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L R Krumholz

Publications and source records attributed to L R Krumholz.

At least 19 recordsLinked to original sources
PubMed2004

In situ bioreduction of technetium and uranium in a nitrate-contaminated aquifer.

The potential to stimulate an indigenous microbial community to reduce a mixture of U(VI) and Tc(VII) in the presence of high (120 mM) initial NO3- co-contamination was evaluated in a shallow unconfined aquifer using a series of single-well, push-pull tests. In the absence of added electron donor, NO3-, Tc(VII), and U(VI) reduction was not detectable. However, in the presence of added ethanol, glucose, or acetate to serve as electron donor, rapid NO3- utilization was observed. The accumulation of NO2-, the absence of detectable NH4+ accumulation, and the production of N2O during in situ acetylene-block experiments suggest that NO3- was being consumed via denitrification. Tc(VII) reduction occurred concurrently with NO3- reduction, but U(VI) reduction was not observed until two or more donor additions resulted in iron-reducing conditions, as detected by the production of Fe(II). Reoxidation/remobilization of U(IV) was also observed in tests conducted with high (approximately 120 mM) but not low (approximately 1 mM) initial NO3- concentrations and not during acetylene-block experiments conducted with high initial NO3-. These results suggest that NO3(-)-dependent microbial U(IV) oxidation may inhibit or reverse U(VI) reduction and decrease the stability of U(IV) in this environment. Changes in viable biomass, community composition, metabolic status, and respiratory state of organisms harvested from down-well microbial samplers deployed during these tests were consistent with the conclusions that electron donor additions resulted in microbial growth, the creation of anaerobic conditions, and an increase in activity of metal-reducing organisms (e.g., Geobacter). The results demonstrate that it is possible to stimulate the simultaneous bioreduction of U(VI) and Tc(VII) mixtures commonly found with NO3- co-contamination at radioactive waste sites.

Biodegradation, Environmental↗
PubMed2004

Impact of clay minerals on sulfate-reducing activity in aquifers.

Previous studies have shown that sulfate-reduction activity occurs in a heterogeneous manner throughout the terrestrial subsurface. Low-activity regions are often observed in the presence of clay minerals. Here we report that clays inhibit sulfate reduction activity in sediments and in a pure culture of Desulfovibrio vulgaris. Clay minerals including bentonite and kaolinite inhibited sulfate reduction by 70-90% in sediments. Intact clays and clay colloids or soluble components, capable of passing through a 0.2-microm filter, were also inhibitory to sulfate-reducing bacteria. Other adsorbent materials, including anion or cation exchangers and a zeolite, did not inhibit sulfate reduction in sediments, suggesting that the effect of clays was not due to their cation-exchange capacity. We observed a strong correlation between the Al2O3 content of clays and their relative ability to inhibit sulfate reduction in sediments (r2 = 0.82). This suggested that inhibition might be a direct effect of Al3+ (aq) on the bacteria. We then tested pure aluminum oxide (Al2O3) and showed it to act in a similar manner to clay. As dissolved aluminum is known to be toxic to a variety of organisms at low concentrations, our results suggest that the effects of clay on sulfate-reducing bacteria may be directly due to aluminum. Thus, our experiments provide an explanation for the lack of sulfate-reduction activity in clay-rich regions and presents a mechanism for the effect.

Aluminum Oxide↗
PubMed2003

Characterization of microbial activities and U reduction in a shallow aquifer contaminated by uranium mill tailings.

