Search

Anthropogenic activities and natural processes release dichloromethane (DCM, methylene chloride), a toxic chemical with substantial ozone-depleting capacity. Specialized anaerobic bacteria metabolize DCM; however, the genetic basis for this process has remained elusive. Comparative genomics of the three known anaerobic DCM-degrading bacterial species revealed a homologous gene cluster, designated the methylene chloride catabolism (mec) gene cassette, comprising 8-10 genes encoding proteins with 79.6%-99.7% amino acid identities. Functional annotation identified genes encoding a corrinoid-dependent methyltransferase system, and shotgun proteomics applied to two DCM-catabolizing cultures revealed high expression of proteins encoded on the mec gene cluster during anaerobic growth with DCM. In a DCM-contaminated groundwater plume, the abundance of mec genes strongly correlated with DCM concentrations (R

Quantitative measurement of process-specific biomarker genes of Dehalococcoides mccartyi (Dhc) supports monitoring at chlorinated ethene contaminated sites. In this study, we varied Dhc cell abunda...

Dehalococcoides mccartyi strains harboring vinyl chloride (VC) reductive dehalogenase (RDase) genes are keystone bacteria for VC detoxification in groundwater aquifers, and bioremediation monitoring regimens focus on D. mccartyi biomarkers. We isolated a novel anaerobic bacterium, “Candidatus Dehalogenimonas etheniformans” strain GP, capable of respiratory dechlorination of VC to ethene. This bacterium couples formate and hydrogen (H(2)) oxidation to the reduction of trichloro-ethene (TCE), all dichloroethene (DCE) isomers, and VC with acetate as the carbon source. Cultures that received formate and H(2) consumed the two electron donors concomitantly at similar rates. A 16S rRNA gene-targeted quantitative PCR (qPCR) assay measured growth yields of (1.2 ± 0.2) × 10(8) and (1.9 ± 0.2) × 10(8) cells per μmol of VC dechlorinated in cultures with H(2) or formate as electron donor, respectively. About 1.5-fold higher cell numbers were measured with qPCR targeting cerA, a single-copy gene encoding a putative VC RDase. A VC dechlorination rate of 215 ± 40 μmol L(−1) day(−1) was measured at 30°C, with about 25% of this activity occurring at 15°C. Increasing NaCl concentrations progressively impacted VC dechlorination rates, and dechlorination ceased at 15 g NaCl L(−1). During growth with TCE, all DCE isomers were intermediates. Tetrachloroethene was not dechlorinated and inhibited dechlorination of other chlorinated ethenes. Carbon monoxide formed and accumulated as a metabolic by-product in dechlorinating cultures and impacted reductive dechlorination activity. The isolation of a new Dehalogenimonas species able to effectively dechlorinate toxic chlorinated ethenes to benign ethene expands our understanding of the reductive dechlorination process, with implications for bioremediation and environmental monitoring. IMPORTANCE Chlorinated ethenes are risk drivers at many contaminated sites, and current bioremediation efforts focus on organohalide-respiring Dehalococcoides mccartyi strains to achieve detoxification. We isolated and characterized the first non-Dehalococcoides bacterium, “Candidatus Dehalogenimonas etheniformans” strain GP, capable of metabolic reductive dechlorination of TCE, all DCE isomers, and VC to environmentally benign ethene. In addition to hydrogen, the new isolate utilizes formate as electron donor for reductive dechlorination, providing opportunities for more effective electron donor delivery to the contaminated subsurface. The discovery that a broader microbial diversity can achieve detoxification of toxic chlorinated ethenes in anoxic aquifers illustrates the potential of naturally occurring microbes for biotechnological applications.

At groundwater sites contaminated with chlorinated ethenes, fermentable substrates are often added to promote reductive dehalogenation by indigenous or augmented microorganisms. Contemporary bioremediation performance monitoring relies on nucleic acid biomarkers of key organohalide-respiring bacteria, such as Dehalococcoides mccartyi (Dhc). Metagenome sequencing of the commercial, Dhc-containing consortium, SDC-9, identified 12 reductive dehalogenase (RDase) genes, including pceA (two copies), vcrA, and tceA, and allowed for specific detection and quantification of RDase peptides using liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS). Shotgun (i.e., untargeted) proteomics applied to the SDC-9 consortium grown with tetrachloroethene (PCE) and lactate identified 143 RDase peptides, and 36 distinct peptides that covered greater than 99% of the protein-coding sequences of the PceA, TceA, and VcrA RDases. Quantification of RDase peptides using multiple reaction monitoring (MRM) assays with 13C-/15N-labeled peptides determined 1.8 × 103 TceA and 1.2 × 102 VcrA RDase molecules per Dhc cell. The MRM mass spectrometry approach allowed for sensitive detection and accurate quantification of relevant Dhc RDases and has potential utility in bioremediation monitoring regimes.

