Comammox Nitrospira Clade B is the most abundant complete ammonia oxidizer in a dairy pasture soil and inhibited by dicyandiamide and high ammonium concentrations

Abstract

The recent discovery of comammox <i>Nitrospira</i>, a complete ammonia oxidizer, capable of completing the nitrification on their own has presented tremendous challenges to our understanding of the nitrification process. There are two divergent clades of comammox <i>Nitrospira</i>, Clade A and B. However, their population abundance, community structure and role in ammonia and nitrite oxidation are poorly understood. We conducted a 94-day microcosm study using a grazed dairy pasture soil amended with urea fertilizers, synthetic cow urine, and the nitrification inhibitor, dicyandiamide (DCD), to investigate the growth and community structure of comammox <i>Nitrospira</i> spp. We discovered that comammox <i>Nitrospira</i> Clade B was two orders of magnitude more abundant than Clade A in this fertile dairy pasture soil and the most abundant subcluster was a distinctive phylogenetic uncultured subcluster Clade B2. We found that comammox <i>Nitrospira</i> Clade B might not play a major role in nitrite oxidation compared to the role of canonical <i>Nitrospira</i> nitrite-oxidizers, however, comammox <i>Nitrospira</i> Clade B is active in nitrification and the growth of comammox <i>Nitrospira</i> Clade B was inhibited by a high ammonium concentration (700 kg synthetic urine-N ha^-1) and the nitrification inhibitor DCD. We concluded that comammox <i>Nitrospira</i> Clade B: (1) was the most abundant comammox in the dairy pasture soil; (2) had a low tolerance to ammonium and can be inhibited by DCD; and (3) was not the dominant nitrite-oxidizer in the soil. This is the first study discovering a new subcluster of comammox <i>Nitrospira</i> Clade B2 from an agricultural soil.