A characterization of the Shiprock, NM, uranium mill tailing site focused on the geochemical and microbiological factors governing in-situ uranium-redox reactions. Groundwater and aqueous extracts of sediment samples contained a wide concentration range of sulfate, nitrate, and U(VI) with median values of 21.2 mM, 16.1 micro M, and 2.7 micro M, respectively. Iron(III) was not detected in groundwater, but a median value of 0.3 mM in sediment extracts was measured. Bacterial diversity down gradient from the disposal pile reflected the predominant geochemistry with relatively high numbers of sulfate- and nitrate-reducing microorganisms, and smaller numbers of acetogenic, methanogenic, nitrate-dependent Fe(II)-oxidizing, Fe(III)-reducing, and sulfide-oxidizing bacteria. In aquifer slurry incubations, nitrate reduction was always preferred and had a negative impact on sulfate-, Fe(III)-, and U-reduction rates. We also found that sulfate-reduction rates decreased sharply in the presence of clay, while Fe(III)-reduction increased with no clear impact on U reduction. In the absence of clay, iron and sulfate reduction correlated with concentrations of Fe(III) and sulfate, respectively. Rates of U(VI) loss did not correlate with the concentration of any electron acceptor. With the exception of Fe(III), electron donor amendment was largely unsuccessful in stimulating electron acceptor loss over a 2-week incubation period, suggesting that endogenous forms of organic matter were sufficient to support microbial activity. Our findings suggest that efforts to accelerate biological U reduction should initially focus on stimulating nitrate removal.

Bacteria↗
PubMed2003

Indigenous and contaminant microbes in ultradeep mines.

Rock, air and service water samples were collected for microbial analyses from 3.2 kilometres depth in a working Au mine in the Witwatersrand basin, South Africa. The approximately metre-wide mined zone was comprised of a carbonaceous, quartz, sulphide, uraninite and Au bearing layer, called the Carbon Leader, sandwiched by quartzite and conglomerate. The microbial community in the service water was dominated by mesophilic aerobic and anaerobic, alpha-, beta- and gamma-Proteobacteria with a total biomass concentration approximately 10(4) cells ml(-1), whereas, that of the mine air was dominated by members of the Chlorobi and Bacteroidetes groups and a fungal component. The microorganisms in the Carbon Leader were predominantly mesophilic, aerobic heterotrophic, nitrate reducing and methylotrophic, beta- and gamma-Proteobacteria that were more closely related to service water microorganisms than to air microbes. Rhodamine WT dye and fluorescent microspheres employed as contaminant tracers, however, indicated that service water contamination of most of the rock samples was < 0.01% during acquisition. The microbial contaminants most likely originated from the service water, infiltrated the low permeability rock through and accumulated within mining-induced fractures where they survived for several days before being mined. Combined PLFA and terminal restriction fragment length profile (T-RFLP) analyses suggest that the maximum concentration of indigenous microorganisms in the Carbon Leader was < 10(2) cells g(-1). PLFA, 35S autoradiography and enrichments suggest that the adjacent quartzite was less contaminated and contained approximately 10(3) cells gram(-1) of thermophilic, sulphate reducing bacteria, SRB, some of which are delta-Proteobacteria. Pore water and rock geochemical analyses suggest that these SRB's may have been sustained by sulphate diffusing from the adjacent U-rich, Carbon Leader where it was formed by radiolysis of sulphide.

Air Microbiology↗
PubMed2003

Importance of Gram-positive naphthalene-degrading bacteria in oil-contaminated tropical marine sediments.

AIMS: The aim of this study was to isolate, characterize and evaluate the importance of naphthalene-degrading bacterial strains from oil-contaminated tropical marine sediments. METHODS AND RESULTS: Three Gram-positive naphthalene-degrading bacteria were isolated from oil-contaminated tropical intertidal marine sediments by direct isolation or enrichment using naphthalene as the sole source of carbon and energy. Bacillus naphthovorans strain MN-003 can also grow on benzene, toluene, xylene and diesel fuel while Micrococcus sp. str. MN-006 can also grow on benzene. Staphylococcus sp. str. MN-005 can only degrade naphthalene and was not able to use the other aromatic hydrocarbons tested. Strain MN-003 possessed the highest maximal specific growth rate with naphthalene as sole carbon source. An enrichment culture fed with naphthalene as sole carbon source exhibited a significant increase in the relative abundances of the three isolates after 21 days of incubation. The three isolates constituted greater than 69% of the culturable naphthalene-degrading microbial community. Strain MN-003 outcompeted and dominated the other two isolates in competition studies involving batch cultures inoculated with equal cell densities of the three isolates and incubated with between 1 and 10 mg l-1 of naphthalene. CONCLUSIONS: Three Gram-positive naphthalene-degrading bacteria were successfully isolated from oil-contaminated tropical marine sediments. Gram-positive bacteria might play an important role in naphthalene degradation in the highly variable environment of oil-contaminated tropical intertidal marine sediments. Among the three isolates, strain MN-003 has the highest maximal specific growth rate when grown on naphthalene, and outgrew the other two isolates in competition experiments. SIGNIFICANCE AND IMPACT OF THE STUDY: This research will aid in the development of bioremediation schemes for oil-contaminated marine environments. Strain MN-003 could potentially be exploited in such schemes.

