Kate Scow | University of California, Davis (original) (raw)

Papers by Kate Scow

This study coupled stable isotope probing with phospholipid fatty acid analysis ( 13 C-PLFA) to d... more This study coupled stable isotope probing with phospholipid fatty acid analysis ( 13 C-PLFA) to describe the role of microbial community composition in the short-term processing (i.e., C incorporation into microbial biomass and/or deposition or respiration of C) of root-versus residue-C and, ultimately, in long-term C sequestration in conventional (annual synthetic fertilizer applications), low-input (synthetic fertilizer and cover crop applied in alternating years), and organic (annual composted manure and cover crop additions) maize-tomato (Zea mays -Lycopersicum esculentum) cropping systems. During the maize growing season, we traced 13 Clabeled hairy vetch (Vicia dasycarpa) roots and residues into PLFAs extracted from soil microaggregates (53-250 μm) and silt-and-clay (<53 μm) particles. Total PLFA biomass was greatest in the organic (41.4 nmol g -1 soil) and similar between the conventional and low-input systems (31.0 and 30.1 nmol g -1 soil, respectively), with Gram-positive bacterial PLFA dominating the microbial communities in all systems. Although total PLFA-C derived from roots was over four times greater than from residues, relative distributions (mol%) of root-and residuederived C into the microbial communities were not different among the three cropping systems. Additionally, neither the PLFA profiles nor the amount of root-and residue-C incorporation into the PLFAs of the microaggregates were consistently different when compared with the silt-andclay particles. More fungal PLFA-C was measured, however, in microaggregates compared with silt-and-clay. The lack of differences between the mol% within the microbial communities of the cropping systems and between the PLFA-C in the microaggregates and the silt-and-clay may have been due to (i) insufficient differences in quality between roots and residues and/or (ii) the high N availability in these N-fertilized cropping systems that augmented the abilities of the microbial communities to process a wide range of substrate qualities. The main implications of this study are that (i) the greater short-term microbial processing of root-than residue-C can be a mechanistic explanation for the higher relative retention of root-over residue-C, but microbial community composition did not influence long-term C sequestration trends in the three cropping systems and (ii) in spite of the similarity between the microbial community profiles of the microaggregates and the silt-and-clay, more C was processed in the microaggregates by fungi, suggesting that the microaggregate is a relatively unique microenvironment for fungal activity.

ABSTRACT Spatial and temporal variations in sediment microbial community structure in a eutrophic... more ABSTRACT Spatial and temporal variations in sediment microbial community structure in a eutrophic lake polluted with inorganic mercury were identified using polar lipid fatty acid (PLFA) analysis. Microbial community structure was strongly related to mercury methylation potential, sediment organic carbon content, and lake location. Pore water sulfate, total mercury concentrations, and organic matter C/N ratios showed no relationships with microbial community structure.

Growers converting from conventional to low-input and organic farming systems must rely on organi... more Growers converting from conventional to low-input and organic farming systems must rely on organic sources for adequate soil fertility. At the Sustainable Agriculture Farming Systems (SAFS) project at UC Davis, we measured soil fertility and biological parameters in four farming systems. By the end of the first 4 years, pH and percent nitrogen were consistently higher in organic and low-input than conventional plots for all crops.

Fatty acid profiles of fungal-feeding nematodes, Aphelenchus avenae and Aphelenchoides compostico... more Fatty acid profiles of fungal-feeding nematodes, Aphelenchus avenae and Aphelenchoides composticola, and selected fungi were determined in microcosm cultures of agar, broth, or sand amended with organic matter. Fatty acids of A. avenae and A. composticola included 16: 0 18: 0, 18: 1ω7, 18: 1ω9, 18: 2, 20: 0, 20: 1, 20: 2, 20: 3 and 20: 4 phospholipid fatty acids (PLFAs) and neutral lipid fatty acids (NLFAs). The nematodes differed in relative amounts of saturated and C18 fatty acids.

Ammonia oxidizing bacteria (AOB) control the rate limiting step of nitrification, the conversion ... more Ammonia oxidizing bacteria (AOB) control the rate limiting step of nitrification, the conversion of ammonia (NH4+) to nitrite (NO2−). The AOB therefore have an important role to play in regulating soil nitrogen cycling. Tillage aerates the soil, stimulating rapid changes in soil N cycling and microbial communities. Here we report results of a study of the short term responses of AOB and net nitrification to simulated tillage and NH4+ addition to soil.

