AGP - Soil biological management with beneficial microorganisms

Successful soil biological management with beneficial microorganisms

Soil microorganisms are the most abundant of all the biota in soil and responsible for driving nutrient and organic matter cycling, soil fertility, soil restoration, plant health and ecosystem primary production. Beneficial microorganisms include those that create symbiotic associations with plant roots (rhizobia, mycorrhizal fungi, actinomycetes, diazotrophic bacteria), promote nutrient mineralization and availability, produce plant growth hormones, and are antagonists of plant pests, parasites or diseases (biocontrol agents). Many of these organisms are already naturally present in the soil, although in some situations it may be beneficial to increase their populations by either inoculation or by applying various agricultural management techniques that enhance their abundance and activity.

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a) Mycorrhizae. More than 90% of the world’s plants are mycorrhizal, with varying degrees of dependence and benefits derived from this association. The most well known and perhaps the most common mycorrhizal symbioses involve arbuscular mycorrhizae (many crop species) and ectomycorrhizae (only woody species; mostly tree and shrub species), although several other types (e.g., Ericaceous, Orchidaceous, Ectendo-mycorrhizae) also exist (Allen et al., 1995). The positive role of mycorrhizae in plant production is well documented, with many cases of growth and yield enhancement, particularly in highly dependent, susceptible plants. The plant response can be due to various reasons, although in most cases it is due to an increase in effective root area for water and nutrient extraction, since the mycorrhizal hyphal network works as a natural extension of the plant root system. The plant donates C to the mycorrhizae in exchange for a greater ability to use native soil resources. Other benefits of the mycorrhizal association are an enhanced protection against pathogens, improved tolerance to pollutants and greater resistence to water stress, high soil temperature, adverse soil pH and transplant ‘shock.’ The wide-spread use of mycorrhizal inoculants in agroecosystems has been hampered, however, by the difficulty in cultivating arbuscular mycorrhizae and producing sufficient inocula at affodable prices. It appears that the most practical current uses of mycorrhizae involve land restoration and reclamation efforts, and arbuscular and ecto-mycorrhizal inoculation of tree and crop seedlings in nurseries. Nonetheless, enhancement of naturally-occuring mycorrhizal populations in agricultural fields (and their potential benefits to the growing crops) is feasible and important benefits can arrise through the adoption of various management practices that enhace mycorrhizal populations and activity such as reduced tillage, crop rotations and lower N and P applications (Abbott and Robson, 1994).

Case study B1. Cropping sequence management and "in situ" production of arbuscular mycorrhiza inoculo (Thompson, 1991, Montanez, 2000)

The objective of all practical methods for management of arbucular mycorrhiza fungi population is to optimize the symbiosis for better crop production. Two main concepts are available to manage AMF populations:

  1. Crop inoculation with selected effective AMF
  2. Crop species are selected for the existing AMF population, making an efficient use of it.

Because plant host can be selective in the reproduction of certain AMF species, cropping sequence may influence the species composition of AMF communities. It is critical to consider how AMF that proliferate within a particular cropping system, might affect crop production. The use a suitable host to increase the infectivity of the soil, prior to the sowing of the main crop, is a potential management practice, which could be an alternative to inoculation.

Figure 1. Dry weight of linseed varied with prior crop and was related to soil densities of AMF spores (modified from Thompson, 1991).

Soil inoculum potential of AMF was increased almost twice after plantation of soybean and reduced to zero after plantation of rape in a microcosm experiment conducted at Reading University (Montanez, 2000). Although, in field trials with linseed (Thompson, 1991) pre-cropping with legumes or sunflowers generated the highest densities of residual AMF spores and resulted in the highest dry weights of linseed (Figure 1).

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b) Rhizobia. The role of the six genera of the Rhizobiaceae bacterial family in agricultural production has also been well documented, with many cases of yield increases with inoculation (Table).

