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Green Phototrophic Bacteria

The green phototrophic Bacteria include three phylogenetic groups: the Green sulfur Bacteria (Chlorobi), the green non-sulfur Bacteria (Chloroflexi), and the cyanobacteria (blue-green algae). They contain bacteriochlorophyl c, d, or e, or chloroohyl a (sometimes with chlorophyl b as well). These give many of these organisms a green color, but overall color is not a consistent trait among these organisms; this color is often masked by the abundant accessory pigments. These organisms also usually contain their antenna complex in discrete membranous organelles, the chlorosomes (green sulfur or non-sulfur Bacteria) or thylakoids (cyanobacteria). Purple phototrophic Bacteria use bacteriochlorophyls a and b, and house their antenna complexes in invaginations of the cytoplasmic membrane.

These three phylogenetic groups are also predominately phototrophic (at least among the familiar species), whereas the purple phototrophic Bacteria and heliobacteria are members of phylogenetic groups (the Proteobacteria and Firmicutes, respectively) that are predominantly non-phototrophic.

Phylum Chloroflexi (Green non-sulfur Bacteria)

Taxonomy

• Phylum Chloroflexi
  • Class Chloroflexi
    • Order Chloroflexales
      • Family Chloroflexaceae
        • Genus Chloroflexus
        • Genus Chloronema
        • Genus Chlorothrix
        • Genus Heliothrix
        • Genus Roseiflexus
        • Genus Kouleothrix
      • Family Oscillochloridaceae
        • Genus Oscillochloris
        • Order Herpetosiphonales
      • Family Herpetosiphonaceae
        • Genus Herptosiphon
  • Class Anaerolineae
    • Order Anaerolinaeles
  • Family Anaerolinaeceae
    • Genus Anaerolinea
  • Order Caldilineales
    • Family Caldilineae
      • Genus Bellilinea
      • Genus Caldilinea
      • Genus Leptolinea
      • Genus Levilinea
      • Genus Longiliea

General characteristics of the Chloroflexi

Diversity
Just over a dozen genera, with only one or sometimes two species in each. Thermomicrobium roseum is sometimes included in this group (and so is included in the tree above), or it may constitute a phylum of its own.

Metabolism
The familiar members of this phylum fall into two general metabolic types: the thermophilic phototrophs (Chloroflexales) and the heterotrophs, some of which are thermophiles (Anerolineae) and some mesophiles (Herpetosiphon).

The phototrophic Chloroflexi carry out anoxygenic photosynthesis; they have a single type of photosystem and carry out cyclic photophosphorylation. They grow best photochemotrophically, but most can fix carbon, but do not use either the Calvin cycle or reverse TCA cycle. Instead they use an unusual pathway found otherwise only in a few Archaea, the hydroxypropionate pathway. Reducing power to reduce CO2 to glyoxylate is from NADPH derived by reverse electron transport from the oxidation of sulfide or hydrogen. Most can also grow by aerobic respiration (heterotrophically).

Morphology
Members of this phylum are flexible unbranched filaments, usually thin (<2μm) with a uniform diameter, and motile by gliding. Septa are present, but not usually visible. Phototrophic species are green or orange en masse, the color depending of which photopigments are produced. Most contain membranous “chlorosomes” resembling individual thylakoids directly beneath the cell membrane; these contain very high concentrations of accessory photopigments (carotinoids and bacteriochlorophyl c), whereas the reaction centers and bacteriochlorophyl a are primarily found in the cytoplasmic membrane. These chlorosomes resemble those of the Chlorobi (see below), but phototrophy in Chloroflexi otherwise resembles that of typical purple bacterial photosynthesis. Phototrophic species grown aerobically become etiolated, and resemble the non-phototrophic species.

The presence of an outer membrane makes this organism formally “Gram-negative”, but they generally seem to lack the lipopolysaccharide (LPS) typical of the Gram-negative envelop. Some are said to have thin sheaths, visible at the ends of filaments, but these may represent cell envelop material left over after breakage of the filaments at dead cells rather than true sheaths.

Habitat
Phototrophic members of this phylum are common and conspicuous in moderate pH hot springs at temperatures from 35°C up to 70°C or more, but are most abundant at about 60°C. Mesophilic heterotrophs are commonly abundant in wastewater sludges. They are also commonly seen in sediments, soil, and freshwater.

