Agricultural Microbiology PDF Lecture Notes

11/23/2021 Agricultural Microbiology Lec. 1 Prof. Dr. Mona S. Zayed 1 Agricultural Microbiology Agricultural microbiology is a bran...

11/23/2021 Agricultural Microbiology Lec. 1 Prof. Dr. Mona S. Zayed 1 Agricultural Microbiology Agricultural microbiology is a branch of science that studies different types of microorganisms that are associated with plants, soil, and even animal (either with positive or negative effect) Soil Microbiology the soil microbiology concern about the study of microorganisms and their processes in soil. In fact, soil is an active habitat for enormous variety of life-forms including microorganisms. The interaction of enormous microorganisms with each other and also with their environments is covered under the branch of soil microbiology. 2 1  11/23/2021 Organization of Ecosystems 3 4 2  11/23/2021 Organization of Ecosystems 1- Biosphere The first level of the ecological pyramid, which is made up of the Earth's surface and atmosphere. It is also known as the zone of life on Earth, (all lifeforms found on the planet coexist on it). Simply: It is the thick envelope of life that surrounds the earth’s surface it is the sum of all the ecosystems of this planet. made up of: hydrosphere (water) lithosphere (soil) atmosphere (air) 5 2- Biomes Climatic regions Biome: is a large region of Earth which is typically characterized by having a certain climate conditions and certain types of dominant living things. Each biome has many ecosystems Some of the most noticeable biomes of the world include The desert biome, Rainforest biome, Savannah biome 6 3  11/23/2021 Ecosystem Ecosystem: it is referring to of the biotic and abiotic factors in an area. The environment that containing all the living organisms (biotic factors such as : plants, animals and microbes) and non-living things (abiotic factors such as: air, soil, and water) are linked together in a particular region and the interaction between them. 7 Communities Community: is all of the different species that live together in the same geographical area and interact with each other. A community is composed of all of the biotic factors of an area. This interaction between the members of these communities often revolves around different concepts such as predator-prey and symbiotic relationships. 8 4  11/23/2021 Population Population: is a group of organisms belonging to the same species living together in the same geographical area and interact with one another 9 Species Is the lowest level of ecological organization Is a group of individuals that are genetically related and can interbreed to produce fertile young. If the individuals cannot interbreed to produce a progeny (so they are not members of the same species) Every single species, (from microscopic bacteria, fungi, plant and animal species to huge blue whale), finds a place at this level of the ecological pyramid. The distribution of these species is governed by abiotic factors of the region. 10 5  11/23/2021 Niche Niche is defined in a general as a cavity, hollow, However, in biologically and ecologically, a niche refer to the following: (1) the specific area where an organism inhabits (2) the role or function of an organism or species in an ecosystem (3) the interrelationship of a species with all the biotic and abiotic factors affecting it. Therefore the ecological niche refers to the interrelationship of a species with all the biotic and abiotic factors affecting it. Small ecosystem 11 Habitat the physical location in the environment to which an organism has adapted Niche overall role that regulator species, or population, serves in a community; nutritional intake, position in the community, and rate of population growth 12 6  11/23/2021 Biosphere made up of: Lithosphere (soil) Atmosphere (air) Hydrosphere (water) Lithosphere: solid, rocky crust that covers the surface of the earth including the bottom of the oceans 13 14 7  11/23/2021 The Soil Environment  Soil is a structured environment that “holds” a wealth of organisms with diverse activities and functions.  microorganisms have a central place, as they play major roles in key soil processes.  The inorganic particles of soil are classified into three major groups according to their size: sand, silt, and clay. The proportions of these particles in any soil determine the soil texture.  soil aggregates are habitats that allow the survival of one or more species of soil microorganisms.  The niches of soil are mainly the soil pore walls.  Soil water passes more rapidly through wider pores by means of gravity mass flow and diffusion than through narrow pores. 15 Schematic of a section through a 2 mm-diameter soil aggregate microsite yielding habitats for bacteria based on physiological requirements. 16 8  11/23/2021 Soil Biology and Microbiology *Mineral Particles *Air Soil consists of: *Water *Soil Organic Matter *Plant Roots *Living Soil Organisms. 