Organisms Found in Soil: 5 Categories

This article throws light upon the five categories of organisms found in soil. The categories are: 1. Animalia 2. Protista 3. Plantae 4. Fungi 5. Monera.

Soil Microorganism: Category # 1. Animalia:

The large animal life-Animalia (Previously macro-faunae)-that inhabit the soil range in size from large burrowing animals, such as badgers to tiny arachnids mites.

a. Burrowing Animals:

Large animals (e.g. moles, mice, rabbits, wood chucks and others) aerate the soil and modify the fertility of soil by influencing soil structure, but they eat and also damage vegetation which makes them more harmful than beneficial.

b. Earthworms:

Earthworms are most important soil macro-animal. Earthworms are members of large groups (Phylum Annelida) of soil inhabiting macro-faunae. They do not destruct living vegetation through eating like other such as cutworms, maggots etc.

They feed on animal and plant residues. The ingested organic matter and fine textured soil are excreted as small granular aggregates, which resist rupture by raindrop impact and provide sufficient and easily available plant nutrients.

Besides this, earthworms are important in many ways. They make holes into the soil through burrowing and these holes serve to increase aeration and drainage.

Moreover, earthworms bring about a transportation of relatively fertile soil mass from the sub-soil to the surface layer. Some earthworm species burrow to 6 metres deep (about 20 ft.) in the soil, but most of them live in the common root zone, which averages 2 m (6.5 ft.) in depth in the temperate regions.

Earthworms prefer moist, well-aerated warm (70°F or 21 °C) soils with soil reaction or pH between 5.0 and 8.4, with adequate palatable organic matter, with low salt concentrations but high available calcium, with fairly deep soil of medium or fine texture and undisturbed by tillage. Soil cover is important in maintaining a high earthworm population.

Enemies of earthworms are heavy farm machinery, sandy salty, arid, acid, cold or hot, bare or barren soils, mice, moles, mites, very toxic insecticides.

Mites, centipedes, insects, ants and termites etc. (Arthropods)-They are joint footed invertebrate organisms and they feed mostly on decaying vegetation and help to aerate the soil with their burrows, however, many species also can be pests because they are phytophagous (Gr. phyto—plant and phagous—to eat).

The ants and termites can radically change or modify the soil structure and till the soil; the net result can be beneficial or harmful.

c. Snails, Slugs etc. (Gastropods):

They feed on decaying vegetation but will eat and damage living plants.

d. Nematodes:

Nematodes are microscopic, un-segmented, thread-like works; they can be classified according to their different feeding habits.

The first (Omnivorous) and second groups (Predaceous) are by far the most abundant in soils and they are important because of their inter-relationships with the soil micro flora.

Nematodes are controlled by chemical fumigants, nematodes, hardwood bark or by rotating with more resistant plant species or the use of resistant crop varieties.

Soil Microorganism: Category # 2. Protista:

Protozoa and slime molds are the main Phyla or Protista kingdom.

a. Protozoa:

The phylum, protozoa are unicellular eukaryotic organisms. They are considerably larger than bacteria. Protozoa based on locomotion or methods of movement can be divided into five classes as follows:

The first three classes are generally found in soils and are show in Fig 18.4. But the latter two classes are not found in soils.

Organisms of the class Mastigophora usually are endowed with one to four flagella, but occasional species pones more than four. The flagellates are most abundant in soils followed by Sarcodina (e.g. Amoeba) and Ciliata. Aeration and the supply of food are possibly the most important criteria for their existence in soils. So they are mostly present on surface soils.

b. Rotifers:

These are called soil micro-animals (micro-fauna) present under moist conditions of the soil. These are microscopic in size. Their anterior is modified into a retractile disk bearing circles of cilia which, in motion, give the appearance of moving wheels. These hairs sweep floating food materials into the animals. The posterior end of the rotifers tapers to a foot by which the rotifer can attach itself to convenient objects (Fig. 18.5).

Soil Microorganism: Category # 3. Plantae:

The plantae organisms obtain energy from the sun and can exist as stationary life. Algae and diatoms are examples of micro Plantae; macro Plantae are Bryophytes (mosses) and Tracheophytes (vascular plants).

a. Macro Plantae:

Most familiar plants have root systems.

There are two kinds of root systems:

(i) A tap root system—a vertical primary root with lateral branches (cotton, beets, carrots) and

(ii) A fibrous root system—many roots of about the same length arising from a common point near ground level (grasses, corn, beans).

