Cyanobacteria · Chapter 2

Cyanobacterial Diversity and Identification

Full text About 25 minutes Last reviewed 2026-11-05

Learning objectives

After studying this chapter, you should be able to:

Distinguish unicellular, colonial and filamentous growth forms.
Identify heterocytes, akinetes, gas vesicles and mucilage and explain the function of each.
Recognize diagnostic features of eight common freshwater genera.
Explain why genus names such as Anabaena and Cylindrospermopsis have changed.
Explain why microscopic identification cannot determine species with certainty or show whether a population produces toxins.

Cyanobacteria come in a remarkable range of shapes for organisms with no internal organelles: single spheres smaller than a red blood cell, jelly colonies of thousands of cells, straight or coiled chains, and tangled mats that can coat a riverbed. Their shapes and specialized cells are what we see under the microscope, so they are the starting point for identification. This chapter introduces the growth forms and structures, profiles eight genera students are likely to meet in Kentucky waters, and explains — just as importantly — what a microscope cannot tell you.

2.1Growth forms

Microscopists group cyanobacteria by how cells are arranged:

Unicellular — cells live singly or in pairs after division.
Colonial — many cells held together in a shared gelatinous mucilage. Microcystis colonies, for example, contain packed spherical cells in an irregular jelly mass that can be visible to the naked eye.
Filamentous — cells divide in one plane and stay attached end-to-end as a chain called a trichome. A trichome together with any surrounding sheath is a filament. Some filaments are straight, some coiled, some branched, and some can glide.

These categories are useful but not taxonomic in themselves: modern genetic studies show that similar shapes evolved repeatedly in unrelated lineages, which is one reason classifications keep changing [1].

2.2Specialized cells and structures

Four features do most of the work in identification, and each has an ecological meaning:

Heterocytes: Thick-walled, usually paler and evenly granular cells where nitrogen fixation happens. They lack oxygen-producing photosystem II, protecting the oxygen-sensitive nitrogenase enzyme. In the model strain Anabaena (Nostoc) PCC 7120, single heterocytes form at regular intervals of roughly 10 to 20 vegetative cells [2]. Their position — along the filament (intercalary) or at its ends (terminal) — is diagnostic. Older texts call them heterocysts.
Akinetes: Enlarged, thick-walled resting cells packed with reserves, formed by members of the order Nostocales. Akinetes sink to the sediment, survive cold and drying, and can germinate to seed the next season's population [3]. Their size, shape and position relative to heterocytes help separate genera and species.
Gas vesicles: Gas-filled protein cylinders that make cells buoyant; aggregates of them (sometimes called aerotopes) make cells look dark, irregular or shimmering in brightfield light. Gas vesicles let planktonic species regulate their depth — rising toward light and, in calm weather, accumulating as surface scums [4].
Mucilage and sheaths: Extracellular polysaccharide layers. A diffuse jelly holds colonies together (Microcystis); a firm, distinct sheath encloses filaments in many mat-forming genera; a tough common matrix gives Nostoc colonies their rubbery feel. India ink added to a wet mount makes mucilage visible as a clear halo.

Mucilage — shared jelly holding the colony together
Gas-vesicle clusters — dark spots that make cells buoyant
Heterocyte — pale, thick-walled nitrogen-fixing cell

Akinete — enlarged resting cell
Vegetative cells of the trichome
Disc-shaped cells, wider than long

Figure 2.1. Three growth forms. (A) Colonial: cells in shared mucilage, with gas vesicles. (B) A coiled filament of the order Nostocales with an intercalary heterocyte and an akinete. (C) A straight filament of short disc-shaped cells with no heterocytes or akinetes; such filaments often glide. Schematic, not to scale; real proportions vary by species.Original illustration, Biology at SCC, CC BY 4.0.

2.3Eight freshwater genera to know

The genera below include the most common bloom-formers in North American lakes and ponds and the most important mat-formers of streams. Fuller descriptions, look-alikes and references are in the Organism Atlas.

