Agricultural microbiology

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Agricultural microbiology is a branch of microbiology dealing with plant-associated microbes and plant and animal diseases. It also deals with the microbiology of soil fertility, such as microbial degradation of organic matter and soil nutrient transformations. The primary goal of agricultural microbiology is to comprehensively explore the interactions between beneficial microorganisms like bacteria and fungi with crops. [1] It also deals with the microbiology of soil fertility, such as microbial degradation of organic matter and soil nutrient transformations.

Contents

Soil microorganisms

Importance of soil microorganisms

Microorganisms as biofertilizers

Biofertilizers are seen as promising, sustainable alternatives to harmful chemical fertilizers due to their ability to increase yield and soil fertility through enhancing crop immunity and development. When applied to the soil, plant, or seed these biofertilizers colonize the rhizosphere or interior of the plant root. Once the microbial community is established, these microorganisms can help to solubilize and break down essential nutrients in the environment which would otherwise be unavailable or difficult for the crop to incorporate into biomass. [2]

Nitrogen

Nitrogen is an essential element needed for the creation of biomass and is usually seen as a limiting nutrient in agricultural systems. Though abundant in the atmosphere, the atmospheric form of nitrogen cannot be utilized by plants and must be transformed into a form that can be taken up directly by the plants; this problem is solved by biological nitrogen fixers. Nitrogen fixing bacteria, also known as diazotrophs, can be broken down into three groups: free-living (ex. Azotobacter , Anabaena, and Clostridium) , symbiotic (ex. Rhizobium and Trichodesmium) and associative symbiotic (ex. Azospirillum ). [3] These organisms have the ability to fix atmospheric nitrogen to bioavailable forms that can be taken up by plants and incorporated into biomass. An important nitrogen fixing symbiosis is that between Rhizobium and leguminous plants. [4] Rhizobium have been shown to contribute upwards of 300 kg N/ha/year in different leguminous plants, and their application to agricultural crops has been shown to increase crop height, seed germination, and nitrogen content within the plant. [5] The use of nitrogen fixing bacteria in agriculture could help reduce the reliance on man-made nitrogen fertilizers that are synthesized via the Haber-Bosch process.

Phosphorus

Phosphorus can be made available to plants via solubilization or mobilization by bacteria or fungi. Under most soil conditions, phosphorus is the least mobile nutrient in the environment and therefore must be converted to solubilized forms in order to be available for plant uptake. Phosphate solubilization is the process by which organic acids are secreted into the environment, this lowers the pH and dissolves phosphate bonds therefore leaving the phosphate solubilized. Phosphate-solubilizing bacteria (PBS) (ex. Bacillus subtilis and Bacillus circulans) are responsible for upwards of 50% of microbial phosphate solubilization. In addition to the solubilized phosphate, PBS can also provide trace elements such as iron and zinc which further enhance plant growth. Fungi (ex. Aspergillus awamori and Penicillium spp.) also perform this process, however their contribution is less than 1% of all activity. [6] [7] A 2019 study showed that when crops were inoculated with Aspergillus niger , there was a significant increase fruit size and yield compared with non-inoculated crops; when the crop was co-inoculated with A. niger and the nitrogen fixing bacteria Azobacter , the crop performance was better than with inoculation using only one of the biofertilizer and the crops that were not inoculated at all. [8] Phosphorus mobilization is the process of transferring phosphorus to the root from the soil; this process is carried out via mycorrhiza (ex. Arbuscular mycorrhiza) . [9] Arbuscular mycorrhiza mobilize phosphate by penetrating and increasing the surface area of the roots which helps to mobilize phosphorus into the plant. Phosphate solubilizing and mobilizing microorganisms can contribute upwards of 30–50 kg P2O5/ha which, in turn, has the potential to increase crop yield by 10–20%. [10]

Example

Microbiology in Sustainable Agriculture

Effective Microorganisms

Effective microorganisms (EM) are essential to the development of sustainable agriculture and consist of a diverse, mixed culture of microorganisms that is naturally occurring in nature. Biopreparations containing effective microorganisms play a crucial role across various sectors, such as environmental protection, food production, and medicine. Furthermore, this application of effective microorganism biotechnology spans a range of agricultural areas, including soil rejuvenation, crop cultivation, livestock farming, and food preservation. These biopreparations prove particularly beneficial for land preparation and field preparation. Effective microorganisms can be applied to crops during the growing season or directly to the soil during preparation, enhancing both soil health and promoting plant growth. The broad utility of effective microorganisms stems from their high enzymatic specificity, allowing them to thrive in various conditions. Moreover, effective microorganism technology is now utilized in more than 140 countries worldwide, with Brazil being the leading adopter. The widespread usage of effective microorganisms displays the power to enhance the agricultural industry and environmentally sustainable farming. [11]

