Factors predictive of the biogeographic distribution of comammox Nitrospira in terrestrial ecosystems

Abstract

Comammox Nitrospira, nitrifiers capable of performing complete nitrification on their own, are widely distributed in terrestrial ecosystems. However, their environmental preferences and factors that predict their biogeographic distribution have not been elucidated. Because most nitrifiers share the same basic life strategies and requirements, the best predictor of large-scale comammox bacterial abundance may be the abundance of other nitrifying guilds. To validate this hypothesis, we assembled data from 60 studies conducted in cropland, grassland, and forest ecosystems to identify abiotic and biotic parameters with the potential to predict comammox bacterial abundance and compare their predictive powers using random forest modelling. As expected, ammonia-oxidizing archaea (AOA) and bacteria (AOB) are the top two factors predicting comammox bacterial abundance, followed by soil pH and nitrate and ammonium (NH4+). Consistent evidence is present from cropland, grassland, and forest landscapes to show that comammox Nitrospira co-vary positively with AOA. On large spatial scales, soil pH and NH4+ are the dominant influence on the abundance of clades A and B, respectively. A negative correlation with rainfall and acidity implies that clade A prefers dry, non-acidic environments, whereas a negative correlation with NH4+ and rainfall indicates that clade B prefers dry, oligotrophic environments. These findings reveal that predictors at the aggregate and clade scales do not overlap, and the predictors of any single genetic clade may not be predictive of total abundance. Comammox Nitrospira prefer to co-metabolize with AOA with the same ecological preferences, hence the strongly positive population co-variation. However, the predictive power of incomplete nitrifiers as predictors may decline when modelling the abundance of a single genetic clade. At the clade level, comammox bacterial abundance is highly modulated by abiotic factors such as pH and NH4+. Niche differentiation between clade A and clade B is influenced more by pH and N status than by water status.