Distinct microbial communities drive methane cycling in below- and above-ground compartments of tropical cloud forests growing on peat

Cloud forests are unique yet understudied ecosystems regarding CH₄ exchange despite their significance in carbon storage. We investigated CH₄ fluxes in peat soil and tree stems of two tropical cloud forests on Réunion Island, one featuring Erica reunionensis and the second a mix of E. reunionensis and Alsophila glaucifolia. The study examined microbiomes across below-ground (soil) and above-ground (canopy soil, leaves, and stems) forest compartments. Metagenomics and qPCR analyses targeted key genes in methanogenesis and methanotrophy in soil and above-ground samples, alongside soil physicochemical measurements. CH₄ fluxes from peat soil and tree stems were measured using gas chromatography and portable trace gas analyzers. Peat soil in both forests acted as a CH₄ sink (- 23.8 ± 4.84 µg C m^{- 2} h^{- 1}) and CO₂ source (55.5 ± 5.51 µg C m^{- 2} h^{- 1}), with higher CH₄ uptake in sites dominated by endemic tree species E. reunionensis. In forest soils, a high abundance of n-DAMO 16 S rRNA gene (3.42 × 10⁷ ± 7 × 10⁶ copies/g dw) was associated with nitrate levels and higher rates of CH₄ uptake and CO₂ emissions. NC-10 bacteria (0.1-0.3%) were detected in only the Erica forest soil, verrucomicrobial methanotrophs (0.1-3.1%) only in the mixed forest soil, whereas alphaproteobacterial methanotrophs (0.1-3.3%) were present in all soils. Tree stems in both forests were weak sinks of CH₄ (-0.94 ± 0.4 µg C m^{- 2} h^{- 1}). The canopy soil hosted verrucomicrobial methanotrophs (0.1-0.3%). The leaves in both forests exhibited metabolic potential for CH₄ production, e.g., exhibiting high mcrA copy numbers (3.5 × 10⁵ ± 2.3 × 10⁵ copies/g dw). However, no CH₄-cycling functional genes were detected in the stem core samples. Tropical cloud forest peat soils showed high anaerobic methanotrophy via the n-DAMO process, while aerobic methanotrophs were abundant in canopy soils. Leaves hosted methanotrophs but predominantly methanogens. These results highlight the significant differences between canopy and soil microbiomes in the CH₄ cycle, emphasizing the importance of above-ground microbiomes in forest CH₄ gas budgets.