Ammonium concentration determines differential growth of comammox and canonical ammonia-oxidizing prokaryotes in soil microcosms

Abstract

An unresolved question in microbial ecology is whether the available ammonium concentration has a differential impact on the growth of newly discovered complete ammonia-oxidizing bacteria (CAOB) and their counterparts, the well-known ammonia-oxidizing bacteria (AOB) and archaea (AOA). To address this issue, soil microcosms were cultured for 40 days with ammonium concentrations of 0, 5, 50, 200, and 500 μg NH+ 4-N g−1 soil. Quantitative PCR analysis suggested that AOB grew in response to the two highest ammonium concentrations, whereas CAOB only grew significantly at native and low ammonium concentrations, demonstrating an AOA-like niche specialization favoring oligotrophic environments but being tolerant to a broader ammonium concentration than AOA. Moreover, phylogenetic and Pearson correlation analysis indicated that species from clade B rather than clade A of CAOB contributed to the nitrification process. This study highlights an important role of the local ammonium concentration in affecting the ecological niche differentiation of comammox and canonical ammonia-oxidizing prokaryotes.