Effective Microorganisms in Sustainable Agriculture

Conventional farming methods use chemical fertilizers, pesticides, and herbicides to safeguard crops from pests and diseases. However, these chemical agents have adverse environmental impacts, contributing to environmental pollution. The use of agricultural chemicals has been linked to the decline of plant and animal species, as well as harm to soil biodiversity, including bacterial and fungal communities. [12] [13] Chemical plant protection products can alter agricultural soils by affecting their physical properties such as texture, permeability, and porosity. Additionally, these products disrupt the nutrient cycles of phosphorus and nitrogen and reduce the diversity of the soil microbiome. Given the challenges posed by a growing global population and the need for more and higher-quality food, the future of agriculture lies in using effective microorganisms to boost yields. This approach offers a sustainable alternative to traditional chemical methods, fostering environmental health and agricultural resilience. [14]

Successful crop production hinges on the health of the soil, which is influenced by a network of biological, chemical, and physical processes driven by microorganisms. Effective microorganisms enhance the soil's beneficial microbial community, paving the way for sustainable agriculture. These microorganisms consist of naturally occurring microbes, such as photosynthesizing bacteria, lactic acid bacteria, yeasts, and fermenting fungi, which can be applied to increase soil microbial diversity. The application of effective microorganisms improves soil structure and fertility while significantly boosting biological diversity. They can inhibit the proliferation of soil-borne pathogens, assist in nitrogen fixation, and enhance plant nutrient uptake. Effective microorganisms also accelerate the decomposition of organic waste, which promotes composting and, therefore, increases the availability of valuable minerals and bolsters the activities of indigenous microbes. By dominating the soil's microbial environment, effective microorganisms encourage other beneficial microbes to thrive and outcompete smaller groups of pathogenic or opportunistic microbes. This natural balancing act leads to stronger, more resilient plants and higher crop yields, positioning effective microorganisms as a key player in the future of sustainable agriculture. [1]

Factors Affecting Microorganisms in Agricultural Systems

Human Impacts

Organic farming methods, which are methods meant to sustain ecosystem health by limiting the use of external inputs like synthetic fertilizers and focusing on natural inputs, [15] can have an effect of increasing the number of microbes in a system and increasing their ability to utilize carbon and nitrogen-based molecules. [16] A method of maintaining ecosystem function in agricultural soils is using crop rotations, where increases in the number of crops used for a crop rotation in farming systems has also been shown to have the effect of increasing microbial diversity and the number of microbial species present. [17] Relatedly, increases in microbial diversity have been shown to have beneficial effects on the health of plants and soils. [18]

There are also agricultural practices that have negative impacts on microorganisms in agricultural systems. Another common farming practice, tillage, can have the immediate effect of decreasing carbon and nitrogen originating from microbial biomass. [12] Conversely, no-till practices have been shown to be able to increase soil health, increase microbial growth, and increase microbial community functionality. [12] However, the negative impacts of tillage are dependent on the intensity of tillage, and the microbial community has been shown to be able to recover over time. [12] To limit the effects of insect behavior on crop growth and health, a common practice is the use of pesticides. These pesticides in turn affect soil microbes in ways such as altering the composition of the microbial community in soils for months after exposure. [13] A type of pesticide, fungicides, have also been shown to have negative effects on microbes not being targeted by the chemical as well as causing changes in the community of microbes living associated with host plant roots. [12]

Environmental Impacts

Climatic changes present themselves in many different ways, and these changes can also impact the microbial members of agricultural soils. Increasing temperatures have been shown to have an effect of limiting plant root growth and thereby reducing the ability of arbuscular mycorrhizal fungi (AMF) to grow associated with these roots. [19] Changing temperatures can have the effect of increasing the abundance and ability of plant pathogens to produce negative impacts in agricultural ecosystems. [20] Increased levels of carbon dioxide (CO2), modify the interactions between plants and pathogens and can lead to changes in what plant pathogens are present and how they are able to negatively impact plants. [20] However, there currently is a lack of information about how to predict how elevated levels of CO2 can change the interactions between plants and potential pathogens across many different plant-pathogen relationships. [20]

There is currently a push to understand the role microbes in soils, including agricultural soils, play in limiting the negative impacts of climate change. For example, soil microbes are able to convert methane into carbon dioxide, thereby modulating greenhouse gas emissions. [21] They also have a wide range of effects on agriculture including conversion of carbon dioxide into usable forms of carbon for plants, releasing chemicals to increase the ability of plants to uptake and store water, and protecting plants from drought. [21]

