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A V Palumbo

Publications and source records attributed to A V Palumbo.

17 recordsLinked to original sources
PubMed2005

Confidence intervals of similarity values determined for cloned SSU rRNA genes from environmental samples.

The goal of this research was to investigate the influence of the error rate of sequence determination on the differentiation of cloned SSU rRNA gene sequences for assessment of community structure. SSU rRNA cloned sequences from groundwater samples that represent different bacterial divisions were sequenced multiple times with the same sequencing primer. From comparison of sequence alignments with unedited data, confidence intervals were obtained from both a 'double binomial' model of sequence comparison and by non-parametric methods. The results indicated that similarity values below 0.9946 are likely derived from dissimilar sequences at a confidence level of 0.95, and not sequencing errors. The results confirmed that screening by direct sequence determination could be reliably used to differentiate at the species level. However, given sequencing errors comparable to those seen in this study, sequences with similarities above 0.9946 should be treated as the same sequence if a 95% confidence is desired.

Base Sequence↗
PubMed2004

Coupling of functional gene diversity and geochemical data from environmental samples.

Genomic techniques commonly used for assessing distributions of microorganisms in the environment often produce small sample sizes. We investigated artificial neural networks for analyzing the distributions of nitrite reductase genes (nirS and nirK) and two sets of dissimilatory sulfite reductase genes (dsrAB1 and dsrAB2) in small sample sets. Data reduction (to reduce the number of input parameters), cross-validation (to measure the generalization error), weight decay (to adjust model parameters to reduce generalization error), and importance analysis (to determine which variables had the most influence) were useful in developing and interpreting neural network models that could be used to infer relationships between geochemistry and gene distributions. A robust relationship was observed between geochemistry and the frequencies of genes that were not closely related to known dissimilatory sulfite reductase genes (dsrAB2). Uranium and sulfate appeared to be the most related to distribution of two groups of these unusual dsrAB-related genes. For the other three groups, the distributions appeared to be related to pH, nickel, nonpurgeable organic carbon, and total organic carbon. The models relating the geochemical parameters to the distributions of the nirS, nirK, and dsrAB1 genes did not generalize as well as the models for dsrAB2. The data also illustrate the danger (generating a model that has a high generalization error) of not using a validation approach in evaluating the meaningfulness of the fit of linear or nonlinear models to such small sample sizes.

Bacteria↗
PubMed2001

Molecular characterization and diversity of thermophilic iron-reducing enrichment cultures from deep subsurface environments.

AIMS: The objectives of this work were to explore the diversity in Fe (III)-reducing enrichment cultures from the deep subsurface and to identify strains involved in metal reduction. METHODS AND RESULTS: Analyses of 16S ribosomal RNA (rRNA) of enrichments, supplemented with hydrogen, acetate or pyruvate as an electron donor, identified three dominant operational taxonomic units (OTUs). All cultures exhibited considerable diversity (36-24 OTUs), even after being transferred at least nine times. Two OTUs were present in all three cultures, constituting about 65% of the total clones examined. CONCLUSION: Dominant OTUs appeared to be most closely related to Thermoanaerobacter ethanolicus or T. kivui. One OTU, which is potentially responsible for autotrophic Fe (III) reduction, was only about 95% similar to T. ethanolicus and may represent a new species. SIGNIFICANCE AND IMPACT OF THE STUDY: An unexpectedly high diversity was found in these enrichments and this diversity may be a feature that can be exploited.

Acetic Acid↗
PubMed2001

Simultaneous recovery of RNA and DNA from soils and sediments.

