Managing Soil Biota in Low-Input and Organic Farming Systems to Enhance Soil Fertility

Final Report for SW95-024

Project Type: Research and Education
Funds awarded in 1995: $175,000.00
Projected End Date: 12/31/1999
Matching Non-Federal Funds: $43,750.00
Region: Western
State: California
Principal Investigator:
Kate Scow
University of California, Dept. of Land, Air, and Water Resources
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Project Information

Abstract:

[Note to online version: The report for this project includes a graphical figure that could not be included here. The regional SARE office will mail a hard copy of the entire report at your request. Just contact Western SARE at (435) 797-2257 or wsare@ext.usu.edu.]

This project’s primary objectives were to compare soil biological communities in conventional, low input and organic farming systems and to explore means to maintain agricultural productivity and enhance sustainability by managing the soil communities. The study was carried out at the Sustainable Agriculture Farming Systems (SAFS) project at UC Davis comparing two- and four-year rotations (including tomatoes, safflower, corn, wheat/beans), managed using conventional, low input or organic practices. We measured microbial biomass and community composition (by phospholipid fatty acid or PLFA fingerprinting) in soils throughout the season, at different spatial locations within the field, under different crops, and within different farming systems. Microbial communities in the different farming systems could be clearly differentiated with communities in the low input system being intermediate between communities in the organic and conventional systems. Crop type also influenced microbial communities with those in wheat and bean soils distinctly different from communities in tomato, safflower and corn soils. The relative importance of environmental variables in governing the composition of microbial communities were ranked in the descending order of importance: time (e.g., seasonal changes) > specific farming operation (e.g., cover crop incorporation or side dressing with mineral fertilizer) > management system > spatial variation in the field. California agricultural soils, particularly the surface layer, are subject to numerous extreme wet/dry cycles within the growing season. Microcosm studies of the effect of wet/dry cycles on soil communities 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. The surface soil community had lower concentrations of stress-related lipids and its composition was not altered by wet/dry cycles as much as was the community in the deeper soil. Both adding organic matter and altering soil moisture (particularly flooding) had major impacts on the microbial community composition of soils.

To determine if managing soil biotic populations can enhance soil fertility, field trials in the SAFS companion plots were carried out for 3 years. We added carbon (straw, straw plus summer cover crop, or straw plus winter cover crop) with or without fall irrigation. Nematode and microbial communities were measured, as well as soil nitrogen and yields of the following tomato crop. The ratio of bacterial:fungal-feeding nematodes was greater relative to the other treatments only when the soil was irrigated in the fall. Dry soil in the fall selected for fungal-feeding nematodes. Fall irrigation plus a late summer cover crop and/or straw application provided significantly greater available N and higher tomato yields the following spring than did treatments without fall irrigation or a late summer cover crop. Carbon inputs without irrigation had no effect on nitrogen or crop yields. We concluded that soil management practices in the late summer and early fall, when soil temperatures are conducive to biological activity, can increase densities of both microorganisms and bacterial-grazing nematodes in the spring with potential benefits for the tomato crop.

Project Objectives:

1. To measure long-term and seasonal changes in the light fraction pool of organic matter in four farming systems and relate these changes to microbial and soil fertility parameters.

2. To test the effect of C:N ratio of organic matter inputs on microbial biomass and community diversity, the abundance and ratio of fungal- and bacterial-feeding nematodes, nitrogen mineralization, labile organic matter pools, and crop productivity.

3. To enhance the rate of cover crop decomposition by fall management practices that enhance nematode populations in spring.

4. To measure nitrogen loss to denitrification as a function of farming system and C/N ratio.

5. To determine causes and impacts of seasonal fluctuations in microbial biomass.

6. To provide analyses of microbial and nematode community size and structure to collaborators.

7. In collaboration with colleagues involved with outreach activities associated with the SAFS project (funded by a training grant), to develop educational material about the importance of soil biology in sustainable agriculture and farming practices that enhance soil communities.

Cooperators

Click linked name(s) to expand
  • Howard Ferris
  • Kate Scow

Research

Research results and discussion:

Objective 1 The light fraction (LF) of soil organic matter, which is an indicator of available carbon and nitrogen, was measured in organic, low input, and conventional tomato plots. The amount of variability in the LF measurements from within each farming system was higher than any differences between farming systems, largely because the LF pool was so small in all soils. Therefore we decided to discontinue these measurements and focus on other means to estimate available carbon (see below).

Objective 2 We broadened this objective to the study of seasonal fluctuations in microbial communities in different farming systems and of the influence of crop type on microbial communities. We found that phospholipid fatty acids (PLFA), found primarily in cell membranes of living organisms, extracted directly from soil provides information on microbial communities in several ways. The sum of all lipids is an estimate of total biomass, specific lipids are biomarkers for certain microbial groups (e.g., bacteria vs fungi, aerobes vs anaerobes), and all lipids together can be used to provide a unique fingerprint for a given soil. A PLFA fingerprint consists of the percentages of different fatty acids detected as peaks in gas chromatograms from a soil extract. Fatty acid percentage values can be entered as multivariate data in principal component analysis to assess similarities among different soil samples. (The PLFA work was co-funded by a grant from the USDA NRI Soil and Soil Biology program).

