Soil consists primarily of inorganic geological materials, which are modified by the biotic community
Soils are dynamic and develop over time
Changes in the activity of the microbial community caused by changes in plant growth, temperature, and other factors can significantly alter soil
In most soils, the major producers of organic material are vascular plants; algae, cyanobacteria and photosynthetic bacteria also contribute
Bacteria, fungi, protozoa, insects, nematodes, worms and many other animals live in soil
Soil varies in terms of the amount of oxygen available to microorganisms
Highly oxygenated areas are found on particle surfaces; microorganisms are often found in thin films of water on these surfaces
The interior of a soil particle can be anaerobic
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
Water logged soil is very similar to anaerobic lake sediments
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
Microorganisms in the Soil Environment
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
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
Protozoa, soil insects, and other animals are located in soil and often feed on bacteria and fungi
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
Microorganisms are constantly being added to soil, but most do not survive
The microbial community makes important contributions to biogeochemical cycling
Soil microorganisms can be categorized on the basis of their preference for easily available or more resistant substrates
Some prefer higher nutrient levels and they respond rapidly to the addition of easily utilizable substrates such as sugars and amino acids
Others are indigenous forms that tend to utilize native organic matter
Some grow in oligotrophic (low nutrient) environments
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
Protozoa influence nutrient cycling by microbivory (feeding on microorganisms), causing an increase in the rates of nitrogen and phosphorus mineralization
Free hydrolytic enzymes released from animals, plants, insects, and microorganisms contribute to soil biochemistry
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
Microorganisms and the Formation of Different Soils
Soil formation
Colonization takes place after newly exposed geological material begins to weather
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
Once formed, most soils are rich sources of nutrients because of the plant and animal life that lives and dies there
Tropical and temperate region soils
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
In temperate region soils, decomposition rates are less than the rate of primary production
In temperate grasslands, deep root penetration leads to formation of fertile soils
In cooler coniferous environments, there can be excessive accumulations of organic matter; fire is a major means to control nutrient cycles
In bog soils, decomposition is slowed by waterlogged, anoxic conditions; this leads to peat accumulation
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
Desert soils-microbial communities called desert crusts, which consist of cyanobacteria and associated commensals, can retain rainfall
Geologically heated hyperthermal soils-populated by bacteria and archaea, many of which are chemolithoautotrophs; chemoorganotrophs are also present
Soil Microorganism Associations with Vascular Plants
Microorganisms on the outside of plants
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
Rhizosphere and rhizoplane microorganisms
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
Numerous rhizosphere bacteria influence plant growth through the release of auxins, gibberellins, cytokinins, and other molecules
Associative nitrogen fixation-nitrogen fixation carried out by bacteria on the rhizoplanes and in the rhizosphere
Microorganism growth within plants
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
The infection process is under the control of a bacterial gene and a plant regulatory protein
Rhizobium is stimulated to produce Nod factors, which activate the host responses necessary for root hair infection and module development
The bacterium induces formation of an infection thread by the plant; the infection thread grows down the root hair
Rhizobium spreads within the infection thread into the underlying root cells
Bacteria multiply and develop into swollen, branched bacteroids enclosed by a plant-derived membrane called the peribacteroid membrane
Further growth and differentiation lead to the formation of nitrogen-fixing forms called symbiosomes
Nitrogen fixation occurs within symbiosomes within the root nodules, and the nitrogen is then assimilated into various organic compounds and distributed throughout the plant
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
A major goal of biotechnology is to introduce nitrogen-fixing genes into plants that do not normally form such associations
Fungal and bacterial endophytes of plants-some fungi and bacteria infect and live within plants as endophytes; can be mutualistic or parasitic (pathogenic)
Mycorrhizae
Fungus-root associations
Five associations have been described; they fall into two broad categories
) 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)
) Endomycorrhizae-fungi that penetrate the outer cortical cells of the plant root, where they form characteristic structures known as arbuscules
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)
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
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
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
Fungi and bacteria as plant pathogens-many fungi and bacteria are plant pathogens, causing rusts, blights, rots and other plant diseases
Viruses-many viruses infect plants and cause disease and economic losses (e.g., TMV)
Tripartite and tetrapartite associations-involve some combination of plant, rhizobia, mycorrhizae, and actinorrhizae; enable plant to better cope with nutrient-deficient environments
Soils, Plants, and Nutrients
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
Several agricultural methods have been developed to promote and maintain soil fertility
No-till and minimum-till practices reduce aeration and use herbicides to control weed infestation
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
Soils are increasingly being impacted by mineral nitrogen releases resulting from human activities
This nitrogen is derived from two major sources: agricultural fertilizers and fossil fuel combustion
The nitrogen releases have had a number of effects
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
Nitrogen fertilizers alter microbial community structure and function
Excessive use of fertilizers can have global-level impacts when nitrogen enters coastal and marine waters
Phosphorus fertilizers cause eutrophication of surface waters when excess phosphorus moves into those waters
Soils, Plants, and the Atmosphere
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
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
Soil microorganisms can influence the global fluxes of both relatively stable and reactive gases
Relatively stable gases include carbon dioxide, nitrous oxide, nitric oxide, and methane
Reactive gases include ammonia, hydrogen sulfide, and dimethylsulfide
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
Methane is produced by methanogens found in ruminants, rice paddies, termite guts, and landfills
Methane is degraded by methanotrophs
The balance between methane production and methane utilization is important for preventing excessive accumulation of this greenhouse gas
Microorganisms and Plant Decomposition
Released soluble materials from plants create a residuesphere, an area between decaying plant material and the soil; residuesphere has much microbial activity
Soluble plant materials are degraded first
Starch, cellulose, and proteins are then degraded, both aerobically and anaerobically
Lignin is degraded primarily by aerobic basidiomycetes, but only after physical rot leads to cavitation of wood
Unusual gases are produced in the process of woody plant decomposition (e.g., chloromethanes, and cyanide)
The Subsurface Biosphere
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
Microbial processes take place in different regions
Shallow subsurface where water flowing from the surface moves below the plant root zone
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
Zones where methane is being synthesized
Soil Microorganisms and Human Health
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)
The growth of soil-related microorganisms in buildings can cause mold problems and "sick building" syndrome
Understanding Microbial Diversity in the Soil
It is estimated that only 1 to 10% of microscopically observable organisms in soils can be cultured in the laboratory
Molecular techniques are now making it possible to assess the range of microbial diversity in soils
However, to fully understand the physiology of these microorganisms, scientists will ultimately need to culture them
