T. C. Onstott

Biogenic iron mineralization accompanying the dissimilatory reduction of hydrous ferric oxide by a groundwater bacterium

Dissimilatory iron-reducing bacteria (DIRB) couple the oxidation of organic matter or H2 to the reduction of iron oxides. The factors controlling the rate and extent of these reduction reactions and the resulting solid phases are complex and poorly understood. Batch experiments were conducted with amorphous hydrous ferric oxide (HFO) and the DIRB Shewanella putrefaciens, strain CN32, in well-defined aqueous solutions to investigate the reduction of HFO and formation of biogenic Fe(II) minerals. Lactate-HFO solutions buffered with either bicarbonate or 1,4-piperazinediethanesulfonic acid (PIPES) containing various combinations of phosphate and anthraquinone-2,6-disulfonate (AQDS), were inoculated with S. putrefaciens CN32. AQDS, a humic acid analog that can be reduced to dihydroanthraquinone by CN32, was included because of its ability to function as an electron shuttle during microbial iron reduction and as an indicator of pe. Iron reduction was measured with time, and the resulting solids were analyzed by X-ray diffraction, scanning electron microscopy (SEM), and transmission electron microscopy (TEM) with energy-dispersive X-ray spectroscopy (EDS) and selected area electron diffraction (SAED). In HCO3− buffered medium with AQDS, HFO was rapidly and extensively reduced, and the resulting solids were dominated by ferrous carbonate (siderite). Ferrous phosphate (vivianite) was also present in HCO3− medium containing P, and fine-grained magnetite was present as a minor phase in HCO3− medium with or without P. In the PIPES-buffered medium, the rate and extent of reduction was strongly influenced by AQDS and P. With AQDS, HFO was rapidly converted to highly crystalline magnetite whereas in its absence, magnetite mineralization was slower and the final material less crystalline. In PIPES with both P and AQDS, a green rust type compound [Fe(6-x)IIFexIII(OH)12]x+[(A2−)x/2 · yH2O]x− was the dominant solid phase formed; in the absence of AQDS a poorly crystalline product was observed. The measured pe and nature of the solids identified were consistent with thermodynamic considerations. The composition of aqueous media in which microbial iron reduction occurred strongly impacted the rate and extent of iron reduction and the nature of the reduced solids. This, in turn, can provide a feedback control mechanism on microbial metabolism. Hence, in sediments where geochemical conditions promote magnetite formation, two-thirds of the Fe(III) will be sequestered in a form that may not be available for anaerobic bacterial respiration.

Archaeal Diversity in Waters from Deep South African Gold Mines

ABSTRACT A culture-independent molecular analysis of archaeal communities in waters collected from deep South African gold mines was performed by performing a PCR-mediated terminal restriction fragment length polymorphism (T-RFLP) analysis of rRNA genes (rDNA) in conjunction with a sequencing analysis of archaeal rDNA clone libraries. The water samples used represented various environments, including deep fissure water, mine service water, and water from an overlying dolomite aquifer. T-RFLP analysis revealed that the ribotype distribution of archaea varied with the source of water. The archaeal communities in the deep gold mine environments exhibited great phylogenetic diversity; the majority of the members were most closely related to uncultivated species. Some archaeal rDNA clones obtained from mine service water and dolomite aquifer water samples were most closely related to environmental rDNA clones from surface soil (soil clones) and marine environments (marine group I [MGI]). Other clones exhibited intermediate phylogenetic affiliation between soil clones and MGI in the Crenarchaeota. Fissure water samples, derived from active or dormant geothermal environments, yielded archaeal sequences that exhibited novel phylogeny, including a novel lineage ofEuryarchaeota. These results suggest that deep South African gold mines harbor novel archaeal communities distinct from those observed in other environments. Based on the phylogenetic analysis of archaeal strains and rDNA clones, including the newly discovered archaeal rDNA clones, the evolutionary relationship and the phylogenetic organization of the domain Archaea are reevaluated.

Environmental genomics reveals a single-species ecosystem deep within earth

DNA from low-biodiversity fracture water collected at 2.8-kilometer depth in a South African gold mine was sequenced and assembled into a single, complete genome. This bacterium, Candidatus Desulforudis audaxviator, composes >99.9% of the microorganisms inhabiting the fluid phase of this particular fracture. Its genome indicates a motile, sporulating, sulfate-reducing, chemoautotrophic thermophile that can fix its own nitrogen and carbon by using machinery shared with archaea. Candidatus Desulforudis audaxviator is capable of an independent life-style well suited to long-term isolation from the photosphere deep within Earths crust and offers an example of a natural ecosystem that appears to have its biological component entirely encoded within a single genome.

