Progress 10/01/04 to 09/30/09
Outputs
OUTPUTS: Release of ethanol into groundwater provides a readily degradable food source that alters the composition of microbial communities as well as influences the fate and transport of pre-existing contaminants. Controlled field experiments, combined with application of DNA fingerprinting methods, were conducted in a shallow aquifer to measure: 1) the impact of ethanol on microbial communities associated with the anaerobic transformation of methyl tert-butyl ether (MTBE) to tert-butanol (TBA), and 2) the impact of TBA on microbial communities under sulfate-reducing conditions. The presence of MTBE and ethanol-induced methane formation were strongly correlated with changes in the composition of microbial communities. Total archael populations were also good predictors of MTBE and ethanol-induced methane levels. Changes in these biological markers thus appear to be a more sensitive indicator of actively occurring degradation than formation of degradation by-products (e.g. methane) or depletion of electron acceptor (e.g. sulfate).This study demonstrated the usefulness and sensitivity of DNA fingerprinting methods, such as terminal restriction fragment length polymorphism (TRFLP), for monitoring changes in microbial communities in response to contaminant dynamics. In Glennville, CA an MTBE bioremediation project was designed to build upon existing fluidized-bed bioreactor technology to provide water that is enriched in oxygen and MTBE degraders for re-injection and in-situ - treatment of the contaminated aquifer. Concurrently, we proposed to treat a portion of the bioreactor output to drinking water standards. The community of Glennville was entirely supplied by private well water prior to aquifer contamination and has been without a local water supply since 1998. The project forged a partnership with members of the community of Glennville; the community water company; the state of California's Department of Health Services; the Central Valley Regional Water Quality Control Board; and Environmental Resolution Inc. (ERI). This was one of the first applications of biological treatment to attempt to meet drinking water standards. Recognizing the importance of open dialogue with the local community, we held two information exchange meetings with Glennville residents. We tested the effluent for concentrations of MTBE and other gasoline components; nutrients added to the bioreactor during the start-up recirculation phase; and potentially pathogenic bacteria. PARTICIPANTS: Nothing significant to report during this reporting period. TARGET AUDIENCES: Target audiences include the general public that relies on groundwater aquifers as a source of drinking water, as well as State and local regulators who are responsible for ensuring clean water and treatment of contaminated water. Other audiences are responsible parties needed to find cost-effective technologies to clean up contaminated groundwater and engineering firms developing treatment methods. PROJECT MODIFICATIONS: Not relevant to this project.
Impacts
The growing interest in developing and utilizing biofuels has driven our research on groundwater contamination and remediation, and addresses the rising need to understand potential environmental impacts. Presentations made to government agencies and industry groups (California Water Resources Control Board, Air Resources Board, National Groundwater Association, California Agriculture Conference, Sustainable Underground Remediation Forum) about our research have increased the awareness of potential environmental impacts of biofuels. Our unique field project has also been noticed beyond the state level and we have received considerable national attention and numerous invitations to give presentations on the subject. We are working with the State of California in developing multi-media guidelines to assess the potential environmental impacts of new fuels. We have been involved in the screening of new biodiesel fuels using controlled laboratory studies and have reported these data back to the State to help guide recommendations about use of these fuels.
Publications
- Dong, L., Cordova-Kreylos, A.L., Yang, J., Yuan, H., Scow, K.M. 2009. Humic acids buffer the effects of urea on soil ammonia oxidizers and potential nitrification. Soil Biology and Biochemistry, 41 (8), pp. 1612-1621.
- Holloway, J.M., Goldhaber, M.B., Scow, K.M., Drenovsky, R.E. 2009. Spatial and seasonal variations in mercury methylation and microbial community structure in a historic mercury mining area, Yolo County, California. Chemical Geology, 267 (1-2), pp. 85-95.
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Progress 01/01/08 to 12/31/08
Outputs
OUTPUTS: The fuel oxygenate, methyl tertiary butyl ether (MTBE), has contaminated numerous groundwater aquifers in the United States, including a number of drinking water aquifers. Despite the fact that MTBE is no longer used as an additive, residual contamination from previous spills is widespread and persistent at many locations. Ethanol is rapidly replacing MTBE as a fuel oxygenate because of the demonstrated recalcitrance of MTBE under the often anaerobic conditions of groundwater aquifers and because of the potential impacts of MTBE breakdown products on human health. Though ethanol is readily degradable, its use as a fuel additive may have unexpected and undesired consequences for the naturally occurring degradation of existing groundwater contaminants from petroleum (e.g., MTBE, benzene). This possibility must be considered in different aquifers and under different conditions. In addition, with the increasing interest and development of ethanol-based biofuels, where ethanol will used in much larger amounts, possible consequences of spills or leakage of these fuels should be addressed. We continue investigations, in collaboration with Doug Mackay at UC Davis, in field studies of natural attenuation and biodegradation of fuels and fuel additives at Vandenberg Air Force Base (VAFB). A large project examined the impact of a controlled release of ethanol on the biodegradation of toluene, benzene and xylene (BTX), as well as on MTBE already present. Ethanol presence led to decreases in the natural attenuation of BTX and caused migration of these pollutants further down gradient from their release point than was the case in the absence of ethanol. Also ethanol substantially stimulated the conversion of MTBE to its recalcitrant metabolite, tertiary butyl alcohol (TBA), and led to reduction in MTBE. TBA is a greater human health concern and more difficult to treat using standard engineering methods than is MTBE. We also found significant changes in the microbial ecology of the aquifer that had been exposed to ethanol groundwater through its stimulation of different microbial communities with different metabolic capabilities. This included the growth of high populations of sulfate reducing bacteria in the same locations where sulfate was utilized and, ultimately, development of high populations of Archaea concurrent with the production of methane. Results from this first large scale field study of the impacts of a biofuel on groundwater biogeochemistry, residual contamination and microbial communities has been disseminated in scientific meetings and industry group meetings. In addition, throughout the project, we have been in communication with California state offices responsible for water quality and public health, with the US Environmental Protection Agency, and with engineering firms. PARTICIPANTS: Participants included Dr. Doug Mackay, Dr. Krassi Hristova (research scientist), Dr. Radomir Schmidt (postdoc), Dr. Mamie Inoue (postdoc), Dr. Ana Lucia Cordova-Kreylos (postdoc), Dr. Kevin Feris, Irina Chakraborty (PhD student). Partner organizations and collaborators included Murray Einarson, Deepa Gandhi, Scott Warner and other staff of Geomatrix Engineers; Patrick Chain, Anu Chakicherla and Staci Kane at Lawrence Livermore National Laboratories; and the Aerojet Corporation. TARGET AUDIENCES: Target audiences include the general public that relies on groundwater aquifers as a source of drinking water, as well as State and local regulators who are responsible for ensuring clean water and treatment of contaminated water. Other audiences are responsible parties needed to find cost-effective technologies to clean up contaminated groundwater and engineering firms developing treatment methods. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.
