Fungal, oomycete, and plasmodiophorid pathogens are the causal agents of potato diseases. These pathogens cause serious economic damage including reduction of potato yield and/or quality of the tubers, thus directly affecting the whole chain of potato production and industry worldwide. The losses are caused in the field where all diseases are initiated and, in the storage, affecting potatoes for consumption as well as on seed tubers for subsequent crops. Moreover, as some of these pathogens are also soilborne, their negative impact on soil contamination requires intensive and expensive measures for the long term. The chapter is focused on the main issues related to the pathogen biology, the disease epidemiology, and the disease management at different stages of development, according to the specific pathogens. The more the understanding of the different diseases, through advanced research, the more tools can be developed to achieve efficient disease management and prevent yield losses. The diseases being discussed in this chapter can be divided according to their targeted plant part: attacking either the above-ground parts causing leaves chlorosis and necrosis, foliar wilt, or the under-ground parts damaging the root system and the tubers. Several of the diseases which intensify during the harvest, storage, and transport of the produce are considered also as postharvest diseases, affecting tubers by causing symptoms such as blemishes, soft and dry rots, leading to a reduction in tuber quality. In the era of climate change and global warming, combating old, new, and re-emerging diseases challenges the scientific community in better knowing “the enemy” for providing acceptable solutions for the growing population on earth. In the current chapter the major pathogens causing severe economic losses and their control will be discussed.

Abstract Potato is an important commodity in Georgia, but the average yields are considerably low (12 t/ha) mainly due to bacterial diseases. During 2020-2021, 73 samples of diseased potato tubers and stems were collected from fields and storage facilities, in different locations in Georgia. Following microbiological and biochemical tests, 54 strains (74%) were gram-negative, facultative anaerobic, oxidase negative, catalase-positive, they developed at 37oC and in 5% NaCl, non-fluorescent on King´s B medium, and produced cavities on CVP, thus indicating they were either Dickeya or Pectobacterium spp. Twenty-seven out of selected 33 strains were identified as Dickeya spp. using conventional PCR and 21 of them were further characterized as D. solani (using TaqMan RT-PCR). According to the present research, D. solani is the major pathogen associated with potato soft rot and black leg in different regions of Georgia. The most prevalent species in Europe, P. brasiliense, as well as D. dianthicola have not been detected in the current research.

A hyperspectral (HS) imaging system in the 400–1650 nm range was developed based on a point spectrometer matched to a double-wedge prism scanner (Risley prism). This type of scanner is efficient and robust in monochromatic laser systems operating under field conditions. Here, we adopted this scanning principle to develop an inexpensive replacement for the HS camera, suitable for application in precision agriculture and environmental monitoring. However, the application of such a scanner in HS imaging is challenging, due to the broadband nature of HS imaging and the dispersive nature of prisms. The sampling characteristics exhibit wavelength-dependent and space-variant behavior, which affect both ground pixel size and location. In this work, we modeled light propagation through the proposed system using a ray-tracing approximation. Based on this model, we proposed a three-step calibration process. A prototype was built and optimized, followed by an intensive validation process that showed a high correlation between the scanner's performance and model prediction of ground sample diameter, as well as accuracy in the spectral measurement of the system. Testing reflectance measurement accuracy showed a normalized sum of absolute difference (NSAD) of 4.24% and less. The calibration process was demonstrated in simulations. Finally, preliminary field experiments with two spectrometers in the range of 400–899 nm (Vis–NIR), and 950–1650 nm shortwave infrared (SWIR) showed that the proposed system can support outdoor monitoring, thus having the potential capabilities for supporting agricultural monitoring tasks.

