Degradation of chlorinated solvents with reactive iron minerals in subsurface sediments from redox transition zones.

Reactive iron (Fe) mineral coatings found in subsurface reduction-oxidation transition zones (RTZs) contribute to the attenuation of contaminants. An 18.3-m anoxic core was collected from the site, where constituents of concern (COCs) in groundwater included chlorinated solvents. Reactive Fe mineral coatings were found to be abundant in the RTZs. This research focused on evaluating reaction kinetics with anoxic sediments bearing ferrous mineral nano-coatings spiked with either tetrachloroethylene (PCE), trichloroethylene (TCE), or 1,4-dichlorobenzene (1,4-DCB). Reaction kinetics with RTZ sediments followed pseudo-first-order reactions for the three contaminants with 90% degradation achieved in less than 39 days. The second-order rate constants for the three COCs ranged from 6.20 × 10-4 to 1.73 × 10-3 Lg-1h-1 with pyrite (FeS2), 4.97 × 10-5 to 1.24 × 10-3 Lg-1h-1with mackinawite (FeS), 1.25 × 10-4 to 1.89 × 10-4 Lg-1h-1 with siderite (FeCO3), and 1.79 × 10-4 to 1.10 × 10-3 Lg-1h-1 with magnetite (Fe3O4). For these three chlorinated solvents, the trend for the rate constants followed: Fe(II) sulfide minerals > magnetite > siderite. The high reactivity of Fe mineral coatings is hypothesized to be due to the large surface areas of the nano-mineral coatings. As a result, these surfaces are expected to play an important role in the attenuation of chlorinated solvents in contaminated subsurface environments.

Characterization and DNA Stable-Isotope Probing of Methanotrophic Bioaerosols.

The growth and activity of bacteria have been extensively studied in nearly every environment on Earth, but there have been limited studies focusing on the air. Suspended bacteria (outside of water droplets) may stay in the atmosphere for time frames that could allow for growth on volatile compounds, including the potent greenhouse gas methane. We investigated the ability of aerosolized methanotrophic bacteria to grow on methane in the airborne state in rotating gas-phase bioreactors. The physical half-life of the aerial bacterium-sized particles was 3 days. To assess the potential for airborne growth, gas-phase bioreactors containing the aerosolized cultures were amended with 1,500 ppmv 13CH4 or 12CH4. Three of seven experiments demonstrated 13C incorporation into DNA, indicating growth in air. Bacteria associated with the genera Methylocystis and Methylocaldum were detected in 13C-DNA fractions, thus indicating that they were synthesizing new DNA, suggesting growth in air. We conclude that methanotrophs outside of water droplets in the air can potentially grow under certain conditions. Based on our data, humidity seems to be a major limitation to bacterial growth in air. Furthermore, low biomass levels can pose problems for detecting 13C-DNA synthesis in our experimental system. IMPORTANCE Currently, the cellular activities of bacteria in the airborne state outside of water droplets have not been heavily studied. Evidence suggests that these airborne bacteria produce ribosomes and metabolize gaseous compounds. Despite having a potentially important impact on atmospheric chemistry, the ability of bacteria in the air to metabolize substrates such as methane is not well understood. Demonstrating that bacteria in the air can metabolize and grow on substrates will expand knowledge about the potential activities and functions of the atmospheric microbiome. This study provides evidence for DNA synthesis and, ultimately, growth of airborne methanotrophs.

Roles of reactive iron mineral coatings in natural attenuation in redox transition zones preserved from a site with historical contamination.

In this study, a protocol was developed to identify reduction-oxidation (redox) transition zones in an effort to exploit natural source zone depletion processes. A sediment core with a total length of 18-m was collected from a site with historical contamination that includes chlorinated benzenes where the redox condition was preserved. In the four redox transition zones investigated, reactive iron coatings are characterized with a suite of analyses under anaerobic conditions. To distinguish surface coating mineralogy, X-ray diffraction, X-ray fluorescence, and field-emission scanning electron microscopy with an energy dispersive X-ray analyzer were applied along with a six-step sequential extraction process. The cycling of Fe and S, as an important contribution and indicator of ongoing natural attenuation processes for constituents of concern (COC), was delineated by using data from multiple and complementary analyses for isolating and identifying iron phases. Along with groundwater chemistry, contaminant concentrations, and microbial genera, attenuation of COCs is expected to be active and sustainable in redox transition zones, where there is an abundance of reactive iron mineral coatings cycling through biogeochemical reactions. Reactions in other redox transition zones may be limited where iron mineral coatings are not dominant.

