Glossary of key subject terms and abbreviations

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A

AAnP	aerobic anoxygenic photosynthesis; the process of photosynthesis occurring under aerobic conditions in which electron donors such as sulfide or organic matter are used, without evolution of oxygen
ABC transporter	ATP-binding cassette transporter; a membrane system comprising a substrate-binding protein, an ATP-hydrolyzing protein, and a channel protein spanning the membrane
acetylene reduction assay	a sensitive assay for measuring the activity of nitrogenase
acquired phototrophy	the process by which phagotrophic protists may transiently retain intact functional algal prey or their plastids, enabling them to carry out photosynthesis; also known as kleptoplastidy
active transport	energy-dependent transport of substances into and out of the cell
acute disease	a disease that has a sudden onset and short duration
adaptive bleaching hypothesis	the hypothesis that corals that have expelled zooxanthellae due to stress (bleaching) are recolonized by genetically different types with greater tolerance of the stress conditions
adenyl cyclase	a key enzyme in membrane transport; continued activation by cholera toxin leads to increased levels of cyclic AMP, leading to excessive fluid and electrolyte loss by activating a transmembrane regulator chloride channel
adherence	the ability of microbes to stick to surfaces
adhesin	a virulence factor enabling a microbe to stick to a host cell surface
adjuvant	a substance (such as mineral oil or aluminum salts) added to vaccines to boost the host’s immune response
ADP-ribosylation	the action of cholera toxin on a regulatory protein in gut cells; leading to excessive loss of electrolytes and fluids
aerobe	an organism that grows in the presence of oxygen
aerobic anoxygenic photosynthesis (AAnP)	the process of photosynthesis occurring under aerobic conditions in which electron donors such as sulfide or organic matter are used, without evolution of oxygen
AFLP	amplified fragment length polymorphism; a genetic fingerprinting method for strain differentiation based on polyacrylamide gel electrophoresis of restriction enzyme digests of DNA
AHL	acyl homoserine lactone, an autoinducer in bacterial quorum sensing
AI	autoinducer; a diffusible molecule that affects the regulation of specific genes when present at threshold concentrations in the cell (quorum sensing)
albedo effect	the reflection of heat by light surfaces (e.g. snow, ice, clouds, coccoliths), which has a major impact on climate
algae	the common name for the polyphyletic group of unicellular or multicellular protists usually obtaining nutrition by photosynthesis (may be mixotrophic)
alpha diversity	the average diversity of species (OTUs) found in a sampled habitat, usually expressed as richness
alveolates	a major clade (superphylum) of protists including the apicomplexa, ciliates, and dinoflagellates; distinguished by distinctive flagella and flattened vesicles (alveoli) under the membrane, which may form armor plates in the dinoflagellates
ammonia-oxidizing archaea (AOA)	a large group of mesophilic and psychrophilic archaea (phylum Thaumoarchaeota) that form a major component of picoplankton, especially in deeper waters, where they have a major role in the nitrogen cycle by carrying out the first stage of nitrification
ammonia-oxidizing bacteria (AOB)	a functional group of bacteria that carry out the first stage of nitrification, generally more dominant than AOA in sediments and water with higher concentrations of ammonia
ammonification	the production of NH3 or NH4+, which is carried out by many types of heterotrophic bacteria and fungi during decomposition of organic material, resulting in readily assimilable N as a nutrient in ocean processes
amnesic shellfish poisoning (ASP)	a disease caused by domoic acid toxin produced by Pseudo-nitzschia diatoms
AMO	(1) anaerobic methane oxidation, a process carried out in sediments by anaerobic methanotrophs (ANME) in syntrophy with sulfate-reducing bacteria; (2) the enzyme ammonia monooxygenase
amoeboid	a type of cellular movement in certain groups of protists, notably the radiolarians and foraminifera, involving a crawling-like movement by protrusions of cytoplasm and fibrils
AMP	adenosine monophosphate, a molecule with major functions in many cellular processes
amplicon sequence variant (ASV)	a term used to describe individual DNA sequences obtained in HTS community studies; following removal or amplification and sequencing errors, sequences inferring true biological origin differing by as little as one nucleotide can be recognized, replacing the need for similarity-based threshold clustering (OTUs); also known as exact sequence variants (ESVs)
AMR	antimicrobial resistance; the ability of a microorganism to resist the effects of treatment with an antibiotic or other antimicrobial compound agent that was previously able to inhibit or kill it
anaerobe	an organism that grows in the absence of oxygen; obligate anaerobes may be killed by its presence
anaerobic respiration	use of substrate other than oxygen in oxidation of a substrate via an electron transport chain
anammox	anaerobic ammonia oxidation; a major reaction in marine nitrogen cycling in sediments and anoxic basins resulting in the release of N2, which is returned to the atmosphere; it is carried out by planctomycete bacteria possessing specialized organelles
ANI	average nucleotide identity (ANI), a quantitative method for measuring the similarity of two genomes at the level of nucleotides
ANME	anaerobic methanotrophic archaea (ANME), which carry out oxidation of methane in sediments, in syntrophy with sulfate-reducing bacteria
annotation	the process of identifying the function of genes in a new genome sequence by comparison with homologous genes of known function
anoxic	oxygen-free (<0.1 μM oxygen detectable)
anoxygenic photosynthesis	the use of light energy to synthesize ATP by cyclic photophosphorylation without the evolution of oxygen
antibiotic	a chemical substance (usually low molecular weight) produced naturally by one microorganism that inhibits or kills another microorganism; in common usage this includes chemically synthesized or modified antimicrobial agents
antibody	a protein (immunoglobulin) produced by the immune system that binds specifically to an antigen
antigen	a substance that elicits an immune response
antimicrobial	a chemical substance that inhibits or kills microorganisms; this includes antibiotics
antimicrobial resistance (AMR)	the ability of a microorganism to resist the effects of treatment with an antibiotic or other antimicrobial compound agent that was previously able to inhibit or kill it
antitumor agent	a cytotoxic substance that inhibits the growth of tumor cells in culture or prevents development of tumors in living animals
AO	acridine orange, a fluorochrome which binds to RNA and DNA
AOA	ammonia-oxidizing archaea; a large group of mesophilic and psychrophilic archaea (phylum Thaumoarchaeota) that form a major component of picoplankton, especially in deeper waters, where they have a major role in the nitrogen cycle by carrying out the first stage of nitrification
AOB	ammonia-oxidizing bacteria; these carry out the first stage of nitrification, generally more dominant than AOA in sediments and water with higher concentrations of ammonia
aOIF	artificial ocean iron fertilization; the process of seeding ocean waters with iron compounds in order to stimulate phytoplankton production
AOM	anaerobic oxidation of methane; a process carried out in sediments by syntrophic consortia of ANME archaea and sulfate-reducing bacteria
apoptosis	one of the types of programmed cell death, showing morphological changes including cell shrinkage, DNA fragmentation, and cell membrane blebbing; an important response to infection by some symbionts and pathogens
aquaculture	the farming of fish, crustaceans, molluscs, algae, and other aquatic organisms
Archaea	the taxonomic name of a phylogenetic domain of organisms characterized by a relatively undifferentiated simple cell structure, isoprenoid glycerol diether or diglycerol tetraether membrane lipids, archaeal rRNA, complex RNA polymerase, and other distinctive properties. For general descriptions, the non-capitalized forms archaea and archaeon (singular) are used.
archaeon (plural, archaea)	an individual member of the domain Archaea
Ascomycota	the largest phylum of Fungi, characterized by a cup-like sac that holds the sexual spores
Asgard	one of the four major clades (supergroups) of Archaea; there is growing evidence that eukaryotes evolved from within this clade
ASP	amnesic shellfish poisoning; caused by domoic acid toxin produced by Pseudo-nitzschia diatoms
assisted evolution (of corals)	a concept that selective breeding of corals may provide a mechanism to repopulate damaged reefs with corals that are more resilient to environmental change
ASV	amplicon sequence variant; a term used to describe individual DNA sequences obtained in HTS community studies; following removal or amplification and sequencing errors, sequences inferring true biological origin differing by as little as one nucleotide can be recognized, replacing the need for similarity-based threshold clustering (OTUs); also known as exact sequence variants (ESVs)
atm	unit of atmospheric pressure [= 0.101 mPa]
atomic force microscopy	instrumentation that can reveal complex surface architectures at the nanometer to micrometer scale
ATP	adenosine triphosphate, the principal energy carrier within cells
attenuated vaccine	a preparation of live bacteria or viruses made reducing the virulence of the pathogen
attenuation	reduction or loss of virulence of a pathogen
autochthonous	a term in ecology to describe organisms that are indigenous to a habitat, rather than introduced from elsewhere
autotroph	an organism able to grow using CO2 as the principal source of carbon
AUV	autonomous underwater vehicles; used for ocean exploration and sampling
average nucleotide identity (ANI)	a quantitative method for measuring the similarity of two genomes at the level of nucleotides
axenic cultures	cultures that are free from living organisms other than the species under study (for example, protist cultures that do not contain their normal bacterial associates)
AZAs	azaspiracids; a group of dinoflagellate toxins that can accumulate in bivalve molluscs, causing diarrhetic shellfish poisoning
azaspiracids	a group of dinoflagellate toxins that can accumulate in bivalve molluscs, causing diarrhetic shellfish poisoning (AZAs)
azooxanthellate	a term used to describe corals or other organisms that do not contain symbiotic zooxanthellae (Symbiodiniaceae)

