Colonization process of olive tissues by Verticillium dahliae and its in planta interaction with the biocontrol root endophyte Pseudomonas fluorescens PICF7

Eco-smart biocontrol strategies utilizing potent microbes for sustainable management of phytopathogenic diseases

Plants have an impact on the economy because they are used in the food and medical industries. Plants are a source of macro- and micronutrients for the health of humans and animals; however, the rise in microbial diseases has put plant health and yield at risk. Because there are insufficient controls, microbial infections annually impact approximately 25 % of the world's plant crops. Alternative strategies, such as biocontrol, are required to fight these illnesses. This review discusses the potential uses of recently discovered microorganisms because they are safe, effective, and unlikely to cause drug resistance. They have no negative effects on soil microbiology or the environment because they are environmentally benign. Biological control enhances indigenous microbiomes by reducing bacterial wilt, brown blotch, fire blight, and crown gall. More research is required to make these biocontrol agents more stable, effective, and less toxic before they can be used in commercial settings.

Endophytic Bacillus velezensis XS142 is an efficient antagonist for Verticillium wilt of potato

Potato Verticillium wilt (PVW) caused by Verticillium dahliae is a vascular disease, that seriously affects potato (Solanum tuberosum L.) yield and quality worldwide. V. dahliae occupies the vascular bundle and therefore it cannot efficiently be treated with fungicides. Further, the application of these pesticides causes serious environmental problems. Therefore, it is of great importance to find environmentally friendly biological control methods. In this study, bacterial strains were isolated from agricultural lands on which potato had been cultured for 5 years. Five strains with a broad-spectrum antagonistic activity were selected. Among these five strains, Bacillus velezensis XS142 showed the highest antagonistic activity. To study the mechanism of XS142, by which this strain might confer tolerance to V. dahliae in potato, the genome of strain XS142 was sequenced. This showed that its genome has a high level of sequence identity with the model strain B. velezensis FZB42 as the OrthoANI (Average Nucleotide Identity by Orthology) value is 98%. The fungal suppressing mechanisms of this model strain are well studied. Based on the genome comparison it can be predicted that XS142 has the potential to suppress the growth of V. dahliae by production of bacillomycin D, fengycin, and chitinase. Further, the transcriptomes of potatoes treated with XS142 were analyzed and this showed that XS142 does not induce ISR, but the expression of genes encoding peptides with antifungal activity. Here we showed that XS142 is an endophyte. Further, it is isolated from a field where potato had been cultured for several years. These properties give it a high potential to be used, in the future, as a biocontrol agent of PVW in agriculture.

Complete genome sequence data of Pseudomonas nitroreducens L4, an endophyte isolated from cotton plants

Pseudomonas nitroreducens L4 was isolated from the interior of cotton plants, which showed strong biocontrol activity against Verticillium dahlia and other fungal pathogens. To elucidate the biocontrol mechanism, the genome sequence of L4 was sequenced using the Illumina and Nanopore sequencing platform. The assembled genome of L4 consisted of a single circular chromosome was 6,229,472 bp, with an average GC content of 64.95 %, 5,629 protein-coding genes, 72 tRNA, 16 rRNA and 1 tm RNA. Six secondary metabolite biosynthetic gene clusters are identified in the genome. The genome sequence provided a theoretical basis for analyzing the biocontrol mechanism of this strain.

The Verticillium dahliae Effector VdPHB1 Promotes Pathogenicity in Cotton and Interacts with the Immune Protein GhMC4

Verticillium dahliae is a kind of pathogenic fungus that brings about wilt disease and great losses in cotton. The molecular mechanism of the effectors in V. dahliae regulating cotton immunity remains largely unknown. Here, we identified an effector of V. dahliae, VdPHB1, whose gene expression is highly induced by infection. The VdPHB1 protein is localized to the intercellular space of cotton plants. Knock-out of the VdPHB1 gene in V. dahliae had no effect on pathogen growth, but decreased the virulence in cotton. VdPHB1 ectopically expressed Arabidopsis plants were growth-inhibited and significantly susceptible to V. dahliae. Further, VdPHB1 interacted with the type II metacaspase GhMC4. GhMC4 gene-silenced cotton plants were more sensitive to V. dahliae with reduced expression of pathogen defense-related and programmed cell death genes. The accumulation of GhMC4 protein was concurrently repressed when VdPHB1 protein was expressed during infection. In summary, these results have revealed a novel molecular mechanism of virulence regulation that the secreted effector VdPHB1 represses the activity of cysteine protease for helping V. dahliae infection in cotton.

Inhibition of Verticillium Wilt in Cotton through the Application of Pseudomonas aeruginosa ZL6 Derived from Fermentation Residue of Kitchen Waste

To isolate and analyze bacteria with Verticillium wilt-resistant properties from the fermentation residue of kitchen wastes, as well as explore their potential for new applications of the residue. A total of six bacterial strains exhibiting Verticillium wilt-resistant capabilities were isolated from the biogas residue of kitchen waste fermentation. Using a polyphasic approach, strain ZL6, which displayed the highest antagonistic activity against cotton Verticillium wilt, was identified as belonging to the Pseudomonas aeruginosa. Bioassay results demonstrated that this strain possessed robust antagonistic abilities, effectively inhibiting V. dahliae spore germination and mycelial growth. Furthermore, P. aeruginosa ZL6 exhibited high temperature resistance (42°C), nitrogen fixation, and phosphorus removal activities. Pot experiments revealed that P. aeruginosa ZL6 fermentation broth treatment achieved a 47.72% biological control effect compared to the control group. Through activity tracking and protein mass spectrometry identification, a neutral metalloproteinase (Nml) was hypothesized as the main virulence factor. The mutant strain ZL6ΔNml exhibited a significant reduction in its ability to inhibit cotton Verticillium wilt compared to the strain P. aeruginosa ZL6. While the inhibitory activities could be partially restored by a complementation of nml gene in the mutant strain ZL6CMΔNml. This research provides a theoretical foundation for the future development and application of biogas residue as biocontrol agents against Verticillium wilt and as biological preservatives for agricultural products. Additionally, this study presents a novel approach for mitigating the substantial amount of biogas residue generated from kitchen waste fermentation.

The role of VdSti1 in Verticillium dahliae: insights into pathogenicity and stress responses

Sti1/Hop, a stress-induced co-chaperone protein, serves as a crucial link between Hsp70 and Hsp90 during cellular stress responses. Despite its importance in stress defense mechanisms, the biological role of Sti1 in Verticillium dahliae, a destructive fungal pathogen, remains largely unexplored. This study focused on identifying and characterizing Sti1 homologues in V. dahliae by comparing them to those found in Saccharomyces cerevisiae. The results indicated that the VdSti1-deficient mutant displayed increased sensitivity to drugs targeting the ergosterol synthesis pathway, leading to a notable inhibition of ergosterol biosynthesis. Moreover, the mutant exhibited reduced production of microsclerotia and melanin, accompanied by decreased expression of microsclerotia and melanin-related genes VDH1, Vayg1, and VaflM. Additionally, the mutant's conidia showed more severe damage under heat shock conditions and displayed growth defects under various stressors such as temperature, SDS, and CR stress, as well as increased sensitivity to H2O2, while osmotic stress did not impact its growth. Importantly, the VdSti1-deficient mutant demonstrated significantly diminished pathogenicity compared to the wild-type strain. This study sheds light on the functional conservation and divergence of Sti1 homologues in fungal biology and underscores the critical role of VdSti1 in microsclerotia development, stress response, and pathogenicity of V. dahliae.

Antimicrobial profile of the culturable olive sporobiota and its potential as a source of biocontrol agents for major phytopathogens in olive agriculture

BACKGROUND

The phytopathogens Xylella fastidiosa and Verticillium dahliae present an unparalleled threat to olive agriculture. However, there is no efficient field treatment available today for either pest. Spore-forming bacteria (i.e., the sporobiota) are known for their extraordinary resistance properties and antimicrobial activity. The aim of this study was thus to identify potential novel sustainable spore-forming biocontrol agents derived from the culturable olive microbiome, termed the sporobiota, in general and in particular against X. fastidiosa and V. dahliae.

