GLOSSARY

ACC deaminase - An enzyme found in some plant growth promoting bacteria and fungi that can cleave the compound ACC (1-aminocyclopropane-1-carboxylate) into ammonia and a-ketobutyrate, ACC is the intermediate precursor  for ethylene biosynthesis in plants.

Acetotroph  - Microorganism that consumes acetate. For instance acetotrophic methanogens  (e.g. Methanosaeta and Methanosarcinae

Acidophile - Microorganism that grow optimally under acidic conditions (low pH).e.g. Sulfolobus

Actinorhiza - Actinorhiza refers to the symbiotic association between certain plants and a group of nitrogen-fixing bacteria known as Frankia. Actinorhiza is commonly observed in plants belonging to the family Rosaceae, such as alders, roses, and certain species of shrubs and trees. 

Acyl homoserine lactone (AHL) - A chemical compound used by some Gram negative bacteria as a signal of cell density in quorum sensing.

Aerobic - Living or active in the presence of oxygen (i.e. in 21% of O2).

Aerotrophism  - The growth or movement of organism towards the air.

Akinetes - They are specialized, non motile, dormant, thick walled, resting cells, protects cyanobacteria against dessication and cold 

Alicyclic compound  -  Compound having a carboxylic ring structure which may be saturated or unsaturated, but not a benzenoid or aromatic compound.

Alkalophile - Microorganism that grows optimally at high pH (alkaline conditions) e.g. Natronobacterium

Amensalism - The process in which one microbial group limits the survival of another one, for example by the production of toxins.

Ammonification - The conversion of organic nitrogen to ammonium ion (NH4+)

Amoebae - Protozoan subgroup of polyphyletic origin, divided into naked and testate amoebae that feed and move on solid surfaces by the protrusion of parts of the cell forming pseudopodia.

Anaerobic - Living or active in the absence of oxygen.

Anammox - Anaerobic ammonium oxidizing bacteria, in which ammonium and nitrite are converted directly to nitrogen gas. e.g. Candidatus Brocadia anommoxidans

Anamorph  -The asexual state of mitosporic fungus

Anatagonist - A microorganism that reduces the growth or activity of another microorganism.

Antagonism - An interactive strategy that involves the inhibitory action of one species on another.

Antibiosis - An antagonistic association of organism in which one produces compounds, for instance antibiotics, harmful to others.

Antibiotic - Compound produced by a microorganism that negatively affects the other organisms, being either-cidal (killing) or -static (growth inhibiting)

Arbuscular mycorrhiza - The most ancient and widespread form of symbiotic mycorrhizal association between a wide range of plant hosts and fungi from the order glomeromycota- characterized by the formation of branching structures or arbuscules. Formerly referred as VAM (Vesicular Arbuscular Mycorrhiza).

Arbuscules - Repeatedly branched hyphal structures formed by glomeromycotan fungi within individual plant root cells. They are thought to be the main sites of nutrient exchange between arbuscular mycorrhizal fungi and other plant hosts.

Arbutoid mycorrhiza - Symbiotic mycorrhizal associations between fungi that are normally ectomycorrhizal and plants in the genera Arbutus, Arctostaphylos and the family Pyrolaceae, where extensive intracellular fungal proliferation occurs.

Ascomycota - The largest fungal phylum, containing fungi which have septate mycelium and produce their sexual spores inside sac like structures called asci.

Autochthonous - Common, indigenous, inhabitant of an environment (e.g. soil) that tend to remain at constant levels, despite fluctuations in local conditions including organic matter levels. Thus they have remained in that place for a significant period of time in the evolutionary scale. e.g. Acidobacteria (soil) and Helicobacter (stomach).

Auxin - Any of the group of plant hormones promoting cell growth.  The primary auxin present in most plants is indole-3-acetic acid.

Auxotroph - A species or strain requiring one or more complex organic nutrients such as amino acids nucleotide bases and enzymatic co-factors for growth

Bacteriocin - Proteinaceous compound produced by bacteria, which is toxic to closely related bacteria or strains of bacteria.

Bacteriophage - Virus that infects bacteria.

Baeocytes - They are differentiated, small spherical motile or nonmotile endospore like reproductive cells produced after multiple fission in certain cyanobacteria. e.g. Pleurocapsa. 

Basidiomycota - A large fungal phylum containing fungi that have septate hyphae and bear their sexual spores on the outside of spore producing bodies called basidia.

