8 Important Microorganisms Present in Soil | Soil Microbiology

The following points highlight the eight important microorganisms present in soil. The microorganisms are: 1. Bacteria 2. Actinomycetes 3. Fungi 4. Cyanobacteria 5. Algae 6. Protozoa 7. Bacteriophages 8. Mycoviruses.

Microorganism # 1. Bacteria:

Bacteria constitute the most dominant group of microorganisms in soil and probably equal one half of the microbial biomass in soil. They are present in all types of soil but their population decreases with increase in the depth of soil.

Generally horizon A of a soil profile consists of more microorganisms than B and C horizons. Under anaerobic conditions (in the absence of oxygen), bacteria dominate the scene and carry on micro­biological activities in soil since fungi and actinomycetes usually do not grow well in the anaerobic conditions.

Bacteria thrive in soil as cocci (spheres, 0.5 μ), bacilli (rods, 0.5 to 3.0 μ), or spirilli (spirals). The bacilli are common in soil, whereas spirilli are very rare in natural environments.

In 1925, Winogradsky classified soil microorganisms in general and bacteria in particular into two broad categories—the autochtonous and the zymogenous organisms. The autochtonous (humus utilizing) or indigenous population is always uniform and constant in soil since their nutrition is derived from native soil organic matter (e.g. Arthrobacter and Nocardia).

On the other hand, zymogenous (opportunistic) or fermentative organisms require an external source of energy and their normal population in soil is low (e.g. Pseudomonas and Bacillus).

When specific substrates are added to soil the number of zymogenous bacteria increases and gradually declines when the added substrate is exhausted. To this category belong the cellulose decomposers, nitrogen utilizing bacteria, and those splitting ammonium into nitrate.

Growth in the presence or absence of oxygen is taken as the criterion to distinguish bacteria into anaerobic, aerobic, and facultative anaerobic, i.e., those capable of developing under oxygenated as well as non- oxygenated conditions.

Under the Bergey’s Manual of Determinative Bacteriology, bacteria are classified into taxonomic groups, orders, families, genera, and species based on the classical Linnaen concept of binomial nomenclature. Ten orders are included in the class Schizomycetes. Of these, three orders—Pseudomonadales, Eubacteriales, and Actinomycetales contain the species of bacteria, which are predominantly reported in soil.

The most commonly occurring soil bacteria belong to the genera Pseudomonas, Arthrobacter, Clostridium, Achromobacter, Bacillus, Micrococcus, Flavobacterium, Corynebacterium, Sarcina, and Mycobacterium. Escherichia is encountered seldom in soils except as a contaminant from sewage, whereas Aerobacter is frequently encountered and is probably a normal inhabitant of certain soils.

Another group of bacteria common in soils is the myxobacteria belonging to the genera Myxococcus, Chondrococcus, Archangium, Polyangium, Cytophaga, and Sporocytophaga. The latter two genera are cellulolytic and hence are dominant in cellulose- rich environments. Myxobacteria feed on other gram-negative bacteria through lysis.

The total population of bacteria in any soil cannot be determined accurately. Apart from the inherent limitations of the soil dilution and plate methods, their numbers vary with the texture, water content, and many other parameters especially the availability of organic substrates in soil. Bacteria can withstand extremes of climate although temperature and moisture influence their population.

In Arctic zones where temperature is below the freezing point, bacteria can thrive as luxuriantly as they do in arid desertic soils where temperatures are very high. The inherent faculty of many bacteria to form spores possessing tough outer covering facilitates the survival of bacteria in all adverse environments.

Survival by spore formation under extreme conditions ought to be differentiated from tolerance to different temperature ranges, which is one of the factors determining the population of bacteria in soil.

Based on this criterion, bacteria are grouped as mesophiles (15 to 45°C), psychrophiles (below 20°C), and thermophiles (45 to 65°C). The mesophilic bacteria, however, constitute the bulk of soil bacteria. Other factors affecting bacterial population in soil are pH, farm practices, fertilizer and pesticide applications, and organic matter amendment.