Example species

Chloroflexus aurantiacus

C. aurantiacus is the most well-studied phototrophic member of this phylum, most of which have not been grown in pure culture. It was originally isolated from photosynthetic mats surrounding hot springs in Yellowstone National Park. It seems to be the primary producer of the distinctive orange mats found in these hot springs (but see below, the discussion of Roseiflexus), and is also abundant in an orange layer directly beneath the light green cyanobacterial mats at somewhat higher temperatures. Filaments are thin (0.5-1.2μm) and glide slowly, ca. 1μm per minute.

Chloroflexus contains chlorosomes and bacteriochlorophyl c, whereas other Chloroflexi do not. These are traits otherwise found only in the green sulfur Bacteria (Chlorobi), and it is likely that the genes encoding these were acquired by Chloroflexus by horizontal transfer.

Although C. aurantiacus is capable of carbon fixation, in most mats they are found in association with cyanobacteria. In these communities, it is the cyanobacteria that are the primary producers, and the Chloroflexi grow photoheterotrophically from organic carbon produced by the cyanobacteria. They are not capable of fixing nitrogen, but acquire their sulfur from sulfate.

Roseiflexus castenholzii

Roseiflexus very closely resembles Chloroflexus except that it lacks chlorosomes and the associated accessory bacteriochlorophyl c. Although Chloroflexus is usually thought to be the primary member of this phylum in hot springs mats, and is readily cultivated from these mats, both molecular phylogenetic analysis (fluorescent in situ hybridization and rRNA-based surveys) and spectral analysis of photopigments suggests that Roseiflexus is far more abundant.

Herpetosiphon aurantiacus

Herpetosiphon is a mesophilic heterotrophic (non-phototrophic) member of this phylum, isolated from the polysacharide matrix of the eukaryotic alga Chara from Birch lake in Minnesota. Herpetosiphon and morphologically similar organisms are commonly seen in soils and sediments, and especially activated sludge in wastewater treatment, but have rarely been cultivated. Although they are always present in activated sludges, their overgrowth causes the bacterial flocs they reside in to retain bulk water, and not form compact sludge. In some cases, these flocs trap gas bubbles and float, producing a thick foam. Microbiologists at wastewater treatment facilities therefore monitor these organisms in the aerobic digestion process, guided by morphological keys to their categorization (rather than cultivation).

Anaerolinea thermophila

A. thermophila was isolated from an industrial thermophilic anaerobic digester (treating fried soybead curd wastewater). It represents a second branch of the Chloroflexi that is poorly understood, comprised of thermophilic heterotrophic filaments. A. thermophila grows at 45-65°C (55°C optimum) and is an obligate anaerobe; other members of this group are facultatively aerobic. Protons are the terminal electron acceptor, generating hydrogen. Growth is strongly inhibited by the accumulation of hydrogen, and so growth is promoted by co-cultivation with hydrogen-consuming methanogens. Unlike others members of this phylum, these are nonmotile.

Phylum Chlorobi (Green sulfur Bacteria)

Taxonomy

• Phylum Chlorobi
  • Class Chlorobia
    • Order Chorobiales
      • Family Chlorobiaceae
        • Genus Chlorobium
        • Genus Anacalochloris
        • Genus Chlorobaculum
        • Genus Chloroherpeton
        • Genus Pelodictyon
        • Genus Prosthecochloris

General characteristics of the Chlorobi

Diversity
This phylum contains only a small number of relatively closely-related species. Most are poorly characterized, and the relationships between them are uncertain. This phylum is related to the phylum Bacteroidetes, and is often grouped with it.

Metabolism
These organisms are strict photoautolithotrophs, using hydrogen or sulfide as the electron donor for reverse electron flow to generate NADH for carbon fixation via the reverse TCA cycle. Energy is generated by cyclic photophosphorylation. Most are also capable of fixing nitrogen, but cannot assimilate sulfate, and so require sulfide as a sulfur source even when using hydrogen as the electron donor for CO2 fixation. Elemental sulfur is the product of sulfide oxidation, and accumulates as extracellular globules.

