Characterization of hydrocarbon-degrading microbial populations in contaminated and pristine Alpine soils

Culture-dependent diversity of bacteria from Laohugou glacier, Qilian Mts., China and their resistance against metals

In the current study, psychrophilic, endolithic, and epilithic bacterial strains were isolated and characterized from the nonpolar Laohugou glacier (LHG) no. 12, the largest valley glacier in the western Qilian Mts. located on the northeastern edge of the Tibetan Plateau. Five different types of samples, rocks, soil, glacial water, ice/snow, and cryoconite, were collected. A total of 48 bacterial strains were isolated by using the R2A bacterial cultural medium. The findings revealed that the Gram-positive bacteria 41 (85.4%) dominated the Gram-negative bacteria 7 (14.6%) in this extremely harsh environment. Molecular characterization based on 16S ribosomal RNA gene sequencing exhibited that the obtained isolates belong to four phyla, among which the diversity of Firmicutes (58.33%) was higher followed by Actinobacteria (23.0%), Proteobacteria (14.6%), and least diversity was reported in Euryarchaeota (4.2%). The bacterial communities were most dominant in soil samples followed by cryoconite sample and least dominant in the ice and snow samples. Moreover, the obtained bacterial isolates were found resistant to high concentrations of heavy metals (Cr³⁺ , Cd²⁺ , Hg²⁺ , and Ar³⁺ ) and sodium chloride, and, therefore, exhibited polyextremophilic characteristics. LHG no. 12 is rich in bacterial and archaeal diversities and provides a potentially curious site for further in-depth exploration of microbial diversity and their biotechnological applications.

Naphthalene exerts substantial nontarget effects on soil nitrogen mineralization processes in a subalpine forest soil: A microcosm study

Naphthalene has been widely used to test the functional roles of soil fauna, but its nontarget effects remain uncertain in various soils. To determine whether there is a potential nontarget effect on soil biochemical properties in subalpine forest soil, soils in a subalpine forest on the western Qinghai-Tibet Plateau were treated by naphthalene in microcosms. The responses of soil microbial activity and nutrients to naphthalene were studied following 52 days of incubation. The results showed that the naphthalene application obviously decreased the microbial respiration rate in the first 10 days of the incubation and then increased the rate in the following days of the incubation. Moreover, the naphthalene application did not significantly affect the microbial activities overall, measured as soil microbial phospholipid fatty acid (PLFA) abundances and biomasses, or most enzyme activities (invertase, nitrate reductase and nitrite reductase) during the whole incubation period. However, naphthalene suppressed increases in the DON, NH4+-N and NO3--N contents and urease activity and led to the net mineralization of inorganic N (NH4+-N + NO3--N), in contrast to the net immobilization result in the controls. These results suggest that naphthalene can exert direct nontarget effects on soil microbial respiration and N mineralization processes in subalpine soils. Caution should be taken when using naphthalene to repel soil animals in field experiments.

Biodegradation of long chain alkanes in halophilic conditions by Alcanivorax sp. strain Est-02 isolated from saline soil

In this study, through a multistep enrichment and isolation procedure, a halophilic bacterial strain was isolated from unpolluted saline soil, which was able to effectively and preferentially degrade long chain alkanes (especially tetracosane and octacosane). The strain was identified by 16S rRNA gene sequence as an Alcanivorax sp. The growth of strain Est-02 was optimized at the presence of tetracosane in different NaCl concentrations, temperatures, and pH. The consumption of different heavy alkanes was also investigated. Optimal culture conditions of the strain were determined to be as follows: 10% NaCl, temperature 25-35 °C and pH 7. Alcanivorax sp. strain Est-02 was able to use a wide range of aliphatic substrates ranging from C₁₄ to C₂₈ with clear tendency to utilize heavy chain hydrocarbons of C₂₄ and C₂₈. During growth on a mixture of alkanes (C₁₄-C₂₈), the strain consumed 60% and 65% of tetracosane and octacosane, respectively, while only about 40% of the lower chain alkanes were degraded. This unique ability of the strain Est-02 in efficient and selective biodegradation of long chain hydrocarbons could be further exploited for remediation of wax and heavy oil contaminated soils or upgrading of heavy crude oils. Comparison of the sequence of alkane hydroxylase gene (alkB) of strain Est-02 with previously reported sequences for Alcanivorax spp. and other hydrocarbon degraders, showed a remarkable phylogenetic distance between the sequence alkB of Est-02 and other alkane-degrading bacteria.

Potential use of endophytic root bacteria and host plants to degrade hydrocarbons

Microbe-assisted phytoremediation depends on competent root-associated microorganisms that enhance remediation efficiency of organic compounds. Endophytic bacteria are a key element of the root microbiome and may assist plant degradation of contaminants. The aim of this study was to investigate the application of four hydrocarbon-degrading endophytic strains previously isolated from an oil sands reclamation area. Strains EA1-17 (Stenotrophomonas sp.), EA2-30 (Flavobacterium sp.), EA4-40 (Pantoea sp.), and EA6-5 (Pseudomonas sp.) were inoculated in white sweet clover growing on soils amended with diesel at 5,000, 10,000, and 20,000 mg·kg^-1. Our results indicate that plant growth inhibition caused by diesel fuel toxicity was overcome in inoculated plants, which showed significantly higher plant biomass. Analysis of soil F2 and F3 hydrocarbon fractions also revealed that these soils were remediated by inoculated plants when diesel was applied at 10,000 mg·kg^-1 and 20,000 mg·kg^-1. In addition, quantification of hydrocarbon-degrading genes suggests that all bacterial strains successfully colonized sweet clover plants. Overall, the endophytic strain EA6-5 (Pseudomonas sp.), which harbored hydrocarbon-degrading genes, was the most effective candidate in phytoremediation experiments and could be a strategy to increase plant tolerance and hydrocarbon degradation in contaminated (e.g., diesel fuel) soils.