Bioaugmentation - Addition of microorganisms to a contaminated site to enhance bioremediation or biodegradation e.g. Pseudomonas putida to degrade oil slicks.

Biocontrol/biological control agent -  an organism used to eliminate or control population of pests, weeds or pathogen or to decrease the damage caused by them.

Biodegradation - The use of organism or enzymes to degrade pollutant compounds, such as recalcitrant compounds in soil. e.g. degradation of BHC, DDT.

Biofertilizer Carriers: - They are inert substances or materials that serve as a medium or carrier for the delivery and application of biofertilizers. The choice of carrier for biofertilizers is important as it determines the viability, stability, and efficacy of the beneficial microorganisms during storage, transportation, and application. The carrier should provide a suitable environment for the survival and multiplication of the microorganisms, protect them from adverse conditions, and facilitate their release and colonization in the soil.

Biofilm - an assemblage of microbial cells on a shared layer of polysaccharides and proteins. A communal living arrangement in which single-celled organisms live in a shared mass of slime.

Biogeochemical cycling - The pathways by which compounds move through both biotic (bio) and abiotic (geo) compartment of an ecosystem. E.g. NH3 form inside cells (in Biosphere inside cells –bio) and N2 form (in atmosphere–geo).

Biological crusts - Biological crusts, also known as biological soil crusts or biocrusts or cyptobiotic crusts, are communities of living organisms that form a thin, cohesive layer on the soil surface in arid, semi-arid, and other ecosystems. These crusts play an essential role in maintaining soil stability and fertility. It includes cyanobacteria (Microcoleus,  Nostoc. Oscillatoria ), green algae (Chlorella, Trebouxia), fungi (Penicillium, Aspergillus, Glomus), lichens (Cladonia, Collema), mossess (Tortula, Grimmia) and bacteria (Azotobacter, Streptomyces, Nocardia).

Biomagnification - An increase in concentration of a chemical, such as DDT, in tissues of organisms during passage from the lower to the higher levels of a food chain.

Biopesticide - Organism or live formulation that prevents or reduces the proliferation of plant pathogens.

Biopiling - A bioremediation process where contaminated soil is placed in piles and various treatments, such s aeration, fertilization and bioaugmentation; can be applied to enhance the removal of contaminants.

Bioremediation - A biological process (usually involving microorganism) that reduces or removes harmful chemical or their toxicity in an environment.

Biosparging - Injection of gaseous nutrients, such as air, oxygen or methane though the saturated zone of a contaminated soil to stimulate biodegradation or bioremediation. e.g. sparging of methane to encourage Methylocystis to degrade trichloroethylene.

Biostimulation - Addition of nutrients to stimulate microbial metabolism at a contaminated site to enhance bioremediation or biodegradation rates.

Biosurfactant - A surface active compound produced by microorganism that can decrease the surface tension of water.

Bioventing - Injecting gaseous nutrients, such as air, oxygen or methane through the vadose (unsaturated) zone of a contaminated soil to enhance biodegradation or bioremediation rates.

Brown-rot fungi - Fungi which decay wood, degrading most of the cellulose and hemicelluloses but which are unable to decay lignin, leaving it as a more or less intact brown substance e.g. Poria and Gloeophyllum.

BTEX - Benzene, toluene, ethylbenzene and xylene.

Coenocytic -  It refers to multinucleate, cell wall (non septate) less mycelium produced by multiple nuclear divisions without accompanying cell division. Thus coenocytic hypha is not compartmentalized. e.g. fungi belonging to the class Zygomycetes like Rhizopus sp.

Candidatus bacteria (விண்ணப்பித்தல்/ பெயர் விண்ணப்பத்தில் இருக்கும் பாக்டீரியா) - Refers to group of bacteria that are non cultured (வளர்க்க முடியாமல் இருக்கும் நுண்ணுயிரிகள்) in laboratory conditions, but exist in nature and well studied by 16S rRNA gene sequencing and genomic studies, meaning well studied but not available in pure culture. e.g. "Candidatus Brocardia anammoxidans" involved in the anaerobic ammonia oxidation in waste water treatment plants. 

Note: here the term candidatus need to be underlined or typed in italic with first letter in Capital, the genus and species name should NOT be underlined and should be non italic; all the words need to be placed within inverted commas  for e.g. "Candidatus Atelocyanobacterium thalassa (UCYN-A)", a cyanobacteria commonly associated  with the formation of nitroplast (nitrogen fixing eukaryotic organelle) with the unicellular green algae Braarudosphaera bigelowii.

