{"id":351,"date":"2019-03-09T06:04:02","date_gmt":"2019-03-09T06:04:02","guid":{"rendered":"http:\/\/esp10.epgpbooks.inflibnet.ac.in\/?post_type=chapter&p=351"},"modified":"2019-04-22T09:49:15","modified_gmt":"2019-04-22T09:49:15","slug":"34-soil-microorganisms-and-their-functions-i","status":"publish","type":"chapter","link":"https:\/\/ebooks.inflibnet.ac.in\/esp10\/chapter\/34-soil-microorganisms-and-their-functions-i\/","title":{"rendered":"Soil microorganisms and their functions – I"},"content":{"raw":"
\"epgp<\/a>\r\n<\/span><\/div>\r\n \r\n\r\n \r\n\r\n \r\n\r\n \r\n\r\n34.1 Introduction<\/strong>\r\n\r\n \r\n

An important factor influencing the productivity of our planet's various ecosystems is the soil that has evolved on our planet. Soil is the natural and dynamic medium for the growth of land plants constituting the habitat of abundant biodiversity. A mass of mineral particles alone do not constitute soil as soil also contains air, water, dead organic matter, and various types of living organisms. The formation of a soil is influenced by organisms, climate, topography, parent material, and time (Steubing, 1994). True soils are influenced, modified, and supplemented by living organisms. Plants and animals aid in the development of a soil through the addition of organic matter. Fungi and bacteria decompose this organic matter into a semi soluble chemical substance known as humus. Larger soil organisms like earthworms, beetles, and termites, vertically redistribute this humus within the mineral matter found beneath the surface of a soil. When water moves downward into the soil, it causes both mechanical and chemical translocations of material (Environment Facts, 1999). Soil contains different types of microorganism, including bacteria, actinomycets, fungi, algae and viruses. Scales of the habitats depend mainly on the size of the organism: a few \u03bcm for bacteria; less than 100 \u03bcm for fungi; between 100 \u03bcm and 2 mm for Acari and Collembola; between 2 and 20 mm for Isopoda (Coleman & Crossley, 1996). Even if the available space is extensive in soil, the biological space, that is, the space occupied by living microorganisms, represents a small proportion, generally less than 5% of the overall available space (Ingham et al<\/em>., 1985).<\/p>\r\n

Soil environment differ from one location to another and from season to season. Therefore factor such as moisture pH, temperature, organic and inorganic content, and oxygen content affect the microbial flora of soil sample (Wankhade et al<\/em>., 2011).<\/p>\r\n

Soil is alive<\/strong><\/p>\r\n

Every gram of a typical healthy soil is home to several thousand different species of bacteria. One square metre of soil can contain about 10 million nematodes and 45 000 microarthropods (springtails and mites). It has more number of species in it than a km of rainforest. In addition to bacteria, soil is home to microscopic fungi, algae, cyanobacteria, actinomycetes, protozoa and nematodes, and macroscopic earthworms and insects.<\/p>\r\n

All of these organisms can be divided between autotrophs such as plants, algae and cyanobacteria, and heterotrophs such as fungi and bacteria, which decompose organic matter.<\/p>\r\n

Soil microbial diversity:<\/strong><\/p>\r\n

Early studies of soil bacterial and fungal diversity have found that less than 10% of the soil microbial community could be readily cultured. In the 1980s Norman Pace and colleagues\u00a0realised that the organisms could be identified in naturally occurring microbial populations without culturing them (Hugenholtz et al<\/em>. 1998) using the techniques that require the extraction and isolation of ribosomal RNA (rRNA) genes directly from cells in soil (as shown in Figure1). After the isolation of the rRNA genes, they are amplified from total community DNA using the polymerase chain reaction (PCR) with rRNA-specific primers. These primers can select different microbial groups at level of the domain (Bacteria, Eukarya, and Archaea), or phylum (e.g. Actinobacteria or Bacteroidetes). Different approaches can be taken to separate and sequence the rRNA genes. Advances in high-throughput DNA sequencing now allow thousands of individuals to be identified in each of thousands of samples in a week (Caporaso et al<\/em>. 2012).<\/p>\r\n \r\n\r\n\"\"<\/a>\r\n\r\nFigure 1: Molecular characterization of soil microbial diversity<\/strong>\r\n\r\n \r\n

Comparison of these sequences with rRNA genes from cultivated species and with sequences in databases such as GenBank allows evolutionary (phylogenetic) relationships between unknown and known organisms to be determined and provides an estimate of the genetic diversity of organisms in the community. Sequence information also allows speculation about the organism\u2019s characteristics, given what is known of its closest cultivated relative. Sometimes, phylogenetic information can also be used to infer physiology; for example, all cyanobacteria form a monophyletic group, as do many sulphate reducing bacteria, halophiles, and methanogenic archaea.<\/p>\r\n

