabolizing a wide range of congeners.

Differential Impacts of Willow and Mineral Fertilizer on Bacterial Communities and Biodegradation in Diesel Fuel Oil-Contaminated Soil

Despite decades of research there is limited understanding of how vegetation impacts the ability of microbial communities to process organic contaminants in soil. Using a combination of traditional and molecular assays, we examined how phytoremediation with willow and/or fertilization affected the microbial community present and active in the transformation of diesel contaminants. In a pot study, willow had a significant role in structuring the total bacterial community and resulted in significant decreases in diesel range organics (DRO). However, stable isotope probing (SIP) indicated that fertilizer drove the differences seen in community structure and function. Finally, analysis of the total variance in both pot and SIP experiments indicated an interactive effect between willow and fertilizer on the bacterial communities. This study clearly demonstrates that a willow native to Alaska accelerates DRO degradation, and together with fertilizer, increases aromatic degradation by shifting microbial community structure and the identity of active naphthalene degraders.

Assessment of the chemical, microbiological and toxicological aspects of post-processing water from underground coal gasification

The purpose of this paper is to provide a comprehensive characterisation (including chemical, microbiological and toxicological parameters) of water after the underground coal gasification (UCG) process. This is the first report in which these parameters were analysed together to assess the environmental risk of the water generated during the simulation of the underground coal gasification (UCG) process performed by the Central Mining Institute (Poland). Chemical analysis of the water indicated many hazardous chemical compounds, including benzene, toluene, ethylbenzene, xylene, phenols and polycyclic aromatic hydrocarbons (PAHs). Additionally, large quantities of inorganic compounds from the coal and ashes produced during the volatilisation process were noted. Due to the presence of refractory and inhibitory compounds in the post-processing water samples, the microbiological and toxicological analyses revealed the high toxicity of the UCG post-processing water. Among the tested microorganisms, mesophilic, thermophilic, psychrophilic, spore-forming, anaerobic and S-oxidizing bacteria were identified. However, the number of detected microorganisms was very low. The psychrophilic bacteria dominated among tested bacteria. There were no fungi or Actinomycetes in any of the water samples. Preliminary study revealed that hydrocarbon-oxidizing bacteria were metabolically active in the water samples. The samples were very toxic to the biotests, with the TU50 reaching 262. None of biotests was the most sensitive to all samples. Cytotoxicity and genotoxicity testing of the water samples in Vicia uncovered strong cytotoxic and clastogenic effects. Furthermore, TUNEL indicated that all of the water samples caused sporadic DNA fragmentation in the nuclei of the roots.

Diversity of planktonic and attached bacterial communities in a phenol-contaminated sandstone aquifer

Polluted aquifers contain indigenous microbial communities with the potential for in situ bioremediation. However, the effect of hydrogeochemical gradients on in situ microbial communities (especially at the plume fringe, where natural attenuation is higher) is still not clear. In this study, we used culture-independent techniques to investigate the diversity of in situ planktonic and attached bacterial communities in a phenol-contaminated sandstone aquifer. Within the upper and lower plume fringes, denaturing gradient gel electrophoresis profiles indicated that planktonic community structure was influenced by the steep hydrogeochemical gradient of the plume rather than the spatial location in the aquifer. Under the same hydrogeochemical conditions (in the lower plume fringe, 30 m below ground level), 16S rRNA gene cloning and sequencing showed that planktonic and attached bacterial communities differed markedly and that the attached community was more diverse. The 16S rRNA gene phylogeny also suggested that a phylogenetically diverse bacterial community operated at this depth (30 mbgl), with biodegradation of phenolic compounds by nitrate-reducing Azoarcus and Acidovorax strains potentially being an important process. The presence of acetogenic and sulphate-reducing bacteria only in the planktonic clone library indicates that some natural attenuation processes may occur preferentially in one of the two growth phases (attached or planktonic). Therefore, this study has provided a better understanding of the microbial ecology of this phenol-contaminated aquifer, and it highlights the need for investigating both planktonic and attached microbial communities when assessing the potential for natural attenuation in contaminated aquifers.

Silver nanotoxicity using a light-emitting biosensor Pseudomonas putida isolated from a wastewater treatment plant

The effect of silver ions, nano- and micro-particles on a luminescent biosensor bacterium Pseudomonas putida originally isolated from activated sludge was assessed. The bacterium carrying a stable chromosomal copy of the lux operon (luxCDABE) was able to detect toxicity of ionic and particulate silver over short term incubations ranging from 30 to 240 min. The IC(50) values obtained at different time intervals showed that highest toxicity (lowest IC(50)) was obtained after 90 min incubation for all toxicants and this is considered the optimum incubation for testing. The data show that ionic silver is the most toxic followed by nanosilver particles with microsilver particles being least toxic. Release of nanomaterials is likely to have an effect on the activated sludge process as indicated by the study using a common sludge bacterium involved in biodegradation of organic wastes.