Pore‐size constraints on the activity and survival of subsurface bacteria in a late cretaceous shale‐sandstone sequence, northwestern New Mexico

To investigate the distribution of microbial biomass and activities to gain insights into the physical controls on microbial activity and potential long‐term survival in the subsurface, 24 shale and sandstone cores were collected from a site in northwestern New Mexico. Bacterial biomass in the core samples ranged from below detection to 31.9 pmol total phospholipid fatty acid (PLFA) g‐1 of rock with no apparent relationship between lithology and PLFA abundance. No metabolic activities, as determined by anaerobic mineralization of [14C]acetate and [14C]glucose and 35SO4 2‐ reduction, were detected in core samples with pore throats <0.2 fan in diameter, smaller than the size of known bacteria. However, enrichments revealed the presence of sulfate‐re‐ducing bacteria, and 35SO4 2‐ reduction was detected upon extended (14 days) incubation in some small‐pore‐throat samples. In contrast, relatively rapid rates of metabolic activity were more common in core samples containing a significant fraction of pore throat...

Mineral transformations associated with the microbial reduction of magnetite

Although dissimilatory iron reducing bacteria DIRB are capable of reducing a number of metals in oxides and soluble forms, the factors controlling the raterextent of magnetite reduction and the nature of the mineral products resulting from magnetite reduction are not well understood. This study was carried out to investigate mechanisms and biogeochemical processes occurring during magnetite reduction by the DIRB, Shewanella putrefaciens strains CN32 and MR-1. Reduction experiments were performed with biogenic and synthetic magnetite in well-defined solutions. Biogenic magnetite was . generated via microbial reduction of hydrous ferric oxide HFO . Biogenic magnetite in solutions buffered with either

39Ar recoil artifacts in chloritized biotite

Biotite separates from the metamorphosed granitic rocks of eastern Taiwan yield disturbed 40Ar39Ar age spectra. Their disturbed profiles become more pronounced with increasing degree of chloritization and are attributed to mixed release of argon from sub-micron scale biotite and chlorite intercalations. 39Ar internal recoil best explains the discordance of the age spectra. Chlorite is randomly intercalated with biotite at scales ranging from 10 A to several tens of microns. Both 40Ar∗ and K were evidently lost during the chloritization reaction. During the neutron irradiation, 39Ar atoms recoil into the chlorite from the adjacent biotite intercalations. The recoil and chloritization combine to produce a variable 40Ar39Ar spatial distribution in the intercalated biotite/chlorite. During 40Ar39Ar step-heating analyses, argon in biotite is released in two pulses centered at ~650°C and 950–1050°C which represent two stages of dehydroxylation of the biotite. Chlorite out-gasses in two pulses centered at ~550°C and 700–900°C during dehydroxylation and then decomposes. This differential thermal release of argon from each mineral phase with variable 40Ar39Ar ratios yields discordant incremental heating age spectra.

Alkaliphilus transvaalensis gen. nov., sp. nov., an extremely alkaliphilic bacterium isolated from a deep South African gold mine.

A novel extreme alkaliphile was isolated from a mine water containment dam at 3.2 km below land surface in an ultra-deep gold mine near Carletonville, South Africa. The cells of this bacterium were straight to slightly curved rods, motile by flagella and formed endospores. Growth was observed over the temperature range 20-50 degrees C (optimum 40 degrees C; 45 min doubling time) and pH range 8.5-12.5 (optimum pH 10.0). The novel isolate, one of the most alkaliphilic micro-organisms yet described, was a strictly anaerobic chemo-organotroph capable of utilizing proteinaceous substrates such as yeast extract, peptone, tryptone and casein. Elemental sulfur, thiosulfate or fumarate, when included as accessory electron acceptors, improved growth. The G+C content of genomic DNA was 36.4 mol %. Phylogenetic analysis based on the 16S rDNA sequence indicated that the isolate is a member of cluster XI within the low G+C gram-positive bacteria, but only distantly related to previously described members. On the basis of physiological and molecular properties, the isolate represents a novel species, for which the name Alkaliphilus transvaalensis gen. nov., sp. nov. is proposed (type strain SAGM1T = JCM 10712T = ATCC 700919T). The mechanism of generation of the highly alkaline microbial habitat and the possible source of the alkaliphile are discussed.

