34 Soil Microorganisms and their functions-II

Babita Khosla

35.1Soil Microorganism – Fungi

Fungi are thought to have colonised land well in advance of plants and have evolved to occupy nearly every ecological niche on earth. They are microscopic plant-like cells that grow in long thread like structures or hyphae that make a mass called mycelium. The mycelium absorbs nutrients from the roots it has colonised, surface organic matter or the soil. It produces special hyphae that create the reproductive spores. Some fungi are single celled (e.g. Yeast) while others form coenocytic thalli. It is estimated that there are 1.5 million to 5 million species of fungi.

Like plants, fungi were historically classified on the basis of reproductive structures. With the advent of next-generation sequencing technologies and the analysis of multiple genetic marker datasets, fungal taxonomy has changed substantially in recent years. Seven fungal phyla are currently recognised: Chytridiomycota, Zygomycota, Deuteromycota, Glomeromycota, Ascomycota, Basidiomycota, and the relatively recently evolved lineage of parasitic endobionts, the Microsporidia, which are sometimes considered to be a sister-group of the fungi (Liu et al.2006)

Figure 1: Classification of Fungi into seven different phyla.

While fungi perform a vast diversity of functions, three functional groups of fungi have particular importance in soil ecosystems: the saprotrophs, the mycorrhizas, and the lichens.

Saprotrophic fungi: Decomposers or saprophytic fungi convert dead organic matter into fungal biomass (i.e. their own bodies), carbon dioxide and organic acids. They are essential for the decomposition of hard woody organic matter. By consuming the nutrients in the organic matter they play an important role in immobilising and retaining nutrients in the soil as well as in the global carbon cycle. The organic acids they produce as by products help create organic matter that is resistant to degradation. Fungi are capable of degrading cellulose, proteins and lignin, some of which are highly resistant to breakdown by producing a wide range of enzymes, including amylases, cellulases, proteases, lipases, and phosphatases. These enzymes are produced by hyphae at the front of the mycelium as it grows through its substrate. From a single germinated spore, the mycelium will often grow radially outwards creating a ring of metabolic activity. The sugars, peptides, amino acids and lipids liberated by the fungal enzymes may not necessarily be acquired by this fungus, but are competed for intensely by bacteria, plants, and other soil biota including other fungi. Thus, by making substrates available to other soil organisms, saprotrophic fungi increase the biomass and diversity of soils and play a critical role in decomposition.

Mutualists: These fungi develop mutually beneficial relationships with plants. They colonise plant roots where they help the plant to obtain nutrients from the soil. Their mass hides roots from pests and pathogens, and provides a greater root area through which the plant can obtain nutrients.