Potato common scab (CS) and peanut pod wart diseases cause substantial economic losses every year in Israel. In this comprehensive study on the Streptomyces spp. population, isolates were collected during 2004–2016 from potato tubers with symptoms grown in Israel, seed tubers imported from Europe and from peanut pods with symptoms grown in Israel. A total of 142 isolates were characterized by PCR using three primer sets ( txtA , tomA and nec1 genes) and by three pathogenicity tests. Seven species were identified among the isolates, S . bottropensis , S . europaeiscabiei , S . griseus , S . scabiei , S . sampsonii , S . turgidiscabies , and S . venezuelae . S . europaeiscabiei was the most dominant among isolates from imported seed tubers, while S . scabiei and S . turgidiscabies were isolated from tubers grown in Israel. Isolates originating from peanuts were significantly more virulent than those from imported seed tubers, as determined by a pathogenicity assay on radish plants. The presence of pathogenic Streptomyces was detected by quantitative PCR (qPCR) in 289 soil samples collected from 31 commercial potato fields with CS history. Eighty percent to 100% of samples collected from fields with a high disease incidence on tubers (50%) gave positive results in qPCR, whereas in samples collected from fields with low CS incidence (2%–30%) the qPCR results were very variable. Potato seed lots imported from Europe during 2008–2021 were found contaminated with CS symptoms at different levels on visual examination. The results of this study indicate that Streptomyces species, in particular S . europaeiscabiei , were introduced to Israel through seed lots imported from Europe.

Half of the harvested food is lost due to rots caused by microorganisms. Plants emit various volatile organic compounds (VOCs) into their surrounding environment, and the VOC profiles of healthy crops are altered upon infection. In this study, a whole-cell bacterial biosensor was used for the early identification of potato tuber soft rot disease caused by the pectinolytic bacteria Pectobacterium in potato tubers. The detection is based on monitoring the luminescent responses of the bacteria panel to changes in the VOC profile following inoculation. First, gas chromatography-mass spectrometry (GC-MS) was used to specify the differences between the VOC patterns of the inoculated and non-inoculated potato tubers during early infection. Five VOCs were identified, 1-octanol, phenylethyl alcohol, 2-ethyl hexanol, nonanal, and 1-octen-3-ol. Then, the infection was detected by the bioreporter bacterial panel, firstly measured in a 96-well plate in solution, and then also tested in potato plugs and validated in whole tubers. Examination of the bacterial panel responses showed an extensive cytotoxic effect over the testing period, as seen by the elevated induction factor (IF) values in the bacterial strain TV1061 after exposure to both potato plugs and whole tubers. Moreover, quorum sensing influences were also observed by the elevated IF values in the bacterial strain K802NR. The developed whole-cell biosensor system based on bacterial detection will allow more efficient crop management during postharvest, storage, and transport of crops, to reduce food losses.

Potato blackleg and tuber soft rot diseases, caused by the pectinolytic bacteria Pectobacterium and Dickeya spp., result in severe yield losses worldwide. Early detection of pectinolytic bacterial infections is an important tool in disease management for sustainable potato production. The main goal of the current study was to profile the volatile composition of tubers inoculated with pectinolytic bacteria, in order to identify biomarkers for inoculation with different pathogens. Potato tubers were inoculated with two genera of bacteria (five species and/or sub-species, 4-5 strains of each). The headspace was sampled via solid-phase microextraction method, and volatiles were further profiled using gas chromatography-mass spectrometry. Using discriminant analysis, we were able to identify volatiles as differentiating biomarkers, indicating either non-specific or species-specific inoculation. Dimethyl ether was increased in all inoculated samples regardless of the genus or species; hexanal was increased in inoculation with Dickeya compared to Pectobacterium; 2-methylbutanol and 2,3-octanedione differentiated between Pectobacterium species inoculation; and 2-pentyl thiophene differentiated between Dickeya species inoculation. Early detection of pectinolytic bacteria through continuous monitoring of storage facility and tuber shipments atmosphere may be a powerful tool in preventing and mitigating tuber soft rots, avoiding severe economic damages and global food loss.

