Prescott's Microbiology,4/e

		Microbiology, 4/e Prescott, Harley, Klein
		Instructor Resources

42 Terrestrial Environments

CHAPTER OVERVIEW

This chapter discusses the general characteristics of microorganisms associated with soils. Soils are dominated by solid materials, and the environment is mostly aerobic. Soils respond to changes in temperature and moisture and to the effects of plowing and other disturbances. Many of these responses are reflected or mediated by the microbial populations found in the soils.

CHAPTER OBJECTIVES

After reading this chapter you should be able to:

! describe the general characteristics of soils from different climates

! discuss the reasons that soil microbial communities are not well-known

! discuss the interactions of microorganisms with the surfaces found in soils

! describe the interaction of microorganisms with insects and other soil animals, and explain how these interactions influence nutrient cycling and other processes

! discuss organic matter accumulation and decomposition in soils

! discuss the various associations between plants and microorganisms and the ways these associations increase the ability of the plants to compete for water and nutrients

! discuss the Rhizobium-legume symbiosis

! discuss mycorrhizal relationships

! discuss the use of composting for maintaining and increasing the fertility of soils

! discuss the degradation and degradability of pesticides in soils, and explain how this affects the function of these substances

! discuss the interactions of soil microbes with the atmosphere and their involvement in gaseous pollutant utilization and modification

CHAPTER OUTLINE

I. The Environments of Soil Microorganisms

A. Soils consist of peds (heterogeneous aggregates of various sizes that contain complex networks of pores and surfaces) that influence nutrient availability and that affect interactions among different microbes

1. Bacteria are found primarily in the microenvironment associated with smaller pores; this protects them from protozoa predation and gives them access to soluble nutrients

2. Filamentous fungi form bridges between separated regions where moisture is available; they move nutrients and water over greater distances in the soil

3. Protozoa, soil insects, and nematodes are located on the outside of the aggregates and feed on the bacteria and fungi

B. Gradients of various environmental factors and nutrients can exist within the pores of the soil (e.g., oxygen gradients)

C. Various soil components= binding affinities for nutrients and other substances can create different microenvironments within the soil; (e.g., anaerobic microsites)

D. Physical factors (e.g., pH) can influence microorganisms that are associated with surfaces

E. Soil clays and humus (partially degraded and stabilized organic matter) attract and bind organic and inorganic substances

F. Clays can serve as genetic microchips where microbially derived enzymes, RNA and DNA allow binding and elongation of nucleic acids

II. Soil Microorganisms, Insects, and AnimalsCContributions to Soils

A. Colonization takes place after geological disturbances begin to form soil

B. Nutrients such as phosphorus and iron must be present, but carbon and nitrogen can be imported by biological processes

C. Once formed, most soils are rich sources of nutrients because of the plant and animal life that lives and dies there, contributing to the nutrient resources

D. Except for the plant component, bacteria and fungi are in greatest abundance in terms of biomass carbon and nitrogen

E. Soil organisms play a major role in the decomposition of plant litter, which would otherwise accumulate in the environment

F. Many of the soil microorganisms have not been cultured and are, therefore, poorly understood; however, DNA analysis and PCR amplification are providing interesting and unexpected information about these unculturable organisms

G. Filamentous actinomycetes, primarily of the genus Streptomyces, produce an odor causing compound called geosmin which give soils their characteristic earthy odor

H. Soil microorganisms can be categorized on the basis of their preference for easily available or more resistant substrates

1. ZymogenousCorganisms that respond rapidly to the addition of easily utilizable substrates such as sugars and amino acids

2. AutochthonousCindigenous forms that tend to utilize native organic matter

I. Microbes that can grow in oligotrophic (low nutrient) environments have developed special strategies to deal with those conditions

J. Soil insects and animals serve as decomposer-reducers, which 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

K. Protozoa influence nutrient cycling by microbivory (feeding on Apalatable@ microorganisms), causing an increase in the rates of nitrogen and phosphorus mineralization

L. Free hydrolytic enzymes released from animals, plants, insects, and lysed microorganisms contribute to soil biochemistry

III. Microorganisms and the Formation of Different Soils

A. An imbalance of primary production and decomposition can lead to either an accumulation of organic matter or the production of an organic-poor, low-fertility soil

B. High temperature (greater than 25EC) favors decomposition

C. Decomposition is a complex process; plant litter, microbial content, soil temperature, water availability, and oxygen availability must be considered

IV. Soil Microorganism Associations with Plants

A. Plants are heavily colonized by microorganisms

B. The presence of microorganisms increases the rate of organic matter released from the roots (exudation)

C. Microorganisms influence plant growth through the release of morphology influencing compounds such as auxins, giberellins and cytokinins