17  The microbial habitat in soil The soil pores is a porous medium that varies both spatially and temporally. The structural form of this porous medium is the product of many different processes. (Biological, physicochemical, and mechanical processes) as they act together to aggregate, compact, crack, and fragment the soil, resulting in a soil structure consisting of solids and pores. The soil habitat generally constitutes an aerobic, oligotrophic (nutrient-poor) environment, which is not conducive to high population densities and activities of microorganisms. In contrast, the rhizosphere provides an environment in which elevated population sizes and activities of fast- growing microorganisms that supported by plant- derived carbon substrates, in the form of exudates and cell lysates. 18 9  11/23/2021 Schematic illustration of the soil environment around plant roots in terms of diffusion of materials (substrate carbon and nutrients) and information (signal molecules). 19 Factors affect Soil life (microorganisms) and Physicochemical Environment) 1) Water, The Essential Factor For Soil Life  “Understanding the movement of water in soil is understanding the most significant feature of the soil as a habitat for microbial life”. Where water moves, so do ions and nutrients.  Water carries dissolved gases and heat, and also bacteria and their predators.  It protects microhabitats from desiccation and opens other potential habitats while closing others. 20 10  11/23/2021 The range of water-influenced soil properties and processes which determine the microbial activity. Eh: redox potential. 21 Moisture Controlling Growth Moisture – Water Activity Water Activity (Aw) is the measure of “free” water available to the microorganism for growth 22 22 11  11/23/2021 The importance of soil water activity to microorganisms Water activity (Aw) is the best determinant of the water requirements of microorganisms. It is the availability of water for reaction in a substrate. The relationship between moisture content and Aw is unique to each soil due to its physical and chemical nature and its organic matter content. This can lead to change soil bacterial communities, Aw can also determine how microbial growth and activity are affected by moisture in soil. 23 Water Activity Aw is affected by the presence of solutes (sugars and salts) Salt or Sugar Lowering aw will reduce the ability for microorganisms to grow 24 24 12  11/23/2021 If a soil's Aw is too low for microbial activity to occur, then even the most biodiverse microbial community with significant biomass will be unable to undertake any ecosystem processes. What is the relationship of a soil’s moisture content to its water activity? The relationship between moisture content and Aw is unique to each soil due to its physical and chemical nature and its organic matter content. 25 26 13  11/23/2021 2) Soil as an energy and nutrient Source soil microorganisms are classified according to how they use their sources of energy and carbon. Light as a source of energy only present at the surface of the soil. The chemical energy for chemoautotrophs is supplied in the form of reduced inorganic chemicals Organic matter provides the energy source for the heterotrophic microbial community of the soil. This organic matter ranges from the readily decomposable and more resistant fractions of plant litter In addition to soil organic matter, the organic carbon that is directly released from plant roots represents a key energy source. 27 Metabolic Classification of Microorganisms E nergy S ource C lassification C arb on S ou rce P hotoautotrophs “Autotrophs” Light (P hototrophs) Ph oto heterotroph s P S I: anaerobic, H 2 S PS I+II: aerobic, H 2O CO2 (A utotrophs) C hem olithoautotrop hs Inorganic (C hem olithotrophs) A erobic (m ajority) C hem olithoheterotro ph s A naerobic (few ) (or M ixotrophs) C hem ical O rgan ic (C hem otrophs) (H eterotrophs) “Heterotrophs” O rganic C hem oorg anoheterotrph s (C hem oorgan otrophs) Ae robic respiration A na erobic respiration Ferm entation C hem oorganoautotrophs 28 14  11/23/2021 29 Carbon Source Autotroph CO2 = principle carbon source Heterotroph Utilize more reduced and complex carbon sources derived from other organisms organic carbon (“nourished by others”) Use organic compounds as a source of carbon 30 15  11/23/2021 Energy Source Phototroph Light energy harvested by photosynthetic processes Chemotroph Organic or inorganic compounds provide energy by oxidative processes 31 “Chemotroph” Lithotrophs Use reduced inorganic compounds as electron source Organotrophs Use organic compounds as H and electron donors 32 16  11/23/2021 Metabolic Classification of Microorganisms En ergy S ou rce C lassification C arbo n S ou rce P h otoautotro phs “Autotrophs” Lig ht (P hototrophs) P h oto heterotroph s P S I: anaerobic, H 2 S P S I+II: aerobic, H 2 O CO2 (A utotrophs) C hem olithoautotro ph s In org anic (C hem olithotrophs) A erobic (m ajority) C h em o lithoheterotroph s A naerobic (few ) (or M