A.H.C. van Bruggen

Fundamental Differences Between Conventional and Organic Tomato Agroecosystems in California

In an integrated, multidisciplinary study we compared ecological characteristics and productivity of commercial farms categorized as either organic (ORG) or conventional (CNV) based on their use of synthetic fertilizers and pesticides or reliance on organic soil amendments and biological pest control. We measured belowground parameters: various soil chemical and biological properties and root disease severity; common agronomic indicators: biomass, fruit yield and insect pest damage; and community level indicators, including arthropod diversity and soil microbial activity and diversity. CNV and ORG production systems could not be distinguished based on agronomic criteria such as fruit yield and arthropod pest damage levels. However, differences were demonstrated in many soil, plant, disease, and diversity indicators suggesting that the ecological processes determining yields and pest levels in these two management systems are distinct. In particular, nitrogen mineralization potential and microbial and parasitoid abundance and diversity were higher in ORG farms. Differences between the agroecosystems were sufficiently robust to be distinguished from environmental variation and suggest that biological processes compensated for reductions in the use of synthetic fertilizers and pesticides.

In search of biological indicators for soil health and disease suppression.

Abstract While soil quality encompasses physical and chemical besides biological characteristics, soil health is primarily an ecological characteristic. Ecosystem health has been defined in terms of ecosystem stability and resilience in response to a disturbance or stress. We therefore, suggest that indicators for soil health could be found by monitoring responses of the soil microbial community to the application of different stress factors at various intensities. The amplitude of a response and time to return to the current state before application of stress could serve as measures of soil health. Root pathogens are an integral part of soil microbial communities, and the occurrence of epiphytotics forms an indication of an ecosystem in distress. Disease suppression can be viewed as a manifestation of ecosystem stability and health. Thus, indicators for soil health could possibly also function as indicators for disease suppressiveness. Previously suggested indicators for soil health and disease suppression have mainly been lists of variables that were correlated to more or less disturbed soils (ranging from conventional to organic agricultural soils, grassland and forest soils) or to conduciveness to disease. We suggest a systematic ecological approach to the search for indicators for soil health and disease suppression, namely, measuring biological responses to various stress factors and the time needed to return to the current state.

Ecology of E. coli O157:H7 and Salmonella enterica in the Primary Vegetable Production Chain

There is an increased concern that plants might be more important as a carrier for human enteric pathogens like E. coli O157:H7 and Salmonella enterica serovars than previously thought. This review summarizes the knowledge available on the ecology of E. coli O157:H7 and Salmonella enterica in the primary production chain of leafy green vegetables (in particular lettuce), including manure, manure-amended soil, and crop. Based on the available literature, suggestions are made for the control of these pathogens. The suggested approach of oligotrophication of agro-ecosystems fits in the wider approach to lower environmental emissions of nutrients from manure application and to enhance the suppression against plant pathogens. Keywords

Comparison of soil N availability and leaching potential, crop yields and weeds in organic, low-input and conventional farming systems in northern California

Increasing dependence on off-farm inputs including, fertilizers, pesticides and energy for food and fiber production in the United States and elsewhere is of questionable sustainability resulting in environmental degradation and human health risks. The organic (no synthetic fertilizer or pesticide use), and low-input (reduced amount of synthetic fertilizer and pesticide use), farming systems are considered to be an alternative to conventional farming systems, to enhance agricultural sustainability and environmental quality. Soil N availability and leaching potential, crop yields and weeds are important factors related to agricultural sustainability and environmental quality, yet information on long-term farming system effects on these factors, especially in the organic and low-input farming systems is limited. Four farming systems: organic, low-input, conventional (synthetic fertilizer and pesticides applied at recommended rates) 4-year rotation (conv-4) and a conventional 2-year rotation (conv-2) were evaluated for soil mineral N, potentially mineralizable N (PMN), crop yields and weed biomass in irrigated processing tomatoes (Lycopersicon esculentumL.) and corn (Zea mays L.) from 1994 to 1998 in California’s Sacramento Valley. Soil mineral N levels during the cropping season varied by crop, farming system, and the amount and source of N fertilization. The organic and low-input systems showed 112 and 36% greater PMN pools than the conventional systems, respectively. However, N mineralization rates of the conventional systems were 100% greater than in the organic and 28% greater than in the low-input system. Average tomato fruit yield for the 5-year period (1994–1998) was 71.0 Mg ha −1 and average corn grain yield was 11.6 Mg ha −1 and both were not significantly different among farming systems. The organic system had a greater aboveground weed biomass at harvest compared to other systems. The lower potential risk of N leaching from lower N mineralization rates in the organic and low-input farming systems appear to improve agricultural sustainability and environmental quality while maintaining similar crop yields.