B

bacteremia/septicemia	the presence of large numbers of bacteria within the bloodstream, usually caused by virulent pathogens that overwhelm the natural host defense mechanisms
Bacteria	the taxonomic name of a phylogenetic domain of organisms characterized by a relatively undifferentiated simple cell structure, diacyl glycerol diester membrane lipids, bacterial rRNA, simple RNA polymerase, and other distinctive properties. For general descriptions, the non-capitalized forms bacteria and bacterium (singular) are used.
bacterial growth efficiency (BGE)	the ratio of biomass or ATP produced to the amount of substrate utilized
bacterin	a suspension of killed or attenuated bacterial cells used as a vaccine
bacteriochlorophyll	a pigment composed of light-sensitive magnesium tetrapyrroles, found in phototrophic bacteria
bacteriocyte	an adapted host cell containing endosymbiotic bacteria
bacteriophage	a virus that infects bacteria; the term phage is now more widely used to indicate agents that infect members of the Bacteria and Archaea
bacterioplankton	free-floating aquatic bacteria
bacteriorhodopsin	a retinal-containing protein found in halophilic Archaea used in light-mediated ATP synthesis
bacterivore	an organism that obtains nutrition from the consumption of bacteria; e.g. predatory protists
barophile	an organism that grows optimally at pressures >30 mPa; the term piezophile is preferred as the prefix piezo- indicates pressure rather than baro-, weight
barotolerant	an organism that is tolerant of a wide range of pressures up to 30–40 mPa, but showing reduced activity above ~20 mPa; the term piezophile is preferred as the prefix piezo- indicates pressure rather than baro-, weight
Basidiomycota	one of the major fungal phyla, occurring in filamentous and yeast forms; distinguished by a pedestal-like structure (basidium) with external sexual spores
BBD	black band disease of corals
BBL	benthic boundary layer; a layer of homogeneous water 10 m or more thick, adjacent to the sediment surface
benthic boundary layer (BBL)	a layer of homogeneous water 10 m or more thick, adjacent to the sediment surface
benthic; benthos	terms used to describe the seafloor or organisms living on or in the sediment of the ocean floor
beta diversity	the amount of change in the number of species (or OTUs or ASVs) between two sampled habitats
BGE	bacterial growth efficiency; the ratio of biomass or ATP produced to the amount of substrate utilized
bicosoecids	a group of bacterivorous nanoflagellate protists; notable examples include Cafeteria and Bodo
binning	a key step in the bioinformatic analysis of genome sequences, in which assembled contigs are sorted into the best estimate of groups that might belong together
bioactive compound	a substance having an effect or causing a response in living cells or tissue
bioaugmentation	the modification of microbial community composition by addition of specific microbes to improve the rate of bioremediation
biodegradation	the breakdown of complex organic compounds
biodeterioration	damage to natural or fabricated materials through microbial activities
biodiversity	the diversity of life forms, including their relationships and functions in ecosystems
biofilm	an organized structure of microbial cells, extracellular products, and associated substances formed on surfaces
biofouling	the colonization of marine surfaces by bacteria and diatoms, followed by successive colonization by algae and invertebrates
biofuel	a fuel derived directly from living organisms, such as oils from microalgae or plants, or methane from microbial decomposition
biogeochemical cycles	movements through the Earth’s system of key elements essential to life, such as carbon, nitrogen, oxygen, sulfur, and phosphorus
bioinformatics	the computational storage, retrieval, and analysis of information about biological structure, sequence, and function
biological pump	the process by which carbon from CO2 at the ocean-atmosphere interface is fixed by photoautotrophs into organic matter and redistributed through the water column to the seafloor and sediments
bioluminescence	the production of light by living organisms
biomagnification	the accumulation and amplification of toxic chemicals at each trophic level so that organisms at the top of the food chain will accumulate high levels of the chemical in their tissues
biomass	the quantity of living matter (weight per unit area or volume)
biomimetics	a design process mimicking processes or principles of assembly found in living organisms
biomolecular electronics	a branch of nanotechnology where the information processing and energy transmission of biological molecules are used to create elements of electronic devices
bioprospecting	the search for pharmaceuticals, enzymes, polymers, and other useful products in living organisms and their genomes
bioremediation	a biological process to enhance the rate or extent of naturally occurring biodegradation of pollutants
biosensor	a device which uses a living organism or biological molecules such as enzymes or antibodies to detect the presence of chemicals
biosphere	the global sum of all ecosystems on Earth
biotechnology	the application of scientific and engineering principles to provide goods and services through mediation of biological agents
bioturbation	the activity of burrowing worms, molluscs, and other animals in sediments, which increases O2 availability to deeper levels of sediments
BKD	bacterial kidney disease of fish
black smoker	a deep-sea hydrothermal vent, emitting super-heated water (200–350oC) containing sulfide and other minerals
BLAST	Basic Local Alignment Similarity Tool; a fundamental step in bioinformatics that finds regions of similarity between nucleotide or protein sequences and calculates the statistical significance of matches
bloom	the rapid multiplication and extensive spread of phytoplankton cells
bloom and bust	the process of rapid multiplication and extensive spread of phytoplankton cells, followed by sudden collapse, often due to viral lysis
bootstrapping	a computational technique to test the validity of phylogenetic trees, in which multiple iterations are made of trees based on subsamples of the sites in an alignment
botulism	a disease characterized by flaccid paralysis, often fatal, caused by ingestion of a neurotoxin produced by Clostridium botulinum
BPV	baculovirus penaei virus; a virus causing disease in shrimp and other crustaceans
brevetoxin	a neurotoxin produced by the dinoflagellate Karenia brevis
brine	water with a very high salinity (e.g. in sea ice and deep-sea hypersaline basins)
burglar alarm hypothesis	a proposed explanation for an ecological function of bioluminescence in dinoflagellates; it suggests that light produced by luminescent prey attracts grazing predators, which in turn sends a signal to larger predators, so that the grazers themselves become prey

C

cable bacteria	a group of filamentous bacteria that oxidize sulfide via long-distance electron transport
calcification	the deposition of calcium carbonate structures by organisms
Calvin–Benson–Bassham (CBB) cycle	the mechanism by which many autotrophic organisms fix carbon dioxide into organic compounds
Candidate Phyla Radiation	a recently described expansion of the tree of life, containing over 70 potential phyla and encompassing a large proportion of bacterial diversity
*Candidatus* *(Ca.)*	an intermediate taxonomic category used for Bacteria and Archaea whose phenotypic characteristics have not been fully documented in accordance with rules defined by the International Committee on Systematics of Prokaryotes
capsid	the shell of proteins that surrounds the genome of a virion
capsomere	the protein subunit of a viral capsid
carbon cycle	the flux of carbon through interconnected reservoirs (atmosphere, terrestrial biosphere, oceans, sediments, and fossil fuels)
carbon fixation	incorporation of CO2 into cellular organic material
carbon sequestration	uptake and storage of carbon via biological and geological processes
carbonate compensation depth	the depth in the ocean below which calcium carbonate dissolves and does not reach the sea floor
carboxysome	a cellular inclusion containing multiple molecules of the enzyme RuBisCO
CARD-FISH	catalyzed reporter deposition fluorescent in situ hybridization; a FISH technique in which the signal is amplified by an enzyme-linked reaction
carotenoids	accessory pigments in photosynthetic organisms, which function primarily to protect cells from harmful photooxidation reactions that can occur in bright light
CBB cycle	Calvin–Benson–Bassham cycle; the mechanism by which many autotrophic organisms fix carbon dioxide into organic compounds
CCN	cloud condensation nuclei; small atmospheric particles that seed the formation of water vapor to liquid
cDNA	complementary DNA; a DNA copy of mRNA made with the enzyme reverse transcriptase
CDV	canine distemper virus (a morbillivirus), which causes a disease of dogs and is closely related to viruses in seals
cercomonads	a group of flagellated protists, abundant in water and sediments
CFB	the Cytophaga–Flavobacterium–Bacteroides group of bacteria
CFP	ciguatera fish poisoning; a disease characterized by severe neurological effects caused by consumption of a dinoflagellate toxin (ciguatoxin) that accumulates in fish tissue by biomagnification
CFU	colony-forming units, used in the enumeration of microorganisms on agar plates
chemocline	a boundary layer in ocean water with a strong gradient of a particular chemical
chemokinesis	a behavioral response of bacteria; an increase in speed of swimming when moving towards or away from an attractant or repellent chemical
chemolithoautotrophy	a microbial process of nutrition, in which CO2 serves as the carbon source and energy and electrons are derived from oxidation of reduced inorganic compounds
chemoorganotrophic heterotroph	an organism using organic compounds as a source of carbon, energy, and electrons
chemosynthesis	a general term to describe the formation of organic compounds which includes chemolithoautotrophy (e.g. using reduced sulfur compounds, hydrogen, or ammonia) and methanotrophy (using methane as source carbon and reducing power)
chemotaxis	a behavior in which microbes move towards attractant chemicals or away from repellents
chemotherapy	the treatment of a disease with antibiotics or synthetic drugs
chitin	a long-chain polymer of N-acetylglucosamine; a component of fungal cell walls and widely distributed in the marine environment as a component of the exoskeleton of crustaceans and internal structures of cephalopods and other animals
chlorophyll	a photosynthetic pigment composed of light-sensitive magnesium tetrapyrroles, in cyanobacteria, algae, and plants
chloroplast	the chlorophyll-containing organelle present in phototropic eukaryotes
choanoflagellate	a free-living unicellular or colonial bacterivorous flagellated protist that is phylogenetically the closest unicellular relative to the obligately multicellular animals
chromogenic media	culture media incorporating a substrate that produces a distinctive color when metabolized by microbial enzymes; used for rapid and reliable detection of specific microorganisms
chromophore	the colored part of a pigmented molecule
chronic disease	a condition that is long-lasting (months or years) that can be controlled but rarely cured completely
chrysomonads	a group of photosynthetic or mixotrophic protists with two flagella; abundant in aquatic environments
Chytridiomycota	One of the major divisions of the fungi, commonly referred to as chytrids; an early diverging lineage characterized by production of reproductive zoospores within a sac-like structure and motile by a single flagellum
chytrids	an early diverging fungal lineage characterized by production of reproductive zoospores within a sac-like structure and motile by a single flagellum
ciguatera fish poisoning (CFP)	a disease characterized by severe neurological effects caused by consumption of a dinoflagellate toxin (ciguatoxin) that accumulates in fish tissue by biomagnification
ciliates	a group of large protists in which some or all of the surface is covered with multiple hair-like structures, which beat to provide motility or to capture food particles
clade	a monophyletic group or lineage of organisms which share common inherited characteristics
clathrate	an ice-like solid form of methane formed with a specific combination of temperature and pressure under the seabed, where it combines with water molecules to form a stable crystalline structure
CLAW hypothesis	a hypothesis developed by Charlson, Lovelock, Andreae and Warren, in which algal DMS production is envisaged as providing a feedback mechanism via production of an albedo effect that regulates the climate
climate change	significant changes in global climate patterns, often synonymous with “global warming”
clone library	a genomic library of different DNA sequences that have been inserted into a host (cloning vector) for propagation of multiple copies
cloning [molecular]	isolation of a DNA sequence and propagation of multiple copies in a host organism, usually a bacterium, for production of large quantities of DNA for molecular analysis
CLSM	confocal laser scanning microscopy
CMV	cetacean morbillivirus, causing a disease of whales and dolphins
coccolithophores	unicellular marine bloom-forming algae with cell surface covered by calcified plates
cold seep	regions of the seabed where fluids containing methane or hydrocarbons enter the water column via fissures in the sediments
coliphage	a virus infecting E. coli or other coliform bacteria
comammox	a process carried out by members of the bacterial genus Nitrospira, whichhave been shown to be capable of complete oxidation of ammonia to nitrate
community fingerprinting	analysis of the genetic sequences in an assemblage of different types of microbes, usually achieved by high-throughput sequencing
compatible solutes	small organic compounds in the cytoplasm that act as osmoprotectants, helping organisms withstand osmotic stress
competence	the ability of bacteria to acquire exogenous DNA via transformation
complement	a cascade system of serum proteins in vertebrates that react to antigen–antibody complexes or bacterial surface components to amplify defense responses to a pathogen
complement resistance	a property of many pathogenic bacteria that enables them to resist the bactericidal properties of serum
concatenation	a bioinformatic method in which sequences from multiple genes are assembled into a large matrix which is used to estimate a phylogenetic tree
conditioning film	a layer of proteins and polysaccharides that coats surfaces within a short period of immersion in seawater; an essential first step in biofilm formation
confocal laser scanning microscopy (CLSM)	a microscopic method in which laser light scans the specimen at one level, yielding an image with high contrast and resolution; especially valuable for examining biofilms and biological tissues
consensus (or conserved) sequence	a DNA sequence in which particular bases are found at the same position when sequences from different organisms are compared
contig	a contiguous length of DNA sequence in which the order of bases is known with high confidence; overlapping segments are used to reconstruct the original genome sequence in shotgun sequencing projects
convective mixing	the vertical transport of seawater driven by density differences due to temperature
convergent evolution	the process whereby unrelated organisms evolve similar traits independently as a result of adaptation to similar environments or ecological niches
copiotroph	an organism capable of using high levels of nutrients
coral bleaching	the loss or impaired function of symbiotic zooxanthellae from corals, usually as a result of environmental stress
coral probiotic hypothesis	the concept of a dynamic interaction between members of the coral microbiome that adapts to changes in environmental conditions, leading to selection of the most favorable microbiome that protects the host from disease
core genome	a set of genes present in the genome of all strains of a collection of bacteria considered to be a species
core microbiome	a set of microbial phylotypes that appear to be stable and consistent residents of an environment or niche within a host; different cut-off thresholds may be set in order to define the “core” members
Coriolis effect	an apparent force arising because of the Earth’s rotation; moving objects, winds, and water masses are deflected to the right in the northern hemisphere and to the left in the southern hemisphere
CPR	Continuous Plankton Recorder; an instrument towed by ships for collection of plankton samples on a moving band of silk
Crenarchaeota	one of the major phyla of the domain Archaea
CRISPR gene-editing	a tool in genetic modification that uses a CRISPR sequence of DNA (short repetitions of base sequences) and its associated enzyme Cas9 to edit the base pairs of a gene
cristae	the infoldings of the inner mitochondrial membrane; important in the classification of protists
cryo-electron tomography	an application of transmission electron microscopy used to produce high-resolution (~1–4 nm) three-dimensional views of biological macromolecules and cells in which samples are viewed at low temperature (liquid nitrogen) and scanned with an electron beam at different tilt angles to produce a 3D image
CTC	5-cyano-2,3-dilotyl tetrazolium chloride; a fluorogenic redox dye that detects an active electron transport chain, used for the assessment of cell viability
CTD	conductivity, temperature, and depth; parameters measured as standard parameters during the collection of ocean water samples
Cyanobacteria	a large phylum of oxygenic photosynthetic Bacteria including dominant members of the phytoplankton with a major contribution to primary production
cyanophage	a phage infecting cyanobacteria
cytoskeleton	a system of hollow microtubules and actin microfilaments that form a scaffold structure in eukaryotic cells
cytotoxin	a chemical substance that is toxic to cells
CZCS	Coastal Zone Color Scanner

