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

Project Overview

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

Annual Reports


  • Agronomic: corn, safflower, wheat, grass (misc. perennial), hay
  • Vegetables: beans, tomatoes


  • Animal Production: manure management, feed/forage
  • Crop Production: nutrient cycling, organic fertilizers
  • Natural Resources/Environment: biodiversity
  • Soil Management: organic matter, composting, nutrient mineralization, soil quality/health


    [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]

    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.

    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.