Biology at SCC
Freshwater Ecology & Watershed Research

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Glossary

Definitions written for introductory biology students. Each term links to the chapter that develops it.

Akinete
A thick-walled, enlarged resting cell formed by some filamentous cyanobacteria (order Nostocales). Akinetes survive cold, darkness or drying in sediments and can germinate to seed a later bloom. Read moreSee also: Heterocyte (heterocyst)
Anatoxin-a
A fast-acting neurotoxin produced by some cyanobacteria (for example some Dolichospermum, Aphanizomenon and benthic Microcoleus). It overstimulates nerve–muscle junctions; dog deaths after contact with benthic mats have often been linked to anatoxins. Read moreSee also: Cyanotoxin, Benthic
Artificial path
In the National Hydrography Dataset, a flowline drawn through a lake, reservoir or wide river so that the stream network stays connected. It represents routing, not a channel you can see. Read moreSee also: National Hydrography Dataset (NHD)
Benthic
Living on or attached to the bottom — rocks, sediment, wood or plants — rather than floating in the water column. Many stream cyanobacteria are benthic and grow as mats or films. Read moreSee also: Planktonic, Biofilm
Biofilm
A community of microorganisms (bacteria, cyanobacteria, algae, fungi, protists) embedded in a self-produced slime on a surface. Stream rocks are typically coated with biofilm. Read moreSee also: Benthic, Periphyton
Biomanipulation
Deliberately changing a food web — usually by removing plankton-eating fish so that large grazers such as Daphnia increase — to reduce algae and improve water clarity. Read moreSee also: Daphnia
Bloom
A rapid increase in the abundance of phytoplankton or attached algae, often visible as discolored water, scum or mats. 'Bloom' describes biomass; it does not by itself mean the bloom is harmful or toxic. Read moreSee also: Harmful algal bloom (HAB), Scum
Blue-green algae
A traditional common name for cyanobacteria, from their blue-green color and their algae-like photosynthesis. Still used in public advisories, but cyanobacteria are bacteria, not algae. Read moreSee also: Cyanobacteria
Carboxysome
A protein-shelled compartment inside cyanobacterial cells that packages the carbon-fixing enzyme Rubisco with concentrated CO₂, making carbon fixation more efficient. Read more
Chlorophyll a
The primary photosynthetic pigment of cyanobacteria, algae and plants. Measured in water as a general index of phytoplankton biomass; it does not distinguish cyanobacteria from other algae. Read moreSee also: Phycocyanin
Co-limitation
When growth responds most strongly to adding two resources together (for example nitrogen and phosphorus) rather than either one alone. Read moreSee also: Limiting nutrient
Cyanobacteria
A phylum of photosynthetic bacteria that carry out oxygen-producing photosynthesis with chlorophyll a. They are prokaryotes — no nucleus or chloroplasts — and range from single cells to colonies and filaments. Read moreSee also: Blue-green algae, Prokaryote
Cyanotoxin
A toxic compound produced by some strains of cyanobacteria. Major groups include liver toxins (microcystins), nerve toxins (anatoxins, saxitoxins) and a cell toxin (cylindrospermopsin). The same species can include toxic and non-toxic strains. Read moreSee also: Microcystin, Anatoxin-a, Cylindrospermopsin, Saxitoxin
Cylindrospermopsin
A cyanotoxin that inhibits protein synthesis and damages the liver, kidney and other organs. Much of it can be dissolved in the water rather than held inside cells. Read moreSee also: Cyanotoxin
Daphnia
Small filter-feeding crustaceans ('water fleas') that graze on phytoplankton. Their response to cyanobacteria is a model system for studying grazer tolerance and coevolution. Read moreSee also: Zooplankton, Grazing
Dissolved (extracellular) toxin
Toxin that is free in the water rather than inside cells, usually released when cells die or are lysed — for example by an algaecide. Read moreSee also: Intracellular toxin
Endosymbiosis (primary)
The engulfment and retention of one cell by another, ending in a permanent partnership. Chloroplasts descend from a cyanobacterium taken up by an ancestral eukaryote. Read more
Eutrophication
Enrichment of a water body with nutrients, especially nitrogen and phosphorus, leading to increased plant and algal growth, reduced clarity and, as organic matter decays, lower dissolved oxygen. Read moreSee also: Limiting nutrient, Internal loading
Gas vesicle
A hollow, gas-filled protein structure inside some cyanobacterial cells that provides buoyancy. Clusters of gas vesicles look dark or refractile under the microscope. Read moreSee also: Planktonic
Grazing
Consumption of algae, cyanobacteria or biofilm by animals such as zooplankton, snails and some fish. Read moreSee also: Daphnia, Zooplankton
Harmful algal bloom (HAB)
A bloom that harms people, animals or the ecosystem — through toxins, oxygen depletion, taste and odor problems or habitat loss. 'Harmful' is a broader claim than 'toxic'. Read moreSee also: Bloom, Cyanotoxin
Heterocyte (heterocyst)
A specialized, thick-walled cell in some filamentous cyanobacteria where nitrogen fixation takes place. It lacks oxygen-producing photosystem II, protecting the oxygen-sensitive nitrogenase enzyme. Usually appears pale and evenly granular. Read moreSee also: Nitrogen fixation, Akinete
Hydrologic connectivity
Whether, when and how water (and what it carries) actually moves from one place to another — over land, through soil, through pipes or underground. Being near something is not the same as being connected to it. Read moreSee also: Watershed, Karst
Hydrologic unit (HUC)