Desulfotomaculum and Methanobacterium spp. dominate a 4-to 5-kilometer-deep fault

ABSTRACT Alkaline, sulfidic, 54 to 60°C, 4 to 53 million-year-old meteoric water emanating from a borehole intersecting quartzite-hosted fractures >3.3 km beneath the surface supported a microbial community dominated by a bacterial species affiliated with Desulfotomaculum spp. and an archaeal species related to Methanobacterium spp. The geochemical homogeneity over the 650-m length of the borehole, the lack of dividing cells, and the absence of these microorganisms in mine service water support an indigenous origin for the microbial community. The coexistence of these two microorganisms is consistent with a limiting flux of inorganic carbon and SO42− in the presence of high pH, high concentrations of H2 and CH4, and minimal free energy for autotrophic methanogenesis. Sulfide isotopic compositions were highly enriched, consistent with microbial SO42− reduction under hydrologic isolation. An analogous microbial couple and similar abiogenic gas chemistry have been reported recently for hydrothermal carbonate vents of the Lost City near the Mid-Atlantic Ridge (D. S. Kelly et al., Science 307:1428-1434, 2005), suggesting that these features may be common to deep subsurface habitats (continental and marine) bearing this geochemical signature. The geochemical setting and microbial communities described here are notably different from microbial ecosystems reported for shallower continental subsurface environments.

Recoil refinements: Implications for the 40Ar/39Ar dating technique

Integration of the neutron energy distribution for a water-moderated reactor with the most recent cross-section data yields mean recoil energies of 177 keV for 39K (n, p) 39Ar, 969 keV for 40Ca (n, α) 37Ar, and 140 eV for 37Cl (n, γ) 38Cl (β) 38Ar. These estimates are insensitive to the anisotropy of reaction products. Utilizing Monte Carlo simulations of collision cascades, we calculate a mean recoil range of 1620 A for 39K (n, p) 39Ar, 3780 A for 40Ca (n, α) 37Ar, and 11 A for 37Cl (n, γ) 38Cl (β) 38Ar. Rutherford backscatter (RBS) measurements of argon implantation experiments into albite confirm the veracity of these estimates. Integration of the recoil range distributions yields a mean depletion depth in a semi-infinite medium of 820 A for 39Ar, 1950 A for 37Ar, and 6 A for 38Ar. The concentration gradients generated by recoil-redistribution between thin slabs were then incorporated into standard diffusion equations. If the exsolution lamellae are the effective diffusion dimension for argon, then the calculations indicate that the argon release rates and 40Ar/39Ar age spectrum derived from incremental heating of minerals exsolved at the micron to submicron scale are significantly affected by recoil-redistribution. The age spectra will be discordant even if the feldspar has not experienced a complex or slow cooling history. Incremental step apparent ages will increase with the fraction of 39Ar released as the potassium poor lamellae degas. The age spectra will exhibit decreasing apparent ages with increasing fraction 39Ar released as the potassium feldstar lamellae degas. The overall profile of the age spectrum will depend upon the composition of the feldspar and the size distribution of the lamellae, if the lamellae are the effective argon diffusion dimension. In principal, these calculations can be used to discriminate between different models for argon diffusion in minerals. Finally, the 11 A mean recoil distance calculated for 38Ar indicates that it is not a proxy for anion-sited excess argon. Instead, published correlations of 38Ar with excess 40Ar probably reflect the degassing of fine-grained, Cl-rich inclusions.

Nematoda from the terrestrial deep subsurface of South Africa

Since its discovery over two decades ago, the deep subsurface biosphere has been considered to be the realm of single-cell organisms, extending over three kilometres into the Earth’s crust and comprising a significant fraction of the global biosphere. The constraints of temperature, energy, dioxygen and space seemed to preclude the possibility of more-complex, multicellular organisms from surviving at these depths. Here we report species of the phylum Nematoda that have been detected in or recovered from 0.9–3.6-kilometre-deep fracture water in the deep mines of South Africa but have not been detected in the mining water. These subsurface nematodes, including a new species, Halicephalobus mephisto, tolerate high temperature, reproduce asexually and preferentially feed upon subsurface bacteria. Carbon-14 data indicate that the fracture water in which the nematodes reside is 3,000–12,000-year-old palaeometeoric water. Our data suggest that nematodes should be found in other deep hypoxic settings where temperature permits, and that they may control the microbial population density by grazing on fracture surface biofilm patches. Our results expand the known metazoan biosphere and demonstrate that deep ecosystems are more complex than previously accepted. The discovery of multicellular life in the deep subsurface of the Earth also has important implications for the search for subsurface life on other planets in our Solar System.