Petroleum-influenced beach sediments of the Campeche Bank, Mexico: diversity and bacterial community structure assessment

Anthropogenic impact accelerates antibiotic resistome diversity in the mangrove sediment of Indian Sundarban

Mangroves are situated in convergence zones between fresh and marine water and are prone to pollution and deforestation. This study explored the microbiome structure, function and antibiotic resistome of Indian Sundarban. The taxonomic Chao1 estimated diversity was highest in uninhabited Kalash (1204.64 ± 12.72) and lowest in Godkhali, which experiences considerable human activities (1158.76 ± 11.18). The alpha diversity showed negative correlation (p < 0.05) with PAH such as Acenaphthene (r = -0.56), Acenaphthylene (r = -0.62), Fluoranthene (r = -0.59), Fluorene (r = -0.55), Phenanthrene (r = -0.57), while the biochemical parameters phosphate (r = 0.58) and salinity (r = 0.58) had a significant (p < 0.05) positive correlation. The data suggest the importance of physicochemical parameters in maintaining the mangrove microbiome. The taxonomic composition was dominated by Proteobacteria (54.12 ± 0.37). All sites were dominated by ARGs such as rpoB2, cpxR, ompR, camP, and bacA. Comparing the Sundarban mangrove sediment resistome with mangrove from other sites in India (Kerala) and China (Guangxi, Hainan, and Shenzhen) suggested that resistome from Indian mangrove has a significantly (p < 0.05) higher ARG diversity compared to Chinese mangroves. Yet, the abundance of the ARG was significantly (p < 0.05) lower in the Indian mangroves posing a much greater risk if enriched. The study suggests that anthropogenic activities and pollution degrade the microbiome diversity, disturb the microbiome functions, and enrich ARGs.

Analyses of community structure and role of immobilized bacteria system in the bioremediation process of diesel pollution seawater

Immobilized bacteria system plays an important role during degradation process in oil contaminated seawater. Although the immobilized bacteria system can be recycled to avoid pollution after remediation, it remains an open question on whether or not the secondary pollution occurs during the degradation process. Additionally, the research on the role of immobilized bacteria system in the process of oil removal is not clear enough. In this study, both the diesel degradation rate of diesel by immobilized bacteria system and changes in marine microbial community structure were determined to explore the role of immobilized bacteria system. The immobilized bacteria system was added to the diesel polluted seawater (1% diesel) for 30 days. The degradation performance was investigated during the process, and the microbial community structure was analyzed simultaneously. The results illustrated that the degradation rate of diesel by immobilized bacteria system reached 78.39% after 30 days, and Alcanivorax (59.09%), Achromobacter (24.34%) and Thalassospira (9.84%) were the dominant genera in the immobilized bacteria system. The addition of immobilized bacteria system increased the content of nitrogen and phosphorus, and then promoted the growth of oil-degrading bacteria. Thus, functional genes related to oil degradation increased. Additionally, there was little difference in the microbial composition between the treated seawater and the unpolluted seawater. Based on all results, it can be inferred that immobilized bacteria system triggered and stimulated diesel degradation process. This study provides a promising way to improve the removal of oil, and provides theoretical support for the wide application of immobilized microorganism technology.

Ecological risk potentials of petroleum hydrocarbons and heavy metals shape the bacterial communities of marine hydrosphere at Atlantic Ocean, Atlas Cove, Nigeria