Bacillus↗
PubMed1999

Importance of Xanthobacter autotrophicus in toluene biodegradation within a contaminated stream.

Toluene-degrading strains T101 and T102 were isolated from rock surface biomass in a toluene-contaminated freshwater stream. These organisms were present at a density of 5.5 x 10(6) cells/g of rock surface biomass. Both are aerobic, rod-shaped, Gram-negative, non-motile, catalase-positive, oxidase-positive, with yellow pigments, and can grow on benzene. Phylogenetic analyses show that strains T101 and T102 have 16S rDNA sequences identical to Xanthobacter autotrophicus. Fatty acid analyses indicate that they are different strains of the same species Xanthobacter autotrophicus, and that they have high levels of cis-11-octadecenoic acid and cis-9-hexadecenoic acid; 3-hydroxyhexadecanoic acid is the major hydroxy fatty acid present. Strains T101 and T102 had maximal velocities (Vmax) for toluene biodegradation of 3.8 +/- 0.5 and 28.3 +/- 2.2 mumoles toluene/mgprotein-hr, and half-saturation constants (Ks) of 0.8 +/- 0.5 and 11.5 +/- 2.4 microM, respectively. Strain T102 has a higher capacity than strain T101 to degrade toluene, and kinetic calculations suggest that strain T102 may be a major contributor to toluene biodegradation in the stream.

Biodegradation, Environmental↗
PubMed1999

Estimation of methanogen biomass by 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.

Biomass↗
PubMed1999

Characterization of two subsurface H2-utilizing bacteria, Desulfomicrobium hypogeium sp. nov. and Acetobacterium psammolithicum sp. nov., and their ecological roles.

We examined the relative roles of acetogenic and sulfate-reducing bacteria in H2 consumption in a previously characterized subsurface sandstone ecosystem. Enrichment cultures originally inoculated with ground sandstone material obtained from a Cretaceous formation in central New Mexico were grown with hydrogen in a mineral medium supplemented with 0.02% yeast extract. Sulfate reduction and acetogenesis occurred in these cultures, and the two most abundant organisms carrying out the reactions were isolated. Based on 16S rRNA analysis data and on substrate utilization patterns, these organisms were named Desulfomicrobium hypogeium sp. nov. and Acetobacterium psammolithicum sp. nov. The steady-state H2 concentrations measured in sandstone-sediment slurries (threshold concentration, 5 nM), in pure cultures of sulfate reducers (threshold concentration, 2 nM), and in pure cultures of acetogens (threshold concentrations 195 to 414 nM) suggest that sulfate reduction is the dominant terminal electron-accepting process in the ecosystem examined. In an experiment in which direct competition for H2 between D. hypogeium and A. psammolithicum was examined, sulfate reduction was the dominant process.

DNA, Bacterial↗
PubMed1998

Two new Mycobacterium strains and their role in toluene degradation in a contaminated stream.