34.2 Soil Microorganism \u2013 Actinomycetes<\/strong><\/p>\r\n

Actinomycetes are numerous and widely distributed in soil and are next to bacteria in abundance. The common genera of actinomycetes are Streptomyces<\/em> (nearly 70%), Nocardia\u00a0\u00a0<\/em>and Micromonospora<\/em> although Actinomycetes<\/em>, Actinoplanes, Micromonospora<\/em> and Streptosporangium <\/em>are also generally encountered in the soil.<\/p>\r\n \r\n

They are widely distributed in the soil, compost etc. The population of actinomycetes increases with depth of soil. They are found on every natural substrate but, prefer non-acidic soils with pH higher than 5. They are heterotrophic, aerobic and mesophilic (25-300C) organisms and some species are commonly present in compost and manures are thermophilic growing at 55-65\u00b0 C temperature. While most bacteria are found in the top foot or so of topsoil, actinomycetes may work many feet below the surface. Deep under the roots they convert dead plant matter to a peat-like substance. While they are decomposing animal and vegetable matter, actinomycetes liberate carbon, nitrogen and ammonia, making nutrients available for higher plants. Five percent or more of the soil\u2019s bacterial population is comprised of actinomycetes and they have the ability to produce antibiotics, chemical substances that inhibit bacterial growth.<\/p>\r\n \r\n\r\n\"\"<\/a>\r\n

These are the organisms with characteristics common to both bacteria and fungi but yet possessing distinctive features to delimit them into a distinct category. They are unicellular like bacteria, but produce a mycelium which is non-septate (coenocytic) and more slender, tike true bacteria they do not have distinct cell-wall and their cell wall is without chitin and cellulose (commonly found in the cell wall of fungi). On culture media unlike slimy distinct colonies of true bacteria which grow quickly, actinomycetes colonies grow slowly, show powdery consistency and stick firmly to agar surface. They produce hyphae and conidia \/ sporangia like fungi. Certain actinomycetes whose hyphae undergo segmentation resemble bacteria, both morphologically and physiologically.<\/p>\r\n

The characteristically earthy smell of newly ploughed soil in the spring is caused by actinomycetes, a higher form of bacteria similar to fungi and moulds. Actinomycetes are\u00a0 especially important in the formation of humus by slowly breaking down humates and humic acids in soils.<\/p>\r\n \r\n\r\nFunctions of actinomycetes:<\/strong>\r\n\r\n \r\n

    \r\n \t
  1. Degrade\/decompose all sorts of organic substances like cellulose, polysaccharides, protein fats, organic-acids etc.<\/li>\r\n \t
  2. Organic residues \/ substances added soil are first attacked by bacteria and fungi and later by actinomycetes, because they are slow in activity and growth than bacteria and fungi.<\/li>\r\n \t
  3. They decompose \/ degrade the more resistant and indecomposable organic substance\/matter and produce a number of dark black to brown pigments which contribute to the dark colour of soil humus.<\/li>\r\n \t
  4. They are also responsible for subsequent further decomposition of humus (resistant material) in soil.<\/li>\r\n \t
  5. They are responsible for earthy \/ musty odor \/ smell of freshly ploughed soils.<\/li>\r\n \t
  6. Many genera species and strains (e.g. Streptomyces if actinomycetes produce\/synthesize number of antibiotics like Streptomycin, Terramycin, Aureomycin etc.<\/li>\r\n \t
  7. One of the species of actinomycetes Streptomyces scabies<\/em> causes disease \"Potato scab\" in potato.<\/li>\r\n<\/ol>\r\n34.3 Soil Microorganism \u2013 Bacteria<\/strong>\r\n\r\n \r\n

