Hybridization Analysis of Microbial DNA from Fuel Oil-Contaminated and Noncontaminated Soil

Reduction in concentration of chromium (VI) by Lysinibacillus macroides isolated from sediments of the Chapala Lake, Mexico

The Chapala Lake is one of the most polluted lakes in Mexico, due to the in flow of effluents from several industrial plants, the lake accumulates pollutants such as chromium(VI) which is considered important for aquatic ecosystem. This study aimed was to evaluate the ability to decrease the concentration of chromium (VI) by Lysinibacillus macroides 2(1B)104A, isolated from sediments of the Chapala Lake. The strain was identified through 16S rRNA sequencing and phylogenetic analysis. Results showed that this strain grows in concentrations of 50, 100, 200 and 300 mgL-1 Cr(VI), in pH ranging 6 to 7, showing 79.508% reduction in concentration 50 mgL-1, determining that the reduction occurs extracellularly. Likewise, it was observed that Lysinibacillus macroides reduced the concentration of Cr(IV) in the broth, it was not observed that the bacteria could sequester Cr(VI) in the membrane or intracellularly. However, it reduced the concentration of Cr(VI) in the broth. Lysinibacillus macroides 2(1B)104A isolate showed having the ability that decrease the concentration of Cr(VI), which makes it a viable options for bioremediation of water polluted with this metal.

Determination of materials present in skeletonized human remains and the associated DNA: Development of a GC/MS protocol

DNA testing of skeletonized human remains is considered to be challenging, especially when the remains have been exposed to inhibitory materials during decomposition. Inhibitors affect the processing of DNA, either by preventing efficient extraction or interfering with down-stream PCR-based processes. Limited studies have been performed on real-world samples that have been exposed to such inhibitors. This paper presents the development of a gas chromatography/mass spectrometry (GC/MS) protocol for the evaluation of materials present in skeletonized human remains recovered from the field, as well as the DNA extracted from the same materials. Twenty-one bone samples and seventeen DNA extracts were evaluated across three solvents and multiple GC/MS parameters to determine the optimal conditions for the recovery of trace materials present. The aim of this work is to provide a technique that can determine the presence of inhibitors prior to DNA extraction, allowing analysts to optimize removal of inhibitory materials.

Diversity and distribution of actinobacterial aromatic ring oxygenase genes across contrasting soil properties

The diversity of a gene family encoding Actinobacterial aromatic ring oxygenases (AAROs) was detected by the PCR-cloning approach using a newly designed PCR primer set. The distribution of AAROs was investigated in 11 soils representing different land management and vegetation zones and was correlated with several geochemical parameters including pH, organic matter (OM), total Kjeldahl nitrogen (TKN), and nitrogen oxides (NO(x)-N: mostly NO3(-)-N). The distribution of individual clades encoding enzymes with potentially different substrates were correlated with different environmental factors, suggesting differential environmental controls on the distribution of specific enzymes as well as sequence diversity. For example, individual clades associated with phthalate dioxygenases were either strongly negatively correlated with pH, or not correlated with pH but showed strong positive correlation with organic carbon content. A large number of clones clustering in a clade related to PAH oxygenases were positively correlated with pH and nitrogen, but not with organic matter. This analysis may yield insight into the ecological forces driving the distribution of these catabolic genes.

Isolation and phylogenic identification of soil haloalkaliphilic strains in the former Texcoco Lake

A wide diversity of organisms exists in soil. Well-adapted groups can be found in extreme environments. A great economic and metabolic potential for extremozymes produced by organisms living at extreme environments has been reported. Extreme characteristics such as high salt content and high pH level make the soil of the former Texcoco Lake a unique place which has not been exploited. Therefore, in this study, 66 strains from soil of the former Texcoco Lake were isolated and phylogenetically analyzed using universal oligonucleotide primers. Different genera such as Kocuria, Micrococcus, Nesterenkonia, Halomonas, Salinicoccus, Kurthia, Gracilibacillus, and Bacillus were found. However, only 22 from all isolated strains were identified at specie level.

