U.S. Department of the Interior

U.S. Geological Survey

Open-File Report 2015–1164

Field and Laboratory Guide to Freshwater Cyanobacteria 

Harmful Algal Blooms for Native American and Alaska 

Native Communities
Cover. Photographs showing 

1. Cyanobacteria, Gloeotrichia echinulata (Midge Eliassen) 

2. Euglenophyta, Euglena sp. (Ann St. Amand) 

3. Euglenophyta, Euglena sanguinea (Barry H. Rosen) 

4. Anabaenopsis arnoldii (Barry H. Rosen) 

5. Dolichospermum circinale (Ann St. Amand) 

6. Dolichospermum crassum (Ann St. Amand) 

7. Dolichospermum lemmermannii (Ann St. Amand) 

8. Haplosiphon hibernicus (Barry H. Rosen)

9. Sphaerospermopsis torques-reginae (Barry H. Rosen) 

10. Microcystis wesenbergii (Barry H. Rosen) 

11. Spirogyra sp. (Ann St. Amand)

123

4

5

6

7

8

9

10 11
Field and Laboratory Guide to Freshwater 

Cyanobacteria Harmful Algal Blooms 

for Native American and Alaska Native 

Communities

By Barry H. Rosen and Ann St. Amand

Open-File Report 2015–1164

U.S. Department of the Interior

U.S. Geological Survey
U.S. Department of the Interior

SALLY JEWELL, Secretary

U.S. Geological Survey

Suzette M. Kimball, Acting Director

U.S. Geological Survey, Reston, Virginia: 2015

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Suggested citation:

Rosen, B.H., and St. Amand, Ann, Field and laboratory guide to freshwater cyanobacteria harmful algal blooms 

for Native American and Alaska Native Communities: U.S. Geological Survey Open-File Report 2015–1164, 44 p., 

http://dx.doi.org/10.3133/ofr20151164. 

ISSN 0196-1497 (print)

ISSN 2331-1258 (online)

ISBN 978-1-4113-3971-2
iii

Contents

Acknowledgments.........................................................................................................................................v

Abstract...........................................................................................................................................................1

Introduction.....................................................................................................................................................1

Field Images....................................................................................................................................................4

Microscope Images.....................................................................................................................................16

Cyanobacteria Microscopic Identification Characteristics ........................................................16

Cyanobacteria .....................................................................................................................................18

Anabaenopsis.............................................................................................................................18

Aphanizomenon .........................................................................................................................19

Chrysosporum (Anabaena) ......................................................................................................20

Cuspidothrix (Aphanizomenon) ...............................................................................................20

Cylindrospermopsis...................................................................................................................20

Dolichospermum (Anabaena)..................................................................................................21

Gloeotrichia.................................................................................................................................24

Haplosiphon................................................................................................................................25

Microcystis .................................................................................................................................26

Nodularia.....................................................................................................................................29

Nostoc sp. ...................................................................................................................................30

Oscillatoria sp.............................................................................................................................31

Planktothrix (Oscillatoria).........................................................................................................31

Plectonema (Lyngbya)...............................................................................................................32

Raphidiopsis................................................................................................................................32

Schizothrix sp. ............................................................................................................................33

Sphaerospermopsis (Anabaena) ............................................................................................33

Woronichinia (Coelospherium)................................................................................................35

Other Organisms Viewed Under the Microscope .........................................................................36

Euglenophyta (Euglenoids).......................................................................................................36

Pyrrhophyta (Dinoflagellates)..................................................................................................37

Haptophyta (Golden Algae)......................................................................................................38

Chlorophyta (Green Algae).......................................................................................................39

References....................................................................................................................................................41
iv

Figures

1. Cyanobacteria, Dolichospermum lemmermannii ....................................................................4

 2. Cyanobacteria, Microcystis aeruginosa...................................................................................4

 3. Cyanobacteria, Microcystis aeruginosa...................................................................................4

 4. Cyanobacteria, Dolichospermum lemmermannii ....................................................................5

 5. Cyanobacteria, Dolichospermum lemmermannii ....................................................................5

 6. Cyanobacteria, Dolichospermum mendotae............................................................................6

 7. Cyanobacteria, Gloeotrichia echinulata ...................................................................................6

 8. Cyanobacteria, Microcystis viridis ............................................................................................7

 9. Cyanobacteria, Dolichospermum lemmermannii ....................................................................7

 10. Cyanobacteria, Aphanizomenon flos-aquae............................................................................8

 11. Cyanobacteria, Aphanizomenon flos-aquae............................................................................8

 12. Cyanobacteria, Nodularia spumigena.......................................................................................9

 13. Cyanobacteria, Plectonema wollei............................................................................................9

 14. Cyanobacteria, Woronichinia naegeliana................................................................................9

 15. Cyanobacteria, Cylindrospermopsis raciborskii....................................................................10

 16. Cyanobacteria, Planktothrix agardhii/prolifica......................................................................10

 17. Green algae, Mougeotia sp. .....................................................................................................11

 18. Green algae, Spirogyra sp. .......................................................................................................11

 19. Green algae, Cladophora sp. ....................................................................................................11

 20. Green algae, Mougeotia sp. .....................................................................................................11

 21. Duckweed: Wolffia columbiana ...............................................................................................12

 22. Duckweed: Wolffia columbiana, Lemna minor......................................................................12

 23. Charophyta, Chara sp. ...............................................................................................................13

 24. Charophyta, Chara sp. ...............................................................................................................13

 25. Rooted macrophytes ..................................................................................................................13

 26. Rooted macrophytes ..................................................................................................................13