RESULTS

We demonstrate the wide-ranging antimicrobial profile of 415 isolates from the culturable olive sporobiota towards human and plant pathogens. We further identified five candidates with antagonistic activity against X. fastidiosa and V. dahliae. These belong to the Bacillus subtilis, Bacillus cereus and Peribacillus simplex clade. The activity was related to the species and their relative origin (soil versus leaf endophytic). It is of particular interest that two of these candidates are already naturally present at the site of disease-development that is, plant interior. We further confirmed the presence of lipopeptide genes potentially associated with the reported bioactivity.

CONCLUSIONS

The study provides insights into how members of the olive sporobiota may support the olive plant to ward off detrimental pathogens. It further yields five promising candidates for the development of eco-friendly, multi-active biocontrol agents in olive agriculture. © 2023 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Microbiome-Mediated Protection against Pathogens in Woody Plants

Pathogens, especially invasive species, have caused significant global ecological, economic, and social losses in forests. Plant disease research has traditionally focused on direct interactions between plants and pathogens in an appropriate environment. However, recent research indicates that the microbiome can interact with the plant host and pathogens to modulate plant resistance or pathogen pathogenicity, thereby altering the outcome of plant-pathogen interactions. Thus, this presents new opportunities for studying the microbial management of forest diseases. Compared to parallel studies on human and crop microbiomes, research into the forest tree microbiome and its critical role in forest disease progression has lagged. The rapid development of microbiome sequencing and analysis technologies has resulted in the rapid accumulation of a large body of evidence regarding the association between forest microbiomes and diseases. These data will aid the development of innovative, effective, and environmentally sustainable methods for the microbial management of forest diseases. Herein, we summarize the most recent findings on the dynamic structure and composition of forest tree microbiomes in belowground and aboveground plant tissues (i.e., rhizosphere, endosphere, and phyllosphere), as well as their pleiotropic impact on plant immunity and pathogen pathogenicity, highlighting representative examples of biological control agents used to modulate relevant tree microbiomes. Lastly, we discuss the potential application of forest tree microbiomes in disease control as well as their future prospects and challenges.

Confronting stresses affecting olive cultivation from the holobiont perspective

The holobiont concept has revolutionized our understanding of plant-associated microbiomes and their significance for the development, fitness, growth and resilience of their host plants. The olive tree holds an iconic status within the Mediterranean Basin. Innovative changes introduced in olive cropping systems, driven by the increasing demand of its derived products, are not only modifying the traditional landscape of this relevant commodity but may also imply that either traditional or emerging stresses can affect it in ways yet to be thoroughly investigated. Incomplete information is currently available about the impact of abiotic and biotic pressures on the olive holobiont, what includes the specific features of its associated microbiome in relation to the host's structural, chemical, genetic and physiological traits. This comprehensive review consolidates the existing knowledge about stress factors affecting olive cultivation and compiles the information available of the microbiota associated with different olive tissues and organs. We aim to offer, based on the existing evidence, an insightful perspective of diverse stressing factors that may disturb the structure, composition and network interactions of the olive-associated microbial communities, underscoring the importance to adopt a more holistic methodology. The identification of knowledge gaps emphasizes the need for multilevel research approaches and to consider the holobiont conceptual framework in future investigations. By doing so, more powerful tools to promote olive's health, productivity and resilience can be envisaged. These tools may assist in the designing of more sustainable agronomic practices and novel breeding strategies to effectively face evolving environmental challenges and the growing demand of high quality food products.

Protein Kinase C Is Involved in Vegetative Development, Stress Response and Pathogenicity in Verticillium dahliae

Potato Verticillium wilt, caused by Verticillium dahliae, is a serious soil-borne vascular disease, which restricts the sustainable development of the potato industry, and the pathogenic mechanism of the fungus is complex. Therefore, it is of great significance to explore the important pathogenic factors of V. dahliae to expand the understanding of its pathology. Protein kinase C (PKC) gene is located in the Ca2+ signaling pathway, which is highly conserved in filamentous fungi and involved in the regulation of a variety of biological processes. In the current study, the PKC gene in V. dahliae (VdPKC) was characterized, and its effects on the fungal pathogenicity and tolerance to fungicide stress were further studied. The results showed that the VdPKC positively regulated the growth and development, conidial germination, and production of V. dahliae, which was necessary for the fungus to achieve pathogenicity. It also affected the formation of melanin and microsclerotia and changed the adaptability of V. dahliae to different environmental stresses. In addition, VdPKC altered the tolerance of V. dahliae to different fungicides, which may be a potential target for polyoxin. Therefore, our results strongly suggest that VdPKC gene is necessary for the vegetative growth, stress response, and pathogenicity of V. dahliae.

DeSUMOylation of a Verticillium dahliae enolase facilitates virulence by derepressing the expression of the effector VdSCP8

The soil-borne fungus Verticillium dahliae, the most notorious plant pathogen of the Verticillium genus, causes vascular wilts in a wide variety of economically important crops. The molecular mechanism of V. dahliae pathogenesis remains largely elusive. Here, we identify a small ubiquitin-like modifier (SUMO)-specific protease (VdUlpB) from V. dahliae, and find that VdUlpB facilitates V. dahliae virulence by deconjugating SUMO from V. dahliae enolase (VdEno). We identify five lysine residues (K96, K254, K259, K313 and K434) that mediate VdEno SUMOylation, and SUMOylated VdEno preferentially localized in nucleus where it functions as a transcription repressor to inhibit the expression of an effector VdSCP8. Importantly, VdUlpB mediates deSUMOylation of VdEno facilitates its cytoplasmic distribution, which allows it to function as a glycolytic enzyme. Our study reveals a sophisticated pathogenic mechanism of VdUlpB-mediated enolase deSUMOylation, which fortifies glycolytic pathway for growth and contributes to V. dahliae virulence through derepressing the expression of an effector.

Insights to Gossypium defense response against Verticillium dahliae: the Cotton Cancer

The soil-borne pathogen Verticillium dahliae, also referred as "The Cotton Cancer," is responsible for causing Verticillium wilt in cotton crops, a destructive disease with a global impact. To infect cotton plants, the pathogen employs multiple virulence mechanisms such as releasing enzymes that degrade cell walls, activating genes that contribute to virulence, and using protein effectors. Conversely, cotton plants have developed numerous defense mechanisms to combat the impact of V. dahliae. These include strengthening the cell wall by producing lignin and depositing callose, discharging reactive oxygen species, and amassing hormones related to defense. Despite the efforts to develop resistant cultivars, there is still no permanent solution to Verticillium wilt due to a limited understanding of the underlying molecular mechanisms that drive both resistance and pathogenesis is currently prevalent. To address this challenge, cutting-edge technologies such as clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9), host-induced gene silencing (HIGS), and gene delivery via nano-carriers could be employed as effective alternatives to control the disease. This article intends to present an overview of V. dahliae virulence mechanisms and discuss the different cotton defense mechanisms against Verticillium wilt, including morphophysiological and biochemical responses and signaling pathways including jasmonic acid (JA), salicylic acid (SA), ethylene (ET), and strigolactones (SLs). Additionally, the article highlights the significance of microRNAs (miRNAs), circular RNAs (circRNAs), and long non-coding RNAs (lncRNAs) in gene expression regulation, as well as the different methods employed to identify and functionally validate genes to achieve resistance against this disease. Gaining a more profound understanding of these mechanisms could potentially result in the creation of more efficient strategies for combating Verticillium wilt in cotton crops.

Systemic Colonization of Potato Plants by Verticillium dahliae Leads to Infection of Tubers and Sprouting Buds

A green fluorescent protein (GFP)-tagged isolate of Verticillium dahliae was used to study its colonization in potato plants and tubers. Three-week-old potato plants of the highly susceptible cultivar 'Shepody' were inoculated with a conidial suspension of a GFP-tagged isolate of V. dahliae using a wound inoculation method. Colonization was studied using confocal microscopy combined with tissue sections. Conidia germinated and hyphae grew along the root hairs, elongation zones, and root caps between 24 and 96 h postinoculation (HPI). At 7 days postinoculation (DPI), the pathogen advanced to cortical tissues and grew into the root vascular bundles. At 8 weeks postinoculation (WPI), the stem epidermal cells, cortical tissues, vascular elements, and petioles were fully colonized by the mycelium of V. dahliae. At 11 WPI, the pathogen was detected in the stolon and progeny tubers, as confirmed by both GFP signals in tissues and reisolation of the pathogen on the semiselective NP-10 medium. Progeny potato tubers were harvested from the inoculated potato plants, and the GFP-signal was observed in the epidermal cells and vascular elements of sprouting buds that emerged from the harvested tubers. The infection rate of progeny tubers detected on semiselective NP-10 medium ranged from 34.55 to 55.56%, with an average of 45.31%. In conclusion, we report, for the first time, the entire progression of colonization by V. dahliae in potato plant tissues, progeny tubers, as well as of the sprouting buds that emerged from progeny tubers.

