ASS 201 Lecture 4 Microbiologically Mediated Processes PDF

Lecture 4: Microbiologically mediated processes Microbiologically mediated processes involve the biochemical and physiological activities of microorganisms that influence or drive chemical reactions, nutrient cycling, energy flow, and material transformations in natural and engineered systems. Lec...

Lecture 4: Microbiologically mediated processes Microbiologically mediated processes involve the biochemical and physiological activities of microorganisms that influence or drive chemical reactions, nutrient cycling, energy flow, and material transformations in natural and engineered systems. Lecturer: Dr. R Yankey  Introduction to Microbiological Processes 1.Biochemical reactions facilitated by microorganisms such as bacteria, fungi, archaea, and algae in i. Nutrient cycling (e.g., nitrogen, carbon, and sulfur cycles); ii. Soil fertility iii. Plant growth and iv. Environmental remediation (phytoremediation, biodegradation/bioremediation). 2  1. Mineralization 1.Organic materials are broken down to release nutrients in a process known as Mineralization. 2.Organic compounds found in organic materials are transformed into inorganic compounds 3.Many of the elements in organic materials are plant nutrients, but they are locked up in the molecular structure of the substance and are unavailable to plants. 4.Mineralization releases these nutrients into the soil in forms that plants can absorb for growth and development. 5.Soil microbes break down organic materials into compounds or ions that plants can use 3  Mineralization 1.When organic material is added to the soil, different types of soil microorganisms begin to break down the organic material. 2.The rate at which soil microorganisms will break down the material depends on environmental factors,  including temperature  moisture availability  soil aeration, and  the carbon-to-nitrogen ratio (C:N) of the material. (If the C:N ratio of the organic material is greater than 30:1, soil microorganisms may "steal" nitrogen from the soil, making it 4 Mineralization The carbon-to-nitrogen ratio (C:N) is a property inherent in any organic material added to the soil (Table 1). All organic materials contain more carbon than nitrogen atoms in their molecular structure. However, the C:N ratio varies in different organic materials. Materials such as wood shavings and wood chips have a high amount of carbon relative to nitrogen, while materials such as fresh poultry manure and grass clippings have a low C:N ratio. A C:N ratio of 700:1 means the material under consideration (e.g., wood chips; Table 1) has 700 parts of carbon to one part of nitrogen, while a ratio of 4:1 (e.g., blood meal; Table 1) means the material has four parts of carbon to one part of nitrogen. Therefore, there is more nitrogen in a material with a C:N ratio of 4:1 compared to 700:1. Since nitrogen is often more limiting than carbon when organic materials are being broken down, materials with a high C:N ratio will take a longer time to break down due to a scarcity of nitrogen, while materials with a low C:N ratio break down faster due 5 to  Mineralization Other factors that can affect the rate of organic matter decomposition include:  The nature and abundance of microorganisms in the soil  The extent of C, N, P, and K  The pH of the soil  The presence or absence of inhibitory substances, such as metals, toxic compounds, and tannins 6  Immobilization  Temporary tying up of nutrients by microbes  Its a process in which soil microorganisms take up nutrients from the soil, especially nitrogen. Why does it happen? 1. Microbes need nitrogen to grow and multiply so they can break down more organic material, especially organic matter with a high C:N ratio. 2. Therefore, the nitrogen can be tied up in microbial biomass or can accumulate in byproducts of microbial activity 3. During the period of immobilization, the soil can undergo nutrient deficiency. Why is it temporal? 7 Nitrogen fixation 8  Nitrogen fixation 1. Conversion Of Atmospheric Nitrogen Gas To Ammonium 2. Nitrogen fixation is a microbially mediated process that converts nitrogen gas to plant-available forms of nitrogen. 3. Mineral/inorganic fertilizers made in the factory, such as ammonium nitrate, contain soluble ammonium and nitrates that plants can directly use for their growth. 