Mycorrhizal fungi are perhaps the best known of the mutualists. The four groups of mycorrhizal fungi are arbuscular, ectomycorrhizal, ericoid and orchid. Arbuscular mycorrhiza (VAM)are the most common form of mycorrhiza, especially in agricultural plant associations. This fungi has arbuscles which are growths formed inside the plant root that have many small projections going into the cells. About 150 arbuscular mycorrhiza species are known. Most plants (90%) have some sort of association with these fungi except for groups such as the Cruciferae family (e.g. mustard, canola, broccoli), Chenopodiaceae (e.g. spinach, beets, saltbush) and Proteaceae (banksia, macadamia). Mycorrhizal fungi form mutually beneficial symbiotic associations with living plant roots. The symbiosis is based on the exchange of resources: the plant receives soil nutrients from the fungus and the plant provides sugars as a source of carbon to the fungus. The vast majority of all land plants form mycorrhizal associations and these allow plants to occupy a much broader range of soil environments than would otherwise be possible. Arbuscular (AM) and ectomycorrhizal (EM)  fungi form symbioses with the broadest range of host plants. AM fungi colonise approximately 80% of all plant species, and are prevalent among herbaceous species including many important crop plants. In these, the site of nutrient exchange is the arbuscule: a finely branched, tree-like hypha that actually penetrates the plant root cell. Mycelia of AM fungi tend to be small compared with those of EM fungi, but they are particularly important for plant access to inorganic soil phosphorus. In temperate regions, most dominant trees and woody plants, including commercially important pine, spruce, fir, oak, beech, poplar and willow, form associations with EM fungi. In EM associations, the fungus remains predominantly on the surface of the root and penetrates only between root cells, but may produce an extensive extra-radical mycelium. Like saprotrophic fungi, EM fungi are critical decomposers of organic materials in soils. Saprotrophic fungi often dominate the surface layers of the soil profile, where they decompose recently shed plant litter, while EM fungi dominate lower in the profile, where they mobilise nitrogen for use by their host plants (Lindahl et al.2007).The extensive mycelium of EM fungi enables their vegetative hyphae to fuse to one another (anastomose); this, and the tendency for EM fungi to be non-specific to host plants, means EM fungi often form extensive, complex under-ground connections known as mycorrhizal networks. Mycorrhizal networks (MNs) occur in all major terrestrial ecosystems and allow materials – including carbon, nutrients, water, defence signals and allele chemicals – to be transferred between plants. Virtually all seeds that germinate in soil do so within an existing mycorrhizal network, allowing the young plant to quickly tap into this pathway of below-ground resource transfer (Teste et al. 2009). Thus, MNs have important effects on plant establishment, survival, and growth, as well as implications for plant community diversity and stability in response to environmental stress. MNs are considered fundamental to ecosystems as complex adaptive systems, because they provide avenues for feedbacks and cross-scale interactionsthat lead to self-organisation and emergent properties (Simard et al. 2012).

Lichens are symbiotic mutualistic associations between a fungus and a green alga (bipartite symbiosis), and sometimes also with cyanobacteria (tripartite symbiosis). The algal partner is usually a unicellular green alga, such as Trebouxia, Pseudotrebouxia, or Myrmecia, or is often a cyanobacterium, such as Nostoc or Scytonema. The fungal partner may be an Ascomycete or Basidiomycete. The fungus contributes the ‘body’ of the symbiosis, protecting the photobionts (algae/ cyanobacteria) from radiation and dehydration, and secreting organic acids that help to break down primary substrates, thereby helping a soil profile to develop and facilitating primary succession of plants onto these new soils. The alga photosynthesises to produce carbon, and the cyanobacteria, if present, fix atmospheric nitrogen into ammonium, a usable form of Nitrogen.

As a symbiosis, lichens are nutritionally independent and are remarkably tolerant to extremes in temperatures and humidity, being particularly adapted to desiccation. This allows them to persist in many habitats inaccessible to plants, including the High Arctic, the Antarctic, and alpine and desert environments. On these barren substrates lichens commonly take on one of three growth forms: crustose(forming a crust), squamulose (tightly clustered and slightly flattened pebble-like units), foliose (leaf like, with flat sheets of tissue not tightly bound), or fruticose (free-standing branching tubes).

Figure 2: Classification of Lichens based on their morphology.

Despite the wide diversity of the basic growth forms, all lichens have a similar internal morphology. The bulk of the lichen’s body is formed from filaments of the fungal partner, and the relative density of these filaments  lichen. At its outer surface, where itdefines the layers within the comes in contact with the environment, the   filaments   are   packed   tightly together to form the cortex. The dense cortex   serves   to   keep   out   other organisms,  and  helps  to  reduce  the organisms,  and  helps  to  reduce  the intensity of light which may damage the alga cells. The algal partner cells are distributed just below the cortex in a layer where the fungal filaments are not so dense. This is very similar to the arrangement in a plant leaf, where the photosynthetic cells are loosely packed to allow air circulation. Below the algal  layer is the medulla, a loosely woven layer of fungal filaments. In foliose lichens, there is a second cortex below the medulla, but in crustose lichens, the medulla is in direct contact with the underlying substrate, to which the lichen is attached.

