Field observations on the variability of crude oil impact on indigenous hydrocarbon-degrading bacteria from sub-Antarctic intertidal sediments

Hydrocarbon bioremediation on Arctic shorelines: Historic perspective and roadway to the future

Climate change has become one of the greatest concerns of the past few decades. In particular, global warming is a growing threat to the Canadian high Arctic and other polar regions. By the middle of this century, an increase in the annual mean temperature of 1.8 °C-2.7 °C for the Canadian North is predicted. Rising temperatures lead to a significant decrease of the sea ice area covered in the Northwest Passage. As a consequence, a surge of maritime activity in that region increases the risk of hydrocarbon pollution due to accidental fuel spills. In this review, we focus on bioremediation approaches on Arctic shorelines. We summarize historical experimental spill studies conducted at Svalbard, Baffin Island, and the Kerguelen Archipelago, and review contemporary studies that used modern omics techniques in various environments. We discuss how omics approaches can facilitate our understanding of Arctic shoreline bioremediation and identify promising research areas that should be further explored. We conclude that specific environmental conditions strongly alter bioremediation outcomes in Arctic environments and future studies must therefore focus on correlating these diverse parameters with the efficacy of hydrocarbon biodegradation.

Hydrocarbon biodegradation potential of microbial communities from high Arctic beaches in Canada's Northwest Passage

Sea ice loss is opening shipping routes in Canada's Northwest Passage, increasing the risk of an oil spill. Harnessing the capabilities of endemic microorganisms to degrade oil may be an effective remediation strategy for contaminated shorelines; however, limited data exists along Canada's Northwest Passage. In this study, hydrocarbon biodegradation potential of microbial communities from eight high Arctic beaches was assessed. Across high Arctic beaches, community composition was distinct, potential hydrocarbon-degrading genera were detected and microbial communities were able to degrade hydrocarbons (hexadecane, naphthalene, and alkanes) at low temperature (4 °C). Hexadecane and naphthalene biodegradation were stimulated by nutrients, but nutrients had little effect on Ultra Low Sulfur Fuel Oil biodegradation. Oiled microcosms showed a significant enrichment of Pseudomonas and Rhodococcus. Nutrient-amended microcosms showed increased abundances of key hydrocarbon biodegradation genes (alkB and CYP153). Ultimately, this work provides insight into hydrocarbon biodegradation on Arctic shorelines and oil-spill remediation in Canada's Northwest Passage.

Rhizoremediation of petroleum hydrocarbon, prospects and future

Oil refineries generate several tones of oily waste which is dumped in an open pit within the vicinity of oil field.

Regime shift in sandy beach microbial communities following Deepwater Horizon oil spill remediation efforts

Sandy beaches support a wide variety of underappreciated biodiversity that is critical to coastal ecosystems. Prior to the 2010 Deepwater Horizon oil spill, the diversity and function of supratidal beach sediment microbial communities along Gulf of Mexico coastlines were not well understood. As such, it was unclear if microbial community compositional changes would occur following exposure to beached oil, if indigenous communities could biodegrade oil, or how cleanup efforts, such as sand washing and sediment redistribution, would impact microbial ecosystem resiliency. Transects perpendicular to the shoreline were sampled from public beaches on Grand Isle, Louisiana, and Dauphin Island, Alabama, over one year. Prior to oil coming onshore, elevated levels of bacteria associated with fecal contamination were detected (e.g., Enterobacteriales and Campylobacterales). Over time, significant shifts within major phyla were identified (e.g., Proteobacteria, Firmicutes, Actinobacteria) and fecal indicator groups were replaced by taxa affiliated with open-ocean and marine systems (e.g., Oceanospirillales, Rhodospirillales, and Rhodobacterales). These new bacterial groups included putative hydrocarbon degraders, similar to those identified near the oil plume offshore. Shifts in the microbial community composition strongly correlated to more poorly sorted sediment and grain size distributional changes. Natural oceanographic processes could not account for the disrupted sediment, especially from the backshore well above the maximum high-tide levels recorded at these sites. Sand washing and tilling occurred on both open beaches from August through at least December 2010, which were mechanisms that could replace fecal indicator groups with open-ocean groups. Consequently, remediation efforts meant to return beaches to pre-spill compositions caused a regime shift that may have added potential ecosystem function, like hydrocarbon degradation, to the sediment. Future research will need to assess the persistence and impact of the newly formed microbial communities to the overall sandy beach ecosystems.

