High-Throughput Amplicon Sequencing Reveals Geographic Structuring and Latent Infections of Bacterial and Fungal Pathogens in Eritrean Potato Production Systems

Potato (Solanum tuberosum L.) is a vital food security and cash crop in Eritrea, yet bacterial and fungal pathogens responsible for 15–30% yield losses remain molecularly uncharacterized across its production systems. Here, we present the first nationwide amplicon-based metagenomic survey of potato pathogen communities, sampling 81 farms across 14 sub-regions spanning four agroclimatic regions during July–August 2024. High-throughput amplicon sequencing targeting the bacterial 16S rRNA V3–V4 region and fungal ITS1–ITS2 loci revealed pronounced geographic heterogeneity in community composition and alpha diversity. Pseudomonas spp. were ubiquitous, with peak relative abundance of 19.5% in Dekemhare. Dominant fungi included Alternaria spp. (14% in Berik), Fusarium spp. (highest diversity 53.8% in Adi Kuala), Botrytis cinerea (37% in Adi Keih), and Rhizoctonia solani (44.4% in Adi Tekeliezan). Bacterial Shannon diversity averaged 5.67; fungal, 4.70. Weighted UniFrac PCoA accounted for 56.5% of bacterial community variance along PC1, confirming distinct geographic clustering. Critically, latent infections of Pseudomonas, Alternaria, Fusarium, and Colletotrichum were detected in every asymptomatic sample examined, demonstrating the inadequacy of visual-only disease surveillance. These findings establish the first molecular baseline for potato pathogen diversity in Eritrea, providing the empirical foundation for region-specific integrated disease management and evidence-based seed certification protocols.