D

DAPI	4’6’-diamidino-2-phenylindole; a fluorochrome that binds to DNA that is used in epifluorescence microscopy and flow cytometry
DDH	DNA–DNA hybridization; a method for determining the relatedness of genetic sequences by determining hybridization of single-stranded DNA extracted from two organisms
ddNTP	dideoxyribonucleotide triphosphate; an intermediate used in Sanger sequencing of DNA
DDT	dichloro-diphenyl-trichloroethane; a persistent organic pollutant previously used as an insecticide
dead zone	a body of shallow water in which the amount of oxygen has been reduced by microbial activity to levels that are too low to support the growth of benthic animals and fish
deep sea	usually considered to be marine waters more than 1000 m deep
denitrification	the reduction of nitrate to nitrogen during anaerobic respiration; decomposition of organic matter by heterotrophic bacteria can lead to the production of the greenhouse gas nitrous oxide
depuration	a method for removing potential pathogens and impurities from shellfish by keeping in circulating UV-treated water
DGGE	denaturing gradient gel electrophoresis; a technique for separating amplified DNA sequences from environmental samples that was widely used for community analysis before the advent of widespread use of high-throughput sequencing
DHA	docosahexaenoic acid; a polyunsaturated long-chain omega-3 fatty acid produced by microalgae, psychrophilic bacteria, and thraustochytrids
diarrhetic shellfish poisoning (DSP)	an intoxication with profuse diarrhea and vomiting caused by eating shellfish that have accumulated okadaic acid and other dinophysiotoxins produced by dinoflagellates
diatoms	a group of photosynthetic unicellular or chain-forming marine and freshwater algal stramenopile protists (microalgae) that are major contributors to primary production
diazocyte	a nitrogen-fixing cell in filamentous cyanobacteria
diazotroph	a microorganism that fixes nitrogen
DIC	dissolved inorganic carbon, in the form of dissolved carbon dioxide, carbonic acid, bicarbonate anion, and carbonate
diel (diurnal) vertical migration	the daily vertical movement over large distances of many motile species of photosynthetic protists, which populate the epipelagic photic zone during the day and migrate to deeper nutrient–rich waters at night, together with associated populations of zooplankton
differentiation	the development of modified cell structures and functions arising by sequential gene expression in response to specific stimuli
DIN	dissolved inorganic nitrogen; nitrate, nitrite, and ammonium
dinoflagellates	unicellular algal protists with two flagella and spinning motion; photosynthetic, phagotrophic, or mixotrophic; many have armored cells; some are important parasites and pathogens
DIP	dissolved inorganic phosphorus; orthophosphate PO43-
diplonemids	a diverse and abundant group of heterotrophic, bacterivorous, euglenid nanoflagellates
disease	a state of disordered physiological responses to internal or external factors
dispersant	a mixture of solvents and emulsifiers used in oil spills that promotes the fragmentation of oil into small droplets
dissolved organic matter (DOM)	an operational definition for the fraction of organic material in seawater that passes through a filter with a pore size of typically 0.22–1.0 µm; DOM is now recognized as containing compounds assembled in colloids and gels, forming a continuum with POM [the related terms DOC, DON, DOP are used for the carbon, nitrogen, or phosphorus components]
diversity index	a quantitative measure of the relative abundance of different types of organism in a community (e.g. species, OTUs, or ASVs) taking account of evenness (Shannon–Wiener index) or dominance, weighted towards the abundance of the most common types (Simpson index)
DMS	dimethyl sulfide; a volatile compound with important effects on climatic processes; produced by the action of a DMSP lyase enzyme from the organic compound DMSP, a major product of marine algae, some bacteria, and corals
DMSP	Dimethylsulfoniopropionate; an organic compound synthesized by marine algae, some bacteria, and corals; its release from phytoplankton supplies a major fraction of the carbon for heterotrophic bacteria and almost all of the sulfur in ocean food webs
DNA vaccination	the direct administration of DNA encoding antigenic proteins into tissue such that the recipient produces an effective immune response
DNA–DNA hybridization (DDH)	method for determining the relatedness of genetic sequences by determining hybridization of single-stranded DNA extracted from two organisms
DNRA	dissimilatory nitrate reduction to ammonium; the result of anaerobic respiration by a range of chemoorganoheterotrophic bacteria, especially in oxygen minimum zones and the upper layer of sediments
dNTP	deoxyribonucleotide triphosphate
DOC	dissolved organic carbon; an operational definition for the fraction of total organic carbon compounds in seawater that passes through a filter with a pore size of typically 0.22–1.0 µm (see DOM)
DOM	dissolved organic matter; an operational definition for the fraction of organic material in seawater that passes through a filter with a pore size of typically 0.22–1.0 µm; DOM is now recognized as containing compounds assembled in colloids and gels, forming a continuum with POM [the related terms DOC, DON, DOP are used for the carbon, nitrogen, or phosphorus components]
DON	dissolved organic nitrogen; an operational definition for the fraction of total organic nitrogen-containing compounds in seawater that passes through a filter with a pore size of typically 0.22–1.0 µm (see DOM)
DOP	dissolved organic phosphorus; an operational definition for the fraction of total organic phosphorus-containing compounds in seawater that passes through a filter with a pore size of typically 0.22–1.0 µm (see DOM)
DPANN	one of the superphyla of the Archaea containing at least 10 major lineages, many of which may be novel obligate symbionts of parasites; the name is an acronym of five of the first groups discovered (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota)
draft genome	a provisional genome sequence compiled from alignment of contiguous nucleotide sequences and assembly into scaffolds, but lacking full detailed annotation of gene function and predicted proteins
DSP	diarrhetic shellfish poisoning; an intoxication with profuse diarrhea and vomiting caused by eating shellfish that have accumulated okadaic acid and other dinophysiotoxins produced by dinoflagellates
dysbiosis	a microbial imbalance in, or on, the body of an animal that may lead to signs of disease

E

ecology	the study of the interrelationships between organisms and their environment
ecosystem engineer	an organism that creates, modifies, maintains, or destroys a habitat; these organisms have a major effect on biodiversity
ecotoxicology	the study of the effects of toxic substances on organisms at the community, ecosystem, and biosphere levels
ectoenzyme	an enzyme secreted to the outside of the cell for the breakdown of high-molecular-weight compounds into monomers that can be absorbed by the cell; this term is sometimes used to distinguish enzymes located on the cell surface from truly extracellular enzymes (exoenzymes)
ectosymbiont	a symbiotic microbe living on the external surface of a host (outside the body)
EhV	Emiliania huxleyi virus
El Niño	extended warming of the central and eastern Pacific that leads to a major shift in ocean currents and weather patterns across the Pacific; occurs at irregular intervals of 2–7 years and often associated with harmful algal blooms or marine disease outbreaks
electron acceptor	a substance that accepts electrons during an oxidation–reduction process
electron donor	a substance that donates electrons during an oxidation–reduction process
electrophoresis	the separation of charged molecules such as nucleic acids or proteins in an electric field
ELISA	enzyme-linked immunosorbent assay; an immunological technique for the detection of antigens or antibodies
emerging diseases	infections that have recently appeared within a population or show a rapid increase in incidence; often caused by previously undetected or unknown agents
endemic	a disease that is naturally present within a human population, involving low numbers of infected individuals (equivalent to epizootic in animals)
endosymbiont	microbe that lives symbiotically within the body of another organism (usually used for intracellular associations)
endotoxin	the lipopolysaccharide of the cell wall of Gram-negative bacteria, responsible for an array of disease signs in vertebrates due to overstimulation of the cytokine system
enrichment culture	the use of particular incubation conditions and culture media to encourage the growth of specific microbes from an environment
enteric viruses	viruses which replicate in the gastrointestinal tract and are the most common cause of gastroenteritis, including seafood-borne infections
environmental genomics	direct extraction and sequencing of nucleic acids from environmental samples, without the need for isolation or culture of the constituent organisms
enzootic	a disease that regularly affects specific animals within a particular region or during a particular season (equivalent to endemic in humans)
epibiont	a symbiotic microbe that lives on the surface of host cells, either within body cavities such as the respiratory or intestinal tract, or on the external surface
epibiotic	microbe that lives on the surface of another organism
epidemic	an outbreak of disease involving an unusually high number of infected persons (the equivalent of epizootic in animals)
epidemiology	the study of the incidence, distribution, and determinants control of diseases and other factors affecting health
epifluorescence light microscopy	method for visualizing bacteria, viruses, and other particles on the surface of a membrane after staining with a fluorochrome, which emits light at a particular wavelength after illumination
epitope	the part of an antigen molecule which is recognized by an antibody
epizootic	an outbreak of disease involving an unusually high number of infected animals (the equivalent of epidemic in humans)
EPS	exopolymeric substances
ESPs	eukaryotic signature proteins; a range of proteins involved in membrane trafficking and production of vesicles thought to be a defining feature of eukaryotic cells, but homologous genes have recently been recognized in Asgard archaea
EST	expressed sequence tag; a short sequence of a transcribed cDNA sequence used in transcriptomic studies
etiology	the specific cause(s) of a disease or condition
ETSP	the Eastern Tropical South Pacific, one of the major permanent open ocean oxygen minimum zones
Eukarya, eukaryotic	Eukarya is the taxonomic name for one of the three domains of life; eukaryotic cells have a membrane-bound nucleus and organelles (the spelling eucaryotic is also used)
euphotic zone	the upper layer of ocean water penetrated by sufficient light of appropriate wavelengths to permit phototrophic metabolism by phytoplankton
Euryarchaeota	one of the major branches of the Archaea, containing many hyperthermophilic and halophilic species
eutrophication	the enrichment of an environment (especially estuaries and coastal waters) by the input of high levels of nutrients (particularly N and P) from terrestrial runoff, encouraging excessive growth of phytoplankton and heterotrophic microbes
Excavata	one of the supergroups of eukaryotic protists, containing a variety of free-living, symbiotic, and parasitic species
exoenzyme	an enzyme secreted to the outside of the cell for the breakdown of high-molecular-weight compounds into monomers that can be absorbed by the cell; this term is sometimes used to distinguish truly extracellular enzymes from those located on the cell surface (ectoenzymes)
exopolymer	a high-molecular-weight polymer excreted by cells; important in the formation of biofilms and in aggregation of particles to form marine snow
exopolymeric substances (EPS)	high-molecular-weight polymers excreted by cells; important in the formation of biofilms and in aggregation of particles to form marine snow
export production	the amount of fixed organic matter produced in the photic zone of the oceans which is exported to deeper waters (carbon flux)

