TY - JOUR AU - Rosenberg, E. AU - Zilber-Rosenberg, I. PY - 2016 DA - 2016// TI - Microbes drive evolution of animals and plants: the hologenome concept JO - MBio VL - 7 UR - https://doi.org/10.1128/mBio.01395-15 DO - 10.1128/mBio.01395-15 ID - Rosenberg2016 ER - TY - STD TI - Gilbert J A, van der Lelie D, Zarraonaindia I. Microbial terroir for wine grapes. Proc Natl Acad Sci U S A. 2014;111:5–6. ID - ref2 ER - TY - JOUR AU - Bokulich, N. AU - Collins, T. AU - Masarweh, C. AU - Allen, G. AU - Heymann, H. AU - Ebeler, S. PY - 2016 DA - 2016// TI - Fermentation behavior suggest microbial contribution to regional wine characteristics JO - MBio VL - 7 UR - https://doi.org/10.1128/mBio.00631-16 DO - 10.1128/mBio.00631-16 ID - Bokulich2016 ER - TY - JOUR AU - Knight, S. AU - Klaere, S. AU - Fedrizzi, B. AU - Goddard, M. R. PY - 2015 DA - 2015// TI - Regional microbial signatures positively correlate with differential wine phenotypes: evidence for a microbial aspect to terroir JO - Sci Rep VL - 5 UR - https://doi.org/10.1038/srep14233 DO - 10.1038/srep14233 ID - Knight2015 ER - TY - JOUR AU - Bokulich, N. A. AU - Thorngate, J. H. AU - Richardson, P. M. AU - Mills, D. A. PY - 2014 DA - 2014// TI - Microbial biogeography of wine grapes is conditioned by cultivar, vintage, and climate JO - Proc Natl Acad Sci U S A VL - 111 UR - https://doi.org/10.1073/pnas.1317377110 DO - 10.1073/pnas.1317377110 ID - Bokulich2014 ER - TY - JOUR AU - Burns, K. N. AU - Kluepfel, D. A. AU - Strauss, S. L. AU - Bokulich, N. A. AU - Cantu, D. AU - Steenwerth, K. L. PY - 2015 DA - 2015// TI - Vineyard soil bacterial diversity and composition revealed by 16S rRNA genes: differentiation by geographic features JO - Soil Biol Biochem Elsevier Ltd VL - 91 UR - https://doi.org/10.1016/j.soilbio.2015.09.002 DO - 10.1016/j.soilbio.2015.09.002 ID - Burns2015 ER - TY - JOUR AU - Martins, G. AU - Lauga, B. AU - Miot-Sertier, C. AU - Mercier, A. AU - Lonvaud, A. AU - Soulas, M. L. PY - 2013 DA - 2013// TI - Characterization of epiphytic bacterial communities from grapes, leaves, bark and soil of grapevine plants grown, and their relations JO - PLoS One VL - 8 UR - https://doi.org/10.1371/journal.pone.0073013 DO - 10.1371/journal.pone.0073013 ID - Martins2013 ER - TY - JOUR AU - Zarraonaindia, I. AU - Owens, S. S. M. AU - Weisenhorn, P. AU - West, K. AU - Hampton-Marcell, J. AU - Lax, S. PY - 2015 DA - 2015// TI - The soil microbiome influences grapevine-associated microbiota JO - MBio VL - 6 UR - https://doi.org/10.1128/mBio.02527-14 DO - 10.1128/mBio.02527-14 ID - Zarraonaindia2015 ER - TY - JOUR AU - Compant, S. AU - Kaplan, H. AU - Sessitsch, A. AU - Nowak, J. AU - Ait Barka, E. AU - Clement, C. PY - 2008 DA - 2008// TI - Endophytic colonization of Vitis vinifera L. by Burkholderia phytofirmans strain PsJN: from the rhizosphere to inflorescence tissues. FEMS Microbiol JO - Ecol VL - 63 ID - Compant2008 ER - TY - STD TI - Whiting J. Selection of grapevine rootstocks and clones: Dept. of Primary Industries; 2003. ID - ref10 ER - TY - JOUR AU - Bonghi, C. AU - Corso, M. AU - Vannozzi, A. AU - Ziliotto, F. AU - Zouine, M. AU - Maza, E. PY - 2016 DA - 2016// TI - Grapevine rootstocks differentially affect the rate of ripening and modulate auxin-related genes in Cabernet Sauvignon berries JO - Front Plant Sci VL - 7 ID - Bonghi2016 ER - TY - JOUR AU - Jin, Z. -. X. AU - Sun, T. -. Y. AU - Sun, H. AU - Yue, Q. -. Y. AU - Yao, Y. -. X. PY - 2016 DA - 2016// TI - Modifications of “Summer Black” grape berry quality as affected by the different rootstocks JO - Sci Hortic VL - 210 UR - https://doi.org/10.1016/j.scienta.2016.07.023 DO - 10.1016/j.scienta.2016.07.023 ID - Jin2016 ER - TY - JOUR AU - Warschefsky, E. J. AU - Klein, L. L. AU - Frank, M. H. AU - Chitwood, D. H. AU - Londo, J. P. AU - Wettberg, E. J. B. PY - 2016 DA - 2016// TI - Rootstocks: diversity, domestication, and