Soil bacteria can also be classified on the basis of their nutritional requirements into those requiring amino acids, B-vitamins, amino acids + B-vitamins, unidentified growth factors in yeast extract or soil extract and soil extract + yeast extract.

The source of B-vitamins and other growth factors in soils is difficult to explain and the occurrence of fastidious species in soil requiring growth substances can only be explained on the basis of mutual dependence of different bacterial strains on extracellular products.

However, soil bacteria are also classified into autotrophic and heterotrophic categories. Autotrophs synthesize their own food, whereas heterotrophs depend on preformed food for nutrition.

Photoautotrophs are those whose food energy is derived through mediation of sunlight, as in the instance of photosynthetic bacteria as opposed to chemoautotrophs which oxidize inorganic materials to derive energy and at the same time utilize the carbon from CO₃ for growth. In the latter category, a group of bacteria known as obligate chemoautotrophs, are included which prefer specific substrates.

Examples of this kind are Nitrobacter which utilizes nitrite, Nitrosomonas which utilizes ammonium, Thiobacillus which converts inorganic sulphur compounds to sulphate and Ferrobacillus capable of converting ferrous iron to ferric iron.

Several of the reactions involved in nitrogen transformations in soil depend on the chemoautotrophic Nitrobacter and Nitrosomonas and hence chemoautotrophy of bacteria in soil is intimately related to crop production.

Microorganism # 2. Actinomycetes:

Actinomycetes  are the soil microorganisms, which have characteristics common to bacteria and fungi and yet possess sufficient distinctive features to delimit them into a distinct category. In the strict taxonomic sense, actinomycetes are clubbed with bacteria in the same class of Schizomycetes but confined to the order Actinomycetales. On agar plates, their colonies can easily be distinguished from true bacteria.

Unlike slimy distinct colonies of true bacteria which grow quickly, actinomycete colonies appear slowly, show powdery consistency, and stick firmly to agar surface. A closer look at a colony under the compound microscope reveals slender unicellular branched mycelium (diameter of the hypha rarely exceeding one micron) forming asexual spores for propagation.

They bear certain similarities to Fungi Imperfecti in the branching of the aerial mycelium which profusely sporulate and in the formation of distinct clumps or pellets in liquid cultures.

Certain actinomycetes, on the other hand, resemble Mycobacterium and Corynebacterium in all respects both morphologically and physiologically including susceptibility to the attack by viruses. Actinomycetes differ from fungi in the composition of their cell wall. They do not have chitin and cellulose, which are commonly found in the cell walls of fungi.

The number of actinomycetes increases in the presence of decomposing organic matter. As a rule, they are intolerant to acidity and their numbers decline at pH 5.0. The most conducive range of pH is between 6.5 and 8.0. Waterlogging of soil is unfavourable for the growth of actinomycetes whereas desertic soils of arid and semi-arid zones sustain sizeable population, probably due to the resistance of spores to desiccation.

The percentage of actinomycetes in the total microbial population increases with the depth of soil and actinomycetes can be isolated in sufficient number even from soil samples obtained from the C horizon of a soil profile.

Delineation of species within different genera of actinomycetales has always been a difficult problem owing to many characteristics which are common with bacteria. For example, Mycobacterium and Mycococcus of the family Mycobacteriaceae have many characteristics common to bacteria and, in fact, are spoken of as filamentous bacteria in common parlance.

Nevertheless, the order Actinomycetales has been classified into four families—Mycobacteriaceae, Actinomycetaceae, Streptomycetaceae and Actinoplanaceae. The commonest genera of actinomycetes in the order of abundance in soils are Streptomyces (nearly 70%), Nocardia and Micromonospora although Actinomyces, Actinoplanes and Streptosporangium have also been encountered occasionally.

Temperatures between 25 and 30°C are conducive for the growth of actinomycetes although thermophilic cultures growing at 55 and 65°C are common in compost heaps where they are numerically extensive and mostly belong to the genera Thermoactinomyces and Streptomyces.

