Utilization of fluoroethene as a surrogate for aerobic vinyl chloride transformation

Fluoroethene (FE) is a stable molecule in aqueous solution and its aerobic transformation potentially yields F-. This work evaluated if FE is a suitable surrogate for monitoring aerobic vinyl chloride (VC) utilization or cometabolic transformation. Experiments were carried out with three isolates, Mycobacterium strain EE13a, Mycobacterium strain JS60, and Nocardioides strain JS614 to evaluate if their affinities for FE and VC and their rates of transformation were comparable and whether the transformation of FE and F- accumulation could be correlated with VC utilization. JS614 grew on FE in addition to VC, making it the first organism reported to use FE as a sole carbon and energy source. EE13a cometabolized VC and FE, and JS60 catabolized VC and cometabolized FE. There was little difference among the three strains in the Ks or kmax values for VC or FE. Competitive inhibition modeled the temporal responses of FE and VC transformations and Cl- and F- release when both substrates were present. Both the rate of FE transformation and rate of F-accumulation could be correlated with the rate of aerobic transformation of VC and showed promise for estimating VC rates in situ using FE as a reactive surrogate.

Evidence for modified mechanisms of chloroethene oxidation in Pseudomonas butanovora mutants containing single amino acid substitutions in the hydroxylase alpha-subunit of butane monooxygenase

The properties of oxidation of dichloroethene (DCE) and trichloroethylene (TCE) by three mutant strains of Pseudomonas butanovora containing single amino acid substitutions in the alpha-subunit of butane monooxygenase hydroxylase (BMOH-alpha) were compared to the properties of the wild-type strain (Rev WT). The rates of oxidation of three chloroethenes (CEs) were reduced in mutant strain G113N and corresponded with a lower maximum rate of butane oxidation. The rate of TCE degradation was reduced by one-half in mutant strain L279F, whereas the rates of DCE oxidation were the same as those in Rev WT. Evidence was obtained that the composition of products of CE oxidation differed between Rev WT and some of the mutant strains. For example, while Rev WT released nearly all available chlorine stoichiometrically during CE oxidation, strain F321Y released about 40% of the chlorine during 1,2-cis-DCE and TCE oxidation, and strain G113N released between 14 and 25% of the available chlorine during oxidation of DCE and 56% of the available chlorine during oxidation of TCE. Whereas Rev WT, strain L279F, and strain F321Y formed stoichiometric amounts of 1,2-cis-DCE epoxide during oxidation of 1,2-cis-DCE, only about 50% of the 1,2-cis-DCE oxidized by strain G113N was detected as the epoxide. Evidence was obtained that 1,2-cis-DCE epoxide was a substrate for butane monooxygenase (BMO) that was oxidized after the parent compound was consumed. Yet all of the mutant strains released less than 40% of the available 1,2-cis-DCE chlorine, suggesting that they have altered activity towards the epoxide. In addition, strain G113N was unable to degrade the epoxide. TCE epoxide was detected during exposure of Rev WT and strain F321Y to TCE but was not detected with strains L279F and G113N. Lactate-dependent O(2) uptake rates were differentially affected by DCE degradation in the mutant strains, providing evidence that some products released by the altered BMOs reduced the impact of CE on cellular toxicity. The use of CEs as substrates in combination with P. butanovora BMOH-alpha mutants might allow insights into the catalytic mechanism of BMO to be obtained.

Global transcriptional response of Nitrosomonas europaea to chloroform and chloromethane

Upon exposure of Nitrosomonas europaea to chloroform (7 microM, 1 h), transcripts for 175 of 2,460 genes were found at higher levels in treated cells than in untreated cells and transcripts for 501 genes were found at lower levels. With chloromethane (3.2 mM, 1 h), transcripts for 67 genes were at higher levels and transcripts for 148 genes were at lower levels. Transcripts for 37 genes were at higher levels following both treatments and included genes for heat shock proteins, sigma-factors of the extracytoplasmic function subfamily, and toxin-antitoxin loci. N. europaea has higher levels of transcripts for a variety of defense genes when exposed to chloroform or chloromethane.