A drainage area in the USGS Watershed Boundary Dataset, identified by a 2- to 16-digit code. Each added pair of digits names a smaller unit nested in the larger one (HUC 8 subbasin, HUC 10 watershed, HUC 12 subwatershed). Read moreSee also: Watershed
Intermittent stream
A stream that flows for part of the year, typically in wet seasons, and is dry or reduced to pools at other times. In NHD this is a map classification that needs field confirmation. Read moreSee also: National Hydrography Dataset (NHD)
Internal loading
Release of nutrients — especially phosphorus — from a lake's own sediments back into the water, often when bottom water loses oxygen. It can sustain blooms after external inputs are reduced. Read moreSee also: Eutrophication
Intracellular toxin
Toxin held inside living cyanobacterial cells. Most microcystin in a healthy bloom is intracellular; it becomes dissolved when cells break. Read moreSee also: Dissolved (extracellular) toxin
Karst
Landscape formed by the dissolution of soluble rock such as limestone, with sinkholes, springs, caves and sinking streams. In karst, water can move underground quickly and cross surface watershed boundaries. Read moreSee also: Sinkhole, Hydrologic connectivity
Limiting nutrient
The nutrient in shortest supply relative to need, so that adding it increases growth. Which nutrient limits can change with place, season and the organisms present. Read moreSee also: Co-limitation
Microcystin
A family of more than 200 related cyclic peptide toxins, mainly affecting the liver, produced by some strains of Microcystis, Planktothrix, Dolichospermum and other genera. The most commonly measured cyanotoxin group in the United States. Read moreSee also: Cyanotoxin
Morphotype
A group of organisms recognized by shared appearance under the microscope. In this portal, a provisional morphotype is a working label used before an identification is confirmed. Read more
Mucilage (sheath)
A gelatinous layer around cells, colonies or filaments. Its shape and visibility help identify genera such as Microcystis and Nostoc. Read more
National Hydrography Dataset (NHD)
The USGS digital map of the nation's streams, rivers, lakes and their connections. A mapped NHD line is evidence of a mapped feature, not of current flow or water quality. Read moreSee also: Artificial path, Hydrologic unit (HUC)
Nitrogen fixation
Conversion of atmospheric N₂ gas into ammonia by the enzyme nitrogenase. Some cyanobacteria can fix nitrogen, which lets them grow when dissolved nitrogen is scarce. Read moreSee also: Heterocyte (heterocyst)
Orthophosphate
Dissolved inorganic phosphate (PO₄³⁻ and related ions), the form of phosphorus most readily used by algae and cyanobacteria. Field kits usually report it as 'reactive phosphate'. Read moreSee also: Eutrophication
Oxygenic photosynthesis
Photosynthesis that splits water as the electron source and releases oxygen, using two linked photosystems. Cyanobacteria invented it; plants and algae inherited it through their chloroplasts. Read moreSee also: Thylakoid
Periphyton
The attached community of algae, cyanobacteria, bacteria and detritus growing on submerged surfaces; the stream ecologist's term for the slippery coating on rocks. Read moreSee also: Biofilm, Benthic
Phycobilisome
A light-harvesting antenna attached to the surface of cyanobacterial thylakoids, built from phycobiliproteins (phycocyanin, allophycocyanin and sometimes phycoerythrin) that pass absorbed light energy to chlorophyll. Read moreSee also: Phycocyanin, Thylakoid
Phycocyanin
A blue accessory pigment (a phycobiliprotein) characteristic of cyanobacteria. Fluorescence sensors that measure phycocyanin give a rough, relative index of cyanobacterial biomass. Read moreSee also: Phycobilisome, Chlorophyll a
Planktonic
Living suspended in the water column, drifting with currents. Bloom-forming lake cyanobacteria such as Microcystis are planktonic. Read moreSee also: Benthic, Gas vesicle
Prokaryote
A cell without a nucleus or membrane-bound organelles; bacteria and archaea are prokaryotes. Read moreSee also: Cyanobacteria
Saxitoxin
A potent nerve toxin that blocks sodium channels; known from marine dinoflagellates ('paralytic shellfish poisoning') and also produced by some freshwater cyanobacteria. Read moreSee also: Cyanotoxin
Scum
A dense layer of buoyant cyanobacteria at the water surface, often concentrated by wind along shorelines. Scums can hold very high toxin concentrations and should not be touched. Read moreSee also: Bloom
Sinkhole
A closed depression formed where soluble bedrock has dissolved or collapsed beneath soil. Sinkholes can route surface runoff directly into groundwater. Read moreSee also: Karst
Thermal stratification
Layering of a lake into warm surface water over colder, denser bottom water, which limits mixing. Calm, stratified conditions favor buoyant cyanobacteria. Read more
Thylakoid
An internal membrane system where the light reactions of photosynthesis occur. In cyanobacteria, thylakoids lie free in the cytoplasm; in algae and plants, they are inside chloroplasts. Read moreSee also: Oxygenic photosynthesis, Phycobilisome
Water residence time
The average time water spends in a lake, reservoir or river reach. Long residence times give slow-growing cyanobacteria time to accumulate; fast-flowing streams flush plankton downstream. Read more
Watershed
The land area that drains to a particular point on a stream, lake or river. Every point on a stream has its own watershed, nested within larger ones. Read moreSee also: Hydrologic unit (HUC), Hydrologic connectivity
Zooplankton
Small animals and animal-like protists drifting in the water — rotifers, copepods and cladocerans such as Daphnia — many of which graze on phytoplankton. Read moreSee also: Daphnia, Grazing