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      Trunk Surgery as a Tool to Reduce Foliar Symptoms in Diseases of the Esca Complex and Its Influence on Vine Wood Microbiota

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          Abstract

          In the last few years, trunk surgery has gained increasing attention as a method to reduce foliar symptoms typical of some of the Esca complex diseases. The technique relies on the mechanical removal of decayed wood by a chainsaw. A study on a 14-year-old Cabernet Sauvignon vineyard was carried out to validate the efficacy of trunk surgery and explore possible explanations behind it. Three levels of treatment were applied to three of the most characteristic symptoms associated with some diseases of the Esca complex, such as leaf stripe symptoms (LS), wilted shoots (WS) and apoplexy (APP). The most promising results were obtained by complete trunk surgery, where the larger decay removal allowed lower symptom re-expression. According to the wood types analyzed (decay, medium and sound wood), different changes in microbiota were observed. Alpha-diversity generally decreased for bacteria and increased for fungi. More specifically, main changes were observed for Fomitiporia mediterranea abundance that decreased considerably after trunk surgery. A possible explanation for LS symptom reduction after trunk surgery could be the microbiota shifting caused by the technique itself affecting a microbic-shared biochemical pathway involved in symptom expression.

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          UCHIME improves sensitivity and speed of chimera detection

          Motivation: Chimeric DNA sequences often form during polymerase chain reaction amplification, especially when sequencing single regions (e.g. 16S rRNA or fungal Internal Transcribed Spacer) to assess diversity or compare populations. Undetected chimeras may be misinterpreted as novel species, causing inflated estimates of diversity and spurious inferences of differences between populations. Detection and removal of chimeras is therefore of critical importance in such experiments. Results: We describe UCHIME, a new program that detects chimeric sequences with two or more segments. UCHIME either uses a database of chimera-free sequences or detects chimeras de novo by exploiting abundance data. UCHIME has better sensitivity than ChimeraSlayer (previously the most sensitive database method), especially with short, noisy sequences. In testing on artificial bacterial communities with known composition, UCHIME de novo sensitivity is shown to be comparable to Perseus. UCHIME is >100× faster than Perseus and >1000× faster than ChimeraSlayer. Contact: robert@drive5.com Availability: Source, binaries and data: http://drive5.com/uchime. Supplementary information: Supplementary data are available at Bioinformatics online.
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            World Map of the Köppen-Geiger climate classification updated

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              The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications

              Abstract UNITE (https://unite.ut.ee/) is a web-based database and sequence management environment for the molecular identification of fungi. It targets the formal fungal barcode—the nuclear ribosomal internal transcribed spacer (ITS) region—and offers all ∼1 000 000 public fungal ITS sequences for reference. These are clustered into ∼459 000 species hypotheses and assigned digital object identifiers (DOIs) to promote unambiguous reference across studies. In-house and web-based third-party sequence curation and annotation have resulted in more than 275 000 improvements to the data over the past 15 years. UNITE serves as a data provider for a range of metabarcoding software pipelines and regularly exchanges data with all major fungal sequence databases and other community resources. Recent improvements include redesigned handling of unclassifiable species hypotheses, integration with the taxonomic backbone of the Global Biodiversity Information Facility, and support for an unlimited number of parallel taxonomic classification systems.
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                Author and article information

                Contributors
                Role: Academic Editor
                Role: Academic Editor
                Journal
                J Fungi (Basel)
                J Fungi (Basel)
                jof
                Journal of Fungi
                MDPI
                2309-608X
                29 June 2021
                July 2021
                : 7
                : 7
                : 521
                Affiliations
                [1 ]Department of Agricultural, Food, Environmental and Forestry Science and Technology (DAGRI), Plant Pathology and Entomology Section, University of Florence, P.le delle Cascine 28, 50144 Firenze, Italy; samuele.moretti@ 123456uha.fr (S.M.); laura.mugnai@ 123456unifi.it (L.M.)
                [2 ]Laboratoire Vigne Biotechnologies et Environnement (LVBE, UR-3991), Université de Haute Alsace, 33 Rue de Herrlisheim, CEDEX, 68000 Colmar, France; sibylle.farine@ 123456uha.fr (S.F.); christophe.bertsch@ 123456uha.fr (C.B.)
                [3 ]Biome Makers, 890 Embarcadero Drive, West Sacramento, CA 95605, USA; catia_carvalho_pinto@ 123456yahoo.com
                [4 ]AIT Austrian Institute of Technology GmbH, Center for Health & Bioresources, Bioresources Unit, Konrad Lorenz Straße 24, 3430 Tulln, Austria; stephane.compant@ 123456ait.ac.at
                Author notes
                Author information
                https://orcid.org/0000-0002-2114-4025
                https://orcid.org/0000-0002-0731-5836
                https://orcid.org/0000-0001-8974-4644
                https://orcid.org/0000-0002-2508-9764
                Article
                jof-07-00521
                10.3390/jof7070521
                8303226
                34210025
                c7981d86-88f6-4350-87d4-36993004d040
                © 2021 by the authors.

                Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license ( https://creativecommons.org/licenses/by/4.0/).

                History
                : 06 June 2021
                : 25 June 2021
                Categories
                Article

                curettage,fomitiporia mediterranea,phaeomoniella chlamydospora,grapevine,decay

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