Potato leak, caused by Pythium ultimum, is characterized by brown to dark-gray lesions on tubers. The efficacy of fungicides applied by foliar spray, in-furrow treatment, or by combination of both methods on disease incidence was evaluated in three field trials. In 2018, a single [50 days after planting (DAP), or 1 week prior to haulm kill (HK)], or two foliar sprays (50 DAP and 1 week pre-HK) of metalaxyl, hymexazol and propamocarb-HCl were evaluated. Disease incidence was significantly reduced only by metalaxyl. In 2019 trials, only metalaxyl treatments were included: a single (50 DAP; 2-weeks pre-HK; 2-days post-HK) or two foliar sprays (50 DAP; 2-weeks pre-HK), in-furrow treatment, alone or combined with foliar spray (2-weeks pre-HK). Disease incidence was significantly reduced by all treatments, except for foliar spray 50 DAP (only in Exp C). The lowest incidence was observed in the in-furrow treatment alone or combined with foliar spray applied 2-weeks before HK.

Powdery scab (PS) caused by Spongospora subterranea, causes lesions on potato tubers and root galling, resulting in significant yield losses. Disease development is affected by soil inoculum and environmental conditions, mainly temperature and soil moisture. A field trial with naturally infested soil was conducted to evaluate the effect of planting date on PS incidence and root galling, using 11 cultivars. Tubers of all tested cultivars had significantly lower levels of PS following the early winter planting dates (7- and 25-October), compared to late planting (15-November). No root galling was observed on plants sampled from the first two planting dates, whereas, in the late planting date, typical root galls were observed at different levels on all tested cultivars. To conclude, planting in fields with a history of PS in warm temperatures and using tolerant cultivars can reduce the risk of PS and considered as a part of disease management.

Fusarium wilt, caused by Fusarium oxysporum, is a major disease of jojoba, causing serious economic losses. This study was aimed at characterizing the Fusarium populations associated with jojoba in Israel. Fifty Fusarium isolates used in this study included 23 isolates from the 1990s ("past") and 27 recently isolated ("recent"). All the isolates were characterized by arbitrarily primed (ap)-PCR and 16 representatives were additionally delineated using multilocus (tef1, rpb1, rpb2) phylogeny and evaluated for their pathogenic potential. Consequently, 88% of the isolates were identified and characterized to the F. oxysporum species complex. The remaining 12% grouped within the F. fujikuroi, F. solani, and F. redolens species complexes. Variations in the infection rate (16.7%-100%), disease symptoms (0.08-1.25, on a scale of 0-3), and fungal colonization index (0.67-2.17, on a scale of 0-4) were observed within the tested isolates, with no significant differences between the past and recent isolates. The representative isolates were assigned to 11 groups based on ap-PCR. Pathogenicity tests showed that isolates from Groups II, IV, and V were the most aggressive, whereas isolates from Groups III, VIII, and IX were the least aggressive. Among the tested isolates, F. oxysporum sensu lato was the most aggressive, followed by F. proliferatum, while F. nygamai was the least aggressive. This study demonstrates the complexity and genetic diversity of Fusarium wilt on jojoba in Israel, indicating possible multiple introductions of infected germplasm into the country.

Pectobacterium brasiliense (Pbr) infects a wide range of crops worldwide, causing potato blackleg and soft rot and vegetable soft rots. This study aimed to characterize the genetic diversity and virulence variability among 68 Pbr strains isolated from either symptomless potato progeny tubers, diseased potato plants, ware potatoes wash water, or vegetables grown in Israel, as well as strains isolated from symptomless seed tubers grown in Europe, or diseased potato plants grown in France. The collection was typed using PCR and TaqMan real-time PCR analyses, dnaX sequence analysis, pulsed-field gel electrophoresis (PFGE), and pectolytic activity. dnaX phylogeny grouped almost all strains in a common genetic clade related to Pbr, which was distinct from the other Pectobacterium species. PFGE analysis identified two main clusters, including one major group of 47 strains with 95%-100% similarity. Maceration assays on two potato cultivars showed significant differences between strains but with no correlations with the source of the strains nor the status of the host (with/without symptoms). Molecular (dnaX sequences and PFGE profiles) and phenotypic analyses (tuber maceration tests) showed that the tested Pbr strains are not a homogeneous group. Analysis of the tested Pbr strains isolated from potato and vegetables grown in fields with a history of potato cultivation suggests that seed tubers imported from Europe may be the main source for Pbr in Israel. To the best of our knowledge, this is the first study that describes biodiversity and population structure of P. brasiliense isolated from potato and vegetables under hot climate conditions.