Trans-Atlantic voyage of petroleum often leads to marine pollution with petroleum hydrocarbons (PHs) and heavy metals (HMs) that defines structures of autochthonous bacteria in the hydrosphere. Bacterial taxa of marine sediments exposed to petroleum transport activities were profiled using 16S rDNA metagenomics and correlated with the geochemistry to establish their impact on the microbiome. The physico-chemistry of the marine systems revealed varied degrees of contamination with PHs and HMs exceeding recommended threshold for aquatic life. Ecological risk assessment based on organic carbon of the sediment established phenanthrene, anthracene, and pyrene posed high risks (index risk quotient >32) to marine life. The most dominant phylum of the 44 bacterial phyla in the marine-sphere was Proteobacteria with relative abundance of 45-77% in the sampling locations. Relative dominance of Proteobacteria in the sediments spanned Gammaproteobacteria (17-25%), Deltaproteobacteria (12-20%), and Alphaproteobacteria (7-14%). Whereas, more operational taxonomic units (OTUs) belonging to Epsilonproteobacteria (19 ± 2.4%) were found in estuarine sediment unlike < 0.5% relative abundances obtained from oceanic sediments. Sulfurimonas apparently dominated the bacterial genera with up to 2.16 ± 0.19% abundance in oceanic sediments. Canonical correspondence analysis revealed that PHs shaped the structure of bacterial OTUs in oceanic sediments where petroleum loading/offloading occurs unlike in some kilometres a yonder where HMs correlated with the bacteria structure. The dominant bacteria might possibly pivotal to ecophysiologies of hydrocarbon contaminated marine environment, and would be pertinent to biotechnological applications for possible bioremediation campaign.

Detection of functional microorganisms in benzene [a] pyrene-contaminated soils using DNA-SIP technology

DNA-SIP technology was used to detect active BaP-degraders involved in the biodegradation of benzo [a] pyrene (BaP) in two soils separately and in mixture. The lowest BaP removal was observed in red soil, and Ramlibacter (OTU830) belonging to the γ-Proteobacteria was labeled as BaP degrader with ¹³C-BaP. The highest diversity of degrading microorganisms occurred in the paddy soil with OTUs belonging to Nocardioids, Micromonospora, Saccharothrix, Lysobacter and Methylium present and a BaP removal efficiency of 29.5% after 14 d. BaP degraders in the mixed microbiome of the soil mixture were Burkholderia and Phenylobacterium, together with Nocardioides and Micromonospora as in the paddy soil. These results indicated that the active BaP-degraders in the mixed microbiome were identical to the active BaP-degraders in paddy soil (OTU356 and OTU328), but also unique in the mixed microbiome, such as OTU393 and OTU392. The functional genes of PAH-ring hydroxylating dioxygenases (PAH-RHD_α) were expressed and were positively related to the removal of BaP, and the active BaP degrading bacteria included both Gram-positive and Gram-negative bacteria. Saccharothrix, Phylobacterium, Micromonospora and Nocardioids are here reported as BaP degraders for the first time using DNA-SIP.

Alterations in the Gut Microbiota of Zebrafish (Danio rerio) in Response to Water-Soluble Crude Oil Components and Its Mixture With a Chemical Dispersant

Crude oil spills have caused substantial impacts to aquatic ecosystems. Chemical dispersants are used to palliate the impact of oil spillages, but their use is polemic due to their additional potential toxic effect when mixed with oil-derived components. In this work, we used a 16S-based metagenomic approach to analyze the changes of the gut microbiota of adult zebrafish (Danio rerio) exposed to the water accommodated fraction (WAF) of a light crude oil (35° API gravity), and the chemically enhanced WAF (CEWAF), prepared with Nokomis 3-F4® dispersant. After 96 h of exposure, WAF induced an increase in the alpha and beta diversity, altering the relative abundance of Vibrio, Flavobacterium, and Novosphingobium. In contrast, CEWAF only caused an increase in the beta diversity, and an enrichment of the genus Pseudomona. Both treatments diminished the abundances of Aeromonas, Cetobacterium, Coxiella, Dinghuibacter, and Paucibacter. Moreover, the co-occurrence network among genera was more complex in WAF than in CEWAF, indicating a greater bacterial interaction in response to WAF. Our results indicate that short-term exposure to WAF and CEWAF can induce a dysbiosis in the gut microbiota of D. rerio, but these changes are specific in each treatment.

