Soil-plant compartments affect fungal microbiome diversity and composition in grapevine

Abarenkov, 2010, The UNITE database for molecular identification of fungi - recent updates and future perspectives, New Phytol., 186, 281, 10.1111/j.1469-8137.2009.03160.x Agler, 2016, Microbial hub taxa link host and abiotic factors to plant microbiome variation, PLoS Biol., 14, 10.1371/journal.pbio.1002352 Agustí-Brisach, 2013, Detection of black-foot and Petri disease pathogens in natural soils of grapevine nurseries and vineyards using bait plants, Plant Soil, 364, 5, 10.1007/s11104-012-1333-1 Almario, 2017, Root-associated fungal microbiota of nonmycorrhizal Arabis alpina and its contribution to plant phosphorus nutrition, Proc. Natl. Acad. Sci. Unit. States Am., 114, E9403, 10.1073/pnas.1710455114 Aronesty, 2011, ea-utils: command-line tools for processing biological sequencing data, Expr. Anal. Durham Bais, 2006, The role of root exudates in rhizosphere interactions with plants and other organisms, Annu. Rev. Plant Biol., 57, 233, 10.1146/annurev.arplant.57.032905.105159 Banos, 2018, A comprehensive fungi-specific 18S rRNA gene sequence primer toolkit suited for diverse research issues and sequencing platforms, BMC Microbiol., 18, 190, 10.1186/s12866-018-1331-4 Berg, 2009, Plant species and soil type cooperatively shape the structure and function of microbial communities in the rhizosphere, FEMS Microbiol. Ecol., 68, 1, 10.1111/j.1574-6941.2009.00654.x Berlanas, 2019, Grapevine rootstock genotype is an important determinant of the rhizosphere bacterial and fungal microbiome, Front. Microbiol., 10, 1142, 10.3389/fmicb.2019.01142 Berlanas, 2017, Estimation of viable propagules of black-foot disease pathogens in grapevine cultivated soils and their relation to production systems and soil properties, Plant Soil, 417, 467, 10.1007/s11104-017-3272-3 Bertin, 2003, The role of root exudates and allelochemicals in the rhizosphere, Plant Soil, 256, 67, 10.1023/A:1026290508166 Blaalid, 2013, ITS1 versus ITS2 as DNA metabarcodes for fungi, Mol. Ecol. Resour., 13, 218, 10.1111/1755-0998.12065 Bulgarelli, 2012, Revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota, Nature, 488, 91, 10.1038/nature11336 Bulgarelli, 2013, Structure and functions of the bacterial microbiota of plants, Annu. Rev. Plant Biol., 64, 807, 10.1146/annurev-arplant-050312-120106 Burns, 2015, Vineyard soil bacterial diversity and composition revealed by 16S rRNA genes: differentiation by geographic features, Soil Biol. Biochem., 91, 232, 10.1016/j.soilbio.2015.09.002 Caporaso, 2010, QIIME allows analysis of high-throughput community sequencing data, Nat. Methods, 7, 335, 10.1038/nmeth.f.303 Castañeda, 2017, Metagenomic analysis exploring taxonomic and functional diversity of soil microbial communities in Chilean vineyards and surrounding native forests, PeerJ, 5, 10.7717/peerj.3098 Chapelle, 2016, Fungal invasion of the rhizosphere microbiome, ISME J., 10, 265, 10.1038/ismej.2015.82 Cherif, 2015, Oasis desert farming selects environment specific date palm root endophytic communities and cultivable bacteria that promote resistance to drought, Environ. Microbiol. Rep., 7, 668, 10.1111/1758-2229.12304 Coleman-Derr, 2016, Plant compartment and biogeography affect microbiome composition in cultivated and native Agave species, New Phytol., 209, 798, 10.1111/nph.13697 Compant, 2008, Endophytic colonization of Burkholderia phytofirmans strain PsJN in Vitis vinifera L: from rhizosphere to infloresence tissues, FEMS Microbiol. Ecol., 63, 84, 10.1111/j.1574-6941.2007.00410.x Corneo, 2014, Moderate warming in microcosm experiment does not affect microbial communities in temperate vineyard soils, Microb. Ecol., 67, 659, 10.1007/s00248-013-0357-2 Costa, 2006, Cultivation-independent analysis of Pseudomonas species in soil and in the rhizosphere of field-grown