The rhizobia infect plant roots, creating nodules where N2 is fixed, providing the plant with most of the N it needs for its development. Well noduled plants with an efficient symbiosis may fix up to several hundred ha-1 of N year-1. Some of this N is added to the soil during plant growth by ‘leaky’ roots, though most remains in plant tissues and is released during decomposition, to the benefit of the following crops or the intercrop.

Previous colonization of the legume roots by mycorrhizae may greatly enhance nodulation by rhizobia, ultimately increasing the potential growth benefits. However, despite the obvious benefits of rhizobial inoculation or management, there are several factors that continue to limit the wide-spread use of this technique to enhance legume yields: use of N fertilizers, lack of incentives to grow legumes, environmental constraints (particularly edaphic; e.g., low P-status), difficulty in producing inocula and its consequent low availability, low genetic compatibility of the host legume with the bacteria (low effectiveness), and lack of appropriate political and economic incentives and infra-structure (Giller et al., 1994; Hungria et al., 1999).

Case study B2. Overview and case studies on biological nitrogen fixation: perspectives and limitations. (Montañez A., 2000)

There are several methods available to enhance nitrogen fixation:

  1. host plant selection (breeding legumes for enhanced nitrogen fixation)
  2. selection of effective strains able to fix more nitrogen
  3. use of different agronomic methods that improve soil conditions for plant and microbial symbiont
  4. inoculation methods

No one approach is better than the others, combining experience from various disciplines in inter-disciplinary research programmes should be pursued.

Several examples are illustrated in this case study showing how different strategies can success, depending on environmental, social and economical conditions.

Complete case study (PDF, 77KB)

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c) Other N2 fixing symbiotic biota. Additional symbiotic N2 fixing relationships of plants with microbes include actinomycete (Frankia) relationships with mostly trees and shrubs (and also some crops such as sorghum), and symbiosis between endophytic diazotrophic bacteria (e.g., Azotobacter, Azospirillum, Acetobacter, Azoarcus, Burkholderia, Herbaspirillum) and grasses (Baldani et al., 1999). The Frankia symbiosis is generally exploited in land reclamation and restoration efforts using principally Casuarinales trees to hold soil (e.g., sand dunes) in place but its potential is still underutilized and further efforts on its development and applications are needed. On the other hand, research on and use of endophytic bacteria have been well developed in tropical regions, particularly Brazil and Mexico. These bacteria not only fix N2 but also modify the shape and increase the number of root hairs, helping the plants to acquire more nutrients. The application of these organisms in inoculants continues to be performed on a wide-scale (mostly in maize, some in rice, wheat, sugar-cane and rice), and yield increases ranging from negligible up to almost 100% have resulted, depending on the crop and bacteria used (Baldani et al., 1999).

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d) Other Plant Growth Promoting Bacteria. Various other beneficial rhizosphere organisms entitled plant growth promoting bacteria (PGPB) have been used, mostly as seed inoculants. PGPB affect plant growth through direct growth promotion (hormonal effects), induced systemic resistence, mineralization, substrate competition, niche exclusion, detoxification of surrounding soil and production of antibiotics, chitinases, cyanide and siderophores (Mahaffee and Kloepper, 1994). Several bacterial species and genera have been used as plant growth promoters, including pseudomonads (e.g., Pseudomonas fluorescens, P. putida, P. gladioli), bacili (e.g., Bacilus subtilis, B. cereus, B. circulans) and others (e.g., Serratia marcescens, Flavobacterium spp., Alcaligenes sp., Agrobacterium radiobacter) (Mahaffee and Kloepper, 1994). Of these, probably the most successful have been Agrobacterium radiobacter, used to control crown gall on several plant families, Bacilus subtilus to suppress Rhizoctonia solani infection (cereal root rots) and various inoculants (mostly Bacilus-based) termed YIB (yield improving bacteria), used widely throughout China on vegetable crops (Chen et al., 1993). Probably the main limitation to more widespread use of these techniques is the poor understanding of the interactions between PGPB and the host plant and the indigenous soil microflora. Improved understanding of these phenomena will permit a more accurate prediction of the effects of inoculation and its potential benefits.