Metagenomic Profiling and Microbial Metabolic Potential of Perdido Fold Belt (NW) and Campeche Knolls (SE) in the Gulf of Mexico

The Gulf of Mexico (GoM) is a particular environment that is continuously exposed to hydrocarbon compounds that may influence the microbial community composition. We carried out a metagenomic assessment of the bacterial community to get an overall view of this geographical zone. We analyzed both taxonomic and metabolic markers profiles to explain how the indigenous GoM microorganims participate in the biogeochemical cycling. Two geographically distant regions in the GoM, one in the north-west (NW) and one in the south-east (SE) of the GoM were analyzed and showed differences in their microbial composition and metabolic potential. These differences provide evidence the delicate equilibrium that sustains microbial communities and biogeochemical cycles. Based on the taxonomy and gene groups, the NW are more oxic sediments than SE ones, which have anaerobic conditions. Both water and sediments show the expected sulfur, nitrogen, and hydrocarbon metabolism genes, with particularly high diversity of the hydrocarbon-degrading ones. Accordingly, many of the assigned genera were associated with hydrocarbon degradation processes, Nitrospira and Sva0081 were the most abundant in sediments, while Vibrio, Alteromonas, and Alcanivorax were mostly detected in water samples. This basal-state analysis presents the GoM as a potential source of aerobic and anaerobic hydrocarbon degradation genes important for the ecological dynamics of hydrocarbons and the potential use for water and sediment bioremediation processes.

Biodegradability enhancement of hydrolyzed polyacrylamide wastewater by a combined Fenton-SBR treatment process

An efficient way to solve the environmental pollution deriving from hydrolyzed polyacrylamide (HPAM)-containing drilling wastewater is urgent. This work adopted a novel method coupling Fenton oxidation with sequencing batch reactor (SBR) to treat gas-field drilling wastewater successively. This Fenton-SBR process reduced COD, HPAM, NH₄⁺-N and total phosphorus (TP) concentrations of drilling wastewater by 98.35%, 87.58%, 94.50% and 93.52%, respectively. While simulated HPAM wastewater with similar HPAM concentration to Fenton-oxidized drilling wastewater was treated only by biological process, and the COD and HPAM removal efficiencies reached 78.26% and 62.95%. The result indicates that the biodegradability of the drilling wastewater was enhanced after Fenton oxidation. Moreover, the analysis on microbial community structure indicates the dominant bacteria in treated drilling wastewater were different from that in treated simulated-wastewater. It can be considered the Fenton-SBR process possesses potential to be applied to treating the drilling wastewater.

Independent and interactive effects of reduced seawater pH and oil contamination on subsurface sediment bacterial communities

Ocean acidification may exacerbate the environmental impact of oil hydrocarbon pollution by disrupting the core composition of the superficial (0-1 cm) benthic bacterial communities. However, at the subsurface sediments (approximately 5 cm below sea floor), the local biochemical characteristics and the superjacent sediment barrier may buffer these environmental changes. In this study, we used a microcosm experimental approach to access the independent and interactive effects of reduced seawater pH and oil contamination on the composition of subsurface benthic bacterial communities, at two time points, by 16S rRNA gene-based high-throughput sequencing. An in-depth taxa-specific variance analysis revealed that the independent effects of reduced seawater pH and oil contamination were significant predictors of changes in the relative abundance of some specific bacterial groups (e.g., Firmicutes, Rhizobiales, and Desulfobulbaceae). However, our results indicated that the overall microbial community structure was not affected by independent and interactive effects of reduced pH and oil contamination. This study provides evidence that bacterial communities inhabiting subsurface sediment may be less susceptible to the effects of oil contamination in a scenario of reduced seawater pH.

