Bacterial community dynamics during bioremediation of diesel oil-contaminated Antarctic soil

Application of xylene-degrading bacteria in the treatment of soil contaminated with petroleum hydrocarbons - A comprehensive laboratory to pilot-scale analysis

Petroleum hydrocarbons, including both aliphatic (gasoline, mineral oil) and aromatic compounds (BTEX), are known for their harmful effects on ecosystems and human health. Despite many studies, large-scale treatment of contaminated soils continues to be challenging, especially at lower temperatures. The use of metabolically-versatile, psychrotolerant, cold-active microorganisms, seems a promising, cost-effective and eco-friendly solution to boost remediation rates. In this study, a suitable microbial consortium was prepared and tested both in lab- and pilot-scale. To achieve the best bioremediation results, bacterial strains were isolated from BTEX-contaminated soil and then tested for the desired traits over a wide range of conditions. Of 5 preselected strains, 3 Pseudomonas strains capable of denitrification and aerobic/anaerobic degradation of hydrocarbons (up to 41.53±7.39 %), further characterized by a broad temperature (4-37 °C), pH (3-4 to 11) and salinity (0-8 %) tolerance, as well as resistance to freezing, were selected. Physiological studies were supported by genetic analyses, which indicated the presence of both alkB and xylM genes, and excluded similarity of the strains to the known opportunistic pathogens. To further confirm the applicability of the consortium, lab-scale analyses were followed by comprehensive pilot-scale tests on ~5 m3 biopile/biocell, at different conditions. The results revealed increased efficacy of the consortium in bioremediation, when compared to biostimulated indigenous strains, for volatile hydrocarbons (93 % vs 88 %) and mineral oil (23 % vs 15 %), as well as 175 % and 136 % acceleration of remediation for the respective compounds in terms of time needed to complete the process. Moreover, the high survivability and metabolic activity of the consortium at different temperatures indicate the possibility of its year-round use for bioremediation of soil contaminated with petroleum hydrocarbons. The study proves the potential of specialized bacteria in the removal of pollutants, and emphasizes the role of bio-based strategies in addressing complex environmental challenges and remediation of contaminated sites.

Regulatory Small RNAs for a Sustained Eco-Agriculture

Small RNA (sRNA) has become an alternate biotechnology tool for sustaining eco-agriculture by enhancing plant solidity and managing environmental hazards over traditional methods. Plants synthesize a variety of sRNA to silence the crucial genes of pests or plant immune inhibitory proteins and counter adverse environmental conditions. These sRNAs can be cultivated using biotechnological methods to apply directly or through bacterial systems to counter the biotic stress. On the other hand, through synthesizing sRNAs, microbial networks indicate toxic elements in the environment, which can be used effectively in environmental monitoring and management. Moreover, microbes possess sRNAs that enhance the degradation of xenobiotics and maintain bio-geo-cycles locally. Selective bacterial and plant sRNA systems can work symbiotically to establish a sustained eco-agriculture system. An sRNA-mediated approach is becoming a greener tool to replace xenobiotic pesticides, fertilizers, and other chemical remediation elements. The review focused on the applications of sRNA in both sustained agriculture and bioremediation. It also discusses limitations and recommends various approaches toward future improvements for a sustained eco-agriculture system.

Full-scale bioremediation of diesel-polluted soil in an Arctic landfarm

A full-scale, experimental landfarm was tested for the capacity to biodegrade oil-polluted soil under high-Arctic tundra conditions in northeast Greenland at the military outpost 9117 Station Mestersvig. Soil contaminated with Arctic diesel was transferred to the landfarm in August 2012 followed by yearly addition of fertilizer and plowing and irrigation to optimize microbial diesel biodegradation. Biodegradation was determined from changes in total petroleum hydrocarbons (TPH), enumeration of specific subpopulations of oil-degrading microorganisms (MPN), and changes in selected classes of alkylated isomers and isomer ratios. Sixty-four percent of the diesel was removed in the landfarm within the first year, but a recalcitrant fraction (18%) remained after five years. n-alkanes and naphthalenes were biodegraded as demonstrated by changing isomer ratios. Dibenzothiophenes and phenanthrenes showed almost constant isomer ratios indicating that their removal was mostly abiotic. Oil-degrading microorganisms were present for the major components of diesel (n-alkanes, alkylbenzenes and alkylnaphthalenes). The degraders showed very large population increases in the landfarm with a peak population of 1.2 × 10⁹ cells g^-1 of total diesel degraders. Some diesel compounds such as cycloalkanes, hydroxy-PAHs and sulfur-heterocycles had very few or no specific degraders, these compounds may consequently be degraded only by slow co-metabolic processes or not at all.

