Patricia A. Sobecky

Microbial Community Analysis of a Coastal Salt Marsh Affected by the Deepwater Horizon Oil Spill

Coastal salt marshes are highly sensitive wetland ecosystems that can sustain long-term impacts from anthropogenic events such as oil spills. In this study, we examined the microbial communities of a Gulf of Mexico coastal salt marsh during and after the influx of petroleum hydrocarbons following the Deepwater Horizon oil spill. Total hydrocarbon concentrations in salt marsh sediments were highest in June and July 2010 and decreased in September 2010. Coupled PhyloChip and GeoChip microarray analyses demonstrated that the microbial community structure and function of the extant salt marsh hydrocarbon-degrading microbial populations changed significantly during the study. The relative richness and abundance of phyla containing previously described hydrocarbon-degrading bacteria (Proteobacteria, Bacteroidetes, and Actinobacteria) increased in hydrocarbon-contaminated sediments and then decreased once hydrocarbons were below detection. Firmicutes, however, continued to increase in relative richness and abundance after hydrocarbon concentrations were below detection. Functional genes involved in hydrocarbon degradation were enriched in hydrocarbon-contaminated sediments then declined significantly (p<0.05) once hydrocarbon concentrations decreased. A greater decrease in hydrocarbon concentrations among marsh grass sediments compared to inlet sediments (lacking marsh grass) suggests that the marsh rhizosphere microbial communities could also be contributing to hydrocarbon degradation. The results of this study provide a comprehensive view of microbial community structural and functional dynamics within perturbed salt marsh ecosystems.

Microbial Responses to the Deepwater Horizon Oil Spill: From Coastal Wetlands to the Deep Sea

The Deepwater Horizon oil spill in the northern Gulf of Mexico represents the largest marine accidental oil spill in history. It is distinguished from past spills in that it occurred at the greatest depth (1,500 m), the amount of hydrocarbon gas (mostly methane) lost was equivalent to the mass of crude oil released, and dispersants were used for the first time in the deep sea in an attempt to remediate the spill. The spill is also unique in that it has been characterized with an unprecedented level of resolution using next-generation sequencing technologies, especially for the ubiquitous hydrocarbon-degrading microbial communities that appeared largely to consume the gases and to degrade a significant fraction of the petroleum. Results have shown an unexpectedly rapid response of deep-sea Gammaproteobacteria to oil and gas and documented a distinct succession correlated with the control of the oil flow and well shut-in. Similar successional events, also involving Gammaproteobacteria, have been observed in nearshore systems as well.

Aerobic biotransformation of n-tetradecylbenzyldimethylammonium chloride by an enriched Pseudomonas spp. community.

The biotransformation of n-tetradecylbenzyldimethylammonium chloride (C(14)BDMA-Cl), a quaternary ammonium compound (QAC), under aerobic conditions by an enriched microbial community growing on benzalkonium chlorides (BACs) was investigated. Biotransformation of C(14)BDMA-Cl commenced with cleavage of the C(alkyl)-N bond and formation of benzyldimethylamine (BDMA). BDMA was further degraded, but in contrast to a previously reported BAC biotransformation pathway, neither benzylmethylamine (BMA) nor benzylamine (BA) was detected as a BDMA biotransformation product. Kinetic assays further confirmed that BMA and BA were not intermediates of C(14)BDMA-Cl transformation by the enriched community. Thus, BDMA is thought to be transformed to dimethylamine and benzoic acid via debenzylation. The biomass-normalized rate of C(14)BDMA-Cl biotransformation was 0.09 μmol/[mg of volatile suspended solids (VSS)·h]. The Microtox acute toxicity EC(50) value of BDMA was 500 times higher than that of C(14)BDMA-Cl. Thus, the aerobic biotransformation of C(14)BDMA-Cl to BDMA results in substantial toxicity reduction. Phylogenetic analysis of Bacteria diversity indicated that the majority of the sequenced clones (98% of the clone library) belonged to the genus Pseudomonas.

