USGS Science⌕ Search

SEARCH · USGS Science

Results for “Microbiology”

Search indexed USGS publications on groundwater, aquifers, geologic maps, mineral resources and earthquakes. Explore source records by subject and place.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 433 records · Page 24Linked to original sources
USGS1991

Electron transport in the dissimilatory iron reducer, GS-15

Mechanisms for electron transport to Fe(III) were investigated in GS-15, a novel anaerobic microorganism which can obtain energy for growth hy coupling the complete oxidation of organic acids or aromatic compounds to the reduction of Fe(III) to Fe(II). The results indicate that Fe(III) reduction proceeds through a type b cytochrome and a membrane-bound Fe(III) reductase which is distinct from the nitrate reductase.

Applied and Environmental Microbiology↗
USGS1991

Inactivation of infectious hematopoietic necrosis virus by low levels of iodine

The fish rhabdovirus infectious hematopoietic necrosis virus (IHNV) was rapidly inactivated by extremely low concentrations of iodine in water. A 99.9% virus reduction was obtained in 7.5 s when virus (10 5 PFU/ml) and iodine (0.1 mg/liter, final concentration) were combined in distilled-deionized or hatchery water. Iodine efficacy decreased at pHs greater than 7.5 or when proteinaceous material was added to the water. Bovine serum albumin blocked iodine inactivation of the virus more effectively than did equal concentrations of fetal bovine serum or river sediment. Sodium thiosulfate effectively neutralized free iodine. Powder, iodophor, and crystalline iodine solutions inactivated IHNV equally. Iodine rapidly inactivated IHNV isolates representing each of the five electropherotypes. Under the conditions used in this study, inactivation was not affected by temperature, salinity, or water hardness. When Dworshak National Fish Hatchery water was continuously treated to provide a free iodine concentration of 0.14 mg/liter, a 7.5-s exposure to iodine was sufficient to inactivate 99.9% of the IHNV. Iodine added to water that contained IHNV prevented infection of rainbow trout ( Oncorhynchus mykiss ) fry. These results suggest that the waterborne route of IHNV transmission can be blocked by adding low iodine concentrations to the water supplies of hatcheries.

Applied and Environmental Microbiology↗
USGS1992

Nitrate is a preferred electron acceptor for growth of freshwater selenate-respiring bacteria

An anaerobic, freshwater enrichment grew with either nitrate or selenate as an electron acceptor. With both ions present, nitrate reduction preceded selenate reduction. An isolate from the enrichment grew on either ion, but the presence of nitrate precluded the reduction of selenate. Stock cultures of denitrifiers grew anaerobically on nitrate but not on selenate.

Applied and Environmental Microbiology↗
USGS1993

Dissimilatory Fe(III) reduction by the marine microorganism Desulfuromonas acetoxidans

The ability of the marine microorganism Desulfuromonas acetoxidans to reduce Fe(III) was investigated because of its close phylogenetic relationship with the freshwater dissimilatory Fe(III) reducer Geobacter metallireducens. Washed cell suspensions of the type strain of D. acetoxidans reduced soluble Fe(III)-citrate and Fe(III) complexed with nitriloacetic acid. The c -type cytochrome(s) of D. acetoxidans was oxidized by Fe(III)-citrate and Mn(IV)-oxalate, as well as by two electron acceptors known to support growth, colloidal sulfur and malate. D. acetoxidans grew in defined anoxic, bicarbonate-buffered medium with acetate as the sole electron donor and poorly crystalline Fe(III) or Mn(IV) as the sole electron acceptor. Magnetite (Fe 3 O 4 ) and siderite (FeCO 3 ) were the major end products of Fe(III) reduction, whereas rhodochrosite (MnCO 3 ) was the end product of Mn(IV) reduction. Ethanol, propanol, pyruvate, and butanol also served as electron donors for Fe(III) reduction. In contrast to D. acetoxidans, G. metallireducens could only grow in freshwater medium and it did not conserve energy to support growth from colloidal S 0 reduction. D. acetoxidans is the first marine microorganism shown to conserve energy to support growth by coupling the complete oxidation of organic compounds to the reduction of Fe(III) or Mn(IV). Thus, D. acetoxidans provides a model enzymatic mechanism for Fe(III) or Mn(IV) oxidation of organic compounds in marine and estuarine sediments. These findings demonstrate that 16S rRNA phylogenetic analyses can suggest previously unrecognized metabolic capabilities of microorganisms.