Morphology
Cellular morphology is diverse in this group, with short chains of rods being the most common. Some produce gas vacuoles, and they are otherwise non-motile except Chloroherpeton, which is a unicellular gliding filament. Cells contain internal membranous chlorosomes along the inside of the cytoplasmic membrane; these house high concentrations of the accessory photopigment bacteriochlorophyls c, d, or e, and carotenoids. Unlike cyanobacterial antenna complexes, in which the pigments are associaated with proteins, these pigments in Chlorobi and Cloroflexi are not bound by protein, existing nearly in a solid state, and transfer light energy in very efficiently. Reaction center chlorophyl is bacteriochlorophyl a, which is located in the cytoplasmic membrane. Sulfur granules are produced externally.

Habitat
Chlorobi are commonly found in anaerobic, sulfide-rich freshwater and marine sediments. Because they require less light than other phototrophic organisms (about 1/4th as much as typical green or purple Bacteria), they can deeper in the more anoxic zones of their environments, and so are less conspicuous than the other green Bacteria. They can be conspicuous, however, in meromictic (permanently stratified) lakes, in which they form a brown or green layer in the water column beneath the red or purple layer of purple Bacteria at the chemocline (the interface between the oxygenated surface water and the denser anaerobic sulfide-rich deep water).

Symbiotic consortia

Some members of this phyla participate in a symbiosis with an uncultivated rod-shaped heterotroph (beta-proteobacteria in known cases). The motile heterotroph is bound by many (about a dozen) non-motile Chlorobi; the heterotroph is provided resources by the green bacteria, which in turn are provided motility by the heterotroph. The two cell types divide synchronously, and the heterotroph swims phototactically, attracted by light of the absorption maximum of bacteriochlorophyl c (740nm) in the phototroph; the cells are in close communication, but the details of this are unknown. The green bacteria can often be cultivated alone (although they are distinct from the free-living species), but the heterotrophs have not. These consortia are common in meromictic lakes, and provide one of the best examples of specific bacterial:bacterial symbiosis.

Example species

Chlorobium limicola

C. limicola strains are sometimes found in symbiosis with motile beta-proteobacteria, as described above, but most often are free-living sediment dwellers. They grow a short chains of rod-shaped cell, each 0.7-1.1 x 0.9-1.5μm, forming large sulfur globules. This species does not produce gas vaculoes. Cultures are green and the predominant photopigment is bacteriochlorophyl c or d.

Pelodictyon phaeoclathratiforme

P. clathratiforme is common in meromictic lakes, and is composed of trapezoidal rod-shaped cells ca. 1 x 2μm that branched chains, circles, and three-dimensional nets. Although non-motile, it produces gas vacuoles that allow it to control its vertical location in the water column. The accessory pigment is primarily bacteriochlorophyl e. Requires very highly reduced conditions for growth, but can use elemental sulfur or thiosulfate as well as sulfide for reducing power for carbon fixation. Unlike most members of this phylum, it is capable of using acetate to grow photoheterotrophically.

Phylum Cyanobacteria (Blue-green algae)

Taxonomy

Because of the large number of genera, only examples are given.

• Phylum Cyanobacteria
  • Class Cyanobacteria
    • Family Chroococcales (e.g. Microcystis, Synechococcus)
    • Family Pleurocapsales (e.g. Dermocarpa, Pleurocapsa)
    • Family Oscillatoriales (e.g. Lyngbya, Oscillatoria, Spirulina)
    • Family Nostocales (e.g. Anabaena, Nostoc, Calothrix)
    • Family Stigonemateles (e.g. Fischerella, Stigonema)
    • Family Prochlorales (Prochloron, Prochlorothrix)
      

General characteristics of the Cyanobacteria

Diversity
The members of this phylum are incredibly diverse phenotypically, but represent a relatively small phylogenetic range. Traditionally mistakenly classified with the eukaryotic “algae”, the taxonomy of this group remains problematic. Most species do not have formal names, and are instead referred to by their genus name and number in the Pasteur Culture Collection (PCC), e.g. Anabaena PCC 6309 rather than Anabaena variabilis.