The nonpathogenic strain of Fusarium oxysporum FO12 induces Fe deficiency responses in cucumber (Cucumis sativus L.) plants

MAIN CONCLUSION

FO12 strain enhances Fe deficiency responses in cucumber plants, probably through the production of ethylene and NO in the subapical regions of the roots. Rhizosphere microorganisms can elicit induced systemic resistance (ISR) in plants. This type of resistance involves complex mechanisms that confer protection to the plant against pathogen attack. Additionally, it has been reported by several studies that ISR and Fe deficiency responses are modulated by common pathways, involving some phytohormones and signaling molecules, like ethylene and nitric oxide (NO). The aim of this study was to determine whether the nonpathogenic strain of Fusarium oxysporum FO12 can induce Fe deficiency responses in cucumber (Cucumis sativus L.) plants. Our results demonstrate that the root inoculation of cucumber plants with the FO12 strain promotes plant growth after several days of cultivation, as well as rhizosphere acidification and enhancement of ferric reductase activity. Moreover, Fe-related genes, such as FRO1, IRT1 and HA1, are upregulated at certain times after FO12 inoculation either upon Fe-deficiency or Fe-sufficient conditions. Furthermore, it has been found that this fungus colonizes root cortical tissues, promoting the upregulation of ethylene synthesis genes and NO production in the root subapical regions. To better understand the effects of the FO12 strain on field conditions, cucumber plants were inoculated and cultivated in a calcareous soil under greenhouse conditions. The results obtained show a modification of some physiological parameters in the inoculated plants, such as flowering and reduction of tissue necrosis. Overall, the results suggest that the FO12 strain could have a great potential as a Fe biofertilizer and biostimulant.

VdERG2 was involved in ergosterol biosynthesis, nutritional differentiation and virulence of Verticillium dahliae

The ergosterol biosynthesis pathway plays an important role in model pathogenic bacteria Saccharomyces cerevisiae, but little is known about the biosynthesis of ergosterol in the pathogenic fungus Verticillium dahliae. In this study, we identified the VdERG2 gene encoding sterol C-8 isomerase from V. dahliae and investigated its function in virulence by generating gene deletion mutants (ΔVdERG2) and complemented mutants (C-ΔVdERG2). Knockout of VdERG2 reduced ergosterol content. The conidial germination rate and conidial yield of ΔVdERG2 significantly decreased and abnormal conidia were produced. In spite of VdERG2 did not affect the utilization of carbon sources by V. dahliae, but the melanin production of ΔVdERG2 was decreased in cellulose and pectin were used as the sole carbon sources. Furthermore, the ΔVdERG2 mutants produced less microsclerotia and melanin with a significant decrease in the expression of microsclerotia and melanin-related genes VaflM, Vayg1, VDH1, VdLAC, VdSCD and VT4HR. In addition, mutants ΔVdERG2 were very sensitive to congo red (CR), sodium dodecyl sulfate (SDS) and hydrogen peroxide (H₂O₂) stresses, indicating that VdERG2 was involved in the cell wall and oxidative stress response. The absence of VdERG2 weakened the penetration ability of mycelium on cellophane and affected the growth of mycelium. Although ΔVdERG2 could infect cotton, its pathogenicity was significantly impaired. These phenotypic defects in ΔVdERG2 could be complemented by the reintroduction of a full-length VdERG2 gene. In summary, as a single conservative secretory protein, VdERG2 played a crucial role in ergosterol biosynthesis, nutritional differentiation and virulence in V. dahliae.

Effect of volatile compounds produced by the cotton endophytic bacterial strain Bacillus sp. T6 against Verticillium wilt

BACKGROUND

Verticillium wilt, caused by the fungus Verticillium dahliae, leads to significant losses in cotton yield worldwide. Biocontrol management is a promising means of suppressing verticillium wilt. The purpose of the study was to obtain and analyze endophytic bacteria with Verticillium wilt-resistant activities from the roots of Gossypium barbadense 'Xinhai15' and to explore the interactions between the soil and plants.

RESULTS

An endophytic bacterium Bacillus sp. T6 was obtained from the Verticillium wilt-resistant cotton G. barbadense 'Xinhai15', which showed significant antagonistic abilities against cotton Verticillium wilt. The bioassay results indicated that the strain possessed strong antagonistic abilities that inhibited V. dahliae spore germination and mycelial growth without contact, and thus it was speculated that the active factor of the bacteria might be volatile compounds. A total of 46 volatile substances were detected via headspace solid-phase microextraction and gas chromatography-mass spectrometry analysis. The pure product verification experiment confirmed that the styrene produced by the T6 strain was the main virulence factor. Transcriptome analysis showed that following styrene induction, 247 genes in V. dahliae, including four hydrolase genes, eight dehydrogenase genes, 11 reductase genes, 17 genes related to transport and transfer were upregulated. Additionally, 72 genes, including two chitinase genes, two protease genes, five transport-related genes, and 33 hypothetical protein genes, were downregulated. The quantitative real-time PCR results confirmed that the expression of the four genes VDAG_02838, VDAG_09554, VDAG_045572, and VDAG_08251 was increased by 3.18, 78.83, 2.71, and 2.92 times, respectively, compared with the uninduced control group.

CONCLUSIONS

The research provides a new reference for the development and application of the volatile compounds of endophytic bacteria as new biocontrol agents for the control of Verticillium wilt and as biological preservatives for agricultural products.

Avoidant/resistant rather than tolerant olive rootstocks are more effective in controlling Verticillium wilt

The identification of rootstocks of low susceptibility to Verticillium dahliae can become a valuable procedure to achieve effective control of Verticillium wilt in the olive grove. This not only involves the identification of suitable genotypes, but also the study of the interaction between the rootstock and the grafted scion. Thus, a rootstock that prevents or minimizes V. dahliae proliferation (avoidance/resistance strategy) can have very different effects on a susceptible scion compared to a rootstock that shows few or no symptoms despite being infected (tolerance strategy). Both resistance and tolerance mechanisms have been recently identified in wild olive genotypes with low susceptibility to V. dahliae. When used as rootstocks of the highly susceptible variety 'Picual', we found that resistant genotypes, including the cultivar 'Frantoio', were more effective than tolerant genotypes in controlling Verticillium wilt. Furthermore, tolerant genotypes were as ineffective as susceptible or extremely susceptible genotypes in controlling Verticillium wilt. We also identified rootstock-scion combinations with behaviours that were not expected according to the degree of susceptibility previously observed in the non-grafted rootstock. Although the rootstocks were able to control Verticillium wilt according to its degree of susceptibility to V. dahliae, the ability to control the infection was not adequately transferred to the grafted scion. Our results confirmed that: the degree of susceptibility to Verticillium wilt of an olive variety does not predict its performance as a rootstock; to use a very low susceptible genotype as rootstock of a susceptible scion increases the susceptibility of the genotype used as rootstock; in any case, avoidant/resistant rootstocks are more effective than tolerant rootstocks in reducing the susceptibility of the grafted plant to V. dahliae.

Physiological and Structural Responses of Olive Leaves Related to Tolerance/Susceptibility to Verticillium dahliae

Verticillium wilt of olive (VWO), caused by the soil borne fungus Verticillium dahliae, is one of the most relevant diseases affecting this crop worldwide. One of the best VWO management strategies is the use of tolerant cultivars. Scarce information is available about physiological and structural responses in the leaves of olive cultivars displaying different levels of tolerance to VWO. To identify links between this phenotype and variations in functional characteristics of the leaves, this study examined the structural and physiological traits and the correlations among them in different olive varieties. This evaluation was conducted in the presence/absence of V. dahliae. On the one hand, no leaf trait but the area was related to VWO tolerance in the absence of the pathogen. On the other hand, after inoculation, susceptible cultivars showed lower leaf area and higher leaf mass per area and dry matter content. Furthermore, at the physiological level, these plants showed severe symptoms resembling water stress. Analyzing the relationships among physiological and structural traits revealed differences between tolerant and susceptible cultivars both in the absence and in the presence of V. dahliae. These results showed that olive leaves of VWO-tolerant and VWO-susceptible cultivars adopt different strategies to cope with the pathogen.