We tested whether there was consistency in the microbial community composition (by PLFA fingerprinting) of tomato soils at SAFS throughout the season, following tillage and fertilization, at different spatial locations within the field, and within different farming systems. PLFA fingerprints were consistent among field blocks within the same farming system, thus field variability represented by blocks in this study did not have a significant impact on the differences in the observed fingerprints. Communities in organic (cover crop and manure) and conventional (mineral fertilizer only) managed plots were significantly different on most dates. Microbial communities in low input (cover crop and mineral fertilizer) plots were intermediate between the conventional and organic communities. Fungi were greater in relative abundance in organic than conventional soils. PLFA data were related to conventional measurements characterizing microbial populations. Measurements of microbial biomass carbon and nitrogen, substrate induced respiration, basal respiration, and potentially mineralizable nitrogen were not as sensitive to season, farming system, and management practices as were the PLFA fingerprints. A comparison was made of PLFA fingerprints of tomato, corn, safflower, bean and wheat soils all collected from the SAFS plot on a single date in the latter part of the growing season. Though communities under some crops could be distinguished from the others (e.g., wheat, beans), others were more similar to one another (e.g., tomatoes, safflower and corn). Samples from the 2-yr conventional rotation plots were distinctly different from the three 4-yr rotation plots.

To investigate the importance of soil fungi and fungal-feeding nematodes in nitrogen mineralization, soil fungi and nematodes were isolated from SAFS soils and inoculated into microcosm column systems with different C:N ratios of organic substrates. Nitrogen-free sand was amended with appropriate amounts of alfalfa and cellulose, with total N held constant, to create C:N ratios ranging from 11:1 to 45:1. Nitrogen mineralization by Aphelenchus avenae and Aphelenchoides composticola feeding on Rhizoctonia solani and Trichoderma sp. was determined by measuring ammonium and nitrate concentrations in the leachate from the columns at 3-d intervals. Nematode population levels and the fatty acid 18:2 (a fungal biomass indicator), were monitored over a period of three weeks. There were differences between fungal species in the amount of N mineralized in the presence of either nematode species. Average N mineralized per nematode per day ranged from 0.0021 ug to 0.0034 ug. N mineralized by fungal-feeding nematodes feeding increased as the C:N ratios of organic substrates increased. Initial and average nematode population densities were significantly higher in columns containing Rhizoctonia than on Trichoderma. Both nematodes reduced the fungal fatty acid 18:2, the biomarker for fungi.

The fungi, Rhizoctonia solani and Trichoderma sp., and nematodes, Aphelenchus avenae and Aphelenchoides composticola, isolated from field soils, were introduced into alfalfa/cellulose/sand microcosms with C:N ratios of 11:1, 20:1, 30:1 and 40:1. The six treatments included each fungus alone or with each nematode. Fungal biomass was measured by identification and quantification of phospholipid fatty acids (PLFAs) extracted from living cell membranes through gas chromatography. Principal component analysis was used to identify key PLFA patterns associated with fungal colonizers and their nematode grazers. Fatty acid 18:2-omega-6c, a fungal indicator, consisted of 52.2 % + 3.8 of total PLFAs in pure broth cultures, and 10.2% + 2.3 in alfalfa/cellulose/sand for R. solani in the absence of nematodes. Biomass of R. solani, as indicated by fungal PLFAs, was reduced in the early stage of decomposition of the organic matter in the presence of A. composticola, but was not reduced by day 21. There was more N mineralized in the presence of nematodes grazing on R. solani than in their absence. Fungal biomass of R. solani was lower at C:N ratios of > 30:1 than at < 20:1 on day 21, but C:N effects were inconsistent for Trichoderma sp. Objective 3 Conversion of N from incorporated crop residues and manure to available mineral forms requires decomposition and mineralization processes mediated by bacteria, fungi and other components of the soil food web. When carbon is abundant, increases in microbial biomass may result in immobilization of N. In that case, mineralization may be increased by organisms that graze on the primary decomposers. In laboratory studies, bacterial-feeding nematodes mineralized between 1.2 and 5.8 ng N per individual per day, depending on body size, while fungal-feeding nematodes mineralized up to 3.3 ng N per individual per day, depending on host status of the fungal substrate. Since bacterial-feeding nematodes have a higher C:N ratio (± 6:1) than their substrate (± 4:1), considerable mineralization of N is associated with their metabolic activity. In consuming sufficient bacteria to provide the C necessary for their body structure and respiration, nematodes assimilate excess N. The excess N is excreted as ammonia. Fungal-feeding nematodes have a body C:N ratio closer to that of their substrate, so the N associated with C used in body structure is not in excess. However, the N associated with C that is respired exceeds body needs and is excreted. Field observations in the organic and low-input tomato plots of the UC Davis Sustainable Agriculture Farming Systems (SAFS) project indicated that population levels of microbivorous and fungivorous nematodes were low early in the growing season. In those plots, which either do not receive mineral fertilizers (organic) or receive them only when necessary (low-input), symptoms of N deficiency are sometimes seen during the early vegetative growth phase. The goal of this study was to manage the soil food web to enhance population levels of microbivorous and fungivorous nematodes in the spring so that their feeding would release N immobilized in the primary decomposer biomass. To avoid delaying planting of tomatoes until nematode populations responded to spring soil temperatures, we attempted to increase numbers of microbivorous nematodes and other microbial grazers the previous fall. Soil temperature conditions are adequate for nematode populations to increase in the late summer and early fall in northern California, but moisture is a constraining factor. The moisture constraint to soil biological activity was relieved by irrigation and a carbon source was provided in the form of a late summer cover crop. Abundance of microbivorous nematodes, and presumably other organisms at similar trophic levels, increased with the enhancement of biological activity the previous fall. Soil N level increased in the spring with nematode abundance. Subsequent tomato yields also increased when N levels were limiting. A convenient biomarker system is necessary to provide a basis for management and monitoring of the soil food web. From the standpoint of soil fertility, greatest amounts of mineralization probably occur at lower trophic interchanges in the food web, where biomass of organisms is greatest. Members of functional guilds of soil nematodes, classified at the family level, respond similarly to food web enrichment and to environmental perturbation and recovery. Indices derived through nematode faunal analysis provide bioindicators for condition of the soil food web and disturbance of the soil environment. Resolution is enhanced by a weighting system for the indicator importance of the presence and abundance of each functional guild in relation to food web enrichment and structure. Graphical representations of food web structure, based on nematode faunal analyses, allow diagnostic interpretation of its condition (e.g. Fig. 1). Simple ratios of the weighted abundance of representatives of specific functional guilds provide useful indicators of food web structure and enrichment, and of the nature of decomposition channels. These analyses can be used as a basis for management decisions and as a means of monitoring management success. Fig.1 Progression of changes in nematode faunal analyses from dry soil in late August in plots where the soil was irrigated and summer and winter cover crops were grown (dark symbols) or were not irrigated and had no cover crop (light symbols). The star indicates the time at which organic material was incorporated into both plots (April). The soil food web of the dry plots was unable to respond rapidly to the enrichment, while that in the irrigated plots responded immediately. The differences were reflected in availability of soil nitrogen in May and in yields of the subsequent tomato crop. Our results confirm that an abundance of nematodes representing opportunist bacterial- and fungal-feeding guilds indicates a biologically-active soil. When such guilds predominate at planting time, N provided by incorporation of organic material will not remain bound in the primary decomposer biomass but will be mineralized through the grazing activities of the nematodes. Despite extensive knowledge of the physiological, population, and trophic ecology of microbivorous nematodes and other soil fauna, the impact of these fauna on community and nutrient dynamics remains unpredictable. We used a novel “field incubator” technique to study populations of soil fauna and their effect on decomposing organic matter in situ. This technique combines the experimental control of the litter bag approach with more realistic contact between soil and decaying litter. Microbivorous nematodes were more abundant early in the decomposition process and fungal feeders (e.g., Aphelenchus avenae) were more abundant in the presence of high C/N ratio organic matter. Experimental exclusion of microarthropods (mostly mites and Collembola) led to reduced mass loss of leaf litter; it did not affect fungi, the primary prey of microarthropods, or populations of fungal feeding nematodes, their potential competitors. However, microarthropod exclusion was associated with elevated populations of predator/omnivore members of the Dorylaimida. Furthermore, in incubators from which microarthropods were not excluded, they were more abundant under the high C/N conditions that favor fungal decomposition. This suggests that microarthropods and predatory nematodes may be linked either directly via predation or indirectly via other members of the food web. The increase in the Dorylaimida is also interesting because it represents colonization by these supposedly disturbance-sensitive nematodes relatively early in the decomposition process. 5. Objectives 4 and 5 Our emphasis was on determining causes and impacts of seasonal fluctuations in microbial communities in SAFS soils. Denitrification measurements were not continued after preliminary results indicated that denitrification rates in all farming systems were minimal during the growing season. Differences in microbial communities among farming systems were not as great as differences over the growing season. Microbial communities, regardless of farming system, showed the same general changes in composition over time. For example, in 1995, changes in microbial community composition between March and August were usually greater than any differences among farming system or among blocks within one farming system. We found similar trends in 1996 through 1998, with all years showing the same general progression with time for all farming systems. Thus similarities in early spring for all 3 years were greater than similarities between early spring and summer samples for the same year or similarities between farming systems for the same year. Even for soil samples collected under different crops and at different times at the SAFS plots, the same systematic progression in community composition with time could still be discerned. For example, corn samples collected in 1995 were more similar to 1995 tomatoes than they were to corn samples collected in 1997. In conclusion, the relative importance of environmental variables in governing the composition of microbial communities could be ranked in the order: time > specific farming operation (e.g., cover crop incorporation or side dressing with mineral fertilizer) > management system > spatial variation in the field.

