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Microbial Ecology

Microbiology of Extreme Environments


Bioactive Compounds of Microorganisms

Health and Disease and Epidemiological Measurements

Methods of Transmission of Diseases

Management of Diseases

Drinking Water Microbiology

Food Borne Disease

Microbial Association in Soil, Water and Air

Microbial ecology is the study of the relationship between microorganisms and their environment. The concept of microbial ecology originated with work of Beijerinck and Winogradsky. Today, microbial ecology has branched out and includes the study of how microbial populations interact with plants and animals in various environments. Microbial communities interact with communities of microorganisms and then abiotic components of the environment to define the entire system.
The microbial association is the interaction between microorganisms, and also to higher organisms, including plants and animals. these interactions may be positive, negative or neutral.
Soil Microorganisms and Their Interactions
The soil is the outer loose material of earth surface different from the underlying bedrocks. The soil is considered to provide the substratum for plant and animal life. The represents a favourable habitat for microorganisms and is inhabited by a wide range of microorganisms, including bacteria ,actinomycetes, fungi, algae and protozoa. The physical structure, aeration, water holding capacity and availability of nutrients are determined by the mineral constituents of soil, which are formed by the weathering of rocks and the degradation of organic wastes due to metabolic activities of microorganisms.
Cultivated the soil has relatively more population of microorganisms than the fallow land, and the soils rich in organic matter contain much more population than sandy and eroded soils. Microbes in the soil are important to us in hormones, organic acids, etc. but certain microbes in soil are the causal agents of various disease in plants and animals.
Soil Bacteria
Bacteria are the most predominant organism in soil, their number varies between 108-1010cells/gm of soil. Based on regular presence, bacteria may be of two types:

  • Soil indigenous or true residents or autochthonous
  • Soil invader or allochthonous

The autochthonous population is always constant in the soil since their nutrition is derived from native soil organic matter. The indigenous flora is relatively stable in its composition. The indigenous species may also possess metabolically dormant morphological forms. Examples;Bacillus(spores),Clostridium, Agrobacterium, Arthrobacter,etc.
Allochthonous population requires an external source of energy. When a specific substrate is added to soil, their number increases and gradually decline when the added substrate is exhausted e.g. cellulose decomposers, nitrogen utilizing bacteria etc.
Role of Soil Bacteria

  1. Nitrogen fixation
  2. Phosphate and sulphur solubilization
  3. Degradation of organic compounds
  4. Some bacteria are pathogenic to the plants and animals
Soil Actinomycetes
They are the transition group of microorganisms which acts as a boundary between bacteria and fungi. Numerically, they are second abundant microbes in the soil after bacteria. The most limiting factor is the pH which governs their abundance in soil. Their luxuriant growth is favoured to be neutral or alkaline pH and they are intolerant to low pH. Many of them are known to produce antibiotics. They also play a role in the decomposition of resistant components of organic matter and in the formation of humus. The most common genera of actinomycetes in soil are;Streptomycin spp.,Nocardia spp., Microbispora spp., Actinomyces spp., Micromonospora spp., Actinoplanes spp., Thermoactinomyces spp.,etc.
Role of Actinomycetes
  1. Actinomycetes can utilize highly complex molecules like polysaccharides, organic acids, lipids, aliphatic and aromatic hydrocarbons, etc. Some species can decompose starch and chitin.Nocardiasppcan metabolize paraffin, phenols, steroids, pyrimidines, etc.Micromonosporacan decompose chitin, cellulose, and even lignin. They also degrade proteins, amino acids, and peptones to release the nitrogen.
  2. Formation of humus through the conversion of raw organic matters into compounds native to soils organic fraction. Main strains of actinomycetes produce compounds that are components of humus.
  3. Thermophilic actinomycetes take part in decaying of compost piles and manures.
  4. Liberation of antibiotics.
Soil Fungi
More than hundreds of different species of fungi inhabit the soil. They prefer to live in the soil in aerobic condition. Fungi perform important functions within the soil in relation to nutrient cycling, disease suppression and water dynamics, all of which help plants become healthier and more vigorous. Fungi exist in both the mycelial and spore stage. Soil fungi are microscopic plant-like cells that grow in long threadlike structures or hyphae that make mass called mycelium. The mycelium absorbs nutrients from the roots it has colonized, surface organic matter or soil. From the mycelia, the fungi are able to throw up its fruiting bodies, the visible part above the soil (e.g.mushrooms), which may contain millions of spores. When the fruiting body bursts, these spores are dispersed through the air to settle in fresh environments and are able to lie dormant for up to years until the right conditions for their activation arise. The physical structure of the soil is improved by the accumulation of mold mycelium within it. Filamentous fungi play important roles in the degradation of cellulose, hemicellulose, starch, pectin and lignin in the organic matter added to the soil. They help in soil aggregation and in the formation of humus from raw organic residues. Most common genera areAlternaria spp., Aspergillus spp., Cladosporium spp., Dematium spp., Gliocladium spp., Penicillium spp., Mucor spp., Cephalosporium spp., Fusarium spp.,etc.

