pH selects for distinct N₂O-reducing microbiomes in tropical soil microcosms

Nitrous oxide (N₂O), a greenhouse gas with ozone destruction potential, is mitigated by the microbial reduction to dinitrogen catalyzed by N₂O reductase (NosZ). Bacteria with NosZ activity have been studied at circumneutral pH but the microbiology of low pH N₂O reduction has remained elusive. Acidic (pH < 5) tropical forest soils were collected in the Luquillo Experimental Forest in Puerto Rico, and microcosms maintained with low (0.02 mM) and high (2 mM) N₂O assessed N₂O reduction at pH 4.5 and 7.3. All microcosms consumed N₂O, with lag times of up to 7 months observed in microcosms with 2 mM N₂O. Comparative metagenome analysis revealed that Rhodocyclaceae dominated in circumneutral microcosms under both N₂O feeding regimes. At pH 4.5, Peptococcaceae dominated in high-N₂O, and Hyphomicrobiaceae in low-N₂O microcosms. Seventeen high-quality metagenome-assembled genomes (MAGs) recovered from the N₂O-reducing microcosms harbored nos operons, with all eight MAGs derived from acidic microcosms carrying the Clade II type nosZ and lacking nitrite reductase genes (nirS/K). Five of the eight MAGs recovered from pH 4.5 microcosms represent novel taxa indicating an unexplored N₂O-reducing diversity exists in acidic tropical soils. A survey of pH 3.5-5.7 soil metagenome datasets revealed that nosZ genes commonly occur, suggesting broad distribution of N₂O reduction potential in acidic soils.