Onion (Allium cepa L.), one of the most widely cultivated and consumed vegetables, is an indispensable culinary ingredient across cultures worldwide. Onion is widely consumed both raw, such as in salads, and as a key component in diverse cuisines due to its characteristic flavor, aroma, and taste (Jin et al., 2024). Although onions are a relatively hardy bulb crop with a longer shelf life than many fresh vegetables, they are prone to considerable postharvest losses primarily due to microbial spoilage during storage and marketing. Existing reports suggest that postharvest losses in onion can range from 20 to 40% depending on storage conditions, cultivar., and geographical region, contributing to significant economic losses and food insecurity (Suravi et al., 2024). Bacterial and fungal infections are major contributors to onion bulb spoilage, intensifying rotting in mechanically damaged bulbs during storage and transport and causing up to 30% of total post-harvest losses (Sharma, 2023). During storage and transport, the onion bulbs positioned in lower layers of storage heaps are subjected to mechanical pressure from the overlying bulbs, resulting in bruising, cracking, or crushing of the bulb tissues, thereby predisposing such bulbs to microbial invasion and accelerated decay. Likewise, storage of onion bulbs in regions with high temperature and elevated relative humidity, such as tropical areas, not only accelerates bulb respiration but also creates favorable conditions for microbial growth, ultimately reducing bulb quality and shortening storage life (Kleman, 2023). Furthermore, the high moisture content and abundant simple sugars present in onion bulbs provides conducive microenvironment for the growth of a wide range of pathogens that contribute significantly to postharvest decay, incurring storage losses (Kiran et al., 2024). The improper curing and drying of onion bulbs prior to storage renders the bulb, neck, and outer scales/skins highly vulnerable to fungal and bacterial pathogens (Schroeder and Du Toit, 2010). Therefore, post-harvest spoilage of onion bulbs remains a major challenge for onion growers, traders, researchers, and stakeholders involved in the onion supply chain. Improper curing and drying of onion bulbs prior to storage renders the bulb, neck, and outer scales/skins highly vulnerable to fungal and bacterial pathogens.

Culture-dependent investigations of onion bulb pathogens have revealed a wide range of fungal pathogens that include different species of Aspergillus, Penicillium, Fusarium, Botrytis, Rhizopus, and Colletotrichum, as well as bacterial pathogens such as Pseudomonas, Lactobacillus, and Erwinia. These microorganisms are well recognized for their role in causing substantial post-harvest losses of onions during storage. Fusarium species are the most frequently reported, with Fusarium oxysporum f. sp. cepae being the causal agent of basal rot, a disease that can persist both in the field and during storage (Diabankana et al., 2024). Aspergillus niger is another major fungal pathogen responsible for black rot and is among the most frequently isolated fungi from infected onion bulb tissues (Alkasim et al., 2025). In addition, other storage fungi such as Penicillium spp. have been implicated in soft rot development in onion bulbs (Duduk et al., 2017). Bacterial pathogens such as Burkholderia spp. are known to cause sour skin disease and bulb rot in onion, leading to significant postharvest losses during storage and marketing (Paudel et al., 2024). Some other bacterial pathogens known to cause post-harvest onion spoilage include Pantoea spp. (De Armas et al., 2022), Pectobacterium carotovorum (Zhang et al., 2023), Dickeya spp. (Ma et al., 2020), Rouxiella badensis (Zhao et al., 2022) and Pseudomonas spp. (Khanal et al., 2022). Traditionally, the studies on these pathogens have relied on culture-based isolation, pathogenicity tests, and targeted molecular identification to establish their role in onion spoilage. While these approaches identify key pathogens like Fusarium, Aspergillus, and Burkholderia, they often overlook the broader microbial communities and potential synergistic interactions that drive disease progression. This underscores the need for microbiome-based studies to unravel complex community interactions beyond individual pathogens.

