A significant portion of oil from the recent Deepwater Horizon (DH) oil spill in the Gulf of Mexico was transported to the shoreline, where it may have severe ecological and economic consequences. The objectives of this study were (i) to identify and characterize predominant oil-degrading taxa that may be used as model hydrocarbon degraders or as microbial indicators of contamination and (ii) to characterize the in situ response of indigenous bacterial communities to oil contamination in beach ecosystems. This study was conducted at municipal Pensacola Beach, FL, where chemical analysis revealed weathered oil petroleum hydrocarbon (C 8 to C 40 ) concentrations ranging from 3.1 to 4,500 mg kg ؊1 in beach sands. A total of 24 bacterial strains from 14 genera were isolated from oiled beach sands and confirmed as oil-degrading microorganisms. Isolated bacterial strains were primarily Gammaproteobacteria, including representatives of genera with known oil degraders (Alcanivorax, Marinobacter, Pseudomonas, and Acinetobacter). Sequence libraries generated from oiled sands revealed phylotypes that showed high sequence identity (up to 99%) to rRNA gene sequences from the oil-degrading bacterial isolates. The abundance of bacterial SSU rRNA gene sequences was ϳ10-fold higher in oiled (0.44 ؋ 10 7 to 10.2 ؋ 10 7 copies g ؊1 ) versus clean (0.024 ؋ 10 7 to 1.4 ؋ 10 7 copies g ؊1 ) sand. Community analysis revealed a distinct response to oil contamination, and SSU rRNA gene abundance derived from the genus Alcanivorax showed the largest increase in relative abundance in contaminated samples. We conclude that oil contamination from the DH spill had a profound impact on the abundance and community composition of indigenous bacteria in Gulf beach sands, and our evidence points to members of the Gammaproteobacteria (Alcanivorax, Marinobacter) and Alphaproteobacteria (Rhodobacteraceae) as key players in oil degradation there.

Bacterial strains 2APBS1 T and 116-2 were isolated from the subsurface of a nuclear legacy waste site where the sediments are co-contaminated with large amounts of acids, nitrate, metal radionuclides and other heavy metals. A combination of physiological and genetic assays indicated that these strains represent the first member of the genus Rhodanobacter shown to be capable of complete denitrification. Cells of strain 2APBS1 T and 116-2 were Gram-negative, non-spore-forming rods, 3-5 mm long and 0.25-0.5 mm in diameter. The isolates were facultative anaerobes, and had temperature and pH optima for growth of 30 6C and pH 6.5; they were able to tolerate up to 2.0 % NaCl, although growth improved in its absence. Strains 2APBS1 T and 116-2 contained fatty acid and quinone (ubiquinone-8; 100 %) profiles that are characteristic features of the genus Rhodanobacter. Although strains 2APBS1 T and 116-2 shared high 16S rRNA gene sequence similarity with Rhodanobacter thiooxydans LCS2 T (.99 %), levels of DNA-DNA relatedness between these strains were substantially below the 70 % threshold used to designate novel species. Thus, based on genotypic, phylogenetic, chemotaxonomic and physiological differences, strains 2APBS1 T and 116-2 are considered to represent a single novel species of the genus Rhodanobacter, for which the name Rhodanobacter denitrificans sp. nov. is proposed. The type strain is 2APBS1 T (5DSM 23569 T 5JCM 17641 T ).

The temperature dependency of denitrification and anaerobic ammonium oxidation (anammox) rates from Arctic fjord sediments was investigated in a temperature gradient block incubator for temperatures ranging from -1 to 40°C. Community structure in intact sediments and slurry incubations was determined using Illumina SSU rRNA gene sequencing. The optimal temperature (Topt ) for denitrification was 25-27°C, whereas anammox rates were optimal at 12-17°C. Both denitrification and anammox exhibited temperature responses consistent with a psychrophilic community, but anammox bacteria may be more specialized for psychrophilic activity. Long-term (1-2 months) warming experiments indicated that temperature increases of 5-10°C above in situ had little effect on the microbial community structure or the temperature response of denitrification and anammox. Increases of 25°C shifted denitrification temperature responses to mesophilic with concurrent community shifts, and anammox activity was eliminated above 25°C. Additions of low molecular weight organic substrates (acetate and lactate) caused increases in denitrification rates, corroborating the hypothesis that the supply of organic substrates is a more dominant control of respiration rates than low temperature. These results suggest that climate-related changes in sinking particulate flux will likely alter rates of N removal more rapidly than warming.

We examined nitrogen cycling over a 1-yr period in shallow, sandy sediments at two contrasting sites near a barrier island in the northeastern Gulf of Mexico, and we provide here the direct determination of dinitrogen gas (N 2 ) production at ambient nitrate concentrations in permeable marine sediments. Nitrogen-stable isotope tracer techniques were used to quantify N 2 -production rates and pathways in sediment cores and slurries. To simulate pore-water advection, the dominant transport process in the upper layer of the permeable sand beds, intact sediment cores were perfused with aerated seawater. This perfusion increased denitrification rates up to 2-fold in Apalachicola Bay sands and up to 17-fold in Gulf of Mexico sublittoral sands, respectively, relative to static cores. Seasonal N 2 -production rates were highest in spring and fall. Denitrified nitrate originated almost entirely from benthic nitrification at the exposed Gulf site, whereas water-column nitrate dominated sedimentary denitrification at the sheltered Bay site. Sediment incubations in stirred chambers were used to determine net fluxes of oxygen (O 2 ), N 2 , nitrate, and ammonium across the sediment-water interface during varied degrees of continuous pore-water exchange. Rates of N 2 efflux correlated with rates of pore-water flow increasing from 0.12 mmol N m 22 d 21 under diffusion-limited transport conditions up to 0.87 mmol N m 22 d 21 with pore-water advection. Mineralized nitrogen was completely converted to N 2 gas in Gulf of Mexico sediments. Our results demonstrate that advective pore-water circulation will accelerate benthic N 2 production by coupled nitrificationdenitrification and that substantial nitrogen loss occurs from coastal permeable sediments.

Abstract. Despite decades of research on the physiology and biochemistry of nitrate/nitrite-respiring microorganisms, little is known regarding their metabolic response to temperature, especially under in situ conditions. The temperature regulation of microbial communities that mediate anammox and denitrification was investigated in near shore permeable sediments at polar, temperate, and subtropical sites with annual mean temperatures ranging from −5 to 23 °C. Total N2 production rates were determined using the isotope pairing technique in intact core incubations under diffusive and simulated advection conditions and ranged from 2 to 359 μmol N m−2 d−1. For the majority of sites studied, N2 removal was 2–7 times more rapid under simulated advective flow conditions. Anammox comprised 6–14% of total N2 production at temperate and polar sites and was not detected at the subtropical site. Potential rates of denitrification and anammox were determined in anaerobic slurries in a temperature gradient block incubator across a temperature range of −1 °C to 42 °C. The highest optimum temperature (Topt) for denitrification was 36 °C and was observed in subtropical sediments, while the lowest Topt of 21 °C was observed at the polar site. Seasonal variation in the Topt was observed at the temperate site with values of 26 and 34 °C in winter and summer, respectively. The Topt values for anammox were 9 and 26 °C at the polar and temperate sites, respectively. The results demonstrate adaptation of denitrifying communities to in situ temperatures in permeable marine sediments across a wide range of temperatures, whereas marine anammox bacteria may be predominately psychrophilic to psychrotolerant. The adaptation of microbial communities to in situ temperatures suggests that the relationship between temperature and rates of N removal is highly dependent on community structure.