F

FACS	fluorescence-activated cell sorting (or sorter)
facultative	a term used to describe an organism that is capable of a particular mode of life or function, but is not restricted to it (e.g. facultative symbiont, facultative anaerobe)
FAME	fatty acid methyl esters; membrane components whose analysis and identification are important in bacterial identification and classification
FAT	fluorescent antibody technique; an immunological technique for detection of antigens or antibodies
Fatty acid methyl esters (FAME)	membrane components whose analysis and identification are important in bacterial identification and classification
fecal indicator organisms (FIOs)	organisms, most commonly bacteria such as E. coli and enterococci whose presence in environmental samples indicates the presence of contamination by fecal pollution and potential health risks
fecal pellets	particles of undigested and partly digested material excreted by protists and animals, especially zooplankton such as copepods and salps; these form part of the aggregated material in marine snow
fermentation	an energy-yielding process in which the substrate is oxidized without an exogenous electron acceptor; organic molecules usually serve as both electron donors and acceptors
fermentation	energy-yielding process in which the substrate is oxidized without an exogenous electron acceptor; organic molecules usually serve as both electron donors and acceptors
Ferrojan Horse Hypothesis	a hypothesis suggesting that the tail fibers of phages bind to iron-binding sites on host cells
fimbriae (singular, fimbria)	hair-like appendage(s) on the surface of bacterial cells that function in attachment to surfaces; frequently used interchangeably with pili
FIOs	fecal indicator organisms; most commonly bacteria such as E. coli and enterococci whose presence in environmental samples indicates the presence of contamination by fecal pollution and potential health risks
FISH	fluorescence in situ hybridization; in which specific genes of taxonomic or functional significance can be recognized within cells or environmental samples using labeled oligonucleotide probes
flagellates	a general term to describe taxonomically diverse protists that have one or more flagella used for movement and feeding; there are numerous phototrophic, heterotrophic, or mixotrophic species
flagellum (plural flagella)	in bacteria, flagella are multi-protein structures consisting of a helical filament, hook, and basal body that imparts rotary movement by H+ or Na+ ion flow; in eukaryotic organisms, flagella are composed of multiple fibrils and produce motility by a whip-like action
flow cytometry	a method for quantifying and determining the properties of particles passed in a “single-file” flow through a laser beam and detected by their fluorescent properties; cells or viruses are usually tagged with a fluorochrome, which is often attached via specific oligonucleotides or antibodies\
fluorescent antibody technique (FAT)	an immunological technique for detection of antigens or antibodies
food web	a graphical representation to show the interconnections of the feeding relationships of a group of organisms within a community
foraminifera
foundation species	an organism that plays a strong role in structuring a community of other organisms; a decline in abundance due to disease often results in major ecosystem disturbance
Fungi	a monophyletic group of heterotrophic eukaryotes with absorptive nutrition; unicellular (yeasts) or mycelial
fusion protein	a protein produced in genetic modification by joining two or more domains encoded by different genes, so that they are transcribed and translated as a single polypeptide

G

Gaia hypothesis	the concept that temperature, gaseous composition, and oxidation state of the atmosphere, oceans, and Earth’s surface are actively controlled by its living organisms behaving as a system to maintain a stability conducive to the maintenance of life
GC ratio	the percentage of guanine + cytosine base pairs in DNA (mol% GC)
GCAT	glycerophospholipid: cholesterol acyltransferase
gene expression	the transcription of a gene into mRNA, followed by translation into a protein
gene probe	an oligonucleotide sequence used in hybridization methods to detect organisms belonging to a specific group
gene transfer agent (GTA)	a virus-like particle containing fragments of DNA that can provide horizontal gene transfer to other cells, but is not capable of infection
generation time	the time taken for a microbial population to double in size
genome	the complete complement of genetic information in a cell or virus
genome reduction	the evolutionary process, common in intracellular parasites and symbionts, by which microbes lose the genes for metabolic functions that are provided by their host (cf. genome streamlining)
genomic fingerprinting	an approach using a variety of techniques based on PCR amplification and electrophoretic separation of DNA fragments to distinguish closely related individuals based on small differences in DNA sequences
genomic streamlining	a phenomenon in which organisms gain a reproductive advantage by evolving to lose non-essential genes; it is common in planktonic microbes growing in low-nutrient, stable niches with large populations (cf. genome reduction)
genomic taxonomy	a system for the classification and naming of organisms based on comparison of their whole genome sequences
genomics	the study of the molecular organization of genomes and gene products using sequence information in coding and noncoding regions
genotype	the complete genetic description of an organism or virus
GFP	green fluorescent protein
giant virus	a nucleocytoplasmic large DNA virus with exceptionally large genomes and virion size, larger than some bacteria; intracellular parasites of protists
gliding motility	the movement of bacteria over surfaces without involvement of flagella; mechanisms include twitching motility via pili and extrusion of slime
glycocalyx	a layer of interconnected polysaccharides surrounding bacterial cells; important in cell interactions and biofilm formation
GMO	a genetically modified organism; one whose genetic material is altered in a way that does not occur naturally by mating and/or natural recombination
GOS	Global Ocean Survey; one of the pioneer ocean multiple sampling surveys revealing the diversity of marine microbes with metagenomic techniques
Gram-negative	a description of bacterial cells with a complex cell wall composed of a thin layer of peptidoglycan plus an outer membrane containing lipopolysaccharide and lipoprotein; based on staining reaction in the Gram stain
Gram-positive	a description of bacterial cells with a simple cell wall composed mainly of peptidoglycan; based on staining reaction in the Gram stain
grazing	the consumption by phagotrophic protists of bacteria, archaea, and other protists; a key process in marine food webs
greenhouse gases	atmospheric gases including water vapor, CO2, methane, nitrous oxide, and chlorofluorocarbons, which induce a warming of the atmosphere by absorbance and re-emission of infrared radiation while allowing shortwave radiation to pass; elevated levels lead to climate change
Gt	gigatonne, 1015 g (= 1 petagram, Pg)
GTA	gene transfer agent; a virus-like particle containing fragments of DNA that can provide horizontal gene transfer to other cells, but is not capable of infection
GTDB	the Genome Taxonomy Database; a standardized taxonomy for bacteria and archaea based on genome phylogeny
gyre	a large system of circulating ocean currents caused by the Coriolis effect

H

HAB	harmful algal bloom; an unusual, excessive growth of cyanobacteria or algae resulting in toxin production, mortalities to marine life, foaming, harm to human health, or other nuisance effects
halophile	a microbe that requires high levels of sodium chloride for growth
haptophytes	a diverse grouping of photosynthetic protists of major importance in ocean processes, containing one or two plastids, together with the yellow–brown accessory pigments diadinoxanthin and fucoxanthin, with two heterokont flagella in one stage of their life cycle
harmful algal bloom (HAB)	an unusual, excessive growth of cyanobacteria or algae resulting in toxin production, mortalities to marine life, foaming, harm to human health, or other nuisance effects
heat-shock response	the expression of a range of proteins in response to sudden exposure to elevated temperatures or other stressful conditions; the response helps to protect cells from damage
helical symmetry	an arrangement of capsomeres and nucleic acid, which are wound together to form a helical tube-like structures in many viruses (especially RNA viruses)
hemolysin	a microbial toxin causing lysis of red blood cells
hemorrhage	the escape of blood from damaged blood vessels into the body or onto body surface
herd immunity	the resistance within a population to the spread of an infectious disease resulting from a sufficiently high proportion of individuals that are immune to the disease
heterocyst	a differentiated nitrogen-fixing cell formed by cyanobacteria; nitrogenase enzymes are segregated from the generation of oxygen because they are strongly inhibited by its presence
heterokont	a term used to describe motile protists belonging to the Stramenopiles supergroup, with two different morphological types of flagella, one smooth and one tinsellated
heterotroph	the short form of chemoorganotrophic heterotroph; an organism that uses organic compounds as a source of carbon, energy, and electrons
HGT	horizontal gene transfer; the transfer of genes from one independent, mature microorganism to another via physical contact (conjugation), transfer of naked DNA (transformation), phages (transduction), or GTAs (HGT); it can also be referred to as lateral gene transfer (LGT)
high-throughput sequencing (HTS)	methods employing various technologies to obtain very large amounts of genomic data at high speed and relatively low cost
HISH	halogen in situ hybridization; a technique employing halogenated oligonucleotide probes used in nanoSIMS for simultaneous phylogenetic identification of specimens and quantification of metabolic activities of single microbial cells in the environment; e.g. the rare element fluorine is used as a label detected by the mass spectrometer, analogous to the visualization of the fluorescent dye in CARD-FISH
HNLC	high-nutrient, low-chlorophyll; a term used to describe ocean regions in which DIN and DIP are never significantly depleted, yet photosynthetic productivity is very low, due to the low concentrations of available iron
holobiont	an animal or plant host plus its associated microorganisms, considered as an integrated whole, rather than as independent components; an assemblage of different species of organisms that function collectively as an ecological unit (sometimes known as a meta-organism)
hologenome concept	a concept that all the genetic components of a host and its microbial partners must be considered as a unit of natural selection in evolution
homology	the relatedness of gene sequences sufficient to suggest common phylogenetic ancestry
horizontal gene transfer	the transfer of genes from one independent, mature microorganism to another via physical contact (conjugation), transfer of naked DNA (transformation), phages (transduction), or GTAs (HGT); it can also be referred to as lateral gene transfer (LGT)
horizontal transmission (of symbionts)	the process by which free-living microbes are acquired from the environment during the early development of the host, leading to a symbiotic association
HPLC-FLD	high-pressure liquid chromatography fluorescence detection
HPV	hepatopancreatic parvovirus, which causes disease in crustaceans
HRP	horseradish peroxidase; an enzyme cross-linked to oligonucleotide probes used in CARD-FISH; enabling amplification of the fluorescence signal
HTS	high-throughput sequencing; methods employing various technologies to obtain very large amounts of genomic data at high speed and relatively low cost
hydrothermal vent	a fissure in the seabed, from which geothermally heated water enriched with gases and minerals is emitted
hyperinfectious	a term used to describe the adaptation of Vibrio cholerae to the human host, resulting in person-to-person transfer with low infectious doses
hyperpiezophile	a deep-sea organism that displays optimal growth rates at pressures >60 mPa
hyperthermophile	an extremely thermophilic bacterium, with optimum growth >80°C
hyphae	the branching filaments that form the mycelium of a fungus

I

ICOMM	International Census of Marine Microbes
icosahedral symmetry	a geometric shape consisting of 20 triangular faces delimited by 12 fivefold vertexes; in many viruses, the individual capsomere subunits assemble into this structure to form the capsid enclosing the nucleic acid
ICTV	the International Committee on Taxonomy of Viruses
IHHN, IHHNV	infectious hypodermal and hematopoietic necrosis, a disease of crustaceans caused by IHHN virus (IHHNV)
IHN, IHNV	infectious hematopoietic necrosis, a disease of fish caused by IHN virus (IHNV)
Illumina	one of the most widely used high-throughput sequencing technologies, based on reversible dye-terminators that enable the identification of single bases as they are introduced into DNA strands
immunostimulant	a drug or nutrient that stimulates the immune system
in vitro	a controlled procedure or experiment conducted outside of an organism (from the Latin for “within glass”)
in vivo	a controlled procedure or experiment conducted in a whole, living organism
inactivated vaccine	a preparation of virus particles, bacteria, or other pathogens that have been grown in culture and killed, usually with formaldehyde or heat
infectious disease	a condition caused by colonization and replication of a pathogenic microbe within the animal body; usually transmissible from one host to another
Internal transcribed spacer (ITS)	a region of nonfunctional DNA flanked between the highly conserved SSU and LSU rRNA genes; variation in sequences provides valuable information for taxonomy and molecular phylogeny among related species
intracellular pathogen	a disease-causing organism that can survive and replicate inside host cells
Ion Torrent	a cost-effective and rapid high-throughput sequencing technology containing electronic systems combining integrated circuits with metal-oxide semiconductors and transistors that detect the change in potential each time a proton is released after a nucleotide is added during DNA synthesis
IPN (IPNV)	infectious pancreatic necrosis (virus)
IROMPs	iron-regulated outer membrane proteins produced by Gram-negative bacteria; induced in pathogens by reduced iron levels in vivo
iron acquisition	an active mechanism by which ocean microbes and pathogens must obtain iron for cellular processes via a system of membrane proteins for secretion of iron-chelating molecules and their receptors, and/or by surface components that adsorb available iron
iron hypothesis	the hypothesis that the concentration of free iron in oceans plays a major regulatory role in phytoplankton productivity; most offshore waters contain very low levels since they are remote from land masses and so receive low inputs of iron from terrestrial sources
ISA (ISAV)	infectious salmon anemia, a disease of salmonid fish caused by ISA virus (ISAV)
ITS	Internal transcribed spacer; a region of nonfunctional DNA flanked between the highly conserved SSU and LSU rRNA genes; variation in sequences provides valuable information for taxonomy and molecular phylogeny among related species