Verticillium dahliae is a soilborne fungal pathogen affecting many economically important crops that can also infect weeds and rotational crops with no apparent disease symptoms. The main research goal was to test the hypothesis that V. dahliae populations recovered from asymptomatic rotational crops and weed species are evolutionarily and genetically distinct from symptomatic hosts. We collected V. dahliae isolates from symptomatic and asymptomatic hosts growing in fields with histories of Verticillium wilt of potato in Israel and Pennsylvania (United States), and used genotyping-by-sequencing to analyze the evolutionary history and genetic differentiation between populations of different hosts. A phylogeny inferred from 26,934 single-nucleotide polymorphisms (SNPs) in 126 V. dahliae isolates displayed a highly clonal structure correlated with vegetative compatibility groups, and isolates grouped in lineages 2A, 2B824, 4A, and 4B, with 77% of the isolates in lineage 4B. The lineages identified in this study were differentiated by host of origin; we found 2A, 2B824, and 4A only in symptomatic hosts but isolates from asymptomatic hosts (weeds, oat, and sorghum) grouped exclusively within lineage 4B, and were genetically indistinguishable from 4B isolates sampled from symptomatic hosts (potato, eggplant, and avocado). Using coalescent analysis of 158 SNPs of lineage 4B, we inferred a genealogy with clades that correlated with geographic origin. In contrast, isolates from asymptomatic and symptomatic hosts shared some of the same haplotypes and were not differentiated. We conclude that asymptomatic weeds and rotational hosts may be potential reservoirs for V. dahliae populations of lineage 4B, which are pathogenic to many cultivated hosts.

Powdery scab (PS), caused by Spongospora subterranea, reduces the quality and marketability of potatoes worldwide. Disease symptoms include lesions on the tuber surface and root galling, which may lead to yield losses. In the current study we report a sustainable approach to reduce PS by manipulating soil temperature during tuber initiation. Plant cover with nonwoven fabric significantly reduced PS on tubers by 54%-69% in 2017 and 84%-93% in 2019, compared to the control, and root galling by 96% in 2019, due to an increased average minimum and maximum soil temperature of 1.8 and 4.2 degrees C in respective years. Additional preplanting soil treatments were also evaluated in naturally infested soil. In 2017, disease incidence and severity were significantly reduced using 2.5 or 5 L a.i./ha fluazinam in broadcast application or in-furrow, and by 0.375 or 0.75 L a.i./ha flusulphamide applied in-furrow. In 2019, disease incidence and severity were significantly reduced by the broadcast application of fluazinam, and 75 kg/ha calcium cyanamide, but the latter had a negative impact on yield. Soil fumigation with metam sodium resulted in a 98% reduction in PS. Root galling was significantly reduced by calcium cyanamide, metam sodium, and fluazinam in the 2019 trial only. Foliar application of resistance-inducing phosphonates combined with fluazinam application had no additive effect on PS incidence and severity. Integrated approaches such as tolerant cultivars, soil testing, preplanting fungicide application, and sustainable means of control such as foliage cover for a short period may be implemented in order to control the disease and minimize damage.

