First microscale data on depth profiles of microbial N₂O reduction, O2 availability, and pore networks inside contrasting single soil aggregates

Abstract

A major greenhouse gas, nitrous oxide (N₂O) significantly emitted from agricultural soils, is reduced to innocuous N₂ gas by the activity of two groups of N₂O-reducing microbes (typical clade I and more recently discovered atypical clade II) having different enzymatic efficiency. Yet, basic information such as the locations of N₂O reduction hotspots and soil factors regulating their formations is still lacking. In addition, oxygen availability, which is strongly constrained by soil pore property, likely dictates their ecology in soil as N₂O reductase enzyme (coded by nosZ genes) is inhibited by O₂. Accordingly, the aim of this study was to assess the mechanistic linkage among soil pore networks, chemical microenvironments (pH, Eh, and O₂ and N₂O abundances), ecology of N₂O-reducing microbes, and the occurrence of N₂O reduction hotspots in single soil aggregates. Using water-stable macroaggregates from two contrasting soil types (highly porous Andosol and less porous clay-rich Acrisol), we determined microscale depth profiles of N₂O and O₂ dynamics, three-dimensional pore properties, and the two N₂O reducer populations in the single aggregates after 48-hour lab incubation under a water-saturated condition. The N₂O and O₂ depth profiles showed the increase in N₂O production with O₂ depletion towards deeper part of the incubated aggregates, indicating denitrification N₂O production especially in Andosol aggregate where O₂ availability was higher. The gene distribution with depth clearly showed higher abundance of nosZ harboring microbes (including both clades I and II) in the Acrisol aggregate than Andosol aggregate especially towards the aggregate interior. In the Acrisol aggregate, the abundance of nosZ clade I harboring microbes was maximum at the middle depth corresponding to N₂O maxima, whereas the nosZ clade II harboring microbes had slightly different niche as their population monotonically increased towards the aggregate core, which were consistent with theoretical O₂ availability and pore connectivity. The current findings underscore the intimate connection between soil physical complexity and microbial ecology, which merits further investigation.