Impacts
Our research on groundwater contamination and remediation, combined with an increasing pressure to develop and utilize biofuels, addresses a rising need to understand the impacts on the environment of new fuels that are replacing petroleum. In addition, our research has advanced society's understanding of how to remediate a widespread groundwater contaminant, methyl tertiary butyl ether (MTBE). This contamination results in major economic losses due to closure of municipal wells and the requirement to import alternate sources of water for public consumption. Numerous presentations made to government agencies and industry groups (California Water Resources Control Board, Air Resources Board, National Groundwater Association, California Agriculture Conference) about our research have increased the awareness of potential environmental impacts of biofuel use. Our unique field project has also been noticed beyond the state level and we have received considerable national attention and numerous invitations to give presentations on the subject. With increasing pressure to reduce dependency upon petroleum, a variety of new fuels are coming onto the market, particularly in California. Based on our experience in the field and lab, we are working with the State of California in developing multi-media guidelines to assess the potential environmental impacts of new fuels. Currently we have begun to screen several of the new biodiesel fuels in laboratory studies. We are trying to develop the funding base and political support to have VAFB designated as a "national test site" for evaluating the impact of biofuels on the groundwater environment.
Publications
- Nozawa-Inoue, M., M. Jien, N. Hamilton, V. Stewart, K.M. Scow and K.R. Hristova. 2008. Quantitative Detection of Perchlorate-Reducing Bacteria by Real-Time PCR Targeting Perchlorate Reductase Gene. Applied Environmental Microbiology 74:1941-1944.
- Feris, K., D. Mackay, N. de Sieyes, I. Chakraborty, M. Einarson, K.R. Hristova, and K. Scow. 2008. Effect of Ethanol on Microbial Community Structure and Function During Natural Attenuation of Benzene, Toluene, and o-Xylene in a Sulfate-reducing Aquifer. Environmental Science and Technology 42(7)2289 - 2294
- Schmidt, R., Battaglia, V., Scow, K., Kane, S. and Hristova, K. 2008. Involvement of a Novel Enzyme, MdpA, in Methyl-tert-Butyl Ether in Degradation in Methylibium petroleiphilum PM1. Applied Environmental Microbiology 74:6631-6638.
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Progress 01/01/07 to 12/31/07
Outputs
OUTPUTS: The fuel oxygenate, methyl tertiary butyl ether (MTBE), has contaminated numerous groundwater aquifers in the US, including a number of drinking water aquifers. Despite the fact that MTBE is no longer used as an additive, residual contamination from previous spills is widespread and persistent at many locations. This contamination results in major economic losses due to closure of municipal wells and the requirement to import alternate sources of water for public consumption. Based on our research, we have developed new molecular tools and generated essential information about one of the few bacteria able to degrade MTBE to harmless constituents. Methylibium petroleiphilum Strain PM1 is the best characterized, most effective and widespread MTBE-degrading microorganism so far described. The completion of PM1's genome sequence provides a strong foundation to investigate aerobic MTBE biodegradation and explore genetic regulation of multiple biodegradation pathways potentially
involved in petroleum remediation. Having the genome sequence available and new progress on the metabolic pathways for MTBE biodegradation will lead to the development of new molecular tools for basic scientific questions as well as environmental applications for aerobic MTBE bioremediation. Strain PM1 is the model organism for MTBE biodegradation and information from this project has international significance for those engaged in research on MTBE biodegradation. We have sent this organism to, and shared research results with, numerous research groups throughout the world.
PARTICIPANTS: Participants included Dr. Krassi Hristova (research scientist), Dr. Mamie Inoue (postdoc), Dr. Ana Lucia Cordova-Kreylos (postdoc), Kun Yang (MS student), Irina Chakraborty (PhD student). Partner organizations and collaborators included Deepa Gandhi, Scott Warner and other staff of Geomatrix Engineers; Patrick Chain, Anu Chakicherla and Staci Kane at Lawrence Livermore National Laboratories; Cindy Nakatsu at Purdue University; and the Aerojet Corporation.
TARGET AUDIENCES: Target audiences include the general public that relies on groundwater aquifers as a source of drinking water, as well as State and local regulators who are responsible for ensuring clean water and treatment of contaminated water. Other audiences are responsible parties needed to find cost-effective technologies to clean up contaminated groundwater and engineering firms developing treatment methods.
Impacts
Our research has advanced society's understanding of how to remediate a widespread groundwater contaminant, methyl tertiary butyl ether (MTBE). One of the few known MTBE-degrading bacteria, PM1, was isolated by our group and described with respect to its phenotype and phylogeny. PM1 is a Gram negative, rod-shaped, motile, non-pigmented, facultative aerobe and was isolated for its ability to completely degrade MTBE. The 16S rRNA gene sequence indicates PM1 is a member of the beta-Proteobacteria. PM1 is a facultative methylotroph that uses methanol as a sole carbon source and is also able to grow on ethanol, toluene, benzene, ethybenzene, and dihydroxybenzoates as sole carbon sources. A new genus and species, Methylibium petroleiphilum gen. nov., sp. nov., was proposed, with the type strain PM1. A whole genome analysis of Methylibium petroleiphilum revealed a 4-Mb circular chromosome and 600-kb megaplasmid containing 3831 and 646 genes, respectively. Aromatic hydrocarbon
and alkane degradation, metal resistance, and methylotrophy are encoded on the chromosome. The megaplasmid contains an unusual t-RNA island, numerous insertion sequences and large repeated elements including a 40 kb region also present on the chromosome and a 29 kb tandem repeat encoding phosphonate transport and cobalamin biosynthesis. The megaplasmid codes for alkane degradation and plays an essential role in MTBE degradation. We identified the unique enzymatic steps involved in the aerobic MTBE degradation pathway of PM1. High-density whole genome cDNA microarrays were used to investigate substrate-dependent gene expression of PM1 grown on MTBE and ethanol as sole carbon sources. An MTBE regulon located on the megaplasmid was identified and putative functions for enzymes encoded in this regulon described with relevance to the predicted MTBE degradation pathway. A new unique dioxygenase enzyme system that carries out the hydroxylation of TBA to 2-methyl-2-hydroxy-1-propanol in M.
petroleiphilum PM1 was discovered. The pathways for toluene, phenol, and alkane oxidation via toluene monooxygenase, phenol hydroxylase, alkane monooxygenase as well as propane monooxygenase, respectively, were upregulated in MTBE-grown cells compared to ethanol-grown cells. Four out of nine putative cyclohexanone monooxygenases were also upregulated in MTBE-grown cells. Results indicated a link between metabolism of MTBE and aromatic compounds present in gasoline mixtures. The expression data aids our understanding of the regulation of metabolic processes that may occur in response to pollutant mixtures and perturbations in the environment. Our research also led to application of a bioremediation technology for application in zero-valent iron (ZVI)/sand bio-barriers placed in an aquifer contaminated with perchlorate and trichloroethylene (TCE). Substantial in situ treatment of both contaminants in mixtures was demonstrated. TCE was readily degraded with ZVI, both with and without
perchlorate, in the presence and absence of microorganisms. Perchlorate could only be degraded biologically and was initially inhibited by the presence of TCE; this inhibition was removed by adding additional hydrogen.