Changes in microbiota of rainbow trout caused by sediments contamination

The abundance, composition and hydrocarbon-degrading bacteria, as possible biomarkers of contamination with oil hydrocarbons, of autochthonous and alochtonous microbiota of the digestive tract of rainbow trout have been estimated. The samples of the bottom sediments for microbiological tests have been collected and a response of natural bacterial communities in the digestive tract of rainbow trout and nutritional changes has been investigated. Experimental fish have been fed with a mixture of three substances with the aim to assess the influence of hydrocarbon-degrading bacteria contained in the sediments on the microbiota of rainbow trout’s digestive tracts. The abundance values of rainbow trout intestinal heterotrophic bacteria were found to change depending on alochtonous microbiota of different bottom sediments given to the experimental fish with food in vitro. According to the results of our research, it is likely that the changes in the abundance values of the microbiota of the digestive tract of fish and in the proportions of functional groups of the bacteria allow us to determine changes in the functional activity of bacteria depending on food composition. Any relative increase or decrease of abundance or activity of alochtonous microbiota allows the prediction of toxic effects of the contaminants on animals and the environment.

Determining the metabolic footprints of hydrocarbon degradation using multivariate analysis

The functional dynamics of microbial communities are largely responsible for the clean-up of hydrocarbons in the environment. However, knowledge of the distinguishing functional genes, known as the metabolic footprint, present in hydrocarbon-impacted sites is still scarcely understood. Here, we conducted several multivariate analyses to characterise the metabolic footprints present in a variety of hydrocarbon-impacted and non-impacted sediments. Non-metric multi-dimensional scaling (NMDS) and canonical analysis of principal coordinates (CAP) showed a clear distinction between the two groups. A high relative abundance of genes associated with cofactors, virulence, phages and fatty acids were present in the non-impacted sediments, accounting for 45.7 % of the overall dissimilarity. In the hydrocarbon-impacted sites, a high relative abundance of genes associated with iron acquisition and metabolism, dormancy and sporulation, motility, metabolism of aromatic compounds and cell signalling were observed, accounting for 22.3 % of the overall dissimilarity. These results suggest a major shift in functionality has occurred with pathways essential to the degradation of hydrocarbons becoming overrepresented at the expense of other, less essential metabolisms.

Intrinsic potential for immediate biodegradation of toluene in a pristine, energy-limited aquifer

Pristine and energy-limited aquifers are considered to have a low resistance and resilience towards organic pollution. An experiment in an indoor aquifer system revealed an unexpected high intrinsic potential for the attenuation of a short-term toluene contamination. A 30 h pulse of 486 mg of toluene, used as a model contaminant, and deuterated water (D2O) through an initially pristine, oxic, and organic carbon poor sandy aquifer revealed an immediate aerobic toluene degradation potential. Based on contaminant and tracer break-through curves, as well as mass balance analyses and reactive transport modelling, a contaminant removal of 40 % over a transport distance of only 4.2 m in less than one week of travel time was obtained. The mean first-order degradation rate constant was λ = 0.178 day(-1), corresponding to a half-life time constant T1/2 of 3.87 days. Toluene-specific stable carbon isotope analysis independently proved that the contaminant mass removal can be attributed to microbial biodegradation. Since average doubling times of indigenous bacterial communities were in the range of months to years, the aerobic biodegradation potential observed is assumed to be present and active in the pristine, energy-limited groundwater ecosystems at any time. Follow-up experiments and field studies will help to quantify the immediate natural attenuation potential of aquifers for selected priority contaminants and will try to identify the key-degraders within the autochthonous microbial communities.

Biodegradation of Toluene Under Seasonal and Diurnal Fluctuations of Soil-Water Temperature

