Glossary of microbial genera and species
Browse through the list to find information about microbial genera and species mentioned in the book. Important: please read the explanatory notes for guidance below.
You can also revise each chapter and test your knowledge of these names with our glossary flashcards.
NOTES FOR GUIDANCE
- The glossary entries briefly describe key features of each genus or species of microorganism or virus mentioned in the book, together with its taxonomy derived from the NCBI Taxonomy Browser (for eukaryotic microbes, bacteria, and archaea) and the ICTV website for viruses.
- In keeping with the convention used in the textbook, only genus and species names are italicized.
- The higher taxa for each organism or virus are listed using the abbreviations: d_domain; k_kingdom; p_phylum; c_class; o_order; f_family; g_genus. Sub divisions, where used, are prefixed by s, such as sp_, sc_, sf_ etc.
- The names of many protist groups do not have formal status; these are shown as “no rank” (nr_).
- Bacteria and archaea which have not been fully characterized according to the Nomenclature Code are shown as Candidatus status. To facilitate searching, they are listed alphabetically in the form “Genus species” (Candidatus species).
- Classification of all microbial groups is undergoing major revision due to application of phylogenetic and genomic approaches, as discussed in the text. Bacteria and archaea—changes in taxonomy according to the new Genomic Taxonomy Database (GTDB) are shown in the list. Also check the List of Prokaryotic Names with Standing in Nomenclature (LPSN). Eukaryotes—see Adl et al. (2018) for proposed revisions. Viruses—check the International Committee on Taxonomy of Viruses (ICTV website).
- The World Register of Marine Species (WoRMS) is an authoritative database of names of all marine organisms.
- For many genera and taxa, the origin of the name is shown, with etymology from Greek (Gr.) or Latin (L.) sources.
Acanthamoeba polyphaga |
A widely distributed, free-living amoeba found in soils, sediments, and seawater which feeds on bacteria, yeast, and microalgae, with an important role in secondary decomposition of organic materials. Important as the host of Mimivirus and related giant viruses. Occasionally pathogenic to immunocompromised humans and a common cause of eye infection due to contaminated contact lens solutions. |
Aerococcus viridans |
A genus of Gram-positive cocci characterized by tetrad clusters of four cells; the causative agent of gaffkemia disease of lobsters. |
Aeromonas |
A genus of heterotrophic, Gram-negative, rod-shaped bacteria widely distributed in wastewater and sewage; can cause infections associated with recreational use of seawater. |
Aeromonas hydrophila |
A heterotrophic, Gram-negative, rod-shaped bacterium mainly found in fresh or brackish water. Possesses many degradative enzymes. Can be pathogenic for fish and humans. |
Aeromonas salmonicida |
A heterotrophic, Gram-negative, rod-shaped bacterium mainly found in fresh or brackish water. Possesses many virulence mechanisms. Subspecies salmonicida is an important pathogen of salmonid fish (subspecies achromogenes, masoucida, pectinolytica, and smithia infect other fish species). |
Agarivorans |
A genus of agarolytic Gram-negative chemoheterotrophs, frequently isolated from seawater and the surface of seaweeds. |
Alcaligenes |
Alcaligenes |
Alcanivorax |
A genus of alkane-degrading bacteria which are dominant in regions surrounding oil seeps and become dominant following oil spills. |
Alexandrium |
A genus of photosynthetic and mixotrophic dinoflagellates, characterized by morphology of the thecal plates, and recently by phylogenetic methods into several clades. Several species, notably A. tamarense and A. catanella, form saxitoxin-producing blooms in nutrient-rich areas that may lead to paralytic shellfish poisoning, mainly via bivalve molluscs. |
Algimonas |
A stalked bacterium commonly attached to the surface of seaweeds, dividing by unequal cell division of an attached sessile cell to produce a flagellated motile stage. |
Aliivibrio fischeri |
A motile (with polar flagellum), heterotrophic, curved, rod-shaped bacterium found globally in marine environments. Bioluminescent. Symbiotic with marine animals, notably the bobtail squid. Formerly classified as Vibrio fischeri and this name is still used in many articles. |
Aliivibrio salmonicida |
A Gram-negative, facultatively anaerobic chemoorganotroph; the causative agent of cold-water vibriosis of fish (Hitra disease). |
Allohahella |
A genus of facultatively anaerobic psychrophilic and mesophilic bacteria isolated from various marine habitats. |
Alternaria |
A large genus of universally distributed ascomycete fungi, mainly saprobic with some major plant pathogens. Can cause opportunistic infections in immunocompromised humans. |
Alteromonas |
A large genus of Gram-negative, motile bacteria with a single polar unsheathed flagellum. Chemoorganotrophic, aerobic with strictly respiratory metabolism using oxygen as the terminal electron. Widely distributed in seawater and in association with marine organisms. |
Aquifex aeolicus |
A rod-shaped, chemolithoautotrophic, hyperthermophilic bacterium found near underwater hydrothermal vents, volcanoes, and hot springs. Highly reduced genome. Thought to be one of the earliest evolving bacteria. |
Aquifex pyrophilus |
A rod-shaped, chemolithoautotrophic, hyperthermophilic bacterium found near underwater hydrothermal vents, volcanoes, and hot springs. Highly reduced genome. Thought to be one of the earliest evolving bacteria. |
Aquisalimonas |
A genus of moderately halophilic aerobic chemoorganotroph isolated from hypersaline environments. |
Archaeoglobus |
A genus of anaerobic hyperthermophilic bacteria found near underwater hydrothermal vents, volcanoes, and hot springs. Motile, with irregular spherical cells. Can cause corrosion and souring in oil extraction. |
Archaeoglobus fulgidus |
An anaerobic hyperthermophilic bacterium found near underwater hydrothermal vents, volcanoes, and hot springs. Motile, with irregular spherical cells. Can cause corrosion and souring in oil extraction. |
Aspergillus |
A large genus of ascomycete fungi, reproducing asexually by conidia; a sexual stage is recognized in about one-third of species. Widely distributed as saprobic contaminants of carbohydrate-containing substrates; many can also grow in nutrient-depleted environments. Several species have been isolated from marine environments, including intertidal mudflats, sponges, and corals. A. sydowii is associated with epizootic disease of sea fans. Some species cause opportunistic infections of humans and animals, including marine mammals. |
Aspergillus sydowii |
A fungusstrongly implicated as the causative agent of epizootic disease of sea fans in the Caribbean. Widely distributed in soil and dust; possibly transmitted to sea fans via a reef snail. (Biotechnological application in the production of metal nanoparticles.) |
Asteroid ambidensovirus |
A ssDNA(+/–) virus in the genus Ambidensovirus, the formal name for sea star associated densovirus, SSaDV. |
Astrolithium cruciatum |
A planktonic, free-living marine protist with long radiating processes composed of strontium sulfate (celestite), used for capturing prey (bacteria and other picoplankton). Common in tropical and subtropical waters worldwide. |
Atelocyanobacterium thalassa (Candidatus species) |
An abundant nitrogen-fixing oceanic cyanobacterium identified as UCYN-A. Does not carry out photosynthesis and forms symbiotic association with prymnesiophyte algae including Braarudosphaera bigelowii. |
Aurantimonas |
A genus of bacteria belonging to the Rhizobiales; includes the coral pathogen A. coralicida associated with white plague of corals. |
Aurantimonas coralicida |
A bacterium belonging to the order Rhizobiales; strongly implicated as the causative agent of white plague of corals. |
Aureobasidium |
A diverse genus of widely distributed saprobic fungi. Often grow on plant or inanimate surfaces as septate hyphae covered with a slimy mass of black or colored conidiospores. Marine strains are often isolated in yeast form from sediments and seawater. |
“Bermanella macondoprimitus” (Candidatus species) |
A heterotrophic, strictly aerobic, motile bacterium from seawater reported to dominate biodegradation of low molecular weight alkanes in a simulation of the Deepwater Horizon oil spill. (Bermanella marisrubri is a validly published species isolated from sediments in the Red Sea.) |
Bacillarnavirus |
A genus of ssRNA(+) viruses, including species infecting the diatoms Chaetoceros socialis and Rhizosolenia setigera. |
Bacillus |
A large genus of organotrophic Gram-positive, rod-shaped bacteria; usually obligate aerobes, but may be facultative anaerobes. Widespread and abundant in sediments and soils. Bacillus spp. have been identified in association with coralline lethal orange disease (CLOD), an infection that affects encrusting coralline algae.Biotechnological applications of Bacillus spp. include the production of biological anti-fouling paints and inclusion of dried endospores in probiotic feed additives in aquaculture. Heat-resistant endospores may cause spoilage in inadequately preserved foodstuffs. |
Bacteroides fragilis |
An obligately anaerobic, Gram-negative, redo-shaped bacterium which is present in large numbers in the human colon as a commensal member of the normal microbiota. The bacteria and its specific phages can be used as an indicator of fecal pollution of seawater by sewage. |
Basidiobolus |
A widely distributed genus of saprotrophic fungi, with some species isolated from the intestines of poikilothermic vertebrates, especially amphibians and reptiles. |
Bdellovibrio bacteriovorus |
An obligately aerobic, motile, Gram-negative bacterium which parasitizes other Gram-negative bacteria by entering the periplasmic space and feeding on the host cell, reproducing to form 15–20 progeny. |
Beggiatoa |
A genus of large filamentous bacteria which is an important member of microbial mats on sulfide-rich sediments. Aerobic, chemolithoautotrophs, oxidizing reduced sulfur compounds; some can also grow heterotrophically. |
Betanodavirus |
A genus of ssRNA(+) viruses causing the disease viral nervous necrosis in cultured marine fish; several species are named after host fish, e.g. Barfin flounder nervous necrosis virus, Redspotted grouper nervous necrosis virus, Striped jack nervous necrosis virus. |
Bicosoeca |
A genus of bicosoecids, heterokont bacterivorous flagellates which are abundant in freshwater and marine habitats, attached to substrates via the shorter of two flagella, whilst the longer flagellum (bearing projections) generates a water current for feeding. |
Bodo saltans |
An abundant and highly active bacterivorous kinetoplastid flagellate, possessing a short anterior projecting “tinsellated” flagellum used to create a water current for feeding and a longer posterior flagellum which may be attached to surfaces. |
Bodomorpha |
A genus of small bacterivorous free-living, amoeboid flagellates, with wide distribution in soils, sediments, marine and freshwater. They have two flagella and produce pseudopodia for phagotrophy. |
Bonamia |
A genus of parasitic rhizarian protists that cause lethal infections of the hemocytes in the tissue of molluscs, especially oysters. Species include Bonamia ostrae, B. exitiosa, B. perspora, and B. roughleyi. |
Bordetella bronchiseptica |
A Gram-negative bacterium causing severe respiratory disease (infectious bronchitis) in a number of animals, including marine mammals. |
Botryococcus braunii |
A unicellular, photosynthetic, pyramid-shaped, planktonic green microalga that produces large amounts triterpene hydrocarbons. It may be suitable for large-scale cultivation for production of feedstock for refining to produce octane, kerosene, and diesel. |
Braarudosphaera bigelowii |
A prymnesiophyte coccolithophore covered with calcareous scales; the host of UCYN-A nitrogen-fixing symbiont. |
Brevidensovirus |
An icosahedral DNA virus infecting shrimp and insects (named species: Dipteran brevidensovirus 1 and 2). |
Breviolum |
A newly designated genus of the symbiotic dinoflagellate family Symbiodiniaceae; corresponding to Symbiodinium clade B. Small cells, primarily associated with cnidarians, but also found in sponges and molluscs; prevalent in the Caribbean. |
Brucella |
A genus of small non-encapsulated, nonmotile, short rod-shaped, facultatively intracellular Gram-negative bacteria. A large range of mammals are infected by specific strains and disease is sometimes transmitted to humans as a zoonosis. Marine mammals can be infected by B. pinnipedalis (seals) and B. ceti (dolphins, porpoises, and whales). |
Brucella ceti |
A small non-encapsulated, nonmotile, short rod-shaped, facultatively intracellular Gram-negative bacterium infecting dolphins, porpoises, and whales. Its main effects are abortion, fatigue, and anorexia; it can also affect the brain, causing disorientation and stranding. Some strains may be transmitted to humans handling sick or dead cetaceans. |