ixotrophs) C hem ical O rg anic (C hem otrophs) (H eterotrop hs) O rgan ic “Heterotrophs” C h em oorgano heterotrp hs (C hem oorgan otrophs) A erobic respiration A naerobic respiration Ferm entation C hem oorgan oautotrophs 33 Energy and Nutritional Flow in Ecosystems Organisms derive nutrients and energy from their habitat. Food chain or energy pyramid summarizes the feeding levels: 34 17  11/23/2021 Insert figure 26.3 Trophic and energy pyramid 35 Producers (called autotrophs) Provide fundamental energy source that initiate the trophic pyramid The only organisms in an ecosystem that can produce organic carbon compounds such as carbohydrates by assimilating simple inorganic sources (CO2 and water) from the atmosphere An organism that uses light energy or other forms of energy to make energy-rich compounds (or their own food) is a producer 36 18  11/23/2021 Consumers They cannot build up carbohydrates from simple inorganic sources. They depend on ready made organic materials. Feed on other living organisms and obtain energy from chemical bonds present in the organic substrates they contain. They break it down enzymatically into simpler compounds which can be absorbed Consumers cannot use the sun’s energy directly like producers. They depend on autotrophs for nutrients and energy. 37 Consumers Consumers must consume or eat producers or other consumers Pyramid usually has several levels of consumers Primary consumers: consume producers Secondary consumers: feed on primary consumers Tertiary consumers: feed on secondary consumers Quaternary consumers: feed on tertiary consumers 38 19  11/23/2021 Types of consumers a. Herbivores- obtain energy by eating only plants b. Carnivores- eat animals (snakes, dogs, owls, etc.) c. Omnivores- eat both plants and animals (e.g. humans) 39 Decomposers Decomposers break down and absorb the organic matter of dead and decaying organisms (plants and animals) into simpler molecules that can be more easily used by other organisms. they recycle materials (organic matter ) into inorganic minerals and gases, mineralize nutrients Decomposers- breaks down organic matter (bacteria and fungi) 40 20  11/23/2021 Carbon source categories Autotrophs (Producers) Carbon dioxide Organic carbon Heterotrophs (Consumers & Decomposers) 41 Autotroph Heterotroph Producer Producer Consumer Decomposer Phototrophic Chemolithotrophic Organotrophic Organotrophic 42 21  11/23/2021 3) Soil temperature Temperature in soil is a key determinant of both the distribution and the activity of soil microorganisms. As temperature directly affects microbial physiology, and it indirectly affects through changes in factors such as nutrient and substrate diffusion and water activity. Soil temperature is the product of solar energy, modified by a series of factors. soil temperature is affected by seasonal factors, as well as “edaphic” factors such as soil type/depth and the nature of the vegetation present. 43 Soil temperature Temperature is a strong selective force and is a key driver of physical, chemical, and physiological reactions. So,…. soil microbial communities can be defined on the basis of temperature values the classification of soil microorganisms on the basis of temperature preference 44 22  11/23/2021 Temperature is Controlling Growth T =Temperature Optimal Growth Thermophiles – like hot conditions Mesophiles – like warm conditions (around body temperature) Psychrotrophs – can grow at refrigeration temperatures 45 45 Temperature Classifications *Based on optimum temperature for growth; *Psychro=cold *Meso = middle *Thermo= warm *Trophic =growing *Duric=withstand *Phil or philic-prefers or loves 46 46 23  11/23/2021 Categories of Microbes Based on Temperature Range Image: Pearson Education Inc. (2004) publishing as Benjamin Cummings 47 Classification of bacteria based on optimum temperature of growth 1) Psychrophiles:  Bacteria that can grow at 0°C or below but the optimum temperature of growth is 15 °C or below and maximum temperature is 20°C are called psychrophiles  Psychrophiles have polyunsaturated fattyacids in their cell membrane which gives fluid nature to the cell membrane even at lower temperature. 2) Psychrotrops (facultative psychrophiles):  Those bacteria that can grow even at 0°C but optimum temperature for growth is (20-30)°C 3) Mesophiles:  Those bacteria that can grow best between (25-40)C but optimum temperature for growth is 37C 48 24  11/23/2021 Classification of bacteria based on optimum temperature of growth 4) Thermophiles:  Those bacteria that can best grow above 45C..  True thermophiles are called as Stenothermophiles, they are obligate thermophiles,  Thermophils contains saturated fatty acids in their cell membrane, so their cell membrane does not become too fluid even at higher temperature.  Thermophiles capable of growing in mesophilic range 6) HypethermophilesThose bacteria that have optimum temperature of growth above 80C.  Mostly Archeobacteria are hyperthermophiles. 