Table 2.1. Diagnostic features of eight freshwater genera
Genus	Form	Heterocytes	Akinetes	Gas vesicles	Typical habitat
Microcystis	Colonial; small spherical cells in mucilage	No	No	Yes	Plankton of warm, enriched lakes and ponds
Dolichospermum	Filament, straight or coiled; round to barrel cells	Intercalary	Yes	Yes	Plankton of lakes and reservoirs
Aphanizomenon	Straight filaments, often in bundles ("grass clippings")	Intercalary	Yes	Yes	Plankton, including cooler waters
Planktothrix	Solitary straight filaments of short cells	No	No	Yes	Plankton of turbid shallow lakes or deep stratified lakes
Oscillatoria and look-alikes	Straight filaments of disc-shaped cells; gliding	No	No	Usually no	Benthic mats; sediments
Raphidiopsis	Short solitary filaments, often tapering	Terminal, or absent	Yes	Yes	Plankton of warm, often turbid waters
Nostoc	Bead-like filaments in a firm jelly colony	Intercalary	Some species	Usually no	Soil, rocks, attached in streams; symbioses
Microcoleus	Filaments, single or bundled in a sheath; mat-forming	No	No	No	Benthic mats in streams and rivers

Two patterns are worth remembering. First, the planktonic bloom-formers (Microcystis, Dolichospermum, Aphanizomenon, Planktothrix, Raphidiopsis) all have gas vesicles, which is how they stay in the light in still water [4, 5]. Second, the stream mat-formers (Microcoleus and Oscillatoria-like filaments) lack gas vesicles and heterocytes and grow attached to surfaces, which is why they matter more for a creek like Allen Branch [6, 7].

Microcystis deserves special mention: it has been recorded blooming in at least 108 countries and is the most frequently cited producer of microcystins [8]. Dolichospermum and Aphanizomenon, both nitrogen fixers, can gain an advantage when dissolved nitrogen is scarce relative to phosphorus — the pattern behind the classic observation that low nitrogen-to-phosphorus ratios favor cyanobacteria, and behind the rise of nitrogen-fixers when nitrogen inputs to an experimental lake were cut [9, 10]. Raphidiopsis (formerly Cylindrospermopsis) is notable for expanding from tropical into temperate waters [11].

2.4Why the names keep changing

Cyanobacteria were classified for over a century almost entirely by appearance. DNA sequencing revealed that many traditional genera mixed unrelated organisms, so names are being revised to match evolutionary relationships — a "polyphasic" approach that combines genes, morphology, ultrastructure and ecology [1]. Between 2014 and 2021 alone, at least 273 new species in 140 genera were described [1]. Three changes affect students in Kentucky directly:

Anabaena → Dolichospermum. Planktonic species with gas vesicles, formerly in Anabaena, were moved to the new genus Dolichospermum in 2009; Anabaena now refers mainly to benthic species without gas vesicles [12, 13]. Older reports — including Kentucky's 1989 livestock poisoning case, attributed to "Anabaena spiroides" — use the old name [14].
Cylindrospermopsis → Raphidiopsis. The two genera were separated only by whether heterocytes were present, a trait that can disappear. A 2018 polyphasic study supported uniting them, and C. raciborskii is now Raphidiopsis raciborskii [15].
Phormidium → Microcoleus. Molecular and morphological work moved the mat-forming Phormidium autumnale group into Microcoleus [16]. River-mat literature from before about 2013 uses Phormidium.

Practical rule: when you read a paper, check the current name in AlgaeBase (opens in a new tab), and record both the name you used and the source you followed.

2.5What a microscope can and cannot tell you

Brightfield microscopy is the right first tool: it is inexpensive, fast and reveals growth form, cell dimensions, heterocytes, akinetes and gas vesicles. It also has firm limits that this portal treats as rules.

Limits of morphological identification

Species are often unresolvable. Colony shape, coiling and cell size vary with growth conditions and change in culture; many traditional morphospecies are not supported by genetic data [8, 13]. Identify to genus — or to a provisional morphotype — unless you have molecular evidence.
Toxicity is invisible. Microcystin-producing and non-producing genotypes of Microcystis coexist in the same lake and look the same; the proportion of toxic genotypes can differ between colony size classes [17]. Toxin genes and toxin concentrations must be measured [18].
The dominant genus does not predict the toxins. In 23 Midwestern blooms, community composition was not strongly correlated with which toxins were present [19].
Look-alikes are common. Colonial green algae, filamentous green algae, diatoms in chains, and even floating plant debris can be mistaken for cyanobacteria in the field [20].

