Lec 2 Diversity of Soil Microorganisms PDF

Diversity of soil microorganisms Lec. 2 Prof. Dr. Mona S. Zayed ▪ There are two types of soil microorganisms based on their evolutionary origin: 1) Indigenous )Native( microorganisms Native to a particular habitat. Indigenous mic...

Diversity of soil microorganisms Lec. 2 Prof. Dr. Mona S. Zayed ▪ There are two types of soil microorganisms based on their evolutionary origin: 1) Indigenous )Native( microorganisms Native to a particular habitat. Indigenous microorganisms are a group of innate microbial consortium that inhabits the soil and have the potentiality to live in it and do different activities (biodegradation, biocomposting, nitrogen fixation, improving soil fertility and as well in the production of plant growth) 2) Nonindigenous )Temporary ( microorganisms Not belonging to a particular habitat Non-indigenous species are species introduced outside their natural past or present range, which might survive and subsequently reproduce. They almost have shortened life expectancy and higher rates of mortality Soil microorganisms can be classified to: 1) Autochthonous species grow at a slow, steady rate, tend to be indigenous or native species, and undergo dormant stages to resist destruction. 1) Zymogenous species have resistant stages, but become active quickly when food sources become available, such as root exudates. 3) Allochthonous species are invaders of an environment (Non-indigenous), enter the soil ecosystem through precipitation, manure, sewage, or diseased plant tissue, do not participate in a sustained way to the soil community, and may die off with time. A) Autochthonous microorganisms 1) Autochthonous microorganisms are native or indigenous to a given soil ecosystem. They are the true inhabitants of an ecosystem; referring to common microbiota of the soil microorganisms that stand to remain constant despite fluctuations in the quantity of fermentable organic matter 2) They can grow and metabolize foods from native soil organic matter under 3) They can grow in soil which contains a limited source of energy (They don’t need an external energy source). 4) Autochthonous microbial population are found in high numbers in the soil 5) They are uniformly spread in soil and relatively constant throughout the soil. 6) The population does not fluctuate in response to nutrient availability. 7) They grow and metabolize under scarce nutrient resources. (they are mostly found in soil that has limited resources). 8) Many of these autochthonous bacteria are oligotrophic, which means that they can grow under conditions of scarcity of resources (i.e., under nutrient limitation) at low growth rates. 9) The microbial autochthonous can decompose humified organic matter 10) Caulobacter sp. and Escherichia coli are two examples of autochthonous bacteria. B) Zymogenous microorganisms 1) Zymogenous term used to describe opportunistic soil microorganisms that grow rapidly on exogenous substrates. (require easily oxidizable substrates for their growth). Once high energy-containing nutrients are added, they show a rapid growth 2) Their number in soil fluctuates frequently 3) Number of zymogenous microorganisms in the soil is low compared to autochthonous bacteria. 4) They need an external source of energy. Once it is provided, they show a rapid growth and rapidly increase to great numbers. 5) When the added nutrient level decreases, they return to undetectable numbers. Therefore, zymogenous bacterial population fluctuates greatly unlike autochthonous bacteria in response to the availability of nutrients. 6) zymogenous bacteria occur in low numbers in the soil. 7) Methylomonas sp., Nitrosomonas sp., Pseudomonas aeruginosa, Nitrospira sp. and Nitrobacter sp. 8) the presence of zymogenous bacteria in soil is temporary. 9) zymogenous can decomposes fresh and soluble organic matter 10) soil microenvironments such as the rhizosphere are dominated by zymogenous bacteria, such as Pseudomonas fluorescens, which grow rapidly on the simple C substrates (glucose). 11) Zymogenous microorganisms are usually copiotrophic  the Difference Between Autochthonous and Zymogenous Bacteria C) Allochthonous 1) They are Nonindigenous )Temporary ( microorganisms 2) They are microorganisms foreign to a given ecosystem. 3) allochthonous microorganisms are grown elsewhere and transported into a given habitat to be there a transient member of community. 4) They do not occupy the functional niches and typically they are weak competitors (although temporary could be abundant) Note Although the definitions of autochthonous and allochthonous microorganisms are mutually exclusive, it is often difficult to determine whether a microorganism found in a particular ecosystem is indeed autochthonous or allochthonous. allochthonous microorganisms that have arrived at a new habitat may be able to survive, grow, and carry out active metabolism and perhaps to become autochthonous microorganisms it is possible that autochthonous microorganisms are not only obligate autochthonous but also zymogenous under nutrient rich conditions. Autochthonous (permanent) is sometimes used with allochthonous (transient) as antonyms  Oligotrophs Oligotroph" Is a combination of the Greek adjective oligos meaning "Few" And the adjective trophikos meaning "Feeding". An oligotroph is an organism that can live and grow in an environment that offers very low levels of nutrients. Oligotrophs are characterize by slow growth low rates of metabolism, generally low population density. ▪ Copiotroph A copiotroph is an organism found in environments rich in nutrients, particularly carbon. They tend to grow only in high organic substrate conditions.  