Agricultural Microbiology Lecture Notes 2023-2024 Ain Shams University PDF

Agricultural Microbiology COL (211) For 2nd level students (Quality Management and Organic Farming Programs) 2023-2024 Dr. Basma Talaat Abd-Elhaim Lecturer of Microbiology, Fac. Agric, Ain Shams University. [email protected]....

Agricultural Microbiology COL (211) For 2nd level students (Quality Management and Organic Farming Programs) 2023-2024 Dr. Basma Talaat Abd-Elhaim Lecturer of Microbiology, Fac. Agric, Ain Shams University. [email protected]  LECTURER 7 SOIL MICROORGANISMS DIVERSITY  Classification of ecosystem microbes. Benefits of soil biodiversity. Types of soil microorganisms. Microorganisms in the soil and soil structure. Microorganisms' function in biogeochemical cycles interactions between soil, plants, and microbes. The "rhizosphere effect" is influenced by the rhizosphere. Plant effects on the rhizosphere. Microorganisms' effect on the rhizosphere. Microbial interactions' effects on the rhizosphere. Rhizosphere effects of plant-microbe interactions.  SOIL MICROORGANISMS DIVERSITY TYPES OF SOIL MICROORGANISMS ALGAE ACTINOMYCETES FUNGI BACTERIA PROTOZOA  SOIL MICROORGANISM DIVERSITY We can classify soil microorganisms according to: Size: their dimensions Algae come before fungi, actinomycetes, yeasts, and bacteria. Fungi come before actinomycetes, yeasts, and bacteria. Bacteria come after fungi, actinomycetes, and yeasts. Function: support plant health. DIVERSITY OF SOIL MICROORGANISMS Cyanobacteria and algae The eukaryotes include the algae and fungi ( organisms with a true cell nucleus). Although certain anaerobes can be found in animal intestines and effluent, most fungus are aerobic heterotrophs. The biomass of these two primary groups in soil is comparable, even though there are many more species of bacteria than fungus (the ratio between the two is dependent on the environment).  ACTINOMYCETES They are gram positive, non-motile, non- capsulated filamentous bacteria. These organisms have been shown to be higher bacteria, but they were thought to be fungi for many years because they have filamentous forms, 0.5 to 0.8 µ in diameter, which appear to branch. It is now clear that they are not fungi but are closely related to the mycobacteria.  FUNGI Eukaryotes include the fungus ( organisms with a true cell nucleus). most fungus are aerobic heterotrophs.  BACTERIA Bacteria are the most varied and prevalent cell type in the soil. Since they lack a nuclear membrane, bacteria are prokaryotes. Bacterial cells can be spherical, rod-shaped, or s-shaped and are typically between 0.4 and 2 m in size. Some bacteria are mobile due to the presence of flagella. However, in the soil, ion exchange is most frequently used to bind them to surfaces.  Microorganisms in the soil and soil structure Stable aggregates of soil particles are necessary for soil structure. The aggregation of soil is greatly influenced by soil organisms. In the aggregation of soil, bacterial cells, mycelial threads of fungus, and actinomycetes all play significant roles. The soil's constituents (organic matter, polysaccharides, lignin, and gums produced by soil bacteria) that play a significant role in cementing soil particles. Soil microorganisms' impact on plant growth Complex organic nutrients are broken down by soil microbes into more easily absorbed inorganic forms that the plant can use for development. Produce several chemicals, such as antibiotics, IAA, and gibberellins, which either directly or indirectly encourage plant development.  Microorganisms' function in biogeochemical cycles Biogeochemical cycles: Chemical element recycling (oxidation and reduction). Cycles of carbon, nitrogen, phosphorus, and Sulphur.  Fractions of soil Microbe-plant-soil interactions Bulk dirt is root-free soil that has been sieved through a 2 mm filter. Rhizosphere: soil particles (0.5–5 mm) gently attached with fine roots. Fine roots (2 mm) at the soil-root interface (sri) with adherent rhizoplane soil (0.5 mm). The main connection between the soil-plant system is the rhizosphere, which makes up half of the "hidden half." The ecosystem's unobserved half is the soil. The Rhizosphere is Half of the Hidden Half and is the Primary Link Between Soil-Plant System.  QUALITIES OF SOIL (BULK SOIL& RHIZOSPHERE) Qualities of Soil can be determined by minerals, soil particle size, organic matter content, and water content, oxygen supply is constrained. Type of organic matter supply source and source of organic substrates determine the distribution of microorganisms (humus and root exudates).  