Anthropogenic activities and natural processes release dichloromethane (DCM), a toxic chemical with substantial ozone-depleting capacity. Specialized anaerobic bacteria metabolize DCM; however, the genetic basis for this process has remained elusive. Comparative genomics of the three known anaerobic DCM-degrading bacterial species revealed a homologous gene cluster, designated the methylene chloride catabolism (mec) gene cassette, comprising eight to ten genes with predicted 79.6 – 99.7% amino acid identity. Functional annotation identified genes encoding a corrinoid-dependent methyltransferase system, and shotgun proteomics applied to two DCM-catabolizing cultures revealed high expression of proteins encoded on the mec gene cluster during anaerobic growth with DCM. In a DCM-contaminated groundwater plume, the abundance of mec genes strongly correlated with DCM concentrations (R2 = 0.71 – 0.85) indicating their value as process-specific bioremediation biomarkers. mec gene clusters were identified in metagenomes representing peat bogs, the deep subsurface, and marine ecosystems including oxygen minimum zones (OMZs), suggesting DCM turnover in diverse habitats. The broad distribution of anaerobic DCM catabolic potential suggests a relevant control function for emissions to the atmosphere, and a role for DCM as a microbial energy source in critical zone environments. The findings imply that the global DCM flux might be far greater than emission measurements suggest.ImportanceDichloromethane (DCM) is an increasing threat to stratospheric ozone with both anthropogenic and natural emission sources. Anaerobic bacterial metabolism of DCM has not yet been taken into consideration as a factor in the global DCM cycle. The discovery of the mec gene cassette associated with anaerobic bacterial DCM metabolism and its widespread distribution in environmental systems highlight a strong attenuation potential for DCM. Knowledge of the mec cassette offers new opportunities to delineate DCM sources, enables more robust estimates of DCM fluxes, supports refined DCM emission modeling and simulation of the stratospheric ozone layer, reveals a novel, ubiquitous C1 carbon metabolic system, and provides prognostic and diagnostic tools supporting bioremediation of groundwater aquifers impacted by DCM.

We report the sequencing, assembly, and draft genome of Shewanella sp. strain BF02_Schw. The assembly contains 5,304,243 bp, with a GC content of 41.43%.

Dichloroacetate (DCA) is ubiquitous in the environment due to natural formation via biological and abiotic chlorination processes and the turnover of chlorinated organic materials (e.g., humic substances). Additional sources include DCA usage as a chemical feedstock and cancer drug and its unintentional formation during drinking water disinfection by chlorination., Dichloroacetate (DCA) commonly occurs in the environment due to natural production and anthropogenic releases, but its fate under anoxic conditions is uncertain. Mixed culture RM comprising “Candidatus Dichloromethanomonas elyunquensis” strain RM utilizes DCA as an energy source, and the transient formation of formate, H2, and carbon monoxide (CO) was observed during growth. Only about half of the DCA was recovered as acetate, suggesting a fermentative catabolic route rather than a reductive dechlorination pathway. Sequencing of 16S rRNA gene amplicons and 16S rRNA gene-targeted quantitative real-time PCR (qPCR) implicated “Candidatus Dichloromethanomonas elyunquensis” strain RM in DCA degradation. An (S)-2-haloacid dehalogenase (HAD) encoded on the genome of strain RM was heterologously expressed, and the purified HAD demonstrated the cofactor-independent stoichiometric conversion of DCA to glyoxylate at a rate of 90 ± 4.6 nkat mg−1 protein. Differential protein expression analysis identified enzymes catalyzing the conversion of DCA to acetyl coenzyme A (acetyl-CoA) via glyoxylate as well as enzymes of the Wood-Ljungdahl pathway. Glyoxylate carboligase, which catalyzes the condensation of two molecules of glyoxylate to form tartronate semialdehyde, was highly abundant in DCA-grown cells. The physiological, biochemical, and proteogenomic data demonstrate the involvement of an HAD and the Wood-Ljungdahl pathway in the anaerobic fermentation of DCA, which has implications for DCA turnover in natural and engineered environments, as well as the metabolism of the cancer drug DCA by gut microbiota.