Identifying redox transition zones in the subsurface of a site with historical contamination.

Reactive iron mineral coatings found throughout reduction-oxidation (redox) transition zones play an important role in contaminant transformation processes. This research focuses on demonstrating a process for effectively delineating redox transition zones at a site with historical contamination. An 18.3 meter core was collected, subsampled, and preserved under anoxic conditions to maintain its original redox status. To ensure a high vertical resolution, sampling increments of 5.08 cm in length were analyzed for elemental concentrations with X-ray fluorescence (XRF), sediment pH, sediment oxidation-reduction potential (ORP), total volatile organic carbon (TVOC) concentration in the sample headspace, and abundant bacteria (16S rRNA sequencing). Over the core's length, gradients observed ranged from 3.74 to 8.03 for sediment pH, -141.4 mV to +651.0 mV for sediment ORP, and from below detection to a maximum of 9.6 ppm TVOC concentration (as chlorobenzene) in the headspace. The Fe and S gradients correlated with the presence of Fe and S reducing bacteria. S concentrations peaked in the Upper Zone and Zone 1 where Desulfosporosinus was abundant, suggesting precipitation of iron sulfide minerals. In Zone 2, Fe concentrations decreased where Geobacter was abundant, potentially resulting in Fe reduction, dissolution, and precipitation of minerals with increased solubility compared to the Fe(III) minerals. Using complementary geochemical and microbial data, five redox transition zones were delineated in the core collected. This research demonstrates a systematic approach to characterizing redox transition zones in a contaminated environment.

Cyanobacteria and Algae in Clouds and Rain in the Area of puy de Dôme, Central France.

The atmosphere contains diverse living microbes, of which the heterotrophic community has been the best studied. Microbes with other trophic modes, such as photoautotrophy, have received much less attention. In this study, culture-independent and dependent methods were used to examine the presence and diversity of oxygenic photoautotrophic microbes in clouds and rain collected at or around puy de Dôme Mountain, central France. Cloud water was collected from the summit of puy de Dôme (1,465 m above sea level [a.s.l.]) for cultivation and metagenomic analysis. Cyanobacteria, diatoms, green algae, and other oxygenic photoautotrophs were found to be recurrent members of clouds, while green algae affiliated with the Chlorellaceae were successfully cultured from three different clouds. Additionally, rain samples were collected below the mountain from Opme meteorological station (680 m a.s.l.). The abundance of chlorophyll a-containing cells and the diversity of cyanobacteria and green algae in rain were assessed by flow cytometry and amplicon sequencing. The corresponding downward flux of chlorophyll a-containing organisms to the ground, entering surface ecosystems with rain, varied with time and was estimated to be between ∼1 and >300 cells cm-2 day-1 during the sampling period. Besides abundant pollen from Pinales and Rosales, cyanobacteria of the Chroococcidiopsidales and green algae of the Trebouxiales were dominant in rain samples. Certain members of these taxa are known to be ubiquitous and stress tolerant and could use the atmosphere for dispersal. Overall, our results indicate that the atmosphere carries diverse, viable oxygenic photoautotrophic microbes and acts as a dispersal vector for this microbial guild.IMPORTANCE Information regarding the diversity and abundance of oxygenic photoautotrophs in the atmosphere is limited. More information from diverse locations is needed. These airborne organisms could have important impacts upon atmospheric processes and on the ecosystems they enter after deposition. Oxygenic photoautotrophic microbes are integral to ecosystem functioning, and some have the potential to affect human health. A better understanding of the diversity and the movements of these aeolian dispersed organisms is needed to understand their ecology, as well as how they could affect ecosystems and human health.

Sources of polychlorinated biphenyls to Upper Hudson River sediment post-dredging.

