Encyclopedia
Please note this is a comparison between Version 1 by Estibaliz Sansinenea and Version 2 by Jason Zhu.
The practice of agriculture has always been a source of food production. The increase in the global population leads to improvements in agriculture, increasing crop quality and yield. Plant growth results from the interaction between roots and their environment, which is the soil or planting medium that provides structural support as well as water and nutrients to the plant. Therefore, good soil management is necessary to prevent problems that will directly affect plant health. Integrated crop management is a pragmatic approach to crop production, which includes integrated pest management focusing on crop protection. Currently, there is an extended idea that many microorganisms, such as fungi or bacteria, are useful in agriculture since they are attractive eco-friendly alternatives to mineral fertilizers and chemical pesticides. The microbes that interact with the plants supply nutrients to crops, control phytopathogens and stimulate plant growth. These actions have beneficial implications in agriculture. Despite the great benefits of microorganisms in agriculture, their use has been quite limited; however, there has been great growth in recent years. This may be because more progress is needed in field applications. One of the most employed genera in agriculture is Bacillus since it has several mechanisms to act as biofertilizers and biopesticides.
- agricultural sustainability
- biofertilizers
- crop protection
- Bacillus sp.
1. Relation between Soil and Plant Health
To develop and apply biofertilizers, before understanding their mechanism of action, it is necessary to first understand the interaction of plants roots with the surrounding environment, which is the soil or planting medium. The soil is formed by solid mineral particles such as sand, silt and clay size, water, air, and organic matter. The soil water, with carbon dioxide’s help, dissolves the mineral particles very slowly and releases nutrients, making them available for the plants. The plants and soil organisms facilitate the cycling of organic matter and nutrients, which allows soil to continue supporting life. Therefore, the soil’s health is key to agricultural sustainability [1][11]. Soil health supports the growth of high-yielding, high-quality, and healthy crops. Scientists use the term soil quality to refer to soil health and define it as the fitness of a specific soil to sustain plant and animal productivity [2][12].
When the soil is healthy the yield of the crops is high, mainly because the roots are able to proliferate easily, there is enough water entering and stored in the soil, there is a sufficient nutrient supply, there are no harmful chemicals in the soil, and beneficial organisms are very active and able to keep potentially harmful ones under control and stimulate plant growth. Healthy soil should have enough nutrients and a good soil structure for the development of plant roots. The soil needs to be well drained and have good aeration. Moreover, the soil should not have pests that can be aggressive to the plants provoking plant diseases and crop losses [3][13].
However, there are several problems associated with soil health such as soil erosion, soil organic matter loss, nutrient imbalance, soil acidification, soil contamination, waterlogging, soil compaction, soil sealing, salinization, and loss of soil biodiversity. There is a relationship between some soil properties. Therefore, when a problem is detected, some properties can be affected. For example, in compacted soils, the pores or spaces are lost, making it difficult or impossible for some of the larger soil organisms to move or even survive.
The soil’s health can be degraded by several agricultural practices, such as tillage [4][14]. This practice breaks down soil aggregates, losing soil organic matter and accelerating erosion. Moreover, when the soil is compacted, it is harder for water to infiltrate, and the roots do not develop properly, causing accelerated erosion and poor crop production. The salinity of soils under irrigation in arid regions is another cause of reduced soil health [5][15]. Irrigation water contains mineral salts, which can reduce water infiltration in soils [6][16].
To achieve good crop yields, several soil-management practices have been applied to grow healthy plants with strong defense capabilities, to suppress pests, and to enhance beneficial organisms. For years, fertilizers and pesticides have been used for agricultural development. Fertilizers are used to supplement the nutrients of the soil and pesticides to diminish the pests and damage caused to plants. Therefore, both are considered crucial elements in agriculture since they increase the fertility of soil and crop productivity [7][17]. However, contradictorily, they also impact the health and environment because they change the soil’s physical properties, disrupt the ecological balance of soil microflora and environment, and disturb many activities of soil. Therefore, these practices have led to poor-quality soil impacting the food security and livelihood supporting systems. Due to chemical fertilizers and pesticides, there are severe signs in and rainfed and irrigated farming areas [8][9][18,19] such as soil erosion, soil organic matter loss, nutrient imbalance.
2. Microorganisms as Biofertilizers
Due to the above-mentioned issues related to chemical fertilizers and pesticides, there has been an important development toward sustainable agriculture using more ecological and clean methods, such as the employment of biopesticides and biofertilizers. Biofertilizers can be inoculated on seeds as well as in the roots of different crop plants under ideal conditions, and they can also be applied directly to the soil [10][20]. Biofertilizer is a substance that contains living microorganisms, which, when applied to seed, plant surfaces, or soil, mobilizes the availability of nutrients particularly by their biological activity, and promotes plant growth [11][3]. Biofertilizers add nutrients through the natural processes of fixing atmospheric nitrogen, solubilizing phosphorus, and stimulating plant growth through the synthesis of growth-promoting substances [12][13][21,22]. They can be grouped in different ways based on their nature and function.