Cellulase - An enzyme that cleaves b-1,4 links in cellulose polymer.

Cellulose - A complex, structural, polymeric carbohydrate composed of long, unbranched chains of glucose [(1,4) linked b-D glucose] molecules that constitutes the chief part of the cell walls of higher plants and algae.

Cellulosome - An extracellular enzyme complex present in some anaerobic cellulose degrading bacteria (e.g. Clostridium sp.) consist of cellulosomal enzymes capable of degrading plant cell walls.

Chelating agent - A chemical compound that forms more than one coordinate bond with metals in solution.

Chemolithotroph - They are also called Chemolithoautorophs. An organism that obtains its energy though oxidation of inorganic compounds (H2S) and fixes carbondioxide for cell biosynthesis

Chemotaxis - Movement of an organism towards or way from a chemical compound.

Chitin - polysaccharide consisting of polymer of b-1,4 linked N-acetyl D –glucose amine that is a major constituent of fungal cell walls and also in the exoskeleton of insects and other arthropods.

Chitinase - An enzyme that hydrolyses glycosidic bonds in chitin to form oligomers and dimers which can be taken up by the cell, providing sources of carbon and nitrogen.

Chitridomycota - The most ancient of fungal phyla, containing the only ‘true fungi’ that produce motile, flagellate zoospores.

Ciliate - Protozoan subgroup consisting of members that swim and feed using hair like cilia.

Cirri - Large organelles of heterotrichous ciliates formed from congregated cilia, that occur on the flattened underside of the cell to propel the organism, for example on the surface of soil particle.

Clamp connection - Lateral connection between two adjacent cells of a dikaryotic fungal hypha which ensure that each cell contains two genetically dissimilar nuclei.

Co-metabolism - Transformation of an organic compound by a microorganism which is not capable of using that as substrate for energy or growth. E.g. enzyme methane monooxygenase involved in the Methane utilization as substrate in Methylocystis also has the ability to degrade the co-substrate Trichloroethylene

Comammox – Complete ammonia oxidizer, refers to bacteria that are capable for complete conversion of ammonia into nitrate, they play important role in N cycling in nature. This property is effected by novel bacterial genera named Nitrospira.

Commensalism - A unidirectional interaction between microorganisms, in which one population benefits, while the latter is unaffected; for example production of vitamins by one population that is used to the sole benefit of the latter.

Competition  - A negative interaction in which more than one partner requires a limiting (nutrient) factor, resulting in a situation where at least one of the partners is adversely effected (for example growth limited).

Conducive soil - A soil that allows the development of plant disease symptoms; the opposite of a suppressive soil.

Copiotrophic - Organism that requires access to plentiful fermentable organic material for growth.

Crop rotation - It is an agricultural farming practice of systematically alternating the type of crops grown on a particular piece of land over a period of time. It offers numerous benefits, including pest and disease management, soil fertility improvement, weed control, and sustainable crop production. E.g. Rice- legume rotation; Wheat-legume rotation.

Culture independent bacterial characterization – refers to molecular level techniques that could tell about the structure and function of microbial communities, without obtaining the members of those communities in pure culture.  

Culture dependent bacterial characterization – culturing of an organism in a specific media (selective or enriched media) and amending the conditions that could facilitate their growth and abundance and thus subsequently recovered in pure culture.

Cytokinin - Any of a group of plant hormones chemically related to the purine adenine.

Cytopharynx - A microtubular organelle that transports food vacuoles further into the cell in some ciliates.

Cytopyge - Also called Cytoprotect the cell anus of protozoa on the cell surface where the cell membrane making up the food vacuole rejoins the outer cell membrane and the food vacuole contents (non digested food parts like bacterial cell walls and organelles) are excreted into the surrounding medium.

Cytostome - Invagination in the cell membrane of some protozoa that form food vacuoles containing collected food particles.

Dechlorination - Removal of chlorine from an organic compound by microorganisms.

Denitrification - Reduction of nitrate to nitrogen gas, via nitrite, nitric and nitrous oxide.

Diazotroph  - A nitrogen fixing bacteria e.g. Rhizobium and Azospirillum.

Dikaryon - Fungal hyphae or mycelium in which each hyphal compartment contains two nuclei representing different mating compatibility groups.

Disease suppressive soil - Refers to soil in which a pathogen causes little or no damage to a host plant, or only transient disease symptoms, although the pathogen may persist in the soil.