49 4) solar energy (light) solar energy is responsible of energy in the soil–plant system. As solar energy affects soil temperature, which in turn influences soil microbial activity. Solar light also directly affects the microbial distribution and activity at or near the soil surface (where light can penetrate), providing energy and driving photoautotrophic soil microorganisms such as algae and cyanobacteria. Under the conditions of high photoautotrophic activity, however, considerable amounts of polysaccharides can be produced in the soil, which play important roles in soil aggregate start and stabilization, thus enhancing the stability of the soil. The most important effect of light, from a soil microbiological point of view, is that it stimulates plant seed germination, seedling establishment, and growth and is necessary for some algae and cyanobacteria to grow on soil surface and other surfaces. 50 25  11/23/2021 5) Soil atmosphere The typical concentrations of the major soil gases in the air and soil atmosphere are indicated in Table 2. soil microbial activity, and the characteristics of the soil atmosphere are strongly related to the soil water regime. Typical Composition of the Soil Atmosphere Compared to the Open Atmosphere N2 O2 CO2 Typical concentration in air (%) 79 21 0.035 Typical concentration in soil atmosphere (%) 79 20–21 0.1–1.0 51 O = Oxygen Based on oxygen requirements;  Aerobic-Need oxygen to grow  Anaerobic-Can grow only if oxygen is absent  Facultative-Can grow with or without oxygen 52 52 26  11/23/2021 Oxygen Controlling Growth Tolerance to oxygen in the surrounding environment Facultative Anaerobic Aerobic Anaerobes 53 53 Classification of bacteria on the basis of gaseous requirement 1. Obligate aerobes: a) Those bacteria require oxygen and cannot grow in the absence of O2. b) Examples; Bacillus sp. 2. Facultative anaerobes: a) Those bacteria that do not require O2 but can use it if available. b) Growth of these bacteria become better in presence of O2 c) Examples: E. coli, Klebsiella sp., Salmonella sp. 3. Aerotolerant anaerobes; a) Those bacteria do not require O2 for growth but can tolerate the presence of O2. b) Growth of these bacteria is not affected by the presence of O2. c) Example: lactobacillus sp. 54 27  11/23/2021 Classification of bacteria on the basis of gaseous requirement 4. Microaerophiles: a) Those bacteria that grow on low concentration of Oxygen but at atmospheric level of Oxygen growth of these bacteria is inhibited. b) These bacteria only have oxidative type of metabolism c) Example: Campylobacter 5. Obligate anaerobes: a) Those bacteria that can grow only in absence of Oxygen. b) Oxygen is harmful to obligate anaerobes c) Examples: Peptococcus, Peptostreptococcus, methanococcus 55 6) Soil pH Soil pH is a major determinant of soil microbial distribution and activity. The pH of a soil, or of a microsite (microbial habitat) in the soil, is the product of numerous factors and processes. 1) First, it is determined by the parent material from which the soil is formed (acid soils tending to form from rocks such as granite and alkaline soils from chalks and limestones), 2) the degree to which mineral weathering has occurred since soil formation. 3) Types of biological processes that can modify the soil pH to varying degrees. acidophiles, preferring low pH conditions; alkaliphiles, preferring high pH conditions 56 28  11/23/2021 Classification of bacteria on the basis of optimum pH of growth 1. Acidophiles: a) Those bacteria that grow best at acidic pH b) The cytoplasm of these bacteria are acidic in nature. c) Some acidopiles are thermophilic in nature, such bacteria are called Thermoacidophiles. d) Examples: Thiobacillus thioxidans, Thiobacillus, ferroxidans, Thermoplasma, Sulfolobus 2. Alkaliphiles:  Those bacteria that grow best at alkaline pH  Example: vibrio cholerae: optimum pH of growth is 8.2 3. Neutriphiles:  Those bacteria that grow best at neutral pH (6.5-7.5)  Most of the bacteria grow at neutral pH  Example: E. coli 57 The distribution and activity of soil microbes as a result of pH Many soil microorganisms can tolerate particular pH conditions that are far from their optimum. For example,  many of the fungi found in acid forest soils are not acidophiles.  When isolated from these environments, some fungi show a favorite for near-neutral conditions, but they are highly competitive under considerable acidity  A further complication in understanding pH-related microbial activity in soils is that most microbes are attached to soil surfaces and many grow in colonies and even biofilms, which can protect them from the pH effects in the soil solution.  The assumptions came from in vitro physiological evidence of the pH requirements of the soi microorganisms, it did not take into account the properties of surface-colonizing populations or of the heterotrophic microorganisms which have wider pH ranges than their autotrophic counter- parts. 58 29  11/23/2021 Thanks 59 30