An increasing interest in bioremediation of hydrocarbon polluted sites raises the question of the influence of seasonal and diurnal changes on soil-water temperature on biodegradation of BTEX, a widespread group of (sub)-surface contaminants. Therefore, we investigated the impact of a wide range of varying soil-water temperature on biodegradation of toluene under aerobic conditions. To see the seasonal impact of temperature, three sets of batch experiments were conducted at three different constant temperatures: 10°C, 21°C, and 30°C. These conditions were considered to represent (1) winter, (2) spring and/or autumn, and (3) summer seasons, respectively, at many polluted sites. Three additional sets of batch experiments were performed under fluctuating soil-water temperature cases (21<>10°C, 30<>21°C, and 10<>30°C) to mimic the day-night temperature patterns expected during the year. The batches were put at two different temperatures alternatively to represent the day (high-temperature) and night (low-temperature) times. The results of constant- and fluctuating-temperature experiments show that toluene degradation is strongly dependent on soil-water temperature level. An almost two-fold increase in toluene degradation time was observed for every 10°C decrease in temperature for constant-temperature cases. Under fluctuating-temperature conditions, toluene degraders were able to overcome the temperature stress and continued thriving during all considered weather scenarios. However, a slightly longer time was taken compared to the corresponding time at daily mean temperature conditions. The findings of this study are directly useful for bioremediation of hydrocarbon-polluted sites having significant diurnal and seasonal variations of soil-water temperature.

Effects of three types of oil dispersants on biodegradation of dispersed crude oil in water surrounding two Persian gulf provinces

OBJECTIVE

To determine the most effective and biodegradable dispersant of spilled oil in water surrounding two Persian Gulf provinces.

METHODS

This study compared the effects of three dispersants, Pars 1, Pars 2, and Gamlen OD4000 on removal of oil in two Persian Gulf provinces' water. Overall, 16 stations were selected. Using the Well method, the growth rate of isolated bacteria and fungi was identified. To specify the growth rate of microorganisms and their usage of oil in the presence of the above-mentioned dispersants, as exclusive sources of carbon, the bacteria were grown in culture medium for 28 days at 120 rpm, 30°C, and their optical density was measured by spectrophotometry. Then, we tested biological oxygen demand (BOD) and chemical oxygen demand (COD) in microorganisms.

RESULTS

The highest growth rate was documented for the growth of microorganisms on either Pars 1 or Pars 2 dispersants or their mixtures with oil. However, the culture having microorganisms grown on Pars 1 had higher BOD and COD than the other two dispersants (9200 and 16800 versus 500 and 960, P < 0.05). Mixture of oil and Pars 2 as well as oil and Pars 1 dispersants showed the highest BODs and CODs, respectively. In the Bahregan province, microorganisms grown on Pars 2 had maximum amount of BOD and COD in comparison with Pars 1 and Gamlen dispersants (7100 and 15200 versus 6000 and 10560, P < 0.05).

CONCLUSION

Pars 1 and Pars 2 were the most effective dispersants with highest degradability comparing Gamlen. In each region, the most suitable compound for removing oil spill from offshores with least secondary contamination should be investigated.

An Overview of Biodegradation of LNAPLs in Coastal (Semi)-arid Environment

Contamination of soil and water due to the release of light non-aqueous phase liquids (LNAPLs) is a ubiquitous problem. The problem is more severe in arid and semi-arid coastal regions where most of the petroleum production and related refinery industries are located. Biological treatment of these organic contaminated resources is receiving increasing interests and where applicable, can serve as a cost-effective remediation alternative. The success of bioremediation greatly depends on the prevailing environmental variables, and their remediation favoring customization requires a sound understanding of their integrated behavior on fate and transport of LNAPLs under site-specific conditions. The arid and semi-arid coastal sites are characterized by specific environmental extremes; primarily, varying low and high temperatures, high salinity, water table dynamics, and fluctuating soil moisture content. An understanding of the behavior of these environmental variables on biological interactions with LNAPLs would be helpful in customizing the bioremediation for restoring problematic sites in these regions. Therefore, this paper reviews the microbial degradation of LNAPLs in soil-water, considering the influences of prevailing environmental parameters of arid and semi-arid coastal regions. First, the mechanism of biodegradation of LNAPLs is discussed briefly, followed by a summary of popular kinetic models used by researchers for describing the degradation rate of these hydrocarbons. Next, the impact of soil moisture content, water table dynamics, and soil-water temperature on the fate and transport of LNAPLs are discussed, including an overview of the studies conducted so far. Finally, based on the reviewed information, a general conclusion is presented with recommendations for future research subjects on optimizing the bioremediation technique in the field under the aforesaid environmental conditions. The present review will be useful to better understand the feasibility of bioremediation technology, in general, and its applicability for remediating LNAPLs polluted lands under aforesaid environments, in particular.