Brucella pinnipedialis |
A small non-encapsulated, nonmotile, short rod-shaped, facultatively intracellular Gram-negative bacterium infecting seals. Although frequently isolated or detected immunologically, its pathogenicity for seals is unclear. It may be transmitted via lungworm parasites. |
Burkholderia pseudomallei |
A Gram-negative, aerobic, motile rod-shaped bacterium associated with soil and plants in tropical and subtropical regions. It is an intracellular opportunist pathogen of humans (causing the serious disease melioidoisis) and animals; captive marine mammals appear to be particularly susceptible. |
Cadophora |
A genus of fungi widely associated with terrestrial plants as saprotrophs and pathogens; some species have been isolated from marine algae and submerged wood. |
Caecitellus |
A genus of bicosoecids; biflagellate, heterokont, bacterivorous gliding flagellates which are abundant in freshwater and marine habitats. |
Cafeteria roenbergensis |
A very small bacterivorous bicosoecid flagellate protist found in high numbers in coastal waters, with rapid motility and high grazing activity on bacterial populations. |
Cafeteriavirus |
A dsDNA giant virus species infecting the protist Cafeteria roenbergensis. |
Calothrix rhizosoleniae |
A nitrogen-fixing, heterocystous freshwater cyanobacterium that is symbiotic with Rhizosolenia diatoms. |
Candida |
A large genus (probably polyphyletic) of ascomycete yeasts, widely distributed as inhabitants of animal skin and mucous membranes; it can be an opportunistic pathogen. Several isolates from marine sources have been investigated for production of bioethanol and inhibitory compounds. |
Carnobacterium |
A genus of Gram-positive heterotrophic bacteria that forms part of the microbial community associated with spoilage of fish and meat. |
Catenovulum |
A genus of Gram-negative heterotrophs, often producing agarolytic and other polysaccharide-degrading enzymes. |
Caulobacter crescentus |
A widely distributed oligotrophic aquatic bacterium distinguished by a stalked sessile cell that produces a motile flagellated cell by an unequal cell division cycle. |
Cenarchaeum symbiosum |
A psychrophilic archaeon associated with a cold-water marine sponge (possibly symbiotic). |
Ceratocorys |
A genus of marine dinoflagellates. |
Cercomonas |
A large genus of naked amoeboid flagellates ~10 µm in length, producing pseudopodia to capture bacteria. Abundant in marine, freshwater, and soil habitats. |
Cetacean morbillivirus(CeMV) |
The species of ssRNA(−) virus, with different strains causing respiratory infections of whales, dolphins, and porpoises, leading to pneumonia and encephalitis; responsible for large epizootics in some cetacean species. |
Chaetoceros |
A very large genus of marine planktonic centric diatoms with frustules containing numerous spines that link to frustules to create a colony of cells. Some species are especially important in polar regions. During blooms of some species, the spines can cause damage to fish gills. |
Chaetoceros debilis |
A member of the large genus of marine planktonic centric diatoms with frustules containing numerous spines that link to frustules to create a colony of cells. Widely distributed in coastal waters. During blooms, the spines can cause damage to fish gills. |
Chaetoceros dichaeta |
A member of the large genus of marine planktonic centric diatoms with frustules containing numerous spines that link to frustules to create a colony of cells. This species is one of the most important diatom species in the Southern Ocean with a major contribution to primary production. Some variants have morphological adaptations enabling them to live in the confined spaces of the brine channels in sea ice. Origin of name: L. chaeto- from Gr. kahite, hair, bristle, spine. |
Chaetoceros muelleri |
A member of the large genus of marine planktonic centric diatoms with frustules containing numerous spines that link to frustules to create a colony of cells. This species has been investigated for use in large-scale culture for production of oils. |
Chelonid alphaherpesvirus 5 (ChHV5) |
The dsDNA virus (genus Scutavirus) responsible for the debilitating surface and visceral fibropapilloma tumors affecting sea turtles. |
Chlorobium |
A genus of green sulfur bacteria; photolithotrophic oxidizers of sulfur utilizing a noncyclic electron transport chain to reduce NAD+. |
Chlorovirus |
A genus of dsDNA viruses including the species Acanthocystis turfacea chlorella virus 1 and Paramecium bursaria Chlorella virus 1. |
Chromatium |
A genus of photoautotrophic sulfur-oxidizing bacteria (purple sulfur bacteria) with straight or curved rod-shaped cells containing sulfur granules. |
Chytridium |
The type genus of the chytrid fungi, a group characterized by the production of motile reproductive zoospores which swim rapidly using a posterior whiplash flagellum and are rapidly dispersed in water and moist habitats. Mostly unicellular or may form colonies with short hyphae. Abundant as saprotrophs in seawater; some species infect diatoms and macroalgae. |
Citrobacter |
A genus of Gram-negative, heterotrophic bacteria in the family Enterobacteriaceae; part of a group known as the coliforms found in the gut of animals, soil, and water. |
Cladochytrium |
A genus of chytrid fungi, including several parasites of algae and seagrasses, as well as terrestrial plants. |
Cladocopium |
A newly designated genus of the symbiotic dinoflagellate family Symbiodiniaceae; corresponding to Symbiodinium clade C.Contains a large number of ecologically abundant species with a broad host range and wide geographic distribution. |
Cladosporium |
A large genus of mycelial ascomycete fungi. Terrestrial species are found as a common inhabitant of plant material (they cause many important plant diseases), textiles, and other inanimate surfaces; spread by aerial conidiospores. Species have been isolated from seawater, algae, and coastal plants. |
Clostridium botulinum |
A Gram-positive bacterium forming highly resistant endospores; widespread in soil and sediments and the intestines of fish. It produces a powerful paralyzing neurotoxin and is the cause of food-borne intoxication sometimes associated with seafood. |
Clostridium perfringens |
A Gram-positive, rod-shaped, anaerobic spore-forming bacterium, widely distributed in marine sediments, soil, decaying vegetation, and the intestinal tract of humans and other animals. It is sometime used as an indicator of long-term sewage pollution. Commonly associated with food poisoning (including poorly preserved seafood products) and polymicrobial tissue infections. |
Coccolithovirus |
A genus in the dsDNA virus family Phycodnaviridae, species Emiliania huxleyi virus 86. |
Colwellia |
A genus of deep-sea psychrophilic, piezophilic, facultatively anaerobic bacteria; shown to be important in the degradation of oil hydrocarbons. |
Coscinodiscus centralis |
A cosmopolitan, oceanic species of photosynthetic, planktonic diatoms with discoid cells, with a distinctive central rosette of large hexagonal holes in a slight depression. |
Crocosphaera watsonii |
A unicellular nitrogen-fixing cyanobacterium found in tropical and sub-tropical waters which separates the processes of photosynthesis and nitrogen fixation via a diel rhythm. |
Cryptococcus |
A large genus of basidiomycete fungi growing as unicellular yeasts enclosed in a gelatin-like polysaccharide capsule. Some species are pathogenic for humans and terrestrial animals, with some reports of disease in marine mammals. Strains have been identified in a variety of marine habitats. |
Cycloclasticus |
A genus of bacteria playing a major role in the aerobic degradation of the polyaromatic hydrocarbons, by breaking the ring structure. Important in areas impacted by marine oil seeps or spills. |
Cyclopsomyces |
A genus of chytrid fungi, widely distributed in a range of freshwater and marine habitats, including Arctic waters. |
Cytophaga |
A genus of Gram-negative, gliding, rod-shaped bacteria commonly found on the surface of sediments and soil; rapidly digests cellulose. Part of the microbial community associated with fish spoilage. Some species are a source of agar-degrading enzymes. |
Dasania |
A genus of obligately aerobic, motile bacteria isolated from Arctic marine sediments. |
Debaryomyces |
A large genus of saprotrophic ascomycete yeasts commonly associated with plants and cheeses, occasionally causing skin infections in humans. Some halotolerant strains have been isolated from seawater and marine invertebrates. Marine isolates have been investigated as probiotic agents. |
Desulfobacter |
A genus of anaerobic sulfate-reducing bacteria widely distributed in sediments. |
Desulfomonas |
A genus of anaerobic sulfate-reducing bacteria widely distributed in sediments. |
Desulfonema |
A genus of anaerobic sulfate-reducing bacteria widely distributed in sediments. |
Desulfovibrio |
A genus of anaerobic sulfate-reducing bacteria widely distributed in sediments. |
Desulfurococcus |
A genus of anaerobic, thermophilic sulfate-reducing archaea found in hydrothermal vents and hot springs. |
Diaphonoeca |
A genus of choanoflagellates found in marine habitats, with some species showing adaptions to steep clines of temperature, salinity, oxygen, and H2S. |
Dinodnavirus |
A dsDNA virus genus comprised of the species Heterocapsa circularisquama DNA virus 01. |
Dinophysis acuti |
A species of photosynthetic, armored dinoflagellate producing toxins (notably okadaic acid) that accumulate in mussels and crabs, leading to diarrhetic shellfish poisoning. |
Dinornavirus |
A genus in the ssRNA(+) virus family Alvernaviridae, containing the species Heterocapsa circularisquama RNA virus 01. |
Dinoroseobacter |
A genus of the alphaproteobacterial Rhodobacteraceae associated with the dinoflagellate Prorocentrum, possibly symbiotic production of vitamins, but can also produce algicidal compounds. Heterotrophic or phototrophic (anoxygenic photosynthesis), with a major role in carbon and sulfur cycling. |
Dokdonia |
Genus of aerobic photoheterotrophic bacteria containing proteorhodopsin. |
Dunaliella tertiolecta |
A unicellular photosynthetic green alga used for large-scale propagation to produce edible oils, carotenoid pigments, and nutritional supplements. |
Durusdinium |
A newly designated genus of the symbiotic dinoflagellate family Symbiodiniaceae; corresponding to Symbiodinium clade D. Species show adaptations to survive fluctuations in temperature or turbidity and are more resistant to environmental disturbance such as coral bleaching. |
“Electronema” (Candidatus genus) |
One of the sulfate-reducing cable bacteria occurring in sediments, producing filaments with long-distance electron transport. |
“Electrothrix” (Candidatus genus) |
One of the sulfate-reducing cable bacteria occurring in sediments, producing filaments with long-distance electron transport. |
“Endobugula sertula” (Candidatus species) |
An intracellular symbiont of the bryozoan Bugula neritans; produces the defensive compound bryostatin, with anti-tumor properties. |
“Endoriftia Persephone” (Candidatus species) |
The uncultivated intracellular sulfur-oxidizing endosymbiont of the hydrothermal vent tubeworm Riftia pachyptila.Genome shows metabolic adaptations for both endosymbiotic and free-living stages. |
“Enterovibrio escacola” (Candidatus species) |
One of the uncultivated bioluminescent endosymbionts in the esca of anglerfish. |
“Enterovibrio luxaltus” (Candidatus species) |
One of the uncultivated bioluminescent endosymbionts in the esca of anglerfish. |
Ectocarpus siliculosus virus (EsV-1) |
A dsDNA species in the genus Phaeovirus responsible for infection of the brown alga Ectocarpus siliculosus, in which virion release is synchronized with the release of spores or gametes, enabling interaction of viruses with their susceptible host cells. |
Ectothiorhodospira |
A genus of the purple sulfur bacteria, depositing sulfur globules outside the cells. Found predominantly in anaerobic conditions, capable of anoxygenic photosynthesis. |
Edwardsiella tarda |
A Gram-negative, fermentative bacterium found in the intestinal tract of aquatic animals, including fish, reptiles, and seals. It has caused small outbreaks of invasive infection in workers handling infected warm-water fish from aquaculture facilities. |
Effrenium |
A newly designated genus of the symbiotic dinoflagellate family Symbiodiniaceae; corresponding to Symbiodinium clade E. One species is known, the non-symbiotic E. voratum, which is exclusively free-living and grazes on bacteria and unicellular eukaryotes. |
Emiliania huxleyi |
A species of photosynthetic coccolithophore found in almost all ocean ecosystems; it is one of the most abundant and important members of the phytoplankton with a major role in carbon cycling due to production of massive blooms which form the base of food webs. The release of calcified plates and sulfur compounds during the collapse of blooms due to viral lysis has major effects on ocean processes and atmospheric chemistry. |