Polyphasic bacterial community analysis of an aerobic activated sludge removing phenols and thiocyanate from coke plant effluent

Biological purification processes are effective tools in the treatment of hazardous wastes such as toxic compounds produced in coal coking. In this study, the microbial community of a lab-scale activated sludge system treating coking effluent was assessed by cultivation-based (strain isolation and identification, biodegradation tests) and culture-independent techniques (sequence-aided T-RFLP, taxon-specific PCR). The results of the applied polyphasic approach showed a simple microbial community dominated by easily culturable heterotrophic bacteria. Comamonas badia was identified as the key microbe of the system, since it was the predominant member of the bacterial community, and its phenol degradation capacity was also proved. Metabolism of phenol, even at elevated concentrations (up to 1500mg/L), was also presented for many other dominant (Pseudomonas, Rhodanobacter, Oligella) and minor (Alcaligenes, Castellaniella, Microbacterium) groups, while some activated sludge bacteria (Sphingomonas, Rhodopseudomonas) did not tolerate it even in lower concentrations (250mg/L). In some cases, closely related strains showed different tolerance and degradation properties. Members of the genus Thiobacillus were detected in the activated sludge, and were supposedly responsible for the intensive thiocyanate biodegradation observed in the system. Additionally, some identified bacteria (e.g. C. badia and the Ottowia-related strains) might also have had a significant impact on the structure of the activated sludge due to their floc-forming abilities.

Identification and genetic characterization of phenol-degrading bacteria from leaf microbial communities

Microbial communities on aerial plant leaves may contribute to the degradation of organic air pollutants such as phenol. Epiphytic bacteria capable of phenol degradation were isolated from the leaves of green ash trees grown at a site rich in airborne pollutants. Bacteria from these communities were subjected, in parallel, to serial enrichments with increasing concentrations of phenol and to direct plating followed by a colony autoradiography screen in the presence of radiolabeled phenol. Ten isolates capable of phenol mineralization were identified. Based on 16S rDNA sequence analysis, these isolates included members of the genera Acinetobacter, Alcaligenes, and Rhodococcus. The sequences of the genes encoding the large subunit of a multicomponent phenol hydroxylase (mPH) in these isolates indicated that the mPHs of the gram-negative isolates belonged to a single kinetic class, and that is one with a moderate affinity for phenol; this affinity was consistent with the predicted phenol levels in the phyllosphere. PCR amplification of genes for catechol 1,2-dioxygenase (C12O) and catechol 2,3-dioxygenase (C23O) in combination with a functional assay for C23O activity provided evidence that the gram-negative strains had the C12O-, but not the C23O-, phenol catabolic pathway. Similarly, the Rhodococcus isolates lacked C23O activity, although consensus primers to the C12O and C23O genes of Rhodococcus could not be identified. Collectively, these results demonstrate that these leaf surface communities contained several taxonomically distinct phenol-degrading bacteria that exhibited diversity in their mPH genes but little diversity in the catabolic pathways they employ for phenol degradation.

Evaluation of different phenol hydroxylase-possessing phenol-degrading pseudomonads by kinetic parameters

Phenol-degrading pseudomonads possessing different phenol hydroxylases (PH) were evaluated by the values of apparent half-saturation constant for phenol-oxygenating activity (K ( S )), maximum specific growth rate (mu (max)), lag-time length (lambda), inhibition constant (K ( I )) and growth yield factor (Y ( X/S )). Strains of the same PH type showed similar kinetic parameters: single-component PH (sPH) harbouring strains had higher values of K ( S ) and lower values of mu (max) than the strains having multicomponent PH (mPH). However, the values of K ( I ) and the dependencies of the lag-time length on initial phenol concentration were strain-specific. The elevated ratio between specific activities of catechol 1,2-dioxygenase (C12O) and muconate cycloisomerase in sPH-strains caused irreversible accumulation of a high amount of exogenous cis,cis-muconate (CCM) which resulted in decreased Y ( X/S ) values. Co-presence of sPH and mPH genes did not give the strains PC16 and P69 any extra advantage and according to determined kinetic parameters only one PH was active during phenol degradation. At the same time simultaneous functioning of catechol ortho and meta cleavage pathways (strain PC20) resulted in higher mu (max) and Y ( X/S ) values. Evaluation of strains showed that the type of PH determined the efficiency of phenol degradation, whereas the tolerance to elevated phenol concentrations was strain-specific.

