TY - JOUR AU - Mendes, L. W. AU - Raaijmakers, J. M. AU - Hollander, M. AU - Mendes, R. AU - Tsai, S. M. PY - 2018 DA - 2018// TI - Influence of resistance breeding in common bean on rhizosphere microbiome composition and function JO - ISME J VL - 12 UR - https://doi.org/10.1038/ismej.2017.158 DO - 10.1038/ismej.2017.158 ID - Mendes2018 ER - TY - JOUR AU - Bakker, P. A. H. M. AU - Pieterse, C. M. J. AU - Jonge, R. AU - Berendsen, R. L. PY - 2018 DA - 2018// TI - The soil-borne legacy JO - Cell VL - 172 UR - https://doi.org/10.1016/j.cell.2018.02.024 DO - 10.1016/j.cell.2018.02.024 ID - Bakker2018 ER - TY - JOUR AU - Goh, C. -. H. AU - Veliz Vallejos, D. F. AU - Nicotra, A. B. AU - Mathesius, U. PY - 2013 DA - 2013// TI - The impact of beneficial plant-associated microbes on plant phenotypic plasticity JO - J Chem Ecol VL - 39 UR - https://doi.org/10.1007/s10886-013-0326-8 DO - 10.1007/s10886-013-0326-8 ID - Goh2013 ER - TY - JOUR AU - Pieterse, C. M. J. AU - Jonge, R. AU - Berendsen, R. L. PY - 2016 DA - 2016// TI - The soil-borne supremacy JO - Trends Plant Sci VL - 21 UR - https://doi.org/10.1016/j.tplants.2016.01.018 DO - 10.1016/j.tplants.2016.01.018 ID - Pieterse2016 ER - TY - JOUR AU - Schlaeppi, K. AU - Bulgarelli, D. PY - 2015 DA - 2015// TI - The plant microbiome at work JO - Mol Plant Microbe Interact VL - 28 UR - https://doi.org/10.1094/MPMI-10-14-0334-FI DO - 10.1094/MPMI-10-14-0334-FI ID - Schlaeppi2015 ER - TY - JOUR AU - Berendsen, R. L. AU - Pieterse, C. M. J. AU - Bakker, P. A. H. M. PY - 2012 DA - 2012// TI - The rhizosphere microbiome and plant health JO - Trends Plant Sci VL - 17 UR - https://doi.org/10.1016/j.tplants.2012.04.001 DO - 10.1016/j.tplants.2012.04.001 ID - Berendsen2012 ER - TY - JOUR AU - Philippot, L. AU - Raaijmakers, J. M. AU - Lemanceau, P. AU - Putten, W. H. PY - 2013 DA - 2013// TI - Going back to the roots: the microbial ecology of the rhizosphere JO - Nat Rev Microbiol VL - 11 UR - https://doi.org/10.1038/nrmicro3109 DO - 10.1038/nrmicro3109 ID - Philippot2013 ER - TY - JOUR AU - Dutta, S. AU - Podile, A. R. PY - 2010 DA - 2010// TI - Plant growth promoting rhizobacteria (PGPR): the bugs to debug the root zone JO - Crit Rev Microbiol VL - 36 UR - https://doi.org/10.3109/10408411003766806 DO - 10.3109/10408411003766806 ID - Dutta2010 ER - TY - JOUR AU - Lundberg, D. S. AU - Lebeis, S. L. AU - Paredes, S. H. AU - Yourstone, S. AU - Gehring, J. AU - Malfatti, S. PY - 2012 DA - 2012// TI - Defining the core Arabidopsis thaliana root microbiome JO - Nature VL - 488 UR - https://doi.org/10.1038/nature11237 DO - 10.1038/nature11237 ID - Lundberg2012 ER - TY - JOUR AU - Peiffer, J. A. AU - Spor, A. AU - Koren, O. AU - Jin, Z. AU - Tringe, S. G. AU - Dangl, J. L. PY - 2013 DA - 2013// TI - Diversity and heritability of the maize rhizosphere microbiome under field conditions JO - Proc Natl Acad Sci VL - 110 UR - https://doi.org/10.1073/pnas.1302837110 DO - 10.1073/pnas.1302837110 ID - Peiffer2013 ER - TY - JOUR AU - Fitzpatrick, C. R. AU - Copeland, J. AU - Wang, P. W. AU - Guttman, D. S. AU - Kotanen, P. M. AU - Johnson, M. T. J. PY - 2018 DA - 2018// TI - Assembly and ecological function of the root microbiome across angiosperm plant species JO - Proc Natl