Publications
- Hristova, K. R., Schmidt, R., Chakicherla, A. Y., Legler, T. C., Wu, J., Chain, P. S., Scow, K. M., Kane, S. R. (2007). Comparative Transcriptome Analysis of Methylibium petroleiphilum PM1 Exposed to the Fuel Oxygenates Methyl tert-Butyl Ether and Ethanol. Appl. Environ. Microbiol. 73: 7347-7357.
- Cavagnaro, T.R., L. E. Jackson, K. M. Scow, and K. R. Hristova. 2007. Effects of arbuscular mycorrhizas on ammonia oxidizing bacteria in an organic farm soil. Microb. Ecol. 54:618-626.
- Kane SR, Chakicherla AY, Chain PS, Schmidt R, Shin MW, Legler TC, Scow KM, Larimer FW, Lucas SM, Richardson PM, Hristova KR. 2007. Whole-genome analysis of the methyl tert-butyl ether-degrading beta-proteobacterium Methylibium petroleiphilum PM1. J Bacteriol. 189:1931-45.
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Progress 01/01/06 to 12/31/06
Outputs
The fuel additive methyl tertiary butyl ether (MTBE), a groundwater contaminant polluting numerous aquifers throughout the US, is now banned from gasoline and other petroleum products. Ethanol, a readily degradable chemical, is replacing MTBE in many gasoline formulations. This poses an interesting challenge for the numerous locations already contaminated by petroleum (including with Superfund chemical benzene and toluene, as well as MTBE) from service station leaks and spills. Natural attenuation processes, such as biodegradation by native microbial communities, keep much of this residual contamination contained and out of water supplies. Leaking of ethanol, which is so readily metabolizable and a preferred microbial substrate, may alter these processes, increasing the potential for human exposure to petroleum compounds. To test this, we conducted a field study at a contaminated groundwater site to measure the effect of a controlled ethanol release on biodegradation
of benzene, other aromatics and MTBE. Ethanol increased the distance that benzene migrated in groundwater and stimulated the conversion of MTBE to the undesirable metabolite, tertiary butyl alcohol (TBA). This was due in part to consumption of electron acceptors that would otherwise have supported biodegradation of the residual contaminants. The significance of this result is that increasing usage of ethanol as a fuel additive may change the potential for human exposure to hazardous chemicals, like benzene, and to other harmful pollutants associated with petroleum. The potential for this situation warrants further study at different sites. Plant invasions alter soil microbial community composition. A study investigated the impacts of invasion-induced changes in the soil microbial community on soil aggregation, an ecosystem property strongly influenced by microorganisms. Soil aggregation is regulated by many biological factors including roots, arbuscular mycorrhizal fungal hyphae, and
microbially-derived carbon compounds. We measured root biomass, fungal-derived glomalin-related soil protein (GRSP), and aggregate mean weight diameter in serpentine soils dominated by an invasive plants (goatgrass or yellow starthistle) or by native plants (lasthenia, plantago or hemizonia). Root biomass tended to increase in invaded soils. GRSP concentrations were lower in goatgrass-dominated soils than native soils. In contrast, starthistle dominated soil contained a higher amount one type of GRSP. Soil aggregation increased with goatgrass invasion, but did not increase with starthistle invasion. In highly aggregated serpentine soils, small increases in soil aggregation accompanying plant invasion were not related to changes in GRSP and likely have limited ecological significance.
Impacts
Readily degradable alternatives to fuel additives such as MTBE, as well as new fuels, may have unexpected impacts on the environment by inhibiting the ability of native microbial communities to naturally attenuate contaminants already present in groundwater and soils. It is essential to study biological and chemical interactions between substances released or leaked to the environment in order to predict and possibly prevent negative impacts of hazardous substances on human health and the environment. Complexities are also evident, and deserve research attention, in the interactions among members of soil microbial communities that determine the impact of invasive plants on terrestrial ecosystems.
Publications
- BATTEN KM, SIX J, SCOW KM, RILLIG MC (2005) Plant invasion of native grassland on serpentine soils has no major effects upon selected physical and biological properties. Soil Biology and Biochemistry 37: 2277-2282
- BATTEN KM, SCOW KM, DAVIES KF, HARRISON SP (2006) Two invasive plants alter soil microbial community composition in serpentine grasslands. Biological Invasions 8: 217-230.
- BOSSIO DA, GIRVAN MS, VERCHOT L, BULLIMORE J, BORELLI T, ALBRECHT A, SCOW KM, BALL AS, PRETTY JN, OSBORN AM (2005) Soil microbial community response to land use change in an agricultural landscape of Western Kenya. Microbial Ecology 49: 50-62.
- CAVAGNARO TR, JACKSON LE, SIX J, FERRIS H, GOYAL S, ASAMI D, SCOW KM (2006) Arbuscular mycorrhizas, microbial communities, nutrient availability, and soil aggregates in organic tomato production. Plant and Soil 282:209-225.
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Progress 01/01/05 to 12/31/05
Outputs
Methyl bromide is highly effective in reducing soil pathogens, however, its use is to be phased out for many applications in the US in the near future. We compared the effects of pre- and postplant treatments and amendments on soil microbial communities and tree vigor in a replanted peach orchard to explore possible replacements for methyl bromide. Soil sterilization treatments and organic carbon amendments changed the composition of microbial communities in the soil. High microbial biomass is generally considered beneficial to agricultural soils; we found that it was usually highest in soils that received the organic carbon amendment and lowest in those with soil sterilization. However, tree vigor was highest with the sterilization treatments. The effects of a microbial inoculants/organic carbon combination on microbial communities and plant vigor were no different from simply adding organic carbon. Furthermore, polyethylene plastic mulch had a similar effect on soil
microbial communities and tree growth as chemical fumigants. The use of polyethylene mulch should be investigated further as an alternative to chemical soil fumigation. In addition, this study suggests that commercial soil inoculants should certainly not be substituted for pre-plant fumigation, and may have very limited value in a commercial orchard setting. During construction of roads, entire hillsides can be cut away, dramatically disturbing the ecosystem. Microbial communities play important, but poorly understood roles in revegetating roadcuts because of the many functions they perform in nutrient cycling, plant symbioses, decomposition, and other ecosystem processes. Our objective was to determine relationships among microbial community composition, soil chemistry, and disturbance on a serpentine soil disturbed by a roadcut and then partially revegetated. We hypothesized that the adjacent undisturbed serpentine soil would have a different microbial community composition from
barren and revegetated sections of the roadcut and that undisturbed soils would have the greatest microbial biomass and diversity. We measured phospholipid fatty acids (PLFA) and soil nutrient concentrations on barren and revegetated sections of the roadcut and on adjacent undisturbed serpentine and nonserpentine soils. Most roadcut samples had soil chemistry similar to the serpentine reference soil. The microbial biomass and diversity of barren sites was lower than that of revegetated or the serpentine reference site. The nonserpentine reference site had significantly greater microbial biomass than serpentine or disturbed sites but significantly lower relative proportions of actinomycetes, and slow growth biomarkers. The barren site had the lowest microbial biomass and a significantly greater proportion of that biomass was fungi. Barren, revegetated, and serpentine sites all had dissimilar microbial community composition. The composition of the revegetated communities, however, was
intermediate between the serpentine reference and barren soils, suggesting that community composition of revegetated soils is approaching that of an undisturbed site with similar soil chemistry.