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e) Biocontrol fungi. Fungal agents have been used extensively for biocontrol of both plant fungal diseases and insect pests. Various non pathogenic (saprophytic) strains of Rhizoctonia, Fusarium, Trichoderma spp. have been used to reduce damage (root rots, wilts, damping off and bare patches) caused by their pathogenic ‘cousins’ and other pathogenic fungi (e.g., Pythium, Sclerotium, Verticillium) (Cook, 1994; Miller, 1990). The fungi Metarrhizium anisopliae, has been successfully used to kill larvae of the grass grubs (scarab beetle) in pastures (Rath, 1992), and several genera of nematode-trapping or nematophagous fungi (e.g., Arthrobotrys, Nematophthora, Dactylella, Verticillium) have shown potential for plant parasitic nematode control, although the level of control is much lower than that which is obtained by use of nematicides (Kerry, 1980; Mankau, 1980; Zunke and Perry, 1997).

However, even though some of these antagonists show excellent potential for wider use (particularly Trichoderma), they continue to be greatly underutilized, primarily due to strict regulations regarding their use and the technical difficulties associated with introducing and maintaning a specific strain of fungi in the soil. Some technical problems to be overcome are: the identification of the factors affecting their survival rates in soils, the best strain for each crop and field conditions, the best methods of field application, the best formulation for delivery, the most appropriate farm management practices to enhance biocontrol, and the education of farmers on the use of the technology (Cook, 1994). Besides the direct method of inoculation, indirect methods of disease and pest control using various agricultural practices that are preventive or antagonistic to the organisms (e.g., soil solarization, crop rotation, use of genetically resistant varieties, organic matter and fertilizer applications, reduced- or no-tillage, natural pesticides and prophylactic control or prevention of disease introduction) are also successful, and can be more easily implemented to promote a integrated soil health management (Rovira et al., 1990; Cook, 1989; Neate, 1994).

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f) Biocontrol nematodes. Entomopathogenic nematodes of the Deladenus, Neoaplectana, Tetradonema, Steinernema and Heterorhabditis genera have been successfully used to control a wide range of insect pests causing damage in horticultural, food cropping, natural and plantation forests: white grubs (scarab beetle larvae), weevils (curculionid beetles), termites, ants, mole crickets, armyworms, fruit flies, sciarid flies, potato, cucumber and flea beetles, locusts, turnip moths, woodwasps and rootworms (Webster, 1980; Klein, 1990). The success of these nematodes lies in the fact that most (up to >90%) of the insect pests spend at least a part of their life cycle in contact with the soil, where they will also meet the biocontrol nematodes, that are not only naturally present, but also have a broad host range and the ability to seek out their host and kill it rapidly. Futhermore, they can be easily mass produced and are environmentally safe. Regarding the role of fungus-feeding nematodes in controlling plant pathogenic fungi we know very little, but can deduce that they may be potentially important. Only a few trials of mass introduction have been performed in the greenhouse, but the results seem promising, with effective control of several root-infecting fungi such as Rhizoctonia, Pythium, Armillaria and Fusarium (Curl and Harper, 1990). Further work, particularly in the field are needed to confirm these results and this potential means of disease biocontrol.

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g) Suppressive soils. Soils or areas in the field and agroecosystem that show greater relative resistance to disease expression in plants (despite the presence of the pathogen, susceptible host plant and favorable climatic conditions) have been termed ‘suppressive soils’ (Alabouvette, 1999). Every soil has a potential for disease suppression and furthermore, agricultural management practices can be enhanced to promote naturally-occurring disease suppressing activities. Most suppressive soils appear to have neutral to alkaline pH values (pH>7), and liming of acid, disease prone soils may effectively reduce severity of some fungal pathogens such as wilts (Alabouvette, 1999). The other strategy for increasing soil suppressiveness involves the process of isolating and selecting efficient antagonistic microorganisms for field inoculation.

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