Correlating the succession of microbial communities from Nigerian soils to petroleum biodegradation.

Whilst biodegradation of different hydrocarbon components has been widely demonstrated to occur by specialist oil-degrading bacteria, less is known about the impact on microbial communities as a function of oil composition by comparing the biodegradation of chemically complex fuels to synthetic products. The objectives of this study were (i) to assess the biodegradation capacity and succession of microbial communities isolated from Nigerian soils in media with crude oil or synthetic oil as sole sources of carbon and energy, and (ii) to assess the temporal variability of the microbial community size. Community profiling was done using 16 S rRNA gene amplicon sequencing (Illumina), and oil profiling using gas chromatography. The biodegradation of natural and synthetic oil differed probably due to the content of sulfur that may interfere with the biodegradation of hydrocarbons. Both alkanes and PAHs in the natural oil were biodegraded faster than in the synthetic oil. Variable community responses were observed during the degradation of alkanes and more simple aromatic compounds, but at later phases of growth they became more homogeneous. The degradation capacity and the size of the community from the more-contaminated soil were higher than those from the less-contaminated soil. Six abundant organisms isolated from the cultures were found to biodegrade oil molecules in pure cultures. Ultimately, this knowledge may contribute to a better understanding of how to improve the biodegradation of crude oil by optimizing culturing conditions through inoculation or bioaugmentation of specific bacteria during ex-situ biodegradation such as biodigesters or landfarming.

Oil Absorbent Polypropylene Particles Stimulate Biodegradation of Crude Oil by Microbial Consortia.

Oil absorbent particles made from surface-modified polypropylene can be used to facilitate the removal of oil from the environment. In this study, we investigated to what extent absorbed oil was biodegraded and how this compared to the biodegradation of oil in water. To do so, we incubated two bacterial communities originating from the Niger Delta, an area subject to frequent oil spills, in the presence and absence of polypropylene particles. One community evolved from untreated soil whereas the second evolved from soil pre-exposed to oil. We observed that the polypropylene particles stimulated the growth of biofilms and enriched species from genera Mycobacterium, Sphingomonas and Parvibaculum. Cultures with polypropylene particles degraded more crude oil than those where the oil was present in suspension regardless of whether they were pre-exposed or not. Moreover, the community pre-exposed to crude oil had a different community structure and degraded more oil than the one from untreated soil. We conclude that the biodegradation rate of crude oil was enhanced by the pre-exposure of the bacterial communities to crude oil and by the use of oil-absorbing polypropylene materials. The data show that bacterial communities in the biofilms growing on the particles have an enhanced degradation capacity for oil.

Analysis of polycyclic aromatic hydrocarbons (PAHs) in surface sediments and edible aquatic species in an oil-contaminated mangrove ecosystem in Bodo, Niger Delta, Nigeria: Bioaccumulation and human health risk assessment.

This work investigated the occurrence and risks associated with polycyclic aromatic hydrocarbons (PAHs) in tissues from five commonly consumed aquatic species (swimming crabs, estuarine shrimp, tiger prawns, periwinkles, and tilapia) and sediment across six sites in the area around Bodo town, in the Niger Delta region of Nigeria. We aimed to establish a relationship between PAH concentrations in sediment and biota, and to derive biota-sediment accumulation factors (BSAFs). Risks to human health associated with consumption of impacted food sources were assessed based on measured biotic concentrations of PAHs. The average concentration of PAHs and the number of PAHs measured above the limit of quantification varied greatly between different biota, with the lowest average concentrations observed in tilapia, followed by tiger prawns, crabs, estuarine shrimp, and the highest concentrations were observed in periwinkles. Similar to biotic concentrations, BSAFs were found to vary greatly across species, sites, and PAHs, though BSAFs for all organisms except periwinkles were below a value of 1. In periwinkles, BSAFs exceeded a value of 1 for phenanthrene (BSAF = 1.7), pyrene (1.5) and benzo[k]fluoranthene (1.7). Risks to human health associated with consumption of these species were assessed using the BaP toxic-equivalent approach for cancer risks and the toxic unit approach which jointly considered carcinogenic but also non-cancer hazards. The BaP toxic-equivalent approach showed that the excess lifetime cancer risk resulting from daily consumption of 0.2 kg of seafood ranged between 1.3 × 10-6 for tiger prawn and tilapia to 4.1 × 10-6 for periwinkles, which is below the excess lifetime cancer risk of 10-4 used by Dutch and Nigerian authorities for sediment intervention values. This finding is supported by the results obtained from the toxic unit approach which indicates that the ratios of the estimated dose and the maximal permissible risk level for summed PAHs never exceeded 1.

Adaptive changes of sediment microbial communities associated with cleanup of oil spills in Nigerian mangrove forests.