Recovery of mRNA from environmental samples for measurement of in situ metabolic activities is a significant challenge. A robust, simple, rapid, and effective method was developed for simultaneous recovery of both RNA and DNA from soils of diverse composition by adapting our previous grinding-based cell lysis method (Zhou et al., Appl. Environ. Microbiol. 62:316-322, 1996) for DNA extraction. One of the key differences is that the samples are ground in a denaturing solution at a temperature below 0 degrees C to inactivate nuclease activity. Two different methods were evaluated for separating RNA from DNA. Among the methods examined for RNA purification, anion exchange resin gave the best results in terms of RNA integrity, yield, and purity. With the optimized protocol, intact RNA and high-molecular-weight DNA were simultaneously recovered from 19 soil and stream sediment samples of diverse composition. The RNA yield from these samples ranged from 1.4 to 56 microg g of soil(-1) dry weight), whereas the DNA yield ranged from 23 to 435 microg g(-1). In addition, studies with the same soil sample showed that the DNA yield was, on average, 40% higher than that in our previous procedure and 68% higher than that in a commercial bead milling method. For the majority of the samples, the DNA and RNA recovered were of sufficient purity for nuclease digestion, microarray hybridization, and PCR or reverse transcription-PCR amplification.

DNA, Bacterial↗
PubMed2001

Evaluation of PCR-generated chimeras, mutations, and heteroduplexes with 16S rRNA gene-based cloning.

To evaluate PCR-generated artifacts (i.e., chimeras, mutations, and heteroduplexes) with the 16S ribosomal DNA (rDNA)-based cloning approach, a model community of four species was constructed from alpha, beta, and gamma subdivisions of the division Proteobacteria as well as gram-positive bacterium, all of which could be distinguished by HhaI restriction digestion patterns. The overall PCR artifacts were significantly different among the three Taq DNA polymerases examined: 20% for Z-Taq, with the highest processitivity; 15% for LA-Taq, with the highest fidelity and intermediate processitivity; and 7% for the conventionally used DNA polymerase, AmpliTaq. In contrast to the theoretical prediction, the frequency of chimeras for both Z-Taq (8.7%) and LA-Taq (6.2%) was higher than that for AmpliTaq (2.5%). The frequencies of chimeras and of heteroduplexes for Z-Taq were almost three times higher than those of AmpliTaq. The total PCR artifacts increased as PCR cycles and template concentrations increased and decreased as elongation time increased. Generally the frequency of chimeras was lower than that of mutations but higher than that of heteroduplexes. The total PCR artifacts as well as the frequency of heteroduplexes increased as the species diversity increased. PCR artifacts were significantly reduced by using AmpliTaq and fewer PCR cycles (fewer than 20 cycles), and the heteroduplexes could be effectively removed from PCR products prior to cloning by polyacrylamide gel purification or T7 endonuclease I digestion. Based upon these results, an optimal approach is proposed to minimize PCR artifacts in 16S rDNA-based microbial community studies.

Artifacts↗
PubMed1997

Sensitive detection of a novel class of toluene-degrading denitrifiers, Azoarcus tolulyticus, with small-subunit rRNA primers and probes.

Azoarcus tolulyticus is a new class of widely distributed toluene-degrading denitrifiers of potential importance in remediating benzene, toluene, ethylbenzene, and xylene (BTEX)-contaminated environments. To detect these organisms in the environment, 16S rRNA gene-based phylogenetic probes were developed. Two sets of specific PCR amplification primers and two oligonucleotide hybridization probes were designed and tested against both closely and distantly related environmental isolates. All of these primers and probes were specific to the species A. tolulyticus. The sensitivity of the PCR amplification primer sets was evaluated with DNA isolated from A. tolulyticus Tol-4 pure culture and from sterile soils seeded with a known number of Tol-4 and Escherichia coli cells. These primer sets were able to detect 1 fg to 1 pg of template DNA from the pure culture and 1.11 x 10(2) to 1.1 x 10(8) Tol-4 cells per g of soil in the presence of 1.56 x 10(10) E. coli cells. These two PCR amplification primers were also successfully tested at two field sites. The primers identified the A. tolulyticus strains among the toluene-degrading bacteria isolated from a low-O2-high-NO(3)- aquifer at Moffett Field, Calif. Also, the presence of A. tolulyticus was detected in the groundwater samples from a BTEX-contaminated aquifer at an industrial site in Detroit, Mich., which showed anaerobic toluene degradation.