The Upper Hudson River (UHR) has been contaminated with polychlorinated biphenyls (PCBs) since the 1940s due to the manufacture of capacitors at two plants near Hudson Falls and Fort Edward, NY by General Electric (GE). Dredging of portions of the UHR was conducted from 2009 to 2015 as a partial remedy for this contamination. In 2017, the New York State Department of Environmental Conservation undertook a comprehensive post-dredging survey of sediment contamination in the UHR. Thousands of samples were collected, and 130 of these were analyzed for PCBs using EPA method 1668A. This data set was analyzed using Positive Matrix Factorization. Six factors were observed. One factor resembled the dominant Aroclors used by GE with little alteration. Three factors represented different pathways and/or extents of microbial dechlorination. One factor resembled a mixture of microbial dechlorination products and a higher molecular weight Aroclor used by GE. The congener patterns of the dechlorination factors suggest that removal of chlorines at the ortho position does occur in the UHR sediment, in agreement with several laboratory studies showing that such ortho dechlorination is possible. This ortho dechlorination could theoretically lead to complete dechlorination of PCBs to biphenyl in UHR sediment. Only one factor was not attributable to GE. It represents inputs of PCBs from tributaries and urban areas and explains 1.7% of the PCB mass in the sediments. The small contribution from the non-GE PCB source suggests that recontamination of the sediment after dredging was minor.

2,3,7,8-Tetrachlorodibenzo-p-dioxin Dechlorination is Differentially Enhanced by Dichlorobenzene Amendment in Passaic River, NJ Sediments.

Polychlorinated dibenzo-p-dioxins (PCDDs) are a class of toxic organic compounds released by a number of industrial processes. Sediments of the Passaic River in New Jersey are contaminated by these compounds. To explore the ability of native organohalide respiring bacteria to dechlorinate PCDDs, we first enriched bacteria from sediments of the Passaic River on two organohalides, trichloroethene (TCE) and 1,2-dichlorobenzene (DCB). We then used these enriched sediment cultures and original, unamended sediment as the inocula in a secondary experiment with 2,3,7,8-tetrachlorodibenzo-p-dioxin (2,3,7,8-TeCDD), 1,2,3,4-tetrachlorodibenzo-p-dioxin (1,2,3,4-TeCDD), and 2,7-dichlorodibenzo-p-dioxin (2,7-DiCDD) as target organohalides. We observed dechlorination of 1,2,3,4-TeCDD by all inocula, although to different extents. We observed progressive dechlorination of 2,3,7,8-TeCDD only in bottles inoculated with the DCB enrichment culture, and dechlorination of 2,7-DiCDD almost exclusively in bottles inoculated with the original, unamended river sediment. Dechlorination of 1,2,3,4-TeCDD was more rapid than that of the other amended congeners. Phylotypes within the class Dehalococcoidia associated with organohalide dechlorination were differentially enriched in DCB versus TCE enrichment cultures, indicating that they may play a role in dechlorination of the PCDDs.

Sewer Sediment Bacterial Communities Suggest Potential to Transform Persistent Organic Pollutants.

Sediments of combined sewers are seeded with microbes from a variety of sources, and experience varying biogeochemical conditions. A variety of redox processes have been demonstrated to occur within sewer systems, as well as transformation of several recalcitrant xenobiotic contaminants. Illumina sequencing of the 16S ribosomal RNA gene from sediments of three combined sewer systems in the northeastern United States resulted in 10 000 to 47 000 operational taxonomic units per sample. Whereas orders Clostridiales and Bacteroidales, considered human fecal indicators, were dominant in one city's sediments; other cities had communities suggestive of diverse redox processes, including reductive dechlorination of chlorinated organic compounds. Collection systems previously associated with polychlorinated biphenyl (PCB) biotransformation, and those with elevated in situ PCB concentrations, had high abundances of Dehalococcoidetes. The results suggest that wastewater collection systems have intrinsic passive treatment capacity, reducing contaminant loads on water resource recovery facilities and, ultimately, on receiving waters.

Using positive matrix factorization to investigate microbial dehalogenation of chlorinated benzenes in groundwater at a historically contaminated site.

