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Bacterial multicomponent monooxygenase gene targets in Pseudonocardia dioxanivorans CB1190 were evaluated for their use as biomarkers to identify the potential for 1,4-dioxane biodegradation in pure cultures and environmental samples. Our studies using laboratory pure cultures and industrial activated sludge samples suggest that the presence of genes associated with dioxane monooxygenase, propane monooxygenase, alcohol dehydrogenase, and aldehyde dehydrogenase are promising indicators of 1,4-dioxane biotransformation; however, gene abundance was insufficient to predict actual biodegradation. A time course gene expression analysis of dioxane and propane monooxygenases in Pseudonocardia dioxanivorans CB1190 and mixed communities in wastewater samples revealed important associations with the rates of 1,4-dioxane removal. In addition, transcripts of alcohol dehydrogenase and aldehyde dehydrogenase genes were upregulated during biodegradation, although only the aldehyde dehydrogenase was significantly correlated with 1,4-dioxane concentrations. Expression of the propane monooxygenase demonstrated a time-dependent relationship with 1,4-dioxane biodegradation in P. dioxanivorans CB1190, with increased expression occurring after over 50% of the 1,4-dioxane had been removed. While the fraction of P. dioxanivorans CB1190-like bacteria among the total bacterial population significantly increased with decrease in 1,4-dioxane concentrations in wastewater treatment samples undergoing active biodegradation, the abundance and expression of monooxygenase-based biomarkers were better predictors of 1,4-dioxane degradation than taxonomic 16S rRNA genes. This study illustrates that specific bacterial monooxygenase and dehydrogenase gene targets together can serve as effective biomarkers for 1,4-dioxane biodegradation in the environment.

Microcosms are used to segregate the effects of two heavy metals (Pb and Cr) and also explore the impact of aromatic hydrocarbons on microbial community structure and function. One of the two energy substrates (glucose or xylene) is added to provide the necessary force for selection to operate and drive changes in community composition.

Research has been conducted on pollutant-biodegrading microorganisms. The authors report the development of real-time PCR procedures for quantification of aromatic catabolic genes in environmental samples.

Objectives/hypothesis: The human papillomavirus (HPV) is known to infect the tissues of the oropharynx as demonstrated in HPV-positive oropharyngeal squamous cell carcinoma (OPSCC). HPV has also been shown to induce benign lymphoid hypertrophy. We sought to investigate an association between obstructive sleep apnea (OSA) and the presence of HPV in palatine and lingual tonsillar oropharyngeal tissue.Study Design: Case series with chart review.Methods: This retrospective laboratory-based study of oropharyngeal tissue from patients with OSA included patients >18 years old who underwent surgical treatment for OSA at a single institution between January 2012 and May 2014. Surgical specimens of adequate size were analyzed for HPV6, 11, and 16 using real-time quantitative polymerase chain reaction from DNA extracted from formalin-fixed paraffin-embedded tissue blocks. Student t test, Pearson χ2 test, and linear logistic regression were used to assess comparisons of body mass index (BMI), apnea-hypopnea index (AHI), age, and gender between HPV-positive and HPV-negative groups.Results: Of 99 cases included in the study, six were positive for HPV: two with HPV16 and four with HPV6. BMI, AHI, age, and gender showed no significant differences between the HPV-positive and HPV-negative groups. Logistic regression to predict HPV positivity accounting for each variable and multivariate analysis were not statistically significant.Conclusions: Our study did not show HPV to have a statistically significant association with OSA. None of the covariates analyzed (BMI, AHI, gender, age) predicted HPV positivity in surgically resected oropharyngeal tissue from OSA patients.Level Of Evidence: 4 Laryngoscope, 127:1231-1234, 2017. [ABSTRACT FROM AUTHOR]

The effect of phenol concentration on phenol biodegradation at an industrial site in the south of Wales, United Kingdom, was investigated using standard Bio-Sep® Bio-Traps® and Bio-Traps® coupled with stable isotope probing (SIP). Unlike many 13C-amendments used in SIP studies (such as hydrocarbons) that physically and reversibly adsorb to the activated carbon component of the Bio-Sep® beads, phenol is known to irreversibly chemisorb to activated carbon. Bio-Traps® were deployed for 32 days in nine site groundwater monitoring wells representing a wide range of phenol concentrations. Bio-Traps® amended with 13C-phenol were deployed together with non-amended Bio-Traps® in three wells. Quantitative polymerase chain reaction (qPCR) analysis of Bio-Traps® post-deployment indicated an inhibitory effect of increasing phenol concentration on both total eubacteria and aerobic phenol-utilizing bacteria as represented by the concentration of phenol hydroxylase gene. Despite the chemisorption of phenol to the Bio-Sep® beads, activated carbon stable isotope analysis showed incorporation of 13C into biomass and dissolved inorganic carbon (DIC) in each SIP Bio-Trap® indicating that chemisorbed amendments are bioavailable. However, there was a clear effect of phenol concentration on 13C incorporation in both biomass and DIC confirming phenol inhibition. These results suggest that physical reductions of the phenol concentrations in some areas of the plume will be required before biodegradation of phenol can proceed at a reasonable rate. © 2013 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

A microbial survey of hydrocarbon-impacted groundwater and vadose zone at a Midwestern refinery employed molecular biological tools to elucidate the microbial processes involved in bioremediation occurring in the subsurface. qPCR analysis of bio-traps incubated in groundwater indicated that a large and diverse microbial community was present throughout the site and suggested that mechanisms of benzene, toluene, ethylbenzene, and xylene ( BTEX) biodegradation included aerobic oxidation, sulfate reduction, methanogenesis, and possibly Fe+3 reduction. To assess the role of vadose zone microorganisms in hydrocarbon attenuation, RNA was extracted from soil core samples, and reverse transcriptase- qPCR ( RT-qPCR) analysis indicated that microbial activity in the vadose zone generally increased with depth, likely supported by hydrocarbons and methane volatilizing from the groundwater. Stable isotope probing ( SIP) with 13C6-benzene provided direct evidence of benzene biodegradation in six of the eight wells studied. The highest levels of 13C were detected in dissolved inorganic carbon ( DIC) extracted from the two monitoring wells closest to the river. The influx of nutrients and oxygen coming from the river may help to maintain a robust population of hydrocarbon degraders in these wells. While qPCR analysis indicated that microorganisms with the genetic potential for hydrocarbon biodegradation were ubiquitous at the site, RT-qPCR and SIP results were used to refine the site conceptual model by identifying areas where that genetic potential was actively being expressed and locations where biodegradation was lagging. [ABSTRACT FROM AUTHOR]