Ectoendomycorrhiza - Mycorrhizal roots which exhibit some of the structural characteristics of both ectomycorrhizal and endomycorrhizas, in particular a high degree of intracellular fungal penetration.

Ectomycorrhiza - Ectotrophic mycorrhizal association formed between long-lived, woody perennial plants and fungi predominantly from the Basidiomycota and Ascomycota.

Ectotrophic - Mycorrhiza association in which the fungus grows on the outside of the root with no or only very limited intracellular penetration.

Ellilcitor  - A surface structure or diffusible compound from a plant pathogen that induced the plant’s systemic resistance to the pathogen as native defense mechanism.

Endobacteria - Intracellular bacteria occurring in roots or in fungal hyphae.

Endocytobiotic - Biotic interaction involving the incorporation of an organism into the cytoplasm of another (eukaryotic) organism by endocytosis.

Endophyte  - A microorganism that growth within the plant, often without showing any symptoms of its presence.

Endosphere - The area within the plant, plant interior.

Endospore - Non-growing cellular form used by some species of Gram positive bacteria that allows for the genome of the ells to be protected during harsh conditions such as those often occurring in soil. Once conditions become favorable again, it can convert back into a vegetative cell.

Endosymbiont - Symbiotic- organism that lives within tissue or cells of another organism.

Epiparasite - Parasite living on the surface of another organism.

Ergosterol  - A sterol present in the cell membranes of yeasts and certain fungi.

Ericoid mycorrhiza - Mycorrhizal association formed in three plant families, the Ericaceae, the Empetraceae and Epacridaceae, all belonging to the Ericales.

Flavonoid  - A specific class of plant metabolites, encompassing compounds that affect gene expression in some microorganism. For instance several compounds that induce nodulation genes in rhizobia and flavonoids.

Fruiting body - A multicellular structure in fungi or sporocarp, on which spore producing structure (e.g. basidia, asci) are borne as part of the sexual phase of the fungal life cycle.  When visible to the naked eye, especially fruits bodies of more or less agaricoid morphology, they are often referred to as mushrooms. Also occur in myxobacteria (myxospore).

Gas vesicles -  are spindle-shaped structures, made up of shell of proteins that are hydrophobic in the inner surface, found in some planktonic bacteria like cyanobacteria, it  provides buoyancy to these cells by decreasing their overall cell density. Positive buoyancy is needed to keep the cells in the upper surface of the water column, so that they can continue to perform photosynthesis. 

Geosmin - The earthy and muddy smell after rain technically referred as petrichor, produced mainly by certain actinobacteria and cyanobacteria. 

Glomeromycota - A fungal phylum comprising the arbuscular mycorrhizal fungi that are characterized by the formation of dichotomously branched arbuscules.

Glomalin - It is a hydrophobic, glycoprotein compounds produced exclusively by arbuscular mycorrhizal (AM) fungi’s (Glomales) as putative (and presently unknown) gene product. It acts like a glue and plays major role in the soil aggregation and stability

Gram-negative - A term used to classify bacteria based on their red color after use of gram stain reagents that stain the cell wall.

Great plate count anomaly - An observation through microscope where in  100 to 1000 times more microorganisms can be directly counted in environmental samples, such as soil, compared to the numbers that may be cultivated (obtained as pure culture in plates).

Greenhouse gas - A gas, usually of anthropogenic or microbial origin, involved in causing the greenhouse effect; for example CO2, CH4, N2O and halocarbons.

Green manure- A manure from cover crops ploughed under and incorporated into the soil.

Guild - The members of a community that perform the same specific function (functional groups).

Halophilic - organism that is optimally active at high salt concentrations.

Hartig net - Branched network of hyphae growing between the cortical cells of an ectomycorrhizal root that maximizes contact between the mycorrhizal fungus and its host plant and is thought to be the interface for exchange of nutrients and carbon between the host and the fungus.

Heterocyst - refers to differentiated cyanobacterial cell, lacks photosystem II, they cannot fix CO2 to cell carbon but carries out nitrogen fixation. 

Hormogonia - They are the filaments of cyanobacteria that break off from main filament and form into small a piece, which helps in dispersal and reproduction 

Humus - Humus refers to the dark, organic component of soil that forms as a result of the decomposition of plant and animal materials. It is a crucial component of healthy soil and plays a vital role in supporting plant growth and overall soil fertility. 

