Abiotic Factors

Non-living factors that can affect life, like soil, nutrients, climate, wind etc.

Absorption Field

An organized system of meticulously constructed narrow trenches, which are partially filled with washed gravel or crushed stone, into which a pipe is placed. Discharges from septic tanks are passed through these trenches.

Acetogenic Bacterium

An aerobic, gram negative bacteria, that is rod-shaped, which is made of non-sporogenous organisms that produce acetic acid as a waste product.

Acetylene Block Assay

Determines the release of nitrous oxide gas from acetylene treated soil, which is used to estimate denitrification.

Acetylene Reduction Assay

This is used to estimate nitrogenase activity by measuring the rate of reduction of ethylene to acetylene.

Acid Soil

Soil which has a pH value lesser than 6.6

Acidophile

An organism that grows well in an acidic medium (up to a pH of 1).

Actinomycete

These are Gram positive, nonmotile, nonsporing, noncapsulated filaments that break into bacillary and coccoid elements. They resemble fungi, and most are free living, particularly in soil.

Actinorhizae

The association present between actinomycetes and roots of plants.

Activated Sludge

Sludge particles which are produced in raw or settled wastewater, by the growth of organisms in aeration tanks. This is all done in the presence of dissolved oxygen. This sludge contains living organisms that can feed on incoming wastewater

Activation Energy

The amount of energy required to bring all molecules in one mole of a substance, to their reactive state, at a given temperature

Active Carrier

An infected person who has visible clinical symptoms of a disease, and is capable of transmitting the disease to other individuals.

Active Site

The location on the surface of the enzyme where the substrate binds.

Adjuvant

The material added to an antigen to increase its immunogenicity, for example, alum

Aerobic

This includes organisms that require molecular oxygen to survive (aerobic organisms), an environment that has molecular oxygen, and processes that happen only in the presence of oxygen (aerobic respiration).

Aerobic Anoxygenic Photosynthesis

Photosynthetic process which takes place under aerobic conditions, but which does not result in the formation of oxygen.

Aerotolerant Anaerobes

Microbes that can survive in both, aerobic and anaerobic conditions, because they obtain their energy by fermentation.

Aflatoxin

A toxin produced by Aspergillus flavus and Aspergillus parasiticus, which contaminate groundnut seedlings. This is said to be a cause of hepatic carcinoma.

Agar

A dried hydrophilic, colloidal substance extracted from red algae species, used as a solid culture media for bacteria and other micro-organisms. Also used as a bulk laxative, in making emulsions and as a supporting medium for immunodiffusion and immunoelectrophoresis

Agarose

Agarose is obtained from seaweed and is used as a resolving medium in electrophoresis. It consists of non-sulfated linear polymer, which contains D-galactose and 3:6-anhydro-L-galactose alternately.

Agglutinates

The visible clumps that are formed as a result of an agglutination reaction.

Agglutination Reaction

The process of clumping together, in suspension of antigen bearing cells, micro-organisms, or particles in the presence of specific antibodies called agglutinins. This leads to the formation of an insoluble immune complex.

Airborne Transmission

A type of transmission, wherein the organism is suspended in or spreads its infection by air.

Akinete

A resting non-motile, dormant, thick-walled spore state of cyanobacteria and algae

Alcoholic Fermentation

A fermentation process that produces alcohol (ethanol) and carbon dioxide from sugars.

Alga

Phototrophic eukaryotic micro-organisms, that maybe unicellular or multicellular. These include phaeophyta: brown algae, spirogyra and red algae.

Aliphatic

Pertaining to any member of one of the two major groups of organic compounds, with the main carbon structure as a straight chain

Alkaline Soil

Soil having pH greater than 7.3.

Alkalophile

Organisms that have an affinity for alkaline media, thus, growing best in such conditions

Allochthonous Flora

Organisms that are not originally found in soil, but reach there by precipitation, sewage, diseased tissue and other such means. They do not contribute much ecologically.

Allosteric Site

A non-active site on the enzyme body, where a non-substrate compound binds. This may result in conformational changes at the active site.

Allotype

Any of various allelic variants of a protein, characterized by antigenic differences.

Alpha Hemolysis

A partial clearing zone, greenish in color, around a bacterial colony that grows on blood agar.

Alpha-proteobacteria

One of the five sub-groups of proteobacteria, each with distinctive 16S rRNA sequences. Mostly contains oligotrophic proteobacteria, many of which have distinctive morphological features.

Alternative Complement Pathway

A pathway of complement activation, including the C3-C9 components of the classical pathway. It is independent of antibody activity.

Alveolar Macrophage

A highly active and aggressive phagocytic macrophage, located on the epithelial lining of the lung alveoli, which ingests and destroys any inhaled particles and micro-organisms.

Amensalism (Antagonism)

A type of symbiosis, wherein one population is adversely affected, while the other is unaffected

Ames Test

A test that uses a special strain of salmonella to test chemicals for mutagenicity and carcinogenicity

Amino Acid Activation

The first stage of synthesis of proteins, where the amino acid is attached to transfer RNA.

Amino Group

The monovalent radical NH2, attached to a carbon skeleton, as seen in amines and amino acids.

Aminoacyl or Acceptor Site (A site)

The site on the ribosome that contains an aminoacyl-tRNA at the beginning of the elongation cycle during protein synthesis.

Ammonia Oxidation

A test which is conducted during manufacturing process, to evaluate ammonia oxidation rate for nitrifiers.

Ammonification

Liberation of ammonia by micro-organisms acting on organic nitrogenous compounds

Amoeba

A minute protozoan, occurring as a single cell with a nucleus, that changes shape by extruding its cytoplasm, leading to the formation of pseudopodia, by means of which it absorbs food and moves

Amoeboid Movement

Movement by means of extrusions of the cytoplasm, leading to formation of foot-like processes called pseudopodia.

Amphibolic Pathways

Metabolic pathways that function both anabolically, as well as catabolically.

Amphitrichous

A cell which has a single flagellum at each end

Amphotericin B

An antibiotic derived from streptomyces nodosus which is effective against many species of fungi and certain species of leishmania.