In this sense, the microorganisms, when applied to the soil or to the plant, that help increase the availability of nutrients to crop plants are known as biofertilizers, which are eco-friendly and cheap alternatives to chemical fertilizers [14][23]. There are different microorganisms that utilize several strategies such as fixing/solubilizing/mobilizing/recycling nutrients in the agricultural ecosystem to be beneficial for the crops, improving plant growth and productivity [15][24].
The plant rhizosphere, the narrow zone of soil surrounding the root system of growing plants, is colonized by a wide range of microbial taxa, out of which bacteria and fungi comprise the most abundant groups [16][25]. Free-living soil bacteria that thrive in the rhizosphere, colonize plant roots, and facilitate plant growth are designated as plant-growth-promoting rhizobacteria that produce and secrete various regulatory chemicals in the plant roots’ vicinity helping in plant growth promotion [17][18][26,27].
Bacteria and fungi that inhabit the rhizosphere can function as biofertilizers that promote plants’ growth and development by facilitating biotic and abiotic stress tolerance and supporting host plants’ nutrition. They can function as biopesticides too since many of the microorganisms kill insects and other pests that threaten crops. Moreover, microorganisms have the ability to degrade and detoxify harmful organic as well as inorganic compounds that accumulate in the soil as contaminating substances, which are the result of many activities, including agriculture practices. They exert the bioremediation action benefiting soil and plant health [19][28].
Bacterial biofertilizers are a group of bacteria that help in fixing different nutrients needed for plant growth in the soil [20][29]. They can fix nitrogen, solubilize phosphorus and potassium or other micronutrients, and secrete organic compounds to suppress plant pathogens or growth-enhancing substances to support plant growth. Examples of the most popular bacterial biofertilizers that have been applied are Azotobacter, Azospirillum, Rhizobium, and Bacillus, among others[21][22][30,31]. Rhizobium is used for legume crops and Azotobacter and Azospirillum for non-legume crops. Acetobacter is more specific for sugarcane [23][2]. Using these bacteria as biofertilizers for promoting plant growth and crop yield, improving soil fertility, and biocontrolling phytopathogens promotes sustainable agriculture by offering eco-friendly alternatives to synthetic agrochemicals, such as chemical fertilizers and pesticides.
The fungal biofertilizers form a symbiotic relationship within the plant roots. Such a relationship is called mycorrhiza, which allows the release and absorption of nutrients, especially phosphorus. Some nutrients cannot diffuse easily into the soil, and the roots deplete these nutrients from the surrounding zone. Arbuscular mycorrhiza are soil beneficial fungi that form a symbiotic relationship with plants and many agricultural crops through the roots of vascular plants [24][32]. The hyphae of these fungi extend into the depletion zone, which increases the absorption surface of plants and improves access to the nutrients [25][33]. The symbiosis of arbuscular mycorrhiza fungi improves the plant rhizosphere microenvironment, increases the absorption of mineral elements by the plant, improves stress and disease resistance, and promotes plant growth [26][34].
The application of microbial biofertilizers has several advantages, as mentioned above, such as their easy use and low cost and their beneficial effects on soil and plants. However, they have some challenges that have hindered their extensive and successful use. Firstly, an initial good laboratory screening is needed for the search of a good and specific biofertilizer strain. In addition, manufacturing and quality control of biofertilizers involve sophisticated technology and qualified and trained human resources, together with lack of enough financial resources to distribute and the unavailability of proper transportation services along with storage facilities, make it a complicated process from the beginning to the end. It should be highlighted among the main issues that can be found, including the poor quality of products, the use of unsuitable strains, the short shelf life, the lack of technical qualified personnel, the lack of awareness among farmers, environmental limitations, etc. [27][35]. Microbial strains should be able to survive in soil, be compatible with the crop on which they are inoculated, and interact with indigenous microflora in soil and abiotic factors to be efficient and successful bioinoculants.
3. Bacillus spp. Beneficial for Plants
The genus Bacillus has several species and strains that have been used as biofertilizers, biopesticides, and important biotechnological tools. These bacteria can suppress pathogens and at the same time promote plant growth using different direct and indirect mechanisms, which can cat simultaneously during plant growth. The direct mechanisms include their ability to obtain nutrient supply such as nitrogen, phosphorus, potassium, and minerals and modulate plant hormone levels. The indirect mechanisms include the secretion of antagonistic substances to inhibit plant pathogens or the induction of resistance to pathogens [28][36]. Therefore, Bacillus strains are effective as biocontrol agents on plant tissues to prevent pathogen colonization by antibiosis towards pathogens and by the induction of systemic resistance in the host plant.
