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  1. Soil as an Environment for Microorganisms
    1. Soil consists primarily of inorganic geological materials, which are modified by the biotic community
    2. Soils are dynamic and develop over time
      1. Changes in the activity of the microbial community caused by changes in plant growth, temperature, and other factors can significantly alter soil
      2. In most soils, the major producers of organic material are vascular plants; algae, cyanobacteria and photosynthetic bacteria also contribute
    3. Bacteria, fungi, protozoa, insects, nematodes, worms and many other animals live in soil
    4. Soil varies in terms of the amount of oxygen available to microorganisms
      1. Highly oxygenated areas are found on particle surfaces; microorganisms are often found in thin films of water on these surfaces
      2. The interior of a soil particle can be anaerobic
      3. Under certain conditions, soil may contain isolated pockets of water, which serve as mini-aquatic environments; oxygen concentrations are generally lower in these pockets of water
      4. Water logged soil is very similar to anaerobic lake sediments
    5. Changes in water content, gas fluxes, and the growth of plant roots can affect the concentration of carbon dioxide and other gases in the soil
  2. Microorganisms in the Soil Environment
    1. Bacteria are found primarily on the surfaces of soil particles, most frequently on surfaces of pores in these particles; this probably protects them from predation by protozoa and gives them access to soluble nutrients
    2. Filamentous fungi form bridges between separated particles or aggregates called peds; this exposes the fungi to high levels of oxygen; filamentous fungi move nutrients and water over great distances in the soil
    3. Protozoa, soil insects, and other animals are located in soil and often feed on bacteria and fungi
    4. Microbial populations can be very high; yet only a small portion of them have been cultured; actinobacteria are important, but less studied, members of terrestrial soil ecosystems
    5. Microorganisms are constantly being added to soil, but most do not survive
    6. The microbial community makes important contributions to biogeochemical cycling
      1. Soil microorganisms can be categorized on the basis of their preference for easily available or more resistant substrates
        1. Some prefer higher nutrient levels and they respond rapidly to the addition of easily utilizable substrates such as sugars and amino acids
        2. Others are indigenous forms that tend to utilize native organic matter
        3. Some grow in oligotrophic (low nutrient) environments
      2. Soil insects and other animals serve as decomposer-reducers; they not only decompose but also physically reduce the size of organic aggregates; this increases the surface area and makes nutrients more available for utilization by bacteria and fungi
      3. Protozoa influence nutrient cycling by microbivory (feeding on microorganisms), causing an increase in the rates of nitrogen and phosphorus mineralization
      4. Free hydrolytic enzymes released from animals, plants, insects, and microorganisms contribute to soil biochemistry
      5. Microbial loop-rapid turn over of organic matter making the nutrients available to plants rather than to higher trophic levels; bacteria and predatory protozoa are involved in this process
  3. Microorganisms and the Formation of Different Soils
    1. Soil formation
      1. Colonization takes place after newly exposed geological material begins to weather
      2. Nutrients such as phosphorus and iron may be present, but carbon and nitrogen must be imported; cyanobacteria are active in the pioneer stage of nutrient accumulation
      3. Once formed, most soils are rich sources of nutrients because of the plant and animal life that lives and dies there
    2. Tropical and temperate region soils
      1. In tropical soils, organic matter is decomposed rapidly and mobile inorganic nutrients can be leached out causing rapid loss of fertility; fertility can be further decreased by slash-and-burn agriculture
      2. In temperate region soils, decomposition rates are less than the rate of primary production
        1. In temperate grasslands, deep root penetration leads to formation of fertile soils
        2. In cooler coniferous environments, there can be excessive accumulations of organic matter; fire is a major means to control nutrient cycles
        3. In bog soils, decomposition is slowed by waterlogged, anoxic conditions; this leads to peat accumulation
    3. Cold moist area soils-colder temperatures decrease both the rate of decomposition and the rate of plant growth; below the plant growth zone is permafrost; these soils are very sensitive to physical disturbances and pollution
    4. Desert soils-microbial communities called desert crusts, which consist of cyanobacteria and associated commensals, can retain rainfall
