Biology subjects

Doron-Faigenboim, A.

Publications and source records attributed to Doron-Faigenboim, A..

11 recordsLinked to original sources

bioRxiv2026

Dual Knockout of StAMY23 and StVINV Improves Postharvest Storage Traits in Potato

Starch is the primary carbohydrate reserve in potato (Solanum tuberosum L.) tubers and a critical determinant of their industrial value. The rate of starch degradation during postharvest storage directly influences key traits such as endodormancy (ED) duration and cold-induced sweetening (CIS), which affect sprouting behavior. In this study, we used CRISPR/Cas9 genome editing to knockout StAMY23, a gene encoding -amylase involved in starch breakdown. stamy23 plants exhibited higher yield and extended tuber ED postharvest, without significantly altering CIS or starch granule content. To further reduce CIS, we knockout StAMY23 in VACUOLAR INVERTASE knockout (stvinv) backgrounds, generating stamy23/stvinv double-knockouts plants. These lines showed significantly reduced CIS, prolonged ED, and elevated starch content, along with altered starch granule content. Collectively, our findings demonstrate that simultaneous downregulation of StAMY23 and StVINV can additively enhance desirable postharvest traits, providing a promising strategy for improving potato storage quality through precision genome editing.

plant biology↗

bioRxiv2026

Isolation and characterization of novel banana rhizosphere bacteria for the control of Fusarium oxysporum f. sp. cubense TR4

Fusarium wilt of banana, caused by Fusarium oxysporum f. sp. cubense race TR4 (Foc), is one of the most destructive diseases threatening global banana production, particularly the Cavendish cultivar. Conventional control strategies, including chemical treatments and quarantine, remain largely ineffective and unsustainable, underscoring the urgent need for alternative approaches. Biological control using rhizosphere-associated microorganisms offers a promising and environmentally friendly strategy. In this study, we isolated 436 bacterial strains from the rhizosphere of healthy banana plants and screened them for antifungal activity against Foc. Out of the screened isolates, 93 exhibited significant in-vitro inhibitions, and 64 of these were subsequently evaluated in greenhouse assays. We found that 22 strains reduced Fusarium wilt severity by 45-85% compared to untreated controls. Among them, two isolates, DDC20 and DDC_NEW2, consistently demonstrated strong biocontrol activity. In addition, cell-free culture media (CFCM) and crude extracts inhibited spore germination in fluorescence-based assays, indicating the involvement of secreted antifungal metabolites. Microscopy and confocal observations of GFP-tagged Foc revealed hyphal abnormalities in the presence of bacterial treatments, including swelling, irregular branching, and distortion, accompanied by excessive sporulation characterized by abundant microconidia, macroconidia, and chlamydospores. Whole-genome sequencing and comparative analyses placed both isolates within the genus Bacillus. Genome mining using antiSMASH identified multiple biosynthetic gene clusters encoding known antifungal compounds such as surfactin, fengycin, bacillibactin, and difficidin, as well as putative novel clusters. LC-MS confirmed the presence of surfactin and fengycin in bacterial extracts, supporting the genomic predictions. Collectively, these findings highlight the potential of DDC20 and DDC_NEW2 (related to Bacillus spp.) from the banana rhizosphere as effective biocontrol agents against Foc TR4. This integrated approach, combining phenotypic assays, microscopy, and genome mining, provides a strong foundation for the development of sustainable strategies to manage Fusarium wilt in banana cultivation.

microbiology↗

bioRxiv2025

Pleiotropic mutation in a tendril TCP gene underlies the yield-enhancing multiple-flowering trait in summer squash (Cucurbita pepo)