Site-directed amino acid substitutions in the hydroxylase alpha subunit of butane monooxygenase from Pseudomonas butanovora: Implications for substrates knocking at the gate

Butane monooxygenase (BMO) from Pseudomonas butanovora has high homology to soluble methane monooxygenase (sMMO), and both oxidize a wide range of hydrocarbons; yet previous studies have not demonstrated methane oxidation by BMO. Studies to understand the basis for this difference were initiated by making single-amino-acid substitutions in the hydroxylase alpha subunit of butane monooxygenase (BMOH-alpha) in P. butanovora. Residues likely to be within hydrophobic cavities, adjacent to the diiron center, and on the surface of BMOH-alpha were altered to the corresponding residues from the alpha subunit of sMMO. In vivo studies of five site-directed mutants were carried out to initiate mechanistic investigations of BMO. Growth rates of mutant strains G113N and L279F on butane were dramatically slower than the rate seen with the control P. butanovora wild-type strain (Rev WT). The specific activities of BMO in these strains were sevenfold lower than those of Rev WT. Strains G113N and L279F also showed 277- and 5.5-fold increases in the ratio of the rates of 2-butanol production to 1-butanol production compared to Rev WT. Propane oxidation by strain G113N was exclusively subterminal and led to accumulation of acetone, which P. butanovora could not further metabolize. Methane oxidation was measurable for all strains, although accumulation of 23 microM methanol led to complete inhibition of methane oxidation in strain Rev WT. In contrast, methane oxidation by strain G113N was not completely inhibited until the methanol concentration reached 83 microM. The structural significance of the results obtained in this study is discussed using a three-dimensional model of BMOH-alpha.

Genome sequence of the chemolithoautotrophic nitrite-oxidizing bacterium Nitrobacter winogradskyi Nb-255

The alphaproteobacterium Nitrobacter winogradskyi (ATCC 25391) is a gram-negative facultative chemolithoautotroph capable of extracting energy from the oxidation of nitrite to nitrate. Sequencing and analysis of its genome revealed a single circular chromosome of 3,402,093 bp encoding 3,143 predicted proteins. There were extensive similarities to genes in two alphaproteobacteria, Bradyrhizobium japonicum USDA110 (1,300 genes) and Rhodopseudomonas palustris CGA009 CG (815 genes). Genes encoding pathways for known modes of chemolithotrophic and chemoorganotrophic growth were identified. Genes encoding multiple enzymes involved in anapleurotic reactions centered on C2 to C4 metabolism, including a glyoxylate bypass, were annotated. The inability of N. winogradskyi to grow on C6 molecules is consistent with the genome sequence, which lacks genes for complete Embden-Meyerhof and Entner-Doudoroff pathways, and active uptake of sugars. Two gene copies of the nitrite oxidoreductase, type I ribulose-1,5-bisphosphate carboxylase/oxygenase, cytochrome c oxidase, and gene homologs encoding an aerobic-type carbon monoxide dehydrogenase were present. Similarity of nitrite oxidoreductases to respiratory nitrate reductases was confirmed. Approximately 10% of the N. winogradskyi genome codes for genes involved in transport and secretion, including the presence of transporters for various organic-nitrogen molecules. The N. winogradskyi genome provides new insight into the phylogenetic identity and physiological capabilities of nitrite-oxidizing bacteria. The genome will serve as a model to study the cellular and molecular processes that control nitrite oxidation and its interaction with other nitrogen-cycling processes.

Product repression of alkane monooxygenase expression in Pseudomonas butanovora

Physiological and regulatory mechanisms that allow the alkane-oxidizing bacterium Pseudomonas butanovora to consume C2 to C8 alkane substrates via butane monooxygenase (BMO) were examined. Striking differences were observed in response to even- versus odd-chain-length alkanes. Propionate, the downstream product of propane oxidation and of the oxidation of other odd-chain-length alkanes following beta-oxidation, was a potent repressor of BMO expression. The transcriptional activity of the BMO promoter was reduced with as little as 10 microM propionate, even in the presence of appropriate inducers. Propionate accumulated stoichiometrically when 1-propanol and propionaldehyde were added to butane- and ethane-grown cells, indicating that propionate catabolism was inactive during growth on even-chain-length alkanes. In contrast, propionate consumption was induced (about 80 nmol propionate consumed.min(-1).mg protein(-1)) following growth on the odd-chain-length alkanes, propane and pentane. The induction of propionate consumption could be brought on by the addition of propionate or pentanoate to the growth medium. In a reporter strain of P. butanovora in which the BMO promoter controls beta-galactosidase expression, only even-chain-length alcohols (C2 to C8) induced beta-galactosidase following growth on acetate or butyrate. In contrast, both even- and odd-chain-length alcohols (C3 to C7) were able to induce beta-galactosidase following the induction of propionate consumption by propionate or pentanoate.