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.

Dynamic membrane bioreactor performance enhancement by powdered activated carbon addition: Evaluation of sludge morphological, aggregative and microbial properties

The effects of powdered activated carbon (PAC) addition on sludge morphological, aggregative and microbial properties in a dynamic membrane bioreactor (DMBR) were investigated to explore the enhancement mechanism of pollutants removal and filtration performance. Sludge properties were analyzed through various analytical measurements. The results showed that the improved sludge aggregation ability and the evolution of microbial communities affected sludge morphology in PAC-DMBR, as evidenced by the formation of large, regularly shaped and strengthened sludge flocs. The modifications of sludge characteristics promoted the formation process and filtration flux of the dynamic membrane (DM) layer. Additionally, PAC addition did not exert very significant influence on the propagation of eukaryotes (protists and metazoans) and microbial metabolic activity. High-throughput pyrosequencing results indicated that adding PAC improved the bacterial diversity in activated sludge, as PAC addition brought about additional microenvironment in the form of biological PAC (BPAC), which promoted the enrichment of Acinetobacter (13.9%), Comamonas (2.9%), Flavobacterium (0.31%) and Pseudomonas (0.62%), all contributing to sludge flocs formation and several (such as Acinetobacter) capable of biodegrading relatively complex organics. Therefore, PAC addition could favorably modify sludge properties from various aspects and thus enhance the DMBR performance.

Pyridine Nucleotide Coenzyme Specificity of p-Hydroxybenzoate Hydroxylase and Related Flavoprotein Monooxygenases

p-Hydroxybenzoate hydroxylase (PHBH; EC 1.14.13.2) is a microbial group A flavoprotein monooxygenase that catalyzes the ortho-hydroxylation of 4-hydroxybenzoate to 3,4-dihydroxybenzoate with the stoichiometric consumption of NAD(P)H and oxygen. PHBH and related enzymes lack a canonical NAD(P)H-binding domain and the way they interact with the pyridine nucleotide coenzyme has remained a conundrum. Previously, we identified a surface exposed protein segment of PHBH from Pseudomonas fluorescens involved in NADPH binding. Here, we report the first amino acid sequences of NADH-preferring PHBHs and a phylogenetic analysis of putative PHBHs identified in currently available bacterial genomes. It was found that PHBHs group into three clades consisting of NADPH-specific, NAD(P)H-dependent and NADH-preferring enzymes. The latter proteins frequently occur in Actinobacteria. To validate the results, we produced several putative PHBHs in Escherichia coli and confirmed their predicted coenzyme preferences. Based on phylogeny, protein energy profiling and lifestyle of PHBH harboring bacteria we propose that the pyridine nucleotide coenzyme specificity of PHBH emerged through adaptive evolution and that the NADH-preferring enzymes are the older versions of PHBH. Structural comparison and distance tree analysis of group A flavoprotein monooxygenases indicated that a similar protein segment as being responsible for the pyridine nucleotide coenzyme specificity of PHBH is involved in determining the pyridine nucleotide coenzyme specificity of the other group A members.

Petroleum Hydrocarbon-Degrading Bacteria for the Remediation of Oil Pollution Under Aerobic Conditions: A Perspective Analysis

With the sharp increase in population and modernization of society, environmental pollution resulting from petroleum hydrocarbons has increased, resulting in an urgent need for remediation. Petroleum hydrocarbon-degrading bacteria are ubiquitous in nature and can utilize these compounds as sources of carbon and energy. Bacteria displaying such capabilities are often exploited for the bioremediation of petroleum oil-contaminated environments. Recently, microbial remediation technology has developed rapidly and achieved major gains. However, this technology is not omnipotent. It is affected by many environmental factors that hinder its practical application, limiting the large-scale application of the technology. This paper provides an overview of the recent literature referring to the usage of bacteria as biodegraders, discusses barriers regarding the implementation of this microbial technology, and provides suggestions for further developments.

Biodegradation of A-fuel oil in soil samples with bacterial mixtures of Rhodococcus and Gordonia strains under low temperature conditions

Bioaugmentation is an effective treatment to clean up polluted sites using contaminant-degrading bacteria. However, this treatment is influenced by various environmental conditions, including temperature. In this study, an effective bioaugmentation system under low temperature condition was developed with three Rhodococcus (strains A, C, and D) and one Gordonia (strain B) oil-degraders, which are officially permitted for bioaugmentation applications in Japan. The oil-degrading ability of each strain and mixture was assessed in liquid culture and in model soils supplemented with A-fuel oil. In liquid culture, Rhodococcus strains A and C degraded the A-fuel oil in cold temperature conditions (15°C and 10°C) as well as in mesophilic condition (30°C). In the model soil samples, the mixture of four degraders was the most effective at removing the A-fuel oil under mesophilic condition (>90%), suggesting that strains B and/or D might have factors that promote degradation. In contrast, A-fuel oil was efficiently removed (>80%) in the soil samples inoculated with A or C as well as that with mixture in cold temperature condition, suggesting that strains A and C were the major degraders under cold condition. Our results indicate that the four degraders could be applied to the bioaugmentation in cold areas.

Characterization of two Pantoea strains isolated from extra-virgin olive oil

The olive oil is an unfavorable substrate for microbial survival and growth. Only few microorganisms use olive oil fatty acids as carbon and energy sources, and survive in the presence of olive oil anti-microbial components. In this study, we have evaluated the occurrence of microorganisms in 1-year-stored extra-virgin olive oil samples. We detected the presence of bacterial and yeast species with a recurrence of the bacterium Stenotrophomonas rhizophila and yeast Sporobolomyces roseus. We then assayed the ability of all isolates to grow in a mineral medium supplemented with a commercial extra-virgin olive oil as a sole carbon and energy source, and analyzed the utilization of olive oil fatty acids during their growth. We finally focused on two bacterial isolates belonging to the species Pantoea septica. Both these isolates produce carotenoids, and one of them synthesizes bioemulsifiers enabling the bacteria to better survive/growth in this unfavorable substrate. Analyses point to a mixture of glycolipids with glucose, galactose and xylose as carbohydrate moieties whereas the lipid domain was constituted by C6-C10 β-hydroxy carboxylic acids.