Impacts
Addition of organic amendments have a greater apparent impact than do microbial inoculants on recovery of the soil communities in fumigated agricultural soils. Revegetation of highly disturbed soils is associated with the recovery of microbial communities similar in composition to those of adjacent undisturbed soils.
Publications
- DRENOVSKY RE, DUNCAN RA, SCOW KM. (2005). Soil sterilization and organic carbon, but not microbial inoculants, change microbial communities in replanted peach orchards. California Agriculture 59: 176-181.
- DEGROOD SH, CLAASSEN VP, SCOW KM (2005) Microbial community composition on native and drastically disturbed serpentine soils. Soil Biology and Biochemistry 37: 1427-1435.
- BURGER M, JACKSON LE, LUNDQUIST EJ, LOUIE DT, MILLER RL, ROLSTON DE, SCOW KM (2005) Microbial responses and nitrous oxide emissions during wetting and drying of organically and conventionally managed soil under tomatoes. Biology and Fertility of Soils 42: 109-118.
- MACHULLA G, BRUNS MA, SCOW, KM (2005) Microbial properties of mine spoil materials in the initial stages of soil development. Soil Science Society of America Journal 69: 1069-1077.
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Progress 01/01/03 to 12/31/03
Outputs
Oxidation of ammonia by autotrophic ammonia-oxidizing bacteria (AOB) is a key process in agricultural and natural ecosystems and has large impacts at the global scale through generation of greenhouse gases. The ecology and physiology of AOB are not well understood because these organisms are notoriously difficult to culture. A real-time PCR assay targeting part of the ammonia monooxygenase gene (amoA) was developed to estimate AOB population size in soil. The effect of ammonium concentration on AOB density was measured in soil microcosms with application of different concentrations of ammonium sulfate. AOB population sizes, as well as ammonium and nitrate concentrations, were monitored for 28 days after application of ammonium sulfate. AOB populations in amended treatments increased proportionally with respect to the amount of ammonium added. The population size of total bacteria (also by real time PCR with a universal bacterial probe) remained the same, regardless of
ammonia concentration. A field experiment was conducted to test whether the changes in AOB density observed in microcosms could also be detected in tomato plots amended with 40g of ammonium sulfate. AOB population size increased almost 5 fold by day 39. In a second field experiment, AOB population size was significantly higher in regularly fertilized vs. unfertilized soil, even though the last ammonium application occurred 8 months prior to measurement, suggesting long-term effects of ammonium fertilization on AOB population size. Plant invasions present a serious threat to native ecosystem structure and function. Little is known about the role rhizosphere microbial communities play in the spread of invasive species into native plant communities. Microbial communities of invasive and native plant rhizospheres in serpentine soils were compared. The two invasive species were Centaurea solstitialis (yellow starthistle) and Aegilops triuncialis (barb goatgrass). The five native species
competitively excluded by the invaders were Lotus wrangelianus, Hemezonia congesta, Holocarpha virgata, Plantago erecta, and Lasthenia californica. Phospholipid Fatty Acid analysis (PLFA) was used to compare the rhizosphere microbial communities of invasive and native plants. Correspondence Analyses (CA) of PLFA data indicated that despite yearly variation, both starthistle and goatgrass appear to change microbial communities in areas they invade, and that invaded and native microbial communities significantly differ. Rhizosphere communities in newly invaded areas were more similar to original native communities than those in areas that had been invaded for several years. In general, invasive plant rhizospheres have higher total microbial biomass and fatty acid diversity and are enriched in PLFA biomarkers for sulfur-oxidizing bacteria, sulfate reducing bacteria, and fungi compared to native plant rhizospheres. Changes in soil microbial community composition induced by plant invasion
may impact native plant fitness and/or ecosystem function.
Impacts
Plant rhizopheres have distinct microbial communities that may play a role in the invasiveness of certain plant species. Quantification of specific microbial populations by quantitative PCR methods will help in understanding specific ecosystem processes and in how microbial communities respond to and recover from disturbances and management practices.
Publications
- BOULTON, AM, JAFFEE BA, SCOW KM (2003) Effects of a common harvester ant (Messor andrei) on richness and abundance of soil biota. Applied Soil Ecology. 23:257-265.
- JOHNSON MJ, LEE KY, and SCOW KM. (2003) DNA fingerprinting reveals links among agricultural crops, soil properties, and the composition of soil microbial communities. Geoderma 114:279-303.
- JACKSON LE, CALDERON F, STEENWERTH K, SCOW KM, and ROLSTON DE. (2003) Responses of soil microbial processes and community structure to tillage events and implications for soil quality. Geoderma 114:305-317.
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Progress 01/01/02 to 12/31/02
Outputs
Methane-oxidizing bacteria (methanotrophs) consume a significant but variable fraction of greenhouse-active methane gas produced in wetlands and rice paddies before it can be emitted to the atmosphere. Temporal and spatial dynamics of methanotroph populations in California rice paddies were quantified using phospholipid biomarker analyses in order to evaluate the relative importance of two groups of methanotrophs, type and type II, with depth and in relation to rice roots. Type I and I organisms differ substantially in their efficiency of methane consumption and in their sensitivity to environmental factors. Methanotroph population fluctuations occurred primarily within the top 0-2 cm of soil, where methanotroph cells increased by a factor of 3-5 over the flooded rice-growing season. The results indicate that rice roots and rhizospheres were less important than the soil-water interface in supporting methanotroph growth. Both type I and type II methanotrophs were
abundant throughout the year. However, only type II populations were strongly correlated with soil porewater methane concentrations and rice growth. In a second project, phospholipid ester-linked fatty acid (PLFA) profiles were used to evaluate soil microbial community composition for 9 land use types in two coastal valleys in California. These included irrigated and non-irrigated agricultural sites, non-native annual grasslands and relict, never-tilled or old field perennial grasslands. We hypothesized that land use history and its associated management inputs and practices may produce a unique soil environment, for which microbes with specific environmental requirements may be selected and supported. We investigated the relationship between soil physical and chemical characteristics, management factors, and vegetation type with microbial community composition. Higher values of total soil C, N, and microbial biomass and lower values of soil pH occurred in the grassland than
cultivated soils. Different soil characteristics, site and management factors, and different land use types showed distinct differences in microbial community composition.
Impacts
Different soils have distinct microbial communities as a function of a soil's physical/chemical properties, land use, and type of management practices employed. These distinct microbial fingerprints will be useful in identifying the type of microbial community required to carry out specific processes and in understanding how communities respond to and recover from disturbances and management practices.
Publications
- COSTELLO, A; AUMAN, A.; MACALADY J; SCOW K; LIDSTROM, M. (2002)Estimation of methanotroph abundance in a freshwater lake sediment. Environ. Micro 4:443-450.
- MACALADY, JL, MCMILLAN AM, DICKENS AF, TYLER SC, SCOW KM. (2002) Population dynamics of type I and II methanotrophic bacteria in rice soils. Environ Microbiol. 4: 148-57.
- ANDREWS, S.S.; MITCHELL, J.P.; MANCINELLI, R.; KARLEN, D.L.; HARTZ, T.K.; HORWATH, W.R.; PETTYGROVE, G.S; SCOW, K.M.; MUNK, D.S. (2002). On-farm assessment of soil quality in California's central valley. Agron. J. 94:12-23.