Changes in bacterial community of anthracene bioremediation in municipal solid waste composting soil

Polycyclic aromatic hydrocarbons (PAHs) are common contaminants in a municipal solid waste (MSW) composting site. Knowledge of changes in microbial structure is useful to identify particular PAH degraders. However, the microbial community in the MSW composting soil and its change associated with prolonged exposure to PAHs and subsequent biodegradation remain largely unknown. In this study, anthracene was selected as a model compound. The bacterial community structure was investigated using terminal restriction fragment length polymorphism (TRFLP) and 16S rRNA gene clone library analysis. The two bimolecular tools revealed a large shift of bacterial community structure after anthracene amendment and subsequent biodegradation. Genera Methylophilus, Mesorhizobium, and Terrimonas had potential links to anthracene biodegradation, suggesting a consortium playing an active role.

Synergistic degradation of 2-naphthol by Fusarium proliferatum and Bacillus subtilis in wastewater

2-Naphthol, which originates widely from various industrial activities, is toxic and thus harmful to human liver and kidney. A new compound biodegradation system was adopted to degrade 2-naphthol-contaminated wastewater. Enzymatic response to 2-naphthol biodegradation in the aqueous phase was also studied. As a co-metabolic substrate, salicylic acid could induce the two microorganisms to produce a large amount of degradation enzymes for 2-naphthol. The key enzymes were confirmed as polyphenol oxidase (PPO) and catechol 2,3-dioxygenase (C23O). The degradation extent of 2-naphthol, determined by high performance liquid chromatography (HPLC), was enhanced by nearly 15% on the 6th day after the addition of the co-metabolic substrate. The results obtained thus clearly indicated that the co-metabolic process was the most important factor affecting the degradation of the target contaminant. The optimal concentration of 2-naphthol was 150 mg L(-1), and the optimal pH value was 7.0. The degradation extent of 2-naphthol was further enhanced by nearly 10% after the addition of Tween 80, which increased the bioavailability of 2-naphthol. In a practical treatment of industrial wastewater from medical manufacture, the synergistic degradation system resulted in a high degradation efficiency of 2-naphthol although its lag time was a little long in the initial stage.

Quantification of aromatic oxygenase genes to evaluate enhanced bioremediation by oxygen releasing materials at a gasoline-contaminated site

Subsurface injection of oxygen-releasing materials (ORMs) is frequently performed at petroleum-contaminated sites to stimulate aerobic bioremediation of benzene, toluene, ethylbenzene, and xylenes (BTEX). In this study, qPCR enumeration of aromatic oxygenase genes and PCR-DGGE profiles of bacterial 16S rRNA genes were combined with groundwater monitoring to determine the impact of ORM injection on BTEX bioremediation at a gasoline-contaminated site. Prior to injection, BTEX concentrations were greater than 3 mg/L and DO levels were typically lessthan 2 mg/L, butphenol hydroxylase (PHE) and ring-hydroxylating toluene monooxygenase (RMO) genes were detected in impacted wells indicating the potential for aerobic BTEX biodegradation. Following injection, DO increased, BTEX concentrations decreased substantially, and PHE and RMO genes copies increased by 1-3 orders of magnitude. In addition, naphthalene dioxygenase (NAH) and xylene monooxygenase (TOL) genes were intermittently detected during periods of increased DO. Following depletion of the ORM, DO decreased, BTEX concentrations rebounded, and oxygenase genes were no longer detected. Temporal changes in PCR-DGGE microbial community profiles reflected the dynamic changes in subsurface conditions. Overall, the combination of chemical and geochemical analyses with quantification of aromatic oxygenase genes demonstrated that injection stimulated BTEX biodegradation until the ORM was depleted.

