S1028: Ecological and genetic diversity of soilborne pathogens and indigenous microflora
Statement of Issues and Justification
This project would apply to SAAESD Priority Areas under Goals 1A (integrated and sustainable agricultural production systems), 4B (natural resource and ecosystem management), and 4F (IPM systems, including biologically-based tactics). Soilborne pathogens are a diverse group of pathogens that reduce plant emergence and infect roots and crowns. The result is reduced plant productivity, increased costs to the grower and potential ecological damage to the adjacent natural environment. Below is a summary of current problems growers face due to soilborne pathogens in four specific plant production systems direct-seeded cotton and soybean, ornamental bedding plants destined for use in the landscape, and vegetable transplants for field production.Cotton seedling diseases are a major factor affecting cotton production worldwide (DeVay, 2001; Hillocks, 1992; Melero-Vara and Jimenaz-Diaz, 1990; Howell, 2001; Howell, 2002). Loss estimates for seedling diseases accounted for 27% of the total estimated losses in lint production from 1991-2000 (DeVay, 2001). The primary pathogens of the cotton seedling disease complex are Rhizoctonia solani, Thielaviopsis basicola, Pythium spp., and Fusarium spp. In addition to stand losses due to damping-off disease, both pre and post-emergence, seedling diseases may delay early season crop growth and result in additional management problems. In severe disease situations replanting may be required. Cotton seed in the U.S. is universally treated with fungicides prior to sale, indicating the severity of seedling disease problems and the efficacy of these fungicides. The producer must decide whether or not to use additional fungicides either on the seed before planting (planter-box, hopper-box, or custom seed treatments) or in the planting furrow (in-furrow treatments). These practices should give greater protection to emerging plants and have been reported to be effective in controlling seedling disease (Chambers, 1995; Colyer et al., 1991; Colyer and Vernon, 2005; Minton and Garber, 1983, Minton et al., 1982). Costs for hopper-box fungicides or custom seed treatments may range from $4.15 to $11.12 per hectare ($1.68 to $4.50 per acre), while in-furrow fungicides may cost the grower from $10.75 to $54.36 per hectare ($4.35 and $22.00 per acre). Replanting costs per hectare are approximately $61.78 ($25.00 per acre) excluding technology fees which are approximately $88.92 per hectare ($35.00 per acre) (Bryant et al., 2003).The soybean cyst nematode, Heterodera glycines Ichinohe, caused yield losses between 4.2 and 3.6 million metric tons in the U.S. between 1999 and 2002 (Wrather et al., 2003). Management strategies for H. glycines acknowledge the clear relationship of increasing H. glycines population densities with decreasing soybean yields (Niblack et al., 1992), and have the common goal of maintaining population densities of the nematode below economic damage threshold levels. These strategies include crop rotation, use of resistant cultivars and chemical control. Sources of host plant resistance against the nematode have been identified and incorporated into soybean germplasm and commercial soybean cultivars. Development of marker-assisted selection methods for H. glycines resistance (Vierling et al., 2000) enables more efficient introgression of soybean cyst nematode resistance genes into commercial cultivars. However, the diversity of soybean cyst nematode populations (Niblack et al., 2002) puts longevity and sustainability of using host plant resistance as the sole management strategy at risk because populations of H. glycines that are virulent on resistant soybean cultivars exist.
Vegetable transplant and bedding plant production are important components of U.S. agriculture in the southeastern states. Bedding plant production at $2.5 billion in 2004 accounted for over 50% of the entire value of floriculture crops in the U.S. (Jarardo, 2005). Vegetable (broccoli, cabbage, pepper, tomato, and others) and strawberry transplants were valued at $173 million in 2003 (USDA, NASS, 2004). Four southern states (FL, TX, GA, and NC) produced 16% of all these crops grown in the U.S. Fresh market tomatoes are an extremely important vegetable commodity. In several states (FL, GA, SC, TN and VA), they are the number one fresh market vegetable crop in terms of dollar value. Nine southern states account for 61% of the U.S. fresh market tomato crop (USDA, NASS, 2005). While of lower value, broccoli is often an important rotational crop for some growers. In Kentucky, for example, it is an important fall crop.
While bedding plants are transplanted into the landscape by people other than the grower, many vegetable producers grow their own transplants. For example, over 4,300 tomato transplants and over 11,000 broccoli transplants are needed per acre. In either situation, the soilborne pathogens that are problematic for cotton seedlingsR. solani and Pythium spp.are also problematic for bedding plants and vegetables in both the transplant and field production phases (Conover, 1949; Jones et al., 1991; Keinath and Farnham, 2001).
Production of many vegetable transplants and bedding plants take place in greenhouses where temperature and moisture conditions can be controlled. Although sanitation is practiced, many greenhouse facilities inadvertently provide conditions favorable for survival of damping-off pathogens such as Pythium spp. and R. solani. In the vegetable transplant and bedding plant commodities there is no tolerance for diseased plants. Thus, even one diseased plant in a flat of otherwise healthy transplants may result in the loss of the entire flat. In addition to damping-off disease, R. solani causes crown and root rot diseases on older transplants that magnifies the amount of loss to the producer due to the length of time plants were utilizing greenhouse resources prior to the loss. Although fungicides are effective in preventing Rhizoctonia crown and root rots, non-target problems can arise in their use since greenhouse operators capture and re-use irrigation water.
Bedding plants and vegetable transplants continue to be challenged by the same soilborne pathogens after planting into the landscape or field. Fungicide use post-plant can be effective but is limited in both situations. Once bedding plants are sold at retail and planted in the landscape around homes and businesses by the consumer, there are few control options other than general cultural practices like mulching and raised beds to limit root disease problems. With vegetables, concerns about worker exposure and fungicide resistance require that other methods of disease control be made available.
