Samir Droby

• Prof.
• Managing Director at Agricultural Research Organization ARO

The exchange of metabolites (i.e., metabolic interactions) between bacteria in the rhizosphere determines various plant-associated functions. Systematically understanding the metabolic interactions in the rhizosphere, as well as in other types of microbial communities, would open the door to the optimization of specific predefined functions of inte...

The exchange of metabolites (i.e., metabolic interactions) between bacteria in the rhizosphere determines various plant-associated functions. Systematically understanding the metabolic interactions in the rhizosphere, as well as in other types of microbial communities, would open the door to the optimization of specific pre-defined functions of int...

The exchange of metabolites (i.e., metabolic interactions) between bacteria in the rhizosphere determines various plant-associated functions. Systematically understanding the metabolic interactions in the rhizosphere, as well as in other types of microbial communities, would open the door to the optimization of specific pre-defined functions of int...

The exchange of metabolites (i.e., metabolic interactions) between bacteria in the rhizosphere determines various plant-associated functions. Systematically understanding the metabolic interactions in the rhizosphere, as well as in other types of microbial communities, would open the door to the optimization of specific pre-defined functions of int...

Kiwifruit vine decline syndrome (KVDS) is characterized by severe root system impairment, which leads to irreversible wilting of the canopy. Plants usually collapse rapidly from the appearance of the first aboveground symptoms, without recovery even in the following seasons. The syndrome has been negatively impacting kiwifruit yield in different ar...

The exchange of metabolites (i.e., metabolic interactions) between bacteria in the rhizosphere determines various plant-associated functions. Systematically understanding the metabolic interactions in the rhizosphere, as well as in other types of microbial communities, would open the door to the optimization of specific pre-defined functions of int...

The surface and internal tissues of fruits host diverse microbial communities but the functional role of this microflora, outside of pathogenic species, in fruit health and quality are largely unknown. The recent use of universal primer sets and advanced sequencing technologies, however, has greatly increased our understanding of these microbial co...

Fruits harbor abundant and diverse microbial communities that protect them from post‐harvest pathogens. Identification of functional traits associated with a given microbiota can provide a better understanding of their potential influence. Here, we focused on the epiphytic microbiome of apple fruit. We suggest that shotgun metagenomic data can indi...

With the introduction of new apple varieties, emerging diseases have been recorded including dry lenticel rot and white haze. Ramularia mali has been identified as the causal agent of dry lenticel rot, whereas species of Golubevia, Tilletiopsis and Entyloma have been associated to white haze, but the epidemiology of these pathogens remains unclear....

Postharvest diseases of fruits and vegetables cause significant economic losses to producers and marketing firms. Many of these diseases are caused by necrotrophic fungal pathogens that require wounded or injured tissues to establish an infection. Biocontrol of postharvest diseases is an evolving science that has moved from the traditional paradigm...

Microbial communities associated with fruit can contribute to quality and pathogen resistance, but little is known about their assembly and dynamics during fruit development and storage. Three apple cultivars growing under the same environmental conditions were utilized to examine the apple carposphere microbiome composition and structure at differ...

Metagenomic sequencing and multi-omic technologies have greatly advanced our understanding of the microbiome of fruit crops and revealed the complex interactions that potentially occur between microbial communities and their host. Strong evidence exists for the involvement of multiple microorganisms in the onset and development of disease in plant...

Biological control of postharvest fruit diseases by antagonistic microorganisms is considered an effective alternative to chemical fungicides. The influence of microbial antagonists on the fruit-associated microbiome provides a new perspective for the in-depth study of the antagonistic mechanism. In this study, the biocontrol effect of A. pullulans...

The control of plant diseases is generally done with the application of synthetic pesticides; however, their use causes problems of environmental contamination and human and animal health. Biocontrol through the application of microbial antagonists is an option to the use of synthetic pesticides. Antagonistic microorganisms have been isolated from...

