Microbial succession and tissue-specific restructuring of bacterial and fungal communities during post-harvest onion bulb rotting

Despite being a relatively hardy bulb crop with a longer shelf life than many fresh vegetables, onions are susceptible to substantial postharvest losses due to microbial spoilage. This study used high-throughput amplicon sequencing to characterize the bacterial and fungal microbiomes associated with healthy (HB), mildly rotten (MRB), and severely rotten (SRB) onion bulbs. Microbial communities were analysed across three distinct bulb tissues comprising neck tissue (NT), outer scale (OS), and central tissue (CT), to generate stage-specific and tissue-specific microbiome profiles. The microbial community analysis based on over 2 million Illumina NGS reads revealed the presence of 85 bacterial OTUs and 53 fungal OTUs across nine bulb samples. Bulb deterioration was marked by pronounced microbial succession, with bacterial diversity increasing from healthy bulbs (8 genera) to mildly rotten bulbs (36 genera), followed by a sharp decline in severely rotten bulbs (11 genera). Several bacterial genera, including <i>Lactobacillus</i>, <i>Novosphingobium</i>, <i>Sphingobium</i>, <i>Pluralibacter</i>, <i>Acetobacter</i>, <i>Gluconobacter</i> and <i>Pantoea</i>, emerged exclusively in rotten bulbs and were absent in healthy tissues, indicating their association with the onion bulb rot. The microbiome of SRB was marked by an overwhelming dominance of <i>Lactobacillus</i> (33.2% in SRB-CT, 16.9% in SRB-NT, 10.8% in SRB-OS), <i>Acetobacter</i> (16.1% in SRB-CT, 15.6% in SRB-NT, 7.0% in SRB-OS), <i>Carnimonas</i> (57.0% in SRB-NT), and <i>Gluconobacter</i> (14.5% in SRB-OS). Fungal communities exhibited a similar successional pattern: healthy bulbs showed negligible fungal presence except in the neck tissue (HB-NT), whereas mildly rotten bulbs showed a sharp increase in fungal diversity dominated by <i>Meyerozyma</i> (21.7%), <i>Blastobotrys</i> (13.3%), and <i>Penicillium</i> (7.0%). In severely rotten bulbs, fungal diversity declined, with <i>Pichia</i> (48.3%) and <i>Kazachstania</i> (8.6%) becoming dominant. Differential abundance analysis using edgeR identified six bacterial genera (<i>Lactobacillus</i>, <i>Novosphingobium</i>, <i>Acetobacter</i>, <i>Pluralibacter</i>, <i>Carnimonas</i>, and <i>Dysgonomonas</i>) and two fungal genera (<i>Pichia</i> and <i>Kazachstania</i>) that exhibited significant stage-dependent shifts during bulb rot progression. Alpha- and beta-diversity analyses revealed strong tissue-specific structuring of fungal communities, identifying the neck region as the primary fungal succession zone. Overall, this study elucidates the ecological restructuring of bacterial and fungal communities during onion bulb deterioration, and would pave the way for devising microbiome-informed interventions to reduce postharvest losses in onions.