Soil microbiology and cycles of the elements


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Soil microbiology and cycles of the elements

  1. 1. What is Soil Microbiology?Soil Microbiology is the branch of soil science concerned with soil inhabiting microorganisms, their functions and activities
  2. 2. What is soil?Soil is the outer, loose earth material which is distinctly different from the underlying bedrock and the region which support plant life.
  3. 3. Soil is made up of manythings, such as weathered rockand decayed plant and animalmatter. Soil is formed over a longperiod of time. Soil is formed from theweathering of rocks andminerals Weathering is the process ofthe breaking down rocks. Thereare three different types ofweathering. Physical, chemicaland biological weathering.
  4. 4. An example of biological weathering of a rock under the influence of clams
  5. 5. Functions of Soil in the Global EcosystemSoils perform five key functions in the global ecosystem.• medium for plant growth,• regulator of water supplies,• recycler of raw materials,• habitat for soil organisms, and• landscaping and engineering medium.
  6. 6. The Components Of Soil• Soils have five basic components:1. Minerals2. Organic Matter3. Water4. Air5. Soil organisms
  7. 7. Gross Soil Composition
  8. 8. 1.Minerals• The mineral part of soil is composed of varying amounts of sand, silt, and clay. These particles are inorganic. Their characteristics greatly influence soil behavior and management needs.
  9. 9. Soil Particle Size• Particle size is an important property that allows us to make distinctions among the different soil minerals.• Soils contain particles that range from very large boulders to minute particles which are invisible to the naked eye.
  10. 10. To further distinguish particles based upon size,particles are separated into the two categories: thecoarse fraction and the fine earth fraction.
  11. 11. Fine Earth Fraction The Fine Earth Fraction Size Texture CharacteristicsSand 2.0 mm -0.05 mm gritty Sand is visible to the naked eye, consists of particles with low surface area, and permits excessive drainage.Silt 0.05 mm - 0.002 buttery Silt is not visible to the naked eye and mm increases the water holding capacity of soil.Clay < 0.002 mm sticky Clay has a high surface area, high water holding capacity, many small pores, and possesses charged surfaces to attract and hold nutrients.
  12. 12. Sand• Sand is mainly small rock fragments and hard minerals such as quartz (silicon dioxide). It contains few plant nutrients• Of the three types of soil particles, sand is the largest in size
  13. 13. • Silt consists of groundSilt up sand (quartz) and rock minerals. Silt contains few nutrients by itself, but it can have nutrients clinging to its surface. • Silt is between sand and clay in terms of size.
  14. 14. Clay• Unlike sand and silt, clays are aluminum- silicate minerals that also have varying amounts of plant nutrients such as potassium, calcium, magnesium, iron, etc.• A good part of a soils native fertility can come from its clay portion
  15. 15. Relative size comparison betweensand, silt, and clay of the fine earth fraction.
  16. 16. COARSE FRACTION The coarse fraction of soil includes anysoil particles greater than 2mm. The coarse fraction includesboulders, stones, gravels, and coarsesands. These are rocky fragments and aregenerally a combination of more thanone type of mineral.
  17. 17. • Organic Matter in the soil includes plant and animal residues at various stages of decomposition, cells and tissues of soil organisms, and substances synthesized by plant roots and soil microorganisms.• Organic matter in the soil is frequently in the form of humus, partially decomposed organic matter that has become dark and crumbly and continues decomposing at a slow rate
  18. 18. Humus benefits the soil in many ways:  It can improve overall physical condition, especially in clay soils.  It can help reduce soil erosion by wind and water because it acts as a "glue" to bind soil particles together into "crumbs," called aggregates, that improve water intake rates and lessen runoff.  It stores and supplies nutrients, especially nitrogen, phosphorus, and sulfur. These are slowly released for use by plant roots as organic matter decomposes  It increases the water-holding capacity of sandy soils.  Its high negative charge helps prevent positively-charged nutrients from leaching. In addition, negative charge improves a soils buffering capacity, or its ability to resist changes in pH.  It can reduce the incidence of some soil-borne diseases and stimulate growth of beneficial soil bacteria, fungi, and earthworms.
  19. 19. Who is at home in the soil?