Verticillium dahliae host plants, Environ. Microbiol., 8, 2136, 10.1111/j.1462-2920.2006.01096.x Dhariwal, 2017, MicrobiomeAnalyst: a web-based tool for comprehensive statistical, visual and meta-analysis of microbiome data, Nucleic Acids Res., 45, W180, 10.1093/nar/gkx295 Dombrowski, 2017, Root microbiota dynamics of perennial Arabis alpina are dependent on soil residence time but independent of flowering time, ISME J., 11, 43, 10.1038/ismej.2016.109 Edgar, 2010, Search and clustering orders of magnitude faster than BLAST, Bioinformatics, 26, 2460, 10.1093/bioinformatics/btq461 Edgar, 2013, UPARSE: highly accurate OTU sequences from microbial amplicon reads, Nat. Methods, 10, 996, 10.1038/nmeth.2604 Edgar Fernández-Calviño, 2010, Microbial community structure of vineyard soils with different pH and copper content, Appl. Soil Ecol., 46, 276, 10.1016/j.apsoil.2010.08.001 Fierer, 2006, The diversity and biogeography of soil bacterial communities, Proc. Natl. Acad. Sci. Unit. States Am. U, 103, 626, 10.1073/pnas.0507535103 Glynou, 2016, The local environment determines the assembly of root endophytic fungi at a continental scale, Environ. Microbiol., 18, 2418, 10.1111/1462-2920.13112 Glynou, 2018, Facultative root-colonizing fungi dominate endophytic assemblages in roots of nonmycorrhizal Microthlaspi species, New Phytol., 217, 1190, 10.1111/nph.14873 Gottel, 2011, Distinct microbial communities within the endosphere and rhizosphere of Populus deltoides roots across contrasting soil types, Appl. Environ. Microbiol., 77, 5934, 10.1128/AEM.05255-11 Gramaje, 2018, Managing grapevine trunk diseases with respects to etiology and epidemiology: current strategies and future prospects, Plant Dis., 102, 12, 10.1094/PDIS-04-17-0512-FE Griffiths, 2011, The bacterial biogeography of British soils, Environ. Microbiol., 13, 1642, 10.1111/j.1462-2920.2011.02480.x Holland, 2016, Evaluating the diversity of soil microbial communities in vineyards relative to adjacent native ecosystems, Appl. Soil Ecol., 100, 91, 10.1016/j.apsoil.2015.12.001 Keller, 2010, Cultivars, clones, and rootstocks, 9 Lauber, 2008, The influence of soil properties on the structure of bacterial and fungal communities across land-use types, Soil Biol. Biochem., 40, 2407, 10.1016/j.soilbio.2008.05.021 Likar, 2017, Ecological and conventional viticulture gives rise to distinct fungal and bacterial microbial communities in vineyard soils, Appl. Soil Ecol., 113, 86, 10.1016/j.apsoil.2017.02.007 Longa, 2017, Soil microbiota respond to green manure in organic vineyards, J. Appl. Microbiol., 123, 1547, 10.1111/jam.13606 Lundberg, 2012, Defining the core Arabidiopsis thaliana root microbiome, Nature, 488, 86, 10.1038/nature11237 Manici, 2017, Long- term grapevine cultivation and agro-environment affect rhizosphere microbiome rather than plant age, Appl. Soil Ecol., 119, 214, 10.1016/j.apsoil.2017.06.027 Marasco, 2018, Grapevine rootstocks shape underground bacterial microbiome and networking but not potential functionality, Microbiome, 6, 10.1186/s40168-017-0391-2 Martins, 2013, Characterization of epiphytic bacterial communities from grapes, leaves, bark and soil of grapevine plants grown, and their relations, PLoS One, 8, 10.1371/journal.pone.0073013 Nguyen, 2015, Parsing ecological signal from noise in next generation amplicon sequencing, New Phytol., 205, 1389, 10.1111/nph.12923 Nguyen, 2016, FUNGuild: an open annotation tool for parsing fungal community datasets by ecological guild, Fungal Ecol., 20, 241, 10.1016/j.funeco.2015.06.006 Nilsson, 2008, Intraspecific ITS variability in the kingdom fungi as expressed in the international sequence database and its implications for molecular species identification, Evol. Bioinform. Online, 26, 193 Ofek, 2014, Host signature effect on plant root-associated microbiomes revealed through analyses of resident versus active