Effect of single and mixed polycyclic aromatic hydrocarbon contamination on plant biomass yield and PAH dissipation during phytoremediation

Polycyclic aromatic hydrocarbon (PAH)-contaminated sites have a mixture of PAH of varying concentration which may affect PAH dissipation differently to contamination with a single PAH. In this study, pot experiments investigated the impact of PAH contamination on Medicago sativa, Lolium perenne, and Festuca arundinacea biomass and PAH dissipation from soils spiked with phenanthrene (Phe), fluoranthene (Flu), and benzo[a]pyrene (B[a]P) in single and mixed treatments. Stimulatory or inhibitory effects of PAH contamination on plant biomass yields were not different for the single and mixed PAH treatments. Results showed significant effect of PAH treatments on plant growth with an increased root biomass yield for F. arundinacea in the Phe (175%) and Flu (86%) treatments and a root biomass decrease in the mixed treatment (4%). The mean residual PAHs in the planted treatments and unplanted control for the single treatments were not significantly different. B[a]P dissipation was enhanced for single and mixed treatments (71-72%) with F. arundinacea compared to the unplanted control (24-50%). On the other hand, B[a]P dissipation was inhibited with L. perenne (6%) in the single treatment and M. sativa (11%) and L. perenne (29%) in the mixed treatment. Abiotic processes had greater contribution to PAH dissipation compared to rhizodegradation in both treatments. In most cases, a stimulatory effect of PAH contamination on plant biomass yield without an enhancement of PAH dissipation was observed. Plant species among other factors affect the relative contribution of PAH dissipation mechanisms during phytoremediation. These factors determine the effectiveness and suitability of phytoremediation as a remedial strategy for PAH-contaminated sites. Further studies on impact of PAH contamination, plant selection, and rhizosphere activities on soil microbial community structure and remediation outcome are required.

Aerobic bacteria degrading both n-alkanes and aromatic hydrocarbons: an undervalued strategy for metabolic diversity and flexibility

Environmental pollution with petroleum toxic products has afflicted various ecosystems, causing devastating damage to natural habitats with serious economic implications. Some crude oil components may serve as growth substrates for microorganisms. A number of bacterial strains reveal metabolic capacities to biotransform various organic compounds. Some of the hydrocarbon degraders are highly biochemically specialized, while the others display a versatile metabolism and can utilize both saturated aliphatic and aromatic hydrocarbons. The extended catabolic profiles of the latter group have been subjected to systematic and complex studies relatively rarely thus far. Growing evidence shows that numerous bacteria produce broad biochemical activities towards different hydrocarbon types and such an enhanced metabolic potential can be found in many more species than the already well-known oil-degraders. These strains may play an important role in the removal of heterogeneous contamination. They are thus considered to be a promising solution in bioremediation applications. The main purpose of this article is to provide an overview of the current knowledge on aerobic bacteria involved in the mineralization or transformation of both n-alkanes and aromatic hydrocarbons. Variant scientific approaches enabling to evaluate these features on biochemical as well as genetic levels are presented. The distribution of multidegradative capabilities between bacterial taxa is systematically shown and the possibility of simultaneous transformation of complex hydrocarbon mixtures is discussed. Bioinformatic analysis of the currently available genetic data is employed to enable generation of phylogenetic relationships between environmental strain isolates belonging to the phyla Actinobacteria, Proteobacteria, and Firmicutes. The study proves that the co-occurrence of genes responsible for concomitant metabolic bioconversion reactions of structurally-diverse hydrocarbons is not unique among various systematic groups.

Use of bacterial acc deaminase to increase oil (especially poly aromatic hydrocarbons) phytoremediation efficiency for maize (zea mays) seedlings

Oil presence in soil, as a stressor, reduces phytoremediation efficiency through an increase in the plant stress ethylene. Bacterial 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase, as a plant stress ethylene reducer, was employed to increase oil phytoremediation efficiency. For this purpose, the ability of ACC deaminase-producing Pseudomonas strains to grow in oil-polluted culture media and withstand various concentrations of oil and also their ability to reduce plant stress ethylene and enhance some growth characteristics of maize and finally their effects on increasing phytoremediation efficiency of poly aromatic hydrocarbons (PAHs) in soil were investigated. Based on the results, of tested strains just P9 and P12 were able to perform oil degradation. Increasing oil concentration from 0 to 10% augmented these two strains population, 15.7% and 12.9%, respectively. The maximum increase in maize growth was observed in presence of P12 strain. Results of high-performance liquid chromatography (HPLC) revealed that PAHs phytoremediation efficiency was higher for inoculated seeds than uninoculated. The highest plant growth and PAHs removal percentage (74.9%) from oil-polluted soil was observed in maize inoculated with P12. These results indicate the significance of ACC deaminase producing bacteria in alleviation of plant stress ethylene in oil-polluted soils and increasing phytoremediation efficiency of such soils.

