Mary E. Watwood

Detection of Euryarchaeota and Crenarchaeota in an oxic basalt aquifer

Groundwater from an oxic, fractured basalt aquifer was examined for the presence of Archaea. DNA was extracted from cells concentrated from groundwater collected from five wells penetrating the eastern Snake River Plain Aquifer (Idaho, USA). Polymerase chain reaction (PCR) amplification of 16S rDNA was performed with Archaea-specific primers using both nested (ca. 200-bp product) and direct (ca. 600-bp product) PCR approaches. Estimates of the archaeal diversity were made by separating PCR products from all five wells by denaturing gradient gel electrophoresis (DGGE) and phylogenetic analysis of partial 16S rDNA sequences from two wells was performed following cloning procedures. Archaea were detected in all wells and the number of DGGE bands per well ranged from two to nine and varied according to PCR approach. There were 30 unique clonal 16S rDNA partial sequences (ca. 600 bp) within a total of 100 clones that were screened from two wells. Twenty-two of the 16S rDNA fragments recovered from the aquifer were related to the Crenarchaeota and Euryarchaeota kingdoms (one large clade of clones in the former and six smaller clades in the latter), with sequences ranging from 23.7 to 95.4% similar to those found in other investigations. The presence of potentially thermophilic or methanogenic Archaea in this fully oxic aquifer may be related to deep thermal sources or elevated dissolved methane concentrations. Many sequences were similar to those that represent non-thermophilic Crenarchaeota of which there are no known cultured members and therefore no putative function.

Activity-dependent fluorescent labeling of bacteria that degrade toluene via toluene 2,3-dioxygenase.

Abstract Alternative substrates for the toluene 2,3-dioxygenase pathway of several pseudomonads served as enzyme-activity-dependent fluorescent probes for the bacteria. Phenylacetylene and cinnamonitrile were transformed to fluorescent and brightly colored products by Pseudomonas putida F1, Pseudomonas fluorescens CFS215, and Burkholderia (Pseudomonas) strain JS150. Active bacteria transformed phenylacetylene, producing bright yellow solutions containing the putative product 2-hydroxy-6-oxo-7-octyn-2,4-dienoate. Transformation of cinnamonitrile resulted in bright orange solutions due to accumulation of the putative product 2-hydroxy-6-oxo-8-cyanoocta-2,4,7-trienoate. Chemical and physical properties of the products supported their identification, which indicated that the first three enzymes of the pathway catalyzed product formation. Phenylacetylene labeled bacteria with green fluorescence emission; bacteria were concentrated on black 0.2-μm-pore-size polycarbonate filters containing polyvinylpyrrolidone (PVP) as a wetting agent. Bacteria labeled with cinnamonitrile were fluorescent orange; labeling was effective with bacteria trapped on PVP-free polycarbonate filters. Production of the enzymes involved in labeling of P. putida F1 and P. fluorescens CFS215 was induced by growth (on arginine) in the presence of toluene; cells grown on arginine without toluene were not labeled. Labeling of P. putida F1 by phenylacetylene was inhibited by toluene, indicating that the same enzymatic pathway was required for transformations of both substrates. Bacteria expressing other toluene-degrading enzymatic pathways were not fluorescently labeled with phenylacetylene.

Use of selective inhibitors and chromogenic substrates to differentiate bacteria based on toluene oxygenase activity

In whole-cell studies, two alkynes, 1-pentyne and phenylacetylene, were selective, irreversible inhibitors of monooxygenase enzymes in catabolic pathways that permit growth of bacteria on toluene. 1-Pentyne selectively inhibited growth of Burkholderia cepacia G4 (toluene 2-monooxygenase [T2MO] pathway) and B. pickettii PKO1 (toluene 3-monooxygenase [T3MO] pathway) on toluene, but did not inhibit growth of bacteria expressing other pathways. In further studies with strain G4, chromogenic transformation of alpha,alpha,alpha-Trifluoro-m-cresol (TFC) was irreversibly inhibited by 1-pentyne, but the presence of phenol prevented this inhibition. Transformation of catechol by G4 was unaffected by 1-pentyne. With respect to the various pathways and bacteria tested, phenylacetylene selectively inhibited growth of Pseudomonas mendocina KR1 (toluene 4-monooxygenase [T4MO] pathway) on toluene, but not on p-cresol. An Escherichia coli transformant expressing T4MO transformed indole or naphthalene in chromogenic reactions, but not after exposure to phenylacetylene. The naphthalene reaction remained diminished in phenylacetylene-treated cells relative to untreated cells after phenylacetylene was removed, indicating irreversible inhibition.These techniques were used to differentiate toluene-degrading isolates from an aquifer. Based on data generated with these indicators and inhibitors, along with results from Biolog analysis for sole carbon source oxidation, the groundwater isolates were assigned to eight separate groups, some of which apparently differ in their mode of toluene catabolism.