Most cell walls are permeable, which enables soil solution to pass through them. Older roots develop thick protective covering mucilage. In contrast, root hairs are single cells of the root surface, with thin walls that allow water and nutrient absorption. The exudates from roots of different crops undoubtedly influence associated microbial populations and hence activities in the soil.

The soil solution near established roots (rhizosphere soil solution) may be an environment of wide diversity than that existing in the soil. Dead roots, sloughed materials and exudates seem to encourage microbial activities.

b. Micro Plantae:

This micro Plantae groups include green algae, yellow-green algae, and diatoms. Soil algae are microscopic, chlorophyll—bearing organisms and are capable of performing photosynthesis.

Soil algae as its vegetative form are most abundant in the surface soil whereas in the sub­soil most algae are present as resting spores or cysts in vegetative forms and they do not depend upon chlorophyll. What were once called blue green algae are now being re-classified into the Monera kingdom as Cyanobacteria (also called blue-green bacteria).

Algae develop well in moist fertile soils. The green colour of a moist soil surface due to application of commercial fertilizers may be an increase of algae. Algae are not important as decomposers of organic matter but are producers of new photosynthetic growth.

Unusual symbiotic algae (either blue green bacteria or green algae) associate with one of several fungi in forms called lichens. The algae fix di-nitrogen, and the fungi attach to a surface and form a protective mat that tenaciously holds water and supplies nutrients to the algae.

Lichens grow very slowly (2/30 mm per year), they help to weather rocks and they can grow on bark and other surfaces. Both fungi and algae can live separately if nutrient supply conditions are sufficient for their growth.

Soil Microorganism: Category # 4. Fungi:

Fungi are organisms without the ability to use the sun for energy. They live on dead or living plants or animal’s tissue. They are eukaryotic lower plants devoid of chlorophyll. Fungi are usually multicellular but are not differentiated into roots, stems and leaves. They range in size and shape from single-celled microscopic yeasts to giant multicellular mushrooms and puffballs.

True fungi are composed of filaments and masses of cells which make up the body of the organism, known as a mycelium. Fungi reproduce by fission, by means of spores borne on fruiting structures that are quite distinctive for certain species. An outline of the classification scheme of fungi is given in Fig 18.6.

Fungi are a curious assortment of one celled organisms (yeasts), multicellular filamentous molds, mildews, smuts and rusts and the well-known mushrooms. So for convenience of discussion, fungi can be broadly grouped into three as follows:

a. Yeasts:

The term yeasts have no taxonomic validity, but these are a group of fungi primarily exist as unicellular organisms and reproduced by budding or fission. Yeasts grow readily at pH 4.0. They can be used for the production of alcoholic beverages and also used as food supplement. They cause different diseases in plants.

b. Molds:

Molds are filamentous, microscopic or semi-microscopic fungi. They are eukaryotic, multicellular with many distinctive structural features and they can be reproduced by asexual (somatic or vegetative reproduction, does not involve the union of nuclei, sex cells or sex organs) and sexual (reproduction carried out by fusion of the compatible nuclei of two parent cells) process.

Molds play an important role in soils than that of the mushroom fungi. They can grow better in a well-aerated soil. The development of molds is also influenced by the soil reaction (acid, neutral and alkaline).

They are most abundant in surface soil layers because of presence of sufficient organic matter and well-aerated condition. Penicillium, Mucor, Fusarium and Aspergillus are important genera that are found in most soils. Some common genera of molds are shown in Fig. 18.7.

c. Mushrooms:

Mushrooms are a group of fleshy macroscopic fungi, which until recently, as other fungi, were included in the plant kingdom because of a cell and spores. They are very unlike green plants because they lack chlorophyll and therefore depend on the performed food for their nutrition.

The mushroom that lives on dead matter is called a saprophyte. Some mushrooms may be parasites, drawing their nutrition from living matter, and some facultative, able to live as saprophytes as well. There are still other mushrooms that exist only in symbiotic association with plants and are called mycorrhizic.

The terms mushroom and toadstool are often used loosely. However, the common view is, the umbrella-shaped fungi belonging to Basidiomycotina, which are edible be called mushrooms and the poisonous-type, toadstools.

In nature, mushrooms grow wild in every country from snowy mountains to sandy deserts on all types of soils, pastures, forests, cultivated fields or water lands. They appear in all seasons, chiefly during the rainy season where well-decomposed organic matters are available.

Mushrooms can be classified as follows:

Brief discussions about edible mushrooms are being given here.