Crop yield is a focal point in plant breeding. Regulation of lateral budding through apical dominance was a central target of crop domestication, directly affecting crop production. The young fruits of Cucurbita pepo, summer squash, are produced on plants characterized by apical dominance and differentiation of a single flower bud per leaf axil. A single recessive mutation, mf, results in differentiation of more than one flower per leaf axil, thereby directly increasing production because of the continual day-to-day harvest of the summer-squash crop. Positional cloning of the Cucurbita pepo mf (Cpmf) gene denoted a frame-shift mutation in a TCP transcription factor, Cp4.1LG13g07780, as causative for the increase in axillary flowering. Cpmf is an ortholog of a tendril-development TCP gene in other cucurbits and, likewise, the recessive allele of Cpmf is associated with distorted tendril development. Gene function is context-dependent, and we propose that multiple-flowering is a unique pleiotropic attribute of mutation in a tendril-development gene of C. pepo. Characterization of a C. pepo collection confirmed a significant association of the Cpmf mutation with multiple-flowering, and showed that the mutant allele is absent in ancestral C. pepo and one of its two cultivated subspecies. The beneficial mutation occurred and was selected after the domestication of the other subspecies, during its cultivation for young fruit production. We demonstrate the discovery of a causative yield-increasing sequence variant and its practical utilization in breeding. Our findings provide a molecular target for creation of high-yielding, multiple-flowering summer-squash cultivars through marker-assisted breeding or precise genome editing. SIGNIFICANCE STATEMENTSummer squash is characterized by apical dominance and a single flower bud per leaf axil. A multiple-flowering trait, conferred by a single recessive gene, mf, significantly increases fruit yield by producing more flowers per leaf axil. We show that a mutation in a tendril-development TCP gene is causative for enhanced axillary flowering, and that the beneficial mutation occurred during the cultivation of summer squash. We demonstrate the successful implementation of mf for development of high-yielding squash cultivars.

plant biology↗

bioRxiv2025

Vacuolar invertase knockout enhances drought tolerance in potato plants

Drought stress is one of the most critical abiotic constraints limiting crop productivity worldwide, exacerbated by ongoing climate change and increasingly frequent extreme weather events. Stomatal regulation and osmoprotective sugar accumulation are critical adaptive mechanisms for plant survival under drought stress. Here, we characterize the enhanced drought resilience observed in CRISPR/Cas9-mediated potato, mutants in their vacuolar invertase gene (StVInv). Knockout plants exhibited improved performance under progressive drought stress and during rewatering drought, maintaining higher stomatal conductance, elevated transpiration rates, and superior photosynthetic efficiency compared to wild-type (WT) plants. These improved performance under similar transpiration rate led to higher agronomic water-use efficiency (AWUE) in stvinv plants resulting in greater biomass production despite reduced water availability. Metabolomic profiling revealed distinct adaptive strategies; stvinv plants preferentially accumulated galactinol and raffinose, indicating enhanced raffinose family oligosaccharide (RFO) metabolism. Furthermore, stvinv plants displayed lower levels of abscisic acid (ABA) and its catabolites under drought, suggesting a moderated ABA response facilitating a more risk-taking growth strategy that supports sustained growth and physiological stability. Our findings identify targeted metabolic and hormonal adjustments underlying drought resilience in potato plant, offering promising strategies for enhancing crop performance under water-limited conditions.

plant biology↗

bioRxiv2025

Entomopathogenic fungi as dual-function biocontrol agents: persistence and microbiome modulation in date palm soils

The effects of entomopathogenic fungi (EPF) on native soil microbiota are poorly understood. Here, we investigated the persistence of the EPF Metarhizium brunneum and Beauveria bassiana as preventive treatments for date palms against the red palm weevil, Rhynchophorus ferrugineus, and monitored the microbial community within the palms. We assessed the changes in the soil microbiota of the palms following application by fungal soil isolation techniques, high-throughput metagenomics, EPF persistence assays, and accompanied that with a continuous monitoring of date palm health. EPF preemptive treatments significantly improved palm protection against the weevil. While both EPF species persisted for 180 days post-application, their effectiveness diverged, with B. bassiana providing longer palm protection. Overall microbial community composition showed no major changes following EPF applications; however, transient alterations increased the relative abundance of local EPF genera, with dominant taxa being more likely to persist. Both EPF treatments enhanced the relative abundance of nitrogen-fixing bacteria, organic matter decomposers, and ammonia-oxidizing archaea, suggesting potential implications for nutrient cycling that require further validation through direct functional measurements. B. bassiana induced the strongest temporal effects on diversity indices, while M. brunneum was more persistent but showed no significant changes in diversity indices compared to the control. These results highlight EPF as a multifunctional biocontrol agent - moderately shaping soil microbiomes for beneficial ecosystem functions.