Effects of dichloroethene isomers on the induction and activity of butane monooxygenase in the alkane-oxidizing bacterium "Pseudomonas butanovora"

We examined cooxidation of three different dichloroethenes (1,1-DCE, 1,2-trans DCE, and 1,2-cis DCE) by butane monooxygenase (BMO) in the butane-utilizing bacterium "Pseudomonas butanovora." Different organic acids were tested as exogenous reductant sources for this process. In addition, we determined if DCEs could serve as surrogate inducers of BMO gene expression. Lactic acid supported greater rates of oxidation of the three DCEs than the other organic acids tested. The impacts of lactic acid-supported DCE oxidation on BMO activity differed among the isomers. In intact cells, 50% of BMO activity was irreversibly lost after consumption of approximately 20 nmol mg protein(-1) of 1,1-DCE and 1,2-trans DCE in 0.5 and 5 min, respectively. In contrast, a comparable loss of activity required the oxidation of 120 nmol 1,2-cis DCE mg protein(-1). Oxidation of similar amounts of each DCE isomer ( approximately 20 nmol mg protein(-1)) produced different negative effects on lactic acid-dependent respiration. Despite 1,1-DCE being consumed 10 times faster than 1,2,-trans DCE, respiration declined at similar rates, suggesting that the product(s) of oxidation of 1,2-trans DCE was more toxic to respiration than 1,1-DCE. Lactate-grown "P. butanovora" did not express BMO activity but gained activity after exposure to butane, ethene, 1,2-cis DCE, or 1,2-trans DCE. The products of BMO activity, ethene oxide and 1-butanol, induced lacZ in a reporter strain containing lacZ fused to the BMO promoter, whereas butane, ethene, and 1,2-cis DCE did not. 1,2-trans DCE was unique among the BMO substrates tested in its ability to induce lacZ expression.

Product and product-independent induction of butane oxidation in Pseudomonas butanovora

Pseudomonas butanovora grows on butane by means of an inducible soluble alkane monooxygenase (sBMO). The induction of sBMO was studied using the wild type and a sBMO reporter strain. The reporter strain has the lacZ::kan cassette inserted into bmoX, the gene that encodes the alpha-subunit of the hydroxylase of sBMO. The beta-galactosidase activity in the reporter strain was not induced by butane, but was induced by 1-butanol and butyraldehyde. P. butanovora expressed sBMO product-independent activity at 3.0+/-1 nmol ethylene oxide min(-1) mg protein(-1) in stationary phase. The sBMO product-independent activity likely primes the expression of sBMO by butane.

Trichloroethylene degradation by butane-oxidizing bacteria causes a spectrum of toxic effects

The physiological consequences of trichloroethylene (TCE) transformation by three butane oxidizers were examined. Pseudomonas butanovora, Mycobacterium vaccae, and Nocardioides sp. CF8 utilize distinctly different butane monooxygenases (BMOs) to initiate degradation of the recalcitrant TCE molecule. Although the primary toxic event resulting from TCE cometabolism by these three strains was loss of BMO activity, species differences were observed. P. butanovora and Nocardioides sp. CF8 maintained only 4% residual BMO activity following exposure to 165 microM TCE for 90 min and 180 min, respectively. In contrast, M. vaccae maintained 34% residual activity even after exposure to 165 microM TCE for 300 min. Culture viability was reduced 83% in P. butanovora, but was unaffected in the other two species. Transformation of 530 nmol of TCE by P. butanovora (1.0 mg total protein) did not affect the viability of BMO-deficient P. butanovora cells, whereas transformation of 482 nmol of TCE by toluene-grown Burkholderia cepacia G4 caused 87% of BMO-deficient P. butanovora cells to lose viability. Together, these results contrast with those previously reported for other bacteria carrying out TCE cometabolism and demonstrate the range of cellular toxicities associated with TCE cometabolism.

Responses of nitrification and ammonia-oxidizing bacteria to reciprocal transfers of soil between adjacent coniferous forest and meadow vegetation in the Cascade Mountains of Oregon

Despite the critical position of nitrification in N cycling in coniferous forest soils of western North America, little information exists on the composition of ammonia-oxidizing bacteria (AOB) in these soils, or their response to treatments that promote or reduce nitrification. To this end, an experiment was conducted in which a set of soil cores was reciprocally transplanted between adjacent forest (low nitrification potential) and meadow (high nitrification potential) environments, at two high-elevation (approximately 1500 m) sites in the H.J. Andrews Experimental Forest located in the Cascade Mountains of Oregon. Half of the cores were placed in screened PVC pipe (closed) to prevent new root colonization, large litter debris inputs, and animal disturbance; the other cores were placed in open mesh bags. A duplicate set of open and closed soil cores was not transferred between sites and was incubated in place. Over the 2-year experiment, net nitrification increased in both open and closed cores transferred from forest to meadow, and to a lesser extent in cores remaining in the forest. In three of four forest soil treatments, net nitrification increases were accompanied by increases in nitrification potential rates (NPR) and 10- to 100-fold increases in AOB populations. In open cores remaining in the forests, however, increases in net nitrification were not accompanied by significant increases in either NPR or AOB populations. Although some meadow soil treatments reduced both net nitrification and nitrification potential rates, significant changes were not detected in most probable number (MPN)-based estimates of AOB population densities. Terminal restriction fragment profiles (T-RFs) of a PCR-amplified 491-bp fragment of the ammonia monooxygenase subunit A gene (amoA) changed significantly in response to some soil treatments, and treatment effects differed among locations and between years. A T-RF previously shown to be a specific biomarker of Nitrosospira cluster 4 (Alu390) was widespread and dominant in the majority of soil samples. Despite some treatments causing substantial increases in AOB population densities and nitrification potential rates, nitrosomonads remained undetectable, and the nitrosospirad AOB community composition did not change radically following treatment.