Physiochemical responses of Ailanthus altissima under the challenge of Verticillium dahliae: elucidating the decline of one of the world’s worst invasive alien plant species

Natural infections of Verticillium spp. (Fungi, Ascomycota) on Ailanthus altissima have suggested to consider the biological control as a promising strategy to counteract this invasive plant, which is otherwise difficult to control by traditional mechanical and chemical treatments. Verticillium wilt is able to lead plants to death, throughout a pathogenic mechanism including vessel occlusions and production of degrading enzymes and phytotoxins. In this study, a 10 weeks open air pot experiment was set to investigate the ecophysiological and biochemical responses of Ailanthus trees artificially inoculated in the trunk with the V. dahliae strain VdGL16, previously isolated in Central Italy from the same host. Inoculated plants showed visible injuries starting from 2 weeks post inoculation (wpi), that progressively developed until a final severe defoliation. The fungal infection rapidly compromised the plant water status, and photosynthesis was impaired due to both stomatal and mesophyll limitations from 4 wpi, with subsequent detrimental effects also on PSII activity. Moreover, the disease altered the translocations of nutrients, as confirmed by cation and carbohydrate contents, probably due to a consumption of simple sugars and starch reserves without replacement of new photosynthesized. An accumulation of osmolytes (abscisic acid and proline) and phenylalanine (a precursor of phenylpropanoids) was also reported at 8 wpi, this being a response mechanism that needs to be further elucidated. However, the activation delay of such defence strategy inevitably did not avoid the premature defoliation of plants and the decline of physiochemical parameters, confirming the key role of Verticillium in Ailanthus decay.

Pseudomonas spp. Enriched in Endophytic Community of Healthy Cotton Plants Inhibit Cotton Verticillium Wilt

The plant microbiome plays a fundamental role in plant growth and health. However, detailed information regarding the plant endophytic microbiome during the infection period of a pathogen is largely unknown. Here, we investigated the microbial community of healthy and diseased cotton plants and the root exudate profiles of susceptible and resistant cultivars utilizing high-throughput sequencing and metabolomics. The results showed that the pathogen infection reduced bacterial diversity and significantly affected the bacterial community composition. The microbiome assembly is shaped predominantly by cultivars. The endophytic microbiome of the infected plants showed greater complexity than the healthy plants in network analysis. The results displayed that a total of 76 compounds were significantly different in the two groups, with 18 compounds showing a higher relative abundance in the resistant cultivars and 58 compounds in the susceptible cultivars. Pathway enrichment analysis showed that pathways related to plant hormone signal transduction, biosynthesis of various secondary metabolites, and biosynthesis and metabolism of amino acids were prominently altered. We also demonstrate that plants inoculated with Pseudomonas sp. strains showed increased resistance to the cotton Verticillium wilt compared with the control plants in pot experiments. Overall, it showed that the pathogen infection affected the community composition, and healthy plants displayed an enriched beneficial microbiome to combat the plant disease. These findings significantly advance our understanding of the endophytic microbiome assembly under the pathogen infection and develop microbiome-based solutions for sustainable crop production systems.

Understanding the Role of PIN Auxin Carrier Genes under Biotic and Abiotic Stresses in Olea europaea L

The PIN-FORMED (PIN) proteins represent the most important polar auxin transporters in plants. Here, we characterized the PIN gene family in two olive genotypes, the Olea europaea subsp. europaea var. sylvestris and the var. europaea (cv. ‘Farga’). Twelve and 17 PIN genes were identified for vars. sylvestris and europaea, respectively, being distributed across 6 subfamilies. Genes encoding canonical OePINs consist of six exons, while genes encoding non-canonical OePINs are composed of five exons, with implications at protein specificities and functionality. A copia-LTR retrotransposon located in intron 4 of OePIN2b of var. europaea and the exaptation of partial sequences of that element as exons of the OePIN2b of var. sylvestris reveals such kind of event as a driving force in the olive PIN evolution. RNA-seq data showed that members from the subfamilies 1, 2, and 3 responded to abiotic and biotic stress factors. Co-expression of OePINs with genes involved in stress signaling and oxidative stress homeostasis were identified. This study highlights the importance of PIN genes on stress responses, contributing for a holistic understanding of the role of auxins in plants.

Identification of Volatile Organic Compounds Emitted by Two Beneficial Endophytic Pseudomonas Strains from Olive Roots

The production of volatile organic compounds (VOCs) represents a promising strategy of plant-beneficial bacteria to control soil-borne phytopathogens. Pseudomonas sp. PICF6 and Pseudomonas simiae PICF7 are two indigenous inhabitants of olive roots displaying effective biological control against Verticillium dahliae. Additionally, strain PICF7 is able to promote the growth of barley and Arabidopsis thaliana, VOCs being involved in the growth of the latter species. In this study, the antagonistic capacity of these endophytic bacteria against relevant phytopathogens (Verticillium spp., Rhizoctonia solani, Sclerotinia sclerotiorum and Fusarium oxysporum f.sp. lycopersici) was assessed. Under in vitro conditions, PICF6 and PICF7 were only able to antagonize representative isolates of V. dahliae and V. longisporum. Remarkably, both strains produced an impressive portfolio of up to twenty VOCs, that included compounds with reported antifungal (e.g., 1-undecene, (methyldisulfanyl) methane and 1-decene) or plant growth promoting (e.g., tridecane, 1-decene) activities. Moreover, their volatilomes differed strongly in the absence and presence of V. dahliae. For example, when co incubated with the defoliating pathotype of V. dahliae, the antifungal compound 4-methyl-2,6-bis(2-methyl-2-propanyl)phenol was produced. Results suggest that volatiles emitted by these endophytes may differ in their modes of action, and that potential benefits for the host needs further investigation in planta.

Functional Traits of Olive Varieties and Their Relationship with the Tolerance Level towards Verticillium Wilt

Verticillium wilt of olive (VWO), caused by the soil-borne pathogen Verticillium dahliae, is considered one of the most important diseases affecting this tree crop. One of the best VWO management measures is the use of tolerant cultivars. Remarkably, no information is available about olive functional traits and their potential relationship with tolerance to V. dahliae. Twenty-five selected functional traits (for leaf, stem, root and whole plant) were evaluated in six olive varieties differing in their VWO tolerance level to identify possible links between this phenotype and functional traits’ variation. High intervarietal diversity was found among cultivars and several functional traits were related with VWO tolerance. Tolerant varieties showed higher leaf area, dry matter content (leaf, stem and plant) and mass fraction for stems, but lower for leaves. Significant differences were also detected for root functional traits, tolerant cultivars displaying larger fine root diameter and lignin content but smaller specific length and area of thick and fine roots. Correlations were found among functional traits both within varieties and between levels of tolerance/susceptibility to VWO. Associations were observed between biomass allocation, dry matter content and VWO tolerance. The most relevant difference between tolerant and susceptible cultivars was related to root system architecture.

Verticillium wilt resistant and susceptible olive cultivars express a very different basal set of genes in roots

BACKGROUND

Olive orchards are threatened by a wide range of pathogens. Of these, Verticillium dahliae has been in the spotlight for its high incidence, the difficulty to control it and the few cultivars that has increased tolerance to the pathogen. Disease resistance not only depends on detection of pathogen invasion and induction of responses by the plant, but also on barriers to avoid the invasion and active resistance mechanisms constitutively expressed in the absence of the pathogen. In a previous work we found that two healthy non-infected plants from cultivars that differ in V. dahliae resistance such as 'Frantoio' (resistant) and 'Picual' (susceptible) had a different root morphology and gene expression pattern. In this work, we have addressed the issue of basal differences in the roots between Resistant and Susceptible cultivars.