Intrinsic rates of petroleum hydrocarbon biodegradation in Gulf of Mexico intertidal sandy sediments and its enhancement by organic substrates

The rates of crude oil degradation by the extant microorganisms in intertidal sediments from a northern Gulf of Mexico beach were determined. The enhancement in crude oil degradation by amending the microbial communities with marine organic matter was also examined. Replicate mesocosm treatments consisted of: (i) controls (intertidal sand), (ii) sand contaminated with crude oil, (iii) sand plus organic matter, and (iv) sand plus crude oil and organic matter. Carbon dioxide (CO(2)) production was measured daily for 42 days and the carbon isotopic ratio of CO(2) (δ(13)CO(2)) was used to determine the fraction of CO(2) derived from microbial respiration of crude oil. Bacterial 16S rRNA clone library analyses indicated members of Actinobacteria, Bacteroidetes, and Chloroflexi occurred exclusively in control sediments whereas Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, and Firmicutes occurred in both control and oil contaminated sediments. Members of the hydrocarbon-degrading genera Hydrocarboniphaga, Pseudomonas, and Pseudoxanthomonas were found primarily in oil contaminated treatments. Hydrocarbon mineralization was 76% higher in the crude oil amended with organic matter treatment compared to the rate in the crude oil only treatment indicating that biodegradation of crude oil in the intertidal zone by an extant microbial community is enhanced by input of organic matter.

Responses of microbial community from northern Gulf of Mexico sandy sediments following exposure to Deepwater Horizon crude oil.

In the present study, microbial community responses to exposure to unweathered Macondo Well crude oil and conventional diesel in a sandy beach environment were determined. Biodegradation was assessed in mesocosm experiments with differing fuel amounts (2,000 and 4,000 mg/kg) and with or without inorganic nutrient amendment. Carbon dioxide production was measured daily for 42 d. Aerobic alkane, total hydrocarbon, and polycyclic aromatic hydrocarbon (PAH) degraders were enumerated in treated and control mesocosms and changes in their abundances were measured weekly. Hydrocarbon mineralization occurred in all treatments. In the inorganic nutrient-amended treatments, the degradation rates were 2.31 and 2.00 times greater in the 2,000 mg/kg diesel and crude oil treatments, respectively, and 3.52 (diesel) and 4.14 (crude) times higher for the fuel types at the 4,000 mg/kg fuel concentrations compared to unamended treatments. Microbial lag phases were short (<3 d) and alkane and total hydrocarbon degrader numbers increased by five orders of magnitude compared to the uncontaminated treatments within 7 d in most treatments. Hydrocarbon degrader numbers in diesel and in crude oil treatments were similar; however, the PAH degraders were more abundant in the crude oil relative to diesel treatment. These findings indicate that hydrocarbon degradation by extant microbial populations in the northern Gulf of Mexico sandy beach environments can be stimulated and enhanced by inorganic nutrient addition.

Microbial Community Responses to Organophosphate Substrate Additions in Contaminated Subsurface Sediments

Background Radionuclide- and heavy metal-contaminated subsurface sediments remain a legacy of Cold War nuclear weapons research and recent nuclear power plant failures. Within such contaminated sediments, remediation activities are necessary to mitigate groundwater contamination. A promising approach makes use of extant microbial communities capable of hydrolyzing organophosphate substrates to promote mineralization of soluble contaminants within deep subsurface environments. Methodology/Principal Findings Uranium-contaminated sediments from the U.S. Department of Energy Oak Ridge Field Research Center (ORFRC) Area 2 site were used in slurry experiments to identify microbial communities involved in hydrolysis of 10 mM organophosphate amendments [i.e., glycerol-2-phosphate (G2P) or glycerol-3-phosphate (G3P)] in synthetic groundwater at pH 5.5 and pH 6.8. Following 36 day (G2P) and 20 day (G3P) amended treatments, maximum phosphate (PO4 3−) concentrations of 4.8 mM and 8.9 mM were measured, respectively. Use of the PhyloChip 16S rRNA microarray identified 2,120 archaeal and bacterial taxa representing 46 phyla, 66 classes, 110 orders, and 186 families among all treatments. Measures of archaeal and bacterial richness were lowest under G2P (pH 5.5) treatments and greatest with G3P (pH 6.8) treatments. Members of the phyla Crenarchaeota, Euryarchaeota, Bacteroidetes, and Proteobacteria demonstrated the greatest enrichment in response to organophosphate amendments and the OTUs that increased in relative abundance by 2-fold or greater accounted for 9%–50% and 3%–17% of total detected Archaea and Bacteria, respectively. Conclusions/Significance This work provided a characterization of the distinct ORFRC subsurface microbial communities that contributed to increased concentrations of extracellular phosphate via hydrolysis of organophosphate substrate amendments. Within subsurface environments that are not ideal for reductive precipitation of uranium, strategies that harness microbial phosphate metabolism to promote uranium phosphate precipitation could offer an alternative approach for in situ sequestration.