Chlorinated benzenes are common groundwater contaminants in the United States, so demonstrating whether they undergo degradation in the subsurface is important in determining the best remedy for this contamination. The purpose of this work was to use a new data mining approach to investigate chlorinated benzene degradation pathways in the subsurface. Positive Matrix Factorization (PMF) was used to analyze long-term measurements of chlorinated benzene concentrations in groundwater at a contaminated site in New Jersey. A dataset containing 597 groundwater samples and 5 chlorinated benzenes and benzene collected from 144 wells over 20 years was investigated using PMF2 software. Despite the heterogeneity of this dataset, PMF analysis revealed patterns indicative of microbial dechlorination in the groundwater and provided insight about where dechlorination is occurring, to what extent, and under which geochemical conditions. PMF resolved a factor indicative of a source of 1,2,4-trichlorobenzene and 1,2-dichlorobenzene and two factors representing stages of dechlorination, one more advanced than the other. The PMF results indicated that virtually all of the 1,2-dichlorobenzene at the site arises from its use onsite, not from the dechlorination of trichlorobenzenes. Factors were further interpreted using ancillary data such as geochemical indicators and field parameters also measured in the samples. Analysis suggested that the partial and advanced dechlorination signals occur under different subsurface physical conditions. The results provided field validation of the current understanding of anaerobic dechlorination of chlorinated benzenes in the subsurface developed from laboratory studies. PMF is thereby shown to be a useful tool for investigating chlorinated benzene dechlorination.

Diastereoisomer-Specific Biotransformation of Hexabromocyclododecanes by a Mixed Culture Containing Dehalococcoides mccartyi Strain 195.

Hexabromocyclododecane (HBCD) stereoisomers may exhibit substantial differences in physicochemical, biological, and toxicological properties. However, there remains a lack of knowledge about stereoisomer-specific toxicity, metabolism, and environmental fate of HBCD. In this study, the biotransformation of (±)α-, (±)ß-, and (±)γ-HBCD contained in technical HBCD by a mixed culture containing the organohalide-respiring bacterium Dehalococcoides mccartyi strain 195 was investigated. Results showed that the mixed culture was able to efficiently biotransform the technical HBCD mixture, with 75% of the initial HBCD (∼12 µM) in the growth medium being removed within 42 days. Based on the metabolites analysis, HBCD might be sequentially debrominated via dibromo elimination reaction to form tetrabromocyclododecene, dibromocyclododecadiene, and 1,5,9-cyclododecatriene. The biotransformation of the technical HBCD was likely diastereoisomer-specific. The transformation rates of α-, ß-, and γ-HBCD were in the following order: α-HBCD > ß-HBCD > γ-HBCD. The enantiomer fractions of (±)α-, (±)ß-, and (±)γ-HBCD were maintained at about 0.5 during the 28 days of incubation, indicating a lack of enantioselective biotransformation of these diastereoisomers. Additionally, the amendment of another halogenated substrate tetrachloroethene (PCE), which supports the growth of strain 195, had a negligible impact on the transformation patterns of HBCD diastereoisomers and enantiomers. This study provided new insights into the stereoisomer-specific transformation patterns of HBCD by anaerobic microbes and has important implications for microbial remediation of anoxic environments contaminated by HBCD using the mixed culture containing Dehalococcoides.

Analysis of airborne microbial communities using 16S ribosomal RNA: Potential bias due to air sampling stress.

A limited number of studies have been conducted to analyze ribosomal RNA (rRNA, present in the ribosome) in bioaerosol samples to identify currently or potentially active airborne microbes, although its genomic counterpart, the rRNA gene (on the chromosome) has been frequently targeted for airborne microbial community analysis. A knowledge gap still exists regarding whether the bioaerosol rRNA abundances are affected by the bioaerosol collection process. We investigated the effect of air sampling stress on the measurement and characterization of 16S rRNA for bioaerosols in the laboratory and field experiments using quantitative polymerase chain reaction (qPCR) and high-throughput sequencing techniques. In a laboratory study, known quantities of freshly grown Escherichia coli cells were spiked onto the filter of a Button Aerosol Sampler and into liquids of BioSampler and SpinCon air samplers and then exposed to sampling stress when the samplers were operated for 2h. We found that the recovered cellular 16S rRNA abundance as determined by qPCR was dependent on sampler type. Further, two devices (Button Aerosol Sampler and BioSampler) that exhibited markedly different efficiency in preserving 16S rRNA were employed in an outdoor environment to collect bioaerosols simultaneously on eight days in two different seasons. The abundance of 16S rRNA in the outdoor air sample (1.3×106-4.9×107copies/m3) was about two orders of magnitude higher than that of 16S rRNA gene (6.9×103-1.5×105copies/m3). The 16S rRNA sequences revealed a different bacterial community compared with 16S rRNA gene-based results across all samples, and this difference depended on the sampling device. In addition, a number of bacterial taxa exhibited higher abundance in the 16S rRNA gene sequences than in 16S rRNA sequences, which suggests the potential activities of certain microbes in airborne phase. Overall, this study highlights the importance of sampling device selection when analyzing RNA in bioaerosols.

