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Quinoa is an expanding crop in southern Spain. Downy mildew, caused by Peronospora variabilis, is the most important quinoa disease in Spain and worldwide. In Spain, this disease has also been observed on the weed Chenopodium album. The objectives of this study were to unravel the origin of the P. variabilis isolates currently infecting quinoa in southern Spain and to study their genetic diversity. We hypothesized that P. variabilis isolates infecting quinoa in Spain could have been introduced through the seeds of the quinoa varieties currently grown in the country or, alternatively, that these isolates are endemic isolates, originally infecting C. album, that jumped to quinoa. In order to test these hypotheses, we sequenced the internal transcribed spacer (ITS), cytochrome c oxidase subunit 1 (cox1), and cox2 regions of 33 P. variabilis isolates infecting C. quinoa and C. album in southern Spain and analyzed their phylogenetic relationship with isolates present in other countries infecting Chenopodium spp. cox1 gene sequences from all of the Spanish P. variabilis isolates were identical and exhibited nine single-nucleotide polymorphisms (SNPs) compared with a single P. variabilis cox1 sequence found at GenBank. Phylogenetic analyses based on the ITS ribosomal DNA region were not suitable to differentiate isolates according to their geographical origin or host. The cox2 sequences from P. variabilis Spanish isolates collected from C. quinoa and C. album were all identical and had a distinctive SNP in the last of four polymorphic sites that distinguished Spanish isolates from isolates from other countries. These results suggest that P. variabilis infecting quinoa in southern Spain could be native isolates that originally infected C. album. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY 4.0 International license .

This work was funded by the United States Department of Agriculture–Agricultural Research Service appropriated project 2034-22000-012-00D and the Xylella fastidiosa Active Containment Through a Multidisciplinary-Oriented Research Strategy (XF-ACTORS) project. Illumina sequencing for BB08-1 was carried out at the University of California, Davis, Genome Center DNA Technologies and Expression Analysis Cores, supported by National Institute of Health Shared Instrumentation Grant 1S10OD010786-01.

The plant pathogenic bacterium Xylella fastidiosa (Xf) is a major threat to agriculture and the environment worldwide. Recent devastating outbreaks in Europe highlight the potential of this pathogen to cause emergent diseases. Xf subsp. multiplex ESVL and IVIA5901 strains that belong to sequence type (ST) 6 were isolated from almond orchards within the outbreak area in Alicante province (Spain). Both strains share more than 99% of the chromosomal sequences), but the ESVL strain harbours two plasmids (pXF64-Hb_ESVL and pUCLA-ESVL). Here, virulence phenotypes and genome content were compared between both strains, using three strains from USA as a reference for the phenotypic analyses. Experiments in microfluidic chambers, used as simulation of xylem vessels, showed that twitching motility was absent in the IVIA5901 strain, while the ESVL strain had reduced twitching motility. Both Spanish strains had less biofilm formation, cell aggregation and lower virulence in tobacco compared with USA reference strains. Genome analysis of the two plasmids from ESVL revealed 51 unique coding sequences (CDS) that were absent in the chromosome of IVIA5901. Comparison of the chromosomes of both strains showed some unique CDS and SNPs in each strain with potential deleterious mutations. Genomic differences found in genes previously associated with adhesion and motility might explain the differences in the phenotypic traits studied. Although additional studies are necessary to infer the potential role of Xf plasmids, our results indicate that the presence of plasmids should be considered in the study of the mechanisms of pathogenicity and adaptation in Xf to new environments.