Two toluene-degrading strains, T103 and T104, were isolated from rock surface biomass in a freshwater stream contaminated with toluene. The strains exhibit different capacities for degradation of toluene and other aromatic compounds and have characteristics of the genus Mycobacterium. Both are aerobic, rod-shaped, gram-positive, nonmotile, and acid-alcohol fast and produce yellow pigments. They have mainly straight-chain saturated and monounsaturated fatty acids with 10 to 20 carbon atoms and large amounts of tuberculostearic acid that are typical of mycobacteria. Fatty acid analyses indicate that T103 and T104 are different mycobacterial strains that are related at the subspecies level. Their identical 16S rDNA sequences are most similar to Mycobacterium aurum and Mycobacterium komossense, and they constitute a new species of fast-growing mycobacteria. Ecological studies reveal that toluene contamination has enriched for toluene-degrading bacteria in the epilithic microbial community. Strains T103 and T104 play only a small role in toluene degradation in the stream, although they are present in the habitat and can degrade toluene. Other microorganisms are consequently implicated in the biodegradation.

Biodegradation, Environmental↗
PubMed1997

Anaerobic aquifer transformations of 2,4-dinitrophenol under different terminal electron accepting conditions.

We evaluated the susceptibility of 2,4-dinitrophenol (2,4-DNP) and 2,4-diaminophenol to anaerobic biodegradation in aquifer slurries. Aquifer microorganisms depleted 2,4-DNP at rates of 25, 9 and 0.4 microM/day under methanogenic, sulfate-reducing and nitrate-reducing conditions, respectively. Rates of abiotic, 2,4-DNP loss in autoclaved control incubations were 7.2, 6.2 and 0.95 microM/day respectively. Abiotic, 2,4-DNP reduction was especially important as the first step in its transformation. 2-Amino-4-nitrophenol was produced by this process, but this compound was further metabolized in methanogenic and sulfate-reducing aquifer slurries. This partially reduced compound persisted in autoclaved controls and in the nitrate-reducing aquifer slurries. Aquifer slurries incubated with either 2,4-DNP or 2,4-diaminophenol produced methane when incubated with no other electron acceptor suggesting that mineralization had occurred under these conditions. In parallel experiments, aquifer slurries amended with 2,6-dinitrophenol or picric acid did not produce methane at levels above the substrate unamended controls.

Journal Article↗
PubMed1997

A rapid and simple method for estimating sulfate reduction activity and quantifying inorganic sulfides.

Volume, 63, no. 4, p. 1627-1630. After publication of this article, it was brought to the attention of the authors that an earlier paper, similar in both methodology and salient findings to ours, was published by Y. P. Hsieh and C. H. Yang. Both papers describe a diffusion method for the extraction and recovery of reduced inorganic sulfides from sediment samples placed in sealed reaction vessels. Our paper describes the application of the method to the measurement of sulfate reduction rates. The earlier work contains important information, but unfortunately, the existence of the work was realized only after publication of our paper. We regret this omission, and the following reference should have been cited in our article. 13a.Hsieh, Y. P., and C. H. Yang. 1989. Diffusion methods for the determination of reduced inorganic sulfur species in sediments. Limnol. Oceanogr. 34: 1126-1130. [This corrects the article on p. 1627 in vol. 63.].

Journal Article↗
PubMed1997

A rapid and simple method for estimating sulfate reduction activity and quantifying inorganic sulfides.

A simplified passive extraction procedure for quantifying reduced inorganic sulfur compounds from sediments and water is presented. This method may also be used for the estimation of sulfate reduction rates. Efficient extraction of FeS, FeS(inf2), and S(sup2-) was obtained with this procedure; however, the efficiency for S(sup0) depended on the form that was tested. Passive extraction can be used with samples containing up to 20 mg of reduced sulfur. We demonstrated the utility of this technique in a determination of both sulfate reduction rates and reduced inorganic sulfur pools in marine and freshwater sediments. A side-by-side comparison of the passive extraction method with the established single-step distillation technique yielded comparable results with a fraction of the effort.

Journal Article↗
PubMed1996

A freshwater anaerobe coupling acetate oxidation to tetrachloroethylene dehalogenation.