Functional gene abundances (nahAc, alkB, xylE) in the assessment of the efficacy of bioremediation

In this study, we compared the mineralization rates of three selected (14)C-labeled hydrocarbon compounds, octacosane, toluene, and naphthalene, with the presence of the corresponding functional genes (alkB, xylE, nahAc) in a large number of soil samples representing different types of soil and petroleum hydrocarbon contamination. Functional genes were enumerated by the replicate limited dilution (RLD) polymerase chain reaction (PCR) technique. RLD-PCR was further compared to real-time PCR measurements for nahAc and xylE for some samples. At a heating oil-contaminated site, octacosane mineralization rates were higher (on average 0.0015 day(-1)) when compared to aerobic naphthalene and toluene mineralization (on average 0.00003 and 0.0007 day(-1)). The corresponding gene abundances measured by RLD-PCR were on average 0.95, 0.3, and 0.13 x 10(3) gene copies g(-1) soil for alkB, nahAc, and xylE, respectively. At a site contaminated with gasoline, the situation was the opposite: Toluene mineralization was the highest (on average 0.0031 day(-1)), and only xylE genes could be detected (on average 0.13 x 10(3) gene copies g(-1) soil by RLD-PCR). XylE and nahAc gene abundances were correlated with the (14)C-toluene and naphthalene mineralization activities, respectively, in samples from aerobic layers. AlkB gene abundances were not correlated with the octacosane mineralization. Real-time PCR was a more sensitive method than RLD-PCR by a factor of 1,200 for nahAc and 300 for xylE. In conclusion, functional gene abundances seemed to reflect the type of the contamination. With optimized assays, the gene abundances can be used to assess bioremediation efficacy.

Enumeration of aromatic oxygenase genes to evaluate monitored natural attenuation at gasoline-contaminated sites

Monitoring groundwater benzene, toluene, ethylbenzene, and xylene (BTEX) concentrations is the typical method to assess monitored natural attenuation (MNA) and bioremediation as corrective actions at gasoline-contaminated sites. Conclusive demonstration of bioremediation, however, relies on converging lines of chemical and biological evidence to support a decision. In this study, real-time PCR quantification of aromatic oxygenase genes was used to evaluate the feasibility of MNA at two gasoline-impacted sites. Phenol hydroxylase (PHE), ring-hydroxylating toluene monooxygenase (RMO), naphthalene dioxygenase (NAH), toluene monooxygenase (TOL), toluene dioxygenase (TOD), and biphenyl dioxygenase (BPH4) genes were routinely detected in BTEX-impacted wells. Aromatic oxygenase genes were not detected in sentinel wells outside the plume indicating that elevated levels of oxygenase genes corresponded to petroleum hydrocarbon contamination. Total aromatic oxygenase gene copy numbers detected in impacted wells were on the order of 10(6)-10(9)copies L(-1). PHE, RMO, NAH, TOD, and BPH4 gene copies positively correlated to total BTEX concentration. Mann-Kendall analysis of benzene concentrations was used to evaluate the status of the dissolved BTEX plume. The combination of trend analysis of contaminant concentrations with quantification of aromatic oxygenase genes was used to assess the feasibility of MNA as corrective measures at both sites.

Isolation and characterization of alkane hydroxylases from a metagenomic library of Pacific deep-sea sediment

Two clones 9E7 and 21G8 in a metagenomic library of the east Pacific deep-sea sediment were found to contain alkane hydroxylase genes (alkB). The whole insert sequences of the two cosmid clones were determined. The insert sequences of 9E7 and 21G8 are 40 and 35 kb, respectively. Besides alkB, several alcohol/aldehyde dehydrogenase genes were also determined. A homolog of rubredoxin 2 of Pseudomonas putida was identified on 9E7 immediately downstream the alkB gene, but was lacking on 21G8. Unlike previous reports, the alkB genes on 9E7 and 21G8 have opposite transcription directions to those of linked alcohol/aldehyde dehydrogenase genes. Phylogenetic analysis put these two deep-sea AlkBs into a unique branch of integral membrane hydroxylases. The two alkB genes (9E7-alkB and 21G8-alkB) were cloned into pCom8 and introduced into two alkB expression host systems P. fluorescens KOB2 Delta 1 and P. putida GPo12 (pGEc47 Delta B). The transformed strains can grow on the n-alkanes from C5 to C16, indicating that both 9E7-AlkB and 21G8-AlkB have a wide substrate range. The data further indicate that the deep sea would be a rich resource for exploring novel alkane-degrading strains and genes.

