Dataset supporting 'Vermicompost alters soil microbial communities and decomposition but increases nitrate leaching in tropical sugarcane'

Agricultural intensification has elevated nitrogen losses that threaten water quality and farm efficiency. Organic amendments such as vermicompost are promoted as tools to enhance soil health and reduce fertiliser demand, yet their effects under tropical field conditions remain uncertain. A six-week field trial in Australian sugarcane soil tested factorial combinations of vermicompost and nitrogen fertiliser. Metabarcoding, trait-based analysis and structural equation modelling were used to assess soil biodiversity, decomposition and nitrate leaching. Bacterial genera diversity increased in the control soils during early wet-season recovery but rose less in vermicompost-amended soils. Vermicompost also shifted bacterial community composition and accelerated decomposition, while fungal and nematode responses were small over the short timeframe. Despite these microbial shifts, vermicompost increased nitrate leaching through a strong direct effect, with indirect pathways via fungi and decomposition remaining weak and uncertain. These findings show that vermicompost can stimulate microbial activity yet still exacerbate nitrogen losses in clay soils with moderate nutrient retention during high rainfall. Management strategies that align organic amendments with crop uptake or combine them with stabilising materials may help capture microbial benefits while reducing off-site impacts.The dataset contains the experimental plot soil environmental and microbial community data. Data tabs:'Environmental Data' - Contains plot and sample ID, experimental treatments, decomposition mass loss and nitrate (as N) leaching measurements, along with pre-experiment baseline soil test results.'16S_Taxa', '18S_Taxa', 'Nematode_Taxa' - contain the taxonomic assignments of sequences from the 16S, 18S and Nematode sequencing respectively.'16S_ASV', '18S_ASV', 'Nematode_ASV' - contain the filtered but untransformed ASV read count from the 16S, 18S and Nematode sequencing respectively.