Strain TT4B has been isolated from anaerobic sediments known to be contaminated with a variety of organic solvents. It is a gram-negative, rod-shaped bacterium and grew anaerobically with acetate as the electron donor and tetrachloroethylene as the electron acceptor in a mineral medium. cis-Dichloroethylene was the halogenated product. This strain did not grow fermentatively and used only acetate or pyruvate as electron donors. Tetrachloroethylene and trichloroethylene were used as electron acceptors, as were ferric nitriloacetate and fumarate. Nitrogen and sulfur oxyanions were not able to substitute as the electron acceptor for this organism. Modest growth occurred in a two-phase system with 1 ml of hexadecane containing 50 to 200 mM tetrachloroethylene (aqueous concentrations, 25 to 100 microM) and 10 ml of anaerobic mineral solution with Na2S as the reducing agent. Growth was completely inhibited at tetrachloroethylene levels above 100 microM.

Acetic Acid↗
PubMed1993

Proposal of Quinella ovalis gen. nov., sp. nov., based on phylogenetic analysis.

Quin's oval is a relatively large bacterium often seen in the rumens of sheep fed diets containing some readily fermented carbohydrates. It has not been obtained in axenic cultures, but a number of its features have been determined by various methods, such as studying cell suspensions purified from rumen fluid by differential centrifugation. We obtained similarly purified suspensions from a sheep fed a diet containing a large amount of molasses. Nearly complete 16S rRNA sequence analysis of these cells as well as cells as Selenomonas ruminantium subsp. ruminantium GA192 (ATCC 12561; type strain) and S. ruminantium subsp. lactilytica HD4 (ATCC 27209) was done. These sequences were compared with those of other bacteria. Evolutionary distance estimates indicated that Quin's oval was most closely related to the Selenomonas-Megasphaera-Sporomusa group in the gram-positive phylum but that it belongs in a new genus. We propose the name Quinella ovalis gen. nov., sp. nov., with its description based on previously known features.

Animals↗
PubMed1992

Characterization of the genes coding for the F1F0 subunits of the sodium dependent ATPase of Propionigenium modestum.

The DNA coding for the eight structural genes and uncI of the sodium dependent ATPase of Propionigenium modestum has been cloned and sequenced. Based on sequence homology, the genes were determined to appear in the order uncBEFHAGDC as in several other bacterial species. Minicell experiments revealed that plasmids containing the P. modestum DNA expressed those ATPase polypeptides in Escherichia coli. These were very similar in molecular mass to those obtained from the purified ATPase of P. modestum. No membrane-bound ATPase activity was observed in E. coli unc deletion strains containing the P. modestum ATPase genes. Amino acid alignments which were done with the Fo subunits revealed only a few conservative changes in the highly conserved regions of the polypeptides.

Adenosine Triphosphatases↗
PubMed1991

Degradation of cellulose and forage fiber fractions by ruminal cellulolytic bacteria alone and in coculture with phenolic monomer-degrading bacteria.

We hypothesized that bacterial species capable of metabolizing phenolic monomers may act as catalysts for forage fiber breakdown by increasing microbial access to cell wall polysaccharides. Ruminal cellulolytic bacteria alone and in combination with phenolic-degrading bacteria were examined for differences in their ability to degrade fiber fractions of alfalfa or bromegrass. Electron micrographs of Fibrobacter succinogenes S85 cultured in combination with the ruminal phenolic-degrading organisms Eubacterium oxidoreducens G41 and Syntrophococcus sucromutans S195 indicated that bromegrass was degraded more extensively by the triculture than by the monoculture. The sequential detergent system was used to quantify the digestibility of fiber components from alfalfa and bromegrass. F. succinogenes incubated with the two phenolic-degrading organisms did not degrade more cell wall material than did F. succinogenes alone. However, with two other ruminal cellulolytic organisms, Clostridium longisporum B6405 and Ruminococcus albus B6403, greater (P less than .05, P less than .10, respectively) amounts of hemicellulose were degraded (72 h in vitro fermentation) from whole-plant alfalfa when E. oxidoreducens and S. sucromutants were combined with the cellulolytic species than when their monocultures were tested. Similar increases were not observed using a NDF preparation of alfalfa as the substrate. Based on these in vitro experiments, it does not seem that E. oxidoreducens and S. sucromutans play an important role in improving forage fiber degradation by cellulolytic ruminal bacteria.

Animals↗