Potato powdery scab caused by Spongospora subterranea subsp . subterranea (Sss) causes extensive damage to the quality and marketability of tubers. Disease outbreaks in potatoes grown in virgin soils in south Israel, lead us to the hypothesis that wind-driven inoculum may also be a source of new infections. Wind and ground traps (13 of each type) were positioned near contaminated commercial potato fields with a history of powdery scab in two plots during 2013–14 (‘Nave 5’ and ‘Nave 89’). Quantification of pathogen density in soil/dust was carried out by DNA extraction and qPCR analysis. In ‘Nave 5’ plot, 58 and 45% (December and January, respectively) and 75 and 50% of the ground and wind traps, respectively, were Sss-positive, with no significant differences in Sss concentrations. In ‘Nave 89’ plot, the percentage of Sss-positive traps increased from 31% and 18% in the ground and wind traps, respectively, in February, to 100% in both trap types, in April, with no significant differences. Evaluation of the dispersal distance of Sss inoculum from contaminated fields was examined in soil samples taken from the top layer of the ground in the uncultivated area adjacent to the contaminated commercial potato fields with a history of powdery scab, in two sites (‘Nave 5’ and ‘Shalom 7’) during 2016. All soil samples, taken from uncultivated areas near the infested fields in various distances of up to 750 m, were Sss positive. This study demonstrated that Sss can be dispersed by wind, particularly in an intensive potato production region where contaminated fields exist.

The global avocado industry is growing, and farmers are seeking to expand their plantations. However, many lands suitable for avocado planting were previously cultivated with hosts of the soil-borne fungal pathogen Verticillium dahliae, which is the causal agent of Verticillium wilt (VW). VW can seriously impair avocado orchards, and therefore, planting on infested soil is not recommended. The use of different rootstock types allows avocado cultivation in various regions with diverse biotic and abiotic constraints. Hence, we tested whether genetic variance among rootstocks may also be used to manage avocado VW. Six hundred trees, mostly Hass and some Ettinger, grafted on 23 selected rootstocks were evaluated for five years in a highly V. dahliae-inoculated plot for VW symptoms, fungal infection, and productivity. The selected rootstocks displayed a significant variation related to VW tolerance, and productive avocado rootstocks with potential VW tolerance were identified. Moreover, the rootstock productivity appears to correlate negatively to the susceptibility level. In conclusion, planting susceptible rootstocks (e.g., VC66, VC152, and VC26) in infested soil increases the likelihood of massive tree loss and low productivity. Whereas, tolerant rootstocks (e.g., VC804 and Dusa) may restrict VW and enable avocado cultivation on infested soils.

Over the past two decades, whole-cell biosensors (WCBs) have been widely used in the environmental field, with only few applications proposed for use in agricultural. This study describes the development and optimization of a WCB for the detection of volatile organic compounds (VOCs) that is produced specifically by infected potato tubers. First, the effect of calcium-alginate matrix formation (beads vs. tablets) on the membrane uniformity and sensing efficiency was evaluated. Then, important parameters in the immobilization process were examined for their effect on the sensitivity to the presence of VOCs. The highest sensitivity to the target VOC was obtained by 20 min polymerization of bacterial suspension with optical density of 0.2 at 600 nm, dissolved in low-viscosity sodium alginate (1.5% w/v) and exposure to VOC at 4 °C. After optimization, the lowest limit of detection for three infection-sourced VOCs (nonanal, 3-methyl-1-butanol, and 1-octen-3-ol) was 0.17-, 2.03-, and 2.09-mg/L, respectively, and the sensor sensitivity was improved by 8.9-, 3.1- and 2-fold, respectively. Then, the new optimized immobilization protocol was implemented for the CMOS-based application, which increased the sensor sensitivity to VOC by 3-fold during real-time measurement. This is the first step in creating a sensor for real-time monitoring of crop quality by identifying changes in VOC patterns.

Pectobacterium and Dickeya spp. are soft rot Pectobacteriaceae that cause aggressive diseases on agricultural crops leading to substantial economic losses. The accurate, rapid and low‐cost detection of these pathogenic bacteria are very important for controlling their spread, reducing the consequent financial loss and for producing uninfected potato seed tubers for future generations. Currently used methods for the identification of these bacterial pathogens at the strain level are based mainly on molecular techniques, which are expensive. We used an alternative method, infrared spectroscopy, to measure 24 strains of five species of Pectobacterium and Dickeya . Measurements were then analyzed using machine learning methods to differentiate among them at the genus, species and strain levels. Our results show that it is possible to differentiate among different bacterial pathogens with a success rate of ~99% at the genus and species levels and with a success rate of over 94% at the strain level.