Base Sequence↗
PubMed1996

Effect of temperature and yeast extract on microbial respiration of sediments from a shallow coastal subsurface and vadose zone.

As a part of our study on microbial heterogeneity in subsurface environments, we have examined the microbial respiration of sediment samples obtained from a coastal site near Oyster, VA. The sediments at the site are unconsolidated, fine to coarse beach sand and gravel. A Columbus Instruments Micro-Oxymax Respirometer was used to measure the rate of carbon dioxide (CO2) production during the respiration of the sediment samples. The rate of respiration of the sediment samples ranged from 0.035-0.6 microL CO2/h/g of the sediment. The sediment samples showing maximum (0.6 microL CO2/h/g) and minimum (0.035 microL CO2/h/g) production of CO2 were selected to study the effect of micronutrient-yeast extract (0.5 and 1.0 micrograms/g of the sediment) and water (0.5 and 1.0 mL) on the rate of CO2 production. The rate of CO2 production increased with the addition of water, but increased approx 2 orders of magnitude (from 0.26 to an average of 23.5 microL CO2/h/g) when 1.0 g/g yeast extract was added to the sediment samples. In these coastal sediments, temperature, depth, and addition of water influenced microbial activity, but the addition of 1.0 microgram/g yeast extract as a micronutrient rapidly increased the rate of CO2 production 2 orders of magnitude.

Biotechnology↗
PubMed1994

Alternative method for rapidly screening microbial isolates for their potential to degrade volatile contaminants.

A method is described for rapidly screening the metabolic potential of bacteria to oxidize semivolatile and volatile compounds as a sole carbon source. The method is based on an automated system that utilizes Microplates manufactured by Biolog, Inc. (Hayward, CA, USA). This system detects bacterial respiratory activity from the oxidation of a carbon source introduced in volatile form. This is in contrast to the original design, which is based on inoculating a carbon source directly into each well. The 96-well (MT) microtiter plates contain nutrients and a tetrazolium dye. When a bacterial species is capable of oxidizing a volatile carbon substrate, the dye turns purple, and a spectrophotometric plate reader quantifies the response. As a test of this method 150 isolates, including isolates known to degrade some of the test compounds and negative controls were evaluated for their potential to oxidize carbon tetrachloride, toluene, and o-xylene. Thirty-seven isolates (25%) were qualitatively identified as contaminant oxidizers, and thirteen of these (35%) showed significant degradation capabilities for both toluene and o-xylene.

Bacteria↗
PubMed1994

The effect of media composition on EDTA degradation by Agrobacterium sp.

EDTA degradation by an Agrobacterium sp. has been examined by quantifying 14C-labeled CO2 produced from iron-[2-14C] EDTA and by measured loss of nonlabeled EDTA by HPLC. Fe-EDTA degradation resulted in a rise in pH, nitrate concentration, and ammonia concentration. Addition of glycerol resulted in suppression of Fe-EDTA degradation and in a decrease in pH and NH4+ concentration in the media. Addition of peptone or yeast extract did not affect degradation. Some of the components (e.g., biotin) of the media are not necessary for growth and biodegradation. Although cobalt-EDTA cannot be degraded, ferrous iron can be added to displace the cobalt.

Biodegradation, Environmental↗
PubMed1994

Bioremediation of petroleum hydrocarbons in soil column lysimeters from Kwajalein island.

Soil column studies were used to evaluate petroleum hydrocarbon (PHC) remediation in soils from Kwajalein Atoll. Treatments included controls, and combinations of water, air, nutrients, and bioaugmentation with indigenous microbes (W, A, N, and M, respectively). Microbial colony forming units (CFU) decreased in the control columns and in treatments without air. Treatments including W+A+N and W+A+N+ exhibited increased CFU. One third of the PHC was removed by water and another third was removed by W+A+N and W+A+N+M treatments. Bioaugmentation with indigenous PHC degraders did not enhance bioremediation. Potential for bioremediation was demonstrated by air, water, and nutrient amendments.