Insights into microbial communities mediating the bioremediation of hydrocarbon-contaminated soil from an Alpine former military site

The study of microbial communities involved in soil bioremediation is important to identify the specific microbial characteristics that determine improved decontamination rates. Here, we characterized bacterial, archaeal, and fungal communities in terms of (i) abundance (using quantitative PCR) and (ii) taxonomic diversity and structure (using Illumina amplicon sequencing) during the bioremediation of long-term hydrocarbon-contaminated soil from an Alpine former military site during 15 weeks comparing biostimulation (inorganic NPK fertilization) vs. natural attenuation and considering the effect of temperature (10 vs. 20 °C). Although a considerable amount of total petroleum hydrocarbon (TPH) loss could be attributed to natural attenuation, significantly higher TPH removal rates were obtained with NPK fertilization and at increased temperature, which were related to the stimulation of the activities of indigenous soil microorganisms. Changing structures of bacterial and fungal communities significantly explained shifts in TPH contents in both natural attenuation and biostimulation treatments at 10 and 20 °C. However, archaeal communities, in general, and changing abundances and diversities in bacterial and fungal communities did not play a decisive role on the effectiveness of soil bioremediation. Gammaproteobacteria and Bacteroidia classes, within bacterial community, and undescribed/novel groups, within fungal community, proved to be actively involved in TPH removal in natural attenuation and biostimulation at both temperatures.

Indigenous 14C-phenanthrene biodegradation in "pristine" woodland and grassland soils from Norway and the United Kingdom

In this study, the indigenous microbial mineralisation of ¹⁴C-phenanthrene in seven background soils (four from Norwegian woodland and three from the UK (two grasslands and one woodland)) was investigated. ∑PAHs ranged from 16.39 to 285.54 ng g^-1 dw soil. Lag phases (time before ¹⁴C-phenanthrene mineralisation reached 5%) were longer in all of the Norwegian soils and correlated positively with TOC, but negatively with ∑PAHs and phenanthrene degraders for all soils. ¹⁴C-phenanthrene mineralisation in the soils varied due to physicochemical properties. The results show that indigenous microorganisms can adapt to ¹⁴C-phenanthrene mineralisation following diffuse PAH contamination. Considering the potential of soil as a secondary PAH source, these findings highlight the important role of indigenous microflora in the processing of PAHs in the environment.

Microbial degradation of total petroleum hydrocarbons in crude oil: a field-scale study at the low-land rainforest of Ecuador

A field-level feasibility study was conducted to determine total petroleum hydrocarbon (TPH)-degrading potential of two bacterial strains, Bacillus thuringiensis B3 and B. cereus B6, and two fungi, Geomyces pannorum HR and Geomyces sp. strain HV, all soil isolates obtained from an oil field located in north-east region of Ecuador. Crude oil-treated soil samples contained in wooden boxes received a mixture of all the four microorganisms and were incubated for 90 days in an open low-land area of Amazon rainforest. The percent removal of TPHs in soil samples that received the mixed microbial inoculum was 87.45, indicating the great potential of the soil isolates in field-scale removal of crude oil. The TPHs-degrading efficiency was verified by determining the toxicity of residues, remained in soil after biodegradation, toward viability of Artemia salina or seed germination and plant growth of cowpea. Our results clearly suggest that the selected soil isolates of bacteria and fungi could be effectively used for large-scale bioremediation of sites contaminated with crude oil.

Polychlorinated Biphenyl (PCB)-Degrading Potential of Microbes Present in a Cryoconite of Jamtalferner Glacier

Aiming to comprehensively survey the potential pollution of an alpine cryoconite (Jamtalferner glacier, Austria), and its bacterial community structure along with its biodegrading potential, first chemical analyses of persistent organic pollutants, explicitly polychlorinated biphenyls (PCBs) and organochlorine pesticides (OCPs) as well as polycyclic aromatic hydrocarbons (PAHs), revealed a significant contamination. In total, 18 PCB congeners were detected by high resolution gas chromatography/mass spectrometry with a mean concentration of 0.8 ng/g dry weight; 16 PAHs with an average concentration of 1,400 ng/g; and 26 out of 29 OCPs with a mean concentration of 2.4 ng/g. Second, the microbial composition was studied using 16S amplicon sequencing. The analysis revealed high abundances of Proteobacteria (66%), the majority representing α-Proteobacteria (87%); as well as Cyanobacteria (32%), however high diversity was due to 11 low abundant phyla comprising 75 genera. Biodegrading potential of cryoconite bacteria was further analyzed using enrichment cultures (microcosms) with PCB mixture Aroclor 1242. 16S rDNA analysis taxonomically classified 37 different biofilm-forming and PCB-degrading bacteria, represented by Pseudomonas, Shigella, Subtercola, Chitinophaga, and Janthinobacterium species. Overall, the combination of culture-dependent and culture-independent methods identified degrading bacteria that can be potential candidates to develop novel bioremediation strategies.

Bioprospection of cold-adapted yeasts with biotechnological potential from Antarctica

The aim of this study was to investigate the ability to produce extracellular hydrolytic enzymes at low temperature of yeasts isolated from 25 de Mayo island, Antarctica, and to identify those exhibiting one or more of the evaluated enzymatic activities. A total of 105 yeast isolates were obtained from different samples and 66 were identified. They belonged to 12 basidiomycetous and four ascomycetous genera. Most of the isolates were ascribed to the genera Cryptococcus, Mrakia, Cystobasidium, Rhodotorula, Gueomyces, Phenoliferia, Leucosporidium, and Pichia. Results from enzymes production at low temperatures revealed that the Antarctic environment contains metabolically diverse cultivable yeasts, which represent potential tools for biotechnological applications. While most the isolates proved to produce 2-4 of the investigated exoenzymes, two of them evidenced the six evaluated enzymatic activities: Pichia caribbica and Guehomyces pullulans, which were characterized as psycrotolerant and psycrophilic, respectively. In addition, P. caribbica could assimilate several n-alkanes and diesel fuel. The enzyme production profile and hydrocarbons assimilation capacity, combined with its high level of biomass production and the extended exponential growth phase make P. caribbica a promising tool for cold environments biotechnological purposes in the field of cold-enzymes production and oil spills bioremediation as well.

