As scientists behind Healthy Hydroponics, we know that it can be difficult and confusing to understand some of the jargon that is used in presentations, discussions, and writings about microbiology. It is why we strive to communicate as clearly as we can with growers who may not be familiar with these terms. One way we are helping growers understand the scientific terminology commonly used when discussing the microbiome is by creating a glossary of terms.
Some of these words may have multiple meanings in other contexts. Here we define these words in the context of microbiology in a simplified manner for growers.
This list will be updated as necessary.
How to Use: Hold CTRL-F (Windows) or cmd-f (Mac) to find the term on the page or scroll down the list below.
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A
Abaxial
Acquired resistance
Adaxial
Aerobic
Aeroponic system
Amplicon
Antibiotic
Antifungal
Antimicrobial
Antiviral
Aquaponics
Archaeum (plural: archaea)
B
Bacterial inoculant
Bacterium (plural: bacteria)
Biocontrol
Biotechnology
By-product
C
Chemotaxis
Chlorotic
Culture-dependent technique
Culture-independent technique
D
E
F
Fungicide
Fungus (plural: fungi)
G
Genome
Genus
Germinate
Gram-negative
Greenhouse
H
I
M
Marker gene
Mesophyll
Microbiome
Microorganism
Mycelium
N
Necrotic
Nutrient Film Technology
P
Pathogen
Pathogenicity
Pesticide
Phenolic compound
Photosynthetic
Plasmid
R
S
Secondary metabolite
Sequencing
Species
Spores
Stoma [plural: stomata]
Susceptible
T
V
W
Definitions
16S rRNA gene (16S ribosomal RNA gene)
A gene encoding the small subunit of the ribosome in Bacteria and Archaea. A partial or complete 16S rRNA gene is commonly used for classification. This gene can be thought of as a barcode for classifying bacteria.
18S rRNA gene (18S ribosomal RNA gene)
A gene encoding the small subunit of the ribosome in Eukaryotes. A partial or complete 18S rRNA gene is commonly used for classification. This gene can be thought of as a barcode for classifying eukaryotes.
Abaxial
The underside of leaves, facing away from the stem.
Adaxial
The upper surface of leaves, facing toward the stem.
Acquired resistance
Resistance which is obtained through mutation or acquisition of genes, in an otherwise susceptible organism
Aerobic
Requiring oxygen to grow.
Aeroponic system
A type of hydroponic growing system where plants are suspended in the air. Roots are then misted with a nutrient-rich solution. Can accommodate most plants, but can be expensive and nozzles can get clogged. However, this system uses the least amount of water!
Amplicon
A piece of DNA that is used as the source or template for producing more copies of the DNA through a process called amplification. For example, an amplicon can be a marker gene that is sequenced to classify organisms.
Antibiotic
An antibiotic is an agent which actively targets bacteria. An antibiotic can kill or inhibit the growth of bacteria.
Antifungal
An antifungal is an agent which specifically targets fungi. This treatment can kill or inhibit the growth of fungus. Fungal infections usually target the hair, skin and nails, therefore treatments are often topical.
Antimicrobial
This is an overarching term for an agent that kills microorganisms, especially pathogens. Antibiotics, antivirals and antifungals are all antimicrobials.
An antiviral is an agent which specifically targets viruses. This agent can kill a virus or suppress its ability to replicate.
Aquaponics
This growing technique combines both hydroponics and aquaculture. In a closed system, the water that the fish live in is pumped through a bio-filter and is used to support the growth of hydroponic crops. This water is ammonia-rich due to the waste produced by the fish.
Archaeum [plural: archaea]
A single-celled organism that lacks a membrane-bound nucleus and has structural and molecular characteristics different from bacteria and eukaryotes. Archaea, along with Bacteria and Eukaryota, is also a domain (highest taxonomic category).
Bacterial inoculant
A product or culture that contains a strain of bacterium or a mixture of bacteria that is used as an agricultural amendment for a beneficial purpose.
Bacterium [plural: bacteria]
A single-celled organism that lacks a membrane-bound nucleus (nucleus: a structure in a cell that contains the genetic material of the cell). Bacteria, along with Eukaryota and Archaea, is also a domain (the highest taxonomic category).
Biocontrol
The use of living organisms or natural substances to prevent or control damage caused by harmful organisms, and does not require pesticides.
Biotechnology
The integration of natural science to engineer a product or service.
By-product
An incidental or secondary product made by an organism, usually as a waste product.
Chemotaxis
The attraction of an organism toward an environmental stimulant or repulsion of an organism away from surroundings it considers a repellent.
Chlorotic
Yellowing of a leaf due to lack of chlorophyll.
Culture-dependent technique
A technique that requires growing (culturing) organisms to study them. For example, visualizing the morphologies of bacteria requires culture-dependent methods to grow the bacteria before being able to see them under a microscope. The majority of microbial species cannot be cultured.
Culture-independent technique
A technique that does not require growing (culturing) organisms to study them. For example, sequencing DNA in a sample is a culture-independent technique to study the types of microorganisms in that sample.
Defoliation
The premature deprivation, or loss, of leaves.
DNA (deoxyribonucleic acid)
A molecule that contains the genetic code (blueprint) for growth, development, and reproduction of an organism. The DNA of an organism or a community of organisms can be sequenced to identify its genes or composition of its member organisms.
