4. Prokaryotic Diversity

4.3 Nonproteobacteria Gram-Negative Bacteria and Phototrophic Bacteria

Learning Objectives

  • Describe the unique features of nonproteobacteria gram-negative bacteria
  • Give an example of a nonproteobacteria bacterium in each category
  • Describe the unique features of phototrophic bacteria
  • Identify phototrophic bacteria

The majority of the gram-negative bacteria belong to the phylum Proteobacteria, discussed in the previous section. Those that do not are called the nonproteobacteria. In this section, we will describe three classes of gram-negative nonproteobacteria: the spirochetes, the CFB group, and the Planctomycetes. A diverse group of phototrophic bacteria that includes Proteobacteria and nonproteobacteria will be discussed at the end of this section.


Spirochetes are characterized by their long (up to 250 μm), spiral-shaped bodies. Most spirochetes are also very thin, which makes it difficult to examine gram-stained preparations under a conventional brightfield microscope. Darkfield fluorescent microscopy is typically used instead. Spirochetes are also difficult or even impossible to culture. They are highly motile, using their axial filament to propel themselves. The axial filament is similar to a flagellum, but it wraps around the cell and runs inside the cell body of a spirochete in the periplasmic space between the outer membrane and the plasma membrane (Figure 4.13).

Light micrograph, electron micrograph and diagrams of spirochetes and their flagella.
Figure 4.13. Spirochetes are typically observed using darkfield microscopy (left). However, electron microscopy (top centre, bottom centre) provides a more detailed view of their cellular morphology. The flagella found between the inner and outer membranes of spirochetes wrap around the bacterium, causing a twisting motion used for locomotion. (credit “spirochetes” micrograph: modification of work by Centers for Disease Control and Prevention; credit “SEM/TEM”: modification of work by Guyard C, Raffel SJ, Schrumpf ME, Dahlstrom E, Sturdevant D, Ricklefs SM, Martens C, Hayes SF, Fischer ER, Hansen BT, Porcella SF, Schwan TG) 

Several genera of spirochetes include human pathogens. For example, the genus Treponema includes a species T. pallidum, which is further classified into four subspecies: T. pallidum pallidum, T. pallidum pertenue, T. pallidum carateum, and T. pallidum endemicum. The subspecies T. pallidum pallidum causes the sexually transmitted infection known as syphilis, the third most prevalent sexually transmitted bacterial infection in the United States, after chlamydia and gonorrhoea. The other subspecies of T. pallidum cause tropical infectious diseases of the skin, bones, and joints.

Another genus of spirochete, Borrelia, contains a number of pathogenic species. B. burgdorferi causes Lyme disease, which is transmitted by several genera of ticks (notably Ixodes and Amblyomma) and often produces a “bull’s eye” rash, fever, fatigue, and, sometimes, debilitating arthritis. B. recurrens causes a condition known as relapsing fever. Appendix D lists the genera, species, and related diseases for spirochetes.

  • Why do scientists typically use darkfield fluorescent microscopy to visualize spirochetes?

Cytophaga, Fusobacterium, and Bacteroides

The gram-negative nonproteobacteria of the genera Cytophaga, Fusobacterium, and Bacteroides are classified together as a phylum and called the CFB group. Although they are phylogenetically diverse, bacteria of the CFB group share some similarities in the sequence of nucleotides in their DNA. They are rod-shaped bacteria adapted to anaerobic environments, such as the tissue of the gums, gut, and rumen of ruminating animals. CFB bacteria are avid fermenters, able to process cellulose in rumen, thus enabling ruminant animals to obtain carbon and energy from grazing.

Cytophaga are motile aquatic bacteria that glide. Fusobacteria inhabit the human mouth and may cause severe infectious diseases. The largest genus of the CFB group is Bacteroides, which includes dozens of species that are prevalent inhabitants of the human large intestine, making up about 30% of the entire gut microbiome (Figure 4.14). One gram of human faeces contains up to 100 billion Bacteroides cells. Most Bacteroides are mutualistic. They benefit from nutrients they find in the gut, and humans benefit from their ability to prevent pathogens from colonizing the large intestine. Indeed, when populations of Bacteroides are reduced in the gut—as often occurs when a patient takes antibiotics—the gut becomes a more favourable environment for pathogenic bacteria and fungi, which can cause secondary infections.

A micrograph of many rod shaped cells.
Figure 4.14. Bacteroides comprise up to 30% of the normal microbiota in the human gut. (credit: NOAA)

Only a few species of Bacteroides are pathogenic. B. melaninogenicus, for example, can cause wound infections in patients with weakened immune systems.