Diversity of ndo genes in mangrove sediments exposed to different sources of polycyclic aromatic hydrocarbon pollution

Polycyclic aromatic hydrocarbon (PAH) pollutants originating from oil spills and wood and fuel combustion are pollutants which are among the major threats to mangrove ecosystems. In this study, the composition and relative abundance in the sediment bacterial communities of naphthalene dioxygenase (ndo) genes which are important for bacterial adaptation to environmental PAH contamination were investigated. Three urban mangrove sites which had characteristic compositions and levels of PAH compounds in the sediments were selected. The diversity and relative abundance of ndo genes in total community DNA were assessed by a newly developed ndo denaturing gradient gel electrophoresis (DGGE) approach and by PCR amplification with primers targeting ndo genes with subsequent Southern blot hybridization analyses. Bacterial populations inhabiting sediments of urban mangroves under the impact of different sources of PAH contamination harbor distinct ndo genotypes. Sequencing of cloned ndo amplicons comigrating with dominant DGGE bands revealed new ndo genotypes. PCR-Southern blot analysis and ndo DGGE showed that the frequently studied nah and phn genotypes were not detected as dominant ndo types in the mangrove sediments. However, ndo genotypes related to nagAc-like genes were detected, but only in oil-contaminated mangrove sediments. The long-term impact of PAH contamination, together with the specific environmental conditions at each site, may have affected the abundance and diversity of ndo genes in sediments of urban mangroves.

Bioremediation and monitoring of aromatic-polluted habitats

Bioremediation may restore contaminated soils through the broad biodegradative capabilities evolved by microorganisms towards undesirable organic compounds. Understanding bioremediation and its effectiveness is rapidly advancing, bringing available molecular approaches for examining the presence and expression of the key genes involved in microbial processes. These methods are continuously improving and require further development and validation of primer- and probe-based analyses and expansion of databases for alternative microbial markers. Phylogenetic marker approaches provide tools to determine which organisms are present or generally active in a community; functional gene markers provide only information concerning the distribution or transcript levels (deoxyribonucleic acid [DNA]- or messenger ribonucleic acid [mRNA]-based approaches) of specific gene populations across environmental gradients. Stable isotope probing methods offer great potential to identify microorganisms that metabolize and assimilate specific substrates in environmental samples, incorporating usually a rare isotope (i.e., (13)C) into their DNA and RNA. DNA and RNA in situ characterization allows the determination of the species actually involved in the processes being measured. DNA microarrays may analyze the expression of thousands of genes in a soil simultaneously. A global analysis of which genes are being expressed under various conditions in contaminated soils will reveal the metabolic status of microorganisms and indicate environmental modifications accelerating bioremediation.

A targeted real-time PCR assay for studying naphthalene degradation in the environment

A quantitative real-time polymerase chain reaction (PCR) assay was developed for monitoring naphthalene degradation during bioremediation processes. The phylogenetic affiliations of known naphthalene-hydroxylating dioxygenase genes were determined to target functionally related bacteria, and degenerate primers were designed on the basis of the close relationships among dioxygenase genes identified from naphthalene-degrading Proteobacteria. Evaluation of the amplification specificity demonstrated that the developed real-time PCR assay represents a rapid, precise means for the group-specific enumeration of naphthalene-degrading bacteria. According to validation with bacterial pure cultures, the assay discriminated between the targeted group of naphthalene dioxygenase sequences and genes in other naphthalene or aromatic hydrocarbon-degrading bacterial strains. Specific amplification of gene fragments sharing a high sequence similarity with the genes included in the assay design was also observed in soil samples recovered from large-scale remediation processes. The target genes could be quantified reproducibly at over five orders of magnitude down to 3 x 10(2) gene copies. To investigate the suitability of the assay in monitoring naphthalene biodegradation, the assay was applied in enumerating the naphthalene dioxygenase genes in a soil slurry microcosm. The results were in good agreement with contaminant mineralization and dot blot quantification of nahAc gene copies. Furthermore, the real-time PCR assay was found to be more sensitive than hybridization-based analysis.

