What Are Cyanobacteria?

Scoop a jar of water from a summer pond, scrape the slick film from a creek rock, or look closely at the dark crust on a damp sidewalk, and you are likely to find cyanobacteria. They are among the most abundant photosynthetic organisms on Earth and among the oldest lineages of life [1, 2]. Their ancestors filled the atmosphere with oxygen; their descendants live on inside every chloroplast; and today a handful of them form the harmful blooms that close lakes to swimming. This chapter explains what kind of organism a cyanobacterium is, and why that matters for everything that follows in this unit.

1.1Bacteria that photosynthesize like plants

Cyanobacteria are a phylum of bacteria that carry out oxygenic photosynthesis: they use light energy to split water, release oxygen gas, and build sugars from carbon dioxide — the same overall process that occurs in algae and plants [3]. Because they photosynthesize this way, are often green or blue-green, and can grow as visible films, filaments and scums, nineteenth- and twentieth-century biologists classified them with the algae as the "blue-green algae" (Cyanophyta or Cyanophyceae). Smith's classic 1983 analysis of lake phytoplankton, for example, still refers to "blue-green algae (Cyanophyta)" [4].

Electron microscopy and, later, molecular phylogenetics settled the question: cyanobacteria are prokaryotes. Their cells have no nucleus, no mitochondria and no chloroplasts, and their genes place them firmly within the domain Bacteria [3, 5]. The name "blue-green algae" survives because it is familiar: public advisories, including Kentucky's, still use it so that people recognize the warning [6]. In this portal we use cyanobacteria for the organisms and treat "blue-green algae" as a common name.

1.2The prokaryotic cell

A cyanobacterial cell is usually only a few micrometers across, but it is far from simple. Its cell envelope is the Gram-negative type: a plasma membrane, a layer of peptidoglycan, and an outer membrane, often wrapped in a sheath or mucilage [3]. Inside, there is no membrane-bound nucleus; the chromosome lies in a region called the nucleoid. The most distinctive feature is a system of internal photosynthetic membranes, the thylakoids, that fills much of the cytoplasm. In algae and plants, thylakoids are enclosed inside chloroplasts; in cyanobacteria, they lie free in the cell [7].

Several other structures are worth recognizing because they explain cyanobacterial ecology:

• Phycobilisomes — light-harvesting antenna complexes attached to the outer surface of the thylakoids (described in Section 1.3) [7].
• Carboxysomes — protein-shelled compartments that package the carbon-fixing enzyme Rubisco together with concentrated CO₂, making carbon fixation efficient even when dissolved CO₂ is scarce [8].
• Gas vesicles — hollow, gas-filled protein structures in many planktonic species that make cells buoyant. Groups of gas vesicles scatter light and make cells look dark or shimmering under the microscope [9].
• Storage granules — reserves of carbohydrate, nitrogen and phosphate. The ability to take up and store phosphorus when it is briefly abundant is one of several traits that help cyanobacteria compete with other phytoplankton [10].

The last row of Table 1.1 is the practical one. Under a student microscope, a cyanobacterial cell usually looks evenly tinted blue-green, olive or reddish throughout, while a green alga shows one or more sharply bounded green chloroplasts — for example, the ribbon-like spiral chloroplast of Spirogyra. Chapter 2 builds on this distinction.

1.3Oxygenic photosynthesis and pigments

Cyanobacteria are the only bacteria that perform oxygenic photosynthesis. Their thylakoid membranes hold the same two linked light reactions — photosystem II and photosystem I — that chloroplasts use. Photosystem II pulls electrons from water, releasing O₂; the electrons pass along an electron transport chain to photosystem I and finally reduce NADP⁺ to NADPH, while the resulting proton gradient drives ATP synthesis. ATP and NADPH then power the Calvin cycle, which fixes CO₂ in the carboxysomes [3, 8].

The primary pigment is chlorophyll a, the same pigment found in every chloroplast. What gives many cyanobacteria their blue-green color is a second set of pigments, the phycobiliproteins. These water-soluble, brightly colored proteins — blue phycocyanin and allophycocyanin, and in some species red phycoerythrin — are assembled into phycobilisomes on the thylakoid surface. Phycobilisomes absorb green, yellow and orange light that chlorophyll absorbs poorly and funnel the energy to the photosystems [7]. Changing the proportions of these pigments lets cyanobacteria use light efficiently in turbid water or deep in a lake [10].

Phycocyanin has a practical use for researchers: because few other organisms make it, instruments that measure phycocyanin fluorescence can estimate how much cyanobacterial biomass is in the water. Chlorophyll a, by contrast, measures all phytoplankton together. Neither pigment says anything about toxins (Chapter 5).

1.4How cyanobacteria changed the planet

Before oxygenic photosynthesis, Earth's atmosphere contained almost no free oxygen. Geochemical evidence records a lasting rise in atmospheric oxygen, the Great Oxidation Event, roughly 2.4 billion years ago; oxygen then rose again much later, toward the end of the Precambrian [12]. Cyanobacteria are the only organisms known to have invented oxygenic photosynthesis, so they are the source of that oxygen [12, 13].