Endozoicomonas |
A genus of diverse heterotrophic bacteria commonly found as part of the microbiome of corals and other marine animals, sometimes considered symbiotic due to carbon and sulfur cycling or provision of vitamins or other nutrients. |
Enterobacter |
A genus of Gram-negative, heterotrophic bacteria in the family Enterobacteriaceae; part of a group known as the coliforms found in the gut of animals, soil, and water. |
Enterococcus |
A large genus of Gram-positive cocci in pairs or short chains that are present in the intestines of animals, sometimes described as fecal streptococci. A key indicator of bathing water analysis. A wide range of species are associated with specific animal hosts, including: Enterococcus avium, E. faecalis, E. faecium, E. durans, and E. gallinarum. |
Enterovirus C |
The ssRNA(+) virus causing poliomyelitis, which can be transmitted in bathing water and infects the central nervous system, causing paralysis and death. |
Epicoccum |
A genus of ascomycete fungus universally distributed as saprotrophs in a wide range of habitats and commonly associated with leaf spot diseases of plants. Marine isolates have been obtained from sediments, algae, and coastal plants. Pigments and other products have agricultural and biotechnological applications, including the synthesis of nanoparticles. |
Epulopiscium fishelsoni |
Extremely large rod-shaped bacterium with unusualviviparous, cell division process. Symbiotic member in the gut of reef fish. |
Erwinia |
A genus of Gram-negative, heterotrophic bacteria in the family Enterobacteriaceae; part of a group known as the coliforms found in the gut of animals, soil, and water. |
Erysipelothrix |
A genus of straight, or slightly curved, slender, nonmotile, weakly Gram-positive rod-shaped bacteria causing a skin infection in animals (including fish and marine mammals) and humans. |
Erysipelothrix rhusiopathiae |
A straight, or slightly curved, slender, nonmotile, weakly Gram-positive rod-shaped bacterium causing a skin infection in animals (including fish and marine mammals). It can be transmitted to humans as a zoonosis in workers handling infected fish or marine mammals. |
Escherichia coli |
A Gram-negative, facultatively anaerobic inhabitant of the human intestine. Mostly harmless, but some strains are pathogenic. Widely used as a model organism in cell biology and as an indicator organism to assess water pollution. |
Euglena |
A genus of unicellular, flagellated, mixotrophic protists with biotechnological applications for the precipitation of metallic nanoparticles. |
Exophiala |
A large and widespread genus of saprotrophic fungi (“black yeast”) most commonly associated with decaying wood and soil and sediments with high organic content. Marine species are isolated from ocean water and sediments and are associated with infections of fish, turtles, and crabs. Some species cause significant epizootics in aquaculture and some cause rare human infections. |
Ferroglobus placidus |
A hyperthermophilic isolated from hydrothermal vent sediment off the coast of Italy. Grows anaerobically by oxidizing aromatic compounds, H2 and H2S coupled to the reduction of ferric iron (Fe3+) to ferrous iron (Fe2+) using nitrate (NO3−) as terminal electron acceptor. |
Flavobacterium |
A genus of Gram-negative aerobic rods, with gliding motility and forming yellow, cream, or orange colonies. Some are opportunistic pathogens of fish. |
Fragilaria |
A large genus of planktonic and benthic marine and freshwater diatoms. They form filamentous colonies of cells joined by protrusions in the center of their valves, forming a ribbon-like structure. |
Fragilariopsis cylindrus |
A pennate diatom widely distributed in the nanoplankton, particularly important in primary production at the base of food webs in sea ice and the ice-edge water column in the Southern Ocean, with metabolic adaptations to allow long-term dark survival under the ice in winter. |
Francisella halioticida |
A pathogenic, intracellular Gram-negative bacterium high mortality in cultured abalone, scallops, and other bivalves. |
Fugacium |
A newly designated genus of the symbiotic dinoflagellate family Symbiodiniaceae; corresponding to Symbiodinium clade F, subclade Fr5. D. Symbionts are found in foraminifera; there are several non-symbiotic species known only from cultured isolates. They probably occur as transient, low-abundance densities in cnidarians. |
Fulvimarina |
A genus of Gram-negative, nonmotile, strictly aerobic bacteria isolated from seawater. |
Fundibacter |
A genus of moderately halophilic hydrocarbon degrading bacteria isolated from marine sediments. |
Gambierdiscus toxicus |
One of the main species of the dinoflagellate genus Gambierdiscus, responsible for epibiotic growth on macroalgae leading to the production of ciguatoxins. Bioaccumulation of toxins can lead to ciguatera fish poisoning following consumption of predatory fish. |
Ganoderma |
A genus of bracket or shelf fungi forming large fruiting bodies. Hyphae of some species have been detected in ocean water and deep-sea sediments. |
Gastrocirrhus monilifer |
A planktonic ciliate with an unusual pattern of cilia, lacking marginal tufts of cilia (cirri) and with an expanded “mouth” cavity and truncate anterior end of the body. |
Geitlerinema |
A filamentous cyanobacterium sometimes isolated from the microbial consortium associated with black band disease of corals. |
Gerakladium |
A newly designated genus of the symbiotic dinoflagellate family Symbiodiniaceae; corresponding to a subclade of metazoan associated Symbiodinium clade G. This is one of the basal lineages of family; ecologically rare. Certain species form association with excavating sponges and black corals. |
Giardia |
A genus of anaerobic flagellated protistan parasites that colonize small intestines of vertebrates. Infection in humans causes severe, protracted diarrhea and abdominal pain (giardiasis). Transmitted from terrestrial animals by water supplies contaminated with highly resistant cysts; marine mammals may also be a reservoir of infection for aquarium staff. |
Glaciecola |
A chemoorganotrophic, psychrophilic, aerobic, motile, slightly halophilic rod-shaped bacterium producing buds and prosthecae; found in sea ice. |
Glaciozyma |
A small genus of psychrophilic, asexually reproducing yeasts, with no known sexual state. G. antarctica is present in Antarctic water and sea ice and its genome indicates an array of adaptations to a changing but persistently cold habitat. |
Gonyaulax |
A genus of armored dinoflagellates, often growing in long chains and associated with red tides, producing yessotoxins which can cause fish mortalities and accumulate in shellfish. Some red tide species have been assigned to other genera (e.g. G. tamarensis, now Alexandrium tamarense; G. grindleyi, now Protoceratium reticulatum; G. polyedra, now Lingulodinium polyedra). |
Gymnodinium |
A genus of marine and freshwater dinoflagellates that lacks the armored cellulosic plates (thecae) typical of dinoflagellates. Some species are primarily photosynthetic, whilst others are phagotrophic or mixotrophic. Many are pigmented and are responsible for blooms; some species are bioluminescent. Some species form long chains. |
Gymnodinium catenatum |
A bloom-forming dinoflagellate; one of the main species responsible for the accumulation of paralytic shellfish poisoning toxins in molluscs, crabs, and lobsters. |
Haematococcus pluvialis |
A unicellular, freshwater green alga that can be cultivated in photobioreactors for large-scale production of the pigment astaxanthin. |
Hafnia |
A genus of Gram-negative, heterotrophic bacteria in the family Enterobacteriaceae; part of a group known as the coliforms found in the gut of animals, soil, and water. |
Hafnia alvei |
One of the bacteria from the normal intestinal microbiota of fish associated with scombroid fish poisoning; it can multiply and convert histidine to histamine, resulting in an allergic-like reaction. |
Hahella |
A genus of facultatively anaerobic psychrophilic and mesophilic bacteria isolated from various marine habitats. |
Haloarcula |
A genus of extremely halophilic archaea found in salterns and hypersaline water, such as the Dead Sea. |
Halobacterium salinarum |
An extremely halophilic, aerobic, rod-shaped archaeon found in salterns, hypersaline brine pools, and salted fish. Used in the production of nam-pla Thai fish sauce. |
Halococcus |
A genus of extremely halophilic archaea found in salterns, hypersaline brine pools, and salted fish. |
Halofolliculina corallasia |
A loricate ciliate associated with Skeletal Eroding Band, a moving dark band of tissue destruction observed on a wide range of branching and massive corals on Indo-Pacific reefs. |
Halomonas aquamarina |
A Gram-negative rod-shaped bacterium, motile via polar flagellum. Found in high salt concentrations, including brine channels in sea ice. |
Halomonas titanicae |
A Gram-negative rod-shaped bacterium, motile via polar flagellum, forming part of the syntrophic consortium responsible for corrosion of iron and steel leading to bioconcretious structures known as rusticles. |
Haloquadratum walsbyi |
A halophilic archaeon isolated from brine pools, distinguished by flat square-shaped cells. |
Halorhodospira |
A genus of moderately halophilic, Gram-negative, anerobic, rod-shaped bacteria. Photosynthetic, sulfide-oxidizing. |
Halorubrum |
A genus of halophilic archaea isolated from salterns. |
Helicostoma nonatum |
A ciliated protist found in large numbers actively feeding on diseased coral tissue, implicated as a cause of “brown jelly” syndrome in aquarium corals. |
Hellea |
A genus of aerobic, heterotrophic stalked bacteria isolated from seawater, attached to particles and surfaces. |
Hemiaulus |
A genus of widely distributed chain-forming marine diatoms; sometimes curved or twisted or with connecting projections forming a symbiotic association with nitrogen-fixing cyanobacteria. |
Hepandensovirus |
A genus of ssDNA(+/–) viruses comprising the hepatopancreatic parvoviruses [HPV] of prawns and shrimp (Decapod hepandensovirus 1). |
Heterosigma akashiwo |
A species of photoautotrophic stramenopiles related to the diatoms, with large cells (50–100 μm) without cell walls and possessing two flagella. Blooms have caused “red tides” responsible for extensive fish mortalities in Japan, Scotland, and Canada; they are thought to kill fish as a result of the production of a range of toxins, including reactive oxygen species, hemolytic substances, and neurotoxins. |
Heterosigma carterae |
A species of photoautotrophic stramenopiles related to the diatom, with large cells (50–100 μm) without cell walls and possessing two flagella. Blooms have caused extensive mortalities in Pacific coast salmon farms; they are thought to kill fish as a result of the production of a range of toxins, including reactive oxygen species, hemolytic substances, and neurotoxins. |
Ideonella sakaiensis |
A novel PET-degrading bacterium isolated from enrichment cultures of sediments at a plastic recycling site. |
Igniococcus hospitalis |
A hyperthermophilic archaeon isolated from undersea hydrothermal systems north of Iceland; the host of the symbiotic or parasitic archaeon Nanoarchaeum equitans. |
Igniococcus islandicus |
A hyperthermophilic archaeon isolated from undersea hydrothermal systems north of Iceland. |
Igniococcus pacificus. |
A hyperthermophilic archaeon isolated from undersea hydrothermal systems on the East Pacific Rise. |
Infectious pancreatic necrosis virus (IPNV) |
A dsRNA virus in the genus Aquabirnavirus causing the disease responsible for heavy mortalities in small fry in freshwater aquaculture hatcheries. |
Jannaschia |
A genus of the roseobacter clade, abundant and widely distributed in seawater. Heterotrophic or photoheterotrophic (anoxygenic photosynthesis), with a major role in carbon and sulfur cycling. |
Kakoeca antarctica |
A choanoflagellate cultured from Antarctic sea ice, with a distinctive basket-like lorica composed of >200 transverse and longitudinal costa (rib-like structures). |
Kangiella |
A genus of heterotrophic, Gram-negative, rod-shaped bacteria isolated from marine sediments and sponges, characterized by strong proteolytic activity. |
Karenia brevis |
A bloom-forming dinoflagellate responsible for classic red tides that affect marine life and have human health effects. The lipophilic, neurotoxic toxin brevetoxin binds to voltage-gated sodium channels in nerve cells, leading to disruption of normal neurological function. |
Katagnymene |
A genus of filamentous cyanobacteria, usually forming coiled trichomes surrounded by a mucilaginous sheath, including marine and freshwater species. |
Katodinium |
A large genus of marine and freshwater dinoflagellates, in which most species lack the armored cellulosic plates (thecae) typical of dinoflagellates. Some species ae primarily photosynthetic, whilst others are phagotrophic or mixotrophic. Some species have a special feeding peduncle for capturing prey. Marine species form dense blooms. |
