The Transition from Conventional to Low-input or Organic Farming Systems: Soil Biology, Soil Chemistry, Soil Physics, Energy Utilization, Economics and Risk

System Descriptions

The Sustainable Agriculture Farming Systems (SAFS) Project was established in 1988 to study agronomic, economic and biological aspects of conventional and alternative farming systems in California’s Sacramento Valley. The study consists of 4 treatment systems which differ primarily in crop rotation and use of external inputs. These include 4-year rotations under conventional (conv-4), low-input, and organic management and a conventionally managed, 2-year rotation (conv-2). The 3, 4-year rotations include tomato, safflower, bean, and corn. In the conv-4 treatment, beans are double-cropped with a winter wheat crop, while in the low-input and organic treatments, beans typically follow a cover crop of oats and vetch. The conv-2 treatment is a tomato and wheat rotation. All systems use “best farmer management practices” which are determined through consultation with growers cooperating on the project. The conv-4 and conv-2 treatments are managed with practices typical of the surrounding area, which include the use of synthetic pesticides and fertilizers. In the low-input system, fertilizer and pesticide inputs are reduced primarily by using legume cover crops to improve soil fertility and mechanical cultivation and cover cropping for weed management. The organic treatment is managed according to the regulations of California Certified Organic Farmers (CCOF). Thus, no synthetic chemical pesticides or fertilizers have been used. Instead, management includes the use of cover crops, composted animal manure, mechanical cultivation, and limited use of CCOF-approved products.

Crop Productivity

Crop Yields. Yields have varied more with year than with management system. Tomato yields from 1989 to 1996 at the SAFS site have ranged from less than 25 tons/acre to over 45 tons/acre; while county averages have typically been 28-34 tons/acre. In general, the organic system has had the lowest yields while the conv-4 system has had the greatest. In 1995 the conv-4 and low-input treatments had significantly higher yields than the organic and conv-2 systems. However, in 1996 the organic system had the highest yields among the four systems for the first time in the 8-year history of the project; though differences were not statistically signficant (Table 1).

Corn yields in the low-input system have been the highest among the 3 management treatments since 1992. In 1995, the corn yield in the low-input system remained relatively stable while those of the conv-4 system increased slightly from the previous year, resulting in no significant differences between those systems. However, organic yields dropped dramatically to 4 tons/acre, apparently due to nitrogen deficiency. In 1996, corn yields in the organic system were improved with higher quality composted manure, and yields among the 3 systems were statistically similar; all at approximately 5 tons/acre (Table 1).

Bean yields in the organic and low-input systems were equal or superior to those of the conv-4 system from 1990, the first year of bean planting, until 1994. However in 1995 and 1996 bean yields have suffered in the organic system due to heavy weed infestations. In 1995, volunteer oats from the previous oats/vetch crop were a problem. Due to a late harvest because of wet conditions, we had a problem with oats shattering during combining. While we were able to spray for weeds in the low input plots, mechanical cultivations in the organic plots were ineffective at reducing weed populations. Weed biomass in the organic system at harvest was almost three times higher than in the low-input system. Nevertheless, the herbicide application was not effective in raising low-input bean yields significantly over the organic yields (Table 1).

Safflower yields in all treatments have steadily increased over the 8 years of the project. While conv-4 safflower yields have generally been slightly higher than those of the alternative systems no statistically significant differences have been observed (Table 1).

Wheat yields in 1995 were quite low due to standing water on the fields over most of the winter. In 1996, yields in the conv-4 system increased by over 1,000 lbs/acre while those of the conv-2 declined slightly. The reason for the poor yields in the conv-2 system may be related to deteriorating soil structure in that system (discussed below). In contrast to wheat, the oats/vetch crop of the low-input and organic systems appeared to thrive from the excess moisture in 1995. Seed yields were 4,500-5,000 lbs/acre in those systems. Seed was not harvested from the oats/vetch crop in 1996. Instead, it was incorporated in the organic system and sold as hay from the low-input system.