 27. Euglenophyta, Euglena sp. ........................................................................................................14

 28. Euglenophyta, Euglena sanguinea...........................................................................................14

 29. Water fern, Azolla sp. ................................................................................................................15

 30. Pine pollen ...................................................................................................................................15

 31. Pyrrhophyta, Durinskia dybowskii ...........................................................................................15

 32. Morphology of cyanobacteria filaments.................................................................................16

 33. Morphology of cyanobacteria colonies..................................................................................17

 34. Anabaenopsis arnoldii ...............................................................................................................18

 35. Aphanizomenon flos-aquae ......................................................................................................19

 36. Aphanizomenon gracile.............................................................................................................19

 37. Chrysosporum ovalisporum ......................................................................................................20

 38. Cuspidothrix issatschenkoi .......................................................................................................20

 39. Cylindrospermopsis raciborskii................................................................................................20

 40. Dolichospermum circinale ........................................................................................................21

 41. Dolichospermum crassum ........................................................................................................22

 42. Dolichospermum lemmermannii ..............................................................................................22

 43. Dolichospermum mendotae......................................................................................................23
v

 44. Dolichospermum planctonicum ...............................................................................................23

 45. Gloeotrichia echinulata .............................................................................................................24

 46. Haplosiphon hibernicus.............................................................................................................25

 47. Microcystis aeruginosa.............................................................................................................26

 48. Microcystis viridis ......................................................................................................................27

 49. Microcystis wesenbergii...........................................................................................................28

 50. Nodularia spumigena.................................................................................................................29

 51. Nodularia spumigena.................................................................................................................29

 52. Nostoc sp. ...................................................................................................................................30

 53. Oscillatoria sp. ............................................................................................................................31

 54. Planktothrix agardhii ..................................................................................................................31

 55. Plectonema wollei ......................................................................................................................32

 56. Raphidiopsis mediterranea .......................................................................................................32

 57. Schizothrix sp. ............................................................................................................................33

 58. Sphaerospermopsis torques-reginae .....................................................................................33

 59. Sphaerospermopsis aphanizomenoides.................................................................................34

 60. Woronichinia naegeliana ..........................................................................................................35

 61. Euglena sp. ..................................................................................................................................36

 62. Euglena sanguinea .....................................................................................................................37

 63. Durinskia dybowskii, Peridinium sp., Ceratium hirundinella ...............................................37

 64. Prymnesium parvum...................................................................................................................38

 65. Green algae: Spirogyra sp., Cladophora sp., Mougeotia sp. ..............................................39

 66. Green algae: Pithophora sp. ....................................................................................................40

Tables

1. Classification, common names, and synonyms for most freshwater algae .......................1

2. Common cyanotoxin-producing cyanobacteria that are illustrated in this guide .....................3

3. Cyanobacteria synonyms (see table 2) .............................................................................................3

Abbreviations

EPA U.S. Environmental Protection Agency

HAB harmful algal bloom

sp. species
vi

Acknowledgments

This project was funded by the U.S. Geological Survey, Office of Tribal Relations. The authors 

thank Monique Fordham and Keith Loftin, U.S. Geological Survey, for their advice and review 

comments. We also thank the numerous photograph contributors who are acknowledged in the 

captions of the figures. All photographs were used with written permission from the respective 

photographers.
Abstract

Cyanobacteria can produce toxins and form harmful algal 

blooms. The Native American and Alaska Native communities 

that are dependent on subsistence fishing have an increased 

risk of exposure to these cyanotoxins. It is important to 

recognize the presence of an algal bloom in a waterbody and 

to distinguish a potentially toxic harmful algal bloom from a 

non-toxic bloom. This guide provides field images that show 

cyanobacteria blooms, some of which can be toxin producers, 

as well as other non-toxic algae blooms and floating plants that 

might be confused with algae. After recognition of a potential 

toxin-producing cyanobacterial bloom in the field, the type(s) 

of cyanobacteria present needs to be identified. Species 

identification, which requires microscopic examination, may 

help distinguish a toxin-producer from a non-toxin producer. 

This guide also provides microscopic images of the common 

cyanobacteria that are known to produce toxins, as well as 

images of algae that form blooms but do not produce toxins.

Introduction

Algae are a group of organisms with similar traits that 

unify them as a group but with specific characteristics that are 

used to separate one organism from another. As an example, 

chlorophyll a, used by algae to capture sunlight for photosynthesis, is common to virtually all organisms called “algae.” 

One major separation of algae is the basic cellular organization 

into prokaryotic organisms, such as the cyanobacteria that 

do not have internal organelles, and eukaryotic organisms, 

which include all the rest of the algal groups. The eukaryotic 

organisms are further divided on the basis of pigments, cell 

wall composition, photosynthetic storage compounds, flagella, 

and genetics. Many flagellated forms have greater affinity and 

are often classified as Protozoa. 

Most recently, genetic affiliations between the hierarchical organization of algae and the individual species has led to 

a continuous flux in the names of organisms. Many approaches 

are available for organizing these groups. Table 1, which is 

based on the “Freshwater Algae of North America, 2015” 

(Wehr and others, 2015), provides a list of the “groups” of 

algae as well as some common names and synonyms for most 

freshwater algae.

Field and Laboratory Guide to Freshwater Cyanobacteria 

Harmful Algal Blooms for Native American and Alaska 

Native Communities 

By Barry H. Rosen1 and Ann St. Amand2

Table 1. Classification, common names, and synonyms for most freshwater algae. 

