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Microbial Insights Inc

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Nobre R.C.M.,Federal University of Alagoas | Nobre M.M.M.,Federal University of Alagoas | Campos T.M.P.,Pontifical Catholic University of Rio de Janeiro | Ogles D.,Microbial Insights Inc
Journal of Hazardous Materials | Year: 2017

This paper investigates the feasibility of applying in-situ Bioremediation (ISB) to three sites contaminated with vinyl chloride and/or chlorinated alkanes such as 1,2-DCA and 1,1,2-TCA, presenting distinct hydrogeological settings and history of contaminant loading. Biotransformation of these compounds is well established in laboratory studies and pure cultures. Due to confidential aspects, however, few field data are available to support real case studies to the predictability of their fate and lifetime in soil and groundwater. Bio-Trap® In Situ Microcosm (ISM) studies were performed in selected monitoring wells, and consisted of a control unit which simulated Monitored Natural Attenuation conditions and other units which were amended with either lactate, emulsified vegetable oil (EVO) or molasses as electron donors. For wells with moderate Dhc counts, the ISM study demonstrated that electron donor addition could stimulate further growth of Dhc and enhance reductive dechlorination. Conversely, for wells with high population counts, substrate addition did not alter results significantly. Site-specific determining factors that most influenced the biodegradation results were microbial activity, soil texture and presence of organic matter, site pH, redox conditions and presence of free phase. © 2017 Elsevier B.V.


Chandler D.P.,Akonni Biosystems Inc. | Kukhtin A.,Akonni Biosystems Inc. | Mokhiber R.,Akonni Biosystems Inc. | Knickerbocker C.,Akonni Biosystems Inc. | And 5 more authors.
Environmental Science and Technology | Year: 2010

The objective of this study was to develop and validate a simple, field-portable, microarray system for monitoring microbial community structure and dynamics in groundwater and subsurface environments, using samples representing site status before acetate injection, during Fe-reduction, in the transition from Fe- to SO4 2--reduction, and into the SO4 2--reduction phase. Limits of detection for the array are approximately 102-103 cell equivalents of DNA per reaction. Sample-to-answer results for the field deployment were obtained in 4 h. Retrospective analysis of 50 samples showed the expected progression of microbial signatures from Fe- to SO4 2- -reducers with changes in acetate amendment and in situ field conditions. The microarray response for Geobacter was highly correlated with qPCR for the same target gene (R2 = 0.84). Microarray results were in concordance with quantitative PCR data, aqueous chemistry, site lithology, and the expected microbial community response, indicating that the field-portable microarray is an accurate indicator of microbial presence and response to in situ remediation of a uranium-contaminated site. © 2010 American Chemical Society.


Gedalanga P.B.,University of California at Los Angeles | Pornwongthong P.,University of California at Los Angeles | Mora R.,AECOM Technology Corporation | Chiang S.-Y.D.,AECOM Technology Corporation | And 3 more authors.
Applied and Environmental Microbiology | Year: 2014

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. © 2014, American Society for Microbiology.


Chiang S.-Y.D.,AECOM Technology Corporation | Mora R.,AECOM Technology Corporation | Diguiseppi W.H.,AECOM Technology Corporation | Diguiseppi W.H.,CH2M HILL | And 4 more authors.
Journal of Environmental Monitoring | Year: 2012

An intrinsic biodegradation study involving the design and implementation of innovative environmental diagnostic tools was conducted to evaluate whether monitored natural attenuation (MNA) could be considered as part of the remedial strategy to treat an aerobic aquifer contaminated with 1,4-dioxane and trichloroethene (TCE). In this study, advanced molecular biological and stable isotopic tools were applied to confirm in situ intrinsic biodegradation of 1,4-dioxane and TCE. Analyses of Bio-Trap® samplers and groundwater samples collected from monitoring wells verified the abundance of bacteria and enzymes capable of aerobically degrading TCE and 1,4-dioxane. Furthermore, phospholipid fatty acid analysis with stable isotope probes (PLFA-SIP) of the microbial community validated the ability for microbial degradation of TCE and 1,4-dioxane. Compound specific isotope analysis (CSIA) of groundwater samples for TCE resulted in δ13C values that indicated likely biodegradation of TCE in three of the four monitoring wells sampled. Results of the MNA evaluation showed that enzymes capable of aerobically degrading TCE and 1,4-dioxane were present, abundant, and active in the aquifer. Taken together, these results provide direct evidence of the occurrence of TCE and 1,4-dioxane biodegradation at the study site, supporting the selection of MNA as part of the final remedy at some point in the future. This journal is © The Royal Society of Chemistry 2012.