The prochlorophytes (Prochloron and Prochlorothrix) are often consider separately from the remainder of the cyanobacteria, although they are phylogenetically members of the Chroococcales. Photosynthesis in prochlorophytes is different in some than in other cyanobacteria, resembling in many ways that of the plastids of eukaryotic phototrophs, which are also members of this group.

Metabolism
Despite the morphological diversity of cyanobacteria, they are physiologically much alike. They carry out oxygenic photosynthesis, using two photosystems in the traditional “Z-scheme” to obtain both energy and reducing power for fixing CO2 via the Calvin cycle. Water is the electron donor for CO2 reduction, generating oxygen. Cyanobacteria use chlorophyl a as their only chlorophyl, and use phycobilins as accessory photopigments. One form of phycobilin, phycocyanin, in combination with chlorophyl a produces the blue-green color from which these organisms get their name, but most familiar members of this group produce phycoerythrin instead, resulting in a rust-red or brown color.

Most cyanobacteria can fix atmospheric nitrogen, but this creates is a dilemma for them. Nitrogenases, the enzymes that reduce N2 to NH4+, are strongly inhibited by O2, the product of oxygenic photosynthesis. As a result, unicellular species generally fix nitrogen at night and photosynthesize by day, separating these mutually-exclusive processes in time. Some filamentous species separate the process physically, by producing specialized cells called heterocysts for fixing nitrogen. Heterocysts are terminally differentiated cells (they cannot reproduce nor revert to vegetative cells) that do not carry out oxygenic photosynthesis; they fix nitrogen and carry out cyclic photophosphorylation. Heterocysts provide fixed nitrogen (in the form of glutamine) to the nearby cells in the filament in exchange for energy (in the form of glutamic acid or sugar). This represents a differentiation between somatic cell lines and germ cell lines; in other words, these filaments are true multicellular organisms.

Morphology
Cyanobacteria very diverse morphologically, coming in all shapes and sizes. Unicellular forms are typically rods or cocci and are found in distinctive organized clusters (see below, the Chroococcales). Filamentous forms are generally motile by gliding, and may have sheaths. Filamentous species can have complex life cycles with a variety of specialized cell types, including nitrogen-fixing heterocycsts and resting akinetes. Only the Stigonematales contain filaments with branches. Cyanobacteria range widely in size, from typical bacterial sizes (about 1μm) to macroscopic; many types of cyanobacterial filaments can be seen distinctly without magnification.

Cells typically contain thylakoids flattened against this cytoplasmic membrane. These can be discrete disks like the chlorosomes of Chlorobi, or concentric layers of thylakoid membrane around the periphery of the cell. Many planktonic species produce gas vacuoles to regulate buoyancy and position in the water column.

Habitat
Cyanobacteria are common in any almost environment there’s sunlight and water. They are found in freshwater and marine environments, soils, on and in the surface of rocks, &c, &c. They are the predominant primary producers in environments that aren’t hospitable for eukaryotic algae. Cyanobacteria are found in acid springs and soda lakes, hot springs and permanently frozen rocks, the open ocean and crusty desert soils.

Many species form symbioses with fungi, animals, plants, various protists, and other bacteria. Lichens are composite organisms, composed to a fungus and an algae, and the phototrophic component are very often cyanobacteria. The Cyanobacteria form endosymbiotic relationships with a wide variety of unicellular eukaryotes, for example diatoms (this is in addition to their usual chloroplasts).The water fern Azolla remains associated with its cyanobacterial symbiont (an Anabaena) throughout its life cycle; specialized lobes on the leaves house the symbionts, which provide their host with fixed nitrogen. Cyanobacteria are commonly associated with freshwater and marine sponges, in the gill arches crustaceans, and in tropical reef clams and corals. The most extreme example of symbiosis of cyanobacteria with eukaryotes are the plastids (chloroplasts) of photosynthetic eukaryotes, which are specialized cyanobacteria.

Family Chroococcales

These cyanobacteria are unicellular, but usually grow as aggregates imbedded in sheaths, capsules or slime. The form of these aggregates depends on which type of covering (if any) the cells have, and how the cells divide. Division is by budding, or binary fission in one, two or three dimensions, or irregularly. Fission in one plane only produces strings of cells, fission in two dimensions (cleavage planes alternate) produce sheets of cells in rowas and columns, and division in three dimensions produces three-dimensional arrays of cells. Irregular cleavage produces irregular cell masses.

