Biology at SCC
Freshwater Ecology & Watershed Research

Identification & taxonomy

Organism Identification Atlas

Reference entries for the organisms SCC students are most likely to meet in local fresh waters, starting with eight cyanobacteria. Each entry gives the features you can see under a microscope, the organisms it is confused with, and the limits of what appearance can tell you.

Confirmed identifications versus provisional morphotypes These are genus-level reference entries, not records from local waters. When students identify organisms from Allen Branch or other sites, each record will state its level: provisional morphotype, genus (morphological), species (morphological) or molecularly confirmed. Student photographs are published only after faculty review. Toxin production is never inferred from appearance.

Microscopy comparison

Choose two organisms to compare their diagnostic features side by side. Photomicrographs — taken at SCC or openly licensed, each with magnification and a calibrated scale bar — will be added as they are reviewed.

The comparison tool needs JavaScript; the full entries are below.

Cyanobacteria

Photosynthetic bacteria: single cells, colonies or filaments, no chloroplasts or nucleus. Seeded with eight freshwater genera.

Microcystis Kützing ex Lemmermann

domain Bacteria › phylum Cyanobacteriota (cyanobacteria) › order Chroococcales › family Microcystaceae

Growth form: colonial

Diagnostic morphology

  • Small spherical cells (a few micrometers across) packed irregularly in a shared mucilage colony
  • Cells look dark or shimmering because they contain gas vesicles
  • Colonies range from small clusters to large, irregular, sometimes perforated masses visible to the eye as green 'paint flecks'
Habitat, look-alikes, limits and toxins
Typical habitat
Planktonic in warm, calm, nutrient-rich lakes, reservoirs and ponds; overwinters on sediments.
Ecological function
Primary producer; the most widespread bloom-former in eutrophic fresh water. Large colonies resist grazing.
Similar-looking organisms
Other colonial coccoid cyanobacteria (e.g., Aphanocapsa, Woronichinia, Snowella); Colonial green algae (have chloroplasts and lack gas vesicles)
Identification limitations
Species have traditionally been named from colony shape and mucilage, which change with conditions and in culture; genetic studies do not support many morphospecies. Toxic and non-toxic strains look the same.
Reported toxin associations
Microcystins: Many, but not all, strains carry microcystin-synthesis genes; the share of toxic genotypes in a population varies. Toxin production cannot be determined by looking at cells.
Local observations
None recorded yet.

Reference entry — no local record Genus-level reference description; no images yet.

Dolichospermum (Ralfs ex Bornet & Flahault) P. Wacklin, L. Hoffmann & J. Komárek

domain Bacteria › phylum Cyanobacteriota (cyanobacteria) › order Nostocales › family Aphanizomenonaceae

Growth form: filamentous · Formerly: Anabaena (planktonic species)

Diagnostic morphology

  • Chains (trichomes) of round to barrel-shaped cells, straight or coiled
  • Gas vesicles in vegetative cells
  • Heterocytes spaced along the filament (intercalary); larger akinetes may be present
Habitat, look-alikes, limits and toxins
Typical habitat
Planktonic in lakes, reservoirs and ponds; often in summer when dissolved nitrogen is low.
Ecological function
Primary producer and nitrogen fixer.
Similar-looking organisms
Benthic Anabaena (no gas vesicles); Sphaerospermopsis; Aphanizomenon; Cuspidothrix
Identification limitations
Species are distinguished by coiling, cell and akinete dimensions and akinete position, which overlap; molecular data are needed for confident species names.
Reported toxin associations
Microcystins, anatoxins, saxitoxins: Reported from some strains; many strains also produce taste-and-odor compounds such as geosmin. Toxin production cannot be determined by looking at cells.
Local observations
None recorded yet.

Reference entry — no local record Genus-level reference description; no images yet.

Aphanizomenon Morren ex Bornet & Flahault

domain Bacteria › phylum Cyanobacteriota (cyanobacteria) › order Nostocales › family Aphanizomenonaceae

Growth form: filamentous

Diagnostic morphology

  • Straight filaments, often aggregated side by side into flakes or bundles that look like floating grass clippings
  • End cells elongated and pale
  • Intercalary heterocytes and elongated akinetes; gas vesicles present
Habitat, look-alikes, limits and toxins
Typical habitat
Planktonic in nutrient-rich lakes and reservoirs, including cooler waters.
Ecological function
Primary producer and nitrogen fixer.
Similar-looking organisms
Dolichospermum; Cuspidothrix; Chrysosporum; Sphaerospermopsis
Identification limitations
The traditional genus contains at least five phylogenetically distant groups; several former species now belong to other genera.
Reported toxin associations
Saxitoxins, cylindrospermopsin, anatoxins: Reported from some members of the traditional genus and related genera; varies by strain. Toxin production cannot be determined by looking at cells.
Local observations
None recorded yet.