Division, Phylum, Group, or Class Common name Synonyms

Cyanobacteria1 Blue-green algae, cyanobacteria, cyanophytes Cyanophyta, Cyanophycota, Cyanophyceae

Chlorophyta2 Green algae Chlorophycota

Charophyceae2 Stoneworts Charophyta

Bacillariophyceae3 Diatoms Bacillariophyta3

Rhodophyta3 Red algae

Euglenophyta3 Euglenoids Euglenophyta

Pyrrhophyta3 Dinoflagellates Dinophyta, Pyrrophyta, Dinophyceae3

Haptophyceae3 Golden algae Haptophyta, Prymnesiophyta

Synurophyceae,3

 Chrysophyceae3 Golden or golden-brown algae Chrysophytes, Synurophytes

Cryptophyta3 Cryptomonads

1

Oren (2004). 2Leliaert and others (2012). 3Wehr and others (2015).

1

U.S. Geological Survey.

2

PhycoTech, Inc.
2 Field and Laboratory Guide to Freshwater Cyanobacteria Harmful Algal Blooms for Native American and Alaska Native Communities

Algae are primary producers and serve as the base of the 

food web in most aquatic habitats. Phytoplankton is a term 

that describes the assemblage of algae that live in the water 

column of a waterbody, including ponds, lakes, reservoirs, 

rivers, and marine habitats. Periphyton are the algae attached 

to plants, rocks, sand, and wood in most aquatic habitats. 

For phytoplankton, each group of algae has unique qualities 

that allow it to thrive at a different time and under specific 

environmental conditions in a waterbody, typically seasonally, 

with one group giving way to another as conditions change in 

the process called succession. For example, diatoms typically 

dominate in colder months and cyanobacteria and green 

algae in warmer months. When the abundance algae causes 

a “problem,” typically a surface scum or accumulation on or 

near a shoreline, it is given the name “algae bloom” and many 

times “harmful algae blooms” (HABs). An algae bloom forms 

under the correct environmental conditions, including nutrient 

abundance, stability of the water column, ample light, and 

optimal temperatures. Although many different types of algae 

are responsible for HABs, cyanobacteria pose the greatest 

problem and are the focus of this guide.

Cyanobacteria, also known as blue-green algae, are a 

group of microorganisms that live in moist terrestrial and 

aquatic habitats throughout the world. Several types of 

cyanobacteria are known to produce a variety of toxins that 

can cause a range of effects from simple skin rashes to liver 

and nerve damage and even mortality of fish, wildlife, and 

rarely, humans (Chorus and Bartrum, 1999). The major groups 

of toxins are the microcystins, saxitoxins, anatoxins, cylindrospermopsins, nodularins, and dermatoxins. These toxins 

typically represent a family of structurally related compounds, 

termed derivatives, which have similar biological effects. 

The complexity of these toxins and their derivatives 

makes attribution of a specific compound to a specific species 

difficult. A field sample is often a mixture of organisms, thus 

the toxin attribution to a given species in a sample is uncertain. 

The best method for attributing a specific compound to a 

specific species involves isolating an organism and culturing it 

to ascertain that it is the source of toxin production; however, 

this is a difficult task and creates a myriad of secondary issues. 

Much of literature describes the dominant organism in a 

bloom and typically attribute the toxin present to that organism. Table 2 provides a synopsis of the toxins found in the 26 

cyanobacteria illustrated in the Microscope Images section 

of this guide. Note that some species are known to produce 

multiple toxins, and it is beyond to scope of this report to 

identify all of the genera and species identified in the literature 

as toxin producers. 

Added to this complexity is the definition of a species 

in the cyanobacteria. The long-standing identification of a 

species is dependent on the morphology of the organism, 

including the shape of the cells, the positioning of key 

features, size, and coloration. Some of these features are stable 

and conservative, while others are more unstable and change 

under certain environmental conditions. With the advent of 

genetic techniques, many of these traditional visual features 

have become secondary to the genetic makeup of an organism; 

however, genetic affiliation relies on being able to analyze an 

individual isolated species. The cyanobacteria have undergone 

substantial name changes to align the genetically affiliated 

organisms into closely related taxa, especially at the genus 

level. Table 3 provides the current name of cyanobacteria 

described in this document, along with the synonyms used 

in the past, to assist in properly identifying organisms and 

interpreting the literature. It is beyond to scope of this report 

to identify all of the synonyms that are used for each purported 

toxin-producing species of cyanobacteria.

Most bloom-forming cyanobacteria can regulate their 

buoyancy to optimize their position in the water column and 

float to the surface. Wind can also cause massive accumulations of phytoplankton on downwind shorelines. Improperly 

treated drinking water containing toxic cyanobacteria can 

cause liver and nervous system impairment in mammals 

including humans (Chorus and Bartram, 1999). Although 

many cyanobacteria often produce taste and odor compounds 

as well, the presence or absence of taste and odor compounds 

is not predictive of the presence of algal toxins.

The human consumption of fish and shellfish exposed 

to a cyanobacteria (and cyanotoxins) is poorly documented. 

Only a few studies have been conducted to examine fish 

and shellfish concentrations for key compounds, such as 

the microcystins (shrimp: Zimba and others, 2006; Ibelings 

and Chorus, 2007; catfish: Zimba and others, 2001; carp: Li 

and other, 2004), the nodularins (mullet: Stewart and others, 

2012), and the saxitoxins (freshwater mussel, Pereira and 

others, 2004). In a report by the National Environmental 

Justice Advisory Council (2002), which provided advice to the 

“Environmental Protection Agency (EPA) on how to improve 

the quality, quantity, and integrity of our Nation’s aquatic 

ecosystems in order to protect the health and safety of people 

consuming or using fish, aquatic plants, and wildlife,” HABs 

are not discussed. This report does recognize that many Native 

American and Alaska Native communities are dependent on 

subsistence fishing, creating an increased risk of exposure 

to traditional toxins, such as mercury and dioxins, which 

accumulate in the aquatic food webs. By comparison, the 

impact of HABs and cyanotoxins on humans, especially the 

Native American and Alaska Native communities, warrants 

additional study. 

