Impact of oil contamination and biostimulation on the diversity of indigenous bacterial communities in soil microcosms

Utilization of-Omic technologies in cold climate hydrocarbon bioremediation: a text-mining approach

Hydrocarbon spills in cold climates are a prominent and enduring form of anthropogenic contamination. Bioremediation is one of a suite of remediation tools that has emerged as a cost-effective strategy for transforming these contaminants in soil, ideally into less harmful products. However, little is understood about the molecular mechanisms driving these complex, microbially mediated processes. The emergence of -omic technologies has led to a revolution within the sphere of environmental microbiology allowing for the identification and study of so called 'unculturable' organisms. In the last decade, -omic technologies have emerged as a powerful tool in filling this gap in our knowledge on the interactions between these organisms and their environment in vivo. Here, we utilize the text mining software Vosviewer to process meta-data and visualize key trends relating to cold climate bioremediation projects. The results of text mining of the literature revealed a shift over time from optimizing bioremediation experiments on the macro/community level to, in more recent years focusing on individual organisms of interest, interactions within the microbiome and the investigation of novel metabolic degradation pathways. This shift in research focus was made possible in large part by the rise of omics studies allowing research to focus not only what organisms/metabolic pathways are present but those which are functional. However, all is not harmonious, as the development of downstream analytical methods and associated processing tools have outpaced sample preparation methods, especially when dealing with the unique challenges posed when analyzing soil-based samples.

Comparative Analysis of Microbial Consortiums and Nanoparticles for Rehabilitating Petroleum Waste Contaminated Soils

Nano-bioremediation application is an ecologically and environmentally friendly technique to overcome the catastrophic situation in soil because of petroleum waste contamination. We evaluated the efficiency of oil-degrading bacterial consortium and silver nanoparticles (AgNPs) with or without fertilizer to remediate soils collected from petroleum waste contaminated oil fields. Physicochemical characteristics of control soil and petroleum contaminated soils were assessed. Four oil-degrading strains, namely Bacillus pumilus (KY010576), Exiguobacteriaum aurantiacum (KY010578), Lysinibacillus fusiformis (KY010586), and Pseudomonas putida (KX580766), were selected based on their in vitrohydrocarbon-degrading efficiency. In a lab experiment, contaminated soils were treated alone and with combined amendments of the bacterial consortium, AgNPs, and fertilizers (ammonium nitrate and diammonium phosphate). We detected the degradation rate of total petroleum hydrocarbons (TPHs) of the soil samples with GC-FID at different intervals of the incubation period (0, 5, 20, 60, 240 days). The bacterial population (CFU/g) was also monitored during the entire period of incubation. The results showed that 70% more TPH was degraded with a consortium with their sole application in 20 days of incubation. There was a positive correlation between TPH degradation and the 100-fold increase in bacterial population in contaminated soils. This study revealed that bacterial consortiums alone showed the maximum increase in the degradation of TPHs at 20 days. The application of nanoparticles and fertilizer has non-significant effects on the consortium degradation potential. Moreover, fertilizer alone or in combination with AgNPs and consortium slows the rate of degradation of TPHs over a short period. Still, it subsequently accelerates the rate of degradation of TPHs, and a negligible amount remains at the end of the incubation period.

Bacteria, Fungi and Microalgae for the Bioremediation of Marine Sediments Contaminated by Petroleum Hydrocarbons in the Omics Era

Petroleum hydrocarbons (PHCs) are one of the most widespread and heterogeneous organic contaminants affecting marine ecosystems. The contamination of marine sediments or coastal areas by PHCs represents a major threat for the ecosystem and human health, calling for urgent, effective, and sustainable remediation solutions. Aside from some physical and chemical treatments that have been established over the years for marine sediment reclamation, bioremediation approaches based on the use of microorganisms are gaining increasing attention for their eco-compatibility, and lower costs. In this work, we review current knowledge concerning the bioremediation of PHCs in marine systems, presenting a synthesis of the most effective microbial taxa (i.e., bacteria, fungi, and microalgae) identified so far for hydrocarbon removal. We also discuss the challenges offered by innovative molecular approaches for the design of effective reclamation strategies based on these three microbial components of marine sediments contaminated by hydrocarbons.

Advances in research on petroleum biodegradability in soil

With the increased demand for petroleum and petroleum products from all parts of the society, environmental pollution caused by petroleum development and production processes is becoming increasingly serious. Soil pollution caused by petroleum seriously affects environmental quality in addition to human lives and productivity. At present, petroleum in soil is mainly degraded by biological methods. In their natural state, native bacteria in the soil spontaneously degrade petroleum pollutants that enter the soil; however, when the pollution levels increase, the degradation rates decrease, and it is necessary to add nutrients, dissolved oxygen, biosurfactants and other additives to improve the degradation ability of the native bacteria in the soil. The degradation process can also be enhanced by adding exogenous petroleum-degrading bacteria, microbial immobilization technologies, and microbial fuel cell technologies.

Crude oil pollution and biodegradation at the Persian Gulf: A comprehensive and review study

The Persian Gulf consider as the fundamental biological marine condition between the seas. There is a different assortment of marine life forms including corals, wipes, and fish in this marine condition. Mangrove timberlands are found all through this sea-going biological system. Sullying of the Persian Gulf to oil-based goods is the principle of danger to this marine condition and this contamination can effectively affect this differing marine condition. Numerous specialists examined the result of oil contamination on Persian Gulf marine creatures including corals sponges, bivalves, and fishes. These analysts affirmed this oil contamination on the Persian Gulf significantly diminished biodiversity. Diverse microorganisms fit to consume oil-based commodities detailed by various scientists from the Persian Gulf and their capacity to the debasement of unrefined petroleum has been examined. There has additionally been little exploration of cyanobacteria, yeast, and unrefined petroleum debasing organisms in this sea-going environment. Biosurfactants are amphipathic molecules that upgrade the disintegration of oil and increment their bioavailability to corrupt microscopic organisms. Additionally, biosurfactant-producing bacteria were discovered from the Persian Gulf, and the capability to degradation of crude oil in microscale was evaluated. The current review article aims to collect the finding of various researches performed in the Persian Gulf on oil pollution and crude-oil biodegradation. It is expected that by applying biological methods in combination with mechanical and chemical methods, the hazard consequences of crude-oil contamination on this important aquatic ecosystem at the world will be mitigated and a step towards preserving this diverse marine environment.