communities, Environ. Microbiol., 16, 2157, 10.1111/1462-2920.12228 Pertot, 2016, Trichoderma atroviride SC1 prevents Phaeomoniella chlamydospora and Phaeoacremonium aleophilum infection of grapevine plants during the grafting process in nurseries, BioControl, 61, 257, 10.1007/s10526-016-9723-6 Petit, 2006, Influence of Glomus intraradices on black foot disease caused by Cylindrocarpon macrodidymum on Vitis rupestris under controlled conditions, Plant Dis., 90, 1481, 10.1094/PD-90-1481 Pinto, 2018, Understand the potential role of Aureobasidium pullulans, a resident microorganism from grapevine, to prevent the infection caused by Diplodia seriata, Front. Microbiol., 9, 3047, 10.3389/fmicb.2018.03047 Prévost-Bouré, 2014, Similar processes but different environmental filters for soil bacterial and fungal community composition turnover on a broad spatial scale, PLoS One, 9 Raaijmakers, 2008, The rhizosphere: a playground and battlefield for soilborne pathogens and beneficial microorganisms, Plant Soil, 321, 341, 10.1007/s11104-008-9568-6 Reinhold-Hurek, 2015, Roots shaping their microbiome: global hotspots for microbial activity, Annu. Rev. Phytopathol., 53, 403, 10.1146/annurev-phyto-082712-102342 Rousk, 2010, Soil bacterial and fungal communities across a pH gradient in an arable soil, ISME J., 4, 1340, 10.1038/ismej.2010.58 Saccà, 2018, Qualitative and quantitative molecular analysis indicate the presence of Phaeomoniella chlamydospora in vineyard soils, J. Phytopathol., 166, 821, 10.1111/jph.12766 Schoch, 2012, Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi, Proc. Natl. Acad. Sci. U.S.A., 109, 6241, 10.1073/pnas.1117018109 Segata, 2011, Metagenomic biomarker discovery and explanation, Genome Biol., 12, R60, 10.1186/gb-2011-12-6-r60 Smalla, 2001, Bulk and rhizosphere soil bacterial communities studied by denaturing gradient gel electrophoresis: plant-dependent enrichment and seasonal shifts revealed, Appl. Environ. Microbiol., 67, 4742, 10.1128/AEM.67.10.4742-4751.2001 Starkey, 1938, Some influences of the development of higher plants upon the microorganisms in the soil: VI. Microscopic examination of the rhizosphere, Soil Sci., 45, 207, 10.1097/00010694-193803000-00005 Terrat, 2017, Correction: mapping and predictive variations of soil bacterial richness across France, PLoS One, 12 Toju, 2012, High-coverage ITS primers for the DNA-based identification of Ascomycetes and Basidiomycetes in environmental samples, PLoS One, 7, 10.1371/journal.pone.0040863 Turner, 2013, The plant microbiome, Genome Biol., 14, 209, 10.1186/gb-2013-14-6-209 Vázquez-Baeza, 2013, EMPeror: a tool for visualizing high-throughput microbial community data, GigaScience, 2, 10.1186/2047-217X-2-16 Wang, 2017, Shifts in microbial communities in soil, rhizosphere and roots of two major crop systems under elevated CO2 and O3, Sci. Rep., 7, 15019, 10.1038/s41598-017-14936-2 White, 1990, Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics, 315 Xia, 2016, Biogeographic distribution patterns of bacteria in typical Chinese forests soils, Front. Microbiol., 7, 1106, 10.3389/fmicb.2016.01106 Xu, 2015, Amplicon-based metagenomics identified candidate organisms in soils that caused yield decline in strawberry, Hortic. Res., 2, 15022, 10.1038/hortres.2015.22 Yang, 2018, Diversity and characteristics of colonization of root-associated fungi of Vaccinium uliginosum, Sci. Rep., 8, 15283, 10.1038/s41598-018-33634-1 Yu, 2018, The role of host genetic signatures on root-microbe interactions in the rhizosphere and endosphere, Front. Plant Sci., 9, 1896, 10.3389/fpls.2018.01896 Zarraonaindia, 2015, Understanding grapevine-microbiome interactions: implications for viticulture industry, Microb. Cell, 2, 171, 10.15698/mic2015.05.204 Zarraonaindia, 2015, The soil microbiome influences grapevine-associated microbiota, mBio, 6, 10.1128/mBio.02527-14