Enhancement of anaerobic degradation of petroleum hydrocarbons by electron intermediate: Performance and mechanism

A quinone-respiring strain capable of degrading multitudinous petroleum hydrocarbons was isolated by selective medium and identified as Bacillus sp. (named as C8). Maximum 76.7% of total petroleum hydrocarbons (TPH) were degraded by the biosurfactant-mediated C8 with the aid of nitrate and electron intermediate (anthraquinone-2,6-disulphonate, AQDS). The quantitative real-time PCR results of several intracellular key functional genes suggested that AQDS could participate in the transformation of intermediates and accelerate the electron transfer in the degradation of TPH and nitrate, thereby eliminating the accumulation of nitrite and increasing the degradation efficiency of TPH. A strengthening mechanism, which promoted electron transport in the anaerobic denitrification degradation of petroleum hydrocarbons by quinone-respiring strain with the aid of electron intermediate, was proposed. The influencing factors were evaluated by using response surface methodology, and the TPH removal was positively related to temperature but negatively to pH.

Antimicrobial Potential of Epiphytic Bacteria Associated With Seaweeds of Little Andaman, India

Seaweeds of the intertidal regions are a rich source of surface associated bacteria and are potential source of antimicrobial molecules. In the present study, 77 epiphytic isolates from eight different algae collected from Little Andaman were enumerated. On testing for their antimicrobial activities against certain pathogens twelve isolates showed positive and six of them showed significant antimicrobial inhibition zone against Shigella boydii type 1, Shigella flexneri type 2a, Shigella dysenteriae type 5, Enterotoxigenic Escherichia coli O115, Enteropathogenic E. coli serotype O114, Vibrio cholera; O1 Ogawa, Aeromonas hydrophila, Klebsiella pneumoniae, Staphylococcus aureus. Based on the activity these six isolates (G1C, G2C, G3C, UK, UVAD, and Tor1) were identified by 16S rRNA gene sequence and were found to belong to the phyla Firmicutes and Proteobacteria. Purified antimicrobial compounds obtained from these isolates were identified by GC-MS. Furan derivatives were identified from G2C Pseudomonas stutzeri KJ849834, UVAD Alcanivorax dieselolei KJ849833, UK Vibrio sp. KJ849837, Tor1 Exiguobacterium profundum KJ849838. While 2-Pyrrolidinone, Phenol, 2, 4-bis (1, 1-dimethylethyl) were from G3C Vibrio owensii KJ849836 and (1-Allylcyclopropyl) methanol from the extracts of G1C Bacillus sp. KJ849835. The results of the present study shows that these six potent isolates isolated from the seaweeds are found to be a source of antimicrobial compounds.

Bacterial communities and chemical parameters in soils and coastal sediments in response to diesel spills at Carlini Station, Antarctica

A diesel spill occurring at Carlini Station (King George Island (Isla 25 de Mayo), South Shetland Islands) in 2009 started the study of the fate of the hydrocarbons and their effect on the bacterial communities of the Potter Cove ecosystem. Soils and sediments were sampled across the 200-meter long diesel plume towards Potter Cove four and 15months after the spill. The sampling revealed a second fuel leakage from an underground pipeline at the spill site. The hydrocarbon fraction spilt over frozen and snow-covered ground reached the sea and dispersed with the currents. Contrary, diesel that infiltrated unfrozen soil remained detectable for years, and was seeping with ground water towards coastal marine sediments. Structural changes of the bacterial communities as well as hydrocarbon, carbon and nitrogen contents were investigated in sediments in front of the station, two affected terrestrial sites, and a terrestrial non-contaminated reference site. Bacterial communities (16S rRNA gene clone libraries) changed over time in contaminated soils and sediments. At the underground seepage site of highest contamination (5812 to 366μgg^-1_dw hydrocarbons from surface to 90-cm depth), communities were dominated by Actinobacteria (18%) and a betaproteobacterium closely related to Polaromonas naphthalenivorans (40%). At one of the spill sites, affected exclusively at the surface, contamination disappeared within one year. The same bacterial groups were enriched at both contaminated sites. This response at community level suggests that the cold-adapted indigenous microbiota in soils of the West Antarctic Peninsula have a high potential for bioremediation and can support soil cleaning actions in the ecosystem. Intensive monitoring of pollution and site assessment after episodic fuel spills is required for decision-making towards remediation strategies.

