Soil microbial diversity

Bacteria

Bacteria and archaea are the smallest independently living unicellular, procaryotic organisms on earth. Bacteria are present in greatest numbers, with archaea 10-fold less. Typical cells range from 0.5 to 1.0 μm in diameter. Bacteria and archaea may occur as cocci, rods, or spirals .They lack a true membrane-bound nucleus, so their DNA lies free in the cell cytoplasm. Their genome typically consists of a single circular molecule of double-stranded DNA, though cells may also harbour smaller DNA elements called plasmids. Bacteria are more numerous than the other four combined. There are more than 400 named genera and an estimated 10⁴ species. Species still unknown quite likely outnumber those already known. They present in all types of soil but their population decreases as the depth of soil increases (Horizon A > B > C). The number of cells of bacteria in the soil is always great, but the individuals are small, (µm in length). Because of the minute size of the bacteria and large cells or filaments of the other 4 groups, the bacteria probably account for appreciably less than half of the total microbial cell mass. Estimates by a number of methods indicate a range of 100 - 4000 kg / ha live weight of bacteria which is, 0.015 - 0.05% of the total soil mass. Fungi often contribute the largest part of the total microbial biomass in soils. In aerated soil, bacteria will be dominating, alone are responsible for all the activities in environment lacking O₂ or little O₂. In transformation process Bacteria stand first, due to their rapid growth and capacity of vigorous decomposition of variety of substrates.

Soil microbiological population (bacteria) has been divided into two broad groups viz., autohcthonous and zymogenous.

Autochthonous or native microbes; Indigenous, which are characteristic of the particular soil and which many be expected always to be found there. eg. Arthrobacter.

Zymogenous, or fermentative organisms require an external source of and their normal population in soil is low (Pseudomonas, Bacillus). When specific substrates are added to soil, the population is increased . Organisms that can take advantage of any sudden increase of nutrients in their environment which enable them to reproduce quickly and abundantly .Then gradually declines when the added substrate is exhausted eg.cellulose decomposers. N utilizing bacteria, nitrifiers etc.,

Transient microbes - comprising organisms that are introduced into the soil by legume inoculation unintentionally as in the case of agents producing animal and plant diseases.

Based on nutritional requirement bacteria are divided into four groups. That creates metabolic diversity.

1. Autotrophs- synthesize their own food, derive energy from light or chemicals.

Photoautotroph - energy from sun light, C from CO_2.

Chemoautotrophs - energy from oxidation of inorganic chemicals, C from CO₂.

2. Heterotrophs- depends on preformed food for nutrition, derive energy and C from organic compounds.

Photoheterotrophs - energy from slight, C from organic compounds.

Chemoheterotrophs- energy & C from organic chemicals.

Although bacteria have been subdivided into more than 100 phyla, fewer than 10 are abundant in soil. The estimated relative abundance of the major phyla varies between different soils (or samples); members of the phyla Proteobacteria, Acidobacteria, and Actinobacteria are widespread and often abundant, whereas members of the Verrucomicrobia, Bacteroidetes, Firmicutes, Chloroflexi, Planctomycetes, and Gemmatimonadetes are generally less prevalent. While the number of phyla in soil is low it appears the species diversity is high compared with other environments. The Proteobacteria are a metabolically diverse group of organisms in several subphyla, four of which, α-, β-, -, and -Proteobacteria, are commonly reported in soil. Members of the α, β, and γ subphyla are considered to be copiotrophs: they are more prevalent where resource availability is high such as in rhizosphere soils

α Proteobacteria: metabolically diverse heterotrophic and autotrophic bacteria. Examples: Sphingomonas, Rhizobium, Mesorhizobium, Methylobacter, Nitrobacter, Rhodospirillum

β Proteobacteria: Heterotrophs, autotrophs, and methanotrophs. Example: Burkholderia, Alcaligenes, Nitrosospira, Thiobacillus, Rhodocyclus. Methylomonas.