Role of Fungi

  1. Fungi play an important role in the degradation of cellulose, hemicellulose, starch, pectin and lignin.
  2. Fungi also helps in the formation of humus from organic residues. Humus improves the soil texture and helps in soil aggregation.
  3. Some fungi are predators on protozoa like amoeba and some of the fungi feed upon nematodes. Thus, they may participate in controlling the soil population.
  4. Some of the fungi remain with plant roots in the symbiotic association (mycorrhizal association) and supply plants with nutrients like nitrogen, phosphorus, sulphur, etc. Examples;Bolletus spp., Glomus spp.
  5. Some of the soil fungi are pathogenic to plants. Example;Aspergillus spp., Alternaria spp.
Soil Algae
Algae population is soil is generally smaller than of either bacteria or fungi. Their number in soil normally 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. Their photosynthetic nature accounts for their predominance on the surface or just below the surface layer of soil. Soil algae are divided into four major classes, i.e. Cyanophyta (blue-green algae), Chlorophyta (grass-green algae), Xanthophyta (yellow-green algae) and Bacillarophyta (diatoms). Out of these four classes, classCyanophyta (blue-green algae) and Chlorophyta (grass green algae) are more abundant in soil. Algae of the class Chlorophyta and bacillarophyta are dominant in the soils of the temperate region while blue-green algae are in tropical soils.Chlorella, Chlamydomonas, Chlorococcumare some of the common genera of grass-green algae (Chlorophyta) present in the soil whereasNavicula, Pinnulariaetc are some of the genera of diatoms present in the soil.
Cyanobacteria, also known as blue-green algae are unicellular, oxygenic photosynthetic prokaryotes grow on the surface of freshly exposed rock where the accumulation of their cells results in simultaneous decomposition of organic matter. This gives a nutrient base that will support the growth of other bacterial species. The dominant genera of blue-green algae in soil are;Chrococcus, Phormidium, Anabaena, Aphanocapra, Oscillatoriaetc. Some blue-green algae help in nitrogen fixation. Cyanobacteria are common in neutral to alkaline soil.
Role of Cyanobacteria
  1. They are responsible for oxygenic soil atmosphere and influence the growth of other microorganisms.
  2. Their capacity to utilize nitrogen gas as a source of nitrogen is great agricultural important. Cyanophycin is the nitrogen storage product in many cyanobacteria. When the nitrogen in the environment becomes deficient this compound is broken down and utilize as a source of nitrogen.
  3. The cyanobacteria play a key role in the transformation rock to soil, a first step rock-plant succession.
Soil Protozoa
Protozoa contains primitive unicellular organisms ranging in size from few microns to few centimeters. They are eukaryotic and lack chlorophyll. the life cycle of protozoa may consist of an active phase and rest phase (cyst). In cyst stage, it can withstand adverse environmental conditions and persists for many years. Reproduction is usually asexual taking place by fission or longitudinal or transverse division. Some can undergo sexual reproduction where two cells fuse, their nuclei unite, genetic material is exchanged and new individuals emerge. the soil protozoa can be classified as:
  1. Flagellates: (Mastigophora)-Oikamonas spp., Bodo spp., Allantoin spp., Cercomonas spp.,etc
  2. Amoeboids: (Sarcodina)-Amoeba, Acanthamoeba, Euglypha, Biomyxa,etc.
  3. Ciliates-Colpoda, Vorticella, Pleotricha, Colpidium,etc.

