Tree microbiomes and methane emissions in upland forests

Rationale: Trees emit methane and harbor methanogens, but the generality, distribution, and ecosystem significance of these associations remain unclear. We investigated methanogenic colonization across 16 upland forest tree species and evaluated relationships between microbial communities and emissions. Methods: We measured 1,148 stem fluxes and 276 soil fluxes, quantified methanogens and methanotrophs via droplet digital PCR in 564 samples, characterized communities through 16S rRNA sequencing, and developed models to upscale fluxes ecosystem-wide. Key results: Methanogens were detected in 97% of heartwood samples (up to 10^7; copies per gram), exceeding mean soil abundances by ~2 orders of magnitude. Wood harbored distinct methanogenic communities (Methanobacteriaceae, Methanomassiliicoccaceae) compared to soils. Species-level methanogen abundance correlated with emissions (R-squared = 0.40), though individual-level correlations were weak, reflecting spatial heterogeneity and complex metabolism and transport interactions. Main conclusion: Methanogens are common in tree microbiomes across diverse species, concentrated in heartwood with substantial individual variation. Species-level abundance patterns partially explain emission variability, establishing internal production as a widespread contributor to upland tree fluxes. Future multi-omics approaches could strengthen abundance-flux relationships, while resolving ecosystem-scale importance requires improved quantification of canopy surface area and flux variability.