Warming global temperatures may exacerbate the 

growth of cyanobacterial blooms (Paerl and Huisman, 2009). 

One reason is that cyanobacteria proliferate in warm water 

temperatures, generally above 25 degrees Celsius (Robarts and 

Zohary, 1987), and are more tolerant of these warmer conditions than their competitors, such as the green algae (Elliott and 

others, 2006; Jöhnk and others, 2008). Warmer surface waters 

also augment vertical stratification (Jöhnk and others, 2008), 

giving the cyanobacteria a unique advantage over eukaryotic 

algae because many the cyanobacteria are able to regulate their 

buoyancy and overcome vertical stratification. Numerous other 

physiological adaptations will give cyanobacteria an advantage 

as global climate changes occur (Carey and others, 2012).
Introduction 3

Anabaenopsis sp.

microcystins (Lanaras and Cook, 1994)

saxitoxins (Ballot and others, 2010b-[genes present])

Aphanizomenon flos-aquae

saxitoxins (Ferreira and others, 2001; Ballot and others, 

2010b-[genes present]) 

cylindrospermopsins (Preussel and others, 2006)

Aphanizomenon gracile

saxitoxins (Ballot and others, 2010b)

cylindrospermopsins (Kokociński and others, 2013)

Chrysosporum ovalisporum

cylindrospermopsins (Akcaalan and others, 2014)

Cuspidothrix issatschenkoi

saxitoxins (Ballot and others, 2010b-[genes present])

anatoxin-a (Ballot and others, 2010a)

Cylindrospermopsis raciborskii

cylindrospermopsins (Sinha and others, 2014)

Dolichospermum circinale

saxitoxins (D’Agostino and others, 2014)

microcystins (Vezie and others, 1998; D’Agostino and 

others, 2014)

anatoxin-a (Sivonen and others, 1989a, 1992a)

Dolichospermum crassum

anatoxin-a(s) (Becker and others, 2010)

Dolichospermum lemmermannii

anatoxin-a(s) (Henriksen and others, 1997)

Dolichospermum mendotae

cylindrospermopsins (Akcaalan and others 2014)

anatoxin-a (Rapala and others, 1993)

Dolichospermum planctonicum

anatoxin-a (Bruno and others, 1994)

Gloeotrichia echinulata

microcystins (Carey and others, 2007)

Haplosiphon hibernicus

microcystins (Prinsep and others, 1992)

Microcystis aeruginosa

microcystins (Rinehart and others, 1994)

Microcystis viridis

microcystins (Watanabe and others, 1986; Kusumi and 

others, 1987)

Microcystis wesenbergii

microcystins (Namikoshi and others, 1992; Tanabe and 

others, 2009)

Nodularia spumigena

nodularins (Carmichael and others, 1988; Sivonen and 

others, 1989b; Stewart and others, 2012)

Nostoc sp.

microcystins (Sivonen and others, 1990, 1992b)

nodularins (Gehringer and others, 2012)

Oscillatoria sp.

anatoxin-a (Aráoz and others, 2005)

Planktothrix agardhii

microcystins (Sivonen and others, 1990)

Plectonema wollei

saxitoxins (Mez and others, 1996)

Raphidiopsis mediterranea

anatoxin-a (Namikoshi and others, 2003; Watanabe and 

others, 2003)

Schizothrix sp.

dermatotoxins (Lippy and Erb, 1976; Mynderse and others, 

1977)

Sphaerospermopsis torques-reginae

anatoxin-a(s) (Molica and others, 2005)

Sphaerospermopsis aphanizomenoides

microcystins (Bittencourt-Oliveira and others, 2011)

cylindrospermopsins (Bittencourt-Oliveira and others, 

2011)

Woronichinia naegeliana

microcystins [perhaps] (Faassen and Lürling 2013)

Table 2. Common cyanotoxin-producing cyanobacteria that are illustrated in this guide.

Table 3. Cyanobacteria synonyms (see table 2).

Currently accepted genus/species Synonym Reference

Chrysosporum ovalisporum Aphanizomenon ovalisporum Zapomelová and others, 2012

Cuspidothrix issatschenkoi Anabaena issatschenkoi

Aphanizomenon issatschenkoi

Rajaniemi and others, 2005

Dolichospermum

 (many species)

Anabaena (most planktonic forms) Wacklin and others, 2009

Planktothrix agardhii 

 (and many other species)

Oscillatoria agardhii Anagnostidis and Komárek, 1988

Sphaerospermopsis aphanizomenoides Aphanizomenon aphanizomenoides Zapomelová and others, 2010

Sphaerospermopsis torques-reginae Anabaena torques-reginae Werner and others, 2012

Woronichinia Coelosphaerium Komárek and Hindák, 1988 

 (for many species)
4 Field and Laboratory Guide to Freshwater Cyanobacteria Harmful Algal Blooms for Native American and Alaska Native Communities

In an effort to help Native American and Alaska Native 

communities develop an awareness of what HABs look like 

in the field and distinguish HABs from a non-toxic bloom, the 

U.S. Geological Survey has developed this guide to illustrate 

the appearance of both typical algal and cyanobacteria blooms. 