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Progress 01/01/01 to 12/31/01
Outputs
The microbial community composition of agricultural soils is influenced by crop type, management practices, and seasonal variations. The objective of this study was to determine if variations in soil microbial biomass and community composition associated with different crops (planted in the previous year) and management practices persisted after these treatments were removed. Sampling in 1998 and 2000 of microbial communities (by phospholipid fatty acid analysis--PLFA) in soils under different crops (tomatoes, corn, wheat/beans, safflower) and management systems (organic, low input, conventional 2 and 4 yr rotation) was performed at the Sustainable Agricultural Farming Systems Project (SAFS) in Davis, CA. One year later (summer, 2001), a single sampling of the same plots now planted uniformly with conventionally managed wheat was conducted. Some of the distinct differences in communities associated with specific crops and management systems observed in 1998 and 2000
disappeared one year after all soils were planted with wheat and managed in the same way. The strongest evidence of the previous treatments was a higher microbial biomass in organic and low input than conventionally managed soils. Analysis of microbial community composition in the 2001 samples revealed small differences between organic and low input treatments versus conventional and high input treatments, but the magnitude of the management differences was small compared to annual differences. These results suggest that differences in microbial biomass are more persistent than are differences in community composition and that community composition is sensitive to the immediate crop and management practices.
Impacts
Information on the composition of microbial communities in agricultural soils should be an important component of agricultural management strategies yet little is. Suprisingly little is known about these communities and what factors influence their composition and size. Understanding how microbial communities respond to management practices and crop type will help to determine what practices are detrimental to or supportive of beneficial soil microorganisms.
Publications
- CHEN, J., H. FERRIS, K.M. SCOW, and K.J. GRAHAM. 2001. Fatty acid composition and dynamics of selected fungal-feeding nematodes and fungi. Comp. Biochem. Physiol. Part B 130:135-144.
- CALDERON, FJ; L.E. JACKSON; K.M. SCOW; and D.E. ROLSTON. 2001. Short-term dynamics of nitrogen, microbial activity, and phospholipid fatty acids after tillage. Soil Sci. Soc. Amer. J. 65:118-126.
- RAMADAN, Z., X.H. SONG, P.K. HOPKE, M.J. JOHNSON, and K.M. SCOW. 2001. Variable selection in classification of environmental soil samples for partial least square and neural network models. Anal. Chem. Acta 446:233-244.
- POUDEL, D.D., H. FERRIS, K. KLONSKY, W.R. HORWATH, K.M. SCOW, A.H.C. VAN BRUGGEN, W.T. LANINI, J.R. MITCHELL, S.T. TEMPLE. 2001. The sustainable agriculture farming system project in California's Sacramento Valley. Outlook on Agriculture. 30: 109-116.
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Progress 01/01/00 to 12/31/00
Outputs
A major objective was to determine if soil microbial communities could be classified into groups according to the type of plant community present, soil mineralogical and chemical properties, land use, and/or geographic location. Microbial communities in a set of 50 agricultural soil samples (representing different crops, locations, and soil taxa) collected in the Central Valley of CA were characterized using Intergenic Transcribed Spacer (ITS), a DNA fingerprinting method. Extracted DNA was amplified using either universal bacterial or fungal primers targeting the region extending from within the 16S rDNA to just into the 23S rDNA and the amplified products were separated on polyacrylamide gels by size. Generally, the bacterial DNA fingerprints (containing 25-30 bands) were more complex and more consistent among field replicates than were the eucaryotic fingerprints (3-12 bands). The greatest similarity among fingerprints was observed among laboratory replicates,
followed by similarity among field replicates, and then by similarity among communities collected under the same crop or at the same location. The DNA community fingerprints were not strongly correlated with any soil property data (pH, organic matter, nitrogen, texture). There was a strong correspondence, however, between how soils grouped on the basis of their microbial community fingerprints and how they grouped on the basis of their reflectance patterns measured by spectral analysis (used to characterize soil in remote sensing), suggesting an underlying relationship between community patterns and certain soil properties. The results demonstrate that ITS-DNA fingerprinting is an effective means of discriminating microbial communities in soils.
Impacts
This result of the project indicate that it is possible to differentiate microbial communities associated with different soils and that community composition responds to management and environmental change. The methods described can be used to assist in making management decisions to improve soil quality and sustainability.
Publications
- SCOW, K.M., E. SCHWARTZ, M.JOHNSON, and J.L. MACALADY. 2000. Measurement of microbial diversity. In: Encylopedia of Biodiversity. (in press).
- SCOW, K.M. 1999. Soil microbiology. In: Encyclopedia of Microbiology. Academic Press (in press).
- FITZGERALD, G., K.M. SCOW, and J. HILL. 2000. Fallow season straw and water management effects on methane emissions in California rice. Global Biogeochemical Cycles 14:767-776.
- CALDERON, F.J., L.E. JACKSON, K.M. SCOW, and D.E. ROLSTON. 2000. Microbial responses to simulated tillage in cultivated and uncultivated soils. Soil Biol. Biochem. 32:1547-1559.
- GREEN, C.T., and K.M. SCOW. 2000. Analysis of phospholipid fatty acids (PLFA) to characterize microbial communities in aquifers. Hydrogeology J. 8:126-141.
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Progress 01/01/99 to 12/31/99
Outputs
The primary objective was to determine how the composition of microbial communities in agricultural soils is influenced by environmental and management factors. Both field and in laboratory microcosm studies were conducted and methods used to characterize communities included Intergenic Transcribed Spacer (ITS) (a DNA fingerprinting method) and Phospholipid Fatty Acid (PLFA). With ITS, a greater diversity of bacteria was found in soils of the organic than low input and conventional farming systems of the Sustainable Agricultural Farming Systems (SAFS) project. Considerably more bacterial than fungal diversity was present in all farming systems. In on-farm studies, PLFA analysis showed that growing cover crops in vineyard soils increased the microbial biomass but did not substantially change community composition relative to that present in soils without cover crops. Differences between vineyard row and furrow communities, however, or between rhizosphere and bulk soil
communities, were very large. Addition of a microbial inoculant did not substantially change the microbial community composition in either vineyard or almond orchard soils. Compaction of pine forest soils had little effect on microbial communities; however, the degree of organic matter removal strongly affected community composition. Using ITS, it was possible to differentiate soil microbial communities in agricultural soils under different crops, including tomatoes, cotton, corn, almonds, and prunes. Communities under annual row crops were more similar to one another than to those under perennial orchards. ITS fingerprints of dust samples collected from these same soils indicated that the dust communities were more similar to their origin soils than to the other dust samples.
Impacts
This results of this project indicate that it is possible to differentiate microbial communities associated with different soils and that community composition responds to management and environmental change. The methods described can be used to assist in making management decisions to improve soil quality and sustainability.
Publications
- SONG, X.-H., P.K. HOPKE, M. A. BRUNS, K. GRAHAM, and K. SCOW. 1999. Pattern recognition of soil samples based on microbial fatty acid contents. Environ. Sci. Technol. 33: 3524-3530.