PCR-DGGE method to assess the diversity of BTEX mono-oxygenase genes at contaminated sites

tmoA and related genes encode the alpha-subunit of the hydroxylase component of the major group (subgroup 1 of subfamily 2) of bacterial multicomponent mono-oxygenase enzyme complexes involved in aerobic benzene, toluene, ethylbenzene and xylene (BTEX) degradation. A PCR-denaturing gradient gel electrophoresis (DGGE) method was developed to assess the diversity of tmoA-like gene sequences in environmental samples using a newly designed moderately degenerate primer set suitable for that purpose. In 35 BTEX-degrading bacterial strains isolated from a hydrocarbon polluted aquifer, tmoA-like genes were only detected in two o-xylene degraders and were identical to the touA gene of Pseudomonas stutzeri OX1. The diversity of tmoA-like genes was examined in DNA extracts from contaminated and non-contaminated subsurface samples at a site containing a BTEX-contaminated groundwater plume. Differences in DGGE patterns were observed between strongly contaminated, less contaminated and non-contaminated samples and between different depths, suggesting that the diversity of tmoA-like genes was determined by environmental conditions including the contamination level. Phylogenetic analysis of the protein sequences deduced from the amplified amplicons showed that the diversity of TmoA-analogues in the environment is larger than suggested from described TmoA-analogues from cultured isolates, which was translated in the DGGE patterns. Although different positions on the DGGE gel can correspond to closely related TmoA-proteins, relationships could be noticed between the position of tmoA-like amplicons in the DGGE profile and the phylogenetic position of the deduced protein sequence.

Assessing the role of alkane hydroxylase genotypes in environmental samples by competitive PCR

AIMS

A molecular tool for extensive detection of prokaryotic alkane hydroxylase genes (alkB) was developed. AlkB genotypes involved in the degradation of short-chain alkanes were quantified in environmental samples in order to assess their occurrence and ecological importance.

METHODS AND RESULTS

Four primer pairs specific for distinct clusters of alkane hydroxylase genes were designed, allowing amplification of alkB-related genes from all tested alkane-degrading strains and from six of seven microcosms. For the primer pair detecting alkB genes related to the Pseudomonas putida GPo1 alkB gene and the one targeting alkB genes of Gram-positive strains, both involved in short-chain alkane degradation (<C10), a quantitative competitive PCR (cPCR) assay was developed and validated on alkB-containing strains. AlkB genes of the two groups were then quantified in hydrocarbon-contaminated and pristine freshwater and soil samples, and their respective frequency was compared to degradation rates of short-chain n-alkanes. Pseudomonas putida-related alkB genes were prevalent in freshwater samples, but Gram-positive alkB-containing strains were more consistently related to alkane degradation activities. The latter genotype was more abundant in soils, although both genotypes increased in the most contaminated soils studied.

CONCLUSIONS

Predominance of alkB genotypes depends on the ecosystem and environmental conditions, but alkane exposure generally leads to an increase of both studied genotypes.

SIGNIFICANCE AND IMPACT OF THE STUDY

The study illustrates the distribution of two different alkB genotypes in two types of ecosystems, and highlights their respective roles in the environment.

Microbial degradation of street dust polycyclic aromatic hydrocarbons in microcosms simulating diffuse pollution of urban soil

Diffuse pollution with polycyclic aromatic hydrocarbons (PAHs) of topsoil in urban regions has caused increasing concerns in recent years. We simulated diffuse pollution of soil in microcosms by spiking sandy topsoil (A-horizon) and coarse, mineral subsoil (C-horizon) with street dust (PM63) isolated from municipal street sweepings from central Copenhagen. The microbial communities adapted to PAH degradation in microcosms spiked with street dust in both A-horizon and C-horizon soils, in spite of low PAH-concentrations. The increased potential for PAH degradation was demonstrated on several levels: by slowly diminishing PAH-concentrations, increased mineralization of 14C-PAHs, increasing numbers of PAH degraders and increased prevalence of nah and pdo1 PAH degradation genes, i.e. the microbial communities quickly adapted to PAH degradation. Three- and 4-ring PAHs from the street dust were biodegraded to some extent (10-20%), but 5- and 6-ring PAHs were not biodegraded in spite of frequent soil mixing and high PAH degradation potentials. In addition to biodegradation, leaching of 2-, 3- and 4-ring PAHs from the A-horizon to the C-horizon seems to reduce PAH-levels in surface soil. Over time, levels of 2-, 3- and 4-ring PAHs in surface soil may reach equilibrium between input and the combination of biodegradation and leaching. However, levels of the environmentally critical 5- and 6-ring PAHs will probably continue to rise. We presume that sorption to black carbon particles is responsible for the persistence and low bioaccessibility of 5- and 6-ring PAHs in diffusely polluted soil.

