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Results for “Geomicrobiology Journal”

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13 recordsLinked to original sources
USGS2010

Characterization of microbial arsenate reduction in the anoxic bottom waters of Mono Lake, California

Dissimilatory reduction of arsenate (DAsR) occurs in the arsenic-rich, anoxic water column of Mono Lake, California, yet the microorganisms responsible for this observed in situ activity have not been identified. To gain insight as to which microorganisms mediate this phenomenon, as well as to some of the biogeochemical constraints on this activity, we conducted incubations of arsenate-enriched bottom water coupled with inhibition/amendment studies and Denaturing Gradient Gel Electrophoresis (DGGE) characterization techniques. DAsR was totally inhibited by filter-sterilization and by nitrate, partially inhibited (~50%) by selenate, but only slightly (~25%) inhibited by oxyanions that block sulfate-reduction (molybdate and tungstate). The apparent inhibition by nitrate, however, was not due to action as a preferred electron acceptor to arsenate. Rather, nitrate addition caused a rapid, microbial re-oxidation of arsenite to arsenate, which gave the overall appearance of no arsenate loss. A similar microbial oxidation of As(III) was also found with Fe(III), a fact that has implications for the recycling of As(V) in Mono Lake's anoxic bottom waters. DAsR could be slightly (10%) stimulated by substrate amendments of lactate, succinate, malate, or glucose, but not by acetate, suggesting that the DAsR microflora is not electron donor limited. DGGE analysis of amplified 16S rDNA gene fragments from incubated arsenate-enriched bottom waters revealed the presence of two bands that were not present in controls without added arsenate. The resolved sequences of these excised bands indicated the presence of members of the epsilon (Sulfurospirillum) and delta (Desulfovibrio) subgroups of the Proteobacteria, both of which have representative species that are capable of anaerobic growth using arsenate as their electron acceptor.

California↗
USGS2003

Immobilization of cobalt by sulfate-reducing bacteria in subsurface sediments

We investigated the impact of sulfate-reduction on immobilization of metals in subsurface aquifers. Co 2+ was used as a model for heavy metals. Factors limiting sulfate-reduction dependent Co 2+ immobilization were tested on pure cultures of sulfate-reducing bacteria, and in sediment columns from a landfill leachate contaminated aquifer. In the presence of 1 mM Co 2+ , the growth of pure cultures of sulfate-reducing bacteria was not impacted. Cultures of Desulfovibrio desulfuricans, Desulfotomaculum gibsoniae , and Desulfomicrobium hypogeia removed greater than 99.99% of the soluble Co 2+ when CoCl 2 was used with no chelators. The above cultures and Desulfoarcula baarsi removed 98-99.94% of the soluble Co(II) when the metal was complexed with the model ligand nitrilotriacetate (Co-NTA). Factors controlling the rate of sulfate-reduction based Co 2+ precipitation were investigated in sediment-cobalt mixtures. Several electron donors were tested and all but toluene accelerated soluble Co 2+ loss. Ethanol and formate showed the greatest stimulation. All complex nitrogen sources tested slowed and decreased the extent of Co 2+ removal from solution relative to formate-amended sediment incubations. A range of pH values were tested (6.35-7.81), with the more alkaline incubations exhibiting the largest precipitation of Co 2+ . The immobilization of Co 2+ in sediments was also investigated with cores to monitor the flow of Co 2+ through undisturbed sediments. An increase in the amount of Co 2+ immobilized as CoS was observed as sulfate reduction activity was stimulated in flow through columns. Both pure culture and sediment incubation data indicate that stimulation of sulfate reduction is a viable strategy in the immobilization of contaminating metals in subsurface systems.