J

JOD

juvenile oyster disease, caused by Roseovarius crassostreae

K

Kanagawa reaction	a diagnostic reaction using a specialized type of blood agar to detect production of hemolysins by Vibrio parahaemolyticus
kDa	kilodalton; an atomic mass unit equal to 1000 Daltons used to describe the molecular weight of large molecules such as proteins
keystone predator	a species whose decline or removal allows an explosive increase in the prey population, often resulting in loss of biodiversity
kill the winner hypothesis (KtW)	a mathematical model of host-parasite dynamics of bacterial and protist hosts, plus predatory grazing protists in which virulent viruses reduce populations of the most active hosts, leading to maintenance of high diversity
kleptoplastidy	the process by which phagotrophic protists may transiently retain intact functional algal prey or their plastids, enabling them to carry out photosynthesis; also known as acquired phototrophy
Koch’s postulates	a set of principles used as evidence for establishing a microorganism as the causative agent of disease
KtW	kill the winner hypothesis; a mathematical model of host-parasite dynamics of bacterial and protist hosts, plus predatory grazing protists in which virulent viruses reduce populations of the most active hosts, leading to maintenance of high diversity

L

labyrinthulids	a group of saprotrophic protists which glide along a network of filaments produced as extensions of the cytoplasmic membrane, associated with the surface of marine macroalgae and seagrasses
Law of the Minimum	a principle derived from crop sciences by Liebig, holding that growth is not dependent on the total amount of resources available, but by the single resource in shortest supply (the limiting nutrient)
limiting nutrient	the nutrient in shortest supply, the concentration of which limits growth and reproduction of particular types of organisms (includes N, P, Si, and Fe)
lineage	a group of organisms descended from a common ancestor
lipopolysaccharide (LPS)	a complex structure of unusual sugar moieties and lipids which is an integral part of the outer membrane of Gram-negative bacteria; it has endotoxin effects and variation in sugar sequences leads to antigenic variation
live attenuated vaccine	a virus or bacterium in which virulence has been eliminated; used to stimulate immunity against infection
LM	light microscopy, or light micrograph
Lokiarchaeota	a novel phylum of Archaea discovered from gene surveys of marine sediments near hydrothermal vents in the Arctic Ocean thought to be the closest link to the Eukarya
lorica	a shell-like protective outer covering, often reinforced with sand grains, produced by some protists such as tintinnid ciliates and choanoflagellates
LPS	lipopolysaccharide; a complex structure of unusual sugar moieties and lipids which is an integral part of the outer membrane of Gram-negative bacteria; it has endotoxin effects and variation in sugar sequences leads to antigenic variation
LPSN	List of Prokaryotic Names with Standing in Nomenclature; a database of names assigned to Bacteria and Archaea indicating their status as validly published names under the international code of nomenclature
LSMS	liquid chromatography mass spectrometry
LSU	the large subunit of ribosomes, a structure of multiple proteins and ribosomal RNA molecules with a sedimentation coefficient of 60S in eukaryotes and 50S in bacteria and archaea; the sequence analysis of the rRNA is used to provide additional resolution of phylogeny derived from the usual SSU analysis
lysogenic conversion	a modification of the phenotype of a bacterial host by the presence of a prophage, such as the acquisition of virulence factors in vibrios
lysogeny	the incorporation of a phage genome into a bacterial genome so that it replicates without initiating a lytic cycle unless stimulated to do so by inducing conditions
lytic cycle	the most common outcome of infection of microorganisms by viruses, in which the viral nucleic is replicated, progeny virions are assembled and finally released by lysis of the cell

M

M	molar
MABV	marine birnavirus(es); a group of widely distributed disease agents in marine invertebrates and fish
MAG	metagenome assembled genome; a bioinformatic method for assembling short reads of DNA sequences obtained from HTS into contiguous sequences, leading to identification of genes and eventual construction of the entire genome of an organism
MALV	marine alveolates; a major clade (superphylum) of protists including the apicomplexa, ciliates, and dinoflagellates; distinguished by distinctive flagella and flattened vesicles (alveoli) under the membrane, which may form armor plates in the dinoflagellates
MAP	modified atmosphere packaging; the use of finely adjusted blends of gases (usually reduced O2 and high levels of CO2 and N2) within a package to improve the quality and safety of food products
MAR	microautoradiography; a technique to visualize the incorporation of radioactively labeled precursors into cells by overlaying with photographic emulsion
MAR-FISH	a technique combining microautoradiography and fluorescent in situ hybridization; a technique allowing visualization of elemental transformations within cells that can be identified as belonging to a particular taxon
marine snow	oceanic particles composed of aggregated cellular detritus, polymers, and living microbes
mass mortality event	an incident that kills a very large number of a single species in a short period of time
MAST	marine stramenopiles; a designation used to group sequences in metagenomic surveys
Mb	megabase (106 nucleotides)
MBV	monodon baculovirus; a virus causing disease in shrimp and other crustaceans
MCP	major capsid protein
MDS plot	multidimensional scaling plot; a graphical method for visualizing the level of similarity (pairwise distances) of individual data within a dataset, widely used in microbial community analysis
mechanosensory function	a response mechanism to mechanical stimuli; in bacterial motility, the flagellar apparatus detects minute changes in viscosity close to surfaces
membrane filtration	a method using vacuum filtration through small pore membranes (typically 0.22 or 0.45 µm) for enumerating bacteria in water or other liquids (also used to sterilize liquids)
mesocosm	an experimental system holding large volumes of seawater to simulate open-water conditions
mesophile	an organism with an optimum growth temperature of 25–40oC
mesozooplankton	planktonic animals in the size range 0.2–20 mm which graze on protists
meta-analysis	a statistical analysis that combines the results of multiple separate scientific studies
metabarcoding	a major method of assessment of biodiversity from environmental samples using high-throughput DNA sequencing based on detection of short sequences, most commonly from SSU rRNA genes
metabolomics	the systematic study of small molecule metabolites within organisms using chromatographic separation and mass spectrometry
metagenome assembled genome (MAG)	a bioinformatic method for assembling short reads of DNA sequences obtained from HTS into contiguous sequences; leading to identification of genes and eventual construction of the entire genome of an organism
metagenome; metagenomics	the entire genetic complement of all biological entities obtained by direct extraction and sequence analysis of nucleic acids from environmental samples, without the need for isolation or culture of the constituent organisms; the science of obtaining the metagenomes
meta-organism	an animal or plant host plus its associated microorganisms, considered as an integrated whole, rather than as independent components; an assemblage of different species of organisms that function collectively as an ecological unit (more commonly referred to as a holobiont)
metaproteomics	the large-scale study of proteins within a microbial community, usually obtained by electrophoretic separation and mass spectrometry
metatranscriptomics	the large-scale study of gene expression within a microbial community, obtained by sequencing DNA complementary to mRNA
methanogens	a group of strictly anaerobic members of the Archaea that obtain energy by producing methane from CO2, H2, acetate, and some other compounds
methanotrophs	microorganisms which obtain nutrition by oxidizing methane to CO2
methylmercury (MeHg)	a highly toxic form of mercury produced by anaerobic bacterial activity in sediments and oxygen-depleted niches within marine snow aggregates
methylotrophs	a group of aerobic microorganisms that oxidize organic compounds without carbon–carbon bonds, including methanol, methylamine, and sometimes methane, as a sole source of carbon and energy (cf. methanotrophs)
MGNV	midgut gland necrosis virus; a virus causing disease in shrimp and other crustaceans
microaerophile	an organism requiring O2, but a lower concentration than that in air
microalgae	microscopic (mostly unicellular) protists, traditionally classified as algae
microarray	a method for determining gene expression by the binding of mRNA or cDNA from cells to an array of oligonucleotides immobilized on a surface
microbe	in this book, a microbe is defined as any microscopic biological entity, including bacteria, archaea, fungi, protists, and viruses
microbial carbon pump	the process by which the integrated activity of microorganisms and viruses alters the nutrient composition of DOM through sequential transformations, leading to production of refractory DOM recalcitrant to further degradation
microbial fuel cell	a bioelectrical system in which bacteria use an electron donor, while the terminal electron acceptor is a working electrode, resulting in generation of current
microbial loop	the process by which organic matter synthesized by photosynthetic organisms is remineralized by the activity of bacteria, archaea, and protists, enabling reuse of minerals and CO2 by primary producers and other heterotrophs
microbial mat	a complex layered community of microbes on aquatic surfaces, characterized by chemical gradients and associated physiological activities
microbial source tracking	a system for identifying the sources of specific microbial contamination in environmental samples or foods
microelectrodes	electrochemical devices which can be used to measure environmental and chemical changes in microhabitats such as sediments
microfluidics	the manipulation and control of the flow of miniscule volumes of fluids in networks of channels with dimensions from tens to hundreds of micrometers
microorganism	this term is used for all cellular microbes (i.e. excluding viruses)
microplastic	a microscopic or barely visible particle or fiber of plastic; generally defined as <5 mm diameter or length [a recent proposal for standardization recommends a size range of 1 to <1000 µm]
MinION	a device for DNA sequencing using nanopore technology, which can produce long single reads
miTags	metagenomic Illumina tags; multiple small fragments of DNA encoding rRNA that can be assembled into overlapping sequences sufficient for taxonomic characterization of a microbial community
mitochondria	the organelles responsible for electron transport and respiration in eukaryotic cells
mixed layer	the uppermost layer of the ocean, mixed by wind; depth varies in different regions, depending on temperature, upwelling, and seasonal effects containing the surface waters
mixotroph	an organism with a mixed mode of nutrition, combining autotrophic and heterotrophic processes; such as sulfur-oxidizing bacteria that require organic compounds or protists that can feed by both phototrophy and engulfment of prey bacteria
MLST	multi-locus sequence typing; a technique for typing multiple gene loci that is widely used in the study of related bacterial strains
modular enzyme	a large enzyme containing separate protein domains that form independently folding, structurally and functionally distinct units; e.g. polyketide synthase
monophyletic	a lineage of organisms belonging to the same phylogenetic cluster or clade
motility	the movement of a microorganism under its own power
MPN	most probable number; a method for determining the microbial population in a liquid based on statistical probability of growth after inoculation of media with various dilutions of the sample
mRNA	messenger RNA
Mt	megatonne, 1012 g (= 1 teragram, Tg)
MUG	methylumbiliferyl-β-glucuronide
multiplex PCR	a PCR in which multiple primers are used for the amplification of different genes
mutualism	a term used to describe a symbiotic association in which it appears that both partners benefit
mycology	the study of fungi

N

NADPH	nicotinamide adenine dinucleotide phosphate (reduced)
NAG	N-acetyl glucosamine
Nanoarchaeota	one of the phyla of DPANN superphylum of Archaea
nanoflagellates	flagellated protists in the nanoplankton size range
nanoplastics	microscopic particles or fibers of plastic [a recent proposal for standardization recommends a size range of 1 to <1000 nm]
nanoSIMS	a technique of secondary ion mass spectrometry enabling elemental transformations to be monitored at subcellular resolution
nanotechnology	the construction of materials and functional objects assembled from basic molecular building blocks
NASA	National Space and Aeronautics Administration
NCBI taxonomy database	a standard international database of nucleotide sequence data for nomenclature and classification of organisms, operated by the US National Center for Biotechnology Information
NCDLV	nucleo-cytoplasmic large DNA virus
necrosis	the death of cells in a tissue organ due to toxins, injury, or failure of the blood supply
neuston	the organisms associated with the surface film between water and the atmosphere
NGS	next-generation sequencing; an outdated term used when the first methods for mass DNA sequencing were introduced, replacing Sanger sequencing (now replaced by HTS, high-throughput sequencing)
nitrification	the oxidation of ammonia to nitrate by certain chemolithotrophic bacteria and archaea
nitrogen fixation	the conversion of atmospheric nitrogen to ammonia, carried out by cyanobacteria and some other microbes (diazotrophy)
NOAA	National Oceanic and Atmospheric Administration
NSP	neurotoxic shellfish poisoning; a disease condition caused by ingestion of shellfish contaminated with brevetoxin produced by the dinoflagellate Karenia brevis
NTP	nucleotide triphosphate
nucleocapsid	the nucleic acid and protein of a virus particle
Nucletmycea	one of the major divisions of the Eukarya containing the fungi
nutraceutical	a high grade processed and standardized dietary supplement or additive