Microbial community–based investigations of onion spoilage are of considerable importance, as internal plant tissues naturally harbor many uncultured endophytic microorganisms that typically exist as symbionts or commensals but can transition to pathogenic forms under specific host-related physiological changes or environmental stresses (Kusstatscher et al., 2020). Therefore, a microbiome perspective highlights the complexity of microbial succession and functional shifts that occur during onion storage and subsequent rotting. Recent advances in microbiome research have revealed that both bacterial and fungal members play crucial roles in determining the progression of spoilage, often through enzymatic degradation of host tissues, competition, or synergistic interactions with other microbes (Kuruppu et al., 2024). Therefore, devising a rational biocontrol strategy for post-harvest bulb storage requires the identification of key microbial players causing bulb spoilage. A deeper understanding of bulb microbiome not only helps to identify the microbial drivers of bulb spoilage, but also highlights the role of opportunistic and functionally dominant taxa which may or may not be well-known pathogens but still crucial in bulb rotting.

While microbiome-based approaches have been applied to many perishable fruits and vegetables like tomato (Ottesen et al., 2013), apple (Shen et al., 2018), grapes (Mezzasalma et al., 2018), oranges (Wang et al., 2018), sugar beets (Kusstatscher et al., 2019) and kiwifruit (Wu et al., 2019), the microbiome associated with onion bulbs, particularly the shifts between healthy and diseased states and tissue-specific microbiome, remains poorly understood. A major contributor to onion spoilage is the dynamic interaction between the bulb tissue and associated microbial communities. Increasing evidence suggests that rot symptoms are often associated with multiple microbial taxa rather than a single pathogen, and that interactions among these microbes can accelerate tissue maceration. Culture-independent amplicon sequencing studies on fruit rot, such as grapevine, have revealed that decaying tissues harbor complex bacterial and fungal communities comprising dozens of genera like Pichia, Zygosaccharomyces, Gluconobacter and Acetobacter, while the traditionally recognized primary pathogens constitute only a subset of the rot-associated microbiome (Brischetto et al., 2024). Therefore, the development of novel and robust disease-control strategies relies on understanding the dynamics of disease emergence on the level of plant-microbiome interaction (Wisniewski and Droby, 2019). This necessitates understanding the microbial interaction of the onion spoilage to devise rather more effective ways to combat spoilage losses based on the microbiome-assisted insights of onion spoilage. To address this gap, the present study investigates bacterial and fungal microbiome dynamics in healthy versus diseased onion bulbs using 16S and ITS amplicon sequencing. By identifying taxonomic differences and key microbial signatures associated with bulb spoilage, this study aims to provide baseline knowledge for developing microbiome-informed strategies to mitigate postharvest onion losses.

In view of the significant postharvest losses encountered during onion bulb storage, understanding the compositional dynamics of microbial communities associated with the rot process is essential for developing effective management strategies. Although several fungal and bacterial species like Botrytis allii, Fusarium oxysporum, Aspergillus niger, and Burkholderia cepacia are known as causal agents of onion bulb decay, the accumulating evidence suggests that rot development is better explained as a microbiome-driven process (pathobiome), arising from dynamic microbial interactions rather than the action of a single pathogenic organism (Droby et al., 2022). This study documented the transitions in both bacterial and fungal community structures across healthy, mildly rotten, and severely rotten onion bulbs, clearly demonstrating that bulb spoilage is a dynamic and microbiome-driven successional process shaped by microbial interactions and host tissue degradation. Overall, a total of 85 bacterial and 53 fungal OTUs were detected across bulb samples representing different stages of rot severity, including healthy, mildly affected, and severely rotten tissues. The presence of 85 bacterial and 53 fungal OTUs in bulb tissues indicates a moderate taxonomic diversity, especially for an internal plant tissue such as an onion bulb, which is considered a selective niche for microbial colonization. In line with this observation, an earlier study by Yurgel et al. reported the presence of 149 bacterial and 40 fungal OTUs across healthy and diseased onion, highlighting taxonomically diverse communities (Yurgel et al., 2018). Even though the healthy onion bulbs exhibited very low microbial colonization, with