Because of an impending ban on burning of residues, more rice growers will be incorporating rice ... more Because of an impending ban on burning of residues, more rice growers will be incorporating rice straw in their fields and will depend more than ever on soil microbes to break down the straw and aid rice production the following season. A variety of methods were used to characterize the effects of various rice straw management methods and winter flooding on the microbial community in a typical rice soil.

The effects of long-term agricultural management on active soil organic matter (SOM) and short-te... more The effects of long-term agricultural management on active soil organic matter (SOM) and short-term microbial C and N dynamics were investigated. Short-term changes in chemical and biological variables after incorporating fresh rye shoots were measured in intact soil cylinders from three contrasting agricultural systems.

This review by a multidisciplinary team maps key components and emerging connections within the i... more This review by a multidisciplinary team maps key components and emerging connections within the intellectual landscape of agroecology. We attempt to extend and preview agroecology as a discipline in which agriculture can be conceptualized within the context of global change and studied as a coupled system involving a wide range of social and natural processes.

Tropical agroecosystems are subject to degradation processes such as losses in soil carbon, nutri... more Tropical agroecosystems are subject to degradation processes such as losses in soil carbon, nutrient depletion, and reduced water holding capacity that occur rapidly resulting in a reduction in soil fertility that can be difficult to reverse. In this research, a polyphasic methodology has been used to investigate changes in microbial community structure and function in a series of tropical soils in western Kenya.

ABSTRACT The kinetics of simultaneous mineralization of p-nitrophenol (PNP) and glucose by Pseudo... more ABSTRACT The kinetics of simultaneous mineralization of p-nitrophenol (PNP) and glucose by Pseudomonas sp. were evaluated by nonlinear regression analysis. Pseudomonas sp. did not mineralize PNP at a concentration of 10 ng/ml but metabolized it at concentrations of 50 ng/ml or higher. The Ks value for PNP mineralization by Pseudomonas sp. was 1.1 micrograms/ml, whereas the Ks values for phenol and glucose mineralization were 0.10 and 0.25 micrograms/ml, respectively.

Abstract Effects of arbuscular mycorrhzal (AM) fungi on plant growth and nutrition are well-known... more Abstract Effects of arbuscular mycorrhzal (AM) fungi on plant growth and nutrition are well-known, but their effects on the wider soil biota are less clear. This is in part due to difficulties with establishing appropriate non-mycorrhizal controls in the field. Here we present results of a field experiment using a new approach to overcome this problem.

Abstract Perchlorate (ClO− 4) contamination of ground water and surface water is a widespread pro... more Abstract Perchlorate (ClO− 4) contamination of ground water and surface water is a widespread problem, particularly in the western United States. This study examined the effect of biodegradation on perchlorate fate and transport in soils. Solute transport experiments were conducted on two surface soils. Pulses of solution containing perchlorate and Br− were applied to saturated soil columns at steady state water flow.

Denitrification beds are containers filled with wood by-products that serve as a carbon and energ... more Denitrification beds are containers filled with wood by-products that serve as a carbon and energy source to denitrifiers, which reduce nitrate (NO3−) from point source discharges into non-reactive dinitrogen (N2) gas. This study investigates a range of alternative carbon sources and determines rates, mechanisms and factors controlling NO3− removal, denitrifying bacterial community, and the adverse effects of these substrates.

Abstract A number of organic compounds were added to soil to determine their effects on the miner... more Abstract A number of organic compounds were added to soil to determine their effects on the mineralization of P-nitrophenol (PNP) by indigenous soil microorganisms. At a concentration of 10 μgg− 1 of soil, phenol slowed the initial rate but increased the final extent of mineralization (cumulative evolution of 14 CO 2) of 5 ng of radiolabeled PNP g− 1 of soil, whereas glucose and glutamate had no effect.

Abstract: Methyl tert-butyl ether (MTBE) is a contaminant of concern to groundwater resources due... more Abstract: 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).

