Long-term rainfall and litter exclusion microbiome dataset

This study provides multi-marker amplicon sequencing datasets to assess how long-term reduction of water inputs and organic substrate supply reshapes forest soil microbiomes. Soil samples were collected in October 2025 from an experimental manipulation site established at the Chiyoda Experimental Station of the Forestry and Forest Products Research Institute (FFPRI), Japan (36.10 N, 140.13 E). The site has been continuously roofed approximately 2 m above the ground since 2017 to exclude both rainfall and litterfall, creating a persistent combination of drying and reduced litter-derived carbon inputs. Surface mineral soils (0-10 cm) were sampled from four points per treatment (rainfall/litter exclusion and an adjacent control), kept cold during transport, and stored at -80 C until analysis. Bacterial and fungal communities were profiled using short-read amplicon sequencing targeting the 16S rRNA gene V4 region (primers 515F/806R) and the fungal ITS2 region (primers gITS7/ITS4), with library preparation and sequencing performed by a commercial service provider (Illumina NextSeq 1000, paired-end). Arbuscular mycorrhizal fungal communities were additionally characterized using long-amplicon sequencing of the SSU-ITS-LSU rDNA region (~2.7 kb) generated by a nested PCR strategy (NS31/LSUmAr13+LSUmAr24 and AML1/LSUmAr13+LSUmAr24, followed by NS31_Glo3/wLSUmBr) and sequenced using the PacBio Revio platform. Detailed PCR parameters and primer information are available via protocols.io. These data enable comparisons between treatments and provide a reference resource for evaluating community shifts, compositional turnover, and potential functional adaptation of forest soil microbiomes under chronic rainfall exclusion and litter limitation in a managed forest setting.