O

OA	ocean acidification; the increase in the concentration of hydrogen ions (fall in pH) due to absorption of CO2 from the atmosphere
obligate	a term used to describe an organism that is restricted to a particular mode of life or function (e.g. obligate parasite, obligate anaerobe)
ocean acidification (OA)	the increase in the concentration of hydrogen ions (fall in pH) due to absorption of CO2 from the atmosphere
ocean color	the color of ocean regions due to the absorption and scattering of light visualized by remote sensing, which is affected by the density and size distribution of phytoplankton
oligonucleotide	a nucleic acid molecule containing a small number of nucleotides; often referring to a synthetic DNA or RNA strand
oligotrophic	a term used to describe an environment with very low nutrient levels, or an organism adapted to such low- nutrient conditions
OM	outer membrane of Gram-negative bacteria
Omics	a generic term that includes genomics, proteomics, transcriptomics, and metabolomics, techniques involving the collection, analysis, and application of data from biological molecules
OMZ	oxygen minimum zone; in common oceanographic usage this defines the suboxic zone found at intermediate depths (usually 1000–1500 m); more specifically, it defines zones at much shallower depths (typically 50–200 m) with extremely low oxygen concentrations (<5 μM) at their core
ONPG	o-nitrophenol-β-galactopyranoside
open reading frame (ORF)	an arrangement of nucleotides in triplet codons in DNA which does not contain a stop codon; sequences larger than 100 are considered to be potential protein-coding regions
operational taxonomic unit (OTU)	usually interpreted as a proxy term for bacterial and archaeal species; used to distinguish organisms defined on the basis of their SSU rRNA gene sequences (typically, bacteria differing by <3% in sequence identity)
operon	a group of genes transcribed into a single mRNA under regulatory control of the same region of the DNA
Opisthokonta	one of the major divisions of the Eukarya containing the fungal and animal lineages
opportunist(ic) pathogen	a disease-causing microbe that can take advantage of an opportunity to infect and multiply within a host, such as physical injury, reduced immunity or other host defense mechanisms, or disrupted normal microbiota
optical tweezers	a micromanipulation procedure which allows the isolation of individual cells using a highly focused laser beam which provides a force, depending on the relative refractive index between the cell and that of the surrounding medium
ORF	open reading frame
ortholog	a gene found in one organism that closely resembles that in another organism, but separated by speciation
osmoprotectant	a compatible solute accumulated in the cytoplasm to protect cells from loss of water to the external environment
osmotrophy	the feeding mechanism of bacteria, archaea, fungi and a small number of protist groups by absorption of low molecular weight nutrients
OTU	operational taxonomic unit; a pragmatic definition to group organisms by similarity, typically used as a proxy for species of bacteria and archaea in analysis of 16S rRNA gene sequences
oxic	a term used to describe an environment containing oxygen at a concentration high enough to permit aerobic growth and respiration
oxidation	a process in which an element or compound loses electrons or H atoms
oxidation–reduction (redox) reaction	a paired reaction in which one compound is oxidized by losing electrons or hydrogen atoms, and another compound is reduced by acquiring these electrons or hydrogen atoms
oxygen-minimum zone (OMZ)	in common oceanographic usage this defines the suboxic zone found at intermediate depths (usually 1000–1500 m); more specifically, it defines zones at much shallower depths (typically 50–200 m) with extremely low oxygen concentrations (<5 μM) at their core

P

PAGE	polyacrylamide gel electrophoresis; a method for separating large molecules such as nucleic acids and proteins
PAH	polyaromatic hydrocarbon
pandemic	an epidemic disease that spreads to many countries worldwide
pangenome	the full complement of genes within a collection of strains in a species of bacteria or archaea in which there is usually a high degree of variation in gene content; it consists of a core genome (genes present in all strains), a dispensable genome (genes shared by two or more strains), and genes unique to individual strains
paralytic shellfish poisoning (PSP)	a disease condition following the ingestion of shellfish contaminated with saxitoxins and related neurotoxic compounds
parasite	an organism that lives on or within the body of a host for all or most of its life and depends on the host for nutrition and shelter without providing benefits to the host; parasites can have a range of effects ranging from almost harmless to pathogenic
pathobiome	a newly developed concept for the understanding of infectious diseases, recognizing pathogenic agents integrated within the biotic context of the host and other microbiota
pathogen	a microbe that causes disease
pathogenicity	the ability of a microbe to cause disease
pathogenicity island	an acquired region identified in a bacterial chromosome containing a cluster of genes associated with survival in the host and production of disease
PBP	periplasmic binding protein; a protein located between the outer and cytoplasmic membranes of Gram-negative bacteria that enables transport of solutes into and out of the cell
PCA	principal components analysis; a statistical method widely used in community analysis for transforming the number of possible correlated variables in a large dataset into a smaller number that makes it easier to identify the principal components accounting for variance
PCB	polychlorinated biphenyl
PCD	programmed cell death; a developmental process, a sequence of events resulting in the death of a cell akin to "cellular suicide"
PCR	the polymerase chain reaction; in vitro amplification of DNA fragments employing sequence-specific oligonucleotide primers and thermostable polymerases
PDV	phocine distemper virus; a morbillivirus causing epizootics in seals
pelagic	the open sea; also used to describe organisms that occupy this habitat
periplasm	the space between the cytoplasmic membrane and the outer membrane of Gram-negative bacteria
periplasmic binding protein (PBP)	a protein located between the outer and cytoplasmic membranes of Gram-negative bacteria that enables transport of solutes into and out of the cell
PFGE	pulsed field gel electrophoresis; a technique used for separating large DNA molecules
PFU	plaque-forming units; used to enumerate viruses which can be propagated in a cultivated host cell
Pg	petagram, 1015 g (= 1 gigatonne, Gt)
phage	a virus infecting bacteria and archaea
phage immunity	a situation where the presence of a prophage also confers resistance to infection of the host bacterium by viruses of the same type
phage therapy (PT)	the use of lytic phages to attack infectious bacteria, for the treatment or prevention of diseases
phagocytosis	a mechanism involving rearrangement of membranes by which cells engulf and ingest other cells or particles
phagotrophy	the process by which some protists feed by ingestion of particles into vacuoles
pharmaceutical	a compound manufactured for use as a medicinal drug
phenotype	the observable characteristics of a culture organism, such as enzyme activities
phosphatase	an enzyme that degrades organic phosphate molecules, releasing orthophosphate (PO4-)
phosphonate	an organic phosphate compound containing a stable C-P bond, which is generally resistant to degradation
photic zone	the upper layer of ocean water penetrated by light; the term euphotic zone may be used to indicate the depth to which sufficient light of appropriate wavelengths permits phototrophic metabolism by phytoplankton
photoautotroph	an organism that grows using light energy, inorganic compound(s) as a source of electrons and CO2 as a carbon source
photobioreactor	a flow-through transparent glass or plastic columns, panels or tubes exposed to light, used for the culture of phototrophic organisms such as microalgae
photoheterotroph (photoorganotroph)	an organism that grows using light energy for generation of ATP, with organic compounds as its source of carbon
photokinesis	a behavioral response of bacteria; an increase in speed of swimming when moving towards or away from a light source
photophosphorylation	the transfer of light energy for synthesis of energy-rich bonds in ATP
photoreactivation	a DNA repair process in which pyrimidine dimers are excised by an enzyme activated by blue light
photosynthesis	the use of light as a source of energy in reactions for the synthesis of ATP and the incorporation of CO2 into organic compounds
photosystem	a functional and structural unit composed of protein complexes and pigments that carries out absorption of light and the transfer of energy and electrons
phototaxis	the movement of a microorganism towards light
phototrophy	use of light as a source of energy for metabolism
phycodnaviruses	a major group of viruses infecting eukaryotic phytoplankton
phycotoxins	algal toxins
phylogenetic classification	a system of classification based on the genetic relatedness and evolutionary history of organisms, rather than similarity of current characteristics
phylogenetic tree	a branching graph or diagram showing the quantitative evolutionary relationships between a group of organisms
phylosymbiosis	a correlation between host phylogenetic relationships and composition of the microbial community
phylotype	a unique sequence of a marker gene in microbial community analysis
phytochelatins	algal compounds that store trace metals
phytoplankton	all free-floating photoautotrophic organisms, including diatoms, dinoflagellates, prymnesiophytes, picoeukaryotes, and other protists, together with cyanobacteria
picoeukaryotes	autotrophic, heterotrophic, and mixotrophic protists in the 0.2–2.0 μm size range (many studies use 0.3 μm as the lower size threshold)
picophytoplankton	photoautotrophic planktonic microbes (cyanobacteria and protists) in the 0.2–2.0 μm size range (many studies use 0.3 μm as the lower size threshold)
picoplankton	planktonic microbes in the 0.2–2.0-μm size range (bacteria, archaea, and some flagellates)
piezophile	a deep-sea organism that displays optimal growth rates at pressures >30 mPa
piezotolerant	the ability of many marine microbes to grow at a wide range of pressures up to 30–40 mPa, with optimum growth rates usually <20 mPa
pili (singular, pilus)	hair-like appendages on the surface of bacterial cells; various kinds function in attachment to surfaces (also known as fimbriae), twitching motility (type IV pili), or bacterial conjugation (sex pili)
plankton	a general term for organisms (mainly microscopic) that float or drift freely in water and are unable to swim against a current
plaque assay	a method for enumerating infective virus particles by counting zones of lysis caused by a virus on a lawn culture of cells
plasmid	a double-stranded DNA molecule in bacteria and archaea that carries genes for specialized functions; it is not part of the chromosome and replicates independently
polymerase chain reaction (PCR)	the in vitro amplification of DNA fragments employing sequence-specific oligonucleotide primers and thermostable polymerases
polymicrobial disease	a disease resulting from simultaneous or sequential infection by multiple microbes
polyphyletic	a term used to describe lineages of organisms belonging to different phylogenetic clusters or clades
polysaccharide	a chain of sugar molecules linked by glycosidic bonds
POM	particulate organic material; defined operationally as material retained by fine pore filtration (typically >0.45 µm); now recognized as containing compounds assembled in colloids and gels, forming a continuum with DOM
POP	persistent organic pollutant
ppm	parts per million
prebiotic	a non-digestible food ingredient that promotes the growth of beneficial microorganisms in the intestines
primary production	the production of organic compounds by autotrophic processes of CO2 fixation in the oceans; it can be defined as either gross (total biomass) or net (gross production less the respiration rate of producing organisms)
primary productivity	the rate of production of organic compounds by autotrophic processes of CO2 fixation in the oceans
primer	a short sequence of DNA (oligonucleotide) required for the initiation of DNA synthesis of a specific gene in PCR amplification
principal components analysis (PCA)	a statistical method widely used in community analysis for transforming the number of possible correlated variables in a large dataset into a smaller number that makes it easier to identify the principal components accounting for variance
probiotic	a live microbial feed supplement that stimulates animal health by inducing beneficial changes in the intestinal microbiota
programmed cell death (PCD)	a developmental process, a sequence of events resulting in the death of a cell akin to "cellular suicide"
prokaryotes	a widely used term to describe organisms whose cells lack a true membrane-bound nucleus, i.e. members of the Bacteria and Archaea; the term is not used in this book, which encourages recognition that these are separate domains with very different properties and evolutionary history
prokaryotic	a term used to describe cells that lack a true membrane-bound nucleus
prophage	the genome of a temperate virus when it is integrated into the host genome
prophylaxis	the prevention of disease
protective antigen	a microbial protein or polysaccharide substance that elicits an immune response that provides protection against infection
proteomics	the analysis of the complete protein content of a cell using two-dimensional electrophoresis, mass spectrometry, and other techniques
proteorhodopsin	a light-sensitive proton-transport membrane protein that is widely found in various groups of planktonic bacteria and archaea
protists	a term used to include simple, usually unicellular eukaryotic microorganisms traditionally classified as algae or protozoa; the term is sometimes used more broadly to include macroscopic algae
proton motive force (PMF)	a source of energy that results from the separation of H+ from OH- ions across a membrane, creating an electrochemical potential that can be used for chemical, osmotic, or mechanical functions
protozoa	the traditional, outdated name for a polyphyletic group of unicellular protists that lack cell walls and usually feed by phagotrophy (some are mixotrophic)
PS	(1) photosystem, a functional and structural unit composed of protein complexes and pigments that carries out absorption of light and the transfer of energy and electrons; or (2) polystyrene
pseudogene	a sequence of a genome that is a defunct relative of a functional gene; often formed during adaptation of a bacterium to pathogenicity in a specific host
pseudolysogeny	a form of viral infection in which phage nucleic acid remains in the host cell for an extended period without initiating a lytic cycle
PSP	paralytic shellfish poisoning; a disease condition following the ingestion of shellfish contaminated with saxitoxins and related neurotoxic compounds
PSTs	paralytic shellfish toxins; saxitoxins and related compounds produced by dinoflagellates
psychrophile	a microbe adapted to low temperatures, with an optimum growth temperature <15°C
psychrotolerant	the ability of a microbe to grow at temperatures at low temperatures, but showing optimal growth at >20°C
PT	phage therapy; the use of lytic phages to attack infectious bacteria, for the treatment or prevention of diseases
PUFA	polyunsaturated fatty acid
pycnocline	a zone having a marked change in density of water as a function of depth
PyMS	pyrolysis mass spectroscopy; a technique that creates a chemical fingerprint of the whole organism, used in microbial identification