Exactly when oxygenic photosynthesis began, and why oxygen took so long to accumulate, are still debated. Single study One molecular-clock analysis concluded that multicellular (filamentous) forms arose before the Great Oxidation Event and that the event coincided with a burst of cyanobacterial diversification [14]. Such dates depend on calibration assumptions and should be read as hypotheses supported by one line of evidence.

The consequences of oxygenation were enormous: an ozone layer, oxidized minerals such as iron oxides in rocks, and eventually the possibility of oxygen-using (aerobic) metabolism that complex animals depend on [12].

1.5From free-living cell to chloroplast

Every chloroplast descends from a cyanobacterium. In a process called primary endosymbiosis, an ancestral eukaryotic cell engulfed a cyanobacterium and, instead of digesting it, kept it. Over time the partner lost most of its genes — many moved to the host's nucleus — and became an organelle [15]. That event gave rise to the Archaeplastida: glaucophytes, red algae, green algae and land plants [16]. The evidence includes the chloroplast's own small circular genome, its bacterial-type ribosomes, its double envelope membrane, and the close relationship between chloroplast genes and cyanobacterial genes.

Single study Which cyanobacterial lineage was the ancestor is less certain. A 2017 phylogenomic analysis concluded that plastids descend from an early-branching freshwater lineage [16]; other studies have proposed different positions. Many other algae — including diatoms, which students will meet constantly in Kentucky streams — obtained their plastids secondhand, by engulfing a eukaryotic alga that already had one [15].

1.6Ecological roles

Cyanobacteria live almost anywhere there is light and at least occasional water: open oceans, lakes and reservoirs, streams, hot springs, soils, desert crusts, rock surfaces and tree bark [17]. Their main ecological roles are:

• Primary production. As photosynthesizers, they convert light and CO₂ into organic matter that supports food webs, and they are important contributors to global carbon cycling [13].
• Nitrogen fixation. Some species convert atmospheric N₂ into ammonia using the enzyme nitrogenase. Because nitrogenase is destroyed by oxygen — which photosynthesis produces — many filamentous species fix nitrogen inside specialized cells called heterocytes (also called heterocysts) that lack oxygen-producing photosystem II [18]. Nitrogen fixation adds new nitrogen to ecosystems and lets these species grow when dissolved nitrogen runs low.
• Partnerships. Cyanobacteria are the photosynthetic partners in many lichens and live inside some plants, supplying fixed nitrogen [17].
• Bloom formation. In warm, nutrient-rich, slow-moving water, a few species can increase rapidly and dominate the phytoplankton, sometimes producing toxins — the subject of Chapters 3–5 [2, 1].

The same traits that make cyanobacteria ecologically important — buoyancy, efficient light harvesting, phosphorus storage, nitrogen fixation and dormant resting cells — are the traits that let some of them outcompete algae in enriched waters [10].

1.7Connection to local research

Key terms

Cyanobacteria

Photosynthetic bacteria that perform oxygenic photosynthesis with chlorophyll a.

Prokaryote

A cell with no nucleus or membrane-bound organelles.

Thylakoid

Internal membrane where the light reactions occur; free in the cytoplasm in cyanobacteria.

Phycobilisome

Antenna complex of phycobiliproteins that captures light for the photosystems.

Phycocyanin

Blue phycobiliprotein characteristic of cyanobacteria; measured as an index of cyanobacterial biomass.

Carboxysome

Protein compartment concentrating Rubisco and CO₂.

Heterocyte

Specialized nitrogen-fixing cell in some filamentous cyanobacteria.

Great Oxidation Event

The lasting rise of atmospheric oxygen roughly 2.4 billion years ago.

Primary endosymbiosis

The engulfment of a cyanobacterium by a eukaryote that produced the first chloroplasts.

More terms: glossary.

Knowledge check

1. A classmate says "blue-green algae are just a kind of algae." What two pieces of evidence would you use to correct them?

   Show answer and explanation

   Cyanobacteria lack a nucleus and membrane-bound organelles such as chloroplasts and mitochondria (cell structure), and their genes group them with other bacteria rather than with eukaryotes (molecular phylogeny). "Blue-green algae" is a historical common name.

2. Why can a phycocyanin sensor estimate cyanobacteria specifically, while a chlorophyll a measurement cannot?

   Show answer and explanation

   Chlorophyll a is present in all photosynthetic phytoplankton, so it measures them together. Phycocyanin is made by cyanobacteria (and very few other organisms), so its fluorescence tracks cyanobacterial biomass more specifically. Neither measures toxins.

3. Nitrogenase is inactivated by oxygen, yet cyanobacteria produce oxygen. How do filamentous species such as Dolichospermum solve this problem?

   Show answer and explanation

   They separate the two processes in space: nitrogen fixation occurs in heterocytes, thick-walled cells that lack oxygen-producing photosystem II, while neighboring vegetative cells photosynthesize and exchange fixed carbon and nitrogen with them.

4. List three lines of evidence that chloroplasts descended from cyanobacteria.

   Show answer and explanation

   Chloroplasts have their own small circular genome; they have bacterial-type ribosomes; they are surrounded by a double membrane; and their genes are most closely related to cyanobacterial genes. Any three of these are correct.