Forensic Analysis of Polychlorinated Dibenzo-p-Dioxin and Furan Fingerprints to Elucidate Dechlorination Pathways.

Polychlorinated dibenzo-p-dioxins and -furans (PCDD/Fs) are persistent organic pollutants whose main removal process in the environment is due to biodegradation, and particularly anaerobic reductive dechlorination. Since PCDD/F congeners that are substituted in the lateral 2, 3, 7, and 8 positions are the most toxic, removal of these chlorines is advantageous, but previous studies have only demonstrated their removal under laboratory conditions. We evaluated a concentration data set of PCDD/F congeners with four or more chlorines along with all 209 polychlorinated biphenyl (PCB) congeners in surface water, treated and untreated wastewater, landfill leachate, and biosolids (NY CARP data set) to determine whether peri and peri/lateral dechlorination of PCDD/Fs occurs in these environments. Positive Matrix Factorization (PMF) applied to the data set revealed a factor indicative of the microbial dechlorination of PCBs, and this factor also contained a variety of non-2,3,7,8 substituted PCDD/F congeners. These results suggest that dechlorination of PCDD/Fs at the lateral positions is facile if not preferred in these environments. The relative lack of tetra- and penta-chlorinated PCDD/Fs suggested that dechlorination proceeds to PCDD/F congeners with less than four chlorines. The PMF results were confirmed by examining three samples that contained >90% PCB dechlorination products from the Fresh Kills Landfill and the Hudson River. Even without factor analysis, these samples demonstrated almost identical PCDD/F congener patterns. This study suggests that PCDD/Fs are reductively dechlorinated to nontoxic non-2,3,7,8 PCDD/F congeners in sewers and landfills as well as in the sediment of the Upper Hudson River.

Electrochemically driven extraction and recovery of ammonia from human urine.

Human urine contains high concentrations of nitrogen, contributing about 75% of the nitrogen in municipal wastewaters yet only 1% of the volume. Source separation of urine produces an ideal waste stream for nitrogen and phosphorus recovery, reducing downstream costs of nutrient treatment at wastewater treatment facilities. We examined the efficiency and feasibility of ammonia extraction and recovery from synthetic and undiluted human urine using an electrochemical cell (EC). EC processing of synthetic urine produced an ammonium flux of 384 ± 8 g N m(-2) d(-1) with a 61 ± 1% current efficiency at an energy input of 12 kWh kg(-1) N removed. EC processing of real urine displayed similar performance, with an average ammonium flux of 275 ± 5 g N m(-2) d(-1) sustained over 10 days with 55 ± 1% current efficiency for ammonia and at an energy input of 13 kWh kg(-1) N removed. With the incorporation of an ammonia stripping and absorption unit into the real urine system, 57 ± 0.5% of the total nitrogen was recovered as ammonium sulfate. A system configuration additionally incorporating stripping of the influent headspace increased total nitrogen recovery to 79% but led to reduced performance of the EC as the urine ammonium concentration decrease. Direct stripping of ammonia (NH3) from urine with no chemical addition achieved only 12% total nitrogen recovery at hydraulic retention times comparable with the EC systems. Our results demonstrate that ammonia can be extracted via electrochemical means at reasonable energy inputs of approximately 12 kWh kg(-1) N. Considering also that the hydrogen generated is worth 4.3 kWh kg(-1) N, the net electrical input for extraction becomes approximately 8 kWh kg(-1) N if the hydrogen can be used. Critical for further development will be the inclusion of a passive means for ammonia stripping to reduce additional energy inputs.

