Global citrus root microbiota unravels assembly cues and core members.

Introduction: Citrus is one of the most important fruit crops worldwide, and the root-associated microbiota can have a profound impact on tree health and growth. Methods: In a collaborative effort, the International Citrus Microbiome Consortium investigated the global citrus root microbiota with samples collected from nine citrus-producing countries across six continents. We analyzed 16S rDNA and ITS2 amplicon sequencing data to identify predominant prokaryotic and fungal taxa in citrus root samples. Comparative analyses were conducted between root-associated microbial communities and those from the corresponding rhizosphere and bulk soil samples. Additionally, genotype-based group-wise comparisons were performed to assess the impact of citrus genotype on root microbiota composition. Results: Ten predominant prokaryotic phyla, containing nine bacterial phyla including Proteobacteria, Actinobacteria, Acidobacteria, and Bacteroidetes and one archaeal phylum (Thaumarchaeota), and multiple fungal phyla including Ascomycota and Basidiomycota were identified in the citrus root samples. Compared with the microbial communities from the corresponding rhizosphere and bulk soil samples from the same trees, the prokaryotic and fungal communities in the roots exhibited lower diversity and complexity but greater modularity compared to those in the rhizosphere. In total, 30 root-enriched and 150 root-depleted genera in bacterial community were identified, whereas 21 fungal genera were enriched, and 147 fungal genera were depleted in the root niche compared with the rhizosphere. The citrus genotype significantly affected the root prokaryotic and fungal communities. In addition, we have identified the core root prokaryotic genera comprising Acidibacter, Allorhizobium, Bradyrhizobium, Chitinophaga, Cupriavidus, Devosia, Dongia, Niastella, Pseudomonas, Sphingobium, Steroidobacter and Streptomyces, and the core fungal genera including Acrocalymma, Cladosporium, Fusarium, Gibberella, Mortierella, Neocosmospora and Volutella. The potential functions of these core genera of root microbiota were predicted. Conclusion: Overall, this study provides new insights into the assembly of microbial communities and identifies core members of citrus root microbiota across a wide geographic range. The findings offer valuable information for manipulating root microbiota to enhance plant growth and health.

Biocontrol Efficacy of Metschnikowia spp. Yeasts in Organic Vineyards against Major Airborne Diseases of Table Grapes in the Field and in Postharvest.

The aim of this work was to evaluate the efficacy of two antagonistic yeasts, Metschnikowia pulcherrima strain MPR3 and M. fructicola strain NRRL Y-27328 (commercial product NOLI), applied in addition to the "on-farm biological treatments" (BIO) carried out during the production season, for the containment of powdery mildew and grey mould diseases on organic table grapes 'Italia'. The yeast strains were applied in the field three times, and their efficacy was evaluated during the production season and under postharvest conditions. Overall, M. pulcherrima MPR3 combined with BIO treatments reduced disease incidence caused by Erysiphe necator and disease incidence and severity caused by Botrytis cinerea with values between 67.8% and 86.2%, showing higher efficacy than BIO treatments applied alone and in combination with NOLI. Field treatments based on BIO+MPR3 maintained their performance also during fruit storage, protecting grape berries from grey mould development to a greater extent than the other treatments (disease reduction of about 98%). Thus, the presence of M. pulcherrima MPR3 seems to improve disease management both in the field and in postharvest environments, without negative impacts on grape microbial communities. These findings highlight the potential of M. pulcherrima MPR3 as a promising alternative strategy for disease control in organic vineyards and in postharvest, providing sustainable solutions to improve food quality and safety.

Assessing Copper-Alternative Products for the Control of Pre- and Postharvest Citrus Anthracnose.

Citrus production is worldwide threatened by Colletotrichum spp., causal agents of pre- and postharvest anthracnose. The recent limitation on the use of copper-based antimicrobials, due to its demonstrated noxious effect on the environment, makes the control of this pathogen difficult. Thus, alternative products able to reduce/phase out copper in organic citrus farming are needed. In this study, the efficacy of 11 commercial alternative products were evaluated in vitro, in growth chamber, in open field and in postharvest environments. In vitro, mineral fertilizers, basic substances, essential oils, plant defense stimulators and biological control agents were able to inhibit the mycelial growth with variable efficacy. On artificially infected citrus fruit, almost all tested products significantly reduced disease incidence and severity, but with lower efficacy than copper. The efficacy of mineral fertilizers-based Kiram and Vitibiosap 458 Plus, citrus essential oil-based Prev-Am Plus and chitosan-based Biorend was confirmed in open field trials, in naturally infected citrus fruits. In these trials Biorend was the best alternative product, significantly reducing disease incidence (71% DI reduction) with better results than copper (47.5%). Field treatments reduced the incidence and severity of the disease in postharvest conditions, especially in fruits field-treated three times. Overall, selected products tested in open field can represent a good alternative to copper compounds in the view of future limitation of its use.

Epiphytic and endophytic microorganisms associated to different cultivar of tomato fruits in greenhouse environment and characterization of beneficial bacterial strains for the control of post-harvest tomato pathogens.