Soil microcosm studies were conducted to identify PLFAs enriched, or decreased, by management practices and environmental perturbations simulated under laboratory conditions. Controlled laboratory experiments were necessary to follow up on hypotheses stemming from results collected in the field. Organic tomato soil from the SAFS Project was incubated with different carbon sources and at several moisture contents to test the following hypotheses:

1. Adding organic matter changes community composition to higher relative proportion of fungal and actinomycete markers.
2. Flooding changes community to greater relative proportion of anaerobic markers and lower relative proportion of fungal marker.
3. Flooding changes community more than organic matter addition.
4. Without addition of organic matter, changing water content has little effect on communities

Soils were incubated at moisture contents of 2%, 11%, field capacity, and flooding. Organic matter additions included cover crops (oats/vetch) only, compost (poultry manure) only, cover crops + compost, or no addition of organic matter. Samples were collected before and at several times (6, 11 and 20 d) during the incubation period. PLFA analysis was used to evaluate these hypotheses.

Both soil moisture content and organic matter addition strongly affected the composition of the soil community. Of all the moisture treatments, flooding caused the most significant change in composition and differences were evident within a week. The flooded treatments amended with organic material were substantially different from the unsaturated treatments (both with and without organic matter). With flooding, there was a high relative abundance of lipids associated with gram-positive anaerobic bacteria and low relative abundance of fungal markers. The PLFA fingerprints of soils incubated at 2, 11 or 22% moisture at all sampling times were relatively similar in the absence of organic matter additions; however in the presence of organic matter, differences were substantial. This suggested that significant changes in microbial communities due to stress are unlikely unless there are carbon sources available for populations to grow on. There was a higher relative abundance of fungal, but not actinomycete, markers in the soils amended with organic matter. In conclusion, both carbon and moisture are likely to have major impacts on the microbial community composition of soils in the field. The next challenge is to link these changes in microbial community composition to processes important to productivity and sustainability. Thus we measured relationships between carbon pools and microbial communities in SAFS soils exposed to wet/dry cycles.

California agricultural soils, particularly the surface layer, are subject to numerous extreme wet/dry cycles within the growing season. To investigate the effect of varying levels of organic amendments and wet/dry cycles on soil microbial communities, we compared soils from conventional, low input, and organic farming systems at SAFS. Differences in C availability to soil microorganisms were apparent among the three farming system soils. Microbial and dissolved organic C (DOC) increased with increasing organic inputs. Respiration following re-wetting was fit to a model describing two carbon pools in soil: one readily available and the other slowly available over a longer period of time. Carbon dioxide released from the more slowly available pool was higher in soils receiving greater long-term organic inputs.