See also

Related Research Articles

<span class="mw-page-title-main">Compost</span> Mixture used to improve soil fertility

Compost is a mixture of ingredients used as plant fertilizer and to improve soil's physical, chemical, and biological properties. It is commonly prepared by decomposing plant and food waste, recycling organic materials, and manure. The resulting mixture is rich in plant nutrients and beneficial organisms, such as bacteria, protozoa, nematodes, and fungi. Compost improves soil fertility in gardens, landscaping, horticulture, urban agriculture, and organic farming, reducing dependency on commercial chemical fertilizers. The benefits of compost include providing nutrients to crops as fertilizer, acting as a soil conditioner, increasing the humus or humic acid contents of the soil, and introducing beneficial microbes that help to suppress pathogens in the soil and reduce soil-borne diseases.

<span class="mw-page-title-main">Crop rotation</span> Agricultural practice of changing crops

Crop rotation is the practice of growing a series of different types of crops in the same area across a sequence of growing seasons. This practice reduces the reliance of crops on one set of nutrients, pest and weed pressure, along with the probability of developing resistant pests and weeds.

<span class="mw-page-title-main">Sustainable agriculture</span> Farming approach that balances environmental, economic and social factors in the long term

Sustainable agriculture is farming in sustainable ways meeting society's present food and textile needs, without compromising the ability for current or future generations to meet their needs. It can be based on an understanding of ecosystem services. There are many methods to increase the sustainability of agriculture. When developing agriculture within sustainable food systems, it is important to develop flexible business processes and farming practices. Agriculture has an enormous environmental footprint, playing a significant role in causing climate change, water scarcity, water pollution, land degradation, deforestation and other processes; it is simultaneously causing environmental changes and being impacted by these changes. Sustainable agriculture consists of environment friendly methods of farming that allow the production of crops or livestock without causing damage to human or natural systems. It involves preventing adverse effects on soil, water, biodiversity, and surrounding or downstream resources, as well as to those working or living on the farm or in neighboring areas. Elements of sustainable agriculture can include permaculture, agroforestry, mixed farming, multiple cropping, and crop rotation.

<span class="mw-page-title-main">Green manure</span> Organic material left on an agricultural field to be used as a mulch or soil amendment

In agriculture, a green manure is a crop specifically cultivated to be incorporated into the soil while still green. Typically, the green manure's biomass is incorporated with a plow or disk, as is often done with (brown) manure. The primary goal is to add organic matter to the soil for its benefits. Green manuring is often used with legume crops to add nitrogen to the soil for following crops, especially in organic farming, but is also used in conventional farming.

<span class="mw-page-title-main">Organic fertilizer</span> Fertilizer developed from natural processes

Organic fertilizers are fertilizers that are naturally produced. Fertilizers are materials that can be added to soil or plants, in order to provide nutrients and sustain growth. Typical organic fertilizers include all animal waste including meat processing waste, manure, slurry, and guano; plus plant based fertilizers such as compost; and biosolids. Inorganic "organic fertilizers" include minerals and ash. Organic refers to the Principles of Organic Agriculture, which determines whether a fertilizer can be used for commercial organic agriculture, not whether the fertilizer consists of organic compounds.

Agrogeology is the study of the origins of minerals known as agrominerals and their applications. These minerals are of importance to farming and horticulture, especially with regard to soil fertility and fertilizer components. These minerals are usually essential plant nutrients. Agrogeology can also be defined as the application of geology to problems in agriculture, particularly in reference to soil productivity and health. This field is a combination of a few different fields, including geology, soil science, agronomy, and chemistry. The overall objective is to advance agricultural production by using geological resources to improve chemical and physical aspects of soil.

<span class="mw-page-title-main">Phosphorus cycle</span> Biogeochemical cycle

The phosphorus cycle is the biogeochemical cycle that involves the movement of phosphorus through the lithosphere, hydrosphere, and biosphere. Unlike many other biogeochemical cycles, the atmosphere does not play a significant role in the movement of phosphorus, because phosphorus and phosphorus-based materials do not enter the gaseous phase readily, as the main source of gaseous phosphorus, phosphine, is only produced in isolated and specific conditions. Therefore, the phosphorus cycle is primarily examined studying the movement of orthophosphate (PO4)3-, the form of phosphorus that is most commonly seen in the environment, through terrestrial and aquatic ecosystems.

