Charpter 4 Soil Microbiology
Few environments on earth have as great a variety of microorganisms as soil. Bacteria, fungi, algae, protozoa and viruses make up this microscopic menagerie, which may reach a total of billions per gram. The great diversity of the microbial flora makes it extremely difficult to determine accurately the total number of microorganisms present. Cultural methods will reveal only those physiological and nutritional types compatible with the cultural environment. Direct microscopic counts theoretically should permit enumeration of all except the viruses, but this technique also has its limitations, especially, in distinguishing living from dead microorganisms. Very often the microbiological analysis of soil is concerned with the isolation and identification of specific physiological types of microorganisms. For this purpose sective media, differential media, and enriched media are appropriate.
1. The Rhizosphere
·Rhizosphere: The region where the soil and roots make contact is designated the rhizosphere which is characterized by a zone of increased microbiological activity.
·The microbial population on and around roots is considerably higher than that of root-free soil. The differences are both quantitative and qualitative. Bacteria predominate, and their growth is enhanced by nutritional substances released from the plant roots, e.g., amino acids, vitamins, and other nutrients. The growth of the plant is influenced by the products of microbial metabolism that are released into soil. It has been reported that amino acid—requiring bacteria exist in rhizosphere in larger numbers than in the root—free soil. It has been demonstrated that the microbiota of the rhizoshere is more active physiologically than that of nonrhizosphere soil. The rhizosphere represents a tremendously complex biological system, and there is a great deal yet to be learned about the interactions which occur between the plant and the microorganisms intimately associated with its root system.
·Electron—microscope techniques have been developed to observe microorganisms directly on the root surfaces.
2. Interactions among soil microorganisms
The microorganisms that inhabit the soil exhibit many different types of associations or interactions. Some of the associations are neutral; some are beneficial or positive; others are negative or detrimental.
2.1 Neutral association
Two different species of microorganisms inhabit the same environment without affecting each other. For example, each could utilize different nutrients without producing metabolic end products that are inhibitory.
2.2 positive associations
mutualism is a symbiotic relationship in which each microorganism benefits from the association.
Lichen: A mutalistic (or symbiotic) association of an alga and a fungus.
Commensalism refers to a relationship between microorganisms in which one species of a pair benefits; the other is not affected. For example, many fungi are able to dissimilate cellulose to glucose. Many bacteria are unable to utilize cellulose, but they can use the fungal breakdown products as energy and carbon sources.
2.3 Negative associations
The killing, injury, or inhibition of growth of one species of microorganism by another when one organism adversely affects the environment of the other. This kind of association is called antagonism.
The antagonistic microorganisms may be of great practical importance in biological control, since they often produce antibiotics or other inhibitory substances which affect the normal growth or survival of other microorganisms (pathogenic microorganisms).
Competition is a negative association among species which compete for essential nutrients. In such situation the best adapted microbial species will predominate, or eliminate other species which are dependent upon the same limited nutrient substance.
Parasitism is defined as a relationship between microorganisms in which one lives in or on another. The parasite feeds on the cells, tissues, or fluids of another microorganism, the host, which is commonly harmed in the process. The parasite is dependent upon the host and lives in intimate physical and metabolic contact with the host. All major groups of plants, animals, and microorganisms are susceptible to attack by microbial parasites.
Viruses that attack bacteria, fungi and algae are strict intracellular parasites since they can not be cultivated as free—living forms.
Eating of an individual of one species by an individual of another species. Protozoa eat bacteria.
3. Biogeochemical role of soil microorganisms
Soil microorganisms serve as biogeochemical agents for the conversion of chemical compounds. The conversion of complex organic compounds into simple inorganic compounds or elements provides for the continuity of elements as nutrients for plants, aminals and microorganisms.
3.1 Biochemical transformations of nitrogen compounds: The nitrogen cycle
·The biochemical process
Proteolysis is the process of enzymatic hydrolysis of proteins. This is accomplished by microorganisms capable of elaborating extracellular proteinase that convert the protein to smaller units (peptides). The peptides are than attacked by peptidases, resulting in the resease of individual amino acid. The overall reactions may be summarized:
·Bacteria: some bacterial species elaborate large amounts of proteolytic enzymes. Among the most active in this respect are some of the clostridia; a lesser degree of activity is found in species of the genera Proteus,Pseudomonas and Bacillus.