Methylation sequencing using bisulfite treatment has revolutionized the field of molecular biology for eukaryotic systems, unveiling levels of intricacy in regulation of gene expression in response to different environmental conditions. While bacteria also utilize methylation to regulate gene expression, bisulfite sequencing does not work as well in bacteria as in eukaryotes, because bacteria methylate adenosine instead of cytosine. Therefore, global bacterial methylation patterns cannot be studied using common Illumina sequencers. In this work, we demonstrate 6mA-seq, a method that can be used to identify patterns in bacteria that methylate adenosines at GATC sites. Furthermore, this method was used on Escherichia coli cultured on four different carbon sources to demonstrate different methylation patterns due to carbon utilization. 6mA-seq can increase the speed in which epigenetic research is conducted in bacteria.

We report the isolation a halophilic bacterium that degrades both aromatic and aliphatic hydrocarbons as the sole sources of carbon at high salinity from produced water. Phylogenetic analysis of 16S rRNA-gene sequences shows the isolate is a close relative of Modicisalibacter tunisiensis isolated from an oil-field water in Tunisia. We designate our isolate as Modicisalibacter sp. strain Wilcox. Genome analysis of strain Wilcox revealed the presence of a repertoire of genes involved in the metabolism of aliphatic and aromatic hydrocarbons. Laboratory culture studies corroborated the predicted hydrocarbon degradation potential. The strain degraded benzene, toluene, ethylbenzene, and xylenes at salinities ranging from 0.016 to 4.0 M NaCl, with optimal degradation at 1 M NaCl. Also, the strain degraded phenol, benzoate, biphenyl and phenylacetate as the sole sources of carbon at 2.5 M NaCl. Among aliphatic compounds, the strain degraded n-decane and n-hexadecane as the sole sources of carbon at 2.5 M NaCl. Genome analysis also predicted the presence of many heavy metal resistance genes including genes for metal efflux pumps, transport proteins, and enzymatic detoxification. Overall, due to its ability to degrade many hydrocarbons and withstand high salt and heavy metals, strain Wilcox may prove useful for remediation of produced waters.

At groundwater sites contaminated with chlorinated ethenes, fermentable substrates are often added to promote reductive dehalogenation by indigenous or augmented microorganisms. Contemporary bioremediation performance monitoring relies on nucleic acid biomarkers of key organohalide-respiring bacteria, such as

Nonylphenol polyethoxylate (NPnEO) surfactants, ubiquitous contaminants in sewage processing facilities, continue to receive attention due to their recalcitrance and diverse toxicity concerns. How the addition of nonylphenol diethoxylate (NP2EO) and its biodegradation products affect microbial community structure in anaerobic semi-continuous digesters was investigated by molecular techniques. Fluorescence in situ hybridization (FISH) and quantitative PCR (qPCR) were used in parallel to monitor total Bacteria, four classes of Proteobacteria, total Archaea, and two genera of acetoclastic methanogens (Methanosarcina and Methanosaeta). Beta- and Gammaproteobacteria were the dominant phyla and the relative abundances of both groups were roughly doubled following NP2EO addition. While Methanosaeta was dominant over Methanosarcina throughout, NP2EO addition and accumulation of NP nearly doubled the relative abundance of Methanosarcina. While digester performance was not affected, this study revealed that relative abundances of the key players in anaerobic digestion were altered by the addition of NP2EO.

Quantitative PCR (qPCR) targeting Dehalococcoides mccartyi (Dhc) biomarker genes supports effective management at sites impacted with chlorinated ethenes. To establish correlations between Dhc biomarker gene abundances and ethene formation (i.e., detoxification), 859 groundwater samples representing 62 sites undergoing monitored natural attenuation or enhanced remediation were analyzed. Dhc 16S rRNA genes and the vinyl chloride (VC) reductive dehalogenase genes bvcA and vcrA were detected in 88% and 61% of samples, respectively, from wells with ethene. Dhc 16S rRNA, bvcA, vcrA, and tceA (implicated in cometabolic reductive VC dechlorination) gene abundances all positively correlated with ethene formation. Significantly greater ethene concentrations were observed when Dhc 16S rRNA gene and VC RDase gene abundances exceeded 10(7) and 10(6) copies L(−1), respectively, and when Dhc 16S rRNA- and bvcA + vcrA-to-total bacterial 16S rRNA gene ratios exceeded 0.1%. Dhc 16S rRNA gene-to-vcrA/bvcA ratios near unity also indicated elevated ethene; however, no increased ethene was observed in 19 wells where vcrA and/or bvcA gene copy numbers exceeded Dhc cell numbers 10- to 10 000-fold. Approximately one-third of samples with detectable ethene lacked bvcA, vcrA, and tceA, suggesting that comprehensive understanding of VC detoxification biomarkers has not been achieved. Although the current biomarker suite is incomplete, the data analysis corroborates the value of the available Dhc DNA biomarkers for prognostic and diagnostic groundwater monitoring at sites impacted with chlorinated ethenes.