Distribution of Anaerobic Hydrocarbon-Degrading Bacteria in Soils from King George Island, Maritime Antarctica

Anaerobic diesel fuel Arctic (DFA) degradation has already been demonstrated in Antarctic soils. However, studies comparing the distribution of anaerobic bacterial groups and of anaerobic hydrocarbon-degrading bacteria in Antarctic soils containing different concentrations of DFA are scarce. In this study, functional genes were used to study the diversity and distribution of anaerobic hydrocarbon-degrading bacteria (bamA, assA, and bssA) and of sulfate-reducing bacteria (SRB-apsR) in highly, intermediate, and non-DFA-contaminated soils collected during the summers of 2009, 2010, and 2011 from King George Island, Antarctica. Signatures of bamA genes were detected in all soils analyzed, whereas bssA and assA were found in only 4 of 10 soils. The concentration of DFA was the main factor influencing the distribution of bamA-containing bacteria and of SRB in the analyzed soils, as shown by PCR-DGGE results. bamA sequences related to genes previously described in Desulfuromonas, Lautropia, Magnetospirillum, Sulfuritalea, Rhodovolum, Rhodomicrobium, Azoarcus, Geobacter, Ramlibacter, and Gemmatimonas genera were dominant in King George Island soils. Although DFA modulated the distribution of bamA-hosting bacteria, DFA concentration was not related to bamA abundance in the soils studied here. This result suggests that King George Island soils show functional redundancy for aromatic hydrocarbon degradation. The results obtained in this study support the hypothesis that specialized anaerobic hydrocarbon-degrading bacteria have been selected by hydrocarbon concentrations present in King George Island soils.

Hydrocarbon degraders establish at the costs of microbial richness, abundance and keystone taxa after crude oil contamination in permafrost environments

Oil spills from pipeline ruptures are a major source of terrestrial petroleum pollution in cold regions. However, our knowledge of the bacterial response to crude oil contamination in cold regions remains to be further expanded, especially in terms of community shifts and potential development of hydrocarbon degraders. In this study we investigated changes of microbial diversity, population size and keystone taxa in permafrost soils at four different sites along the China-Russia crude oil pipeline prior to and after perturbation with crude oil. We found that crude oil caused a decrease of cell numbers together with a reduction of the species richness and shifts in the dominant phylotypes, while bacterial community diversity was highly site-specific after exposure to crude oil, reflecting different environmental conditions. Keystone taxa that strongly co-occurred were found to form networks based on trophic interactions, that is co-metabolism regarding degradation of hydrocarbons (in contaminated samples) or syntrophic carbon cycling (in uncontaminated samples). With this study we demonstrate that after severe crude oil contamination a rapid establishment of endemic hydrocarbon degrading communities takes place under favorable temperature conditions. Therefore, both endemism and trophic correlations of bacterial degraders need to be considered in order to develop effective cleanup strategies.

Application of a Bayesian nonparametric model to derive toxicity estimates based on the response of Antarctic microbial communities to fuel-contaminated soil

Ecotoxicology is primarily concerned with predicting the effects of toxic substances on the biological components of the ecosystem. In remote, high latitude environments such as Antarctica, where field work is logistically difficult and expensive, and where access to adequate numbers of soil invertebrates is limited and response times of biota are slow, appropriate modeling tools using microbial community responses can be valuable as an alternative to traditional single-species toxicity tests. In this study, we apply a Bayesian nonparametric model to a soil microbial data set acquired across a hydrocarbon contamination gradient at the site of a fuel spill in Antarctica. We model community change in terms of OTUs (operational taxonomic units) in response to a range of total petroleum hydrocarbon (TPH) concentrations. The Shannon diversity of the microbial community, clustering of OTUs into groups with similar behavior with respect to TPH, and effective concentration values at level x, which represent the TPH concentration that causes x% change in the community, are presented. This model is broadly applicable to other complex data sets with similar data structure and inferential requirements on the response of communities to environmental parameters and stressors.

