Introduction:

Microbial environment is complex and continually changing. It frequently has low nutrient concentrations (oligotrophic) and exposes microbes to several overlapping gradients of nutrients and other environmental factors. Physicochemical factors govern growth and survival of microbes in these environments and methods used in their isolation, study and quantification.

Soil microbiology:

The soil (as ecosystem) is the natural medium for terrestrial plant growth. It is made up of varying proportions of organic and inorganic components that arise due to interactions between several complex procedures like weathering of rocks, decomposition of plants and animal's materials, and redistribution of materials by water movement and human activities. Some of the particles forming soil come together to create aggregates or clumps. The way in which they are arranged spatially gives the soil a structure.

Functions of soil Fungi:

1. One of the most significant functions of soil fungi is degradation of complex plant structures such as hemicelluloses, pectin, cellulose etc in simple molecules that are made available to plants as nutrients. They help in formation of stable soil by binding soil through hyphal penetration.

2. Fungi are able to breakdown complex proteinous materials, producing ammonia and sulphur compounds that could be utilized by higher plants.

3. Soil fungi may function as parasites in soil under certain conditions to the disadvantage of higher plants

Methods of study and isolation of soil microorganisms:

Soil serves as the reservoir of several microbial pathogens of plants and animals that play the significant role in soil economy. Two major difficulties are usually connected with isolation of soil microorganisms. These are:-

a) Inability of soil microorganism to grow and complete their life cycles in defined synthetic media.

b) Contamination particularly by bacteria and fast growing fungi.

The different methods that can be used in isolation of soil microorganisms comprise:-

1. Soil Plate Dilution Method/Serial Dilution Method: In this method, the known amount of soil is taken with the known volume of sterile distilled water; then serial of dilutions are made. Sample volumes of each dilution are then included with just molten agar in Petri dishes, allowed to cool and then incubated.

Advantages: It provides both quantitative and qualitative accounts of microbial spore load of soil

Disadvantages:  Petri dishes have detailed nutrients and specific environmental conditions (pH, temperature. etc) so fungal colonies appearing are those favored by environmental conditions and those not favored are inhibited. Because some microorganisms grow faster than others, fast growing ones may over grow and suppress slow growers.

2. Soil Plate Method: In this method, some quantities of soil is dispersed in Petri dishes having just molten agar and incubated for some days to permit for germination and growth of microbial spores.

Advantages: The method provides both total and individual species of microorganisms present per gram of soil. It provides more complete count as both spores join coarse and fine particles will appear.

Disadvantages: The method is also indirect method and most of the disadvantages of dilution method will be valid.

3. Rossi - Cholodny Slide (Rossi; 1928): According to Rossi, the method comprises of pressing slides against undisturbed vertical soil surface. After removal and staining, picture of microorganisms as they usually occur in soil will be obtained. Cholodny altered this method by permitting slide to stay in soil for five days to three weeks before removal. Presently, this method has been really altered and may involve burial of microscope slides coated with agar in soil.

Disadvantages: Substrates (agar) are not natural to soil. Introduction of slide to the soil is a type of disturbance. The isolation of hyphae for successive colony differentiation might be hard.

Factors affecting microbial growth in soil (Soil as the environment for micro organisms):

a) Soil Components: Soil comprises of the mixture of weathered rock of different sizes. Proportion of size determines soil texture. Clay particles are significant components of soil environment; and they really influence other physical and chemical properties of soil.

b) Soil water/moisture content: Soil water is usually present as a thin film around the soil particles. Dissolve a known weight of soil in the known volume of water (generally, soil: water in ration 1:2); dry to constant weight and then:

Moisture Content = less in weight on drying/ initial weight x 100%

Water is helpful in keeping microbial cells turgid. Water plays some roles in dispersal of spores. Water gives the medium for movement of reproductive structures in some species.

c) Soil Aeration: Amount of air present in the soil differs, and this frequently has some relationship with soil water content. There is also the exchange of gases between soil and atmosphere through air spaces in soil. Amount of air present the soil differs with soil type and different points in the soil e.g. in regions of intense microbial activity, particularly near plant roots (rhizosphere) the concentration of air will be considerably altered due to metabolism by rhizosphere organisms. Most fungal species are aerobic.

d) Soil profile/depth: This denotes changes as you go in soil. Microbial populations in soil reduce with increase in soil depth. That is, on soil surface, many microbial activities are occurring. Thus population of microorganisms in this zone is generally higher. Other reasons to describe these trends comprise:

• Presence of substrates that serve as food for microorganisms on surface layer.
• Effect of sun rays on surface soil temperature has some connection with enzymatic activities.
• Due to agricultural activities and microbial interactions, soil particles on surface are not too strongly held together and this provides room for aeration.