New alk genes detected in Antarctic marine sediments

Alkane monooxygenases (Alk) are the key enzymes for alkane degradation. In order to understand the dispersion and diversity of alk genes in Antarctic marine environments, this study analysed by clone libraries the presence and diversity of alk genes (alkB and alkM) in sediments from Admiralty Bay, King George Island, Peninsula Antarctica. The results show a differential distribution of alk genes between the sites, and the predominant presence of new alk genes, mainly in the pristine site. Sequences presented 53.10-69.60% nucleotide identity and 50.90-73.40% amino acid identity to alkB genes described in Silicibacter pomeroyi, Gordonia sp., Prauserella rugosa, Nocardioides sp., Rhodococcus sp., Nocardia farcinica, Pseudomonas putida, Acidisphaera sp., Alcanivorax borkumensis, and alkM described in Acinetobacter sp. This is the first time that the gene alkM was detected and described in Antarctic marine environments. The presence of a range of previously undescribed alk genes indicates the need for further studies in this environment.

Effects of spilled oil on bacterial communities of mediterranean coastal anoxic sediments chronically subjected to oil hydrocarbon contamination

The effects of spilled oil on sedimentary bacterial communities were examined in situ at 20 m water depth in a Mediterranean coastal area. Sediment collected at an experimental site chronically subjected to hydrocarbon inputs was reworked into PVC cores with or without a massive addition of crude Arabian light oil ( approximately 20 g kg(-1) dry weight). Cores were reinserted into the sediment and incubated in situ at the sampling site (20 m water depth) for 135 and 503 days. The massive oil contamination induced significant shifts in the structure of the indigenous bacterial communities as shown by ribosomal intergenic spacer analysis (RISA). The vertical heterogeneity of the bacterial communities within the sediment was more pronounced in the oiled sediments particularly after 503 days of incubation. Response to oil of the deeper depth communities (8-10 cm) was slower than that of superficial depth communities (0-1 and 2-4 cm). Analysis of the oil composition by gas chromatography revealed a typical microbial alteration of n-alkanes during the experiment. Predominant RISA bands in oiled sediments were affiliated to hydrocarbonoclastic bacteria sequences. In particular, a 395-bp RISA band, which was the dominant band in all the oiled sediments for both incubation times, was closely related to hydrocarbonoclastic sulfate-reducing bacteria (SRB). These bacteria may have contributed to the main fingerprint changes and to the observed biodegradation of n-alkanes. This study provides useful information on bacterial dynamics in anoxic contaminated infralittoral sediments and highlights the need to assess more precisely the contribution of SRB to bioremediation in oil anoxic contaminated areas.

Persistence and biodegradation of kerosene in high-arctic intertidal sediment

A kerosene type hydrocarbon fraction (equivalent to 7 L m(-2)) was added to enclosures in the surface layer of high-arctic intertidal beach sediment. The experimental spill was repeated in two consecutive years in the period July-September. The rate and extent of hydrocarbon removal and the accompanying bacterial response were monitored for 79 days (2002) and 78 days (2003). The bulk of added kerosene, i.e. 94-98%, was lost from the upper 5 cm layer by putatively abiotic processes within 2 days and a residual fraction in the range 0.6-1.2mg per g dry sediment was stably retained. Concomitant addition of oleophilic fertilizer led to higher initial retention, as 24% of the kerosene remained after 2 days in the presence of a modified, cold-climate adapted version of the well-known Inipol EAP 22 bioremediation agent. In these enclosures, which showed an increase in hydrocarbon-degrader counts from 6.5 x 10(3) to 4.1 x 10(7) per g dry sediment within 8 days, a 17% contribution by biodegradation to subsequent hydrocarbon removal was estimated. Stimulation in hydrocarbon-degrader counts in fertilizer-alone control enclosures was indistinguishable from the stimulation observed with both kerosene and fertilizer present, suggesting that the dynamics in numbers of hydrocarbon-degrading bacteria was primarily impacted by the bioremediation agent.

Sustainable oil and grease removal from synthetic stormwater runoff using bench-scale bioretention studies

One of the principal components of the contaminant load in urban stormwater runoff is oil and grease (O&G) pollution, resulting from vehicle emissions. A mulch layer was used as a contaminant trap to remove O&G (dissolved and particulate-associated naphthalene, dissolved toluene, and dissolved motor oil hydrocarbons) from a synthetic runoff during a bench-scale infiltration study. Approximately 80 to 95% removal of all contaminants from synthetic runoff was found via sorption and filtration. Subsequently, approximately 90% of the sorbed naphthalene, toluene, oil, and particulate-associated naphthalene was biodegraded within approximately 3, 4, 8, and 2 days after the event, respectively, based on decreases in contaminant concentrations coupled with increases of microbial populations. These results indicate the effectiveness and sustainability of placing a thin layer of mulch on the surface of a bioretention facility for reducing O&G pollution from urban stormwater runoff.