BASIC program for reduction of data from community-level physiological profiling using biolog microplates: rationale and critical interpretation of data.

A BASIC program is offered that reduces data resulting from mixed-species inoculations into Biolog microplates. The procedures of the program are supported by a critical review of the literature relating to Biolog data reduction. The availability of standardized, accelerated data reduction protocols will facilitate study comparisons and allow efficient evaluation of new data reduction approaches.

Soil amidase activity in polyacrylamide-treated soils and potential activity toward common amide-containing pesticides

Abstract Polyacrylamide (PAM) is currently used as an irrigation water additive to significantly reduce the amount of soil erosion that occurs during furrow irrigation of crops. Elevated soil amidase activity specific toward the large PAM polymer has been reported in PAM-treated field soils; the substrate specificity of the induced amidase is uncertain. PAM-treated and untreated soils were assayed for their capacity to hydrolyze the amide bond in carbaryl (Sevin), diphenamid (Dymid), and naphthalene acetamide. Based on results obtained with a soil amidase assay, there was no difference between PAM-treated and untreated soils with respect to the rate of amide bond hydrolysis of any of the agrochemicals tested. It appears that under these assay conditions the PAM-induced soil amidase is not active toward the amide bonds within these molecules. However, carbaryl was hydrolyzed by a different soil amidase. To our knowledge, this is the first soil enzyme assay-based demonstration of the hydrolysis of carbaryl by a soil amidase.

A Comparison of Ultrasonication and Soxhlet Methods for DDT Extraction from Soil

The goal of this study was to determine the efficacy of ultrasonication extraction of 1,1,1-trichloro-2,2-bis[p-chlorophenyl]ethane (DDT), 1,1-dichloro-2,2-bis[p-chlorophenyl]ethane (DDD), and 2,2-bis[p-chlorophenyl]1,1-dichloro-ethylene (DDE) residues in soil for the purposes of saving time, minimizing generation of hazardous solvent wastes, and reducing costs associated with monitoring contaminant concentrations at remediation sites. An ultrasonic extraction method was developed for DDT, DDD, and DDE residues in soil, and the efficiency of extraction using an ultrasonic cavitator was compared to the traditional soxhlet method by GC-MS. Un-contaminated soil was spiked with analytes DDT, DDD, and DDE at 0.1,1.0,10.0, and 100.0 mg/ kg. Experiments were performed in triplicate, and recoveries of analytes were determined and statistically compared. Results indicate that ultrasonic extraction is a suitable preparatory method for analysis of DDT, DDD, and DDE residues in soil. For spike concentrations of 1 mg/...

Exchangeable ammonium and nitrate from different nitrogen fertilizer preparations in polyacrylamide-treated and untreated agricultural soils

Abstract High molecular weight, anionic polyacrylamide (PAM) is currently being used as an irrigation water additive to significantly reduce soil erosion associated with furrow irrigation. PAM contains amide-N, and PAM application to soils has been correlated with increased activity of soil enzymes, such as urease and amidase, involved in N cycling. Therefore we investigated potential impacts of PAM treatment on the rate at which fertilizer N is transformed into NH4+ and NO3– in soil. PAM-treated and untreated soil microcosms were amended with a variety of fertilizers, ranging from common rapid-release forms, such as ammonium sulfate [(NH4)2SO4] and urea, to a variety of slow-release formulations, including polymerized urea and polymer-encapsulated urea. Ammonium sulfate was also tested together with the nitrification inhibitor dicyandiamide (DCD). The fertilizers were applied at a concentration of 1.0 mg g–1, which is comparable to 100 lb acre–l, or 112 kg ha–1. Potassium chloride-extractable NH4+-N and NO3–-N were quantified periodically during 2–4 week incubations. PAM treatment had no significant effect on NH4+ release rates for any of the fertilizers tested and did not alter the efficacy of DCD as a nitrification inhibitor. However, the nitrification rate of urea and encapsulated urea-derived NH4+-N was slightly accelerated in the PAM-treated soil.