  20. 20. Soil organisms are creatures that spend all or part of their lives in the soilSoil organisms can be grouped on thebasis of: Size: how big they are Species: ecological functions Function: how they make their living
  21. 21. Size of Soil OrganismsMacro or large Meso or mid-size Micro or small (>2 mm) (2–0.2 mm) (<0.2mm) Earthworm Springtail Yeast Alfalfa root Bacteria Mite
  22. 22. Based on the ecological function:(1) herbivores that subsist on living plants,(2) detritivores that subsist on dead plant debris,(3) predators that consume animals,(4) fungivores that eat fungi,(5) bacterivores that eat bacteria,(6) parasites that live off, but do not consume, otherorganisms.  Another classification of soil organisms groups them into: (1) heterotrophs that rely on organic compounds for energy (2) autotrophs that obtain their energy from photosynthesis
  23. 23. Commensalist ParasiticDietrich Werner, Marburg, Germany Symbiotic
  24. 24. • Earthworms – Mix fresh organic materials into the soil – Brings organic matter into contact with soil microorganisms • Soil insects and other arthropods – Shred fresh organic material into much smaller particles – Allows soil microbes to access all parts of the organic residue
  25. 25. Soil Microorganisms• BacteriaMost numerous in soilMost diverse metabolismCan be aerobic or anaerobicOptimal growth at pH 6-8
  26. 26. Nitrogen-fixing bacteria form symbiotic associationswith the roots of legumes. The plant supplies simplecarbon compounds to the bacteria, and the bacteriaconvert nitrogen (N2) from air into a form the planthost can use Nitrifying bacteria change ammonium (NH4+) tonitrite (NO2-) then to nitrate (NO3-) – a preferred formof nitrogen for grasses and most row crops. Denitrifying bacteria convert nitrate to nitrogen (N2)or nitrous oxide (N2O) gas; anaerobic
  27. 27. Actinomycetes• a large group of bacteria that grow as hyphae like fungi• Transitional group between bacteria and fungi• Active in degrading more resistant organic compounds• Optimal growth at alkaline pH
  28. 28. • 2 important products: – produce antibodies (streptomycin is produced by an actinomycetes) – produce geosmin; responsible for the characteristically “earthy” smell of freshly turned, healthy soil• Negative impact - potato scab (Streptomyces scabies)
  29. 29. Soil Microorganisms • Fungi Dominate the soil biomass Obligate aerobes Can survive desiccation Dominate in acid soils Negative impacts: – Apple replant disease (Rhizoctonia, Pythium, Fusarium, andPhytophtora) – Powdery mildew is caused by a fungus Beneficials:– Penicillium
  30. 30. What are mycorrhizal fungi?• Mycorrhizas are associations between fungi and plant roots that can be beneficial to both the plant and the fungi• The fungi link the plant with soil by acting as agents of nutrient exchange• In general, mycorrhizas play an important role in sustainable plant productivity and maintenance of soil structure.• Mycorrhizal associations occur on almost all terrestrial plants and are not as plant-specific as other plant-microbe associations that formed between some plants (e.g. legumes) and bacteria (e.g. rhizobia).
  31. 31. Mycorrhizal fungi Soil structure benefitMycorrhizal fungi present Mycorrhizal fungi absent• Soil structure stabilized and • Soil structure is weak strengthened • Structure is not maintained when• Structure is maintained when immersed in water immersed in water
  32. 32. Protists and nematodes- the predators –Feed on the primary Rotifer decomposers (bacteria, fungi, actinomycetes) Amoeba –Release nutrients (nitrogen) contained in the bodies of the Predatory nematode primary decomposers
  33. 33. Abundance of soil organisms Number Biomass1Organism per gram soil (lbs per (~1 tsp) acre 6”) Earthworms – 100 – 1,500 Mites 1-10 5 – 150 Nematodes 10 – 100 10 – 150 Protozoa up to 100 thousand 20 – 200 Algae up to 100 thousand 10 – 500 Fungi up to 1 million 1,000 – 15,000 Actinomycetes up to 100 million 400 – 5,000 Bacteria up to 1 billion 400 – 5,000 1 Biomass is the weight of living organisms
  34. 34. Why are soil organisms important? Soil animals perform several functions in soil that make them a vital part of all ecosystems, including agriculture. Soil animals are involved in:• degradation of organic matter and mineralisation of nutrients,• controlling populations of pathogens,• improving and maintaining soil structure and• mixing organic matter through the soil.