Draft Genome Sequence of Sphingomonas sp. Strain Ant20, Isolated from Oil-Contaminated Soil on Ross Island, Antarctica

Here, we present the draft genome of Sphingomonas sp. strain Ant20, isolated from oil-polluted soil near Scott Base, Ross Island, Antarctica. The genome of this aromatic hydrocarbon-degrading bacterium provides valuable information on the microbially mediated biodegradation of aromatic compounds in cold-climate systems.

Microbe-assisted phytoremediation of hydrocarbons in estuarine environments

Estuaries are sinks for various anthropogenic contaminants, such as petroleum hydrocarbons, giving rise to significant environmental concern. The demand for organisms and processes capable of degrading pollutants in a clean, effective, and less expensive process is of great importance. Phytoremedition approaches involving plant/bacteria interactions have been explored as an alternative, and halophyte vegetation has potential for use in phytoremedition of hydrocarbon contamination. Studies with plant species potentially suitable for microbe-assisted phytoremediation are widely represented in scientific literature. However, the in-depth understanding of the biological processes associated with the re-introduction of indigenous bacteria and plants and their performance in the degradation of hydrocarbons is still the limiting step for the application of these bioremediation solutions in a field context. The intent of the present review is to summarize the sources and effects of hydrocarbon contamination in estuarine environments, the strategies currently available for bioremediation (potential and limitations), and the perspectives of the use of halophyte plants in microbe-assisted phytoremediation approaches.

Bacterial community response to petroleum contamination and nutrient addition in sediments from a temperate salt marsh

Microbial communities play an important role in the biodegradation of organic pollutants in sediments, including hydrocarbons. The aim of this study was to evaluate the response of temperate salt marsh microbial communities to petroleum contamination, in terms of community structure, abundance and capacity to degrade hydrocarbons. Sediments un-colonized and colonized (rhizosediments) by Juncus maritimus, Phragmites australis and Triglochin striata were collected in a temperate estuary (Lima, NW Portugal), spiked with petroleum under variable nutritional conditions, and incubated for 15 days. Results showed that plant speciation emerged as the major factor for shaping the rhizosphere community structure, overriding the petroleum influence. Moreover, when exposed to petroleum contamination, the distinct salt marsh microbial communities responded similarly with (i) increased abundance, (ii) changes in structure, and (iii) decreased diversity. Communities, particularly those associated to J. maritimus and P. australis roots displayed a potential to degrade petroleum hydrocarbons, with degradation percentages between 15% and 41%, depending on sediment type and nutritional conditions. In conclusion, distinct salt marsh microbial communities responded similarly to petroleum contamination, but presented different pace, nutritional requirements, and potential for its biodegradation, which should be taken into account when developing bioremediation strategies.

Direct assessment of viral diversity in soils by random PCR amplification of polymorphic DNA

Viruses are the most abundant and diverse biological entities within soils, yet their ecological impact is largely unknown. Defining how soil viral communities change with perturbation or across environments will contribute to understanding the larger ecological significance of soil viruses. A new approach to examining the composition of soil viral communities based on random PCR amplification of polymorphic DNA (RAPD-PCR) was developed. A key methodological improvement was the use of viral metagenomic sequence data for the design of RAPD-PCR primers. This metagenomically informed approach to primer design enabled the optimization of RAPD-PCR sensitivity for examining changes in soil viral communities. Initial application of RAPD-PCR viral fingerprinting to soil viral communities demonstrated that the composition of autochthonous soil viral assemblages noticeably changed over a distance of meters along a transect of Antarctic soils and across soils subjected to different land uses. For Antarctic soils, viral assemblages segregated upslope from the edge of dry valley lakes. In the case of temperate soils at the Kellogg Biological Station, viral communities clustered according to land use treatment. In both environments, soil viral communities changed along with environmental factors known to shape the composition of bacterial host communities. Overall, this work demonstrates that RAPD-PCR fingerprinting is an inexpensive, high-throughput means for addressing first-order questions of viral community dynamics within environmental samples and thus fills a methodological gap between narrow single-gene approaches and comprehensive shotgun metagenomic sequencing for the analysis of viral community diversity.

Biodegradation of benzene, toluene, and xylene (BTX) in liquid culture and in soil by Bacillus subtilis and Pseudomonas aeruginosa strains and a formulated bacterial consortium

PURPOSE

The major aromatic constituents of petroleum products viz. benzene, toluene, and mixture of xylenes (BTX) are responsible for environmental pollution and inflict serious public concern. Therefore, BTX biodegradation potential of individual as well as formulated bacterial consortium was evaluated. This study highlighted the role of hydrogen peroxide (H(2)O(2)), nitrate, and phosphate in stimulating the biodegradation of BTX compounds under hypoxic condition.