Microbial community dynamics associated with rhizosphere carbon flow

Root-deposited photosynthate (rhizodeposition) is an important source of readily available carbon (C) for microbes in the vicinity of growing roots. Plant nutrient availability is controlled, to a large extent, by the cycling of this and other organic materials through the soil microbial community. Currently, our understanding of microbial community dynamics associated with rhizodeposition is limited. We used a (13)C pulse-chase labeling procedure to examine the incorporation of rhizodeposition into individual phospholipid fatty acids (PLFAs) in the bulk and rhizosphere soils of greenhouse-grown annual ryegrass (Lolium multiflorum Lam. var. Gulf). Labeling took place during a growth stage in transition between active root growth and rapid shoot growth on one set of plants (labeling period 1) and 9 days later during the rapid shoot growth stage on another set of plants (labeling period 2). Temporal differences in microbial community composition were more apparent than spatial differences, with a greater relative abundance of PLFAs from gram-positive organisms (i15:0 and a15:0) in the second labeling period. Although more abundant, gram-positive organisms appeared to be less actively utilizing rhizodeposited C in labeling period 2 than in labeling period 1. Gram-negative bacteria associated with the 16:1omega5 PLFA were more active in utilizing (13)C-labeled rhizodeposits in the second labeling period than in the first labeling period. In both labeling periods, however, the fungal PLFA 18:2omega6,9 was the most highly labeled. These results demonstrate the effectiveness of using (13)C labeling and PLFA analysis to examine the microbial dynamics associated with rhizosphere C cycling by focusing on the members actively involved.

Community composition and functioning of denitrifying bacteria from adjacent meadow and forest soils

We investigated communities of denitrifying bacteria from adjacent meadow and forest soils. Our objectives were to explore spatial gradients in denitrifier communities from meadow to forest, examine whether community composition was related to ecological properties (such as vegetation type and process rates), and determine phylogenetic relationships among denitrifiers. nosZ, a key gene in the denitrification pathway for nitrous oxide reductase, served as a marker for denitrifying bacteria. Denitrifying enzyme activity (DEA) was measured as a proxy for function. Other variables, such as nitrification potential and soil C/N ratio, were also measured. Soil samples were taken along transects that spanned meadow-forest boundaries at two sites in the H. J. Andrews Experimental Forest in the Western Cascade Mountains of Oregon. Results indicated strong functional and structural community differences between the meadow and forest soils. Levels of DEA were an order of magnitude higher in the meadow soils. Denitrifying community composition was related to process rates and vegetation type as determined on the basis of multivariate analyses of nosZ terminal restriction fragment length polymorphism profiles. Denitrifier communities formed distinct groups according to vegetation type and site. Screening 225 nosZ clones yielded 47 unique denitrifying genotypes; the most dominant genotype occurred 31 times, and half the genotypes occurred once. Several dominant and less-dominant denitrifying genotypes were more characteristic of either meadow or forest soils. The majority of nosZ fragments sequenced from meadow or forest soils were most similar to nosZ from the Rhizobiaceae group in alpha-Proteobacteria species. Denitrifying community composition, as well as environmental factors, may contribute to the variability of denitrification rates in these systems.

Trichloroethylene Degradation by Toluene-Oxidizing Bacteria Grown on Non-aromatic Substrates

The potential of trichloroethylene (TCE) to induce and non-aromatic growth substrates to support TCE degradation in five strains (Pseudomonas mendocina KR1, Ralstonia pickettii PKO1, Pseudomonas putida F1, Burkholderia cepacia G4, B. cepacia PR1) of toluene-oxidizing bacteria was examined. LB broth and acetate did not support TCE degradation in any of the wild-type strains. In contrast, fructose supported the highest specific levels of TCE oxidation observed in each of the strains tested, except B. cepacia G4. We discuss the potential mechanisms and implications of this observation. In particular, cells of P. mendocina KR1 degraded significant amounts of TCE during cell growth on non-aromatic substrates. Apparently, TCE degradation was not completely constrained by any given factor in this microorganism, as was observed with P. putida F1 (TCE was an extremely poor substrate) or B. cepacia G4 (lack of oxygenase induction by TCE). Our results indicate that multiple physiological traits are required to enable useful TCE degradation by toluene-oxidizing bacteria in the absence of aromatic cosubstrates. These traits include oxygenase induction, effective TCE turnover, and some level of resistance to TCE mediated toxicity.