Chromium(VI) transport and fate in unsaturated zone and aquifer: 3D Sandbox results.

The simulation of Cr(VI) behavior in an unsaturated zone and aquifer, using a 3D experimental set-up were performed to illustrate the distribution, transport and transformation of Cr(VI), and further to reveal the potential harm of Cr(VI) after entering the groundwater. The result indicated that chromium(VI) was transported in the vertical direction, meanwhile, was transported in the horizontal direction under the influence of groundwater flow. The direction and distance away from the pollution source zone had great effect on the chromium(VI) concentration. At the sampling sites near the pollution source zone, there was a sudden increase of chromium(VI) concentration. The concentration of chromium(III) concentration in some random effluent samples was not detected. Chromium had not only transported but also had fraction and specie transformation in the unsaturated zone and aquifer. The relative concentration of residue fraction chromium was decreased with time. The content of Fe-Mn oxide fraction chromium was increased with time. The relative content of exchangeable and carbonate-bound fraction chromium was lower and the content variations were not obvious. Chromium(VI) (91-98%) was first reduced to chromium(III) rapidly. The oxidation reaction occurred later and the relative content of chromium(VI) was increased again. The presence of manganese oxides under favorable soil conditions can promote the reoxidation of Cr(III) to Cr(VI).

Phosphate-Mediated Remediation of Metals and Radionuclides

Worldwide industrialization activities create vast amounts of organic and inorganic waste streams that frequently result in significant soil and groundwater contamination. Metals and radionuclides are of particular concern due to their mobility and long-term persistence in aquatic and terrestrial environments. As the global population increases, the demand for safe, contaminant-free soil and groundwater will increase as will the need for effective and inexpensive remediation strategies. Remediation strategies that include physical and chemical methods (i.e., abiotic) or biological activities have been shown to impede the migration of radionuclide and metal contaminants within soil and groundwater. However, abiotic remediation methods are often too costly owing to the quantities and volumes of soils and/or groundwater requiring treatment. The in situ sequestration of metals and radionuclides mediated by biological activities associated with microbial phosphorus metabolism is a promising and less costly addition to our existing remediation methods. This review highlights the current strategies for abiotic and microbial phosphate-mediated techniques for uranium and metal remediation.

Complete Genome Sequence of Rahnella aquatilis CIP 78.65

Rahnella aquatilis CIP 78.65 is a gammaproteobacterium isolated from a drinking water source in Lille, France. Here we report the complete genome sequence of Rahnella aquatilis CIP 78.65, the type strain of R. aquatilis.

Enhancing the biodegradation of oil in sandy sediments with choline: A naturally methylated nitrogen compound

We investigated how additions of choline, a naturally occurring methylated nitrogen-containing compound, accelerated hydrocarbon degradation in sandy sediments contaminated with moderately weathered crude oil (4000 mg kg(-1) sediment). Addition of lauroylcholine chloride (LCC) and tricholine citrate (TCC) to oil contaminated sediments resulted in 1.6 times higher hydrocarbon degradation rates compared to treatments without added choline derivatives. However, the degradation rate constant for the oil contaminated sediments amended with LCC was similar to that in contaminated sediments amended with inorganic nitrogen, phosphorus, and glucose. Additions of LLC and TCC to sediments containing extensively weathered oil also resulted in enhanced mineralization rates. Cultivation-free 16S rRNA analysis revealed the presence of an extant microbial community with clones closely related to known hydrocarbon degraders from the Gammaproteobacteria, Alphaproteobacteria, and Firmicutes phyla. The results demonstrate that the addition of minimal amounts of organic compounds to oil contaminated sediments enhances the degradation of hydrocarbons.