The plant pathogenic bacterium Xylella fastidiosa (Xf) is a major threat to agriculture and the environment worldwide. Recent devastating outbreaks in Europe highlight the potential of this pathogen to cause emergent diseases. Xf subsp. multiplex ESVL and IVIA5901 strains that belong to sequence type (ST) 6 were isolated from almond orchards within the outbreak area in Alicante province (Spain). Both strains share more than 99% of the chromosomal sequences), but the ESVL strain harbours two plasmids (pXF64-Hb_ESVL and pUCLA-ESVL). Here, virulence phenotypes and genome content were compared between both strains, using three strains from USA as a reference for the phenotypic analyses. Experiments in microfluidic chambers, used as simulation of xylem vessels, showed that twitching motility was absent in the IVIA5901 strain, while the ESVL strain had reduced twitching motility. Both Spanish strains had less biofilm formation, cell aggregation and lower virulence in tobacco compared with USA reference strains. Genome analysis of the two plasmids from ESVL revealed 51 unique coding sequences (CDS) that were absent in the chromosome of IVIA5901. Comparison of the chromosomes of both strains showed some unique CDS and SNPs in each strain with potential deleterious mutations. Genomic differences found in genes previously associated with adhesion and motility might explain the differences in the phenotypic traits studied. Although additional studies are necessary to infer the potential role of Xf plasmids, our results indicate that the presence of plasmids should be considered in the study of the mechanisms of pathogenicity and adaptation in Xf to new environments.

Trabajo desarrollado bajo la financiación del proyecto “Soil Hydrology research platform underpinning innovation to manage water scarcity in European and Chinese cropping Systems” (773903), coordinado por José Alfonso Gómez Calero, investigador del Instituto de Agricultura Sostenible (IAS)., Among the agricultural practices promoted by the Common Agricultural Policy to increase soil functions, the use of cover crops is a recommended tool to improve the sustainability of Mediterranean woody crops such as olive orchards. However, there is a broad range of cover crop typologies in relation to its implementation, control and species composition. In that sense, the influence of different plant species on soil quality indicators in olive orchards remains unknown yet. This study describes the effects of four treatments based on the implementation of different ground covers (CC-GRA: sown cover crop with gramineous, CC-MIX: sown cover crop with a mixture of species and CC-NAT: cover crop with spontaneous vegetation) and conventional tillage (TILL) on soil erosion, soil physicochemical and biological properties after 8 years of cover crop establishment. Our results demonstrated that the presence of a temporary cover crop (CC), compared to a soil under tillage (TILL), can reduce soil losses and maintain good soil physicochemical properties and modify greatly the structure and diversity of soil bacterial communities and its functioning. The presence of a homogeneous CC of gramineous (Lolium rigidum or Lolilum multiflorum) (CC-GR) for 8 years increased the functional properties of the soil as compared to TILL; although the most relevant change was a modification on the bacterial community composition that was clearly different from the rest of treatments. On the other hand, the use of a mixture of plant species (CC-MIX) as a CC for only two years although did not modify greatly the structure and diversity of soil bacterial communities compared to the TILL soil, induced significant changes on the functional properties of the soil and reverted those properties to a level similar to that of an undisturbed soil that had maintained a natural cover of spontaneous vegetation for decades (CC-NAT)., This work was supported by the EU SoilMan project (grant number 01LC1620) funded through the 2015–2016 BiodivERsA COFUND call for research proposals, with national funds through PCIN-2016-048 project by the Spanish Ministry of Economy and Competitiveness (MINECO), SHui project (GA 773903), and by projects PID2019-105793RB-I00, AGL2008-00344 from ‘Ministerio de Ciencia e Innovación’, AGL-2012–37521 from ‘Ministerio de Economia y Competitividad’ of Spain, Project P10-AGR-5908 from ‘Consejería de Economía, Innovación y Ciencia’ Junta de Andalucía, and FEDER financial support from the European Union.