impacts on shoot phenotypes JO - Trends Plant Sci VL - 21 UR - https://doi.org/10.1016/j.tplants.2015.11.008 DO - 10.1016/j.tplants.2015.11.008 ID - Warschefsky2016 ER - TY - JOUR AU - Wallis, C. M. AU - Wallingford, A. K. AU - Chen, J. PY - 2013 DA - 2013// TI - Grapevine rootstock effects on scion sap phenolic levels, resistance to Xylella fastidiosa infection, and progression of Pierce’s disease JO - Front Plant Sci VL - 4 UR - https://doi.org/10.3389/fpls.2013.00502 DO - 10.3389/fpls.2013.00502 ID - Wallis2013 ER - TY - JOUR AU - Berdeja, M. AU - Nicolas, P. AU - Kappel, C. AU - Dai, Z. W. AU - Hilbert, G. AU - Peccoux, A. PY - 2015 DA - 2015// TI - Water limitation and rootstock genotype interact to alter grape berry metabolism through transcriptome reprogramming JO - Hortic Res VL - 2 UR - https://doi.org/10.1038/hortres.2015.12 DO - 10.1038/hortres.2015.12 ID - Berdeja2015 ER - TY - JOUR AU - Hamrouni, L. H. M. AU - Abdelly, C. H. K. PY - 2015 DA - 2015// TI - Influence of the rootstock/scion combination on the Grapevine’s behavior under salt stress JO - J Plant Biochem Physiol VL - 3 UR - https://doi.org/10.4172/2329-9029.1000154 DO - 10.4172/2329-9029.1000154 ID - Hamrouni2015 ER - TY - JOUR AU - Bert, P. -. F. AU - Bordenave, L. AU - Donnart, M. AU - Hévin, C. AU - Ollat, N. AU - Decroocq, S. PY - 2013 DA - 2013// TI - Mapping genetic loci for tolerance to lime-induced iron deficiency chlorosis in grapevine rootstocks (Vitis sp.) JO - Theor Appl Genet VL - 126 UR - https://doi.org/10.1007/s00122-012-1993-5 DO - 10.1007/s00122-012-1993-5 ID - Bert2013 ER - TY - JOUR AU - Habran, A. AU - Commisso, M. AU - Helwi, P. AU - Hilbert, G. AU - Negri, S. PY - 2016 DA - 2016// TI - Roostocks/scion/nitrogen interactions affect secondary metabolism in the grape berry JO - Front Plant Sci VL - 7 UR - https://doi.org/10.3389/fpls.2016.01134 DO - 10.3389/fpls.2016.01134 ID - Habran2016 ER - TY - JOUR AU - Van der Heijden, M. G. A. AU - Hartmann, M. PY - 2016 DA - 2016// TI - Networking in the plant microbiome JO - PLoS Biol VL - 14 UR - https://doi.org/10.1371/journal.pbio.1002378 DO - 10.1371/journal.pbio.1002378 ID - Van der Heijden2016 ER - TY - JOUR AU - Aryan, A. AU - Brader, G. AU - Mörtel, J. AU - Pastar, M. AU - Riedle-Bauer, M. PY - 2014 DA - 2014// TI - An abundant “Candidatus Phytoplasma solani” tuf b strain is associated with grapevine, stinging nettle and Hyalesthes obsoletus JO - Eur J Plant Pathol VL - 140 UR - https://doi.org/10.1007/s10658-014-0455-0 DO - 10.1007/s10658-014-0455-0 ID - Aryan2014 ER - TY - JOUR AU - Mapelli, F. AU - Marasco, R. AU - Balloi, A. AU - Rolli, E. AU - Cappitelli, F. AU - Daffonchio, D. PY - 2012 DA - 2012// TI - Mineral–microbe interactions: biotechnological potential of bioweathering JO - J Biotechnol VL - 157 UR - https://doi.org/10.1016/j.jbiotec.2011.11.013 DO - 10.1016/j.jbiotec.2011.11.013 ID - Mapelli2012 ER - TY - JOUR AU - Hayat, R. AU - Ali, S. AU - Amara, U. AU - Khalid, R. AU - Ahmed, I. PY - 2010 DA - 2010// TI - Soil beneficial bacteria and their role in plant growth promotion: a review JO - Ann Microbiol VL - 60 UR - https://doi.org/10.1007/s13213-010-0117-1 DO - 10.1007/s13213-010-0117-1 ID - Hayat2010 ER - TY - STD TI - Bulgarelli D, Schlaeppi K, Spaepen S, van Themaat EVL, Schulze-Lefert P, Ver Loren van Themaat E, et al. Structure and functions of the bacterial microbiota of plants. Annu Rev Plant Biol 2013;64:807–838. ID - ref23 ER - TY - JOUR AU - Compant, S. AU - Clément, C. AU - Sessitsch, A. PY - 2010 DA - 2010// TI - Plant growth-promoting bacteria in the rhizo- and endosphere of plants: their role, colonization, mechanisms involved and prospects for utilization JO - Soil Biol Biochem VL - 42 UR - https://doi.org/10.1016/j.soilbio.2009.11.024 DO - 10.1016/j.soilbio.2009.11.024 ID - Compant2010 ER - TY - JOUR AU - Samad, A. AU - Trognitz, F. AU - Compant, S. AU - Antonielli, L. AU - Sessitsch, A. PY - 2017 DA - 2017// TI - Shared and host-specific microbiome diversity and functioning of grapevine and accompanying weed plants JO - Environ Microbiol VL - 19 UR - https://doi.org/10.1111/1462-2920.13618 DO - 10.1111/1462-2920.13618 ID - Samad2017 ER - TY - JOUR AU - Hardoim, P. R. AU - van Overbeek, L. S. AU - Elsas, J. D. PY - 2008 DA - 2008// TI - Properties of bacterial endophytes and their proposed role in plant growth JO - Trends Microbiol VL - 16 UR - https://doi.org/10.1016/j.tim.2008.07.008 DO - 10.1016/j.tim.2008.07.008 ID - Hardoim2008 ER - TY - JOUR AU - Martín-Moldes, Z. AU - Zamarro, M. T. AU - del Cerro, C. AU - Valencia, A. AU - Gómez, M. J. AU - Arcas, A. PY - 2015 DA - 2015// TI - Whole-genome analysis of Azoarcus sp. strain CIB provides genetic insights to its different lifestyles and predicts novel metabolic features JO - Syst Appl Microbiol VL - 38 UR - https://doi.org/10.1016/j.syapm.2015.07.002 DO - 10.1016/j.syapm.2015.07.002 ID - Martín-Moldes2015 ER - TY - JOUR AU - DeAngelis, K. M. AU - Brodie, E. L. AU - DeSantis, T. Z. AU - Andersen, G. L. AU - Lindow, S. E. AU - Firestone, M. K. PY - 2009 DA - 2009// TI - Selective progressive response of soil microbial community to wild oat roots JO - ISME J. VL - 3 UR - https://doi.org/10.1038/ismej.2008.103 DO - 10.1038/ismej.2008.103 ID - DeAngelis2009 ER - TY - JOUR AU - Marasco, R. AU - Rolli, E. AU - Fusi, M. AU - Cherif, A. AU - Abou-Hadid, A. AU - El-Bahairy, U. PY - 2013 DA - 2013// TI - Plant growth promotion potential is equally represented in diverse grapevine root-associated bacterial communities from different biopedoclimatic environments JO - Biomed Res Int VL - 2013 UR - https://doi.org/10.1155/2013/491091 DO - 10.1155/2013/491091 ID - Marasco2013 ER - TY - JOUR AU - Castañeda, L. E. AU - Godoy, K. AU - Manzano, M. AU - Marquet, P. A. AU - Barbosa, O. PY - 2015 DA - 2015// TI - Comparison of soil microbial communities inhabiting vineyards and native sclerophyllous forests in central Chile JO - Ecol Evol VL - 5 UR - https://doi.org/10.1002/ece3.1652 DO - 10.1002/ece3.1652 ID - Castañeda2015 ER - TY - STD TI - Campisano A, Antonielli L, Pancher M, Yousaf S, Pindo M, Pertot I. Bacterial endophytic communities in the grapevine depend on pest management. van Overbeek LS, editor. PLoS One. 2014;9:e112763. ID - ref31 ER - TY - JOUR AU - Jiang, Y. AU - Li, S. AU - Li, R. AU - Zhang, J. AU - Liu, Y. AU - Lv, L. PY - 2017 DA - 2017// TI - Plant cultivars imprint the rhizosphere bacterial community composition and association networks JO - Soil Biol Biochem VL - 109 UR - https://doi.org/10.1016/j.soilbio.2017.02.010 DO - 10.1016/j.soilbio.2017.02.010 ID - Jiang2017 ER - TY - JOUR AU - Wagner, M. R. AU - Lundberg, D. S. AU - del Rio, T. G. AU - Tringe, S. G. AU - Dangl, J. L. AU - Mitchell-Olds, T. PY - 2016 DA - 2016// TI - Host genotype and age shape the leaf and root microbiomes of a wild perennial plant JO - Nat Commun VL - 7 UR - https://doi.org/10.1038/ncomms12151 DO - 10.1038/ncomms12151 ID - Wagner2016 ER - TY - JOUR AU - Haney, C. H. AU - Samuel, B. S. AU - Bush, J. AU - Ausubel, F. M. PY - 2015 DA - 2015// TI - Associations with rhizosphere bacteria can confer an adaptive advantage to plants JO - Nat Plants VL - 1 UR - https://doi.org/10.1038/nplants.2015.51 DO - 10.1038/nplants.2015.51 ID - Haney2015 ER - TY - JOUR AU - Pagliarani, C. AU - Vitali, M. AU - Ferrero, M. AU - Vitulo, N. AU - Incarbone, M. AU - Lovisolo, C. PY - 2017 DA - 2017// TI - The accumulation of miRNAs differentially modulated by drought stress is affected by grafting in grapevine JO - Plant Physiol VL - 173 UR - https://doi.org/10.1104/pp.16.01119 DO - 10.1104/pp.16.01119 ID - Pagliarani2017 ER - TY - JOUR AU - Shenton, M. AU - Iwamoto, C. AU - Kurata, N. AU - Ikeo, K. PY - 2016 DA - 2016// TI - Effect of wild and cultivated rice genotypes