Many references suggest that an increase in weed, pest and disease pressure in agroecosystems is due to changes in agricultural practices and cropping systems especially rotation, fertilization and application of agrochemicals that contribute to greater intensification (Altieri and Nicholls 2003). Conventional farming tends to rely on synthetic chemicals and some genetically modified crop varieties for pest, disease and weed control, but these are explicitly avoided in organic farming systems, which utilize crop rotation, natural enemies, resistant crop varieties and limited biological intervention (Hani et al. 1998; Lampkin and Measures 1999). Combining these approaches in integrated management strategies aims to: increase crop and animal health and make conditions for pests, diseases and weeds less favourable; enhance the activities of the natural enemies of pests, diseases and weeds including other insects, fungal, bacterial and other living organisms as biological control agents (Lampkin 1999; Speiser et al. 2006). Agronomic practices and the use of organic fertilizers in which nutrient release is gradual, can reduce weed competition and possible damages. A study demonstrated that it should be possible to reduce weed competition by ensuring that the amount of nitrogen in soil before sowing is around 100 kg/ha (Valantin-Morison and Meynard 2008).
Poor soil aeration caused by poor soil structure, soil type or water logging was associated with the development of cavity spot (Pythium spp.) disease in carrot (Hiltunen and White 2002). The pea root rot complex (Fusarium spp.) is known to be affected by compaction, temperature and moisture of the soils. Chang (1994) showed that an increase in soil bulk density due to compaction significantly increased root rot incidence and disease severity, and drastically reduced the fresh weight of pea plants due to the disease. Tillage practices that reduce soil compaction, increase drainage and increase soil temperature have been shown to generally reduce the severity and damage caused by root rot pathogens to many vegetables such as beans (Abawi and Widmer 2000).
Soil microbial biomass may contribute to crop protection in general, and mycor-rhizal organisms to the control of plant root pathogens in particular. Mycorrhizae act in a number of ways such as: improving nutrient acquisition by host plant; competitive exclusion of pathogens at infection sites and within the rhizosphere; inducing anatomical and structural changes in the root thereby creating physical barriers to pathogen entry; production of antagonistic substances against root pathogens and activation of plant defence mechanisms (Sullivan 2001). Agricultural practices can have major short- or long-term impacts on mycorrhizal fungi as well as on other soil micro-organisms. In an experiment examining the effectiveness of mycorrhizal spores from organically and conventionally managed soils in promoting the growth of leek and white clover cultivars, it was shown that white clover only benefited from mycorrhizal infection in a low-fertile organically managed soil. Furthermore, in this study inocula from organic soils were more effective in both achieving mycorrhizal infection and in allowing more efficient P uptake in both crops (Scullion et al. 1998). Intensive farming practices probably reduce the benefits of indigenous mycorrhizal fungi.
Biological control agents, especially plant-pathogenic fungi, offer possible alternatives to chemical pesticides (Ghorbani et al. 2005). By using biocontrol agents instead of chemical pesticides as Speiser et al. (2006) suggested, organic farming substitutes 'agrochemicals' such as pesticides or veterinary drugs with 'organic inputs' such as biocontrol agents. However, crop protection is particularly critical in the early stages of conversion from conventional to organic farming because natural enemies and biocontrol agents are not fully available and need time to reach equilibrium (Lampkin 1999). Biological control methods are accepted as practical, safe, environmentally beneficial management techniques applicable to agroecosys-tems (Charudatan 2001). Mechanisms by which endophytes can act as biocontrol agents include production of antibiotic agents (Lambert et al. 1987; Chen et al. 1993; Sturz et al. 1998, 2000), siderophore production (Kloepper et al. 1980), nutrient competition (Kloepper et al. 1980), niche exclusion (Cook and Baker 1983) and induction of systemic acquired host resistance (Chen et al. 1995).
Since early observations that biodiversity in agricultural systems tended to be associated with less incidence of plant disease and high ecological stability, it has been demonstrated by many scientists that a range of soil micro-organisms actively support plant health (Dehne 1982; Fitter and Garbaye 1994; Azcon-Aguilar and Barea 1996). Soil microbial biomass changes as a consequence of switching from conventional to organic management (Shannon et al. 2002), and therefore plant pathogens in the community will be changed and the absence of synthetic pesticides improves biodiversity and increases occurrence of beneficial organisms (Klingen et al. 2002).
Choice of crop in a rotation with plants less susceptible to specific pathogens causes a decline in population due to natural mortality and the antagonistic activities of co-existent root zone micro-organisms (Fry 1982). Crop rotation may also provide microbial benefits beyond those normally associated with pathogen host range and saprophytic survival (Peters et al. 2003). Rotation is most successful in limiting the impact of biotrophic pathogens that require living host tissues, or those pathogens with low saprophytic survival capability (Bailey and Duczek 1996). However, crop rotation is least successful in reducing diseases caused by pathogens with a wide host range or those that produce long-lived survival structures such as sclerotia or oospores (Umaerus et al. 1989). Legume plant age was also the parameter that most strongly influenced the quality of the legume residues, and consequently its N and P release dynamics, with potentially significant consequences for N and P uptake recovery and losses and, ultimately, cropping system sustainability (Vanlauwe et al. 2008). Seed quality is also a major issue for crop establishment especially in low-input farming systems, where varieties often grow under more stressful conditions than in conventional farming systems. In the absence of organic seeds from varieties bred specifically for organic systems, non-GMO crop genotypes selected for high seed quality in a conventional system will also have high seed quality when grown in a low-input, organic system (Yara et al. 2008).