approximately 89% of the total sequences corresponded to host-derived chloroplast/mitochondrial DNA. This dominance of host sequences indicates that the internal tissues of healthy bulbs harbor a substantially lower microbial load compared to tissues from rotten onion bulbs. The dominance of host-derived sequences in healthy onion bulb tissues is a well-documented phenomenon, with studies such as Yurgel et al. reporting that ~95% of sequences recovered from healthy bulbs were of host chloroplast origin in comparative microbiome analyses of healthy and diseased tissues (Yurgel et al., 2018). Conversely, some amplicon sequencing–based studies have reported no detectable bacterial ASVs altogether in asymptomatic healthy bulbs; nevertheless, this observation could be a technical limitation arising from low sequencing coverage, rather than evidence for the absence of bacterial endophytes (Liakos et al., 2025). Since, in the present study, the rarefaction analysis revealed the saturation with no further increase in species richness with sequencing depth in healthy bulbs (Supplementary Figure S1), it is likely that the observed patterns reflected good capture of the microbial diversity present in the healthy onion bulbs. Despite the lower microbial abundance in healthy bulbs, OTUs representing four phyla (Proteobacteria, Firmicutes, Bacteroidota, and Planctomycetota) and eight bacterial genera were detected, indicating that although microbial presence was low, the healthy bulb environment still harbored a diverse bacterial community. Since onions are widely consumed raw in the form of salads, the insights in to microbiome of healthy bulbs may have health implications. The presence of bacterial sequences representing genera like Prevotella, especially in central tissues of healthy bulbs, is noteworthy, given that members of this genus are well-recognized beneficial inhabitants of the human gut microbiome (Tett et al., 2021). These findings suggest that raw onion consumption may serve as a source of beneficial gut-associated bacteria such as Prevotella; however, this remains a preliminary inference based on the prevalence of Prevotella sequences in healthy bulbs, in light of existing studies describing diet-mediated acquisition of the human gut microbiome (Wicaksono et al., 2023), and therefore requires further validation through strain-level, culture-based studies.

Our analysis of the bacterial community revealed that the bacterial genera like Acinetobacter, Pseudomonas, and Carnimonas were detected in both healthy and rotten onion bulbs, suggesting that these are inhabitant taxa capable of surviving in intact tissues as well as proliferating under conditions of tissue degradation. Although present at a very low abundance in healthy bulbs, their relative abundance increased markedly in mildly and severely rotten bulbs, indicating that taxa respond to changed biochemical environment of the bulb during the rotting process. Their increased abundance also supports the view that these bacteria may persist in a latent or quiescent state within healthy bulbs and proliferate as the bulb microenvironment becomes permissive during decay. The detection of these genera in healthy bulb tissues, and their increased abundance during rot progression, suggests that they may persist as low-abundance resident taxa and proliferate as the bulb microenvironment becomes permissive, raising the possibility of vertical acquisition as part of the native bulb microbiota (Pereira et al., 2023). The presence of Acinetobacter and Pseudomonas in the healthy onion bulbs and their increased abundance with onion bulb rot has been reported previously in uncultured survey of onion bulbs from Annapolis Valley, Canada (Yurgel et al., 2018). Moreover, several studies have reported the frequent occurrence of Acinetobacter in many fruits and vegetables as their native microflora (Karumathil et al., 2016; Ababneh et al., 2022). In contrast, other genera such as Lactobacillus, Novosphingobium, Acetobacter, Sphingobium, Pluralibacter, and Pantoea were observed only in rotten bulbs, suggesting that they represent opportunistic secondary invaders of the onion bulb during progressive bulb rotting. The sharp increase in abundance observed in MRB suggests that early tissue damage and partial loss of bulb integrity create permissive niches that allow colonization of these taxa possibly through horizontal acquisition as their appearance during storage points to their acquisition through air, handling surfaces, storage crates, and soil residues (Frank et al., 2017). The neck tissue appears to function as a primary entry point for microbial invasion, as evidenced by the pronounced enrichment of diverse bacterial genera in MRB-NT. The neck region is anatomically more exposed and physiologically vulnerable, particularly under unregulated storage conditions, making it susceptible to horizontal microbial ingression. Once established in the