Large differences in microbial process rates and community composition suggested greater adaptation to wet/dry cycles in the surface (0-3 cm) than deeper (3-15 cm) layer in all farming system soils. The increase in microbial biomass carbon (MBC) as a proportion of total MBC after soil re-wetting was greater in the surface than deeper layer. Respiration kinetics of the surface layer showed a more rapid response to soil re-wetting, as indicated by higher rate constants for both the rapidly and slowly used C pools, and by greater CO2 mineralized from the slowly used pool. The surface and deeper layers had distinctly different community compositions with higher ratios of cyclopropyl fatty acids to their precursors suggesting greater bacterial stress in response to wet/dry cycles in the deeper layer. This study suggested that adaptation to wet/dry cycles by surface microorganisms had occurred during the several months between the time of field preparation and tillage in April and the later sampling date in July, leading to changes both in microbial process rates and community composition.

Objective 6 We collaborated with Prof. Bruce Jaffee, Dept. of Nematology, and Cooperative Extension Specialist, Jeff Mitchell, in the Dept. of Vegetable Crops. With Prof. Jaffee, we published a paper linking information on microbial substrate induced respiration and nematode community size and structure to data on the density of nematode-trapping fungi. With Dr. Mitchell, we measured nematode community structure and microbial community composition in tomato and cover cropped plots that are part of the Biologically Integrated Farming Systems (BIFS) study near Fresno, California. Scow was involved in a project evaluating potential indices of soil quality with the USDA Soil Tilth Lab in Ames, Iowa. Scow also collaborated with Louise Jackson and Dennis Rolston on the effects of short term disturbance, such as irrigation and tillage, on N dynamics and microbial communities in agricultural soils. Scow’s lab also ran microbial community analysis for numerous growers, farm advisors, and grower groups. These include Bruce Roberts, Ed Weber, Chuck Ingels, and Roger Duncan (farm advisors), as well as the Sonoma Valley Growers Group and the Prune Board. Making these measurements provides our collaborators with valuable data on microbial communities, possibly of use in decision making. In turn, the collaborations give us on-farm applications of our measurements and opportunities to link our measurements to soil and agronomic properties of concern to growers.

Objective 7 Outreach is a significant part of our project and both PIs have been active participants in outreach activities for the past 3 years. This is despite the fact that the general SAFS project had no outreach coordinator past 1997. Scow and Ferris played a major role in two workshops put on by the BIOS (Biologically Integrated Orchard Study) Project during 1998. This involved running afternoon workshops on the soil food web. Also, Dr. Ferris and Scow were keynote speakers and participated in a panel discussion on how to measure soil organisms in a Soil Biology workshop hosted by John Luna and Mary Stabens at Oregon State University. We are a central resource for the FARMS program, a unique educational outreach program for high school students, which provides exposure to and research opportunities in agricultural science. Jessica Hanson, a graduate student in the Scow lab, was a coordinator for the program during 1997 and continued to be heavily involved in the program in 1998. Specific outreach activities are listed in the following section.

Research conclusions:

Our ultimate goal is to improve out understanding of the complex interactions between the availability of plant nutrients and the soil food web, specifically the microbial community and their nematode predators. As part of the larger USDA SARE funded project, “A Comparison of Conventional, Low Input and Organic Farming Systems: The Transition Phase and Long Term Viability,” the findings of our project have implications for the larger project. Management of the fertility of the organic farming system is one of the project’s major challenges. One potential contribution is the finding a relatively low cost management practice in the fall, irrigation, can lead to a 15% increase in available nitrogen from the cover crop. If adopted, such practices would diminish reliance on mineral fertilizers in low input type systems and reduce the need for supplemental forms of fertilizers (e.g., foliar sprays) in organic systems. Adoption may also result in reduced leaching of nitrate because the N is now assimilated during the fall and winter in the biomass of the cover crop and soil biota.

Another major contribution is the generation of new information about soil microbial and nematode communities in agricultural systems. Interest in soil biology has recently intensified among growers, agronomic researchers, and advisors, as the need to manage the below-, as well as above-ground, part of farming systems has become evident. Our progress in this area has been severely constrained by methods that limit information about microbial communities to biomass, counts, and process rates. Without information about community composition, it is impossible to target which groups of organisms have desirable traits and thus develop management strategies to enhance these groups. Analysis of PLFAs has high potential for providing meaningful information to researchers, as well as to a larger audience, beyond just confirming microorganisms are present in their soil. Currently, we know the PLFA method can provide a unique fingerprint for a particular soil. With more data, these fingerprints can be used to determine traits of the microbial community likely to be associated with productive, fertile, and/or “healthy” soils. Many microbial products (e.g., inoculants) have flooded the market and it is difficult for growers and advisors to evaluate the claims of efficacy associated with them. The PLFA method can provide direct information about changes, if any, in soil communities with use of such products. As our data base of agricultural soils increases, we will more groups of PLFAs (and organism groups) that are consistently associated with good and poor soil management. With the identification of practical and consistent relationships between farming practices and microbial communities, analysis of PLFAs will likely be developed as a service by private microbial analytical labs that support growers, advisors, and researchers.

Participation Summary

Educational & Outreach Activities

Participation Summary

Education/outreach description:

Peer-reviewed Publications.

Bongers, T. and H. Ferris. 1999. Nematode community structure as a bioindicator in environmental monitoring. Trends in Evolution and Ecology 14:224-228.

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.

Bossio, D.A., and K.M. Scow. 1998. Impact of carbon and flooding on PLFA profiles and substrate utilization patterns of soil microbial communities. Microb. Ecol. 35:265-278.