Edible Mushrooms:

At present there are three types of mushroom being cultivated in India. These are: the white button mushroom (Agaricus bisporus), the paddy straw mushroom (Volvariella volvacea) and the Oyster mushroom (Pleurotus sajor—Cajci).

Of these, A bisporus is the most popular and economically sound to grow and is extensively cultivated throughout the world. Besides these there are also other edible mushrooms that are not generally cultivated in India like Agaricus bitorguis; Flammulina velutipes, Pholiota nameko etc. The principal parts of mushroom are depicted in figure 18.8.

The advantages of mushroom cultivation are to utilize the different agricultural wastes such as crop residues and organic wastes, industrial materials as through the conversion of substrate for their growth and the spent substrate can again be utilized as manure. Many wastelands can also be utilized through growing of mushrooms on such lands.

d. Fungi-Organic Matter Decomposers:

Fungi are the most versatile soil organisms. One of the most important evidences of decomposition of some materials especially organic matters is the appearance of fungal mycelia, a vegetative mass of threadlike branching filaments (hyphae—a filament or a thread of a mycelium).

Molds on bread, on cheeses, on many rotting foods, and in forest litter exhibit mycelia. Fungi are tremendous decomposers of organic waste materials and most readily attack cellulose (woody materials), lignins, gums and other organic complex substances.

Fungi can act also under a wide range of soil reaction i.e. from acidic to alkaline soil reactions. Fungi also compete with plants for different nutrients liberated from the decomposition of different organic waste materials, especially nitrogen, phosphorus and sulphur. Fungi also secrete different organic substances which help in the formation of water-stable soil aggregates.

Moreover, fungi function more economically than bacteria in that they transform into their tissues a large production of the carbon and nitrogen of the compounds attached and give off as by-products less CO₂ and NH₄⁺. However, fungi apparently cannot oxidize ammonium compounds (NH₄⁺) to nitrates (NO₃^–) as do some bacteria, nor can they fix or bind elemental nitrogen into combined forms.

e. Harmful Fungi:

Some fungi exist as predators on living cells. Hyphae of fungi can penetrate protozoa and when they become immobile, slowly digest them. Even nematodes can be entagled in mycelia and devoured. Although a very few types of soil fungi are found to be predatory, their importance is major. Various fungi cause different types of diseases in plants like, smuts, rusts, powdery and downy mildews, scabs, root rots etc.

Even the fungal decomposers are not all harmless. Aflatoxins produced by molds growing on grains (mostly Aspergillus flavus). Some toxins (produced by fungi) are carcinogens (Cancer-causing) and that are harmful to human beings.

f. Mycorrhizae:

A mycorrhiza is an infected root system arising from the rootlets of a seed plant. The word mycorrhiza (my-koe-rye-zee), derived from the Greek, meaning “fungus root”. Mycorrhizae are fungi that form symbiotic association of a fungus with the roots of a higher plant.

Mycorrhizae-enhance mineral absorption by the green plants. Some mycorrhizae form a king of sheath around the root, sometimes giving it a hairy, cottony appearance. The plant root transmits substances (some produced by exudation) to the fungi, and the fungi help in transmitting nutrients and water to the plant roots.

The fungal hyphae growing out from the plant root reach to the additional soil areas and help absorb many nutrients for transmission to the plant, particularly less mobile nutrients, such as phosphate (PO₄^3-), Zn²⁺, Cu²⁺ and MoO₄^2-. Because they provide a protective cover, mycorrhizae increase the plant seedlings tolerance to drought to high temperatures, to infection by disease fungi, and even to extreme soil acidity.

Mycorrhizae can be divided and described as follows:

The formation of mycorrhizae is particularly pronounced in soils low in phosphorus and nitrogen, and high nutrient levels are collected with poor mycorrhizal development.

The production of such mycorrhizal structures is most vigorous when the roots have a large-reserve of available carbohydrates followed by intensive photosynthesis. The formation of mycorrhizae also protect the roots of plant from any extreme soil conditions like strong-alkalinity, strong acidity etc.

Mycorrhizae are usually found on tree roots. The use of fertilizers negates much of the nutritive assistance that could be given to host plant by mycorrhizae, but as the cost of fertilizers increases, relatively cheap mycorrhizal inoculations will likely become more common.

It has been found that the inoculation of vesicular arbuscular (VA) endomycorrhizal fungi helps to increase phosphorus uptake from the soil. An additional benefit of the VA fungi helps in the establishment of bacteria which can fix atmospheric nitrogen in soils of low available phosphorus. A simple sketch of ectomycorrhiza is depicted in Fig. 18.9.