Effect of temperature and additional carbon sources on phenol degradation by an indigenous soil Pseudomonad

A new indigenous soil bacterium Pseudomonas sp. growing on phenol and on a mixture of phenol, toluene, o-cresol, naphthalene and 1,2,3-trimethylbenzene (1,2,3-TMB) was isolated and characterized. Phylogenetic analysis suggested its classification to Pseudomonadaceae family and showed 99.8% DNA sequence identity to Pseudomonas pseudoalcaligenes species. The isolate was psychrotroph, with growth temperatures ranging from ca. 0 to 40 degrees C. The GC-MS structural analysis of metabolic products of phenol degradation by this microorganism indicated a possible ortho cleavage pathway for high concentrations (over 200 mg L(-1)) of phenol. Biodegradation rates by this species were found to be three times more effective than those previously reported by other Pseudomonas strains. The effect of temperature on phenol degradation was studied in batch cultures at temperatures ranging from 10 to 40 degrees C and different initial phenol concentrations (up to 500 mg L(-1)). Above 300 mg L(-1) of initial phenol concentration no considerable depletion was recorded at both 10 and 40 degrees C. Maximum degradation rates for phenol were recorded at 30 degrees C. The biodegradation rate of phenol was studied also in the presence of additional carbon sources (o-cresol, toluene, naphthalene, 1,2,3-TMB) at the optimum growth temperature and was found significantly lower by a factor of eight in respect to the strong competitive inhibition between the substrates and the more available sources of carbon and energy. The Haldane equation mu = mum S/(Ks + S + S2/K1) was found to best fit the experimental data at the optimum temperature of 30 degrees C than the Monod equation with kinetic constants mum = 0.27 h(-1), KS = 56.70 mg L(-1), KI = 249.08 mg L(-1).

Exploring the microbial biodegradation and biotransformation gene pool

Similar to the New World explorers of the 16th and 17th century, microbiologists today find themselves at the edge of unknown territory. It is estimated that only 0.1-1% of microorganisms can be cultivated using current techniques; the vastness of microbial lifestyles remains to be explored. Because the microbial metagenome is the largest reservoir of genes that determine enzymatic reactions, new techniques are being developed to identify the genes that underlie many valuable chemical biotransformations carried out by microbes, particularly in pathways for biodegradation of recalcitrant and xenobiotic molecules. Our knowledge of catabolic routes built on research during the past 40 years is a solid basis from which to venture on to the little-explored pathways that might exist in nature. However, it is clear that the vastness of information to be obtained requires astute experimental strategies for finding novel reactions.

Bacterial diversity and function of aerobic granules engineered in a sequencing batch reactor for phenol degradation

Aerobic granules are self-immobilized aggregates of microorganisms and represent a relatively new form of cell immobilization developed for biological wastewater treatment. In this study, both culture-based and culture-independent techniques were used to investigate the bacterial diversity and function in aerobic phenol- degrading granules cultivated in a sequencing batch reactor. Denaturing gradient gel electrophoresis (DGGE) analysis of PCR-amplified 16S rRNA genes demonstrated a major shift in the microbial community as the seed sludge developed into granules. Culture isolation and DGGE assays confirmed the dominance of beta-Proteobacteria and high-G+C gram-positive bacteria in the phenol-degrading aerobic granules. Of the 10 phenol-degrading bacterial strains isolated from the granules, strains PG-01, PG-02, and PG-08 possessed 16S rRNA gene sequences that matched the partial sequences of dominant bands in the DGGE fingerprint belonging to the aerobic granules. The numerical dominance of strain PG-01 was confirmed by isolation, DGGE, and in situ hybridization with a strain-specific probe, and key physiological traits possessed by PG-01 that allowed it to outcompete and dominate other microorganisms within the granules were then identified. This strain could be regarded as a functionally dominant strain and may have contributed significantly to phenol degradation in the granules. On the other hand, strain PG-08 had low specific growth rate and low phenol degradation ability but showed a high propensity to autoaggregate. By analyzing the roles played by these two isolates within the aerobic granules, a functional model of the microbial community within the aerobic granules was proposed. This model has important implications for rationalizing the engineering of ecological systems.

