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 10⁷ copies g⁻¹), exceeding mean soil abundances by ∼2 orders of magnitude. Wood harbored distinct methanogenic communities (Methanobacteriaceae, Methanomassiliicoccaceae) compared to soils. Individual tree-level gene-flux correlations were weak, reflecting spatial heterogeneity and complex metabolism and transport interactions. However, aggregated tree species-level methanogen:methanotroph ratios correlated significantly with emissions (R² = 0.54), with methanogen abundance alone explaining 40% of variation.

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 flux magnitude requires improved quantification of canopy surface area and flux variability.