Ammonia-oxidizing bacteria along meadow-to-forest transects in the Oregon Cascade Mountains

Although nitrification has been well studied in coniferous forests of Western North America, communities of NH(3)-oxidizing bacteria in these forests have not been characterized. Studies were conducted along meadow-to-forest transects at two sites (Lookout and Carpenter) in the H. J. Andrews Experimental Forest, located in the Cascade Mountains of Oregon. Soil samples taken at 10- or 20-m intervals along the transects showed that several soil properties, including net nitrogen mineralization and nitrification potential rates changed significantly between vegetation zones. Nonetheless, terminal restriction fragment length polymorphism (T-RFLP) analysis of the PCR-amplified NH(3) monooxygenase subunit A gene (amoA) showed the same DNA fragments (TaqI [283 bp], CfoI [66 bp], and AluI [392 bp]) to dominate >/=45 of 47 soil samples recovered from both sites. Two fragments (491-bp AluI [AluI491] and CfoI135) were found more frequently in meadow and transition zone soil samples than in forest samples at both sites. At the Lookout site the combination AluI491-CfoI135 was found primarily in meadow samples expressing the highest N mineralization rates. Four unique amoA sequences were identified among 15 isolates recovered into pure culture from various transect locations. Six isolates possessed the most common T-RFLP amoA fingerprint of the soil samples (TaqI283-AluI392-CfoI66), and their amoA sequences shared 99.8% similarity with a cultured species, Nitrosospira sp. strain Ka4 (cluster 4). The other three amoA sequences were most similar to sequences of Nitrosospira sp. strain Nsp1 and Nitrosospira briensis (cluster 3). 16S ribosomal DNA sequence analysis confirmed the affiliation of these isolates with Nitrosospira clusters 3 and 4. Two amoA clone sequences matched T-RFLP fingerprints found in soil, but they were not found among the isolates.

Treatment of atrazine in nursery irrigation runoff by a constructed wetland

To investigate the treatment capability of a surface flow wetland at a container nursery near Portland, Oregon, atrazine was introduced during simulated runoff events. Treatment efficiency was evaluated as the percent atrazine recovered (as percent of applied) in the water column at the wetland's outlet. Atrazine treatment efficiency at the outlet of the constructed wetland during a 7-d period ranged from 18-24% in 1998 (experiments 1-3) and 16-17% in 1999 (experiments 4 and 5). Changes in total flow, or frequency and intensity of runoff events did not affect treatment. For experiment 6 in 1999, where the amount, frequency, and duration of runoff events exceeded all other experiments, treatment was compromised. For all experiments, deethylatrazine (DEA) and deisopropylatrazine (DIA) accounted for 13-21% of the initial application. Hydroxyatrazine (HA) was rarely detected in the water. Organic carbon adsorption coefficients (Koc) were determined from batch equilibrium sorption isotherms with wetland sediment, and they decreased in the order of HA > DIA > atrazine > DEA. Static water-sediment column experiments indicated that sorption is an important mechanism for atrazine loss from water passing through the constructed wetland. The results of the MPN assay indicated the existence in the wetland of a low-density population of microorganisms with the potential to mineralize atrazine's ethyl side chain.

Biodegradation of monohalogenated alkanes by soil NH(3)-oxidizing bacteria

Although cooxidative biodegradation of monohalogenated hydrocarbons has been well studied in the model NH(3)-oxidizing bacterium, Nitrosomonas europaea, virtually no information exists about cooxidation of these compounds by native populations of NH(3)-oxidizing bacteria. To address this subject, nitrifying activity was stimulated to 125-400 nmol NO(3)(-) produced g(-1) soil h(-1) by first incubating a Ca(OH)(2)-amended, silt loam soil (pH 7.0+/-0.2) at field capacity (270 g H(2)O kg(-1) soil) with 10 micro mol NH(4)(+) g(-1) soil for 14 days, followed by another 10 days of incubation in a shaken slurry (2:1 water:soil, v/w) with periodic pH adjustment and maintenance of 10 mM NH(4)(+). These slurries actively degraded both methyl bromide (MeBr) and ethyl chloride (EtCl) at maximum rates of 20-30 nmol ml(-1) h(-1) that could be sustained for approximately 12 h. Although the MeBr degradation rates were linear for the first 10-12 h of incubation, they could not be sustained regardless of NH(4)(+) level and declined to zero over 20 h of incubation. The transformation capacity of the slurry enrichments (~1 micro mol MeBr ml(-1) soil slurry) was similar to the value measured previously in cell suspensions of N. europaea with similar NH(3)-oxidizing activity. Several MeBr-degrading characteristics of the nitrifying enrichments were found to be similar to those documented in the literature for MeBr-degrading methanotrophs and facultatively methylotrophic bacteria.