Potential Environmental Factors Affecting Oil-Degrading Bacterial Populations in Deep and Surface Waters of the Northern Gulf of Mexico

Understanding bacterial community dynamics as a result of an oil spill is important for predicting the fate of oil released to the environment and developing bioremediation strategies in the Gulf of Mexico. In this study, we aimed to elucidate the roles of temperature, water chemistry (nutrients), and initial bacterial community in selecting oil degraders through a series of incubation experiments. Surface (2 m) and bottom (1537 m) waters, collected near the Deepwater Horizon site, were amended with 200 ppm light Louisiana sweet crude oil and bacterial inoculums from surface or bottom water, and incubated at 4 or 24°C for 50 days. Bacterial community and residual oil were analyzed by pyrosequencing and gas chromatography-mass spectrometry (GC-MS), respectively. The results showed that temperature played a key role in selecting oil-degrading bacteria. Incubation at 4°C favored the development of Cycloclasticus, Pseudoalteromonas, Sulfitobacter, and Reinekea, while 24°C incubations enhanced Oleibacter, Thalassobius, Phaeobacter, and Roseobacter. Water chemistry and the initial community also had potential roles in the development of hydrocarbon-degrading bacterial communities. Pseudoalteromonas, Oleibacter, and Winogradskyella developed well in the nutrient-enriched bottom water, while Reinekea and Thalassobius were favored by low-nutrient surface water. We revealed that the combination of 4°C, crude oil and bottom inoculum was a key factor for the growth of Cycloclasticus, while the combination of surface inoculum and bottom water chemistry was important for the growth of Pseudoalteromonas. Moreover, regardless of the source of inoculum, bottom water at 24°C was a favorable condition for Oleibacter. Redundancy analysis further showed that temperature and initial community explained 57 and 19% of the variation observed, while oil and water chemistry contributed 14 and 10%, respectively. Overall, this study revealed the relative roles of temperature, water chemistry, and initial bacterial community in selecting oil degraders and regulating their evolution in the northern Gulf of Mexico.

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.

The effect of soil type on the bioremediation of petroleum contaminated soils

In this research the bioremediation of four different types of contaminated soils was monitored as a function of time and moisture content. The soils were categorized as sandy soil containing 100% sand (type I), clay soil containing more than 95% clay (type II), coarse grained soil containing 68% gravel and 32% sand (type III), and coarse grained with high clay content containing 40% gravel, 20% sand, and 40% clay (type IV). The initially clean soils were contaminated with gasoil to the concentration of 100 g/kg, and left on the floor for the evaporation of light hydrocarbons. A full factorial experimental design with soil type (four levels), and moisture content (10 and 20%) as the factors was employed. The soils were inoculated with petroleum degrading microorganisms. Soil samples were taken on days 90, 180, and 270, and the residual total petroleum hydrocarbon (TPH) was extracted using soxhlet apparatus. The moisture content of the soils was kept almost constant during the process by intermittent addition of water. The results showed that the efficiency of bioremediation was affected significantly by the soil type (Pvalue < 0.05). The removal percentage was the highest (70%) for the sandy soil with the initial TPH content of 69.62 g/kg, and the lowest for the clay soil (23.5%) with the initial TPH content of 69.70 g/kg. The effect of moisture content on bioremediation was not statistically significant for the investigated levels. The removal percentage in the clay soil was improved to 57% (within a month) in a separate experiment by more frequent mixing of the soil, indicating low availability of oxygen as a reason for low degradation of hydrocarbons in the clay soil.

A novel bioremediation strategy for petroleum hydrocarbon pollutants using salt tolerant Corynebacterium variabile HRJ4 and biochar

The present work aimed to develop a novel strategy to bioremediate the petroleum hydrocarbon contaminants in the environment. Salt tolerant bacterium was isolated from Dagang oilfield, China and identified as Corynebacterium variabile HRJ4 based on 16S rRNA gene sequence analysis. The bacterium had a high salt tolerant capability and biochar was developed as carrier for the bacterium. The bacteria with biochar were most effective in degradation of n-alkanes (C16, C18, C19, C26, C28) and polycyclic aromatic hydrocarbons (NAP, PYR) mixture. The result demonstrated that immobilization of C. variabile HRJ4 with biochar showed higher degradation of total petroleum hydrocarbons (THPs) up to 78.9% after 7-day of incubation as compared to the free leaving bacteria. The approach of this study will be helpful in clean-up of petroleum-contamination in the environments through bioremediation process using eco-friendly and cost effective materials like biochar.

Enhanced crude oil biodegradation in soil via biostimulation

Research on feasible methods for the enhancement of bioremediation in soil contaminated by crude oil is vital in oil-exporting countries such as Kuwait, where crude oil is a major pollutant and the environment is hostile to biodegradation. This study investigated the possibility of enhancing crude oil bioremediation by supplementing soil with cost-effective organic materials derived from two widespread locally grown trees, Conocarpus and Tamarix. Amendments in soils increased the counts of soil microbiota by up to 98% and enhanced their activity by up to 95.5%. The increase in the biodegradation of crude oil (75%) and high levels of alkB expression substantiated the efficiency of the proposed amendment technology for the bioremediation of hydrocarbon-contaminated sites. The identification of crude-oil-degrading bacteria revealed the dominance of the genus Microbacterium (39.6%), Sphingopyxis soli (19.3%), and Bordetella petrii (19.6%) in unamended, Conocarpus-amended, and Tamarix-amended contaminated soils, respectively. Although soil amendments favored the growth of Gram-negative bacteria and reduced bacterial diversity, the structures of bacterial communities were not significantly altered.

