Mycobiome Characterisation and Mycotoxin Ecology of the Groundnut Post-Harvest System in Northern Nigeria: A Multi-Site Longitudinal Study

The groundnut post-harvest system in northern Nigeria is a complex ecological environment shaped by dynamic interactions between fungal communities, substrate characteristics, climate variables, and human management practices. Existing mycotoxin research in this context has predominantly applied culture-dependent methods targeting Aspergillus species, leaving the broader mycobiome and its ecological drivers inadequately characterised. This study conducted a multi-site longitudinal characterisation of the complete mycobiome and mycotoxin ecology of the groundnut post-harvest system across five states in northern Nigeria (Kano, Kaduna, Sokoto, Borno, and Katsina) over three consecutive post-harvest seasons. Culture-independent metabarcoding of the ITS1 region using Illumina MiSeq sequencing was applied to 420 post-harvest system samples collected from farms, aggregation centres, markets, and small-scale processing facilities. Mycotoxin profiles (aflatoxins, ochratoxin A, fumonisins, and cyclopiazonic acid) were determined by ultra-high performance liquid chromatography with mass spectrometry. Ecological determinants of mycobiome composition were modelled using multivariate ordination and generalised additive mixed models. Results revealed 312 fungal operational taxonomic units, with Aspergillus section Flavi, Penicillium, and Fusarium constituting the dominant pathogenic genera. Mycobiome diversity was inversely correlated with aflatoxin contamination intensity, suggesting competitive exclusion dynamics. Climate variables (relative humidity and temperature amplitude) were the strongest predictors of seasonal mycobiome shifts. The study produces the first comprehensive mycobiome atlas for this system and provides novel mechanistic data for designing targeted biocontrol interventions. Keywords: mycobiome, mycotoxins, groundnut, metabarcoding, northern Nigeria.