The introduction of temporary grassland into an annual crop rotation is recognized to improve soil ecosystem services, and resulting legacies can be beneficial for the following crops. In this context, the aim of the present study was to evaluate legacy effects of introducing temporary grassland into an annual crop rotation on five ecosystem services (i) soil structure maintenance (aggregate stability), (ii) water regulation (saturated hydraulic conductivity), (iii) biodiversity conservation (microbial biomass and microbial metabolic activity, as well as microorganism, enchytraeid, springtail and earthworm communities), (iv) pathogen regulation (soil suppressiveness to Verticillium dahliae), and (v) forage production and quality. Three crop rotation schemes, maintained for twelve years, were compared in four random blocks, one being an annual crop rotation without grassland (0%), another with a medium percentage of grassland (50%, corresponding to 3 years of continuous grassland in the crop rotation), and a third one with a high percentage of grassland in the crop rotation (75%, corresponding to 6 years of continuous grassland in the crop rotation). The results showed that the grassland introduction into an annual crop rotation improved, whatever the duration of the grassland, soil structure maintenance and biodiversity conservation, while it decreased pathogen regulation and did not modify water regulation. Comparing the two crop rotations that included grassland, indicated a stronger beneficial grassland legacy effect for the higher proportion of grassland concerning soil structure maintenance and biodiversity conservation. By contrast, water regulation, pathogen regulation and forage production were not affected by the legacy of the 75% grassland during the rotation. Overall, our findings demonstrated the extent to which grassland legacies are affecting the current state of soil properties and possible ecosystem services provided. To improve ecosystem services, soil management should take legacy effects into account and consider longer timeframes to apply beneficial practices., This work was supported by the EU SoilMan project (grant number 01LC1620) funded through the 2015–2016 BiodivERsA COFUND call for research proposals, with national funders the Federal Ministry of Education and Research (BMBF), the French National Research Agency (ANR), the Swedish Research Council for Environment, Agricultural Sciences and Spatial Planning (FORMAS), the Spanish Ministry of Economy and Competitiveness (MINECO), the Executive Agency for Higher Education, Research, Development and Innovation Funding (UEFISCDI), the European Regional Development Fund (Centre of Excellence EcolChange). We would like to thank the National Research Infrastructure “Agro-écosystèmes, Cycles Biogéochimique et Biodiversité” (ACBB) http://www.soere-acbb for providing access to an excellent field experiment and the “the AnaEE France (ANR-11-INBS-0001)”, “AllEnvi” and “CNRS-INSU” which support it. We thank Météo France for meteorological data.

This article belongs to the Special Issue Role of Human Interventions in Spread of Soilborne Forest Pathogens and Methods for Mitigation., Disease outbreaks caused by introduced Phytophthora species have been increasing in British forests and woodlands in recent years. A better knowledge of the Phytophthora communities already present in the UK is of great importance when developing management and mitigation strategies for these diseases. To do this, soils were sampled in “disturbed” sites, meaning sites frequently visited by the public, with recent and new plantings or soil disturbances versus more “natural” forest and woodland sites with little disturbance or management. Phytophthora diversity was assessed using high-throughput Illumina sequencing targeting the widely accepted barcoding Internal Transcribed Spacer 1 (ITS1) region of rRNA and comparing it with the mitochondrial cytochrome c oxidase I (COI) gene. Isolation of Phytophthora was run in parallel. Nothophytophthora spp. and Phytophthora spp. were detected in 79 and 41 of the 132 locations of the 14 studied sites when using ITS or COI, respectively. A total of 20 Phytophthora amplicon sequence variants (ASVs) were assigned to known Phytophthora species from eight clades (1a, 2, 2b, 3a, 5, 6b, 7a, 8b, 8c, 8d, 10a, and 10b) and 12 ASVs from six clades (1a, 2c, 3a, 3b, 6b, 7a, 8b, 8c, and 8d) when using ITS or COI, respectively. Only at two locations were the results in agreement for ITS, COI, and isolation. Additionally, 21 and 17 unknown Phytophthora phylotypes were detected using the ITS and COI, respectively. Several Phytophthora spp. within clades 7 and 8, including very important forest pathogens such as P. austrocedri and P. ramorum, were identified and found more frequently at “disturbed” sites. Additionally, eight ASVs identified as Nothophytophthora spp. were detected representing the first report of species within this new genus in Britain. Only three species not known to be present in Britain (P. castaneae, P. capsici, and P. fallax) were detected with the ITS primers and not with COI. To confirm the presence of these or any potential new Phytophthora species, sites should be re-sampled for confirmation. Additionally, there is a need to confirm if these species are a threat to British trees and try to establish any eradication measures required to mitigate Phytophthora spread in Britain., This work has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 635646, POnTE (Pest Organisms Threatening Europe).