Many of the organisms require the use of a microscope to 

correctly determine the type of bloom that is present. Included 

in this guide are microscopic images that illustrate many of 

the most common HABs and others that are known to be 

a nuisance or produce toxins that are not obvious surface 

bloom-forming organisms. Graham and others (2008) provide 

guidelines for the design and sampling for cyanotoxins in 

lakes and reservoirs. 

Field Images

When approaching a water bloom, caution and safety 

procedures should be used to prevent direct contact with the 

bloom because some cyanotoxins can be absorbed through the 

skin. These field photographs illustrate the color, “texture,” 

and general appearance of water blooms, both harmful and 

non-toxic, including nuisance blooms of green algae, certain 

floating plants, and other known blooms that may be encountered. Recognizing a cyanobacterial bloom in a waterbody 

and distinguishing it from other blooms that may or may not 

be harmful is the first step in becoming aware of the potential 

risk in surface water blooms. Figure 1 illustrates the common 

coloration of a blue-green algae bloom, or cyanobacterium; 

many variations of blue-green algae exist as illustrated in 

figures 2–16. Coloration is not an indicator of the genus of 

the organism(s), although repeated sampling and microscopic 

confirmation from the same waterbody should increase the 

likelihood of correctly identifying the key organisms seen 

when in the field.

Many cyanobacteria float and often accumlate along the 

shoreline as illustrated in figures 2–7. These accumulations 

ofen appear clumped or scummed (figs. 3–5). Cells standed 

on the shoreline often leak their pigments. Phycocyanin is a 

blue pigment and can turn a waterbody or shoreline turquoise 

(fig. 6) or chartreuse (fig. 7). Blooms can also be evenly 

dispersed in the water (figs. 8–10) or evenly dispersed as 

clumps (fig. 11). Some cyanobacteria appear brown in color 

due to the red pigment phycoerythrin and its combination with 

other pigments (figs. 12–15). Red to pink blooms are another 

phenonmenon due to phycoerythrin (fig. 16). 

Figure 1. Cyanobacteria, Dolichospermum lemmermannii. 

(Photograph: Ann St. Amand)

Figure 2. Cyanobacteria, Microcystis aeruginosa. (Photograph: 

Ann St. Amand)

Figure 3. Cyanobacteria, Microcystis aeruginosa. (Photograph: 

Ann St. Amand)
Field Images 5

Figure 4. Cyanobacteria, Dolichospermum lemmermannii. (Photograph: Ann St. Amand)

Figure 5. Cyanobacteria, Dolichospermum lemmermannii. (Photograph: Ann St. Amand)
6 Field and Laboratory Guide to Freshwater Cyanobacteria Harmful Algal Blooms for Native American and Alaska Native Communities

Figure 6. Cyanobacteria, Dolichospermum mendotae. (Photograph: Ann St. Amand)

Figure 7. Cyanobacteria, Gloeotrichia echinulata.

(Photograph: Midge Eliassen)
Field Images 7

Figure 8. Cyanobacteria, Microcystis viridis. (Photograph: Ann St. Amand)

Figure 9. Cyanobacteria, Dolichospermum lemmermannii. (Photograph: Ann St. Amand)
8 Field and Laboratory Guide to Freshwater Cyanobacteria Harmful Algal Blooms for Native American and Alaska Native Communities

Figure 10. Cyanobacteria, Aphanizomenon flos-aquae.

(Photograph: Ann St. Amand)

Figure 11. Cyanobacteria, Aphanizomenon flos-aquae. (Photograph: Jacob Kann)
Field Images 9

Figure 12. Cyanobacteria, Nodularia spumigena. 

(Photograph: Wayne Wurtsbaugh)

Figure 13. Cyanobacteria, Plectonema wollei. 

(Photograph: Ken Wagner)

Figure 14. Cyanobacteria, Woronichinia naegeliana. (Photograph: Ann St. Amand)
10 Field and Laboratory Guide to Freshwater Cyanobacteria Harmful Algal Blooms for Native American and Alaska Native Communities

Figure 15. Cyanobacteria, Cylindrospermopsis raciborskii. (Photograph: Ann St. Amand)

Figure 16. Cyanobacteria, Planktothrix agardhii/prolifica. (Photograph: Richard Holmes)
Field Images 11

Other types of HABs and floating plants can be 

distinguished from cyanobacteria blooms by color and texture. 

Green algae commonly are encountered and typically are 

grass-green in color (figs. 17–19). Many types of green algae 

consist of long, stringy filaments (fig. 20) that feel either 

slippery or like cotton. Some floating aquatic plants may 

look like algae (fig. 21), but close examination shows that 

individual plants are present, such as watermeal (fig. 22) and 

duckweed. One group of algae, the charophytes, are macroscopic and typically are rooted but can get dislodged and float 

in a waterbody (fig. 23). Although they may look like vascular 

plants, a closer look shows their characteristic features 

(fig. 24). Aquatic plants are distinct from algae (figs. 25–26). 

Another group of algae, the euglenoids (Euglenophyta), often 

form surface blooms—some are green in color (fig. 27), and 

others are red (fig. 28). Azolla, a small floating aquatic fern 

also forms a red surface mat (fig. 29). Occasionally, pollen 

from plants can form a thick accumulation, typically with a 

distinct yellowish color (fig. 30). Dinoflagellate (Pyrrhophyta) 

blooms, although typically found in saline waters, occasionally bloom in freshwater and typically have a tan-brown and 

sometimes blackish appearance (fig. 31).