Example: Microcystis

Microcystis is a common freshwater and estuarine specie. Cells are coccoid, 3-5μm in diameter, clustered irregularly in gelatinous masses. It flourishes in the summer months, and in polluted waters can form blooms that looks like bright green latex paint floating on and in the water. May produce toxins (microcystins) that cause skin irritation or gastrointestinal discomfort (in the short run) or liver damage (in the long run) if ingested.

Family Pleurocapsales

Members of this family reproduce by multiple fission, a single large cell producing a number of small spore-like cells known as baeocytes. The simplest forms are unicellular, a single baeocyte growing into a large vegetative cell which divides into many baeocytes. If the cell divisions are in alternating planes, the baeocytes are arranged in orderly three-dimensional cubical arrays. In some species, an early single asymmetric binary fission of the baeocyte produces a large cell that continues to grow, and then divides by multiple fission. The smaller “mother” cell then grows and divides again in an asymmetric binary fission, regenerating both the mother cell and a cell destined for multiple fission. In the genus Pleurocapsa and its relatives, the growing baeocyte also divides early into two cells; one of these cells expands and ultimately undergoes multiple fission. The other cell goes through a series of asymmetric divisions, creating branched pseudohyphae of vegetative cells. These can be simple masses of cells, or complex three-dimensional structures. Eventually, cells within these pseudohyphae can undergo multiple fission, releasing baeocytes.

Example: Dermocarpa

Dermocarpa has a relatively simple life cycle, in which the baeocytes (which are transiently motile, by gliding) grow into large vegetative cells, then divide by multiple fission into many baeocytes. These baocytes are contained in the spherical husk of the mother cells, which splits open to release the baeocytes into the environment.

Family Oscillatorales

These very common and conspicuous cyanobacteria are filamentous and divide only by binary fission. The only cellular differentiation in these filaments are the terminal cells in some cases, which can be rounded, tapered, or pointed. The form of the ends of filaments is important in the identification of these species. Filaments can be straight, loosely coiled, or tightly helical. The individual cells of the filament can be obvious, or the septa can be difficult to see. Sheaths are common, and most are motile by gliding.

Example: Oscillatoria

Oscillatoria is a common member of this group, ubiquitous in freshwater environments. They are often large enough to be mistaken for filamentous eukaryotic green algae. Filaments typically have a light sheath, if any, and the individual cells are cylindrical disks. Filaments are rigid, and rotate during gliding; this can make them appear to writhe as they rotate around slight curves and bends in the filament.

Family Nostocales

These cyanobacteria are morphologically similar to the Oscillatoriales, growing in linear filaments, but have complex life cycles and cellular differentiation. In nitrogen-limiting conditions, some cells differentiate into nitrogen-fixing heterocysts. This is a terminal differentiation; heterocysts can neither divide nor develop back into vegetative cells. Heterocysts have a heavy cell wall, and are much lighter in color than are vegetative cells, and so are readily identified. These heterocycsts provide fixed nitrogen to the nearby cells. As the distance between heterocycsts increases as the vegetative cells between continue to grow and divide, those cells midway between heterocysts become starved for fixed nitrogen, and one will therefore develop into a new heterocyst.

Most members of this group also produce “resting” stage cells called akinetes when filaments are nutritionally limited. Akinetes are usually larger than vegetative cells, contain good reserves of storage granules, and are depleted for photopigments. It is common, however, for akinetes to accumulate other pigments, making them appear dark or brown. Akinetes are resistant to a variety of environmental insults, but not heat. Filaments are prone to breakage at the junctions between akinetes or heterocycts and the adjacent vegetative cells, and so it is common to see filaments with these specialized cells at one or both ends. When provided a fresh supply of nutrients, akinetes germinate to produce a new filament.

Some members of this group, especially the plant symboints, also produce specialized filaments called hormogonia. Hormogonia are short filaments composed of small cells that glide rapidly. Hormogonia are produced in response to the detection by the vegetative filament of a soluble factor produced by the plant. The hormogonia glide rapidly toward the source of this “hormone”, develop heterocysts, and then the remainder of the cells of the hormogonia develop into vegetative cells

Example: Anabaena

Anabaena is a common freshwater specie. Cells are in the shape of flattened beads to short barrel-like cylinders. Filaments are not covered in slime or sheaths, and akinetes are not only produced adjacent to heterocycts. Does not produce hormongonia. Filaments are not tapered.

