Soil pH, not land-use type, predicts microbial motility and denitrification genes after rainforest conversion in Sumatra and Borneo

Abstract Conversion of lowland rainforest to rubber and oil palm alters soil microbial communities, but whether functional gene responses are consistent across regions, and what drives them, is unclear. Public soil shotgun metagenomes from Jambi, Sumatra (32 plots: rainforest, jungle rubber, rubber, oil palm) and Sabah, Borneo (24 plots: unlogged forest, logged forest, oil palm) were reanalysed. The Sumatran workflow reproduced published fold changes (r = 0.998). In Sumatra, land use explained 41% of the variation in functional composition (permutation test, p = 0.0001); flagellar assembly genes declined by 27–35%, chemotaxis genes by 17–20% and secretion-system genes by 10–12% in converted systems, while denitrification genes increased in oil palm ( nirS + 220%, nosZ + 164%). In Sabah, oil palm differed little from unlogged forest, and oil palm effects pooled across sites were not significant and highly heterogeneous (I² = 83–99%). In contrast, relationships with soil pH were consistent in both regions: denitrification (combined ρ = 0.69) and nitrogen-fixation genes (ρ = 0.50) increased with pH, whereas type VI secretion (ρ = −0.64), flagellar motility (ρ = −0.53) and chemotaxis genes (ρ = −0.41) decreased (all p ≤ 0.002). Plantations raised soil pH consistently in Sumatra but not in Sabah. Decimal errors in 32 published soil values and a misassigned mcrA gene were also corrected. Soil chemistry, particularly pH altered by liming, predicts microbial functional responses to rainforest conversion better than land-use type alone. Measuring soil pH alongside metagenomes should improve predictions of microbial denitrification potential in plantation landscapes, including in the Philippines.