Microorganism # 3. Fungi:

Fungi are next only to bacteria in abundance in soil. They dominate all soils and possess filamentous mycelium composed of individual hyphae. The hyphae may be uni-, bi- or multinucleate and non-septate (without cross walls) or septate. Asexual reproduction takes place by the production of spores or conidia mitotically.

A well- defined sexual cycle involving gametic fusion and subsequent production of spores through meiotic or reduction division may take place in fungi. The size, shape and colour of conidia or spores and the physiological characteristics of cultures in artificial, as well as natural substrates provide valuable taxonomic criteria in the classification of fungal isolates into well-defined genera and species.

All the environmental factors that influence the distribution of bacteria and actinomycetes also influence the fungal flora of soil. The quality and quantity of organic matter present in soil have a direct effect on fungal numbers in soil since most fungi are heterotrophic in nutrition.

Fungi are dominant in acid soils because acidic environment is not conducive for the existence of either bacteria or actinomycetes, resulting in the monopoly of fungi for utilization of native substrates in soil.

They are also present in neutral or alkaline soils and some can tolerate pH beyond 9.0. Arable soils contain abundant fungi since they are strictly aerobic and excess of soil moisture decreases their numbers. Isolation of fungi from different horizons of soil profiles demonstrates that these microorganisms exhibit selective preference for various depths of soil.

Those fungi that are common in lower depths are rarely encountered on the surface of soils which may be explained on the basis of the availability of organic matter and the ratio between oxygen and carbon dioxide in the soil atmosphere at varying depths.

Seasonal fluctuations in fungal numbers are not uncommon. Farm practices including crop rotation and fertilizer or pesticide applications influence the nature and dominance of fungal species.

Broadly speaking, the soil fungi are classified into Phycomycetes, Ascomycetes, Basidiomycetes, and Fungi Imperfecti. Many fungi which are commonly isolated from soil come under the class Fungi Imperfecti by virtue of the fact that they produce abundant asexual spores and lack sexual cycle. Members of this class are distinguished by their septate mycelium and a structure called conidiophore from which conidia or spores are continuously produced.

The other three classes of fungi have both sexual and asexual means of reproduction. Phycomycetous members possess non-septate and unicellular hyphae and possess sacs called sporangia containing spores. A specialized sporangium known as ascus is characteristic of Ascomycetes which contains a definite number of ascospores usually numbering 4 or 8. Unlike Phycomycetes, Ascomycetes have septate mycelia.

As a rule, the members of Basidiomycetes (which are characterized by specialized reproductive structure known as basidium, producing basidiospores) are difficult to isolate from soil on agar plates for the simple reason that the nutritional requirements of many of the basidiomycetes are exacting and the conventional method of soil-dilution plating is inadequate to isolate them in pure culture.

Many of the wood- rotting fungi such as Polyporus and ectotrophic mycorrhizal fungi (e.g., Boletus), which inhabit the root region of forest trees come under soil Basidiomycetes.

They need B-vitamins and special growth factors contained in root exudates for growth in laboratory media. Nevertheless, Basidiomycetes are usually present in soil in a mycelial state and can be recognized by the fructifications or fruit bodies which they produce on the surface of soil or decaying wood.

Suitable baits can be buried in soils and Basidiomycetes may be selectively isolated by such baiting techniques. Many of the Basidiomycetes are capable of utilizing cellulose and in this respect they appear to be good colonizers of soils in the forest.

The genera of fungi which are most commonly encountered in soils and which can be isolated by conventional methods are the following. Acrostalagmus, Aspergillus, Botrytis, Cephalosporium, Gliocladium, Monilla, Cladosporium, Penicillium, Trichoderma, Trichothecium, Verticillium, Alternaria, Pullularia, Cylindrocarpon, Scopulariopsis, Spicaria, and Fusarium (Fungi Imperfecti); Mortierella, Absidia, Cunninghamella, Zygorynchus, Mucor, Rhizopus, and Pythium (Phycomycetes); Chaetomium (Ascomycetes) and Rhizoctonia (Mycelia sterilia, which fail to produce reproductive structures).