Anaerobic

Refers to organisms that survive in the absence of oxygen (anearobic organisms), the absence of molecular oxygen, processes occurring in the absence of oxygen like anearobic respiration.

Anamorph

A stage of fungal reproduction, where cells are asexually formed by the process of mitosis.

Anaplerotic Reactions

Reactions that help replenish intermediates in the tricarboxylic acid cycle when their reserves are depleted.

Anergy

Decreased responsiveness to antigens, to the extent that there is an inability to react to substances that are expected to be antigenic

Anion Exchange Capacity

Total exchangeable anions that a soil can adsorb. The unit used to express the amount is in centimoles of negative charge per kilogram of soil.

Annotation

The process of determining the exact location of specific genes in a genome map

Anoxic

A condition or state which is devoid of oxygen.

Anoxygenic Photosynthesis

A type of photosynthesis where oxygen is not produced. This phenomenon is seen in green and purple bacteria.

Antagonist

A drug that binds to a hormone, neurotransmitter, or another drug, thus, blocking the action of the other substance.

Antheridium

The male gametangium found in phylum Oomycota (kingdom Stramenopila) and phylum Ascomyta (kingdom Fungi)

Anthrax

An often fatal and infectious disease, caused by ingestion or inhalation of spores of Bacillus anthracis, which are normally found in soil. It is acquired by humans through contaminated wool or animal products or by inhalation of airborne spores

Anthropogenic

Something that is derived from human activities.

Antibiosis

Lysis of an organism brought about by metabolic products of the antagonist. This can be caused by enzymes, lytic agents or other toxic compounds

Antibiotic

A chemical substance produced by a microorganism, which has the capacity to inhibit the growth of, or kill other micro-organisms

Antibody

An immunoglobulin molecule that reacts with a specific antigen that induced its synthesis and with molecules that have a similar structure

Antibody-Dependent Cell-Mediated Cytotoxicity (ADCC)

A type of reaction wherein, cells with Fc receptors that recognize the Fc region of the bound antibody, kill the antibody-coated target cells.

Anticodon Triplet

A triplet of nucleotides in transfer RNA that is complementary to the codon in messenger RNA.

Antigen

Any substance capable of instigating the immune system into action, inciting a specific immune response and of reacting with the products of that response.

Antimetabolite

A substance that interferes with a specific metabolic pathway, by inhibiting a key enzyme, due its resemblance with the normal enzyme substrate.

Antimicrobial Agent

An agent that has the capacity to kill or inhibit the growth of micro-organisms

Antisense RNA

One of the strands of a double-stranded molecule, which does not directly encode the product, but is complementary to it, thus, inhibiting its activity.

Antiseptic

A substance that inhibits the growth and development of micro-organisms, but does not necessarily kill them.

Aplanospore

A spore that is formed during asexual reproduction, which is nonflagellated and nonmotile.

Apoenzyme

A protein part of an enzyme that is separable from the prosthetic group (the coenzyme).

Apoptosis

A pattern of cell death which is often called 'programmed death' or 'suicide of cells', wherein the cell breaks up into fragments, which are membrane bound. These fragments are then eliminated by phagocytosis. This is a protective mechanism, by which the cell prevents spread of infection to other cells by sacrificing itself.

Aporepressor

A product of regulator genes, that combines with the corepressor to form the complete repressor.

Arbuscule

Special structure formed in the root cortical cells by arbuscular mycorrhizal fungi. The structure formed resembles a tree.

Artificially Acquired Passive Immunity

A type of temporary immunity that results from the introduction of antibodies produced by another organism or by in vitro methods, into the body.

Aseptic Technique

Procedures that are performed under strict sterile conditions. These procedures maybe laboratory procedures such as microbiological cultures.

Assimilatory Nitrate Reduction

Reduction of nitrate to compounds like ammonium, for the synthesis of amino acids and proteins.

Associative Dinitrogen Fixation

An enhanced rate of dinitrogen fixation, brought about by a close relationship between free-living diazotrophic organisms and a higher plant.

Associative Symbiosis

Interaction between two dissimilar organisms or biological systems, which is normally mutually beneficial.

Autogenous Infection

An infection which occurs due to the microbiota of the patient himself.

Autoimmune Disease

A disease where the target is the body's own tissues, that is, there is attacking of self-antigens.

Autoimmunity

A condition where a specific humoral or cell mediated immune response is initiated against the constituents of the body's own tissues. It normally leads to hypersesitivity reactions, and if it persists, can even escalate to an autoimmune disease.

Autolysins

A lysin that originates in an organism, which is capable of destroying its own cells and tissues.

Autoradiography

Making a radiograph of an object or tissue by recording the radiation emitted by it on a photographic plate. The radiation is emitted by radioactive material within the object or tissue.

Autotrophic Nitrification

The combined nitrification action of two autotrophic organisms, one converting ammonium to nitrite and the other oxidizing nitrite to nitrate.

Auxotroph

A mutated type of organism that requires specific organic growth factors, in addition to the carbon source present in a minimal medium.

Axenic

Pure cultures of micro-organisms, that is, which are not contaminated by any foreign organisms.

Axial Filament

Found in spirochetes, it is the organ of motility.

B-cell (B lymphocyte)

Bursa-dependent lymphocytes which are precursors of antibody-producing cells (plasma cells) and the cells primarily responsible for humoral immunity.

B-cell Antigen Receptor (BCR)

The membrane which is formed of membrane immunoglobulin or surface immunoglobulin, which allows a B-cell to detect, when a specific antigen is present in the body, and triggers B-cell activation.

Bacteria

A domain that contains prokaryotic cells that are not multicellular. Read more on bacteria.

Bacteremia

Presence of bacteria in the blood.

Bacterial Artificial Chromosome

A cloning vector that is derived from E. coli, which is used to clone foreign DNA fragments in E. coli.

Bacterial Photosynthesis

A mode of metabolism, which is light-dependent and where carbon dioxide is reduced to glucose, which is used for energy production and biosynthesis. It is an anaerobic reaction.

Bactericide

A substance that kills bacteria

Bacteriochlorophyll

A light absorbing pigment found in phototrophic bacteria, like green sulfur and purple sulfur bacteria.