Family Stigonematales

These cyanobacteria divide in more than one plane, producing branched filaments or filaments composed of clusters of cells (multiseriate). Side branches are often morphologically distinct from the main filament. In some species, filaments are easily disrupted, producing clusters of cells that are easily confused with Chroococcales, but unlike these non-filamantous forms will often contain heterocysts or akinetes. Hormonogonia are common.

Example: Fischerella

Fischerella is composed of multiceriate main filaments and uniseriate side branches. Grow to become large, dense mats of filaments than can glide along the substrate. Heterocysts form in both the main filament and side branches, whereas akinets form only on the main filaments. The main filament, but not the side branches, and usually covered in a dense sheath.

Family Prochlorales

Members of this family resemble the chloroplasts of eukaryotic algae and plants more than any other cyanobacteria. Chloroplasts are, in fact, specific relatives of the Prochlorales (thus the name), and so are formally members of this Family as well.

Prochlorales utilize both chlorophyl a and chlorophyll b as primary photopigments for oxygenic photosynthesis. Cells contain distinct thylakoids, but these lack phycobilins or phycobilisomes. Thylakoids are generally stacked, reminiscent of those of chloroplasts.

These organisms are sometimes considered separately from the other cyanobacteria, and in this context are referred to as the Oxychlorobacteria. Nevertheless, they are phylogenetic members of the cyanobacteria. Species of the genus Prochlorococcus, which also contain chlorophyl b instead of phycobilin, were originally thought to be members of this group, but seem to have evolved this trait independently (or by horizontal transfer), and are in reality members of the Chroococcales.

Example: Prochloron

Prochloron is a symbiont of ascidians (sea squirts), in which it resides on the surface and imbedded in the surface test of the animals, and especially in the communal cloacal cavity (these are colonial species), where they form visible green patches. Although usually considered an exosymbiont, it is also found in vacuoles of the host cells living as an endosymbiont. They are especially common in sea squirts living in shady zones of the coral reefs. Prochloron provides up to half of the organic carbon requirements of the host animal. The cells are individual spheres or ovals 10-30μm in diameter

Other Green phototrophs

The Heliobacteria are green, anoxygenic phototrophs using bacteriochlorophyl g. However, these organisms are members of the phylum Firmicutes, and so are described elsewhere.

Bacterial photosynthesis

Phototrophism is the biological process of converting (capturing) light energy into chemical energy. The process by which green Bacteria and the purple Bacteria carry out phototrophism share a common basic mechanism, usually referred to as photosynthesis, which is only briefly reviewed here.

Cyclic photophosphorylation

Photosynthetic Bacteria generally perform cyclic photophosporylation. Light energy, captured by antenna chlorophyls and accessory pigments, is channeled to reaction center complexes. This light energy excites an electron in the reaction center chlorophyl, and makes the reaction center a strong electron donor (reductant). An electron is transfered from the reaction center (which becomes oxidized) to the electron transport chain. The electron traverses the electron transport chain, resulting in the pumping of protons from the cytoplasm to the periplasm or lumen of the thylakoid. At the end of the electron transport chain the electron is transferred back to the oxidized reaction center in the ground state. The reduced reaction center is now ready to accept another packet of light energy and repeat the cycle. With each cycle comes an increase in the proton motive force, which is used by ATPase to generate ATP from ADP and phosphate. The net reaction of cyclic photophosphorylation is: light + ADP + phosphate -> ATP. All of the components of the cycle are regenerated within the cycle; no other inputs are required.

Obtaining reducing power for carbon fixation

Cyclic photophosphorylation generates only ATP. Photosynthetic organisms have several approaches to obtain NADH; organic compounds (photoheterotrophs), reverse electron flow (purple photoautotrophs and Chloroflexi), from ferridoxin from the electron transport chain (Chlorobi and heliobacteria), or oxygenic photosynthesis (cyanobacteria).