Stucker V.,Colorado School of Mines | Ranville J.,Colorado School of Mines | Newman M.,University of Florida | Peacock A.,Microbial Insights Inc | And 2 more authors.
Water Research | Year: 2011

Laboratory tests and a field validation experiment were performed to evaluate anion exchange resins for uranium sorption and desorption in order to develop a uranium passive flux meter (PFM). The mass of uranium sorbed to the resin and corresponding masses of alcohol tracers eluted over the duration of groundwater installation are then used to determine the groundwater and uranium contaminant fluxes. Laboratory based batch experiments were performed using Purolite A500, Dowex 21K and 21K XLT, Lewatit S6328 A resins and silver impregnated activated carbon to examine uranium sorption and extraction for each material. The Dowex resins had the highest uranium sorption, followed by Lewatit, Purolite and the activated carbon. Recoveries from all ion exchange resins were in the range of 94-99% for aqueous uranium in the environmentally relevant concentration range studied (0.01-200 ppb). Due to the lower price and well-characterized tracer capacity, Lewatit S6328 A was used for field-testing of PFMs at the DOE UMTRA site in Rifle, CO. The effect on the flux measurements of extractant (nitric acid)/resin ratio, and uranium loading were investigated. Higher cumulative uranium fluxes (as seen with concentrations > 1 ug U/gram resin) yielded more homogeneous resin samples versus lower cumulative fluxes (<1 ug U/gram resin), which caused the PFM to have areas of localized concentration of uranium. Resin homogenization and larger volume extractions yield reproducible results for all levels of uranium fluxes. Although PFM design can be improved to measure flux and groundwater flow direction, the current methodology can be applied to uranium transport studies. © 2011 Elsevier Ltd.


Baird C.,Georgia Pacific Corporation | Ogles D.,Microbial Insights Inc | Baldwin B.R.,Microbial Insights Inc
NACE - International Corrosion Conference Series | Year: 2016

MIC often contributes to corrosion in paper mills despite the seemingly inhospitable conditions for microbial growth. Molecular microbiological methods most notably quantitative polymerase chain reaction (qPCR) were employed to examine MIC at three paper mills with unique operations and construction materials. Despite raw water treatment, qPCR quantification of total bacteria and specific MIC associated microbial groups revealed growth of substantial and diverse microbial populations which had not been identified with cultivation based methods. Moreover, qPCR quantification of several microbial groups highlighted their roles in MIC. At most facilities including one experiencing corrosion of UNS S31254, iron oxidizing bacteria (IOB) were detected at high concentrations (1.00 × 108 cells/g). The actions of IOB were confirmed by x-ray diffraction analysis demonstrating production of iron oxyhydroxides (e.g. hematite). Fermenting bacteria were also routinely detected. Along with direct impacts, volatile fatty acids and hydrogen produced during fermentation support growth of other anaerobic microorganisms linked to MIC. Consistent with tubercle formation and biofilm maturation, sulfate reducing bacteria (SRB) and methanogens were detected in some solid phase samples. Overall, the qPCR results suggest biomass growth within the system, IOB activity and tubercle formation followed by proliferation of fermenters and eventually SRB and methanogens under the deposits. © 2016 by NACE International.


Baldwin B.R.,Microbial Insights Inc | Biernacki A.,Microbial Insights Inc | Blair J.,Arctos Environmental | Purchase M.P.,Arctos Environmental | And 4 more authors.
Environmental Science and Technology | Year: 2010

Increasingly, molecular biological tools, most notably quantitative polymerase chain reaction (qPCR), are being employed to provide a more comprehensive assessment of bioremediation of petroleum hydrocarbons and fuel oxygenates. While qPCR enumeration of key organisms or catabolic genes can aid in site management decisions, evaluation of site activities conducted to stimulate biodegradation would ideally include a direct measure of gene expression to infer activity. In the current study, reverse-transcriptase (RT) qPCR was used to monitor gene expression to evaluate the effectiveness of an oxygen infusion system to promote biodegradation of BTEX and MTBE. During system operation, dissolved oxygen (DO) levels at the infusion points were greater than 30 mg/L, contaminant concentrations decreased, and transcription of two aromatic oxygenase genes and Methylibium petroleiphilum PM1-like 16S rRNA copies increased by as many as 5 orders of magnitude. Moreover, aromatic oxygenase gene transcription and PM1 16s rRNA increased at downgradient locations despite low DO levels even during system operation. Conversely, target gene expression substantially decreased when the system was deactivated. RT-qPCR results also corresponded to increases in benzene and MTBE attenuation rates. Overall, monitoring gene expression complemented traditional groundwater analyses and conclusively demonstrated that the oxygen infusion system promoted BTEX and MTBE biodegradation. © 2010 American Chemical Society.