Bacteriocin

Substances that are produced by bacteria which kill other strains of bacteria by inducing a metabolic block.

Bacteriorhodopsin

A protein involved in light mediated ATP synthesis, which contains retinal. It is one of the main characteristics of archaebacteria.

Bacteriostatic

An agent that inhibits the growth or multiplication of bacteria, but does not kill them.

Bacteroid

A genus of bacteroides, these are Gram negative, rod-shaped, anaerobic bacteria which are normal inhabitants of the oral, respiratory, urogenital and intestinal cavities of animals and humans.

Baeocytes

Reproductive cells formed by cyanobacteria through multiple fission. They are small and spherical in shape.

Balanced Growth

Microbial growth where all cellular constituents are synthesized at constant rates, in relation to each other.

Barophile

An organism that thrives in conditions of high hydrostatic pressure.

Barotolerant

An organism that can tolerate high hydrostatic pressure, although it will grow better under normal pressure.

Basal Body

A cylindrical structure that attaches the flagella to the cell body at the base of prokaryotic or eukaryotic organisms.

Basal Medium

A basal medium allows the growth of many types of micro-organisms which do not require special nutrient supplements.

Base Composition

The proportion of total bases consisting of guanine plus cytosine or thymine plus adenine base pairs.

Basidioma

Fruiting body that produces the basidia.

Basidiospore

The sexual spore of the Basidiomycotina, which is formed on the basidium.

Batch Culture

A culture of micro-organisms which is obtained by inoculating a dish containing a single batch of medium.

Batch Process

A treatment procedure wherein, a tank or reactor is filled, the solution is treated, and the tank is emptied. Batch processes are mostly used to cleanse, stabilize, or condition chemical solutions for use in industries.

Benthic Zone

The ecological region at the lowest level of a water body, including the sediment surface and some sub-surface layers.

Beta Hemolysis

A clear zone seen around a bacterial colony growing on blood agar.

Bio-Tower

A tower filled with a media similar to a rachet or plastic rings, where air and water are forced up the tower by a counterflow movement. It is an attached culture system.

Bioaccumulation

Intracellular accumulation of chemical substances in living tissue.

Bioaugmentation

Addition to the micro-organism's environment that can metabolize and grow on specific organic compounds.

Bioavailability

The extent to which a drug or other substance becomes available to the target tissue after administration.

Biochemical Oxygen Demand

The amount of dissolved oxygen consumed in five days by biological processes breaking down organic matter. It is a test that measures the oxygen consumed (in mg/L) over five days at 20 degrees Celsius.

Biodegradable

The property by which a substance is capable of being degraded by biological processes, like bacterial or enzymatic action.

Biodegradation

The process of breakdown of substances by chemical reactions, thus rendering these substances less harmful to the environment.

Bioinsecticide

A pathogen (either bacteria, virus or fungi) used to kill or inhibit the activity of unwanted insect pests.

Bioluminescence

The production of light in living organisms by the enzyme luciferase.

Biomagnification

Increase in the concentration of a chemical substance, as its position progresses in the food chain.

Biostimulation

A process which helps catalyze the activity of micro-organisms involved in biodegradation

Biosynthesis

Production of cellular constituents from simpler compounds.

Biotransformation

The chemical alterations of a drug, occurring in the body, due to enzymatic activity.

Biotrophic

Close associations seen between two different organisms, that work mutually to benefit each other.

Bioventing

A procedure where the subsurface is aerated to enhance biological activity of naturally occurring micro-organisms in the soil.

Blastomycosis

An infection caused due to Blastomyces dermatitidis, it predominantly affects skin, lungs and bones.

Burst size

The number of phages ejected by a host cell over the course of its lytic life cycle.

Butanediol Fermentation

A kind of fermentation found in Enterobacteriaceae family, where 2,3-Butanediol is a major product.

Capsid

The outer proteinaceous coat of a virus.

Capsomere

A protein sub-unit of the capsid of a virus.

Carbon Cycle

The cycle where carbon-dioxide is taken in and converted to organic compunds by photosynthesis or chemosynthesis, after which it is partially incorporated into sediments, and then returned to the atmosphere by respiration or combustion

Carbon Fixation

Conversion of carbon-dioxide and other single carbon compounds to organic compunds such as carbohydrates.

Carbon-Nitrogen (C/N) ratio

Ratio of carbon mass to nitrogen mass in soil or other organic material.

Carboxyl Group

The -COOH group found attached to the main carbon skeleton in certain compounds, like carboxylic acids and fatty acids.

Carboxysomes

Polyhedral cell inclusions which form the key enzyme of the Calvin cycle.

Carcinogen

An often mutated substance which is implicated as one of the causing agents of cancer.

Catabolism

A process by which complex substances are broken down into simpler compounds, often accompanied by the release of energy.

Catabolite Repression

Transcription-level inhibition of inducible enzymes by glucose, or other easily available carbon sources.

Cell-mediated Immunity

Immunity resulting from destruction of foreign organisms and infected cells by the active action of T-lymphocytes on them. It can be acquired by individuals by the transfer of cells.

Cellular Slime Molds

Slime molds with a vegetative phase containing amoeboid cells that come together to form a pseudoplasmodium.

Cellulitis

A diffused inflammation of the soft or connective tissue, in which a thin and watery exudate spreads through tissue spaces, often leading to ulceration and abscess formation.

Cephalosporin

A group of broad-spectrum, penicillinase resistant antibiotics, derived from Cephalosporium. Read more on different types of antibiotics.

Chaperonin

Heat shock proteins that oversee correct folding and assembly of polypeptides in bacteria, plasmids, eukaryotic, cytosol, and mitochondria.

Chelate

A chemical compound in which a metallic ion is firmly bound into a ring within the chelating molecule. Chelates are used in metal poisoning.

Chemoautotroph

Organisms that obtain their enegry from the oxidation of inorganic chemicals and other carbon compounds.

Chemoheterotroph

Organisms that obtain energy and carbon from the oxidation of organic compunds.

Chemolithotroph

Living organisms that obtain their energy from oxidation of inorganic compunds, which act as electron donors.