Microbial community evolution during the aerobic biodegradation of petroleum hydrocarbons in marine sediment microcosms: Effect of biostimulation and seasonal variations

Evolution of the microbial community structure in crude oil contaminated marine sediments was assessed under aerobic biodegradation during wet (18 °C) and dry (28 °C) seasons experiments, to account for seasonal variations in nutrients and temperature, under biostimulation and natural attenuation conditions. NMDS showed significant variation in the microbial communities between the wet and the dry season experiments, and between the biostimulation and the natural attenuation treatments in the dry season microcosms. No significant variation in the microbial community and oil biodegradation was observed during the wet season experiments due to high background nitrogen levels eliminating the effect of biostimulation. Larger variations were observed in the dry season experiments and were correlated to enhanced alkanes removal in the biostimulated microcosms, where Alphaproteobacteria dominated the total microbial community by the end of biodegradation (54%). Many hydrocarbonoclastic bacterial genera showed successive dominance during the operation affecting the ultimate performance of the microcosms.

Adaptative transcriptional response of Dietzia cinnamea P4 strain to sunlight simulator

Responses to sunlight exposure of the oil-degrading Dietzia cinnamea P4 strain were evaluated by transcriptional levels of SOS genes, photoreactivation and genes involved in tolerance to high levels of reactive oxygen species. The P4 strain was exposed for 1 and 2 h and the magnitude of level changes in the mRNA was evaluated by qPCR. The results described the activation of the SOS system, with the decline of the repressor lexA gene levels and the concomitant increase of recA and uvrAD genes levels. The genes that participate in the photoreactivation process were also responsive to sunlight. The phrB gene encoding deoxyribodipyrimidine photo-lyase had its expression increased after 1-h exposure, while the phytAB genes showed a progressive increase over the studied period. The protective genes against reactive oxygen species, catalases, superoxides, peroxidases, and thioredoxins, had their expression rates detected under the conditions validated in this study. These results show a fast and coordinated response of genes from different DNA repair and tolerance mechanisms employed by strain P4, suggesting a complex concerted protective action against environmental stressors.

Ecological impact evaluation by constructing in situ microcosm with porous ceramic arrowhead

In recent years, bioremediation has been used as an effective technique for the cleaning of polluted sites. However, bioremediation treatment efficacy varies considerably; thus, characterization of indigenous pollutant-degrading soil microorganisms and assessment of the changes in microbial composition by pollutants are essential for designing efficient bioremediation methods. In this study, an ecological impact evaluation method that is cost-efficient and has low contamination risk was developed to assess the indigenous microbial composition. An "in situ microcosm" was constructed using a porous ceramic arrowhead. Phenol, a common environmental pollutant, was used to assess the evaluation efficacy of this method. Our data showed that phenol gradually percolated into the soil adjacent to the arrowhead and stimulated unique indigenous microorganisms (Bacillus sp., Streptomyces sp., and Cupriavidus sp.). Furthermore, the arrowhead approach enabled efficient evaluation of the ecological impact of phenol on soil microorganisms. Thus, the arrowhead method will contribute to the development of bioremediation methods.

The responses of two native plant species to soil petroleum contamination in the Yellow River Delta, China

Petroleum contamination is a significant environmental problem in the Yellow River Delta. The responses of two native salt-tolerant plant species, alfalfa (Medicago sativa) and bristle grass (Setaria uiridis Beauv), to soil petroleum contamination were investigated at five levels between 0 and 2.0% (w/w). Results showed that the total, aboveground and underground plant biomasses of both species were significantly reduced by petroleum contamination (p < 0.05), with the inhibition enhanced with increased petroleum levels. However, the emergence rate of bristle grass was promoted by petroleum contamination. Following 100 days of exposure, the number of soil petroleum degraders increased greatly, with a trend of initial increase followed by a decrease at 1.5% contamination or higher. Compared to bulk soils, bacteria-degrading alkanes, total hydrocarbons and PAHs in alfalfa rhizosphere soils increased by 1.33-4.18-, 0.85-3.01- and 4.12-12.75-fold, respectively, with an increase of 2.80-10.00-, 4.42-14.44- and 7.30-26.00-fold in bristle grass rhizosphere soils, respectively. The greatest number of petroleum degraders in bristle grass rhizosphere soils resulted in the highest petroleum degradation rate. Bristle grass may be the optimal species for petroleum remediation in the studied area.

The complete genome sequence of the cold adapted crude-oil degrader: Pedobacter steynii DX4

Pedobacter steynii DX4 was isolated from the soil of Tibetan Plateau and it can use crude oil as sole carbon and energy source at 15 °C. The genome of Pedobacter steynii DX4 has been sequenced and served as basis for analysis its metabolic mechanism. It is the first genome of crude oil degrading strain in Pedobacter genus. The 6.58 Mb genome has an average G + C content of 41.31% and encodes 5464 genes. In addition, annotation revealed that Pedobacter steynii DX4 has cold shock proteins, abundant response regulators for cell motility, and enzymes involved in energy conversion and fatty acid metabolism. The genomic characteristics could provide information for further study of oil-degrading microbes for recovery of crude oil polluted environment.

Horizontal gene transfer versus biostimulation: A strategy for bioremediation in Goa

Bioaugmentation, Biostimulation and Horizontal gene transfer (HGT) of catabolic genes have been proven for their role in bioremediation of hydrocarbons. It also has been proved that selection of either biostimulation or bioremediation varies for every contaminated site. The reliability of HGT compared to biostimulation and bioremediation was not tested. The present study focuses on reliability of biostimulatiion, bioaugmentation and HGT during biodegradation of Diesel oil and Non aqueous phase liquids (NAPL). Pseudomonas aeruginosa (AEBBITS1) having alkB and NDO genes was used for bioaugmentation and the experiment was conducted using seawater as medium. Based on Gas chromatography results diesel was found to be degraded to 100% in both presence and absence of AEBBITS1. Denturing gradient gel electrophoresis result showed same pattern in presence and absence of AEBBITS1 indicating no HGT. NAPL degradation was found to be more by Biostimulated Bioaugmentation compared to biostimulation and bioaugmentation alone. This proves that biostimulated bioaugmentation is better strategy for oil contamination (tarabll) in Velsao beach, Goa.

The Interaction between Plants and Bacteria in the Remediation of Petroleum Hydrocarbons: An Environmental Perspective

