Microbial Interkingdom Interactions in Roots Promote Arabidopsis Survival

[1]  Kazutaka Katoh,et al.  MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization , 2017, Briefings Bioinform..

[2]  S. Hacquard,et al.  Microbial interactions within the plant holobiont , 2018, Microbiome.

[3]  Eoin L. Brodie,et al.  Dynamic root exudate chemistry and microbial substrate preferences drive patterns in rhizosphere microbial community assembly , 2018, Nature Microbiology.

[4]  J. Tiedje,et al.  FlowPot axenic plant growth system for microbiota research , 2018, bioRxiv.

[5]  G. Coupland,et al.  Root-associated fungal microbiota of nonmycorrhizal Arabis alpina and its contribution to plant phosphorus nutrition , 2017, Proceedings of the National Academy of Sciences.

[6]  Sur Herrera Paredes,et al.  Root microbiota drive direct integration of phosphate stress and immunity , 2017, Nature.

[7]  J. Maciá‐Vicente,et al.  Influence of phylogenetic conservatism and trait convergence on the interactions between fungal root endophytes and plants , 2016, The ISME Journal.

[8]  R. Garrido-Oter,et al.  Root nodule symbiosis in Lotus japonicus drives the establishment of distinctive rhizosphere, root, and nodule bacterial communities , 2016, Proceedings of the National Academy of Sciences.

[9]  Bernard Henrissat,et al.  Survival trade-offs in plant roots during colonization by closely related beneficial and pathogenic fungi , 2016, Nature Communications.

[10]  Peer Bork,et al.  Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees , 2016, Nucleic Acids Res..

[11]  P. Schulze-Lefert,et al.  Root Endophyte Colletotrichum tofieldiae Confers Plant Fitness Benefits that Are Phosphate Status Dependent , 2016, Cell.

[12]  P. Greenfield,et al.  Fungal identification using a Bayesian classifier and the Warcup training set of internal transcribed spacer sequences , 2016, Mycologia.

[13]  Detlef Weigel,et al.  Microbial Hub Taxa Link Host and Abiotic Factors to Plant Microbiome Variation , 2016, PLoS biology.

[14]  S. Tringe,et al.  Plant compartment and biogeography affect microbiome composition in cultivated and native Agave species , 2015, The New phytologist.

[15]  R. Logtestijn,et al.  A widespread plant-fungal-bacterial symbiosis promotes plant biodiversity, plant nutrition and seedling recruitment , 2015, The ISME Journal.

[16]  Karoline Faust,et al.  CoNet app: inference of biological association networks using Cytoscape , 2016, F1000Research.

[17]  Alice C. McHardy,et al.  Functional overlap of the Arabidopsis leaf and root microbiota , 2015, Nature.

[18]  I. Baldwin,et al.  Native root-associated bacteria rescue a plant from a sudden-wilt disease that emerged during continuous cropping , 2015, Proceedings of the National Academy of Sciences.

[19]  Sur Herrera Paredes,et al.  Salicylic acid modulates colonization of the root microbiome by specific bacterial taxa , 2015, Science.

[20]  R. Knight,et al.  Microbiota and Host Nutrition across Plant and Animal Kingdoms. , 2015, Cell host & microbe.

[21]  Nicolas Bailly,et al.  A Higher Level Classification of All Living Organisms , 2015, PloS one.

[22]  R. Henrik Nilsson,et al.  A Comprehensive, Automatically Updated Fungal ITS Sequence Dataset for Reference-Based Chimera Control in Environmental Sequencing Efforts , 2015, Microbes and environments.

[23]  Cameron Johnson,et al.  Structure, variation, and assembly of the root-associated microbiomes of rice , 2015, Proceedings of the National Academy of Sciences.

[24]  I. Maldonado-Mendoza,et al.  A high‐throughput screening assay to identify bacterial antagonists against Fusarium verticillioides , 2014, Journal of basic microbiology.

[25]  M. Thines,et al.  Root-associated fungi of Arabidopsis thaliana and Microthlaspi perfoliatum , 2014, Fungal Diversity.

[26]  K. Peay,et al.  Endemism and functional convergence across the North American soil mycobiome , 2014, Proceedings of the National Academy of Sciences.

[27]  C. Schadt,et al.  A Multifactor Analysis of Fungal and Bacterial Community Structure in the Root Microbiome of Mature Populus deltoides Trees , 2013, PloS one.

[28]  R. Henrik Nilsson,et al.  Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for analysis of environmental sequencing data , 2013 .

[29]  Mihai Pop,et al.  Robust methods for differential abundance analysis in marker gene surveys , 2013, Nature Methods.

[30]  Robert C. Edgar,et al.  UPARSE: highly accurate OTU sequences from microbial amplicon reads , 2013, Nature Methods.

[31]  P. Poole,et al.  The plant microbiome , 2013, Genome Biology.

[32]  Jonathan Friedman,et al.  Inferring Correlation Networks from Genomic Survey Data , 2012, PLoS Comput. Biol..

[33]  Robert C. Edgar,et al.  Defining the core Arabidopsis thaliana root microbiome , 2012, Nature.

[34]  R. Amann,et al.  Revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota , 2012, Nature.

[35]  Vladimir Makarenkov,et al.  T-REX: a web server for inferring, validating and visualizing phylogenetic trees and networks , 2012, Nucleic Acids Res..

[36]  William A. Walters,et al.  QIIME allows analysis of high-throughput community sequencing data , 2010, Nature Methods.

[37]  Rob Knight,et al.  PyNAST: a flexible tool for aligning sequences to a template alignment , 2009, Bioinform..

[38]  Andrea Lancichinetti,et al.  Community detection algorithms: a comparative analysis: invited presentation, extended abstract , 2009, VALUETOOLS.

[39]  J. Tiedje,et al.  Naïve Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy , 2007, Applied and Environmental Microbiology.

[40]  C. Emmerling,et al.  Methods for evaluating human impact on soil microorganisms based on their activity, biomass, and diversity in agricultural soils , 2006 .

[41]  Eoin L. Brodie,et al.  Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB , 2006, Applied and Environmental Microbiology.

[42]  P. Shannon,et al.  Cytoscape: a software environment for integrated models of biomolecular interaction networks. , 2003, Genome research.

[43]  J. Garbaye Tansley Review No. 76 Helper bacteria: a new dimension to the mycorrhizal symbiosis. , 1994, The New phytologist.

[44]  Daniel R. Mishell,et al.  A multifactor analysis , 1979 .