Evaluating compost and lime effects on soil organic matter, soil microbial communities and the control of Fusarium wilt in commercial tomato grown in Florida's sandy soils

Final Report for OS10-054

Project Type: On-Farm Research
Funds awarded in 2010: $14,955.00
Projected End Date: 12/31/2012
Region: Southern
State: Florida
Principal Investigator:
Amy Shober
University of Florida
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Project Information


Single applications of composted yard waste and lime amendments to Florida soils used for commercial tomato production had minimal effect on soil chemical properties and no effect on the incidence of Fusarium wilt. Soil organic matter was higher in soils receiving compost at the 30 ton/acre rate than when compost was applied at lower rates (5 to 20 ton/acre). Soils amended with 20-30 ton/acre compost supported statistically higher numbers of culturable bacteria and lower numbers of culturable fungi during mid-season only. The grower received little benefit from compost and lime additions, suggesting unrecovered costs of processing and applying the compost.


Vegetable production in Florida and throughout the southeastern U.S. commonly occurs on sandy coastal plains soils. These soils tend to be acidic with low organic matter content. As a result, soils used for vegetable production tend to have low fertility, water holding capacity, and biological activity (Muchovej et al., 2008). Fertility has typically been managed by applying inorganic fertilizers and lime as needed, while soil diseases, nematodes and weeds have traditionally been controlled by fumigation with methyl bromide.

Producer reliance on inorganic fertilizers to meet crop nutrient requirements does nothing to enhance soil organic matter levels. In addition, fields are commonly left fallow between crop cycles allowing the loss of organic matter as topsoil is eroded by wind or water. The use of methyl bromide effectively sterilizes soils, reducing the level of soilborne pests and pathogens as well as beneficial microorganisms that function to cycle plant nutrients and potentially suppress the effects of harmful organisms. Agricultural transition from methyl bromide has led to a resurgence of diseases caused by soilborne pathogens, especially wilt caused by Fusarium oxysporum f.sp. lycopersici (FOL).

The management of soil pH with lime has been shown to reduce Fusarium wilt, when nitrate-based N fertilizers are used in place of ammonium-based sources (Jones and Woltz, 1967, 1969, and 1972). Such practices were paramount for the control of FOL race 2 (Jones and Woltz, 1967 and 1969), but efficacy has not been assessed for race 3 isolates. However, pH management varies among tomato growers and is not currently used as a disease management tool because of widespread soil fumigant use (Geraldson et al., 1966; Jones et al., 1966). While commercial tomato cultivars with resistance to FOL race 3 are available, they lack the horticultural traits or resistance to other pathogens that are critical for successful production in Florida. These breeding issues were considered insignificant until recent changes in fumigation practices.

Research suggests that repeated applications of organic amendments, such as animal manures, biosolids, and composts, can increase soil organic matter level (Darby et al., 2006; Tester, 1990), even in the southeastern U.S., where the organic matter oxidation is rapid (Ozores-Hampton et al., 1998). Soil organic matter has many known benefits, such as increased water holding capacity, improved soil aeration through reduced bulk densities and increased soil fertility (Tester, 1990). Increasing soil organic matter can also enhance microbial activity, which improves plant nutrient uptake and suppression of certain plant diseases (Darby et al., 2006; Stone et al., 2003; Vallad et al., 2003).

Research clearly indicates that the use of organic amendments and lime can improve soil physical and chemical properties and increase overall crop growth. However, it is unclear whether these practices alone or in combination can sufficiently control soilborne pathogens, such as FOL, when vegetables are produced in sandy soils within a humid, sub-tropical climate regime. It is possible that such practices, if not properly monitored, could actually exacerbate certain diseases caused by soilborne pathogens or lead to physiological disorders due to reduced availability of certain essential nutrients.

Project Objectives:

The objective of this study was to determine the effect of compost and lime on soil chemical properties (including organic matter), the soil microbial community, including Fusarium spp., and the incidence and severity of diseases caused by soil borne pathogens, such as FOL. Specifically, we evaluated the effect of compost and lime amendments on the severity of Fusarium wilt and soil microbial community structure.