Widespread pollution of terrestrial ecosystems with petroleum hydrocarbons (PHCs) has generated a need for remediation and, given that many PHCs are biodegradable, bio- and phyto-remediation are often viable approaches for active and passive remediation. This review focuses on phytoremediation with particular interest on the interactions between and use of plant-associated bacteria to restore PHC polluted sites. Plant-associated bacteria include endophytic, phyllospheric, and rhizospheric bacteria, and cooperation between these bacteria and their host plants allows for greater plant survivability and treatment outcomes in contaminated sites. Bacterially driven PHC bioremediation is attributed to the presence of diverse suites of metabolic genes for aliphatic and aromatic hydrocarbons, along with a broader suite of physiological properties including biosurfactant production, biofilm formation, chemotaxis to hydrocarbons, and flexibility in cell-surface hydrophobicity. In soils impacted by PHC contamination, microbial bioremediation generally relies on the addition of high-energy electron acceptors (e.g., oxygen) and fertilization to supply limiting nutrients (e.g., nitrogen, phosphorous, potassium) in the face of excess PHC carbon. As an alternative, the addition of plants can greatly improve bioremediation rates and outcomes as plants provide microbial habitats, improve soil porosity (thereby increasing mass transfer of substrates and electron acceptors), and exchange limiting nutrients with their microbial counterparts. In return, plant-associated microorganisms improve plant growth by reducing soil toxicity through contaminant removal, producing plant growth promoting metabolites, liberating sequestered plant nutrients from soil, fixing nitrogen, and more generally establishing the foundations of soil nutrient cycling. In a practical and applied sense, the collective action of plants and their associated microorganisms is advantageous for remediation of PHC contaminated soil in terms of overall cost and success rates for in situ implementation in a diversity of environments. Mechanistically, there remain biological unknowns that present challenges for applying bio- and phyto-remediation technologies without having a deep prior understanding of individual target sites. In this review, evidence from traditional and modern omics technologies is discussed to provide a framework for plant-microbe interactions during PHC remediation. The potential for integrating multiple molecular and computational techniques to evaluate linkages between microbial communities, plant communities and ecosystem processes is explored with an eye on improving phytoremediation of PHC contaminated sites.

Multiwall carbon nanotubes increase the microbial community in crude oil contaminated fresh water sediments

Since crude oil contamination is one of the biggest environmental concerns, its removal from contaminated sites is of interest for both researchers and industries. In situ bioremediation is a promising technique for decreasing or even eliminating crude oil and hydrocarbon contamination. However, since these compounds are potentially toxic for many microorganisms, high loads of contamination can inhibit the microbial community and therefore reduce the removal rate. Therefore, any strategy with the ability to increase the microbial population in such circumstances can be of promise in improving the remediation process. In this study, multiwall carbon nanotubes were employed to support microbial growth in sediments contaminated with crude oil. Following spiking of fresh water sediments with different concentrations of crude oil alone and in a mixture with carbon nanotubes for 30days, the microbial profiles in these sediments were obtained using FLX-pyrosequencing. Next, the ratios of each member of the microbial population in these sediments were compared with those values in the untreated control sediment. This study showed that combination of crude oil and carbon nanotubes can increase the diversity of the total microbial population. Furthermore, these treatments could increase the ratios of several microorganisms that are known to be effective in the degradation of hydrocarbons.

Microbial density and diversity in constructed wetland systems and the relation to pollutant removal efficiency

Microbes are believed to be at the core of the wastewater treatment processes in constructed wetlands (CWs). The aim of this study was to assess the microbial biomass carbon (MBC) and Shannon's diversity index (SDI) in the substrate of CWs planted with Phragmites australis, Hymenocallis littoralis, Canna indica and Cyperus flabelliformis, and to relate MBC and SDI to the pollutant removal in the systems. Significant higher MBC was observed in CWs with H. littoralis and C. indica than in CWs with P. australis, and the MBC differed with season and substrate depth. The microbial community in the wetlands included four phyla: Cyanobacteria, Proteobacteria, Chloroflexi, and Acidobacteria, with a more diverse community structure in wetlands with C. flabelliformis. The MBC in the substrate and the SDI of the 15-20 cm depth correlated with the removal of biochemical oxygen demand, NH4-N and NO3-N. Our results indicate that substrate SDI and MBC can both be regarded as bioindicators of the pollutant removal ability in CWs.

Evaluating the efficacy of bioremediating a diesel-contaminated soil using ecotoxicological and bacterial community indices

Diesel represents a common environmental contaminant as a result of operation, storage, and transportation accidents. The bioremediation of diesel in a contaminated soil is seen as an environmentally safe approach to treat contaminated land. The effectiveness of the remediation process is usually assessed by the degradation of the total petroleum hydrocarbon (TPH) concentration, without considering ecotoxicological effects. The aim of this study was to assess the efficacy of two bioremediation strategies in terms of reduction in TPH concentration together with ecotoxicity indices and changes in the bacterial diversity assessed using PCR-denaturing gradient gel electrophoresis (DGGE). The biostimulation strategy resulted in a 90 % reduction in the TPH concentration versus 78 % reduction from the natural attenuation strategy over 12 weeks incubation in a laboratory mesocosm-containing diesel-contaminated soil. In contrast, the reduction in the ecotoxicity resulting from the natural attenuation treatment using the Microtox and earthworm toxicity assays was more than double the reduction resulting from the biostimulation treatment (45 and 20 % reduction, respectively). The biostimulated treatment involved the addition of nitrogen and phosphorus in order to stimulate the microorganisms by creating an optimal C:N:P molar ratio. An increased concentration of ammonium and phosphate was detected in the biostimulated soil compared with the naturally attenuated samples before and after the remediation process. Furthermore, through PCR-DGGE, significant changes in the bacterial community were observed as a consequence of adding the nutrients together with the diesel (biostimulation), resulting in the formation of distinctly different bacterial communities in the soil subjected to the two strategies used in this study. These findings indicate the suitability of both bioremediation approaches in treating hydrocarbon-contaminated soil, particularly biostimulation. Although biostimulation represents a commercially viable bioremediation technology for use in diesel-contaminated soils, further research is required to determine the ecotoxicological impacts of the intervention.

Bacterial community shift in the coastal Gulf of Mexico salt-marsh sediment microcosm in vitro following exposure to the Mississippi Canyon Block 252 oil (MC252)

In this study, we examined the responses by the indigenous bacterial communities in salt-marsh sediment microcosms in vitro following treatment with Mississippi Canyon Block 252 oil (MC252). Microcosms were constructed of sediment and seawater collected from Bayou La Batre located in coastal Alabama on the Gulf of Mexico. We used an amplicon pyrosequencing approach on microcosm sediment metagenome targeting the V3–V5 region of the 16S rRNA gene. Overall, we identified a shift in the bacterial community in three distinct groups. The first group was the early responders (orders Pseudomonadales and Oceanospirillales within class Gammaproteobacteria), which increased their relative abundance within 2 weeks and were maintained 3 weeks after oil treatment. The second group was identified as early, but transient responders (order Rhodobacterales within class Alphaproteobacteria; class Epsilonproteobacteria), which increased their population by 2 weeks, but returned to the basal level 3 weeks after oil treatment. The third group was the late responders (order Clostridiales within phylum Firmicutes; order Methylococcales within class Gammaproteobacteria; and phylum Tenericutes), which only increased 3 weeks after oil treatment. Furthermore, we identified oil-sensitive bacterial taxa (order Chromatiales within class Gammaproteobacteria; order Syntrophobacterales within class Deltaproteobacteria), which decreased in their population after 2 weeks of oil treatment. Detection of alkane (alkB), catechol (C2,3DO) and biphenyl (bph) biodegradation genes by PCR, particularly in oil-treated sediment metacommunity DNA, delineates proliferation of  the hydrocarbon degrading bacterial community. Overall, the indigenous bacterial communities in our salt-marsh sediment in vitro microcosm study responded rapidly and shifted towards members of the taxonomic groups that are capable of surviving in an MC252 oil-contaminated environment.