- BRUNS, M. A., and K. M. SCOW. 1999. DNA fingerprinting as a means to identify sources of soil-derived dust: problems and potential, p. 193-205. In: Scow et al. (eds) Integrated assessment of ecosystem health. Lewis Publishers, Boca Raton, FL.
- SUDARSHANA, P., J.R. HANSON, and K.M. SCOW. 1999. Application of random amplified polymorphic DNA (RAPD) method for characterization of soil microbial communities, p. 223-231. In: Scow et al. (eds) Integrated assessment of ecosystem health. Lewis Publishers, Boca Raton, FL.
- LUNDQUIST, E.J., L.E. JACKSON, C. JOHNSON, S. UESUGI, and K.M. SCOW. 1999. Rapid response of soil microbial communities from conventional, low input, and organic farming systems to a wet/dry cycle. Soil Biol. Biochem 31:1661-1675.
- LUNDQUIST, E.J., L.E. JACKSON, and K.M. SCOW. 1999. Wet-dry cycles affect dissolved organic carbon in two California agricultural soils. Soil Biol. Biochem 31:1031-1038.
- LUNDQUIST, E.J., L.E. JACKSON, K.M. SCOW, and C. HSU. 1999. Changes in microbial biomass and community composition, and soil carbon and nitrogen pools after incorporation of rye into three California agricultural soils. Soil Biol. Biochem. 31:221-236.
- CLARK, M.S., W.R. HORWATH, C. SHENNAN, C, K.M. SCOW, W. T. LANINI, and H. FERRIS. 1999. Nitrogen, weeds and water as yield-limiting factors in conventional, low-input, and organic tomato systems. Agric. Ecosyst. Environ. 73:257-270.
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Progress 01/01/98 to 12/01/98
Outputs
Major research objectives included: i) developing methods for characterizing soil microbial communities; ii) identifying and prioritizing environmental and management factors that influence community composition and iii) determining organisms and functional groups that differ among soils. Analysis of phospholipid fatty acids (PLFA) proved able to distinguish soils from different locations, as well as the same soil subjected to different conditions. The relative importance of environmental variables influencing community composition was soil type>time of season>crop = texture>management system>spatial variation in the field. When flooded, soil became depleted in fungal and actinomycete fatty acids and enriched in fatty acids associated with gram positive, anaerobic bacteria. Adding organic residues enriched fungal and actinomycete fatty acids. DNA-based methods were explored for fingerprinting communities in soil. Intergenic Transcribed Spacer analysis (ITS) and
Thermal Denaturing Gel Electrophoresis (TGGE) were effective for fingerprinting and differentiating soil communities. Sequencing of specific bands within gels permitted identification of individual species. Using neural network based approaches for classifying data differentiated microbial communities in soils, using fatty acid data, more accurately than did principal components analysis. >.
Impacts
(N/A)
Publications
- CLARK, M.S., W.R. HORWATH, C. SHENNAN, and K.M. SCOW. 1998. Changes in soil chemical properties resulting from organic and low-input farming practices. Agron. J. 90:662-671.
- GUNAPALA, N., R.C. VENETTE, H. FERRIS, and K.M. SCOW. 1998. Effects of soil management history on the rate of organic matter decomposition. Soil Biol. Biochem. 30:1917-1927.
- SONG, X.H., P.K. HOPKE, M. BRUNS, D.A. BOSSIO, and K.M. SCOW. 1998. A fuzzy adaptive resonance theory--supervised predictive mapping neural network applied to the classification of multivariate data. Chemomet. Intell. Lab. Syst. 41:161-170
- LUNDQUIST, E.J., L.E. JACKSON, and K.M. SCOW. 1998. Effects of wet/dry cycles on dissolved organic carbon in two California agricultural soils. Soil Biol. Biochem (in press).
- LUNDQUIST, E.J., L.E. JACKSON, K.M. SCOW, and C. HSU. 1998. Changes in microbial biomass and community composition, and soil carbon and nitrogen pools after incorporation of rye into three California agricultural soils. Soil Biol. Biochem.
- GUNAPALA, N., and K.M. SCOW. 1998. Dynamics of soil microbial biomass and activity in conventional and organic farming systems. Soil Biol. Biochem. 30:805-816.
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Progress 01/01/97 to 12/01/97
Outputs
Biodegradation of pesticides is strongly influenced by the composition of soil microbial communities; however, little is known about the community composition of many soils. We conducted phospholipid fatty acid (PLFA) analyses to characterize microbial communities in numerous California agricultural soils. Microbial communities could be clearly distinguished, with a sharp contrast between communities in saturated or high clay soils and unsaturated, well-drained soils. Redundancy analysis revealed that both soil texture and crop type were significantly correlated with variation in PLFA fingerprints in a set of agricultural soils from the Central Valley. The soil fumigant, metam sodium, caused substantial declines in the density, diversity and activity of soil microbial communities, even at rates equal to or 50% of typical application rates. Recovery of communities in soil microcosms to their original state was very slow. Agricultural soils in California are subjected
to extreme fluctuations in soil moisture due to irrigation and high temperatures. Microcosm studies of the effect of wet/dry cycles on microbial communities in tomato soils indicated large differences in microbial communities in the surface and deeper layers of soil. Adaptation to wet/dry cycles by surface, but not deeper soil, microbial populations was evident within several months of exposure to wet/cycles. After exposure to stress, surface soil populations had lower concentrations of lipids associated with stress and the communit.
Impacts
(N/A)
Publications
- MACALADY, J., and K.M. SCOW. 1997. Effects of fumigation with metam sodium on soil microbial activity and community structure. J.
- BOSSIO, D.A., K. M. SCOW, N. GUNAPALA, and K.J. GRAHAM. 1997. Determinants of soil microbial communities: effects of agricultural management, season, and soil type on phospholipid fatty acid
- BOSSIO, D.A., and K. M. SCOW. 1997. Impact of carbon and flooding on PLFA profiles and substrate utilization patterns of soil microbial communities. Microb. Ecol. (in press).
- BOSSIO, D.A., and K.M. SCOW. 1997. Microbial ecology in agricultural ecosystems: impacts of management changes on the microbial community in a rice production system. Cal. Agric. 51: 33-40.
- LAU, S. S., M. E. FULLER, H. FERRIS, R. C. VENETTE and K. M. SCOW. 1997. Development and testing of an assay for soil-ecosystem health using the bacterial-feeding nematode Cruznema tripartitum. Ecotoxicology and Environmental Safety 36:133-
- FULLER, M.E., and K. M. SCOW. 1997. Impacts of trichloroethylene (TCE) and toluene on nitrogen cycling in soil. Appl. Environ.