Geomicrobiology Journal↗
USGS2005

Geochemical controls on microbial nitrate-dependent U(IV) oxidation

After reductive immobilization of uranium, the element may be oxidized and remobilized in the presence of nitrate by the activity of dissimilatory nitrate-reducing bacteria. We examined controls on microbially mediated nitrate-dependent U(IV) oxidation in landfill leachate-impacted subsurface sediments. Nitrate-dependent U(IV)-oxidizing bacteria were at least two orders of magnitude less numerous in these sediments than glucose- or Fe(II)-oxidizing nitrate-reducing bacteria and grew more slowly than the latter organisms, suggesting that U(IV) is ultimately oxidized by Fe(III) produced by nitrate-dependent Fe(II)-oxidizing bacteria or by oxidation of Fe(II) by nitrite that accumulates during organotrophic dissimilatory nitrate reduction. We examined the effect of nitrate and reductant concentration on nitrate-dependent U(IV) oxidation in sediment incubations and used the initial reductive capacity (RDC = [reducing equivalents] - [oxidizing equivalents]) of the incubations as a unified measurement of the nitrate or reductant concentration. When we lowered the RDC with progressively higher nitrate concentrations, we observed a corresponding increase in the extent of U(IV) oxidation, but did not observe this relationship between RDC and U(IV) oxidation rate, especially when RDC > 0, suggesting that nitrate concentration strongly controls the extent, but not the rate of nitrate-dependent U(IV) oxidation. On the other hand, when we raised the RDC in sediment incubations with progressively higher reductant (acetate, sulfide, soluble Fe(II), or FeS) concentrations, we observed progressively lower extents and rates of nitrate-dependent U(IV) oxidation. Acetate was a relatively poor inhibitor of nitrate-dependent U(IV) oxidation, while Fe(II) was the most effective inhibitor. Based on these results, we propose that it may be possible to predict the stability of U(IV) in a bioremediated aquifer based on the geochemical characteristics of that aquifer.

Geomicrobiology Journal↗
USGS2009

Arsenic in the evolution of earth and extraterrestrial ecosystems

If you were asked to speculate about the form extra-terrestrial life on Mars might take, which geomicrobial phenomenon might you select as a model system, assuming that life on Mars would be ‘primitive’? Give your reasons. At the end of my senior year at Rensselaer Polytechnic Institute in 1968, I took Professor Ehrlich's final for his Geomicrobiology course. The above question beckoned to me like the Sirens to Odysseus, for if I answered, it would take so much time and thought that I would never get around to the exam's other essay questions and consequently, would be “shipwrecked” by flunking the course. So, I passed it up. With this 41-year perspective in mind, this manuscript is now submitted to Professor Ehrlich for (belated) “extra-credit.” R.S. Oremland

Geomicrobiology Journal↗
USGS2013

A biogeochemical and genetic survey of acetylene fermentation by environmental samples and bacterial isolates

Anoxic samples (sediment and groundwater) from 13 chemically diverse field sites were assayed for their ability to consume acetylene (C 2 H 2 ). Over incubation periods ranging from ˜ 10 to 80 days, selected samples from 7 of the 13 tested sites displayed significant C2H2 removal. No significant formation of ethylene was noted in these incubations; therefore, C 2 H 2 consumption could be attributed to acetylene hydratase (AH) rather than nitrogenase activity. This putative AH (PAH) activity was observed in only 21% of the total of assayed samples, while amplification of AH genes from extracted DNA using degenerate primers derived from Pelobacter acetylenicus occurred in even fewer (9.8%) samples. Acetylene-fermenting bacteria were isolated as a pure culture from the sediments of a tidal mudflat in San Francisco Bay (SFB93) and as an enrichment culture from freshwater Searsville Lake (SV7). Comparison of 16S rDNA clone libraries revealed that SFB93 was closely related to P. carbolinicus, while SV7 consisted of several unrelated bacteria. AH gene was amplified from SFB93 but not SV7. The inability of the primers to generate amplicons in the SV7 enrichment, as well as from several of the environmental samples that displayed PAH activity, implied that either the primers were too highly constrained in their specificity or that there was a different type of AH gene in these environmental samples than occurs in P. acetylenicus. The significance of this work with regard to the search for life in the outer Solar System, where C 2 HL 2 is abundant, is discussed.

Geomicrobiology Journal↗
USGS2014

The transport of nonindigenous microorganisms into caves by human visitation: a case study at Carlsbad Caverns National Park

A series of atmospheric investigations was conducted in Carlsbad Cavern to determine if human visitation is a possible cause for the contamination of the cave system with non-indigenous microorganisms. In 2004, site-specific culture-based data demonstrated that Staphylococcus spp. colony-forming units (CFUs) were the most prevalent members of the atmospheric community along the paved visitor trail (avg. 18.8% of CFU), while Knoellia spp. CFUs dominated off-trail locations (40.1% of CFU). Fungal culture data revealed that Penicillium and Aspergillus were prevalent in the Lunch Room where food is stored, sold, and consumed. Ubiquitous genera such as Cladosporium and Alternaria were prevalent near the Natural Entrance of the cave, and the general trend was a decrease in fungal CFUs with progression into the cave system, except for the area near the Lunch Room. Management practices such as prohibition of crumb-generating types of foods could be considered to protect cave health. In 2009, nonculture-based analyses demonstrated that Enterobacteriaceae were the dominant microbiota at sites along the descent trail and within the Lunch Room. Dominance of Enterobacteriaceae has not been previously demonstrated in caves. Either they are naturally occurring indigenous members, or their presence is a marker of anthropogenic contamination.