Calibration and deployment of custom-designed bioreporters for protecting biological remediation consortia from toxic shock

We have previously described the development of a panel of site-specific lux-based bioreporters from an industrial wastewater treatment system remediating coking effluents. The Pseudomonad strains carry a stable chromosomal copy of the luxCDABE operon from Photorhabdus luminescens and display proportional responses in bioluminescence decay with increasing phenol concentration up to 800 mg l-1. In this work we describe their deployment to provide a strategic sensing network for protecting bacterial communities involved in the biological breakdown of coking effluents. This evaluation demonstrated the utility of strategic placement of reporters around heavy industry treatment systems and the reliability of the reporter strains under normal operational conditions. Mono-phenol or total phenolic variation within the treatment system accounted for>65-80% of the luminescence response. The reporters exhibited stable luminescence output during normal operations with maximum standard deviations of luminescence over time of c. 5-15% depending on the treatment compartment. Furthermore, deployment of the bioreporters over a 5-month period allowed the determination of an operational range (OR) for each reporter for effluent samples from each compartment. The OR allowed a convenient measure of toxicity effects between treatment compartments and accurately reflected a specific pollution event occurring within compartments of the treatment system. This work demonstrates the utility of genetic modification to provide ecologically relevant bioreporters, extends the sensing capabilities currently obtained through marine derived biosensors and significantly enhances the potential for in situ deployment of reporting agents.

Assessing wastewater toxicity to activated sludge: recent research and developments

Toxicants in municipal sewage treatment plant (STP) influent wastewater may inhibit the biological activity of the activated sludge and cause treatment plant process upsets. Such process upsets may be avoided if influent wastewater is monitored for toxicity and protective actions are taken when toxicity is detected. A comprehensive review of the methods that can be used for assessing wastewater toxicity to biological treatment systems was conducted several years ago and the resultant report was published in 2000 by Water Environment Research Foundation (WERF). The WERF report also specified the criteria for influent wastewater toxicity monitoring methods and suggested research needs to be addressed. A significant amount of effort was made since the publication of the WERF report to develop new assays or devices and to improve existing ones. In this manuscript, recent research and developments in methods for assessing wastewater toxicity to activated sludge were reviewed. The literature indicates that bioluminescence- and respirometry-based methods received much attention in recent research. A comparison of the new/improved methods with the criteria described in the WERF report reveals that none of these methods has been shown to meet all the specified criteria. The present review also indicates that research efforts since 2000 have not fully taken into account the criteria for influent wastewater toxicity monitoring methods and have not addressed the research needs proposed in the WERF report.

Methods evaluating vanadium tolerance in bacteria isolated from crude oil contaminated land

Investigations into bacterial responses to vanadium are rare, and in this study were initiated by isolating cultures from crude oil contaminated soil from Russia and Saudi Arabia. Addition of vanadyl sulphate and vanadium pentoxide created acid conditions in the media whilst sodium metavanadate and sodium orthovanadate produced neutral and alkaline effects, respectively. Buffers were introduced for wider comparison of the sample set treatments and to distinguish between the effects of pH and compound toxicity. This study has resulted in the creation of protocols for the pH stabilisation of media containing vanadium compounds and revealed that, although vanadium salts demonstrated some toxic effects, as revealed by MIC and bioluminescence decay tests, the effects were mainly due to pH rather than inherent toxicity of the metal. Capacity for sorption of vanadium to biomass was also investigated.

N-acyl-l-homoserine lactones (AHLs) affect microbial community composition and function in activated sludge

The role of intercellular signalling in the regulation of genes and phenotypes in a broad range of bacterial species is now firmly established. In contrast, the impact of intercellular signalling on microbial community parameters, such as species diversity and function, is less well understood. In this study the role of N-acyl-l-homoserine lactones (AHLs) in microbial community dynamics in an industrial wastewater treatment system is addressed. Seven proteobacterial strains producing compounds with AHL-like activity were isolated from the treatment plant. Three of these belong to genera with no previously identified AHL producing species. Addition of AHLs at 2 micro M to sludge samples generated changes in both community function (phenol degradation) and composition as determined by length heterogeneity PCR and denaturing gradient gel electrophoresis. Phenol degradation was more stable as a result of the AHL augmentation. A dominant functional member of the Thauera genus was transiently supplanted by a member of the Comomonas genus in response to AHL addition. This suggests that AHLs can play a role in mediating microbial community parameters and has implications for ecosystem function and industrial wastewater treatment.