microbiology↗

bioRxiv2025

Systematic discovery of bacterial symbionts in rumen ciliate protozoa

Microbial interactions are fundamental to global ecological and evolutionary processes, exemplified by endosymbiosis between prokaryotes and single-cell eukaryotes that gave rise to organelles. While such associations remain widespread and ecologically important, the diversity and evolutionary dynamics of intracellular symbioses in many microbial ecosystems remain poorly understood. Here, we uncover a hidden layer of microbial complexity in the rumen ecosystem by identifying multiple endosymbiotic associations between ciliate protozoa and bacteria. Using genome-resolved metagenomics on protozoa enriched rumen fractions, we reveal diverse bacterial genomes exhibiting hallmarks of an obligate intracellular lifestyle. These candidate symbionts span several bacterial phyla and include close relatives of known endosymbionts and parasites of protists as well as previously unclassified or presumed free-living bacterial lineages that likely represent overlooked symbiont specialists. Our findings therefore expand the known distribution of bacterial endosymbiosis, establish the rumen - a key site of global carbon and nitrogen cycling - as a promising model for symbiosis research, and demonstrate the power of our approach to uncover hidden symbiotic associations across complex microbial communities. Overall, our results highlight the ubiquity and evolutionary significance of intracellular symbiosis as a shaping force in microbial ecosystems.

microbiology↗

bioRxiv2025

Deciphering the Survival Strategies of the Entomopathogenic Nematode Steinernema carpocapsae Using Rapid Desiccation Assisted by Nanoparticle-Based Emulsion

Water retention is essential for survival under desiccating conditions, especially for entomopathogenic nematodes (EPNs) used as biocontrol agents. Foliar application of EPNs causes rapid desiccation (RD), severely reducing their survival and efficacy. We investigated the physiological and molecular responses of Steinernema carpocapsae to RD, delivered in a novel nanoparticle-stabilized emulsion to improve tolerance under variable humidity. We hypothesized that the formulation would enhance EPNs survival, by promoting early stress-responsive pathways and water-retention mechanisms. Formulated nematodes exhibited delayed water loss and increased survival under low humidity compared with non-formulated controls. The emulsion mitigated RD by enhanced hydration retention and reduced water loss, effects that were strongly associated with differential trehalose accumulation. In addition, maintenance of basement membrane integrity and cytoskeletal organization, emerged as a critical component of desiccation. These findings advance understanding of RD tolerance in EPNs and demonstrate how tailored formulation strategies can protect biocontrol agents under desiccation stress.

developmental biology↗

bioRxiv2025

Contribution of the Tobamovirus resistance gene Tm-1 to control of ToBRFV resistance in tomato

Tomato brown rugose fruit virus (ToBRFV) is a rapidly spreading pathogen that poses a significant threat to tomato production worldwide. We previously identified a locus on tomato chromosome 11 controlling tolerance to the virus. We further established that combining this locus with one that maps to the Tm-1 region on chromosome 2 confers resistance to the virus. Here we sought to determine whether, and how, the Tm-1 gene itself is involved in ToBRFV resistance. Overexpression of Tm-1 in a tolerant genotype significantly reduced viral accumulation, conferring resistance to ToBRFV. On the other hand, overexpression of Tm-1 in a susceptible genotype only delayed symptom appearance. Moreover, effective RNAi-silencing of Tm-1 in the resistant genotype yielded susceptible plants. These findings show that the Tm-1 gene interacts genetically with the locus controlling tolerance on chromosome 11 and that this interaction is critical for achieving effective resistance to ToBRFV. In addition, the symptomatic plants obtained following silencing of Tm-1 in the resistant genotype indicate that tolerance is also dependent on normal expression levels of the recessive tm-1 allele.

plant biology↗

bioRxiv2023

A metabolic modeling-based framework for predicting trophic dependencies in native rhizobiomes of crop plants