Use of Bacillus thuringiensis supernatant from a fermentation process to improve bioremediation of chlorpyrifos in contaminated soils

The aim of this research was to investigate the potential of a nutrient-rich organic waste, namely the cell-free supernatant of Bacillus thuringiensis (BtS) gathered from fermentation, as a biostimulating agent to improve and sustain microbial populations and their enzymatic activities, thereby assisting in the bioremediation of chlorpyrifos-contaminated soil at a high dose (70 mg kg(-1)). Experiments were performed for up to 80 d. Chlorpyrifos degradation and its major metabolic product, 3,5,6-trichloro-2-pyridinol (TCP), were quantified by high-performance liquid chromatography (HPLC); total microbial populations were enumerated by direct counts in specific medium; and fluorescein diacetate (FDA) hydrolysis was measured as an index of soil microbial activity. Throughout the experiment, there was higher chlorpyrifos degradation in soil supplemented with BtS (83.1%) as compared to non-supplemented soil. TCP formation and degradation occurred in all soils, but the greatest degradation (30.34%) was observed in soil supplemented with BtS. The total microbial populations were significantly improved by supplementation with BtS. The application of chlorpyrifos to soil inhibited the enzymatic activity; however, this negative effect was counteracted by BtS, inducing an increase of approximately 16% in FDA hydrolysis. These results demonstrate the potential of B. thuringiensis supernatant as a suitable biostimulation agent for enhancing chlorpyrifos and TCP biodegradation in chlorpyrifos-contaminated soils.

Bioremediation potential of microorganisms derived from petroleum reservoirs

Bacterial strains and metagenomic clones, both obtained from petroleum reservoirs, were evaluated for petroleum degradation abilities either individually or in pools using seawater microcosms for 21 days. Gas Chromatography-Flame Ionization Detector (GC-FID) and Gas Chromatography-Mass Spectrometry (GC-MS) analyses were carried out to evaluate crude oil degradation. The results showed that metagenomic clones 1A and 2B were able to biodegrade n-alkanes (C14 to C33) and isoprenoids (phytane and pristane), with rates ranging from 31% to 47%, respectively. The bacteria Dietzia maris CBMAI 705 and Micrococcus sp. CBMAI 636 showed higher rates reaching 99% after 21 days. The metagenomic clone pool biodegraded these compounds at rates ranging from 11% to 45%. Regarding aromatic compound biodegradation, metagenomic clones 2B and 10A were able to biodegrade up to 94% of phenanthrene and methylphenanthrenes (3-MP, 2-MP, 9-MP and 1-MP) with rates ranging from 55% to 70% after 21 days, while the bacteria Dietzia maris CBMAI 705 and Micrococcus sp. CBMAI 636 were able to biodegrade 63% and up to 99% of phenanthrene, respectively, and methylphenanthrenes (3-MP, 2-MP, 9-MP and 1-MP) with rates ranging from 23% to 99% after 21 days. In this work, isolated strains as well as metagenomic clones were capable of degrading several petroleum compounds, revealing an innovative strategy and a great potential for further biotechnological and bioremediation applications.

Using liquid crystals to reveal how mechanical anisotropy changes interfacial behaviors of motile bacteria

Bacteria often inhabit and exhibit distinct dynamical behaviors at interfaces, but the physical mechanisms by which interfaces cue bacteria are still poorly understood. In this work, we use interfaces formed between coexisting isotropic and liquid crystal (LC) phases to provide insight into how mechanical anisotropy and defects in LC ordering influence fundamental bacterial behaviors. Specifically, we measure the anisotropic elasticity of the LC to change fundamental behaviors of motile, rod-shaped Proteus mirabilis cells (3 μm in length) adsorbed to the LC interface, including the orientation, speed, and direction of motion of the cells (the cells follow the director of the LC at the interface), transient multicellular self-association, and dynamical escape from the interface. In this latter context, we measure motile bacteria to escape from the interfaces preferentially into the isotropic phase, consistent with the predicted effects of an elastic penalty associated with strain of the LC about the bacteria when escape occurs into the nematic phase. We also observe boojums (surface topological defects) present at the interfaces of droplets of nematic LC (tactoids) to play a central role in mediating the escape of motile bacteria from the LC interface. Whereas the bacteria escape the interface of nematic droplets via a mechanism that involved nematic director-guided motion through one of the two boojums, for isotropic droplets in a continuous nematic phase, the elasticity of the LC generally prevented single bacteria from escaping. Instead, assemblies of bacteria piled up at boojums and escape occurred through a cooperative, multicellular phenomenon. Overall, our studies show that the dynamical behaviors of motile bacteria at anisotropic LC interfaces can be understood within a conceptual framework that reflects the interplay of LC elasticity, surface-induced order, and topological defects.

Potential impact of soil microbial heterogeneity on the persistence of hydrocarbons in contaminated subsurface soils

In situ bioremediation is potentially a cost effective treatment strategy for subsurface soils contaminated with petroleum hydrocarbons, however, limited information is available regarding the impact of soil spatial heterogeneity on bioremediation efficacy. In this study, we assessed issues associated with hydrocarbon biodegradation and soil spatial heterogeneity (samples designated as FTF 1, 5 and 8) from a site in which in situ bioremediation was proposed for hydrocarbon removal. Test pit activities showed similarities in FTF soil profiles with elevated hydrocarbon concentrations detected in all soils at 2 m below ground surface. However, PCR-DGGE-based cluster analysis showed that the bacterial community in FTF 5 (at 2 m) was substantially different (53% dissimilar) and 2-3 fold more diverse than communities in FTF 1 and 8 (with 80% similarity). When hydrocarbon degrading potential was assessed, differences were observed in the extent of (14)C-benzene mineralisation under aerobic conditions with FTF 5 exhibiting the highest hydrocarbon removal potential compared to FTF 1 and 8. Further analysis indicated that the FTF 5 microbial community was substantially different from other FTF samples and dominated by putative hydrocarbon degraders belonging to Pseudomonads, Xanthomonads and Enterobacteria. However, hydrocarbon removal in FTF 5 under anaerobic conditions with nitrate and sulphate electron acceptors was limited suggesting that aerobic conditions were crucial for hydrocarbon removal. This study highlights the importance of assessing available microbial capacity prior to bioremediation and shows that the site's spatial heterogeneity can adversely affect the success of in situ bioremediation unless area-specific optimizations are performed.

