Comammox and ammonia-oxidizing archaea dominated the nitrification under different nitrogen fertilizer levels in acid purple soil of Southwest China

Abstract

Ammoxidation represents the initial phase of nitrification and the rate-limiting step of the whole process, primarily influenced by complete ammonia oxidizers (comammox), ammonia-oxidizing archaea (AOA), and ammonia-oxidizing bacteria (AOB). However, in the co-existence of comammox, AOA and AOB, the dominant microorganism of ammoxidation process remains unclear. To elucidate the relative roles of these ammonia oxidizers in ammoxidation under sustained N application, we conducted a long-term fertilization experiment involving five N application rates (0 kg·ha⁻¹, N0; 90 kg·ha⁻¹, N1; 180 kg·ha⁻¹, N2, 270 kg·ha⁻¹, N3; 360 kg·ha⁻¹, N4) and determined the potential nitrification rate (PNR), soil chemical properties, and the diversity and community structure of ammonia oxidizers. Compared to N0, the N application treatments enhanced the PNR, soil organic carbon (SOC), total nitrogen (TN), ammonium (NH₄⁺), nitrate (NO₃⁻), and reduced pH and available phosphorus (AP). Furthermore, the four N application treatments increased the shannon index of AOA, AOB and comammox, while also altered the β-diversity of these groups, and N4 treatments increased the Chao1 index of these groups. The proportion of Archaeo (AOA), Nitrosospira (AOB), and Nitrospira (comammox) increasing progressively as N fertilizer dosage increased, while the proportion of Crenarchaeota (AOA) and Bacteria (AOB) exhibited a declining trend. Redundancy analysis indicated that N application influences the composition of AOA through the pH and AP, the composition of AOB via SOC and NO₃⁻, and the composition of comammox through pH. The results of structural equation model showed that PNR was significantly affected by N rate, pH, AOA α-diversity and comammox α-diversity. In addition, the standardized total effect of AOA α-diversity (0.41) and comammox α-diversity (0.53) on PNR is much greater than that of AOB (0.064). Consequently, comammox may preferentially inhabit acidic and nutrient-poor soil environments, AOA and comammox were identified as the principal contributors to ammoxidation in acid soil under long-term treatment with different N fertilizer levels.