Pathogens: This group includes the well-known fungi such as Verticillium, Phytophthora, Rhizoctonia and Pythium. The pathogenic fungi are usually the dominant organism in the soil. These organisms penetrate the plant and decompose the living tissue, creating a weakened, nutrient deficient plant, or death. In addition to destroying plant tissue directly, some plant pathogens spoil crops by producing potent toxins. Fungi are also responsible for food spoilage and the rotting of stored crops. For example, the fungus Claviceps purpurea causes ergot, a disease of cereal crops (especially of rye). Although the fungus reduces the yield of cereals, the effects of the ergot’s alkaloid toxins on humans and animals are of much greater significance. In animals, the disease is referred to as ergotism. The most common signs and symptoms are convulsions, hallucinations, gangrene, and loss of milk in cattle. The active ingredient of ergot is lysergic acid, which is a precursor of the drug LSD.

Another kind of toxin named aflatoxins released by fungi of the genus Aspergillus are carcinogenic compounds. Periodically, harvests of nuts and grains are contaminated by aflatoxins, leading to massive recall of produce. This sometimes ruins producers and causes food shortages in developing countries.

Functions of Fungi

1. Fungi plays significant role in soils and plant nutrition.

2. They plays important role in the degradation / decomposition of cellulose, hemi cellulose, starch, pectin, lignin in the organic matter added to the soil. Lignin which is resistant to decomposition by bacteria is mainly decomposed by fungi. They also plays important role in soil aggregation and in the formation of humus.
3. Certain fungi belonging to sub-division Zygomycotina and Deuteromycotina are predators in nature and attack on protozoa & nematodes in soil and thus, maintain biological equilibrium in soil.
4. Some soil fungi are parasitic and causes number of plant diseases such as wilts, root rots, damping-off and seedling blights e.g. Pythium, Phyiophlhora, Fusarium, Verticillium etc.

Number of soil fungi forms mycorrhizal association with the roots of higher plants (symbiotic association of a fungus with the roots of a higher plant) and helps in   mobilization of soil phosphorus and nitrogen e.g. Glomus, Gigaspora, Aculospora, (Endomycorrhiza) and Amanita, Boletus, Entoloma, Lactarius (Ectomycorrhiza).

35.2Soil Microorganism – Algae

Algae are present in most of the soils where moisture and sunlight are available. Their number in soil usually ranges from 100 to 10,000 per gram of soil. They are photoautotrophic, aerobic organisms and obtain CO2 from atmosphere and energy from sunlight and synthesize their own food. They are unicellular, filamentous or colonial. Soil algae are divided in to four main classes or phyla as follows:

1. Cyanophyta (Blue-green algae)
2. Chlorophyta (Grass-green algae)
3. Xanthophyta (Yellow-green algae)
4. Bacillariophyta (diatoms or golden-brown algae)

Out of these four classes / phyla, blue-green algae and grass-green algae are more abundant in soil. The green-grass algae and diatoms are dominant in the soils of temperate region while blue-green algae predominate in tropical soils. Green-algae prefer acid soils while blue green algae are commonly found in neutral and alkaline soils. The most common genera of green algae found in soil are: Chlorella, Chlamydomonas, Chlorococcum, Protosiphonetc. and that of diatoms are Navicula, Pinnularia. Synedra, Frangilaria.

Blue green algae are unicellular, photoautotrophic prokaryotes containing Phycocyanin pigment in addition to chlorophyll. They do not posses flagella and do not reproduce sexually. They are common in neutral to alkaline soils. The dominant genera of BGA in soil are: Chrococcus, Phormidium, Anabaena, Aphanocapra, Oscillatoriaetc. Some BGA posses specialized cells known as “Heterocyst“ which is the sites of nitrogen fixation. BGA fixes nitrogen (non-symbiotically) in puddle paddy/water logged paddy fields (20-30 kg/ha/season). There are certain BGA which possess the character of symbiotic nitrogen fixation in association with other organisms like fungi, mosses, liverworts and aquatic ferns Azolla, eg Anabaena-Azollaassociation fix nitrogen symbiotically in rice fields.

