Geology topics

Lee R. Krumholz

Publications and source records attributed to Lee R. Krumholz.

8 recordsLinked to original sources

USGS2005

Role for Fe(III) minerals in nitrate-dependent microbial U(IV) oxidation

Microbiological reduction of soluble U(VI) to insoluble U(IV) is a means of preventing the migration of that element in groundwater, but the presence of nitrate in U(IV)-containing sediments leads to U(IV) oxidation and remobilizaton. Nitrite or iron(III) oxyhydroxides may oxidize U(IV) under nitrate-reducing conditions, and we determined the rate and extent of U(IV) oxidation by these compounds. Fe(III) oxidized U(IV) at a greater rate than nitrite (130 and 10 μM U(IV)/day, respectively). In aquifer sediments, Fe(III) may be produced during microbial nitrate reduction by oxidation of Fe(II) with nitrite, or by enzymatic Fe(II) oxidation coupled to nitrate reduction. To determine which of these mechanisms was dominant, we isolated a nitrate-dependent acetate- and Fe(II)-oxidizing bacterium from a U(VI)- and nitrate-contaminated aquifer. This organism oxidized U(IV) at a greater rate and to a greater extent under acetate-oxidizing (where nitrite accumulated to 50 mM) than under Fe(II)-oxidizing conditions. We show that the observed differences in rate and extent of U(IV) oxidation are due to mineralogical differences between Fe(III) produced by reaction of Fe(II) with nitrite (amorphous) and Fe(III) produced enzymatically (goethite or lepidocrocite). Our results suggest the mineralogy and surface area of Fe(III) minerals produced under nitrate-reducing conditions affect the rate and extent of U(IV) oxidation. These results may be useful for predicting the stability of U(IV) in aquifers.

Environmental Science & Technology↗

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↗

USGS2005

A method adapting microarray technology for signature tagged mutagenesis of Dusulfovibrio dusulfuricans G20 and Shewanella oneidensis MR-1 in anaerobic sediment survival experiments

Signature-tagged mutagenesis (STM) is a powerful technique that can be used to identify genes expressed by bacteria during exposure to conditions in their natural environments. To date, there have been no reports of studies in which this approach was used to study organisms of environmental, rather than pathogenic, significance. We used a mini-Tn 10 transposon-bearing plasmid, pBSL180, that efficiently and randomly mutagenized Desulfovibrio desulfuricans G20 in addition to Shewanella oneidensis MR-1. Using these organisms as model sediment-dwelling anaerobic bacteria, we developed a new screening system, modified from former STM procedures, to identify genes that are critical for sediment survival. The screening system uses microarray technology to visualize tags from input and output pools, allowing us to identify those lost during sediment incubations. While the majority of data on survival genes identified will be presented in future papers, we report here on chemotaxis-related genes identified by our STM method in both bacteria in order to validate our method. This system may be applicable to the study of numerous environmental bacteria, allowing us to identify functions and roles of survival genes in various habitats.

Applied and Environmental Microbiology↗

USGS2005

Effect of the oxidation rate and Fe(II) state on microbial nitrate-dependent Fe(III) mineral formation

A nitrate-dependent Fe(II)-oxidizing bacterium was isolated and used to evaluate whether Fe(II) chemical form or oxidation rate had an effect on the mineralogy of biogenic Fe(III) (hydr)oxides resulting from nitrate-dependent Fe(II) oxidation. The isolate (designated FW33AN) had 99% 16S rRNA sequence similarity to Klebsiella oxytoca. FW33AN produced Fe(III) (hydr)oxides by oxidation of soluble Fe(II) [Fe(II) sol ] or FeS under nitrate-reducing conditions. Based on X-ray diffraction (XRD) analysis, Fe(III) (hydr)oxide produced by oxidation of FeS was shown to be amorphous, while oxidation of Fe(II) sol yielded goethite. The rate of Fe(II) oxidation was then manipulated by incubating various cell concentrations of FW33AN with Fe(II) sol and nitrate. Characterization of products revealed that as Fe(II) oxidation rates slowed, a stronger goethite signal was observed by XRD and a larger proportion of Fe(III) was in the crystalline fraction. Since the mineralogy of Fe(III) (hydr)oxides may control the extent of subsequent Fe(III) reduction, the variables we identify here may have an effect on the biogeochemical cycling of Fe in anoxic ecosystems.