Identification of Anaerobic Aniline-Degrading Bacteria at a Contaminated Industrial Site.

Anaerobic aniline biodegradation was investigated under different electron-accepting conditions using contaminated canal and groundwater aquifer sediments from an industrial site. Aniline loss was observed in nitrate- and sulfate-amended microcosms and in microcosms established to promote methanogenic conditions. Lag times of 37 days (sulfate amended) to more than 100 days (methanogenic) were observed prior to activity. Time-series DNA-stable isotope probing (SIP) was used to identify bacteria that incorporated (13)C-labeled aniline in the microcosms established to promote methanogenic conditions. In microcosms from heavily contaminated aquifer sediments, a phylotype with 92.7% sequence similarity to Ignavibacterium album was identified as a dominant aniline degrader as indicated by incorporation of (13)C-aniline into its DNA. In microcosms from contaminated canal sediments, a bacterial phylotype within the family Anaerolineaceae, but without a match to any known genus, demonstrated the assimilation of (13)C-aniline. Acidovorax spp. were also identified as putative aniline degraders in both of these two treatments, indicating that these species were present and active in both the canal and aquifer sediments. There were multiple bacterial phylotypes associated with anaerobic degradation of aniline at this complex industrial site, which suggests that anaerobic transformation of aniline is an important process at the site. Furthermore, the aniline degrading phylotypes identified in the current study are not related to any known aniline-degrading bacteria. The identification of novel putative aniline degraders expands current knowledge regarding the potential fate of aniline under anaerobic conditions.

Development of a dual-internal-reference technique to improve accuracy when determining bacterial 16S rRNA:16S rRNA gene ratio with application to Escherichia coli liquid and aerosol samples.

Accurate enumeration of rRNA content in microbial cells, e.g. by using the 16S rRNA:16S rRNA gene ratio, is critical to properly understand its relationship to microbial activities. However, few studies have considered possible methodological artifacts that may contribute to the variability of rRNA analysis results. In this study, a technique utilizing genomic DNA and 16S rRNA from an exogenous species (Pseudomonas fluorescens) as dual internal references was developed to improve accuracy when determining the 16S rRNA:16S rRNA gene ratio of a target organism, Escherichia coli. This technique was able to adequately control the variability in sample processing and analysis procedures due to nucleic acid (DNA and RNA) losses, inefficient reverse transcription of RNA, and inefficient PCR amplification. The measured 16S rRNA:16S rRNA gene ratio of E. coli increased by 2-3 fold when E. coli 16S rRNA gene and 16S rRNA quantities were normalized to the sample-specific fractional recoveries of reference (P. fluorescens) 16S rRNA gene and 16S rRNA, respectively. In addition, the intra-sample variation of this ratio, represented by coefficients of variation from replicate samples, decreased significantly after normalization. This technique was applied to investigate the temporal variation of 16S rRNA:16S rRNA gene ratio of E. coli during its non-steady-state growth in a complex liquid medium, and to E. coli aerosols when exposed to particle-free air after their collection on a filter. The 16S rRNA:16S rRNA gene ratio of E. coli increased significantly during its early exponential phase of growth; when E. coli aerosols were exposed to extended filtration stress after sample collection, the ratio also increased. In contrast, no significant temporal trend in E. coli 16S rRNA:16S rRNA gene ratio was observed when the determined ratios were not normalized based on the recoveries of dual references. The developed technique could be widely applied in studies of relationship between cellular rRNA abundance and bacterial activity.

Identifying the Correct Biotransformation Model from Polychlorinated Biphenyl and Dioxin Dechlorination Batch Studies.

