6.2.4: pH

pH tells us the extent to which an environment is acidic or basic. Similarly to pressure, microbial life extends over a broad pH range. Only a few species can grow in environments with pH less than \(2\) and above \(10\) (Madigan et al., 2003), but microbial growth has been demonstrated at external pH as low as \(0\) and as high as about \(13\) (Pikuta et al., 2007; Roadcap et al., 2006; Schleper et al., 1995). To fully appreciate the extent of this range, we have to recall that pH is calculated as the negative log (base 10) of hydrogen ion activity: \[\text{pH} = -\log \left[ \text{H}^{+} \right]\] Thus, for each pH unit, hydrogen ion activity changes by a factor of ten. In other words, microbial life extends over at least 13 orders of magnitude in hydrogen ion activity.

Within these extremes, most individual species can only grow over a pH range of three to four pH units (Rosso et al., 1995). Neutrophiles grow optimally at pH levels between \(5\) and \(9\) (Konhauser, 2007). Acidophiles grow best at pH less than \(5\) and alkaliphiles grow best at pH greater than \(9\) (Baker-Austin and Dopson, 2007; Horikoshi, 1999). The pH requirements for growth of these groups represents the pH of the external environment. Internal pH, the pH of a cell’s cytoplasm, is typically near neutral values, even for acidophiles and alkaliphiles (Lowe et al., 1993).

External pH influences microbial communities in several ways. As summarized by Jin and Kirk (2018a, 2018b), pH affects geochemical reactions that affect the salinity and composition of aqueous solutions and the bioavailability of nutrients, it impacts the function and activity of microbial enzymes and other biomolecules, and it affects the amount of energy released by microbial reactions and reaction rates because many microbial reactions include hydrogen ions either as a product or reactant.

Reflecting these impacts, many studies have found that pH is a significant environmental control on microbial community composition. As an example, Fierer and Jackson (2006) examined microbial communities in 98 soil samples from across North and South America. They considered environmental factors that influenced microbial community diversity, which includes richness (the number of different species) and evenness (distribution of abundance across the species). Their analysis showed that soil pH was a more important driver of diversity than even mean annual temperature and other factors that typically predict plant and animal diversity. They also found that soil pH was the strongest predictor of microbial community composition. As a second example, Power et al. (2018) examined microbial communities in 925 geothermal springs in New Zealand. The springs had pH ranging from \(<1\) to \(9.7\) and temperature ranging from \(13.9 \text{-} 100.6^{\circ}\text{C}\). They found that pH was the primary driver of diversity in springs with temperature below \(70^{\circ}\text{C}\). Above \(70^{\circ}\text{C}\), temperature became a significant driver.

In both of these studies, species richness was found to be greatest at near-neutral pH. Similarly, Thompson et al. (2017) observed the same result in an even larger scale study, which examined bacterial and archaeal rRNA gene sequences collected from sites around the world. Their analysis included 3,986 samples collected mostly from freshwater and soil environments. Taken together, the results indicate that most bacterial and archaeal species are neutrophiles.

Lastly, the extent to which pH impacts soil microbial communities appears to be greater for bacteria than fungi. Rousk et al. (2010) examined microbial communities in soils from a long-term field experiment where soil microbes were exposed to pH ranging from \(4\) to \(8.3\). The relative abundance and diversity of bacteria in the community were significantly related to pH. In contrast, they found that the relative abundance of fungi was unaffected by pH and fungal diversity was only weakly related to pH. They interpreted that differences in the response of bacteria and fungi to pH may reflect narrower pH ranges for bacterial species than fungal species within the communities