<span class="mw-page-title-main">Rhizobacteria</span> Group of bacteria affecting plant growth

Rhizobacteria are root-associated bacteria that can have a detrimental, neutral or beneficial effect on plant growth. The name comes from the Greek rhiza, meaning root. The term usually refers to bacteria that form symbiotic relationships with many plants (mutualism). Rhizobacteria are often referred to as plant growth-promoting rhizobacteria, or PGPRs. The term PGPRs was first used by Joseph W. Kloepper in the late 1970s and has become commonly used in scientific literature.

<span class="mw-page-title-main">Phototrophic biofilm</span> Microbial communities including microorganisms which use light as their energy source

Phototrophic biofilms are microbial communities generally comprising both phototrophic microorganisms, which use light as their energy source, and chemoheterotrophs. Thick laminated multilayered phototrophic biofilms are usually referred to as microbial mats or phototrophic mats. These organisms, which can be prokaryotic or eukaryotic organisms like bacteria, cyanobacteria, fungi, and microalgae, make up diverse microbial communities that are affixed in a mucous matrix, or film. These biofilms occur on contact surfaces in a range of terrestrial and aquatic environments. The formation of biofilms is a complex process and is dependent upon the availability of light as well as the relationships between the microorganisms. Biofilms serve a variety of roles in aquatic, terrestrial, and extreme environments; these roles include functions which are both beneficial and detrimental to the environment. In addition to these natural roles, phototrophic biofilms have also been adapted for applications such as crop production and protection, bioremediation, and wastewater treatment.

Microbial inoculants, also known as soil inoculants or bioinoculants, are agricultural amendments that use beneficial rhizosphericic or endophytic microbes to promote plant health. Many of the microbes involved form symbiotic relationships with the target crops where both parties benefit (mutualism). While microbial inoculants are applied to improve plant nutrition, they can also be used to promote plant growth by stimulating plant hormone production. Although bacterial and fungal inoculants are common, inoculation with archaea to promote plant growth is being increasingly studied.

<span class="mw-page-title-main">Agricultural pollution</span> Type of pollution caused by agriculture

Agricultural pollution refers to biotic and abiotic byproducts of farming practices that result in contamination or degradation of the environment and surrounding ecosystems, and/or cause injury to humans and their economic interests. The pollution may come from a variety of sources, ranging from point source water pollution to more diffuse, landscape-level causes, also known as non-point source pollution and air pollution. Once in the environment these pollutants can have both direct effects in surrounding ecosystems, i.e. killing local wildlife or contaminating drinking water, and downstream effects such as dead zones caused by agricultural runoff is concentrated in large water bodies.

<span class="mw-page-title-main">Biofertilizer</span> Substance with micro-organisms

A biofertilizer is a substance which contains living micro-organisms which, when applied to seeds, plant surfaces, or soil, colonize the rhizosphere or the interior of the plant and promotes growth by increasing the supply or availability of primary nutrients to the host plant. Biofertilizers add nutrients through the natural processes of nitrogen fixation, solubilizing phosphorus, and stimulating plant growth through the synthesis of growth-promoting substances. The micro-organisms in biofertilizers restore the soil's natural nutrient cycle and build soil organic matter. Through the use of biofertilizers, healthy plants can be grown, while enhancing the sustainability and the health of the soil. Biofertilizers can be expected to reduce the use of synthetic fertilizers and pesticides, but they are not yet able to replace their use. As of 2024, more than 340 biofertilizer products have been approved for commercial use in the US.

<span class="mw-page-title-main">Manure</span> Organic matter, mostly derived from animal feces, which can be used as fertilizer

Manure is organic matter that is used as organic fertilizer in agriculture. Most manure consists of animal feces; other sources include compost and green manure. Manures contribute to the fertility of soil by adding organic matter and nutrients, such as nitrogen, that are utilised by bacteria, fungi and other organisms in the soil. Higher organisms then feed on the fungi and bacteria in a chain of life that comprises the soil food web.