The endophytic microbiome of plants is believed to have a significant impact on its physiology and disease resistance, however, the role of host genotype in determining the composition of the endophytic microbiome of apple root systems remains an open question that has important implications for defining breeding objectives. In the current study, t...

In the current scenario of climate change, the uncertainty of environmental factors and adverse impacts of chemical pesticides on the texture and productivity of soil along with increasing health concerns to humans appear as a global challenge in the management of agricultural yield to meet the food demand of burgeoning global populations. However,...

Postharvest diseases of fruits caused by phytopathogens cause losses up to 50% of global production. Phytopathogens control is performed with synthetic fungicides, but the application causes environmental contamination problems and human and animal health in addition to generating resistance. Yeasts are antagonist microorganisms that have been used...

Plants evolved in association with a diverse community of microorganisms. The effect of plant phylogeny and domestication on host–microbiome co‐evolutionary dynamics are poorly understood. Here we examined the effect of domestication and plant lineage on the composition of the endophytic microbiome of 11 Malus species, representing three major grou...

Recently, increasing focus has been placed on exploring fruit microbiomes and their association with their hosts. Investigation of the fruit surface microbiome of apple has revealed variations in the composition and structure depending on management practices, phenological stages, and spatial distribution on the fruit itself. However, the fate of t...

Wheat grains are colonized by complex microbial communities that have the potential to affect seed quality and susceptibility to disease. Some of the beneficial microbes in these communities have been shown to protect plants against pathogens through antagonism. We evaluated the role of the microbiome in seed health: in particular, against mycotoxi...

In the current scenario of changing climatic conditions and the rising global population, there is an urgent need to explore novel, efficient, and economical natural products for the benefit of humankind. Biosurfactants are one of the latest explored microbial synthesized biomolecules that have been used in numerous fields, including agriculture, p...

Endophytic microorganisms present inside the host plant play an essential role in host fitness, nutrient supply and stress tolerance. Endophytes are often used in sustainable agriculture as biofertilizers, biopesticides and as inoculants to mitigate abiotic stresses including salinity, drought, cold and pH variation in the soil. In changing climati...

Microbial Management of Plant Stresses: Current Trends, Application and Challenges explores plant microbiota including isolated microbial communities that have been used to study the functional capacities, ecological structure and dynamics of the plant-microbe interaction with focus on agricultural crops. Presenting multiple examples and evidence o...

Apple trees host diverse communities of bacteria, fungi, viruses, and other microbes that occupy all plant surfaces and internal tissues. In the past two decades, our understanding of these communities has burgeoned due to new technologies that allow culture-independent characterisation of microbial communities. In this chapter, we provide a compre...

Fruit‐based diets are recognized for their benefits to human health. The safety of fruit is a global concern for scientists. Fruit microbiome represents the whole microorganisms that are associated with a fruit. These microbes are either found on the surfaces (epiphytes) or in the tissues of the fruit (endophytes). The recent knowledge gained from...

Plant-associated microbial communities form complex co-associations that play a role in promoting plant productivity and health, although the underlying mechanisms have not been fully elucidated. The functional role of the microbiome provides a new perspective on how we can potentially utilize the microbiome to maintain the postharvest quality and...

We present the first worldwide study on the apple (Malus × domestica) fruit microbiome that examines questions regarding the composition and the assembly of microbial communities on and in apple fruit. Results revealed that the composition and structure of the fungal and bacterial communities associated with apple fruit vary and are highly dependen...

Citrus fruit are highly susceptible to infection by several fungal pathogens during postharvest storage. Therefore, harvested citrus fruit receive a series of treatments in the packhouse such as initial drenching, washing and disinfection, immersion in heated solutions of chemical fungicides and waxing that also include fungicides to reduce the ino...

Globalization has a dramatic effect on the trade and movement of seeds, fruits and vegetables, with a corresponding increase in economic losses caused by the introduction of transboundary plant pathogens. Current diagnostic techniques provide a useful and precise tool to enact surveillance protocols regarding specific organisms, but this approach i...