The N-heterocyclic bases, 2-ethyltetrahydropyridine (1), 2-acetyl-1-pyrroline (2), and 2-acetylte... more The N-heterocyclic bases, 2-ethyltetrahydropyridine (1), 2-acetyl-1-pyrroline (2), and 2-acetyltetrahydropyridine (3) are associated with the occurrence of mousy off-flavor in wine. The biosynthesis of these N-heterocycles by the wine lactic acid bacterium, Lactobacillus hilgardii DSM 20176, was studied by high-cell-density incubation in combination with a minimal chemically defined N-heterocycle assay medium.

Abstract Climate change predictions for California indicate that agriculture will need to substan... more Abstract Climate change predictions for California indicate that agriculture will need to substantially adapt to reduced water availability, changing crops, and changes in temperatures, in order to sustain the level and diversity of crop production in California. California legislators recently passed the California Global Warming Solutions Act of 2006 (AB 32) that requires all industries to reduce the three major greenhouse gases (GHGs)(CO 2, N 2 O, and CH 4) to 1990 levels by 2020.

Abstract Metam sodium (MS) is a widely used soil fumigant with broad biocidal activity. The impac... more Abstract Metam sodium (MS) is a widely used soil fumigant with broad biocidal activity. The impact of MS on soil microbial community structure and function is largely unknown. We investigated the effects of fumigation with field-relevant doses of MS in soil microcosms using traditional heterotrophic activity measures (C and N mineralization), a substrate-utilization assay, and fatty acid analysis.

We tested the hypotheses that management of the soil food web in the fall would enhance grazing o... more We tested the hypotheses that management of the soil food web in the fall would enhance grazing on bacteria and fungi by microbivorous nematodes in the spring, consequently increasing N availability in cover-crop driven organic and low-input farming systems. The food web was manipulated by irrigating the dry soil of late summer and/or providing carbon sources.

ABSTRACT Nematode-trapping fungi, nematodes, and microbial biomass were quantified in conventiona... more ABSTRACT Nematode-trapping fungi, nematodes, and microbial biomass were quantified in conventionally and organically managed field plots in the Sustainable Agriculture Farming Systems Project at the University of California at Davis. There were four replicate plots (0.135 ha per plot) for each management system, and plots were sampled three times each year for 2 years.

This study coupled stable isotope probing with phospholipid fatty acid analysis ( 13 C-PLFA) to d... more This study coupled stable isotope probing with phospholipid fatty acid analysis ( 13 C-PLFA) to describe the role of microbial community composition in the short-term processing (i.e., C incorporation into microbial biomass and/or deposition or respiration of C) of root-versus residue-C and, ultimately, in long-term C sequestration in conventional (annual synthetic fertilizer applications), low-input (synthetic fertilizer and cover crop applied in alternating years), and organic (annual composted manure and cover crop additions) maize-tomato (Zea mays -Lycopersicum esculentum) cropping systems. During the maize growing season, we traced 13 Clabeled hairy vetch (Vicia dasycarpa) roots and residues into PLFAs extracted from soil microaggregates (53-250 μm) and silt-and-clay (<53 μm) particles. Total PLFA biomass was greatest in the organic (41.4 nmol g -1 soil) and similar between the conventional and low-input systems (31.0 and 30.1 nmol g -1 soil, respectively), with Gram-positive bacterial PLFA dominating the microbial communities in all systems. Although total PLFA-C derived from roots was over four times greater than from residues, relative distributions (mol%) of root-and residuederived C into the microbial communities were not different among the three cropping systems. Additionally, neither the PLFA profiles nor the amount of root-and residue-C incorporation into the PLFAs of the microaggregates were consistently different when compared with the silt-andclay particles. More fungal PLFA-C was measured, however, in microaggregates compared with silt-and-clay. The lack of differences between the mol% within the microbial communities of the cropping systems and between the PLFA-C in the microaggregates and the silt-and-clay may have been due to (i) insufficient differences in quality between roots and residues and/or (ii) the high N availability in these N-fertilized cropping systems that augmented the abilities of the microbial communities to process a wide range of substrate qualities. The main implications of this study are that (i) the greater short-term microbial processing of root-than residue-C can be a mechanistic explanation for the higher relative retention of root-over residue-C, but microbial community composition did not influence long-term C sequestration trends in the three cropping systems and (ii) in spite of the similarity between the microbial community profiles of the microaggregates and the silt-and-clay, more C was processed in the microaggregates by fungi, suggesting that the microaggregate is a relatively unique microenvironment for fungal activity.