The objectives of this study were to assess the influence on microbial communities resulting from i) the physical removal of free oil (pre-treatment or post-treatment), and ii) the level of oiling within a contaminated former mangrove forest. Sediment samples were collected before and after the removal of free oil. Before the process of remediation, a highly biodiverse mangrove microbiome which had adapted to history of recurring oil spills was observed. After removing the surface oil, the microbial diversity of the sediments reduced, with members of the phyla Firmicutes and Proteobacteria becoming dominant. This indicates that while water flushing reduced overall microbial diversity, it stimulated the growth of a more specialized bacterial community reported to be involved in hydrocarbon biodegradation. These results provide new insights on microbial communities and their succession in mangrove forest sediments, that will be useful for monitoring oil cleaning programs using water flushing to remove free oil.

Distribution of ETBE-degrading microorganisms and functional capability in groundwater, and implications for characterising aquifer ETBE biodegradation potential.

Microbes in aquifers are present suspended in groundwater or attached to the aquifer sediment. Groundwater is often sampled at gasoline ether oxygenate (GEO)-impacted sites to assess the potential biodegradation of organic constituents. However, the distribution of GEO-degrading microorganisms between the groundwater and aquifer sediment must be understood to interpret this potential. In this study, the distribution of ethyl tert-butyl ether (ETBE)-degrading organisms and ETBE biodegradation potential was investigated in laboratory microcosm studies and mixed groundwater-aquifer sediment samples obtained from pumped monitoring wells at ETBE-impacted sites. ETBE biodegradation potential (as determined by quantification of the ethB gene) was detected predominantly in the attached microbial communities and was below detection limit in the groundwater communities. The copy number of ethB genes varied with borehole purge volume at the field sites. Members of the Comamonadaceae and Gammaproteobacteria families were identified as responders for ETBE biodegradation. However, the detection of the ethB gene is a more appropriate function-based indicator of ETBE biodegradation potential than taxonomic analysis of the microbial community. The study shows that a mixed groundwater-aquifer sediment (slurry) sample collected from monitoring wells after minimal purging can be used to assess the aquifer ETBE biodegradation potential at ETBE-release sites using this function-based concept.

Core sediments and oil chemistry from contaminated mangroves in eastern Niger Delta, Ogoniland, Nigeria.

Thirty cores to maximum depth of 3.7 m were taken in 2018 to investigate sedimentary characteristics and hydrocarbon penetration within mangrove sediments in Bodo (southeastern Niger Delta), an area contaminated by numerous ongoing oil spills but most significantly in 2008. Sediments were dominated by organically rich (Chikoko) mud underlain by clay with sandier sediments at deeper core depths and adjacent to shorelines. Analysis of 202 samples showed high median hydrocarbon concentrations at the surface (39,000 mg/kg) and shallow subsurface (10-25 cm, 25,000 mg/kg), decreasing with depth: 430 mg/kg at 40-70 cm; 157 mg/kg at 75-120 cm, and <30 mg/kg at depths ≥150 cm. Most (85%) EPA-16 priority polycyclic aromatic hydrocarbons and all monoaromatics were below detection limit. Shallow subsurface oil penetration was aided by crab burrows and presence of mangrove remnants and was inhibited from deeper depths by groundwater at ~25 cm and increased sediment compaction.

Effects of DNA preservation solution and DNA extraction methods on microbial community profiling of soil.

Microbial community profiling using high-throughput sequencing relies in part on the preservation of the DNA and the effectiveness of the DNA extraction method. This study aimed at understanding to what extent these parameters affect the profiling. We obtained samples treated with and without a preservation solution. Also, we compared DNA extraction kits from Qiagen and Zymo-Research. The types of samples were defined strains, both as single species and mixtures, as well as undefined indigenous microbial communities from soil. We show that the use of a preservation solution resulted in substantial changes in the 16S rRNA gene profiles either due to an overrepresentation of Gram-positive bacteria or to an underrepresentation of Gram-negative bacteria. In addition, 16S rRNA gene profiles were substantially different depending on the type of kit that was used for extraction. The kit from Zymo extracted DNA from different types of bacteria in roughly equal amounts. In contrast, the kit from Qiagen preferentially extracted DNA from Gram-negative bacteria while DNA from Gram-positive bacteria was extracted less effectively. These differences in kit performance strongly influenced the interpretation of our microbial ecology studies.

Assessing the suitability of a manometric test system for determining the biodegradability of volatile hydrocarbons.