Bossio, D.A., K.M. Scow, N. Gunapala, and K.J. Graham. 1998. Determinants of soil microbial communities: Effects of agricultural management, season, soil type on phospholipid fatty acid profiles. Microb. Ecol. 36:1-12.

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.

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. (in press).

Chen, J and H. Ferris. 1998. Mineralization of nitrogen by Aphelenchoides composticola. Journal of Nematology 30:490.

Chen, J. and H. Ferris. 1999. The effects of nematode grazing on nitrogen mineralization during fungal decomposition of organic matter. Soil Biology and Biochemistry 31:1265-1279.

Chen, J. and H. Ferris. 2000. Growth and nitrogen mineralization of selected fungi and fungal-feeding nematodes on sand amended with organic matter. Plant and Soil 218:91-101.

Chen, J., H. Ferris, K. M. Scow and K. J.
Graham. 1999. The effect of fungal-feeding nematodes on fungal biomass during decomposition of organic matter . Journal of Nematology 31:517.

Clark, M. S., H. Ferris, K. Klonsky, W.T. Lanini, A.H.C. vanBruggen, & F.G. Zalom. 1998. Agronomic, economic, and environmental comparison of pest management in conventional and alternative tomato and corn systems in northern California. Agriculture, Ecosystems & Environment. 68:51-71.

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.

Clark, M.S., W.R. Horwath, C. Shennan, 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. Agriculture, Ecosystems and Environment 73:257-270.

Ferris, H. and L. Zheng. 1998. Toward a prescriptive phytopharmacognosy for management of plant-parasitic nematodes. Journal of Nematology 30:496.

Ferris, H., R. C. Venette, and S. S. Lau. 1997. Population energetics of bacterial-feeding nematodes: Carbon and nitrogen budgets. Soil Biol. and Biochem. 29: 1183-1194.

Ferris, H., R. C. Venette, H. R. van der Meulen and K. M. Scow. 1998. Nitrogen fertility and soil food web management. Journal of Nematology 30:495-496.

Ferris, H., R. C. Venette, H. R. van der Meulen and S. S. Lau. 1998. Nitrogen mineralization by bacterial-feeding nematodes: verification and measurement. Plant and Soil 203:159-171.

Ferris, H., T. Bongers and R. G. M. de Goede. 1999. Nematode faunal indicators of soil food web condition. Journal of Nematology 31:534-535.

Fuller, M.E., and K.M. Scow. 1997. Effect of exopolymers on biodegradation of organic compounds by Pseudomonas sp. strains JSA and JS150. Microb. Ecol. 34:248-253.

Fuller, M.E., and K.M. Scow. 1997. Impacts of trichloroethylene (TCE) and toluene on nitrogen cycling in soil. Appl. Environ. Microbiol. 68:120-129

Fuller, M.E., K.M. Scow, S.S. Lau and H. Ferris. 1997. Trichloroethylene (TCE) and toluene effects on the structure and function of the soil community Soil Biol. and Biochem.29:75-89.

Gunapala, N. and K.M. Scow. 1998. Dynamics of soil microbial biomass and activity in conventional and organic farming systems. Soil Biol. and Biochem. 30:805-816.

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. and Biochem. 30:1917-1927.

Hanson, J.R., J.L. Macalady, D. Harris, and K.M. Scow. Linking toluene degradation with specific microbial populations in soil. Appl. Environ. Microbiol. 65:5403-5408.

Jaffee, B.A., H.Ferris, and K.M. Scow. 1998. Nematode-trapping fungi in organic and conventional cropping systems. Phytopathology 88:344-349.

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 36:133-139.

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, 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, 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.

Macalady, J., M. Fuller, and K.M. Scow. 1998. Effects of fumigation with metam sodium on soil microbial activity and community structure. J. Environ. Qual. 27:54-63.

Rillig, M.C., K.M. Scow, J.N. Klironomos, and M.F. Allen. 1997. Microbial carbon-substrate utilization in the rhizosphere of Gutierrezia sarothrae grown in elevated atmospheric carbon dioxide. Soil Biol. Biochem. 29:1387-1394.

Scow, K.M. 1997. Soil microbial communities and carbon flow in agroecosystems, p. 361-407. In: Jackson, L.E.(ed.) Ecology in Agriculture. Academic Press, N.Y.

Scow, K.M. 1999. Soil microbiology. In: Encyclopedia of Microbiology. Academic Press (in press).

Scow, K.M. 1997. Soil microbial communities and carbon flow in agroecosystems, p. 361-407. In: Jackson, L.E. (ed.) Ecology in Agriculture. Academic Press, N.Y.

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., G.E. Fogg, D.E. Hinton, and M.L. Johnson (editors). 1999. Integrated assessment of ecosystem health. Lewis Publishers, Boca Raton, FL.

Shouse, B. N. and H. Ferris. 1999. Microbe-grazer-predator community dynamics during organic matter decomposition. Journal of Nematology 31:570.

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

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.

Sudarshana, P., J.R. Hanson, and K.M. Scow. 1998. Application of random amplified polymorphic (RAPD) DNA method for characterization of soil microbial communities. In: Scow et al. (eds) Critical methodologies for the study of ecosystem health. Ann Arbor Press, Inc. (in press)

Venette, R. C. and H. Ferris. 1997. Thermal restraints to population growth of bacterial-feeding nematodes. Soil Biol. and Biochem. 29:63-74.

Venette, R.C., and H. Ferris. 1998. Influence of bacterial type and density on population growth of bacterial-feeding nematodes. Soil Biol. and Biochem. 30:949-960.

Venette, R.C., F.A. M. Mostafa, and H. Ferris. 1997. Trophic interactions between bacterial feeding nematodes and the nematophagous fungus Hirsutella rhossiliensis in plant rhizospheres to supress Heterodera schachtii. Plant Soil 191:213-223.