Development of bespoke bioluminescent reporters with the potential for in situ deployment within a phenolic-remediating wastewater treatment system

A suite of ecologically relevant, site-specific bioreporters was constructed by transposon mutagenesis of microorganisms isolated from a polluted phenolic-remediating wastewater treatment system. Four Pseudomonad species were engineered to carry a stable chromosomal copy of the lux operon (luxCDABE) derived from Photorhabdus luminescens. These recombinant reporter microorganisms were tested for bioluminescence response to relevant phenol concentrations in the laboratory and to phenolic-containing effluents generated by an industrial wastewater treatment plant. The reporters displayed proportional responses of bioluminescence decay with increasing phenol concentrations up to 800 mg l(-1) of phenol. When deployed against samples from the treatment system, they showed superior operational range and sensing capabilities to that observed for industry standard microorganisms such as Vibrio fischeri. Specifically, the engineered strains accurately predicted toxicity shifts in all the treatment compartments under study (with phenolic concentrations ranging from approximately 10 to 600 mg l(-1)) with a low coefficient of variation of replicate determinations (between 1.16% and 8.32%). This work highlights the utility of genetic modification of native microorganisms from sites of interest to provide robust and ecologically relevant organism-based reagents for toxicity monitoring with the potential for in situ deployment.

RNA stable isotope probing, a novel means of linking microbial community function to phylogeny

Identifying microorganisms responsible for recognized environmental processes remains a great challenge in contemporary microbial ecology. Only in the last few years have methodological innovations provided access to the relationship between the function of a microbial community and the phylogeny of the organisms accountable for it. In this study stable-isotope-labeled [13C]phenol was fed into a phenol-degrading community from an aerobic industrial bioreactor, and the 13C-labeled RNA produced was used to identify the bacteria responsible for the process. Stable-isotope-labeled RNA was analyzed by equilibrium density centrifugation in concert with reverse transcription-PCR and denaturing gradient gel electrophoresis. In contradiction with findings from conventional methodologies, this unique approach revealed that phenol degradation in the microbial community under investigation is dominated by a member of the Thauera genus. Our results suggest that this organism is important for the function of this bioreactor.

Technical considerations for RNA-based stable isotope probing: an approach to associating microbial diversity with microbial community function

An ongoing challenge within microbial ecology is the development of methodologies that attribute microbial community functions to microbial diversity. One approach, involving the incorporation of stable isotopes from labelled tracer compounds into biological signature molecules (biomarkers), may overcome this current limitation. To examine the potential of RNA as the biomarker in stable isotope probing we have generated a series of atom % (13)C-enriched RNA samples through exploitation of the anabolic abilities of a phenol-degrading environmental isolate. Isotope ratio mass spectrometry was used to determine the atom % (13)C of each RNA sample (ca. 1-100%). The corresponding buoyant density (1.755-1.795 g mL(-1)) was determined by equilibrium density gradient centrifugation and agarose gel electrophoresis. This empirically defined relationship between the atom % (13)C of RNA and its buoyant density suggests ribonucleic acids with atom % (13)C enrichments greater than 10% can be isolated by equilibrium density centrifugation. The processing and analysis of isolated RNA by reverse transcription polymerase chain reaction, denaturing gradient gel electrophoresis, cloning and sequencing are discussed. The RNA-based stable isotope probing protocol presented here will find particular utility in assessing the roles of microbial community members in the biodegradation of natural and anthropogenic xenobiotic compounds.

Analysis of river pollution data from low-flow period by means of multivariate techniques: a case study from the oil-shale industry region, northeastern Estonia

The oil-shale industry has created serious pollution problems in northeastern Estonia. Untreated, phenol-rich leachate from semi-coke mounds formed as a by-product of oil-shale processing is discharged into the Baltic Sea via channels and rivers. An exploratory analysis of water chemical and microbiological data sets from the low-flow period was carried out using different multivariate analysis techniques. Principal component analysis allowed us to distinguish different locations in the river system. The riverine microbial community response to water chemical parameters was assessed by co-inertia analysis. Water pH, COD and total nitrogen were negatively related to the number of biodegradative bacteria, while oxygen concentration promoted the abundance of these bacteria. The results demonstrate the utility of multivariate statistical techniques as tools for estimating the magnitude and extent of pollution based on river water chemical and microbiological parameters. An evaluation of river chemical and microbiological data suggests that the ambient natural attenuation mechanisms only partly eliminate pollutants from river water, and that a sufficient reduction of more recalcitrant compounds could be achieved through the reduction of wastewater discharge from the oil-shale chemical industry into the rivers.