on rhizosphere bacterial community composition JO - Rice VL - 9 UR - https://doi.org/10.1186/s12284-016-0111-8 DO - 10.1186/s12284-016-0111-8 ID - Shenton2016 ER - TY - JOUR AU - Pinto, C. AU - Pinho, D. AU - Sousa, S. AU - Pinheiro, M. AU - Egas, C. AU - Gomes, A. C. PY - 2014 DA - 2014// TI - Unravelling the diversity of grapevine microbiome JO - PLoS One VL - 9 UR - https://doi.org/10.1371/journal.pone.0085622 DO - 10.1371/journal.pone.0085622 ID - Pinto2014 ER - TY - JOUR AU - Vega-Avila, A. D. AU - Gumiere, T. AU - Andrade, P. A. M. AU - Lima-Perim, J. E. AU - Durrer, A. AU - Baigori, M. PY - 2015 DA - 2015// TI - Bacterial communities in the rhizosphere of Vitis vinifera L. cultivated under distinct agricultural practices in Argentina JO - Antonie Van Leeuwenhoek VL - 107 UR - https://doi.org/10.1007/s10482-014-0353-7 DO - 10.1007/s10482-014-0353-7 ID - Vega-Avila2015 ER - TY - JOUR AU - Layeghifard, M. AU - Hwang, D. M. AU - Guttman, D. S. PY - 2017 DA - 2017// TI - Disentangling interactions in the microbiome: a network perspective JO - Trends Microbiol VL - 25 UR - https://doi.org/10.1016/j.tim.2016.11.008 DO - 10.1016/j.tim.2016.11.008 ID - Layeghifard2017 ER - TY - JOUR AU - Fierer, N. AU - Lennon, J. T. PY - 2011 DA - 2011// TI - The generation and maintenance of diversity in microbial communities JO - Am J Bot VL - 98 UR - https://doi.org/10.3732/ajb.1000498 DO - 10.3732/ajb.1000498 ID - Fierer2011 ER - TY - JOUR AU - Jones, S. E. AU - Lennon, J. T. PY - 2010 DA - 2010// TI - Dormancy contributes to the maintenance of microbial diversity JO - Proc Natl Acad Sci VL - 107 UR - https://doi.org/10.1073/pnas.0912765107 DO - 10.1073/pnas.0912765107 ID - Jones2010 ER - TY - JOUR AU - Connor, N. AU - Barberán, A. AU - Clauset, A. PY - 2017 DA - 2017// TI - Using null models to infer microbial co-occurrence networks JO - PLoS One VL - 12 UR - https://doi.org/10.1371/journal.pone.0176751 DO - 10.1371/journal.pone.0176751 ID - Connor2017 ER - TY - JOUR AU - Wei, W. AU - Kakizawa, S. AU - Suzuki, S. AU - Jung, H. -. Y. AU - Nishigawa, H. AU - Miyata, S. PY - 2004 DA - 2004// TI - In planta dynamic analysis of onion yellows Phytoplasma using localized inoculation by insect transmission JO - Phytopathology VL - 94 UR - https://doi.org/10.1094/PHYTO.2004.94.3.244 DO - 10.1094/PHYTO.2004.94.3.244 ID - Wei2004 ER - TY - JOUR AU - Lherminier, J. AU - Courtois, M. AU - Caudwell, A. PY - 1994 DA - 1994// TI - Determination of the distribution and multiplication sites of Flavescence Dorée mycoplasma-like organisms in the host plant Vicia faba by ELISA and immunocytochemistry JO - Physiol Mol Plant Pathol VL - 45 UR - https://doi.org/10.1016/S0885-5765(05)80071-2 DO - 10.1016/S0885-5765(05)80071-2 ID - Lherminier1994 ER - TY - JOUR AU - Mazmanian, S. K. AU - Round, J. L. AU - Kasper, D. L. PY - 2008 DA - 2008// TI - A microbial symbiosis factor prevents intestinal inflammatory disease JO - Nature VL - 453 UR - https://doi.org/10.1038/nature07008 DO - 10.1038/nature07008 ID - Mazmanian2008 ER - TY - JOUR AU - Trivedi, P. AU - Duan, Y. AU - Wang, N. PY - 2010 DA - 2010// TI - Huanglongbing, a systemic disease, restructures the bacterial community associated with citrus roots JO - Appl Environ Microbiol VL - 76 UR - https://doi.org/10.1128/AEM.02901-09 DO - 10.1128/AEM.02901-09 ID - Trivedi2010 ER - TY - JOUR AU - Bulgari, D. AU - Quaglino, F. AU - Bianco, P. A. AU - Casati, P. PY - 2011 DA - 2011// TI - Preliminary results on endophytic bacterial community fluctuation during phytoplasma infection JO - Bull Insectology VL - 64 ID - Bulgari2011 ER - TY - JOUR AU - Bulgari, D. AU - Casati, P. AU - Quaglino, F. AU - Bianco, P. A. PY - 2014 DA - 2014// TI - Endophytic bacterial community of grapevine leaves influenced by sampling date and phytoplasma infection process JO - BMC Microbiol VL - 14 UR - https://doi.org/10.1186/1471-2180-14-198 