Hustoria  - Specialized feeding structures of a fungal pathogen that is capable of direct penetration into and nutrient absorption from a host plant

Horizontal gene transfer (HGT) -  Movement of a gene or group of genes from one organism to another by mechanisms other than vertical transmission. It may occur among bacteria via transduction, transformation or conjugation but not by binary fission. It occurs between Agrobacterium and plants via the conjugative tumor-inducing (Ti) plasmid. It is also called as lateral gene transfer.

Hydrogenotroph - Microorganism that consumes hydrogen e.g. hydrogenotrophic methanogens (e.g. Methanobrevibacter and Methanogenium) which produce methane in soil according to the following reaction:

4H2 + CO2 >>>  CH4 + 2H2O

Hydrogenase or Uptake hydrogenase - An enzyme system that is capable of using hydogen molecules (that evolve as by products) formed during N2 fixation, this H2 is oxidized by the uptake hydrogenase to produce ATP for the cell, the strains possessing such an enzyme system are referred as Hup+ strains.

Hyperaccumulator (Plant) - A plant that is able to accumulate a large concentrations of certain metals from water or soil. e.g. Thlaspi sp. accumulates Zn.

Hyperparasitism - The parasitism of an organism which itself is a parasite. e.g. Trichoderma harzianum

Hyperthermophilic - Extremely thermophilic (heat loving) organism i.e. an organism that is optimally active under extremely warm conditions (often >100oC).

Hypovirulence - Reduced ability of selected isolates within a population of a fungal pathogen to infect, colonize, kill and/or multiply on susceptible host tissues.

Ice nucleation activity - The ability to catalyze ice formation in supercooled water based on the presence of a bacterial-encoded protein (inaZ product) that serves as nucleus for ice crystal formation and that can lead to frost damage in plants e.g. Pseudomonas sp.

Indole acetic acid (IAA) - A plant growth hormone (Auxin type) that is also produced in some microorganisms.

Induced systemic resistance (ISR) -  It encompasses a broad range of phenomena elicited by necrosis inducing plant pathogens or herbivory that allow the plant to restrict the pathogen to certain tissues, this resistance is initiated by the signals Jasmonates and ethylene synthesis in plants.

Key stone species - An organism which has low numerical representation within a community but play a specialized niche role in the environment that is essential to community function and survival.   e.g. Leptospirillum group III possessing nif gene is identified as key stone species among the acid mine drainage communities obtained through metagenomics analysis.

Leghemoglobin: is a red coloured haem protein produced by the leguminous host plants in response to the presence of nitrogen-fixing bacteria within the nodules. The primary function of leghemoglobin is to scavenge the oxygen present, within the nodule. Nitrogen fixation is an oxygen-sensitive process, and excessive oxygen can inhibit the nitrogenase enzyme responsible for fixing atmospheric nitrogen.

Lichen - Symbiotic association between a fungus and photosynthetic partner, which can be either a green alga or cyanobacterium.

Lignin - A group of high molecular weight amorphous compounds, comprising polymers of phenylpropanoid compounds, that is a component of many plant cell walls and is highly resistance to chemical and enzymatic degradation, providing strength to the plant tissues.

Lignocellulose - A major chemical component of wood composed of covalently linked molecules of lignin and cellulose

Melanin - A range of black or brown pigments of amorphous structure.

Mesophile - A microorganism able to grow in the temperature range 20-50oC; optimal growth often occurs at about 37oC.

Metagenome - The collective genomes of a total community in a given habitat.

Methanogenesis - Production of the greenhouse gas methane by methanogenic archaea.

Methanotroph - Microorganism that oxidizes methane as an energy yielding reaction for growth, usually belonging to aerobic bacteria that are common in soil, but also anaerobic methane oxidizing (AMO) archaea that are common in marine sediments.

Methyl co-enzyme M reductase (Mcr) - Key enzyme in methane production that is unique to methanogens.

Methylotrophic (organisms) - Methanol-consuming organisms

Microbiome - The genomes of all microbial community members living within a particular environment, a collective genome representing all community members, it is also called metagenomic DNA.

Mineralization - Catabolism of an organic compound into inorganic components, such as water, carbon dioxide and sometimes salts by microorganisms.

Mitosporic fungi - Ascomycetous fungi that produce conidia but whose sexual states are absent, rare or unknown; previously referred to as the Deutromycota or “Fungi Imperfecti”.

Monotropoid mycorrhiza - Symbiotic mycorrhizal association between fungi and achlorophyllous plants in the family Monotropaceae.