RESULTS

The gene expression pattern of roots from 29 olive cultivars with different degree of resistance/susceptibility to V. dahliae was analyzed by RNA-Seq. However, only the Highly Resistant and Extremely Susceptible cultivars showed significant differences in gene expression among various groups of cultivars. A set of 421 genes showing an inverse differential expression level between the Highly Resistant to Extremely Susceptible cultivars was found and analyzed. The main differences involved higher expression of a series of transcription factors and genes involved in processes of molecules importation to nucleus, plant defense genes and lower expression of root growth and development genes in Highly Resistant cultivars, while a reverse pattern in Moderately Susceptible and more pronounced in Extremely Susceptible cultivars were observed.

CONCLUSION

According to the different gene expression patterns, it seems that the roots of the Extremely Susceptible cultivars focus more on growth and development, while some other functions, such as defense against pathogens, have a higher expression level in roots of Highly Resistant cultivars. Therefore, it seems that there are constitutive differences in the roots between Resistant and Susceptible cultivars, and that susceptible roots seem to provide a more suitable environment for the pathogen than the resistant ones.

Assessing the Involvement of Selected Phenotypes of Pseudomonas simiae PICF7 in Olive Root Colonization and Biological Control of Verticillium dahliae

Pseudomonas simiae PICF7 is an indigenous inhabitant of the olive (Olea europaea L.) rhizosphere/root endosphere and an effective biocontrol agent against Verticillium wilt of olive (VWO), caused by the soil-borne fungus Verticillium dahliae. This study aimed to evaluate the potential involvement of selected phenotypes of strain PICF7 in root colonization ability and VWO biocontrol. Therefore, a random transposon-insertion mutant bank of P. simiae PICF7 was screened for the loss of phenotypes likely involved in rhizosphere/soil persistence (copper resistance), root colonization (biofilm formation) and plant growth promotion (phytase activity). Transposon insertions in genes putatively coding for the transcriptional regulator CusR or the chemotaxis protein CheV were found to affect copper resistance, whereas an insertion in fleQ gene putatively encoding a flagellar regulatory protein hampered the ability to form a biofilm. However, these mutants displayed the same antagonistic effect against V. dahliae as the parental strain. Remarkably, two mutants impaired in biofilm formation were never found inside olive roots, whereas their ability to colonize the root exterior and to control VWO remained unaffected. Endophytic colonization of olive roots was unaltered in mutants impaired in copper resistance and phytase production. Results demonstrated that the phenotypes studied were irrelevant for VWO biocontrol.

Biological Control of Verticillium Wilt on Olive Trees by the Salt-Tolerant Strain Bacillus velezensis XT1

Verticillium wilt, caused by the pathogen Verticillium dahliae, is extremely devastating to olive trees (Olea europea). Currently, no successful control measure is available against it. The objective of this work was to evaluate the antifungal activity of Bacillus velezensis XT1, a well-characterized salt-tolerant biocontrol strain, against the highly virulent defoliating V. dahliae V024. In vitro, strain XT1 showed to reduce fungal mycelium from 34 to 100%, depending on if the assay was conducted with the supernatant, volatile compounds, lipopeptides or whole bacterial culture. In preventive treatments, when applied directly on young olive trees, it reduced Verticillium incidence rate and percentage of severity by 54 and ~80%, respectively. It increased polyphenol oxidase (PPO) activity by 395%, indicating an enhancement of disease resistance in plant tissues, and it decreased by 20.2% the number of fungal microsclerotia in soil. In adult infected trees, palliative inoculation of strain XT1 in the soil resulted in a reduction in Verticillium symptom severity by ~63%. Strain XT1 is biosafe, stable in soil and able to colonize olive roots endophytically. All the traits described above make B. velezensis XT1 a promising alternative to be used in agriculture for the management of Verticillium wilt.

The Role of Microbial Inoculants on Plant Protection, Growth Stimulation, and Crop Productivity of the Olive Tree (Olea europea L.)

The olive tree (Olea europaea L.) is an emblematic, long-living fruit tree species of profound economic and environmental importance. This study is a literature review of articles published during the last 10 years about the role of beneficial microbes [Arbuscular Mycorrhizal Fungi (AMF), Plant Growth Promoting Rhizobacteria (PGPR), Plant Growth Promoting Fungi (PGPF), and Endophytes] on olive tree plant growth and productivity, pathogen control, and alleviation from abiotic stress. The majority of the studies examined the AMF effect using mostly Rhizophagus irregularis and Glomus mosseae species. These AMF species stimulate the root growth improving the resistance of olive plants to environmental and transplantation stresses. Among the PGPR, the nitrogen-fixing bacteria Azospirillum sp. and potassium- and phosphorous-solubilizing Bacillus sp. species were studied extensively. These PGPR species were combined with proper cultural practices and improved considerably olive plant’s growth. The endophytic bacterial species Pseudomonas fluorescens and Bacillus sp., as well as the fungal species Trichoderma sp. were identified as the most effective biocontrol agents against olive tree diseases (e.g., Verticillium wilt, root rot, and anthracnose).

Verticillium Wilt of Olive and its Control: What Did We Learn during the Last Decade?

Verticillium (Verticillium dahliae Kleb.) wilt is one of the most devastating diseases affecting olive (Olea europaea L. subsp. europaea var. europaea) cultivation. Its effective control strongly relies on integrated management strategies. Olive cultivation systems are experiencing important changes (e.g., high-density orchards, etc.) aiming at improving productivity. The impact of these changes on soil biology and the incidence/severity of olive pests and diseases has not yet been sufficiently evaluated. A comprehensive understanding of the biology of the pathogen and its populations, the epidemiological factors contributing to exacerbating the disease, the underlying mechanisms of tolerance/resistance, and the involvement of the olive-associated microbiota in the tree's health is needed. This knowledge will be instrumental to developing more effective control measures to confront the disease in regions where the pathogen is present, or to exclude it from V. dahliae-free areas. This review compiles the most recent advances achieved to understand the olive-V. dahliae interaction as well as measures to control the disease. Aspects such as the molecular basis of the host-pathogen interaction, the identification of new biocontrol agents, the implementation of "-omics" approaches to unravel the basis of disease tolerance, and the utilization of remote sensing technology for the early detection of pathogen attacks are highlighted.

Management of Verticillium Wilt of Avocado Using Tolerant Rootstocks

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.

An Overview of the Molecular Genetics of Plant Resistance to the Verticillium Wilt Pathogen Verticillium dahliae

Verticillium dahliae is a soil-borne hemibiotrophic fungus that can lead to plant vascular disease and significant economic loss worldwide. Its hosts include over 400 dicotyledon plant species, such as annual herbs, perennials, and woody plants. The average yield loss of cotton crop caused by Verticillium wilt is approximately 10–35%. As the control of this disease is an urgent task for many countries, further understanding of the interaction between plants and V. dahliae is essential. Fungi can promote or inhibit plant growth, which is important; however, the most important relationship between plants and fungi is the host–pathogen relationship. Plants can become resistant to V. dahliae through diverse mechanisms such as cell wall modifications, extracellular enzymes, pattern recognition receptors, transcription factors, and salicylic acid (SA)/jasmonic acid (JA)/ethylene (ET)-related signal transduction pathways. Over the last decade, several studies on the physiological and molecular mechanisms of plant resistance to V. dahliae have been undertaken. In this review, many resistance-related genes are summarised to provide a theoretical basis for better understanding of the molecular genetic mechanisms of plant resistance to V. dahliae. Moreover, it is intended to serve as a resource for research focused on the development of genetic resistance mechanisms to combat Verticillium wilt.

Effect of Cultivar Resistance and Soil Management on Spatial-Temporal Development of Verticillium Wilt of Olive: A Long-Term Study

Verticillium wilt, caused by Verticillium dahliae, challenges olive cultivation and an Integrated Disease Management (IDM) approach is the best-suited tool to combat it. Since 1998, an IDM strategy in an orchard (called Granon, Spain) of the susceptible cv. Picual was conducted by increasing planting density with moderately resistant cv. Frantoio, chemical weed control, and replanting of dead olives with cv. Frantoio following soil solarization. The Verticillium wilt epidemic in Granon orchard was compared to the epidemic in a non-IDM orchard (called Ancla, Spain) with plowed soil and dead Picual olives replanted with the same cultivar. Field evaluations (2012-2013) showed an incidence and severity of the disease as Picual-Ancla > Picual-Granon > Frantoio-Granon. The spatiotemporal dynamics of the Verticillium epidemics from 1998 to 2010 were monitored with digital images using SIG. The annual tree mortalities were 5.6% for Picual olives in Ancla orchard, and 3.1 and 0.7% for Picual and Frantoio olives in Granon orchard, respectively. There was a negative relationship between the mortality of olive trees (%) by the pathogen and the height (m) above sea level. The annual mortality of cv. Picual olives was positively correlated with spring rainfalls. The Index of Dispersion and beta-binomial distribution showed aggregation of Verticillium-dead olives. In conclusion, this IDM strategy considerably reduced the disease in comparison with traditional agronomic practices.