4. However, there are bacteria in the soil that can convert nitrogen gas to soluble forms of nitrogen for crop 9  Nitrogen fixation Two types of nitrogen fixation can happen in the soil. performed by bacteria called free-living nitrogen fixers. Eg include Azotobacter and Cynobacteria non- The estimate of nitrogen fixed by the free-living microbes in arid symbiotic agricultural lands is relatively low at about 4 lb nitrogen/acre/year However, in arid rangelands and unmanaged lands, nitrogen fixation by nitrogen soil cyanobacteria can be much higher, especially when they form soil fixation surface aggregates known as biological soil crusts this occurs between the Rhizobium bacteria and legumes where a legume plant forms a mutually beneficial relationship with Rhizobium bacteria legume plant secretes specific chemicals (flavonoids) into the soil through its roots. Once the bacteria have “infected” the root hairs, the plant cells respond by dividing and creating root nodules, which house the bacteria symbiotic The Rhizobium bacteria in the nodules convert nitrogen gas, which is abundant in the soil, into ammonia, which plants can utilize The legume receives the bacterially fixed nitrogen products, while the bacteria in the nodules receive carbohydrates from the legume, allowing them to thrive 10 Nitrogen fixation Cyanobacteria in rangelands and unmanaged lands can form biological soil crusts, which represent living soil aggregates that stabilize the desert soil. Biological soil crusts are home to myriad diverse microorganisms, including cyanobacteria, other bacteria, eukaryotic algae, mosses, and lichens. Shown here are lichen and cyanobacteria crusts 11  Nitrogen fixation Root nodules attached to the roots of a legume plant. 12  Nitrification 1. Conversion Of Ammonium To Nitrate-Nitrogen 2. Nitrification is the conversion of ammonia or ammonium ions to nitrate through bacterial action. Nitrification is a two-step process in the soil 3. The ammonia or ammonium compound is converted to nitrite by bacteria in the genus Nitrosomonas 4. the nitrite is converted to nitrate by bacteria in the genus Nitrobacter 13  Nitrification Nitrification process in the soil. 1. Since nitrification is an oxidative process (a process requiring oxygen), the soil must be well aerated for nitrification to take place. 2. Nitrification also requires a warm temperature for optimal processing (Why?), often greater than 20 degree Celsius, and thus progresses very slowly at low temperatures. 3. Plants can make use of both nitrate and ammonium forms of nitrogen 4. Ammonium-nitrogen is a positively charged ion that often gets attached to the small humus or clay particles in the soil in a process called adsorption 5. When this happens, ammonium-nitrogen may be more difficult for the plants to access 6. Nitrate, in contrast, is a more readily available form of nitrogen in the soil, and it can be absorbed by the plants faster than ammonium-nitrogen 14  Nitrification 1. When too much nitrate is in the soil, it can easily dissolve in soil water and be leached as water moves through the soil. When the nitrate- nitrogen is moved down through the soil beyond the rooting zone, it becomes unavailable for crop uptake, and it can eventually end up in the groundwater. 2. Another problem of excessive nitrate in the soil is the possibility for it to be denitrified 3. Ammonium-nitrogen can be introduced to the soil through manure, composts, decomposing crop residues, and mineral fertilizers used in commercial agriculture. Nitrification inhibitors – improves the nitrogen use efficiency of plants 15  Denitrification 1. Conversion Of Nitrate To Nitrogen Gas 2. Denitrification is the chemical conversion by microbes of nitrates (NO3-) and nitrites (NO2-) present in the soil to nitric oxide (NO), nitrous oxide (N2O), and nitrogen gases (N2) 3. Denitrifying bacteria are facultative anaerobes - ordinarily flourish in an oxygen-rich environment, but when oxygen is scarce, they shift their metabolism 16  Denitrification 4. This implies that important plant-accessible nitrogen in the soil can be lost through denitrification, lowering the quantity of nitrogen available for crop production. Thiobacillus denitrificans, Micrococcus denitrificans, Pseudomonas, and Serratia species are among the bacteria that can cause denitrification in the soil. 5. Averagely 20% of applied nitrogen could be lost to denitrification. 6. Another detrimental effect of denitrification occurs if the end product of the denitrification is nitrous oxide (N2O) because this gas is known to be 300 times more 17  Mycorrhizal Association 1. Beneficial fungal association with plant roots 2. Mycorrhizal association occurs in the soil when mycorrhizal fungi (MF) form a symbiotic partnership with plant roots to help the plant with the uptake of water and nutrients, especially phosphorus and helps in plant communication. 3. In return, the plants provide simple carbohydrates for the growth of the MF 4. The MF association is very common among most 18  Mycorrhizal Fungi (MF) Association Based on the way that the MF associate with plants, two major types of association can be defined: ectomycorrhizal and endomycorrhizal fungi. Ectomycorrhizal association Endomycorrhizal association 1. The MF infect the plant roots and multiply in 1. The MF penetrate the cell wall and grow into the cell wall region without penetrating the the plant cell wall. They grow around…but not into the cells plants cell wall 2. Endomycorrhizal fungi develop tiny, highly 2. Ectomycorrhizal fungi wrap themselves branching structures inside plant cells, called around the outer portion of the roots and arbuscules, that are used to exchange grow outward into the soil nutrients and carbohydrates between the plant and the fungi. 