    5. Geologically heated hyperthermal soils-populated by bacteria and archaea, many of which are chemolithoautotrophs; chemoorganotrophs are also present
  4. Soil Microorganism Associations with Vascular Plants
    1. Microorganisms on the outside of plants
      1. Phyllosphere microorganisms-a wide variety of microorganisms are found on and in the aerial surfaces of plants (phyllosphere), where they can utilize organic compounds released by the leaves and stems; phyllosphere microorganisms can either protect or harm the plant host
      2. Rhizosphere and rhizoplane microorganisms
        1. The rhizosphere is the volume of soil around plant roots influenced by materials released by the plants; the rhizoplane is the root surface; both provide unique environments for microorganisms; microorganisms in the rhizosphere serve as a labile source of nutrients and play a critical role in organic matter synthesis and degradation
        2. Numerous rhizosphere bacteria influence plant growth through the release of auxins, gibberellins, cytokinins, and other molecules
        3. Associative nitrogen fixation-nitrogen fixation carried out by bacteria on the rhizoplanes and in the rhizosphere
    2. Microorganism growth within plants
      1. Rhizobium-a prominent member of the rhizosphere community; it can also establish an endosymbiotic association with legumes and fix nitrogen for use by the plant
        1. The infection process is under the control of a bacterial gene and a plant regulatory protein
        2. Rhizobium is stimulated to produce Nod factors, which activate the host responses necessary for root hair infection and module development
        3. The bacterium induces formation of an infection thread by the plant; the infection thread grows down the root hair
        4. Rhizobium spreads within the infection thread into the underlying root cells
        5. Bacteria multiply and develop into swollen, branched bacteroids enclosed by a plant-derived membrane called the peribacteroid membrane
        6. Further growth and differentiation lead to the formation of nitrogen-fixing forms called symbiosomes
        7. Nitrogen fixation occurs within symbiosomes within the root nodules, and the nitrogen is then assimilated into various organic compounds and distributed throughout the plant
        8. Once differentiated, the bacterial cells cannot reproduce; this sacrifice has been called altruism in the rhizosphere: it may promote root exudation and the maintenance of high levels of Rhizobium in the rhizosphere
        9. A major goal of biotechnology is to introduce nitrogen-fixing genes into plants that do not normally form such associations
      2. Fungal and bacterial endophytes of plants-some fungi and bacteria infect and live within plants as endophytes; can be mutualistic or parasitic (pathogenic)
      3. Mycorrhizae
        1. Fungus-root associations
        2. Five associations have been described; they fall into two broad categories
          1. ) Ectomycorrhizae-grow as an external sheath around the root with limited penetration of the fungus into the cortical regions of the root; found primarily in temperate regions; mycelia extend far into the soil forming a mycorrhizosphere and mediate nutrient transfer to the plant; process is aided by mycorrhizal helper bacteria (MRB)
          2. ) Endomycorrhizae-fungi that penetrate the outer cortical cells of the plant root, where they form characteristic structures known as arbuscules
        3. Mycorrhizae increase the competitiveness of the plant and increase water uptake by the plant in arid environments; they also make it possible to share resources (e.g., carbon, minerals and water)
      4. Actinorrhizae-actinomycete-root associations between members of the genus Frankia and woody plants; Frankia can fix nitrogen and are important in the life of woody, shrublike plants
      5. Stem-nodulating rhizobia-bacteria that form nodules at the base of adventitious roots branching out of the stem part above the soil surface; observed primarily in tropical legumes
      6. Agrobacterium-members of this genus containing the Ti (tumor-inducing) plasmid cause the formation of galls (tumors) on the plant; is a complex process that involves transfer of Ti DNA into the plant host; recent interest in these bacteria centers on the use of the Ti plasmid as a vector to transfer new genetic characteristics (eg., herbicide resistance, bioluminescence) to plants
      7. Fungi and bacteria as plant pathogens-many fungi and bacteria are plant pathogens, causing rusts, blights, rots and other plant diseases
      8. Viruses-many viruses infect plants and cause disease and economic losses (e.g., TMV)
    3. Tripartite and tetrapartite associations-involve some combination of plant, rhizobia, mycorrhizae, and actinorrhizae; enable plant to better cope with nutrient-deficient environments
  5. Soils, Plants, and Nutrients