Functions / role of algae or BGA:

• Plays important role in the maintenance of soil fertility especially in tropical soils.
• Add organic matter to soil when die and thus increase the amount of organic carbon in soil.
• Most of soil algae (especially BGA) act as cementing agent in binding soil particles and thereby reduce/prevent soil erosion.
• Mucilage secreted by the BGA is hygroscopic in nature and thus helps in increasing water retention capacity of soil for longer time/period.
• Soil algae through the process of photosynthesis liberate large quantity of oxygen in the soil environment and thus facilitate the aeration in submerged soils or oxygenate the soil environment.
• They help in checking the loss of nitrates through leaching and drainage especially in un-cropped soils.

3. They help in weathering of rocks and building up of soil structure

35.3Soil Microorganism – Protozoa

These are unicellular, eukaryotic, colourless, and animal like organisms (Animal kingdom). They are larger than bacteria and size varying from few microns to a few centimeters. Their population in arable soil ranges from l0,000 to 1,00,000 per gram of soil and are abundant in surface soil. They can withstand adverse soil conditions as they are characterized by “cyst stage” in their life cycle. Except few genera which reproduce sexually by fusion of cells, rest of them reproduces asexually by fission / binary fission. Most of the soil protozoa are motile by flagella or cilia or pseudopodia as locomotors organs. Depending upon the type of appendages provided for locomotion, protozoa are classified into four classes

• Rhizopoda (Sarcondia)
• Mastigophora
• Ciliophora (Ciliata)
• Sporophora (not common Inhabitants of soil)

Rhizopoda: The class consists protozoa without appendages usually have naked protoplasm without cell-wall, pseudopodia as temporary locomotory organs are present some times. Important genera are Amoeba, Biomyxa, Euglypha, etc.

Mastigophora: This class contains flagellated protozoa, which are predominant in soil. Important genera are: Allention, Bodo, Cercobodo, Cercomonas, EntosiphonSpiromonas, Spongomions and Testramitus. Many members are saprophytic and some possess chlorophyll and are autotrophic in nature. In this respect, they resemble unicellular algae and hence are known as “Phytoflagellates”.

Ciliophora: The soil protozoa belonging to the class ciliate / ciliophora are characterized by the presence of cilia (short hair-like appendages) around their body, which helps in locomotion. The important soil inhabitants of this class are Colpidium, Colpoda, Balantiophorus, Gastrostyla, Halteria, Uroleptus, Vortiicella, Pleurotricha etc.

Protozoa are abundant in the upper layer (15 cm) of soil. Organic manures protozoa. Soil moisture, aeration, temperature and PH are the important factors affecting soil protozoa.

Functions of Protozoa:

1. Most of protozoans derive their nutrition by feeding or ingesting soil bacteria belonging to the genera Enterobacter, Agrobacterium, Bacillus, Escherichia, Micrococcus, and Pseudomonas and thus, they play important role in maintaining microbial / bacterial equilibrium in the soil.
2. Some protozoa have been recently used as biological control agents against phytopathogens.
3. Species of the bacterial genera viz. Enterobacter and Aerobacter are commonly used as the food base for isolation and enumeration of soil protozoans.
4. Several soil protozoa cause diseases in human beings which are carried through water and other vectors, e.g. Amoebic dysentery caused by Entomobea histolytica.

