Influence of microbial species and functional diversity in soils on pathogen dispersal and ecosystem processes in organic and conventional agroecosystems

Influence of microbial species and functional diversity in soils on pathogen dispersal and ecosystem processes in organic and conventional agroecosystems

Summary

Organic production systems have increased in recent years in many areas of the United States. Organic systems do not use synthetic pesticides and in the long term may be more sustainable than conventional systems. It is often assumed that soils from conventional agroecosystems will be more prone to pathogen invasion then soils from organic agroecosystems, since species diversity is greater in soils from organic agroecosystems. However, this hypothesis has never been critically examined in the field using spatial statistical modeling and dispersal gradient analysis with introduced plant pathogens. We know little about how to manage soil microbial communities to reduce pathogen invasion and optimize plant disease suppression and ecosystem level processes. Is it more important to manage functional or species diversity of microbial communities to enhance suppressiveness of soils to plant pathogens? Only a few comparative studies have been conducted to examine the relationship between plant disease suppression, soil physical and chemical factors and the biological communities present in soils from organic and conventional agroecosystems. None of these studies have been conducted on a spatial scale in the southeastern US.

This research began in the summer of 2001. A portion of the field research was conducted at the Horticultural Crops Research Station (HCRS) in Clinton, North Carolina in field plots that were established in the fall of 1996 on a previous SARE grant. The objectives of our research are to examine the influence of microbial species and functional diversity and composition on the invasion of soils from conventional and organic agroecosystems by the Basidiomycete plant pathogen Sclerotium rolfsii, causal agent of Southern blight. Specifically, we will contrast conventional soil fertility amendments including synthetic fertilizers, and organic soil fertility amendments, including either composted plant materials, animal manures, or incorporated green manures on the spread of this pathogen and the community dynamics of selected microflora in field plots. In on-farm tests, we will evaluate the resistance of conventional versus organic agrecosystems to species invasion and colonization by S. rolfsii. We will sample soils on both organic and conventional farms that have received either organic or conventional soil fertility amendments and compare disease suppressiveness of these soils and determine the functional components of soil microbial communities associated with disease suppression. We continue to enhance our educational efforts at N. C. State University by teaching several classes including courses in Agriculture, Ethics, and the Environment, Soil Ecology, Ecology, Evolution and Diversity, and Applied Multivariate and Spatial Statistics. We participated in an on-farm educational presentation at the SARE regional conference in the fall of 2001 and data from the project will br presented at the American Phytopathological Society Meeting in Charlotte in August of 2003.

Objectives/Performance Targets

Objective 1. Are soils from organic agroecosystems more resistant than soils from conventional agroecosystems to invasion by the soilborne plant pathogen S. rolfsii? How do the spatial patterns of disease symptom expression relate to pathogen propagules of S. rolfsii in soils in field plots from conventional and organic agroecosystems?

Objective 2: Are grower field soils from organic farms amended with organic fertility amendments more suppressive to disease caused by S. rolfsii than soils from conventional farms amended with synthetic fertility amendments? Is species diversity, functional diversity or the composition of the soil microflora most closely related to disease suppressiveness?

Objective 3: Continue education and outreach plans by teaching graduate level courses relevant to sustainable agriculture research, conducting on-farm research and education, and presenting data at conferences with a focus on ecology in agriculture.

Accomplishments/Milestones

Objective 1. Are soils from organic agroecosystems more resistant than soils from conventional agroecosystems to invasion by the soilborne plant pathogen S. rolfsii?

This portion of the field research is underway at the Horticultural Crops Research Station (HCRS) in Clinton, North Carolina in field plots that were established in the fall of 1996 on a previous SARE grant. The experimental design consists of a split plot. The frequency of disturbance (tillage) during the growing season differs between the main plot treatments (2 levels) and includes either biweekly tillage on bare-soil plots or surface-mulch with wheat straw after a single initial tillage on mulched plots. The mainplots are arranged in 4 blocks. Subplots (4 levels) include: a conventional synthetic fertilizer or organic fertility amendments including either a composted cotton-gin trash (CGT), composted poultry manure (PM), or an incorporated rye-vetch green manure (RV) (cover crop planted in previous fall). Rates of each soil amendment were standardized to obtain 112 kg plant available nitrogen per hectare. Each experimental unit consists of six rows that are 7.6-m long and 1.6-m wide. Treatments were replicated four times. Six-week old tomato seedlings were transplanted 14 days after soil amendment in single rows at 30 cm within-row spacing, and overhead irrigation was utilized as needed through the season (2.5-3.0 cm per week without rain). Main plots received tillage biweekly until plants were too large for a tractor to clear. Wheat straw was applied to the other main plot treatments 2 weeks after transplanting.