Generalists and Specialists soil Microorganisms Generalist microorganisms microorganisms which exhibit broad environmental tolerances with even distributions across many habitats, Many bacteria and archaea in soil can be characterized as soil “generalists”; as, they are found (often in high numbers) in practically every soil on Earth. Examples of such soil generalists are members of the genus Bacillus and related genera, actinobacteria, Pseudomonas sp. Such generalists can, however, adapt to the selective processes that are present in a particular microsite in the soil. Specialist microorganisms specialists, which are strongly restricted to one specific habitat due to narrow tolerances Ex: an extremely low or high soil pH may favor acidophilic or alkaliphilic bacteria or archaea whereas completely anoxic conditions (anaerobic), such as those following soil flooding, may favor anaerobic bacteria Moreover, the presence of specific plants like legumes may favor specific bacterial types, such as the rhizobia that form root nodules and carry out nitrogen fixation in symbiosis with legumes Types of microorganisms in Soil Bacteria Actinomycetes Fungi Algae protozoa  Diversity of soil microorganisms Soil organisms can be grouped based on: Size: how big they are fungi > actinomycetes > yeasts > bacteria Species: their numbers bacteria > fungi > actinomycetes > yeasts Function: how they make their living Soil depth  Examples : Fungi like Rhizopus sp., Mucor sp., Chaetomium , Fusarium sp., Cladosporium sp., Rhizoctonia sp., Aspergillus sp., Trichoderma sp. Bacteria like Azotobacter sp., Rhizobium sp., Bacillus sp., Xanthomonas sp. Actinomycetes Streptomyces sp., Nocardia sp. Yeasts Saccharomyces sp. , Cryptococcus sp. , Candida sp.  Benefits of Soil Biodiversity Soil has the ability to bound back from a Ecosystem Stability. severe disturbance Ecosystem Flexibility. Soil has several ways to accomplish the same function (system redundancy) Soil Close-Up = Cyanobacteria = Actinomycetes Bacteria Bacteria are the most diverse group in the soil, and the most abundant cell type. Bacteria are prokaryotes, (lacking a nuclear membrane. Bacterial cells are usually in the range of 0.4-2 μm, and can be spherical, rod-shaped or S shaped. Some bacteria have flagella making them mobile. However, in the soil they are most often attached to surfaces by ion exchange.  Fungi Unlike the bacteria, fungi belong to the eukaryotes, ( organisms with a true cell nucleus). Most fungi are aerobic heterotrophs; some anaerobes occur in guts of animals and in wastewater. Although there are far more species of bacteria than fungi - the ratio between both being dependent on the environment - the biomass of these two major groups in soil is comparable.  Cyanobacteria and Algae Taxonomically, cyanobacteria and algae belong to two different domains: cyanobacteria are prokaryotic eubacteria, algae are eukaryotes. However, due to their functional and morphological similarities, the cyanobacteria were previously grouped together with the algae under the name: algae. Both cyanobacteria and algae are photosynthetic organisms; cyanobacteria are also commonly capable of fixing nitrogen. Cyanobacteria are believed to be one of the oldest life forms on earth, dating back more than 3.5 billion years, and were probably the primary agents in oxygenating the atmosphere and earth. Both algae and cyanobacteria are found in all soils. Although they need light to grow, they can be found even in deeper soil layers. Actinomycetes 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.  Effect of Soil microorganisms on soil structure Soil structure dependent on stable aggregates of soil particles Soil organisms play important role in soil aggregation Bacterial cells and mycelial strands of fungi and actinomycetes play important role in soil aggregation Constituents of soil playing important role in cementing of soil particles organic matter polysaccharides lignin and gums synthesized by soil microbes  Role of Soil microorganisms in plant growth Convert complex organic nutrients into simpler inorganic forms which are readily absorbed by the plant for growth. Produce variety of substances like IAA, gibberellins, antibiotics etc. which directly or indirectly promote the plant growth. Role of microorganisms in Biogeochemical Cycles Biogeochemical Cycles: Recycling (oxidation and reduction) of chemical elements 1. Carbon Cycle 2. Nitrogen Cycle 3. Sulfur Cycle 4. Phosphorus Cycle Soil - Plant –Microbe Interaction  Soil Fractions Bulk soil – root free soil which passes through a 2mm mesh sieve Rhizosphere soil – aggregates (0.5-5 mm) removed from fine roots by gentle shaking Soil-root interface (SRI) – fine roots (