DO - 10.1186/1471-2180-14-198 ID - Bulgari2014 ER - TY - JOUR AU - Trivedi, P. AU - He, Z. AU - Van Nostrand, J. D. AU - Albrigo, G. AU - Zhou, J. AU - Wang, N. PY - 2012 DA - 2012// TI - Huanglongbing alters the structure and functional diversity of microbial communities associated with citrus rhizosphere JO - ISME J. VL - 6 UR - https://doi.org/10.1038/ismej.2011.100 DO - 10.1038/ismej.2011.100 ID - Trivedi2012 ER - TY - JOUR AU - Trivedi, P. AU - Wang, N. PY - 2014 DA - 2014// TI - Host immune responses accelerate pathogen evolution JO - ISME J. VL - 8 UR - https://doi.org/10.1038/ismej.2013.215 DO - 10.1038/ismej.2013.215 ID - Trivedi2014 ER - TY - JOUR AU - Berry, D. AU - Widder, S. PY - 2014 DA - 2014// TI - Deciphering microbial interactions and detecting keystone species with co-occurrence networks JO - Front Microbiol VL - 5 UR - https://doi.org/10.3389/fmicb.2014.00219 DO - 10.3389/fmicb.2014.00219 ID - Berry2014 ER - TY - JOUR AU - Hamedi, J. AU - Mohammadipanah, F. PY - 2015 DA - 2015// TI - Biotechnological application and taxonomical distribution of plant growth promoting actinobacteria JO - J Ind Microbiol Biotechnol VL - 42 UR - https://doi.org/10.1007/s10295-014-1537-x DO - 10.1007/s10295-014-1537-x ID - Hamedi2015 ER - TY - JOUR AU - Finkel, O. M. AU - Castrillo, G. AU - Herrera Paredes, S. AU - Salas González, I. AU - Dangl, J. L. PY - 2017 DA - 2017// TI - Understanding and exploiting plant beneficial microbes JO - Curr Opin Plant Biol VL - 38 UR - https://doi.org/10.1016/j.pbi.2017.04.018 DO - 10.1016/j.pbi.2017.04.018 ID - Finkel2017 ER - TY - JOUR AU - Gopal, M. AU - Gupta, A. PY - 2016 DA - 2016// TI - Microbiome selection could spur next-generation plant breeding JO - Front Microbiol VL - 7 UR - https://doi.org/10.3389/fmicb.2016.01971 DO - 10.3389/fmicb.2016.01971 ID - Gopal2016 ER - TY - JOUR AU - Mendes, L. W. AU - Kuramae, E. E. AU - Navarrete, A. A. AU - van Veen, J. A. AU - Tsai, S. M. PY - 2014 DA - 2014// TI - Taxonomical and functional microbial community selection in soybean rhizosphere JO - ISME J. VL - 8 UR - https://doi.org/10.1038/ismej.2014.17 DO - 10.1038/ismej.2014.17 ID - Mendes2014 ER - TY - JOUR AU - Biasolo, G. A. D. AU - Kucmanski, D. A. AU - Salamoni, S. P. AU - Gardin, J. P. P. AU - Minotto, E. AU - Baratto, C. M. PY - 2016 DA - 2016// TI - Isolation, characterization and selection of bacteria that promote plant growth in grapevines (Vitis sp.) JO - J Agric Sci VL - 9 ID - Biasolo2016 ER - TY - JOUR AU - Compant, S. AU - Mitter, B. AU - Colli-Mull, J. G. AU - Gangl, H. AU - Sessitsch, A. PY - 2011 DA - 2011// TI - Endophytes of grapevine flowers, berries, and seeds: identification of cultivable bacteria, comparison with other plant parts, and visualization of niches of colonization JO - Microb Ecol VL - 62 UR - https://doi.org/10.1007/s00248-011-9883-y DO - 10.1007/s00248-011-9883-y ID - Compant2011 ER - TY - JOUR AU - Baldan, E. AU - Nigris, S. AU - Romualdi, C. AU - D’Alessandro, S. AU - Clocchiatti, A. AU - Zottini, M. PY - 2015 DA - 2015// TI - Beneficial bacteria isolated from grapevine inner tissues shape Arabidopsis thaliana roots JO - PLoS One VL - 10 UR - https://doi.org/10.1371/journal.pone.0140252 DO - 10.1371/journal.pone.0140252 ID - Baldan2015 ER - TY - JOUR AU - Rolli, E. AU - Marasco, R. AU - Vigani, G. AU - Ettoumi, B. AU - Mapelli, F. AU - Deangelis, M. L. PY - 2015 DA - 2015// TI - Improved plant resistance to drought is promoted by the root-associated microbiome as a water stress-dependent trait JO - Environ Microbiol VL - 17 UR - https://doi.org/10.1111/1462-2920.12439 DO - 10.1111/1462-2920.12439 ID - Rolli2015 ER - TY - JOUR AU - Rolli, E. AU - Marasco, R. AU - Saderi, S. AU - Corretto, E. AU - Mapelli, F. AU - Cherif, A. PY - 2017 DA - 2017// TI - Root-associated bacteria promote grapevine growth: from the laboratory to the field JO - Plant Soil VL - 