MATERIALS AND METHODS

The individual bacterium viz. Bacillus subtilis DM-04 and Pseudomonas aeruginosa M and NM strains and a consortium comprising of the above bacteria were inoculated to BTX-containing liquid medium and in soil. The bioremediation experiment was carried out for 120 h in BTX-containing liquid culture and for 90 days in BTX-contaminated soil. The kinetics of BTX degradation either in presence or absence of H(2)O(2), nitrate, and phosphate was analyzed using biochemical and gas chromatographic (GC) technique.

RESULTS

Bacterial consortium was found to be superior in degrading BTX either in soil or in liquid medium as compared to degradation of same compounds by individual strains of the consortium. The rate of BTX biodegradation was further enhanced when the liquid medium/soil was exogenously supplemented with 0.01 % (v/v) H(2)O(2), phosphate, and nitrate(.) The GC analysis of BTX biodegradation (90 days post-inoculation) in soil by bacterial consortium confirmed the preferential degradation of benzene compared to m-xylene and toluene.

CONCLUSIONS

It may be concluded that the bacterial consortium in the present study can degrade BTX compounds at a significantly higher rate as compared to the degradation of the same compounds by individual members of the consortium. Further, addition of H(2)O(2) in the culture medium as an additional source of oxygen, and nitrate and phosphate as an alternative electron acceptor and macronutrient, respectively, significantly enhanced the rate of BTX biodegradation under oxygen-limited condition.

Comparison of denitrifier communities in the biofilms of bioaugmented and non-augmented zeolite-biological aerated filters

The denitrifier communities of a bioaugmented and non-augmented zeolite-biological aerated filter (Z-BAFs) were investigated and compared because the bioaugmented Z-BAF provided better and more stable treatment efficiency for nitrate and nitrite removal. Terminal restriction fragment length polymorphism (T-RFLP) and reverse transcription T-RFLP (RT-T-RFLP) were applied to analyse the denitrifier community diversity in the biofilm collected from each Z-BAF. The results showed that the bioaugmentation technology favourably changed the indigenous denitrifier community and enhanced denitrification under nitrogen loading shocks. The cDNA clone libraries were developed to explore the active denitrifier community structures of both filters. The results showed that the active denitrifiers in both the bioaugmented and non-bioaugmented Z-BAF belonged to alpha-, beta- and gamma-proteobacteria. However, the sequence of the introduced denitrifier (Paracoccus sp. BW001) was not found in the clone library of the bioaugmented filter, which implied that the removal of nitrate and nitrite was attributed mainly to the indigenous denitrifiers in the adjusted bacterial community in the bioaugmented Z-BAF.

Plant litter and soil type drive abundance, activity and community structure of alkB harbouring microbes in different soil compartments

Alkanes are major constituents of plant-derived waxy materials. In this study, we investigated the abundance, community structure and activity of bacteria harbouring the alkane monooxygenase gene alkB, which catalyses a major step in the pathway of aerobic alkane degradation in the litter layer, the litter-soil interface and in bulk soil at three time points during the degradation of maize and pea plant litter (2, 8 and 30 weeks) to improve our understanding about drivers for microbial performance in different soil compartments. Soil cores of different soil textures (sandy and silty) were taken from an agricultural field and incubated at constant laboratory conditions. The abundance of alkB genes and transcripts (by qPCR) as well as the community structure (by terminal restriction fragment polymorphism fingerprinting) were measured in combination with the concentrations and composition of alkanes. The results obtained indicate a clear response pattern of all investigated biotic and abiotic parameters depending on the applied litter material, the type of soil used, the time point of sampling and the soil compartment studied. As expected the distribution of alkanes of different chain length formed a steep gradient from the litter layer to the bulk soil. Mainly in the two upper soil compartments community structure and abundance patterns of alkB were driven by the applied litter type and its degradation. Surprisingly, the differences between the compartments in one soil were more pronounced than the differences between similar compartments in the two soils studied. This indicates the necessity for analysing processes in different soil compartments to improve our mechanistic understanding of the dynamics of distinct functional groups of microbes.