Volume 10, no. 5, e02039-19, 2019, [https://doi.org/10.1128/mBio.02039-19][1]. The affiliation of coauthor Frank E. Loffler with Oak Ridge National Laboratory was inadvertently omitted. The corrected author affiliations are shown above. [1]: /lookup/doi/10.1128/mBio.02039-19

Microorganisms of the superphylum Asgard Archaea are considered to be the closest living prokaryotic relatives of eukaryotes (including plants and animals) and thus promise to give insights into the early evolution of more complex life forms. However, very little is known about their biology as none of the organisms has yet been cultivated in the laboratory. Here we report on the ecological distribution of Asgard Archaea and on four newly sequenced genomes of the Lokiarchaeota and Thorarchaeota lineages that give insight into possible metabolic features that might eventually help to identify these enigmatic groups of archaea in the environment and to culture them., The genomes of Asgard Archaea, a novel archaeal proposed superphylum, share an enriched repertoire of eukaryotic signature genes and thus promise to provide insights into early eukaryote evolution. However, the distribution, metabolisms, cellular structures, and ecology of the members within this superphylum are not well understood. Here we provide a meta-analysis of the environmental distribution of the Asgard archaea, based on available 16S rRNA gene sequences. Metagenome sequencing of samples from a salt-crusted lagoon on the Baja California Peninsula of Mexico allowed the assembly of a new Thorarchaeota and three Lokiarchaeota genomes. Comparative analyses of all known Lokiarchaeota and Thorarchaeota genomes revealed overlapping genome content, including central carbon metabolism. Members of both groups contained putative reductive dehalogenase genes, suggesting that these organisms might be able to metabolize halogenated organic compounds. Unlike the first report on Lokiarchaeota, we identified genes encoding glycerol-1-phosphate dehydrogenase in all Loki- and Thorarchaeota genomes, suggesting that these organisms are able to synthesize bona fide archaeal lipids with their characteristic glycerol stereochemistry.

Dichloromethane (DCM) is susceptible to microbial degradation under anoxic conditions and is metabolized via the Wood-Ljungdahl pathway; however, mechanistic understanding of carbon-chlorine bond cleavage is lacking. The microbial consortium RM contains the DCM degrader “Candidatus Dichloromethanomonas elyunquensis” strain RM, which strictly requires DCM as a growth substrate. Proteomic workflows applied to DCM-grown consortium RM biomass revealed a total of 1,705 nonredundant proteins, 521 of which could be assigned to strain RM. In the presence of DCM, strain RM expressed a complete set of Wood-Ljungdahl pathway enzymes, as well as proteins implicated in chemotaxis, motility, sporulation, and vitamin/cofactor synthesis. Four corrinoid-dependent methyltransferases were among the most abundant proteins. Notably, two of three putative reductive dehalogenases (RDases) encoded within strain RM’s genome were also detected in high abundance. Expressed RDase 1 and RDase 2 shared 30% amino acid identity, and RDase 1 was most similar to an RDase of Dehalococcoides mccartyi strain WBC-2 (AOV99960, 52% amino acid identity), while RDase 2 was most similar to an RDase of Dehalobacter sp. strain UNSWDHB (EQB22800, 72% amino acid identity). Although the involvement of RDases in anaerobic DCM metabolism has yet to be experimentally verified, the proteome characterization results implicated the possible participation of one or more reductive dechlorination steps and methyl group transfer reactions, leading to a revised proposal for an anaerobic DCM degradation pathway. IMPORTANCE Naturally produced and anthropogenically released DCM can reside in anoxic environments, yet little is known about the diversity of organisms, enzymes, and mechanisms involved in carbon-chlorine bond cleavage in the absence of oxygen. A proteogenomic approach identified two RDases and four corrinoid-dependent methyltransferases expressed by the DCM degrader “Candidatus Dichloromethanomonas elyunquensis” strain RM, suggesting that reductive dechlorination and methyl group transfer play roles in anaerobic DCM degradation. These findings suggest that the characterized DCM-degrading bacterium Dehalobacterium formicoaceticum and “Candidatus Dichloromethanomonas elyunquensis” strain RM utilize distinct strategies for carbon-chlorine bond cleavage, indicating that multiple pathways evolved for anaerobic DCM metabolism. The specific proteins (e.g., RDases and methyltransferases) identified in strain RM may have value as biomarkers for monitoring anaerobic DCM degradation in natural and contaminated environments.