Moving waves of bacterial populations and total organic carbon along roots of wheat

A bstractTo determine if spatial variation in soluble carbon sources along the root coincides with different trophic groups of bacteria, copiotrophic and oligotrophic bacteria were enumerated from bulk soil and rhizosphere samples at 2 cm intervals along wheat roots 2, 3, and 4 weeks after planting. There was a moderate rhizosphere effect in one experiment with soil rich in fresh plant debris, and a very pronounced rhizosphere effect in the second experiment with soil low in organic matter. We obtained wavelike patterns of both trophic groups of bacteria as well as water-soluble total organic carbon (TOC) along the whole root length (60 or 90 cm). TOC concentrations were maximal at the root tip and base and minimal in the middle part of the roots. Oscillations in populations of copiotrophic and oligotrophic bacteria had two maxima close to the root tip and at the root base, or three maxima close to the tip, in the middle section, and at the root base. The location and pattern of the waves in bacterial populations changed progressively from week to week and was not consistently correlated with TOC concentrations or the location of lateral root formation. Thus, the traditional view that patterns in bacterial numbers along the root directly reflect patterns in exudation and rhizodeposition from several fixed sources along the root may not be true. We attributed the observed wavelike patterns in bacterial populations to bacterial growth and death cycles (due to autolysis or grazing by predators). Considering the root tip as a moving nutrient source, temporal oscillations in bacterial populations at any location where the root tip passed would result in moving waves along the root. This change in concept about bacterial populations in the rhizosphere could have significant implications for plant growth promotion and bioremediation.

Percolation and Survival of Escherichia coli O157:H7 and Salmonella enterica Serovar Typhimurium in Soil Amended with Contaminated Dairy Manure or Slurry

ABSTRACT The effect of cattle manure and slurry application on percolation and survival of Escherichia coli O157:H7 and Salmonella enterica serovar Typhimurium was investigated for different soil depths after the addition of water. Four treatments were chosen for the first set of experiments: (i) addition of inoculated farmyard manure on the soil surface, (ii) mixing of inoculated farmyard manure with the top 10 cm of soil, (iii) addition of inoculated slurry on the soil surface, and (iv) injection of inoculated slurry into the top 10 cm of the soil. Homogeneity of water distribution in the soil profile was confirmed by a nondestructive nuclear magnetic resonance method. Survival data were fitted to a modified logistic model, and estimated survival times were compared. In the second set of experiments, pathogen-inoculated farmyard manure or slurry was applied to soil columns with 1-month-old lettuce plants. More pathogen cells percolated to greater depths after slurry than after manure application. Survival of E. coli O157:H7 was significantly longer in soil with slurry than in that with manure, while survival of Salmonella serovar Typhimurium was equally high with manure and slurry. The densities of the pathogens were not different in the rhizosphere compared to the bulk soil with manure, while the densities were higher by 0.88 ± 0.11 and 0.71 ± 0.23 log CFU per g (dry weight), respectively, in the rhizosphere than in bulk soil after slurry application. Our results suggest that surface application of manure may decrease the risk of contamination of groundwater and lettuce roots compared to injection of slurry.

Effects of long-term crop management on nematode trophic levels other than plant feeders disappear after 1 year of disruptive soil management

Nematode community analysis may provide a useful tool to quantify soil health. Nematode communities were monitored for 5 years during a 12-year period in the sustainable agriculture farming systems (SAFS) project at UC Davis, where conventional (CONV), low-input (LOW) and organic (ORG) management treatments were compared. After the completion of three 4-year crop rotation cycles, a uniform crop of oats was grown in 2001. The composition of the nematode genera was different from year to year, but there were significant management effects on genus composition in each year, with the CONV treatment being significantly different from the LOW and ORG treatments. Important contributors to the differences in genus composition among treatments were plant parasitic nematodes. Nematode community indices (enrichment (EI), basal (BI) and channel (CI) indices) of the CONV treatment differed from those of the ORG and LOW treatments in 1993, 1994, 1995 and 2000, but not in 2001. The difference in structure index (SI) among management treatments was significant in 1995 and 2000. EI and SI were generally lower, and BI and CI higher in CONV than in LOW and ORG treatments. There were significant crop effects on the community indices throughout the years. Even in 2001, there was a residual effect of the crop grown in 2000 on most nematode community indices. Differences in EI, BI and CI among crops were consistent, while those in SI were not. Meloidogyne javanica(Treub) Chitwood, juveniles added to various soil samples were reduced by 68% in soil where nematode trapping fungi had been added and which had low BI (12) and low CI (20) values. Soil from SAFS plots with a high BI (47) and high CI (70) after 1 year of oats and ploughing, suppressed root knot juveniles much less. There were significant negative correlations between BI and root knot nematode (RKN) suppression ( −0.72) and between CI and RKN suppression (−0.74). Thus, BI and CI appeared to be most valuable as indicators for long-term effects of management on nematode suppression. However, BI and SI may be more suitable as general indicators for the health status of a soil, since CI can be high in highly disturbed agro-ecosystems as well as in undisturbed natural ecosystems. A high BI would indicate poor ecosystem health, while a high SI would indicate a well-regulated, healthy ecosystem. For agricultural soils the presence of large populations of plant parasitic nematodes forms an additional indication of poor ecosystem health, as natural regulation is limited in this case.