35.4Ecological significance of Soil microorganisms: The importance of microbes in soil is fundamental. Without them life on the planet would not be possible. Microbes play essential roles in maintaining soil fertility trough recycling nutrients and influencing their availability to plants, improving soil structure, supporting healthy plant growth and degrading organic pollutants.  The  functions  and  processes  microbes  perform  or  facilitate  in  our  soil  are incredibly complex. Soil microbiological ecosystems either preform or facilitate a number of key cycles such as the nitrogen, water and carbon cycles They can alter the physico-chemicalcharacteristics of the environment, directly participating in the transformations of nitrogen, phosphorus,  and  sulphur,  and  forming  mutualistic  associations  with  plants,  all  of  these activities  resulting  in  greater  plant  growth  (Sylvia  et  al.,  2005).Symbiotic  associations between fungi and plants are present in a broad range of terrestrial ecosystems and involve a large proportion of plant taxa (Brundrett, 2009). It is believed that at least 85% of plant species are able to establish symbiotic associations with fungi, of which 70% are associated with individuals of the phylum Glomeromycota, forming the arbuscular mycorrhizas (Wang& Qiu, 2006).

Living organisms both plant and animal types constitute an important component of soil. Though these organisms form only a fraction (less than one percent) of the total soil mass, but they play important role in supporting plant communities on the earth surface.

35.4.1 Soil microbes and plant growth: Microorganisms being minute and microscopic, they are universally present in soil, water and air. Besides supporting the growth of various biological systems, soil and soil microbes serve as a best medium for plant growth. Soil fauna

• & flora convert complex organic nutrients into simpler inorganic forms which are readily absorbed by the plant for growth. Further, they produce variety of substances like IAA, gibberellins, antibiotics etc. which directly or indirectly promote the plant growth

35.4.2 Soil microbes and soil structure: Soil structure is dependent on stable aggregates of soil particles-Soil organisms play important role in soil aggregation. Constituents of soil are viz. organic matter, polysaccharides, lignins and gums, synthesized by soil microbes plays important role in cementing / binding of soil particles. Further, cells and mycelial strands of fungi and actinomycetes, wormi casts from earthworm is also found to play important role in soil aggregation. Different soil microorganisms, having soil aggregation / soil binding properties are graded in the order as fungi >actinomycetes> gum producing bacteria > yeasts.

35.4.3 Soil microbes and organic matter decomposition: The organic matter serves not only as a source of food for microorganisms but also supplies energy for the vital processes of metabolism that are characteristics of living beings. Microorganisms such as fungi, actinomycetes, bacteria, protozoa etc. and macro organisms such as earthworms, termites, insects etc. plays important role in the process of decomposition of organic matter and release of plant nutrients in soil. Thus, organic matter added to the soil is converted by oxidative decomposition to simpler nutrients / substances for plant growth and the residue is transformed into humus. Organic matter / substances include cellulose, lignins and proteins (in cell wall of plants), glycogen (animal tissues), proteins and fats (plants, animals). Cellulose is degraded by bacteria, especially those of genus Cytophaga and other genera (Bacillus, Pseudomonas, Cellulomonas, and Vibrio Achromobacter) and fungal genera (Aspergillus, Penicilliun, Trichoderma, Chactomium, Curvularia). Lignins and proteins are partially digested by fungi, protozoa and nematodes. Proteins are degraded to individual amino acids mainly by fungi, actinomycetes and Clostridium. Under unaerobic conditions of waterlogged soils, methane are main carbon containing product which is produced by the bacterial genera (strict anaerobes) Methanococcus and Methanobacterium.

35.4.4 Soil microbes and humus formation: Humus is the organic residue in the soil resulting from decomposition of plant and animal residues in soil, or it is the highly complex organic residual matter in soil which is not readily degraded by microorganism, or it is the soft brown/dark coloured amorphous substance composed of residual organic matter along with dead microorganisms.

35.4.5 Soil microbes and cycling of elements: Life on earth is dependent on cycling of elements from their organic / elemental state to inorganic compounds, then to organic compounds and back to their elemental states. The biogeochemical process through which organic compounds are broken down to inorganic compounds or their constituent elements is known “Mineralization”, or microbial conversion of complex organic compounds into simple inorganic compounds & their constituent elements is known as mineralization.