Applied and Environmental Microbiology↗

USGS2003

A procedure for quantitation of total oxidized uranium for bioremediation studies

A procedure was developed for the quantitation of complexed U(VI) during studies on U(VI) bioremediation. These studies typically involve conversion of soluble or complexed U(VI) (oxidized) to U(IV) (the reduced form which is much less soluble). Since U(VI) freely exchanges between material adsorbed to the solid phase and the dissolved phase, uranium bioremediation experiments require a mass balance of U in both its soluble and adsorbed forms as well as in the reduced sediment bound phase. We set out to optimize a procedure for extraction and quantitation of sediment bound U(VI). Various extractant volumes to sediment ratios were tested and it was found that between 1:1 to 8:1 ratios (v/w) there was a steady increase in U(VI) recovered, but no change with further increases in v/w ratio. Various strengths of NaHCO 3 , Na-EDTA, and Na-citrate were used to evaluate complexed U(VI) recovery, while the efficiency of a single versus repeated extraction steps was compared with synthesized uranyl-phosphate and uranyl-hydroxide. Total recovery with 1 M NaHCO 3 was 95.7% and 97.9% from uranyl-phosphate and uranyl-hydroxide, respectively, compared to 80.7% and 89.9% using 450 mM NaHCO 3 . Performing the procedure once yielded an efficiency of 81.1% and 92.3% for uranyl-phosphate and uranyl-hydroxide, respectively, as compared to three times. All other extractants yielded 7.9–82.0% in both experiments.

Journal of Microbiological Methods↗

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↗

USGS2002

In-situ evidence for uranium immobilization and remobilization

The in-situ microbial reduction and immobilization of uranium was assessed as a means of preventing the migration of this element in the terrestrial subsurface. Uranium immobilization (putatively identified as reduction) and microbial respiratory activities were evaluated in the presence of exogenous electron donors and acceptors with field push−pull tests using wells installed in an anoxic aquifer contaminated with landfill leachate. Uranium(VI) amended at 1.5 μM was reduced to less than 1 nM in groundwater in less than 8 d during all field experiments. Amendments of 0.5 mM sulfate or 5 mM nitrate slowed U(VI) immobilization and allowed for the recovery of 10% and 54% of the injected element, respectively, as compared to 4% in the unamended treatment. Laboratory incubations confirmed the field tests and showed that the majority of the U(VI) immobilized was due to microbial reduction. In these tests, nitrate treatment (7.5 mM) inhibited U(VI) reduction, and nitrite was transiently produced. Further push−pull tests were performed in which either 1 or 5 mM nitrate was added with 1.0 μM U(VI) to sediments that already contained immobilized uranium. After an initial loss of the amendments, the concentration of soluble U(VI) increased and eventually exceeded the injected concentration, indicating that previously immobilized uranium was remobilized as nitrate was reduced. Laboratory experiments using heat-inactivated sediment slurries suggested that the intermediates of dissimilatory nitrate reduction (denitrification or dissimilatory nitrate reduction to ammonia), nitrite, nitrous oxide, and nitric oxide were all capable of oxidizing and mobilizing U(IV). These findings indicate that in-situ subsurface U(VI) immobilization can be expected to take place under anaerobic conditions, but the permanence of the approach can be impaired by disimilatory nitrate reduction intermediates that can mobilize previously reduced uranium.

Environmental Science & Technology↗

USGS1999

Estimation of methanogen biomass via quantitation of coenzyme M

Determination of the role of methanogenic bacteria in an anaerobic ecosystem often requires quantitation of the organisms. Because of the extreme oxygen sensitivity of these organisms and the inherent limitations of cultural techniques, an accurate biomass value is very difficult to obtain. We standardized a simple method for estimating methanogen biomass in a variety of environmental matrices. In this procedure we used the thiol biomarker coenzyme M (CoM) (2-mercaptoethanesulfonic acid), which is known to be present in all methanogenic bacteria. A high-performance liquid chromatography-based method for detecting thiols in pore water (A. Vairavamurthy and M. Mopper, Anal. Chim. Acta 78:363–370, 1990) was modified in order to quantify CoM in pure cultures, sediments, and sewage water samples. The identity of the CoM derivative was verified by using liquid chromatography-mass spectroscopy. The assay was linear for CoM amounts ranging from 2 to 2,000 pmol, and the detection limit was 2 pmol of CoM/ml of sample. CoM was not adsorbed to sediments. The methanogens tested contained an average of 19.5 nmol of CoM/mg of protein and 0.39 ± 0.07 fmol of CoM/cell. Environmental samples contained an average of 0.41 ± 0.17 fmol/cell based on most-probable-number estimates. CoM was extracted by using 1% tri-( N )-butylphosphine in isopropanol. More than 90% of the CoM was recovered from pure cultures and environmental samples. We observed no interference from sediments in the CoM recovery process, and the method could be completed aerobically within 3 h. Freezing sediment samples resulted in 46 to 83% decreases in the amounts of detectable CoM, whereas freezing had no effect on the amounts of CoM determined in pure cultures. The method described here provides a quick and relatively simple way to estimate methanogenic biomass.

Applied and Environmental Microbiology↗