Bioremediation assessment of diesel-biodiesel-contaminated soil using an alternative bioaugmentation strategy

This study investigated the effectiveness of successive bioaugmentation, conventional bioaugmentation, and biostimulation of biodegradation of B10 in soil. In addition, the structure of the soil microbial community was assessed by polymerase chain reaction-denaturing gradient gel electrophoresis. The consortium was inoculated on the initial and the 11th day of incubation for successive bioaugmentation and only on the initial day for bioaugmentation and conventional bioaugmentation. The experiment was conducted for 32 days. The microbial consortium was identified based on sequencing of 16S rRNA gene and consisted as Pseudomonas aeruginosa, Achromobacter xylosoxidans, and Ochrobactrum intermedium. Nutrient introduction (biostimulation) promoted a positive effect on microbial populations. The results indicate that the edaphic community structure and dynamics were different according to the treatments employed. CO2 evolution demonstrated no significant difference in soil microbial activity between biostimulation and bioaugmentation treatments. The total petroleum hydrocarbon (TPH) analysis indicated a biodegradation level of 35.7 and 32.2 % for the biostimulation and successive bioaugmentation treatments, respectively. Successive bioaugmentation displayed positive effects on biodegradation, with a substantial reduction in TPH levels.

Transcriptional profiling of genes involved in n-hexadecane compounds assimilation in the hydrocarbon degrading Dietzia cinnamea P4 strain

The petroleum-derived degrading Dietzia cinnamea strain P4 recently had its genome sequenced and annotated. This allowed employing the data on genes that are involved in the degradation of n-alkanes. To examine the physiological behavior of strain P4 in the presence of n-alkanes, the strain was grown under varying conditions of pH and temperature. D. cinnamea P4 was able to grow at pH 7.0–9.0 and at temperatures ranging from 35 ºC to 45 ºC. Experiments of gene expression by real-time quantitative RT-PCR throughout the complete growth cycle clearly indicated the induction of the regulatory gene alkU (TetR family) during early growth. During the logarithmic phase, a large increase in transcriptional levels of a lipid transporter gene was noted. Also, the expression of a gene that encodes the protein fused rubredoxin-alkane monooxygenase was enhanced. Both genes are probably under the influence of the AlkU regulator.

Dynamics of indigenous bacterial communities associated with crude oil degradation in soil microcosms during nutrient-enhanced bioremediation

Bacterial population dynamics were examined during bioremediation of an African soil contaminated with Arabian light crude oil and nutrient enrichment (biostimulation). Polymerase chain reaction followed by denaturing gradient gel electrophoresis (DGGE) were used to generate bacterial community fingerprints of the different treatments employing the 16S ribosomal ribonucleic acid (rRNA) gene as molecular marker. The DGGE patterns of the nutrient-amended soils indicated the presence of distinguishable bands corresponding to the oil-contaminated-nutrient-enriched soils, which were not present in the oil-contaminated and pristine control soils. Further characterization of the dominant DGGE bands after excision, reamplification and sequencing revealed that Corynebacterium spp., Dietzia spp., Rhodococcus erythropolis sp., Nocardioides sp., Low G+C (guanine plus cytosine) Gram positive bacterial clones and several uncultured bacterial clones were the dominant bacterial groups after biostimulation. Prominent Corynebacterium sp. IC10 sequence was detected across all nutrient-amended soils but not in oil-contaminated control soil. Total heterotrophic and hydrocarbon utilizing bacterial counts increased significantly in the nutrient-amended soils 2 weeks post contamination whereas oil-contaminated and pristine control soils remained fairly stable throughout the experimental period. Gas chromatographic analysis of residual hydrocarbons in biostimulated soils showed marked attenuation of contaminants starting from the second to the sixth week after contamination whereas no significant reduction in hydrocarbon peaks were seen in the oil-contaminated control soil throughout the 6-week experimental period. Results obtained indicated that nutrient amendment of oil-contaminated soil selected and enriched the bacterial communities mainly of the Actinobacteria phylogenetic group capable of surviving in toxic contamination with concomitant biodegradation of the hydrocarbons. The present study therefore demonstrated that the soil investigated harbours hydrocarbon-degrading bacterial populations which can be biostimulated to achieve effective bioremediation of oil-contaminated soil.

Detection by denaturing gradient gel electrophoresis of ammonia-oxidizing bacteria in microcosms of crude oil-contaminated mangrove sediments

Currently, the effect of crude oil on ammonia-oxidizing bacterium communities from mangrove sediments is little understood. We studied the diversity of ammonia-oxidizing bacteria in mangrove microcosm experiments using mangrove sediments contaminated with 0.1, 0.5, 1, 2, and 5% crude oil as well as non-contaminated control and landfarm soil from near an oil refinery in Camamu Bay in Bahia, Brazil. The evolution of CO(2) production in all crude oil-contaminated microcosms showed potential for mineralization. Cluster analysis of denaturing gradient gel electrophoresis-derived samples generated with primers for gene amoA, which encodes the functional enzyme ammonia monooxygenase, showed differences in the sample contaminated with 5% compared to the other samples. Principal component analysis showed divergence of the non-contaminated samples from the 5% crude oil-contaminated sediment. A Venn diagram generated from the banding pattern of PCR-denaturing gradient gel electrophoresis was used to look for operational taxonomic units (OTUs) in common. Eight OTUs were found in non-contaminated sediments and in samples contaminated with 0.5, 1, or 2% crude oil. A Jaccard similarity index of 50% was found for samples contaminated with 0.1, 0.5, 1, and 2% crude oil. This is the first study that focuses on the impact of crude oil on the ammonia-oxidizing bacterium community in mangrove sediments from Camamu Bay.

Monitoring of microbial hydrocarbon remediation in the soil

Bioremediation of hydrocarbon pollutants is advantageous owing to the cost-effectiveness of the technology and the ubiquity of hydrocarbon-degrading microorganisms in the soil. Soil microbial diversity is affected by hydrocarbon perturbation, thus selective enrichment of hydrocarbon utilizers occurs. Hydrocarbons interact with the soil matrix and soil microorganisms determining the fate of the contaminants relative to their chemical nature and microbial degradative capabilities, respectively. Provided the polluted soil has requisite values for environmental factors that influence microbial activities and there are no inhibitors of microbial metabolism, there is a good chance that there will be a viable and active population of hydrocarbon-utilizing microorganisms in the soil. Microbial methods for monitoring bioremediation of hydrocarbons include chemical, biochemical and microbiological molecular indices that measure rates of microbial activities to show that in the end the target goal of pollutant reduction to a safe and permissible level has been achieved. Enumeration and characterization of hydrocarbon degraders, use of micro titer plate-based most probable number technique, community level physiological profiling, phospholipid fatty acid analysis, 16S rRNA- and other nucleic acid-based molecular fingerprinting techniques, metagenomics, microarray analysis, respirometry and gas chromatography are some of the methods employed in bio-monitoring of hydrocarbon remediation as presented in this review.