  • Why are Cytophaga, Fusobacterium, and Bacteroides classified together as the CFB group?


The Planctomycetes are found in aquatic environments, inhabiting freshwater, saltwater, and brackish water. Planctomycetes are unusual in that they reproduce by budding, meaning that instead of one maternal cell splitting into two equal daughter cells in the process of binary fission, the mother cell forms a bud that detaches from the mother cell and lives as an independent cell. These so-called swarmer cells are motile and not attached to a surface. However, they will soon differentiate into sessile (immobile) cells with an appendage called a holdfast that allows them to attach to surfaces in the water (Figure 4.15). Only the sessile cells are able to reproduce. Another unusual feature of certain Planctomycetes genera is the presence of a membrane-bound structure called the anammoxasome. These bacteria are obligately anaerobic lithotrophs and this structure is so-named because it is where the anaerobic ammonia oxidation occurs. The process yields hydrazine (N2H4 — rocket fuel) as an intermediate. To deal with the high toxicity of hydrazine, the anammoxasome membrane is made of ladderane lipids. These lipids are unusual and highly compact, presumably providing protection against diffusion of the hydrazine.

a) A micrograph of an oval cell with long projections attached to a root-shaped structure labeled holdfast. The oval cell is approximately 500 nm in diameter. B) A micrograph of a similar looking cell with a long projection that is not attached to a holdfast.
Figure 4.15. (a) Sessile Planctomycetes have a holdfast that allows them to adhere to surfaces in aquatic environments. (b) Swarmers are motile and lack a holdfast. (credit: modification of work by American Society for Microbiology)

Table 4.7 summarizes the characteristics of some of the most clinically relevant genera of nonproteobacteria.

Table 4.7: Characteristics of Some Clinically Relevant Nonproteobacteria

Example Genus Microscopic Morphology Unique Characteristics
Bacteroides Gram-negative bacillus Obligate anaerobic bacteria; abundant in the human gastrointestinal tract; usually mutualistic, although some species are opportunistic pathogens
Cytophaga Gram-negative bacillus Motile by gliding; live in soil or water; decompose cellulose; may cause disease in fish
Fusobacterium Gram-negative bacillus with pointed ends Anaerobic; form; biofilms; some species cause disease in humans (periodontitis, ulcers)
Leptospira Spiral-shaped bacterium (spirochetes); gram negative-like (better viewed by darkfield microscopy); very thin Aerobic, abundant in shallow water reservoirs; infect rodents and domestic animals; can be transmitted to humans by infected animals’ urine; may cause severe disease
Sphingobacterium Gram-negative bacillus Oxidase positive; nonmotile; contain high amounts of sphingophospholipids; rarely cause disease in humans
Treponema Gram-negative-like spirochete; very thin; better viewed by darkfield microscopy Motile; do not grow in culture; T. pallidum (subspecies T. pallidum pallidum) causes syphilis
  • How do Planctomycetes reproduce?

Phototrophic Bacteria

The phototrophic bacteria are a large and diverse category of bacteria that do not represent a taxon but, rather, a group of bacteria that use sunlight as their primary source of energy. This group contains both Proteobacteria and nonproteobacteria. They use solar energy to synthesize ATP through photosynthesis. When they produce oxygen, they perform oxygenic photosynthesis. When they do not produce oxygen, they perform anoxygenic photosynthesis. With the exception of some cyanobacteria, the majority of phototrophic bacteria perform anoxygenic photosynthesis.

One large group of phototrophic bacteria includes the purple or green bacteria that perform photosynthesis with the help of bacteriochlorophylls, which are green, purple, or blue pigments similar to chlorophyll in plants. Some of these bacteria have a varying amount of red or orange accessory pigments called carotenoids. Their colour varies from orange to red to purple to green (Figure 4.16), and they are able to absorb light of various wavelengths. Traditionally, these bacteria are classified into sulphur and nonsulphur bacteria; they are further differentiated by colour.

A thick glass tube filled with purple regions labeled purple bacteria and green regions labeled green bacteria.
Figure 4.16. Purple and green sulphur bacteria use bacteriochlorophylls to perform photosynthesis.

The sulphur bacteria perform anoxygenic photosynthesis, using sulphites as electron donors and releasing free elemental sulphur. Nonsulphur bacteria use organic substrates, such as succinate and malate, as donors of electrons.

The purple sulphur bacteria oxidize hydrogen sulphide into elemental sulphur and sulphuric acid and get their purple colour from the pigments bacteriochlorophylls and carotenoids. Bacteria of the genus Chromatium are purple sulphur Gammaproteobacteria. These microorganisms are strict anaerobes and live in water. They use carbon dioxide as their only source of carbon, but their survival and growth are possible only in the presence of sulphites, which they use as electron donors. Chromatium has been used as a model for studies of bacterial photosynthesis since the 1950s.[1]

The green sulphur bacteria use sulphide for oxidation and produce large amounts of green bacteriochlorophyll. The genus Chlorobium is a green sulphur bacterium that is implicated in climate change because it produces methane, a greenhouse gas. These bacteria use at least four types of chlorophyll for photosynthesis. The most prevalent of these, bacteriochlorophyll, is stored in special vesicle-like organelles called chlorosomes.

Purple nonsulphur bacteria are similar to purple sulphur bacteria, except that they use hydrogen rather than hydrogen sulphide for oxidation. Among the purple nonsulphur bacteria is the genus Rhodospirillum. These microorganisms are facultative anaerobes, which are actually pink rather than purple, and can metabolize (“fix”) nitrogen. They may be valuable in the field of biotechnology because of their potential ability to produce biological plastic and hydrogen fuel.[2]

The green nonsulphur bacteria are similar to green sulphur bacteria but they use substrates other than sulphides for oxidation. Chloroflexus is an example of a green nonsulphur bacterium. It often has an orange colour when it grows in the dark, but it becomes green when it grows in sunlight. It stores bacteriochlorophyll in chlorosomes, similar to Chlorobium, and performs anoxygenic photosynthesis, using organic sulphites (low concentrations) or molecular hydrogen as electron donors, so it can survive in the dark if oxygen is available. Chloroflexus does not have flagella but can glide, like Cytophaga. It grows at a wide range of temperatures, from 35 °C to 70 °C, thus can be thermophilic.

Another large, diverse group of phototrophic bacteria compose the phylum Cyanobacteria; they get their blue-green colour from the chlorophyll contained in their cells (Figure 4.17). Species of this group perform oxygenic photosynthesis, producing megatons of gaseous oxygen. Scientists hypothesize that cyanobacteria played a critical role in the change of our planet’s anoxic atmosphere 1–2 billion years ago to the oxygen-rich environment we have today.[3]

a) A micrograph of green spherical cells. B) A photo of a green lake
Figure 4.17. (a) Microcystis aeruginosa is a type of cyanobacteria commonly found in freshwater environments. (b) In warm temperatures, M. aeruginosa and other cyanobacteria can multiply rapidly and produce neurotoxins, resulting in blooms that are harmful to fish and other aquatic animals. (credit a: modification of work by Dr. Barry H. Rosen/U.S. Geological Survey; credit b: modification of work by NOAA)

Cyanobacteria have other remarkable properties. Amazingly adaptable, they thrive in many habitats, including marine and freshwater environments, soil, and even rocks. They can live at a wide range of temperatures, even in the extreme temperatures of the Antarctic. They can live as unicellular organisms or in colonies, and they can be filamentous, forming sheaths or biofilms. Many of them fix nitrogen, converting molecular nitrogen into nitrites and nitrates that other bacteria, plants, and animals can use. In filamentous cyanobacteria, the reactions of nitrogen fixation occur in specialized cells called heterocysts.

Photosynthesis in Cyanobacteria is oxygenic, using the same type of chlorophyll a found in plants and algae as the primary photosynthetic pigment. In addition to carotenoid accessory pigments, Cyanobacteria also use phycocyanin and cyanophycin, two accessory photosynthetic pigments that give them their characteristic blue colour. They are located in special organelles called phycobilisomes and in folds of the cellular membrane called thylakoids, which are remarkably similar to the photosynthetic apparatus of plants. Recall that it was an ancestor of Cyanobacteria that gave rise to the eukaryotic chloroplast through endosymbiosis.[4] Thus the type of photosynthesis seen in plants is the same as in Cyanobacteria. Cyanobacteria are also an interesting object of research in biochemistry,[5] with studies investigating their potential as biosorbents[6] and products of human nutrition.[7]

Unfortunately, cyanobacteria can sometimes have a negative impact on human health. Genera such as Microcystis can form harmful cyanobacterial blooms, forming dense mats on bodies of water and producing large quantities of toxins that can harm wildlife and humans. These toxins have been implicated in tumours of the liver and diseases of the nervous system in animals and humans.[8]

Table 4.8 summarizes the characteristics of important phototrophic bacteria.

Table 4.8: Characteristics of Important Phototrophic Bacteria

Phototrophic Bacteria
Phylum Class Example Genus or Species Common Name Oxygenic or Anoxygenic Sulfur Deposition
Cyanobacteria Cyanophyceae Microcystis aeruginosa Blue-green bacteria Oxygenic None
Chlorobi Chlorobia Chlorobium Green sulphur bacteria Anoxygenic Outside the cell
Chloroflexi (Division) Chloroflexi Chloroflexus Green nonsulphur bacteria Anoxygenic None
Proteobacteria Alphaproteobacteria Rhodospirillum Purple nonsulphur bacteria Anoxygenic None
Betaproteobacteria Rhodocyclus Purple nonsulphur bacteria Anoxygenic None
Gammaproteobacteria Chromatium Purple sulphur bacteria Anoxygenic Inside the cell
  • What characteristic makes phototrophic bacteria different from other prokaryotes?

Key Takeaways

  • Gram-negative nonproteobacteria include the taxa spirochetes; the Cytophaga, Fusobacterium, Bacteroides group; Planctomycetes; and many representatives of phototrophic bacteria.
  • Spirochetes are motile, spiral bacteria with a long, narrow body; they are difficult or impossible to culture.
  • Several genera of spirochetes contain human pathogens that cause such diseases as syphilis and Lyme disease.
  • Cytophaga, Fusobacterium, and Bacteroides are classified together as a phylum called the CFB group. They are rod-shaped anaerobic organoheterotrophs and avid fermenters. Cytophaga are aquatic bacteria with the gliding motility. Fusobacteria inhabit the human mouth and may cause severe infectious diseases. Bacteroides are present in vast numbers in the human gut, most of them being mutualistic but some are pathogenic.
  • Planctomycetes are aquatic bacteria that reproduce by budding; they may form large colonies, and develop a holdfast.
  • Phototrophic bacteria are not a taxon but, rather, a group categorized by their ability to use the energy of sunlight. They include Proteobacteria and nonproteobacteria, as well as sulphur and nonsulphur bacteria coloured purple or green.
  • Sulfur bacteria perform anoxygenic photosynthesis, using sulphur compounds as donors of electrons, whereas nonsulphur bacteria use organic compounds (succinate, malate) as donors of electrons.
  • Some phototrophic bacteria are able to fix nitrogen, providing the usable forms of nitrogen to other organisms.
  • Cyanobacteria are oxygen-producing bacteria thought to have played a critical role in the forming of the earth’s atmosphere.

Multiple Choice

Fill in the Blank

Short Answer

  1. Explain the term CFB group and name the genera that this group includes.
  2. Name and briefly describe the bacterium that causes Lyme disease.
  3. Characterize the phylum Cyanobacteria.



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  1. R.C. Fuller et al. “Carbon Metabolism in Chromatium.” Journal of Biological Chemistry 236 (1961):2140–2149.
  2. T.T. Selao et al. “Comparative Proteomic Studies in Rhodospirillum rubrum Grown Under Different Nitrogen Conditions.” Journal of Proteome Research 7 no. 8 (2008):3267–3275.
  3. A. De los Rios et al. “Ultrastructural and Genetic Characteristics of Endolithic Cyanobacterial Biofilms Colonizing Antarctic Granite Rocks.” FEMS Microbiology Ecology 59 no. 2 (2007):386–395.
  4. T. Cavalier-Smith. “Membrane Heredity and Early Chloroplast Evolution.” Trends in Plant Science 5 no. 4 (2000):174–182.
  5. S. Zhang, D.A. Bryant. “The Tricarboxylic Acid Cycle in Cyanobacteria.” Science 334 no. 6062 (2011):1551–1553.
  6. A. Cain et al. “Cyanobacteria as a Biosorbent for Mercuric Ion.” Bioresource Technology 99 no. 14 (2008):6578–6586.
  7. C.S. Ku et al. “Edible Blue-Green Algae Reduce the Production of Pro-Inflammatory Cytokines by Inhibiting NF-κB Pathway in Macrophages and Splenocytes.” Biochimica et Biophysica Acta 1830 no. 4 (2013):2981–2988.
  8. I. Stewart et al. Cyanobacterial Poisoning in Livestock, Wild Mammals and Birds – an Overview. Advances in Experimental Medicine and Biology 619 (2008):613–637.


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