In addition, we evaluated the effect of compost amendments on soil organic matter under Florida’s humid sub-tropical climate. We also determined the effect of the compost and lime treatments on the availability of essential plant nutrients, including P, K, Ca, and Mg. Both Ca and Mg can form complexes with dissolved organic carbon and be leached from the soil when composts are applied. Losses of Ca and Mg from soils can lead to abnormal fruit development (blossom end rot) and large yield losses.

Results from this study were shared with the cooperating grower and the greater grower community to provide guidance in the use of soil amendments and soil pH management in commercial tomato. This research was part of a long-term effort by both UF investigators to identify cost-effective cultural practices that reduce the need for chemical pesticides and fertilizers by improving soil conditions that enhance soil microbial populations and activity. Such practices are sustainable, environmentally benign, and have practical applications for conventional and organic crop production in Florida and other southeastern states.


Click linked name(s) to expand
  • Gary Vallad


Materials and methods:
Experimental Design

Field trials were established at a commercial tomato production farm in Manatee County, FL in spring and fall seasons of 2010. Composted yard waste (compost) and lime (High CAL) were applied as soil treatments to all field trials to manipulate soil organic matter and pH on 18 Jan. 2010 and 20 July 2010 for the spring and fall seasons, respectively. Soil treatments during the spring 2010 trial included:
1) 5 tons/acre compost + 0.50 tons/acre SuperMag;
2) 10 tons/acre compost + 0.25 tons/acre SuperMag;
3) 1 ton/acre High Cal + 0.50 tons/acre SuperMag; and
4) 4) 0.25 tons/acre SuperMag (unamended control).

During the fall 2010 season, soils treatments were:
1) 10 tons/acre compost + 0.25 tons/acre SuperMag;
2) 20 tons/acre compost + 0.50 tons/acre SuperMag;
3) 30 tons/acre compost + 0.75 tons/acre SuperMag;
4) 1 ton/acre High Cal + 0.50 tons/acre SuperMag; and
5) 0.25 tons/acre SuperMag (unamended control).

Soil treatments were applied to individual 35 ft × 600 ft field plots in a randomized complete block design with three replications (total = 15 plots; approx. 9 acres total) using a calibrated tractor spreader. Lime (High CAL) was applied (when designated as part of the soil treatment) at an appropriate rate needed to raise the soil pH from native levels (approximately pH 6.0) to pH 7.0 based on the buffer pH test (Adams-Evens buffer) (Mylavarapu, 2009). Mulched, raised beds (6 beds per plot) were prepared with 5 ft center-to-center bed spacing. Tomatoes were produced on an approximately 110-day production cycle. The planting dates were 3 Mar. 2010 and 1 Sept. 2010 for the spring and fall seasons, respectively. Other aspects of land preparation, fertility and water management, pest and disease control, and harvest were performed using best management practices at the discretion of the grower cooperator.

Compost and Soil Samples

Composted municipal yard waste was prepared by the grower from municipal yard waste collected by the city of St. Petersburg, FL. The composted material was set in windrows of 12 to 15 ft tall by 20 to 25 ft wide, which were turned once per month on average. Windrow temperatures were monitored weekly and were never allowed to exceed 145°F. Windrow was turned 6 to 8 times and screened prior to application to field plots. Compost pH, electrical conductivity (EC), moisture content, organic C, organic matter (OM), carbon to nitrogen (C:N) ratio, total Kjeldahl N (TKN), total digestible P, total digestible K, and maturity were determined using standard test methods for the examination of compost and composting (Test Methods for Evaluation of Compost and Composting) (US Composting Council, 2002) at the Soil Control Lab (Watsonville, CA).