neck tissue, these microorganisms may progressively spread to the outer scales and central tissues, following nutrient gradients created by tissue softening and cell wall breakdown. The bacterial genera like Lactobacillus (Bonasera et al., 2017), Pantoea (Zhang et al., 2022) are well described pathogens of onion bulb, the role of Novosphingobium, Sphingobium, Pluralibacter and Acetobacter has not been previously described in onion bulb decay, and therefore these taxa may represent opportunistic or saprophytic colonizers that proliferate following the tissue damage or changes in bulb tissues during storage. The detection of these taxa may also reflect ecological succession within the bulb microenvironment, where shifts in oxygen availability, pH, and available carbon sources during rot selectively favor certain bacterial groups. Overall, these findings support a horizontal environmental acquisition of microbes where initial tissue damage facilitates microbial ingression from the environment, followed by niche-driven selection and dominance of decay-adapted taxa as the bulb rot progresses to advance stages (SRB). In a shotgun metagenomic study, metagenome-assembled genomes (MAGs) affiliated with Acetobacter were recovered from symptomatic, decaying onion bulbs (Liakos et al., 2025). However, the absence of onion pathogenicity-related genes in the metagenome-assembled genomes (MAGs) of Acetobacter suggests that they function as opportunistic colonizers rather than primary pathogens. Collectively, these findings suggest that the onset of onion bulb rotting is associated with a gradual shift from a restricted, latent microbial community to a more diverse, enriched opportunistic assemblage rather than the single dominant pathogen driven process. Microbial diversity analysis was used to assess the transition from a relatively low-diversity microbiome in healthy bulb (HB) tissue to a more diverse and complex community in mildly rotten bulbs (MRB), followed by a marked decline in microbial diversity in severely rotten bulbs (SRB). The loss of microbial diversity is often associated with disease development across plant, animal, and human systems (Trivedi et al., 2020). In plant systems, this relationship is best documented in soils and rhizospheres, where healthy or disease-suppressive soils consistently exhibit higher microbial diversity and greater network complexity than disease-conducive soils (Dundore-Arias et al., 2023). Mendes et al. (2011) demonstrated that suppression of Rhizoctonia solani relied on a diverse and interactive microbial consortium rather than a single antagonistic taxon, and that disruption of this diversity compromised disease resistance. Similarly, Berendsen et al. (2012) and Trivedi et al. (2020) emphasized that loss of microbial diversity reduces ecosystem resilience and increases susceptibility to pathogen invasion.

Beyond plant systems, a similar pattern is observed in animal and human hosts, particularly in the gut, where high microbial diversity is observed for healthy states and the loss of microbial diversity is to inflammatory and infectious diseases (Lozupone et al., 2012). However, the association between loss of microbial diversity and disease is not universal and is highly system-dependent. In internal plant tissues and endophytic systems, where tight host filtering operates, the healthy state is characterized by lower but stable microbial diversity. In such systems, disease state can be associated with increased microbial diversity due to relaxed host control and invasion by opportunistic or saprophytic microorganisms. Consequently, the endophytic microbial composition is strongly influenced by plant genotype, tissue type, host defense responses, and the local metabolite landscape that collectively regulate microbial entry and persistence. The lower microbial diversity in healthy onion bulb tissues can be attributed to effective host filtering that maintains a restricted yet stable microbial community. The transient increase in diversity in MRB tissues is attributed to the weakening host control and increased microbial ingression during early decay. The subsequent decline in diversity in SRB tissues reflects the dominance of a few decay-adapted taxa under advanced tissue degradation. In light of strong host filtering as a driver of low diversity in healthy plant tissues, the human gut presents an interesting contrast, where active host filtering coexists with high microbial diversity in healthy states and a loss of diversity during disease. In the gut, host filtering operates within an open, nutrient-rich ecosystem, where high microbial diversity provides functional redundancy, colonization resistance, and metabolic stability, supporting host health. Thus, the relationship between microbial diversity and host health is system-dependent, shaped by host physiology, tissue type, nutrient availability, and the ecological role of the microbiome.