Effects of Phytoremediation Treatment on Bacterial Community Structure and Diversity in Different Petroleum-Contaminated Soils

Increased exploitation and use of petroleum resources is leading to increased risk of petroleum contamination of soil and groundwater. Although phytoremediation is a widely-used and cost-effective method for rehabilitating soils polluted by petroleum, bacterial community structure and diversity in soils undergoing phytoremediation is poorly understood. We investigate bacterial community response to phytoremediation in two distinct petroleum-contaminated soils (add prepared petroleum-contaminated soils) from northwest China, Weihe Terrace soil and silty loam from loess tableland. High-throughput sequencing technology was used to compare the bacterial communities in 24 different samples, yielding 18,670 operational taxonomic units (OTUs). The dominant bacterial groups, Proteobacteria (31.92%), Actinobacteria (16.67%), Acidobacteria (13.29%) and Bacteroidetes (6.58%), increased with increasing petroleum concentration from 3000 mg/kg–10,000 mg/kg, while Crenarchaeota (13.58%) and Chloroflexi (4.7%) decreased. At the order level, RB41, Actinomycetales, Cytophagales, envOPS12, Rhodospirillales, MND1 and Xanthomonadales, except Nitrososphaerales, were dominant in Weihe Terrace soil. Bacterial community structure and diversity in the two soils were significantly different at similar petroleum concentrations. In addition, the dominant genera were affected by available nitrogen, which is strongly associated with the plants used for remediation. Overall, the bacterial community structure and diversity were markedly different in the two soils, depending on the species of plants used and the petroleum concentration.

Assessment of the bacterial community structure in shallow and deep sediments of the Perdido Fold Belt region in the Gulf of Mexico

The Mexican region of the Perdido Fold Belt (PFB), in northwestern Gulf of Mexico (GoM), is a geological province with important oil reservoirs that will be subjected to forthcoming oil exploration and extraction activities. To date, little is known about the native microbial communities of this region, and how these change relative to water depth. In this study we assessed the bacterial community structure of surficial sediments by high-throughput sequencing of the 16S rRNA gene at 11 sites in the PFB, along a water column depth gradient from 20 to 3,700 m, including five shallow (20–600 m) and six deep (2,800–3,700 m) samples. The results indicated that OTUs richness and diversity were higher for shallow sites (OTUs = 2,888.2 ± 567.88; H′ = 9.6 ± 0.85) than for deep sites (OTUs = 1,884.7 ± 464.2; H′ = 7.74 ± 1.02). Nonmetric multidimensional scaling (NMDS) ordination revealed that shallow microbial communities grouped separately from deep samples. Additionally, the shallow sites plotted further from each other on the NMDS whereas samples from the deeper sites (abyssal plains) plotted much more closely to each other. These differences were related to depth, redox potential, sulfur concentration, and grain size (lime and clay), based on the environmental variables fitted with the axis of the NMDS ordination. In addition, differential abundance analysis identified 147 OTUs with significant fold changes among the zones (107 from shallow and 40 from deep sites), which constituted 10 to 40% of the total relative abundances of the microbial communities. The most abundant OTUs with significant fold changes in shallow samples corresponded to Kordiimonadales, Rhodospirillales, Desulfobacterales (Desulfococcus), Syntrophobacterales and Nitrospirales (GOUTA 19, BD2-6, LCP-6), whilst Chromatiales, Oceanospirillales (Amphritea, Alcanivorax), Methylococcales, Flavobacteriales, Alteromonadales (Shewanella, ZD0117) and Rhodobacterales were the better represented taxa in deep samples. Several of the OTUs detected in both deep and shallow sites have been previously related to hydrocarbons consumption. Thus, this metabolism seems to be well represented in the studied sites, and it could abate future hydrocarbon contamination in this ecosystem. The results presented herein, along with biological and physicochemical data, constitute an available reference for further monitoring of the bacterial communities in this economically important region in the GoM.