Aeromicrobiology:

This is a study of micro-organisms in air. Similar to soil and other environments, micro-organisms are symbolize in the air and maybe because of their role in the transmission of some air-borne infectious diseases and dispersal of microorganisms, the study of aero microorganisms has been getting attention from microbiologists and scientists usually. Components of aerial environment are differed and generally comprise dust particles, pollen grains, bacterial spores, fungal spores, fungal hyphal fraqments, actinomycetes, spores of bryophytes and pteridophytes etc. Generally, micro-organisms in air are in the state of suspended animation. Several of them are easy killed by desiccation, ultra violet rays and other adverse situations. Dispersal of air - borne particles has 3 stages

• Liberation and take off into air
• Dispersion in air current
• Deposition on surfaces at the end of journey before germination and growth.

a) Liberation: Before a particle becomes airborne, several problems have to be overcome. Example, energy is needed to overcome adhesive forces joining particles to the surface of substrates; also the particle has to be of the size which will be airborne. Degree of adaptation to air borne dispersal differs really between different groups of micro-organisms and this is reflected in the relative abundance in the air.

b) Dispersion: Dispersion of air-borne micro-organisms can be considered at two levels. Fate of individual spores and behavior of groups or cloud of spores. These features are associated and depend on physical characteristics of the spores and that of atmosphere. The significant features of spores in this respect are shape, size, and degree of surface roughness, density and electrostatic charges; while those of environment comprise turbulences, wind movements, layering convention, wind gradient near ground and pattern of atmospheric circulation.

c) Deposition: Last stage of airborne dispersal of microorganisms is deposition. Microbes are returned to the surface layer of plants, animals or soil so that they can no longer be blown by normal wind, although they may still be washed off. Deposition may happen in precipitation or from dry air by numerous different methods like impaction, sedimentation, rain washing and so on.

Factors affecting concentration of microorganisms in atmosphere:

Wind Speed: Fast moving air blows force with it and so eagerly gives energy for detachment of spores from vegetative structure and other surfaces. Generally, it is hard for spores to be deposited at the spot except where there is the obstacle or wind breaker along the wind course.

Rain Splashes: Rain washes air-borne spores to the soils and as such the amount of rain attained by the area may have some impact on number of air-borne spores and microorganisms. Where the area has an evidently stated raining and dry seasons, amount of dust particles and spores in the air may differ with the seasons of the year.

Temperature: During dry season, those air-borne spores which are thin walled are simply dehydrated to benefit of those with thick warty walls that are more adapted to endure high temperatures. There is also relationship between temperature and humidity, then temperature and wind movement.

Methods of study and isolation of aerial micro-organisms:

a) Settle Plate (Simple Gravity Plate) Technique: This is the most extensively utilized method for isolating air-borne micro-organisms. It engages exposing Petri dishes having nutrient agar medium on the stool outside for time interval. After settling of particles on medium for said time interval dishes are then collected incubated and after the particular time of incubation, colonies are counted and recognized.

b) Filtration Techniques: This may be filtration using membrane or glass fibers. Though, extreme desiccation of propagules may limit the value to culturing only resistant cells. Filters may gather cell by impaction, sieving, diffusion or electrostatic attraction; each of these working alone or in mixture with another depending on kinds of filter.

c) Impostors: This has also been extensively utilized in aerobiology. Examples are Cascade impactors and automatic volumetric trap that traps spores on coated microscope slides. We have Anderson slit sampler that has been designed to keep spores on agar media in Petri dishes. It also separates catches to different size fashions.

Practical application and significance of aeromicrobiological studies:

The application of aero microbiology is of great significance in disease epidemiology, forecasting and modeling. Epidemiology is a study of incidence, distribution and control of diseases inside populations or sum of factors managing the presence or absence of the disease or pathogen. Aerobiology can make precious contributions to epidemiology of animal and plant diseases. Sinnecker (1976) identified six kinds of diseases with aerogenic transmission depending on:

• the resistance of infective agents in droplets;
• the drop's nuclei or dust;
• the ability to infect from secondary aerosols formed when dust is re-suspended;
• the host range;
• whether there are alternative means of transmission and;
• whether infective agent can survival for long in droplet form.