Soil samples were collected three times per season: immediately following application of soil treatments, at flowering, and at fruit set. Soil samples were not taken at final harvest due to early termination of the field trials by the cooperating grower due to low market prices. Composite soil samples were collected by randomly removing 24 to 30 soil cores from the top 15 cm of each land and stored in coolers until transported back to the laboratory for processing. A portion of each soil sample was air-dried, sieved to pass a 2-mm screen, and analyzed for soil pH (1:2 soil to deionized water ratio), EC (1:2 soil to deionized water ratio), and OM (loss on ignition) using standard methods (Mylavarapu, 2009). Soil test P, K, Ca, and Mg were determined by analyzing Mehlich 3 soil extracts (Mehlich, 1984) using inductively coupled plasma-atomic emission spectroscopy (ICP-AEP) (Perkin Elmer, Waltham, MA). Soil CO2 flux was measured on-site weekly (during the growing season) using a Li-Cor soil CO2 flux chamber (Li-Cor Biosciences, Lincoln, NE).

Soilborne Fungi and Bacteria

The remaining (field moist) portion of each composite soil sample was used to assess soil microbial populations using standard dilution plating techniques. Total culturable aerobic bacteria and Pseudomonas spp. were enumerated on 0.3% tryptic soy agar and King’s B medium (King et al., 1954), respectively, each amended with cyclohexamide (10 mg•L-1) and pentachloronitrobenzene (1 g•L-1) to suppress fungal growth. Total culturable fungi were enumerated on potato dextrose agar and a V-8 medium amended with rifampicin (50 mg•L-1), streptomycin (200 mg•L-1), and chloramphenicol (250 mg•L-1) to suppress bacterial growth. Fusarium oxysporum were assessed by dilution plating dried 1-g soil samples onto a modified Komada’s medium (Hansen et al., 1990). The colony forming units (cfu) per gram of soil were collected from each dilution series and converted to a logarithmic scale prior to statistical analysis.

Disease Ratings

Both trials were established on land with a history of vascular wilt disease caused by FOL, race 3 (G. Vallad, personal communication), with an average disease incidence of 20%, but as high as 80% in some areas of the field. However, the incidence of any soil-borne disease issues was assessed on a periodic basis over the course of tomato production. Fusarium wilt was confirmed through standard aseptic isolation of FOL from stem and petioles. Several collected isolates from randomly selected colonies of both morphology types were selected to verify pathogenic status (Attitalla et al., 2011).

Statistical Analysis

Soil chemical properties were analyzed by season using a repeated measures model, with soil treatment and sampling date as fixed effects and block as a random effect using PROC MIXED in SAS (SAS Institute, 2003). Normality was checked by examining histograms and normality plots of the conditional residuals (generated by the command “plots = pearsonpanel”). No significant soil treatment × date effects were reported for soil chemical properties allowing data to be pooled over each trial. All pairwise comparisons were completed on transformed data using the Tukey’s honestly significant difference (HSD) test with a significance level of ?= 0.05. Arithmetic means are reported in figures and tables.

Generalized linear models in the PROC GLIMMIX procedure of SAS, Version 9.2 (SAS Institute, Inc., Cary, NC) were used to determine the effect of compost and lime treatments on disease incidence and culturable soil bacteria and fungi counts. Soil amendment treatment was considered a fixed effect, while block and block × treatment were treated as random effects in the model. Disease incidence data were square root transformed, while culturable soil bacteria and fungi counts were log base 10 transformed prior to statistical analyses. Fisher’s protected LSD (? = 0.05) test was used to compare least squares means among treatments at each date.

Research results and discussion:

Field trials were conducted during the spring 2010 (February – June) and in the fall 2010 (August – December) production cycles at the growers site located in Manatee County, Florida. Replication of the experiment in an additional fall growing season (2011) was aborted by the grower due to low market prices.

Compost and Soil Samples

Compost that was applied to the soil was fully mature and supported plant growth (data not shown). The pH of the compost applied during the spring 2010 and fall 2010 seasons was slightly alkaline (Table 1). Our compost chemical properties (Table 1) were similar to properties of composts used in vegetable production in central Florida (Ozores-Hampton et al., 2011), except for C:N ratio. Ozores-Hampton et al. (2011) reported a C:N ratio of 14.5 compared to the C:N ratio of 25 and 22 for compost applied in our study during the spring and fall seasons, respectively. The lower C:N ratio reported by Ozores-Hampton et al. (2011) is probably a result of compost feedstock that consisted of biosolids in addition to yard waste. Compost applied as part of our study contained only yard waste materials. However, both composts would oxidize readily and N will be mineralized and available for plant uptake during the growing season.