The Transcriptome of Verticillium dahliae Responds Differentially Depending on the Disease Susceptibility Level of the Olive (Olea europaea L.) Cultivar

Among biotic constraints affecting olive trees cultivation worldwide, the soil-borne fungus Verticillium dahliae is considered one of the most serious threats. Olive cultivars display differential susceptibility to the disease, but our knowledge on the pathogen’s responses when infecting varieties differing in susceptibility is scarce. A comparative transcriptomic analysis (RNA-seq) was conducted in olive cultivars Picual (susceptible) and Frantoio (tolerant). RNA samples originated from roots during the first two weeks after inoculation with V. dahliae defoliating (D) pathotype. Verticillium dahliae mRNA amount was overwhelmingly higher in roots of the susceptible cultivar, indicating that proliferation of pathogen biomass is favored in ‘Picual’. A significant larger number of V. dahliae unigenes (11 fold) were only induced in this cultivar. Seven clusters of differentially expressed genes (DEG) were identified according to time-course expression patterns. Unigenes potentially coding for niche-adaptation, pathogenicity, virulence and microsclerotia development were induced in ‘Picual’, while in ‘Frantoio’ expression remained negligible or null. Verticillium dahliae D pathotype transcriptome responses are qualitatively and quantitatively different, and depend on cultivar susceptibility level. The much larger V. dahliae biomass found in ‘Picual’ roots is a consequence of both host and pathogen DEG explaining, to a large extent, the higher aggressiveness exerted over this cultivar.

Use of RGB Vegetation Indexes in Assessing Early Effects of Verticillium Wilt of Olive in Asymptomatic Plants in High and Low Fertility Scenarios

Verticillium Wilt of Olive, a disease caused by the hemibiotrophic vascular fungus Verticillium dahliae Kleb. presents one of the most important constraints to olive production in the world, with an especially notable impact in Mediterranean agriculture. This study evaluates the use of RGB vegetation indexes in assessing the effects of this disease during the biotrophic phase of host-pathogen interaction, in which symptoms of wilt are not yet evident. While no differences were detected by measuring stomatal conductance and chlorophyll fluorescence, results obtained from RGB indexes showed significant differences between control and inoculated plants for indexes Saturation, a*, b*, green Area (GA), normalized green-red difference index (NGRDI) and triangular greenness index (TGI), presenting a reduction in plant growth as well as in green and yellow color components as an effect of inoculation. These results were contrasted across two scenarios of mineral fertilization in soil and soil amended with two different olive mill waste composts, presenting a clear interaction between the host-pathogen relationship and plant nutrition and suggesting the effect of V. dahliae infection during the biotrophic phase was not related to plant water status.

Screening of bacterial isolates related to olive orchard pests in Tunisia using 16S ribosomal RNA and evaluation of their biotechnological potential

AIM

This study investigated the bacterial diversity of dead insects collected from olive tree orchards widely cultivated in Tunisia. We aimed to explore metabolic diversity, screen enzymatic activities for biotechnological applications and carry out preliminary bioassays for bio-insecticide development.

METHODS AND RESULTS

A total of 50 bacteria strains were randomly isolated from four different biotopes situated in Sfax (Tunisia). 16S rRNA gene sequencing was used to identify 24 species, and isolates were evaluated for enzymatic activity and antimicrobial potential. Nineteen of the total number of Bacillus strains have enzymatic activity compared to strains from the other genera (14/50). Our bacterial collection was evaluated for antimicrobial potential against bacterial and fungal isolates. Isolates B8-2 (Bacillus subtilis) showed strong antibacterial activities and isolates B2-3 (Bacillus licheniformis) and B10-1 (Serratia marcescens) showed the highest antifungal activity. Seventeen of the total number of isolates caused greater than 50% mortality rate of second and fourth instar larvae of Ephestia kuehniella.

CONCLUSION

The selected species from olive orchards represent a broad spectrum of antimicrobial and insecticidal activities and can be considered promising resources in biological control.

SIGNIFICANCE AND IMPACT OF THE STUDY

Bacteria isolated from olive pests in olive orchards were investigated for detecting their potential biotechnological applications.

Visualization of the impatiens downy mildew pathogen using fluorescence in situ hybridization (FISH)

BACKGROUND

Plasmopara obducens is the biotrophic oomycete responsible for impatiens downy mildew, a destructive disease of Impatiens that causes high crop loss. Currently, there are no available methods for the microscopic detection of P. obducens from leaves of impatiens, which may be contributing to the spread of the disease. Fluorescence in situ hybridization (FISH) is a sensitive and robust method that uses sequence-specific, fluorescence-labeled oligonucleotide probes to detect target organisms from the environment. To study this important pathogen, we developed and standardized a FISH technique for the visualization of P. obducens from Impatiens walleriana tissues using a species-specific 24-mer oligonucleotide probe designed to target a region of the rRNA internal transcribed spacer 2 (ITS2).

RESULTS

Since P. obducens cannot be propagated in vitro, we developed a custom E. coli expression vector that transcribes the P. obducens rRNA-ITS target sequence (clone-FISH) for use as a control and to optimize hybridization conditions. The FISH assay could detect P. obducens sporangiophores, sporangia and oospores, and hyphae from naturally infected I. walleriana leaves and stems. Cross-reactivity was not observed from plant tissue, and the assay did not react when applied to E. coli with self-ligated plasmids and non-target oomycete species.

CONCLUSIONS

This FISH protocol may provide a valuable tool for the study of this disease and could potentially be used to improve early monitoring of P. obducens, substantially reducing the persistence and spread of this destructive plant pathogen.

Belowground Microbiota and the Health of Tree Crops

Trees are crucial for sustaining life on our planet. Forests and land devoted to tree crops do not only supply essential edible products to humans and animals, but also additional goods such as paper or wood. They also prevent soil erosion, support microbial, animal, and plant biodiversity, play key roles in nutrient and water cycling processes, and mitigate the effects of climate change acting as carbon dioxide sinks. Hence, the health of forests and tree cropping systems is of particular significance. In particular, soil/rhizosphere/root-associated microbial communities (known as microbiota) are decisive to sustain the fitness, development, and productivity of trees. These benefits rely on processes aiming to enhance nutrient assimilation efficiency (plant growth promotion) and/or to protect against a number of (a)biotic constraints. Moreover, specific members of the microbial communities associated with perennial tree crops interact with soil invertebrate food webs, underpinning many density regulation mechanisms. This review discusses belowground microbiota interactions influencing the growth of tree crops. The study of tree-(micro)organism interactions taking place at the belowground level is crucial to understand how they contribute to processes like carbon sequestration, regulation of ecosystem functioning, and nutrient cycling. A comprehensive understanding of the relationship between roots and their associate microbiota can also facilitate the design of novel sustainable approaches for the benefit of these relevant agro-ecosystems. Here, we summarize the methodological approaches to unravel the composition and function of belowground microbiota, the factors influencing their interaction with tree crops, their benefits and harms, with a focus on representative examples of Biological Control Agents (BCA) used against relevant biotic constraints of tree crops. Finally, we add some concluding remarks and suggest future perspectives concerning the microbiota-assisted management strategies to sustain tree crops.