γ Proteobacteria: heterotrophs, lithotrophs, and phototrophs. Examples: Pseudomonas and Xanthamonas, Thiocapsa and Chromatium

δ Proteobacteria: sulphate- and iron reducing bacteria; Examples: Desulfovibrio, Bdellovibrio

Acidobacteria: Oligotrophs- They also appear well suited to low nutrient conditions, tolerate fluctuations in soil moisture, and are capable of nitrate and nitrite reduction Example: Acidobacterium

Archaea

Archaea were originally thought to exist only in harsh environments and were often described as ‘extremophiles’, but we now know they are widely distributed and are found alongside bacteria in many environments including soil. Archaea and bacteria are difficult to distinguish on the basis of their morphology. However, 16S ribosomal rRNA sequences can differentiate these groups. Nitrification in agricultural soil; methanogenesis in rice field are some of the soil processes mediated by archaea.

Actinobacteria

A transitional group between the simple Bacteria and Fungi are the actinomycetes, now grouped as actinobacteria. Actinobacteria are a group of Gram-positive bacteria with high guanine and cytosine content in their DNA, which can be terrestrial or aquatic. Though they are unicellular like bacteria, they do not have distinct cell wall, but they produce a mycelium that is nonseptate and more slender. Actinobacteria include some of the most common soil, freshwater and marine type, playing an important role in decomposition of organic materials, such as cellulose and chitin, thereby playing a vital part in organic matter turnover and carbon cycle, replenishing the supply of nutrients in the soil, and is an important part of humus formation.

Distribution and abundance

Actinobacteria are numerous and widely distributed not only in soil but in a variety of other habitats including composts, river muds and lake bottoms. Present in surface soil and also in lower horizons to considerable depth. In abundance they are second only to the Bacteria and the viable counts almost equal to both. Saprophytic existence, but a few species can cause diseases of plants, domestic animals and even humans.

Population is 10⁵ to 10⁸/g in temperate zone, but lower counts in waterlogged soils, acid peat, arctic, Tundra regions. In alkaline areas, especially when dry, the relative abundance is high.

Common genera in soils

The common genera present in the soil are Streptomyces (70%), Nocardia, Micromonaspora, Frankia which occur in all types of soil including desert soil. When comparing the Actinobacterial diversity in terrestrial environment, the greatest biodiversity lies in the oceans. The marine environment is an untapped source of novel Actinobacteria diversity and thus of new metabolites. Marine Actinobacteria dwelling in extremely different environment produce different types of bioactive compounds compared with terrestrial ones.

The genus Streptomyces they elaborate musty odour; an odour reminiscent of freshly turned soil. The metabolite of Streptomyces, geosmin and other volatile products are responsible for the characteristic earth odor/ smell.

Functions:

• Decomposition of resistant components of plant and animal tissue.
• Transformations at high temperature particularly in the manure and compost pits – thermophiles dominant
• Cause certain soil borne diseases of plants, potato scab of apple, sweet potato pox.
• Cause infection to humans, animals.
• Play important role in microbial antagonism by production of antibiotics and production of enzymes.

Fungi

As the important constituent group of the soil population, they are widely distributed in most well – cultivated soils. Fungi account for a large part of the total microbial biomass. Though they are not the major inhabitants, they do in fact makeup the significant part of the biomass because of the large diameter and extensive network of the filaments. Fungi exist in soil in the form of vegetative mycelium and spores. Characteristically the fungi possess a filamentous mycelium network of individual hyphal stands. The hypha itself is rather broad and has a diameter appreciably greater than that found in the common actinomycetes. In nature asexual spores are abundant and widespread, the sexual spores relatively uncommon. In contrast with bacteria,it can be effectively differentiated into Genera and species on the basis of morphology.

Distribution and abundance

Estimates of microbial density reveal the presence in soil is ranging a few as 20,000 to as many as 1,000,000 fungal propagules per gram, the propagule being considered as any spore, or hyphal filament that is capable at giving rise to a colony. The length of the fungal mycelium has been reported to range from 10 to 100 m per g surface soil, but varies up to 500 and sometimes in excess of 1000 meter have also been obtained. It would appear that the weight of fungi ranges from 500 to 5000 kg per ha of surface soil. Thus the filaments make up a significant part of the soil mass.