Photoheterotrophs use light only for their energy needs; reducing power and carbon are from organic compounds. This is independent of cyclic photophosphorylation.

Purple photoautotrophic Bacteria and Chloroflexi rely on a source of a strong chemical reductant, such as sulfide, thiosulfate, elemental sulfur, ferrous cation, or hydrogen as a source of electrons. These electrons are used to reduce cytochrome c, and the electrons traverse the electron transport chain in reverse, at the expense of the proton motive force (and so ultimately at the expense of ATP), and used to reduce NAD+ to NADH used for carbon fixation. This uses the same electron transport chain as photophosphorylation, but is otherwise an independent process.

Chlorobi have reaction centers that are more strongly reducing that are those of other organisms. As a result, the electrons transferred to the electron transport chain pass first through iron-sulfur proteins that can be used to generate reduced ferridoxin as a source of reducing power for carbon fixation. Electrons removed from the electron transport chain to reduce ferridoxin are replaced in the system from external sources of reductant, typically sulfide, sulfur, thiosulfate, ferrous cation, or hydrogen. Although these electrons are transferred to cyctochrome c, as in the purple photoautotrophs, they subsequently are transferred to the oxidized reaction center, rather than undergoing reverse electron flow. Therefore, photosynthesis in these organisms generations both ATP and reducing power for carbon fixation, but requires a chemical reductant as well as light.

Cyanobacteria, including chloroplasts, carry out oxygenic photosynthesis; the traditional “Z-scheme” of photosynthesis. This process is based on the same cyclic photophophorylation used by other photosynthetic Bacteria. As in the other green Bacteria, reducing power (NADH or NADPH) is siphoned out of the system at the stage of ferridoxin. These electrons must be replaced for cyclic photophosphorylation to continue. Rather than directly use an external chemical reductants, however, cyanobacteria use a second reaction center (photosystem II; photosystem I is the reaction center used for cyclic photophosphorylation). This reaction center transfers electrons to the electron transport chain via reduced quinone. These electrons must be replaced, but photosystem II is so strongly oxidizing that it can accept electrons from water, generating molecular oxygen in the process.

Rhodopsin phototrophy

It has recently been discovered that a wide range of Bacteria can capture light energy for ATP production using rhodopsin, a simple light-driven proton pump composed on a single protein (rhodopsin) and photopigment (retinal). This is apparently a significant form of phototrophy in the ocean, and perhaps other ecosystems, but is best known only from genes found in uncultivated organisms. This form of phototrophy seems to have spread widely, by horizontal transfer, from its origin in the halophilic Archaea. The mechanism of rhodopsin phototrophy is therefore discussed elsewhere, and likewise the discovery of these genes in uncultivated Bacteria.

Carbon fixation

Most phototrophic organisms can fix carbon for growth; they are photoautotrophic. These three phyla of green phototrophic Bacteria each use a different pathway for carbon (CO2) fixation: the Calvin cycle (cyanobacteria), reverse TCA cycle (Chlorobi) and the hydroxypropionate pathway (Chloroflexi). Although each is an entirely independent pathway, they share several fundamental features imposed by chemistry: they are cyclical, and require reductant and energy. Another, noncyclical pathway for carbon fixation is known from nonphototrophic acetogenic Bacteria and some methanogens; the reductive acetyl-CoA pathway.

Calvin cycle
The Calvin cycle is the most familiar and common carbon fixation pathway. The key enzyme in this pathway is ribulose bis-phosphate carboxylase/oxidase (“rubisco”), that carboxylates ribulose 1,5-bis-phosphate to form two molecules of 3-phosphoglycerate; this is the step in which CO2 is incorporated into organic carbon. After phosphorylation, the resulting 1,3-diphosphoglycerate is reduced glyceraldehyde 3-phosphate. The remainder of the steps are sugar rearrangements, using enzymes common in carbohydrate metabolism in most organisms, ending in the phosphorylation of ribulose 5-phosphate to regenerate ribulose 1,5-bis-phosphate. For each three molecules of ribulose 1,5-bis-phosphate that enter the cycle, 3 molecules of CO2 are fixed, generating a net of one molecule of glyceraldehyde 3-phosphate that can be siphoned off for metabolism after regenerating three more molecules of ribulose 1,5-bis-phosphate to close the cycle. This glyceraldehyde 3-phosphate feeds directly into general carbohydrate metabolism.

