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Background Despite their importance as a reservoir of biodiversity, the factors shaping soil microbial communities and the extent by which these are impacted by cultivation are still poorly understood. Using 16S rRNA gene and ITS sequencing, we characterized the soil microbiota of vineyards and of neighboring permanent grassland soils in the Italian province of Trentino, and correlated their structure and composition to location, chemical properties of the soil, and land management. Results Bacterial communities had a core of conserved taxa accounting for more than 60% of the reads of each sample, that was influenced both by geography and cultivation. The core fungal microbiota was much smaller and dominated by geography alone. Cultivation altered the structure and composition of the soil microbiota both for bacteria and fungi, with site-specific effects on their diversity. The diversity of bacterial and fungal communities was generally inversely correlated across locations. We identified several taxa that were impacted by the chemical properties and texture of the soil. Conclusions Our results highlight the different responses of bacterial and fungal communities to environmental factors and highlight the need to characterize both components of the soil microbiota to fully understand the factors that drive their variability.

Despite the increasing interest in using microbial-based technologies to support human space exploration, many unknowns remain not only on bioprocesses but also on microbial survivability and genetic stability under non-Earth conditions. Here the desert cyanobacterium Chroococcidiopsis sp. CCMEE 029 was investigated for robustness of the repair capability of DNA lesions accumulated under Mars-like conditions (UV radiation and atmosphere) simulated in low Earth orbit using the EXPOSE-R2 facility installed outside the International Space Station. Genomic alterations were determined in a space-derivate of Chroococcidiopsis sp. CCMEE 029 obtained upon reactivation on Earth of the space-exposed cells. Comparative analysis of whole-genome sequences showed no increased variant numbers in the space-derivate compared to triplicates of the reference strain maintained on the ground. This result advanced cyanobacteria-based technologies to support human space exploration.

We present a draft assembly of the genome of European pear (Pyrus communis) `Bartlett'. Our assembly was developed employing second generation sequencing technology (Roche 454), from single-end, 2 kb, and 7 kb insert paired-end reads using Newbler (version 2.7). It contains 142,083 scaffolds greater than 499 bases (maximum scaffold length of 1.2 Mb) and covers a total of 577.3 Mb, representing most of the expected 600 Mb Pyrus genome. A total of 829,823 putative single nucleotide polymorphisms (SNPs) were detected using re-sequencing of `Louise Bonne de Jersey' and `Old Home'. A total of 2,279 genetically mapped SNP markers anchor 171 Mb of the assembled genome. Ab initio gene prediction combined with prediction based on homology searching detected 43,419 putative gene models. Of these, 1219 proteins (556 clusters) are unique to European pear compared to 12 other sequenced plant genomes. Analysis of the expansin gene family provided an example of the quality of the gene prediction and an insight into the relationships among one class of cell wall related genes that control fruit softening in both European pear and apple (Malusxdomestica). The `Bartlett' genome assembly v1.0 (http://www.rosaceae.org/species/pyrus/pyrus_communis/genome_v1.0) is an invaluable tool for identifying the genetic control of key horticultural traits in pear and will enable the wide application of marker-assisted and genomic selection that will enhance the speed and efficiency of pear cultivar development.

CRISPR/Cas9 genome editing is a modern biotechnological approach used to improve plant varieties, modifying only one or a few traits of a specific variety. However, this technology cannot be easily used to improve fruit quality traits in citrus, due to the lack of knowledge of key genes, long juvenile stage, and the difficulty regenerating whole plants of specific varieties. Here, we introduce a genome editing approach with the aim of producing citrus plantlets whose fruits contain both lycopene and anthocyanins. Our method employs a dual single guide RNA (sgRNA)-directed genome editing approach to knockout the fruit-specific β-cyclase 2 gene, responsible for the conversion of lycopene to beta-carotene. The gene is targeted by two sgRNAs simultaneously to create a large deletion, as well as to induce point mutations in both sgRNA targets. The EHA105 strain of Agrobacterium tumefaciens was used to transform five different anthocyanin-pigmented sweet oranges, belonging to the Tarocco and Sanguigno varietal groups, and ‘Carrizo’ citrange, a citrus rootstock as a model for citrus transformation. Among 58 plantlets sequenced in the target region, 86% of them were successfully edited. The most frequent mutations were deletions (from -1 to -74 nucleotides) and insertions (+1 nucleotide). Moreover, a novel event was identified in six plantlets, consisting of the inversion of the region between the two sgRNAs. For 20 plantlets in which a single mutation occurred, we excluded chimeric events. Plantlets did not show an altered phenotype in vegetative tissues. To the best of our knowledge, this work represents the first example of the use of a genome editing approach to potentially improve qualitative traits of citrus fruit.