Klebsiella |
A genus of Gram-negative, heterotrophic bacteria in the family Enterobacteriaceae; part of a group known as the coliforms found in the gut of animals, soil, and water. Some species are opportunistic pathogens. |
Kluyveromyces |
A genus of ascomycete yeasts usually associated with dairy products. Some marine species have been identified. |
Labyrinthula zosterae |
A parasitic protist that forms a net-like ectoplasmic membrane and infects seagrasses, leading to degradation of plant cell walls, blackening and destruction of tissue (“wasting disease”). |
Lactobacillus |
A genus of Gram-positive, facultative anaerobic or microaerophilic, rod-shaped, non-spore-forming bacteria; a significant component of the microbiome of humans and other animals. Marine strains have important applications as aquaculture probiotics. |
Lactococcus garviae |
A Gram-positive bacterium infecting marine fish in Asian aquaculture causing lesions in the vascular endothelium, leading to hemorrhage of internal organs and damage to the central nervous system. |
Leptolyngbya |
A genus of filamentous cyanobacteria sometimes isolated from the microbial consortium associated with black band disease of corals. |
Leptospira |
A genus of highly motile, helically coiled bacteria widespread in water, sediments, and soil. Some species are pathogenic for animals, including seals and sea lions, in which it causes cyclical epizootics of leptospirosis, characterized by kidney disease. |
Leucothrix |
A genus of large, filamentous chemoorganotrophic bacteria, which grow on the surface of seagrasses, seaweeds, and other marine surfaces. Attached filaments release cells which colonize new surfaces via a holdfast. |
Lingulodinium polyedra |
Bioluminescent bloom-forming armored dinoflagellate associated with fish mortality. (Formerly named Gonyaulax polyedra and L. polyedrum.) |
Listeria monocytogenes |
A food-borne pathogen of particular concern in lightly preserved ready-to-eat products such as cold-smoked fish and shellfish because of its ability to grow over a very wide temperature range and salinity. |
Lobulomyces |
A genus of chytrid fungi, with isolates found in ocean and coastal waters. |
Lymphocystsis disease virus |
A dsDNA virus in the genus Lymphocystivirus causing papilloma-like lesions on the skin, fins, and tail of cultured and wild fish. |
Lyngbya |
A genus of cyanobacteria forming long, unbranching filaments inside a rigid mucilaginous sheath, which form mats in combination with other phytoplankton. Common around coral atolls and salt marshes, can also form dense floating mats. May have toxicity for humans (via ingestion or skin contact). |
“Magnetoglobus multicellularis” (Candidatus species) |
A bacterial species that forms a compact spherical aggregate of highly organized flagellated cells containing magnetic membrane-enclosed crystals. The aggregates behave like multicellular organisms that swim in either helical or straight trajectories in response to a magnetic field. |
Magnetococcus |
A genus of motile alphaproteobacteria found in sediments whose cells contain chains of membrane-enclosed structures containing single magnetic domain crystals that enable the bacterium to orientate itself in the Earth’s magnetic field. |
Magnetospira |
A genus of motile alphaproteobacteria found in sediments whose cells contain chains of membrane-enclosed structures containing single magnetic domain crystals that enable the bacterium to orientate itself in the Earth’s magnetic field. |
Magnetospirillum |
A genus of motile alphaproteobacteria found in sediments whose cells contain chains of membrane-enclosed structures containing single magnetic domain crystals that enable the bacterium to orientate itself in the Earth’s magnetic field. |
Magnetovibrio |
A genus of motile alphaproteobacteria found in sediments whose cells contain chains of membrane-enclosed structures containing single magnetic domain crystals that enable the bacterium to orientate itself in the Earth’s magnetic field. |
Malassezia |
A genus of basidiomycete yeasts known for many years to be associated with human skin conditions such as dandruff and eczema, but now known to be universally distributed in plants and soils, as an epibiont of animals, deep-sea sediments, hydrothermal vents, seawater, corals, and other invertebrates. |
Marinobacter |
A large genus of heterotrophic gammaproteobacteria found in numerous marine habitats spanning aerobic to anoxic gradients. Species have diverse metabolic capabilities, important in degradation of organic molecules and detoxification of metals. M. pelagius has been used for production of metallic nanoparticles. |
Marteilia |
A genus of protistan parasites of mussels and oysters, causing loss of condition, emaciation, tissue necrosis, and mortalities. Species include Marteilia refringens (in Europe) and M. sydneyii (in Australia). |
Martelella mediterranea |
A species of Gram-negative, oxidase-, and catalase-positive, strictly aerobic heterotrophic bacteria isolated from saline lakes and tidal mudflats. |
Mavirus |
A genus of dsDNA viruses comprised of the virophage species Cafeteriavirus-dependent mavirus. |
Megavirus chilensis |
A giant virus infecting marine amoebae, related to Acanthamoeba polyphaga mimivirus (APMV). |
Melosira arctica |
A psychrophilic centric diatom identified as one of the major primary producers in Arctic sea ice. |
Melosira moniliformis |
A centric diatom with thick cell walls, usually connected in straight chains. Most common in cold waters from late winter to early spring in Northern European Seas and abundant in the summer on the Oregon coast. Commonly identified as one of the major primary producers in Arctic sea ice. |
Merismopedia |
A genus of cyanobacteria that has been isolated from oil-rich sediments; possesses hydrocarbon-degrading ability. (Formerly known as Agmenellum.) |
Mesochytrium |
A genus of chytrid fungi, with some isolates from seawater. |
Mesodinium rubrum |
An important bloom-forming ciliate which has lost phagotrophic capability and is a strict phototroph, making a major contribution to primary production in coastal waters; responsible for seasonal red tides (non-toxic). |
Methanobrevibacter |
A genus of methanogenic archaea that seem to be restricted to the mouth and intestines of animals. M. smithii appears to be a human-specific species and may be a useful indicator species for water testing. |
Methanocaldococcus jannaschii |
A hyperthermophilic methanogenic archaeon found in hydrothermal vents. |
Methanococcoides |
A genus of methanogenic archaea isolated from sediments and Antarctic lakes that are also methylotrophic. |
Methanoculleus |
A genus of methanogenic Archaea isolated from brackish waters, soils, and wastewater. Can utilize ethanol and secondary alcohols as electron donors for methane production. |
Methanogenium |
A genus of coccoid methanogenic Archaea isolated from anoxic marine and lake sediments. |
Methanolacinia |
A genus of irregularly shaped methanogenic Archaea isolated from anoxic sediments. |
Methanopyrus kandleri |
A hyperthermophilic, halotolerant, methanogenic archaeon, originally isolated from sediments associated with undersea hydrothermal vents. |
Methanosarcina |
A versatile methanogenic archaeon found in deep sea vents and oxygen-depleted sediments. Can produce methane via three pathways: from H2 reduction of CO2, from acetate, and via methylotrophy. |
Methanosarcina acetivorans |
A versatile methanogenic archaeon found in deep sea vents and oxygen-depleted sediments. Can produce methane via three pathways: from H2 reduction of CO2, from acetate, and via methylotrophy. |
Methanospirillum |
A genus of motile, filamentous methanogenic archaea found in wetland soils and waste treatment systems. Can form methane from H2 reduction of CO2, or from formate. |
Methanothermococcus |
A genus of hyperthermophilic, methanogenic archaea isolated from hydrothermal vents. |
Methanotorris |
A genus of hyperthermophilic methanogenic archaea isolated from hydrothermal vent black smoker chimneys. |
Methylobacterium |
A genus of methylotrophic bacteria using C1 compounds such as methanol and methylamine, as well as C2, C3, and C4 compounds, for growth. Mainly found in soil and on plants; some species have been isolated from seawater. |
Methylobrevis pamukkalensis |
An aerobic, halotolerant methylotrophic bacterium with short cells isolated from a saline hot spring. Can utilize methanol, methylamine, and mannitol as carbon and energy sources. |
Methylocystis |
A genus of methanotrophic bacteria that may form lipid cysts, containing intracellular membranes parallel to the cell wall. Aerobic obligate chemolithoautotrophs, utilizing C1 compounds via the serine pathway and capable of nitrogen fixation. Mostly isolated from soil and mosses. |
Methylophaga |
A genus of halophilic methylotrophic bacteria, all of which were isolated from marine or otherwise low water activity environments such as hypersaline lakes. The cells are rod-shaped and are motile by a single polar flagellum. |
Methyloprofundus |
A genus of methanotrophic bacteria isolated from deep sea methane seeps; free-living and as gill endosymbionts of Bathymodiolus mussel. |
Methylosinus |
A small genus of methanotrophic bacteria. |
Microcoleus |
A genus of cyanobacteria that has been isolated from oil-rich sediments; possesses hydrocarbon-degrading ability. |
Microcystis |
A genus of cyanobacteria characterized by small, buoyant cells with gas-filled vesicles producing microcystin toxins affecting liver function; mainly found in fresh and brackish water. Responsible for large summer blooms in estuarine and coastal waters, especially in the Baltic Sea. |
Micromonas pusilla |
A small, highly motile, mixotrophic green alga responsible for a large fraction of the picophytoplankton; it is becoming of increasing importance (due to climate change) as a primary producer and grazing predator in Arctic waters. |
Micromonospora |
A genus of Gram-positive, spore-forming bacteria, generally aerobic, and forming a branched mycelium. They are saprotrophic in sediments, soil, and water. Various species are sources of antibiotics. |
Mimivirus |
A genus of dsDNA giant viruses, containing the species Acanthamoeba polyphaga mimivirus infecting the amoeba of that name. |
Monosiga brevicollis |
A bacterivorous choanoflagellate forming an important link between nanoplankton and larger organisms in marine food webs. A model organism for the study of key developmental processes in the evolution of animals. |
Moraxella |
A genus of Gram-negative short rod-shaped bacteria; one of the group of bacteria causing fish spoilage. |
Morbillivirus |
The genus of ssRNA(−) viruses which includes the species infecting marine mammals, Cetacean morbillivirus (CeMV)and Phocine morbillivirus (PDV); these are related to Measles morbillivirus (MeV), Canine morbillivirus (CDV), Rinderpest morbillivirus (RPV), and others. |
Morganella morganii |
One of the bacteria from the normal intestinal microbiota of fish associated with scombroid fish poisoning; it can multiply and convert histidine to histamine, resulting in an allergic-like reaction. |
Moritella |
A genus of facultatively anaerobic, heterotrophic, Gram-negative bacteria. Some are piezopsychrophilic, characterized by production of large amounts of polyunsaturated fatty acids. M. viscosa is associated with skin disease in fish. |
Moritella viscosa |
A facultatively anaerobic, heterotrophic, Gram-negative bacterium causing ulcers on the skin of farmed fish, usually in low temperatures. |
Mrakia |
A genus of psychrophilic basidiomycete yeasts isolated from polar soils and cold-water sediments. |
Mycobacterium bovis |
A Gram-positive, acid-fast, aerobic rod-shaped bacterium, causing the systemic disease tuberculosis in humans and animals, principally cattle and sometimes marine mammals. |
Mycobacterium fortuitum |
A Gram-positive, acid-fast, aerobic rod-shaped bacterium, causing lesions in the skin and lungs of humans and animals, sometimes including marine mammals. |
Mycobacterium marinum |
A Gram-positive, acid-fast, aerobic rod-shaped bacterium, causing lesions in the skin and lungs of humans and animals, sometimes including fish and marine mammals; it can cause zoonotic infection in aquarium workers. |
Mycobacterium tuberculosis |
A Gram-positive, acid-fast, aerobic rod-shaped bacterium, causing the systemic disease tuberculosis in humans and animals, sometimes including marine mammals. |
Mycosphaerella |
A very large genus of ascomycte fungi, containing many important plant pathogens. Several species have been identified in seawater samples and in association with macroalgae. |
Nannochloropis |
A genus of small, marine, nonmotile, heterokont, microalgae with biotechnological applications for production of biodiesel and aquaculture feeds. It produces high levels of polyunsaturated fatty acids and pigments such as astaxanthin and is also used for the precipitation of metallic nanoparticles. |
“Nitrosocaldus islandicus” (Candidatus species) |