Biological controls could offer an alternative, if they were safe, effective and economical. Biological control using antagonistic microbes, alone or as supplements, to minimize the use of chemical pesticides has received increasing attention for cotton in recent years (Aqil and Batson, 1999; Hagedorn et al., 1993; Howell, 2002; Howell et al., 2000). Biological controls have been registered and used on cotton as an alternative and supplement to fungicides. Regional testing of seed treatment biological agents indicates that these agents do not perform as consistently as fungicides and suggest different strategies need to be examined. In-furrow treatments are commonly used on cotton, and planters are equipped for liquid or granular application in the planting furrow and may offer a method to increase the likelihood of establishing a biological agent and controlling seedling diseases.
The advantage of bedding plants and vegetable transplants treated with biocontrol agents during greenhouse production is that those plants may carry the biocontrol agent along on the root system when planted in the landscape or field. In the case of a biocontrol agent that is rhizosphere competent, this could extend the disease protection period through the life of the crop in the landscape or field. Isolates of binucleate Rhizoctonia sp. (BNR) have proven effective in preliminary experiments for control of both Pythium and Rhizoctonia damping-off in bedding plants (Burns and Benson, 2000; Honeycutt and Benson, 2001) and may also be effective in preliminary experiments for control of damping-off of vegetable transplants.
Plant growth-promoting rhizobacteria (PGPR) are naturally occurring root-colonizing bacteria which can induce increased plant growth (Cleyet-Marcel et al., 2001; Kloepper, 1994; Glick, 1995), often with concomitant reductions in plant diseases. The beneficial effects of PGPR for disease control have been reported for many crops and pathogens (Raupach et al., 1996; Raupach and Kloepper, 1998; Reddy et al., 1999; Reddy et al., 2000). The best strains and mixtures of PGPR activate the plants natural defense mechanisms in a phenomenon termed induced systemic resistance (ISR) (Raupach and Kloepper, 2000; Jetiyanon and Kloepper, 2002). Gustafson LLC commercialized a PGPR preparation under the name BioYieldä. The product is incorporated into the potting mix used to grow transplants and is a combination of two spore-forming PGPR Bacillus strains. Treated transplants show increased shoot and root growth leading to more rapid development than nontreated transplants. An ISR response is frequently observed.
Beauveria bassiana is a ubiquitous fungus with entomopathogenic properties and an extensive host range of pest insects. With few exceptions, research on B. bassiana as a control for plant pathogens has been limited to laboratory studies on growth and cell lysis. The potential of B. bassiana to control important seedling pathogens, such as R. solani and Pythium myriotylum has recently been demonstrated (Bishop, 1999; Ownley et al., 2000; Ownley et al., 2004; Seth et al., 2001; Seth, 2001; Marshall et al., unpublished data).
Introduction of commercial biological agents to field soils, whether for disease management or enhancing plant productivity, has not been consistently successful across all crops or even within a defined geographic region on a single crop. For example, our previous cooperative research suggested that biological-based seed treatments did not increase stand of snap bean in the southeastern U.S, although they were beneficial on other crops. A likely cause of the failures is our lack of understanding of the genetic diversity of soilborne pathogen populations and the indigenous soil microflora associated with plant roots. While state-to-state differences will exist, there are common underlying themes. Genera and species of deleterious and beneficial soil microflora often belong to the same culturable groups, even when isolated from different soil types, but genetic and physiological relationships apparently determine the specific role these organisms play in sustainable crop production. The same is also apparent for the organisms that cannot be cultured, but that now can be examined at the molecular level. Plant pathogens may appear morphologically similar, but they may be genetically different (or similar) within and among field locations.
Considerable diversity of R. solani exists in the southeastern U. S., with two of the three most recent anastomosis groups (AG-11 and AG-13) being identified from plants and soil in this region. The question is, Where do these fungi originate? Research has demonstrated that AG-3 associated with potatoes may have migrated in one direction (northeastern U.S. to N.C.) due to movement of seed potatoes (Ceresini et al., 2002a/b; Ceresini et al., 2003). How do other R. solani AG groups move? Do natural areas harbor R. solani and serve as new genetic material for this pathogen in field and greenhouse situations? While ornamental bedding plants, and to a lesser extent vegetable transplants, can be moved great distances within the region (and so move pathogens with them), direct seeded crop plants, such as cotton and soybean, do not move.
The soilborne pathogens Rhizoctonia and Pythium and the diseases they cause are common throughout the southeastern U.S. for virtually all plants, whether direct seeded into a field or initially grown in a greenhouse. Yet, we know little of their genetic background or origin. Because fungicides are not consistently efficacious, economical, ecologically desirable or commercially desirable to use (organic plant production), biological control and/or PGPR agents should be considered a component of an ecologically-based approach to manage these pathogens. Successful completion of the research in this proposed project will help to reduce our reliance on chemical pesticides and increase the sustainability of U.S. agriculture, while providing insight into the pathogen itself.
This group of scientists is not capable of conducting the proposed research project on an individual scientist basis. It requires a multi-state, team approach. Each scientist brings their own expertise and their own individual states perspective to the problems outlined. Within each state is a diversity of crop-growing regions that often bear no similarity to each other, but which are similar to a region in another state. We expand our knowledge of the problems by conducting similar experiments in diverse locations and then closely examining our results at our annual meetings in preparation for publication and outreach to the agricultural community.
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