Separating and characterizing functional alkane degraders from crude-oil-contaminated sites via magnetic nanoparticle-mediated isolation

Uncultivable microorganisms account for over 99% of all species on the planet, but their functions are yet not well characterized. Though many cultivable degraders for n-alkanes have been intensively investigated, the roles of functional n-alkane degraders remain hidden in the natural environment. This study introduces the novel magnetic nanoparticle-mediated isolation (MMI) technology in Nigerian soils and successfully separates functional microbes belonging to the families Oxalobacteraceae and Moraxellaceae, which are dominant and responsible for alkane metabolism in situ. The alkR-type n-alkane monooxygenase genes, instead of alkA- or alkP-type, were the key functional genes involved in the n-alkane degradation process. Further physiological investigation via a BIOLOG PM plate revealed some carbon (Tween 20, Tween 40 and Tween 80) and nitrogen (tyramine, l-glutamine and d-aspartic acid) sources promoting microbial respiration and n-alkane degradation. With further addition of promoter carbon or nitrogen sources, the separated functional alkane degraders significantly improved n-alkane biodegradation rates. This suggests that MMI is a promising technology for separating functional microbes from complex microbiota, with deeper insight into their ecological functions and influencing factors. The technique also broadens the application of the BIOLOG PM plate for physiological research on functional yet uncultivable microorganisms.

Microbial diversity and community structure in an antimony-rich tailings dump

To assess the impact of antimony (Sb) on microbial community structure, 12 samples were taken from an Sb tailings pile in Guizhou Province, Southwest China. All 12 samples exhibited elevated Sb concentrations, but the mobile and bioaccessible fractions were small in comparison to total Sb concentrations. Besides the geochemical analyses, microbial communities inhabiting the tailing samples were characterized to investigate the interplay between the microorganisms and environmental factors in mine tailings. In all samples, Proteobacteria and Actinobacteria were the most dominant phyla. At the genus level, Thiobacillus, Limnobacter, Nocardioides, Lysobacter, Phormidium, and Kaistobacter demonstrated relatively high abundances. The two most abundant genera, Thiobacillus and Limnobacter, are characterized as sulfur-oxidizing bacteria and thiosulfate-oxidizing bacteria, respectively, while the genus Lysobacter contains arsenic (As)-resistant bacteria. Canonical correspondence analysis (CCA) indicates that TOC and the sulfate to sulfide ratio strongly shaped the microbial communities, suggesting the influence of the environmental factors in the indigenous microbial communities.

Long-term oil contamination causes similar changes in microbial communities of two distinct soils

Since total petroleum hydrocarbons (TPH) are toxic and persistent in environments, studying the impact of oil contamination on microbial communities in different soils is vital to oil production engineering, effective soil management and pollution control. This study analyzed the impact of oil contamination on the structure, activity and function in carbon metabolism of microbial communities of Chernozem soil from Daqing oil field and Cinnamon soil from Huabei oil field through both culture-dependent techniques and a culture-independent technique-pyrosequencing. Results revealed that pristine microbial communities in these two soils presented disparate patterns, where Cinnamon soil showed higher abundance of alkane, (polycyclic aromatic hydrocarbons) PAHs and TPH degraders, number of cultivable microbes, bacterial richness, bacterial biodiversity, and stronger microbial activity and function in carbon metabolism than Chernozem soil. It suggested that complicated properties of microbes and soils resulted in the difference in soil microbial patterns. However, the changes of microbial communities caused by oil contamination were similar in respect of two dominant phenomena. Firstly, the microbial community structures were greatly changed, with higher abundance, higher bacterial biodiversity, occurrence of Candidate_division_BRC1 and TAO6, disappearance of BD1-5 and Candidate_division_OD1, dominance of Streptomyces, higher percentage of hydrocarbon-degrading groups, and lower percentage of nitrogen-transforming groups. Secondly, microbial activity and function in carbon metabolism were significantly enhanced. Based on the characteristics of microbial communities in the two soils, appropriate strategy for in situ bioremediation was provided for each oil field. This research underscored the usefulness of combination of culture-dependent techniques and next-generation sequencing techniques both to unravel the microbial patterns and understand the ecological impact of contamination.

Enrichment experiment changes microbial interactions in an ultra-oligotrophic environment

The increase of nutrients in water bodies, in particular nitrogen (N) and phosphorus (P) due to the recent expansion of agricultural and other human activities is accelerating environmental degradation of these water bodies, elevating the risk of eutrophication and reducing biodiversity. To evaluate the ecological effects of the influx of nutrients in an oligotrophic and stoichiometrically imbalanced environment, we performed a replicated in situ mesocosm experiment. We analyzed the effects of a N- and P-enrichment on the bacterial interspecific interactions in an experiment conducted in the Cuatro Cienegas Basin (CCB) in Mexico. This is a desert ecosystem comprised of several aquatic systems with a large number of microbial endemic species. The abundance of key nutrients in this basin exhibits strong stoichiometric imbalance (high N:P ratios), suggesting that species diversity is maintained mostly by competition for resources. We focused on the biofilm formation and antibiotic resistance of 960 strains of cultivated bacteria in two habitats, water and sediment, before and after 3 weeks of fertilization. The water habitat was dominated by Pseudomonas, while Halomonas dominated the sediment. Strong antibiotic resistance was found among the isolates at time zero in the nutrient-poor bacterial communities, but resistance declined in the bacteria isolated in the nutrient-rich environments, suggesting that in the nutrient-poor original environment, negative inter-specific interactions were important, while in the nutrient-rich environments, competitive interactions are not so important. In water, a significant increase in the percentage of biofilm-forming strains was observed for all treatments involving nutrient addition.