There is growing interest in using organic amendments and compost extracts not only to improve biological, chemical and physical soil conditions, but also to provide direct and indirect control of crop pests and diseases in tropical, arid and temperate climates (Abbasi et al. 2002; Litterick et al. 2004). Organic farmers routinely use organic fertilizers, composts and additions of rock minerals for these purposes to help ensure acceptable yields of high-quality produce particularly in intensive vegetable production systems (Zhang et al., 1998; Diver et al. 1999; Montemurro et al. 2005; Barker and Bryson 2006; Toor et al. 2006). However, the effects of applications of plant residues and compost to the soil or aqueous extracts to soil and/or crop foliage are very much related to the degree of decomposition of the plant material or compost feedstock (Ghorbani et al 2008b). Matured composts are generally more suppressive although readily available carbon compounds found in low-quality, immature compost suppressed Pythium and Rhizoctonia (Nelson et al. 1994). Beneficial organisms may be used to inoculate composts: for example, strains of Trichoderma and Flavobacterium, added to suppress Rhizoctonia solani in potatoes. Trichoderma harzianum acts against a broad range of soil-borne fungal crop pathogens, including R. solani, by production of anti-fungal exudates (Sullivan 2001). Composts' contribution to nitrogen fertility must also be taken into account as nutrient status may influence the severity of pathogens. Phytophthora die-back of Rhodododendron, Fusarium wilt of cyclamen and fire blight are examples of diseases that increase in severity as a result of excessive nitrogen fertility introduced into container media with composted biosolids (Ceuster and Hoitink 1999). Direct changes in host susceptibility to infection in response to nitrogen supply have also been postulated but are still controversial (Savary et al. 1995). It is known, for example, that fertilization with large amounts of nitrogen increases the susceptibility of pear to fire blight (Erwinia amylovora (Burrill) Winslow), and of wheat to rust (Puccinia graminis Pers.) and powdery mildew (Erysiphe graminis DC. f. sp. tritici Marchal) (Agrios 1997). Sheath blight (R. solani Kuhn) in rice fields increases with increasing N level (Cu et al. 1996). Applications of urea increase the severity of Rhizoctonia blight (Colbach et al. 1996). Growth and disease responses to high levels of NH4-N have been documented with a range of plants and pathogens (Sasseville and Mills 1979; Marti and Mills 1991). In contrast, reduced availability of nitrogen may increase the susceptibility of tomato to Fusarium wilt, of many solanaceous plants to Alternaria solani (Ell. & Mart.) Jones & Grout. early blight and Pseudomonas solanacearum (Smith) Smith wilt; of sugar beets to Sclerotium rolfsii, and of most seedlings to Pythium damping off (Agrios 1997). Similarly ammonium fertilizer can decrease disease levels and infection cycles of take-all (Gaeumannomyces graminis (Sacc) Arx & Olivier var. tritici Walker (Ggt) in wheat (Colbach et al. 1996). Thus, there is a real need to determine the effect of soil nutrient supply on disease development and biocontrol activities of biocontrol agents.
Application of organic matters and all treatments that increase the total micro-bial activity in the soil and increasing competition for nutrients might enhance general suppression of pathogens (Ghorbani et al 2008b), improve plant health and induce disease resistance in many plants (Sullivan 2001). Application of poultry manure showed lower disease incidence, as shown by 80% healthy tomato, compared with the chemical fertilizers (Ghorbani et al 2008a). As the active microbial biomass increases, the capacity to utilize carbon, nutrients and energy in the soil is increased and thus these resources will be very limited for the soil-borne pathogens. In this situation, substantial quantities of soil nutrients are tied up in soil microbial bodies, so that there will be very high competition for nutrients. Organic fertilizers and especially composts act as food sources and shelters for antagonists that compete with plant pathogens; organisms that prey on and parasitize pathogens and beneficial micro-organisms that produce antibiotics (Sullivan 2001). Anyway, as Ceuster and Hoitink (1999) suggested, many aspects of organic amendments must be controlled to obtain consistent results because of their variable nature. The composition of the organic matter from which the organic fertilizer is prepared, the processing method, the stability or maturity of the finished product, the quantity of available plant nutrients provided and time of application all must be carefully considered.
Organic farmers should know the C/N and N/P ratios in organic fertilizer before application of N-P-K in order to formulate an overall pest or disease management strategy. Most high C/N ratio composts (>70:1) immobilize nitrogen and plants grown in such products suffer from chronic nitrogen deficiency resulting in lack of growth and increased susceptibility to pathogens or insects (Ceuster and Hoitink 1999). High C/N ratio tree bark compost may suppress Fusarium wilts, but with lower C/N ratio composts, they may become more severe as a result of the excess nitrogen, which favours Fusarium (Hoitink et al. 1997). The moisture content following the peak heating stage of compost is critical to the range of organisms inhabiting the finished product. Compost with at least 40-50% moisture will be colonized by both bacteria and fungi and will be suppressive for Pythium disease (Hoitink et al. 1997).
Various alternative, non-chemosynthetic treatments have been developed for the direct control and management of plant pathogens, particularly for use in organic systems, but which are also applicable in conventional cropping. These include aqueous extracts of plant material or compost, mineral preparations and also specifically selected microbial populations applied to the soil and/or crop foliage, usually at low dose rates. They may have direct anti-disease effects and/or induce plant resistance or stimulate competitor micro-organisms or otherwise be antagonistic to target plant pathogens (Ghorbani et al. 2006). The components of composts responsible for induced activity may be biological or chemical in nature (Zhang et al. 1998) and nutrient supply may be involved with regard to effects of organic manures on plant pests.
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