An obligately thermophilic, aerobic ammonia-oxidizing chemolithoautotrophic, growing as small irregular shaped cocci. Isolated from a terrestrial hot spring in Iceland. |
“Nitrosopelagicus brevis” (Candidatus species) |
An obligately aerobic chemolithoautotrophic ammonia-oxidizing archaeon ubiquitous in the open ocean, with a major role in the nitrogen cycle. |
“Nitrosopumilus koreensis” (Candidatus species) |
A member of the genus of obligately aerobic chemolithoautotrophic ammonia-oxidizing archaea ubiquitous in the open ocean, with a major role in the nitrogen cycle. Isolated from Arctic marine sediment, currently uncultivated and fully characterized. |
“Nitrosopumilus salaria” (Candidatus species) |
A member of the genus of obligately aerobic chemolithoautotrophic ammonia-oxidizing archaea ubiquitous in the open ocean, with a major role in the nitrogen cycle. Currently uncultivated. |
“Nitrosopumilus sediminis” (Candidatus species) |
A member of the genus of obligately aerobic chemolithoautotrophic ammonia-oxidizing archaea ubiquitous in the open ocean, with a major role in the nitrogen cycle. Currently uncultivated. |
Nanoarchaeum equitans |
A tiny archaeon (~400 nm) with one of the smallest known genomes, occurring in intimate association (possibly parasitic or symbiotic) with cells of another archaeon Igniococcus hospitalis. |
Neptunomomas |
A genus comprising several species of rod-shaped, facultatively anaerobic marine bacteria. N. naphthovorans has been isolated from coastal marine sediments contaminated with polycyclic aromatic hydrocarbons, used as a sole carbon and energy source for growth. N. japonicus has been isolated from deep sea whale falls and is closely related to the Osedax symbionts. |
Nitrobacter
|
A genus of rod-shaped Gram-negative, aerobic, chemolithoautotrophic bacteria with a major role in the nitrogen cycle, oxidizing nitrite to nitrate in marine systems and soils. |
Nitrococcus |
Genus of chemolithoautotrophic bacteria obtaining energy by oxidation of ammonia to nitrite (first step in nitrification). |
Nitrosococcus oceani |
A chemolithoautotrophic bacterium with a major role in the marine nitrogen cycle, obtaining energy by oxidation of ammonia to nitrite (first step in nitrification). |
Nitrosococcus oceani |
A chemolithoautotrophic bacterium with a major role in the marine nitrogen cycle, obtaining energy by oxidation of ammonia to nitrite (first step in nitrification). |
Nitrosomonas |
A genus of chemolithoautotrophic bacteria obtaining energy by oxidation of ammonia to nitrite (first step in nitrification). |
Nitrosopumilus |
A genus of obligately aerobic chemolithoautotrophic ammonia-oxidizing archaea ubiquitous in the open ocean, with a major role in the nitrogen cycle. |
Nitrosopumilus adriaticus |
A member of the genus of obligately aerobic chemolithoautotrophic ammonia-oxidizing archaea ubiquitous in the open ocean, with a major role in the nitrogen cycle. Cultivated from seawater. |
Nitrosopumilus cobalaminigenes |
A member of the genus of obligately aerobic chemolithoautotrophic ammonia-oxidizing archaea ubiquitous in the open ocean, with a major role in the nitrogen cycle. Cultivated from seawater. |
Nitrosopumilus maritimus |
A member of the genus of obligately aerobic chemolithoautotrophic ammonia-oxidizing archaea ubiquitous in the open ocean, with a major role in the nitrogen cycle. First cultivated member of the genus; originally isolated from aquarium sediment. |
Nitrosopumilus oxyclinae |
A member of the genus of obligately aerobic chemolithoautotrophic ammonia-oxidizing archaea ubiquitous in the open ocean, with a major role in the nitrogen cycle. Cultivated from seawater oxycline. |
Nitrosopumilus piranensis |
A member of the genus of obligately aerobic chemolithoautotrophic ammonia-oxidizing archaea ubiquitous in the open ocean, with a major role in the nitrogen cycle. Cultivated from seawater. |
Nitrosopumilus ureiphilus |
A member of the genus of obligately aerobic chemolithoautotrophic ammonia-oxidizing archaea ubiquitous in the open ocean, with a major role in the nitrogen cycle. Isolated from near shore seawater. |
Nitrospina |
A genus of chemolithoautotrophic bacteria obtaining energy by oxidation of nitrite to nitrate (second step in nitrification). |
Nitrospira |
A genus of chemolithoautotrophic bacteria obtaining energy by oxidation of nitrite to nitrate (second step in nitrification). |
Nocardia crassostreae |
An actinomycete bacterium that infects oysters, Crassostreae gigas and Ostrea edulis. The bacteria occur mainly in gonadal follicles, vesicular connective tissue, gills, heart, and adductor muscle, but they eventually invade every tissue, causing mortalities in late summer. |
Nodularia |
A genus of filamentous cyanobacteria characterized by small, buoyant cells with gas-filled vesicles producing nodularin toxins affecting liver function; found in brackish and saline water. Responsible for large summer blooms in estuarine and coastal waters, especially in the Baltic Sea. |
Norwalk virus |
The sole species of the ssRNA(+) Norovirus genus, responsible for acute gastroenteritis (vomiting and diarrhea) following consumption of contaminated food and water or person-to-person contact, often occurring in local epidemics in hospitals, cruise ships, hotels etc. Shellfish are often implicated. |
Novirhabdovirus |
A genus of ssRNA(−) viruses which cause viral hemorrhagic septicemia in fish; species from different hosts include Piscine novirhabdovirus; Salmonid novirhabdovirus, and Snakehead novirhabdovirus. |
Oceanicaulis |
A genus of aerobic, Gram-negative, straight or curved rods with dimorphic cells. The sessile stage has stalks (or prosthecae) and cells divide to produce progeny cells, motile via a single polar flagellum. Associated with dinoflagellates, other marine algae and surfaces. |
Oceanimonas |
A genus of Gram-negative, rod-shaped, aerobic, chemoorganotrophic bacteria isolated from seawater. |
Oceaniserpentilla haliotis |
A Gram-negative, aerobic, heterotrophic bacterium originally isolated from Halioitis rubra, a member of the abalone family of gastropods. Identified as a major contributor to the degradation of crude oil in the Deep Horizonoil spill. |
Oceanospirillum |
A genus of Gram-negative bacteria with rigid helical cells, motile by bipolar tufts of flagella. Chemoorganotrophic aerobes, with respiratory metabolism with oxygen as terminal electron acceptor. Numerous species have been associated from coastal seawater and shellfish. |
Ochromonas |
A genus of unicellular, mixotrophic, flagellated, golden-brown microalgae; some isolates have been shown to degrade phenolic and hydrocarbon compounds. |
Oleispira antarctica |
A psychrophilic Gram-negative bacterium, active in the degradation of hydrocarbons. |
Oscillatoria |
A genus of filamentous cyanobacteria forming colonies which orient towards a light source by oscillatory movement, gliding over surfaces using microfibrils. Numerous species, both marine and freshwater—abundant in plankton, microbial mats and the surface of sediments. Can grow heterotrophically in areas with high organic material, producing toxic blooms in estuaries and areas such as the Baltic Sea. |
Ostreid herpesvirus 1 (OsHV1) |
A dsDNA virus in the genus Ostreavirus, responsible for mass mortalities in cultured Pacific oysters (Crassostrea gigas). |
Ostreococcus tauri |
A coccid prasinophyte alga in the picophytoplankton with a major impact on ocean ecology and carbon cycling in many areas. The smallest known free-living eukaryote (~0.8 µm). |
Ostreopsis |
A genus of planktonic bloom-forming dinoflagellates which have been implicated in ciguatera-like illness due to production of a toxin which may result from presence of the toxin in aerosols produced by wind and wave action. |
“Pelagibacter ubique” (Candidatus species) |
A crescent-shaped heterotrophic bacterium; a cultured example of the SAR11 clade which is the most dominant group of bacteria in the ocean picoplankton. |
“Photodesmus katoptron” (Candidatus species) |
The uncultured bacterial bioluminescent symbiont of the flashlight fish Anomalops katoptron; genome analysis shows that the bacterium is reliant on the host for nutrition but can escape from the host and survive in water for transmission to new hosts. Origin of name: Gr. phôs -otos,light; desmus,servant; species named after host Anomalops katoptron. Taxonomy: (full): d_Bacteria; p_Proteobacteria; c_Gammaproteobacteria; o_Vibrionales; f_Vibrionaceae. GTDB assigns to o_Enterobacterales. |
Parafavella parumdentata |
A tintinnid ciliate with a distinctive vase-shaped lorica. |
Paraglaciecola |
Psychrophilic, aerobic, motile, slightly halophilic ovoid, rod-shaped or slightly curved bacterium. Chemoorganotrophic. |
Paraphysomonas |
A genus of solitary, colorless flagellates covered with numerous silica scales which are free-swimming in the plankton or attached to surfaces via a slender stalk. They feed on bacteria, diatoms, or small algae which are pulled in via the motion of a long flagellum and ingested by phagocytosis. |
Pasteurella |
A genus of Gram-negative, facultatively anaerobic, nonmotile bacteria which can cause disease in a range of animals; occasionally identified in diseased captive cetaceans. |
Pediococcus |
A genus of Gram-positive lactic acid bacteria with homofermentative metabolism, usually occurring in pairs or tetrads, due to division along two planes of symmetry. Used as a probiotic in food products and aquaculture feeds. |
Pelagimonas varians |
A member of the abundant and widely distributed chemoorganotrophic roseobacter clade, in seawater. Heterotrophic or photoheterotrophic (anoxygenic photosynthesis) isolated from the North Sea. |
Pelagomonas calceolata |
A photosynthetic heterokont flagellate adapted to low light. |
Penicillium |
One of the best-known genera of filamentous fungi, because of its abundance in soils, stored foods, growth on damp surfaces and for the production of the antibiotic penicillin and cheeses. Spores are widely spread in the air. Several strains have been isolated from marine habitats, including deep-sea sediments. |
Penstyldensovirus |
A genus of ssDNA(+/–) viruses comprising Decapod penstyldensovirus 1, the causative agent of infectious hypodermal and hematopoietic necrosis (IHHN) disease of prawns and shrimp. |
Pepper mild mottle virus (PMMoV) |
A virus in the genus Tobamovirus that causes a disease of peppers and is abundant in human feces, due to its presence in spicy foods. It can be used as novel indicator of sewage pollution of seawater. |
Peranema |
A genus of phagotrophic free-living euglinid flagellates, using a cytostomal feeding apparatus supported by a pair of rigid rods. |
Perkinsus marinus |
A species of dinoflagellate-like alveolate protists which is a major pathogen of oysters, causing degradation of oyster tissues and leading to high mortality in oyster populations on the North American coast, Mexico, and Brazil. The disease is known as dermo or perkinsosis. |
Petalomonas |
A large genus of phagotrophic free-living euglinid flagellates, which lack chloroplasts and feed on bacteria, yeasts, and small protists abundant within freshwater environments with a few marine species found in the plankton and sediments. |
Pfiesteria piscicida |
A mixotrophic dinoflagellate implicated as the cause of large-scale fish mortalities in the 1980s and 1990s on the coast of North Carolina and in tributaries of the Chesapeake Bay with controversial links to neuropsychological effects in humans. |
Phaeobacter |
A member of the abundant and widely distributed chemoorganotrophic roseobacter clade. Several species are effective colonizers of abiotic and biotic (including algae) marine surfaces and produce a range of antibiotic compounds that inhibit biofouling. |
Phaeobacterium |
A Gram-negative, rod-shaped, phototrophic and motile bacterium isolated from mangrove forest sediment. |
Phaeocystis |
A genus of haptophyte microalgae often grouped in the prymnesiophytes. A widespread member of the phytoplankton with a major role in carbon and sulfur cycling. Forms large floating colonies causing seasonal blooms, especially in polar and temperate regions, which can cause problems on beaches and coastal waters due to production of foam and sulfur smells (due to copious production of dimethyl sulfide from dimethylsulfonioprpionate). |
Phaeocystis globosa |
A prominent species of this genus of haptophyte microalgae, often grouped in the prymnesiophytes. A widespread member of the phytoplankton with a major role in carbon and sulfur cycling. Forms large floating colonies causing seasonal blooms, especially in nutrient-rich temperate regions, which can cause problems on beaches and coastal waters due to production of foam and sulfur smells (due to copious production of dimethyl sulfide from dimethylsulfoniopropionate). |
Phaeodactylum tricornutum |
A diatom that exists in a variety of cell shapes with distinct benthic and planktonic forms. It is widely used as a model eukaryotic organism for cell biology and genetic modification and is suitable for large-scale culture for production of biofuel precursor oils. |