Drip System
A type of hydroponic system in which the nutrient-rich water is pumped directly into the plant base and any excess water will drip out.
Ebb and Flow
AKA “flood and drain”, is a popular type of hydroponic system and is often a large setup, due to the spacing of plants. Plants are flooded and drained with nutrient-rich water using a pump. Great for diverse plant types, (e.g. root vegetables) but issues can arise with pump malfunctions.
Eukaryote
An organism that can be multicellular (composed of multiple cells) or unicellular/single-celled (composed of one cell) where each cell contains a membrane-bound nucleus (nucleus: a structure in a cell that contains the genetic material of the cell). Some examples of eukaryotes include: fungi/moulds, yeasts, Pythium, nematodes, and algae. Eukaryota, along with Bacteria and Archaea, is also a domain (the highest taxonomic category).
Fungus [plural: fungi]
A member of Eukaryotes that includes moulds, yeasts, and mushrooms. Fungi produce spores (microscopic particles needed for reproduction) and feed on organic matter (carbon-based compounds).
Fungicide
A chemical that targets and destroys fungus.
An organism’s entire set of genetic material or DNA encoding instructions for growth, development, and reproduction of the organism.
Genus
The level of taxonomic identification for an organism that is below the family level.
Germinate
A seed developing shoots.
A group of bacteria which counterstain (turn pink) using the Gram staining method.
Greenhouse
An enclosed space made of glass or plastic to let it natural light. Semi-controlled environment with (usually) a single layer of planted crops. A more traditional form of agriculture.
Hydroponics
A technique often used in vertical farming and is a form of agriculture without soil. Instead, plants are grown in a nutrient rich solution. This environment is highly controlled (e.g. pH, temperature, humidity, nutrient concentrations etc.).
ITS (intergenic transcribed spacer)
A sequence of nucleotides between genes encoding the small and large subunit of the ribosome in fungi, commonly used as a marker gene. This sequence can be thought of as a barcode for classifying fungi.
Marker gene
A specific sequence of DNA signifying a partial or complete gene or intergenic region (region between genes) that is used to differentiate between taxonomic groups.
Mesophyll
The inner tissue of a leaf containing chloroplasts (contains chlorophyll and is where photosynthesis takes place)
Microbiome
It is the combined genetic material of microorganisms in a particular environment.
Microbiota
The microorganisms in a specific environment. Microbiome and microbiota are sometimes used interchangeably.
Microorganism
A microscopic organism that can be unicellular or multicellular. Microorganisms include bacteria, archaea, fungi, etc.
Mycelium (plural: mycelia)
A root like structure of a fungus which consists of branching.
Necrotic
Producing death in a localized area of a living tissue.
Nutrient Film Technology
This is a type of hydroponic system which scales up well. The nutrient rich water is pumped into sloped channels, with excess solution flowing back into the reservoir. Great for plants with small roots and for large commercialized farms.
Pathogen
A microorganism (e.g. bacteria, fungus or virus) which can cause disease or illness.
Pathogenicity
The ability of a microorganism to cause disease.
Pesticide
A chemical that destroys pests and/or other organisms which are harmful to plants and/or animals.
Phenolic compound
A chemical compound which contains aromatic rings with hydroxy groups that is directly attached to a phenyl, substituted phenyl or aryl group.
Photosynthetic
Relating to the process of photosynthesis.
Plasmid
A piece of DNA in a cell that is separate from the chromosome (necessary DNA for survival of an organism), can move/be transferred between organisms and can carry beneficial or survival genes.
Rhizosphere
The area of soil surrounding the roots of plants.
Ribosome
A ribosome is a structure in cells that synthesizes proteins.
Ri-plasmid
Rhizogenic plasmid, which causes root growth (aka hairy root disease) and is found in Agrobacterium rhizogenes.
Secondary metabolites
Not required for growth of an organism, but are produced to provide an advantage to the organism, such as inhibiting growth of a competitive organism.
Sequencing
The process of determining the order of nucleotides (building blocks of DNA) in DNA.
Species
Level of taxonomic identification for an organism, one level below genus
Spores
Microscopic particle which allows for fungus to reproduce.
Stoma (plural: stomata)
A pore found in the epidermis of a plant which allows for the exchange of gas.
Susceptible
An organism’s ability to suffer if exposed to a particular threat.
T-DNA
The transferred-DNA from the host bacteria into the plants genome, the Ti-plasmid is found in Agrobacterium tumefaciens and causes tumour growth in plants.
Taxonomy
The system of classifying organisms. The order of taxonomic categories of organisms from the broad to specific: domain, phylum, class, order, family, genus, species.
Ti-plasmid
Tumorigenic plasmid, which causes tumor growth (aka crown gall disease)
Vertical Farming
This method is similar to a greenhouse, however trays containing crops are stacked from floor to ceiling. This is a much more controlled environment, containing LED lighting, humidity and temperature control. More expensive than greenhouses (6-10x) but utilizes every inch of space.
Water Culture
AKA “Deep water systems”, are similar to wick systems, but the roots are directly submerged. They also have an air stone or diffuser to oxygenate the water. This system provides substantial nutrient uptake, but there is potential for root disease if the system is not maintained/cleaned properly.
Wick Systems
Among the simplest hydroponic designs – function without the use of electricity, pumps or aerators! Water travels up the wick to nourish the plant. Limited nutrients are supplied to the plant, but this system is great for small gardens!