Response of Core Microbial Consortia to Chronic Hydrocarbon Contaminations in Coastal Sediment Habitats

Traditionally, microbial surveys investigating the effect of chronic anthropogenic pressure such as polyaromatic hydrocarbons (PAHs) contaminations consider just the alpha and beta diversity and ignore the interactions among the different taxa forming the microbial community. Here, we investigated the ecological relationships between the three domains of life (i.e., Bacteria, Archaea, and Eukarya) using 454 pyrosequencing on the 16S rRNA and 18S rRNA genes from chronically impacted and pristine sediments, along the coasts of the Mediterranean Sea (Gulf of Lion, Vermillion coast, Corsica, Bizerte lagoon and Lebanon) and the French Atlantic Ocean (Bay of Biscay and English Channel). Our approach provided a robust ecological framework for the partition of the taxa abundance distribution into 859 core Operational taxonomic units (OTUs) and 6629 satellite OTUs. OTUs forming the core microbial community showed the highest sensitivity to changes in environmental and contaminant variations, with salinity, latitude, temperature, particle size distribution, total organic carbon (TOC) and PAH concentrations as main drivers of community assembly. The core communities were dominated by Gammaproteobacteria and Deltaproteobacteria for Bacteria, by Thaumarchaeota, Bathyarchaeota and Thermoplasmata for Archaea and Metazoa and Dinoflagellata for Eukarya. In order to find associations among microorganisms, we generated a co-occurrence network in which PAHs were found to impact significantly the potential predator – prey relationship in one microbial consortium composed of ciliates and Actinobacteria. Comparison of network topological properties between contaminated and non-contaminated samples showed substantial differences in the network structure and indicated a higher vulnerability to environmental perturbations in the contaminated sediments.

Chronic Polyaromatic Hydrocarbon (PAH) Contamination Is a Marginal Driver for Community Diversity and Prokaryotic Predicted Functioning in Coastal Sediments

Benthic microorganisms are key players in the recycling of organic matter and recalcitrant compounds such as polyaromatic hydrocarbons (PAHs) in coastal sediments. Despite their ecological importance, the response of microbial communities to chronic PAH pollution, one of the major threats to coastal ecosystems, has received very little attention. In one of the largest surveys performed so far on coastal sediments, the diversity and composition of microbial communities inhabiting both chronically contaminated and non-contaminated coastal sediments were investigated using high-throughput sequencing on the 18S and 16S rRNA genes. Prokaryotic alpha-diversity showed significant association with salinity, temperature, and organic carbon content. The effect of particle size distribution was strong on eukaryotic diversity. Similarly to alpha-diversity, beta-diversity patterns were strongly influenced by the environmental filter, while PAHs had no influence on the prokaryotic community structure and a weak impact on the eukaryotic community structure at the continental scale. However, at the regional scale, PAHs became the main driver shaping the structure of bacterial and eukaryotic communities. These patterns were not found for PICRUSt predicted prokaryotic functions, thus indicating some degree of functional redundancy. Eukaryotes presented a greater potential for their use as PAH contamination biomarkers, owing to their stronger response at both regional and continental scales.

Bacteria capable of degrading anthracene, phenanthrene, and fluoranthene as revealed by DNA based stable-isotope probing in a forest soil

Information on microorganisms possessing the ability to metabolize different polycyclic aromatic hydrocarbons (PAHs) in complex environments helps in understanding PAHs behavior in natural environment and developing bioremediation strategies. In the present study, stable-isotope probing (SIP) was applied to investigate degraders of PAHs in a forest soil with the addition of individually (13)C-labeled phenanthrene, anthracene, and fluoranthene. Three distinct phylotypes were identified as the active phenanthrene-, anthracene- and fluoranthene-degrading bacteria. The putative phenanthrene degraders were classified as belonging to the genus Sphingomona. For anthracene, bacteria of the genus Rhodanobacter were the putative degraders, and in the microcosm amended with fluoranthene, the putative degraders were identified as belonging to the phylum Acidobacteria. Our results from DNA-SIP are the first to directly link Rhodanobacter- and Acidobacteria-related bacteria with anthracene and fluoranthene degradation, respectively. The results also illustrate the specificity and diversity of three- and four-ring PAHs degraders in forest soil, contributes to our understanding on natural PAHs biodegradation processes, and also proves the feasibility and practicality of DNA-based SIP for linking functions with identity especially uncultured microorganisms in complex microbial biota.