A marked reduction in microbial diversity in SRB tissues accompanied by dominance of a few bacterial genera like Lactobacillus, Acetobacter, Carnimonas, and Gluconobacter was observed. The bacterial genera such as Lactobacillus and Gluconobacter, which are enriched in advanced rot stages, are primarily fermentative or oxidative bacteria. These taxa are known to produce organic acids (lactic acid, gluconic acid, acetic acid), leading to localized acidification of host tissues. Thus, these bacteria may indirectly accelerate rot progression by making the bulb microenvironment more permissive for decay rather than directly degrading plant polymers. This suggests that the advanced stages of bulb rotting are accompanied with collapse in microbial community complexity. This shift is due to the changed microenvironment of the bulb as a result of loss of bulb tissue integrity and consequent enrichment of fermentable sugars, organic acids, creating acidic microenvironments favoring proliferation of acid-tolerant, fermentative, and oxidative bacteria (Parra-Aguilar et al., 2025). These observations suggest that microbial dysbiosis in rotting bulbs is largely a consequence of tissue decay rather than its sole cause. Our findings in the context of onion bulb rot, suggest that the tissue degradation likely disrupts physical barriers and releases nutrients, creating permissive and heterogeneous microenvironments that facilitate opportunistic colonization and variable microbial succession and therefore satisfies Anna Karenina principle (Arnault et al., 2023). However, it is also possible that the enriched bacterial and fungal taxa, once established, may further accelerate rot progression through enzymatic degradation and metabolic interactions. Therefore, the increasing heterogeneity of microbial communities with disease severity reflects a feedback loop in which host tissue breakdown and microbial proliferation reinforce each other, rather than a single deterministic pathogenic pathway. Importantly, the concurrent shifts in bacterial and fungal communities also indicate the possibility of cross-kingdom (bacteria-fungi) cooperation in onion tissue degradation. Fungi are well recognized for initiating cell-wall breakdown through secretion of cellulolytic and pectinolytic enzymes, thereby releasing soluble substrates that can be exploited by bacteria (Lattanzio et al., 2006; Deveau et al., 2018). Such fungal–bacterial interactions have been shown to enhance disease progression in plant systems by accelerating nutrient cycling and modifying local microenvironments. The coordinated succession patterns observed in this onion rot studysupport a model in which host tissue decay, microbial dysbiosis, and inter-microbial cooperation operate as an interconnected feedback loop rather than as isolated processes.

This study also examined the composition and succession of fungal communities associated with healthy and rotten onion bulbs. A clear restructuring of the onion bulb mycobiome was observed with differential rot severity, highlighting strong tissue specificity and stage-dependent fungal succession. Overall, 53 fungal OTUs were detected across the nine onion bulb samples, with very low fungal colonization observed in healthy bulbs, and this level of diversity is comparable to the 40 fungal OTUs reported by Yurgel et al. (2018) in their onion microbiome study. Overall, healthy bulbs harbored a very limited fungal community, particularly in the central and outer scale tissues, indicating that intact bulb tissues are largely resistant to fungal colonization. The comparatively higher fungal presence in the neck tissue of healthy bulbs (Shannon index = 0.53), dominated by Aspergillus, contrasted with the markedly lower fungal sequences observed in the outer scales (Shannon index = 0.10) and central tissues (Shannon index = 0.04). The transition from healthy to mildly rotten bulbs was marked by the emergence of several fungal genera that were completely absent in healthy tissues, particularly enrichment was more apparent in the neck region. The appearance and dominance of Meyerozyma, Blastobotrys, and Penicillium in mildly rotten neck tissue suggests that early tissue degradation creates favorable niches for opportunistic yeasts and filamentous fungi. Although Penicillium is widely reported as a pathogen of storage onion bulbs (Çakır and Maden, 2015), the yeast like ascomycetes fungi Meyerozyma and Blastobotrys are not reported as onion bulb pathogens, however, Meyerozyma enrichment in rotten bulbs has also been observed in other amplicon-based studies of diseased onion tissues (Yurgel et al., 2018), which suggests a recurrent association of this fungal genus with bulb decay rather than a sporadic occurrence in this study. The neck tissue remained the primary site of fungal colonization in mildly rotten bulbs, exhibiting a higher Shannon diversity index (MRB-NT = 1.74) than the outer scales (MRB-OS = 0.54) and central tissue (MRB-CT = 0.52). Since maximum fungal activity occurs through the neck tissue, the importance of proper curing and complete neck closure is essential to ensure better storability, as incomplete neck closure resulting from improper curing has been reported to predispose bulbs to bacterial and fungal ingression, resulting in faster bulb spoilage (Schroeder and Du Toit, 2010; Vahling-Armstrong et al., 2016). As rot progressed to the severe stage, a pronounced dominance of fermentative yeasts, particularly Pichia and Kazachstania, was observed across all bulb tissues, including the central tissue. This marked shift toward yeast-dominated communities indicates a major ecological transition within the bulb microenvironment, favoring fermentative processes. The predominance of Kazachstania has been shown