    1. Organic matter in soil helps retain nutrients, maintain soil structure, and hold water for plant use; plowing, irrigation, and other soil disturbances can increase microbial degradation of this organic matter, thereby decreasing soil fertility
    2. Several agricultural methods have been developed to promote and maintain soil fertility
      1. No-till and minimum-till practices reduce aeration and use herbicides to control weed infestation
      2. Composting allows for controlled decomposition and produces physiologically stabilized compost material; this material, when added to the soil, increases the organic content without stimulating soil microorganisms to increase decomposition
    3. Soils are increasingly being impacted by mineral nitrogen releases resulting from human activities
      1. This nitrogen is derived from two major sources: agricultural fertilizers and fossil fuel combustion
      2. The nitrogen releases have had a number of effects
        1. When the nitrogen added is greater than can be used by plants, it remains in mobile form and can enter surface water and groundwater; higher nitrate levels in water are related to a number of animal health problems
        2. Nitrogen fertilizers alter microbial community structure and function
        3. Excessive use of fertilizers can have global-level impacts when nitrogen enters coastal and marine waters
    4. Phosphorus fertilizers cause eutrophication of surface waters when excess phosphorus moves into those waters
  6. Soils, Plants, and the Atmosphere
    1. Ice-nucleating bacteria serve as nucleation centers for snow and precipitation formation; genetically engineered ice-minus bacteria can be sprayed on frost-sensitive plants to protect the plants from frost-damage; however, the release of such genetically engineered microorganisms into the environment is of continuing concern
    2. Soil microorganisms can influence the atmosphere by degrading airborne pollutants such as methane, hydrogen, and carbons dioxide; they can also improve air in closed buildings
    3. Soil microorganisms can influence the global fluxes of both relatively stable and reactive gases
      1. Relatively stable gases include carbon dioxide, nitrous oxide, nitric oxide, and methane
      2. Reactive gases include ammonia, hydrogen sulfide, and dimethylsulfide
    4. Use of nitrogen-containing fertilizers, use of automobiles, conversion of soils to agricultural use, and use of landfills can stimulate production of NO, N20, methane and other greenhouse gases
      1. Methane is produced by methanogens found in ruminants, rice paddies, termite guts, and landfills
      2. Methane is degraded by methanotrophs
      3. The balance between methane production and methane utilization is important for preventing excessive accumulation of this greenhouse gas
  7. Microorganisms and Plant Decomposition
    1. Released soluble materials from plants create a residuesphere, an area between decaying plant material and the soil; residuesphere has much microbial activity
      1. Soluble plant materials are degraded first
      2. Starch, cellulose, and proteins are then degraded, both aerobically and anaerobically
      3. Lignin is degraded primarily by aerobic basidiomycetes, but only after physical rot leads to cavitation of wood
    2. Unusual gases are produced in the process of woody plant decomposition (e.g., chloromethanes, and cyanide)
  8. The Subsurface Biosphere
    1. Studied by examining outcrops, surface excavations, petroleum hydrocarbons, well corings, and materials from deep mine sites; the use of improved techniques has led to the acceptance of the idea that microorganisms exist far below Earth's surface
    2. Microbial processes take place in different regions
      1. Shallow subsurface where water flowing from the surface moves below the plant root zone
      2. Subsurface regions where organic matter has been transformed by chemical and biological processes to yield coal, kerogens, and oil and gas; mobile materials move up into more porous geological structures where microorganisms can be active
      3. Zones where methane is being synthesized
  9. Soil Microorganisms and Human Health
    1. Soils contain a wide variety of pathogenic organisms, which can cause disease if they have an entry point into the human body and find favorable conditions there (e.g., Clostridium, Acanthamoeba, and Cyclospora)
    2. The growth of soil-related microorganisms in buildings can cause mold problems and "sick building" syndrome
  10. Understanding Microbial Diversity in the Soil
    1. It is estimated that only 1 to 10% of microscopically observable organisms in soils can be cultured in the laboratory
    2. Molecular techniques are now making it possible to assess the range of microbial diversity in soils
    3. However, to fully understand the physiology of these microorganisms, scientists will ultimately need to culture them

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