Soil microbes’ plays important role in the biochemical cycling of elements in the biosphere where the essential elements (C, P, S, N & Iron etc.) undergo chemical transformations. Through the process of mineralization organic carbon, nitrogen, phosphorus, sulphur, iron etc. are made available for reuse by plants.

35.4.6 Soil microbes and biological N2 fixation: Conversion of atmospheric nitrogen in to ammonia and nitrate by microorganisms is known as biological nitrogen fixation.

Fixation of atmospheric nitrogen is essential because of the reasons:

1. Fixed nitrogen is lost through the process of nitrogen cycle through de-nitrification.
2. Demand for fixed nitrogen by the biosphere always exceeds its availability.
3. The amount of nitrogen fixed chemically and lightning process is very less (i.e. 0.5%) as compared to biologically fixed nitrogen
4. Nitrogenous fertilizers contribute only 25% of the total world requirement while biological nitrogen fixation contributes about 60% of the earth’s fixed nitrogen
5. Manufacture of  nitrogenous  fertilizers  by  “Haber”  process  is  costly  and  timeconsuming.

The numbers of soil microorganisms carry out the process of biological nitrogen fixation at normal atmospheric pressure (1 atmosphere) and temperature (around 20 °C). Two groups of microorganisms are involved in the process of biological nitrogen fixation Non-symbiotic (free living): Depending upon the presence or absence of oxygen, non-symbiotic N2 fixation prokaryotic organisms may be aerobic heterotrophs (Azotobacter, Pseudomonas, Achromobacter) or aerobic autotrophs (blue green algae as Nostoc, Anabena Calothrix,) and anaerobic heterotrophs (Clostridium, Kelbsiella. Desulfovibrio) or anaerobic Autotrophs (Chlorobium, Chromnatium, Rhodospirillum, Meihanobacterium etc.)

Symbiotic (Associative): The organisms involved are Rhizobium, Bradyrhizobium in legumes; Azospirillum in grasses; Actinonycetes Frankia in Casuarinas and Alder.

35.4.7 Soil microbes as biocontrol agents: Several eco-friendly bioformulations of microbial origin are used in agriculture for the effective management of plant diseases, insect pests, weeds etc. e.g. Trichoderma sp. and Gleocladium sp. are used for biological control of seed and soil borne diseases. Fungal genera Entomophthora, Beauveria, Metarrhizium are used in the management of insect pests and Nuclear polyhydrosis virus (NPV) is used for the control of Heliothis/American boll worm. Bacteria like Bacillus thuringiensis, Pseudomonas are used in cotton against Angular leaf spot and boll worms. The suppression mechanisms include the suite of native organisms out-competing the pathogenic organisms, physically protecting roots and providing better nutrition to the plant.

35.4.8 Degradation of pesticides in soil by microorganisms: Soil receives different toxic chemicals in various forms and causes adverse effects on beneficial soil micro flora / micro fauna, plants, animals and human beings. Various microbes present in soil act as the scavengers of these harmful chemicals in soil. The pesticides/chemicals reaching the soil are acted upon by several physical, chemical and biological forces exerted by microbes in the soil and they are degraded into non-toxic substances and thereby minimize the damage caused by the pesticides to the ecosystem. For example, bacterial genera like Pseudomonas, Clostridium, Bacillus, Thiobacillus, Achromobacter etc. and fungal genera like Trichoderma, Penicillium, Aspergillus, Rhizopus, and Fusarium are playing important role in the degradation of the toxic chemicals / pesticides in soil.

35.4.9 Biodegradation of hydrocarbons: Natural hydrocarbons in soil like waxes, paraffin’s, oils etc. are degraded by fungi, bacteria and actinomycetes e.g. paraffinic hydrocarbons are metabolized and degraded by Mycobacteria, Nocardia, Streptomyces Pseudomonas, Flavobacterium and several fungi.

References

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