in the fermentative onion foods along with many other yeast genera like Candida, and Saccharomyces (Cheng et al., 2014). Since the bacterial community analysis also revealed a concurrent increase in fermentative and oxidative bacterial genera in severely rotten bulb tissues, such as Lactobacillus (33.2%) and Acetobacter (16.1%), together with fermentative fungal genera, these patterns indicate that onion bulb rotting progresses predominantly through fermentation-driven processes. Severe tissue maceration, oxygen limitation, and accumulation of fermentable substrates likely favor yeast proliferation over filamentous fungi at this stage. The overwhelming abundance of Pichia in severely rotten tissues suggests its strong competitive advantage under advanced decay conditions and points to its potential role in driving secondary fermentation processes that accelerate bulb softening and tissue collapse. Previous studies on spoiled vegetable microbiota have shown that the production of extracellular hydrolases like cellulases, xylanases, and pectinases (pectin lyase and polygalacturonase), protease, amylase, and lipases correlates with the severity of rot, with pectinases often playing a dominant role in cell wall breakdown (Lee et al., 2013). Several bacterial taxa enriched in decayed onion tissues (e.g., Acinetobacter) have been reported to produce pectinase activity on plant substrates, supporting the possibility that similar hydrolytic mechanisms contribute to tissue degradation in onion bulb rot (Bhardwaj, 2023). Similarly, many species of fungal genera Aspergillus enriched in rotten tissue are also the well-documented producer of hydrolases like cellulase, pectinase, β-glucosidases, and xylanases, which can break down structural polysaccharides in plant tissues (Rehman et al., 2014; Matsuzawa, 2024). Other fungal genera enriched in rotten bulb tissues included Penicillium, several species of which are known to produce extracellular plant cell wall–degrading enzymes such as pectinases and cellulases. Enrichment of hydrolase-producing microorganisms in rotten tissues suggests their potential involvement in onion bulb tissue degradation through cell wall polysaccharide weakening and subsequent tissue maceration. The increased abundance of bacterial genera such as Lactobacillus and Gluconobacter, and fungal genera such as Pichia and Kazachstania, in advanced rot stages (SRB) suggests that their role in bulb decay may be mediated through microenvironmental changes, such as acidification, rather than direct hydrolase action, as these genera are primarily associated with fermentative metabolism rather than the production of cellulases or pectinases. This study underscores the need to reconsider onion bulb rotting as a dynamic process of microbial succession rather than a disease driven by a single pathogen. Our findings reveal that several bacterial and fungal genera which are classically not recognized as major postharvest pathogens of fruits and vegetables becomes abundant during bulb rot progression, thereby highlighting their potential role in bulb decay. The present study adopts a tissue- and stage-resolved sampling strategy to capture microbiome restructuring associated with progressive onion bulb rot. By focusing on representative bulbs across defined health states and dissecting distinct tissues, the analysis emphasizes qualitative shifts in dominant taxa, community composition, and ecological transitions along the bulb rot stages. Such an approach is particularly suited to generating information of niche-specific microbial colonization, potential pathogen reservoirs, and tissue-dependent host–microbe interactions, while increased biological replication would further strengthen quantitative inference, the patterns observed here provide a first framework for understanding tissue-specific microbial assembly during bulb deterioration and serve as a basis for future studies incorporating larger sample sizes for predictive modeling. Elucidating the ecological functions, growth requirements (including pH and temperature optima), and interaction dynamics of these dominant microbial taxa will be critical for developing targeted and stage-specific strategies to slow or prevent bulb rotting during storage and postharvest handling.

This study characterized the bacterial and fungal communities associated with healthy and rotten onion bulbs across distinct bulb tissues. High-throughput amplicon sequencing revealed a structured succession of both bacterial and fungal communities characterized by an initial expansion of taxonomic diversity during early decay, followed by a pronounced dominance of a few specialized taxa at severe rot stages. The increased abundance of bacterial genera such as Lactobacillus, Acetobacter, Gluconobacter, and Carnimonas, together with yeasts including Pichia and Kazachstania, underscore their potential roles in driving bulb tissue degradation although many of these genera are not classically described as common pathogens of onion bulb. Further functional and culture-based studies will be required to clarify the specific roles of these taxa in rot development and to translate these insights into effective postharvest management strategies. Tissue-specific analyses further revealed the bulb neck tissue as the primary fungal succession zone, likely facilitating initial colonization and subsequent inward spread during progression of rotting. Overall, these findings highlight onion bulb rotting as a microbiome-driven, successional process shaped by bulb tissue niche and rot severity. By elucidating the rot-stage and tissue-specific changes in bacterial and fungal community compositions, this study advances our understanding of microbial processes associated with postharvest bulb decay.