Exploration of inorganic C and N assimilation by soil microbes with time-of-flight secondary ion mass spectrometry

Stable C and N isotopes have long been used to examine properties of various C and N cycling processes in soils. Unfortunately, relatively large sample sizes are needed for accurate gas phase isotope ratio mass spectrometric analysis. This limitation has prevented researchers from addressing C and N cycling issues on microbially meaningful scales. Here we explored the use of time-of-flight secondary ion mass spectrometry (TOF-SIMS) to detect 13C and 15N assimilation by individual bacterial cells and to quantify N isotope ratios in bacterial samples and individual fungal hyphae. This was accomplished by measuring the relative abundances of mass 26 (12C14N-) and mass 27 (13C14N- and 12C15N-) ions sputtered with a Ga+ probe from cells adhered to an Si contact slide. TOF-SIMS was successfully used to locate and quantify the relative 15N contents of individual hyphae that grew onto Si contact slides in intimate contact with a model organomineral porous matrix composed of kaolin, straw fragments, and freshly deposited manure that was supplemented with 15NO3-. We observed that the 15N content of fungal hyphae grown on the slides was significantly lower in regions where the hyphae were influenced by N-rich manure than in regions influenced by N-deficient straw. This effect occurred over distances of tens to hundreds of microns. Our data illustrate that TOF-SIMS has the potential to locate N-assimilating microorganisms in soil and to quantify the 15N content of cells that have assimilated 15N-labeled mineral N and shows promise as a tool with which to explore the factors controlling microsite heterogeneities in soil.

Noninvasive quantitative measurement of bacterial growth in porous media under unsaturated-flow conditions

Glucose-dependent growth of the luxCDABE reporter bacterium Pseudomonas fluorescens HK44 was monitored noninvasively in quartz sand under unsaturated-flow conditions within a 45- by 56- by 1-cm two-dimensional light transmission chamber. The spatial and temporal development of growth were mapped daily over 7 days by quantifying salicylate-induced bioluminescence. A nonlinear model relating the rate of increase in light emission after salicylate exposure to microbial density successfully predicted growth over 4 orders of magnitude (r(2) = 0.95). Total model-predicted growth agreed with growth calculated from the mass balance of the system by using previously established growth parameters of HK44 (predicted, 1.2 x 10(12) cells; calculated, 1.7 x 10(12) cells). Colonization expanded in all directions from the inoculation region, including upward migration against the liquid flow. Both the daily rate of expansion of the colonized zone and the population density of the first day's growth in each newly colonized region remained relatively constant throughout the experiment. Nonetheless, substantial growth continued to occur on subsequent days in the older regions of the colonized zone. The proportion of daily potential growth that remained within the chamber declined progressively between days 2 and 7 (from 97 to 13%). A densely populated, anoxic region developed in the interior of the colonized zone even though the sand was unsaturated and fresh growth medium continued to flow through the colonized zone. These data illustrate the potential of a light transmission chamber, bioluminescent bacteria, and sensitive digital camera technology to noninvasively study real-time hydrology-microbiology interactions associated with unsaturated flow in porous media.

Requirement of DNA repair mechanisms for survival of Burkholderia cepacia G4 upon degradation of trichloroethylene

A Tn5-based mutagenesis strategy was used to generate a collection of trichloroethylene (TCE)-sensitive (TCS) mutants in order to identify repair systems or protective mechanisms that shield Burkholderia cepacia G4 from the toxic effects associated with TCE oxidation. Single Tn5 insertion sites were mapped within open reading frames putatively encoding enzymes involved in DNA repair (UvrB, RuvB, RecA, and RecG) in 7 of the 11 TCS strains obtained (4 of the TCS strains had a single Tn5 insertion within a uvrB homolog). The data revealed that the uvrB-disrupted strains were exceptionally susceptible to killing by TCE oxidation, followed by the recA strain, while the ruvB and recG strains were just slightly more sensitive to TCE than the wild type. The uvrB and recA strains were also extremely sensitive to UV light and, to a lesser extent, to exposure to mitomycin C and H(2)O(2). The data from this study establishes that there is a link between DNA repair and the ability of B. cepacia G4 cells to survive following TCE transformation. A possible role for nucleotide excision repair and recombination repair activities in TCE-damaged cells is discussed.