- SCOW, K.M. 1997. Soil microbial communities and carbon flow in agroecosystems, p. 361-407. In: Jackson, L.E.(ed.) Ecology in
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Progress 01/01/96 to 12/30/96
Outputs
The microbial communities of soils from numerous California agricultural systemsand compost were characterized using phospholipid fatty acid analysis (PLFA) of whole soil extracts. Communities could be clearly differentiated using multivariate statistics. This result indicated PLFA analysis to be a powerful approach for characterizing microbial communities and for studying how factors such as pollution, climate, soil type, management, and others can change community composition. In field studies of rice and tomato soils, the impact of various factors on community composition could be ranked in the following order of importance: in-field variability < agricultural management = seasonal changes < soil type/location. High levels of fungal and actinomycete PLFAs were found in soils that were well-drained and with high carbon inputs, whereas high levels of PLFAs associated with anaerobic bacteria were found in flooded soils. Many of the PLFAs proposed as markers for other
microbial groups were not found and many previously unidentified PLFAs were found in the soils. This indicates the need for future research to identify environmentally important microbial species and functional groups associated with certain PLFAs. Patterns based on PLFA data did not always agree with patterns based on carbon source utilization patterns, the latter method which is also used to characterize soil communities. It was concluded that PLFA analysis was the more reliable method because it does not require culturing, and.
Impacts
(N/A)
Publications
- RILLIG, M.C., K.M. SCOW, J.N. KLIRONOMOS, and M.F. ALLEN. 1996. Microbial carbon-substrate utilization in the rhizosphere of Gutierrezia sarothrae grown in elevated atmospheric carbon dioxide. Soil Biol. Biochem. (in press).
- LAU, S.S., M.E. FULLER, H. FERRIS, R.C. VENETTE, and K.M. SCOW. 1996. Development and testing of an assay for soil-ecosystem health using the bacterial-feeding nematode Cruznema tripartitum. Ecotox. Environ. (in press) SCOW, K.
- M., and M.R. WERNER. 1996. The soil ecology of cover cropped vineyards. In: Ingels, C. (ed.) Use of cover crops in vineyards. UC Sustainable AgricultureResearch and Education Program Press (in press).
- SCOW, K.M. 1996. Interrelationships between soil microbial communities and carbon flow in agroecosystems. In: Jackson, L.E.(ed.) Agricultural Ecology (in press).
- GUNAPALA, N., and K.M. SCOW. 1996. Dynamics of soil microbial biomass and activity in conventional and organic farming systems. Soil Biol. Biochem. (in press).
- FULLER, M.E., K.M. SCOW, S. LAU, and H. FERRIS. 1996. Trichloroethylene and toluene effects on the structure and function of the soil community. Soil Biol. Biochem. (in press).
- FULLER, M. E., and K.M. SCOW. 1996. Effects of toluene on microbial-mediated processes involved in the soil nitrogen cycle. Microb. Ecol. 32:171-184.
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Progress 01/01/95 to 12/30/95
Outputs
Pollutants and agrichemicals selectively influence the structure and function ofmicrobial communities. Analysis of phospholipid fatty acids extracted directly from soil and of carbon source utilization patterns were used to develop fingerprints of soil microbial communities. Trichloroethylene (TCE) and toluene, both ubiquitous soil contaminants, substantially decreased nitrification and caused sharp increases in soil ammonium. Inhibition of nitrification was due, in part, to competitive inhibition of the ammonium monoxygenase and is likely to occur with many pollutants requiring oxygenases for metabolism. Exposure to toluene and TCE caused significant shifts in the heterotrophic metabolic diversity of the microbial community. Respiration, mineralization, and denitrification were unaffected even by high toluene and TCE concentrations. Metham sodium, a commonly used pesticide, substantially reduced respiration and heterotrophic metabolic diversity at low pesticide
application rates and recovery of processes to original rates was slow. In a field study of rice straw decomposition, distinct soil microbial communities under different straw management systems could be discriminated based on their carbon utilization patterns. Using canonical correspondence analysis, the variables of carbon and water content were found to explain much of the variation in communities across the plots.
Impacts
(N/A)
Publications
- FULLER, M.E., and K.M. SCOW. 1995. Effects of toluene on microbial-mediated processes involved in the soil nitrogen cycle. Microb. Ecol. (in-press).
- BOSSIO, D.A., and K.M. SCOW. 1995. Impact of carbon and flooding on the metabolic diversity of microbial communities in soil. Appl. Environ. Microb. 61:4043-4050.
- HOYLE, B., K.M. SCOW, G. FOGG, and J. DARBY. 1995. Effect of carbon:nitrogen ratio on kinetics of phenol biodegradation by Acinetobacter in saturated sand. Biodegradation 6:283-293.
- MORGENROTH, E., E.D. SCHROEDER, D.P.Y. CHANG, and K.M. SCOW. 1995. Nutrient limitation in a compost biofilter degrading hexane. Proc. Air and Waste Management Association, 88th Annual Meeting, San Antonio, Texas, June 18-23, 1995.
- FULLER, M., D. MU, and K.M. SCOW. 1995. Biodegradation of trichloroethylene and toluene by indigenous microbial populations in vadose sediments. Microb. Ecol. 29:311-325.
- SCOW, K.M., S. FAN, C. JOHNSON, and G.M. MA. 1994. Biodegradation of sorbed chemicals in soil. Environ. Health Perspec. 103:93-95.
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Progress 01/01/94 to 12/30/94
Outputs
Sorption and biological factors control rates of biodegradation of sorbed chemicals in soil. For phenanthrene, no relationship was found between sorption parameters (Kc, Kd) and biodegradation rate in seven soils. Sorption strongly influenced biodegradation when halloysite clay was added to soil; a marked reduction in rate was due to greater and irreversible sorption of phenanthrene onto clay. Aging of phenanthrene in soil significantly reduced its biodegradability. Inoculation of soils with a bacterial strain substantially enhanced phenanthrene biodegradation; however, a very high population density was required. Addition of surfactants or secondary carbon sources did not enhance phenanthrene biodegradation. Differences in the kinetics of mineralization of phenol and para-nitrophenol were due, in part, to phenol's ability to form irreversible bonds with soil organic matte and thus making it unavailable for degradation. Both trichloroethylene (TCE) and toluene were
readily degraded by indigenous microbial populations in soils and unsaturated subsurface sediments. Success of TCE removal, however, required the presence of toluene and was sensitive to the ratio of toluene to TCE concentration because of the role of competitive inhibition and toxicity. Unlike in surface soil, degradation of both TCE and toluene in the subsurface required the addition of mineral nutrients. A biofilter composed of compost removed toluene and methylene chloride, but not TCE.
Impacts
(N/A)
Publications
- SCOW, K.M., SOMASCO, O., GUNAPALA, N. SAU, S., VENETTE, R., FERRIS, H., MILLER, R., AND SHENNAN, C. 1994. Changes in soil fertility and biology during the transition from conventional to low-input ... Agric. Calif. 48:20-26.
- ERGAS, S.J., KINNEY, K., FULLER, M.E., AND SCOW, K.M. 1994. Control of dichloromethane emissions using biofiltration. Proc. I&EC Special Symposium, American Chemical Society, Atlanta, GA, Sept. 19-21, 1994.
- ERGAS, S.J., SCHROEDER, E.D., CHANG, D.P.Y., AND SCOW, K.M. 1994. Spatial distribution of microbial populations in biofilters. Proc. Air and Waste Management Association, 87th Annual Meeting, Cincinatti, OH, June 19-24, 1994.
- SCHROEDER, E.D., CHANG, D.P.Y., ERGAS, S.J., KINNEY, K.A., AND SCOW, K.M. 1994. Biofiltration for cleanup of VOC-impacted air streams. Proc. Hazmacon, San Jose, CA; March 1, 1994.