Air↗
PubMed1991

Methanol suppression of trichloroethylene degradation by Methylosinus trichosporium (OB3b) and methane-oxidizing mixed cultures.

The effect of methanol on trichloroethylene (TCE) degradation by mixed and pure methylotrophic cultures was examined in batch culture experiments. Methanol was found to relieve growth inhibition of Methylosinus trichosporium (OB3b) at high (14 mg/L) TCE concentrations. Degradation of TCE was determined by both radiolabeling and gas chromatography techniques. When cultures were grown on methanol over 10 to 14 d with 0.3 mg/L TCE, OB3b degraded 16.89 +/- 0.82% (mean +/- SD) of the TCE, and a mixed culture (DT type II) degraded 4.55 +/- 0.11%. Mixed culture (JS type I) degraded 4.34 +/- 0.06% of the TCE. When grown on methane with 0.3 mg/L TCE, 32.93 +/- 2.01% of the TCE was degraded by OB3b, whereas the JS culture degraded 24.3 +/- 1.38% of the TCE, and the DT culture degraded 34.3 +/- 2.97% of the TCE. The addition of methanol to cultures grown on methane reduced TCE degradation to 16.21 +/- 1.17% for OB3b and to 5.08 +/- 0.56% for JS. Although methanol reduces the toxicity of TCE to the cultures, biodegradation of TCE cannot be sustained in methanol-grown cultures. Since high TCE concentrations appear to inhibit methane uptake and growth, we suggest the primary toxicity of TCE is directed towards the methane monooxygenase.

Biodegradation, Environmental↗
PubMed1988

Trichloroethylene biodegradation by a methane-oxidizing bacterium.

Trichloroethylene (TCE), a common groundwater contaminant, is a suspected carcinogen that is highly resistant to aerobic biodegradation. An aerobic, methane-oxidizing bacterium was isolated that degrades TCE in pure culture at concentrations commonly observed in contaminated groundwater. Strain 46-1, a type I methanotrophic bacterium, degraded TCE if grown on methane or methanol, producing CO(2) and water-soluble products. Gas chromatography and C radiotracer techniques were used to determine the rate, methane dependence, and mechanism of TCE biodegradation. TCE biodegradation by strain 46-1 appears to be a cometabolic process that occurs when the organism is actively metabolizing a suitable growth substrate such as methane or methanol. It is proposed that TCE biodegradation by methanotrophs occurs by formation of TCE epoxide, which breaks down spontaneously in water to form dichloroacetic and glyoxylic acids and one-carbon products.

Journal Article↗
PubMed1987

Bacterial communities in acidic and circumneutral streams.

The relationship between pH and the abundance and activity of bacteria in streams was examined as part of a study of the effect of acidification on stream communities. Of the bacterial communities examined, the epilithic community appeared to be the most significantly affected by acidification. Microbial biomass, as quantified by measuring the ATP level, on rock surfaces was significantly correlated with pH. Also, bacterial production by the epilithic bacteria, indicated by incorporation of tritiated thymidine into DNA, was always higher at high-pH sites than at low-pH sites of the same stream order and elevation. Bacterioplankton concentrations varied between 0.53 x 10 and 9.42 x 10 cells . ml in the first- to fourth-order streams examined. The bacterioplankton concentration in one sample from a spring was 0.17 x 10 cells . ml. Bacterioplankton concentrations were not correlated with pH but were significantly correlated with seston concentrations. The correlation with seston is a result of increases in particle-associated bacteria at high seston concentrations. The proportion of bacterioplankton attached to particles varied from 0 to 70%. Bacterial numbers and production in the sediments were significantly correlated with the organic content of the sediment rather than with the pH of the overlying water. Thus, reduced abundance and activity of bacteria as a result of acidification could be detected only for the relatively active community on rock surfaces; this community was exposed to the low pH because of the unbuffered nature of its environment.

Journal Article↗
PubMed1984

Response of marine bacterioplankton to differential filtration and confinement.