Manometric test systems, adapted from those used to measure biochemical oxygen demand (BOD), and the OxiTop® test system in particular, are being increasingly used to determine the biodegradability of chemicals in accordance to OECD 301F guidelines. In this study, the suitability of the OxiTop® test system for determining the biodegradability of volatile hydrophobic substances has been explored. Experiments in biotic and abiotic systems were conducted with readily biodegradable complex aliphatic hydrocarbons covering a range of volatilities. Results indicated that abiotic losses of test substances were occurring due to sorption of the test substance to plastic components used in the OxiTop® system. A further 'plastic-free' biodegradation test system was designed using PreSens optical dissolved oxygen (DO) sensors. This significantly improved the measured biodegradation due to reduced abiotic losses and better retention of the test substance. These results highlight the importance of considering the physico-chemical properties of test substances when selecting test methods and equipment. They also highlight the value of incorporating chemical analysis and abiotic controls to improve the interpretation of biodegradation studies.

Comparison of landfarming amendments to improve bioremediation of petroleum hydrocarbons in Niger Delta soils.

Large scale landfarming experiments, using an extensive range of treatments, were conducted in the Niger-Delta, Nigeria to study the degradation of oil in contaminated soils. In this work the effect of nutrient addition, biosurfactant, Eisenia fetida (earthworm) enzyme extract, bulking and sorption agents and soil neutralization were tested. It was found that these treatments were successful in removing up to 53% of the total petroleum hydrocarbon in the soil within 16 weeks. A comparison between treatments demonstrated that most were no more effective than agricultural fertilizer addition alone. One strategy that did show better performance was a combination of nutrients, biochar and biosurfactant, which was found to remove 23% more Total Petroleum Hydrocarbons (TPH) than fertilizer alone. However, when performance normalized costs were considered, this treatment became less attractive as a remedial option. Based on this same analysis it was concluded that fertilizer only was the most cost effective treatment. As a consequence, it is recommended that fertilizer is used to enhance the landfarming of hydrocarbon contaminated soils in the Niger Delta. The attenuation rates of both bulk TPH and Total Petroleum Hydrocarbon Criteria Working Group (TPHCWG) fractions are also provided. These values represent one of the first large scale and scientifically tested datasets for treatment of contaminated soil in the Niger Delta region. An inverse correlation between attenuation rates and hydrocarbon molecular weight was observed with heavy fractions showing much slower degradation rates than lighter fractions. Despite this difference, the bioremediation process resulted in significant removal of all TPH compounds independent of carbon number.

A Simple Analytical Formula for the Leakage Flux Through a Perforated Aquitard.

In this methods note, we present a simple analytical formula to quantify the steady-state leakage flux (Q) over a perforated aquitard. The flux depends on the aquitard thickness (D), the radius of the perforation (R), the hydraulic conductivity of the material inside the perforation (kfill ), the conductivities of the overlying and underlying aquifers (k1 and k2 , respectively), and the head difference between the two aquifers (ΔH): [Formula: see text]. This equation assumes an aquitard separating two homogeneous and infinite aquifers (R ≪ aquifer thickness) in which radial flow to and from the perforation occurs, with no other recharge or discharge boundaries near the perforation. The flux through a perforation in a hypothetical case study with D = 10 m, k1 = 10 m/d, k2 = 20 m/d, R = 0.072 m, and ΔH = 1 m ranges between less than 1 mL/d if the hole is backfilled with bentonite (k(fill ) = 10(-4) m/d), to several liters per day if the perforation is backfilled with sand from the overlying aquifer (k(fill) = 10 m/d), to several m(3) /d if the perforation forms an open conduit (k(fill) = 10(5) m/d). The leakage fluxes calculated with this model agree well with those calculated using a numerical model (MODFLOW).

Reactive transport modeling of thermal column experiments to investigate the impacts of aquifer thermal energy storage on groundwater quality.

Aquifer thermal energy storage (ATES) systems are increasingly being used to acclimatize buildings and are often constructed in aquifers used for drinking water supply. This raises the question of potential groundwater quality impact. Here, we use laboratory column experiments to develop and calibrate a reactive transport model (PHREEQC) simulating the thermally induced (5-60 °C) water quality changes in anoxic sandy sediments. Temperature-dependent surface complexation, cation-exchange, and kinetic dissolution of K-feldspar were included in the model. Optimization results combined with an extensive literature survey showed surface complexation of (oxy)anions (As, B, and PO4) is consistently exothermic, whereas surface complexation of cations (Ca and Mg) and cationic heavy metals (Cd, Pb, and Zn) is endothermic. The calibrated model was applied to simulate arsenic mobility in an ATES system using a simple yet powerful mirrored axi-symmetrical grid. Results showed that ATES mobilizes arsenic toward the fringe of the warm water bubble and the center of the cold water bubble. This transient redistribution of arsenic causes its aqueous concentrations in the cold and warm groundwater bubbles to become similar through multiple heating cycles, with a final concentration depending on the average injection temperature of the warm and cold ATES wells.