·Fungi: Rhizopus, Mucor, Aspergillus
·Many microorganisms can deaminate amino acids. The production of ammonia is referred as ammonification.
·Microorganisms (nitrifying bacteria) convert ammonia to nitrate. This process is called nitrification. The process occurs in two steps, each step performed by a different group of bacteria.
Nitrifying bacteria, including ammonia oxidizers and nitrite oxidizers, are gram—negative chemolithotrophs. Their main source of carbon is obtained through CO2 fixation; energy is derived by the oxidation of NH3 or NO2depending upon the group.
·The transformation of nitrate to gaseous nitrogen is accomplished by microorganisms in a series of biochemical reactions. This process is called denitrification.
There are diverse groups of bacteria in soil, sewage and aquatic environments that can transform NOto N2. They include some chemotrophs, phototrophs, heterotrophs and autotrophs.
·Environmental conditions in a soil have a significant effect on the level of denitrification. The process is enhanced in soils by ①oxygen supply is limited, ② an abundance of organic matter, ③ elevated temperature (25~65℃),④ neutral or alkaline pH.
·From the standpoint of griculture and environment, both nitrification and denitrification are undesirable pocesses.
3.1.5 Biological Nitrogen Fixation
A number of microorganisms are able to use molecular nitrogen in the atmosphere as their source of nitrogen. The conversion of molecular nitrogen into ammonia is known as biological nitrogen fixation.
220.127.116.11 Nitrogen fixing Microorganisms
·Two groups of microorganisms are involved in biological nitrogen fixation
·nonsymbiotic microorganisms, those living freely in the soil. e.g. Azotobacter. The process to fix nitrogen by this group of bacteria is called nonsymbiotic nitrogen fixation.
·Symbiotic microorganisms, those living in roots of plants. e.g. Rhizobium. The process to fix nitrogen by this group of bacteria is called symbiotic nitrogen fixation.
18.104.22.168 The essential reactants in the biological nitrogen fixation process
·The nitrogenase enzyme complex
This has been characterized as two components, and neither is active without the other. Component I is known as the Mo-Fe protein. Component II, which is a smaller molecule is Fe protein. Both molecules contain sulfur.
·A strong reducing agent
·A requlating system for NH3 production and utilization
·A system that protects the nitrogen-fixing system from inhibition by molecular oxgen.
22.214.171.124 The overall biochemical reaction for BNF
126.96.36.199 Nonsymbictic nitrogen fixation
nonsymbiotic nitrogen fixation has been studied extensively with clostridium pasteurianum and species of Azotobacter. The former is an anaerobic bacillus, and the latter are aerobic spherical cells. Both are widely distributed in soils.
188.8.131.52 Symbiotic nitrogen fixation
symbiotic nitrogen fixation is accomplished by the bacteria of the genus Rhizobium in association with legumes (e.g. soybean, peanut, clover, pea)
·Symbiotic properties of Rhizobium
① Infection: Rhizobia invade plant root, through root hairs and form nodules.
② Host specificity: not all species of Rhizobium produce nodulation and fix nitrogen with any legume. There is specificity between the bacteria and legumes.
③ Effectiveness: The amount of nitrogen fixed.
How to estimate the effectiveness?
·Plant growth: Dry weight, fresh weight, height.
·Nodulation: nodule number and weight,
·The Nitrogenase activity
Acetylene reduction method
·The amount of nitrogen fixed
·To demonstrate growth in jensen’s N-free medium. Plant total nitrogen of inoculated — plant total nitrogen of uninoculated.
④ Competitiveness, one strain compete nodulation with other rhizobial strains.
Methods to study rhizobial competiveness —marker techniques
·Insertion of marker genes
·AFLP fingerprint technique.
184.108.40.206 Rhizobial phylogeny and taxonomy？