A model that uses the induction phase of lux gene-dependent bioluminescence in Pseudomonas fluorescens HK44 to quantify cell density in translucent porous media

A cooled charge-coupled device (CCD) camera was used to follow the kinetics of induction of lux gene-dependent bioluminescence in Pseudomonas fluorescens HK44 held either in aqueous suspensions minus sand, saturated or unsaturated translucent sand (0.348 and 0.07 cm(3) H(2)O/cm(3) of sand, respectively), and at cell densities ranging between 1 x 10(6) and 8.5 x 10(8) cells/ml. Before O(2) availability became a limiting factor, the rate of light emission (L) increased with the square of time (t) and linearly with increasing cell density (c). A nonlinear model was developed that contains a "rate of increase in light emission" constant, B', which is determined directly from the slope of a plot of radical L/c against t. The model predicted the behavior of lux induction in HK44 under a variety of conditions. Similar B' values were determined [49.0-57.6 x 10(-10) light units/(cell min(2))] for cell suspensions held in aqueous medium minus sand, in saturated or unsaturated 40/50 grade sand (0.36 mm grain diameter) and in two other textural classes of translucent sand. Although both the growth phase, and the presence of glucose during lux induction affected the first detectable time (FDT) of bioluminescence by HK44 in sand, the kinetics of induction of light emission were similar among treatments (stationary phase cells plus glucose, B'=61.6+/-3.2, log phase cells plus glucose, B'=63.2+/-7.2). The potential exists to use a combination of a CCD camera system, an inducible lux gene containing bioluminescent bacterium, and a light transmission chamber to nonintrusively visualize and quantify in real time the interactions between bacterial growth and unsaturated flow of water and solutes in porous media.

Atrazine degradation by bioaugmented sediment from constructed wetlands

The potential to establish pesticide biodegradation in constructed wetland sediment was investigated. Under microcosm conditions, bioaugmentation of sediment with small quantities of an atrazine spill-site soil (1:100 w/w) resulted in the mineralization of 25-30% of 14C ethyl atrazine (1-10 microg g(-1) sediment) as 14CO2 under both unsaturated and water-saturated conditions; atrazine and its common metabolites were almost undetectable after 30 days incubation. By comparison, unbioaugmented sediment supplemented with organic amendments (cellulose or cattail leaves) mineralized only 2-3% of 14C ethyl atrazine, and extractable atrazine and its common metabolites comprised approximately 70% of the original application. The population density of atrazine-degrading microorganisms in unbioaugmented sediment was increased from approximately 10(2)/g to 10(4)/g by bioaugmentation (1:100 w/w), and increased by another 60-fold (6.0x10(5) g(-1)) after incubation with 10 microg g(-1) of atrazine. A high population of atrazine degraders (approximately 10(6) g(-1)) and enhanced rates of atrazine mineralization also developed in bioaugmented sediment after incubation in flooded mesocosms planted with cattails (Typha latifolia) and supplemented with atrazine (3.2 mg l(-1), 1 microg g(-1) sediment). In the absence of atrazine, neither the population of atrazine degraders, nor the atrazine mineralizing potential of bioaugmented sediment increased, regardless of the presence or absence of cattails. Bioaugmentation might be a simple method to promote pesticide degradation in nursery run-off channeled through constructed wetlands, if persistence of degraders in the absence of pesticide is not a serious constraint.

Atrazine remediation in wetland microcosms

Laboratory wetland microcosms were used to study treatment of atrazine in irrigation runoff by a field-scale-constructed wetland under controlled conditions. Three experiments, in which 1 ppm atrazine was added to the water column of three wetland, one soil control, and one water control microcosm, were conducted. Atrazine dissipation from the water column and degradate formation (deethylatrazine [DEA]; deisopropylatrazine [DIA]; and hydroxyatrazine [HA]) were monitored. Atrazine dissipation from the water column of wetland microcosms was biphasic. Less than 12% of the atrazine applied to wetland microcosms remained in the water column on day 56. Atrazine degradates were observed in water and sediment, with HA the predominant degradate. Analysis of day 56 sediment samples indicated that a significant portion of the initial application was detected as the parent compound and HA. Most probable number (MPN) assays demonstrated that atrazine degrader populations were small in wetland sediment. Wetland microcosms were able to reduce atrazine concentration in the water column via sorption and degradation. Based on results from this study, it is hypothesized that plant uptake contributed to atrazine dissipation from the water column.