Reference entry — no local record Genus-level reference description; no images yet.

Planktothrix Anagnostidis & Komárek

domain Bacteria › phylum Cyanobacteriota (cyanobacteria) › order Oscillatoriales › family Microcoleaceae

Growth form: filamentous · Formerly: Oscillatoria (planktonic species such as O. agardhii and O. rubescens)

Diagnostic morphology

  • Solitary, straight, unbranched filaments without heterocytes or akinetes
  • Cells shorter than wide, with gas vesicles
  • Some species are red-pigmented (phycoerythrin-rich) and live deep in stratified lakes
Habitat, look-alikes, limits and toxins
Typical habitat
Planktonic in shallow turbid lakes (P. agardhii) and deep stratified lakes (P. rubescens).
Ecological function
Primary producer that tolerates low light.
Similar-looking organisms
Oscillatoria; Limnothrix; Planktolyngbya; Pseudanabaena
Identification limitations
Separation from similar unbranched filaments needs gas-vesicle observation and cell dimensions; species identity often requires molecular data.
Reported toxin associations
Microcystins: Commonly reported; toxic and non-toxic strains co-occur. Toxin production cannot be determined by looking at cells.
Local observations
None recorded yet.

Reference entry — no local record Genus-level reference description; no images yet.

Oscillatoria and similar filaments Vaucher ex Gomont (Oscillatoria)

domain Bacteria › phylum Cyanobacteriota (cyanobacteria) › order Oscillatoriales › family Oscillatoriaceae (Oscillatoria)

Growth form: filamentous

Diagnostic morphology

  • Unbranched filaments of short, disc-like cells (much wider than long)
  • No heterocytes or akinetes
  • Filaments glide and slowly rotate or wave — the 'oscillating' movement behind the name
Habitat, look-alikes, limits and toxins
Typical habitat
Benthic mats on sediment, rocks and wood in streams, ponds and lake margins; some in the plankton.
Ecological function
Primary producer; mat-former that stabilizes sediments.
Similar-looking organisms
Phormidium; Microcoleus; Lyngbya; Planktothrix; Tychonema
Identification limitations
'Oscillatoria' was historically used for almost any unbranched filament of this type. Many such organisms now belong to other genera, so older reports — including toxin reports — may refer to different taxa. Treat field identifications as a morphotype ('Oscillatoria-like').
Reported toxin associations
Anatoxins, microcystins (historical reports): Older reports under this name often concern organisms now placed in other genera; check the current name of any cited strain. Toxin production cannot be determined by looking at cells.
Local observations
None recorded yet.

Reference entry — no local record Treated as a morphotype group, not a single genus.

Raphidiopsis F.E. Fritsch & F. Rich

domain Bacteria › phylum Cyanobacteriota (cyanobacteria) › order Nostocales › family Aphanizomenonaceae

Growth form: filamentous · Formerly: Cylindrospermopsis (e.g., C. raciborskii, now R. raciborskii)

Diagnostic morphology

  • Solitary, short to medium filaments, straight, curved or coiled, often tapering at the ends
  • When present, heterocytes are at the filament ends (terminal), not along the middle
  • Akinetes may form near the ends or along the filament
Habitat, look-alikes, limits and toxins
Typical habitat
Planktonic in warm, often turbid lakes and reservoirs; has expanded into temperate regions.
Ecological function
Primary producer; competitive under low light and variable nutrients.
Similar-looking organisms
Other Nostocales filaments without visible heterocytes; Planktolyngbya
Identification limitations
Raphidiopsis and Cylindrospermopsis were separated only by the presence of heterocytes, which can be absent; genetic data supported uniting them. Filaments without heterocytes are easy to misidentify.
Reported toxin associations
Cylindrospermopsin, saxitoxins: Production differs among strains and regions. Toxin production cannot be determined by looking at cells.
Local observations
None recorded yet.