Insight from the draft genome of Dietzia cinnamea P4 reveals mechanisms of survival in complex tropical soil habitats and biotechnology potential

The draft genome of Dietzia cinnamea strain P4 was determined using pyrosequencing. In total, 428 supercontigs were obtained and analyzed. We here describe and interpret the main features of the draft genome. The genome contained a total of 3,555,295 bp, arranged in a single replicon with an average G+C percentage of 70.9%. It revealed the presence of complete pathways for basically all central metabolic routes. Also present were complete sets of genes for the glyoxalate and reductive carboxylate cycles. Autotrophic growth was suggested to occur by the presence of genes for aerobic CO oxidation, formate/formaldehyde oxidation, the reverse tricarboxylic acid cycle and the 3-hydropropionate cycle for CO₂ fixation. Secondary metabolism was evidenced by the presence of genes for the biosynthesis of terpene compounds, frenolicin, nanaomycin and avilamycin A antibiotics. Furthermore, a probable role in azinomycin B synthesis, an important product with antitumor activity, was indicated. The complete alk operon for the degradation of n-alkanes was found to be present, as were clusters of genes for biphenyl ring dihydroxylation. This study brings new insights in the genetics and physiology of D. cinnamea P4, which is useful in biotechnology and bioremediation.

Removal of petroleum pollutants and monitoring of bacterial community structure in a membrane bioreactor

The long-term operational stability (159 d) in removal of organics and ammonia from synthetic wastewater was investigated. The experiment was carried out in two identical plug flow membrane bioreactors (MBR) (each with a submerged A4 Kubota membrane) operated under aerobic conditions. The vacuum distillate of a crude oil fraction in the emulsified state, which was used to model the petroleum pollutants, was added into the feed medium. The performance of biological treatment was evaluated by physicochemical analyses such as nitrogen forms, COD, and BOD. Additionally, monitoring of PAHs in the wastewaters was performed using HPLC-diode array detector. Moreover, the community structure of bacteria was analyzed by polymerase chain reaction-denaturing gradient gel electrophoresis. The MBR treatment was very effective with reduction by more than 90% of COD and Total Organic Carbon. Nearly complete removal of petroleum originated non-polar micropollutants was observed. The influence of the highest dosage of petroleum pollutants (1000 μLL(-1)) on the bacterial community was noted.

Succession of bacterial community along with the removal of heavy crude oil pollutants by multiple biostimulation treatments in the Yellow River Delta, China

Multiple biostimulation treatments were applied to enhance the removal of heavy crude oil pollutants in the saline soil of Yellow River Delta. Changes of the soil bacterial community were monitored using the terminal restriction fragment length polymorphism (T-RFLP) and clone library analyses. The 140-day microcosm experiments showed that low C:N:P ratio, high availability of surfactant and addition of bulking agent significantly enhanced the performance, leading to the highest total petroleum hydrocarbon removal. Meanwhile, the bacterial community was remarkably changed by the multiple biostimulation treatments, with the Deltaproteobacteria, Firmicutes, Actinobacteria, Acidobacteria and Planctomycetes being inhibited and the Alpha- and Beta-proteobacteria and some unknown Gammaproteobacteria bacteria being enriched. In addition, different hydrocarbon-degraders came to power in the following turn. At the first stage, the Alcanivorax-related Gammaproteobacteria bacteria dominated in the biostimulated soil and contributed mainly to the biodegradation of easily degradable portion of the heavy crude oil. Then the bacteria belonging to Alphaproteobacteria, followed by bacteria belonging to Candidate division OD1, became the dominant oil-degraders to degrade the remaining recalcitrant constituents of the heavy crude oil.

Temporal changes in Sphingomonas and Mycobacterium populations in mangrove sediments contaminated with different concentrations of polycyclic aromatic hydrocarbons (PAHs)

The change in community diversity and structure of the indigenous, dominant, polycyclic aromatic hydrocarbon (PAH)-degrading bacterial genera, Sphingomonas and Mycobacterium, due to contamination in the environment is not very well known. A combination of PCR-DGGE with specific primers and a cultivation-dependent microbiological method was used to detect different populations of Sphingomonas and Mycobacterium in mangrove sediments. The structure of the entire bacterial community (including Sphingomonas) did not show a shift due to environmental contamination, whereas the diversity of Mycobacterium populations in mangrove sediments with higher PAH contamination increased from exposure between Day 0 and Day 30. The isolated Mycobacterium strains migrated to the same position as the major bands of the bacterial communities in Mycobacterium-specific DGGE. A dioxygenase gene system, nidA, which is commonly found in PAH-degrading Mycobacterium strains, was also detected in the more highly contaminated sediment slurries. The present study revealed that Mycobacterium species were the dominant PAH-degraders and played an important role in degrading PAHs in contaminated mangrove sediments.

Bacterial diversity dynamics in a long-term petroleum-contaminated soil

Bacterial diversity dynamics were investigated in the soil samples in different distances and depths from/at a long-term petroleum-contaminated site. Microbial activity in the soil samples showed ATP values closely correlated with organic matter content (OC) and total petroleum hydrocarbon (TPH). Bacterial community diversity (H) and evenness (J) using PCR-DGGE (polymerase chain reaction-denaturing gradient gel electrophoresis) and PCR-T-RFLP (terminal restriction fragment length polymorphism) results showed positive correlation with concentration of TPH or OC, but tmoA (toluene monooxygenase gene)-based bacterial H and J using a PCR-T-RFLP result did not. No significant difference of H and J values in the bacterial and the tmoA communities was observed. The bacterial community structure characterized by PCR-DGGE and PCR-T-RFLP techniques showed similarity according to soil sampling distance rather than soil sampling depth. Canonical correspondence analysis demonstrated that OC including TPH had the most significant effect on the bacterial community diversity at the long-term petroleum-contaminated site.

How a bacterial community originating from a contaminated coastal sediment responds to an oil input

Bacterial communities inhabiting coastal sediments are subjected to oil spills. In order to examine the early structural response of a complex bacterial community to oil pollution, a kinetic study of the crude oil impact on bacterial communities inhabiting sediments from the contaminated Etang-de-Berre lagoon was performed. The sediments were maintained in slurries in presence or absence of crude oil and the kinetic study was carried out 14 days. During this period, 54% of crude oil was biodegraded showing the importance of the early degradation step. The metabolically active community (16S rRNA transcript analysis) was immediately impacted by the oil input, observed as an apparent decrease of species richness in the first hour of incubation. Nevertheless, this shift was quickly reversed, highlighting a fast, adaptative and efficient response of the metabolically active bacterial population. The high proportion of sequences related to hydrocarbonoclastic strains or petroleum-associated clones in active oiled community was consistent with significant increasing numbers of cultivable hydrocarbonoclastic bacteria at the end of the experiment. We concluded that "Etang-de-Berre" bacterial communities inhabiting oiled sediments for decades adopted a specific structure depending on oil presence and were able to face hydrocarbon contamination quickly and efficiently.