Popular-Press Publications

Scow, K.M., and M.R. Werner. 1999. The soil ecology of cover cropped vineyards, p. 69-79. In: Ingels, C. (ed.) Cover cropping in vineyards. University of California Division of Agriculture and Natural Resources. Publication 3338. DANR, Oakland, CA.

Clark, M.S., K. Scow, H. Ferris, S. Ewing, J. Mitchell, and W. Horwath. 1998. Evaluating soil quality in Organic, Low-Input, and Conventional Farming Systems. Sustainable Agriculture Farming Systems Project Bulletin 2 (1): 1-3.

Clark, M. S., H. Ferris, K. Klonsky, W.T. Lanini, A.H.C. van Bruggen, F.G. Zalom, & S. Temple. 1997. Pesticide use reduced by 50-100% in low-input and organic cropping systems. Sustainable Agricutlture Farming Systems Project Bulletin 1 (3): 1-3.

Clark, M. S., H. Ferris, K. Klonsky, S. Ewing, J. Mitchell, and W. Horwath. 1998. Evaluating soil quality in organic, low-input, and conventional farming systems. Sustainable Agriculture Farming Systems Project Newsletter 2(1):1-3.

Conference Presentations

Scow, K. 1997. Agricultural microbial communities. EPA Center for Ecological Health Research Annual Meeting. University of California, Davi (3/17)

Scow, K. 1997. Impact of metam sodium on Soil Microbial Communities. EPA Center for Ecological Health Research Annual Meeting. University of California, Davis. (3/17)

Scow, K. 1997. Use of information on microbial communities in soil quality assessment. Kearney Foundation of Soil Science: Soil Quality Symposium, Berkeley, CA. (3/25)

Ferris, H. 1997. Invasion Biology: Bacterial-feeding nematodes as a model system. Ecology Graduate Group, UC Davis (5/5)

Scow, K. 1997. Microbial communities in agricultural soils. Soil Ecology Meetings, Manhattan, Kansas. (5/28)

Ferris, H. 1997. Microbivorous nematodes and soil fertility. University of Hawaii. 20 participants.

Scow, K. 1997. Use of information on microbial communities in soil quality assessment. Soil quality symposium. Corvallis, Oregon. (6/24)

Scow, K. 1997. Microbial communities in agricultural soils. Woodbridge-Lodi Growers Association (vineyards), Lodi, CA. (7/22)

Ferris, H. 1997. Invasion Biology: Bacterial-feeding nematodes as a model system. Department of Plant Pathology, North Carolina State University. (10/6)

Ferris, H. 1997. Invasion Biology: Bacterial-feeding nematodes as a model system. Institute of Ecology, University of Georgia. (10/9)

Ferris, H. 1997. Invasion Biology: Bacterial-feeding nematodes as a model system. Department Entomology, University of Minnesota. (10/20)

Scow, K. 1997. Comparison of PLFA to SFAME as Methods for Characterizing Soil Microbial Communities. Soil Science Society of America meetings, Anaheim, CA (10/28).

Scow, K. 1997. Characterization of Soil Microbial Communities in California Agricultural Soils. Soil Science Society of America meetings, Anaheim, CA (10/28)

Chen, J. and H. Ferris. 1998. Nitrogen mineralization by Aphelechus avenae associated with Rhizoctonia sp. and barley straw. Annual Meeting of the Society of Nematologists.

Clark, M. S. (+ 13 additional authors). 1998. Comparison of conventional, low-input, and organic farming systems in the Sacramento Valley of California. Soil and Water Conservation Society Conference: Cover Crops, Soil Quality, and Ecosystems, Sacramento, CA, (January).

Clark, M. S., F.G. Zalom , H. Ferris, K. Klonsky, W.T. Lanini, & A.H.C. vanBruggen. 1998. Multidisciplinary comparison of pest management in conventional, low-input, and organic cropping systems. Entomol. Soc. Amer. Annual Meeting, Nashville, TN.

Ferris, H., R.C. Venette, H.R. van der Meulen, and K.M. Scow. 1998. N-fertility and soil food web management. Annual Meeting of the Society of Nematologists.

Ferris, H., R. C. Venette, H. R. van der Meulen, and S. S. Lau. Nitrogen mineralization by bacterial-feeding nematodes. Annual Meeting of the Society of Nematologists.

Scow, K. 1998. Microbial Community Analysis. Center for Ecological Health Annual Meeting, Davis. (March)

Scow, K. 1998. Biological Fingerprinting of Fugitive Dust. Invited talk at Air and Waste Management Conference, San Diego, CA. (June)

Scow, K. 1998. Biological Fingerprinting of Fugitive Dust. Invited talk at USDA Air Quality Workshop, Davis, CA. (July)

Scow, K. 1998. Determinants of microbial communities in agricultural soils. International Society for Microbial Ecology, Halifax, Nova Scotia, Canada. (August)

Scow, K. 1998. Microbial Community Analysis. EPA Centre for Ecological Health Research, Science Advisory Committee Meeting, Davis, CA. (September)

Scow, K. 1998. Linking microbial community composition to function in agricultural soils. Invited talk at Soil Science Society of America, Baltimore, MD (October).

Scow, K.M. 1998. Microbiology and Soil Quality. Invited talk at Soil Biology Workshop, Corvallis, OR. (11/17).

Scow, K.M. 1998. Microbiology of agricultural soils. Invited talk at the Vegetable Crops Symposium, Davis, CA (11/3)

Ferris, H., R. C. Venette, H. R. van der Meulen and K. M. Scow. 1998. Nitrogen fertility and soil food web management. Annual Meeting of the Society of Nematologists.

Chen, J and H. Ferris. 1998. Mineralization of nitrogen by Aphelenchoides composticola. Annual Meeting of the Society of Nematologists.