Chemoorganotroph

Organisms that obtain energy and electrons from the oxidation of organic compounds.

Chemostat

A continuously used culture device, controlled by limited amounts of nutrients and dilution rates.

Chemotaxis

Movement of a motile organism under the influence of a chemical. It maybe attracted towards the chemical or maybe repulsed by it.

Chemotrophs

Organisms that obtain their energy by the oxidation of chemical compounds.

Chlamydospore

A thick walled intercalary or terminal asexual spore which is not shed. It is formed by rounding up of a cell.

Chronic Carrier

An individual carrying a pathogen over an extended period of time.

Chytrid

A fungus belonging to the genus Chytridomycota. It is spherical in shape and has rhizoids, which are short, thin filamentous branches, that resemble fine roots.

Cilia

Minute hairlike extensions present on a cell surface, which move in a rhythmic manner.

Ciliate

A protozoan that moves with the help of cilia.

Clarification

The process of purification of water, where suspended material in the water is removed. It can be done by using sedimentation, filtration or by the use of adsorbing chemicals like alum.

Clone

Cells which have descended from a single parent cell. Organisms having identical copies of DNA structure, which is obtained by replication.

Colonization

Establishment of an entire community of micro-organisms at a designated site.

Colorless Sulfur Bacteria

A group of nonphotosynthetic bacteria that oxidize sulfur compounds, thus deriving their energy by this process.

Combinatorial Biology

The process of transfer of genetic material from one microorganism to another. Mostly used to synthesize products such as antibiotics. It is also used in genetic engineering.

Cometabolism

Transformation of a substrate by a microorganism without deriving energy or nutrients from the substrate.

Competent

The ability to take up DNA.

Complementary DNA

A DNA copy of any RNA molecule, like mRNA or tRNA

Complex Viruses

Viruses with capsids that are neither icosahedral nor helical. They have a complicated symmetry.

Conditional Mutations

Mutations occurring only under certain specific conditions.

Conidiospore

A thin-walled, asexual spore seen on hyphae which is not contained in sporangium.

Conjugants

Mating partners that participate in conjugation, which is a type of sexual reproduction, seen in protozoans.

Conjugative Plasmid

A self transmissible plasmid, or a plasmid that can encode all functions required to bring about its conjugation.

Consortium

Two or more members working together, where each organism benefits from the other, thus often performing functions that may not be possible to carry out individually.

Constitutive Enzyme

Enzymes synthesized in the cell, irrespective of the environmental conditions surrounding the cell.

Cosmid

A plasmid vector which can be packed in a phage capsid. It is useful for cloning large fragments of DNA.

Cyanobacterium

A photosynthetic, nitrogen fixing bacteria which includes the blue-green bacteria.

Cyst

Resting stage of certain bacteria and protozoans, wherein the entire cell is surrounded by a protective layer.

Cytokine

Non-antibody proteins released by a cell when it comes in contact with specific antigens.

Cytoplasm

The protoplasm of a cell, exclusive of the nucleus. Read more on the structure and functions of cytoplasm.

Cytoplasmic Membrane

A selectively permeable membrane which is present around the cytoplasm of the cell.

Decomposition

Chemical breakdown of a compound into smaller and simpler compounds by micro-organisms.

Defined Medium

A medium whose quantitative and chemical composition is exactly known.

Degradation

Process by which a compound is transformed into simpler compounds.

Denaturation

Process by which double stranded DNA unwinds into two single strands.

Denitrification

Reduction of nitrate or nitrite into simpler nitrogenous compounds like molecular nitrogen or nitrogen oxides.

Derepressible Enzyme

Enzyme produced in the absence of a specific inhibitory compound.

Dew point

The temperature to which air must be cooled to bring about the condensation of water vapor.

Diazotroph

Organism capable of using dinitrogen as its sole nitrogen source.

Differential Medium

A medium with certain indicators, which helps distinguish between different chemical reactions during growth of organisms on it.

Diffused Air Aeration

A diffused air activated sludge plant takes air, compresses it and discharges it with force, below the surface of water.

Dikaryon

When two nuclei are present in the same hyphal compartment (they maybe homokaryon or heterokaryon), it is known as dikaryon.

Dilution Plate Count Method

A method of estimating the number of viable micro-organisms in a sample.

Dinitrogen Fixation

Conversion of molecular dinitrogen into ammonia and other organic combinations useful in other biological processes.

Direct Count

Using direct microscopic examination to determine the number of micro-organisms present in a given mass of soil.

Disinfectant

An agent that kills micro-organisms.

DNA Fingerprinting

Techniques by which possible differences between different DNA samples can be assessed.

Dolipore Septum

Specialized cross-wall that separates hypha of fungi belonging to the genus Basidiomycota.

Domain

The highest level of biological classification which goes beyond kingdoms. The three domains of biological organisms are Bacteria, Eukarya, and Archaea.

Doubling Time

The time needed for a certain population to double in number.

Endoenzyme

Enzyme that acts along the internal portion of a polymer.

Endonuclease

The endoenzyme responsible for breaking the phosphodiester bonds in a nucleic acid molecule.

Endophyte

An organism, which maybe parasitic or symbiotic, with a plant that is grown within.

Endospore

A cell which is formed by certain gram-positive bacteria in unfavorable conditions. An endospore is extremely resistant to heat and other harmful agents.

Enhanced Rhizosphere Degradation

Enhanced activity of micro-organisms involved with biodegradation of contaminants near plant roots which is brought about by compounds exuded by the plant roots.

Enrichment Culture

Technique wherein environmental conditions are altered to aid the growth of a specific organism or group of organisms.

Enteric Bacteria

These are bacteria present in the intestinal tract of humans and other animals. They maybe physiologic or pathologic.

Episome

An extrachromosomal replicating genetic element found in certain bacteria.

Epitope

An antigenic determinant of known structure. It is the region of the antigen to which the variable region of the antibody binds.

Ericoid Mycorrhizae

The type of mycorrhizae found in Ericales plants. These hyphae are capable of penetrating cortical cells.

Estuaries

Water bodies located at river ends. They are subjected to tidal fluctuations.

Eubacteria

A genus of bacteria belonging to the family Propionibacteriaceae, found as saprophytes in soil and water.

