Compost for Management of Plant Pathogens and Weed Seeds

Final Report for ONE10-123

Project Type: Partnership
Funds awarded in 2010: $15,000.00
Projected End Date: 12/31/2011
Region: Northeast
State: Vermont
Project Leader:
Dr. Deborah Neher, PhD
University of Vermont
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Project Information


We demonstrated that compost prepared with a C:N ratio of 25-40:1 and attaining temperatures of 55-77oC (131-171oF) for 15 days will kill disease early blight inoculum and large crab grass seeds. When applied at a rate of 20 tons per acre, compost made with hardwood bark suppressed severity of early blight disease more than compost made with softwood, hay or manure-silage. Using compost as part of the management package keeps more nutrients and organic matter on the farm and saves purchase of external inputs.


Early blight is widespread and devastating on crops within the Solanaceae, Crucifer (Brassica) and Apiaceae (carrot) families in Vermont. The primary inoculum of the pathogen is typically splashed onto the foliage from infested soil. Inoculum load is influenced by the soil texture and abundance of the pathogen on surface soils or mulches. Sanitation is important to reduce initial inoculum and, thus, diseased material must be disposed of in a manner to destroy the pathogen. Given that the early blight pathogen has saprophytic capabilities that facilitate survival and dispersal, on site disposal techniques are avoided in favor of diverting material to the landfill. However, composting these materials on local farms has the potential to kill these pathogens and weeds, which would allow producers to reduce export of nutrients and organic matter from their operation and generate a local source of disease- and weed-free (Liebman and Davis 2000, Larney and Blackshaw 2003) potting medium. Furthermore, composted organic wastes can serve as a biological inoculant for field soils to reduce the severity of root diseases caused by plant pathogens in natural and field systems (Stone et al. 2001, Hoitink and Boehm 1999)

Organic certification outlines minimum temperature requirements to kill pathogens and weed seeds. Compost made in windrows is considered suitable for organic production has an established carbon-to-nitrogen (C:N) ratio of 25-40:1 attaining temperatures of 55-77oC (131-171oF) for 15 days, during which time the pile is turned at least five times. The problem is that most farmers do not follow these recommendations. In Vermont, farms may attempt to compost manure but have insufficient carbon to develop an appropriate ratio, or do not turn the pile frequently enough to reach proper aeration and temperatures.

If properly prepared, most compost naturally suppresses Pythium and Phytophthora (Chen et al. 1988, Chung et al. 1988, Harris et al. 1997). However, diseases with saprophytic phases such as Rhizoctonia (Voland and Epstein 1997) and Alternaria are more difficult to control and require accommodating the antagonist microbe during composting. Composts prepared from lignocellulosic substrates such as tree barks become colonized by Trichoderma spp. which is an effective biocontrol of Rhizoctonia (Hoitink and Boehm 1999). Trichoderma works by producing a chitinase which lyses the fungal pathogen hyphae. Populations of biocontrol agents are linked with carbohydrate content. Once carbohydrates are depleted, the microbial communities degrading them decline. The concentration of cellulose and lignin in compost determines the longevity of the suppressive effect

Nitrogen and other nutrients cycled as organic matter are decomposed by soil microbes. A proper compost recipe that provides nitrogen sufficient to basic metabolism, activity and reproduction of microbes is critical to efficient production of quality soil amendment product. Hardwoods typically have a higher C:N than softwoods and straw. Frequent turning aerates piles to reach temperatures lethal to plant pathogens and weed seeds. Curing of piles allows recolonization of fungi such as Trichoderma (Hoitink and Boehm 1999).

Project Objectives:
  1. Demonstrate that compost, properly made, will heat and kill disease early blight inoculum and giant crab grass weed seeds.
    Compare the ability of compost made from to suppress early blight disease on crucifer crops at two partner farms.


Click linked name(s) to expand/collapse or show everyone's info
  • Tom Gilbert
  • Andy Jones
  • Bruce Kauffman


Materials and methods:

Feedstock materials to make compost were analyzed for C:N content in May 2010 through the UVM Agriculture and Environmental Testing Laboratory (Table 1). Four types of compost were built in June 2010: 1) manure similar to what farmers create ('compost' but not to recipe), 2) proper recipe with hay, 3) proper recipe with softwood, and 4) proper recipe with hardwood (Table 2). All recipes were optimized for C:N and moisture, except control.