In spring 2010, the application of compost or lime to soils prior to bedding had no effect on soil pH, EC, OM, or Mehlich 3 nutrients (Table 2). Similarly, no significant soil treatment effects were reported for pH, EC, or Mehlich 3 P, K, and Ca during the fall 2010 production cycle (Table 3). Our results differed from those of Ozores-Hampton et al. (2011), who reported an increase in soil OM, pH, and Mehlich 1-extractable P, K, Ca, and Mg. However, Ozores-Hampton et al. (2011) measured soil parameters following repeated composted applications over a 10-year time frame, whereas compost in our study was applied as a single application during one growing season. Also, Ozores-Hampton et al. (2011) reported an initial compost application rate of 80.4 ton/acre (180 Mg•ha-1), which was approximately three times higher than our highest application rate.

Application of compost affected soil OM and Mehlich 3 Mg in the fall 2010 season (Table 3). The application of compost at the 30 tons/acre rate led to significant increases in soil OM compared to soils that did not receive compost (Table 3). In the spring 2010 growing season, temperatures were much higher and application rates were lower than in the fall 2010 season, which could have had an effect on the rate of OM decomposition. Loper et al. (2010) reported a significant increase in soil OM when composted dairy manure solids were applied to simulated residential landscapes at an application rate of 256 Mg•ha-1, which was three times higher than the highest rate (30 ton/acre) in our study. In contrast, Hanlon et al. (2009) reported a modest 2.2 % increase in soil organic matter when compost was applied at a rate of 5 to 7 tons/acre (personal communication) to a sandy soil over a 10-year period. The U.S. Compost Council (2001) states that applications of compost at rates up to 50 or 60 dry tons/acre can be beneficial to vegetable production, but application rates that are that high are rarely used. The average compost application rate for vegetables is 1 to 2 tons/acre (U.S. Compost Council, 2001). Therefore, it may take repeated applications of compost over a longer time period to see a significant increase in soil OM, unless high rates are applied during a single compost application.

We also observed an increase in Mehlich 3 Mg when compost was applied to soil at the 20 and 30 tons/acre rates (Table 3). Our compost contained 31 lb Mg per ton; therefore, application of compost at the 20 and 30 tons/acre rates added 620 and 930 lb of Mg, respectively. Stoffella and Kahn (2001) reported that Mg concentrations in compost ranged from 1 to 5 g•kg-1 (2 to 10 lb/ton). The increase in Mehlich 3 Mg may be related to the application of Super MAG in combination with the compost at the higher rates.

Soilborne Fungi and Bacteria

During the spring 2010 season, soil treatments had no effect on total soil bacteria or total fungi (data not shown). However, compost and lime applications led to an increase in the total soil bacteria during the fall 2010 season, with an increase in the total soil bacteria and a decrease in the total fungi only for the 7 Oct. 2010 collection date (Table 4). We suggest that the reported higher counts of bacteria initially, followed by succession of fungi (increased fungi counts) could be due to the increase in soil organic matter that occurred with the application of compost at high application rates (20 to 30 tons/acre). Kornillowicz-Kowalska and Bohacz (2010) reported similar results following application of composted feather waste to soils, where an initial spike in bacteria was succeeded by higher counts of fungi. In contrast, we did not see a re-colonization of F. oxysporum in the soil regardless of the compost amendments, despite that fact that F. oxysporum persists in soil as chlamdospores and lives off soil organic matter (Olivain et al., 2006).

Our data exhibited a numerical increase in the amount of fluorescent pseudomonads counts over the course of the fall season for some of the treatments (Table 4). Pseudomonads are antagonistic microbes that have been shown to be suppressive against the fungal pathogen Fusarium (Sylvia et al., 2005). However, we reported no effects of soil treatments on F. oxysporum population (Table 4). We were unable to determine if F. oxysporum re-colonized the soil beds over the course of the study due to the fact that our counts were near the limit of detection.

