Yogurt, pickles, sauerkraut, and lime-seasoned dishes all owe their tangy taste to a high acid content (Figure 3.34). Recall that acidity is a function of the concentration of hydrogen ions [H⁺] and is measured as pH. Environments with pH values below 7.0 are acidic, with a high concentration of H+ ions; those with pH values above 7.0 are considered basic. Extreme pH affects the structure of all macromolecules. The hydrogen bonds holding together strands of DNA break up at high pH. Lipids are hydrolyzed by an extremely basic pH. The proton motive force responsible for production of ATP in cellular respiration depends on the concentration gradient of H⁺ across the plasma membrane (see Cellular Respiration). If H⁺ ions are neutralized by hydroxide ions, the concentration gradient collapses and impairs energy production. But the component most sensitive to pH in the cell is its workhorse, the protein. Moderate changes in pH modify the ionization of amino-acid functional groups and disrupt hydrogen bonding, which, in turn, promotes changes in the folding of the molecule, promoting denaturation and destroying activity.

The optimum growth pH is the most favourable pH for the growth of an organism. The lowest pH value that an organism can tolerate is called the minimum growth pH and the highest pH is the maximum growth pH (Figure 3.35). These values can cover a wide range, which is important for the preservation of food and to microorganisms’ survival in the stomach. For example, the optimum growth pH of Salmonella spp. is 7.0–7.5, but the minimum growth pH is closer to 4.2.

Neutrophiles

Most bacteria are neutrophiles, meaning they grow optimally at a pH within one or two pH units of the neutral pH of 7, between 5 and 8 (see Figure 3.35). Most familiar bacteria, like Escherichia coli, staphylococci, and Salmonella spp. are neutrophiles and do not fare well in the acidic pH of the stomach. However, there are pathogenic strains of E. coli, S. typhi, and other species of intestinal pathogens that are much more resistant to stomach acid. In comparison, fungi thrive at slightly acidic pH values of 5.0–6.0.

Acidophiles

Microorganisms that grow optimally at a pH less than 5 are called acidophiles. For example, the sulphur-oxidizing Sulfolobus spp. isolated from sulphur mud fields and hot springs in Yellowstone National Park are extreme acidophiles. These archaea survive at pH values of 2.5–3.5. Species of the archaean genus Ferroplasma live in acid mine drainage at pH values of 0–2.9 (Figure 3.36). Lactobacillus bacteria, which are an important part of the normal microbiota of the vagina, can tolerate acidic environments at pH values 3.5–6.8 and also contribute to the acidity of the vagina (pH of 4, except at the onset of menstruation) through their metabolic production of lactic acid. The vagina’s acidity plays an important role in inhibiting other microbes that are less tolerant of acidity. Acidophilic microorganisms display a number of adaptations to survive in strong acidic environments. While the membrane is slightly leaky to protons, the cytoplasmic pH of most acidophiles is generally only slightly acidic. One of the major reasons for this is their ability to actively transport of H⁺ ions out of the cell. In addition, cytoplasmic proteins have evolved to function better at a slightly acidic pH with increased negative surface charges compared to their neutrophilic homologues. The ether linkage of the archaeal membrane lipids is more acid stable than the typical ester linked phospholipids, but in addition, acidophilic archaea typically possess tetraether membrane lipids. The resulting monolayer structure  makes their membranes a much better barrier to proton leakage in extremely low pH environments. And since these organisms may also be adapted to growing at high temperatures, the membranes also maintain their semi-fluid consistency. While the cytoplasmic proteins of acidophiles have relatively normal pH optima, those that are secreted have acidic pH optima compared to their neutrophile homologues. The gene sequences for acidophilic secreted proteins have evolved to give secondary, tertiary and quaternary structures that are resistant to the protonating effects of the acidic environment. These proteins are of great interest for their possible biotechnological applications.

Alkaliphiles

At the other end of the spectrum are alkaliphiles, microorganisms that have pH optima between 8.0 and 11. Vibrio cholerae, the pathogenic agent of cholera, grows best at the slightly basic pH of 8.0; it can survive pH values of 11.0 but is inactivated by the acid of the stomach. When it comes to survival at high pH, the bright pink halophilic archaeon Natronobacterium, found in the soda lakes of the African Rift Valley, may hold the record at a pH of 10.5 (Fig. 3.37). Extreme alkaliphiles have adapted to their harsh environment through various evolutionary modifications. Alkaliphilic archaea have diether lipid membranes. The ether linkage is more resistant to chemical or thermal degradation compared to the ester-linked phospholipids. Given the paucity of protons in alkaline environments, maintaining a proton motive force is probably the most pressing challenge for alkaliphiles. One of the adaptations of alkaliphilic halophilic bacteria and archaea in soda lakes and other highly salty environments is the evolution of coupled transporters and flagella that exploit sodium motive force, thus conserving the PMF for oxidative and photophosphorylation by the ATP synthase. The cell surface of alkaliphiles has a high concentration of acidic (i.e. negatively charged) molecules and it has been suggested this acts as a “proton sponge”, allowing a more rapid lateral diffusion of protons from the ETS, to the ATP synthase, compared to the rate of diffusion into the surrounding waters^[1] Finally, alkaliphiles may use Na⁺/H⁺ antiport to create a sodium motive force. For example, the alkaliphile Bacillus firmus derives the energy for transport reactions and motility from SMF rather than a proton motive force. As with the acidophiles, the genes for secreted proteins of alkaliphiles have evolved to give enzymes that resist deprotonation/denaturation and chemical degradation at the high pH of their environment. These enzymes are also of interest to biotechnology companies. In fact, laundry detergents, which are alkaline in nature, contain alkaliphilic lipases and proteases to improve their stain-removing abilities.

Adapting to Changes in Environmental pH

Outside of the lab, the physicochemical conditions faced by microbes may fluctuate rapidly. This is also true of host-associated microbes. The bacteria and archaea of the developing gut microbiota, as well as gastrointestinal pathogens such as the various pathogenic strains of E. coli, must be able to survive exposure to the acid pH of the stomach in order to colonize intestinal tract. These organisms therefore require the ability to adapt to a sudden and temporary drop in pH. One major strategy such organisms use is a global stress response system known as the “acid shock” response. This response results in acid tolerance and involves the induction (turning on) of a suite of genes, and the repression of others to essentially reprogram the cell. Among the molecules that are expressed as a result of acid stress are chaperones. These function to help fold, or refold, unfolded proteins. This response helps neutrophiles survive exposure to acid pH but below the minimum, proteins are irreversibly denatured and the cell dies. This has been exploited as a means of food preservation (Figure 3.34), for example in pickling (vinegar is dilute acetic acid).