Acad Sci VL - 115 UR - https://doi.org/10.1073/pnas.1717617115 DO - 10.1073/pnas.1717617115 ID - Fitzpatrick2018 ER - TY - JOUR AU - Lu, T. AU - Ke, M. AU - Peijnenburg, W. J. G. M. AU - Zhu, Y. AU - Zhang, M. AU - Sun, L. PY - 2018 DA - 2018// TI - Investigation of rhizospheric microbial communities in wheat, barley, and two rice varieties at the seedling stage JO - J Agric Food Chem VL - 66 UR - https://doi.org/10.1021/acs.jafc.7b06155 DO - 10.1021/acs.jafc.7b06155 ID - Lu2018 ER - TY - JOUR AU - Turner, T. R. AU - Ramakrishnan, K. AU - Walshaw, J. AU - Heavens, D. AU - Alston, M. AU - Swarbreck, D. PY - 2013 DA - 2013// TI - Comparative metatranscriptomics reveals kingdom level changes in the rhizosphere microbiome of plants JO - ISME J VL - 7 UR - https://doi.org/10.1038/ismej.2013.119 DO - 10.1038/ismej.2013.119 ID - Turner2013 ER - TY - JOUR AU - Warembourg, F. R. AU - Roumet, C. AU - Lafont, F. PY - 2003 DA - 2003// TI - Differences in rhizosphere carbon-partitioning among plant species of different families JO - Plant Soil VL - 256 UR - https://doi.org/10.1023/A:1026147622800 DO - 10.1023/A:1026147622800 ID - Warembourg2003 ER - TY - JOUR AU - Bulgarelli, D. AU - Garrido-Oter, R. AU - Münch, P. C. AU - Weiman, A. AU - Dröge, J. AU - Pan, Y. PY - 2015 DA - 2015// TI - Structure and function of the bacterial root microbiota in wild and domesticated barley JO - Cell Host Microbe VL - 17 UR - https://doi.org/10.1016/j.chom.2015.01.011 DO - 10.1016/j.chom.2015.01.011 ID - Bulgarelli2015 ER - TY - JOUR AU - Timm, C. M. AU - Carter, K. R. AU - Carrell, A. A. AU - Jun, S. R. AU - Jawdy, S. S. PY - 2018 DA - 2018// TI - Abiotic stresses shift belowground populus-associated bacteria toward a core stress microbiome JO - mSystems VL - 3 UR - https://doi.org/10.1128/mSystems.00070-17 DO - 10.1128/mSystems.00070-17 ID - Timm2018 ER - TY - JOUR AU - Castrillo, G. AU - Teixeira, P. J. P. L. AU - Paredes, S. H. AU - Law, T. F. AU - Lorenzo, L. AU - Feltcher, M. E. PY - 2017 DA - 2017// TI - Root microbiota drive direct integration of phosphate stress and immunity JO - Nature VL - 543 UR - https://doi.org/10.1038/nature21417 DO - 10.1038/nature21417 ID - Castrillo2017 ER - TY - JOUR AU - Pérez-Jaramillo, J. E. AU - Mendes, R. AU - Raaijmakers, J. M. PY - 2016 DA - 2016// TI - Impact of plant domestication on rhizosphere microbiome assembly and functions JO - Plant Mol Biol VL - 90 UR - https://doi.org/10.1007/s11103-015-0337-7 DO - 10.1007/s11103-015-0337-7 ID - Pérez-Jaramillo2016 ER - TY - JOUR AU - Edwards, J. AU - Johnson, C. AU - Santos-Medellín, C. AU - Lurie, E. AU - Podishetty, N. K. AU - Bhatnagar, S. PY - 2015 DA - 2015// TI - Structure, variation, and assembly of the root-associated microbiomes of rice JO - Proc Natl Acad Sci VL - 112 UR - https://doi.org/10.1073/pnas.1414592112 DO - 10.1073/pnas.1414592112 ID - Edwards2015 ER - TY - JOUR AU - Panke-Buisse, K. AU - Poole, A. C. AU - Goodrich, J. K. AU - Ley, R. E. AU - Kao-Kniffin, J. PY - 2015 DA - 2015// TI - Selection on soil microbiomes reveals reproducible impacts on plant function JO - ISME J VL - 9 UR - https://doi.org/10.1038/ismej.2014.196 DO - 10.1038/ismej.2014.196 ID - Panke-Buisse2015 ER - TY - JOUR AU - Lebeis, S. L. AU - Paredes, S. H. AU - Lundberg, D. S. AU - Breakfield, N. AU - Gehring, J. AU - McDonald, M. PY - 2015 DA - 2015// TI - Salicylic acid modulates colonization of the root microbiome by specific bacterial taxa JO - Science VL - 349 UR - https://doi.org/10.1126/science.aaa8764 DO - 10.1126/science.aaa8764 ID - Lebeis2015 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 - Hartman, G. L. AU - West, E. D. AU - Herman, T. K. PY - 2011 DA - 2011// TI - Crops that feed the world 2. Soybean-worldwide production, use, and constraints caused by pathogens and pests JO - Food Security VL - 3 UR - https://doi.org/10.1007/s12571-010-0108-x DO - 10.1007/s12571-010-0108-x ID - Hartman2011 ER - TY - JOUR AU - Hill, J. AU - Nelson, E. AU - Tilman, D. AU - Polasky, S. AU - Tiffany, D. PY - 2006 DA - 2006// TI - Environmental, economic, and energetic costs and benefits of biodiesel and ethanol biofuels JO - Proc Natl Acad Sci VL - 103 UR - https://doi.org/10.1073/pnas.0604600103 DO - 10.1073/pnas.0604600103 ID - Hill2006 ER - TY - JOUR AU - Herridge, D. F. AU - Peoples, M. B. AU - Boddey, R. M. PY - 2008 DA - 2008// TI - Global inputs of biological nitrogen fixation in agricultural systems JO - Plant Soil VL - 311 UR - https://doi.org/10.1007/s11104-008-9668-3 DO - 10.1007/s11104-008-9668-3 ID - Herridge2008 ER - TY - STD TI - Monthly biodiesel production report - energy information administration. https://www.eia.gov/biofuels/biodiesel/production/. Accessed 8 Oct 2018. UR - https://www.eia.gov/biofuels/biodiesel/production/ ID - ref26 ER - TY - JOUR AU - Vance, C. P. PY - 2001 DA - 2001// TI - Symbiotic nitrogen fixation and phosphorus acquisition. Plant nutrition in a world of declining renewable resources JO - Plant Physiol VL - 127 UR - https://doi.org/10.1104/pp.010331 DO - 10.1104/pp.010331 ID - Vance2001 ER - TY - JOUR AU - Zahran, H. H. PY - 1999 DA - 1999// TI - Rhizobium-legume symbiosis and nitrogen fixation under severe conditions and in an arid climate JO - Microbiol Mol Biol Rev VL - 63 ID - Zahran1999 ER - TY - JOUR AU - Salvagiotti, F. AU - Cassman, K. G. AU - Specht, J. E. AU - Walters, D. T. AU - Weiss, A. AU - Dobermann, A. PY - 2008 DA - 2008// TI - Nitrogen uptake, fixation and response to fertilizer N in soybeans: A review JO - Field Crops Res VL - 108 UR - https://doi.org/10.1016/j.fcr.2008.03.001 DO - 10.1016/j.fcr.2008.03.001 ID - Salvagiotti2008 ER - TY - JOUR AU - Hartman, K. AU - Heijden, M. G. AU - Roussely-Provent, V. AU - Walser, J. -. C. AU - Schlaeppi, K. PY - 2017 DA - 2017// TI - Deciphering composition and function of the root microbiome of a legume plant JO - Microbiome VL - 5 UR - https://doi.org/10.1186/s40168-016-0220-z DO - 10.1186/s40168-016-0220-z ID - Hartman2017 ER - TY - JOUR AU - Hassani, M. A. AU - Durán, P. AU - Hacquard, S. PY - 2018 DA - 2018// TI - Microbial interactions within the plant holobiont JO - Microbiome VL - 6 UR - https://doi.org/10.1186/s40168-018-0445-0 DO - 10.1186/s40168-018-0445-0 ID - Hassani2018 ER - TY - JOUR AU - Anderson, M. J. AU - Willis, T. J. PY - 2003 DA - 2003// TI - Canonical analysis of principal coordinates: a useful method of constrained ordination for ecology JO - Ecology VL - 84 UR - https://doi.org/10.1890/0012-9658(2003)084[0511:CAOPCA]2.0.CO;2 