We performed Monte Carlo simulations of batch transformations of hydrophobic compounds using typical numbers of data points, extent of reaction, and measurement error, to identify the most appropriate biotransformation model to describe such data under different conditions. Highly hydrophobic compounds such as polychlorinated biphenyls (PCBs) and dioxins present special challenges for parameterization due to low environmental concentrations and slow biotransformation rates, which result in high sample variability, few samples, and limited substrate concentration range. Four models of varying complexity (zero-order, first-order, Monod, and Best) were fit to simulated data. Various combinations of initial concentration (S0), half saturation concentration (KS), maximum substrate utilization rate (qmax), measurement error, number of data points per batch run, and extent of biotransformation were simulated. One thousand Monte-Carlo runs were performed for each parameter combination, and AICc (Akaike's information criterion corrected for small numbers of data points) was used to determine the most appropriate model. Neither the Best model nor the zero-order model ever produced the lowest AICc for a majority of simulations under any combination of test conditions. With 10% measurement error, the first-order model always outperformed the others. In the case of 1% measurement error with 10 evenly-spaced data points, the Monod model was the better choice when S0>KS and the system was not mass transfer limited [Formula: see text] otherwise, the first-order model was indicated. S0 is constrained by the compound's aqueous solubility; therefore, for highly hydrophobic compounds such as PCBs or polychlorinated dibenzo-p-dioxins and dibenzofurans, a first-order model is likely to fit batch biotransformation data as well or better than a more complicated model.

Reductive dechlorination of 1,2,3,7,8-pentachlorodibenzo-p-dioxin and Aroclor 1260, 1254 and 1242 by a mixed culture containing Dehalococcoides mccartyi strain 195.

A mixed culture containing Dehalococcoides mccartyi strain 195 dechlorinated 1,2,3,7,8-pentachlorodibenzo-p-dioxin (1,2,3,7,8-PeCDD) and selected polychlorinated biphenyl (PCB) congeners in Aroclors 1260, 1254 and 1242. 1,2,3,7,8-PeCDD was dechlorinated to 1,3,7-trichlorodibenzo-p-dioxin (1,3,7-TrCDD) and/or 1,3,8-TrCDD via 1,3,7,8-tetrachlorodibenzo-p-dioxin (1,3,7,8-TeCDD), a pathway that excludes the production of the toxic congener 2,3,7,8-TeCDD. Dechlorination rate and extent was greatly enhanced by the addition of 1,2,3,4-tetrachlorobenzene (1,2,3,4-TeCB) as an alternate halogenated substrate and/or incubation temperature increase from 25 °C to 35 °C. The most extensive dechlorination of PCBs occurred for Aroclor 1260 with 13 major congeners making up 44.1 mol% of the original PCBs dechlorinated by 42% over 250 days at 25 °C. When 1,2,3,4-TeCB was amended as co-substrate, the extent of dechlorination increased to 82%, over 250 days. The mixed culture primarily dechlorinated the doubly-flanked chlorines on 2,3,4-, 2,3,4,6-, and 2,3,4,5,6-substituted chlorophenyl rings, whereas it primarily removed the doubly-flanked para chlorine from the 2,3,4,5-substituted chlorophenyl ring. Experiments using a 20% dilution of culture with 31.8 µg/mL 1,2,3,4-TeCDD or 2,3,4,4',5-pentachlorobiphenyl (PCB 114) as sole halogenated substrate exhibited less than 0.1 mol% dechlorination over 120 days. Further, dechlorination of PCBs and PCDDs by the fully grown culture in the absence of 1,2,3,4-TeCB eventually stopped or greatly slowed over the incubation period. Since Dehalococcoides spp. only gain energy for growth from organohalide respiration, absence of reductive dechlorination upon transfer and dilution or cessation of dechlorination after long incubation times suggest that it is unlikely that strain 195 can grow using the PCDDs or PCBs utilized in this study.

Release of free DNA by membrane-impaired bacterial aerosols due to aerosolization and air sampling.

