Tree microbiomes and methane emissions in upland forests

Gewirtzman, J.; Arnold, W.; Taylor, M.; Burrows, H.; Merenstein, C.; Woodbury, D.; Whitlock, N.; Kraut, K.; Gonzalez, L.; Brodersen, C. R.; Duguid, M.; Raymond, P. A.; Peccia, J.; Bradford, M. A.

doi:10.1101/2025.09.30.679632

bioRxiv · 10.1101/2025.09.30.679632

Tree microbiomes and methane emissions in upland forests

Gewirtzman, J.·Arnold, W.·Taylor, M.·Burrows, H.·Merenstein, C.·Woodbury, D.·Whitlock, N.·Kraut, K.·Gonzalez, L.·Brodersen, C. R.·Duguid, M.·Raymond, P. A.·Peccia, J.·Bradford, M. A.

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Abstract

RationaleUpland forest trees emit CH , but whether emissions derive from internal microbial production or soil-derived transport remains debated. Methanogens have been detected in heartwood of several species, yet the prevalence of wood-associated methanogenesis, its metabolic basis, and its relationship to co-occurring methanotrophy are poorly understood. MethodsWe measured 1,148 stem fluxes and 276 soil fluxes, sampled internal stem gases including {delta}{superscript 1}3CH , quantified methanogens and methanotrophs via ddPCR in 564 samples, characterized communities via 16S rRNA sequencing, and upscaled fluxes. Key resultsMethanogens were detected in 97% of heartwood samples (up to 10 copies g {superscript 1}) at concentrations exceeding soil by [~]2 orders of magnitude; methane consumers were likewise near-ubiquitous across forest compartments. Wood harbored distinct microbial communities dominated by hydrogenotrophic Methanobacteriaceae, corroborated by depleted {delta}{superscript 1}3CH . Vertical flux profiles indicated soil transport only in wet microsites, with uniform emissions across height consistent with internal production across most upland species. Species-level methanogen:methanotroph ratios predicted emissions (R{superscript 2} = 0.51), indicating net flux reflects the balance between production and oxidation. Main conclusionMethane-cycling microbes are widespread in upland trees, and net methane flux reflects the species-level balance between production and consumption. Internal methanogenesis contributes widely to upland tree emissions; resolving ecosystem-scale magnitude requires improved quantification of woody surface area and vertical flux variability.

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Gewirtzman, J., Arnold, W., Taylor, M., Burrows, H., Merenstein, C., Woodbury, D., Whitlock, N., Kraut, K., Gonzalez, L., Brodersen, C. R., Duguid, M., Raymond, P. A., Peccia, J., Bradford, M. A.. 2025-09-30. Tree microbiomes and methane emissions in upland forests. https://doi.org/10.1101/2025.09.30.679632

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