Many soil yeasts belonging to true Ascomycetes such as Saccharomyces and those belonging to Fungi Imperfecti such as Candida can also be isolated on acidified media (pH 4.0). Their numbers in soil are low and their significance in soil is poorly understood.

Degradation of organic matter and help in soil aggregation is one of the main functions of fungi in soil. Besides this property, certain species of Alternaria, Aspergillus, Cladosporium, Dematium, Gliocladium, Helminthosporium, Humicola and Metarhizium produce substances similar to humic substances in soil and hence may be important in the maintenance of soil organic matter.

Some of the fungi that usually form ectotrophic associations on the root system of forest trees such as pine belonging to the genera Boletus and Lactarius help in the mobilization of soil phosphorus and nitrogen into plants. In many instances, establishment of new forests becomes difficult unless mycorrhizal fungi are artificially introduced into soil by inoculation.

Microorganism # 4. Cyanobacteria:

Several cyanobacteria such as Anabaena, Nostoc, Aulosira, Cylindrospermum, Tolypothrix, Gloeotrichia, Wollea, Lyngbya, Calothrix, Chroococcus, Gloeocapsa, Plectonema, Microcystis, etc. generally occur in soil and are reported to possess the power of fixing atmospheric nitrogen from the air, an important part in enrichment of the soil with N₂.

Many soil cyanobacteria can resist long spells of drought. When remoistened, these cyanobacteria develop slowly in comparison to bacteria and coccoid green algae but quickly become dominant. Nostoc muscorum and Nodularia harveyana appeared from soil that had been dried for 79 years. Similarly, Nostoc passeriniaum and Anabaena oscillarioides var. terrestris were obtained from a soil dried for 59 yrs.

Microorganism # 5. Algae:

Algae differ from other organisms occurring in soil by having photosynthetic pigments that enable them to synthesize carbon compounds and form carbon dioxide in the presence of light. The need for light gives an immediate clue to their distribution in soil; they are indeed found most abundantly in the top inch or so of the soil.

The maximum depth to which microalgae have been recorded in soil is 2 m. Also, because of their requirement for light, microalgae develop most abundantly when the soil is not heavily shaded by vegetation or surface litter.

Green microalgae (Chlorophyceae) are the group most commonly present in soil. Genera often found include Hormidium, Chlorella and Chlamydomonas. The characteristic empty silicaceous shells of diatoms (Bacillariophyceae) are often seen during microscopic examination of the soil, and indicate that live diatoms must have been present. Yellow green algae (Xanthophyceae) are less common in soil than the other groups mentioned and red algae (Rhodophyceae) are rarely found except in abnormal saline soils.

Besides their photosynthetic activities, soil microalgae add certain compounds to the soil, either through death or by secretion from the cells. Members of Chlorophyceae have been shown to release polysaccharides in culture and this probably occurs in nature. Certain microalgae, e.g., Chlorella produce growth substances and antibiotics which may affect the soil flora.

Microorganism # 6. Protozoa:

Protozoa that occur in soil are unicellular and generally they lack chlorophyll barring few exceptions. They are characterized by a cyst-stage in their life cycle which can help them to withstand adverse soil conditions.

Besides a few genera which reproduce sexually by fusion of cells, the rest of the protozoans reproduce asexually by fission. Important genera of protozoans that occur in soil are Allantion, Bodo, Cercobodo, Cercomonas, Entosiphon, Heteromita, Oikomonas, Sainouran, Monas. Spiromonas, Spongomonas and Tetramitus.

Unlike the flagellate forms of protozoa which move with the help of their flagella numbering up to four, there are protozoa in soil which move with the help of extrusions of protoplasm known as false feet or pseudopodia. The protoplasm may be naked or as in some genera encased in shells. Important soil inhabitants of this class known as Sarcodina are Amoeba, Biomyxa, Difflugia, Hartmanella, Euglypha, Lecythium, Nuclearia, Naegleria, and Trinema.