Disease Ratings

The greatest number of symptomatic plants with fusarium wilt was identified toward the end of the spring 2010 trial, regardless of soil treatment (Figure 1). In fall 2010, we found that beds receiving compost at the 20 ton/acre rate produced tomato plants with the lowest number of fusarium wilt symptoms when compared with other treatments (Figure 2). By the end of the trial, tomatoes produced on beds that were composted at the 30 tons/acre rate showed the highest incidence of wilt (Figure 2); however, these treatment effects were not statistically significant. Wilt incidence was seen much earlier in the fall season than in the spring trial (Figures 1 and 2). This trend for earlier disease occurrence could be because optimal temperature conditions were reached earlier in the fall growing season than that of the spring season. Larkin (2002) reported that fusarium wilt disease incidence were apparent at the tested range of temperatures of 22°C to 32°C, but the greatest incidence rates were optimal at an ambient air temperature of 27°C.

Participation Summary

Educational & Outreach Activities

Participation Summary

Education/outreach description:

Results were disseminated to certified crop advisers (CCA) during the state-wide CCA training event on 11 Oct. 2011. We will also present results of the on-farm project at a full-day training event for county extension faculty on 1 June 2012 and at the 2012 Florida AgExpo, which is held annually at the Gulf Coast Research and Education Center. Pre- and post-test surveys at training events will evaluate knowledge gained by participants. For example, 71 CCAs attending increased their knowledge by 10% (on average) by attending the 11 Oct. 2011 training event.

Results of this study are presented in a non-thesis MS student paper by Mr. John Gum that will be published on the University of Florida Soil and Water Science Department website after an initial holding period (to allow for peer-reviewed publication). We will also deliver the project findings and recommendations to stakeholders (including agricultural producers, extension personnel and government officials) via a peer-reviewed fact sheet published through the University of Florida – IFAS Extension EDIS database (http://edis.ifas.ufl.edu/) and through peer-reviewed research publications.

Project Outcomes

Project outcomes:

Our results suggest that the grower is seeing little benefit from applications of composted yard waste to sandy soils prior to planting. Although the 30 ton/acre compost rate used in the fall 2010 is 3 times the typical rate applied by the cooperating grower, it appears that applications of compost may have no treatment effect on the incidence of fusarium wilt. It is possible that growers may benefit from longer-term applications of composted material; however, this cannot be assessed in our study.

Therefore, we cannot recommend the addition of compost on a large scale for the commercial production of tomato to achieve suppression of fusarium wilt during a single year or season. Large application of organic amendments can increase overall organic matter within a short amount of time; however, it is unclear if the increase in soil OM will translate to increased tomato yields, have an effect on future seasons, or reduce the incidence of fusarium wilt.

Economic Analysis

The grower received all yard waste from the cities of Sarasota and St. Petersburg, FL at no cost to the grower. The material was windrowed on site. Approximately 40 acres of land were dedicated to composting on-site. This practice did not remove viable land from production, so little cost was associated with the practice. The yard waste was windrowed and piles were turned every 3 months using existing farm equipment (front end loader). Grower estimated cost for producing the compost at $7 per a ton, which includes labor, fuel, land value, cost of operating/maintaining a front end loader, and cost of applying composted material prior to planting cover crops. The grower typically applies the material twice a year to 1,000 acres at 5 tons per an acre on average, for an annual cost of $70,000.

Farmer Adoption

While other studies suggest that there are soil quality and disease suppression benefits of long-term compost applications in vegetable production, we cannot recommend the use of compost during tomato production for the control of Fusarium wilt based on the results of our study.


Areas needing additional study

Future studies should determine if repeated applications of organic amendments and/or lime have a long-term effect on soil chemical and physical properties or on the incidence of Fusarium wilt in tomato when applied directly to soils prior to bed preparation or in between seasons for cover crop establishment. Future studies should be conducted under more controlled conditions than can be achieved on working farms to ensure that disease ratings are available through the entire growing season.

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.