DO - 10.1890/0012-9658(2003)084[0511:CAOPCA]2.0.CO;2 ID - Anderson2003 ER - TY - JOUR AU - Hayashi, M. AU - Saeki, Y. AU - Haga, M. AU - Harada, K. AU - Kouchi, H. AU - Umehara, Y. PY - 2012 DA - 2012// TI - Rj (rj) genes involved in nitrogen-fixing root nodule formation in soybean JO - Breed Sci VL - 61 UR - https://doi.org/10.1270/jsbbs.61.544 DO - 10.1270/jsbbs.61.544 ID - Hayashi2012 ER - TY - JOUR AU - Mendes, L. W. AU - Kuramae, E. E. AU - Navarrete, A. A. AU - 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 - Sugiyama, A. AU - Ueda, Y. AU - Zushi, T. AU - Takase, H. AU - Yazaki, K. PY - 2014 DA - 2014// TI - Changes in the bacterial community of soybean rhizospheres during growth in the field JO - PLoS One VL - 9 UR - https://doi.org/10.1371/journal.pone.0100709 DO - 10.1371/journal.pone.0100709 ID - Sugiyama2014 ER - TY - JOUR AU - Xiao, X. AU - Chen, W. AU - Zong, L. AU - Yang, J. AU - Jiao, S. AU - Lin, Y. PY - 2017 DA - 2017// TI - Two cultivated legume plants reveal the enrichment process of the microbiome in the rhizocompartments JO - Mol Ecol VL - 26 UR - https://doi.org/10.1111/mec.14027 DO - 10.1111/mec.14027 ID - Xiao2017 ER - TY - JOUR AU - Beckers, B. AU - Beeck, M. AU - Weyens, N. AU - Boerjan, W. AU - Vangronsveld, J. PY - 2017 DA - 2017// TI - Structural variability and niche differentiation in the rhizosphere and endosphere bacterial microbiome of field-grown poplar trees JO - Microbiome VL - 5 UR - https://doi.org/10.1186/s40168-017-0241-2 DO - 10.1186/s40168-017-0241-2 ID - Beckers2017 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 - Souza, R. S. C. AU - Okura, V. K. AU - Armanhi, J. S. L. AU - Jorrín, B. AU - Lozano, N. AU - Silva, M. J. PY - 2016 DA - 2016// TI - Unlocking the bacterial and fungal communities assemblages of sugarcane microbiome JO - Sci Rep VL - 6 UR - https://doi.org/10.1038/srep28774 DO - 10.1038/srep28774 ID - Souza2016 ER - TY - JOUR AU - Sasse, J. AU - Martinoia, E. AU - Northen, T. PY - 2018 DA - 2018// TI - Feed your friends: do plant exudates shape the root microbiome? JO - Trends Plant Sci VL - 23 UR - https://doi.org/10.1016/j.tplants.2017.09.003 DO - 10.1016/j.tplants.2017.09.003 ID - Sasse2018 ER - TY - JOUR AU - Zgadzaj, R. AU - Garrido-Oter, R. AU - Jensen, D. B. AU - Koprivova, A. AU - Schulze-Lefert, P. AU - Radutoiu, S. PY - 2016 DA - 2016// TI - Root nodule symbiosis in Lotus japonicus drives the establishment of distinctive rhizosphere, root, and nodule bacterial communities JO - Proc Natl Acad Sci VL - 113 UR - https://doi.org/10.1073/pnas.1616564113 DO - 10.1073/pnas.1616564113 ID - Zgadzaj2016 ER - TY - JOUR AU - White, L. J. AU - Jothibasu, K. AU - Reese, R. N. AU - Brözel, V. S. AU - Subramanian, S. PY - 2015 DA - 2015// TI - Spatio temporal influence of isoflavonoids on bacterial diversity in the soybean rhizosphere JO - Mol Plant Microbe Interact VL - 28 UR - https://doi.org/10.1094/MPMI-08-14-0247-R DO - 10.1094/MPMI-08-14-0247-R ID - White2015 ER - TY - JOUR AU - Shameer, S. AU - Prasad, T. N. V. K. V. PY - 2018 DA - 2018// TI - Plant growth promoting rhizobacteria for sustainable agricultural practices with special reference to biotic and abiotic stresses JO - Plant Growth Regul VL - 