Exoenzyme

An enzyme which acts outside the cell that secretes it.

Exons

The region of a split DNA that codes for RNA.

Extracellular

Outside the cell.

Exudate

A fluid high in protein and cellular debris which has escaped from blood vessels, usually as a result of inflammation.

Facultative Organism

An organism which is able to adjust to a particular circumstance or has the ability to take up different roles in a process.

Feedback Initiation

Inhibition by an end product of the biosynthetic pathway involved in its synthesis.

Fertilizer

Any organic or inorganic material added to the soil to enhance the growth of plants.

Field Capacity

Content of water remaining in the soil after being saturated with water.

Filamentous

In the form of very long rods, mostly seen in bacteria. Seen as branching strands in fungi.

Fimbria

Short filamentous structure present on a bacterial cell, involved with adhesion of the bacteria to other surfaces it comes in contact with.

Frustule

Siliceous wall and protoplasm seen in diatoms.

Fulvic Acid

The yellow organic material that remains behind after removal of humic acid by the process of acidification.

Fungistasis

Suppression of growth of new fungal cells, due to excessive competition for nutrients, or due to the presence of excessive inhibitory compounds in the soil.

Fungus

Eukaryotic heterotrophic organisms that live as saprophytes or parasites. This group includes mushrooms, yeast and molds. They have a rigid cell wall.

Fluorescent Antibody

This is a laboratory test that is done, wherein antibodies are tagged with fluorescent dye to detect the presence of micro-organisms.

Gas Vacuole

A sub:cellular organelle, found only in prokaryotes, which are gas filled vesicles.

Gene Cloning

Isolation of a desired gene from an organism and its replication in large amounts. It is used extensively in DNA research.

Gene Probe

A strand of nucleic acid which can be labeled and hybridized to a complementary molecule from a mixture of other nucleic acids. It is helpful in DNA sequencing.

Generation Time

The time required for a population to double in number.

Genetic Code

The information on the DNA, which is required for the synthesis of proteins.

Glycosidase

The enzyme responsible for hydrolizing a glucosidic linkage between two sugar molecules.

Gram Stain

A differential stain that divides bacteria into two groups, as Gram positive and Gram negative, depending on the ability of the organism to retain crystal violet when decolorized with an organic solvent like ethanol.

Growth

An increase in the number of cells, and the size and constituents present in the cells.

Growth Factor

Organic compound essential for growth which is required in trace amounts, and which cannot be synthesized by the organism itself.

Growth Rate

The rate at which growth occurs.

Growth Rate Constant

Slope of log10 of the number of cells per unit volume plotted against time.

Growth Yield Coefficient

Quantity of carbon formed per unit of substrate carbon consumed.

Halophile

An organism that thrives, or at least which can survive in a saline environment.

Halotolerant

An organism that can survive in a saline environment, but does not require a saline environment for growth.

Hapten

A substance not inducing antibody formation, but which is able to combine with a specific antibody.

Heterokaryon

Hypha that contains at least two genetically dissimilar nuclei.

Heterolactic Fermentation

A kind of lactic acid fermentation, wherein various sugars are fermented into different products.

Heterothallic

Hyphae that are incompatible with each other, thus requiring another compatible hypha to mate with, to form a dikaryon or a diploid.

Heterotrophic Nitrification

The oxidation of ammonium to nitrite and nitrate by heterotrophic organisms.

Hexose Monophosphate Pathway

A metabolic pathway involving the oxidative decarboxylation of glucose:6:phosphate.

Holomictic

These are those lakes, wherein the water in them at some point of time will have a uniform temperature and density from top to bottom, thus allowing the lake waters to mix completely.

Holomorph

A fungus which consists of all sexual and asexual stages in its life cycle.

Homofermentation

A type of fermentation where there is only one type of end product generated.

Homokaryon

A fungal hypha containing nuclei which are genetically identical.

Homolactic Fermentation

A type of lactic acid fermentation, in which all sugars involved are converted into lactic acid.

Homothallic

Hyphae that are self:compatible, that is, sexual reproduction occurs in the same organism by meiosis and genetic recombination. Fusion of these hyphae lead to the formation of dikaryon or diploid.

Host

An organism that can harbor or nourish another organism.

Heterofermentation

Any fermentation where there is more than one main end product.

Humic Acid

Dark colored organic material extracted from the soil by the use of reagents and which is precipitated by acid.

Humic Substances

High molecular weight substances formed by secondary synthesis reactions, for example, humic acid and fulvic acid.

Humification

The process of conversion of organic residues into humic substances by biochemical processes.

Hybridization

Natural or artificial construction of a duplex nucleic acid molecule by complementary base pairing between two nucleic acid strands derived from different sources.

Hydrocarbon

An organic compound containing carbon and hydrogen only.

Hydrogen Oxidizing Bacterium

These are bacteria that oxidize hydrogen for energy and synthesize carbohydrates, using carbon dioxide as their source of carbon in the absence of other organic compounds.

Hyperparasite

Parasite that feeds on another parasite.

Hyperthermophile

An organism that thrives in temperatures ranging around 80 degrees Celsius or more.

Hypolimnion

This is the dense, bottom layer of water, that lies below the thermocline, in a thermally stratified lake.

Illuviation

Repositioning of soil removed from one horizon to another.

Immobilization

Conversion of an element from inorganic to organic form.

Immunity

The protection mechanism against infections caused by micro-organisms or toxins, that is inherent in the body.

Immunoblot

The technique for analyzing or identifying proteins via antigen:antibody specific reactions.

Immunofluoresence

The technique to determine the location of an antigen or antibody in a tissue section or smear by fluorescence.

Immunogen

A substance that has the capacity to bring about an immune response.

Immunoglobulin

A protein which has antibody activity.

In vivo

Inside the body.

Inducible Enzyme

An enzyme generated in response to an external factor.

Infection

Invasion and multiplication of micro-organisms in body tissues, leading to various diseases and disorders.

Infection Thread

The tube in root hair, through which rhizobia reach and infect roots.

Infrared (IR)

The portion of the electromagnetic spectrum whose wavelength ranges from 0.75 microns to 1 millimeter.