3. The ectomycorrhizal association is more prevalent among forest trees. 3. Arbuscular mycorrhizal fungi (AMF) is of greater importance in farming because most native plants, field crops, and vegetable crops can form a symbiotic relationship with the AMF. 19 Ectomycorrhizal fungi (left, blue) and endomycorrhizal (arbuscular) fungi (right, purple) interactions with a plant root. The ectomycorrhiza grow around—but not into— the plant cell walls, while the endomycorrhiza grow into plant cells and form arbuscules 20  Mycorrhizal Association 5. In both types of association, after the MF associate with the plant roots, they keep growing outward, potentially extending the zone from which nutrients and water can be extracted and directed back to plant roots. At the same time, the MF receive simple carbohydrates from the plant to enable the fungi to continue to grow. 6. The MF are also called “root extenders,” and due to this root-extending function, the MF association increases the efficiency of plant mineral uptake from the soil and helps plants to be more drought-resilient. Some studies have also shown that the AMF can solubilize nutrient elements like phosphorus and sulfur and make them available for crops. It has also been shown that the AMF can help alleviate other stresses on plants, such as extreme temperature, pH, toxic metals, soil pathogens, and soil salinity 7. Another key advantage of the AMF is their ability to enhance stable soil structure. They do this directly with their hyphae (vegetative growth structures), forming a physical network around the soil particles, and indirectly by exuding an iron-containing protein called glomalin. Glomalin is a very sticky substance that acts as a “biological glue” for the soil crumbs. Although many plants can form AMF associations, their occurrence may be limited in croplands because of frequent soil tillage, and it has been shown that the AMF association is more abundant in untilled soils compared to frequently tilled soils 21 Rhizophagy Cycle Another way that plants obtain nutrients from the soil is through a process called the rhizophagy cycle. In the rhizophagy cycle, non-pathogenic soil microbes called endophytes are attracted to plant roots through the exudates secreted by plants into the soil. Some of the endophytes eventually enter the roots and start to live in the plant tissues. Through certain substances in the plant roots called “superoxides,” the cell walls of the microbes are dissolved, and nutrients contained within the microbes are released into the plants. After the extraction of nutrients from the microbes, they move back into the soil via the root tips, where they acquire more nutrients before re-entering the plant roots. In this way, these microbes alternate between living inside the plants and living freely in the soil. The 22 rhizophagy cycle is highly beneficial to Key Mechanisms in Microbiologically Mediated Processes 1. Metabolism as the Driving Force: Catabolism: Breakdown of complex molecules to release energy. Anabolism: Synthesis of complex molecules from simpler ones, requiring energy. Redox Reactions: Microorganisms mediate electron transfer, enabling oxidation and reduction processes crucial for energy production. 2. Enzymatic Activity: Microbes produce specific enzymes that catalyze reactions, lowering activation energy and increasing reaction rates. Examples: Amylases (breakdown of starch), cellulases (cellulose degradation), and nitrogenase (nitrogen fixation). 3. Biofilms and Microbial Communities: Microbes often form biofilms (structured communities attached to surfaces), enhancing their efficiency in processes like degradation or corrosion. Microbial consortia enable synergistic processes, such as syntrophy (mutually beneficial metabolic exchange). 23  Conclusio Soil microorganisms are essential for improving soil health and ensuring its sustainability. n They do this by affecting nutrient transformation and availability in the soil through a variety of processes. They also play a crucial role in the transformation of organic materials that are added to the soil. To be able to manage the soil sustainably, it is necessary to understand the roles that microbes perform in the soil and the numerous activities that they carry out. Soils of arid and semiarid regions are particularly challenging to manage, and a major issue is lower biological activities in such soils due to low organic matter contents. Adding organic material to the soil, such as plant 24