Characterization of two homeodomain transcription factors with critical but distinct roles in virulence in the vascular pathogen Verticillium dahliae

Vascular wilt caused by Verticillium dahliae is a destructive disease that represents a chronic economic problem for crop production worldwide. In this work, we characterized two new regulators of pathogenicity in this species. Vph1 (VDAG_06555) was identified in a candidate gene approach as a putative homologue of the transcription factor Ste12. Vhb1 (VDAG_08786), identified in a forward genetics approach, is similar to the homeobox transcription factor Htf1, reported as a regulator of conidiogenesis in several fungi. Deletion of vph1 did not affect vegetative growth, whereas deletion of vhb1 greatly reduced sporulation rates in liquid medium. Both mutants failed to induce Verticillium wilt symptoms. However, unlike Δvph1, Δvhb1 could be re-isolated from the vascular system of some asymptomatic plants. Confocal microscopy further indicated that Δvph1 and Δvhb1 differed in their behaviour in planta; Δvph1 could not penetrate the root cortex, whereas Δvhb1 was impaired in its ability to colonize the xylem. In agreement with these observations, only Δvhb1 could penetrate cellophane paper. On cellophane, wild-type and Δvhb1 strains produced numerous short branches with swollen tips, resembling the hyphopodia formed on root surfaces, contrasting with Δvph1, which generated unbranched long filaments without swollen tips. A microarray analysis showed that these differences in growth were associated with differences in global transcription patterns, and allowed us to identify a large set of novel genes potentially involved in virulence in V. dahliae. Ste12 homologues are known regulators of invasive growth, but Vhb1 is the first putative Htf1 homologue identified with a critical role in virulence.

On the origins and domestication of the olive: a review and perspectives

Background

Unravelling domestication processes is crucial for understanding how species respond to anthropogenic pressures, forecasting crop responses to future global changes and improving breeding programmes. Domestication processes for clonally propagated perennials differ markedly from those for seed-propagated annual crops, mostly due to long generation times, clonal propagation and recurrent admixture with local forms, leading to a limited number of generations of selection from wild ancestors. However, additional case studies are required to document this process more fully.

Scope

The olive is an iconic species in Mediterranean cultural history. Its multiple uses and omnipresence in traditional agrosystems have made this species an economic pillar and cornerstone of Mediterranean agriculture. However, major questions about the domestication history of the olive remain unanswered. New paleobotanical, archeological, historical and molecular data have recently accumulated for olive, making it timely to carry out a critical re-evaluation of the biogeography of wild olives and the history of their cultivation. We review here the chronological history of wild olives and discuss the questions that remain unanswered, or even unasked, about their domestication history in the Mediterranean Basin. We argue that more detailed ecological genomics studies of wild and cultivated olives are crucial to improve our understanding of olive domestication. Multidisciplinary research integrating genomics, metagenomics and community ecology will make it possible to decipher the evolutionary ecology of one of the most iconic domesticated fruit trees worldwide.

Conclusion

The olive is a relevant model for improving our knowledge of domestication processes in clonally propagated perennial crops, particularly those of the Mediterranean Basin. Future studies on the ecological and genomic shifts linked to domestication in olive and its associated community will provide insight into the phenotypic and molecular bases of crop adaptation to human uses.

Indigenous Pseudomonas spp. Strains from the Olive (Olea europaea L.) Rhizosphere as Effective Biocontrol Agents against Verticillium dahliae: From the Host Roots to the Bacterial Genomes

The use of biological control agents (BCA), alone or in combination with other management measures, has gained attention over the past decades, driven by the need to seek for sustainable and eco-friendly alternatives to confront plant pathogens. The rhizosphere of olive (Olea europaea L.) plants is a source of bacteria with potential as biocontrol tools against Verticillium wilt of olive (VWO) caused by Verticillium dahliae Kleb. A collection of bacterial isolates from healthy nursery-produced olive (cultivar Picual, susceptible to VWO) plants was generated based on morphological, biochemical and metabolic characteristics, chemical sensitivities, and on their in vitro antagonistic activity against several olive pathogens. Three strains (PIC25, PIC105, and PICF141) showing high in vitro inhibition ability of pathogens' growth, particularly against V. dahliae, were eventually selected. Their effectiveness against VWO caused by the defoliating pathotype of V. dahliae was also demonstrated, strain PICF141 being the rhizobacteria showing the best performance as BCA. Genotypic and phenotypic traits traditionally associated with plant growth promotion and/or biocontrol abilities were evaluated as well (e.g., phytase, xylanase, catalase, cellulase, chitinase, glucanase activities, and siderophore and HCN production). Multi-locus sequence analyses of conserved genes enabled the identification of these strains as Pseudomonas spp. Strain PICF141 was affiliated to the “Pseudomonas mandelii subgroup,” within the “Pseudomonas fluorescens group,” Pseudomonas lini being the closest species. Strains PIC25 and PIC105 were affiliated to the “Pseudomonas aeruginosa group,” Pseudomonas indica being the closest relative. Moreover, we identified P. indica (PIC105) for the first time as a BCA. Genome sequencing and in silico analyses allowed the identification of traits commonly associated with plant-bacteria interactions. Finally, the root colonization ability of these olive rhizobacteria was assessed, providing valuable information for the future development of formulations based on these strains. A set of actions, from rhizosphere isolation to genome analysis, is proposed and discussed for selecting indigenous rhizobacteria as effective BCAs.

Tolerance of olive (Olea europaea) cv Frantoio to Verticillium dahliae relies on both basal and pathogen-induced differential transcriptomic responses

Verticillium wilt of olive (VWO) is one of the most serious biotic constraints for this tree crop. Our knowledge of the genetics of the tolerance/resistance to this disease is very limited. Here we show that tolerance of the cv Frantoio relies on both basal and early pathogen-induced differential transcriptomic responses. A comparative transcriptomic analysis (RNA-seq) was conducted in root tissues of cvs Frantoio (VWO-tolerant) and Picual (VWO-susceptible). RNA samples originated from roots of inoculated olive plants during the early infection stages by Verticillium dahliae (highly virulent, defoliating pathotype). A huge number of differentially expressed genes (DEGs) were found between 'Frantoio' and 'Picual' (27 312 unigenes) in the absence of the pathogen. Upon infection with V. dahliae, 'Picual' and 'Frantoio' plants responded differently too. In the early infection stages, four clusters of DEGs could be identified according to their time-course expression patterns. Among others, a pathogenesis-related protein of the Bet v I family and a dirigent-like protein involved in lignification, and several BAK1, NHL1, reactive oxygen species stress response and BAM unigenes showed noticeable differences between cultivars. Tolerance of 'Frantoio' plants to VWO is a consequence of a complex and multifaceted process which involves many plant traits.

Desirable Traits of a Good Biocontrol Agent against Verticillium Wilt

The soil-borne fungus Verticillium causes serious vascular disease in a wide variety of annual crops and woody perennials. Verticillium wilt is notoriously difficult to control by conventional methods, so there is great potential for biocontrol to manage this disease. In this study we aimed to review the research about Verticillium biocontrol to get a better understanding of characteristics that are desirable in a biocontrol agent (BCA) against Verticillium wilt. We only considered studies in which the BCAs were tested on plants. Most biocontrol studies were focused on plants of the Solanaceae, Malvaceae, and Brassicaceae and within these families eggplant, cotton, and oilseed rape were the most studied crops. The list of bacterial BCAs with potential against Verticillium was dominated by endophytic Bacillus and Pseudomonas isolates, while non-pathogenic xylem-colonizing Verticillium and Fusarium isolates topped the fungal list. Predominant modes of action involved in biocontrol were inhibition of primary inoculum germination, plant growth promotion, competition and induced resistance. Many BCAs showed in vitro antibiosis and mycoparasitism but these traits were not correlated with activity in vivo and there is no evidence that they play a role in planta. Good BCAs were obtained from soils suppressive to Verticillium wilt, disease suppressive composts, and healthy plants in infested fields. Desirable characteristics in a BCA against Verticillium are the ability to (1) affect the survival or germination of microsclerotia, (2) colonize the xylem and/or cortex and compete with the pathogen for nutrients and/or space, (3) induce resistance responses in the plant and/or (4) promote plant growth. Potential BCAs should be screened in conditions that resemble the field situation to increase the chance of successful use in practice. Furthermore, issues such as large scale production, formulation, preservation conditions, shelf life, and application methods should be considered early in the process of selecting BCAs against Verticillium.