Figure 17. Green algae, Mougeotia sp. (Photograph: Steve 

Heiskary, Minnesota Pollution Control Agency)

Figure 18. Green algae, Spirogyra sp. (Photograph: Ken Wagner)

Figure 19. Green algae, Cladophora sp. (Photograph: Ann St. 

Amand)

Figure 20. Green algae, Mougeotia sp. (Photograph: Steve 

Heiskary, Minnesota Pollution Control Agency)
12 Field and Laboratory Guide to Freshwater Cyanobacteria Harmful Algal Blooms for Native American and Alaska Native Communities

Figure 21. Duckweed: Wolffia columbiana (also called watermeal). (Photograph: Ann St. Amand)

Figure 22. Duckweed: Left, Wolffia columbiana; Right, Lemna minor. (Photographs: Barry H. Rosen)
Field Images 13

Figure 23. Charophyta, Chara sp. (Photograph: Barry H. Rosen)

Figure 24. Charophyta, Chara sp. (Photograph: Ann St. Amand)

Figure 25. Rooted macrophytes. (Photograph: Ann St. Amand)

Figure 26. Rooted macrophytes. (Photograph: Ann St. Amand)
14 Field and Laboratory Guide to Freshwater Cyanobacteria Harmful Algal Blooms for Native American and Alaska Native Communities

Figure 27. Euglenophyta, Euglena sp. (Photograph: Ann St. Amand)

Figure 28. Euglenophyta, Euglena sanguinea, a known toxin 

producer. (Photograph: Barry H. Rosen)
Field Images 15

Figure 29. Water fern, 

Azolla sp. (Photograph: 

Bob Kirschner, Chicago 

Botanic Garden, Illinois)

Figure 30. Pine pollen. (Photograph: Linda Green, University of 

Rhode Island Watershed Watch)

Figure 31. Pyrrhophyta, Durinskia dybowskii. 

(Photograph: Brian Magott, Oklahoma 

Department of Environmental Quality)
16 Field and Laboratory Guide to Freshwater Cyanobacteria Harmful Algal Blooms for Native American and Alaska Native Communities

Microscope Images

Field collections of potentially HABs need followup 

examination with a microscope to determine that the bloom 

is in fact cyanobacteria and if it is or is not a known toxin 

producer. The following collection of images include some of 

the same organisms in the field image section of this guide, as 

well as additional organisms that are of importance because 

of the toxins they produce. In addition, some of the harmless 

organisms are illustrated so the user can distinguish between 

harmful and non-toxic organisms. Various laboratories are 

located around the country that specialize in the identification 

of organisms and perform toxin analyses. Each laboratory has 

a preferred collection methodology and preservation techniques that should be followed for the most accurate results. 

Cyanobacteria Microscopic Identification 

Characteristics

Recognizing a cyanobacterium under the microscope 

involves observing characteristics associated with that 

morphology. Proper identification often relies on a species 

dichotomous key (Komárek and Anagnostidis, 2001, 2005; 

Komárek, 2013) to determine what the organism might be. 

Often times the shape and dimensions of the cells (length 

and width) are required for resolving a specimen to the 

species level.

Filament – a chain or stack of cells

• Some of these filaments consist of cells stacked like a 

roll of coins, with the individual cells being a single 

coin (fig. 32, image on the left). 

• Some are round cells attached end to end like a string 

of pearls (fig. 32, image on the right). 

• Some filaments are straight, some are coiled (fig. 32, 

the two images on the left and on the right, respectively). 

• Some species make a resting spore, an akinete (fig. 32, 

label A) along the length or at the end of a filament. 

• Some species have heterocytes, specialized cells in 

the filament that fix atmospheric nitrogen (previously 

termed heterocysts) (fig. 32, label H), along the length 

or at the end of a filament. 

A

H

Figure 32. Morphology of cyanobacteria filaments. Straight and coiled forms, as well as features important in 

distinguishing the grouping of organisms. (Photographs: Left and right, Barry H. Rosen; Center, Ann St. Amand)
Microscope Images 17

Colony – a collection of cells, most with a distinct or irregular 

pattern

• Many species are embedded in a common mucilaginous matrix that may or not be visible under the 

microscope (fig. 33).

• Some species have a set number of cells per colony, 

others are more heterogeneous.

• Some colonies are made up of filaments (fig. 33, 

bottom image).

Figure 33. Morphology of cyanobacteria colonies. Round to oval cells or filaments embedded in a mucilaginous 

matrix; features important in distinguishing the grouping of organisms. (Photographs from Rosen and others, 2010)
18 Field and Laboratory Guide to Freshwater Cyanobacteria Harmful Algal Blooms for Native American and Alaska Native Communities

Cyanobacteria

The following images are grouped alphabetically by genus and are based on the latest naming conventions at the time 

of publication. The recent use of genetics has led to the renaming of many organisms and the traditional genera; where 

appropriate, the previous name is included in parentheses.

Anabaenopsis

Figure 34. Anabaenopsis arnoldii. Two focal planes of the same filament. Note the heterocyte at 

both ends of this curled filament in the image on the left (arrow). (Photographs: Barry H. Rosen)
Microscope Images 19

Aphanizomenon

Aphanizomenon flos-aquae

Figure 35. Aphanizomenon flos-aquae. Filaments clustered in bundles (upper) and individual filaments (lower). 