Q

Q-PCR	quantitative (real-time) polymerase chain reaction; a method for diagnostic detection of microbes in the environment and tissues
QQ	quorum quenching; a process of disrupting bacterial quorum sensing signaling by degrading inducer molecules or blocking their receptors
QS	quorum sensing; a mechanism of regulating gene expression in bacteria depending on secretion and sensing of inducer molecules within a population; when these reach a certain critical level, the bacteria will express specific genes
quorum quenching (QQ)	a process of disrupting bacterial quorum sensing signaling by degrading inducer molecules or blocking their receptors
quorum sensing (QS)	a mechanism of regulating gene expression in bacteria depending on secretion and sensing of inducer molecules within a population; when these reach a certain critical level, the bacteria will express specific genes

R

radioisotope	an unstable isotope of an element that decays or disintegrates spontaneously, emitting radiation; compounds labeled with 14C, 3H, 32P, or 35S are commonly used to study metabolic pathways and the rate of reactions
radiolarians	unicellular, phagotrophic protists with cells producing intricate silica skeletons
RAPD	random amplified polymorphic DNA, a PCR technique using several short primers with the aim of amplifying a large number of different sequences from a genomic template which can be separated by electrophoresis; the technique is valuable as a rapid method of comparing multiple bacterial strains
rare biosphere	a term used to describe the large number of microbial species on Earth that are present at very low abundance
RDOM	recalcitrant DOM; dissolved organic matter which has been modified by the integrated activity of microorganisms and viruses through sequential transformations, which may persist for hundreds or thousands of years in the deep ocean; also known as refractory DOM
reactive oxygen species (ROS)	unstable derivatives of oxygen (free radicals) that react avidly with molecules in the cell
recalcitrant DOM (RDOM)	dissolved organic matter which has been modified by the integrated activity of microorganisms and viruses through sequential transformations, which may persist for hundreds or thousands of years in the deep ocean; also known as refractory DOM
recombinant DNA technology	the insertion of a gene into a cloning vector such as a plasmid and transfer into another organism to produce a recombinant molecule (genetic engineering)
red tide	a bloom in which water is discolored due to excessive growth of pigmented algae; these are frequently harmful due to depletion of oxygen and production of toxins
Redfield ratio	the relatively constant proportions maintained between the elements C, N, P, and O taken up during synthesis of cellular material by marine organisms and released by subsequent remineralization
redox reaction	a paired reaction in which one compound is oxidized by losing electrons or H atoms, and another compound is reduced by acquiring these electrons or H atoms
reductive tricarboxylic acid (rTCA) cycle	reductive (or reverse) tricarboxylic acid (rTCA) cycle, in which CO2 is fixed in many chemoautotrophs
regulon	a set of multiple genes which are regulated by a master gene in response to a single stimulus
remote sensing	the collection and interpretation of information about an object without being in physical contact; it usually refers to measurement of physical and chemical properties of the oceans via instruments carried on aircraft or orbiting satellites
rep-PCR	a simple and rapid PCR method for comparing microbial strains, based on the fact that bacterial DNA naturally contains interspersed repetitive sequences; after amplification, bands can be separated by electrophoresis
reservoir (of infection)	a secondary host or environmental niche in which an infectious microbe can survive and possible multiply
respiration	the energy-yielding metabolic process in which the substrate is oxidized by transfer in an electron transport chain to an exogenous terminal electron acceptor such as O2, nitrate, or certain organic compounds, leading to production of ATP
RFLP	restriction fragment length polymorphism; a method for comparing microbial strains involving the cutting of genomic DNA with a combination of restriction endonucleases and separating the fragments according to size by gel electrophoresis
Rhizaria	one of the protist supergroups containing radiolarians and foraminifera, characterized by an amoeboid body form with pseudopodia used for locomotion and feeding
rhodopsin	a protein covalently bound to a carotenoid pigment, retinal, which absorbs light and generates a proton motive force for the production of ATP
ribotyping	the identification of microorganisms by analysis of DNA fragments produced by restriction enzyme digestion of rRNA genes
richness	a simple measure of diversity which counts the number of species in a sample
RNA	ribonucleic acid
ROD	Roseovarius oyster disease
ROS	reactive oxygen species; unstable derivatives of oxygen (free radicals) that react avidly with molecules in the cell
ROV	remotely operated vehicle
rRNA	ribosomal RNA
rRNA analysis	the analysis of the nucleotide sequence of ribosomal RNA molecules or (more usually) of the genes that encode them, together with noncoding spacer regions; the most common method used in microbial phylogenetic classification and diversity studies
rTCA cycle	the reductive or reverse TCA cycle; a sequence of metabolic reactions used for CO2 fixation by many autotrophic bacteria and archaea
RTN	rapid tissue necrosis; a disease of corals
RT-PCR	reverse transcriptase PCR; a method for detecting gene expression by quantifying messenger RNA; a complementary copy (cDNA) of the mRNA is made with the enzyme reverse transcriptase
RuBisCO	ribulose bisphosphate carboxylase; the key CO2-fixing enzyme found in many autotrophic organisms
RUBP	ribulose bisphosphate
rusticles	porous, fragile aggregations of rust similar to a stalactite or icicle formed by microbial corrosion of iron in deep water

S

S	Svedberg unit
SA	surface area
SAD	species abundance distribution; a graphical plot of the number of species in a sample (richness) against the number of individual organisms collected
SAG	single (cell) amplified genome; the assembled genome of a single cell isolated from the environment obtained by whole genome amplification using a phage DNA polymerase, providing enough DNA for use in high-throughput sequencing
saprotrophy	a term used to describe the nutrition of chemoheterotrophic fungi and bacteria, which feed by absorbing the small molecules produced extracellular enzymes that digest organic material
saxitoxins	a class of toxins produced by dinoflagellates responsible for paralytic shellfish poisoning
SBP	sphingolipid biosynthesis pathway
scaffold	in metagenomics, a portion of the genome sequence reconstructed from end-sequenced whole-genome shotgun clones comprising contiguous sequences (contigs) and gaps
SCG	single cell genomics; a method for obtaining the genome sequence from an isolated individual microbial cell using whole genome amplification and high-throughput sequencing of the DNA
scombroid fish poisoning	an allergic-like response to the ingestion of scombroid fish in which histidine in the tissue has been converted by post mortem bacterial activity to histidine
SCUBA	self-contained underwater breathing apparatus
SDS-PAGE	sodium dodecyl sulfate polyacrylamide electrophoresis; a technique for separation of proteins
SeaWiFs	Sea-viewing Wide Field-of-view Sensor; a NASA satellite-borne sensor that measured ocean color and other parameters from 1997–2010
secondary endosymbiosis	a likely explanation for the origin of the chloroplast in stramenopiles, thought to have arisen 700–1200 MYA, through engulfment of a red alga ancestor by a heterotrophic eukaryote
SEM	scanning electron microscopy
sense (of RNA viruses)	a term used to indicate the coding potential of the genome of single-stranded RNA viruses; a positive-sense RNA genome can serve as mRNA directly, whereas negative-sense RNA must first be converted to a complementary mRNA by RNA-dependent RNA polymerase
septicemia	an infection leading to massive entry of bacteria in the bloodstream, accompanied by toxins and adverse immunological reactions that may progress to septic shock
shotgun sequencing	the random sequencing of DNA from small fragments of a genome followed by assembly of contiguous sequences (contigs) to reconstruct the genome sequence
siboglinids	a family of polychaete annelid tubeworms which have no mouth, gut, or anus in their adult form and are dependent on chemolithotrophic symbiotic bacteria for their nutrition
siderophore	organic molecule excreted by bacteria, which complexes with iron in the environment and transports it into the cell
signature sequence	an oligonucleotide sequence (commonly in rRNA) that characterizes a particular group of organisms and is used to design gene probes
silicification	the process of assembling a silica cell wall or skeleton in diatoms and radiolarians
SIMS	secondary ion mass spectrometry
single (cell) amplified genome (SAG)	single (cell) amplified genome; the assembled genome of a single cell isolated from the environment obtained by whole genome amplification using a phage DNA polymerase, providing sufficient DNA for use in high-throughput sequencing
single cell genomics (SCG)	a method for obtaining the genome sequence from an isolated individual microbial cell using whole genome amplification and high-throughput sequencing of the DNA
singleton	in DNA sequencing, a sequence that has only a single representative in a dataset, often removed in earlier sequencing projects to simplify comparison between samples (unnecessary with modern algorithms)
SIP	stable isotope probing; the analysis of “heavy” and “light” forms of an element used to distinguish biological from purely geochemical processes; for example, by measuring the ratio of 13C:12C or 34S:32S in organic material
S-layer	a paracrystalline layer of protein subunits found on the surface of many bacterial cells and the main type of cell wall in archaea
smart packaging	packaging used for fish and other foodstuffs which incorporates biochemical or electronic sensors to provide a visual indicator of freshness and safety
SML	surface microlayer; the biofilm-like interface between the ocean surface and the atmosphere
SMRT	small molecule, real time; a DNA sequencing technology using arrays of fabricated nanostructures
SMV	spawner mortality virus; a virus infecting crustaceans
solubility pump	the ocean process that produces a vertical gradient of dissolved inorganic carbon due to increased solubility of CO2 in cold water; deep water with high carbon content is formed in high latitudes and is transported by deep ocean currents with upwelling at low latitudes
Southern blotting	a technique for transferring denatured DNA fragments from an agarose gel to a nitrocellulose sheet for identification using a hybridization probe
species	in microbiology, a monophyletic group whose properties can be distinguished from those of other species by multiple criteria, i.e. a collection of strains that share many relatively stable common properties but differ significantly from other collections of strains; in eukaryotic microbes, morphological features and sexual reproduction are important features
species abundance distribution (SAD)	a graphical plot of the number of species in a sample (richness) against the number of individual organisms collected
specific pathogen-free (SPF)	a term used for animals or animal products that are guaranteed free of a particular pathogen; especially important for the control of aquaculture diseases
SPF	specific pathogen-free; a term used for animals or animal products that are guaranteed free of a particular pathogen; especially important for the control of aquaculture diseases
SRB	sulfate-reducing bacteria; bacteria able to use sulfate or elemental sulfur as a terminal electron acceptor during anaerobic respiration
SST	sea surface temperature
SSU	the small subunit of ribosomes, a structure of multiple proteins and ribosomal RNA molecules with a sedimentation coefficient of 40S in eukaryotes and 30S in bacteria and archaea; sequence analysis of the rRNA molecules is used to provide evidence of phylogeny
stable isotope analysis (or probing, SIP)	the analysis of “heavy” and “light” forms of an element used to distinguish biological from purely geochemical processes; for example, by measuring the ratio of 13C:12C or 34S:32S in organic material
strain (of bacteria)	a population descended from an isolate in pure culture
stramenopiles	one of the major supergroups of protists, also known as the heterokonts, encompassing a wide diversity of phototrophic, heterotrophic, and mixotrophic forms characterized by a tinsellated “hairy” flagellum and the presence of membrane systems indicating secondary endosymbiosis during evolution; major groups include the diatoms, chrysophytes, phaeophytes, and oomycetes
stratification	an ocean phenomenon when water with different properties such as salinity, density, and temperature form layers, which act as barrier for passive mixing of the water; increasing stratification is one consequence of rising global temperatures
suboxic	a term used to describe an environment containing a low level of dissolved oxygen (<20 μM); usually referring to the base of the photic zone or a layer occurring at intermediate depths (usually 1000–1500 m)
sulfate-reducing bacteria (SRB)	bacteria able to use sulfate or elemental sulfur as a terminal electron acceptor during anaerobic respiration
supergroup or superphylum	a taxonomic grouping (clade) of phyla, used in some classification systems for protists and archaea
surface microlayer (SML)	the biofilm-like interface between the ocean surface and the atmosphere
SWI	sediment-water interface
Symbiodiniaceae	a newly designated family of dinoflagellates created from reclassification of clades within the genus Symbiodinium, many of which form symbioses with marine invertebrates and protists
symbiosis	living together; a close association of two different organisms, usually interpreted as mutualism where both partners appear to gain benefit
syndrome	a collection of characteristic signs and disease lesions associated with a specific cause
syntrophy	a cooperative association between microbes in which the growth of one or both partners depends on the provision of nutrients or growth factors from the activities of the other
systematics	the study of the diversity and relationships of organisms, including their taxonomy and phylogeny

