Cold Atmospheric Plasma Decontaminates Arabidopsis thaliana Seeds and Remodels Seedling Fungal Microbiota

Seed-associated microorganisms influence seed quality, seedling establishment, and plant health and also constitute a major source of seed-borne pathogens. Cold atmospheric plasma (CAP) has emerged as a promising alternative to chemical seed treatments because of its antimicrobial activity, although its effects on fungal communities associated with developing seedlings remain poorly understood. Here, Arabidopsis thaliana seeds from two ecotypes (Columbia and Landsberg erecta) were exposed to CAP for 5 or 15 min. Seed decontamination efficiency was assessed by culturing on malt extract agar and nephelometric analyses, while fungal communities associated with seedlings derived from treated and untreated seeds were characterized by ITS1 amplicon sequencing. CAP efficiently reduced fungal contamination without affecting seed germination. CAP altered the composition of fungal communities associated with developing seedlings, but the magnitude of these changes depended on seed batch and ecotype. Dominant taxa markedly declined after treatment, whereas several low-abundance taxa increased in relative abundance. These findings demonstrate that CAP is an effective pesticide-free technology for seed decontamination and can also reshape fungal communities associated with developing seedlings, highlighting broader ecological consequences of plasma-based seed treatments.