The nutrition is holozoic in which the ingested food particle is surrounded by vacuole and digested. Holozoic protozoa derive their nutrition by predating soil bacteria such asE. coli, Pseudomonas, Bacillus, Clostridiumetc. Some of the protozoa may also be saprophytic.
The population of protozoa is dense in the soil with a large number of bacteria and are limited to the upper layer of soil. their growth is affected by soil moisture. water logged conditions make the environment anaerobic and retard their growth. Most of them are aerobic. they have low sensitivity towards pH and grow over a pH range 3.5->9 (optimum pH 6-9). The temperature for growth is specific but the higher temperature is detrimental to them.

Role of Protozoa in Soil
The function of protozoan in soil is little known however, they are thought to be responsible for following:

  1. They serve to regulate the size of the bacterial community.
  2. They allow competing bacteria to co-exist in soil in which one bacterial species might have other eliminated.
  3. Decomposition of organic matter, for example, polysaccharides are easily metabolised by protozoa.
  4. The protozoa may be pathogenic to plants and animals.
Water Microorganisms and Their Interactions
Water covers 71% of Earth's surface. It is vital for the every known being in this world. And it is the another favourable habitat for microorganisms and is inhabited by wide range of microorganisms, including bacteria, cyanobacteria, molds and yeasts, algae, protozoa, diatoms, dinoflagellates, phytoflagellates, rotifers, and crustaceans. Water is indispensible for microorganisms. Because of its fluidity, it brings nutrients into cells and helps in expelling waste material out of cell. Different metabolic reaction require water molecule to run within the cell. The hydro -ecosphere is divided into fresh water habitat and marine habitat and the microorganisms are divided accoding to this.
Fresh Water Ecosystem
Fresh water habitat consist of lakes, ponds, swamps, streams and rivers. Fresh water habitats are classified on the basis of their physical and chemcal properties. The standing water such as lakes and ponds are called lentic or littorol habitats and those with running water are called lotic habitats.
Distribution of Microorganisms in Lentic Ecosystem
The microorganisms may occur at all depth ranging from the surface region to bottom. The top layer and bottom sediments consist of higher concentration of microorganisms.
Microorganisms on the surface (Neuston)
Microorganisms at neuston layer comprises of Bacteria-Pseudomonas spp., Caulobacter spp., Neuskia spp., Achromobacter spp., Flavobacterium spp., Alcaligens spp., Brevibacterium spp., Letothrix spp., Micrococcus spp.etc.
Cyanobacteria-Anabaena spp., Aphanizomenon spp., Microcystis spp., etc
Molds & Yeasts-Claudosporium spp(molds),Torulopsis spp., Candida spp., Cryptococcus spp., Rhodotorula spp.etc
Algae-Chromulina spp., Botrydiopsis spp., Codosiga spp., Nautococcus spp., Navicula spp., Proterogonia spp., Sohaeroeca spp.etc
Protozoa-Difflugia spp., Vorticella spp., Arcella spp., Acineta spp., Clathurulina spp., Stylonychia spp., Amoeba spp., Paramecium spp.etc
Diatoms (Phytoplanktons)-Coscinodiscus spp., Skeletonema spp.etc
Dinoflagellates-Gonyoulax spp., Gymnodium spp.etc
Phytoflagellates-Dictyocha spp., Pyraminonas spp.etc
Rotifers (Wheel animals)-Branchionas spp.etc
Crustaceans-Euphausia spp., Calanus spp., Euchaeta spp.etc.