Microbial Dynamics Associated with Multiphasic Decomposition of 14C-Labeled Cellulose in Soil

A bstractRecent emphasis on residue management in sustainable agriculture highlights the importance of elucidating the mechanisms of microbial degradation of cellulose. Cellulose decomposition and its associated microbial dynamics in soil were investigated in incubation experiments. Population dynamics of actinomycetes, bacteria, and fungi were monitored by direct counts. Populations of oligotrophic bacteria in cellulose-amended soil were determined by plate count using a low C medium containing 4 mg C liter−1 agar, and copiotrophs using a high C medium. Cumulative 14CO2 evolution from 14C-labeled cellulose was best described by a multiphasic curve in a 28-day incubation experiment. The initial phase of decomposition was attributed mainly to the activity of bacterial populations with a low oligotroph-to-copiotroph ratio, and the second phase mainly to fungal populations. An increase in oligotroph-to-copiotroph ratio coincided with the emergence of a rapid 14CO2 evolution stage. Streptomycin reduced 14CO2 evolution during the first phase and prompted earlier emergence of the second phase, compared to the control. Cycloheximide initially promoted 14CO2 evolution but subsequently had a lasting negative effect on 14CO2 evolution. Cycloheximide addition significantly increased bacterial biomass and resulted in substantially stronger oscillation of active bacterial populations, whereas it initially reduced, and then stimulated, active fungal biomass. The observed changes in 14CO2 evolution could not be explained by observed shifts in fungal and bacterial biomass, probably because functional groups of fungi and bacteria could not be distinguished. However, it was suggested that oligotrophic bacteria prompted activation of cellulolytic enzumes in fungi and played an important role in leading to fungal dominance of cellulose decomposition.

Bacterial Community Structure in Relation to the Carbon Environments in Lettuce and Tomato Rhizospheres and in Bulk Soil

A bstractCrop roots provide dynamic nutrient environments within agroecosystems that can influence the relative abundance and activity of oligotrophic and copiotrophic microorganisms. Copiotrophic organisms grow in carbon (C)-rich environments and their distribution implies that C abundance favors their survival. Survival of oligotrophic organisms is dependent on their ability to multiply and maintain activity in habitats of low C flux. To determine if spatial variation in available C along the root coincides with different physiological groups of bacteria, we isolated bacteria from the rhizosphere at different locations along the tap root of lettuce and tomato plants grown under greenhouse and field conditions. In all five experiments, the overall numbers of both oligotrophs and copiotrophs were high at the upper portions of the root and lower at tip locations and in the bulk soil environment. Consistent patterns in the ratio of copiotrophic to oligotrophic (C:O) bacteria along the roots of lettuce and tomato were obtained and clearly showed that the C:O ratio was different for these two crop species. With lettuce, C:O ratios were high at the root tip (1.22 to 1.61) and upper mid-root locations (0.90 to 1.30), intermediate at the lower mid-root locations (0.73 to 0.95), and low at the root base (0.56 to 0.76). With tomato, C:O ratios were low at root tip locations (0.50 to 0.68) and high at mid and base locations along the root (1.20 to 1.28). These differences may reflect qualitative and quantitative differences in root exudates between these crop species. In our experiments, nitrogen (N) concentrations and lateral branch sites, providing C sources, were important factors influencing bacterial populations in the rhizosphere of lettuce and tomato. Competitive interactions between microorganisms and physiological constraints with respect to substrate affinity may be two important mechanisms influencing bacterial populations and structure of rhizosphere communities.

Agronomic, economic, and environmental comparison of pest management in conventional and alternative tomato and corn systems in northern California

The effectiveness, economic efficiency, and environmental impact of pest management practices was compared in conventional, low-input, and organic processing tomato and field corn systems in northern California. Pests, including arthropods, weeds, pathogens, and nematodes, were monitored over an 8-year period. Although both crops responded agronomically to the production-system treatments, arthropods, pathogens, and nematodes were found to play a relatively small role in influencing yields. In contrast, weed abundance was negatively correlated with tomato and corn yields and appeared to partially account for lower yields in the alternative systems compared to the conventional systems. Lower pesticide use in the organic and low-input systems resulted in considerably less potential environmental impact but the economic feasibility of reducing pesticide use differed dramatically between the two crops. The performances of the organic and low-input systems indicate that pesticide use could be reduced by 50% or more in corn with little or no yield reduction. Furthermore, the substitution of mechanical cultivation for herbicide applications in corn could reduce pest management costs. By contrast, pesticide reductions in tomato would be economically costly due to the dependence on hand hoeing as a substitution for herbicides. Based on the performance of the low-input and organic tomato systems, a 50% pesticide reduction would increase average pest management costs by 50%.