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 interest, and therefore to the harnessing of the functionality of various types of microbiomes. However, mechanistic knowledge regarding the gathering and interpretation of these interactions is limited. Here, we present a framework utilizing genomics and constraint based modeling approaches, aiming to interpret the hierarchical trophic interactions in the soil environment. 243 genome-scale metabolic models of bacteria associated with a specific disease suppressive vs disease conducive apple rhizospheres were drafted based on genome resolved metagenomes, comprising an in-silico native microbial community. Iteratively simulating microbial community members growth in a metabolomics-based apple root-like environment produced novel data on potential trophic successions, used to form a network of communal trophic dependencies. Network-based analyses have characterized interactions associated with beneficial vs non-beneficial microbiome functioning, pinpointing specific compounds and microbial species as potential disease supporting and suppressing agents. This framework provides a means for capturing trophic interactions and formulating a range of testable hypotheses regarding the metabolic capabilities of microbial communities within their natural environment. Essentially, it can be applied to different environments and biological landscapes, elucidating the conditions for the targeted manipulation of various microbiomes, and the execution of countless predefined functions.

microbiology↗

bioRxiv2021

Revealing the genetic components responsible for the unique photosynthetic stem capability of the wild almond Prunus arabica (Olivier) Meikle

Almond (Prunus dulcis (Mill.) D. A. Webb) is a major deciduous fruit tree crop worldwide. During dormancy, under warmer temperatures and inadequate chilling hours, the plant metabolic activity increases and may lead to carbohydrate deficiency. Prunus arabica (Olivier) Meikle is a bushy wild almond species known for its green, un-barked stem, which stays green even during the dormancy period. Our study revealed that P. arabica green stems assimilate significantly high rates of CO2 during the winter as compared to P. dulcis cv. Um el Fahem (U.E.F), and may improve carbohydrate status throughout dormancy. To uncover the genetic inheritance and mechanism behind the P. arabica Stem Photosynthetic Capability (SPC), a segregated F1 population was generated by crossing P. arabica to U.E.F. Both parents whole genome was sequenced, and a single nucleotide polymorphism (SNP) calling identified 4,887 informative SNPs for genotyping. A robust genetic map for U.E.F and P. arabica was constructed (971 and 571 markers, respectively). QTL mapping and association study for the SPC phenotype revealed major QTL (log of odd (LOD)=20.8) on chromosome 7, and another minor but significant QTL on chromosome 1 (LOD=3.9). Finally, a list of 73 candidate genes was generated. This work sets the stage for future research to investigate the mechanism regulating the SPC trait, how it affects the trees physiology, and its importance for breeding new cultivars better adapted to high winter temperatures.

plant biology↗

bioRxiv2019

Endogenous sugar level is associated with differential heat tolerance in onion bulb scales

Postharvest heat treatment stimulates desiccation and browning of outer scales of onion (Allium cepa. L) bulb to dry papery skins. Inner scales resist the heat treatment, as evidenced by high moisture levels. During heating, inner scales showed increasing soluble sugar levels followed by higher osmolarity, vs. a dramatic decrease in both in the outer scales. Exogenous feeding of outer scales with sucrose, glucose or fructose solutions before heat treatment reduced water loss during heating, suggesting a role for soluble sugars in water retention and therefore, heat tolerance. Vacuolar invertase (VInv) is a key enzyme regulating the levels of sucrose, glucose and fructose in plant tissue. VInv-silencing in potato plants prevented the accumulation of reducing sugars in heated leaves, increasing water loss. In onion outer scales, VInv activity increased during heating but reducing sugars decreased, possibly due to their rapid metabolism during scale senescence to form skin. Transcriptomic analysis demonstrated upregulation of genes involved in lignin biosynthesis and secondary cell-wall formation in outer scales during heat exposure, and upregulation of genes involved in energy-related pathways in inner scales. This study reveals the dual role of soluble sugars in different onion scales, as osmoprotectants or building blocks, under heat stress. HighlightHexose formation in the inner scales of onion is associated with heat tolerance, while in the outer scales, the hexoses are metabolized for onion skin formation.

plant biology↗