Bacterial diversity in oil-polluted marine coastal sediments

Marine environments harbour a persistent microbial seed which can be shaped by changes of the environmental conditions such as contamination by petroleum components. Oil spills, together with small but continuous discharges of oil from transportation and recreational activities, are important sources of hydrocarbon pollution within the marine realm. Consequently, prokaryotic communities have become well pre-adapted toward oil pollution, and many microorganisms that are exposed to its presence develop an active degradative response. The natural attenuation of oil pollutants, as has been demonstrated in many sites, is modulated according to the intrinsic environmental properties such as the availability of terminal electron acceptors and elemental nutrients, together with the degree of pollution and the type of hydrocarbon fractions present. Whilst dynamics in the bacterial communities in the aerobic zones of coastal sediments are well characterized and the key players in hydrocarbon biodegradation have been identified, the subtidal ecology of the anaerobic community is still not well understood. However, current data suggest common patterns of response in these ecosystems.

Characterization of the microbial community structure and nitrosamine-reducing isolates in drinking water biofilters

Two biofilters were constructed using biological activated carbon (BAC) and nitrosamine-containing water from two drinking water treatment plants. The microbiome of each biofilter was characterized by 454 high-throughput pyrosequencing, and one nitrosamine-reducing bacterium was isolated. The results showed that nitrosamines changed the relative abundance at both the phylum and class levels, and the new genera were observed in the microbial communities of the two BAC filters after cultivation. As such, the genus Rhodococcus, which includes many nitrosamine-reducing strains reported in previous studies, was only detected in the BAC2 filter after cultivation. These findings indicate that nitrosamines can significantly affect the genus level in the microbial communities. Furthermore, the isolated bacterial culture Rhodococcus cercidiphylli A41 AS-1 exhibited the ability to reduce five nitrosamines (N-nitrosodimethylamine, N-nitrosodiethylamine, N-nitrosodi-n-propylamine, N-nitrosopyrrolidine, and N-nitrosodi-n-butylamine) with removal ratios that ranged from 38.1% to 85.4%. The isolate exhibited a better biodegradation ability with nitrosamine as the carbon source when compared with nitrosamine as the nitrogen source. This study increases our understanding of the microbial community in drinking water biofilters with trace quantities of nitrosamines, and provides information on the metabolism of nitrosamine-reducing bacteria.

Novel Phenanthrene-Degrading Bacteria Identified by DNA-Stable Isotope Probing

Microorganisms responsible for the degradation of phenanthrene in a clean forest soil sample were identified by DNA-based stable isotope probing (SIP). The soil was artificially amended with either 12C- or 13C-labeled phenanthrene, and soil DNA was extracted on days 3, 6 and 9. Terminal restriction fragment length polymorphism (TRFLP) results revealed that the fragments of 219- and 241-bp in HaeIII digests were distributed throughout the gradient profile at three different sampling time points, and both fragments were more dominant in the heavy fractions of the samples exposed to the 13C-labeled contaminant. 16S rRNA sequencing of the 13C-enriched fraction suggested that Acidobacterium spp. within the class Acidobacteria, and Collimonas spp. within the class Betaproteobacteria, were directly involved in the uptake and degradation of phenanthrene at different times. To our knowledge, this is the first report that the genus Collimonas has the ability to degrade PAHs. Two PAH-RHDα genes were identified in 13C-labeled DNA. However, isolation of pure cultures indicated that strains of Staphylococcus sp. PHE-3, Pseudomonas sp. PHE-1, and Pseudomonas sp. PHE-2 in the soil had high phenanthrene-degrading ability. This emphasizes the role of a culture-independent method in the functional understanding of microbial communities in situ.