The abundance of nahAc genes correlates with the 14C-naphthalene mineralization potential in petroleum hydrocarbon-contaminated oxic soil layers

In this study, we evaluated whether the abundance of the functional gene nahAc reflects aerobic naphthalene degradation potential in subsurface and surface samples taken from three petroleum hydrocarbon contaminated sites in southern Finland. The type of the contamination at the sites varied from lightweight diesel oil to high molecular weight residuals of crude oil. Samples were collected from both oxic and anoxic soil layers. The naphthalene dioxygenase gene nahAc was quantified using a replicate limiting dilution-polymerase chain reaction (RLD-PCR) method with a degenerate primer pair. In the non-contaminated samples nahAc genes were not detected. In the petroleum hydrocarbon-contaminated oxic soil samples nahAc gene abundance [range 3 x 10(1)-9 x 10(4) copies (g dry wt soil)(-1)] was correlated (Kendall non-parametric correlation r2=0.459, p<0.01) with the aerobic 14C-naphthalene mineralization potential (range 1 x 10(-5)-0.1 d(-1)) measured in microcosms at in situ temperatures (8 degrees C for subsurface and 20 degrees C for surface soil samples). In these samples nahAc gene abundance was also correlated with total microbial cell counts (r2=0.471, p<0.01), respiration rate (r2=0.401, p<0.01) and organic matter content (r2=0.341, p<0.05). NahAc genes were amplified from anoxic soil layers indicating that, although involved in aerobic biodegradation of naphthalene, these genes or related sequences were also present in the anoxic subsurface. In the samples taken from the anoxic layers, the aerobic 14C-naphthalene mineralization rates were not correlated with nahAc gene abundance. In conclusion, current sequence information provides the basis for a robust tool to estimate the naphthalene degradation potential at oxic zones of different petroleum hydrocarbon-contaminated sites undergoing in situ bioremediation.

Dynamics of an oligotrophic bacterial aquifer community during contact with a groundwater plume contaminated with benzene, toluene, ethylbenzene, and xylenes: an in situ mesocosm study

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

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

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

Biodegradation of total organic carbons (TOC) in Jordanian petroleum sludge

Biodegradation is cost-effective, environmentally friendly treatment for oily contaminated sites by the use of microorganisms. In this study, laboratory experiments were conducted to establish the performance of bacterial isolates in degradation of organic compounds contained in oily sludge from the Jordanian Oil Refinery plant. As a result of the laboratory screening, three natural bacterial consortia capable of degrading total organic carbons (TOC) were prepared from isolates enriched from the oil sludge. Experiments were conducted in Erlenmeyer flasks under aerobic conditions, with TOC removal percentage varied from 0.3 to 28% depending on consortia type and concentration. Consortia 7B and 13B exhibited the highest TOC removal percentage of 28 and 22%, respectively, before nutrient addition. TOC removal rate was enhanced after addition of nutrients to incubated flasks. The highest TOC reduction (43%) was estimated after addition of combination of nitrogen, phosphorus and sulphur to consortia 7B. A significant variation (P<0.005) was observed between the effect of consortia type and concentration on TOC% reduction. No significant variation was observed between incubation at 10 and 18 days in TOC% reduction. This is the first report concerning biological treatment of TOC by bacteria isolated from the oil refinery plants, where it lays the ground for full integrated studies recommended for the degradation of organic compounds that assist in solving sludge problems.

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.

Methods of studying soil microbial diversity

Soil microorganisms, such as bacteria and fungi, play central roles in soil fertility and promoting plant health. This review examines and compares the various methods used to study microbial diversity in soil.