Disease incidence and yield

Final disease incidence in 2002 caused by S. rolfisi in tomato ranged from 12-68%. Soil fertility amendments significantly affected the incidence of disease, the area under the disease progress curve, and yield (Table 1). Disease was significantly reduced by organic soil fertility amendments. Disease incidence and the area under the disease progress curve were lowest in plots amended with cotton gin trash and highest in plots amended with synthetic fertility amendments. Yields were also highest in plots amended with cotton gin trash while lowest yields were in plots with the rye vetch green manure (Table 1).

Spatial patterns of disease symptom expression in field plots from conventional and organic agroecosystems?

The center four rows of the six row plots were divided into 1m quadrats containing 3 plants and coordinates were determined and marked. Each treatment and rep combination (32) contained 28 quadrats and a total of 896 quadrats were monitored for disease across the field. The spatial and temporal dynamics of disease spread were evaluated over time by monitoring the incidence and severity of infected plants in each quadrat. Disease severity was recorded on individual plants on a quadrat basis, one time per week for a period of seven weeks. The spatial dynamics of disease spread were affected by soil fertility amendment. Disease spread less rapidly through plots amended with cotton gin trash than synthetic fertilizer. Further statistical analysis of the spatial data is underway to quantify the dynamics of disease spread over space and time.

Soil microbial communities, microbial biomass, respiration, carbon and nitrogen, physical and chemical factors

Population densities of thermophilic organisms (organisms that grow at temperatures > 40 C) were significantly higher in soils amended with composted cotton gin trash than in the other soils. Population densities of thermophiles were 3.1 x 104 colony-forming units per gram of dry soil (cfu/g dry soil) in plots amended with composted cotton gin trash and 1.6 x 104, 1.0 x 104 and 1.2 x 104 cfu/g dry soil in soils amended with synthetic fertilizers, composted poultry manure or a rye vetch green manure, respectively. Population densities of oomycete fungi were also higher in soils amended with cotton gin trash (2.2 x 102 cfu/g dry soil) than soils amended with synthetic fertilizers (1.1 x 101 cfu/g), composted poultry manure (6.6 x 101 cfu/g dry soil) or a rye vetch green manure (1.4 x 102 cfu/g), respectively. There were no differences in population densities of total fungi, Trichoderma or Gliocladium species, culturable bacteria or enteric bacteria among treatments.

Mulching and amendments significantly influenced soil extractable carbon (C). Compared to tillage, mulching increased soil extractable C in the 2002 samples. Highest extractable C (43-88 mg C kg -1) was found in plots amended with cotton gin trash, followed by poultry manure (34-68 mg C kg-1) rye vetch (20-44 mg C kg-1), and synthetic fertilizer (17-41 mg C kg-1). There were no interactions between tillage/mulch and amendments. Soil extractable N was higher in plots amended with cotton gin trash than in other treatments in the August sample. Interactions between tillage/mulch and amendments were recorded in the June samples for both years.

Microbial biomass C (MBC) was significantly higher in plots mulched with wheat straw than in the tilled plots. Amendments had consistently significant influences on MBC. The largest microbial biomass C was found in the plots treated with cotton gin trash (200 to 520 mg kg-1) followed by the poultry manure (120 to 270 mg kg-1), rye vetch cover crop (114 to 278 mg kg-1) and synthetic fertilizer (98 to 208 mg kg-1). The MBC was found to be significantly correlated with extractable C, microbial biomass nitrogen (MBN), and microbial respiration, and in most cases with extractable N and net mineralizable N.