Inoculate

To treat a medium with micro-organisms for the purpose of creating a favorable response.

Inoculum

The material used to introduce an organism into a certain medium for growth.

Insertion

A type of genetic mutation, wherein single or multiple nucleotides are added to DNA.

Insertion Sequence

The simplest possible type of transposable elements.

Integration

The process by which a DNA molecule becomes incorporated into another genome.

Interspecies Hydrogen Transfer

The process of hydrogen production and consumption reactions, occurring by the interaction of various micro-organisms.

Intracellular

Inside the cell.

Isoenzyme

When two different enzymes, which maybe different in their composition, act as catalysts for the same reaction, or set of reactions.

Isolation

A procedure wherein a pure culture of an organism is obtained from a sample or an environment.

Isomorphous Substitution

The substitution of an atom by a similarly sized atom of lower valence, in a crystalline clay sheet.

Jaccard's Coefficient

An association coefficient of numerical taxonomy, which is the proportion of characters that match, excluding those that both organisms lack.

K- Strategy

Ecological strategy where organisms depend on adapting physiologically to the resources available in their immediate environment.

Koch's Postulates

Laws given by Robert Koch which prove that an organism is the causative agent of a disease.

Lag Phase

The time period when there is no increase in the number of micro-organisms, seen after inoculation of fresh growth medium.

Lamella

Seen in plants as the layers of protoplasmic membranes in chloroplast that contain photosynthetic pigments.

Leaching

Removal of metals from ores by the help of micro-organisms.

Lectins

Plant proteins with a high affinity for specific sugar residues.

Leghemoglobin

Red colored pigments rich in iron, which are produced in root nodules during symbiotic association between rhizobia and leguminous plants.

Ligand

A molecule, ion or group of molecules or ions, bound to the central atom by means of a chelate or coordination compound.

Light Compensation Point

The point where the rate of respiration is higher than the rate of photosynthesis, which usually occurs at about 1% of sunlight intensity.

Lime (agricultural)

Soil amendment containing high levels of calcium compounds, like calcium carbonate and other such mineral which are used to neutralize soil acidity, and provide calcium for plant growth.

Lipopolysaccharide (LPS)

Complex lipid structure containing sugars and fatty acids, which is commonly found in most Gram negative bacteria.

Lithotroph

An organism that uses inorganic substrate such as ammonia or hydrogen to act as electron donors in energy metabolism. They maybe chemolithotrophs or photolithotrophs.

Litter

The surface layer of forests which is laden with leaves, twigs, fruits etc.

Lophotrichous

An organism that has a tuft of flagella that is polar in nature.

Luxury Uptake

Uptake of nutrients in excess of what is required by an organism for its normal growth.

Lysis

The rupture and destruction of a cell, resulting in loss of cellular contents.

Lysogeny

An association where a prokaryote contains a prophage and the virus genome is replicated in sync with the chromosome of the host.

Lysosome

A cell organelle which contains lytic enzymes.

Macronutrient

A substance required in large amounts for normal growth of an individual.

Macropore

Larger soil pores from which water drains readily by gravity.

Magnetosome

Small particles of magnetite, which is a compound containing magnesium, present in cells that exhibit magnetotaxis.

Magnetotactic Bacteria

Bacteria that orient themselves according to the earth's magnetic field due to the presence of the magnetosomes.

Manure

Animal excreta, with or without a bedding of litter at various stages of decomposition. It's normally considered to be a good fertilizer.

Mass Flow (nutrient)

The movement of solutes in relation to the movement of water.

Medium

A source where micro-organisms are grown.

Mesofauna

Animals residing in the soil which are 200 to 1000 microns in length. This group includes nematodes, oligochaete worms, smaller insect larvae and certain anthropods.

Mesophile

An organism that thrives in temperatures ranging from 15 - 40 degrees Celsius.

Methanogenesis

The production of methane by biological reactions.

Methanogenic Bacterium

Bacteria that produce methane as a by:product of their chemical reactions.

Methanotroph

An organism capable of oxidizing methane.

Microaerophile

Micro-organisms that grow well in relatively low oxygen concentration environments.

Microaggregate

Clusters of clay stabilized by organic matter and precipitated inorganic matter.

Microbial Biomass

Total mass of micro-organisms living in a given mass or volume of soil.

Microbial Population

Total number of micro-organisms living in a given mass or volume of soil.

Microbiology

The study of micro-organisms, often with the aid of a microscope.

Microcosm

A community or any other unit that is representative of a larger community.

Microenvironment

The immediate physical and chemical surroundings of a microorganism.

Microfauna

Protozoa, nematodes and anthropods that are smaller than 200 microns.

Microflora

This includes bacteria, virus, fungi and algae.

Micrometer

One millionth of a meter (10-6 meters).

Micronutrient

Elements that are required for growth in trace amounts. These include copper, iron, zinc etc.

Micro-organism

An organism that is too small to be seen by the naked eye. Also called microbes, these include bacteria, fungi, protozoans, algae and viruses.

Micropore

A small sized soil pore (approximately less than 30 microns in diameter) which is normally found within structural aggregates.

Microsite

A small part of the soil where the biological or chemical processes are different from the rest of the soil.

Mixotroph

Organisms that are capable of assimilating organic compounds as carbon sources, while using inorganic compounds as electron donors.

Mold

A group of saprobic or parasitic fungi causing a cottony growth on organic substances.

Monoclonal Antibody

Antibody produced from a single clone of cells, which has a uniform structure and specificity.

Monokaryon

Fungal hyphae where the compartments contain only nucleus.

Morphometric Characters

These are characteristics regarding the depth, dimension, sediment distribution, water currents etc.

Motility

The ability of a cell to move from one place to another.

Mucigel

Gelatinous material found on the surface of roots growing in normal soil.

Mucilage

Gelatinous secretions and exudates produced by plant roots and most micro-organisms.

Mulch

Materials which are laid down on soil to protect it from rain, crusting, freezing etc. these materials could be sawdust, plastic, leaves etc.

Municipal Solid Waste

The total consumer and commercial waste generated in a certain confined and restricted geographic area.