<span class="mw-page-title-main">Phosphate solubilizing bacteria</span> Bacteria

Phosphate solubilizing bacteria (PSB) are beneficial bacteria capable of solubilizing inorganic phosphorus from insoluble compounds. P-solubilization ability of rhizosphere microorganisms is considered to be one of the most important traits associated with plant phosphate nutrition. It is generally accepted that the mechanism of mineral phosphate solubilization by PSB strains is associated with the release of low molecular weight organic acids, through which their hydroxyl and carboxyl groups chelate the cations [an ion that have positive charge on it.] bound to phosphate, thereby converting it into soluble forms. PSB have been introduced to the Agricultural community as phosphate Biofertilizer. Phosphorus (P) is one of the major essential macronutrients for plants and is applied to soil in the form of phosphate fertilizers. However, a large portion of soluble inorganic phosphate which is applied to the soil as chemical fertilizer is immobilized rapidly and becomes unavailable to plants. Currently, the main purpose in managing soil phosphorus is to optimize crop production and minimize P loss from soils. PSB have attracted the attention of agriculturists as soil inoculums to improve the plant growth and yield. When PSB is used with rock phosphate, it can save about 50% of the crop requirement of phosphatic fertilizer. The use of PSB as inoculants increases P uptake by plants. Simple inoculation of seeds with PSB gives crop yield responses equivalent to 30 kg P2O5 /ha or 50 percent of the need for phosphatic fertilizers. Alternatively, PSB can be applied through fertigation or in hydroponic operations. Many different strains of these bacteria have been identified as PSB, including Pantoea agglomerans (P5), Microbacterium laevaniformans (P7) and Pseudomonas putida (P13) strains are highly efficient insoluble phosphate solubilizers. Recently, researchers at Colorado State University demonstrated that a consortium of four bacteria, synergistically solubilize phosphorus at a much faster rate than any single strain alone. Mahamuni and Patil (2012) isolated four strains of phosphate solubilizing bacteria from sugarcane (VIMP01 and VIMP02) and sugar beet rhizosphere (VIMP03 and VIMP 04). Isolates were strains of Burkholderia named as VIMP01, VIMP02, VIMP03 and VIMP04. VIMP (Vasantdada Sugar Institute Isolate by Mahamuni and Patil) cultures were identified as Burkholderia cenocepacia strain VIMP01 (JQ867371), Burkholderia gladioli strain VIMP02 (JQ811557), Burkholderia gladioli strain VIMP03 (JQ867372) and Burkholderia species strain VIMP04 (JQ867373).

Soil microbiology is the study of microorganisms in soil, their functions, and how they affect soil properties. It is believed that between two and four billion years ago, the first ancient bacteria and microorganisms came about on Earth's oceans. These bacteria could fix nitrogen, in time multiplied, and as a result released oxygen into the atmosphere. This led to more advanced microorganisms, which are important because they affect soil structure and fertility. Soil microorganisms can be classified as bacteria, actinomycetes, fungi, algae and protozoa. Each of these groups has characteristics that define them and their functions in soil.

<span class="mw-page-title-main">Root microbiome</span> Microbe community of plant roots

The root microbiome is the dynamic community of microorganisms associated with plant roots. Because they are rich in a variety of carbon compounds, plant roots provide unique environments for a diverse assemblage of soil microorganisms, including bacteria, fungi, and archaea. The microbial communities inside the root and in the rhizosphere are distinct from each other, and from the microbial communities of bulk soil, although there is some overlap in species composition.

Korean natural farming (KNF) is an organic agricultural method that takes advantage of indigenous microorganisms (IMO) to produce rich soil that yields high output without the use of herbicides or pesticides.

<span class="mw-page-title-main">Mycorrhiza helper bacteria</span> Group of organisms

Mycorrhiza helper bacteria (MHB) are a group of organisms that form symbiotic associations with both ectomycorrhiza and arbuscular mycorrhiza. MHBs are diverse and belong to a wide variety of bacterial phyla including both Gram-negative and Gram-positive bacteria. Some of the most common MHBs observed in studies belong to the genera Pseudomonas and Streptomyces. MHBs have been seen to have extremely specific interactions with their fungal hosts at times, but this specificity is lost with plants. MHBs enhance mycorrhizal function, growth, nutrient uptake to the fungus and plant, improve soil conductance, aid against certain pathogens, and help promote defense mechanisms. These bacteria are naturally present in the soil, and form these complex interactions with fungi as plant root development starts to take shape. The mechanisms through which these interactions take shape are not well-understood and needs further study.

<span class="mw-page-title-main">Viral shunt</span>

The viral shunt is a mechanism that prevents marine microbial particulate organic matter (POM) from migrating up trophic levels by recycling them into dissolved organic matter (DOM), which can be readily taken up by microorganisms. The DOM recycled by the viral shunt pathway is comparable to the amount generated by the other main sources of marine DOM.

Seaweed fertiliser is organic fertilizer made from seaweed that is used in agriculture to increase soil fertility and plant growth. The use of seaweed fertilizer dates back to antiquity and has a broad array of benefits for soils. Seaweed fertilizer can be applied in a number of different forms, including refined liquid extracts and dried, pulverized organic material. Through its composition of various bioactive molecules, seaweed functions as a strong soil conditioner, bio-remediator, and biological pest control, with each seaweed phylum offering various benefits to soil and crop health. These benefits can include increased tolerance to abiotic stressors, improved soil texture and water retention, and reduced occurrence of diseases.

References

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