A bacterium was isolated from activated sewage sludge that has the ability to use ibuprofen as its sole carbon and energy source. Phylogenetic analysis of the 16S rRNA gene sequence placed the strain in the Variovorax genus within the β-proteobacteria. When grown on ibuprofen it accumulated a transient yellow intermediate that disappeared upon acidification, a trait consistent with meta ring-fission metabolites. GC/MS analysis of derivatized culture supernatant yielded two spectra consistent with trihydroxyibuprofen bearing all three hydroxyl groups on the aromatic ring. These metabolites were only detected when 3-fluorocatechol, a meta ring-fission inhibitor, was added to Ibu-1 cultures and the supernatant was then derivatized with aqueous acetic anhydride and diazomethane. These findings suggest the possibility of ibuprofen metabolism proceeding via a trihydroxyibuprofen meta ring-fission pathway. Identical spectra, consistent with these putative ring-hydroxylated trihydroxyibuprofen metabolites, were also obtained from ibuprofen-spiked sewage sludge, but only when it was poisoned with 3-fluorocatechol. The presence of the same trihydroxylated metabolites in both spiked sewage sludge and culture supernatants suggests that this trihydroxyibuprofen extradiol ring-cleavage pathway for the degradation of ibuprofen may have environmental relevance.

Dehalobacterium formicoaceticum utilizes dichloromethane as the sole energy source in defined anoxic bicarbonate-buffered mineral salt medium. The products are formate, acetate, inorganic chloride, and biomass. The bacterium’s genome was sequenced using PacBio, assembled, and annotated. The complete genome consists of one 3.77-Mb circular chromosome harboring 3,935 predicted protein-encoding genes.

The US Environmental Protection Agency (EPA) published a National Ambient Air Quality Standard (NAAQS) and the accompanying Federal Reference Method (FRM) for PM 10 in 1987. The EPA revised the particle standards and FRM in 1997 to include PM 2.5. In 2005, EPA proposed revisions to this NAAQS to include PM 10–2.5 but only finalized revisions with a PM 2.5 FRM and the development of a national monitoring network in 2006. Presently, no EPA designated reference or equivalent method sampler has the ability to directly measure the mass concentrations of PM 10 , PM 10–2.5 , and PM 2.5 simultaneously. An additive approach has been used for samplers like the dichotomous monitors to calculate PM 10 mass concentrations from independent measures of PM 10–2.5 and PM 2.5 (i.e. PM 10 = PM 10–2.5 + PM 2.5 ). A differential approach has been used to calculate PM 10–2.5 from identical collocated PM 10 and PM 2.5 samplers (i.e. PM 10–2.5 = PM 10 –PM 2.5 ). Since these two approaches have been used widely for PM measurements, it is informative to evaluate their precision and comparability. EPA performed collocated tests of five different particle samplers in the Research Triangle Park area of North Carolina to evaluate the comparability and to characterize the additive and differential approaches used to determine particle mass concentrations. The intra-sampler precision of MiniVol, Omni, and dichotomous samplers was less than 8.4%. The precision of PM 10 measurements using the additive approach with dichotomous samplers was less than 3.5%. The poorest precision of the various PM 10–2.5 differential approaches was less than 15.1%. No zero or negative PM 10–2.5 concentrations were calculated using the differential approach. A coefficient of determination of 0.81 or higher was obtained for all paired comparison of PM 10–2.5. The reported test results show that concentrations calculated from both the additive and differential approaches generally agree among the portable samplers, the more established dichotomous sampler and the Federal Reference Methods