Mycophagous

Organisms that eat fungi.

Mycovirus

Viruses that infect fungi.

Nanopore

Soil pore having dimensions in nanometers.

NAPL

A non-aqueous phase liquid which maybe lighter or denser than water.

Necrotrophic

A mechanism by which an organism produces lytic enzymes that kill and then breakdown host cells for its nutrition.

Nematode

Eukaryotes that are unsegmented, usually microscopic roundworm.

Neutralism

Lack of interaction between two organisms in the same habitat.

Niche

Functional role of an organism in a certain habitat.

Nictotinamide Adenine Dinucleotide (NAD+)

An important oxidized coenzyme that is a hydrogen and electron carrier in redox reactions.

Nicotinamide Adenine Dinucleotide Phosphate (NADP+)

An important oxidized coenzyme that acts as a hydrogen and electron carrier in various redox reactions.

Nitrate Reduction (biological)

The process of reduction of nitrate to simpler forms like ammonium by plant and micro-organisms.

Nitrification

Biological oxidation of ammonium to nitrite and nitrate.

Nitrifying Bacteria

Chemolithotrophs that can carry out the transformation from ammonia to nitrite or nitrate.

Nitrogen Cycle

The cycle where nitrogen is used by a living organism, then after the organism dies is restored to soil, followed by its final conversion to its original state of oxidation.

Nitrogenase

The enzyme required for biological nitrogen fixation.

Nodulin

Proteins produced in root hairs or nodules in response to rhizobial infection.

Nonpolar

A substance that is hydrophobic and does not easily dissolve in water.

Northern Blot

Hybridization of single stranded DNA or RNA to RNA fragments.

Nucleic Acid

A high molecular weight nucleotide polymer.

Nucleoid

The nuclear region of certain organisms like bacteria, which contains chromosomes, but which is not limited by a nuclear membrane.

Nucleophilic Compound

An electron donor in chemical reactions involving covalent catalysis in which the donated electrons bond with other chemical groups.

Oligonucleotide

A short nucleic acid chain, which is obtained from an organism or is synthesized chemically.

Oligotroph

A microorganism that has adapted itself to grow in environments that are low in nutrients.

Oospore

Thick walled spore formed in an oogonium by fungus like organisms like the phylum Oomycota.

Operon

Genes whose expression is controlled by a single operator.

Parasitism

Feeding by one organism on the cells of a second, normally larger organism, thus, harming the host.

Parasexual Cycle

A nuclear cycle wherein genes of haploid nuclei recombine without meiosis.

Particle Density

Density of particles present in soil.

Particle Size

Effective diameter of a particle measured by sedimentation or micrometric mathods.

Pasteurization

Process of using heat to kill or reduce the activity of micro-organisms in heat:sensitive materials.

Pathogen

An organism that is capable of causing an infection, or harming a host cell.

Pathogen Suppressive soil

Soil where a pathogen does not persist, either in its own survival or in its pathogenicity.

Pathogenicity

The ability of a parasite to infect or inflict damage on a host.

Peat

Unconsolidated soil material consisting mostly of undecomposed organic matter with excessive moisture content.

Pellicle

A rigid protein layer just below the cell membrane.

Peptidoglycan

Rigid cell wall layer seen in bacteria. It's also called murein.

Peribacteroid Membrane

A plant derived membrane which surrounds rhizobia in host cells of legume nodules.

Periplasmic space

The area between the cell membrane and cell wall in Gram negative bacteria.

Perithecium

Flask shaped ascocarp open at the tip.

Peritrichous Flagellation

Multiple flagella present all over the cell surface.

Permanent Wilting Point

The highest concentration of soil at which plants present in it, will irreversibly wilt when placed in a humid chamber.

Phosphobacterium

Bacteria that are good at dissolving insoluble inorganic phosphate that is present in soil.

Photoautotroph

Self:sufficient organisms that can generate energy from light and carbon dioxide.

Photoheterotroph

Organisms able to use light as source of energy and organic materials as carbon source.

Photophosphorylation

Synthesis of high energy phosphate bonds by the use of light as source of energy.

Phototaxis

Movement of an organism, or a part of it, towards light.

Phytoextraction

The use of plants or algae for removing contaminants from soil, sediments or water, and turning them into harvestable plant biomass.

Phycobilin

Water soluble pigment that is seen in cyanobacteria and is the light harvesting pigment for Photosystem II.

Pilus

Fimbria like substance present on fertile cells that deals with transfer of DNA during the process of conjugation.

Plaque

A localized area of lysis or cell inhibition which is caused due to virus infection.

Plasmogamy

Fusion of two cell contents, inclusive of the cytoplasm and nuclei.

Plate Count

Number of colonies formed on a solid culture medium, when uniformly inoculated with a known amount of soil.

Polar Flagellation

The presence of flagella at one or both ends.

Protoplast

A cell devoid of cell wall.

Pour Plate

The method of performing a plate count of micro-organisms.

Psychrotroph

An organism that is able to grow at zero degrees and above twenty degrees Celsius.

Pure Culture

A microorganism population of a single strain.

Radioimmunoassay

An immunological assay that makes use of radioactive antibodies or antigens to detect certain substances.

Reaction Center

A photosynthetic complex containing chlorophyll and other compounds.

Reannealing

The process seen on cooling, where two complementary strands of DNA hybridize back into a single strand.

Recalcitrant

Resistance of an organism to a microbial attack.

Recombination

Process by which genetic elements in two separate genomes are brought together in one unit. This is an important step in gene therapy.

Replication

Conversion of one double stranded DNA molecule into two identical double stranded DNA molecules.

Repression

Process by which an enzyme synthesis is suppressed due to the presence of certain external substance.

Reverse Transcription

Process of copying information from RNA to DNA.

Rhizobacteria

Bacteria that are found in roots, where they aggressively colonize.

Rhizobia

Bacteria capable of living symbiotically in leguminous plant roots, from where they receive energy and commonly fix molecular dinitrogen.

Rhizomorph

Mass of fungal hyphae that are organized in long, thick strands with a darkly pigmented outer rind that contains specialized tissues for absorption and water transport.