410 UR - https://doi.org/10.1007/s11104-016-3019-6 DO - 10.1007/s11104-016-3019-6 ID - Rolli2017 ER - TY - STD TI - Cherif H, Marasco R, Rolli E, Ferjani R, Fusi M, Soussi A, Mapelli F, Blilou I, Borin S, Boudabous A, Cherif A. Oasis desert farming selects environment-specific date palm root endophytic communities and cultivable bacteria that promote resistance to drought. Environ Microbiol Rep. 2015;7:668–78. ID - ref61 ER - TY - JOUR AU - Kuczynski, J. AU - Lauber, C. L. AU - Walters, W. A. AU - Parfrey, L. W. AU - Clemente, J. C. AU - Gevers, D. PY - 2012 DA - 2012// TI - Experimental and analytical tools for studying the human microbiome JO - Nat Rev Genet VL - 13 UR - https://doi.org/10.1038/nrg3129 DO - 10.1038/nrg3129 ID - Kuczynski2012 ER - TY - JOUR AU - Edgar, R. C. PY - 2013 DA - 2013// TI - UPARSE: highly accurate OTU sequences from microbial amplicon reads JO - Nat Methods VL - 10 UR - https://doi.org/10.1038/nmeth.2604 DO - 10.1038/nmeth.2604 ID - Edgar2013 ER - TY - JOUR AU - Caporaso, J. G. AU - Kuczynski, J. AU - Stombaugh, J. AU - Bittinger, K. AU - Bushman, F. D. AU - Costello, E. K. PY - 2010 DA - 2010// TI - QIIME allows analysis of high-throughput community sequencing data JO - Nat Methods VL - 7 UR - https://doi.org/10.1038/nmeth.f.303 DO - 10.1038/nmeth.f.303 ID - Caporaso2010 ER - TY - JOUR AU - McDonald, D. AU - Price, M. N. AU - Goodrich, J. AU - Nawrocki, E. P. AU - DeSantis, T. Z. AU - Probst, A. PY - 2012 DA - 2012// TI - An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea JO - ISME J. VL - 6 UR - https://doi.org/10.1038/ismej.2011.139 DO - 10.1038/ismej.2011.139 ID - McDonald2012 ER - TY - JOUR AU - Price, M. N. AU - Dehal, P. S. AU - Arkin, A. P. PY - 2010 DA - 2010// TI - FastTree 2—approximately maximum-likelihood trees for large alignments JO - PLoS One VL - 5 UR - https://doi.org/10.1371/journal.pone.0009490 DO - 10.1371/journal.pone.0009490 ID - Price2010 ER - TY - JOUR AU - McMurdie, P. J. AU - Holmes, S. PY - 2014 DA - 2014// TI - Waste not, want not: why rarefying microbiome data is inadmissible JO - PLoS Comput Biol VL - 10 UR - https://doi.org/10.1371/journal.pcbi.1003531 DO - 10.1371/journal.pcbi.1003531 ID - McMurdie2014 ER - TY - JOUR AU - Dormann, C. F. AU - Gruber, B. AU - Fründ, J. PY - 2008 DA - 2008// TI - Introducing the bipartite package: analysing ecological networks JO - R News VL - 8 ID - Dormann2008 ER - TY - JOUR AU - Shannon, P. AU - Markiel, A. AU - Ozier, O. AU - Baliga, N. S. AU - Wang, J. T. AU - Ramage, D. PY - 2003 DA - 2003// TI - Cytoscape: a software environment for integrated models of biomolecular interaction networks JO - Genome Res VL - 13 UR - https://doi.org/10.1101/gr.1239303 DO - 10.1101/gr.1239303 ID - Shannon2003 ER - TY - STD TI - Ramette A. Multivariate analyses in microbial ecology. FEMS Microbiol Ecol. 2007;62:142–60. ID - ref70 ER - TY - STD TI - Buttigieg PL, Ramette A. A guide to statistical analysis in microbial ecology: a community-focused, living review of multivariate data analyses. FEMS Microbiol Ecol. 2014;90(3):543-50. ID - ref71 ER - TY - STD TI - Anderson MMJ, Gorley RNRN, Clarke KR. PERMANOVA + for PRIMER: guide to software and statistical methods. Plymouth; 2008. ID - ref72 ER - TY - JOUR AU - Nuccio, E. E. AU - Anderson-Furgeson, J. AU - Estera, K. Y. AU - Pett-Ridge, J. AU - De Valpine, P. AU - Brodie, E. L. PY - 2016 DA - 2016// TI - Climate and edaphic controllers influence rhizosphere community assembly for a wild annual grass JO - Ecology VL - 97 UR - https://doi.org/10.1890/15-0882.1 DO - 10.1890/15-0882.1 ID - Nuccio2016 ER - TY - JOUR AU - Horstemeyer, M. F. AU - Wang, P. PY - 2003 DA - 2003// TI - Cradle-to-grave simulation-based design incorporating multiscale microstructure-property modeling: reinvigorating design with science JO - J Comput Mater Des VL - 10 UR - https://doi.org/10.1023/B:JCAD.0000024171.13480.24 DO - 10.1023/B:JCAD.0000024171.13480.24 ID - Horstemeyer2003 ER - TY - JOUR AU - Segata, N. AU - Izard, J. AU - Waldron, L. AU - Gevers, D. AU - Miropolsky, L. AU - Garrett, W. S. PY - 2011 DA - 2011// TI - Metagenomic biomarker discovery and explanation JO - Genome Biol VL - 12 UR - https://doi.org/10.1186/gb-2011-12-6-r60 DO - 10.1186/gb-2011-12-6-r60 ID - Segata2011 ER - TY - STD TI - Clarke K, Warwick R. Change in marine communities: an approach to statistical analysis and interpretation. 