Subsequent to the 1997 promulgation of the Federal Reference Method (FRM) for monitoring fine particulate matter (PM2.5) in ambient air, U.S. Environmental Protection Agency (EPA) received reports that the DOW 704 diffusion oil used in the method's Well Impactor Ninety-Six (WINS) fractionator would occasionally crystallize during field use, particularly under wintertime conditions. Although the frequency of occurrence on a nationwide basis was low, uncertainties existed as to whether crystallization of the DOW 704 oil may adversely affect a sampling event's data quality. In response to these concerns, EPA and the State of Connecticut Department of Environmental Protection jointly conducted a series of specialized tests to determine whether crystallized oil adversely affected the performance of the WINS fractionator. In the laboratory, an experimental setup used dry ice to artificially induce crystallization of the diffusion oil under controlled conditions. Using primary polystyrene latex calibration aerosols, standard size-selective performance tests of the WINS fractionator showed that neither the position nor the shape of the WINS particle size fractionation curve was substantially influenced by the crystallization of the DOW 704 oil. No large particle bounce from the crystallized impaction surface was observed. During wintertime field tests, crystallization of the DOW 704 oil did not adversely affect measured PM2.5 concentrations. Regression of measurements with crystallized DOW 704 versus liquid dioctyl sebacate (DOS) oil produced slope, intercept, and R2 values of 0.98, 0.1, and 0.997 microg/m3, respectively. Additional field tests validated the use of DOS as an effective impaction substrate. As a result of these laboratory and field tests, DOS oil has been approved by EPA as a substitute for DOW 704 oil. Since the field deployment of DOS oil in 2001, users of this alternative oil have not reported any operational problems associated with its use in the PM2.5 FRM. Limited field evaluation of the BGI very sharp cut cyclone indicates that it provides a viable alternative to the WINS fractionator.

The results of several research field studies were evaluated to estimate the precision and bias of various designated PM2.5 Federal Reference Method (FRM) samplers. Precision was favorable in these carefully conducted research studies where all operational activities were strictly controlled, with an average coefficient of variation (CV) ranging from 2 to 6%. No significant bias was found between the method designations. Comparisons between the designated reference method samplers meet the EPA Equivalent Method Criteria for comparability except for one pair of samplers. In this instance, the

Sphingomonas Ibu-2 has the unusual ability to cleave the acid side chain from the pharmaceutical ibuprofen and related arylacetic acid derivatives to yield corresponding catechols under aerobic conditions via a previously uncharacterized mechanism. Screening a chromosomal library of Ibu-2 DNA in Escherichia coli EPI300 allowed us to identify one fosmid clone (pFOS3G7) that conferred the ability to metabolize ibuprofen to isobutylcatechol. Characterization of pFOS3G7 loss-of-function transposon mutants permitted identification of five ORFs, ipfABDEF, whose predicted amino acid sequences bore similarity to the large and small units of an aromatic dioxygenase (ipfAB), a sterol carrier protein X (SCPx) thiolase (ipfD), a domain of unknown function 35 (DUF35) protein (ipfE) and an aromatic CoA ligase (ipfF). Two additional ORFs, ipfH and ipfI, which encode putative ferredoxin reductase and ferredoxin components of an aromatic dioxygenase system, respectively, were also identified on pFOS3G7. Complementation of a markerless loss-of-function ipfD deletion mutant restored catechol production as did complementation of the ipfF Tn mutant. Expression of subcloned ipfABDEF alone in E. coli did not impart full metabolic activity unless coexpressed with ipfHI. CoA ligation followed by ring oxidation is common to phenylacetic acid pathways. However, the need for a putative SCPx thiolase (IpfD) and DUF35 protein (IpfE) in aerobic arylacetic acid degradation is unprecedented. This work provides preliminary insights into the mechanism behind this novel arylacetic acid-deacylating, catechol-generating activity.

The degree to which small natural dams affect the native bacterial nitrogen cycling community was explored by molecular methods. The identities and relative abundances of ammonia oxidizing bacteria in the sediment surrounding an artificial dam both at the surface and in the hyporheic zone were characterized. Analyses were performed using tRFLP of the conserved amoA gene using a semi-nested degenerate PCR approach. Additionally, an amoA gene library was constructed to characterize the most dominant sediment genotypes. The results of the tRFLP analyses showed clear differences between the upstream and downstream communities at different depths in the sediment column. Non-metric multidimensional scaling ordination of the tRFLP data set produced a stable one-dimensional solution with significant correlations to oxygen, pH, nitrate, and dissolved organic nitrogen levels. The sample corresponding to the hyporheic zone downstream of the dam showed 28–50% higher amoA richness and higher diversity than the other samples. All gene fragments sequenced from the samples grouped with sequences of the Nitrosospira type. Ordination of 16S rDNA tRFLP data revealed a two dimensional data structure, one axis of which had similar chemical correlation characteristics as the amoA model axis. Taken together, the results from this study suggest that the presence of the dam creates physical and chemical heterogeneity that may foster genetic diversity and community changes amongst ammonia oxidizing bacteria.