Rhizoplane

Plant root surface and strongly adhering soil particles.

Rhizosphere

The zone of soil immediately adjacent to plant roots in which the activity and type of micro-organisms present differ from that in the rest of the soil.

Rhizosphere Competence

Ability of an organism to colonize the rhizosphere.

Sanitization

Elimination of pathogenic or harmful organisms, including insect larvae, intestinal parasites and weed seeds.

Sclerotium

Modified fungal hyphae that form a compact and hard vegetative resting structure with a thick pigmented outer rind.

Secondary Metabolite

Product of intermediary metabolism released from a cell, for example, antibiotic.

Selective Medium

A medium that is biased in allowing only certain types of micro-organisms to grow.

Serial Dilution

Series of stepwise dilutions, normally done in sterile water, which is done to reduce microorganism populations to manageable numbers.

Serology

Study of reactions that take place between antigens and antibodies in vitro.

Sheath

Tubular structure that is found either around a chain of cells or around a bundle of filaments.

Siderochromes

The compounds that are synthesized by the micro-organisms themselves, which are responsible for iron uptake.

Siderophore

A metabolite that is formed by some micro-organisms, that forms a strong coordination compound with iron.

Slime Layer

A diffuse layer found immediately outside the cell wall in certain bacteria.

Slime Mold

Micro-organisms that are eukaryotic and which lack cell walls.

Solarization

A technique to control the growth of pathogens, wherein a plastic sheet is used to cover moistened soil in hot climates, thereby trapping the incoming radiation.

Specific Activity

Expressed as micromoles formed per unit time per milligram of protein, this is the amount of enzyme activity units per mass of protein.

Spermosphere

The area seen around a germinating seed, where there is increased microbiological activity.

Spread Plate

A technique for performing a plate count of micro-organisms.

Sterilization

The process whereby an object or surface is rendered free of any living micro-organisms.

Storage Polysaccharide

The energy reserves which are stored in a cell when there is excess of carbon available.

Strain

Population of cells, all of which arise from a single pure isolate.

Substrate

A base on which an organism is grown. They can also be the substances on which compounds and enzymes act.

Sulfur Cycle

The cycle wherein sulfur, the element is taken up by living organisms, then released upon the death of the organism, and then converted to its final state of oxidation.

Symbiosis

Two dissimilar organisms, living together. Their association maybe commensal or mutualistic.

Synergism

Association between two organisms that is mutually beneficial.

Syntrophy

Interaction between two or more populations that supply each other's nutritional needs.

Systemic

Something that involves the entire body and is not localized in the body.

Teichoic Acids

All wall, membrane or capsular polymers containing glycerophosphate or ribitol phosphate residues.

Telemorph

One of the stages of sexual reproduction, wherein cells are formed by meiosis and genetic recombination.

Temperate Virus

A virus that does not cause destruction and lysis of the cells of its host, but instead, its genome may replicate in sync with that of the host.

Terminal Electron Acceptor

The last acceptor of the electron, as it exits the electron transport chain.

Thermocline

That point in a lake, where there is a drastic drop in temperature with increase in depth.

Thermophile

An organism that grows best at temperatures around 45 and 80 degrees Celsius.

Ti plasmid

A conjugative tumor inducing plasmid that can transfer genes into plants. Seen in the bacterium Agrobacterium tunefaciens.

Toxin

A foreign substance present in the body, which is mostly generated by micro-organisms, that is capable of inflicting damage on the host cell.

Transduction

The process where host genetic information is transferred through an agent like a virus or a bacteriophage.

Transgenic

Genetically modified plants or organisms, which contain foreign genes, which have been inserted by means of recombinant DNA techniques.

Transposable Element

A genetic element that can be transposed from one site on a chromosome to another.

Transposon

Transposable element which, in addition to transposable genes, carries other genes.

Transposon Mutagenesis

A mutant phenotype is formed by inactivation of the host gene, which occurs due to the insertion of a transposon.

Tricarboxylic Acid Cycle

A series of metabolic reactions, by which pyruvate is oxidized to carbon dioxide.

Trophic Level

Describes the residence of nutrients in various organisms along a food chain ranging from the primary nutrient assimilating autotrophs to carnivorous animals.

Uronic Acid

A class of acidic compounds that contain both carboxylic and aldehydic groups and are oxidation products of sugars. They occur mainly in polysaccharides.

Vadose Zone

Unsaturated zone of soil which is above the groundwater, extending from the bottom of the capillary fringe to the soil surface.

Vector

An agent that can carry pathogens from one host to another. It can also denote a plasmid or virus used in genetic engineering to insert genes into a cell.

Vegetative Cell

A growing or actively feeding form of a cell, as against a spore.

Vesicles

Spherical structures formed intra:cellularly, by certain arbuscular mycorrhizal fungi.

Viable but Nonculturable

Living organisms that cannot be cultured on artificial media.

Viable Count

Measurement of the concentration of live cells in a microbial population.

Vibrio

Curved, rod-shaped bacteria that cause cholera, belonging to the genus Vibrio.

Virion

The virus particle and the virus nucleic acid surrounded by a protein coat.

Virulence

The degree of pathogenicity of a parasite.

Water Content

The amount of water contained in a material, which is expressed as the mass of water per unit mass of oven:dry material.

Water Retention Curve

A graph showing soil water content as a function of increasingly negative soil water potential.

White Rot Fungus

Fungus that attacks lignin, along with cellulose and hemicellulose, leading to marked lightening of the infected wood.

Wild Type

Strain of a microorganism that is isolated from nature. The native and original form of a gene or organism.

Winogradsky Column

A glass column that allows growth of micro-organisms under conditions similar to those found in nutrient rich water and sediment. This column contains an anerobic lower zone and an aerobic upper zone.

Woronin Body

A spherical structure found in fungi belonging to the phylum Ascomycota, which are associated with the simple pore in the septa separating the hyphal compartments.

Xenobiotic

A compound that is foreign to the biological systems.

Xerophile

An organism that is capable of growing at low water potentials, that is, in very dry habitats.

Zymogenous Flora

Refers to micro-organisms that respond rapidly by enzyme production and growth when simple organic substrates become available.