- ROSSNER, U., HOYLE, B.L., AND SCOW, K.M. 1994. Effect of carbon:nitrogen ratios on growth kinetics of acinetobacter johnsonii metabolizing phenol in liquid and.
- MU, D.Y., AND K.M. SCOW. 1994. Effect of trichloroethylene (TCE) and toluene concentrations on TCE and toluene biodegradation and the population density of TCE and toluene degraders in soil. Appl. Environ. Microbiol. 60:2661-266.
- TEMPLE, S.R., FRIEDMAN, D., SOMASCO, O., FERRIS, H., SCOW, K. AND KLONSKY, K. 1994. A multidisciplinary and experiment station based participatory comparison of alternative crop management systems..Amer. J. Altern. Agric. 9:64-71.
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Progress 01/01/93 to 12/30/93
Outputs
Studies continued on the biodegradation of volatile organic and sorbed chemicalsin soil. Population dynamic studies of biodegrading organisms revealed that the lengthy lag period preceding toluene and TCE degradation was due to the slow growth of an initially very small, microbial population able to degrade these chemicals. High concentrations of TCE resulted in significant reductions in the size of the population able to degrade toluene and TCE. Aging of phenanthrene, but not TCE, in soil reduced its biodegradability. In contrast to TCE, methylene chloride was degraded by soil indigenous populations in the absence, but not presence of toluene. A biofilter composed of compost and microorganisms from sludge and pure cultures removed toluene and methylene chloride, but not TCE, from a contaminated airstream. Differences in the kinetics of mineralization of phenol and para-nitrophenol were due to phenol's ability to form irreversible bonds with soil organic matter and
thus making it unavailable for degradation. Intensive monitoring of microbial, nematode and soil fertility parameters was conducted in conventional and organic tomato plots. Microbial biomass and activity measures were significantly higher in organic than conventional systems on most sampling dates. Bacterial-feeding nematode populations increased in organic plots following vetch incorporation. Mineral N levels remained low in organic, whereas they rose to high levels following sidedressing in the conventional system.
Impacts
(N/A)
Publications
- MU, D.Y., and K.M. SCOW. 1994. Effect of TCE and toluene concentration on biodegradation and the population density of TCE- and toluene-degraders in soil. Appl. Environ. Microbiol. (under revision).
- TEMPLE, S.R., D. FRIEDMAN, O. SOMASCO, H. FERRIS, K. SCOW and K. KLONSKY. 1994. A multidisciplinary and experiment station based participatory comparison of alternative crop management systems for California's Sacramento Valley. Amer.
- SCOW, K.M., O. SOMASCO, N. GUNAPALA, S. LAU, R. VENETTE, H. FERRIS, R. MILLER, and C. SHENNAN. 1994. Changes in soil fertility and biology during the transition from conventional to low-input and organic farming systems. Calif. Agric.
- FAN, S., and K.M. SCOW. 1993. Biodegradation of TCE and toluene by indigenous microbial populations in soil. Appl. Environ. Microbiol. 59:1911-1918.
- CHUNG, G.-Y., B.J. MCCOY, and K.M. SCOW. 1993. Criteria to assess when biodegradation is kinetically limited by intraparticle diffusion and sorption. Biotechnol. and Bioeng. 41:625-632.
- SCOW, K.M. 1993. Effect of sorption-desorption and diffusion processes on the kinetics of biodegradation of organic chemicals in soil, pp 73-114. In: Linn, D. (ed.) Sorption and Degradation of Pesticides and Organic Chemicals in Soil.
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Progress 01/01/92 to 12/30/92
Outputs
The most significant results of the past year are from studies on the biodegradation of sorbed polyaromatic hydrocarbons and volatile organic chemicals in soil. An inverse relationship was measured between the rate of biodegradation of phenanthrene and its sorption partition coefficient in six soils from the same soil series. Addition of nontronite and halloysite, but not other clays, enhanced the rate of phenanthrene biodegradation in Yolo soil. Phenanthrene degradation was significantly greater in Yolo silt loam that had received cover crop residues over the past 12 years than in unamended Yolo or other soils with similar organic matter content. The rate and extent of degradation of trichloroethylene (TCE) was dependent on initial concentrations of both TCE and its cosubstrate, toluene, and the lag period decreased with increasing times of exposure. Continual exposure of soil to high concentrations of TCE did not result in the termination of toluene and TCE
degradation. Non-pollutant aromatics (L-phenylalanine, L-tryptophan, cinnamic acid, L-tyrosine, vanillin, and salicylic acid) supported some degradation of TCE; however, not as much as that supported by toluene and phenol. Biodegradation of TCE and toluene in vadose zone samples from Lawrence Livermore National Laboratories required the addition of nutrients; nitrogen was essential and phosphorus further enhanced the rate.
Impacts
(N/A)
Publications
- SCOW, K.M. 1992. Effect of sorption-desorption and diffusion processes on the kinetics of biodegradation of organic chemicals in soil. In: Linn, D., and T. Carski (ed.) Sorption and Degradation of Agricultural Chemicals in Soil.
- CHUNG, G.-Y., B.J. MCCOY, and K.M. SCOW. 1992. Criterion to assess when biodegradation is kinetically limited by intraparticle diffusion and sorption. (in press: Biotechnology and Bioengineering).
- FAN, S., and K.M. SCOW. 1992. Biodegradation of TCE and toluene by indigenous microbial populations in Soil. (accepted: Appl. Environ. Microbiol.).
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Progress 01/01/91 to 12/30/91
Outputs
Trichloroethylene (TCE) is readily biodegraded by indigenous microbial populations in several soils only in the presence of toluene or phenol as a co-substrate. Methanol and ethylene slightly stimulate TCE degradation; glucose, benzoate and extracted soil carbon do not. The rate and percentage of TCE degraded increases as the initial toluene concentration is increased. As the initial TCE concentration is increased, however, the rate and extent of toluene and TCE degradation declines. Previous exposure to toluene, with or without TCE, results in a significantly higher rate of degradation of both chemicals. Vadose zone samples from a site contaminated with TCE, a diesel spill, or uncontaminated support degradation of toluene and TCE in some samples; however, there is no systematic relationship between degradation potential and previous exposure to contaminants. Numerous bacterial strains--including pseudomonads, Rhodococcus sp. and other actinomycetes-isolated from
the test soils and vadose samples degrade TCE in the presence of toluene. An antibiotic resistant strain of Pseudomonas putida introduced into both sterile and nonsterile soil survived for 600 h in the presence of toluene. The Diffusion-Sorption-Biodegradation (DSB) model describes the biodegradation of chemicals limited in availability to microorganisms by diffusion and sorption.
Impacts
(N/A)
Publications
- SCOW, K.M. and HUTSON, J. 1992. Effect of diffusion and sorption on the kinetics of biodegradation: theoretical considerations. Soil Sci. Soc. Amer. J. 56:119-127.
- SCOW, K.M. and ALEXANDER, M. 1992. Effect of diffusion and sorption on the kinetics of biodegradation: experimental results with synthetic aggregates. Soil. Sci. Soc. Amer. J. 56:128-134.
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