Yield Stability. An important aspect of yield is stability over time. Stability is of particular interest in comparing alternative to conventional systems because of the potential implications for farm income when adopting non-conventional practices. We assessed yield stability by calculating the coefficient of variation (CV) for each cropping system under conventional and alternative management for the first four years (1989-1992), second four years (1993-1996), and the entire eight-year period (1989-1996) (Table 2). In general crop yields were more variable during the second rotation compared to the first rotation for all systems. Only yields of low-input corn and bean and conv-4 bean were less variable during the second rotation. Corn showed the only statistically significant difference across farming systems. Organic management, and to a somewhat lesser extent, low-input management, resulted in greater corn yield variability than the conv-4 system over the 8 years of production (Table 2). However, low-input corn yields over the last 4 years have been just as stable as those of the conv-4 system.

Soil Characteristics
Soil Fertility. Nitrogen deficiency has been largely responsible for reduced tomato and corn yields in the organic treatment (Scow et al. 1994; Friedman et al. submitted; Cavero et al. submitted). However, there has not been a clear relationship between soil and plant mineral nitrogen levels and yield. Nitrate levels measured in tomato petioles have typically been greater in the conventional compared to the alternative systems throughout the experiment and patterns observed in 1995 and 1996 were no exception (Table 3). Petiole nitrate levels in the organic system were considered deficient, according to conventional standards (Geraldson & Tyler 1990), at the first bloom, one-inch fruit, and first color stages in both years. By contrast, the low-input and two conventional systems were found to be deficient only at the first color stage.

In 1995, other measurements of tomato plant growth showed that by mid-June, leaf area index, total biomass and whole plant N were also the lowest in the organic system. At harvest, total N uptake in the organic tomatoes were considerably less than the other three systems (Table 5) strongly supporting the observation that organic tomatoes were N deficient. While these data seem to indicate nitrogen deficiency early in the growing season as a primary cause of lower yields in the alternative systems, there has not been a consistent, significant correlation between yield and petiole nitrate at any of these stages. In 1996, total plant nitrogen at harvest was similar across treatments (Table 5). However, petiole nitrate and blade percent nitrogen patterns (Tables 3 & 4) indicate that the early season nitrogen deficiency was compensated for by greater nitrogen uptake later in the season.

Because N deficiency appears to be a common problem in the organic system and conventional fertility indicators have not proven useful, we are studying the effects of management of the soil fauna on nitrogen release to better understand nitrogen processes in organically-managed systems. In laboratory experiments, additions of bacterial-feeding nematodes enhanced nitrogen mineralization by 50%. However, bacterial-feeding nematodes are at low levels in field soils in the spring when plants sometimes exhibit nitrogen stress. Bacterial-feeding nematodes were abundant and diverse across and within farming systems with greater abundance in the organic and low input systems. We have established an experiment in the companion plot area to test the effect of late-summer/fall cultural and cropping practices on levels of bacterial-feeding nematodes in the spring, and to determine the effect of those practices on nitrogen availability to transplanted tomatoes.

An additional experiment in the companion area, designed to evaluate the effects of varying nitrogen inputs and C:N ratios on immobilization and mineralization patterns, plant uptake, and yield, has been run for 3 years. In this experiment, published “sufficiency” and “deficiency” values for petiole nitrate did not reflect yield response in any year and therefore do not appear to be an appropriate tool for managing organic and low input tomato systems. For example, in 1994 petiole nitrate levels in the straw treatment and the straw plus cover crop treatment were close throughout the season, yet the straw treatment was the lowest yielding while the straw plus cover crop treatment was the highest yielding (Table 6).

Identifying petiole nitrate sufficiency and deficiency levels as yield predictors for organic and low input systems is problematic. This is shown by the small difference in petiole nitrate levels between the highest yielding and lowest yielding treatments in 1994, and also by the large spread in petiole nitrate levels with no corresponding yield differences in 1995. Soil nitrate levels were directly related to the C:N ratio of the inputs. High C:N ratio correlated with low soil nitrate, low C:N with higher nitrate levels. Higher nitrate levels in the soil did not correspond to higher yields. High C:N ratios did not necessarily correspond to lower yields, though in 1994 we observed that a C:N ratio of 93:1 did result in reduced yields.

