Species and Tissue-Specific Microbiomes Drive Methane Fluxes from Trees

Trees contribute to methane (CH₄) cycling through internal microbial processes and transport, with tree-mediated CH₄ emissions documented across various forest types, including upland ecosystems where soils typically act as CH₄ sinks. To investigate the microbial drivers of these emissions, we measured CH₄ fluxes from tree stems and surrounding soils across upland, intermediate, and wetland sites at Yale-Myers Forest, Connecticut, USA. While upland soils consistently consumed CH₄, tree stems emitted CH₄ at all landscape positions. Fluxes from upland tree stems showed no height-dependent decline, indicating internal methane production rather than soil-to-stem transport. Using droplet digital PCR (ddPCR) to quantify the mcrA gene, methanogen abundance in heartwood was over two orders of magnitude higher than in surrounding soils, with copy numbers ranging from 10⁴ to 10⁵ g⁻¹ in tree tissues compared to 10¹ to 10² g⁻¹ in soils.

Microbial sequencing revealed distinct methanogenic communities, including Methanobacterium and Methanomassiliicoccus, indicating primarily hydrogenotrophic pathways of methane production. Functional inference showed that methanogenesis pathways strongly correlated with fermentation pathways, including those producing hydrogen and acetate, suggesting syntrophic interactions between fermentative bacteria and methanogens. In contrast, methanogenesis pathways were anticorrelated with aerobic respiration and sulfur metabolism, indicating redox conditions suppress methane production in outer tissues. These findings emphasize that heartwood serves as a niche for anaerobic processes driving CH₄ production.

The internal tree microbiome was highly partitioned between tissues. Heartwood and sapwood microbiomes showed distinct microbial compositions and minimal similarity to surrounding soil communities. Heartwood was dominated by anaerobic bacteria and archaea, while sapwood and bark harbored methanotroph-related genes (pmoA, mmoX), indicating potential internal methane oxidation.

Internal gas sampling confirmed elevated CH₄ concentrations within stems, particularly at mid-stem heights, corresponding with visible heartwood decay. Methanotroph-related genes detected in sapwood and bark suggest some gross methane oxidation, but methanogenesis pathways dominated, resulting in net positive fluxes from tree stem to atmosphere. These findings underscore tree microbiomes' importance in methane cycling, with heartwood providing an anaerobic niche for microbial methane metabolism in upland forests.