Investigations of soil autotrophic ammonia oxidizers in farmlands through genetics and big data analysis

Highlights: • AOA, AOB, comammox, anammox and feammox commonly co-existed in agricultural soils. • Feammox showed significant contribution to autotrophic ammonia oxidation in soils. • Direct and indirect effects of dominated factors on ammonia oxidizers were identified. • The relationship between reactive heavy metals and ammonia oxidation was first studied. Soil ammonia oxidation is a key and rate-limiting process of nitrogen cycle in agriculture. Diverse autotrophic ammonia oxidizers, including ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), anaerobic ammonium oxidation (anammox), complete ammonia oxidation (comammox), and anaerobic ammonium oxidation coupled to iron reduction (feammox), were found to drive the process. However, limited studies have investigated the co-occurrence, abundance and relative contributions of these microbes in agricultural soils. Here, we report the diversity, abundance, environmental factors influencing these microbes and their contributions to soil ammonia oxidation. Results suggest that AOA, AOB, comammox, anammox, and feammox commonly co-existed in soil microbial community regardless of land uses (rice, soybean, orchard, nursery stock, and weed); and had a higher abundance in the topsoil (0–15 cm) than the subsoil (15–30 cm). Both AOA and AOB were important drivers of autotrophic ammonia oxidation in rice soils, with predicted ammonia oxidation rates of 0.48 ± 0.56 and 0.93 ± 1.32 μmol N·g dry soil⁻¹·d⁻¹, respectively. Interestingly, feammox, Acidimicrobiaceae sp. A6, showed an equivalent or even greater predicted ammonia oxidation rate (1.23 ± 0.98 μmol N·g dry soil⁻¹·d⁻¹) than AOA or AOB in rice soils, suggesting the significant contribution of feammox to soil ammonia oxidation. Multiple factors, including nutrients, pH, moisture content, total organic carbon, and reactive heavy metals were confirmed to directly or indirectly affect the autotrophic ammonia oxidizers. Notably, the increase of heavy metal availability enriched the autotrophic ammonia oxidizers, which implied the negative effect of heavy metals on soil nitrogen management. These results suggest that multi-engineering measures, e.g., slow-release fertilizer, soil acidification mitigation, and heavy metal immobilization should be taken together to slow the ammonia oxidation for improving nitrogen-use efficiency in agriculture.