Ferris, H. and L. Zheng. 1998. Toward a prescriptive phytopharmacognosy for management of plant-parasitic nematodes. Annual Meeting of the Society of Nematologists.

Ferris, H., T. Bongers and R. G. M. de Goede. 1999. Nematode faunal indicators of soil food web condition. Annual Meeting of the Society of Nematologists.

Chen, J., H. Ferris, K. M. Scow and K. J. Graham. 1999. The effect of fungal-feeding nematodes on fungal biomass during decomposition of organic matter . Annual Meeting of the Society of Nematologists.

Shouse, B. N. and H. Ferris. 1999. Microbe-grazer-predator community dynamics during organic matter decomposition. Annual Meeting of the Society of Nematologists.

Scow, K.M. 1999. A bug’s story. Invited talk in Dept. of LAWR. (2/10)

Scow, K.M. 1999. Developing Relationships between Soil Communities and Soil Quality in Agroecosystems. Kearney Symposium (3/23)

Scow, K.M. 1999. Role of microorganisms in the soil/atmospheric interface. Air Quality Workshop, Davis, CA (7/27).

Field Days/Presentations/Outreach
1996-1997

Scow and Ferris. 1996. September 18 (96) SAFS Soil Biology Workshop. Full day of lectures and labs on soil biology and the soil food web. 45 participants. Included: The soil food web, Food web theory, Soil biology and nutrient cycling.

Scow, 1997. FARMS program: visit Winters High School to meet with students. 200 participants. (1/7).

Scow, 1997. Presentation to Longterm Research in Agricultural Systems (LTRAS) seminar. 30 participants (1/23)

Scow, 1997. Presentation to growers associated with BIOS (Biologically Integrated Orchard Systems) project, Turlock, CA. 70 participants (1/30)

Scow, 1997. Arlene Tugel (USDA Soil Quality Initiative) visits project (2/13)

Scow, 1997. FARMS program: high school student visit to working farm. 30 participants.(2/15)

Scow, 1997. Presentation to Soil Microbiology class, UC Davis campus. 50 participants.(2/19)

Ferris and Scow. 1997. SAFS/BIFS (Biological Integrated Farming Systems) Project Joint workshop. Afternoon was devoted to soil biology with Ferris and Scow. 75 participants. (2/21)

Ferris, 1997. The importance of long-term cropping systems research, UC-SAREP Policy Advisory Committee. 20 participants. (2/22)

Scow, 1997. FARMS program: Field Day at Sierra Orchards 50 participants. (3/11)

Ferris, 1997. The importance of long-term cropping systems research, USDA-SARE Technical Advisory Committee. 15 participants. (3/21)

Ferris, 1997. Lab Exercises and Demonstration: Nematodes and nitrogen mineralization. SAFS Cover Crop Workshop. 45 participants. (3/22)

Ferris, 1997. Microbivorous nematodes and soil fertility. California Nematology Workshop, Riverside. 100 participants. (3/24)

Ferris, 1997. The role of bacterial-feeding nematodes in soil fertility. California Nematology Workshop, Davis. 100 participants. (3/27)

Scow. 1997. Microbial ecology and environmental assessment. Lecture for course: Ecotoxicology. (4/22)

Ferris, 1997. Nematodes and Cover Crops. SAFS Cover Crop Workshop, Davis. 30 participants (4/24)

Scow. 1997. Soil is alive! Science fair at Caesar Chavez Elementary School, Davis, CA. 200 participants. (5/8)

Scow. 1997. Joint group meeting with Mary Firestone’s soil microbiology lab, Berkeley, CA (5/16)

Scow. 1997. FARMS program: presentation of student research projects. 40 participants. (5/20)

Scow. 1997. Soil micobial ecology. Lecture for course: Rhizosphere Ecology. (6/3)

Scow. 1997. Presentation and field tour for Soil Fertility class, UC Davis campus. 40 participants.

Ferris and Scow. 9th Annual SAFS Field Day. 160 participants. (6/19)

Scow. 1997. Soil biology. FARMS workshop for high school teachers, Winters, CA. 30 participants. (6/17)

Scow. 1997. Soil microbiology. 2 day workshop for Soil Science Institute (CRS, Forest Service employees). 50 participants. (8/25-8/26).

Scow. 1997. FARMS program: Student-mentor meetings at UC Davis. 50 participants. (9/25)

Scow. 1997. FARMS program: Field day at Sierra Orchards. 90 participants. (10/15)

Scow. 1997. Soil microbial ecology. Lecture for course: Fundamentals of Ecology. (11/3)

Scow. 1997. FARMS program: student tour of SAFS project. 40 participants. (11/20)

1998

Scow, K. 1998. Determinants of microbial communities in agricultural soils. Invited talk at Sonoma Grape Day, Santa Rosa, CA. (February)

Scow, K. 1998. Determinants of microbial communities in agricultural soils. Talk at Agricultural Technology Day, University of California, Davis, CA. (June)

Scow, K. 1998. Influence of environmental factors on microbial communities in agricultural soils. Invited talk at Vineyard Growers Group, Madera, CA. (June)

Scow. 1997. Soil microbiology. Workshop for CRS, Forest Service employees. (July)

Presentation to Dr. Doug Karlen and Dr. Susan Andrews, USDA National Soil Tilth Lab, Ames, IA. (August).

Scow lab. 1998. Soil food web. BIOS Workshop Woodland (October)

Scow lab. 1998. Soil food web. BIOS Workshop Fresno (October)

Scow, K. 1998. Linking microbial community composition to function in agricultural soils. Invited talk at Soil Science Society of America, Baltimore, MD (October).

Scow, K. 1998. Microbial communities in California agricultural soils. Invited talk at Soil Biology Workshop. Corvallis, Oregon (November).

