Tree stem methane emissions are regulated by site‐level biogeochemistry over species identity in Amazon floodplain forests

•Tree stems in Amazonian floodplains emit substantial methane (CH4), yet controls on emission variability remain unclear. Emissions span orders of magnitude between várzea (nutrient-rich) and igapó (nutrient-poor) forests and among trees, suggesting controls beyond flooding.
•We tested whether site-level biogeochemistry better explains stem CH4 variability than species identity by measuring emissions from two co-occurring species with contrasting wood densities – Eschweilera coriacea and Hevea spruceana – across várzea and igapó forests. Emissions were paired with porewater chemistry (electrical conductivity, dissolved oxygen, dissolved CH4, and dissolved organic carbon), methane production potential (MPP), and root biomass.
•Stem CH4 emissions were significantly higher in várzea than in igapó, independent of species or stem height. Várzea porewaters displayed higher conductivity, dissolved CH4 and MPP, near-neutral pH, and lower oxygen, with fine roots concentrated in the 0- to 50-cm soil layer, indicating a shallow CH4 supply zone. Basal stem emissions in várzea correlated with shallow porewater chemistry and fine-root biomass, whereas relationships in igapó were weak.
•These findings show that Amazonian floodplain stem CH4 emissions are governed by shallow site-level biogeochemistry, rather than species identity alone and should be incorporated into basin-scale CH4 budgets and process models to capture spatial variability.