(Photographs: Left, Barry H. Rosen; Right, Ann St. Amand)

Figure 36. Aphanizomenon gracile. Filament showing akinetes (left) and a heterocyte (right). (Photographs: 

Ann St. Amand)

Aphanizomenon gracile
20 Field and Laboratory Guide to Freshwater Cyanobacteria Harmful Algal Blooms for Native American and Alaska Native Communities

Chrysosporum (Anabaena)

Figure 37. Chrysosporum ovalisporum. Filament showing 

akinetes and heterocytes. (Photograph: Ann St. Amand)

Cuspidothrix (Aphanizomenon)

Figure 38. Cuspidothrix issatschenkoi. Filament showing a 

heterocyte. (Photographs: Barry H. Rosen)

Cylindrospermopsis 

Figure 39. Cylindrospermopsis raciborskii. Filament showing 

straight and curled morphs. Heterocytes are found at the end of 

the filaments; akinete found adjacent to heterocyte (lower left). 

(Photographs: Barry H. Rosen)
Microscope Images 21

Dolichospermum (Anabaena)

Dolichospermum circinale

Figure 40. Dolichospermum circinale. Spherical cells in the curved filaments. Heterocytes are along the length of the filaments and 

are about the same size as the vegetative cells. (Photograph: Ann St. Amand)
22 Field and Laboratory Guide to Freshwater Cyanobacteria Harmful Algal Blooms for Native American and Alaska Native Communities

Dolichospermum crassum

Figure 41. Dolichospermum crassum. Spherical cells in the coiled filament. Heterocytes are along 

the length of the filaments and are about the same size as the vegetative cells. (Photograph: Ann 

St. Amand)

Dolichospermum lemmermannii 

Figure 42. Dolichospermum lemmermannii. Coiled filaments connecting to form a colony. Akinetes enlarged, slightly bent 

(right image). (Photographs: Left, Ann St. Amand; Right, Margaret K. Spoo-Chupka)
Microscope Images 23

Dolichospermum mendotae

Figure 43. Dolichospermum mendotae. Irregularly coiled filaments with heterocytes and elongated akinetes. 

(Photograph: Andrew Chapman)

Figure 44. Dolichospermum planctonicum. Round cells in a straight filament; enlarged akinetes. (Photograph: 

Ann St. Amand) 

Dolichospermum planctonicum
24 Field and Laboratory Guide to Freshwater Cyanobacteria Harmful Algal Blooms for Native American and Alaska Native Communities

Gloeotrichia 

Figure 45. Gloeotrichia echinulata. Filaments tapered, forming a colony, with an overall appearance of a pin cushion 

(lower left image). The base of each filament terminates in a heterocyte (lower right image). (Photographs: Barry H. 

Rosen)

200 μm
Microscope Images 25

Haplosiphon 

Figure 46. Haplosiphon hibernicus. Filament has true branching and rectangular heterocytes. 

(Photographs: Barry H. Rosen)

5 μm
26 Field and Laboratory Guide to Freshwater Cyanobacteria Harmful Algal Blooms for Native American and Alaska Native Communities

Microcystis

Microcystis aeruginosa

Figure 47. Microcystis aeruginosa. Round to oval cells embedding a mucilaginous matrix. Cell color varies from 

brown to various shades of green and blue-green. (Photographs: Barry H. Rosen) 
Microscope Images 27

Microcystis viridis

Figure 48. Microcystis viridis. Paired cells round to oval cells in “packets” embedded in a 

mucilaginous matrix. (Photographs: Ann St. Amand)
28 Field and Laboratory Guide to Freshwater Cyanobacteria Harmful Algal Blooms for Native American and Alaska Native Communities

Microcystis wesenbergii

Figure 49. Microcystis wesenbergii. Round cells dispersed in a 

robust, well defined common mucilaginous envelope; individual. 

(Photographs: Barry H. Rosen)
Microscope Images 29

Nodularia

Nodularia spumigena

Figure 50. Nodularia spumigena. Cells arranged in filaments, heterocytes common 

and at somewhat regular intervals, with distinct constrictions at the junction 

between barrel-shaped cells. (Photograph: Ann St. Amand)

Nodularia spumigena

Figure 51. Nodularia spumigena. Cells arranged in filaments, 

heterocytes common, with distinct constrictions at the junction 

between cells. (Photograph: Ann St. Amand) 
30 Field and Laboratory Guide to Freshwater Cyanobacteria Harmful Algal Blooms for Native American and Alaska Native Communities

Nostoc sp.

Figure 52. Nostoc sp. Filaments have round cells (elongated before cell division). Filaments embedded both 

individual and a common mucilaginous matrix. (Photographs: Barry H. Rosen) 
Microscope Images 31

Oscillatoria sp.

Figure 53. Oscillatoria sp. Cells in filaments, shorter than 

wide. Color varies from green, blue-green, to dark brown. Upper 

photograph is O. limosa. (Photographs: Barry H. Rosen) 

Planktothrix (Oscillatoria)

Figure 54. Planktothrix agardhii. Filaments composed of 

cells that range from longer than wide to slightly shorter 

than wide. Lightly pigmented. Can have both terminal cells 

tapered; often one end of a filament is rounded and the other 

end tapered. (Photographs: Upper and middle, Barry H. Rosen; 

Bottom, Ann St. Amand)
32 Field and Laboratory Guide to Freshwater Cyanobacteria Harmful Algal Blooms for Native American and Alaska Native Communities

Plectonema (Lyngbya)

Figure 55. Plectonema wollei. Cells in filaments with sheaths. 

Large diameter filaments, with cells stacked like coins in the 

filaments. Bottom image illustrates a cell turned on its side. 

Most dark brown in color. (Photographs: Top, Barry H. Rosen; 

Bottom, Ann St. Amand)

Raphidiopsis

Figure 56. Raphidiopsis mediterranea. This genus is characterized by curving filaments and the presence of akinetes but not 

heterocytes. This genus may eventually be merged with Cylindrospermopsis. (Photographs: Barry H. Rosen)
Microscope Images 33

Schizothrix sp.