2nd ed. Plymouth: Prim. Ltd Plymouth; 2001. ID - ref76 ER - TY - JOUR AU - Aßhauer, K. P. AU - Wemheuer, B. AU - Daniel, R. AU - Meinicke, P. PY - 2015 DA - 2015// TI - Tax4Fun: predicting functional profiles from metagenomic 16S rRNA data JO - Bioinformatics VL - 31 UR - https://doi.org/10.1093/bioinformatics/btv287 DO - 10.1093/bioinformatics/btv287 ID - Aßhauer2015 ER - TY - JOUR AU - Quast, C. AU - Pruesse, E. AU - Yilmaz, P. AU - Gerken, J. AU - Schweer, T. AU - Yarza, P. PY - 2012 DA - 2012// TI - The SILVA ribosomal RNA gene database project: improved data processing and web-based tools JO - Nucleic Acids Res VL - 41 UR - https://doi.org/10.1093/nar/gks1219 DO - 10.1093/nar/gks1219 ID - Quast2012 ER - TY - JOUR AU - Ogata, H. AU - Goto, S. AU - Sato, K. AU - Fujibuchi, W. AU - Bono, H. AU - Kanehisa, M. PY - 1999 DA - 1999// TI - KEGG: Kyoto encyclopedia of genes and genomes JO - Nucleic Acids Res VL - 27 UR - https://doi.org/10.1093/nar/27.1.29 DO - 10.1093/nar/27.1.29 ID - Ogata1999 ER - TY - JOUR AU - Kanehisa, M. AU - Goto, S. AU - Sato, Y. AU - Kawashima, M. AU - Furumichi, M. AU - Tanabe, M. PY - 2014 DA - 2014// TI - Data, information, knowledge and principle: back to metabolism in KEGG JO - Nucleic Acids Res VL - 42 UR - https://doi.org/10.1093/nar/gkt1076 DO - 10.1093/nar/gkt1076 ID - Kanehisa2014 ER - TY - JOUR AU - Kanehisa, M. AU - Furumichi, M. AU - Tanabe, M. AU - Sato, Y. AU - Morishima, K. PY - 2017 DA - 2017// TI - KEGG: new perspectives on genomes, pathways, diseases and drugs JO - Nucleic Acids Res VL - 45 UR - https://doi.org/10.1093/nar/gkw1092 DO - 10.1093/nar/gkw1092 ID - Kanehisa2017 ER - TY - JOUR AU - Kaiser, K. AU - Wemheuer, B. AU - Korolkow, V. AU - Wemheuer, F. AU - Nacke, H. AU - Schöning, I. PY - 2016 DA - 2016// TI - Driving forces of soil bacterial community structure, diversity, and function in temperate grasslands and forests JO - Sci Rep VL - 6 UR - https://doi.org/10.1038/srep33696 DO - 10.1038/srep33696 ID - Kaiser2016 ER - TY - JOUR AU - Sashidhar, B. AU - Podile, A. R. PY - 2010 DA - 2010// TI - Mineral phosphate solubilization by rhizosphere bacteria and scope for manipulation of the direct oxidation pathway involving glucose dehydrogenase JO - J Appl Microbiol VL - 109 ID - Sashidhar2010 ER - TY - JOUR AU - Weiss, S. AU - Van Treuren, W. AU - Lozupone, C. AU - Faust, K. AU - Friedman, J. AU - Deng, Y. PY - 2016 DA - 2016// TI - Correlation detection strategies in microbial data sets vary widely in sensitivity and precision JO - ISME J Nature Publishing Group VL - 10 ID - Weiss2016 ER - TY - JOUR AU - Faust, K. AU - Sathirapongsasuti, J. F. AU - Izard, J. AU - Segata, N. AU - Gevers, D. AU - Raes, J. PY - 2012 DA - 2012// TI - Microbial co-occurrence relationships in the human microbiome. Ouzounis CA, editor JO - PLoS Comput Biol VL - 8 UR - https://doi.org/10.1371/journal.pcbi.1002606 DO - 10.1371/journal.pcbi.1002606 ID - Faust2012 ER - TY - JOUR AU - Faust, K. AU - Raes, J. PY - 2016 DA - 2016// TI - CoNet app: inference of biological association networks using Cytoscape JO - F1000 Res VL - 5 UR - https://doi.org/10.12688/f1000research.9050.2 DO - 10.12688/f1000research.9050.2 ID - Faust2016 ER - TY - JOUR AU - Barberán, A. AU - Bates, S. T. AU - Casamayor, E. O. AU - Fierer, N. PY - 2012 DA - 2012// TI - Using network analysis to explore co-occurrence patterns in soil microbial communities