ABSTRACT Spatial and temporal variations in sediment microbial community structure in a eutrophic... more ABSTRACT Spatial and temporal variations in sediment microbial community structure in a eutrophic lake polluted with inorganic mercury were identified using polar lipid fatty acid (PLFA) analysis. Microbial community structure was strongly related to mercury methylation potential, sediment organic carbon content, and lake location. Pore water sulfate, total mercury concentrations, and organic matter C/N ratios showed no relationships with microbial community structure.

Growers converting from conventional to low-input and organic farming systems must rely on organi... more Growers converting from conventional to low-input and organic farming systems must rely on organic sources for adequate soil fertility. At the Sustainable Agriculture Farming Systems (SAFS) project at UC Davis, we measured soil fertility and biological parameters in four farming systems. By the end of the first 4 years, pH and percent nitrogen were consistently higher in organic and low-input than conventional plots for all crops.

Fatty acid profiles of fungal-feeding nematodes, Aphelenchus avenae and Aphelenchoides compostico... more Fatty acid profiles of fungal-feeding nematodes, Aphelenchus avenae and Aphelenchoides composticola, and selected fungi were determined in microcosm cultures of agar, broth, or sand amended with organic matter. Fatty acids of A. avenae and A. composticola included 16: 0 18: 0, 18: 1ω7, 18: 1ω9, 18: 2, 20: 0, 20: 1, 20: 2, 20: 3 and 20: 4 phospholipid fatty acids (PLFAs) and neutral lipid fatty acids (NLFAs). The nematodes differed in relative amounts of saturated and C18 fatty acids.

Ammonia oxidizing bacteria (AOB) control the rate limiting step of nitrification, the conversion ... more Ammonia oxidizing bacteria (AOB) control the rate limiting step of nitrification, the conversion of ammonia (NH4+) to nitrite (NO2−). The AOB therefore have an important role to play in regulating soil nitrogen cycling. Tillage aerates the soil, stimulating rapid changes in soil N cycling and microbial communities. Here we report results of a study of the short term responses of AOB and net nitrification to simulated tillage and NH4+ addition to soil.

Because of an impending ban on burning of residues, more rice growers will be incorporating rice ... more Because of an impending ban on burning of residues, more rice growers will be incorporating rice straw in their fields and will depend more than ever on soil microbes to break down the straw and aid rice production the following season. A variety of methods were used to characterize the effects of various rice straw management methods and winter flooding on the microbial community in a typical rice soil.

The effects of long-term agricultural management on active soil organic matter (SOM) and short-te... more The effects of long-term agricultural management on active soil organic matter (SOM) and short-term microbial C and N dynamics were investigated. Short-term changes in chemical and biological variables after incorporating fresh rye shoots were measured in intact soil cylinders from three contrasting agricultural systems.

This review by a multidisciplinary team maps key components and emerging connections within the i... more This review by a multidisciplinary team maps key components and emerging connections within the intellectual landscape of agroecology. We attempt to extend and preview agroecology as a discipline in which agriculture can be conceptualized within the context of global change and studied as a coupled system involving a wide range of social and natural processes.

Tropical agroecosystems are subject to degradation processes such as losses in soil carbon, nutri... more Tropical agroecosystems are subject to degradation processes such as losses in soil carbon, nutrient depletion, and reduced water holding capacity that occur rapidly resulting in a reduction in soil fertility that can be difficult to reverse. In this research, a polyphasic methodology has been used to investigate changes in microbial community structure and function in a series of tropical soils in western Kenya.

ABSTRACT The kinetics of simultaneous mineralization of p-nitrophenol (PNP) and glucose by Pseudo... more ABSTRACT The kinetics of simultaneous mineralization of p-nitrophenol (PNP) and glucose by Pseudomonas sp. were evaluated by nonlinear regression analysis. Pseudomonas sp. did not mineralize PNP at a concentration of 10 ng/ml but metabolized it at concentrations of 50 ng/ml or higher. The Ks value for PNP mineralization by Pseudomonas sp. was 1.1 micrograms/ml, whereas the Ks values for phenol and glucose mineralization were 0.10 and 0.25 micrograms/ml, respectively.