Grant
Agency: National Science Foundation | Branch: | Program: SBIR | Phase: Phase I | Award Amount: 100.00K | Year: 2009

This Small Business Innovation Research Phase I project will result in a suite of microbial source tracking assays to provide cost-effective identification of fecal contamination sources in surface waters. Beach closures and advisories exceeded 20,000 days in each of the past 3 years with more than 60% caused by fecal pollution. Overall, 13% of surface waters do not meet quality standards due to fecal contamination. The problem continues more than 30 years after the Clean Water Act because traditional methods cannot identify fecal inputs from the myriad of human (wastewater treatment plants, septic fields), agricultural (confined animal feeding operations), and natural wildlife activities. Microbial source tracking (MST) using quantitative polymerase chain reaction (qPCR) offers a rapid but sensitive approach to quantify fecal inputs and most importantly identify the source. The primary milestone of the project will be rigorously validated qPCR assays that provide conclusive identification of fecal contamination sources allowing end users to eliminate fecal inputs and protect human health. The broader impact of this research is the development and validation of an mtDNA based qPCR method to identify fecal contamination sources which will ultimately lead to improved water quality. Fecal contamination of water resources currently results in beach closures and restrictions on shellfish harvesting that severely impact waterfront communities. Moreover, periodic outbreaks of waterborne diseases clearly highlight the need for improved detection of fecal contamination indicators to protect human health. This award is funded under the American Recovery and Reinvestment Act of 2009 (Public Law 111-5).


Grant
Agency: National Science Foundation | Branch: | Program: SBIR | Phase: Phase II | Award Amount: 500.00K | Year: 2011

This Small Business Innovation Research (SBIR) Phase II project will result in field validated microbial source tracking (MST) assays that provide cost-effective identification of sources of fecal pollution. Despite efforts mandated under the BEACH and Clean Water Acts, beach closures have exceeded 20,000 days in each of the last four years primarily due to fecal pollution. The problem continues because traditional methods cannot identify the sources of fecal contamination (sewage, livestock, domestic animals, wildlife). MST assays employing quantitative polymerase chain reaction (qPCR) were developed to quantify source-specific genetic markers encoded on the mitochondrial DNA (mtDNA) of the source animal (human, cattle, dog, etc.). The Phase I results demonstrated that mtDNA-based assays combined with bacterial source tracking methods will provide conclusive identification of fecal contamination sources allowing implementation of corrective measures to improve water quality and protect human health. Phase II studies will include a modification of the DNA extraction procedure to permit quantification of live fecal bacteria to aid in risk assessment and extended field validation studies at two beaches and two coastal watersheds impaired by unknown sources of fecal pollution. The broader impacts of this research are that the MST assays developed and validated during the Phase II project will empower stakeholders with the type of actionable data required to identify fecal contamination sources, implement appropriate corrective actions, and safeguard the nation?s waters. Fecal contamination of water resources currently exacts a severe toll in terms of increased risks to human health and impacts on coastal economies.


Grant
Agency: NSF | Branch: Standard Grant | Program: | Phase: | Award Amount: 500.00K | Year: 2011

This Small Business Innovation Research (SBIR) Phase II project will result in field validated microbial source tracking (MST) assays that provide cost-effective identification of sources of fecal pollution. Despite efforts mandated under the BEACH and Clean Water Acts, beach closures have exceeded 20,000 days in each of the last four years primarily due to fecal pollution. The problem continues because traditional methods cannot identify the sources of fecal contamination (sewage, livestock, domestic animals, wildlife). MST assays employing quantitative polymerase chain reaction (qPCR) were developed to quantify source-specific genetic markers encoded on the mitochondrial DNA (mtDNA) of the source animal (human, cattle, dog, etc.). The Phase I results demonstrated that mtDNA-based assays combined with bacterial source tracking methods will provide conclusive identification of fecal contamination sources allowing implementation of corrective measures to improve water quality and protect human health. Phase II studies will include a modification of the DNA extraction procedure to permit quantification of live fecal bacteria to aid in risk assessment and extended field validation studies at two beaches and two coastal watersheds impaired by unknown sources of fecal pollution.
The broader impacts of this research are that the MST assays developed and validated during the Phase II project will empower stakeholders with the type of actionable data required to identify fecal contamination sources, implement appropriate corrective actions, and safeguard the nation?s waters. Fecal contamination of water resources currently exacts a severe toll in terms of increased risks to human health and impacts on coastal economies.

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