Background: Apple is one of the most highly consumed fruits worldwide and is the largest fruit crop produced in temperate regions. Fruit quality, safety and long-term storage are issues that are important to growers, distributors, and consumers. We present the first worldwide study on the apple fruit microbiome that examines questions regarding the...

Each plant has a microbiome that is consisted of epiphytic and endophytic microbial communities. The plant microbiome may play a prominent role in different functions such as growth, disease, suppressing pathogens and potential influence of the physiology of reproductive plant organs (e.g., fruit). Endophytic microbiomes of any plant organs have mu...

Penicillium expansum is a ubiquitous postharvest pathogen that infects a wide range of fruits, including pome and a variety of stone fruit. Virulence factors that mediate pathogenicity in postharvest-decay fungi have not been fully defined, especially in regard to if and how the pathogen is able to modulate fruit defense mechanisms, particularly at...

Wheat is the primary source of carbohydrates and considered as a widely consumed food worldwide. Due to its biologic composition and structure, wheat grains are one of the more highly food sources that can be stored and used for a long time. Preservation techniques have been used to extend the shelf life of wheat and wheat-based products, primarily...

Accumulating evidence indicates that the composition of the microbiota inhabiting an organism (both endo- and epiphytically) can have a profound effect on host physiology and defense responses. The role of the microbiota in plant health and physiology, however, is poorly understood, and few studies have focused on temperate fruit trees. A global ef...

Penicillium expansum is a destructive phytopathogen causing postharvest decay on many stored fruits. To develop effective and safe management strategies, it is important to investigate its pathogenicity-related mechanisms. In this study, a bioinformatic pipeline was constructed and 50 core effector genes were identified in P. expansum using multipl...

Microbial volatiles (MVOCs) are low molecular weight compounds synthesized by range of microbial strains including bacteria and fungi. The chemical diversity of volatiles is variable and strain specific. Although low boiling point, and high vapour pressure of volatiles make easy transition between soil particles associated water and environment, th...

In the recent past edible films and coatings have been extensively used as an alternative packaging system over conventional systems to enhance shelf life, fruit quality and antagonistic properties against phytopathogens. The coatings are composed of various materials including polysaccharides, lipids, and proteins along with some other additives,...

This is the Introductory chapter in the book 'Microbiome Stimulants for Crops: Mechanisms and Applications' (Elsevier). This book will be in print late 2020 or early 2021.

There is growing recognition of the role that the microbiome plays in the health and physiology of many plant species. However, considerably less research has been conducted on the postharvest microbiome of produce and the impact that postharvest processing may have on its composition. Here, amplicon sequencing was used to study the effect of washi...

Chapter for book 'Microbial Endophytes: Functional Biology and Applications': Inside plants, microbial communities live as endophytes without causing any disease symptoms or adverse impacts to the host plant. These microbial communities may comprise bacteria, fungi, archaea. In the last few decades endophytic microbes have been broadly used in sust...

Date palm (Phoenix dactylifera) is considered to be a highly important food crop in several African and Middle Eastern countries due to its nutritional value and health-promoting properties. Microbial contamination of dates has been of concern to consumers, but very few works have analyzed in detail the microbial load of the different parts of date...

Fungal pathogens in fruits and vegetables cause significant losses during handling, transportation, and storage. Biological control with microbial antagonists replacing the use of chemical fungicides is a major approach in postharvest disease control, and several products based on single antagonists have been developed but have limitations related...

Candida oleophila is an effective biocontrol agent used to control post-harvest diseases of fruits and vegetables. C. oleophila I-182 was the active agent used in the first-generation yeast-based commercial product, Aspire®, for post-harvest disease management. Several action modes, like competition for nutrients and space, induction of pathogenesi...

In the current scenario of climate change, numerous strategies have been employed in the area of sustainable agriculture or plant science to generate plants, which can withstand various types of biotic and abiotic stresses. Currently, a range of biotic and abiotic stresses such as cold, draught, salinity, water deficit, or extreme pH is present tha...