There are several Bacillus species that can fix atmospheric nitrogen, which has been probed by the presence of the nifH gene or through the experiment on nitrogenase activity [29][37]. Phosphorus is an important nutrient for soil health and plant growth, but it is scarce in soil in its inorganic form, which is the form absorbed by the plants. However, Bacillus can solubilize in its unavailable form of phosphorus to available phosphorus probably associated with the release of low-molecular-weight organic acids, such as succinic acid, that help to solubilize the fixed phosphorus into an exchangeable form [30][38]. Different species of Bacillus can also produce siderophores, which bind iron and zinc, increasing the availability of soluble metals in the soil and helping plants in the acquisition of iron and zinc [31][39].
Moreover, several species of Bacillus are able to secrete phytohormones, such as auxins, gibberellins, cytokinins, and abscisic acid, which play different roles in affecting plant cell enlargement and division and enlargement of roots [32][40]. Several genes have been identified participating in IAA biosynthetic pathways in Bacillus, observing an increase in root growth of several crops, such as potato [33][34][41,42]. Cytokinins and gibberellins are also produced by several strains of Bacillus and are involved in plant growth promotion [32][40]. Abscisic acid is involved in plant responses of tolerance to abiotic stresses (drought, chilling, heat, salinity, etc.) and in the dormancy process, which is present in several Bacillus species [32][40]. Three phytohormones, which are involved directly in defense responses to biotic stresses, such as salicylic acid, mainly against biotrophic pathogens, and jasmonic acid and ethylene, mainly against necrotrophic pathogens and pests, have been reported in different Bacillus species [35][43].
The importance of soil health for plant development and the role of the microorganisms, such as Bacillus, as biofertilizers has been mentioned before. However, there is another problem related to the crops. Several fungi and insects act as parasites for different types of plants, destroying important crops. The genus of Bacillus sp. has extraordinary machinery to secrete several secondary metabolites, lytic enzymes, and toxins against the phytopathogens, which cause plant diseases, promoting plant growth [11][3]. The control of fungal diseases by Bacillus-based biopesticides represents an interesting opportunity for agricultural biotechnology since these microorganisms improve soil quality, soil health, and the growth, yield, as well as quality of crops. There are several Bacillus-based biopesticides that have been commercialized.
Antagonistic metabolites that Bacillus secrete include lipopeptide surfactants, such as surfactin, fengycin, and iturin families, which are potent biofungicides and have been applied in several crops against fungal plant pathogens, such as Botrytis cinerea, Magnaporthe oryzae, Fusarium graminearum, Fusarium oxysporum, among others [36][44]. Bacillus spp. also secrete several lytic enzymes, such as chitinases, β-1,3-glucanases, β-glucosidase, lipases, and proteases, which have the ability to degrade the components of the fungal cell wall, such as chitin, β-glucans, and proteins. However, the antagonistic activity of enzymes can rely on quorum quenching, which interferes with quorum-sensing molecules used by several pathogens. This is the case of lactonase enzymes, which have been found in several Bacillus and which interfere with N-acyl-L-homoserine lactones, well-known quorum-sensing molecules. Moreover, Bacillus strains have a wide arsenal of chemical compounds with antifungal and antibacterial activity against different phytopathogens, such as macrolactins or bacteriocins. A recent study suggested that B. amyloliquefaciens L-1 was a good biocontrol agent against pear ring rot [37][45]. Bacillus species can produce some metabolites, molecules, or chemical compounds inducing systemic resistance, which is an immune response expressed in all plant organs [38][46].
As mentioned before, the Bacillus genus is a great factory that produces several chemical compounds with different activities that benefit the health of the crops. However, there are some factors affecting the production of these secondary metabolites, which can be important to better understand the real impact of these compounds on crops and agriculture. Abiotic factors, such as temperature, pH, and oxygen availability, have been the most studied, which influence the production of several metabolites in plant-associated microbes [36][44]. Biotic factors are also very important. For rhizosphere establishment, root exudates are essential, which provide nutrients for the plant-associated bacteria. Additionally, in this complex ecosystem of the rhizosphere, Bacillus has to compete with other microorganisms secreting several metabolites to fight against fungal and bacterial competitors [36][44].
It is mandatory to highlight the extended use of B. thuringiensis as a biopesticide worldwide. This bacterium secretes, along with spores, specific insecticidal proteins called Cry proteins, which are toxic against different insect orders, including some pests that attack important crops causing economic losses. These insecticidal delta-endotoxins are applied on the plant leaves or mixed with the soil and are specifically toxic against lepidopteran, coleopteran, or dipteran insects, as well as nematodes, depending on the type of Cry toxin secreted by each subspecies. Upon ingesting, the toxins are solubilized by the alkaline conditions in the insect midgut and are subsequently proteolytically converted into a toxic core fragment, which binds to the receptors of the apical microvillus membranes of epithelial midgut cells [39][48]. Then, the toxins’ conformation changes and gets inserted into the cell membrane and forms pores, which leads to an osmotic imbalance until the cell rupture. This leads to the loss of midgut epithelium integrity, resulting in insect death caused by bacteremia and tissue colonization [39][48]. For this reason, many commercial products of B. thuringiensis bioinsecticides have been available in the market [40][49].