Impact of Polyacrylamide Treatment on Sorptive Dynamics and Degradation of 2,4-D and Atrazine in Agricultural Soil

High-molecular-weight, anionic polyacrylamide (PAM) is added to irrigation water to reduce soil erosion during furrow irrigation of crops. The chemical nature of PAM, together with the observation that the polymer can be biotransformed by soil bacteria, led us to question the impact of PAM treatment on the fate of coapplied agrochemicals. The herbicides, atrazine (nonionic) and 2,4-D (anionic), were tested for pesticide sorption, desorption, and degradation in PAM-treated and untreated soils. Sorption of atrazine and 2,4-D in soil was unaffected by PAMtreatment, as was atrazine desorption. However, 2,4-D desorbedmore readily from the PAM-treated soil than from untreated soil. With respect to pesticide degradation, mineralization of the 2,4-D aromatic ring was not impacted by PAM treatment, but decarboxylation of the 2,4-D carboxylic acid side chain was significantly reduced in the PAM-treated soil. Limited mineralization (7 to 10%) of atrazine was observed in both soils. However, in PAM-treated soils atrazine conversion to 14CO2 and bound residue components was significantly reduced, and there was an increase in the level of methanol extractable metabolites. These results may indicate that PAM application can alter the environmental fate of some pesticides in soils, especially under the high dose treatment conditions examined in this study.

Stable carbon isotope fractionation in chlorinated ethene degradation by bacteria expressing three toluene oxygenases

One difficulty in using bioremediation at a contaminated site is demonstrating that biodegradation is actually occurring in situ. The stable isotope composition of contaminants may help with this, since they can serve as an indicator of biological activity. To use this approach it is necessary to establish how a particular biodegradation pathway affects the isotopic composition of a contaminant. This study examined bacterial strains expressing three aerobic enzymes for their effect on the 13C/12C ratio when degrading both trichloroethene (TCE) and cis-1,2-dichloroethene (c-DCE): toluene 3-monoxygenase, toluene 4-monooxygenase, and toluene 2,3-dioxygenase. We found no significant differences in fractionation among the three enzymes for either compound. Aerobic degradation of c-DCE occurred with low fractionation producing δ13C enrichment factors of −0.9 ± 0.5 to −1.2 ± 0.5, in contrast to reported anaerobic degradation δ13C enrichment factors of −14.1 to −20.4‰. Aerobic degradation of TCE resulted in δ13C enrichment factors of −11.6 ± 4.1 to −14.7 ± 3.0‰ which overlap reported δ13C enrichment factors for anaerobic TCE degradation of −2.5 to −13.8‰. The data from this study suggest that stable isotopes could serve as a diagnostic for detecting aerobic biodegradation of TCE by toluene oxygenases at contaminated sites.

Transition Metal Catalyst-Assisted Reductive Dechlorination of Perchloroethylene by Anaerobic Aquifer Enrichments

Bioremediation of groundwater contaminated with chlorinated solvents, such as perchloroethylene (PCE) or carbon tetrachloride, can be accomplished by adding nutrients to stimulate a microbial community capable of reductive dechlorination. However, biotransformation of these solvents, especially PCE, typically occurs very slowly or not at all. Experiments were conducted to evaluate whether the addition of transition metal tetrapyrrole catalysts would increase the reductive transformation of PCE to trichloroethylene (TCE) by sulfate-reducing enrichment cultures. Batch assays were used to test vitamin B12 and two synthetic sulfonatophenyl porphine catalysts for the stimulation of reductive dechlorination of PCE by sulfate-reducing bacteria (SRB) enriched from aquifer sediments from two locations at Dover Air Force Base. Cells from the enrichments were concentrated and added to batch assay vials. Vials containing SRB cells amended with vitamin B12 exhibited enhanced transformation of PCE to TCE compared with reactors amended with either synthetic catalysts or reactors containing cells alone. Methane production was observed in reactors that exhibited maximum levels of dechlorination. Storage of aquifer sediments between enrichments led to decreased levels of PCE dechlorination in subsequent assays.