Methyl tert-butyl ether (MTBE) is a contaminant of concern to groundwater resources due to its pe... more Methyl tert-butyl ether (MTBE) is a contaminant of concern to groundwater resources due to its persistence in subsurface environments. MTBE appears to be degraded readily in the presence of oxygen but is recalcitrant under the anaerobic conditions prevalent in the subsurface, and can be converted into the more toxic compound tert-butanol (TBA). As ethanol is being promoted as a renewable fuel and a replacement for MTBE in gasoline formulations, its potential impact on the biodegradation of preexisting contaminants and on other components of petroleum must be examined. The purpose of this study is to investigate the effect of ethanol release on existing MTBE plumes and the fate of TBA under sulfate-reducing conditions. Our results suggest that TBA, MTBE and ethanol-induced methane concentrations are strong determinants of the composition of the indigenous microbial community that develops during MTBE transformation. Some of the changes in microbial communities induced by ethanol may ...
Philosophical Transactions of the Royal Society B: Biological Sciences
Soil and soil biodiversity play critical roles in Nature's Contributions to People (NCP) # 10... more Soil and soil biodiversity play critical roles in Nature's Contributions to People (NCP) # 10, defined as Nature's ability to regulate direct detrimental effects on humans, and on human-important plants and animals, through the control or regulation of particular organisms considered to be harmful. We provide an overview of pathogens in soil, focusing on human and crop pathogens, and discuss general strategies, and examples, of how soils' extraordinarily diverse microbial communities regulate soil-borne pathogens. We review the ecological principles underpinning the regulation of soil pathogens, as well as relationships between pathogen suppression and soil health. Mechanisms and specific examples are presented of how soil and soil biota are involved in regulating pathogens of humans and plants. We evaluate how specific agricultural management practices can either promote or interfere with soil's ability to regulate pathogens. Finally, we conclude with how integratin...
Increasing soil organic carbon (SOC) stocks in agricultural soils can contribute to stabilizing o... more Increasing soil organic carbon (SOC) stocks in agricultural soils can contribute to stabilizing or even lowering atmospheric greenhouse gas (GHG) concentrations. Cover crop rotation has been shown to increase SOC and provide productivity benefits for agriculture. Here we used a split field design to evaluate the short-term effect of cover crop on SOC distribution and chemistry using a combination of bulk, isotopic, and spectroscopic analyses of size-and density-separated soil aggregates. Macroaggregates (>250 µm) incorporated additional plant material with cover crop as evidenced by more negative δ13C values (−25.4‰ with cover crop compared to −25.1‰ without cover crop) and increased phenolic (plant-like) resonance in carbon NEXAFS spectra. Iron EXAFS data showed that the Fe pool was composed of 17–21% Fe oxide with the remainder a mix of primary and secondary minerals. Comparison of oxalate and dithionite extractions suggests that cover crop may also increase Fe oxide crystallin...
The Century Experiment at the Russell Ranch Sustainable Agriculture Facility at the University of... more The Century Experiment at the Russell Ranch Sustainable Agriculture Facility at the University of California, Davis provides long-term agroecological data from row crop systems in California's Central Valley starting in 1993. The Century Experiment was initially designed to study the effects of a gradient of water and nitrogen availability on soil properties and crop performance in ten different cropping systems to measure tradeoffs and synergies between agricultural productivity and sustainability. Currently systems include 11 different cropping systems-consisting of four different crops and a cover crop mixture-and one native grass system. This paper describes the long-term core data from the Century Experiment from 1993-2014, including crop yields and biomass, crop elemental contents, aerial-photo-based Normalized Difference Vegetation Index data, soil properties, weather, chemical constituents in irrigation water, winter weed populations, and operational data including ferti...
Methyl-tert-butyl ether (MTBE) and its degradation by-product, tert-butyl alcohol (TBA), are wide... more Methyl-tert-butyl ether (MTBE) and its degradation by-product, tert-butyl alcohol (TBA), are widespread contaminants detected frequently in groundwater in California. Since MTBE was used as a fuel oxygenate for almost two decades, leaking underground fuel storage tanks are an important source of contamination. Gasoline components such as BTEX (benzene, toluene, ethylbenzene and xylenes) are often present in mixtures with MTBE and TBA. Investigations of interactions between BTEX and MTBE degradation have not yielded consistent trends, and the molecular mechanisms of BTEX compounds' impact on MTBE degradation are not well understood. We investigated trends in transcription of biodegradation genes in the MTBE-degrading bacterium, Methylibium petroleiphilum PM1 upon exposure to MTBE, TBA, ethylbenzene and benzene as individual compounds or in mixtures. We designed real-time quantitative PCR assays to target functional genes of strain PM1 and provide evidence for induction of genes m...
