Evidence for iron-mediated anaerobic methane oxidation in a crude oil-contaminated aquifer.

In a methanogenic crude oil contaminated aquifer near Bemidji, Minnesota, the decrease in dissolved CH(4) concentrations along the groundwater flow path, along with the positive shift in δ(13) C(CH) (4) and negative shift in δ(13) C(DIC) , is indicative of microbially mediated CH(4) oxidation. Calculations of electron acceptor transport across the water table, through diffusion, recharge, and the entrapment and release of gas bubbles, suggest that these processes can account for at most 15% of the observed total reduced carbon oxidation, including CH(4) . In the anaerobic plume, the characteristic Fe(III)-reducing genus Geobacter was the most abundant of the microbial groups tested, and depletion of labile sediment iron is observed over time, confirming that reduced carbon oxidation coupled to iron reduction is an important process. Electron mass balance calculations suggest that organic carbon sources in the aquifer, BTEX and non-volatile dissolved organic carbon, are insufficient to account for the loss in sediment Fe(III), implying that CH(4) oxidation may also be related to Fe(III) reduction. The results support a hypothesis of Fe(III)-mediated CH(4) oxidation in the contaminated aquifer.

Description of Tessaracoccus profundi sp.nov., a deep-subsurface actinobacterium isolated from a Chesapeake impact crater drill core (940 m depth).

A novel actinobacterium, designated CB31(T), was isolated from a 940 m depth sample of a drilling core obtained from the Chesapeake meteor impact crater. The strain was isolated aerobically on R2A medium agar plates supplemented with NaCl (20 g l(-1)) and MgCl2 x 6 H2O (3 g l(-1)). The colonies were circular, convex, smooth and orange. Cells were slightly curved, rod-shaped in young cultures and often appeared in pairs. In older cultures cells were coccoid. Cells stained Gram-positive, were non-motile and did not form endospores. The diagnostic diamino acid of the peptidoglycan was LL: -diaminopimelic acid. The polar lipids included phosphatidylglycerol, diphosphatidglycerol, four different glycolipids, two further phospholipids and one unidentified lipid. The dominant menaquinone was MK-9(H(4)) (70%). The major cellular fatty acid was anteiso C15:0 (83%). The DNA G + C content was 68 mol%. The strain grew anaerobically by reducing nitrate to nitrite or by fermenting glucose. It was catalase positive and oxidase negative. It grew between 10 and 45 degrees C, with an optimum between 35 and 40 degrees C. The pH range for growth was 5.7-9.3, with an optimum at pH 7.5. The closest phylogenetic neighbors based on 16S rRNA gene sequence identity were members of the genus Tessaracoccus (95-96% identity). On the basis of phenotypic and phylogenetic distinctiveness, strain CB31(T) is considered to represent a novel species of the genus Tessaracoccus, for which we propose the name Tessaracoccus profundi sp. nov.. It is the first member of this genus that has been isolated from a deep subsurface environment. The type strain is CB31(T) (=NCIMB 14440(T) = DSM 21240(T)).

Complete and draft genome sequences of six members of the Aquificales.

The Aquificales are widespread in marine and terrestrial hydrothermal environments. Here, we report the complete and draft genome sequences of six new members of the Aquificales: two marine species, Persephonella marina strain EX-H1 and Hydrogenivirga strain 128-5-R1 (from the East Pacific Rise, 9 degrees 50.3'N, 104 degrees 17.5'W, and the Eastern Lau Spreading Center, 176 degrees 11.5'W, 20 degrees 45.8'S, respectively), and four terrestrial isolates, Sulfurihydrogenibium azorense strain Az-Fu1, Sulfurihydrogenibium yellowstonense strain SS-5, and Sulfurihydrogenibium strain Y03AOP1 (from Furnas, Azores, Portugal, and Calcite Springs and Obsidian Pool in Yellowstone National Park, United States, respectively), and the only thermoacidophilic isolate, Hydrogenobaculum strain Y04AAS1 (from a stream adjacent to Obsidian Pool). Significant differences among the different species exist that include nitrogen metabolism, hydrogen utilization, chemotaxis, and signal transduction, providing insights into their ecological niche adaptations.

Deep drilling into the Chesapeake Bay impact structure.

Samples from a 1.76-kilometer-deep corehole drilled near the center of the late Eocene Chesapeake Bay impact structure (Virginia, USA) reveal its geologic, hydrologic, and biologic history. We conducted stratigraphic and petrologic analyses of the cores to elucidate the timing and results of impact-melt creation and distribution, transient-cavity collapse, and ocean-water resurge. Comparison of post-impact sedimentary sequences inside and outside the structure indicates that compaction of the crater fill influenced long-term sedimentation patterns in the mid-Atlantic region. Salty connate water of the target remains in the crater fill today, where it poses a potential threat to the regional groundwater resource. Observed depth variations in microbial abundance indicate a complex history of impact-related thermal sterilization and habitat modification, and subsequent post-impact repopulation.

Geomicrobiology of subglacial ice above Lake Vostok, Antarctica.

Data from ice 3590 meters below Vostok Station indicate that the ice was accreted from liquid water associated with Lake Vostok. Microbes were observed at concentrations ranging from 2.8 x 10(3) to 3.6 x 10(4) cells per milliliter; no biological incorporation of selected organic substrates or bicarbonate was detected. Bacterial 16S ribosomal DNA genes revealed low diversity in the gene population. The phylotypes were closely related to extant members of the alpha- and beta-Proteobacteria and the Actinomycetes. Extrapolation of the data from accretion ice to Lake Vostok implies that Lake Vostok may support a microbial population, despite more than 10(6) years of isolation from the atmosphere.

Detection of ammonium-oxidizing bacteria of the beta-subclass of the class Proteobacteria in aquatic samples with the PCR.

The PCR was used as the basis for the development of a sensitive and specific assay for the detection of ammonium-oxidizing bacteria belonging to the beta-subclass of the class Proteobacteria. PCR primers were selected on the basis of nucleic acid sequence data available for seven species of nitrifiers in this subclass. The specificity of the ammonium oxidizer primers was evaluated by testing known strains of nitrifiers, several serotyped environmental nitrifier isolates, and other members of the Proteobacteria, including four very closely related, nonnitrifying species (as determined by rRNA sequence analysis). DNA extracts from 19 bacterio-plankton samples collected from Lake Bonney, Antarctica, and the Southern California Bight were assayed for the presence of ammonium oxidizers. By using a two-stage amplification procedure, ammonium oxidizers were detected in samples collected from both sites. Chemical data collected simultaneously support the occurrence of nitrification and the presence of nitrifiers. This is the first report describing PCR primers specific for ammonium-oxidizing bacteria and the successful amplification of nitrifier genes coding for rRNA from DNA extracts from natural samples. This application of PCR is of particular importance for the detection and study of microbes, such as autotrophic nitrifiers, which are difficult or impossible to isolate from indigenous microbial communities.

Phytoplankton division rates in light-limited environments: two adaptations.

Red tide-forming dinoflagellates maximize cell numbers during periods of low light intensities in two ways. For short-term exposures to suboptimal light intensities such as might occur during recirculation in frontal convergences, cell division rates can be maintained at the expense of stored carbon for up to two generation times. During longer periods, corresponding to subsurface transport below a pycnocline, cell division rates eventually decrease as a portion of the fixed carbon is diverted to replenishing stored carbon. As a result, maximum rates of cell division can be resumed rapidly upon advection into surface waters where light intensities are optimal for growth.