Botrytis cinerea is the causal agent of grey mould rot of apples. The efficacy of biofumigation with thyme (Thymus vulgaris), savoury (Satureja montana), and basil (Ocimum basilicum) essential oils (EOs) at 1%, 0.5%, and 0.1% concentrations were tested against B. cinerea. In vitro, the results showed 100% growth inhibition at 1% concentration for all oils. Subsequent biofumigation experiments on apples of cultivar ‘Opal’ with 1% EOs showed that, after 60 d storage, thyme and savoury EOs significantly reduced grey mould rot incidence (average incidence 2% for both treatments) compared to the control (7%). Analyses of quality indicated slightly higher fruit firmness for 1% thyme at 30 d and slightly higher titratable acidity for 1% thyme and savoury at 60 d. Sampling of the atmosphere inside the cabinets was performed to characterize and quantify the volatile components of EOs released through biofumigation. Though thymol and p-cymene were the main components of thyme EO, the antimicrobial activity was mainly due to the presence of thymol and, to a lower extent, of carvacrol. In savoury EO, carvacrol and p-cymene were the main components, whereas in basil EO, linalool and estragole were mainly present. Metabarcoding analyses showed that the epiphytic microbiome had higher richness and evenness compared to their endophytic counterpart. By the end of shelf-life, treatments with thyme EO reduced B. cinerea abundance compared to the inoculated control for both endophytes (from 36.5% to 1.5%) and epiphytes (from 7.0% to 0.7%), while favouring a significant increase in Penicillium species both in endophytes (from 0.2% to 21.5%) and epiphytes (from 0.5% to 18.6%). Results indicate that thyme EO (1%) and savoury EO (1%) are equally effective in hampering grey mould rot development in vivo.

Nectarines can be affected by many diseases, resulting in significant production losses. Natural products, such as essential oils (EOs), are promising alternatives to pesticides to control storage rots. This work aimed to test the efficacy of biofumigation with EOs in the control of nectarine postharvest diseases while also evaluating the effect on the quality parameters (firmness, total soluble solids, and titratable acidity) and on the fruit fungal microbiome. Basil, fennel, lemon, oregano, and thyme EOs were first tested in vitro at 0.1, 0.5, and 1.0% concentrations to evaluate their inhibition activity against Monilinia fructicola. Subsequently, an in vivo screening trial was performed by treating nectarines inoculated with M. fructicola, with the five EOs at 2.0% concentration by biofumigation, performed using slow-release diffusers placed inside the storage cabinets. Fennel, lemon, and basil EOs were the most effective after storage and were selected to be tested in efficacy trials using naturally infected nectarines. After 28 days of storage, all treatments showed a significant rot reduction compared to the untreated control. Additionally, no evident phytotoxic effects were observed on the treated fruits. EO vapors did not affect the overall quality of the fruits but showed a positive effect in reducing firmness loss. Metabarcoding analysis showed a significant impact of tissue, treatment, and sampling time on the fruit microbiome composition. Treatments were able to reduce the abundance of Monilinia spp., but basil EO favored a significant increase in Penicillium spp. Moreover, the abundance of other fungal genera was found to be modified.

White haze, an emerging disorder caused by extensive fungal growth on the apple surface, results in a compromised fruit quality and decreased marketability. The use of biological control agents could be an interesting tool to reduce its development. This work aimed to test the efficacy of two Aureobasidium pullulans strains (AP2 and PL5) in controlling white haze on stored apples. An in vivo trial was conducted by inoculating fruits with white haze causal agents (Entyloma belangeri, Golubevia pallescens, Tilletiopsis washingtonensis) and treating them with the antagonistic yeasts. Three commercial biofungicides were also included in the trial. Both A. pullulans strains, along with the Metschnikowia fructicola-based product, reduced white haze incidence after 110 days of storage at 1 ± 1 °C and after 7 days of shelf life. Furthermore, the effect of A. pullulans application on the fruit fungal microbiome was assessed. A significant impact of apple matrix and treatment on the mycobiome composition was observed. Analyses showed a good colonization of A. pullulans on the treated apples, both epiphytically and endophytically. A decrease in white haze-related fungi abundance was observed in the treated fruits. Additionally, a reduction of Ramularia spp. and modifications in the abundance of other fungal genera were detected after storage and shelf life.

Preserving ex situ soil microbial communities is essential for bacterial biodiversity conservation in microbiome biobanking, accurate microbiome research, and future biotechnological applications in sustainable agriculture. The effect of three soil preservation methods—cryopreservation at −80 °C, refrigeration at 4 °C, and lyophilization—on the viability, diversity and metabolic functionality of the soil microbiome was evaluated using soil from untreated and solarized strawberry fields stored at 0, 6 and 12 months. Microbial viability, ecological strategies, functionality, and diversity were assessed using plate counts, r/K strategist profiling, BIOLOG EcoPlates, and 16S rRNA/ITS gene amplicon-based sequencing, respectively. Cryopreservation outperformed the other preservation strategies by generally maintaining total bacterial counts, especially in control soil, preserving the balance between oligotrophic and copiotrophic communities, and sustaining high alpha diversity indices over 12 months. Refrigeration provided moderate preservation, though microbial viability and community stability declined over time. In contrast, lyophilization significantly reduced microbial abundance, altered community composition, and diminished metabolic diversity and substrate utilization. Beta diversity analyses confirmed that cryopreserved samples remained similar in microbial structure to the initial timepoint, while lyophilized samples diverged substantially. Functional analyses also revealed reduced metabolic activity in lyophilized soils, underscoring the negative impact on the microbiome’s ecological roles. Overall, the results of this study identify cryopreservation as the most effective storage method for maintaining soil microbiome integrity, providing critical guidance for preserving soil samples in microbiome research and sustainable agricultural biotechnology.