Individual species and genera have been recorded in diverse and highly dissimilar habits. They are the inhabitants of peats, flooded soils planted to rice, regions with low and extremely high salt contents, locations in many deserts, sites in Antartica, as well as in the tundra.

Fungi generally dominate microbial biomass and activity (i.e., respiration) in soil organic horizons, particularly in forests .Bacterial-to-fungal ratios tend to be lower in acidic, low-nutrient soils with recalcitrant litter and high C-to-N ratios, whereas bacteria are increasingly prominent in high N+P, saline, alkaline, and anaerobic (waterlogged) soils. Fungal distributions are more influenced by N and P availability than pH.

Importance

1. Fungi mediate nearly every aspect of organic matter production, decomposition and sequestration, with concomitant roles in the mineralization and cycling of N and P.
2. Contribute more biomass to the soil.

Function and activity

• Produce a wide range of enzymes, including amylases, proteases, lipases, and phosphatases.
• Involved in the degradation of the major plant constituents – cellulose, hemicellulose, pectins, starch and lignin.
• Participate in humus formation from fresh organic residues.
• Carry out inorganic transformations and influences the formation of stable aggregates by means of hyphal penetration and the mechanical binding of the particles. Aggregate formation promotes soil C sequestration by providing physical protection from decomposers and their degradative enzymes
• Pathogenecity is common character associated with several soil borne fungi- Fusarium, Helminthosporium.
• Cause disease among humans, animals
• They are the predator against protozoa. The hyphae penetrate the protozoan with a resulting decrease in motility of the animal and an eventual total cessation of movement. The Fungi slowly digests the cellular components and assimilates the substances released.
• Nematodes are also trapped by the Fungi by hyphal extensions. Eg: Arthrobotrys, Dactylaria, Dactylella,
• Support plant production through mycorrhizal associations that enhance the acquisition of water and nutrients
• Fungal endophytes can confer resistance to thermal and drought stress
• Fungi also support C and N fixation by algae and cyanobacteria through lichen associations.

Algae

Algae are ubiquitous; they occur in almost every habitable environment on earth, in soils, permanent ice, snow fields, hot springs, and hot and cold deserts. Algae are present in most of the soils where moisture and sunlight are available. They occur in small numbers in soil. 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. They add biomass to the extent of 7 to 300 kg / ha.Soil algae are divided in to four main classes or phyla as follows:Cyanophyta (Blue-green algae); Chlorophyta (Grass-green algae); Xanthophyta (Yellow-green algae); 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, Protosiphon etc. and that of diatoms are Navicula, Pinnularia. The dominant genera of BGA in soil are: Chrococcus, Phormidium, Anabaena, Aphanocapra, Oscillatoria etc. Some BGA possess 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-Azolla association fix nitrogen symbiotically in rice fields.

Importance of algae

• Colonizes the barren surface and corrode and weather rocks and contribute to soil formation.
• Algal layer covers the rocks; on death it favors secondary colonizers.
• Surface bloom reduces erosion losses probably by binding together with soil particles.
• Most of soil algae (especially BGA) act as cementing agent in binding soil particles and thereby reduce/prevent soil erosion ,Improve soil structure, texture and add fertility to soil after decay.
• Involved in CO₂ fixation. Add organic matter to soil when die and thus increase the amount of organic carbon in soil
• 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 and thus provides O₂ to the roots and other microorganisms.
• Plays important role in the maintenance of soil fertility especially in tropical soils.
• Under flooded paddy field,involved in nitrogen fixation as symbiotic and free-living organisms.
• Production of metabolites.
• Single cell protein production, β-carotene.

Protozoa

These are unicellular, eukaryotic, colourless, and animal like organisms .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. Most of the soil protozoa are motile by flagella or cilia or pseudopodia as locomotors organs.

Functions of Protozoa

• 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.
• Protozoa have been recently used as biological control agents against phytopathogens.
• Several soil protozoa cause diseases in human beings which are carried through water and other vectors, eg. Amoebic dysentery caused by Entomobea histolytica.