    Bacteria are some of the smallest; single-celled may be shaped like a sphere, rod, or a spiral twist and most abundant microbes in the soil. One gram of soil in good conditions can contain 600 million bacteria belonging to an estimated 60,000 different species, most which have yet to be even named, and each has its own particular roles and capabilities. Most bacteria are colourless and produce colonies; others are free-living. All reproduce by means of binary fission, in which the nucleus splits in two and a new cell wall grows crosswise over the middle of the cell. Each half contains one of the two nuclei, so that a new individual is produced from a single bacterial cell. Under the best conditions, a colony of bacteria can multiply into billions in a very short time. The life span of one generation of bacteria is about 20 to 30 minutes, so that one cell may yield a progeny of billions of individuals in half a day. The microorganisms exist throughout the soil but predominate in top surface soil (10 cm approx), where food sources are plentiful and around the macropores (channels lined with organic matter and formed by the growing roots and the activity of earthworms, insects and\u00a0other soil biota). As they are dependent on exudates and sloughed-off cells of roots, which is a readily available food source so, they are especially abundant in the area immediately next to plant roots. The unique soil microbial ecosystem associated with the immediate vicinity of plant roots is called the rhizosphere. The rhizosphere is the narrow region of soil that is directly influenced by the roots and associated soil organisms, which are primary decomposers of organic matter, but they do other things, such as provide nitrogen through fixation to help growing plants, detoxify harmful chemicals (toxins), suppress disease organisms, and produce products that might stimulate plant growth.<\/p>\r\n

    Amongst the different microorganisms inhabiting in the soil, bacteria are the most abundant and predominant organisms. These are primitive, prokaryotic, microscopic and unicellular microorganisms without chlorophyll. Morphologically, soil bacteria are divided into three groups viz Cocci (round\/spherical), Bacilli (rod-shaped) and Spirilla (cells with long wavy chains). Bacilli are most numerous followed by Cocci and Spirilla in soil.<\/p>\r\n

    The most common method used for isolation of soil bacteria is the \"dilution plate count\" method which allows the enumeration of only viable\/living cells in the soil. The size of soil bacteria varies from 0.5 to 1.0 micron in diameter and 1.0 to 10.0 microns in length. They are motile with locomotory organs flagella.<\/p>\r\n

    Bacterial population is one-half of the total microbial biomass in the soil ranging from 1,00000 to several hundred millions per gram of soil, depending upon the physical, chemical and biological conditions of the soil.<\/p>\r\n \r\n

    Winogradsky (1925), on the basis of ecological characteristics classified soil microorganisms in general and bacteria in particular into two broad categories i.e. Autochnotus (Indigenous species) and the Zymogenous (fermentative). Autochnotus bacterial population is uniform and constant in soil, since their nutrition is derived from native soil organic matter (e.g. Arthrobacter <\/em>and Nocardia <\/em>whereas Zymogenous bacterial population in soil is low, as they require an external source of energy, e.g. Pseudomonas<\/em> & Bacillus<\/em>. The population of Zymogenous bacteria increases gradually when a specific substrate is added to the soil. To this category belong the cellulose decomposers, nitrogen utilizing bacteria and ammonifiers.<\/p>\r\n

    As per the system proposed in the Bergey's Manual of Systematic Bacteriology, most of the bacteria which are predominantly encountered in soil are taxonomically included in the three orders, Pseudomonadales, Eubacteriales and Actinomycetales of the class Schizomycetes. The most common soil bacteria belong to the genera Pseudomonas, Arthrobacter,<\/em> Clostridium Achromobacter, Sarcina, Enterobacter <\/em>etc. The another group of bacteria\u00a0common in soils is the Myxobacteria belonging to the genera Micrococcus, Chondrococcus,<\/em> Archangium, Polyangium, Cyptophaga.<\/em><\/p>\r\n \r\n

    Bacteria are also classified on the basis of physiological activity or mode of nutrition, especially the manner in which they obtain their carbon, nitrogen, energy and other nutrient requirements. They are broadly divided into two groups<\/p>\r\n \r\n

      \r\n \t
    1. Autotrophic bacteria <\/strong>are capable synthesizing their food from simple inorganic nutrients, while heterotrophic bacteria depend on pre-formed food for nutrition. All autotrophic bacteria utilize CO2 (from atmosphere) as carbon source and derive energy either from sunlight (photoautotrophs, e.g. Chromatrum. Chlorobium.<\/em> Rhadopseudomonas <\/em>or from the oxidation of simple inorganic substances present in soil (chemoautotrophs e.g. Nitrobacter, Nitrosomonas, Thiaobacillus<\/em>).<\/li>\r\n<\/ol>\r\n \r\n
        \r\n \t
      1. Heterotrophic bacteria: <\/strong>Bacteria are the most nutritionally diverse of all organisms, which is to say, as a group, they can eat nearly anything. Majority of soil bacteria are heterotrophic in nature and derive their carbon and energy from complex organic substances\/organic matter, decaying roots and plant residues. Since bacteria are smaller, less mobile and less complex than most organisms, they are less able to escape an environment that becomes unfavourable. They obtain their nitrogen from nitrates and ammonia compounds (proteins) present in soil and other nutrients from soil or from the decomposing organic matter. The heterotrophic bacteria are of various types like:<\/li>\r\n<\/ol>\r\n \r\n