Abstract Effects of arbuscular mycorrhzal (AM) fungi on plant growth and nutrition are well-known... more Abstract Effects of arbuscular mycorrhzal (AM) fungi on plant growth and nutrition are well-known, but their effects on the wider soil biota are less clear. This is in part due to difficulties with establishing appropriate non-mycorrhizal controls in the field. Here we present results of a field experiment using a new approach to overcome this problem.

Abstract Perchlorate (ClO− 4) contamination of ground water and surface water is a widespread pro... more Abstract Perchlorate (ClO− 4) contamination of ground water and surface water is a widespread problem, particularly in the western United States. This study examined the effect of biodegradation on perchlorate fate and transport in soils. Solute transport experiments were conducted on two surface soils. Pulses of solution containing perchlorate and Br− were applied to saturated soil columns at steady state water flow.

Denitrification beds are containers filled with wood by-products that serve as a carbon and energ... more Denitrification beds are containers filled with wood by-products that serve as a carbon and energy source to denitrifiers, which reduce nitrate (NO3−) from point source discharges into non-reactive dinitrogen (N2) gas. This study investigates a range of alternative carbon sources and determines rates, mechanisms and factors controlling NO3− removal, denitrifying bacterial community, and the adverse effects of these substrates.

Abstract A number of organic compounds were added to soil to determine their effects on the miner... more Abstract A number of organic compounds were added to soil to determine their effects on the mineralization of P-nitrophenol (PNP) by indigenous soil microorganisms. At a concentration of 10 μgg− 1 of soil, phenol slowed the initial rate but increased the final extent of mineralization (cumulative evolution of 14 CO 2) of 5 ng of radiolabeled PNP g− 1 of soil, whereas glucose and glutamate had no effect.

Abstract: Methyl tert-butyl ether (MTBE) is a contaminant of concern to groundwater resources due... more Abstract: 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).

The N-heterocyclic bases, 2-ethyltetrahydropyridine (1), 2-acetyl-1-pyrroline (2), and 2-acetylte... more The N-heterocyclic bases, 2-ethyltetrahydropyridine (1), 2-acetyl-1-pyrroline (2), and 2-acetyltetrahydropyridine (3) are associated with the occurrence of mousy off-flavor in wine. The biosynthesis of these N-heterocycles by the wine lactic acid bacterium, Lactobacillus hilgardii DSM 20176, was studied by high-cell-density incubation in combination with a minimal chemically defined N-heterocycle assay medium.

Abstract Climate change predictions for California indicate that agriculture will need to substan... more Abstract Climate change predictions for California indicate that agriculture will need to substantially adapt to reduced water availability, changing crops, and changes in temperatures, in order to sustain the level and diversity of crop production in California. California legislators recently passed the California Global Warming Solutions Act of 2006 (AB 32) that requires all industries to reduce the three major greenhouse gases (GHGs)(CO 2, N 2 O, and CH 4) to 1990 levels by 2020.

Abstract Metam sodium (MS) is a widely used soil fumigant with broad biocidal activity. The impac... more Abstract Metam sodium (MS) is a widely used soil fumigant with broad biocidal activity. The impact of MS on soil microbial community structure and function is largely unknown. We investigated the effects of fumigation with field-relevant doses of MS in soil microcosms using traditional heterotrophic activity measures (C and N mineralization), a substrate-utilization assay, and fatty acid analysis.

We tested the hypotheses that management of the soil food web in the fall would enhance grazing o... more We tested the hypotheses that management of the soil food web in the fall would enhance grazing on bacteria and fungi by microbivorous nematodes in the spring, consequently increasing N availability in cover-crop driven organic and low-input farming systems. The food web was manipulated by irrigating the dry soil of late summer and/or providing carbon sources.

ABSTRACT Nematode-trapping fungi, nematodes, and microbial biomass were quantified in conventiona... more ABSTRACT Nematode-trapping fungi, nematodes, and microbial biomass were quantified in conventionally and organically managed field plots in the Sustainable Agriculture Farming Systems Project at the University of California at Davis. There were four replicate plots (0.135 ha per plot) for each management system, and plots were sampled three times each year for 2 years.