Abundance and diversity of functional genes involved in the degradation of aromatic hydrocarbons in Antarctic soils and sediments around Syowa Station

Hydrocarbon catabolic genes were investigated in soils and sediments in nine different locations around Syowa Station, Antarctica, using conventional PCR, real-time PCR, cloning, and sequencing analysis. Polycyclic aromatic hydrocarbon ring-hydroxylating dioxygenase (PAH-RHD)-coding genes from both Gram-positive and Gram-negative bacteria were observed. Clone libraries of Gram-positive RHD genes were related to (i) nidA3 of Mycobacterium sp. py146, (ii) pdoA of Terrabacter sp. HH4, (iii) nidA of Diaphorobacter sp. KOTLB, and (iv) pdoA2 of Mycobacterium sp. CH-2, with 95-99% similarity. Clone libraries of Gram-negative RHD genes were related to the following: (i) naphthalene dioxygenase of Burkholderia glathei, (ii) phnAc of Burkholderia sartisoli, and (iii) RHD alpha subunit of uncultured bacterium, with 41-46% similarity. Interestingly, the diversity of the Gram-positive RHD genes found around this area was higher than those of the Gram-negative RHD genes. Real-time PCR showed different abundance of dioxygenase genes between locations. Moreover, the PCR-denaturing gradient gel electrophoresis (DGGE) profile demonstrated diverse bacterial populations, according to their location. Forty dominant fragments in the DGGE profiles were excised and sequenced. All of the sequences belonged to ten bacterial phyla: Proteobacteria, Actinobacteria, Verrucomicrobia, Bacteroidetes, Firmicutes, Chloroflexi, Gemmatimonadetes, Cyanobacteria, Chlorobium, and Acidobacteria. In addition, the bacterial genus Sphingomonas, which has been suggested to be one of the major PAH degraders in the environment, was observed in some locations. The results demonstrated that indigenous bacteria have the potential ability to degrade PAHs and provided information to support the conclusion that bioremediation processes can occur in the Antarctic soils and sediments studied here.

Horizontal arrangement of anodes of microbial fuel cells enhances remediation of petroleum hydrocarbon-contaminated soil

With the aim of in situ bioremediation of soil contaminated by hydrocarbons, anodes arranged with two different ways (horizontal or vertical) were compared in microbial fuel cells (MFCs). Charge outputs as high as 833 and 762C were achieved in reactors with anodes horizontally arranged (HA) and vertically arranged (VA). Up to 12.5 % of the total petroleum hydrocarbon (TPH) was removed in HA after 135 days, which was 50.6 % higher than that in VA (8.3 %) and 95.3 % higher than that in the disconnected control (6.4 %). Hydrocarbon fingerprint analysis showed that the degradation rates of both alkanes and polycyclic aromatic hydrocarbons (PAHs) in HA were higher than those in VA. Lower mass transport resistance in the HA than that of the VA seems to result in more power and more TPH degradation. Soil pH was increased from 8.26 to 9.12 in HA and from 8.26 to 8.64 in VA, whereas the conductivity was decreased from 1.99 to 1.54 mS/cm in HA and from 1.99 to 1.46 mS/cm in VA accompanied with the removal of TPH. Considering both enhanced biodegradation of hydrocarbon and generation of charge in HA, the MFC with anodes horizontally arranged is a promising configuration for future applications.

Refinement of biodegradation tests methodologies and the proposed utility of new microbial ecology techniques

Society's reliance upon chemicals over the last few decades has led to their increased production, application and release into the environment. Determination of chemical persistence is crucial for risk assessment and management of chemicals. Current established OECD biodegradation guidelines enable testing of chemicals under laboratory conditions but with an incomplete consideration of factors that can impact on chemical persistence in the environment. The suite of OECD biodegradation tests do not characterise microbial inoculum and often provide little insight into pathways of degradation. The present review considers limitations with the current OECD biodegradation tests and highlights novel scientific approaches to chemical fate studies. We demonstrate how the incorporation of molecular microbial ecology methods (i.e., 'omics') may improve the underlying mechanistic understanding of biodegradation processes, and enable better extrapolation of data from laboratory based test systems to the relevant environment, which would potentially improve chemical risk assessment and decision making. We outline future challenges for relevant stakeholders to modernise OECD biodegradation tests and put the 'bio' back into biodegradation.

Complete genome sequence analysis of Pseudomonas aeruginosa N002 reveals its genetic adaptation for crude oil degradation

The present research work reports the whole genome sequence analysis of Pseudomonas aeruginosa strain N002 isolated from crude oil contaminated soil of Assam, India having high crude oil degradation ability. The whole genome of the strain N002 was sequenced by shotgun sequencing using Ion Torrent method and complete genome sequence analysis was done. It was found that the strain N002 revealed versatility for degradation, emulsification and metabolizing of crude oil. Analysis of cluster of orthologous group (COG) revealed that N002 has significantly higher gene abundance for cell motility, lipid transport and metabolism, intracellular trafficking, secretion and vesicular transport, secondary metabolite biosynthesis, transport and catabolism, signal transduction mechanism and transcription than average levels found in other genome sequences of the same bacterial species. However, lower gene abundance for carbohydrate transport and metabolism, replication, recombination and repair, translation, ribosomal structure, biogenesis was observed in N002 than average levels of other bacterial species.

Alkane hydroxylase genes in psychrophile genomes and the potential for cold active catalysis

BACKGROUND

Psychrophiles are presumed to play a large role in the catabolism of alkanes and other components of crude oil in natural low temperature environments. In this study we analyzed the functional diversity of genes for alkane hydroxylases, the enzymes responsible for converting alkanes to more labile alcohols, as found in the genomes of nineteen psychrophiles for which alkane degradation has not been reported. To identify possible mechanisms of low temperature optimization we compared putative alkane hydroxylases from these psychrophiles with homologues from nineteen taxonomically related mesophilic strains.

RESULTS

Seven of the analyzed psychrophile genomes contained a total of 27 candidate alkane hydroxylase genes, only two of which are currently annotated as alkane hydroxylase. These candidates were mostly related to the AlkB and cytochrome p450 alkane hydroxylases, but several homologues of the LadA and AlmA enzymes, significant for their ability to degrade long-chain alkanes, were also detected. These putative alkane hydroxylases showed significant differences in primary structure from their mesophile homologues, with preferences for specific amino acids and increased flexibility on loops, bends, and α-helices.