        Decomposers: <\/strong>Bacteria play an important role in decomposition of organic materials, especially in the early stages of decomposition when moisture levels are high. Bacillus subtilis <\/em>and Pseudomonas fluorescens <\/em>are examples of decomposer bacteria. The compost bacteria are decomposers as they decompose living or dead organic materials. Some are so adaptable that they can use more than a hundred different organic compounds as their source of carbon because of their ability to produce a variety of enzymes. Usually, they can produce the appropriate enzyme to digest whatever material they find themselves on.<\/p>\r\n

        Nitrogen fixing bacteria<\/strong><\/p>\r\n

        Nitrogen is required for cellular synthesis of enzymes, proteins, chlorophyll, DNA and RNA, and is therefore important in plant growth and production of food and feed. The ability of crop plants to thrive is frequently limited by the supply of available nitrogen; although there is a lot of it in the atmosphere, plants are unable to utilise it,\u00a0instead rely on an inorganic supply (naturally-occurring and in the form of fertilisers). However, certain bacterial species are able to \u2018fix\u2019 atmospheric nitrogen into a usable form. This form of nitrogen fixation can add the equivalent of more than 100kg of nitrogen per hectare per year.<\/p>\r\n \r\n

        Some of these bacteria exist free living in the soil and often associated with non-legume plants. Among the free-living bacteria that can fix nitrogen are aerobic species such as Azotobacter, Azospirillum<\/em>, Gluconobacter<\/em>, Flavobacterium<\/em> and Herbaspirillum. <\/em>These aerobic organisms apparently shield the anaerobic nitrogenase enzyme from oxygen by, among other things, having a very high rate of oxygen use that minimizes the di\ufb00usion of oxygen into the interior of the cell, where the enzyme is located. Another free-living obligate aerobe that fixes nitrogen is Beijerinckia<\/em>. Some anaerobic bacteria, such as certain species of Clostridium<\/em> also fix nitrogen.<\/p>\r\n\"\"<\/a>\r\n

        Another group of bacteria capable of fixing nitrogen in the soil namely Rhizobium,<\/em> Mesorhizobium, Bradyrhizobium, Azorhizobium, Allorhizobium and Sinorhizobium <\/em>live in special root nodules on legume plants (clover, peas, peanuts, beans, alfalfa etc.) as symbionts. The free-living Rhizobium enters the plant via its root hairs, forming an infection thread and infecting more and more cells. Normally rod-shaped, they proliferate as irregularly-shaped bacteroids, densely packing the cells and causing them to swell, forming root nodules.<\/p>\r\n \r\n

        There are similar examples of symbiotic nitrogen fixation in nonleguminous plants, such as alder trees. The alder tree is symbiotically infected with an actinomycete (Frankia<\/em>) and forms nitrogen-fixing root nodules.<\/p>\r\n \r\n

        Nitrogen-fixing bacteria belong to different phyla of the domain Eubacteria and may associate with the roots of plants in a more or less specific manner (Franche et al<\/em>., 2009). Bacteria capable of symbiotically associating with the roots of plants, leading to the formation of structures called nodules, have a higher specificity in relation to the host (Masson-Boivin et al<\/em>., 2009). However, some bacteria may inhabit the root surface or the plant rhizosphere, forming associations with low degree of specificity with the host (Bhattacharjee et al<\/em>., 2008). Plants associated with these bacteria benefit themselves due to the increased nitrogen supply, and in the case of symbiotic associations, over 90% of nitrogen contained in the plant can be fixed by bacteria (Franche et al<\/em>., 2009). Thus, the presence of N-fixing bacteria in the rhizosphere of plants can improve plant growth in nitrogen-poor environments, as well as promote increased nitrogen content in the soil, which is often related to the facilitative effect that legume species have on other plant species (Walker et al., 2003). Phosphate-solubilizing microorganisms <\/strong>(PSB) are naturally present in soils associated or not with plant roots (Rodr\u00fd\u00ecguez & Fraga, 1999; Gyaneshwar et al<\/em>., 2002). Phosphate-solubilizing microorganisms are very important, especially in tropical soils as they are able to indirectly provide phosphorus to plants by solubilizing P precipitated with iron, aluminum and calcium (Gyaneshwar et al<\/em>., 2002). These microorganisms solubilize phosphorus\u00a0adsorbed by soil minerals by means of various mechanisms and have great potential to promote plant growth.<\/p>\r\n\"\"<\/a>\r\n