Impacts of shallow geothermal energy production on redox processes and microbial communities.

Shallow geothermal systems are increasingly being used to store or harvest thermal energy for heating or cooling purposes. This technology causes temperature perturbations exceeding the natural variations in aquifers, which may impact groundwater quality. Here, we report the results of laboratory experiments on the effect of temperature variations (5-80 °C) on redox processes and associated microbial communities in anoxic unconsolidated subsurface sediments. Both hydrochemical and microbiological data showed that a temperature increase from 11 °C (in situ) to 25 °C caused a shift from iron-reducing to sulfate-reducing and methanogenic conditions. Bioenergetic calculations could explain this shift. A further temperature increase (>45 °C) resulted in the emergence of a thermophilic microbial community specialized in fermentation and sulfate reduction. Two distinct maxima in sulfate reduction rates, of similar orders of magnitude (5 × 10(-10) M s(-1)), were observed at 40 and 70 °C. Thermophilic sulfate reduction, however, had a higher activation energy (100-160 kJ mol(-1)) than mesophilic sulfate reduction (30-60 kJ mol(-1)), which might be due to a trade-off between enzyme stability and activity with thermostable enzymes being less efficient catalysts that require higher activation energies. These results reveal that while sulfate-reducing functionality can withstand a substantial temperature rise, other key biochemical processes appear more temperature sensitive.

Temperature-induced impacts on groundwater quality and arsenic mobility in anoxic aquifer sediments used for both drinking water and shallow geothermal energy production.

Aquifers used for the production of drinking water are increasingly being used for the generation of shallow geothermal energy. This causes temperature perturbations far beyond the natural variations in aquifers and the effects of these temperature variations on groundwater quality, in particular trace elements, have not been investigated. Here, we report the results of column experiments to assess the impacts of temperature variations (5°C, 11°C, 25°C and 60°C) on groundwater quality in anoxic reactive unconsolidated sandy sediments derived from an aquifer system widely used for drinking water production in the Netherlands. Our results showed that at 5 °C no effects on water quality were observed compared to the reference of 11°C (in situ temperature). At 25°C, As concentrations were significantly increased and at 60 °C, significant increases were observed pH and DOC, P, K, Si, As, Mo, V, B, and F concentrations. These elements should therefore be considered for water quality monitoring programs of shallow geothermal energy projects. No consistent temperature effects were observed on Na, Ca, Mg, Sr, Fe, Mn, Al, Ba, Co, Cu, Ni, Pb, Zn, Eu, Ho, Sb, Sc, Yb, Ga, La, and Th concentrations, all of which were present in the sediment. The temperature-induced chemical effects were probably caused by (incongruent) dissolution of silicate minerals (K and Si), desorption from, and potentially reductive dissolution of, iron oxides (As, B, Mo, V, and possibly P and DOC), and mineralisation of sedimentary organic matter (DOC and P).

Climate change induced salinisation of artificial lakes in the Netherlands and consequences for drinking water production.

In this paper we present a modelling study to investigate the impacts of climate change on the chloride concentration and salinisation processes in two man-made freshwater lakes in the Netherlands, Lake IJsselmeer and Lake Markermeer. We used a transient compartmental chloride and water balance model to elucidate the salinisation processes occurring under present conditions and assess future salinisation under two climate forcing scenarios. The model results showed that the Rhine River is the dominant determinant for the chloride concentration in both lakes, followed by drainage of brackish groundwater from the surrounding polders. The results further show that especially during dry years, seawater intrusion through the tidal closure dam is an important source of chloride to Lake IJsselmeer. The results from the climatic forcing scenarios show that Lake IJsselmeer is especially vulnerable to climate-induced salinisation whereas effects on Lake Markermeer are relatively small. Peak chloride concentrations at the raw water intake of the Andijk drinking water facility on Lake IJsselmeer are projected to increase to values above 250 mg/l in the most far-reaching climate change scenario W+ in 2050 for dry years. This is well above the maximum allowable concentration of 150 mg/l for chloride in drinking water. Modelling showed that climate change impacts the chloride concentrations in a variety of ways: 1) an increasing occurrence of low river flows from summer to autumn reduces the dilution of the chloride that is emitted to the Rhine with a constant load thereby increasing its concentration; 2) increased open water evaporation and reduced rainfall during summer periods and droughts increases the chloride concentration in the water; and 3) rises in sea level increase seawater intrusion through the tidal closure dam of Lake IJsselmeer. The processes described here are likely to affect many other tidal rivers or lakes and should be considered when planning future raw water intake stations for drinking water production or agricultural water supply.