Assessing degradation capability of aerobic indigenous microflora in PAH-contaminated brackish sediments

A study was conducted to determine polycyclic aromatic hydrocarbons (PAHs) distribution and microbial population changes in brackish sediments from an Italian lagoon included in the Ramsar List of Wetlands of International Importance. The presence and level of PAH-degrading bacteria were estimated by the most probable number (MPN) enumeration technique, whereas degradation capability towards target compounds was checked against loss of spiked PAHs (Phenanthrene, Anthracene and Fluoranthene) in MPN tubes after incubation in optimal conditions. Chemical analyses and microbiological counts suggested a potential for PAHs biodegradation by natural occurring populations of sediment microorganisms, thus indicating an "optimal range" in sediment PAHs concentrations, outside of which the natural selection of the indigenous microflora did not occur. The MPN procedure here described, provided an effective and reliable way to simultaneously determine microbial population densities and subsequent confirmation of the biodegradation capability of sediment indigenous microflora when exposed to laboratory and environmental concentrations of PAHs.

Impact of crude oil on bacteriocenosis of the digestive tract of mollusks

In this study the effect of crude oil on intestinal bacterial populations of the mollusk Viviparus contactus was investigated. The addition of crude oil into an environment of mollusks induced no clear changes in the saprophytic, amylolytic, and total coliform bacterial counts in the digestive tract of the mollusk. After 10 days of contamination, the saprophytic, amylolytic, and total coliform bacterial numbers were of the same order of magnitude as the initial numbers. Significant numbers of indigenous hydrocarbon-degrading bacteria were observed in the intestinal tracts of mollusks before contamination with crude oil. Introduction of crude oil into the mollusk environment resulted in an increase of 2 orders of magnitude in the number of hydrocarbon-degrading bacteria in the digestive tract. Therefore, measuring the hydrocarbon-degrading bacterial populations in the digestive tracts of hydrobionts can be considered an important component of contaminated-site assessment studies.

PCR-based detection of non-indigenous microorganisms in 'pristine' environments

PCR-based technologies are widely employed for the detection of specific microorganisms, and may be applied to the identification of non-indigenous microorganisms in 'pristine' environments. For 'pristine' environments such as those found on the Antarctic continent, the application of these methods to the assessment of environmental contamination from human activities must be treated with caution. Issues such as the possibility of non-human dispersal of organisms, stability and survival of non-indigenous organisms in vivo, the sensitivity, reproducibility and specificity of the PCR process (and particularly primer design) and the sampling regime employed must all be considered in detail. We conclude that despite these limitations, PCR and related technologies offer enormous scope for assessment of both natural and non-indigenous microbial distributions.

Bacterioplanktonic abundance, productivity and petroleum hydrocarbon biodegradation in marinas and other coastal waters in North Carolina, USA

The purpose of this study was to assess the differences in the abundance and activity of the bacterioplankton at sites with varied boating activity, and to determine the response of the communities to additional petroleum pollution. Three sites, including two marinas and a site on Bogue Sound in coastal North Carolina, were selected for monthly experiments. Seasonal patterns of bacterioplanktonic abundance and diesel fuel biodegradation for each site were examined, and possible correlations with intensity of boating activities were explored. Bacterioplanktonic communities at the three sites in this study were more similar in their structure and biodegradation potential than would have been expected from previous studies. We found no differences in the abundance and biodegradation potential of theses communities at the three sites, and only a slightly elevated number of hydrocarbon degraders at one of the marinas. Patterns of biodegradation were more closely related to total bacterial abundance, rather than number of petroleum hydrocarbon degraders. There was a strong seasonal pattern in bacterial abundance and biodegradation at all three sites. The bacterioplanktonic Community at all sites responded similarly to additions of diesel fuel. Bacterial abundance and productivity were both elevated to some extent, and number of petroleum hydrocarbon degraders changed relatively little. These data indicate that marinas may not profoundly after the bacterioplankton and that coastal waters often have resident bacterial communities capable of degrading petroleum hydrocarbon pollution.