D. The Rhizosphere and Rhizobium

1. The rhizosphere is the area of the soil in the immediate vicinity of the plant roots

2. Release of organic materials from the roots causes localized changes

3. In low-fertility soils (e.g., desert soils) this may have a tremendous impact on the microbial community, while in high-fertility soils this effect may not be as pronounced

4. Microorganisms in the rhizosphere serve as a labile source of nutrients and play a critical role in organic matter synthesis and degradation

5. Environment around certain types of plants promotes association with mutualistic nitrogen-fixing bacteria; the genus Rhizobium is a prominent member of the rhizosphere community

a. Rhizobium is stimulated to produce Nod factors that promote activate the host symbiotic process necessary for root hair infection and module development

b. An infection thread forms and grows down the root hair

c. Rhizobium spreads within the infection thread into the underlying root cells

d. Bacteria multiply and develop into swollen, branched bacteroids enclosed by a plant-derived membrane called the peribacteroid membrane

e. Further growth and differentiation lead to the formation of nitrogen-fixing forms called symbiosomes

f. Nitrogen fixation occurs within the symbiosome and the nitrogen is then assimilated into various organic compounds and distributed throughout the plant

g. Associative nitrogen fixation also occurs and is mediated by free-living bacteria in the rhizosphere; however, recent evidence suggests that the major contribution of these bacteria may be the reduction of nitrate to ammonia, which is then available for use by the plant

h. A major goal of biotechnology is to introduce nitrogen fixing genes into plants that do not normally form such associations

E. ActinorrhizaeCactinomycete-root associations between members of the genus Frankia and woody plants; they can fix nitrogen and are important in the life of woody, shrublike plants

F. MycorrhizaeCfungus-root associations; 5 associations have been described

1. EctomycorrhizaeCgrow 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 mycorhizal helper bacteria (MRB)

2. EndomycorrhizaeCfungal hyphae penetrate the outer cortical cells of the plant root, where they form characteristic structures known as arbuscules; they increase the competitiveness of the plant and increase water uptake by the plant in arid environments

G. Tripartite and Tetrapartite AssociationCinvolve some combination of plant, rhizobia, mycorrhizae, and actinorrhizae; enable plant to better cope with nutrient-deficient environments

1. Capable of nitrogen fixation

2. Important in the lives of these plants

H. Fungal and Bacterial Endophytes of PlantsCsome fungi and bacteria infect and live within plants as endophytes; can be mutualistic or parasitic (pathogenic)

I. Tumorigenicity or AgrobacteriuCGenetic ApplicationsCAgrobacterium containing the Ti (tumor-inducing) plasmid cause the formation of galls (tumors) on the plant; recent interest centers around the use of the Ti plasmid as a vector to transfer new genetic characteristics (eg., herbicide resistance; bioluminescence) to the plant

V. Soil Organic Matter and Soil FertilityCmicrobial degradation must be balanced by the need for organic matter in order to retain nutrients, to maintain soil structure, and to hold water for plant use

A. Plowing and other soil disturbances aerate soil and increase microbial degradation

B. No-till and minimum-till practices reduce aeration but require more herbicides to control weed infestation

C. Composting allows for controlled decomposition which produces physiologically stabilized compost material that, when added to the soil, increases the organic content without stimulating soil microorganisms to increase decomposition

VI. Degradation and MicroorganismsCFallibility and Recalcitrance

A. FallibilityCnot all organic compounds can be degraded by microorganisms

B. RecalcitranceCthe degree to which an organic compound can resist microbial degradation

C. Degradation is promoted by the presence of easily usable energy sourcesCcometabolism

D. A balance is needed such that a pesticide will remain active in the soil long enough to do its job, but degrade quickly enough so that it will not linger beyond its useful period and thereby have an adverse effect

E. Degradation usually takes place in several stages

F. Degradation processes can be harnessed to degrade agricultural wastes and waste water by land farming, where the waste is incorporated into the soil or allowed to flow over the soil where degradation occurs

G. Phytoremediation involves planting fast-growing plants in contaminated soil; stimulates microbial growth through release of organic nutrients; this allows cometabolic processes that stimulate degradation

VII. Soil Microorganism Interactions with the Atmosphere

A. Ice-nucleating bacteria serve as nucleation centers for snow and precipitation formation

B. AIce-minus@ strains that have been genetically engineered seem to protect strawberries from frost damage when sprayed on the plant; however, the release of such genetically engineered microorganisms (GEMs) into the environment is of continuing concern

C. 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

3. Methane has become of increasing concern and it is questionable if consumption can keep up with production rates; this may lead to atmospheric accumulation with a rise in average atmospheric temperature (greenhouse effect)

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