Reverse TCA cycle
Many autotrophic organisms that don’t use the Calvin cycle to fix carbon (e.g. the Chlorobi) use the reverse TCA cycle, also know as the reductive TCA cycle. This is the same pathway as the familiar TCA cycle, but all of the reactions are run in the reverse direction. The TCA cycle usually consumes pyruvate, generating ATP, NADH or NADPH, reduced ferridoxin, and waste CO2. The reverse TCA cycle therefore consumes CO2, ATP, NADH/NADPH and reduced ferridoxin to produce pyruvate. In the Chlorobi, two key steps use the oxidation of ferridoxin rather than NADH to drive the reactions in the reverse direction. The acetyl-CoA generated by this pathway can be used directly, or carboxylated further to produce pyruvate in a reverse of the “transition reaction”.

Hydroxypropionate pathway
The Chloroflexi and many Crenarchaea use a third carbon fixation method, the hydroxypropionate pathway. Some of the reactions used in this pathway are common to the TCA cycle, but it is a unique pathway. The hydroxypropionate generates glyoxylate, which can feed into central metabolism after amidation to glycine.

Reductive acetyl-CoA pathway
Acetogenic Bacteria, as well as some sulfate reducers and some methanogenic Archaea, fix carbon using molecular hydrogen in the Wood reaction, also known as the reductive acetyl-CoA pathway. Unlike the other pathways for carbon fixation, the reductive acetyl-CoA pathway is not cyclic; it has two branches, one the formation of a methyl-corrinoid and the other the generation of carbon monoxide, that come together to produce acetyl-CoA. Unlike in the other pathways, the carbon from CO2 is carried through the reductive transformations on one-carbon carrier cofactors; tetrahydrofolate (in the case of Bacteria) or tetrahydromethanopterin (in the case of Archaea). This pathway is also unusual in that the electrons for reduction of CO2 come directly from hydrogenase rather than NADH or other reduced cofactors. As in the case of the reductive TCA pathway, acetyl-CoA produced can be further carboxylated (fixing another CO2 molecule) to pyruvate by the reverse of the transition reaction. Although acetogenic Bacteria fix carbon using this pathway, they also generate energy (in the form of ATP) using this same pathway, by cleaving acetate from the acetyl-CoA coupled to phosphorylation of ADP to ATP. This acetate is excreted as a waste product.

This pathway shares many of the reactions of methanogenesis, in which the methyl group from methanopterin or the corrinoid protein would otherwise be transferred to coenzyme M, reduced one step further, and released as methane.

Questions for thought

• Can you think of any bacterial:bacterial symbioses other than that of Chlorobium? What about bacterial:eukaryotic symbioses?
  
  
• Some cyanobacteria can grow photoheterotrophically rather than photosynthetically. What does this mean? What affect would this have on PSI and PSII?
  
  
• Some cyanobacteria can grow using sulfide instead of water as the donor of electrons for reducing power for CO2 fixation. Can you develop some hypotheses about how they might be doing this? How would you test these?
  
  
• Chloroflexus contains chlorosomes and chlorophyl c, unlike other Chloroflexi, and it has been suggested that these were acquired by horizontal transfer from the Chlorobi. How would you test this hypothesis?
  
  
• Most phototrophic Bacteria are capable of fixing carbon (i.e. the are photoautotrophic). Why do you suppose this is? Why are so many also able to fix atmospheric nitrogen?
  
  
• Why do you suppose it is that most phototrophic Bacteria except the cyanobacteria are anaerobic?
  
  
• The final proof that chloroplasts originated from cyanobacteria came from phylogenetic analysis of chloroplast genes, especially the ribosomal RNA genes. Given that chloroplasts did arise from the cyanobacteria (and in particular the Prochlorales), do you see chloroplasts as descendants of cyanobacteria, or as a kind of cyanobacteria?
  
  
• The chloroplasts of various types of algae (green, golden-brown, red, &c) are quite distinct, and it remains controversial whether the all descend from a single chloroplast ancestor or each represent an independent symbiosis event. How would you test these opposing hypotheses? What are the complications that might cloud your answer(s)?

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