Phaeosphaeria |
A genus of filamentous ascomycete fungi, most of which are pathogenic for grasses and weeds, but several marine examples have been isolated, feeding on decaying macroalgae and plant debris. They are a rich source of structurally diverse bioactive natural compounds with cytotoxic and antimicrobial properties. |
Phaeovirus |
A genus in the dsDNA virus family Phycodnaviridae, infecting brown macroalgae; species include Ectocarpus siliculosus virus 1 and Feldmannia irregularis virus a. |
Phocine morbillivirus (PDV) |
The ssRNA(−) virus causing phocine distemper, a fatal respiratory disease that causes large epizootics in seals. |
Phormidium |
A large genus of cyanobacteria, including mainly freshwater and a few marine species. Forms trichomes enclosed in a sheath, which can act as a defense against grazing protists. Strains have been associated with colonization of plastics and degradation of hydrocarbons in the marine environment. |
Phormidium corallyticum |
A species of cyanobacteria characterized by trichomes enclosed in a sheath producing a network of filaments; a prominent member of the microbiome implicated in black band disease of corals. |
Photobacterium |
A genus of chemoorganotrophic, halophilic rod-shaped bacterium, motile by single polar sheathed flagellum. Widely distributed in seawater and in association with marine animals; an important factor in fish spoilage. |
Photobacterium damselae subsp. piscicida |
A chemoorganotrophic, halophilic rod-shaped bacterium, motile by single polar sheathed flagellum. Important pathogen of fish, with serious impacts in marine aquaculture, e.g. seabass and sea bream culture. |
Photobacterium leiognathi |
A chemoorganotrophic, halophilic rod-shaped bacterium, motile by single polar sheathed flagellum. A facultative bioluminescent symbiont of marine animals, notably fish. |
Photobacterium phosphoreum |
A chemoorganotrophic, halophilic rod-shaped bacterium, motile by single polar sheathed flagellum. A facultative bioluminescent symbiont of marine animals, notably fish. One of the bacteria from the normal intestinal microbiota of fish associated with scombroid fish poisoning; it can multiply and convert histidine to histamine, resulting in an allergic-like reaction. |
Photobacterium piscicida |
A chemoorganotrophic, halophilic rod-shaped bacterium, motile by single polar sheathed flagellum. Important pathogen of fish, with serious impacts in marine aquaculture, e.g. seabass and sea bream culture. The correct taxonomic designation is Photobacterium damselae subsp. piscicida. |
Photobacterium profundum |
Psychrophilic, piezophilic bacterium isolated from the deep sea (>5000 m). Chemoorganotrophic, motile by single polar sheathed flagellum. |
Phytopthora gemini |
A member of the plant pathogenic Oomycetes (water molds), which kills dormant seeds and developing seedlings of Zostera seagrass. |
Pichia |
A genus of ascomycete saprotrophic yeasts with spherical or elliptical cells. Most known species are associated with decaying plant material and some cause spoilage of wines. Several species have been isolated from seawater, marine sediments, and marine algae. Occasionally associated with opportunistic human infections. Some have antibiotic effects against other fungi and produce other bioactive compounds and enzymes, some with biotechnological potential. |
Piscirickettsia salmonis |
A bacterium causing a serious epizootic disease in salmonid fishes; it grows intracellularly within membrane-bound cytoplasmic vacuoles in host cells. It has a major impact on salmon populations, especially in Chilean aquaculture. |
Planctopirus limnophila |
A member of the order Planctomycetales, a group of budding aquatic microorganisms with unusual cell wall structure and internal membranes. This species, isolated from a lake, has been the model for studies of planctomycete cell biology. |
Planococcus |
A genus of aerobic, motile, Gram-positive cocci usually found in sediments and soils; isolates have been identified in association with coralline lethal orange disease (CLOD), an infection that affects encrusting coralline algae. |
Podochytrium |
A genus of chytrid fungi; some have been identified as parasites of diatoms. |
Polychytrium |
A genus of chytrid fungi; some have been identified in marine samples. |
Prasinovirus |
A genus in the dsDNA virus family Phycodnaviridae infecting prasinophyte algae; species include Micromonas pusilla virus SP1 and Ostreococcus tauri virus OtV5. |
Prevotella |
A genus of Gram-negative anaerobic bacteria forming part of the normal microbiota of the mouth, intestinal tract, and vagina of humans and animals. Useful in tracking sources of water pollution from different animal sources. |
Prochlorococcus |
A genus of very small (~0.6 µm) cocci containing divinyl chlorophylls. Dominant photosynthetic ocean bacteria, especially in tropical and sub-tropical waters down to limits of light penetration. Only one species (P. marinus) is officially recognized, but this conceals great genetic and physiological diversity. |
Prochlorococcus marinus |
A species of very small (~0.6 µm) cocci containing divinyl chlorophylls. Dominant photosynthetic ocean bacteria, especially in tropical and sub-tropical waters down to limits of light penetration. |
Prochloron |
A genus of unicellular oxygenic, photosynthetic cyanobacteria frequently found as symbionts of ascidians. |
Proplectella |
A tintinnid ciliate with a distinctive vase-shaped lorica. |
Prorocentrum |
A widely distributed and highly diverse genus of bloom-forming, planktonic, photosynthetic dinoflagellates. Some species may produce toxins (notably okadaic acid) that accumulate in mussels and crabs, leading to diarrhetic shellfish poisoning. |
Protoperidinium |
A large genus of globally distributed heterotrophic dinoflagellates 50–100 um in size, often colored red, brown, or yellow in the inner parts of the organism, possessing armored cellulosic plates and horns or spines. They feed by capturing prey (usually other dinoflagellates and diatoms) by phagotrophy or via a peduncle. Includes the species P. defectum; P. incognitum; P. antarcticum. |
Prymnesiovirus |
A genus in the dsDNA virus family Phycodnaviridae infecting prymnesiophyte algae; species Chrysochromulina brevifilum virus PW1. |
Pseudoalteromonas |
A genus of curved rod-shaped bacterium. Motile with single polar flagellum. Heterotrophic. Widely distributed in ocean and coastal waters. |
Pseudoalteromonas agarivorans |
A curved rod-shaped heterotrophic, Gram-negative bacterium, motile with single polar flagellum; described as a cause of disease in the reef sponge Rhopaloeides odorabile. |
Pseudoalteromonas haloplanktis |
A curved rod-shaped heterotrophic, Gram-negative bacterium, motile with single polar flagellum; widely distributed in ocean and coastal waters. |
Pseudomonas |
A large genus of Gram-negative chemoorganotrophic bacteria widely distributed in soil and water (but less common in marine). Motile by single polar flagellum. Mainly saprotrophic, but some strains are pathogenic for plants and animals (including opportunist pathogens associated with infection of cuts and grazing from swimming). Also associated with fish spoilage. Biotechnological applications include the development of anti-fouling surface treatments, aquaculture probiotics, and agar-degrading enzymes. |
Pseudo-nitzschia |
A genus of several species of widely distributed pennate diatoms, some of which produce toxic domoic acid. |
Pseudo-nitzschia multiseries |
A species of widely distributed pennate bloom-forming diatoms, which produces toxic domoic acid. |
Pseudo-nitzschia pseudodelicatissima |
A species of widely distributed pennate bloom-forming diatoms, which produces toxic domoic acid. |
Pseudoscillatoria coralii |
One of the filamentous cyanobacteria sometimes isolated from the microbial consortium associated with black band disease of Favia sp. corals in the Red Sea. |
Pseuodoalteromonas haloplanktis |
A curved rod-shaped bacterium. Motile with single polar flagellum. Heterotrophic. Widely distributed in ocean and coastal waters. |
Psychrobium conchae |
A psychrophilic (optimum growth temperature 12oC), chemoorganotrophic, aerobic bacterium; motile with a single polar flagellum. |
Pyrobaculum aerophilum |
A hyperthermophilic archaeon with rod-shaped cells possessing terminal spherical bodies, isolated from hydrothermal vents. Capable of aerobic respiration, using both organic and inorganic compounds. |
Pyrococcus furiosus |
A hyperthermophilic archaeon isolated from deep sea hydrothermal vents. Optimum growth temperature ~100oC. Chemoorganotrophic, using a range of carbohydrate and protein sources. It produces a thermostable DNA polymerase used in the PCR. |
Pyrococcus strain GB-D |
A hyperthermophilic archaeon isolated from deep sea hydrothermal vents that produces a thermostable DNA polymerase with proof reading, used in the PCR. |
Pyrococcus yayanossi |
A hyperthermophilic archaeon isolated from deep sea hydrothermal vents. Optimum growth temperature ~100oC. Chemoorganotrophic, using a range of carbohydrate and protein sources. |
Pyrocystis lunula |
A large, epipelagic dinoflagellate used in an ecotoxicological bioassay. |
Pyrodictium occultum |
A hyperthermophilic sulfur-reducing archaeon found in the chimneys of hydrothermal vents. Possesses flat disk-shaped cells of variable size, growing in a network of flake-like structures held together by hollow tubules, attached to sulfur crystals. |
Pyrodinium bahamense |
A bloom-forming dinoflagellate; one of the main species in tropical waters responsible for the accumulation of paralytic shellfish poisoning toxins in molluscs, crabs, and lobsters. |
Pyrolobus fumarii |
A hyperthermophilic sulfur-reducing archaeon with coccoid cells; found in the black smoker chimneys of hydrothermal vents, with an optimum growth temperature of 106oC. An obligate chemolithoautotroph, coupling the oxidation of H2 to reduction of NO3-, S2O32-, or O2 at very low concentrations. |
Pythium porphyrae |
An oomycete (water mold) causing infection of the red alga Porphyra. |
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“Riegeria santandreae” (Candidatus species) |
Chemolithoautotrophic (sulfide-oxidizing) intracellular symbiont of Paracatenula gutless flatworm; has reduced genome but stores carbon and energy sources for transfer to host via outer membrane vesicles. |
Ralstonia |
A genus of chemoorganotrophic bacteria that can also grow autotrophically, fixing CO2 using hydrogen as reductant when organic nutrients are absent. No marine species described. Terrestrial species include major pathogens of plants and opportunistic infections of humans (often mistaken for Pseudomonas). |
Raoultella planticola |
One of the bacteria from the normal intestinal microbiota of fish associated with scombroid fish poisoning; it can multiply and convert histidine to histamine, resulting in an allergic-like reaction. |
Raphidovirus |
A genus in the dsDNA virus family Phycodnaviridae infecting raphidophyte algae; species Heterosigma akashiwo virus 01. |
Renibacterium salmoninarum |
A Gram-positive intracellular pathogen; causative agent of bacterial kidney disease, a chronic infection of salmon. |
Rhizobium |
A genus of nitrogen-fixing bacteria, best known for their symbiotic association in root nodules of leguminous plants. Several marine strains associated with seagrasses and as epibionts of invertebrates have been described. |
Rhizobium |
A genus of nitrogen-fixing bacteria that fix nitrogen; numerous species are associated with soil and plants, notably as symbionts within root nodules of various plants such as legumes. Some species have been isolated from seawater. |
Rhizoclosmatium |
A genus of chytrid fungi; several have been identified in marine samples. |
Rhizophydium |
A genus of chytrid fungi with several species identified in marine samples as saprotrophs and parasites of diatoms. |
Rhizosolenia |
A genus of weakly silicified centric diatoms with cylindrical cells, with conical valves narrowing into a long, straight, and needle-like spine. Shape of cells limits zooplankton grazing and blooms may lead to anoxia and clogging of fish gills. Can form large floating mats in coastal areas. Important in nitrogen-cycling due to the presence of cyanobacterial endosymbionts. |
Rhodobacter |
A genus belonging to the large group of phototrophs originally described as purple non-sulfur bacteria, although they can in fact use sulfur or hydrogen as electron donor for CO2 reduction. They are found in numerous marine habitats and are metabolically diverse and can grow in the dark anaerobic respiration or fermentation, or aerobically by respiration. |
Rhodococcus |
A genus of aerobic, nonmotile, Gram-positive bacteria isolated from sediments and seawater, used for the production of metallic nanoparticles. |
Rhodopirellula islandica |