Ferris, H. 1998. Importance of microbivorous nematodes at the SAFS project. Invited talk at Soil Biology Workshop. Corvallis, Oregon (November).

Scow, K. 1998. SAFS Field Day. 30 high school students of the Farming Agriculture and Resources Management for Sustainability (FARMS). (November).

Ferris, H. 1998. Microbivorous Nematodes and Soil Fertility – Soil Biology Workshop Oregon State University (Dr. John Luna) 11/17/98

Ferris, H. . 1998. Characteristics, Identification and Faunal Analysis of Soil Nematodes (two laboratory sessions) – Soil Biology Workshop Oregon State University (Dr. John Luna) 11/17/98

Ferris, H. . 1998. Measurement and Interpretation of Soil Biological Parameters (Panel discussion) – Soil Biology Workshop Oregon State University (Dr. John Luna) 11/17/98

1999

Scow, K.M. 1999. Microbial blood and claws. Science Fair, Caesar Chavez Elementary School, Davis, CA. (4/28)

Scow, K.M. 1999. Microbiology of vineyard soils. Sonoma Valley Growers Association, Geyserville, CA. (5/7)

Scow. 1997. Soil microbiology. Workshop for CRS, Forest Service employees. (7/28)

Ferris, H. 1999. Soil Sampling and Interpretation of Nematode Count Data – California Nematology Workshop, Yuba City 3/29/99

Ferris, H. 1999. Nematodes and Fruit Trees: Analysis of Soil Fauna. Davis. 11/04/99

Ferris, H. 1999. The Soil Food Web and Indicators of its Condition, Southern California Turfgrass Institute, Buerna Park, 12/15/99

Ferris, H. 1999. Beneficial Soil Organisms: Understanding Soil Food Webs. Association of Applied Insect Ecologists, Sacramento, 2/1/00

Ferris, H. 1999. Beneficial Soil Nematodes: Understanding Soil Food Webs Tehama County Walnut Day, Red Bluff, 2/9/00

Ferris, H. 1999. Invisible Allies: Soil Food Web Management to Enhance Nitrogen Availability. SARE Conference, Portland. 3/7/00

Ferris, H. 1999. Twelve Years of SAFS: Farming System Differences if Soil Chemistry, Soil Biology and Soil Structure. SARE Conference, Portland. 3/8/00

Ferris, H. 1999. Structure and Function of Soil Food Webs: CAPCA Field Day, Fresno. 3/23/00

For all three years of the project, the UC Davis courses, Nematology 100: Plant and Soil Nematodes (Ferris), Soil Science 111: Soil Microbiology (Scow), and Soil Sci. 112: Soil Ecology (Scow/Jaffee) make extensive use of information and the field site associated with the SAFS project.

Project Outcomes

Project outcomes:

Farmer Adoption

A significant impact of our studies has been changes in management of the winter cover crop in the SAFS main plot low-input and organic management systems. Previous approaches were to leave the soil bare and dry during the fall and to sow the winter cover crop in November, to be germinated by winter rains. Now the standard procedure at SAFS involves planting the cover crop by mid-September and germinating it through irrigation, consistent with the results of our fall management project. This information has been shared with farmers and extension specialists at the numerous workshops in which we have been involved. Fall management of cover crops conceivably would diminish reliance on mineral fertilizers and may result in reduced leaching of N due to immobilization in cover crop and soil biota biomass during the fall and winter.

Another impact of our project is that our presentations and workshops at numerous outreach activities have promoted a dialogue with, and generated feedback from, growers about the importance of soil biology in agriculture and about methods for measuring soil organisms. Many growers are interested in having their soils analyzed for microbial populations and nematodes. Through our research we are providing information to help growers determine the usefulness of such measurements, which technologies to use, and how to interpret these results in the context of soil quality. Both Scow and Ferris have been and continue to be involved in numerous outreach activities concerned with this topic.

Producer Involvement

1997 Conferences: 250; Field Days: 130
1998 Workshops: 22 at UC Davis; 53 at Oregon State; Field Days: 192
1999 Workshops: 150; Field Days: 125

Recommendations:

Areas needing additional study

A logical extension of our studies of soil biological processes in low input and organic agricultural production systems is to move in the direction of minimum or conservation tillage. Clearly there is a need to develop and implement such practices to conserve and build soil structure, reduce soil compaction, conserve fossil fuel energy, and to reduce erosion and respirable dusts. Implementation of the practices in irrigated agriculture will create different challenges in conventional, low-input and organic farming systems. Among the new hypotheses generated by these new research directions are:

1. The most undisturbed and carbon-rich soils will have the most intact and extensive food webs.

2. The most disturbed systems (conventional/tilled) will have the least extensive foodweb, but are also least reliant on food web dynamics for soil fertility and structure.

3. In each farming system the food web in the two tillage systems will be a function of the interplay between C availability (possibly higher in the tilled) and the effects of disturbance (least in the minimum till).

4. In the carbon-driven (cover crop) farming systems (low-input and organic), opportunist organisms at lower trophic levels will abound in tilled soils; the food web will be more balanced and self-regulated in minimum-tilled soils than in disturbed (tilled) soils.

5. Turnover rates of the microbial biomass will be greater in the minimum-tilled than the tilled systems due to the prevalence of grazers throughout the web.

6. Consequently in the carbon-driven plots, mineralization per unit of C, or per unit of microbial biomass, should be greater in the minimum till plots. However, total mineral levels may be greatest in tilled plots as a result of the total C, total abundance of primary decomposer organisms, and their turnover (even though turnover rates are lower).

7. Nematode faunal analyses will provide a useful monitoring system for the condition of the soil food web under each treatment regime.

Any opinions, findings, conclusions, or recommendations expressed in this publication are those of the author(s) and do not necessarily reflect the view of the U.S. Department of Agriculture or SARE.