The greatest growth responses to mycorrhizae are probably to plants in highly weathered tropical soils because the leached oxisols and ultisols are low in basic cations, are acidic, are low in phosphorus, and may have toxic levels of aluminium. The mycorrhizae improve various soil conditions and thereby stimulate growth and development of various crops.

Soil Microorganism: Category # 5. Monera:

Soil organisms, bacteria, cyanobacteria (formerly blue green algae) and actinomycetes belong to the Monera kingdom. Bacteria and actinomycetes decompose organic matter, although atinomycetes are not as effective as bacteria. Actinomycetes are the source of large number of beneficial antibiotics, but they can also produce musty tastes and odour to waters.

a. Soil Bacteria:

Bacteria are unicellular microorganisms; the name comes from the Greek word for “rod” designating the usual bacterial shape. The numbers of bacteria in the soil generally exceeded all other micro-organisms, although fungi may exceed bacteria in weight. Bacteria can be simple classified on the basis of nutritional pattern, oxygen needs and symbiotic relationships as (Fig. 18.10).

b. Autotrophic Bacteria:

Autotrophic (meaning—self nutritive) bacteria manufacture their food by the synthesis of inorganic materials e.g. plants do in photosynthesis. Autotrophic bacteria are further divided into photoautotrophs and chemo autotrophs as mentioned in the above classification scheme.

Specific groups of autotrophic bacteria can oxidize ammonium, nitrites, sulphides, sulphur, ferrous iron (Fe²⁺), manganous manganese (Mn²⁺), hydrogen gas and carbon dioxides. The oxidation transforms mineral forms which are usually less beneficial to plants (nitrites, NO₂^–), sulphides, carbon monoxide (CO), to useful forms nitrates (NO₃^–) sulphates (SO₄^2-), carbon dioxide (CO₂).

Other oxidations eliminate toxic forms of carbon and manganese. The most important groups of autotrophic soil bacteria are those that are responsible for the oxidation of ammonium (NH₄⁺) to nitrates (NO₃^–) available to plants via a toxic transitory form of nitrogen, nitrites (NO₂^–).

The organisms carrying out such nitrifying process achieve maximum activities under the following conditions:

(i) The presence of proteins to release ammonium as they decompose, or the presence of ammonium salts e.g. ammonium sulphate (NH₄)₂SO₄.

(ii) Sufficient aeration.

(iii) Field moist soil but not saturated or waterlogged

(iv) A large quantity of calcium (not too much acidic soil conditions)

(v) Optimum temperature between 20-40°C.

Nitrification is of great concern to the quality of our environment because the conversion of stable NH₄⁺ into NO₃^– permits movement of NO₃^– into groundwater’s. Eutrophication, an increase in the concentration of nutrients in water is evident by the increased algal growths which, when dead and decomposing, require oxygen that otherwise could be used by water fauna. Generally phosphorus concentrations are the most limiting nutrient in eutrophication.

The chemoautotrophic bacteria may be sub-divided on the basis of the element whose oxidation provides the energy for growth and cell synthesis as follows:

A. Nitrogen compounds oxidised.

(i) Ammonium (NH₄⁺) oxidised to nitrite (NO₂^–), Nitrosomonas

(ii) Nitrite (NO₂^–) oxidised to nitrate (NO₃^–), Nitrobacter

B. Inorganic sulphur compounds converted to sulphate (SO₄^2-). Thiobacillus

C. Ferrous iron (Fe²⁺) converted to the ferric form (Fe³⁺). Ferro bacillus, Gallionella.

D. Hydrogen (H₂) oxidised. Hydro genomonas, Desulphovibrio Methanobacillus

E. Carbon monoxide (CO) oxidised to CO₂ Carboxydomonas’. Many other bacteria have also been considered as chemoautotrophs. Chemoautotrophic bacteria are important in nature because of the energy yielding reactions they catalyze, and various processes for which they are responsible are essential for crop production.

c. Blue Green Bacteria (Cyanobacteria):

Blue green bacteria are ubiquitous in distribution. They are completely autotrophic and require only, light, water, free N₂, CO₂, and other salts containing nutrients.

Blue green bacteria or cyano bacteria exhibit a wide diversity of shapes and arrangements from unicellular cocci or rods to long trichomes-(chain like structure having much larger area of contact between the adjacent cells). Gas vacuoles may be formed by many species. Some cyanobacteria are surrounded by a sheath that surrounds the aggregates or trichomes.