Among the few bacteria known to utilize methyl tert-butyl ether (MTBE) as a sole carbon source, M... more Among the few bacteria known to utilize methyl tert-butyl ether (MTBE) as a sole carbon source, Methylibium petroleiphilum PM1 is a well-characterized organism with a sequenced genome; however, knowledge of the genetic regulation of its MTBE degradation pathway is limited. We investigated the role of a putative transcriptional activator gene, mdpC, in the induction of MTBE-degradation genes mdpA (encoding MTBE monooxygenase) and mdpJ (encoding tert-butyl alcohol hydroxylase) of strain PM1 in a gene-knockout mutant mdpC(-). We also utilized quantitative reverse transcriptase PCR assays targeting genes mdpA, mdpJ and mdpC to determine the effects of the mutation on transcription of these genes. Our results indicate that gene mdpC is involved in the induction of both mdpA and mdpJ in response to MTBE and tert-butyl alcohol (TBA) exposure in PM1. An additional independent mechanism may be involved in the induction of mdpJ in the presence of TBA.
Microbial diversity is the measure of the number or relative abundance of microbial species in a ... more Microbial diversity is the measure of the number or relative abundance of microbial species in a local area or region. Measuring microbial diversity may involve counting individual species, numbers of functional groups, or units operationally defined by the particular method being used.
Although the anaerobic biodegradation of methyl tert-butyl ether (MTBE) and tert-butyl alcohol (T... more Although the anaerobic biodegradation of methyl tert-butyl ether (MTBE) and tert-butyl alcohol (TBA) has been documented in the laboratory and the field, knowledge of the microorganisms and mechanisms involved is still lacking. In this study, DNA-stable isotope probing (SIP) was used to identify microorganisms involved in anaerobic fuel oxygenate biodegradation in a sulfate-reducing MTBE and TBA plume. Microorganisms were collected in the field using Bio-Sep® beads amended with (13)C5-MTBE, (13)C1-MTBE (only methoxy carbon labeled), or(13)C4-TBA. (13)C-DNA and (12)C-DNA extracted from the Bio-Sep beads were cloned and 16S rRNA gene sequences were used to identify the indigenous microorganisms involved in degrading the methoxy group of MTBE and the tert-butyl group of MTBE and TBA. Results indicated that microorganisms were actively degrading (13)C-labeled MTBE and TBA in situ and the (13)C was incorporated into their DNA. Several sequences related to known MTBE- and TBA-degraders in...
Methyl tert-butyl ether (MTBE) is a contaminant of concern to groundwater resources due to its pe... more Methyl tert-butyl ether (MTBE) is a contaminant of concern to groundwater resources due to its persistence in subsurface environments. MTBE appears to be degraded readily in the presence of oxygen but is recalcitrant under the anaerobic conditions prevalent in the subsurface, and can be converted into the more toxic compound tert-butanol (TBA). As ethanol is being promoted as a renewable fuel and a replacement for MTBE in gasoline formulations, its potential impact on the biodegradation of preexisting contaminants and on other components of petroleum must be examined. The purpose of this study is to investigate the effect of ethanol release on existing MTBE plumes and the fate of TBA under sulfate-reducing conditions. Our results suggest that TBA, MTBE and ethanol-induced methane concentrations are strong determinants of the composition of the indigenous microbial community that develops during MTBE transformation. Some of the changes in microbial communities induced by ethanol may ...
Philosophical Transactions of the Royal Society B: Biological Sciences
Soil and soil biodiversity play critical roles in Nature's Contributions to People (NCP) # 10... more Soil and soil biodiversity play critical roles in Nature's Contributions to People (NCP) # 10, defined as Nature's ability to regulate direct detrimental effects on humans, and on human-important plants and animals, through the control or regulation of particular organisms considered to be harmful. We provide an overview of pathogens in soil, focusing on human and crop pathogens, and discuss general strategies, and examples, of how soils' extraordinarily diverse microbial communities regulate soil-borne pathogens. We review the ecological principles underpinning the regulation of soil pathogens, as well as relationships between pathogen suppression and soil health. Mechanisms and specific examples are presented of how soil and soil biota are involved in regulating pathogens of humans and plants. We evaluate how specific agricultural management practices can either promote or interfere with soil's ability to regulate pathogens. Finally, we conclude with how integratin...
Increasing soil organic carbon (SOC) stocks in agricultural soils can contribute to stabilizing o... more Increasing soil organic carbon (SOC) stocks in agricultural soils can contribute to stabilizing or even lowering atmospheric greenhouse gas (GHG) concentrations. Cover crop rotation has been shown to increase SOC and provide productivity benefits for agriculture. Here we used a split field design to evaluate the short-term effect of cover crop on SOC distribution and chemistry using a combination of bulk, isotopic, and spectroscopic analyses of size-and density-separated soil aggregates. Macroaggregates (>250 µm) incorporated additional plant material with cover crop as evidenced by more negative δ13C values (−25.4‰ with cover crop compared to −25.1‰ without cover crop) and increased phenolic (plant-like) resonance in carbon NEXAFS spectra. Iron EXAFS data showed that the Fe pool was composed of 17–21% Fe oxide with the remainder a mix of primary and secondary minerals. Comparison of oxalate and dithionite extractions suggests that cover crop may also increase Fe oxide crystallin...