There was significantly higher microbial biomass N in the mulched soils than the tilled soils (Tables 2). Surface residue treatment had more pronounced effects in 2002 than in 2001. Amendments also significantly influenced MBN. The CGT had the greatest effects with a decreasing order of CGT > PM > RV ¡Ö SF. The MBN was significantly correlated with extractable C and MBC, and in most cases with extractable N, microbial respiration and net mineralizable N. Organic amendment and wheat straw treatments did not show influences on the microbial biomass C to N ratios in most cases (Table 2).

Mulching significantly increased microbial respiration (Table 2). Soil microbial respiration was higher in plots amended with cotton gin trash and poultry manure than synthetic fertilizer or rye vetch. There were interactions between mulch and amendment for the August samples. The microbial respiration was significantly correlated with MBC, MBN, NMN, and extractable- C for most sample dates.

Straw surface application led to higher net nitrogen mineralization (potential N availability) than did tillage, except the samples of August 2001. Organic amendments had significant effects on N mineralization. Highest net mineralized N were found in plots amended with cotton gin trash, while plots amended with rye vetch, poultry manure and synthetic fertilizers released much less N. No significant interactions were observed between mulch and amendments for nitrogen mineralization. Net mineralizable N was significantly correlated with extractable C, and in most cases to MBC, MBN, extractable N and microbial respiration.

Soil fertility amendments had a significant effect on all the chemical factors that were measured in the plots with the exception of zinc, copper and % humic matter. Cation exchange capacity was highest in soils amended with cotton gin trash. The base saturation and pH of soils amended with the organic fertility amendments were also higher than soils amended with synthetic fertilizer. In general, P, K, Ca, Mg, and Mn levels were higher in soils with compost amendments than synthetic fertility amendments.

Objective 2: Are grower field soils from organic farms amended with organic fertility amendments more suppressive to disease caused by S. rolfsii than soils from conventional farms amended with synthetic fertility amendments?

We are interested in asking the question ¡°Will soils from organic grower fields with a history of organic fertility amendment use be more suppressive to pathogen dispersal, sclerotia germination and disease then soils from conventional fields amended with synthetic fertilizers?¡± In spring of 2002, 20 kilograms of soil was removed in a uniform pattern from 3 sites at 3 organic (Dawson, Hartmann, Harman), 3 sustainable (Hitt, Letendre, HCRS-Clinton) and 4 conventional (Hope, Holland, Hall, Cottle) farms. The organic farms used cover crops and organic soil amendments (composted animal manures, feather meal or yard waste) and the conventional farms used synthetic fertilizers for plant nutrition. Two undisturbed cores were removed from three locations at each farm for bulk density and soil water release measurements. Soil cores were removed from three areas at each farm to a depth of 8 inches and bulked. Germination of S. rolfsii sclerotia varied by grower type. In greenhouse assays, disease incidence caused by S. rolfsii on bell pepper was higher in soils from conventional farms (28.3%) than in soils from sustainable (11.1%) or organic (15.6%) farms. The area under the disease progress curve and disease severity were also higher in soils from conventional than sustainable and organic farms. The greenhouse experiments will be repeated with soil sampled from grower fields in 2003. Mycelial growth of S. rolfsii in soils was not affected grower type. Weed biomass in a greenhouse pot assay was higher in soils from organic than sustainable or conventional farms.

Is species diversity, functional diversity or the composition of the soil microflora most closely related to disease suppressiveness?

Culture dependent assays were used to measure the relative abundance of various microbial populations using 10-fold serial dilutions of soil and selective media. Numbers of culturable bacteria, enteric bacteria, total fungi, and thermophilic microorganisms were quantified. In addition, numbers of species of Trichoderma and fluorescent Pseudomonas species were assessed since they have been associated with suppressive soils and are known biological control agents or have growth-promoting effects on plants. The abundance of total culturable fungi, bacteria, and enteric bacteria were not different among farms (Table 3). However, the number of fluorescent Pseudomonas species and thermophilic microorganisms were higher in soils from organic and sustainable than conventional farms, while the reverse was true for Trichoderma species. Sampling will be repeated in the spring of 2003 to confirm results.

Total and active fungal and bacterial biomass was also measured in the soils from organic, sustainable and conventional farms in the spring of 2002. Total fungal biomass was lower in soils from conventional than organic and sustainable farms (Table 4). However, total bacterial biomass was higher in soils from conventional than sustainable and organic farms. Soils from sustainable farms had the highest active bacterial and fungal biomass and the highest ratio of active to total fungal biomass and bacterial biomass.