The Verticillium-specific protein VdSCP7 localizes to the plant nucleus and modulates immunity to fungal infections

Fungal pathogens secrete effector proteins to suppress plant basal defense for successful colonization. Resistant plants, however, can recognize effectors by cognate R proteins to induce effector-triggered immunity (ETI). By analyzing secretomes of the vascular fungal pathogen Verticillium dahliae, we identified a novel secreted protein VdSCP7 that targets the plant nucleus. The green fluorescent protein (GFP)-tagged VdSCP7 gene with either a mutated nuclear localization signal motif or with additional nuclear export signal was transiently expressed in Nicotiana benthamiana, and investigated for induction of plant immunity. The role of VdSCP7 in V. dahliae pathogenicity was characterized by gene knockout and complementation, and GFP labeling. Expression of the VdSCP7 gene in N. benthamiana activated both salicylic acid and jasmonate signaling, and altered the plant's susceptibility to the pathogens Botrytis cinerea and Phytophthora capsici. The immune response activated by VdSCP7 was highly dependent on its initial extracellular secretion and subsequent nuclear localization in plants. Knockout of the VdSCP7 gene significantly enhanced V. dahliae aggressiveness on cotton. GFP-labeled VdSCP7 is secreted by V. dahliae and accumulates in the plant nucleus. We conclude that VdSCP7 is a novel effector protein that targets the host nucleus to modulate plant immunity, and suggest that plants can recognize VdSCP7 to activate ETI during fungal infection.

Selection and evaluation of micro-organisms for biocontrol of Verticillium dahliae in olive

AIMS

To identify potential biological control agents against Verticillium wilt in olive through a mass screening approach.

METHOD AND RESULTS

A total of 47 strains and nine mixtures of micro-organisms were evaluated against Verticillium dahliae in a three stage screening: (i) in vitro, by the effect on the mycelial growth and spore germination of the pathogen; (ii) in natural infested soil, by the effect on the reduction of microsclerotia of the pathogen; (iii) in planta, by the effect on the infection of olive plants under controlled conditions. Various fungal and bacterial strains and mixtures inhibited the pathogen and showed consistent biocontrol activity against Verticillium wilt of olive.

CONCLUSION

The screening has resulted in promising fungi and bacteria strains with antagonistic activity against Verticillium, such as two non-pathogenic Fusarium oxysporum, one Phoma sp., one Pseudomonas fluorescens and two mixtures of micro-organisms that may possess multiple modes of action.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study provides a practical basis for the potential use of selected strains as biocontrol agents for the protection of olive plants against V. dahliae infection. In addition, our study presented an effective method to evaluate antagonistic micro-organisms of V. dahliae in olive.

Pseudomonas fluorescens PICF7 displays an endophytic lifestyle in cultivated cereals and enhances yield in barley

Pseudomonas fluorescens PICF7, an indigenous inhabitant of olive roots, displays an endophytic lifestyle in this woody crop and exerts biocontrol against the fungal phytopathogen Verticillium dahliae Here we report microscopy evidence that the strain PICF7 is also able to colonize and persist on or in wheat and barley root tissues. Root colonization of both cereal species followed a similar pattern to that previously reported in olive, including inner colonization of the root hairs. This demonstrates that strain PICF7 can colonize root systems of distant botanical species. Barley plants germinated from PICF7-treated seeds showed enhanced vegetative growth. Moreover, significant increases in the number of grains (up to 19.5%) and grain weight (up to 20.5%) per plant were scored in this species. In contrast, growth and yield were not significantly affected in wheat plants by the presence of PICF7. Proteomics analysis of the root systems revealed that different proteins were exclusively found depending on the presence or absence of PICF7 and only one protein with hydrogen ion transmembrane transporter activity was exclusively found in both PICF7-inoculated barley and wheat plants but not in the controls.

Amplicon-based metagenomics identified candidate organisms in soils that caused yield decline in strawberry

A phenomenon of yield decline due to weak plant growth in strawberry was recently observed in non-chemo-fumigated soils, which was not associated with the soil fungal pathogen Verticillium dahliae, the main target of fumigation. Amplicon-based metagenomics was used to profile soil microbiota in order to identify microbial organisms that may have caused the yield decline. A total of 36 soil samples were obtained in 2013 and 2014 from four sites for metagenomic studies; two of the four sites had a yield-decline problem, the other two did not. More than 2000 fungal or bacterial operational taxonomy units (OTUs) were found in these samples. Relative abundance of individual OTUs was statistically compared for differences between samples from sites with or without yield decline. A total of 721 individual comparisons were statistically significant - involving 366 unique bacterial and 44 unique fungal OTUs. Based on further selection criteria, we focused on 34 bacterial and 17 fungal OTUs and found that yield decline resulted probably from one or more of the following four factors: (1) low abundance of Bacillus and Pseudomonas populations, which are well known for their ability of supressing pathogen development and/or promoting plant growth; (2) lack of the nematophagous fungus (Paecilomyces species); (3) a high level of two non-specific fungal root rot pathogens; and (4) wet soil conditions. This study demonstrated the usefulness of an amplicon-based metagenomics approach to profile soil microbiota and to detect differential abundance in microbes.

Arabidopsis thaliana as a tool to identify traits involved in Verticillium dahliae biocontrol by the olive root endophyte Pseudomonas fluorescens PICF7

The effective management of Verticillium wilts (VW), diseases affecting many crops and caused by some species of the soil-borne fungus Verticillium, is problematic. The use of microbial antagonists to control these pathologies fits modern sustainable agriculture criteria. Pseudomonas fluorescens PICF7 is an endophytic bacterium isolated from olive roots with demonstrated ability to control VW of olive caused by the highly virulent, defoliating (D) pathotype of Verticillium dahliae Kleb. However, the study of the PICF7-V. dahliae-olive tripartite interaction poses difficulties because of the inherent characteristics of woody, long-living plants. To overcome these problems we explored the use of the model plant Arabidopsis thaliana. Results obtained in this study showed that: (i) olive D and non-defoliating V. dahliae pathotypes produce differential disease severity in A. thaliana plants; (ii) strain PICF7 is able to colonize and persist in the A. thaliana rhizosphere but is not endophytic in Arabidopsis; and (iii) strain PICF7 controls VW in Arabidopsis. Additionally, as previously observed in olive, neither swimming motility nor siderophore production by PICF7 are required for VW control in A. thaliana, whilst cysteine auxotrophy decreased the effectiveness of PICF7. Moreover, when applied to the roots PICF7 controlled Botrytis cinerea infection in the leaves of Arabidopsis, suggesting that this strain is able to induce systemic resistance. A. thaliana is therefore a suitable alternative to olive bioassays to unravel biocontrol traits involved in biological control of V. dahliae by P. fluorescens PICF7.

Plant genotype-specific archaeal and bacterial endophytes but similar Bacillus antagonists colonize Mediterranean olive trees

Endophytes have an intimate and often symbiotic interaction with their hosts. Less is known about the composition and function of endophytes in trees. In order to evaluate our hypothesis that plant genotype and origin have a strong impact on both, endophytes of leaves from 10 Olea europaea L. cultivars from the Mediterranean basin growing at a single agricultural site in Spain and from nine wild olive trees located in natural habitats in Greece, Cyprus, and on Madeira Island were studied. The composition of the bacterial endophytic communities as revealed by 16S rRNA gene amplicon sequencing and the subsequent PCoA analysis showed a strong correlation to the plant genotypes. The bacterial distribution patterns were congruent with the plant origins in "Eastern" and "Western" areas of the Mediterranean basin. Subsequently, the endophytic microbiome of wild olives was shown to be closely related to those of cultivated olives of the corresponding geographic origins. The olive leaf endosphere harbored mostly Proteobacteria, followed by Firmicutes, Actinobacteria, and Bacteroidetes. The detection of a high portion of archaeal taxa belonging to the phyla Thaumarchaeota, Crenarchaeota, and Euryarchaeota in the amplicon libraries was an unexpected discovery, which was confirmed by quantitative real-time PCR revealing an archaeal portion of up to 35.8%. Although the function of these Archaea for their host plant remains speculative, this finding suggests a significant relevance of archaeal endophytes for plant-microbe interactions. In addition, the antagonistic potential of culturable endophytes was determined; all isolates with antagonistic activity against the olive-pathogenic fungus Verticillium dahliae Kleb. belong to Bacillus amyloliquefaciens. In contrast to the specific global structural diversity, BOX-fingerprints of the antagonistic Bacillus isolates were highly similar and independent of the olive genotype from which they were isolated.