84 UR - https://doi.org/10.1007/s10725-017-0365-1 DO - 10.1007/s10725-017-0365-1 ID - Shameer2018 ER - TY - JOUR AU - Gupta, G. AU - Parihar, S. S. AU - Ahirwar, N. K. AU - Snehi, S. K. AU - Singh, V. PY - 2015 DA - 2015// TI - Plant growth promoting rhizobacteria (PGPR): current and future prospects for development of sustainable agriculture JO - J Microb Biochem Technol VL - 7 ID - Gupta2015 ER - TY - JOUR AU - Bulgarelli, D. AU - Schlaeppi, K. AU - Spaepen, S. AU - Loren van Themaat, E. AU - Schulze-Lefert, P. PY - 2013 DA - 2013// TI - Structure and functions of the bacterial microbiota of plants JO - Annu Rev Plant Biol VL - 64 UR - https://doi.org/10.1146/annurev-arplant-050312-120106 DO - 10.1146/annurev-arplant-050312-120106 ID - Bulgarelli2013 ER - TY - JOUR AU - Weisskopf, L. AU - Heller, S. AU - Eberl, L. PY - 2011 DA - 2011// TI - Burkholderia species are major inhabitants of white lupin cluster roots JO - Appl Environ Microbiol VL - 77 UR - https://doi.org/10.1128/AEM.05845-11 DO - 10.1128/AEM.05845-11 ID - Weisskopf2011 ER - TY - JOUR AU - Neumann, G. AU - Martinoia, E. PY - 2002 DA - 2002// TI - Cluster roots-an underground adaptation for survival in extreme environments JO - Trends Plant Sci VL - 7 UR - https://doi.org/10.1016/S1360-1385(02)02241-0 DO - 10.1016/S1360-1385(02)02241-0 ID - Neumann2002 ER - TY - JOUR AU - Zhalnina, K. AU - Louie, K. B. AU - Hao, Z. AU - Mansoori, N. AU - Rocha, U. N. AU - Shi, S. PY - 2018 DA - 2018// TI - Dynamic root exudate chemistry and microbial substrate preferences drive patterns in rhizosphere microbial community assembly JO - Nat Microbiol VL - 3 UR - https://doi.org/10.1038/s41564-018-0129-3 DO - 10.1038/s41564-018-0129-3 ID - Zhalnina2018 ER - TY - JOUR AU - Pérez-Jaramillo, J. E. AU - Carrión, V. J. AU - Bosse, M. AU - Ferrão, L. F. V. AU - Hollander, M. AU - Garcia, A. A. F. PY - 2017 DA - 2017// TI - Linking rhizosphere microbiome composition of wild and domesticated Phaseolus vulgaris to genotypic and root phenotypic traits JO - ISME J VL - 11 UR - https://doi.org/10.1038/ismej.2017.85 DO - 10.1038/ismej.2017.85 ID - Pérez-Jaramillo2017 ER - TY - JOUR AU - Cardinale, M. AU - Grube, M. AU - Erlacher, A. AU - Quehenberger, J. AU - Berg, G. PY - 2015 DA - 2015// TI - Bacterial networks and co-occurrence relationships in the lettuce root microbiota JO - Environ Microbiol VL - 17 UR - https://doi.org/10.1111/1462-2920.12686 DO - 10.1111/1462-2920.12686 ID - Cardinale2015 ER - TY - JOUR AU - Zachow, C. AU - Müller, H. AU - Tilcher, R. AU - Berg, G. PY - 2014 DA - 2014// TI - Differences between the rhizosphere microbiome of Beta vulgaris ssp. maritima - ancestor of all beet crops - and modern sugar beets JO - Front Microbiol VL - 5 UR - https://doi.org/10.3389/fmicb.2014.00415 DO - 10.3389/fmicb.2014.00415 ID - Zachow2014 ER - TY - JOUR AU - Zhao, J. AU - Fu, J. AU - Liao, H. AU - He, Y. AU - Nian, H. AU - Hu, Y. PY - 2004 DA - 2004// TI - Characterization of root architecture in an applied core collection for phosphorus efficiency of soybean germplasm JO - Chin Sci Bull VL - 49 UR - https://doi.org/10.1007/BF03184131 DO - 10.1007/BF03184131 ID - Zhao2004 ER - TY - JOUR AU - Hunt, S. AU - Layzell, D. B. PY - 1993 DA - 1993// TI - Gas