Cytotoxicity associated with trichloroethylene oxidation in Burkholderia cepacia G4

The effects of trichloroethylene (TCE) oxidation on toluene 2-monooxygenase activity, general respiratory activity, and cell culturability were examined in the toluene-oxidizing bacterium Burkholderia cepacia G4. Nonspecific damage outpaced inactivation of toluene 2-monooxygenase in B. cepacia G4 cells. Cells that had degraded approximately 0.5 micromol of TCE (mg of cells(-1)) lost 95% of their acetate-dependent O(2) uptake activity (a measure of general respiratory activity), yet toluene-dependent O(2) uptake activity decreased only 35%. Cell culturability also decreased upon TCE oxidation; however, the extent of loss varied greatly (up to 3 orders of magnitude) with the method of assessment. Addition of catalase or sodium pyruvate to the surfaces of agar plates increased enumeration of TCE-injured cells by as much as 100-fold, indicating that the TCE-injured cells were ultrasensitive to oxidative stress. Cell suspensions that had oxidized TCE recovered the ability to grow in liquid minimal medium containing lactate or phenol, but recovery was delayed substantially when TCE degradation approached 0.5 micromol (mg of cells(-1)) or 66% of the cells' transformation capacity for TCE at the cell density utilized. Furthermore, among B. cepacia G4 cells isolated on Luria-Bertani agar plates from cultures that had degraded approximately 0.5 micromol of TCE (mg of cells(-1)), up to 90% were Tol(-) variants, no longer capable of TCE degradation. These results indicate that a toxicity threshold for TCE oxidation exists in B. cepacia G4 and that once a cell suspension has exceeded this toxicity threshold, the likelihood of reestablishing an active, TCE-degrading biomass from the cells will decrease significantly.

New insights into methyl bromide cooxidation by Nitrosomonas europaea obtained by experimenting with moderately low density cell suspensions

We examined the rates and sustainability of methyl bromide (MeBr) oxidation in moderately low density cell suspensions ( approximately 6 x 10(7) cells ml(-1)) of the NH(3)-oxidizing bacterium Nitrosomonas europaea. In the presence of 10 mM NH(4)(+) and 0.44, 0. 22, and 0.11 mM MeBr, the initial rates of MeBr oxidation were sustained for 12, 12, and 24 h, respectively, despite the fact that only 10% of the NH(4)(+), 18% of the NH(4)(+), and 35% of the NH(4)(+), respectively, were consumed. Although the duration of active MeBr oxidation generally decreased as the MeBr concentration increased, similar amounts of MeBr were oxidized with a large number of the NH(4)(+)-MeBr combinations examined (10 to 20 micromol mg [dry weight] of cells(-1)). Approximately 90% of the NH(3)-dependent O(2) uptake activity and the NO(2)(-)-producing activity were lost after N. europaea was exposed to 0.44 mM MeBr for 24 h. After MeBr was removed and the cells were resuspended in fresh growth medium, NO(2)(-) production increased exponentially, and 48 to 60 h was required to reach the level of activity observed initially in control cells that were not exposed to MeBr. It is not clear what percentage of the cells were capable of cell division after MeBr oxidation because NO(2)(-) accumulated more slowly in the exposed cells than in the unexposed cells despite the fact that the latter were diluted 10-fold to create inocula which exhibited equal initial activities. The decreases in NO(2)(-)-producing and MeBr-oxidizing activities could not be attributed directly to NH(4)(+) or NH(3) limitation, to a decrease in the pH, to the composition of the incubation medium, or to toxic effects caused by accumulation of the end products of oxidation (NO(2)(-) and formaldehyde) in the medium. Additional cooxidation-related studies of N. europaea are needed to identify the mechanism(s) responsible for the MeBr-induced loss of cell activity and/or viability, to determine what percentages of cells damaged by cooxidative activities are culturable, and to determine if cooxidative activity interferes with the regulation of NH(3)-oxidizing activity.

Effects of soil and water content on methyl bromide oxidation by the ammonia-oxidizing bacterium Nitrosomonas europaea

Little information exists on the potential of NH(3)-oxidizing bacteria to cooxidize halogenated hydrocarbons in soil. A study was conducted to examine the cooxidation of methyl bromide (MeBr) by an NH(3)-oxidizing bacterium, Nitrosomonas europaea, under soil conditions. Soil and its water content modified the availability of NH(4)(+) and MeBr and influenced the relative rates of substrate (NH(3)) and cosubstrate (MeBr) oxidations. These observations highlight the complexity associated with characterizing soil cooxidative activities when soil and water interact to differentially affect substrate and cosubstrate availabilities.