Nitrogen deficiency has also been a problem in the organic corn system. Although large differences in soil nitrate levels across systems have not been detected, organic corn yields were low in 1993 and 1995. In those years total nitrogen uptake in the organic system was only 55-65% of that in the low-input and conv-4 systems (Table 7). However, in 1994 and 1996 total nitrogen uptake and yield in the organic system equaled or exceeded the other treatments. The lower yields in 1993 and 1995 were apparently due to inadequate nitrogen mineralization from the applied manure. Predicting available nitrogen in the organic system is difficult because it is dependent upon the amount, quality, and type of manure applied as well as the activity and structure of the soil food web. This unpredictability is overcome in the low-input system by using a combination of legume cover crops and supplemental synthetic fertilizer. The use of cover crops contributes nitrogen and enhances soil microbial activity while the mineral fertilizer eliminates nitrogen deficiency at critical periods of crop growth.

Soil Biology. For the past 6 years, levels of the soil microbial biomass have been higher in the organic and low input than conventional tomato farming systems (see previous Progress Reports). Levels of microbial activity have also been correspondingly higher in organic and low-input systems. To provide an indication of the structure and diversity of the microbial community in the soils from these 3 farming systems, phospholipid fatty acids (PLFA) (primarily associated with microbial membranes) were extracted from tomato soil samples collected over the growing season in 1995 and then analyzed by gas chromatography. The PLFA profile consists of various peaks representing different fatty acids, some of which correspond to particular microbial groups but, together which can be used as a "fingerprint" of the entire community. Patterns in the fingerprints, across farming systems and over time through the growing season, were determined using multivariate statistics (principal component analysis, constrained ordination analysis).

PLFA profiles from organic and conventional systems differed substantially from one another throughout the season from April to July. PLFA profiles from the low-input system were intermediate between organic and conventional on most sample dates. Low-input converged with the organic system following incorporation of the cover crop and converged with the conventional system following side dressing with mineral fertilizer. Field level spatial variation, represented by field blocks, was not significant in this study. Seasonal change was found to have a larger impact on PLFA profiles than management except over short time periods of two to four weeks following major farming operations.

Diversity indices, using several approaches, were calculated for the microbial communities in each of the farming systems based on the assumption that one PLFA peak corresponds to a species. There was little difference in the PLFA diversity among the conventional, low-input and organic farming systems using any of the approaches. This indicated that the differences in the PLFA profiles among the farming systems were due more to differences in the relative abundances of the same group of species rather than to differences in the species composition in the farming systems.

When the SAFS soil samples were compared to clay soils under rice management at a different location, PLFA profiles from two different soil types were completely separated by principal component analysis despite significant variation due to management and seasonal variation within each soil type. Thus we believe that PLFA analysis is a very promising method for discriminating microbial communities in different soil types, as well as responses of the communities to management and seasonal variation within a soil type.

Soil Structure. Soil aggregate stability was compared across treatments in 1994 and 1995 using a modified wet sieving technique. Results from 1994 showed that soil aggregation was more stable in the organic compared to the conventional systems. Microbial biomass carbon appeared to be responsible for this difference. However, the results of 1995 suggest that the 4-year rotation produces more stable aggregation than the 2-year rotation in this soil, and that the presence of a growing crop in the summer months has a greater effect on aggregate stability than the amount of organic matter applied to the soil or the type or amount of fertilizer used. Presence or absence of cover crops did not appear to greatly affect the stability. Future research will attempt to determine how seasonal trends in aggregate stability relate to shifts in microbial activity in response to the presence of a growing crop and whether organic matter present in the soil shows structural variation across treatments and over time.

Pests

Weeds. Among the major pest classes, weeds have been the most costly to manage throughout the experiment, typically accounting for 25% of total operating costs. Hand hoeing contributes the greatest to weed management costs and, while it has been utilized in all systems, it has been most important in the alternative systems, where synthetic herbicides are not used. During the first 5 years of the experiment (1989-1993) weed pressure was similar across the treatments (Lanini et al. 1994). Similarly, in 1994 and 1995 there were no statistical differences in weed biomass at harvest. Summer weed cover in 1996 was generally higher than was observed in 1994 (Table 8). Abnormal weather in 1995 allowed many weeds to escape control, and set seed (Table 9). The weed seeds of 1995 increased the weed pressure, and in spite of good weather for weed control operations, weed cover was higher than in 1994. The exception to this trend was the tomato plots which were hand weeded, in addition to herbicides and/or machine cultivation. In 1996, corn was not treated with an herbicide in any plots and weed pressure was close to what was observed in 1995.