Summary Blueberries are critical for food production due to their widespread consumption and nutritional value. Beyond agriculture, wild Vaccinium species play essential ecological roles, including supporting pollinators and enhancing soil health. This dual importance underscores their relevance to both food security and ecosystem sustainability. The fruit-associated microbiome, both internal and surface-dwelling, includes a wide range of microorganisms. These microbial communities play a dual role: they influence fruit quality (e.g., taste, texture, shelf life) and are also involved in the degradation processes that occur during fruit senescence or postharvest storage.”. Despite their importance, the specific factors shaping the microbiomes of blueberry fruits, as well as their relationship with other above-ground parts of the plant and their stability over different years, remain poorly understood. We conducted a field experiment to characterize the taxonomic composition of fungal and bacterial communities colonizing the leaves and the surface and pulp of fruits on a collection of 10 different cultivars of blueberry over two years. Independently from the sampling time, pulp of the fruit, surface and leaves harbor specific and distinct microbiomes. A major factor determining the microbiome of blueberry fruits and leaves was plant cultivar, followed by tissue. We further identified the core microbiome for each plant tissue and demonstrated that core taxa account for the dominant fraction of the microbiota of each plant. As trade and production of blueberries is expanding, our results provide a foundation for advancing the development of targeted microbiome management strategies, with potential applications in enhancing plant health and productivity.

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Plasmopara viticola is the causal agent of grapevine downy mildew (DM). DM resistant varieties deploy effector-triggered immunity (ETI) to inhibit pathogen growth, which is activated by major resistance loci, the most common of which are Rpv3 and Rpv12 . We previously showed that a quick metabolome response lies behind the ETI conferred by Rpv3 TIR-NB-LRR genes. Here we used a grape variety operating Rpv12 -mediated ETI, which is conferred by an independent locus containing CC-NB-LRR genes, to investigate the defence response using GC/MS, UPLC, UHPLC and RNA-Seq analyses. Eighty-eight metabolites showed significantly different concentration and 432 genes showed differential expression between inoculated resistant leaves and controls. Most metabolite changes in sugars, fatty acids and phenols were similar in timing and direction to those observed in Rpv3 -mediated ETI but some of them were stronger or more persistent. Activators, elicitors and signal transducers for the formation of reactive oxygen species were early observed in samples undergoing Rpv12 -mediated ETI and were paralleled and followed by the upregulation of genes belonging to ontology categories associated with salicylic acid signalling, signal transduction, WRKY transcription factors and synthesis of PR-1, PR-2, PR-5 pathogenesis-related proteins.

‘Glera’ and ‘Ribolla Gialla’ are the most economically relevant local grapevine cultivars of Friuli Venezia Giulia region (north-eastern Italy). ‘Glera’ is used to produce the world-renowned Prosecco wine. ‘Ribolla Gialla’ cultivation is constantly increasing due to the strong demand for sparkling wine and is the most important variety in Brda (Slovenia). Knowledge of local varieties history in terms of migration and pedigree relationships has scientific and marketing appeal. Following prospections, genotyping and ampelographic characterization of minor germplasm in Friuli Venezia Giulia, a further research was developed to understand the parentage relationships among the grapevine varieties grown in this region. An integrated strategy was followed combining the analysis of nuclear and chloroplast microsatellites with the Vitis 18k SNP chip. Two main recurrent parents were found, which can be regarded as “founders”: ‘Vulpea’, an Austrian variety parent-offspring related with at least ten Friuli Venezia Giulia cultivars, among them ‘Glera’, and ‘Refosco Nostrano’, first degree related with other six Friuli Venezia Giulia varieties. ‘Ribolla Gialla’ was shown to be another member of the impressively long list of offspring derived from the prolific ‘Heunisch Weiss’. Combining molecular markers and historical references was a high-performance strategy for retracing and adjusting the history of cultivars.

Context: Diabetes is reported as a risk factor for severe COVID-19, but whether this risk is similar in all categories of age remains unclear.Objective: To investigate the risk of severe COVID-19 outcomes in hospitalized patients with and without diabetes according to age categories.Design setting and participants: We conducted a retrospective observational cohort study of 6,314 consecutive patients hospitalized for COVID-19 between February and June 30 2020, and follow-up recorded until 30 September 2020, in the Paris metropolitan area, France.Main outcome measure(s): The main outcome was a composite outcome of mortality and orotracheal intubation in subjects with diabetes compared with subjects without diabetes, after adjustment for confounding variables and according to age categories.Results: Diabetes was recorded in 39% of subjects. Main outcome was higher in patients with diabetes, independently of confounding variables (HR 1.13 [1.03-1.24]) and increased with age in individuals without diabetes, from 23% for those <50 to 35% for those >80 years but reached a plateau after 70 in those with diabetes. In direct comparison between patients with and without diabetes, diabetes-associated risk was inversely proportional to age, highest in <50 and similar after 70 years. Similarly, mortality was higher in patients with diabetes (26%) than in those without diabetes (22%, p<0.001), but adjusted HR for diabetes was significant only in patients under 50 (HR 1.81 [1.14-2.87]).Conclusions: Diabetes should be considered as an independent risk factor for the severity of COVID-19 in young adults more so than in older adults, especially for individuals younger than 70 years.