Bacterial diversity of polluted surface sediments in the northern Adriatic Sea

Samples were collected from sea sediments at seven sites in the northern Adriatic Sea that included six sites next to industrial complexes and one from a tourist site (recreational beach). The samples were assayed for alkanes and polycyclic aromatic hydrocarbons. The composition of the hydrocarbon samples suggested that industrial pollution was present in most cases. A sample from one site was also grown aerobically under crude oil enrichment in order to evaluate the response of indigenous bacterial populations to crude oil exposure. Analysis of 16S rRNA gene sequences showed varying microbial biodiversity depending on the level of pollution--ranging from low (200 detected genera) to high (1000+ genera) biodiversity, with lowest biodiversity observed in polluted samples. This indicated that there was considerable biodiversity in all sediment samples but it was severely restricted after exposure to crude oil selection pressure. Phylogenetic analysis of putative alkB genes showed high evolutionary diversity of the enzymes in the samples and suggested great potential for bioremediation and bioprospecting. The first systematic analysis of bacterial communities from sediments of the northern Adriatic Sea is presented, and it will provide a baseline assessment that may serve as a reference point for ecosystem changes and hydrocarbon degrading potential--a potential that could soon gain importance due to plans for oil exploitation in the area.

Microbial metabolism and community structure in response to bioelectrochemically enhanced remediation of petroleum hydrocarbon-contaminated soil

This study demonstrates that electrodes in a bioelectrochemical system (BES) can potentially serve as a nonexhaustible electron acceptor for in situ bioremediation of hydrocarbon contaminated soil. The deployment of BES not only eliminates aeration or supplement of electron acceptors as in contemporary bioremediation but also significantly shortens the remediation period and produces sustainable electricity. More interestingly, the study reveals that microbial metabolism and community structure distinctively respond to the bioelectrochemically enhanced remediation. Tubular BESs with carbon cloth anode (CCA) or biochar anode (BCA) were inserted into raw water saturated soils containing petroleum hydrocarbons for enhancing in situ remediation. Results show that total petroleum hydrocarbon (TPH) removal rate almost doubled in soils close to the anode (63.5-78.7%) than that in the open circuit positive controls (37.6-43.4%) during a period of 64 days. The maximum current density from the BESs ranged from 73 to 86 mA/m(2). Comprehensive microbial and chemical characterizations and statistical analyses show that the residual TPH has a strongly positive correlation with hydrocarbon-degrading microorganisms (HDM) numbers, dehydrogenase activity, and lipase activity and a negative correlation with soil pH, conductivity, and catalase activity. Distinctive microbial communities were identified at the anode, in soil with electrodes, and soil without electrodes. Uncommon electrochemically active bacteria capable of hydrocarbon degradation such as Comamonas testosteroni, Pseudomonas putida, and Ochrobactrum anthropi were selectively enriched on the anode, while hydrocarbon oxidizing bacteria were dominant in soil samples. Results from genus or phylum level characterizations well agree with the data from cluster analysis. Data from this study suggests that a unique constitution of microbial communities may play a key role in BES enhancement of petroleum hydrocarbons biodegradation in soils.

Marine coastal sediments microbial hydrocarbon degradation processes: contribution of experimental ecology in the omics'era

