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

1995 Annual 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

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



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 carbon(C):nitrogen (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.


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 UCD 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, and spatial variation in the field.

California’s 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 three 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.

Potential Benefits

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 Western SARE funded project, “A Comparison of Conventional, Low Input and Organic Farming Systems: The Transition Phase and Long Term Viability” (see SW96-012), 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 percent 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.

Farmer Adoption and Direct Impact

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.

This summary was prepared by the project coordinator for the 2000 reporting cycle.


Kate Scow

UC Davis
CA 95616
Howard Ferris

UC Davis
CA 95616