Figure 57. Schizothrix sp. Thin, slender filaments with cells 

longer than wide, within a sheath and typically multiple 

filaments intertwined. (Photographs: Barry H. Rosen)

Sphaerospermopsis (Anabaena)

Figure 58. Sphaerospermopsis torques-reginae. Filaments 

composed of round cells and coiled, with some regularity. 

Heterocyte with two adjacent, spherical akinetes (top image), 

often on both sides of the heterocyte. (Photographs: Barry H. 

Rosen)
34 Field and Laboratory Guide to Freshwater Cyanobacteria Harmful Algal Blooms for Native American and Alaska Native Communities

Figure 59. Sphaerospermopsis aphanizomenoides. Filaments composed of rounded cells but not 

coiled, akinetes adjacent to both sides of heterocytes (not in this image). (Photograph: Ann St. Amand)
Microscope Images 35

Woronichinia (Coelospherium)

Figure 60. Woronichinia naegeliana. Cells, round to oval, in colonies embedded on the outer edge of the mucilaginous 

matrix (not throughout like Microcystis). (Photographs: Barry H. Rosen)
36 Field and Laboratory Guide to Freshwater Cyanobacteria Harmful Algal Blooms for Native American and Alaska Native Communities

Other Organisms Viewed Under the Microscope

The remaining collection of images include some of the same organisms in the field image section of this guide, as 

well as additional organisms that are of importance because they can cause issues in a waterbody or may be an indicator 

of a water quality concern. In addition, some of the harmless organisms are illustrated so the user can distinguish between 

harmful and harmless organisms.

Euglenophyta (Euglenoids)

Euglena 

This organism can form a surface scum on waterbodies that have been enriched with nutrients that look almost oily. 

One species, Euglena sanguinea, is known to produce the alkaloid fish and mammal toxin, euglenophycin (Zimba and 

others, 2010).

Figure 61. Euglena sp. (see figure 27). Surface scums indicate nutrient enrichment. Euglena cells can swim using a long flagellum, 

and they typically have a visible red eyespot (inset). (Photograph: Ann St. Amand; Inset photograph: Barry H. Rosen)
Microscope Images 37

Euglena sanguinea

Figure 62. Euglena sanguinea (see figure 28). This organism 

accumulates the pigment astaxanthin and imparts a red color 

to individual cells and to surface scums. (Photograph: Barry H. 

Rosen)

Pyrrhophyta (Dinoflagellates)

The Pyrrhophyta, more commonly called dinoflagellates, include both freshwater and marine representatives. In the 

marine environment, approximately 5 percent are known to produce toxins. These toxins are associated with red tides and 

shellfish poisoning. Saxitoxin is a common and potent paralytic neurotoxin produced by some marine species. The following 

figure illustrates some common freshwater dinoflagellates that may bloom, but they are not known to produce toxins.

Figure 63. Left: Durinskia dybowskii (see figure 31). Right: 

Peridinium sp.; Bottom: Ceratium hirundinella. (Photographs: 

Top left, Ann St. Amand; Top right and bottom: Barry H. Rosen)
38 Field and Laboratory Guide to Freshwater Cyanobacteria Harmful Algal Blooms for Native American and Alaska Native Communities

Haptophyta (Golden Algae)

This group of algae is infamous because of one species, Prymnesium parvum. It is known to cause large fish kills in 

brackish waters and is widely distributed, but does not seem to affect humans. Texas, Oklahoma, New Mexico, Colorado, 

Wyoming, North Carolina, South Carolina, Georgia, Arkansas, and Alabama have all reported waterbodies with this 

organism. 

Figure 64. Prymnesium parvum. Note the color of the chromoplast (left) and 

the two flagella (right) that allow this organism to swim. (Photographs: Left, 

Barry H. Rosen; Right, Ann St. Amand)
Microscope Images 39

Chlorophyta (Green Algae)

The green algae generally do not produce toxins; however, enriched waterbodies often experience excess green 

algal growth, visible as long bright or grassy green and sometime dark green filaments. These filaments are typically 

slippery or cottony to the touch, depending on which group of organisms they are associated with. The following figure 

shows three characteristic filamentous green algae and can be compared to the cyanobacteria images.

Figure 65. Green algae. Top: Spirogyra sp., with helical or spiral chloroplast (see figure 19). Middle: Cladophora sp., 

showing branched filaments (see figure 18). Bottom: Mougeotia sp., with flat, plate-like chloroplast (see figure 20). 

(Photographs: Top and middle, Ann St. Amand; Bottom, Barry H. Rosen) 
40 Field and Laboratory Guide to Freshwater Cyanobacteria Harmful Algal Blooms for Native American and Alaska Native Communities

Figure 66. Green algae, Pithophora sp. with characteristic swollen “akinetes” (Photographs: Ann St. Amand)
References 41

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References 43

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Manuscript was approved on August 24, 2015.

Prepared by the U.S. Geological Survey Science Publishing 

Network, Raleigh Publishing Service Center

For more information concerning this publication, contact

Barry Rosen, Biologist

U.S. Geological Survey

Caribbean-Florida Water Science Center

12703 Research Parkway

Orlando, FL 32826

(407) 803-5508

brosen@usgs.gov
Rosen and St. Amand—Field and Laboratory Guide to Freshwater Cyanobacteria Harmful Algal Blooms for Native American and Alaska Native Communities—Open-File Report 2015–1164

ISSN 0196-1497 (print)

ISSN 2331-1258 (online)

http://dx.doi.org/10.3133/ofr20151164