Coastal marine sediments, where important biological processes take place, supply essential ecosystem services. By their location, such ecosystems are particularly exposed to human activities as evidenced by the recent Deepwater Horizon disaster. This catastrophe revealed the importance to better understand the microbial processes involved on hydrocarbon degradation in marine sediments raising strong interests of the scientific community. During the last decade, several studies have shown the key role played by microorganisms in determining the fate of hydrocarbons in oil-polluted sediments but only few have taken into consideration the whole sediment’s complexity. Marine coastal sediment ecosystems are characterized by remarkable heterogeneity, owning high biodiversity and are subjected to fluctuations in environmental conditions, especially to important oxygen oscillations due to tides. Thus, for understanding the fate of hydrocarbons in such environments, it is crucial to study microbial activities, taking into account sediment characteristics, physical-chemical factors (electron acceptors, temperature), nutrients, co-metabolites availability as well as sediment’s reworking due to bioturbation activities. Key information could be collected from in situ studies, which provide an overview of microbial processes, but it is difficult to integrate all parameters involved. Microcosm experiments allow to dissect in-depth some mechanisms involved in hydrocarbon degradation but exclude environmental complexity. To overcome these lacks, strategies have been developed, by creating experiments as close as possible to environmental conditions, for studying natural microbial communities subjected to oil pollution. We present here a review of these approaches, their results and limitation, as well as the promising future of applying “omics” approaches to characterize in-depth microbial communities and metabolic networks involved in hydrocarbon degradation. In addition, we present the main conclusions of our studies in this field.

Remarkable impact of PAHs and TPHs on the richness and diversity of bacterial species in surface soils exposed to long-term hydrocarbon pollution

Nowadays, because of substantial use of petroleum-derived fuels the number and extension of hydrocarbon polluted terrestrial ecosystems is in growth worldwide. In remediation of aforementioned sites bioremediation still tends to be an innovative, environmentally attractive technology. Although huge amount of information is available concerning the hydrocarbon degradation potential of cultivable hydrocarbonoclastic bacteria little is known about the in situ long-term effects of petroleum derived compounds on the structure of soil microbiota. Therefore, in this study our aim was to determine the long-term impact of total petroleum hydrocarbons (TPHs), volatile petroleum hydrocarbons (VPHs), total alkyl benzenes (TABs) as well as of polycyclic aromatic hydrocarbons (PAHs) on the structure of bacterial communities of four different contaminated soil samples. Our results indicated that a very high amount of TPH affected positively the diversity of hydrocarbonoclastic bacteria. This finding was supported by the occurrence of representatives of the α-, β-, γ-Proteobacteria, Actinobacteria, Flavobacteriia and Bacilli classes. High concentration of VPHs and TABs contributed to the predominance of actinobacterial isolates. In PAH impacted samples the concentration of PAHs negatively correlated with the diversity of bacterial species. Heavily PAH polluted soil samples were mainly inhabited by the representatives of the β-, γ-Proteobacteria (overwhelming dominance of Pseudomonas sp.) and Actinobacteria.

Alkane biodegradation genes from chronically polluted subantarctic coastal sediments and their shifts in response to oil exposure

Although sediments are the natural hydrocarbon sink in the marine environment, the ecology of hydrocarbon-degrading bacteria in sediments is poorly understood, especially in cold regions. We studied the diversity of alkane-degrading bacterial populations and their response to oil exposure in sediments of a chronically polluted Subantarctic coastal environment, by analyzing alkane monooxygenase (alkB) gene libraries. Sequences from the sediment clone libraries were affiliated with genes described in Proteobacteria and Actinobacteria, with 67 % amino acid identity in average to sequences from isolated microorganisms. The majority of the sequences were most closely related to uncultured microorganisms from cold marine sediments or soils from high latitude regions, highlighting the role of temperature in the structuring of this bacterial guild. The distribution of alkB sequences among samples of different sites and years, and selection after experimental oil exposure allowed us to identify ecologically relevant alkB genes in Subantarctic sediments, which could be used as biomarkers for alkane biodegradation in this environment. 16 S rRNA amplicon pyrosequencing indicated the abundance of several genera for which no alkB genes have yet been described (Oleispira, Thalassospira) or that have not been previously associated with oil biodegradation (Spongiibacter-formerly Melitea-, Maribius, Robiginitomaculum, Bizionia and Gillisia). These genera constitute candidates for future work involving identification of hydrocarbon biodegradation pathway genes.