Microbial Mythology

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Various misconceptions and simple errors commonly appear in textbooks. Here we provide a place for microbiology educators to set the record straight.
Authors: Please provide primary references, in open-access sources whenever possible.

Aerobic or anaerobic: Is a shaken flask truly aerobic?

For decades, researchers have cultured E. coli and other bacteria in a flask shaken or rotated to aerate, providing access to oxygen for respiration. But is the culture truely "aerobic;" that is, does it actually get enough oxygen to respire? It turns out that only during the early part of the growth curve do the bacteria receive enough oxygen to be fully "aerobic" (that is, respiring as fast as they can.) An oxygen electrode shows that up to about optical density of 0.2-0.3 (measured at 600nm), the oxygen concentration declines to zero. Above OD of 0.3, the cells are using oxygen faster than it can be replaced; thus, their respiration is underutilized. The culture is called "microanaerobic," meaning that it uses partly anaerobic metabolism. Later in stationary phase, when metabolism slows down, the culture becomes "aerobic" again. For discussion, see for example Svetlana Alexeeva et al., 2001, J. Bacteriol. 184:1402.
Actually, the situation is even more complicated, depending on the growth medium. Enteric bacteria grown on glucose convert everything to acetate first, no matter how much oxygen they get. Then later, they they take back the acetate and send it to the TCA cycle. For very full discussion, see Alan Wolfe, 2005, MMBR 69:12. (Note: This very long review takes a while to download.)

Centrifugation: Is it a harmless way to "collect" bacteria?

The time-honored way of collecting bacteria from a suspended culture is to centrifuge the suspension; that is, subject the cells to thousands of time gravity (g) so that they sediment in a pellet at the bottom of a tube. But what effect does centrifugation have on cells? They experience g force, loss of oxygen (if previously aerated), nutrient depletion, and cold shock (if previously warmed to 37 deg. C). And the cells experince surface changes that alter their adhesive properties. See for example this article by Caitlin H. Bell, 2005, J. Young Investigators 12:6.

Conjugation in bacteria: Do pili mediate DNA transfer?

During bacterial conjugation, the donor and recipient cells are brought together by protein filaments called pili. Since the pili are composed of hollow tubes of protein subunits, like a turret, it was thought for a while that DNA might travel down the hollow tube. The hollow tube theory is still taught; see example.

Actually, DNA is transferred across the bacterial envelope by a protein complex embedded in the membranes. For review of classic experiments, see Brigette Dreiseikelmann, 1994. For a more current review, see Inês Chen et al, 2005.

Fossil microbes: Do they exist?

The oldest fossil organisms are actually microbes. The earliest convincing microfossils are of colonial cyanobacteria dated to 2 Gya (two billion years ago). More recent fossils known as stromatolites are also the products of microbes affecting the deposition of sediment clasts and the precipitation of chemical sediments.
But microbial fossils are hard to define. Some formations claimed to be fossils have actually turned out to be non-biological. There are no objective criteria for what constitutes a "true" microbial fossil; only a consensus that certain formations have never been seen to result from non-biological chemical or physical processes. For a good general discussion of microbial fossils, see Life on a Young Planet: The First Three Billion Years of Evolution on Earth by Andrew H. Knoll.

Nuclear membrane: Do bacteria have one?

Introductory texts often give the impression that bacterial DNA lacks organization, basically distributed in the cytoplasm. In fact, however, bacterial DNA is tightly organized in looped domains of the nucleoid. See for example "The bacterial nucleoid: a highly organized and dynamic structure," Thanbichler et al 2005. Furthermore, some bacteria actually contain their DNA within a membrane very much like a "nuclear membrane." Such bacteria include the Planctomycetes, studied by John Fuerst and colleagues. Planctomycetes are commonly found in soil and water, where they have important ecological functions such as association with invertebrates, and the conduct of anaerobic ammonia oxidation (anammox metabolism). Some archaea associated with sponges also appear to possess something like "nuclear" membranes.

TCA cycle: Does succinyl-CoA synthetase use ATP or GTP?

Succinyl-CoA synthetase, also known as succinate thiokinase, is the enzyme of the TCA cycle that interconverts succinyl-CoA with succinate, coupled to formation of a nucleotide triphosphate. Many textbooks and web sites state that succinyl-CoA synthetase phosphorylates only GDP to GTP. See example.

According to the primary literature, however, ADP phosphorylation predominates in E. coli (Margaret Birney et al, 1996) whereas in Pseudomonas sp., various nucleotide diphosphates are phosphorylated (Vinayak Kapatral et al, 2000). Human mitochondria have two forms of the enzyme, which phosphorylate ATP and GTP respectively (David Lambeth et al, 2004).

Viruses: Can a virus be a cell?

Viruses are traditionally defined as non-cellular infective particles. Yet some giant viruses, such as Mimivirus (which infects amebas) have a genome comparable in size to that of bacteria (1.2 million base pairs) and carry numerous cellular enzymes. ASM News 71:278, 2005 Bioinformatic analysis shows that Mimivirus probably evolved from bacteria by reductive evolution. Similar reductive evolution is likely for other large DNA viruses such as herpesviruses. Mimivirus can even be parasitized by smaller viruses called "virophages." NatureNews 6 Aug. 2008