The capacity of microorganisms from water kefir (WK) to control Aspergillus flavus growth during the aerobic phase of ensiled sorghum grains was determined. Sorghum inoculated with A. flavus was treated with filter-sterilized and non-sterilized water kefir, ensiled, and incubated 7 days at 25 °C. A. flavus growth was quantified by qPCR after incuba...

Biological control of postharvest diseases has been suggested as a viable alternative to synthetic chemicals and has been the focus of considerable research worldwide for the last 30 years by many scientists and several commercial companies. Microbiome-based research has opened a whole new frontier that will greatly expand our knowledge of postharv...

Penicillium expansum is a major postharvest pathogen that infects different fruits, mainly through injuries inflicted during harvest or subsequent handling after harvest. Several effectors were suggested to mediate pathogenicity of P. expansum in fruit tissue. Among these effectors Nep1-like proteins (NLPs), produced by various microorganisms with...

While the wheat-associated microbiome is of major agricultural importance, little is known about the alterations in wheat grain microbial community composition during storage. Characterization of the bacterial and fungal communities in stored wheat grains revealed the impact of phosphine fumigation, one of the most effective methods to eliminate in...

Blue mold caused by Penicillium expansum is a major postharvest disease of pome fruit. Several mechanisms possibly involved in P. expansum pathogenicity and virulence. However, factors that mediate pathogenicity and virulence are largely not yet characterized. In this work we analyzed P. expansum predicted secretome to reveal potential genes that h...

Microorganisms are an integral part of the composition of fruits and vegetables and are found as epiphytes on the surface or as endophytes within tissues. The realization that fruit surfaces harbor beneficial microorganisms fostered the field of biological control using epiphytic microorganisms which led to the development of several commercial bio...

The yeast Metschnikowia fructicola was reported as an efficient biological control agent of postharvest diseases of fruits and vegetables, and it is the bases of the commercial formulated product “Shemer.” Several mechanisms of action by which M. fructicola inhibits postharvest pathogens were suggested including iron-binding compounds, induction of...

Fasta file of transcripts of MF.

Fasta file of CDSs of MF.

fpkm expression data and statistical differences among conditions analyzed with RNAseq.

Fasta file of proteins of MF.

Annotation file of MF, produced by Blast2GO.

List of GO terms related to the mutation or repair of the DNA sequence.

Annotation of Mf transcripts.

Proteinortho analysis of M. fructicola, M. bicuspidata, C. auris and C. lusitaniae.

Vcf file, obtained by mapping the M. fructicola strain AP47 reads on the genome of strain 277.

CAZymes predicted in the M. fructicola 277 genome.

Bacterial contamination is a growing concern worldwide. The aim of this work was to develop an antimicrobial coating based on curcumin-cyclodextrin inclusion complex and using polyethylene terephthalate (PET) film as a support matrix. After a pre-treatment aimed to provide sufficient electric charge to the PET surface, it was electrostatically coat...

Background: High-throughput amplicon sequencing spanning conserved portions of microbial genomes (16s rRNA and ITS) was used in the present study to describe the endophytic microbiota associated with three apple varieties, "Royal Gala," "Golden Delicious," and "Honey Crisp," and two rootstocks, M.9 and M.M.111. The objectives were to (1) determine...

Malus sieversii from Central Asia is a progenitor of the modern domesticated apple (Malus × domestica). Several accessions of M. sieversii are highly resistant to the postharvest pathogen Penicillium expansum. A previous study identified the qM–Pe3.1 QTL on LG3 for resistance to P. expansum in the mapping population GMAL4593, developed using the re...

We have developed a series of synthetic constructs suitable to genetically manipulate a broad range of yeast species belonging to the fungal CTG clade. This molecular toolbox notably allows heterologous gene expression, single or dual fluorescence labeling and construction of luciferase-expressing strains for bioluminescence imaging.

P. expansum is regarded as one of the most important postharvest rots of apple fruit and is also of great concern to fruit processing industries. Elucidating the pathogenicity mechanism of this pathogen is of utmost importance for the development of effective and safe management strategies. Although, many studies on modification of the host environ...