A species of Rhodopirellula first isolated in waters off Iceland. The genus is distinguished by unusual cell morphology, with reproduction by budding and internal membrane compartments. Heterotrophic, degrading a wide range of complex carbohydrates in sediments and marine snow. |
Rhodopseudomonas |
A genus belonging to the large group of phototrophs originally described as purple non-sulfur bacteria, although they can in fact use sulfur or hydrogen as electron donor for CO2 reduction. They are found in numerous marine habitats and are metabolically diverse and can grow in the dark anaerobic respiration or fermentation, or aerobically by respiration. |
Rhodospirillum |
A genus belonging to the large group of phototrophs originally described as purple non-sulfur bacteria, although they can in fact use sulfur or hydrogen as electron donor for CO2 reduction. They are found in numerous marine habitats and are metabolically diverse and can grow in the dark, anaerobic respiration or fermentation, or aerobically, by respiration. |
Rhodosporidium |
A genus of oleaginous basidiomycete red-pigmented yeasts. Several marine species have been isolated from coastal waters and the deep sea, with potential biotechnological applications in biodiesel production and aquaculture. |
Rhodotorula |
A genus of oleaginous basidiomycete red-pigmented yeasts. Several marine species have been isolated from coastal waters and the deep sea, some with potential biotechnological applications in biodiesel production and aquaculture. Used in the fermentation of fish product ika-shiokara. |
Rhynchomonas nasuta |
A raptorial feeding kinetoplastid flagellate, grazes on bacteria and picoeukaryotes. |
Richelia intracellularis |
A nitrogen-fixing cyanobacterium that lives symbiotically in the space between the cell membrane and silica frustule of diatoms such as Rhizosolenia and Hemiaulus. |
Roseobacter |
A genus of the alphaproteobacterial Rhodobacteraceae; members of this genus and the roseobacterclade are among the most abundant bacteria in the surface ocean. Heterotrophic or photoheterotrophic (anoxygenic photosynthesis), with a major role in carbon and sulfur cycling. |
Roseofilum reptotaenium |
One of the gliding, filamentous cyanobacteria isolated from the microbial consortium associated with black band disease in the Caribbean coral Siderastrea siderea; the filaments from the structure of the migrating mat. The bacterium produces microcystin toxins and can tolerate high levels of sulfide produced by sulfate-reducing bacteria in the black band. |
Roseovarius |
A large genus of the alphaproteobacterial Rhodobacteraceae; members of this clade are among the most abundant bacteria in the surface ocean. Some species are isolated from the deep sea and in association with marine invertebrates. Heterotrophic or photoheterotrophic (anoxygenic photosynthesis), with a major role in carbon and sulfur cycling. |
Roseovarius crassostreae |
A member of the alphaproteobacterial Roseobacter clade; the etiological agent of juvenile oyster disease (JOD) causing seasonal mortalities of hatchery-produced juvenile oysters raised in the north-eastern USA. |
Roseovarius nubinhibens |
A member of the large genus of the alphaproteobacterial Rhodobacteraceae; members of this clade are among the most abundant bacteria in the surface ocean. Some species are isolated from the deep sea and in association with marine invertebrates. Heterotrophic or photoheterotrophic (anoxygenic photosynthesis), with a major role in carbon and sulfur cycling (degradation of DMSP). |
Ruegeria |
A large genus of the alphaproteobacterial Rhodobacteraceae; members of this genus and the roseobacterclade are among the most abundant bacteria in the surface ocean. Heterotrophic or photoheterotrophic (anoxygenic photosynthesis), with a major role in carbon and sulfur cycling. Originally isolated from seawater by enrichment with DMSP. |
Ruegeria pomeroyi |
A member of the alphaproteobacterial Rhodobacteraceae; members of this genus and the roseobacterclade are among the most abundant bacteria in the surface ocean. Heterotrophic or photoheterotrophic (anoxygenic photosynthesis), with a major role in carbon and sulfur cycling. Originally isolated from seawater by enrichment with DMSP. (Closely related to Silicibacter pomeroyi, but currently retained in separate genera.) |
Salinibacter ruber |
Extremely halophilic (optimum 20–30% NaCl), red-pigmented bacterium isolated from salterns where it can comprise up to 25% of the microbial community. |
Salinispora |
A genus of high CC Gram-positive actinomycete bacteria which occurs in marine sediments and are the subject of intensive study into the large number of secondary metabolites, many with potential applications as pharmaceuticals. |
Salmon isavirus (ISAV) |
A ssRNA(−) virus in the genus Isavirus that infects erythrocytes, causing the disease infectious salmon anemia. |
Salmonella |
A heterotrophic bacterium found in the intestinal tract of animals and humans; often responsible for gastrointestinal infections. Numerous subspecies and serovars. |
Salmonella typhi |
A Gram-negative enteric bacterium causing the serious epidemic disease typhoid fever. |
Salpingoeca rosetta |
A choanoflagellate with a complex life cycle, transitioning between single and colonial collar cell types used as a model organism in investigation of cell-cell connections and cell differentiation, revealing important insights into the early evolution of the animals. |
Schizochytrium |
A genus of unicellular thraustochytrids found widely in coastal habitats, playing an important role in marine food webs by degradation of complex organic material by and production of polyunsaturated fatty acids which are essential nutrients for larval development and fish nutrition. Schizochytrium is exploited in biotechnology for production of docosahexaenoic acid (DHA) for human nutrition and aquaculture, and also as a delivery agent for aquaculture vaccines. |
Serratia |
A genus of Gram-negative, heterotrophic bacteria in the family Enterobacteriaceae; part of a group known as the coliforms found in the gut of animals, soil, and water. |
Serratia marcescens |
A rod-shaped, Gram-negative, facultatively anaerobic bacterium abundant in soil and damp environments, and as a member of the human intestinal microbiota (can be an opportunistic pathogen of humans). A specific strain was shown to be the causative agent of white pox disease of Acropora corals in the Caribbean, due to sewage pollution of reefs. |
Shewanella |
A genus of Gram-negative, heterotrophic, facultative anaerobic bacterium that can use Fe and Mn as terminal electron acceptor in place of O2 which has applications in bioremediation and development of microbial fuel cells. Some species are associated with fish spoilage and decay, with production of trimethylamine. |
Shewanella putrefaciens |
A Gram-negative, heterotrophic, facultative anaerobic bacterium that can use Fe and Mn as terminal electron acceptor in place of O2. Associated with fish spoilage and decay, with production of trimethylamine. |
Shigella |
A genus of Gram-negative, facultative aerobic, non-spore-forming, nonmotile, rod-shaped bacteria genetically closely related to E. coli and responsible for the epidemic disease dysentery. |
Silicibacter pomeroyi |
A member of the alphaproteobacterial Rhodobacteraceae; members of this genus and the roseobacterclade are among the most abundant bacteria in the surface ocean. Heterotrophic or photoheterotrophic (anoxygenic photosynthesis), with a major role in carbon and sulfur cycling. Originally isolated from seawater by enrichment with DMSP. (Closely related to Ruegeria pomeroyi, but currently retained in separate genera.) |
Skeletonema |
A primarily marine and estuarine genus of large diatoms usually connected in long chains; responsible for high levels of primary production during spring blooms in nutrient upwelling area, often dominant in waters characterized by salinity fluctuations and high silicate concentrations. |
Sphingomonas |
A large and diverse genus of Gram-negative, rod-shaped, chemoorganotrophic, strictly aerobic bacteria. They are distinguished by possession of glycosphingolipids (GSLs) instead of lipopolysaccharide in their cell envelopes. They can metabolize a diverse range of organic compounds present in low concentrations and some strains have been used for bioremediation of polluted habitats. |
Spizellomyces |
A genus of chytrid fungi with several species identified in marine samples as saprotrophs and parasites of diatoms. |
Spongiibacter |
A genus of halophilic, chemoorganotrophic Gram-negative rods; motile by a polar flagellum isolated from marine sponges and seawater. |
Sporobolomyces |
A genus of basidomycete yeasts widely distributed as saprotrophs on the surface of terrestrial plants; some marine species have been described. |
Spumella |
A highly diverse genus of colorless, non-scaled, bacterivorous nanoflagellates widely distributed in marine and freshwater and sediments, with an important role in food webs. |
Sputnikvirus |
A genus of dsDNA viruses comprising the species Mimivirus-dependent virus Sputnik; a virophage infecting Acanthamaoeba polyphaga cells already infected with Mimivirus. |
Staphylococcus |
A genus of Gram-positive, facultatively anaerobic bacteria forming cocci in grape-like clusters. Found on the skin and mucous membranes of humans and other animals including marine mammals. Virulent strains produce serious systemic infections. |
Staphylothermus marinus |
Hyperthermophilic archaeon forming large grape-like clusters. Obligately anaerobic, heterotrophic. |
Streptococcus iniae |
A Gram-positive bacterium, typically occurring in chains, the causative agent of a disease of fish in warm-water aquaculture and fish kills in the Caribbean. It can also cause zoonotic infection by infection of wounds in workers handling infected fish, leading to severe cellulolytic infection. |
Streptomyces |
A genus of Gram-positive, filamentous bacteria found in soil and sediments. It produces antimicrobial secondary metabolites and has been used for the development of biological antifouling treatments. |
Sulfitobacter |
A member of the alphaproteobacterial Rhodobacteraceae; members of this genus and the roseobacterclade are among the most abundant bacteria in the surface ocean. Heterotrophic or photoheterotrophic (anoxygenic photosynthesis), with a major role in carbon and sulfur cycling. Particularly abundant in environments with a constant source of inorganic sulfur. May produce algicidal compounds that affect Emiliania huxleyi blooms. |
Sulfolobus |
A genus of hyperthermophilic and acidophilic archaea with irregularly shaped cells found worldwide in volcanic springs and hydrothermal vents. Can grow chemolithoautotrophically via sulfur oxidation or heterotrophically by using sulfur to oxidize simple organic compounds. |
Symbiodinium |
A genus of endosymbiotic photosynthetic dinoflagellates inhabiting corals, anemones, clams, jellyfish, foraminifera, and other hosts, commonly known as zooxanthellae, playing a critical role in nutrition of their host. Distinct clades are recognized using molecular phylogenetic methods; these are now reclassified into different genera and the genus name Symbiodinium is now retained only for clade type A. |
Synechococcus |
A unicellular cyanobacterium with cells 0.6–1.6 µm. One of the most important members of the picophytoplankton making a major contribution to ocean productivity. Distributed worldwide, with higher densities in waters with high nutrient levels. |
Synechocystis |
A photosynthetic cyanobacterium mostly found in freshwater; a few marine strains have been isolated. Can also be cultured heterotrophically. Extensively used for studies of the molecular biology of circadian clocks. |
“Thiodiazotropha endoloripes” (Candidatus species) |
A sulfur-oxidizing and nitrogen-fixing bacterium that is an endosymbiont of the clam Loripes lucinales, resulting in a major impact on the bioturbation and fertility of seagrass meadows. |
“Thiosymbion” (Candidatus genus) |
Chemolithoautotrophic (sulfide-oxidizing) intracellular symbiont of Inanidrilus gutless oligochaete worm. |
Taura syndrome virus |
A small, non-enveloped, icosahedral, ssRNA(+) virus belonging to the genus Aparivirus causing heavy mortalities in prawn and shrimp culture. |
Tenacibaculum maritimum |
The causative agent of a skin disease of fish, referred to as marine flexibacteriosis (the bacterium was previously classified in the genus Flexibacter), marine columnaris, or black patch necrosis. It is characterized by excess mucus production, damage to the gills, tissue necrosis around the mouth and fins, skin lesions, and eventual death. It is widely distributed in numerous species of wild and farmed fish in Europe, Japan, North America, and Australia. |
Teredinibacter turnerae |
A Gram-negative rod, motile with a single polar flagellum. Symbiotic inhabitant of the gills of wood-boring molluscs (shipworms) in the family Teredinidae, secreting polysaccharide-degrading enzymes that enable the host to digest wood; it also provides the host with nitrogen compounds via nitrogen fixation. |
Thalassiosira |