Most probable number (MPN) method - Technique for enumeration of microorganisms, for example in soil, on the basis of multiple end-point dilutions and statistical inference of estimated cell numbers.  The number of positive observations in different sample dilutions is entered in an MPN table, to obtain an estimate of the number of microorganism in the sample.

Mucigel - Gelatinous layer that covers that root surface.

Mutualism - An interaction between organisms in which the partners receive mutual benefits.

Mycorrhiza - Symbiotic relationship between plant roots and certain groups of fungi.

Mycorrhizosphere - The soil volume influenced by the combined activities of a root and its associated mycorrhizal hyphae.

Mycota - The classical taxonomic kingdom of true fungi sometimes referred to as the Eumycota

Mycoparasitism - Parasitism of one fungus by another fungus, whereby the parasite gains some or all of its nutrient while conferring no benefit in return.

Myxospore - Complex structure in the life cycle of myxobacteria, consisting of a rounded cll with a thick cell wall that forms from a vegetative myxobacterial cell when nutrient are scarce; a process mediated by contact signaling.

Naked amoeba - Amoeba lacking an outer test or shell

Necrotrophic - Strictly, feeding on dead cells and tissues, however the term is also used to distinguish necrotrophic pathogen (those killing their hosts before feeding on the dead tissues) from biotrophic pathogen which feed on living host tissues.

Neutralism - lack of interaction between microbial populations, for example due to spatial separation, the inability to contact or sense each other or lack of growth.

Nematophagous fungi - They are carnivorous fungi specialized in trapping and digesting nematodes. Around 160 species are known to exist. For example, Arthrobotrys dactyloides effective in controlling the cosmopolitan plant-parasitic root-knot nematode Meloidogyne javanica. Some species of nematophagous fungi are being investigated for use in biological control agent.  E.g. Purpureocillium lilacinum, infests the plant-parasitic Meloidogyne incognita, which attacks the roots of many cultivated plants.

Nitrogen oxide (NO) - A nitrogen oxide that plays an important role in the chemistry of the atmosphere and is produced mainly by nitrifying and denitrifying bacteria.

Nitroplast - a unique eukaryotic organelle that is invovled in the N2 fixation, it was evolved from cyanobacterial symbiont named "Candidatus Atelocyanobacterium thalassa" (UCYN-A), that is commonly associated with the unicellular green algae Braarudosphaera bigelowii. 

Nitrification - The oxidation of reduced form of nitrogen to nitrate.

Nitrifier - A microorganism involved in the transformation of reduced form of nitrogen to nitrate.

Nitrogen cycle -  the cyclic steps involve dint he transformation of different forms of organic and inorganic nitrogen.

Nitrous oxide (N2O) - A greenhouse gas produced mainly by nitrifying and denitrifying bacteria

Nitrosome – theoretically refers to organelle in a diazotrophic bacteria which may be formed during the course of evolution.

Nod factor - A molecule produced in some bacteria such as rhizobia, serving as a plant-responsive signal during nodule formation.

Nod genes - Nodulation genes associated with production of nodulation factors in some bacteria , such as rhizobia.

Nodule - A structure formed within plant tissue, e.g. in roots of legumes during invasion by some bacteria such as rhizobia.

Oligotrophic (organism) - organism that can metabolize and grow under conditions of scarcity of resources (that is, under nutrient limitation) with relatively low growth rate.

Pathogenesis-Related (PR) proteins - They are a group of proteins produced by plants in response to pathogenic infections, environmental stress, or exposure to certain chemicals. They play a crucial role in plant defense mechanisms and are often associated with systemic acquired resistance. 

Photoautotroph - A microorganism that derived energy from photosynthesis and obtains carbon form CO2. e.g. Cyanobacteria.

Phyllosphere - The phyllosphere refers to the above-ground parts of plants, specifically the surfaces of leaves, stems, and other aerial plant structures. It is a unique and dynamic ecological niche that supports a diverse community of microorganisms, including bacteria, fungi, algae, and viruses. 

Phytoalexin - Low molecular mass, lipophilic, antimicrobial compound that accumulates at some sites of pathogen infection, mediating, systemically acquired resistance (SAR) it further inhibits the growth and spread of fungus. e.g. rishitin, solanidine, scopalin and caffeic acids synthesized in cotton, alfa alfa and red clover plants. 

Phytohormones - Plant hormones such as Auxin, gibberelin, cytokinin, abscisic acid and ethylene.