Aquatic microbiology (Micro-Organism in Natural Waters)

Majority of microbial environments are aquatic, in that sometime, vegetative organism live in aqueous media like animal and plant fluids, water soil and many other related habitats. Aquatic microbiology though refers to that microorganism that live in earth's natural waters ranging from small ponds to great oceans.

Kinds of aquatic environments

Aquatic environment are frequently individual in oceans and inland waters. Inland waters can be categorized in ground and surface waters. Ground water is that water contained in permeable rocks below water table. It accumulates as water in the soil percolates through it. Several nutrients are thus filtered out. Surface water includes of lotic or running waters comprising of springs, streams and rivers. Second group are lentic or standing waters comprising of lakes, ponds, swamps and bogs. Springs can take place where ground water breaks surface and therefore like ground water, they are nutrient poor near origin.

Special habitats in aquatic environments

Important special habitats can be found in aquatic environments and the micro-organism inhabiting such habitats has special features of survival in such areas. Such feature may be structural or physiological. These vary considerably from sand to mud and silt. These can be classified into three major components according to the origin.

1. Lithogeneous Components: those mainly derived from rock, soil and volcanic ash.

2. Biogenious Components: those made up of skeletal remains of macro- and micro-organisms like diatoms

3. Hydrogenous Components: those components resulting from inorganic and chemical reactions occurring in water. Bottom sediments may be a mainly significant reservoir of organic and inorganic nutrients and when highly decreased they may give habitat for anaerobic organisms.

Physical and Chemical Factors in aquatic environments

a) Dissolved gases: The two most significant dissolved gases in aquatic environments are oxygen and carbon dioxide. Oxygen is impotent due to its significance in aerobic bioprocesses and in relation to oxidation - reduction potentials; while carbon dioxide is significant for photosynthesis and pH equilibrium. Concentration of oxygen in water is dependent on water temperature, partial pressure, salinity and biological activities. In water, equilibrium is established between carbon dioxide, carbonic acid and bicarbonate as follows:

CO₂+ H₂O ↔ H₂CO₃ ↔ HCO₃+H⁺ ↔ CO₃^2- +2H⁺

b) Hydrogen Ion Concentration (PH): Optimum PH for most aquatic bacteria is between pH 6.5-8.5 and this corresponds with PH of most large water bodies. Approximate PH of sea water generally lies below PH 8-8.3 while those of lakes are about pH7; though substantial fluctuations may take place.

c) Salinity: Although salinity is not itself a physical factor, changes in salinity can have profound osmotic effect that attimes can be lethal and can also be toxic through denaturation of cellular components. Many marine bacteria are halophytic and some have specific needs for sodium ions and some will not tolerate very high salt concentrations.

Microflora in aquatic environment:

Micro- organisms present in aquatic environment are mostly phytoplanktons. They comprise bacteria, algae and fungi; others are protozoa and viruses.

Bacteria: Generally, bacterial flora of the river may illustrate the peculiar close relationship with surrounding terrestrial population due to constant injection of soil, water run offs and organic matters. few aquatic bacteria are phototrophic while chemotrophic ones are also lengthily distributed, but usually distribution and plenty of majority of the heterotrophs is mainly managed by concentration of available organic materials, thus in nutrients poor spring, bacteria present are mainly of Gram negative rods such as Gallionella, Pseudomonas etc.

Microalgae: Aquatic microalgae play the very significant role in aquatic environments as main producers of organic compounds. They are essentially autotrophic, but some of them can be heterotrophic. In small bodies of water, like ponds, much of the main productivity may be performed by benthic algae but in large bodies of water like large lakes and oceans, algal phytoplanktons are the major producers.

Fungi: All fugal species are heterotrophic. Algae are the producers. Aquatic fungi are significant in decomposition as they are able to break down fat, hemicellulose, cellulose, liqnin, proteins, chitin, and carbohydrates etc in water. Fungi are more significant than bacteria in breakdown of complex materials. Representatives of four main classes of fungi are found in aquatic environments, either free living or more frequently growing on surfaces.

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