        \r\n

        Several mechanisms have been proposed to explain the P solubilisation. One of the primary mechanisms is the release of organic, inorganic acids and the excretion of protons that accompanies to the NH4+ assimilation (Whitelaw 2000). Equally, phosphates may also be released from solid compounds by carbonic acid formed as a result of the decomposition of organic residues (Memon, 1996).The bacteria namely Nitrosomonas<\/em> and Thiobacillus<\/em> are reported to mobilize inorganic phosphates by producing nitric and sulphuric acid.<\/p>\r\n \r\n

        Many organic acids produced by rhizosphere microorganisms are effective in solubilizing soil phosphates by decreasing the sorption of Pon the clay surfaces, favouring the solubilization of hydroxyapatite (rock phosphate) and plant P uptake. Some of the organic acids commonly found are gluconic acid, oxalic acid, citric acid, lactic acid, tartaric acid and aspartic acid produced due to oxidative respiration or by fermentation of organic carbon sources in the microbial metabolism. Such biological reactions occur in the rhizosphere where carbonaceous compounds are used by phosphorus solubilising rhizobacteria (PSRB) and the phosphate released is taken up by the roots. On the other hand, organic anions produced by PSRB also compete with phosphates for fixation sites on the surface of soil colloids.<\/p>\r\n \r\n

        In addition to above discussed mechanisms, the release of phosphatase enzymes by phosphorus solubilising microorganisms, that mineralize organic P compounds has been also suggested as another mechanism involved (Stevenson 1986). Various studies have shown that\u00a0inoculation of this group of microorganisms in the rhizosphere of many plant species led to increased uptake of phosphorus by the plants and higher growth.<\/span><\/p>\r\n\r\n<\/div>\r\n \r\n\r\n\"\"<\/a>\r\n

        Plant Growth promoting rhizobacteria (PGPR): <\/strong>A large group of bacteria called PGPR plays an important role in promoting plant growth by different mechanisms. By participating in key ecosystem processes or acting specifically on certain plant species, these bacteria can play a central role in the composition of plant communities in different environments.<\/p>\r\n

        The bacteria termed PGPR are able to promote plant performance by means of a wide variety of mechanisms (Saharan & Nehra, 2011). The studies have shown that inoculation of plants with PGPR can increase nutrient content (Orhan et al<\/em>., 2006; Karthikeyan et al<\/em>., 2010) and resistance to pathogens (Saravana kumar et al<\/em>., 2007; Maksimov et al<\/em>., 2011). Moreover, some PGPR are able to produce phytohormones, increase the population of other beneficial microorganisms and control the population of harmful ones in the rhizosphere (Saharan & Nehra, 2011). Thus, plants able to recruit greater populations of these microorganisms into their rhizospheres present greater survival, growth, and reproduction (Gholami et al<\/em>., 2009), and consequently higher competitive ability.<\/p>\r\n \r\n\r\nDisease suppressors<\/strong>\r\n\r\n \r\n

        A number of bacteria have been commercialised worldwide for disease suppression. However, suppression is often specific to particular diseases of particular crops and may only be effective in certain circumstances.<\/p>\r\n \r\n

        Bacillus megaterium<\/em>, Pseudomonas fluorescens <\/em>are example of such bacteria that has been used on some crops to suppress the disease-causing fungus Rhizoctonia solani.<\/em> Similarly the bacteria Bacillus subtilis<\/em> has also been reported to be used to suppress seedling blight of sunflowers caused by Alternaria helianthi<\/em>.<\/p>\r\n \r\n\r\nSulphur oxidisers<\/strong>\r\n\r\n \r\n

        In the magmatic crust of our planet, sulphur is present in its reduced form as sulfide of metals. Many soil minerals contain sulphides, a form of sulphur largely unavailable to plants. The biological oxidation of hydrogen sulphide to sulphate (form of sulphur which plants can use) is one of the major reactions of the global sulphur-cycle performed by sulphur oxidising bacteria present in soil. The sulphur oxidizing microorganisms are primarily the gram negative bacteria currently classified as species of Thiobacillus, Thiomicrospira<\/em>and Thiosphaera<\/em>, but heterotrophs, such as some species of Paracoccus, Xanthobacter, Alcaligens <\/em>and Pseudomonas <\/em>can also exhibit chemolithotrophic growth on inorganic sulphur.<\/p>\r\n\r\n\r\n\r\n\r\n
        you can view video on Soil microorganisms and their functions - I<\/strong><\/td>\r\n\"\"<\/a><\/td>\r\n<\/tr>\r\n<\/tbody>\r\n<\/table>\r\nReferences:<\/strong>\r\n