We isolated Alternaria brassicinae from Brussels sprout leaves and A. carotiincultae and A. dauci from carrot leaves from Intervale Community Farm in fall 2009 (Figure 1). Known quantities of early blight infested plant material and seeds (i.e., crab grass Digitaria sanguinalis) will be placed into two types of bags, one with a mesh and the other sealed in plastic (Figure 2). The mesh bag tested the effect of heat and biota and the sealed bag tested the effect of heat alone. Each recipe was replicated in three piles (Figure 3) in a randomized complete block design (Figure 4). Pathogen and weed seed bags were removed from each of 12 piles at three times during the compost process: baseline, compost duration required for organic certification, and end of the thermophilic phase (Figure 5). Turning of piles was based on temperatures at 1’ and 3’ (Figure 6). Pathogen viability was testing by swabbing moistened inoculum on 3 independent leaves of Brussels spouts to determine whether it generated disease symptoms (Figure 1 lower right). Seed germination assessment was quantified by plating 3 replicate dishes of 100 seeds each to determine percentage germination.

2) Field demonstration of disease suppression properties of compost (season 2)
Field trials were established in 2011 as demonstration plots at two locations: Intervale Community Farm (Burlington, VT) and Riverside Farm (East Hardwick, VT). We worked with the existing cropping management plan of the farm and took precautions not to introduce any pathogens or seed. On each farm, we established six treatments (4 compost types and 2 controls), replicated in a Randomized Complete Block design, blocked by row position. Experimental units were 25’meter lengths of a cropping row with a buffer strip to avoid interplot interference (Figure 7 Intervale, Figure 8 Riverside). Compost treatments were applied after the first cultivation at 20 tons per acre (twice the typical application rate), and spread manually to avoid transplant damage (Figure 9). The three compost treatments (hay, softwood, hardwood compost with proper C:N ratio) were tested for their relative ability to suppress disease by a combination of a physical barrier mulch and antagonistic fungi or bacteria acting as biological control agents. Two controls were included: sterile rice hull mulch as a control to test the role of a physical barrier only and bare soil as no physical barrier.

Effectiveness of compost as a physical barrier and/or substrate for colonization of antagonistic fungi was measured by comparing the onset, incidence and severity of early blight and any other diseases that develop that occurred naturally by residential wind-blown or splash-dispersed fungi or bacteria. Each of 8 plants in the center of each plot was evaluated for early blight symptoms. Numbers of lesions were counted for each of the four lowest leaves from the plant. In addition, the physiological status of each leaf was recorded (H: healthy, C: chlorotic, S: senescent). Diesaese severity was computed as ? (# leaves x # lesions per leaf) plant. Assessments were made up to six times after the initial symptoms were apparent and continued until secondary spread of the disease was prevalent.

Research results and discussion:
Viability of pathogen and weed seeds

Properly made compost appears to effectively kill the early blight pathogen and giant crabgrass weed seeds by the time that compost attained temperatures of 55-77oC (131-171oF) for 15 days by turning a minimum of 5 times (Figure 6). Germination of crab grass seed was reduced to 0% by the start of the thermophilic stage (T1) when exposed to both microbes and heat. In contrast, seeds were not killed until the end of the thermophilic stage (T2) when exposed to heat only (Figure 10 left panels). Similarly, virulence of the early blight pathogen was reduced to 0% by the start of the thermophilic phase (T1) when exposed to microbes and heat, and more variable when exposed to heat only (Figure 10 right panel).

Disease suppression in field demonstration

In 2011, we conducted trials using the brassica cropping system on the two farms proposed.
The Intervale Community Farm was flooded most of May, so we were not able to begin the field trial there until mid-July. We were able to collect two time points of disease before tropical storm Irene flooded the fields leading to termination of the experiment.
At Riverside Farm, we experienced substantial variation in plant growth because the farmer was unable to provide an even spread of manure/compost at the beginning of the season. We were able to collect six time points of disease at Riverside Farm, three before and three after Tropical Storm Irene. Noticeable increases in early blight disease were observed post-storm. At Riverside, we noted a trend toward suppressed early blight incidence and severity when hardwood compost was applied in comparison to manure, softwood or hay, although the results were not different statistically. The controls appeared similar, suggesting that it is not just a physical barrier effect of rice hulls.

