et al., 2012).
2.5.6 Gemmatimonadetes
The most recently discovered group of phototrophic bacteria are the Gemmatimonadetes (Zeng et al., 2014). These organisms contain bacteriochlorophyll a, are semiaerobic, and are incapable of assimilating inorganic carbon. Their photosynthetic apparatus is remarkably similar to that found in purple bacteria, and they have almost certainly acquired the ability to carry out photosynthesis by large‐scale horizontal gene transfer.
2.5.7 Cyanobacteria
The cyanobacteria are a large and diverse group of photosynthetic prokaryotes (Bryant, 1994; Flores and Herrero, 2014). They are the only group of photosynthetic bacteria that have oxygenic metabolism, producing molecular oxygen as a byproduct of photosynthesis. Cyanobacteria were previously known as blue‐green algae, although this name is misleading as they are not true algae, which are all eukaryotes. As we will explore in more detail in later chapters, the mechanism of photosynthesis in cyanobacteria is remarkably similar to that in photosynthetic eukaryotes, which therefore makes study of them of special interest. Cyanobacteria are remarkably tough and resilient organisms that inhabit almost any environment where light is available, ranging from freshwater, marine, and terrestrial environments to extreme environments such as hot springs and even the surfaces and subsurface regions of rocks in both Antarctica and scorching hot deserts. Nearly all cyanobacteria are photoautotrophs, although some species can also grow photoheterotrophically. An electron micrograph of a representative cyanobacterium is shown in Fig. 2.4.
The cyanobacterial group includes all phototrophic bacteria that produce oxygen as a byproduct of photosynthesis. Most species contain chlorophyll a and phycobiliproteins, which function as antenna complexes. However, some types of oxygenic photosynthetic prokaryotes deviate from this pattern. These include the chlorophyll b‐containing prochlorophytes and the chlorophyll d‐containing organisms. Phylogenetic studies have shown that all these organisms form a single large phylum according to 16S rRNA (Flores and Herrero, 2014). This phylum is dominated by traditional cyanobacteria, so all prokaryotic oxygenic phototrophs are now usually called cyanobacteria for simplicity.
Figure 2.4 Thin section transmission electron micrograph of the cyanobacterium Synechocystis PCC 6803 prepared by high‐pressure cryofixation. Scale bar 0.4 μm.
Source: Courtesy of Robert Roberson.
Many species of cyanobacteria can fix nitrogen from N2 to NH3, although, to do this, they face a special challenge. The enzyme system that fixes N2, called nitrogenase, is very sensitive to O2. The O2 produced by Photosystem II in cyanobacteria is therefore incompatible with N2 fixation. Cyanobacteria solve this problem in one of several different ways. In some filamentous forms, which grow as strings of cells, approximately every tenth cell will change its characteristics and become a special N2‐fixing cell called a heterocyst (Wolk et al., 1994). In these cells, Photosystem II is absent, an exceptionally thick cell wall inhibits diffusion of O2 into the cell, and O2 scavenging systems keep these cells anaerobic to protect the nitrogenase. The other major strategy employed is to carry out N2 fixation only when it is dark, when the cells are not producing O2. An unusual group of nitrogen fixing cyanobacteria has lost all genes that code for Photosystem II and is an obligate symbiont with a eukaryotic alga (Thompson et al., 2012).
A few groups of cyanobacteria can switch from using H2O as an electron donor to using H2S, with elemental sulfur as the product (Padan, 1979; Liu et al., 2020). They are thus capable of true anoxygenic photosynthesis, although if H2S is absent they produce O2 in much the same way as other cyanobacteria. The anoxygenic metabolism therefore represents an additional capability in these organisms, and they thus differ significantly from the other anoxygenic phototrophic prokaryotes, which cannot produce O2 under any environmental conditions.
Most cyanobacteria contain an extensive internal system of membranes called thylakoids. These membranes contain the photosynthetic apparatus (van de Meene et al., 2006; Liberton et al., 2011). All cyanobacteria contain chlorophyll a. Most species lack chlorophyll b and contain bilin pigments that are organized into large antenna complexes called phycobilisomes (Chapter 5). A group of cyanobacteria, called prochlorophytes, contain chlorophyll b in addition to chlorophyll a (Matthijs et al., 1994). This chlorophyll b‐containing group might logically be assumed to be closely related to the organisms that became the chloroplasts of green algae and higher plants, which contain chlorophyll b. However, this relationship is not supported by analyses of some genetic markers (see below and Chapter 12). The chlorophyll b in these organisms is contained in antenna complexes that are structurally quite different from those of plant and algal chloroplasts. The prochlorophytes do not contain organized phycobilisomes, although some of them do contain genetic information for certain phycobiliproteins.
An important group of prochlorophytes is the genus Prochlorococcus (Partensky et al., 1999). These cells are found in the deeper regions of the photic zone in the oceans. They were overlooked for many years because they are extremely small organisms, less than 1 μm in diameter, and passed through the holes in standard collection filters. Because of their small size, they are sometimes called picoplankton, along with other small marine cyanobacteria. They are also unusual in that the chlorophyll a present, divinyl chlorophyll a, is chemically slightly different from the chlorophyll a found in all other oxygenic phototrophs (Chapter 4), a change that adapts them better to the photic environment where they are found. Other prochlorophytes include Prochloron, which was the first to be discovered. It grows as a symbiont with a marine animal known as an ascidian in the Great Barrier Reef off Australia and in other places in the South Pacific. Evidence strongly suggests that the prochlorophytes are polyphyletic in origin (Palenik and Haselkorn, 1992; Urbach et al., 1992).
Two recently discovered groups of cyanobacteria are of particular interest. They contain the long‐wavelength‐absorbing pigments chlorophyll d and chlorophyll f, which absorb out to nearly 750 nm in the near infrared (Miyashita et al., 1996; Chen et al., 2010). These organisms live primarily in filtered light environments where other organisms above them absorb most of the visible light, so that only the near infrared radiation penetrates more deeply where these organisms live.
2.6 Photosynthetic eukaryotes
Eukaryotic photosynthetic organisms all contain the subcellular organelle called the chloroplast. An overview diagram of the photosynthetic complexes in the chloroplasts of a variety of photosynthetic eukaryotes is shown in Fig. 2.2 (right panel). Chloroplasts are one of a larger group of organelles known as plastids, some of which carry out other functions, such as starch or pigment storage in flowers and fruits. As discussed above, a variety of evidence clearly shows that chloroplasts originated by a process called endosymbiosis, in which a cyanobacterial‐like cell was initially a symbiont with a protoeukaryotic cell and then eventually became a semiautonomous but essential part of the host cell (Margulis, 1993). The chloroplast contains DNA, which is organized and regulated in a manner typical of bacteria, not eukaryotes. This DNA encodes a number of chloroplast proteins that function in photosynthesis and