JO - ISME J VL - 6 UR - https://doi.org/10.1038/ismej.2011.119 DO - 10.1038/ismej.2011.119 ID - Barberán2012 ER - TY - JOUR AU - Blondel, V. D. AU - Guillaume, J. -. L. AU - Lambiotte, R. AU - Lefebvre, E. PY - 2008 DA - 2008// TI - Fast unfolding of communities in large networks JO - J Stat Mech Theory Exp VL - 2008 UR - https://doi.org/10.1088/1742-5468/2008/10/P10008 DO - 10.1088/1742-5468/2008/10/P10008 ID - Blondel2008 ER - TY - STD TI - Bastian M, Heymann S, Jacomy M. Gephi: an open source software for exploring and manipulating networks. Third Int AAAI Conf Weblogs Soc Media. 2009;8:361–2. ID - ref89 ER - TY - JOUR AU - O’Hara, R. B. AU - Kotze, D. J. PY - 2010 DA - 2010// TI - Do not log-transform count data JO - Methods Ecol Evol VL - 1 UR - https://doi.org/10.1111/j.2041-210X.2010.00021.x DO - 10.1111/j.2041-210X.2010.00021.x ID - O’Hara2010 ER - TY - JOUR AU - Penrose, D. M. AU - Glick, B. R. PY - 2003 DA - 2003// TI - Methods for isolating and characterizing ACC deaminase-containing plant growth-promoting rhizobacteria JO - Physiol Plant VL - 118 UR - https://doi.org/10.1034/j.1399-3054.2003.00086.x DO - 10.1034/j.1399-3054.2003.00086.x ID - Penrose2003 ER - TY - JOUR AU - Daffonchio, D. AU - Cherif, A. AU - Borin, S. PY - 2000 DA - 2000// TI - Homoduplex and heteroduplex polymorphisms of the amplified ribosomal 16S-23S Internal Transcribed Spacers describe genetic relationships in the “Bacillus cereus group.” JO - Appl Environ Microbiol VL - 66 UR - https://doi.org/10.1128/AEM.66.12.5460-5468.2000 DO - 10.1128/AEM.66.12.5460-5468.2000 ID - Daffonchio2000 ER - TY - JOUR AU - Marasco, R. AU - Rolli, E. AU - Ettoumi, B. AU - Vigani, G. AU - Mapelli, F. AU - Borin, S. PY - 2012 DA - 2012// TI - A drought resistance-promoting microbiome is selected by root system under desert farming JO - PLoS One VL - 7 UR - https://doi.org/10.1371/journal.pone.0048479 DO - 10.1371/journal.pone.0048479 ID - Marasco2012 ER - TY - JOUR AU - Pruesse, E. AU - Peplies, J. AU - Glöckner, F. O. PY - 2012 DA - 2012// TI - SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes JO - Bioinformatics VL - 28 UR - https://doi.org/10.1093/bioinformatics/bts252 DO - 10.1093/bioinformatics/bts252 ID - Pruesse2012 ER - TY - JOUR AU - Talavera, G. AU - Castresana, J. AU - Kjer, K. AU - Page, R. AU - Sullivan, J. PY - 2007 DA - 2007// TI - Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments JO - Syst Biol VL - 56 UR - https://doi.org/10.1080/10635150701472164 DO - 10.1080/10635150701472164 ID - Talavera2007 ER - TY - JOUR AU - Kumar, S. AU - Stecher, G. AU - Tamura, K. PY - 2016 DA - 2016// TI - MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets JO - Mol Biol Evol VL - 33 UR - https://doi.org/10.1093/molbev/msw054 DO - 10.1093/molbev/msw054 ID - Kumar2016 ER - TY - JOUR AU - Saitou, N. AU - Nei, M. PY - 1987 DA - 1987// TI - The neighbor-joining method: a new method for reconstructing phylogenetic trees JO - Mol Biol Evol VL - 4 ID - Saitou1987 ER - TY - JOUR AU - Bric, J. M. AU - Bostock, R. M. AU - Silverstone, S. E. AU - Bric, J. M. AU - Bostock, R. M. AU - Silverstonet, S. E. PY - 1991 DA - 1991// TI - Rapid in situ assay for Indoleacetic acid production by bacteria immobilized on a nitrocellulose membrane JO - Appl Environ Microbiol VL - 57 ID - Bric1991 ER - TY - JOUR AU - Nautiyal, C. S. PY - 1999 DA - 1999// TI - An efficient microbiological growth medium for screening phosphate solubilizing microorganisms JO - FEMS Microbiol Lett VL - 170 UR - https://doi.org/10.1111/j.1574-6968.1999.tb13383.x DO - 10.1111/j.1574-6968.1999.tb13383.x ID - Nautiyal1999 ER - TY - JOUR AU - Schwyn, B. AU - Neilands, J. PY - 1987 DA - 1987// TI - Universal chemical assay for the detection determination of siderophores JO - Anal Biochem VL - 160 UR - https://doi.org/10.1016/0003-2697(87)90612-9 DO - 10.1016/0003-2697(87)90612-9 ID - Schwyn1987 ER -