A genus of diatoms, with multiple freshwater and marine species; the latter are widely distributed in all oceanic regions and are major contributors to primary production in temperate to polar regions. |
Thalassiosira nordenskiioeldi |
A photosynthetic, planktonic diatoms connected in long flexible chains by organic threads. Mainly found in cold and temperate regions, often forming extensive blooms in spring and autumn. |
Thalassobacillus |
A genus of Gram-positive, moderately halophilic chemoorganotrophic bacteria isolated from hypersaline environments; some degrade phenolic compounds. |
Thalassomonas |
A genus of Gram-negative aerobic, chemoorganotrophic rod-shaped bacteria isolated from marine animals. T. loyana has been implicated as a cause of white plague disease of corals in the Red Sea. |
Thalassomonas loyana |
A Gram-negative aerobic, chemoorganotrophic rod-shaped bacterium implicated as a cause of white plague disease of corals in the Red Sea. |
Thermococcus celer |
A coccoid, hyperthermophilic archaeon which is highly motile due to a tuft of polar flagella. An obligately anaerobic chemoorganotroph, metabolizing proteins and other organic molecules using elemental sulfur as electron acceptor. Found in shallow sulfur-rich hydrothermal systems, notably in Vulcano, Italy. The source of thermostable DNA polymerase used in the PCR. |
Thermococcus litoralis |
A coccoid, hyperthermophilic archaeon which is highly motile due to a tuft of polar flagella. An obligately anaerobic chemoorganotroph, metabolizing proteins and other organic molecules using elemental sulfur as electron acceptor. Found on a beach near Naples, Italy. The source of thermostable DNA polymerase used in the PCR. |
Thermodesulfobacterium |
A genus containing thermophilic chemolithoautotrophic sulfate-reducing bacteria isolated from deep sea hydrothermal vents. They can utilize acetate and other fatty acids as electron donors for sulfate reduction to H2S and contain unusual non-isoprenoid ether-linked lipids in their cell membranes. |
Thermodiscus |
A hyperthermophilic archaeon with disc-shaped cells. |
Thermotoga maritima |
A hyperthermophilic bacterium from hydrothermal vents. Optimum growth temperature is 80oC and maximum 90oC; this is the only member of the Bacteria known to grow at such high temperatures. Deep lineage in phylogenetic trees suggests ancient origin. Distinguished by a toga-like envelope. The source of a thermostable DNA polymerase for use in the PCR. |
Thermus aquaticus |
A hyperthermophilic bacterium isolated from terrestrial hot springs; the source of the original thermostable DNA polymerase (Taq) for use in the PCR. |
Thermus thermophilus |
A hyperthermophilic bacterium isolated from terrestrial hot springs; the source of a thermostable DNA polymerase for use in the PCR. |
Thiobacillus |
A genus of obligately chemolithoautotrophic bacteria, oxidizing sulfur, thiosulfate or polythionates as energy sources. |
Thiococcus pfennigii |
A Gram-negative, non‐motile, obligately phototrophic and strictly anaerobic species of bacteria isolated from salt marshes. |
Thiomargarita |
A sulfur-oxidizing bacterium distinguished by very large cells up to 750 µm containing a large vacuole for storage of nitrate used as oxidant. |
Thiomicrospira crunogena |
A colorless chemolithoautotrophic spiral shaped bacterium isolated from deep sea hydrothermal vents, oxidizing sulfide, thiosulfate and sulfur. |
Thioploca auraucae |
Large sulfur-oxidizing bacterium that live in multicellular, filamentous bundles surrounded by a braided sheath, forming dense mats on sediments below oxygen minimum zones. |
Thiospirillum |
A genus of the purple sulfur bacteria, carrying out anoxygenic photosynthesis via oxidation of H2S. Large spiral-shaped cells with polar flagella. Found in shallow anoxic waters and microbial mats. |
Thiothrix |
A genus of filamentous sulfur-oxidizing bacteria, related to the genera Beggiatoa and Thioploca, forming sheathed multicellular filaments. Motile by gliding. |
Thiothrix |
A genus of filamentous sulfur-oxidizing bacteria, related to the genera Beggiatoa and Thioploca, forming sheathed multicellular filaments. Motile by gliding. |
Thiovulum |
A genus of spiral sulfur-oxidizing bacteria which show exceptionally fast swimming (up to 615 µm s-1) at H2S/O2 interfaces. |
Trichodesmium |
A genus of cyanobacteria responsible for a large proportion of nitrogen fixation in the oceans. Filaments aggregate to form large reddish-brown colonies on the ocean surface, visible from space. Specialized cells separate the processes of photosynthesis and nitrogen fixation. |
Trichodesmium contortum |
A cyanobacterium closely related to the more familiar T. erythraeum, which is responsible for a large proportion of nitrogen fixation in the oceans. Filaments aggregate to form colonies on the ocean surface. Specialized cells separate the processes of photosynthesis and nitrogen fixation. Distinguished from T. erythraeum by pigment production and cell structure, including arrangement of gas vesicles and glycogen storage clusters. |
Trichodesmium erythraeum |
A cyanobacterium responsible for a large proportion of nitrogen fixation in the oceans. Filaments aggregate to form large reddish-brown colonies on the ocean surface, visible from space. Specialized cells separate the processes of photosynthesis and nitrogen fixation. |
Trichodesmium hildebrandtii |
A cyanobacterium closely related to the more familiar T. erythraeum, which is responsible for a large proportion of nitrogen fixation in the oceans. Filaments aggregate to form colonies on the ocean surface. Specialized cells separate the processes of photosynthesis and nitrogen fixation. Distinguished from T. erythraeum by pigment production and cell structure, including arrangement of gas vesicles and glycogen storage clusters. |
Trichodesmium tenue |
A cyanobacterium closely related to the more familiar T. erythraeum, which is responsible for a large proportion of nitrogen fixation in the oceans. Filaments aggregate to form colonies on the ocean surface. Specialized cells separate the processes of photosynthesis and nitrogen fixation. Distinguished from T. erythraeum by pigment production and cell structure, including arrangement of gas vesicles and glycogen storage clusters. |
Trichosporon |
A large genus of basidiomycte yeasts, common as saprotrophs in soil; some cause opportunistic skin infections of humans and animals. Some strains have been isolated from seawater and marine sediments. |
Tupanvirus |
The name given to two strains of giant tailed viruses isolated from deep ocean sediment and a soda lake, distinguished by the exceptionally large virions (up to 1.25 µm) and an almost complete apparatus for the translation of all 20 standard amino acids in proteins. |
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Vibrio |
A large genus of highly motile bacteria with curved rod-shaped cells common in coastal environments and associated with surfaces and with animal and human diseases. |
Vibrio alginolyticus |
A facultatively anaerobic chemoorganotroph, widely distributed in association with marine organisms and surfaces. Curved rods, rapid motility by polar flagella. Grow rapidly in culture, moderately halophilic, produces swarming colonies on agar. Sometimes responsible for cellulitis following infection of wounds. |
Vibrio anguillarum |
A facultatively anaerobic chemoorganotroph responsible for vibriosis infection of fish and mortalities in invertebrate aquaculture. Curved rods, rapid motility by polar flagella. |
Vibrio carchariae |
A facultatively anaerobic chemoorganotroph sometimes implicated as a cause of white band disease of Acropora corals. |
Vibrio cholerae |
A facultatively anaerobic chemoorganotroph inhabiting coastal and estuarine waters, with adaptations for rapid proliferation in the human intestine, causing the severe epidemic diarrheal disease cholera. Curved rods, rapid motility by polar flagella. |
Vibrio coralliilyticus |
A facultatively anaerobic chemoorganotroph which is pathogenic for corals and a range of other organisms, responsible for mortalities in invertebrate aquaculture. Curved rods, rapid motility by polar flagella. |
Vibrio fischeri (reclassified as Aliivibrio fischeri) |
A widely distributed facultatively anaerobic chemoorganotroph occurring in planktonic form and in association with marine organisms. Notable for its bioluminescent properties, especially in symbiotic association with squid. Curved rods, rapid motility by polar flagella. |
Vibrio harveyi
|
A facultatively anaerobic chemoorganotroph which occurs widely in the plankton of tropical and sub-tropical waters, reaching high densities in association with algal blooms. Distinguished by its pronounced bioluminescence. Also occurs widely in association with marine animals, and an important pathogen in fish, molluscs, and crustaceans and sometimes implicated in coral disease. Curved rods, rapid motility by polar flagella. |
Vibrio nigripulchritudo |
A facultatively anaerobic chemoorganotroph with curved rods and rapid motility by polar flagella. A highly virulent pathogen of cultured crustaceans in New Caledonia and other areas of the Indo-Pacific. Distinguished by striking blue-black colonies on agar. |
Vibrio ordalii |
A facultatively anaerobic chemoorganotroph with curved rods and rapid motility by polar flagella. A highly virulent pathogen causing mortality in salmon aquaculture in Pacific coastal waters off Oregon, Washington State, and British Columbia. |
Vibrio owensii |
A facultatively anaerobic chemoorganotroph with curved rods and rapid motility by polar flagella. A highly virulent pathogen of cultured crustaceans isolated in Queensland, Australia. |
Vibrio parahaemolyticus |
A facultatively anaerobic chemoorganotroph, widely distributed in association with marine organisms and surfaces. Curved rods, rapid motility by polar flagella (or peritrichous on surfaces). Grows rapidly in culture, moderately halophilic, produces swarming colonies on agar. Sometimes responsible for cellulitis following infection of wounds. |
Vibrio penaeicida |
A facultatively anaerobic chemoorganotroph. A major pathogen of tropical prawn and shrimp aquaculture. |
Vibrio proteolyticus |
A facultatively anaerobic chemoorganotroph, commonly associated with marine invertebrates and implicated in yellow blotch/band disease of corals. |
Vibrio rotiferianus |
A facultatively anaerobic chemoorganotroph, commonly associated with marine invertebrates and implicated in yellow blotch/band disease of corals. |
Vibrio shilonii |
A facultatively anaerobic chemoorganotroph with curved rods and rapid motility by polar flagella. First named as V. shiloi (this name is still used by some authors) as the causative agent of bacterial bleaching in the coral Oculina patagonica. |
Vibrio splendidus |
A facultatively anaerobic chemoorganotroph which occurs widely and is readily cultivated from coastal seawater, sediments, and marine invertebrates. Curved rods, rapid motility by polar flagella. It is a major pathogen in cultured molluscs (especially oysters) and crustaceans. |
Vibrio tapetis |
The causative agent of brown ring disease leading to high mortality in cultured Manila clams (Ruditapes philippinarum); the pathogen attaches to the clam tissue, causing abnormal thickening and a characteristic brown ring along the edge of the shell. |
Vibrio tubiashii |
A facultatively anaerobic chemoorganotroph which is responsible for mortalities in invertebrate aquaculture, especially the larval stage of molluscs. Curved rods, rapid motility by polar flagella. |
Vibrio vulnificus |
A facultatively anaerobic chemoorganotroph, responsible for fatal human infections (septicemia) following consumption of infected oysters or infection of wounds. Curved rods, rapid motility by polar flagella. |
Vibro alginolyticus |
A facultatively anaerobic chemoorganotroph, widely distributed in association with marine organisms and surfaces. Sometimes implicated in coral diseases. Curved rods, rapid motility by polar flagella. Grow rapidly in culture, moderately halophilic, produces swarming colonies on agar. Sometimes responsible for cellulitis following infection of wounds. |
Whispovirus |
The genus of the dsDNA White spot syndrome virus of crustaceans; a major cause of mortality in tropical shrimp culture. |
Woodsholea maritima |
A Gram-negative, curved rod-shaped bacterium possessing a stalk, which adheres to surfaces in seawater. Chemoorganotrophic, aerobic, distinguished by presence of particular fatty acids. |
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Yersinia |
A genus of Gram-negative fermentative enteropathogenic bacteria present in the intestines of animals, responsible for human infections via contaminated food products, or blood by flea bites in the case of plague. |
Zobellia galactanivorans |
A Gram-negative, chemoorganotrophic rod-shaped bacterium isolated from the surface of red algae. Distinguished by the possession of enzymes for degradation of complex algal polysaccharides including agar and carageenans. |