New Mexico↗
USGS2016

A microbial arsenic cycle in sediments of an acidic mine impoundment: Herman Pit, Clear Lake, California

The involvement of prokaryotes in the redox reactions of arsenic occurring between its +5 [arsenate; As(V)] and +3 [arsenite; As(III)] oxidation states has been well established. Most research to date has focused upon circum-neutral pH environments (e.g., freshwater or estuarine sediments) or arsenic-rich “extreme” environments like hot springs and soda lakes. In contrast, relatively little work has been conducted in acidic environments. With this in mind we conducted experiments with sediments taken from the Herman Pit, an acid mine drainage impoundment of a former mercury (cinnabar) mine. Due to the large adsorptive capacity of the abundant Fe(III)-rich minerals, we were unable to initially detect in solution either As(V) or As(III) added to the aqueous phase of live sediment slurries or autoclaved controls, although the former consumed added electron donors (i.e., lactate, acetate, hydrogen), while the latter did not. This prompted us to conduct further experiments with diluted slurries using the live materials from the first incubation as inoculum. In these experiments we observed reduction of As(V) to As(III) under anoxic conditions and reduction rates were enhanced by addition of electron donors. We also observed oxidation of As(III) to As(V) in oxic slurries as well as in anoxic slurries amended with nitrate. We noted an acid-tolerant trend for sediment slurries in the cases of As(III) oxidation (aerobic and anaerobic) as well as for anaerobic As(V) reduction. These observations indicate the presence of a viable microbial arsenic redox cycle in the sediments of this extreme environment, a result reinforced by the successful amplification of arsenic functional genes ( aioA , and arrA ) from these materials.

California↗
USGS2016

Filamentous hydrous ferric oxide biosignatures in a pipeline carrying acid mine drainage at Iron Mountain Mine, California

A pipeline carrying acidic mine effluent at Iron Mountain, CA, developed Fe(III)-rich precipitate caused by oxidation of Fe(II) aq . The native microbial community in the pipe included filamentous microbes. The pipe scale consisted of microbial filaments, and schwertmannite (ferric oxyhydroxysulfate, FOHS) mineral spheres and filaments. FOHS filaments contained central lumina with diameters similar to those of microbial filaments. FOHS filament geometry, the geochemical environment, and the presence of filamentous microbes suggest that FOHS filaments are mineralized microbial filaments. This formation of textural biosignatures provides the basis for a conceptual model for the development and preservation of biosignatures in other environments.

Geomicrobiology Journal↗
USGS2016

Dissolution of fluorapatite by Pseudomonas fluorescens P35 resulting in fluorine release

Chemical weathering of fluorine-bearing minerals is widely accepted as the main mechanism for the release of fluorine (F) to groundwater. Here, we propose a potential mechanism of F release via microbial dissolution of fluorapatite (Ca 5 (PO 4 ) 3 F), which has been neglected previously. Batch culture experiments were conducted at 30°C with a phosphate-solubilizing bacteria strain, Pseudomonas fluorescens P35, and rock phosphates as the sole source of phosphate for microbial growth in parallel with abiotic controls. Rock phosphates consisted of 55–91% of fluorapatite and 5–10% of dolomite before microbial dissolution as indicated by X-ray diffraction (XRD). Mineral composition and morphology changed after microbial dissolution characterized by the disappearance of dolomite and the development of etched cavities on rock phosphate surfaces. The pH of media used was approximately 7.4 at the beginning and increased gradually to 7.7 in abiotic controls; with the inoculum, the pH decreased to acidic values of 3.7–3.8 after 27 h. Phosphate, calcium, and fluoride were released from the rock phosphate to the acidified medium. At 42 h, the concentration of F reached 8.1–10.3 mg L −1 . The elevated F concentration was two times higher than the F levels in groundwater in regions diagnosed with fluorosis, and was toxic to the bacteria, as demonstrated by a precipitous decrease in live cells. Geochemical modeling demonstrated that the oxidation of glucose (the carbon source for microbial growth in the medium) to gluconic acid could decrease the pH to 3.7–3.8 and result in the dissolution of fluorapatite and dolomite. Dolomite and fluorapatite remained unsaturated, while concentrations of dissolved phosphorus (P), calcium (Ca), and F increased throughout the time course Fluorite reached saturation [saturation index (SI) 0.22–0.42] after 42 h in rock phosphate–amended biotic systems. However, fluorite was not detected in XRD patterns of the final residue from microcosms. Given that phosphate-solubilizing bacteria are ubiquitous in soil and groundwater ecosystems, they could play an important role in fluorapatite dissolution and the release of F to groundwater.