exchange of legume nodules and the regulation of nitrogenase activity JO - Annu Rev Plant Physiol Plant Mol Biol VL - 44 UR - https://doi.org/10.1146/annurev.pp.44.060193.002411 DO - 10.1146/annurev.pp.44.060193.002411 ID - Hunt1993 ER - TY - JOUR AU - Agler, M. T. AU - Ruhe, J. AU - Kroll, S. AU - Morhenn, C. AU - Kim, S. -. T. AU - Weigel, D. PY - 2016 DA - 2016// TI - Microbial hub taxa link host and abiotic factors to plant microbiome variation JO - PLoS Biol VL - 14 UR - https://doi.org/10.1371/journal.pbio.1002352 DO - 10.1371/journal.pbio.1002352 ID - Agler2016 ER - TY - JOUR AU - Poudel, R. AU - Jumpponen, A. AU - Schlatter, D. C. AU - Paulitz, T. C. AU - Gardener, B. B. M. AU - Kinkel, L. L. PY - 2016 DA - 2016// TI - Microbiome networks: A systems framework for identifying candidate microbial assemblages for disease management JO - Phytopathology VL - 106 UR - https://doi.org/10.1094/PHYTO-02-16-0058-FI DO - 10.1094/PHYTO-02-16-0058-FI ID - Poudel2016 ER - TY - JOUR AU - Matilla, M. A. AU - Espinosa-Urgel, M. AU - Rodríguez-Herva, J. J. AU - Ramos, J. L. AU - Ramos-González, M. I. PY - 2007 DA - 2007// TI - Genomic analysis reveals the major driving forces of bacterial life in the rhizosphere JO - Genome Biol VL - 8 UR - https://doi.org/10.1186/gb-2007-8-9-r179 DO - 10.1186/gb-2007-8-9-r179 ID - Matilla2007 ER - TY - JOUR AU - Levy, A. AU - Salas Gonzalez, I. AU - Mittelviefhaus, M. AU - Clingenpeel, S. AU - Herrera Paredes, S. AU - Miao, J. PY - 2018 DA - 2018// TI - Genomic features of bacterial adaptation to plants JO - Nat Genet VL - 50 UR - https://doi.org/10.1038/s41588-017-0012-9 DO - 10.1038/s41588-017-0012-9 ID - Levy2018 ER - TY - JOUR AU - Allison, S. D. AU - Martiny, J. B. H. PY - 2008 DA - 2008// TI - Resistance, resilience, and redundancy in microbial communities JO - Proc Natl Acad Sci VL - 105 UR - https://doi.org/10.1073/pnas.0801925105 DO - 10.1073/pnas.0801925105 ID - Allison2008 ER - TY - JOUR AU - Baetz, U. AU - Martinoia, E. PY - 2014 DA - 2014// TI - Root exudates: the hidden part of plant defense JO - Trends Plant Sci VL - 19 UR - https://doi.org/10.1016/j.tplants.2013.11.006 DO - 10.1016/j.tplants.2013.11.006 ID - Baetz2014 ER - TY - JOUR AU - Görke, B. AU - Stülke, J. PY - 2008 DA - 2008// TI - Carbon catabolite repression in bacteria: many ways to make the most out of nutrients JO - Nat Rev Microbiol VL - 6 UR - https://doi.org/10.1038/nrmicro1932 DO - 10.1038/nrmicro1932 ID - Görke2008 ER - TY - JOUR AU - Seo, J. -. S. AU - Keum, Y. -. S. AU - Li, Q. X. PY - 2009 DA - 2009// TI - Bacterial degradation of aromatic compounds JO - Int J Environ Res Public Health VL - 6 UR - https://doi.org/10.3390/ijerph6010278 DO - 10.3390/ijerph6010278 ID - Seo2009 ER - TY - JOUR AU - Wenke, K. AU - Kai, M. AU - Piechulla, B. PY - 2010 DA - 2010// TI - Belowground volatiles facilitate interactions between plant roots and soil organisms JO - Planta VL - 231 UR - https://doi.org/10.1007/s00425-009-1076-2 DO - 10.1007/s00425-009-1076-2 ID - Wenke2010 ER - TY - JOUR AU - Mahoney, A. K. AU - Yin, C. AU - Hulbert, S. H. PY - 2017 DA - 2017// TI - Community structure, species variation, and potential functions of rhizosphere-associated bacteria of different winter wheat (Triticum