Soils from organic farms had significantly greater levels of phosphorus, calcium, magnesium, sodium, manganese, zinc, and copper than soils from conventional farms (data not shown). Percent humic matter, CEC, % base saturation, pH, were also higher in soils from organic and sustainable than conventional farms.

Microbial biomass C (MBC) was 758, 455.2, and 110.1 mg kg-1 in soils from organic, sustainable, and conventional farms, respectively. Higher labile C, soil respiration, microbial biomass nitrogen, extractable N and net mineralizable N were also observed in soils from organic farms and sustainable than conventional farms (Table 5).

Three subsamples of each soil from each site at the five conventional and five organic grower locations were immediately stored in a freezer (-20oC) and will be used to assess the microbial community structure by analyzing the phospholipid fatty acid (PLFA) biomarkers. Genetic diversity of the fungal and bacterial communities in soil will be assessed using DNA directly extracted from soil and amplified with primers in a polymerase chain reaction. The above assays have not been conducted yet. Community level physiological profiling (CLPP) was conducted within 3 weeks after sampling by examining sole-C substrate use patterns of the microbial communities on Biolog microplates. We are in the process of analyzing the substrate utilization pattern data and will report this at a later time.

Tables submitted as hard copies

Impacts and Contributions/Outcomes

The Project coordinator has been involved in research and outreach at the Horticultural Crops Research Station (HCRS) in Clinton, NC since 1987 and has taught soil quality workshops and participated in numerous field days for county agents and growers at many locations within North Carolina and at commodity group meetings across the southeast. This year the PI and co-PI (Hu) and her research team attended the Southern SARE meeting in Raleigh, North Carolina and presented a poster. They also participated in a field presentation of data at Alex Hitt’s farm. County agents Debbie Roos in Chatham County, NC and Alan Thornton in Sampson County, NC have facilitated farm visits and grower meetings. A farm survey has also been developed and sent to the growers to gather more information on their farming practices and history of plant disease.

The co-PI (Hu) organized a new class in Soil Ecology that was taught for the first time in the fall of 2001. The project coordinator teaches a class called “Agriculture, Ethics and the Environment” (http:www.cals.ncsu.edu/course/pp590a) in the fall of 2002 in the Department of Plant Pathology at N. C. State University. Students enrolled in the class have included graduate students from many departments in CALS, county agents, North Carolina Dept. of Agriculture pesticide administrators, N.C. Department of Environment and Natural Resources statisticians, and growers. Written reviews from students who have taken the class have been excellent. The class is taught every other year and will be taught again in the fall of 2002. Students use role playing and case studies to discuss issues such as populations and food, ozone depletion, animal waste management, water quality, intellectual property rights and the third world, genetically modified crop plants, organic and sustainable agriculture, pesticide resistance development, and research ethics. The other co-PI (Gumpertz) teaches classes in multivariate and spatial statistical techniques. The PI and coPI (Hu) also recently began team teaching a new class in BT 595E “Ecology, Evolution and Diversity”. The PI and co-PI (Hu) are also members of the Ecological Society of America and attended and presented data from previous SARE funded research at the ESA meeting in Madison, WI in August of 2001.

Three publications have been published from the previous SARE funded project conducted at the Horticultural Crops Research Station, the Center for Environmental Farming Systems, and grower fields including:

Bulluck, L. R., Evanylou, G. K., and Ristaino, J. B. 2002. Influence of Alternative and Synthetic Soil Fertility Amendments on Soil Microbial Communities and Physical and Chemical Properties on Organic and Conventional Farms. Appl. Soil. Ecol. 19:147-160.

Bulluck, L. R., and Ristaino, J. B. 2002. Synthetic and organic amendments affect Southern blight, soil microbial communities and yield of processing tomatoes. Phytopathology 92:181-189.

Bulluck, L. R., Barker, K. R., and Ristaino, J. B. 2002. Nematode trophic group and community dynamics on tomato as influenced by organic and synthetic soil fertility amendments. Appl. Soil Ecology 21:233-255.

Collaborators: