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Recombinant DNA Cut And Tape Classroom Activity

Nonproteobacteria Gram-Negative Bacteria and phototrophic Bacteria

Learning Objectives

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 ([link]).

Spirochetes are typically observed using darkfield microscopy (left). However, electron microscopy (top center, bottom center) 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)
A light micrograph of long spiral shaped cells. A TEM cross-section of these shows a circle outlined by a cell membrane. Inside the cell is the cytoplasm and a darker region labeled nucleoid. Outside of this is the periplasmic space and outside of that is an outer membrane. A bulge within the periplasmic space is labeled axial filament. Small dots within the axial filament are labeled endoflagella. An SEM from the original light micrograph shows what looks like a thin rope wound around a thicker rope. The thin rope is labeled axial filament.

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 gonorrhea. 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.

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 ([link]). One gram of human feces 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 favorable environment for pathogenic bacteria and fungi, which can cause secondary infections.

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

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


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 ([link]). Only the sessile cells are able to reproduce.

(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)
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.

[link] summarizes the characteristics of some of the most clinically relevant genera of 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

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 pigments called carotenoids. Their color varies from orange to red to purple to green ([link]), and they are able to absorb light of various wavelengths. Traditionally, these bacteria are classified into sulfur and nonsulfur bacteria; they are further differentiated by color.

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

The sulfur bacteria perform anoxygenic photosynthesis, using sulfites as electron donors and releasing free elemental sulfur. Nonsulfur bacteria use organic substrates, such as succinate and malate, as donors of electrons.

The purple sulfur bacteria oxidize hydrogen sulfide into elemental sulfur and sulfuric acid and get their purple color from the pigments bacteriochlorophylls and carotenoids. Bacteria of the genus Chromatium are purple sulfur 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 sulfites, which they use as electron donors. Chromatium has been used as a model for studies of bacterial photosynthesis since the 1950s.1

The green sulfur bacteria use sulfide for oxidation and produce large amounts of green bacteriochlorophyll. The genus Chlorobium is a green sulfur 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 nonsulfur bacteria are similar to purple sulfur bacteria, except that they use hydrogen rather than hydrogen sulfide for oxidation. Among the purple nonsulfur 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 nonsulfur bacteria are similar to green sulfur bacteria but they use substrates other than sulfides for oxidation. Chloroflexus is an example of a green nonsulfur bacterium. It often has an orange color 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 sulfites (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 color from the chlorophyll contained in their cells ([link]). 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) 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)
a) A micrograph of green spherical cells. B) A photo of a green lake

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. 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. Cyanobacteria also use phycocyanin and cyanophycin, two secondary photosynthetic pigments that give them their characteristic blue color. 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. Scientists hypothesize that plants originated from endosymbiosis of ancestral eukaryotic cells and ancestral photosynthetic bacteria.4 Cyanobacteria are also an interesting object of research in biochemistry,5 with studies investigating their potential as biosorbents6 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 tumors of the liver and diseases of the nervous system in animals and humans.8

[link] summarizes the 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 sulfur bacteria Anoxygenic Outside the cell
Chloroflexi (Division) Chloroflexi Chloroflexus Green nonsulfur bacteria Anoxygenic None
Proteobacteria Alphaproteobacteria Rhodospirillum Purple nonsulfur bacteria Anoxygenic None
Betaproteobacteria Rhodocyclus Purple nonsulfur bacteria Anoxygenic None
Gammaproteobacteria Chromatium Purple sulfur bacteria Anoxygenic Inside the cell

Key Concepts and Summary

Multiple Choice

Which of the following is the organelle that spirochetes use to propel themselves?

  1. plasma membrane
  2. axial filament
  3. pilum
  4. fimbria


Which of the following bacteria are the most prevalent in the human gut?

  1. cyanobacteria
  2. staphylococci
  3. Borrelia
  4. Bacteroides


Which of the following refers to photosynthesis performed by bacteria with the use of water as the donor of electrons?

  1. oxygenic
  2. anoxygenic
  3. heterotrophic
  4. phototrophic


Fill in the Blank

The bacterium that causes syphilis is called ________.

Treponema pallidum pallidum

Bacteria in the genus Rhodospirillum that use hydrogen for oxidation and fix nitrogen are ________ bacteria.

purple nonsulfur

Short Answer

Explain the term CFB group and name the genera that this group includes.

Name and briefly describe the bacterium that causes Lyme disease.

Characterize the phylum Cyanobacteria.


  1. 1 R.C. Fuller et al. “Carbon Metabolism in Chromatium.” Journal of Biological Chemistry 236 (1961):2140–2149.
  2. 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. 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. 4 T. Cavalier-Smith. “Membrane Heredity and Early Chloroplast Evolution.” Trends in Plant Science 5 no. 4 (2000):174–182.
  5. 5 S. Zhang, D.A. Bryant. “The Tricarboxylic Acid Cycle in Cyanobacteria.” Science 334 no. 6062 (2011):1551–1553.
  6. 6 A. Cain et al. “Cyanobacteria as a Biosorbent for Mercuric Ion.” Bioresource Technology 99 no. 14 (2008):6578–6586.
  7. 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. 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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