Geomicrobiology Journal↗
USGS1991

Mineral remains of early life on Earth? On Mars?

The oldest sedimentary rocks on Earth, the 3.8‐Ga Isua Iron‐Formation in southwestern Greenland, are metamorphosed past the point where organic‐walled fossils would remain. Acid residues and thin sections of these rocks reveal ferric microstructures that have filamentous, hollow rod, and spherical shapes not characteristic of crystalline minerals. Instead, they resemble ferric‐coated remains of bacteria. Modern so‐called iron bacteria were therefore studied to enhance a search image for oxide minerals precipitated by early bacteria. Iron bacteria become coated with ferrihydrite, a metastable mineral that converts to hematite, which is stable under high temperatures. If these unusual morphotypes are mineral remains of microfossils, then life must have evolved somewhat earlier than 3.8 Ga, and may have involved the interaction of sediments and molecular oxygen in water, with iron as a catalyst. Timing is constrained by the early in fall of planetary materials that would have heated the planet's surface. Because there are no earlier sedimentary rocks to study on Earth, it may be necessary to expand the search elsewhere in the solar system for clues to any biotic precursors or other types of early life. Evidence from Mars shows geophysical and geochemical differentiation at a very early stage, which makes it an important candidate for such a search if sedimentation is an important process in life's origins. Not only does Mars have iron oxide‐rich soils, but its oldest regions have river channels where surface water and sediment may have been carried, and seepage areas where groundwater may have discharged. Mars may have had an atmosphere and liquid water in the crucial time frame of 3.9–4.0 Ga. A study of morphologies of iron oxide minerals collected in the southern highlands during a Mars sample return mission may therefore help to fill in important gaps in the history of Earth's earliest biosphere.

Geomicrobiology Journal↗
USGS1993

Does lead affect microbial metabolism in aquifer sediments under different terminal electron accepting conditions?

High concentrations of aliphatic organic acids (∼1 mM acetate) in groundwater from a petroleum hydrocarbon‐contaminated aquifer are associated with elevated concentrations (∼30 μg/L) of lead. This pattern suggests that toxic effects of lead have contributed to the observed accumulation of organic acids. This hypothesis was tested by examining the effects of lead on carbon mineralization and organic acid accumulation in petroleum‐contaminated aquifer material incubated under different terminal electron‐accepting conditions. Lead was found to inhibit fermentation (organic acid accumulation) as well as microbial carbon mineralization (CO 2 or CH 4 production) under aerobic, nitrate‐reducing, sulfate‐reducing, and methanogenic conditions. Thus Pb does not appear to be the primary cause of organic acid accumulation at the field site. Rather, substantial accumulation of aliphatic organic acids occurred only in methanogenic microcosms, and only trace amounts of acetic acid were detected in sulfate‐reducing microcosms. This pattern parallels field observations in which high organic acid concentrations were detected in methanogenic zones, but only low concentrations of acetic acid were detected in sulfate‐reducing zones.

Geomicrobiology Journal↗
USGS1994

Protists from a sewage‐contaminated aquifer on cape cod, Massachusetts

Several species of flagellates (genera Bodo, Cercomonas, Cryptaulax, Cyathomonas, Goniomonas, Spumella ) have been identified in cultures from a plume of organic contamination (treated sewage effluent) within an aquifer on Cape Cod, Massachusetts. Amoebae and numerous unidentifiable 2‐ to 3‐μm flagellates have also been observed. As a rule, flagellates were associated with solid surfaces, or were capable of temporary surface attachment, corroborating earlier observations from in situ and column transport experiments suggesting that protists in the Massachusetts aquifer have a high propensity for association with sediment grain surfaces. Based on the fact that cultures from the uncontaminated part of the aquifer yielded only a few species of protists, it is hypothesized that the greater abundance and variety of food sources in the contaminant plume is capable of supporting a greater number of protistan species.

Geomicrobiology Journal↗