Integrated perspective for effective bioremediation

Identification of factors which can influence the natural attenuation process with available microbial genetic capacities can support the bioremediation which has been viewed as the safest procedure to combat with anthropogenic compounds in ecosystems. With the advent of molecular techniques, assimilatory capacity of an ecosystem can be defined with changing community dynamics, and if required, the essential genetic potential can be met through bioaugmentation. At the same time, intensification of microbial processes with nutrient balancing, expressing and enhancing the degradative capacities, could reduce the time frame of restoration of the ecosystem. The new concept of ecosystems biology has added greatly to conceptualize the networking of the evolving microbiota of the niche that helps in effective application of bioremediation tools to manage pollutants as additional carbon source.

Abundance and diversity of n-alkane-degrading bacteria in a forest soil co-contaminated with hydrocarbons and metals: a molecular study on alkB homologous genes

Unraveling functional genes related to biodegradation of organic compounds has profoundly improved our understanding of biological remediation processes, yet the ecology of such genes is only poorly understood. We used a culture-independent approach to assess the abundance and diversity of bacteria catalyzing the degradation of n-alkanes with a chain length between C(5) and C(16) at a forest site co-contaminated with mineral oil hydrocarbons and metals for nearly 60 years. The alkB gene coding for a rubredoxin-dependent alkane monooxygenase enzyme involved in the initial activation step of aerobic aliphatic hydrocarbon metabolism was used as biomarker. Within the area of study, four different zones were evaluated: one highly contaminated, two intermediately contaminated, and a noncontaminated zone. Contaminant concentrations, hydrocarbon profiles, and soil microbial respiration and biomass were studied. Abundance of n-alkane-degrading bacteria was quantified via real-time PCR of alkB, whereas genetic diversity was examined using molecular fingerprints (T-RFLP) and clone libraries. Along the contamination plume, hydrocarbon profiles and increased respiration rates suggested on-going natural attenuation at the site. Gene copy numbers of alkB were similar in contaminated and control areas. However, T-RFLP-based fingerprints suggested lower diversity and evenness of the n-alkane-degrading bacterial community in the highly contaminated zone compared to the other areas; both diversity and evenness were negatively correlated with metal and hydrocarbon concentrations. Phylogenetic analysis of alkB denoted a shift of the hydrocarbon-degrading bacterial community from Gram-positive bacteria in the control zone (most similar to Mycobacterium and Nocardia types) to Gram-negative genotypes in the contaminated zones (Acinetobacter and alkB sequences with little similarity to those of known bacteria). Our results underscore a qualitative rather than a quantitative response of hydrocarbon-degrading bacteria to the contamination at the molecular level.

Bioremediation and reclamation of soil contaminated with petroleum oil hydrocarbons by exogenously seeded bacterial consortium: a pilot-scale study

PURPOSE

Spillage of petroleum hydrocarbons causes significant environmental pollution. Bioremediation is an effective process to remediate petroleum oil contaminant from the ecosystem. The aim of the present study was to reclaim a petroleum oil-contaminated soil which was unsuitable for the cultivation of crop plants by using petroleum oil hydrocarbon-degrading microbial consortium.

MATERIALS AND METHODS

Bacterial consortium consisting of Bacillus subtilis DM-04 and Pseudomonas aeruginosa M and NM strains were seeded to 20% (v/w) petroleum oil-contaminated soil, and bioremediation experiment was carried out for 180 days under laboratory condition. The kinetics of hydrocarbon degradation was analyzed using biochemical and gas chromatographic (GC) techniques. The ecotoxicity of the elutriates obtained from petroleum oil-contaminated soil before and post-treatment with microbial consortium was tested on germination and growth of Bengal gram (Cicer aretinum) and green gram (Phaseolus mungo) seeds.

RESULTS

Bacterial consortium showed a significant reduction in total petroleum hydrocarbon level in contaminated soil (76% degradation) as compared to the control soil (3.6% degradation) 180 days post-inoculation. The GC analysis confirmed that bacterial consortium was more effective in degrading the alkane fraction compared to aromatic fraction of crude petroleum oil hydrocarbons in soil. The nitrogen, sulfur, and oxygen compounds fraction was least degraded. The reclaimed soil supported the germination and growth of crop plants (C. aretinum and P. mungo). In contrast, seeds could not be germinated in petroleum oil-contaminated soil.

CONCLUSIONS

The present study reinforces the application of bacterial consortium rather than individual bacterium for the effective bioremediation and reclamation of soil contaminated with petroleum oil.