THE RHIZOSPHERE AND RHIZOPLANE The root environment zone known as the rhizosphere promotes the development of microorganisms that utilize chemicals found in roots as sources of C, N, and energy. Rhizoplane: the surface of a plant's root where soil particles creates a microenvironment at the plant-soil interface for microbial activity. Sperm sphere: 1 to 20 mm zone of elevated microbial activity surrounding seed (imbibing/germinating).  Rhizosphere effects When microbial density Affect microbial variety is affected, there are reduces the diversity of more bacteria in the bacteria in the rhizosphere than in the rhizosphere with bulk of the soil. comparison to bulk soil.  Influences on the "rhizosphere effect" Due to the low levels of accessible C and N in "bulk soil" and the nature of the root exudates, root exudates are seen as having a significant influence. lysates, mucilage, and secretion. chemotaxis (signal compounds) oriented the motile organisms' motion in relation to a chemical agent. depending on the chemical gradient, it might be either positive (toward) or negative (away). It could direct rhizobacteria to affect plant root locations. Low soil water potential due to moisture microsites (atmospheric concentration or CO2 levels) has a significant impact on microbial development since it can hinder motility and nutrient transfer. A considerable portion of the pore space is water-filled at higher soil water potentials, and oxygen may be limiting pH changes. Biofilm Assemblages (accumulations) of microorganisms and the extracellular materials they produce at the root-soil interface that are generally adhered to the surface of the root or "rhizoplane.“ Phases of biofilm development 1. Reversible bacterial adsorption. 2. Irreversible bacterial adhesion. 3. Bacterial growth and division. 4. Exopolymer synthesis and biofilm development. 5. Other creatures' attachment to the biofilm.  Rhizobacteria: (bacteria closely associated with plant roots) "Plant-growth-promoting rhizobacteria" or "PGPR“. Increase plant growth or seed germination through a variety of processes (pathogen-repelling substances, chemicals that promote plant development, etc.). Such as...Pseudomonas spp. DRMO stands for "deleterious rhizosphere microorganisms." DRB stands for "delete rhizobacteria." Impede or reduce plant development through a variety of ways (inhibitory or toxic compounds, enzymes, over- production of growth promoters).  Endophytic microbes (endon gr., Within; & phyton, plant). The definition of endophyte is "in the plant." Endorhizal microbes' endo" (endon gr., Inside; & "rhiza" signifies root - Endorhiza (internal root tissues)) bacteria invading inner cellular layers of plant roots.  ECOLOGICAL RHIZOSPHERE A. Plant effects on the rhizosphere. B. Microorganisms' effect on the rhizosphere. C. Rhizosphere effects of plant-microbe interactions. D. Microbial interactions' effects on the rhizosphere.  A. Plant effect on the rhizosphere Rhizodeposition All that the plant roots lose. These substances, which include water- soluble exudates, secretions of insoluble components, lysates, and dead fine root gases like CO2 and ethylene, are quickly digested by rhizosphere microbes. Influence of root respiration on co2 ph Nutritional absorption from inorganic sources. Effect of plants specifically on the microbial ecology in the rhizosphere (positive or negative).  B. MICROORGANISMS' EFFECTS ON THE RHIZOSPHERE Make compounds that encourage growth (auxins, gibberellins, cytokinin’s). High phosphatase activity, organic acids generation, phosphorus availability, and antimicrobial factors (AMF). Transferring Mn, Fe, and Zn to plants after assimilation toxicity or availability of elements. Urease and proteases have enzymatic activity (mineralized n for plant uptake). Production of antibiotics to fight root infections (actinomycetes create more than 50 distinct types of antibiotics, including streptomycin and neomycin). Production of siderophores. Siderophores are substances that microorganisms release under conditions of low iron stress and which function as ferric iron chelating agents. Production of phytotoxins - both PGPR and DRB (deleterious rhizobacteria) can inhibit the growth of seeds and plants by creating (HCN, herbicidal compounds, complex phytotoxins) citrus growth is suppressed because of DRB.