Weed seedbank data indicated major differences between systems in terms of total weed populations and in species composition (Table 9). Redroot pigweed was a major problem in the corn in 1995 and was the dominant summer weed in the seedbank. The conv-2 plots, which do not have corn in the rotation, had much less pigweed seed than what was observed in other plots. Lambsquarters was the principal weed in safflower and again was much less common in the conv-2 plots which do not have safflower in the rotation. Black nightshade seed was more common in the conv-4 and conv-2 tomato plots where herbicides were used in place of cultivation. Cultivation, used in the low-input and organic tomato plots was more effective at removing black nightshade plants (and seed). Barnyardgrass was 4 to 10 times higher in the organic and low input plots compared to the conventional plots. Cultivation has not been effective in stopping late season germination and seed set of this species which remains an unsolved problem in these systems.

Although winter weeds have infested the cover crops to various degrees throughout the study period, they have generally not resulted in yield reductions in the subsequent crops. The only weed to show a large change among treatments is the chickweed, which has produced a large number of seed (Table 2). The low growth habit and non-competitive nature of this species has not resulted in this plant causing any problems in spite of its abundance.

Pathogens. For the second time since the start of the SAFS project (1989), root disease severity was assessed for all tomato plots. Twenty plants per plot were uprooted one week before harvest. Visual disease assessments were made for corky root (Pyrenochaeta lycopersici), root rots caused by Pythium, Phytophthora, Rhizoctonia, or Fusarium spp., root knot nematode galls (Meloidogyne sp.), and knobby root tips (cause unknown). The scoring scales are indicated under Table 10. Disease severities were generally low. Symptoms of corky root were significantly more severe in the conv-2 treatment relative to the others in 1995 and 1996. Pythium root rot was significantly less severe in the conv-4 than other treatments, while knobby root was significantly more severe in both conventional treatments. Phytophthora root rot was significantly more severe in the organic than other treatments. Symptoms of Verticillium wilt were not observed since the tomato cultivar was resistant to this disease.

Fungi were isolated from 20 roots per plot, 6 sections per root, on selective agar media for Pythium and Phytophthora sp. (PARP), Pyrenochaeta lycopersici (CRM), and Verticillium dahliae (sodium polypectate medium), and on non-selective media (WA and APDA) for Rhizoctonia, Fusarium and other fungi. The numbers of Rhizoctonia and Fusarium isolates were higher in the 2-year rotation plots than in all other plots (Table 2). This trend was reversed for Macrophomina. Pythium was more frequently isolated from the low-input and organic plots than from the conventional plots, while there were no differences in Phytophthora among the treatments. There were no significant differences among treatments for the percentages of roots from which Verticillium dahliae was isolated.

Root knot nematodes were identified as Meloidogyne javanica in 1995 (samples were not submitted for identification in 1996). Rhizosphere samples from plants with knobby roots were examined for Xiphinema but this nematode was not observed. However, these soil samples contained low to moderate numbers of root lesion nematodes (about 415 per liter of soil in 1996).
In conclusion, tomato root disease severity was much lower in 1996 than in 1995. The differences among treatments were consistent from year to year for corky root and knobby root but not for the other diseases.

Insects. Plot size limits the study of farming system effects on mobile, above-ground insects, however, economically important arthropod pests have been monitored throughout the experiment to identify the need for pest control intervention and determine the effects of pests on crop quality and yield. Insecticides have been used in the conventional tomatoes 5 out of the 8 years of the project, while conventional corn has required insecticides in only 2 of the 8 years. Tomato quality has been acceptable for paste for all systems during the entire 8 years. However, stink bug damage in 1992 and 1995 would have rendered the low-input and organic tomatoes, which received no insecticide treatment, unacceptable for dicing and whole pack. Seedcorn maggot and wireworms have been occasional pests in the low-input and organic safflower and corn due to inadequate waiting periods between cover crop incorporation and cash crop planting. Replanting has been needed in some years. Future work will be focused on the relationship between cover crop management methods and timing and the effects of pests on seedlings.