Detection and enumeration of aromatic oxygenase genes by multiplex and real-time PCR

Our abilities to detect and enumerate pollutant-biodegrading microorganisms in the environment are rapidly advancing with the development of molecular genetic techniques. Techniques based on multiplex and real-time PCR amplification of aromatic oxygenase genes were developed to detect and quantify aromatic catabolic pathways, respectively. PCR primer sets were identified for the large subunits of aromatic oxygenases from alignments of known gene sequences and tested with genetically well-characterized strains. In all, primer sets which allowed amplification of naphthalene dioxygenase, biphenyl dioxygenase, toluene dioxygenase, xylene monooxygenase, phenol monooxygenase, and ring-hydroxylating toluene monooxygenase genes were identified. For each primer set, the length of the observed amplification product matched the length predicted from published sequences, and specificity was confirmed by hybridization. Primer sets were grouped according to the annealing temperature for multiplex PCR permitting simultaneous detection of various genotypes responsible for aromatic hydrocarbon biodegradation. Real-time PCR using SYBR green I was employed with the individual primer sets to determine the gene copy number. Optimum polymerization temperatures for real-time PCR were determined on the basis of the observed melting temperatures of the desired products. When a polymerization temperature of 4 to 5 degrees C below the melting temperature was used, background fluorescence signals were greatly reduced, allowing detection limits of 2 x 10(2) copies per reaction mixture. Improved in situ microbial characterization will provide more accurate assessment of pollutant biodegradation, enhance studies of the ecology of contaminated sites, and facilitate assessment of the impact of remediation technologies on indigenous microbial populations.

Response of bacterial community during bioremediation of an oil-polluted soil

AIM

To study the response of the bacterial community to bioremediation of a soil with an aged contamination of crude oil.

METHODS AND RESULTS

The bacterial community in laboratory soil columns during a 72-day biostimulation treatment was followed by analysing the number of total cultivable hydrocarbon-degrading bacteria, soil respiratory activity and the 16S-23S rDNA internal transcribed spacer homoduplex heteroduplex polymorphisms (ITS-HHP) of total soil bacterial DNA. ITS-HHP permits an estimate of both length and sequence polymorphism in a 16S-23S rDNA spacer population, using to advantage the homoduplex and heteroduplex fragments that are generated during PCR. The treatment, made by air sparging and biostimulation with a mineral nutrient and surfactant solution, resulted in a 39.5% decrease of the total hydrocarbon content. Within 4 days of treatment onset the bacterial community underwent a first phase of activation that led to a substantial increase in the observable diversity. Subsequently, after a 12-day period of stability, another activation phase was observed with further shifts of the community structure and an increase in the abundance and diversity of catechol-2,3-dioxygenase (C23O) genes.

CONCLUSIONS

The overall data suggest an important contribution of uncultivable bacteria to the soil bioremediation, since, during the second activation phase, the increases of the respiratory activity, bacterial diversity and C23O gene abundance and diversity were not accompanied by a corresponding increase of the cultivable bacteria number.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study shows that successive phases of activation of bacterial populations occur during a bioremediation treatment of oil-polluted soil.

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.

Quantifying functional gene populations: comparing gene abundance and corresponding enzymatic activity using denitrification and nitrogen fixation in pulp and paper mill effluent treatment systems

The relationship between the abundance of three functional genes and their corresponding biochemical reaction rates was investigated in several activated sludge and mill effluent microbial communities. Gene probes were prepared for two key denitrification genes (nirS and nirK) and for one nitrogen-fixation gene (nifH) and were validated using a variety of strains of known nir and nif genotype. ATP-based measures of viable cell numbers were used to provide total population sizes. In certain microbial communities (activated sludge enrichment cultures and multiple samples taken from the same mill primary clarifier), a strong correlation was observed between gene abundance and biochemical activity rates. However, when comparing several different nonenriched activated sludge bioreactors and separate primary clarifier microbial communities, the ratio of specific gene abundance to biochemical activity rates varied widely. These results suggest that in cases where a microbial community is not fully induced for a given biochemical activity or when very different communities are compared, quantitative gene probing can give a better measure of a community's potential to carry out the encoded function than can the relevant biochemical assay. However, the gene quantitation method employed here probably underestimated the true number of probed genes present in the microbial communities due to nirS and nifH genes in the communities having reduced DNA sequence similarity with the probes used.