T

T3SS	type III secretion system; a cellular structure produced by some pathogenic bacteria, which functions like a molecular syringe to deliver toxins and other molecules into host cells
T6SS	type VI secretion system; a cellular structure produced by Vibrio spp., which functions like a molecular syringe whose primary function is to deliver effector molecules that kill other bacteria in the environment
TACK	a superphylum in the domain Archaea, containing the phyla Thaumarchaeota, Aigarchaeota, Crenarchaeota, and Korarchaeota
taxon (plural taxa)	a group of one or more populations of an organism considered to be a unit in a classification system because they are phylogenetically related and share common characteristics
taxonomy	the process of classifying and naming organisms and viruses according to prescribed rules appropriate to the different microbial groups
TBT	tributyl tin; a now banned component of antifouling paints with severe environmental effects
TCA cycle	tricarboxylic acid cycle; a series of metabolic reactions in which a molecule of acetyl CoA is completely oxidized to CO2, generating precursors for biosynthesis and NADH and FADH2, which are oxidized in the electron transport chain; also known as the Krebs cycle and citric acid cycle
TCBS	thiosulfate-citrate-bile-sucrose; an ingredient of selective media for cultivation of vibrios
TCP	toxin co-regulated pili; a major virulence factor of Vibrio cholerae
TDH	thermostable direct hemolysin; a virulence factor of Vibrio parahaemolyticus
TEM	transmission electron microscopy
temperate phage	a phage that causes the infected bacterium to enter a lysogenic cycle; usually by integration of the phage genome into the host bacterium’s chromosome
TEP	transparent exopolymer particles; gel-like transparent, sticky particles formed from acidic polysaccharides that are important in formation of aggregates and links between the ocean surface and atmospheric processes
tetrodotoxin (TTX)	a potent neurotoxin associated with Fugu fish poisoning, believed to be of microbial origin
Tg	teragram, 1012 g (= 1 megatonne, Mt)
TGGE	temperature gradient gel electrophoresis; a technique for separating amplified DNA sequences from environmental samples that was widely used for community analysis before the advent of widespread use of high-throughput sequencing
Thaumarchaeota	one of the major phyla of the domain Archaea
thecae	the armored cellulose plates characteristic of many dinoflagellates
thermocline	the boundary layer in ocean water separating water of different temperatures
thermophile	an organism that grows above 55–60°C
thiotroph	a chemolithoautotrophic microbe that uses sulfur or reduced sulfur compounds as a source of reducing power
thraustochytrids	a group of protists which feed by osmotrophy, producing a slime net containing multiple extracellular enzymes for digestion of organic compounds; widely distributed in coastal and open ocean waters at low densities
tintinnids	a group of voracious bacterivorous ciliates characterized by production of a lorica, a shell-like protective outer covering, often reinforced with sand grains
Tm	the "melting point" of DNA; the specific temperature at which strands of the double helix dissociate, dependent on the ratio of GC:AT bases
toxin	a substance produced by microorganisms that induces host damage
transcriptome	the total set of mRNA molecules expressed from the genes of an organism
TRFLP	terminal restriction fragment length polymorphism; a PCR method in which DNA from a mixed community is amplified and cut with restriction enzymes, resulting in fragments that can be separated by gel electrophoresis to indicate community diversity
TRGs	toxin-related genes; a set of genes found in symbionts of invertebrates that are similar to genes encoding toxins in animal pathogens
TRH	thermostable related hemolysin; a possible virulence factor of Vibrio parahaemolyticus
tRNA	transfer RNA
trophosome	the trunk of tubeworms, containing symbiont-filled bacteriocytes and an extensive blood supply
TSV	Taura syndrome virus; a virus infecting crustaceans
TTX	tetrodotoxin; a potent neurotoxin associated with Fugu fish poisoning, believed to be of microbial origin
TVB-N	total volatile base nitrogen; ammonia, trimethylamine, and other volatile nitrogenated bases produced during decomposition of fish; it is measured as an indicator of freshness and quality of fish
twitching motility	a jerky movement of bacterial cells on surfaces generated by type IV pili
two-component regulatory system	a system comprising a sensor kinase protein in the membrane that becomes phosphorylated in response to an external signal and passes the phosphoryl group (directly or via a cascade mechanism) to a response regulator protein, which usually affects transcription of specific genes (in bacterial chemotaxis there is a direct effect on flagellar motility)
type III secretion system (T3SS)	a cellular structure produced by some pathogenic bacteria, which functions like a molecular syringe to deliver toxins and other molecules into host cells
type species	the species of bacterium or archaeon on which the genus and higher taxa are based and for which cultures are deposited in international culture collections for reference purposes
type VI secretion system (T6SS)	a cellular structure produced by Vibrio spp., which functions like a molecular syringe whose primary function is to deliver effector molecules that kill other bacteria in the environment

U

ultramicrobacteria	a term used to describe very small bacteria (~0.2 μm diameter) occurring naturally in seawater or formed by miniaturization under low-nutrient conditions
upwelling	the upward motion of deep water, driven by effects of winds, temperature, and density, bringing nutrients to the upper layers of the ocean
USEPA	United States Environment Protection Agency
UV	ultraviolet

V

V	volume
vaccination	the administration of antigenic material (a vaccine) to stimulate the immune system to develop adaptive immunity to a pathogen
VBNC	viable but nonculturable; a term used to describe a physiological state in which it is not possible to culture an organism on media that normally supports its growth, although cells retain indicators of metabolic activity
vector	an organism that carries pathogens from one host to another
vertical migration	the diel (or diurnal) migration of motile phytoplankton such as dinoflagellates and diatoms (together with associated zooplankton) to and from the well-lit surface waters in the day to deeper waters at night
vertical transmission	the direct transmission of symbionts from adult hosts to their progeny, usually via the eggs
VHML	a phage (myovirus) infecting Vibrio harveyi
VHS; VHSV	viral hemorrhagic septicemia, a disease of fish; VHS virus
viable but nonculturable (VBNC)	a term used to describe a physiological state in which it is not possible to culture an organism on media that normally supports its growth, although cells retain indicators of metabolic activity
vibriophages	phages that infect Vibrio spp.
vibrios	the colloquial term for members of the family Vibrionaceae
viral eukaryogenesis hypothesis	the proposal that the first eukaryotic cell was a multimember consortium consisting of a viral ancestor of the nucleus, an archaeal ancestor of the eukaryotic cytoplasm, and a bacterial ancestor of the mitochondria
viral shunt	the mechanism by which viral lysis of cells results in recycling of nutrients in microbial loop processes, resulting in retention of nutrients for heterotrophic metabolism and lessening transfer to other trophic levels
viral shuttle	a recent extension of the viral shunt concept, due to recognition that viral lysis of host cells leads to release of polymers that form aggregates which accelerate carbon export via the biological pump
virion	the extracellular particle form of a virus; the nucleic acid enclosed in protein
virion factory	a large organelle-like inclusion formed in cells infected by NCDLVs, in which viral replication and assembly takes place
virocell	a term used to describe a cell (a bacterium, archaeon, or eukaryote) that has been transformed by viral infection so that its major function becomes the propagation of viral genes, rather than cell division; this concept recognizes this as the living form of the virus
virome	a viral metagenome; the entire complement of all viral genes collected from a particular environment
virulence	the degree of pathogenicity of a microorganism as indicated by the production of disease signs
virulence factor	a molecule produced by a pathogenic microbe that enables colonization and replication within a host, resulting in damage
virus	a biological entity containing either DNA or RNA that can only replicate inside living cells as an obligate intracellular parasite
virus decay	the decline in numbers of viruses observed over time in seawater in the absence of new viral production, due mainly to inactivation by visible and UV light
virus dilution (reduction) method	a method to quantify the production of viruses in seawater removing free VLPs by filtration and measuring the production of new particles by epifluorescence or flow cytometry
VLP	virus-like particle(s); structures recognized by transmission electron microscopy or flow cytometry as having the characteristic morphology of virions, but which cannot be designated as viruses because these methods cannot show if they are infectious
VPI	Vibrio pathogenicity island; a genomic region in Vibrio cholerae containing the genes encoding toxin co-regulated pili

W

w/v	weight per volume
WBD	white band disease of corals
WGS	whole genome shotgun sequencing
whale falls	a term used to describe sites where the carcasses of whales have sunk to the ocean floor, depositing large amounts of organic matter, which supports diverse microbial and animal communities
whale pump	a term used to describe the periodic deposition of large amounts of organic carbon to the ocean floor by the sinking of whale carcasses
WHO	World Health Organization
Winogradsky column	a glass column packed with sediment and overlaid with seawater to mimic a natural community for the enrichment of different microbial species
WPD	white plague disease of corals
WS	white syndrome of corals
WSSV	white spot syndrome virus (Whispovirus), which causes a disease of prawns

X

xanthophylls	yellow-brown carotenoid pigments, especially prominent in dinoflagellates
xenobiotic	an artificial synthetic compound that does not occur naturally
xenophyophores	foraminifera found on the sea floor with cytoplasmic spines for prey capture; these can reach very large sizes and high densities on sea mounts and trenches beneath productive waters, with aggregates of waste material

Y

yeasts

unicellular fungi

Z

zoonosis	a disease generally associated with animals that can be transmitted to humans
zooplankton	free-floating small animals and non-photosynthetic protists
zooxanthellae	the dinoflagellates (family Symbiodiniaceae) present as intracellular symbionts of many corals, clams, jellyfish, and other marine invertebrates, named for their golden-brown color due to xanthophyll pigments