Medical treatments and personal hygiene lead to the steady release of pharmaceutical and personal care products (PPCPs) into the environment. Some of these PPCPs have been shown to have detrimental environmental effects and could potentially impact human health. Understanding the biological transformation of PPCPs is essential for accurately determining their ultimate environmental fate, conducting accurate risk assessments, and improving PPCP removal. We summarize the current literature concerning the biological transformation of PPCPs in wastewater treatment plants, the environment, and by pure cultures of bacterial isolates. Although some PPCPs, such as ibuprofen, are readily degraded under most studied conditions, others, such as carbamazepine, tend to be recalcitrant. This variation in the biodegradability of PPCPs can be attributed to structural differences, because PPCPs are classified by application, not chemical structure. The degradation pathways of octylphenol by Sphingomonas sp. strain PWE1, ibuprofen by Sphingomonas sp. strain Ibu-2, and DEET by Pseudomonas putida DTB are discussed in more detail.

Medical treatments and personal hygiene lead to the steady release of pharmaceutical and personal care products (PPCPs) into the environment. Some of these PPCPs have been shown to have detrimental environmental effects and could potentially impact human health. Understanding the biological transformation of PPCPs is essential for accurately determining their ultimate environmental fate, conducting accurate risk assessments, and improving PPCP removal. We summarize the current literature concerning the biological transformation of PPCPs in wastewater treatment plants, the environment, and by pure cultures of bacterial isolates. Although some PPCPs, such as ibuprofen, are readily degraded under most studied conditions, others, such as carbamazepine, tend to be recalcitrant. This variation in the biodegradability of PPCPs can be attributed to structural differences, because PPCPs are classified by application, not chemical structure. The degradation pathways of octylphenol by Sphingomonas sp. strain PWE1, ibuprofen by Sphingomonas sp. strain Ibu-2, and DEET by Pseudomonas putida DTB are discussed in more detail.

Although ibuprofen [2-(4-isobutylphenyl)-propionic acid] is one of the most widely consumed drugs in the world, little is known regarding its degradation by environmental bacteria. Sphingomonas sp. strain Ibu-2 was isolated from a wastewater treatment plant based on its ability to use ibuprofen as a sole carbon and energy source. A slight preference toward the R enantiomer was observed, though both ibuprofen enantiomers were metabolized. A yellow color, indicative of meta -cleavage, accumulated transiently in the culture supernatant when Ibu-2 was grown on ibuprofen. When and only when 3-flurocatechol was used to poison the meta -cleavage system, isobutylcatechol was identified in the culture supernatant via gas chromatography-mass spectrometry analysis. Ibuprofen-induced washed-cell suspensions also metabolized phenylacetic acid and 2-phenylpropionic acid to catechol, while 3- and 4-tolylacetic acids and 2-(4-tolyl)-propionic acid were metabolized to the corresponding methyl catechols before ring cleavage. These data suggest that, in contrast to the widely distributed coenzyme A ligase, homogentisate, or homoprotocatechuate pathway for metabolism of phenylacetic acid and similar compounds, Ibu-2 removes the acidic side chain of ibuprofen and related compounds prior to ring cleavage.

Gas dilution systems can be used for multipoint calibrations of pollutant gas analyzers and for the analysis and certification of compressed gas calibration standards. This laboratory evaluation obtained estimates of the accuracy and precision of four representative gas dilution systems. Diluted and undiluted gas mixtures containing carbon monoxide, nitric oxide or sulfur dioxide in nitrogen were sampled by pollutant gas analyzers. Accuracies were estimated from the difference between the slopes of regression lines from measurements of the diluted and undiluted gas mixtures. These accuracy estimates ranged from −3.3 to 10.0 percent. Precisions were estimated from the 95-percent uncertainty for regression-predicted concentrations. These precision estimates ranged from 0.3 to 14.9 percent of the predicted concentration for mid-range dilutions.