As typical with integrating studies in a farmer’s field, timing was occasionally imprecise, we had one block of treatments that was applied before cultivation and was incorporated into the soil. Under this circumstance, the hardwood compost continued to suppress disease and was as effective as the other blocks when compost was added after cultivation. This result indicates a microbial mechanism and not simply a physical barrier.


Early blight disease has a wide host range including Solanaceae (tomato, eggplant, potato), Crucifer or Brassica (Brussels sprouts, cabbage), and Apiaceae (carrots). It is caused by Alternaria species. Our focus was on early blight because it is widespread, has a wide host range, and currently has no known genetic resistance in seed. In addition to the sanitizing process of composting, achieved through heating, we know that compost made with hardwood materials are known to be substrates that attract colonization of biological control fungi such as Trichoderma during the curing phase of compost. Compost preparation in this study involved a complete thermophilic phase and curing to allow natural colonization by biocontrol organisms. This is the first report on use of compost to suppress early blight.

Literature Cited

Chen W, HAJ Hoitink, AF Schmitthenner, OH Tuovinen (1988) The role of microbial activity in suppression of damping-off caused by Pythium ultimum. Phytopathology 78: 314-322.

Chung YR, HAJ Hoitink, PE Lipps (1988) Interactions between organic-matter decomposition level and soilborne disease severity. Agriculture, Ecosystems & Environment 24: 183-193.

Harris AR, K Siwek, BM Wiseman (1997) Interactions between damping-off fungi, antagonists and Capsicum seedlings. Applied Soil Ecology 6: 251-263.

Hoitink HAJ, MJ Boehm (1999) Biocontrol within the context of soil microbial communities: A substrate-dependant phenomenon. Annual Review of Phytopathology 37: 427-446.

Larney FJ, RE Blackshaw (2003) Weed seed viability in composted beef cattle feedlot manure. Journal of Environmental Quality 32: 1105-1113.

Liebman M, A Davis (2000) Integration of soil, crop and weed management in low-external-input farming systems. Weed Research 40: 27-47.

Stone AG, SJ Traina, HAJ Hoitink (2001) Particulate organic matter composition and Pythium damping-off of cucumber. Soil Science Society of America Journal 65: 761–770.

Voland RP, AH Epstein (1997) Development of suppressiveness to diseases caused by Rhizoctonia solani in soils amended with composted and noncomposted manure. Plant Disease 78: 461-466.

Research conclusions:
  • Biological control strategies support organic and low input practices. Using compost as part of the management package keeps more nutrients and organic matter on the farm and saves purchase of external inputs.
    The two partner farms were chosen because of their high visibility. ICF is surrounded by a neighborhood of vegetable producers and is a common farm tour stop. Riverside farm is near Highfields Center for composting (HCC). HCC staff directly reaches 100-300 farmers or more per year through workshops, lectures, and other presentations, and an immeasurable number of producers at events and through media. Through these avenues, HCC staff can effectively communicate the results of our research and trials to the farm community.
    More than 100 participants attended each of two presentations at the NOFA-VT meeting and 40 participants attended the presentation at the VORS meeting (see below).
Participation Summary

Education & Outreach Activities and Participation Summary

Participation Summary:

Education/outreach description:
  • PI Neher presented the project to potential applicants for the 2011 SARE Partnership applicants.
    Two invited presentations on 11 February 2012 at the Northeast Organic Farming Association of Vermont held at University of Vermont, Burlington: 1) Neher, D.A. General Soil Science for Beginning Farmers; and 2) Neher, D.A. Biological Indicators of Soil Health
    One invited presentation on 29 March 2012 at the Vermont Organic Recycling Summit meeting held at Vermont Technical College in Randolph, Vermont: Neher, D.A. Crafting compost to manage plant pathogens and weed seeds.

Project Outcomes

Project outcomes:


Farmer Adoption


Assessment of Project Approach and Areas of Further Study:

Areas needing additional study

  • Application rates
    Standardized method and recipe for curing to foster biological control agents
    Identify metrics of compost maturity
    Expand to other crops and disease systems: potato/common scab; Rhizoctonia seed and seedling rots caused by damping-off pathogens including Pythium, Phythophthora, Rhizoctonia, and Xanthomonas campestris pv campestris. expand our crops to include snap beans, cucumbers and cabbage.
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.