Applied and Environmental Microbiology↗
USGS1993

Selective inhibition of ammonium oxidation and nitrification-linked N2O formation by methyl fluoride and dimethyl ether

Methyl fluoride (CH 3 F) and dimethyl ether (DME) inhibited nitrification in washed-cell suspensions of Nitrosomonas europaea and in a variety of oxygenated soils and sediments. Headspace additions of CH 3 F (10% [vol/vol]) and DME (25% [vol/vol]) fully inhibited NO 2 - and N 2 O production from NH 4 + in incubations of N. europaea , while lower concentrations of these gases resulted in partial inhibition. Oxidation of hydroxylamine (NH 2 OH) by N. europaea and oxidation of NO 2 - by a Nitrobacter sp. were unaffected by CH 3 F or DME. In nitrifying soils, CH 3 F and DME inhibited N 2 O production. In field experiments with surface flux chambers and intact cores, CH 3 F reduced the release of N 2 O from soils to the atmosphere by 20- to 30-fold. Inhibition by CH 3 F also resulted in decreased NO 3 - + NO 2 - levels and increased NH 4 + levels in soils. CH 3 F did not affect patterns of dissimilatory nitrate reduction to ammonia in cell suspensions of a nitrate-respiring bacterium, nor did it affect N 2 O metabolism in denitrifying soils. CH 3 F and DME will be useful in discriminating N 2 O production via nitrification and denitrification when both processes occur and in decoupling these processes by blocking NO 2 - and NO 3 - production.

Applied and Environmental Microbiology↗
USGS1993

Degradation of trichloroethylene by Pseudomonas cepacia G4 and the constitutive mutant strain G4 5223 PR1 in aquifer microcosms

Pseudomonas cepacia G4 degrades trichloroethylene (TCE) via a degradation pathway for aromatic compounds which is induced by substrates such as phenol and tryptophan. P. cepacia G4 5223 PR1 (PR1) is a Tn5 insertion mutant which constitutively expresses the toluene ortho -monooxygenase responsible for TCE degradation. In groundwater microcosms, phenol-induced strain G4 and noninduced strain PR1 degraded TCE (20 and 50 μM) to nondetectable levels (< 0.1 μM) within 24 h at densities of 10 8 cells per ml; at lower densities, degradation of TCE was not observed after 48 h. In aquifer sediment microcosms, TCE was reduced from 60 to < 0.1 μM within 24 h at 5 x 10 8 PR1 organisms per g (wet weight) of sediment and from 60 to 26 μM over a period of 10 weeks at 5 x 10 7 PR1 organisms per g. Viable G4 and PR1 cells decreased from approximately 10 7 to 10 4 per g over the 10-week period.

Applied and Environmental Microbiology↗
USGS1994

Spatial variability in biodegradation rates as evidenced by methane production from an aquifer

Accurate predictions of carbon and energy cycling rates in the environment depend on sampling frequencies and on the spatial variability associated with biological activities. We examined the variability associated with anaerobic biodegradation rates at two sites in an alluvial sand aquifer polluted by municipal landfill leachate. In situ rates of methane production were measured for almost a year, using anaerobic wells installed at two sites. Methane production ranged from 0 to 560 μmol · m -2 · day -1 at one site (A), while a range of 0 to 120,000 μmol · m -2 · day -1 was measured at site B. The mean and standard deviations associated with methane production at site A were 17 and 57 μmol · m -2 · day -1 , respectively. The comparable summary statistics for site B were 2,000 and 9,900 μmol · m -2 · day -1 . The coefficients of variation at sites A and B were 340 and 490%, respectively. Despite these differences, the two sites had similar seasonal trends, with the maximal rate of methane production occurring in summer. However, the relative variability associated with the seasonal rates changed very little. Our results suggest that (i) two spatially distinct sites exist in the aquifer, (ii) methanogenesis is a highly variable process, (iii) the coefficient of variation varied little with the rate of methane production, and (iv) in situ anaerobic biodegradation rates are lognormally distributed.

Applied and Environmental Microbiology↗
USGS1994

Degradation of methyl bromide by methanotrophic bacteria in cell suspensions and soils

Cell suspensions of Methylococcus capsulatus mineralized methyl bromide (MeBr), as evidenced by its removal from the gas phase, the quantitative recovery of Br - in the spent medium, and the production of 14 CO 2 from [ 14 C]MeBr. Methyl fluoride (MeF) inhibited oxidation of methane as well as that of [ 14 C]MeBr. The rate of MeBr consumption by cells varied inversely with the supply of methane, which suggested a competitive relationship between these two substrates. However, MeBr did not support growth of the methanotroph. In soils exposed to high levels (10,000 ppm) of MeBr, methane oxidation was completely inhibited. At this concentration, MeBr removal rates were equivalent in killed and live controls, which indicated a chemical rather than biological removal reaction. At lower concentrations (1,000 ppm) of MeBr, methanotrophs were active and MeBr consumption rates were 10-fold higher in live controls than in killed controls. Soils exposed to trace levels (10 ppm) of MeBr demonstrated complete consumption within 5 h of incubation, while controls inhibited with MeF or incubated without O 2 had 50% lower removal rates. Aerobic soils oxidized [ 14 C]MeBr to 14 CO 2 , and MeF inhibited oxidation by 72%. Field experiments demonstrated slightly lower MeBr removal rates in chambers containing MeF than in chambers lacking MeF. Collectively, these results show that soil methanotrophic bacteria, as well as other microbes, can degrade MeBr present in the environment.

Applied and Environmental Microbiology↗
USGS1994

Use of molecular techniques to evaluate the survival of a microorganism injected into an aquifer

A PCR primer set and an internal probe that are specific for Pseudomonas sp. strain B13, a 3-chlorobenzoate-metabolizing strain, were developed. Using this primer set and probe, we were able to detect Pseudomonas sp. strain B13 DNA sequences in DNA extracted from aquifer samples 14.5 months after Pseudomonas sp. strain B13 had been injected into a sand and gravel aquifer. This primer set and probe were also used to analyze isolates from 3-chlorobenzoate enrichments of the aquifer samples by Southern blot analysis. Hybridization of Southern blots with the Pseudomonas sp. strain B13-specific probe and a catabolic probe in conjunction with restriction fragment length polymorphism (RFLP) analysis of ribosome genes was used to determine that viable Pseudomonas sp. strain B13 persisted in this environment. We isolated a new 3-chlorobenzoate-degrading strain from one of these enrichment cultures. The B13-specific probe does not hybridize to DNA from this isolate. The new strain could be the result of gene exchange between Pseudomonas sp. strain B13 and an indigenous bacterium. This speculation is based on an RFLP pattern of ribosome genes that differs from that of Pseudomonas sp. strain B13, the fact that identically sized restriction fragments hybridized to the catabolic gene probe, and the absence of any enrichable 3-chlorobenzoate-degrading strains in the aquifer prior to inoculation.

Massachusetts↗
USGS1994

Autotrophic, hydrogen-oxidizing, denitrifying bacteria in groundwater, potential agents for bioremediation of nitrate contamination

Addition of hydrogen or formate significantly enhanced the rate of consumption of nitrate in slurried core samples obtained from an active zone of denitrification in a nitrate-contaminated sand and gravel aquifer (Cape Cod, Mass.). Hydrogen uptake by the core material was immediate and rapid, with an apparent K m of 0.45 to 0.60 μM and a V max of 18.7 nmol cm -3 h -1 at 30°C. Nine strains of hydrogen-oxidizing denitrifying bacteria were subsequently isolated from the aquifer. Eight of the strains grew autotrophically on hydrogen with either oxygen or nitrate as the electron acceptor. One strain grew mixotrophically. All of the isolates were capable of heterotrophic growth, but none were similar to Paracoccus denitrificans , a well-characterized hydrogen-oxidizing denitrifier. The kinetics for hydrogen uptake during denitrification were determined for each isolate with substrate depletion progress curves; the K m s ranged from 0.30 to 3.32 μM, with V max s of 1.85 to 13.29 fmol cell -1 h -1 . Because these organisms appear to be common constituents of the in situ population of the aquifer, produce innocuous end products, and could be manipulated to sequentially consume oxygen and then nitrate when both were present, these results suggest that these organisms may have significant potential for in situ bioremediation of nitrate contamination in groundwater.

Massachusetts↗
USGS1994

Microbial transformation of nitroaromatics in surface soils and aquifer materials

Microorganisms indigenous to surface soils and aquifer materials collected at a munitions-contaminated site transformed 2,4,6-trinitrotoluene (TNT), 2,4-dinitrotoluene (2,4-DNT), and 2,6-dinitrotoluene (2,6-DNT) to amino-nitro intermediates within 20 to 70 days. Carbon mineralization studies with both unlabeled (TNT, 2,4-DNT, and 2,6-DNT) and radiolabeled ([ 14 C]TNT) substrates indicated that a significant fraction of these source compounds was degraded to CO 2 .

Missouri↗
USGS1994

Accuracy, reproducibility, and interpretation of fatty acid methyl ester profiles of model bacterial communities

We determined the accuracy and reproducibility of whole-community fatty acid methyl ester (FAME) analysis with two model bacterial communities differing in composition by using the Microbial ID, Inc. (MIDI), system. The biomass, taxonomic structure, and expected MIDI-FAME profiles under a variety of environmental conditions were known for these model communities a priori. Not all members of each community could be detected in the composite profile because of lack of fatty acid 'signatures' in some isolates or because of variations (approximately fivefold) in fatty acid yield across taxa. MIDI- FAME profiles of replicate subsamples of a given community were similar in terms of fatty acid yield per unit of community dry weight and relative proportions of specific fatty acids. Principal-components analysis (PCA) of MIDI-FAME profiles resulted in a clear separation of the two different communities and a clustering of replicates of each community from two separate experiments on the first PCA axis. The first PCA axis accounted for 57.1% of the variance in the data and was correlated with fatty acids that varied significantly between communities and reflected the underlying community taxonomic structure. On the basis of our data, community fatty acid profiles can be used to assess the relative similarities and differences of microbial communities that differ in taxonomic composition. However, detailed interpretation of community fatty acid profiles in terms of biomass or community taxonomic composition must be viewed with caution until our knowledge of the quantitative and qualitative distribution of fatty acids over a wide variety of taxa and the effects of growth conditions on fatty acid profiles is more extensive.

Applied and Environmental Microbiology↗
USGS1994

Isolation, growth, and metabolism of an obligately anaerobic, selenate- respiring bacterium, strain SES-3

A gram-negative, strictly anaerobic, motile vibrio was isolated from a selenate-respiring enrichment culture. The isolate, designated strain SES-3, grew by coupling the oxidation of lactate to acetate plus CO 2 with the concomitant reduction of selenate to selenite or of nitrate to ammonium. No growth was observed on sulfate or selenite, but cell suspensions readily reduced selenite to elemental selenium (Se 0 ). Hence, SES-3 can carry out a complete reduction of selenate to Se 0 . Washed cell suspensions of selenate-grown cells did not reduce nitrate, and nitrate-grown cells did not reduce selenate, indicating that these reductions are achieved by separate inducible enzyme systems. However, both nitrate-grown and selenate-grown cells have a constitutive ability to reduce selenite or nitrite. The oxidation of [ 14 C]lactate to 14 CO 2 coupled to the reduction of selenate or nitrate by cell suspensions was inhibited by CCCP (carbonyl cyanide m -chlorophenylhydrazone), cyanide, and azide. High concentrations of selenite (5 mM) were readily reduced to Se 0 by selenate-grown cells, but selenite appeared to block the synthesis of pyruvate dehydrogenase. Tracer experiments with [ 75 Se]selenite indicated that cell suspensions could achieve a rapid and quantitative reduction of selenite to Se 0 . This reduction was totally inhibited by sulfite, partially inhibited by selenate or nitrite, but unaffected by sulfate or nitrate. Cell suspensions could reduce thiosulfate, but not sulfite, to sulfide. These results suggest that reduction of selenite to Se 0 may proceed, in part, by some of the components of a dissimilatory system for sulfur oxyanions.

Nevada↗
USGS1995

Transport behavior of groundwater protozoa and protozoan-sized microspheres in sandy aquifer sediments

Transport behaviors of unidentified flagellated protozoa (flagellates) and flagellate-sized carboxylated microspheres in sandy, organically contaminated aquifer sediments were investigated in a small-scale (1 to 4-m travel distance) natural-gradient tracer test on Cape Cod and in flow-through columns packed with sieved (0.5-to 1.0-mm grain size) aquifer sediments. The minute (average in situ cell size, 2 to 3 μ m) flagellates, which are relatively abundant in the Cape Cod aquifer, were isolated from core samples, grown in a grass extract medium, labeled with hydroethidine (a vital eukaryotic stain), and coinjected into aquifer sediments along with bromide, a conservative tracer. The 2- μ m flagellates appeared to be near the optimal size for transport, judging from flowthrough column experiments involving a polydispersed (0.7 to 6.2 μ m in diameter) suspension of carboxylated microspheres. However, immobilization within the aquifer sediments accounted for a log unit reduction over the first meter of travel compared with a log unit reduction over the first 10 m of travel for indigenous, free-living groundwater bacteria in earlier tests. High rates of flagellate immobilization in the presence of aquifer sediments also was observed in the laboratory. However, immobilization rates for the laboratory-grown flagellates (initially 4 to 5 μ m) injected into the aquifer were not constant and decreased noticeably with increasing time and distance of travel. The decrease in propensity for grain surfaces was accompanied by a decrease in cell size, as the flagellates presumably readapted to aquifer conditions. Retardation and apparent dispersion were generally at least twofold greater than those observed earlier for indigenous groundwater bacteria but were much closer to those observed for highly surface active carboxylated latex microspheres. Field and laboratory results suggest that 2- μ m carboxylated microspheres may be useful as analogs in investigating several abiotic aspects of flagellate transport behavior in groundwater.

Massachusetts↗
USGS1995

Growth of strain SES-3 with arsenate and other diverse electron acceptors

The selenate-respiring bacterial strain SES-3 was able to use a variety of inorganic electron acceptors to sustain growth. SES-3 grew with the reduction of arsenate to arsenite, Fe(III) to Fe(II), or thiosulfate to sulfide. It also grew in medium in which elemental sulfur, Mn(IV), nitrite, trimethylamine N -oxide, or fumarate was provided as an electron acceptor. Growth on oxygen was microaerophilic. There was no growth with arsenite or chromate. Washed suspensions of cells grown on selenate or nitrate had a constitutive ability to reduce arsenate but were unable to reduce arsenite. These results suggest that strain SES-3 may occupy a niche as an environmental opportunist by being able to take advantage of a diversity of electron acceptors.

Applied and Environmental Microbiology↗
USGS1995

Analysis of factors affecting the accuracy, reproducibility, and interpretation of microbial community carbon source utilization patterns

We determined factors that affect responses of bacterial isolates and model bacterial communities to the 95 carbon substrates in Biolog microliter plates. For isolates and communities of three to six bacterial strains, substrate oxidation rates were typically nonlinear and were delayed by dilution of the inoculum. When inoculum density was controlled, patterns of positive and negative responses exhibited by microbial communities to each of the carbon sources were reproducible. Rates and extents of substrate oxidation by the communities were also reproducible but were not simply the sum of those exhibited by community members when tested separately. Replicates of the same model community clustered when analyzed by principal- components analysis (PCA), and model communities with different compositions were clearly separated un the first PCA axis, which accounted for >60% of the dataset variation. PCA discrimination among different model communities depended on the extent to which specific substrates were oxidized. However, the substrates interpreted by PCA to be most significant in distinguishing the communities changed with reading time, reflecting the nonlinearity of substrate oxidation rates. Although whole-community substrate utilization profiles were reproducible signatures for a given community, the extent of oxidation of specific substrates and the numbers or activities of microorganisms using those substrates in a given community were not correlated. Replicate soil samples varied significantly in the rate and extent of oxidation of seven tested substrates, suggesting microscale heterogeneity in composition of the soil microbial community.