Bethic Microorganism (Benthos)
There are fewer microorganisms at depth than at surface because of the lack of sunlight and other nutrients availability. And they are:

  • Anaerobic Prokaryotes

Heterotrophic-Vibrio spp., Pseudomonas spp.
Chemolithotrophic-Nitrobacter spp., Nitrosomonas spp., Thiobacillus spp., Methanogens, Clostridium spp.

  • Few protozoa (shallow)- Ciliates ,Amoeba,Flagellates
Marine Environments
The marine environment represents a major portion of the biosphere and contains 97% of the Earth's water. Much of this is in the deep sea at adepth greater than 1,000 meters, representing 75% of the ocean's volume. The ocean has been called a "high-pressure refrigrator", with most of the volume below 100 meters at a constant 3°C temperature and high pressure. It also has high salt concentration. Because of high pressure and high salt concentration, the number of microorganisms is relatively lower than in fresh water. The microorganisms having ability to tolerate high salt concentration and preferring high pressure can only survive in this environment.

Microorganisms in marine environment
Microorganisms on the surface (pleuston) of ocean/sea

Bacteria-Erythrobacter, Erythromicrobium, Protaminobacter, Roseobacter, Vibrio, Cytophyga, Bacillus, Alcaligens, Flavobacterium, Spirillum
Algae- Mostly Phaeophyta (brown algae)-Sargassum,also some chlorophyta, Cryptophyta, Rhodophaeophyta
Protozoa-Acantharia, Radiolaria, Tintinnidium
Yeast-Candida, Torulopsis, Trichosporon, Cryptococcus, Rhodosporidium

Microorganisms in Benthic region (Deep sea microorgnasims)
The bottom of the sea is characterised by low temoerature- high pressure and low level of nutrients. At certain environment, there are hydrothermal vents and coral reefs.
Barophilic Bacteria-Moritella
Hydrothermal vents-Thiomicrosporo, Thermococcus, Beggiatoa, Pyrodictium, Methanopyros, Pyrolobs, Thiobacillus, Thiovulvum
Coral reefs-Calothrix, Crustacea

Microorganisms in Atmosphere/ Air
Atmosphere is composed pf nearly 79% nitrogen, 21% oxygen, 0.04% of CO2 and trace amount of other gases. It consists of water vapours, water droplets, ice crystals and dust particles.
The troposphere interface with hydrosphere and lithosphere and is composed of many air microflora. Atmosphere does not favour growth and multiplication of microorganisms because of the limitations in physical and chemical parameters and exposure to UV rays from the sun. However, there are substantial numbers of microorganisms in lower troposphere that have adapted to survive and disperse through the atmosphere.

Microorganisms are dispersed in air through soil, water, animal and plant surfaces. During dispersal, the microorganisms enter and pass through the atmosphere before reaching other favourable ecosystems for growth and multiplication. Dispersal through environment reflects continued survival of microorganisms in air. The microorganisms may remain as vegetative cells, spores or cysts. Spores are better adapted to atmosphere.
Fungal spores found in air Puccinia, Helminthosporium, Agaricus, Lycoperdon, Cladosporium, Alternaria, Penicillium BacteriaCorynebacterium, Bacillus, Clostridium, Halobacter, Sulfalobus, Halococcus, Streptococcus, Staphylococcus, Mycobacterium, Coxiella, Campylobacter, Yersinia, Salmonella, Pasteurella, Serratia, Escherichia, Brucella, Mycoplasma, Klebsiella, Leptospira, Neisseria Blue green algae-NostocActinomycetes-Nocardia, Streptomyces


Atlas, RM and R Bartha. Microbial Ecology:Fundamentals and Applications. The Benjamin Cummins Publication co. Inc., 1998.
Gordis, L. Epidemiology. third edition. 2004.
Maier, RM, IL Pepper and CP Gerba. Environmental Microbiology. Academic press Elsevier Publication, 2006.
Park, K. Park's Text Book of social and prevention Medicine. 18th edition. 2008.




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