From deforestation to regeneration: How do land-use changes shape soil microbes and methane-cycling genes in the Eastern Amazon?

• Land-use change affects the structure and composition, and diversity of soil microbial communities in the Eastern Amazon rainforest. • Forest-to-pasture conversion increases the abundance of methanogenesis genes. • Seasonality amplifies the effects of land-use change on methane-related genes, increasing methanogenesis during the wet season in pasture soils. • Soil pH regulates the resilience of the CH₄ cycle. Land-use change in the Amazon Rainforest impacts soil properties and belowground microbial communities, with far-reaching implications for soil ecosystem services, including methane cycle processes. However, it is unclear whether the known methane sink-to-source shift observed after forest-to-pasture conversion occurs consistently throughout the year, or whether forest regeneration can help us restore this crucial ecosystem process. Here, we assessed the impacts of forest-to-pasture conversion and forest regeneration in the Amazon Rainforest on its soil properties and microbial communities, focusing on methane-related microbiota, using 16S rRNA sequencing and quantitative real-time PCR. Conversion resulted in significant changes in soil chemistry and microbial communities, while seasonality and its interaction with land use intensified those differences. Land-use change also increased the abundance of methanotrophs and methanogens, but the ratio between both groups was altered, consistent with pastures as potential sources of methane and forests as sinks. Seasonality further increased the impact of the conversion on methane-cycling microorganisms. Our findings also highlight the potential of passive forest regeneration to restore certain soil chemistry and microbiological patterns similar to those of primary forests, including methane-related genes. Although these results provide strategies to support methane mitigation, they indicate that the functional and taxonomic potential of microbial communities may not be equally recovered. This highlights the importance of maintaining primary forests to preserve critical ecosystem services.