Understanding nitrous oxide emission from agricultural system through the functional ecophysiological traits of ammonia-oxidizing microorganisms

• Grant number: 24/15775-2
• Support Opportunities: Scholarships abroad - Research Internship - Post-doctor
• Start date: April 30, 2025
• End date: September 01, 2025
• Field of knowledge: Agronomical Sciences - Agronomy - Soil Science
• Principal Investigator: Maurício Roberto Cherubin
• Grantee: Lucas Pecci Canisares
• Supervisor: Graeme William Nicol
• Host Institution: Escola Superior de Agricultura Luiz de Queiroz (ESALQ). Universidade de São Paulo (USP). Piracicaba , SP, Brazil
• Institution abroad: Université Claude Bernard Lyon 1, France
• Associated to the scholarship: 23/08814-9 - MONS: Mechanisms of nitrous oxide emission in tropical soil, BP.PD

Abstract

Nitrous oxide (N2O) emission in tropical agroecosystems predominantly occurs through nitrification due to well-aerated conditions that rarely support denitrification. Nitrification, a key process in the nitrogen (N) cycle, converts ammonium to nitrate. The limiting step in this process is ammonia oxidation, carried out by ammonia-oxidizing microorganisms (AOM) such as ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA), and complete ammonia oxidizers (comammox). These organisms play distinct roles in N2O production, with AOB typically yielding more N2O compared to AOA. Understanding the niche differentiation of AOB, AOA and comammox is crucial for predicting and mitigating N2O emissions in agroecosystems. AOB and AOA occupy different niches based on soil pH and substrate concentrations. AOA tend to oxidize ammonia from organic sources due to higher substrate affinity that makes this group to growth in environments with lower ammonium concentration, while AOB tend to oxidize ammonia derived from fertilizers due to their lower substrate affinity that allow them to growth in soil rich in ammonium. For example, organic amendments result in lower soil ammonium content than inorganic fertilizers like ammonium-based fertilizers (e.g. ammonium sulfate, urea and ammonium nitrate) due to slower release of ammonium during the organic N mineralization. Consequently, organic amendments favor AOA while inorganic fertilizers favor AOB. However, differences have been observed within AOB and AOA, where certain lineages of AOA have similar substrate affinities as some AOB groups while other lineages do not grow if a high concentration of N substrate supplied. Therefore, agricultural practices that alter soil ammonium content concentrations might impact AOM populations based on their resource utilization traits. Cover crops, widely used for enhancing soil health and carbon sequestration, also influence inorganic nitrogen availability and N2O emissions. Legume cover crops, with lower C:N ratios, release inorganic nitrogen rapidly, potentially increasing AOB populations and AOA with lower affinities for substrate. Grass cover crops, with higher C:N ratios, immobilize inorganic nitrogen, favoring AOA lineages with high affinity for substrate. Understanding these interactions is essential for optimizing agroecosystems to maximize carbon sequestration while minimizing N2O emissions. This project aims to investigate the impact of different cover crop species on the composition of active AOB, AOA, and comammox in agricultural soils where N is supplied by different N substrates (organic and inorganic). By evaluating soil microcosms with various cover crop treatments, we will assess how different N substrates influence AOM communities and their contribution to N2O emissions. The findings will inform sustainable agricultural management practices to mitigate greenhouse gas emissions and enhance soil health.