Monitoring the impact of hydrocarbon contamination and nutrient addition on microbial density, activity, and diversity in soil

The development of optimal in situ bioremediation strategies requires a better knowledge of their impact on the soil microbial communities. We have evaluated the impact of hexadecane contamination and different nutrient amendments on soil microbial density and activity. Microbial density was measured via total DNA quantification, and microbial activity via respiration and RNA variation. The RNA/DNA ratio was also determined, as it is a potential indicator of microbial activity. PCR-amplified 16S rRNA genes were cloned and sequenced to analyze the diversity of bacterial communities. Nutrient addition significantly increased respiration and DNA and RNA concentrations in contaminated soil, indicating a limitation of degradation and growth by the availability of nitrogen and phosphorus in unamended microcosms. Hexadecane treatment slightly affected the diversity of the bacterial community, while it was dramatically reduced by nutrient treatments, particularly the addition of nitrogen and phosphorus. Microbial community composition was also altered with the enrichment of populations related to Nocardia in bioremediated soils, while uncultured Proteobacteria were mostly detected in uncontaminated soil.

Effects of temperature and fertilization on total vs. active bacterial communities exposed to crude and diesel oil pollution in NW Mediterranean Sea

The dynamics of total and active microbial communities were studied in seawater microcosms amended with crude or diesel oil at different temperatures (25, 10 and 4 degrees C) in the presence/absence of organic fertilization (Inipol EAP 22). Total and hydrocarbon-degrading microbes were enumerated by fluorescence microscopy and Most Probable Number (MPN) method, respectively. Total (16S rDNA-based) vs. active (16S rRNA) bacterial community structure was monitored by Capillary-Electrophoresis Single Strand Conformation Polymorphism (CE-SSCP) fingerprinting. Hydrocarbons were analyzed after 12 weeks of incubation by gas chromatography-mass spectrometry. Total and hydrocarbon-degrading microbial counts were highly influenced by fertilization while no important differences were observed between temperatures. Higher biodegradation levels were observed in fertilized microcosms. Temperature and fertilization induced changes in structure of total bacterial communities. However, fertilization showed a more important effect on active bacterial structure. The calculation of Simpson's diversity index showed similar trends among temperatures whereas fertilization reduced diversity index of both total and active bacterial communities.

Microbiological polyphasic approach for soil health evaluation in an Italian polluted site

The use of microorganisms as bioindicators of soil health is quite a new feature, rarely considered for the soil health evaluation in chronically-polluted industrial sites, and still suffering of the bias related to the technique applied. In this work we applied a microbiological polyphasic approach, relying on soil indigenous microorganisms as bioindicators and combining culture-dependent and -independent methods, in order to evaluate soil health of four sites (1a, 1b, 2a and 2b) inside a chemical factory with a centenary activity. Functional as well as structural aspects were comprehensively considered. Results were related to the kind of pollutants found in each site. Heavy metal pollution was recorded in sites 1b and 2b, while both organic and inorganic substances were detected in sites 1a and 2a. Based on the chemical and physical properties of the four soils, site 1b and 2b grouped together, while 1a and 2a were separated from the others. The density of the culturable bacteria was very low in site 2a, where only gram-positive were found. According to the identification of culturable bacteria, site 2a showed the lowest similarity with the other sites. Microbial activity was detected only in sites 1b and 2b. PCR-DGGE (Denaturing Gradient Gel Electrophoresis), was performed on the culturable, total and active microbial communities. Consistently with the identification of culturable bacterial strains, the molecular profile of the culturable fraction of site 2a, was clearly separated from the molecular profiles of other sites in cluster analysis. Molecular fingerprintings of the whole and active bacterial communities differed among the sites, but clustered according to the pollutants present in each site. The presence of possible key species in each site has been discussed according to the whole and active species. Since the results obtained by microbiological analysis are consistent with the chemical data, we suggest that the use of this microbiological polyphasic approach and of microorganisms as intrinsic bioindicators, can be suitable for the evaluation of soil health.

Selective enhancement of the fluorescent pseudomonad population after amending the recirculating nutrient solution of hydroponically grown plants with a nitrogen stabilizer

Fluorescent pseudomonads have been associated, via diverse mechanisms, with suppression of root disease caused by numerous fungal and fungal-like pathogens. However, inconsistent performance in disease abatement, after their employment, has been a problem. This has been attributed, in part, to the inability of the biocontrol bacterium to maintain a critical threshold population necessary for sustained biocontrol activity. Our results indicate that a nitrogen stabilizer (N-Serve, Dow Agrosciences) selectively and significantly enhanced, by two to three orders of magnitude, the resident population of fluorescent pseudomonads in the amended (i.e., 25 microg ml(-1) nitrapyrin, the active ingredient) and recycled nutrient solution used in the cultivation of hydroponically grown gerbera and pepper plants. Pseudomonas putida was confirmed as the predominant bacterium selectively enhanced. Terminal restriction fragment length polymorphism (T-RFLP) analysis of 16S rDNA suggested that N-Serve selectively increased P. putida and reduced bacterial diversity 72 h after application. In vitro tests revealed that the observed population increases of fluorescent pseudomonads were preceded by an early growth suppression of indigenous aerobic heterotrophic bacteria (AHB) population. Interestingly, the fluorescent pseudomonad population did not undergo this decrease, as shown in competition assays. Xylene and 1,2,4-trimethylbenzene (i.e., the inert ingredients in N-Serve) were responsible for a significant percentage of the fluorescent pseudomonad population increase. Furthermore, those increases were significantly higher when the active ingredient (i.e., nitrapyrin) and the inert ingredients were combined, which suggests a synergistic response. P. putida strains were screened for the ability to produce antifungal compounds and for the antifungal activity against Pythium aphanidermatum and Phytophthora capsici. The results of this study suggest the presence of diverse mechanisms with disease-suppressing potential. This study demonstrates the possibility of using a specific substrate to selectively enhance and maintain desired populations of a natural-occurring bacterium such as P. putida, a trait considered to have great potential in biocontrol applications for plant protection.

Diversity of ring-hydroxylating dioxygenases in pristine and oil contaminated microbial mats at genomic and transcriptomic levels

The aim of this work was to characterize bacterial ring-hydroxylating dioxygenase (RHD) diversity in a pristine microbial mat and follow their diversity changes in response to heavy fuel oil contamination. In order to describe the RHDs diversity, new degenerate primers were designed and a nested-PCR approach was developed to gain sensitivity and wider diversity. RHD diversity in artificially contaminated mats maintained in microcosms and in chronically contaminated mats was analysed by clone libraries and terminal restriction fragment length polymorphism (T-RFLP) at genomic and transcriptomic levels. The RHD diversity in the pristine microbial mat was represented by Pseudomonas putida nahAc-like genes and no increase of diversity was detected after 1 year of oil contamination. The diversity observed in a 30 year chronically polluted microbial mat was represented by four main RHD clusters and two new genes revealing higher polyaromatic hydrocarbon (PAH) degradation capacity. This study illustrates that a single petroleum contamination (such as oil spill) is not enough to involve a detectable modification of RHD diversity. The new degenerate primers described here allowed RHD gene amplification from pristine and contaminated samples thereby showing their diversity. The proposed approach solves one of the main problems of functional gene analysis providing effective amplification of the environmental diversity of the targeted genes.