Reference entry — no local record Genus-level reference description; no images yet.

Nostoc Vaucher ex Bornet & Flahault

domain Bacteria › phylum Cyanobacteriota (cyanobacteria) › order Nostocales › family Nostocaceae

Growth form: filamentous (in gelatinous colonies) · Common name: Star jelly; witch's butter (for some terrestrial colonies)

Diagnostic morphology

  • Bead-like chains of round cells tangled inside a firm, shared gelatinous matrix
  • Colonies form jelly balls, sheets or crusts visible to the naked eye
  • Intercalary heterocytes; akinetes in some species
Habitat, look-alikes, limits and toxins
Typical habitat
On soil, rocks and plants in damp places, attached in streams and ponds; also as symbionts of some plants and fungi (lichens).
Ecological function
Nitrogen fixer that adds nitrogen to soils and partner organisms.
Similar-looking organisms
Anabaena (no firm colonial matrix); Trichormus; Desmonostoc
Identification limitations
Colony form is helpful but several genera have been split from Nostoc on genetic grounds.
Reported toxin associations
Microcystins: Reported from some strains; most Nostoc are not known bloom-formers. Toxin production cannot be determined by looking at cells.
Local observations
None recorded yet.

Reference entry — no local record Genus-level reference description; no images yet.

Microcoleus Desmazières ex Gomont

domain Bacteria › phylum Cyanobacteriota (cyanobacteria) › order Oscillatoriales › family Microcoleaceae

Growth form: filamentous · Formerly: Phormidium autumnale group (now Microcoleus autumnalis and relatives)

Diagnostic morphology

  • Unbranched filaments without heterocytes, single or bundled within a common sheath
  • End cell often rounded or capped (a calyptra)
  • Forms dark green to brown-black leathery mats on rocks and gravel
Habitat, look-alikes, limits and toxins
Typical habitat
Benthic in streams and rivers, especially on cobbles in clear, flowing water; also soils and desert crusts.
Ecological function
Primary producer and mat-builder; mats can detach and float downstream.
Similar-looking organisms
Phormidium; Oscillatoria; Tychonema
Identification limitations
Requires careful observation of sheaths, end cells and cell dimensions; reassignments from Phormidium are recent, so older literature uses other names.
Reported toxin associations
Anatoxins: Benthic mats of this group have been linked to dog deaths in rivers elsewhere; toxicity varies greatly among mats. Toxin production cannot be determined by looking at cells.
Local observations
None recorded yet.

Reference entry — no local record Highly relevant to stream sites such as Allen Branch; no local records yet.

Green algae

Eukaryotic algae with grass-green chloroplasts — common look-alikes for cyanobacteria in ponds and streams. Entries planned for Phase 2.

No entries yet in this category.

Diatoms

Eukaryotic algae with glass (silica) cell walls; dominant on many stream rocks. Entries planned for Phase 2.

No entries yet in this category.

Other freshwater protists

Euglenoids, dinoflagellates, ciliates, amoebae and flagellates. Entries planned for Phase 2.

No entries yet in this category.

Zooplankton

Rotifers, copepods and cladocerans that graze phytoplankton. One entry (Daphnia); more in Phase 2.

Daphnia O.F. Müller

domain Eukaryota › phylum Arthropoda › class Branchiopoda › order Anomopoda (Cladocera) › family Daphniidae

Growth form: animal (crustacean, about 0.5–5 mm) · Common name: Water flea

Diagnostic morphology

  • Body enclosed in a clear, two-sided carapace ending in a tail spine
  • Large compound eye; branched second antennae used for swimming in jerky hops
  • Filtering legs visible beating inside the carapace; eggs often visible in a dorsal brood chamber
Habitat, look-alikes, limits and toxins
Typical habitat
Ponds and lakes; rare in fast-flowing streams.
Ecological function
Key filter-feeding grazer linking phytoplankton to fish; target of biomanipulation.
Similar-looking organisms
Ceriodaphnia; Simocephalus; Bosmina
Identification limitations
Species identification needs close examination of the head, spines and postabdomen; hybrids occur.
Local observations
None recorded yet.

Reference entry — no local record Included as the model grazer discussed in Chapter 6.

Aquatic macroinvertebrates

Insect larvae, snails, crustaceans and worms visible without a microscope; classic stream-health indicators. Entries planned for Phase 2.

No entries yet in this category.