Stable isotope probing with ¹⁸O-water to investigate growth and mortality of ammonia oxidizing bacteria and archaea in soil

Ammonia oxidizing bacteria (AOB) and archaea oxidize ammonia to nitrite, the first and rate-limiting step in the important ecosystem process of nitrification. Growth and mortality of ammonia oxidizers in soil are difficult to quantify but accurate measurements would offer important insights into how environmental parameters regulate the population dynamics of these organisms. Stable isotope probing (SIP) is a recently developed technique that can identify microorganisms that assimilate labeled substrates and can be adapted to quantify the growth of organisms in soil. Here, we describe the use of SIP with ¹⁸O-water to investigate the growth and mortality of ammonia oxidizers in a soil taken from a ponderosa pine forest in northern Arizona, USA. Addition of ammonia to soil stimulated the growth of AOB but not ammonia oxidizing archaea (AOA). The mortality of AOA was increased upon addition of ammonia to soil; however, the variance in these measurements was high. The mortality of AOB, in contrast, was not impacted by addition of ammonia to soil. The results suggest that increased ammonia availability in soil favors AOB over AOA.