CONCLUSION

A focused analysis on psychrophile genomes led to discovery of numerous candidate alkane hydroxylase genes not currently annotated as alkane hydroxylase. Gene products show signs of optimization to low temperature, including regions of increased flexibility and amino acid preferences typical of psychrophilic proteins. These findings are consistent with observations of microbial degradation of crude oil in cold environments and identify proteins that can be targeted in rate studies and in the design of molecular tools for low temperature bioremediation.

Bacterial diversity in a contaminated Alpine glacier as determined by culture-based and molecular approaches

Glaciers are important ecosystems, hosting bacterial communities that are adapted to cold conditions and scarcity of available nutrients. Several works focused on the composition of bacterial communities in glaciers and on the long-range atmospheric deposition of pollutants in glaciers, but it is not clear yet if ski resorts can represent a source of point pollution in near-by glaciers, and if these pollutants can influence the residing bacterial communities. To test these hypotheses, 12 samples were analyzed in Madaccio Glacier, in a 3200 ma.s.l. from two areas, one undisturbed and one close to a summer ski resort that is active since the 1930s. Chemical analyses found concentrations up to 43 ng L(-1) for PCBs and up to 168 μg L(-1) for PAHs in the contaminated area: these values are significantly higher than the ones found in undisturbed glaciers because of long-range atmospheric deposition events, and can be explained as being related to the near-by ski resort activities. Isolation of strains on rich medium plates and PCR-DGGE analyses followed by sequencing of bands allowed the identification of a bacterial community with phylogenetic patterns close to other glacier environments, with Proteobacteria and Actinobacteria the mostly abundant phyla, with Acidobacteria, Firmicutes and Cyanobacteria also represented in the culture-independent analyses. A number of isolates were identified by molecular and biochemical methods as phylogenetic related to known xenobiotic-degrading strains: glaciers subjected to chemical contamination can be important reservoirs of bacterial strains with potential applications in bioremediation.

Distribution of naphthalene dioxygenase genes in crude oil-contaminated soils

Polycyclic aromatic hydrocarbons (PAHs) are one of the major pollutants in soils in oil exploring areas. Biodegradation is the major process for natural elimination of PAHs from contaminated soils. Functional genes can be used as biomarkers to assess the biodegradation potential of indigenous microbial populations. However, little is known about the distribution of PAH-degrading genes in the environment. The links between environmental parameters and the distribution of PAH metabolic genes remain essentially unclear. The present study investigated the abundance and diversity of naphthalene dioxygenase genes in the oil-contaminated soils in the Shengli Oil Field (China). Spatial variations in the density and diversity of naphthalene dioxygenase genes occurred in this area. Four different sequence genotypes were observed in the contaminated soils, with the predominance of novel PAH-degrading genes. Pearson's correlation analysis illustrated that gene abundance had positive correlations with the levels of total organic carbon and aromatic hydrocarbons, while gene diversity showed a negative correlation with the level of polar aromatics. This work could provide some new insights toward the distribution of PAH metabolic genes and PAH biodegradation potential in oil-contaminated ecosystems.

Features of pseudomonads growing at low temperatures: another facet of their versatility

Pseudomonads are a diverse and ecologically successful group of γ-proteobacteria present in many environments (terrestrial, freshwater and marine), either free living or associated with plants or animals. Their success is at least partly based on their ability to grow over a wide range of temperatures, their capacity to withstand different kinds of stress and their great metabolic versatility. Although the optimal growth temperature of pseudomonads is usually close to 25–30°C, many strains can also grow between 5°C and 10°C, and some of them even close to 0°C. Such low temperatures strongly affect the physicochemical properties of macromolecules, forcing cells to evolve traits that optimize growth and help them withstand cold-induced stresses such as increased levels of reactive oxygen species, reduced membrane fluidity and enzyme activity, cold-induced protein denaturation and the greater stability of DNA and RNA secondary structures. This review gathers the information available on the strategies used by pseudomonads to adapt to low temperature growth, and briefly describes some of the biotechnological applications that might benefit from cold-adapted bacterial strains and enzymes, e.g., biotransformation or bioremediation processes to be performed at low temperatures.

Biodegradation of variable-chain-length n-alkanes in Rhodococcus opacus R7 and the involvement of an alkane hydroxylase system in the metabolism

Rhodococcus opacus R7 is a Gram-positive bacterium isolated from a polycyclic aromatic hydrocarbon contaminated soil for its versatile metabolism; indeed the strain is able to grow on naphthalene, o-xylene, and several long- and medium-chain n-alkanes. In this work we determined the degradation of n-alkanes in Rhodococcus opacus R7 in presence of n-dodecane (C12), n-hexadecane (C16), n-eicosane (C20), n-tetracosane (C24) and the metabolic pathway in presence of C12. The consumption rate of C12 was 88%, of C16 was 69%, of C20 was 51% and of C24 it was 78%. The decrement of the degradation rate seems to be correlated to the length of the aliphatic chain of these hydrocarbons. On the basis of the metabolic intermediates determined by the R7 growth on C12, our data indicated that R. opacus R7 metabolizes medium-chain n-alkanes by the primary alcohol formation. This represents a difference in comparison with other Rhodococcus strains, in which a mixture of the two alcohols was observed. By GC-MSD analysis we also identified the monocarboxylic acid, confirming the terminal oxidation.

Moreover, the alkB gene cluster from R. opacus R7 was isolated and its involvement in the n-alkane degradation system was investigated by the cloning of this genomic region into a shuttle-vector E. coli-Rhodococcus to evaluate the alkane hydroxylase activity. Our results showed an increased biodegradation of C12 in the recombinant strain R. erythropolis AP (pTipQT1-alkR7) in comparison with the wild type strain R. erythropolis AP. These data supported the involvement of the alkB gene cluster in the n-alkane degradation in the R7 strain.