A third group of soil protozoa belong to the class Ciliata. They are distinguished by the possession of minute hairs called cilia around their bodies which help in locomotion.

Important genera of this class are Balantiophorus, Colpoda, Colpidium, Enchelys, Halteria, Gastrostyla, Oxytricha, Pleurotricha, Uroleptus and Vortkella. Apart from the classes Mastigophora, Sarcodina and Ciliata which are soil inhabitants, the phylum protozoa has two more classes (Suctoria and Sporozoa) which are not considered here.

The protozoans prefer certain species of bacteria for their nutrition. They thrive in soil at the expense of bacteria belonging to the genera Aerobacter, Agrobacterium, Bacillus, Escherichia, Micrococcus and Pseudomonas by ingesting them into their protoplasm.

In fact, Aerobacter cultures are recommended as a food base for isolation and enumeration of soil protozoans. When the food base (bacteria) diminishes in soils, the protozoa get encysted (form cysts) for survival against the harmful action of high temperature, drought, application of pesticides, etc.

Protozoa abundantly occur in the upper layer of the soil and their numbers are directly dependent on bacterial population. Use of organic manures in soil increases the number of soil protozoans which is again a reflection on the corresponding increase in the bacterial flora due to the application of organic matter.

Owing to inadequate studies on soil protozoa, it is difficult to define the role of individual factors such as pH and temperature on protozoan population in soil. Nevertheless, it is clear that protozoa are abundant in soil and their main function is to regulate the number of bacteria.

Nothing is known about the associative effects of protozoa with other soil microorganisms for the simple reason that very few workers have been attracted to this field, more so, because isolation and quantification of soil protozoans involve time-consuming procedures.

Microorganism # 7. Bacteriophages:

Bacteriophages, the bacteria-eating viruses and usually called phages, are the smallest inhabitants of the soil and they are known to attack the cells of bacteria and actinomycetes. Unlike bacteria, fungi, actinomycetes and protozoa that can be easily observed under a compound microscope, bacteriophages can be seen only under an electron microscope because of their minute size.

Some workers prefer to make a sub-division known as actinophages while referring to phages attacking actinomycetes. The phages attacking cyanobacteria are known as cyanophages. Although phages cannot be seen without the help of an electron microscope, the lysis caused by the action of specific phages on their hosts can be seen as ‘plaques’ on agar plates. Bacteriophages can pass through bacterial filters since their size rarely exceeds 0.05 to 0.01 µ in diameter.

The bacteriophages possess a head-like and a tail-like structure. The tail attaches itself to the surface of the bacterium and gains entry into host’s protoplasm. Lysis sets in when the bacteriophage multiplies resulting in the liberation of many more progeny phages to re infect new bacterial cells. It is too early to assess the importance of bacteriophages in the overall influence of soil on agricultural productivity because the information on this aspect is not sufficient to make any generalization.

Microorganism # 8. Mycoviruses (Fungal viruses):

Although it was stated earlier that fungi are distinguishable from bacteria and actinomycetes in the sense that they are free from virus attack, several workers have come to recognize the existence of fungi-attacking viruses (mycoviruses) in recent years.

Prior to 1968 convincing evidence did not come forth regarding the presence or replication of mycoviruses and they were invariably referred to as virus-like bodies. Mycoviruses have been reported to occur in over 60 species from some 50 genera of fungi and most reports include studies using an electron microscope.

The most extensively studied system is the mycovirus of Penicillium chrysogenum. Examinations of virus particles for electrophoretic mobility, sedimentation coefficient, buoyant density, and serological specificity reveal differences among those viruses infecting species of Penicillium, Aspergillus, Periconia, and Ustilago.

Accurate determinations of molecular weight and amino acid content of different mycoviruses have been made and electron microscope studies suggest that young apical regions of hyphae of Penicillium are free of virus particles whereas the older regions of hyphae contain many particles. In three species of Penicillium, viruses are sometimes associated with lytic plaque formation which are not often reproducible, probably due to altered sensitivity of the host.