aestivum) cultivars JO - Front Plant Sci VL - 8 UR - https://doi.org/10.3389/fpls.2017.00132 DO - 10.3389/fpls.2017.00132 ID - Mahoney2017 ER - TY - JOUR AU - Takahashi, S. AU - Tomita, J. AU - Nishioka, K. AU - Hisada, T. AU - Nishijima, M. PY - 2014 DA - 2014// TI - Development of a prokaryotic universal primer for simultaneous analysis of Bacteria and Archaea using next-generation sequencing JO - PLoS One VL - 9 UR - https://doi.org/10.1371/journal.pone.0105592 DO - 10.1371/journal.pone.0105592 ID - Takahashi2014 ER - TY - JOUR AU - Lundberg, D. S. AU - Yourstone, S. AU - Mieczkowski, P. AU - Jones, C. D. AU - Dangl, J. L. PY - 2013 DA - 2013// TI - Practical innovations for high-throughput amplicon sequencing JO - Nat Methods VL - 10 UR - https://doi.org/10.1038/nmeth.2634 DO - 10.1038/nmeth.2634 ID - Lundberg2013 ER - TY - JOUR AU - Kozich, J. J. AU - Westcott, S. L. AU - Baxter, N. T. AU - Highlander, S. K. AU - Schloss, P. D. PY - 2013 DA - 2013// TI - Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform JO - Appl Environ Microbiol VL - 79 UR - https://doi.org/10.1128/AEM.01043-13 DO - 10.1128/AEM.01043-13 ID - Kozich2013 ER - TY - JOUR AU - Rognes, T. AU - Flouri, T. AU - Nichols, B. AU - Quince, C. AU - Mahé, F. PY - 2016 DA - 2016// TI - VSEARCH: a versatile open source tool for metagenomics JO - PeerJ VL - 4 UR - https://doi.org/10.7717/peerj.2584 DO - 10.7717/peerj.2584 ID - Rognes2016 ER - TY - JOUR AU - Edgar, R. C. AU - Haas, B. J. AU - Clemente, J. C. AU - Quince, C. AU - Knight, R. PY - 2011 DA - 2011// TI - UCHIME improves sensitivity and speed of chimera detection JO - Bioinformatics VL - 27 UR - https://doi.org/10.1093/bioinformatics/btr381 DO - 10.1093/bioinformatics/btr381 ID - Edgar2011 ER - TY - JOUR AU - Clarke, K. R. PY - 1993 DA - 1993// TI - Non-parametric multivariate analyses of changes in community structure JO - Austral Ecol VL - 18 UR - https://doi.org/10.1111/j.1442-9993.1993.tb00438.x DO - 10.1111/j.1442-9993.1993.tb00438.x ID - Clarke1993 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 - JOUR AU - Asnicar, F. AU - Weingart, G. AU - Tickle, T. L. AU - Huttenhower, C. AU - Segata, N. PY - 2015 DA - 2015// TI - Compact graphical representation of phylogenetic data and metadata with GraPhlAn JO - PeerJ VL - 3 UR - https://doi.org/10.7717/peerj.1029 DO - 10.7717/peerj.1029 ID - Asnicar2015 ER - TY - JOUR AU - Friedman, J. AU - Alm, E. J. PY - 2012 DA - 2012// TI - Inferring correlation networks from genomic survey data JO - PLoS Comput Biol VL - 8 UR - https://doi.org/10.1371/journal.pcbi.1002687 DO - 10.1371/journal.pcbi.1002687 ID - Friedman2012 ER - TY - JOUR AU - Csardi, G. AU - Nepusz, T. PY - 2006 DA - 2006// TI - The igraph software package for complex network research JO - InterJournal Complex Syst VL - 1695 ID - Csardi2006 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 - Love, M. I. AU - Huber, W. AU - Anders, S. PY - 2014 DA - 2014// TI - Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 JO - Genome Biol VL - 15 UR - https://doi.org/10.1186/s13059-014-0550-8 DO - 10.1186/s13059-014-0550-8 ID - Love2014 ER - TY - BOOK AU - Kolde, R. PY - 2015 DA - 2015// TI - pheatmap: pretty heatmaps. R package version 1.0. 8 ID - Kolde2015 ER -