Phytoremediation  - The use of plant to remove toxicants (either metals or organics) from soil or water.  The plant roots may directly take up some pollutant molecules, such as heavy metals, or the roots can serve as a vehicle for spreading degrading bacteria in the soil.

Phytostimulators -  They also known as plant growth stimulators or plant biostimulants, refer to a group of substances or products that are applied to plants to enhance their growth, development, and overall performance. Phytostimulators do not provide essential nutrients like fertilizers but work through various physiological and biochemical mechanisms to promote plant growth and improve plant health. E.g. Auxins, seaweed extracts and humic and fulvic acids

Plant growth promoting rhizobacteria (PGPR) - Bacterial which colonize roots and increase plant growth.  They may act directly by improving nutrient availability or through hormone production, or indirectly by acting as biocontrol agents. The term was introduced by Kloepper and Schroth .

Prototroph - A species or strain of microbe capable of growing on minimal medium consist of simple carbohydrate or CO2 as carbon source with inorganic sources of all other nutrients requirements.

Psychrophile - A microorganism that grows optimally at low temperatures.

Quality control - Quality control of biofertilizers involves ensuring that the products meet specific standards and criteria for their intended purpose. This process includes various tests and assessments to determine the viability, purity, and effectiveness of the biofertilizers. The test involved are viability testing, purity testing, shelf life testing. E.g. Phosphobacteria purity assured by testing for P solubilization in Pikovaskaya agar; In glucose peptone agar - absence of Rhizobium growth indicates its purity.

Rhizobia  - A group of nitrogen fixing bacteria that can form a symbiotic association with legume plants.  In most cases, nitrogen fixation occurs in specialized structure called nodules on the plant root.

Rhizosphere - The soil region influenced by plant roots that is the site of many key interactions between plant and microorganisms.

Rhizobacteria - Induced systemic resistance (RISR) – is a type of resistance induced by beneficial soil borne microorganisms and rhizobacteria, like pathogens this organism’s molecular pattern is also recognized by plants mainly by induction of reactive oxygen species, resulting in mild but effective activation of immune response.

Root exudates - Materials released by plant roots containing a variety of monomeric compounds (sugars, amino acids, fatty acids, carboxylic acids) that are important for bacterial growth in the rhizosphere.

r-strategist - Organism that can metabolize and grow rapidly (r) (has a high growth rate) when nutrient supply is high and that has a survival advantage in uncrowded situations.

Saprotroph - An organism that feeds on dead organic matter.

Scytonemin - Refers to sunscreen pigments excreted into their extracellular sheaths or capsules, it offers a passive protective mechanism against UV radiation. 

Septate hyphae -  Hyphae of certain fungi contain cross walls called septa, that divides them into distinct uninucleate cell like units.  e.g. Aspergillus hypha

Sheath fungi - A mantle-like structure of fungal hyphae enclosing an ectomycorrhizal root tip.

Soft-rot fungi - Fungi growing on wood in damp environments, usually within the lumen of individual woody cells but with little ability to degrade lignin.

Soil Aggregate - They are composed of number of components ranging from clay microstructures to fine particulate organic matter to form microaggregate (50-250 µm), this microaggregates entangle to form macro aggregate (>250 µm diameter).

Spermosphere - It refers to zone surrounding the imbibing or germinating seeds in soil 1-20 mm zone. Thus its a zone of intense interaction between the soil, microbial communities and germinating seeds.

Stress ethylene - In plants, a larger burst of ethylene produced following a biotic or abiotic stress.

Symbionts - A close and usually obligatory association of two organisms of different species living together, not necessarily to their mutual benefit, but often used exclusively for associations in which both partner benefit which is more correctly term as mutualism.

Symbiosome - Rhizobia released from the infection thread into the root cortical cells are enclosed within a plant derived membrane called as peribacteroid membrane, thus rhizobia are physically isolated from the host (plant) cell cytoplasm. Thus each membrane enclosed bacterium is referred as symbiosome.

Synergism - A facultatively metabolic interaction between microorganisms in which two or more microbial populations are not capable of growth and survival in the absence of the other.  For example, one population may produce a metabolic compound that the other population can further metabolize, allowing the growth of both populations.

Systemic acquired resistance (SAR) -  Long-lasting and broad host-range defense mechanism in plants that can be brought about by previously treating a plant or parts of it with pathogenic microorganism or chemicals that induce reactive oxygen species leading to localized cell death and induction of salicylic acid production that eventually induce the expression of pathogen related (PR) genes.

Telomorph  - The sexual stage of Mitosporic fungus.