Unicellular Cyanobacteria are generally non-motile, but trichome-formers usually possess glinding motility. Flagella are absent. Cyanobacteria are widespread in soil, freshwater and marine habitats. Some species of cyanobacteria are thermophilic which can grow in hot springs.

Cyanobacteria can grow as mats on the surface of bare soil as primary colonizers. They are most important in adding organic matter and nitrogen to the soil and in preventing incipient erosion.

Some cyanobacteria grow in symbiosis with other organisms e.g. symbionts of lichens. They are also associated with certain protozoa that are called cyanellae. Some of them live within the plant bodies of a naked seed plants like water fems (Azolla), cycads and angiosperms (plants whose seeds are borne within a fruit) where they fix nitrogen.

Again, some of them possess a peculiar structure known as “heterocyst” and all heterocystons forms can fix nitrogen from the atmosphere. Recently some cyanobacteria without heterocyst’s have also been found to fix nitrogen under specific conditions like low oxygen tension.

An outline of the classification system of some of the well-known genera is appended in table 18.2.

The Heterocyst, a Botanical Enigma, usually occurs in the filamentous blue green bacteria or cyanobacteria. Heterocyst may be situated at the both ends i.e. terminal and basal positions of the filament and also between the vegetative cells of the filament in an “intercalary” positions.

They are rounded in shape and usually larger in size with conspicuous thick envelope (three layers-outermost fibrous the middle homogenous and eliminated inherent excepting at the polar region) as compared to ordinary vegetative cells. They have homogeneous cell content due to the absence of cytoplasmic granular inclusions.

They look like yellowish green colour due to absence or reduction of phycocyanin (substance for pigment). They are produced during active growth stage of the cyanobacteria. Heterocyst’s serve in vegetative reproduction by promoting the fragmentation of filaments. They are involved in nitrogen fixation and may be the actual sites of effective nitrogenase activity.

Nitrogen fixation by cyanobacteria is of economic significance in hot climates, particularly in sub-tropical and tropical rice soils. There is an important symbiotic relationship between Anabaena azolla (Cyanobacteria) and Azolla (a water fern) in temperate and tropical waters.

The blue green bacteria located in cavities in leaves of the water fern is protected from external adverse conditions and it is capable of supplying all of the nitrogen needs of the host plant. The characteristics feature of this association is the water fern’s very large light harvesting surface that limits the N₂-fixing capacity of the free living cyanobacteria.

d. Actinomycetes:

Actinomycetes (ak-tino-mye-seets) are gram-positive bacteria of Monera Kingdom that are characterized by the formation of branching filaments. They are characterized by branched mycelia similar to fungi, and resemble bacteria when the mycelia break into short fragments. Another difference from the fungi is the absence from the actinomycetes cell wall of the chitin cellulose commonly found among the molds.

It belongs to the order Actinomycetales which contains for families (Mycobacteriaceae, Actinomycetaceae, Streptomycetaceae and Actinoplanaceae) and nine genera (Mycobacterium, Mycococcus, Actinomyces, Nocardia, Streptomyces, Micromonospora, Thermoactinomyces, Actinoplanes and Streptosporangium).

Recently actinomycetes have attracted worldwide attention after it was discovered that they produce a number of beneficial antibiotics. About 500 antibiotics have been so far isolated, of which the most important are streptomycin, aureomycin, terramycin and neomycin.

The activities of actinomycetes in soil transformations are outlined below:

(a) Helps for the decomposition of the resistant components of plants and animals.

(b) Helps for the formation of humus through the decomposition of organic materials.

(c) Can decompose different green manures, hay, compost piles and animal manures at high temperatures.

(d) Cause of certain soil-borne diseases of plants like potato scab etc.

(e) Possible importance in microbial antagonism through the liberation of antibiotics.

Besides these, actinomycetes (e.g. Frankia) were found to form symbiotic N-fixing relationships with a diversified type of plants. Definite actinomycete, plant symbiosis has been established for many plant like coffee-berry, flooded rice, alders etc.

The great interest in symbiotic actinomycetes is partly due to the fact that actinomycetes infect at least seven different botanical families whereas Rhizobia bacteria infect only the Leguminosae (with a few exceptions). Actinomycetes are found in large quantities in soils containing high fresh organic matter, having neutral to slightly acidic reaction and also moist conditions.