The bacterioplankton community of confined seawater at 25 degrees C changed significantly within 16 h of collection. Confinement increased CFU, total cell number (by epifluorescence microscopy), and average cell volume of bacterioplankton and increased the turnover rate of amino acids in seawater sampled at Frying Pan Shoals, N.C. The bacterioplankton community was characterized by two components: differential doubling times during confinement shifted dominance from bacteria which were nonculturable to bacteria which were culturable on a complex nutrient medium. Culturable cells (especially those of the genera Pseudomonas, Alcaligenes, and Acinetobacter) increased from 0.08% of the total cell number in the seawater immediately after collection to 13% at 16 h and 41% at 32 h of confinement. Differential filtration before confinement indicated that particles passing through a 3.9-microns-, but retained by a 0.2-micron-, pore-size Nuclepore filter may be a major source of primary amines to the confined population. The 3.0-microns filtration increased growth rate and ultimate numbers of culturable cells through the removal of bacterial predators or the release of primary amines from cells damaged during filtration or both.

Amines↗
PubMed1984

Size of suspended bacterial cells and association of heterotrophic activity with size fractions of particles in estuarine and coastal waters.

The size of bacteria and the size distribution of heterotrophic activity were examined in estuarine, neritic, and coastal waters. The data indicated the small size of suspended marine bacteria and the predominance of free-living cells in numerical abundance and in the incorporation of dissolved amino acids. The average per-cell volume of suspended marine bacteria in all environments was less than 0.1 mum. Cell volume ranged from 0.072 to 0.096 mum at salinities of 0 to 34.3 per thousand in the Newport River estuary, N.C., and from 0.078 to 0.096 mum in diverse areas of the Gulf of Mexico. Thus, the free-living bacteria were too small to be susceptible to predation by copepods. In the Newport River estuary, ca. 93 to 99% of the total number of cells and 75 to 97% of incorporated tritium (from H-labeled mixed amino acids) retained by a 0.2-mum-pore-size filter passed through a 3.0-mum-pore-size filter. Although the amino acid turnover rate per cell was higher for the bacteria in the >3.0-mum size fraction than in the <3.0-mum size fraction, the small number of bacteria associated with the >3.0-mum size particles resulted in the low relative contribution of attached bacteria to total heterotrophic activity in the estuary. For coastal and neritic samples, collected off the coast of Georgia and northeast Florida and in the plume of the Mississippi River, 56 to 98% of incorporated label passed through a 3.0-mum-pore-size filter. The greatest activity in the >3.0-mum fraction in the Georgia Bight was at nearshore stations and in the bottom samples. Our data were consistent with the hypothesis that resuspension of bottom material is an important factor in influencing the proportion of heterotrophic activity attributable to particle-associated bacteria.

Journal Article↗
PubMedDate not supplied

Effects of nutrient dosing on subsurface methanotrophic populations and trichloroethylene degradation.

In in situ bioremediation demonstration at the Savannah River Site in Aiken, South Carolina, trichloroethyle degrading microorganisms were stimulated by delivering nutrients to the TCE-contaminated subsurface via horizontal injection wells. Microbial and chemical monitoring of groundwater from 12 vertical wells was used to examine the effects of methane and nutrient (nitrogen and phosphorus) dosing on the methanotrophic populations and on the potential of the subsurface microbial communities to degrade TCE. Densities of methanotrophs increased 3-5 orders of magnitude during the methane- and nutrient-injection phases; this increase coinclded with the higher methane levels observed in the monitoring wells. TCE degradation capacity, although not directly tied to methane concentration, responded to the methane injection, and responded more dramatically to the multiple-nutrient injection. tion. These results support the crucial role of methane, nitrogen, and phosphorus as amended nutrients in TCE bioremediation. The enhancing effects of nutrient dosing on microbial abundance and degradative potentials, coupled with increased chloride concentrations, provided multiple lines of evidence substantiating the effectiveness of this integrated in situ bioremediation process.

Biodegradation, Environmental↗