We report here that stress experienced by bacteria due to aerosolization and air sampling can result in severe membrane impairment, leading to the release of DNA as free molecules. Escherichia coli and Bacillus atrophaeus bacteria were aerosolized and then either collected directly into liquid or collected using other collection media and then transferred into liquid. The amount of DNA released was quantified as the cell membrane damage index (ID), i.e., the number of 16S rRNA gene copies in the supernatant liquid relative to the total number in the bioaerosol sample. During aerosolization by a Collison nebulizer, the ID of E. coli and B. atrophaeus in the nebulizer suspension gradually increased during 60 min of continuous aerosolization. We found that the ID of bacteria during aerosolization was statistically significantly affected by the material of the Collison jar (glass > polycarbonate; P < 0.001) and by the bacterial species (E. coli > B. atrophaeus; P < 0.001). When E. coli was collected for 5 min by filtration, impaction, and impingement, its ID values were within the following ranges: 0.051 to 0.085, 0.16 to 0.37, and 0.068 to 0.23, respectively; when it was collected by electrostatic precipitation, the ID values (0.011 to 0.034) were significantly lower (P < 0.05) than those with other sampling methods. Air samples collected inside an equine facility for 2 h by filtration and impingement exhibited ID values in the range of 0.30 to 0.54. The data indicate that the amount of cell damage during bioaerosol sampling and the resulting release of DNA can be substantial and that this should be taken into account when analyzing bioaerosol samples.

Microbially mediated reductive dechlorination of weathered polychlorinated dibenzofurans in Kymijoki sediment mesocosms.

Little is known about the potential for indigenous microorganisms to reductively dechlorinate weathered polychlorinated dibenzo-p-dioxins (PCDDs) and dibenzofurans (PCDFs) in contaminated sediments. The sediments of River Kymijoki, Finland are heavily contaminated with PCDFs originating from manufacture of the chlorophenol-based fungicide Ky-5. Reductive dechlorination of weathered PCDFs was monitored to examine strategies for stimulating such activities. Amendments with electron donors, a halogenated co-substrate (tetrachlorobenzene, TeCBz), and bioaugmentation with a mixed culture containing Dehalococcoides mccartyi strain 195 were used to stimulate dechlorination activity in 30 L River Kymijoki sediment mesocosms incubated from 18 °C to 21 °C. An initial onset of dechlorination of octa-, hepta- and hexa-CDFs was observed in all mesocosms in the first 2 years of incubation. During this initial 2-year period, the decrease in the mol% contribution of these PCDFs was coupled with an increase in the mol% contribution of tetra- and penta-CDFs. The ratio of 1,2,3,4,6,7,8- to 1,2,3,4,6,8,9-hepta-CDF increased significantly. Subtle differences were observed between amended and unamended mesocosms. For penta-CDFs, a decreasing mol% ratio of peri vs. total chlorines and increasing mol% ratio of lateral vs. total chlorines was observed in mesocosms amended with TeCBz, suggesting that the amendments may affect pathways of dechlorination. Analysis of congener patterns using principal components analysis supported the observation that dechlorination was most pronounced during the first 2 years. Polymerase chain reaction and denaturing gradient gel electrophoresis (PCR-DGGE) analysis of 16S rRNA genes revealed a diverse Chloroflexi community. This study showed evidence for dechlorination of weathered PCDFs in Kymijoki sediment mesocosms mediated by indigenous microorganisms.

Ecogenomics of microbial communities in bioremediation of chlorinated contaminated sites.

Organohalide compounds such as chloroethenes, chloroethanes, and polychlorinated benzenes are among the most significant pollutants in the world. These compounds are often found in contamination plumes with other pollutants such as solvents, pesticides, and petroleum derivatives. Microbial bioremediation of contaminated sites, has become commonplace whereby key processes involved in bioremediation include anaerobic degradation and transformation of these organohalides by organohalide respiring bacteria and also via hydrolytic, oxygenic, and reductive mechanisms by aerobic bacteria. Microbial ecogenomics has enabled us to not only study the microbiology involved in these complex processes but also develop tools to better monitor and assess these sites during bioremediation. Microbial ecogenomics have capitalized on recent advances in high-throughput and -output genomics technologies in combination with microbial physiology studies to address these complex bioremediation problems at a system level. Advances in environmental metagenomics, transcriptomics, and proteomics have provided insights into key genes and their regulation in the environment. They have also given us clues into microbial community structures, dynamics, and functions at contaminated sites. These techniques have not only aided us in understanding the lifestyles of common organohalide respirers, for example Dehalococcoides, Dehalobacter, and Desulfitobacterium, but also provided insights into novel and yet uncultured microorganisms found in organohalide respiring consortia. In this paper, we look at how ecogenomic studies have aided us to understand the microbial structures and functions in response to environmental stimuli such as the presence of chlorinated pollutants.