[Background]: The olive tree is of particular economic interest in the Mediterranean basin. Researchers have conducted several studies on one of the most devastating disorders affecting this tree, the Verticillium wilt, which causes substantial economic losses in numerous areas. We analyzed metatranscriptomic samples taken from a previous study conducted on leaves and roots of Olea europaea that were infected with Verticillium dahliae. In addition, we also analyzed mechanically damaged roots. The aim of our approach is to describe the dynamics of the root microbiome after severe perturbations., [Results]: Our results not only describe the dynamics of the microbial community associated with the disturbance, but also show the high complexity of these systems and explain how this can lead to a conflicting assignment of the various types of parasitism observed in a specific organism., [Conclusions]: Our findings indicate that this infection, although led by Verticillium, is driven not by a single species, but by a polymicrobial consortium that also includes natural endophytes of the olive tree. This community contains both biotrophic and necrotrophic organisms that alternate and live together during the infection. In addition, opportunistic organisms appear that take profit not from plant tissues, but from new emerging populations of microorganisms. Therefore, this system can be described as a complex biological system composed of different interacting communities. Notably, our work has important considerations when it comes to classifying the type of parasitism of a given species.

The olive tree is of particular economic interest in the Mediterranean basin. Researchers have conducted several studies on one of the most devastating disorders affecting this tree, the Verticillium wilt of olive, which causes significant economic damage in numerous areas of this crop. We have analyzed the temporal metagenomic samples of a transcriptomic study in Olea europaea roots and leaves after root-damage and after a root Verticillium dahliae infection (Jimenez-Ruiz et al. 2017). Our results indicate that this infection, although led by Verticillium, is driven not by a single species but by a polymicrobial community, including their natural endophytes, which acts as a consortium in the attack to the host plant. This community includes both biotrophic and necrotrophic organisms that alternate and live together during the infection. Our results not only describe how the microbial community progresses along these processes, but also explain the high complexity of these systems, that in turn, could justify at least in part the occasional changes and disparity found at the time of classifying the kind of parasitism of a determined organism.

Xylella fastidiosa is an economically important plant pathogenic bacterium of global importance associated, since 2013, with a devastating epidemic in olive trees in Italy. Since then, several outbreaks of this pathogen have been reported in other European member countries including Spain, France, and Portugal. In Spain, the three major subspecies (subsp. fastidiosa, multiplex, and pauca) of the bacterium have been detected in the Balearic Islands, but only subspecies multiplex in the mainland (Alicante). We present the first complete genome sequences of two Spanish strains: X. fastidiosa subsp. fastidiosa IVIA5235 from Mallorca and X. fastidiosa subsp. multiplex IVIA5901 from Alicante, using Oxford Nanopore and Illumina sequence reads, and two hybrid approaches for genome assembly. These completed genomes will provide a resource to better understand the biology of these X. fastidiosa strains., This work was funded by European Union’s Horizon 2020 Framework Research Programme Projects XF-ACTORS (Xylella fastidiosa Active Containment Through a Multidisciplinary Oriented Research Strategy grant 727987) and POnTE (Pest Organisms Threatening Europe grant 635646), and Desarrollo de estrategias de erradicación, contención y control de Xylella fastidiosa en España: Diagnóstico, estructura genética y gama de huéspedes (Project E-RTA2017-00004-C06-02) from Programa Estatal de I+D+I Orientada a los Retos de la Sociedad of the Spanish Government and COST Action CA16107 EuroXanth supported by European Cooperation in Science and Technology.e