Michigan↗
USGS1995

Fe(III) and S0 reduction by Pelobacter carbinolicus

There is a close phylogenetic relationship between Pelobacter species and members of the genera Desulfuromonas and Geobacter , and yet there has been a perplexing lack of physiological similarities. Pelobacter species have been considered to have a fermentative metabolism. In contrast, Desulfuromonas and Geobacter species have a respiratory metabolism with Fe(III) serving as the common terminal electron acceptor in all species. However, the ability of Pelobacter species to reduce Fe(III) had not been previously evaluated. When a culture of Pelobacter carbinolicus that had grown by fermentation of 2,3- butanediol was inoculated into the same medium supplemented with Fe(III), the Fe(III) was reduced. There was less accumulation of ethanol and more production of acetate in the presence of Fe(III). P. carbinolicus grew with ethanol as the sole electron donor and Fe(III) as the sole electron acceptor. Ethanol was metabolized to acetate. Growth was also possible on Fe(III) with the oxidation of propanol to propionate or butanol to butyrate if acetate was provided as a carbon source. P. carbinolicus appears capable of conserving energy to support growth from Fe(III) respiration as it also grew with H 2 or formate as the electron donor and Fe(III) as the electron acceptor. Once adapted to Fe(III) reduction, P. carbinolicus could also grow on ethanol or H 2 with S 0 as the electron acceptor. P. carbinolicus did not contain detectable concentrations of the c -type cytochromes that previous studies have suggested are involved in electron transport to Fe(III) in other organisms that conserve energy to support growth from Fe(III) reduction. These results demonstrate that P. carbinolicus may survive in some sediments as an Fe(III) or S 0 reducer rather than growing fermentatively on rare substrates or syntrophically as an ethanol-oxidizing acetogen. These studies also suggest that the ability to use Fe(III) as a terminal electron acceptor may be an important unifying feature of the Geobacter-Desulfuromonas- Pelobacter branch of the delta Proteobacteria .

Applied and Environmental Microbiology↗
USGS1995

Methylmercury oxidative degradation potentials in contaminated and pristine sediments of the Carson River, Nevada

Sediments from mercury-contaminated and uncontaminated reaches of the Carson River, Nevada, were assayed for sulfate reduction, methanogenesis, denitrification, and monomethylmercury (MeHg) degradation. Demethylation of [ 14 C]MeHg was detected at all sites as indicated by the formation of 14 CO 2 and 14 CH 4 . Oxidative demethylation was indicated by the formation of 14 CO 2 and was present at significant levels in all samples. Oxidized/reduced demethylation product ratios (i.e., 14 CO 2 / 14 CH 4 ratios) generally ranged from 4.0 in surface layers to as low as 0.5 at depth. Production of 14 CO 2 was most pronounced at sediment surfaces which were zones of active denitrification and sulfate reduction but was also significant within zones of methanogenesis. In a core taken from an uncontaminated site having a high proportion of oxidized, coarse-grain sediments, sulfate reduction and methanogenic activity levels were very low and 14 CO 2 accounted for 98% of the product formed from [ 14 C]MeHg. There was no apparent relationship between the degree of mercury contamination of the sediments and the occurrence of oxidative demethylation. However, sediments from Fort Churchill, the most contaminated site, were most active in terms of demethylation potentials. Inhibition of sulfate reduction with molybdate resulted in significantly depressed oxidized/reduced demethylation product ratios, but overall demethylation rates of inhibited and uninhibited samples were comparable. Addition of sulfate to sediment slurries stimulated production of 14 CO 2 from [ 14 C]MeHg, while 2-bromoethanesulfonic acid blocked production of 14 CH 4 . These results reveal the importance of sulfate-reducing and methanogenic bacteria in oxidative demethylation of MeHg in anoxic environments.

Nevada↗