Microcosm experiments of oil degradation by microbial mats. II. The changes in microbial species

The influence of microbial mats on the degradation of two crude oils (Casablanca and Maya) and the effect of oil pollution on the mat structure were assessed using model ecosystems, prepared under laboratory conditions subject to tidal movements, from pristine Ebro Delta microbial-mat ecosystems. Both selected oils are examples of those currently used for commercial purposes. Casablanca crude oil is aliphatic with a low viscosity; Maya represents a sulphur-rich heavy crude oil that is predominantly aromatic. In the unpolluted microcosms, Microcoleus chthonoplastes-, Phormidium- and Oscillatoria-like were the dominant filamentous cyanobacterial morphotypes, whilst Synechoccocus-, Synechocystis- and Gloeocapsa-like were the most abundant unicellular cyanobacteria. After oil contamination, no significant changes of chlorophyll a and protein concentrations were observed, though cyanobacterial diversity shifts were monitored. Among filamentous cyanobacteria, M. chthonoplastes-like morphotype was the most resistant for both oils, unlike the other cyanobacteria, which tolerated Casablanca but not Maya. Unicellular cyanobacteria seemed to be resistant to pollution with both essayed oils, with the exception of the morphotype resembling Gloeocapsa, which was sensitive to both oils. The crude-oil addition also had a significant effect on certain components of the heterotrophic microbial community. Casablanca oil induced an increase in anaerobic heterotrophic bacteria, whereas the opposite effect was observed in those heterotrophs when polluted with Maya oil. The overall results, microbiological and crude-oil transformation analysis, indicate that the indigenous community has a considerable potential to degrade oil components by means of the metabolic cooperation of phototrophic and heterotrophic populations.

Responses of microbial communities in Arctic sea ice after contamination by crude petroleum oil

Microbial communities associated with Arctic fjord ice polluted with petroleum oils were investigated in this study. A winter field experiment was conducted in the Van Mijen Fjord (Svalbard) from February to June 2004, in which the ice was contaminated with a North Sea paraffinic oil. Holes were drilled in the ice and oil samples frozen into the ice at the start of the experiment. Samples, including cores of both oil-contaminated and clean ice, were collected from the field site 33, 74, and 112 days after oil application. The sampled cores were separated into three sections and processed for microbiological and chemical analyses. In the oil-contaminated cores, enumerations of total prokaryotic cells by fluorescence microscopy and colony-forming units (CFU) counts of heterotrophic prokaryotes both showed stimulation of microbial growth, while concentrations of oil-degrading prokaryotes remained at similar levels in contaminated and clean ice. Analysis of polymerase chain reaction (PCR)-amplified bacterial 16S rRNA gene fragments by denaturing gradient gel electrophoresis (DGGE) revealed that bacterial communities in oil-contaminated ice generated fewer bands than communities in clean ice, although banding patterns changed both in contaminated and clean ice during the experimental period. Microbial communities in unpolluted ice and in cores contaminated with the paraffinic oil were examined by cloning and sequence analysis. In the contaminated cores, the communities became predominated by Gammaproteobacteria related to the genera Colwellia, Marinomonas, and Glaciecola, while clean ice included more heterogeneous populations. Chemical analysis of the oil-contaminated ice cores with determinations of n-C17/Pristane and naphthalene/phenanthrene ratios indicated slow oil biodegradation in the ice, primarily in the deeper parts of the ice with low hydrocarbon concentrations.

Effects of heavy fuel oil on the bacterial community structure of a pristine microbial mat

The effects of petroleum contamination on the bacterial community of a pristine microbial mat from Salins-de-Giraud (Camargue, France) have been investigated. Mats were maintained as microcosms and contaminated with no. 2 fuel oil from the wreck of the Erika. The evolution of the complex bacterial community was monitored by combining analyses based on 16S rRNA genes and their transcripts. 16S rRNA gene-based terminal restriction fragment length polymorphism (T-RFLP) analyses clearly showed the effects of the heavy fuel oil after 60 days of incubation. At the end of the experiment, the initial community structure was recovered, illustrating the resilience of this microbial ecosystem. In addition, the responses of the metabolically active bacterial community were evaluated by T-RFLP and clone library analyses based on 16S rRNA. Immediately after the heavy fuel oil was added to the microcosms, the structure of the active bacterial community was modified, indicating a rapid microbial mat response. Members of the Gammaproteobacteria were initially dominant in the contaminated microcosms. Pseudomonas and Acinetobacter were the main genera representative of this class. After 90 days of incubation, the Gammaproteobacteria were superseded by "Bacilli" and Alphaproteobacteria. This study shows the major changes that occur in the microbial mat community at different time periods following contamination. At the conclusion of the experiment, the RNA approach also demonstrated the resilience of the microbial mat community in resisting environmental stress resulting from oil pollution.

Identification and biodegradation potential of a novel strain of Dietzia cinnamea isolated from a petroleum-contaminated tropical soil

A bacterial strain, named P4, isolated previously from microcosms containing oil-contaminated soil collected from an environmentally protected area of a tropical Atlantic forest (Biological Reserve of Poço das Antas) located in Brazil was identified as Dietzia cinnamea by morphological, biochemical and genotypic tests. Arabian Light and Marlin oils were both degraded when strain P4 was tested for oil degradation ability in microplates. Total Petroleum Hydrocarbons (TPH) analysis, determined by gas chromatography, showed that strain P4 degraded a wide range of n-alkanes, and also pristane and phytane. Furthermore, this strain was also able to grow in mineral liquid media amended with carbazole, quinoline, naphthalene, toluene, gasoline and diesel as the sole carbon sources. The species D. cinnamea has been previously described with only one representative strain isolated from a perianal swab of a patient with a bone marrow transplant. With the results presented here this species is implicated not only as a human pathogen but also as a potential strain for further studies concerning its role for bioremediation of oil contaminated soil.

New group-specific 16S rDNA primers for monitoring foaming mycolata during saline waste-water treatment

Newly designed group-specific PCR primers for denaturing gradient gel electrophoresis (DGGE) were used to investigate foaming mycolata from a bioreactor treating an industrial saline waste-water. Genetic profiles on DGGE gels were different with NaCl at 1.65 and 8.24 g l(-1), demonstrating that mycolata community was affected by salinity. A semi-nested PCR strategy resulted in more bands in community genetic profiles than direct amplification. DNA sequencing of bands confirmed the efficacy of the novel primers with sequences recovered being most similar to foam producing mycolata. The new group-specific primers/DGGE approach is a new step toward a more complete understanding of functionally important groups of bacteria involved in biological treatment of waste-water.