Statistic analysis of radial growth of ΔPeLysM3 null mutants (Δ3) compared to WT (P. e 100) and ectopic mutant (E). (DOCX)

Statistic analysis of ΔPeLysM1 pathogenicity test. (DOCX)

Statistic analysis of ΔPeLysM3 pathogenicity test. (DOCX)

Effect of targeted deletion of PeLysM1, PeLysM2, PeLysM3 and PeLysM4 on spore production. Average number of spore produced after 11 days of growth on potato dextrose agar medium based on three independent experiments. Bars indicate standard error. Letters indicate significant differences at P<0.05 based on nested one-way ANOVA followed by Tukey’s h...

Statistic analysis of ΔPeLysM2 pathogenicity test. (DOCX)

Partial results of the yeast-two hybrid analysis of the interactions between LysM from P. expansum and apple proteins. Five out 37 of positive clones are presented. The LysM domain (240 nt) from PeLysM1 was amplified by PCR, fused with the GAL4 DNA binding domain in the pGBKT7 vector and used as a bait. Empty vector was used as negative control. Th...

Statistic analysis of ΔPeLysM4 pathogenicity test. (DOCX)

Deletion of PeLysM1, PeLysM2, PeLysM3 and PeLysM4 in Penicillium expansum PE100. (A) Diagram of the wild type and deleted PeLysM1, PeLysM2, PeLysM3 and PeLysM4 loci. The hygromycin selectable marker present in the T-DNA of plasmids pRFHU2-PeLysM1, pRFHU2-PeLysM2, pRFHU2-PeLysM3 and pRFHU2-PeLysM4 replaces the corresponding PeLysM genes by homologou...

Primers used in the study. (DOCX)

Original gel images. (PPTX)

Curcumin has been known for a long time for its antimicrobial properties that are further increased by exposure to light. Due to the low aqueous solubility of curcumin, appropriate delivery systems are required to facilitate its implementation. In this work, we compared the antimicrobial activity toward Escherichia coli of two curcumin formulations...

During storage and ripening, mango fruit develop stem-end rots (SER) that reduce quality, causing significant losses of harvested fruit. The presented results indicate that pathogens, endophytically colonizing the fruit’s stem end, awaken during fruit ripening and cause SER. The main pathogens causing SER in mango grown in Israel were found to be A...

Blue mold caused by Penicillium expansum is the most important postharvest disease of apple worldwide and results in significant financial losses. There are no defined sources of resistance to blue mold in domesticated apple. However, resistance has been described in wild Malus sieversii accessions, including plant introduction (PI)613981. The obje...

QTL analysis scores for Kruskal-Wallis test, interval mapping and multiple QTL modeling on LG3 and LG10. Source: “RG” = marker heterozygous (informative) only in ‘Royal Gala’, “Ms” = informative only in PI613981, and “Both” = informative in both parents. Mapping LOD scores for “All Years” = score calculated based on blue mold LSmean lesion diameter...

Genotype data of GMAL4593 genetic linkage map. Text file listing markers and their respective genotype in 169 GMAL4593 progeny used to develop to genetic linkage map. Segregation type: (ab × cd) represents four distinct alleles among the two parents; (ef × eg) represents three alleles with a common allele shared between parents (ab × ac); (hk × hk)...

Images of genetic linkage maps for 17 linkage groups of GMAL4593 population. Images (.pdf) illustrate maps for ‘Royal Gala’ (maternal parent, left), PI613981 (paternal parent, right) and combined GMAL4593 mapping population (center). Anchor markers used to combine parental maps and connected with lines. The genetic linkage maps were calculated usin...

M. sieversii PI613981 marker S3_30831583 of LG3 qM-Pe3.1 QTL has major effect on the LSmean of blue mold lesion diameter 7 dpi. The parental haplotypes of M. sieversii PI613981 markers S3_29877372 and S3_30831583 were presumed to be nn-np and np-nn, respectively, based upon the number of individuals with each haplotypes. Both the np-nn parental hap...