Mixtures of environmental pollutants: effects on microorganisms and their activities in soils

Soil is the ultimate sink for most contaminants and rarely has only a single contaminant. More than is generally acknowledge, environmental pollutants exist as mixtures (organic-organic, inorganic-inorganic, and organic-inorganic). It is much more difficult to study chemical mixtures than individual chemicals, especially in the complex soil environment. Similarly, understanding the toxicity of a chemical mixture on different microbial species is much more complex, time consuming and expensive, because multiple testing designs are needed for an increased array of variables. Therefore, until now, scientific enquiries worldwide have extensively addressed the effects of only individual pollutants toward nontarget microorganisms. In this review, we emphasize the present status of research on (i) the environmental occurrence of pollutant mixtures; (ii) the interactions between pollutant mixtures and ecologically beneficial microorganisms; and (iii) the impact of such interactions on environmental quality. We also address the limitations of traditional cultivation based methods for monitoring the effects of pollutant mixtures on microorganisms. Long-term monitoring of the effects of pollutant mixtures on microorganisms, particularly in soil and aquatic ecosystems, has received little attention. Microbial communities that can degrade or can degrade or can develop tolerance to, or are inhibited by chemical mixtures greatly contribute to resilience and resistance in soil environments. We also stress in this review the important emerging trend associated with the employment of molecular methods for establishing the effects of pollutant mixtures on microbial communities. There is currently a lack of sufficient cogent toxicological data on chemical mixtures for making informed decision making in risk assessment by regulators. Therefore, not only more toxicology information on mixtures is needed but also there is an urgent need to generate sufficient, suitable, and long-term modeling data that have higher predictability when assessing pollutant mixture effects on microorganisms. Such data would improve risk assessment at contaminated sites and would help devise more effective bioremediation strategies.

Advances in molecular and "-omics" technologies to gauge microbial communities and bioremediation at xenobiotic/anthropogen contaminated sites

Microbial bioremediation has been well-demonstrated as an ecofriendly and cost-competitive strategy for elimination of xenobiotic and or anthropogenic compounds from the polluted environments. However, successful execution of these versatile bioremediation strategies requires a thorough understanding of factors governing the growth, metabolism, dynamics and functions of indigenous microbial communities at contaminated sites. Recent innovative breakthroughs in genotypic profiling, ultrafast genome pyrosequencing, metagenomics, metatranscriptomics, metaproteomics and metabolomics along with bioinformatics tools have provided crucial in-sights of microbial communities and their mechanisms in bioremediation of environmental pollutants. Moreover, advances in these technologies have significantly improved the process of efficacy determination and implementation of microbial bioremediation strategies. The current review is focused on application of these molecular and "-omics" technologies in gauging the innate microbial community structures, dynamics and functions at contaminated sites or pollution containment facilities.

Microarray and real-time PCR analyses of the responses of high-arctic soil bacteria to hydrocarbon pollution and bioremediation treatments

High-Arctic soils have low nutrient availability, low moisture content, and very low temperatures and, as such, they pose a particular problem in terms of hydrocarbon bioremediation. An in-depth knowledge of the microbiology involved in this process is likely to be crucial to understand and optimize the factors most influencing bioremediation. Here, we compared two distinct large-scale field bioremediation experiments, located at the Canadian high-Arctic stations of Alert (ex situ approach) and Eureka (in situ approach). Bacterial community structure and function were assessed using microarrays targeting the 16S rRNA genes of bacteria found in cold environments and hydrocarbon degradation genes as well as quantitative reverse transcriptase PCR targeting key functional genes. The results indicated a large difference between sampling sites in terms of both soil microbiology and decontamination rates. A rapid reorganization of the bacterial community structure and functional potential as well as rapid increases in the expression of alkane monooxygenases and polyaromatic hydrocarbon-ring-hydroxylating dioxygenases were observed 1 month after the bioremediation treatment commenced in the Alert soils. In contrast, no clear changes in community structure were observed in Eureka soils, while key gene expression increased after a relatively long lag period (1 year). Such discrepancies are likely caused by differences in bioremediation treatments (i.e., ex situ versus in situ), weathering of the hydrocarbons, indigenous microbial communities, and environmental factors such as soil humidity and temperature. In addition, this study demonstrates the value of molecular tools for the monitoring of polar bacteria and their associated functions during bioremediation.