A genetically and functionally diverse group of non-diazotrophic Bradyrhizobium spp. colonizes the root endophytic compartment of Arabidopsis thaliana

[1]  D. R. Hoagland,et al.  The Water-Culture Method for Growing Plants Without Soil , 2018 .

[2]  D. Latrasse,et al.  Plant-Specific Histone Deacetylases HDT1/2 Regulate GIBBERELLIN 2-OXIDASE2 Expression to Control Arabidopsis Root Meristem Cell Number[OPEN] , 2017, Plant Cell.

[3]  M. Ragan,et al.  Evolutionary conservation of a core root microbiome across plant phyla along a tropical soil chronosequence , 2017, Nature Communications.

[4]  M. Bosse,et al.  Linking rhizosphere microbiome composition of wild and domesticated Phaseolus vulgaris to genotypic and root phenotypic traits , 2017, The ISME Journal.

[5]  R. Kolter,et al.  Simplified and representative bacterial community of maize roots , 2017, Proceedings of the National Academy of Sciences.

[6]  Takahiro Tsukui,et al.  Complete Genome Sequence of Bradyrhizobium diazoefficiens USDA 122, a Nitrogen-Fixing Soybean Symbiont , 2017, Genome Announcements.

[7]  J. Chun,et al.  A large-scale evaluation of algorithms to calculate average nucleotide identity , 2017, Antonie van Leeuwenhoek.

[8]  M. Woodward,et al.  Novel European free-living, non-diazotrophic Bradyrhizobium isolates from contrasting soils that lack nodulation and nitrogen fixation genes – a genome comparison , 2016, Scientific Reports.

[9]  J. Fuhrman,et al.  Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples. , 2016, Environmental microbiology.

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

[12]  Evgeny M. Zdobnov,et al.  BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs , 2015, Bioinform..

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

[14]  S. Hallam,et al.  Non-symbiotic Bradyrhizobium ecotypes dominate North American forest soils , 2015, The ISME Journal.

[15]  James E. Johnson,et al.  NCBI BLAST+ integrated into Galaxy , 2015, bioRxiv.

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

[17]  S. Tringe,et al.  MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm , 2014, Microbiome.

[18]  Torsten Seemann,et al.  Prokka: rapid prokaryotic genome annotation , 2014, Bioinform..

[19]  Björn Usadel,et al.  Trimmomatic: a flexible trimmer for Illumina sequence data , 2014, Bioinform..

[20]  C. Tian,et al.  Genetic Divergence of Bradyrhizobium Strains Nodulating Soybeans as Revealed by Multilocus Sequence Analysis of Genes Inside and Outside the Symbiosis Island , 2014, Applied and Environmental Microbiology.

[21]  Aidan C. Parte,et al.  LPSN—list of prokaryotic names with standing in nomenclature , 2013, Nucleic Acids Res..

[22]  M. Udvardi,et al.  Transport and metabolism in legume-rhizobia symbioses. , 2013, Annual review of plant biology.

[23]  Alexey A. Gurevich,et al.  QUAST: quality assessment tool for genome assemblies , 2013, Bioinform..

[24]  Richard Christen,et al.  Significant and persistent impact of timber harvesting on soil microbial communities in Northern coniferous forests , 2012, The ISME Journal.

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

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

[27]  Sergey I. Nikolenko,et al.  SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing , 2012, J. Comput. Biol..

[28]  D. Higgins,et al.  Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega , 2011, Molecular systems biology.

[29]  Joel L. Sachs,et al.  Evolutionary transitions in bacterial symbiosis , 2011, Proceedings of the National Academy of Sciences.

[30]  E. Simms,et al.  Origins of cheating and loss of symbiosis in wild Bradyrhizobium , 2010, Journal of evolutionary biology.

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

[32]  F. Martin,et al.  Pyrosequencing reveals a contrasted bacterial diversity between oak rhizosphere and surrounding soil. , 2010, Environmental microbiology reports.

[33]  Miriam L. Land,et al.  Trace: Tennessee Research and Creative Exchange Prodigal: Prokaryotic Gene Recognition and Translation Initiation Site Identification Recommended Citation Prodigal: Prokaryotic Gene Recognition and Translation Initiation Site Identification , 2022 .

[34]  J. Batut,et al.  Establishing nitrogen-fixing symbiosis with legumes: how many rhizobium recipes? , 2009, Trends in microbiology.

[35]  A. Willems,et al.  Multilocus sequence analysis of the genus Bradyrhizobium. , 2009, Systematic and applied microbiology.

[36]  J. Eisen,et al.  A simple, fast, and accurate method of phylogenomic inference , 2008, Genome Biology.

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

[38]  S. Andersson,et al.  The evolution of chronic infection strategies in the α-proteobacteria , 2004, Nature Reviews Microbiology.

[39]  Wei Qian,et al.  Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. , 2000, Molecular biology and evolution.

[40]  J. Vanderleyden,et al.  The Rhizobium-plant symbiosis. , 1995, Microbiological reviews.

[41]  Jun Zhu,et al.  Symbiosis within Symbiosis: Evolving Nitrogen-Fixing Legume Symbionts. , 2016, Trends in microbiology.

[42]  F. Bushman,et al.  QIIME allows integration and analysis of high-throughput community sequencing data. Nat. Meth. , 2010 .

[43]  S. Tabata,et al.  Complete genomic sequence of nitrogen-fixing symbiotic bacterium Bradyrhizobium japonicum USDA110. , 2002, DNA research : an international journal for rapid publication of reports on genes and genomes.

[44]  Susumu Goto,et al.  KEGG: Kyoto Encyclopedia of Genes and Genomes , 2000, Nucleic Acids Res..

[45]  Hiroyuki Ogata,et al.  KEGG: Kyoto Encyclopedia of Genes and Genomes , 1999, Nucleic Acids Res..

[46]  Sean R. Eddy,et al.  Profile hidden Markov models , 1998, Bioinform..

[47]  D. C. Jordan NOTES: Transfer of Rhizobium japonicum Buchanan 1980 to Bradyrhizobium gen. nov., a Genus of Slow-Growing, Root Nodule Bacteria from Leguminous Plants , 1982 .