Testate Amoebae - Amoebae partially enclosed in a shell or test, made of organic material, agglutinated particles, calcium carbonate or silica e.g. Diffugia globulosa

Thermophile - A microorganism that grows optimally at high temperatures an important source of thermostable enzymes.

Uptake Hydrogenase  - As inevitable side reaction of nitrogenase, electrons are transferred to protons resulting in ATP dependent evolution of H2. Diazotrophs like Azotobacter, Bradyrhizobium, Azorhizobium and some cyanobacteria found to possess an O2 dependent enzyme system named uptake hydrogenase (strain with this enzyme system are referred as Hup+) Which oxidizes H2 to yield ATP, this reaction referred as Knall gas reaction. Thus this enzyme provides respiratory protection against O2 and protection of the nitrogenase from inhibitory effects of H2.

 2H2 + O2 >>>>>  2H2O (-237 KJ mol-1).

Vampyrellidae - A family of naked amoebae with a spherical body shape that in soil have been associated with feeding on (plant pathogenic) fungi.

Vesicles - Spherical or ovoid swellings in the hyphae of some arbuscular mycorrhizal fungi.

Vesicular-arbuscular (mycorrhizae) - An older name for arbuscular mycorrhizal fungi, derived from  the fact that some glomeromycotan fungi, in addition to forming arbuscules, also form swollen storage structures termed vesicles.

Viable-but-nonculturable (VBNC) - A state in which a microorganism is alive but unable to grow on medium that normally supports its growth and that is reversible, meaning that the cells can be resuscitated to be able to grow if conditions become favourable. Commonly occur in medically important pathogenic bacteria. e.g. Vibrio cholerae cell exhibit VBNC state.

White-rot fungi -  Fungi that is able to achieve the complete degradation of lignin. E.g. Phanerochaete chrysosporium. 

Xenobiotics - man made molecules that are foreign to life, for example a range of pesticides of varying chemical nature and polychlorinated biphenyls (PCBs).

Zygomycota - A diverse group of fungi characterized by sexual reproduction by fusion of gametangia to produce resting sexual spores (zygospores) and asexual reproduction by non-motile spores.

Zygospore - Thick walled sexual spore resulting from the fusion of gametangia in zygomyceteous fungi.

Zymogenous (organism) -  Fast growing microorganism that consumes organic substrates.

Phytoalexin Activities

Phytoalexins are antibiotics produced by plants that are under attack. Phytoalexins tend to fall into several classes including terpenoids, glycosteroids and alkaloids; however, researchers often find it convenient to extend the definition to include all phytochemicals that are part of the plant't defensive arsenal.

Phytoalexins produced in plants act as toxins to the attacking organism. They may puncture the cell wall, delay maturation, disrupt metabolism or prevent reproduction of the pathogen in question. However, phytoalexins are often targeted to specific predators; a plant that has anti-insect phytoalexins may not have the ability to repel a fungal attack.

When a plant cell recognized particles from damaged cells or particles from the pathogen, the plant launches a two-pronged resistance: a general short-term response and a delayed long-term specific response.

As part of the induced resistance, the short-term response, the plant deploys free radicals such as superoxide and hydrogen peroxide to kill invading cells. In pathogen interactions, the common short-term response is the hypersensitive response, wherin apoptosis-compromised cells commit suicide in order to create a physical barrier for the invader.

Long-term resistance, or systemic acquired resistance (SAT, involves communication of the damaged tissue with the rest of the plant using plant hormones such as jasmonic acid, ethylene, abscisic acid or salicylic acid. The reception of the signal leads to global changes within teh plant, which induce genes that protect from further pathogen intrusion, including enzymes involved in the production of phytoalexins.

Often, if jasmonates or ethylene (both gaseous hormones) is released from the wounded tissue, neighboring plants also manufacture phytoalexins in response. For herbivores, common vectors for disease, these and other wound response aromatics seem to act as a warning that the plant is no longer edible. Also, in accordance with the old adage, "an enemy of my enemy is my friend," the aromatics may alert natural enemies of the plant invaders that lunch is available

A simple definition to C:N ratio

It refers to the ratio of carbon to nitrogen available in an organic material,  this ratio in turn  determine whether that organic addition to soil, enhance mineralization or immobilization in soil

Low/Narrow C:N (<25:1) ratio – mineralization & High/wider C:N ratio (>25:1)- Immobilization

For an ideal composting process to get started, a C:N ratio of 25-30:1 need to be maintained