Several bacterial and fungal diseases affect greenhouse-grown tomato crops, causing severe annual yield losses worldwide. The need to reduce chemical compound applications has encouraged the search of alternative approach for the control of tomato diseases, including the use of biological control agents. The presence of total and beneficial microbial populations was investigated on the surface and in the pulp of seven cultivars of tomato fruit coming from eleven greenhouses in the Pachino district (south-east of Sicily), recognized by the European Community with the "Protected Geographical Indication" label. Principal component analysis (PCA) showed that epiphytic and endophytic microbial populations clustered into groups according to the areas of origin. Approximately 240 tomato fruit-associated bacterial isolates were selected and a high percentage of them showed antagonistic activity against Clavibacter michiganensis subsp. michiganensis, Pseudomonas syringae pv. tomato, Xanthomonas euvesicatoria pv. perforans, Botrytis cinerea and Alternaria alternata. Analysis of the 16S rRNA gene sequences revealed a predominance of bacteria in Bacillus and Pseudomonas genera, followed by Citrobacter and Enterobacter. The presence of these genera differed according to the geographical areas of tomato samples, whereas their antagonistic capabilities varied according to the five tomato pathogens. The in vitro effectiveness of eight representative bacterial strains belonging to Pseudomonas, Bacillus and Enterobacter genera was confirmed in in vivo assays, carried out on tomato fruit artificially inoculated with A. alternata and B. cinerea. Altogether, these results revealed differences in population density of native microbiota of "Pomodoro di Pachino" fruits and allowed the selection of antagonistic bacterial strains that can be applied in field and in postharvest conditions as alternatives to chemical compounds.

COS-OGA Applications in Organic Vineyard Manage Major Airborne Diseases and Maintain Postharvest Quality of Wine Grapes.

In most wine-growing countries of the world the interest for organic viticulture and eco-friendly grape production processes increased significantly in the last decade. Organic viticulture is currently dependent on the availability of Cu and S compounds, but their massive use over time has led to negative effects on environment health. Consequently, the purpose of this study was to evaluate the effectiveness of alternative and sustainable treatments against powdery mildew, gray mold and sour rot under the field conditions on Nero d'Avola and Inzolia Sicilian cultivars. In detail, the efficacy of COS-OGA, composed by a complex of oligochitosans and oligopectates, and its effects in combination with arbuscular mycorrhizal fungi (AMF) were evaluated to reduce airborne disease infections of grape. COS-OGA combined with AMF induced a significant reduction in powdery mildew severity both on Nero d'Avola and Inzolia with a mean percentage decrease of about 15% and 33%, respectively. Moreover, COS-OGA alone and combined with AMF gave a good protection against gray mold and sour rot with results similar to the Cu-S complex (performance in disease reduction ranging from 65 to 100%) on tested cultivars. Similarly, the COS-OGA and AMF integration provided good performances in enhancing average yield and did not negatively impact quality and microbial communities of wine grape. Overall, COS-OGA alone and in combination could be proposed as a valid and safer option for the sustainable management of the main grapevine pathogens in organic agroecosystems.

Combined application of antagonistic Wickerhamomyces anomalus BS91 strain and Cynara cardunculus L. leaf extracts for the control of postharvest decay of citrus fruit.

Combined use of biocontrol agents and plant extracts can be considered a viable and promising strategy for protecting plant tissues with different synergistic mechanisms of action that improve the antimicrobial activity of the mixtures. Treatments of citrus fruits with Wickerhamomyces anomalus BS91 have been previously reported as effective measures to reduce the incidence of green mold caused by Penicillium digitatum. On the opposite, the knowledge of the antifungal activity of cultivated cardoon (Cynara cardunculus L. var. altilis DC.) leaf extract, vegetable widespread in some Mediterranean areas, is still very limited. In this study, experimental trials were conducted to evaluate the effectiveness in vitro of leaf aqueous, methanolic and ethanolic extracts of C. cardunculus against seven fungal pathogens responsible for considerable food losses in the postharvest stage. In addition, biocontrol yeast W. anomalus BS91 and the three C. cardunculus extracts were tested in vivo both as a single treatment and in mixture, against Penicillium digitatum on 'Tarocco' oranges and 'Femminello' lemons. The combination of W. anomalus BS91 and leaf ethanolic extract reduced with the highest efficacy the incidence and severity of green mold on orange and lemon fruits with respect to the control, and was more effective than treatment with antagonistic yeast or leaf extracts applied alone. Incidence and severity of citrus decay were more consistently reduced when mixtures were applied 24 h before the inoculation of the pathogen, thus suggesting the relevance of preventive treatments. The mixtures of antagonistic W. anomalus BS91 and ethanolic leaf extract were more effective in controlling green mold decay on oranges than on lemons. These results indicate that biocontrol agents and leaf extracts, used in appropriate combination, can provide a stronger protection than when used singularly. However, compatibility between microbial antagonist and antimicrobial extract should be preliminary verified.