2.6A teaching key to growth forms

The steps below sort a wet-mount specimen into a growth form and a starting genus to check against the Atlas. It is a teaching tool, not a definitive key; consult the USGS field and laboratory guide for photographs of each group and its look-alikes [20].

Are there distinct chloroplasts (sharply bounded green bodies), a visible nucleus or flagella? Yes → a eukaryotic alga or protist, not a cyanobacterium. No, pigment is diffuse → continue.
Are the cells joined in chains (trichomes)? No → step 3. Yes → step 4.
Single cells or a colony? Many small round cells with dark gas-vesicle clusters in an irregular jelly colony → check Microcystis. Without gas vesicles → other colonial coccoid genera; record as a morphotype.
Are there heterocytes (pale, thick-walled cells)? Yes → step 5. No → step 6.
Heterocytes along the chain: filaments in a firm jelly ball or sheet → Nostoc; free filaments with gas vesicles, round or barrel cells → Dolichospermum; straight filaments in bundles with elongated pale end cells → Aphanizomenon. Heterocytes only at the ends of short filaments → Raphidiopsis.
No heterocytes: solitary straight filaments with gas vesicles, floating → Planktothrix (or Raphidiopsis lacking heterocytes); filaments without gas vesicles, attached or in mats, cells disc-shaped and gliding → Oscillatoria-like; several filaments bundled within one sheath, forming dark leathery stream mats → Microcoleus.

Record what you saw (form, dimensions in micrometers measured with a calibrated ocular micrometer, presence of each structure), your provisional identification, and your confidence. The Methods page explains calibration and photomicrography.

2.7Connection to local research

At Allen Branch

Hypothesis If cyanobacteria are present in Allen Branch, benthic, mat-forming filaments without heterocytes (Oscillatoria-like or Microcoleus-like) are more likely than planktonic bloom-formers, because the stream is flowing and shaded. This is a prediction to test, not a finding.

A good first dataset: scrape a measured area of rock at several stations, prepare wet mounts, photograph every distinct morphotype with a scale bar, and record provisional identifications for faculty review. See Chapter 10 and the observation records.

Key terms

Trichome: A chain of cells; with its sheath, a filament.
Mucilage: Extracellular jelly holding colonies or filaments together.
Heterocyte: Nitrogen-fixing cell; intercalary or terminal.
Akinete: Thick-walled resting cell of Nostocales.
Gas vesicle: Gas-filled protein structure providing buoyancy.
Morphotype: A group recognized by appearance; a provisional identification.
Polyphasic taxonomy: Classification combining genetic, morphological, ultrastructural and ecological data.

Knowledge check

You see a straight filament of disc-shaped cells gliding slowly across the slide, with no heterocytes. What is the most defensible label, and why not a species name?

Show answer and explanation
"Oscillatoria-like filament" (a provisional morphotype). Several genera share this appearance, and species-level identification of such filaments needs more characters and usually molecular data.
A pond sample is dominated by Microcystis colonies. A classmate concludes the pond is toxic. What is wrong with that reasoning?

Show answer and explanation
Toxic and non-toxic Microcystis strains look the same; toxin production depends on genotype and conditions. Only a toxin measurement (or, as supporting evidence, toxin-gene analysis) can show whether microcystins are present.
Why do most planktonic bloom-formers have gas vesicles while stream mat-formers usually do not?

Show answer and explanation
In still water, buoyancy lets plankton stay in the lit surface layer; in a stream, cells attached to the bottom are held in place, and flowing water would carry floating cells away.
A 2005 paper reports Anabaena flos-aquae blooms in a reservoir. What name would you check today, and where?

Show answer and explanation
Planktonic Anabaena species were transferred to Dolichospermum (e.g., D. flos-aquae). Check the current accepted name and synonyms in AlgaeBase.

References

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