The Century Experiment at the Russell Ranch Sustainable Agriculture Facility at the University of... more The Century Experiment at the Russell Ranch Sustainable Agriculture Facility at the University of California, Davis provides long-term agroecological data from row crop systems in California's Central Valley starting in 1993. The Century Experiment was initially designed to study the effects of a gradient of water and nitrogen availability on soil properties and crop performance in ten different cropping systems to measure tradeoffs and synergies between agricultural productivity and sustainability. Currently systems include 11 different cropping systems-consisting of four different crops and a cover crop mixture-and one native grass system. This paper describes the long-term core data from the Century Experiment from 1993-2014, including crop yields and biomass, crop elemental contents, aerial-photo-based Normalized Difference Vegetation Index data, soil properties, weather, chemical constituents in irrigation water, winter weed populations, and operational data including ferti...
Methyl-tert-butyl ether (MTBE) and its degradation by-product, tert-butyl alcohol (TBA), are wide... more Methyl-tert-butyl ether (MTBE) and its degradation by-product, tert-butyl alcohol (TBA), are widespread contaminants detected frequently in groundwater in California. Since MTBE was used as a fuel oxygenate for almost two decades, leaking underground fuel storage tanks are an important source of contamination. Gasoline components such as BTEX (benzene, toluene, ethylbenzene and xylenes) are often present in mixtures with MTBE and TBA. Investigations of interactions between BTEX and MTBE degradation have not yielded consistent trends, and the molecular mechanisms of BTEX compounds' impact on MTBE degradation are not well understood. We investigated trends in transcription of biodegradation genes in the MTBE-degrading bacterium, Methylibium petroleiphilum PM1 upon exposure to MTBE, TBA, ethylbenzene and benzene as individual compounds or in mixtures. We designed real-time quantitative PCR assays to target functional genes of strain PM1 and provide evidence for induction of genes m...
Among the few bacteria known to utilize methyl tert-butyl ether (MTBE) as a sole carbon source, M... more Among the few bacteria known to utilize methyl tert-butyl ether (MTBE) as a sole carbon source, Methylibium petroleiphilum PM1 is a well-characterized organism with a sequenced genome; however, knowledge of the genetic regulation of its MTBE degradation pathway is limited. We investigated the role of a putative transcriptional activator gene, mdpC, in the induction of MTBE-degradation genes mdpA (encoding MTBE monooxygenase) and mdpJ (encoding tert-butyl alcohol hydroxylase) of strain PM1 in a gene-knockout mutant mdpC(-). We also utilized quantitative reverse transcriptase PCR assays targeting genes mdpA, mdpJ and mdpC to determine the effects of the mutation on transcription of these genes. Our results indicate that gene mdpC is involved in the induction of both mdpA and mdpJ in response to MTBE and tert-butyl alcohol (TBA) exposure in PM1. An additional independent mechanism may be involved in the induction of mdpJ in the presence of TBA.
Microbial diversity is the measure of the number or relative abundance of microbial species in a ... more Microbial diversity is the measure of the number or relative abundance of microbial species in a local area or region. Measuring microbial diversity may involve counting individual species, numbers of functional groups, or units operationally defined by the particular method being used.
Although the anaerobic biodegradation of methyl tert-butyl ether (MTBE) and tert-butyl alcohol (T... more Although the anaerobic biodegradation of methyl tert-butyl ether (MTBE) and tert-butyl alcohol (TBA) has been documented in the laboratory and the field, knowledge of the microorganisms and mechanisms involved is still lacking. In this study, DNA-stable isotope probing (SIP) was used to identify microorganisms involved in anaerobic fuel oxygenate biodegradation in a sulfate-reducing MTBE and TBA plume. Microorganisms were collected in the field using Bio-Sep® beads amended with (13)C5-MTBE, (13)C1-MTBE (only methoxy carbon labeled), or(13)C4-TBA. (13)C-DNA and (12)C-DNA extracted from the Bio-Sep beads were cloned and 16S rRNA gene sequences were used to identify the indigenous microorganisms involved in degrading the methoxy group of MTBE and the tert-butyl group of MTBE and TBA. Results indicated that microorganisms were actively degrading (13)C-labeled MTBE and TBA in situ and the (13)C was incorporated into their DNA. Several sequences related to known MTBE- and TBA-degraders in...
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Papers by Kate Scow