Vertical Distribution of Denitrification Potential, Denitrifying Bacteria, and Benzoate Utilization in Intertidal Microbial Mat Communities

Aspects of denitrification and benzoate degradation were studied in two estuarine microbial mat communities on the California coast by measuring the depth distributions of potential denitrification rates, genetic potential for denitrification, nitrate concentration, benzoate mineralization rates, total bacterial abundance, and abundance of a denitrifying strain (TBD-8b) isolated from one of the sites. Potential denitrification was detected in microbial mat cores from both Elkhorn Slough and Tomales Bay. Maximum denitrification rates were more than two orders of magnitude higher at Elkhorn Slough (3.14 mmol N m -2 d -1) than at Tomales Bay (0.02 mmol N m -2 d -1), and at both sites, the maximum rates occurred in the 0-2 mm depth interval. Ambient pore [NO 3 + NO 2] was substantially higher at Elkhorn Slough than at Tomales Bay. Incorporation and mineralization of benzoate was maximal near the mat surface at Elkhorn Slough. The areal rate of benzoate utilization was 1045 nmol C m -2 d -1, which represented utilization of 70% of the added substrate in 24 h. Total bacterial and TBD-8b abundances were greatest near the surface at both Tomales Bay and Elkhorn Slough, and TBD-8b represented less than 0.2% of the total. Genetic potential for denitrification, quantified by hybridization with a nitrite reductase gene fragment, was present below the mat surface at average levels representing presence of the gene in approximately 10% of the total cells.

Evaluation of inoculum addition to stimulate in situ bioremediation of oily-sludge-contaminated soil

A full-scale study evaluating an inoculum addition to stimulate in situ bioremediation of oily-sludge-contaminated soil was conducted at an oil refinery where the indigenous population of hydrocarbon-degrading bacteria in the soil was very low (10(3) to 10(4) CFU/g of soil). A feasibility study was conducted prior to the full-scale bioremediation study. In this feasibility study, out of six treatments, the application of a bacterial consortium and nutrients resulted in maximum biodegradation of total petroleum hydrocarbon (TPH) in 120 days. Therefore, this treatment was selected for the full-scale study. In the full-scale study, plots A and B were treated with a bacterial consortium and nutrients, which resulted in 92.0 and 89.7% removal of TPH, respectively, in 1 year, compared to 14.0% removal of TPH in the control plot C. In plot A, the alkane fraction of TPH was reduced by 94.2%, the aromatic fraction of TPH was reduced by 91.9%, and NSO (nitrogen-, sulfur-, and oxygen-containing compound) and asphaltene fractions of TPH were reduced by 85.2% in 1 year. Similarly, in plot B the degradation of alkane, aromatic, and NSO plus asphaltene fractions of TPH was 95.1, 94.8, and 63.5%, respectively, in 345 days. However, in plot C, removal of alkane (17.3%), aromatic (12.9%), and NSO plus asphaltene (5.8%) fractions was much less. The population of introduced Acinetobacter baumannii strains in plots A and B was stable even after 1 year. Physical and chemical properties of the soil at the bioremediation site improved significantly in 1 year.

Structural diversity of microorganisms in chemically perturbed soil assessed by molecular and cytochemical approaches

Until recently, our understanding of microbial community development in soil ecosystems exposed to different inorganic and organic pollutants has been limited to culturable microorganisms because of the techniques available. The discovery that most soil microorganisms are non-culturable but potentially viable and metabolically active accelerated the application of different culture-independent methods for structural diversity assessments of the microbial community. This review examines the results of recent studies on the impact of heavy metals and organic pollutants on the diversity of the microflora obtained with methods based on analyses of signature biomarkers such as nucleic acids and fatty acids. The application of these techniques allowed researchers to pinpoint reduction of microbial diversity in contaminated soil, and significant shifts in the community structure, leading to the dominance of only a few populations (species) and the disappearance of others, some of which were never isolated by conventional methods (e.g. an increase in Acidobacterium or a decrease in terrestrial non-thermophilic Crenarchaeota). Although the new techniques are not free from limitations, they allow the monitoring of the virtual impact of stressors on soil microorganisms and the direction of resuscitation of the microbial community during natural or induced bioremediation, especially when using combined approaches.