Wild plant species growing closely connected in a subalpine meadow host distinct root-associated bacterial communities

Aleklett, 2013, The root microbiota—a fingerprint in the soil?, Plant and Soil, 370, 671, 10.1007/s11104-013-1647-7

Alford, 2009, The effects of flavonoid allelochemicals from knapweeds on legume-rhizobia candidates for restoration, Restoration Ecology, 17, 506, 10.1111/j.1526-100X.2008.00405.x

Altschul, 1990, Basic local alignment search tool, Journal of Molecular Biology, 215, 403, 10.1016/S0022-2836(05)80360-2

Anderson, 2004, PERMDISP: a FORTRAN computer program for permutational analysis of multivariate dispersions (for any two-factor ANOVA design) using permutation tests

Anderson, 2005, PERMANOVA: a FORTRAN computer program for permutational multivariate analysis of variance

Anderson, 2013, PERMANOVA, ANOSIM, and the Mantel test in the face of heterogeneous dispersions: What null hypothesis are you testing?, Ecological Monographs, 83, 557, 10.1890/12-2010.1

Bailey, 2005, Host plant genetics affect hidden ecological players: links among Populus, condensed tannins, and fungal endophyte infection, Canadian Journal of Botany, 83, 356, 10.1139/b05-008

Bais, 2004, How plants communicate using the underground information superhighway, Trends in Plant Science, 9, 26, 10.1016/j.tplants.2003.11.008

Bais, 2006, The role of root exudates in rhizosphere interactions with plants and other organisms, Annual Review of Plant Biology, 57, 233, 10.1146/annurev.arplant.57.032905.105159

Baldani, 1997, Recent advances in BNF with non-legume plants, Soil Biology and Biochemistry, 29, 911, 10.1016/S0038-0717(96)00218-0

Bardgett, 2014, Going underground: root traits as drivers of ecosystem processes, Trends in Ecology and Evolution, 29, 692, 10.1016/j.tree.2014.10.006

Becklin, 2012, Host identity impacts rhizosphere fungal communities associated with three alpine plant species, Microbial Ecology, 63, 682, 10.1007/s00248-011-9968-7

Bell, 2014, Rhizosphere stoichiometry: are C:N:P ratios of plants, soils, and enzymes conserved at the plant species-level?, New Phytologist, 201, 505, 10.1111/nph.12531

Berg, 2009, Plant species and soil type cooperatively shape the structure and function of microbial communities in the rhizosphere, FEMS Microbiology Ecology, 68, 1, 10.1111/j.1574-6941.2009.00654.x

Bodenhausen, 2013, Bacterial communities associated with the leaves and the roots of Arabidopsis thaliana, PLoS ONE, 8, e56329, 10.1371/journal.pone.0056329

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, Annual Review of Plant Biology, 64, 807, 10.1146/annurev-arplant-050312-120106

Caporaso, 2010, QIIME allows analysis of high-throughput community sequencing data, Nature Methods, 7, 335, 10.1038/nmeth.f.303

Chaparro, 2013, Root exudation of phytochemicals in Arabidopsis follows specific patterns that are developmentally programmed and correlate with soil microbial functions, PLoS ONE, 8, e55731, 10.1371/journal.pone.0055731

Chelius, 2001, The diversity of archaea and bacteria in association with the roots of Zea mays L, Microbial Ecology, 41, 252, 10.1007/s002480000087

Clarke, 2006, PRIMER v6: user manual/tutorial

Costa, 2006, Effects of site and plant species on rhizosphere community structure as revealed by molecular analysis of microbial guilds, FEMS Microbiology Ecology, 56, 236, 10.1111/j.1574-6941.2005.00026.x

de Ridder-Duine, 2005, Rhizosphere bacterial community composition in natural stands of Carex arenaria (sand sedge) is determined by bulk soil community composition, Soil Biology and Biochemistry, 37, 349, 10.1016/j.soilbio.2004.08.005

DeSantis, 2006, Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB, Applied and Environmental Microbiology, 72, 5069, 10.1128/AEM.03006-05

Doornbos, 2011, Impact of root exudates and plant defense signaling on bacterial communities in the rhizosphere. A review, Agronomy for Sustainable Development, 32, 227, 10.1007/s13593-011-0028-y

Farrar, 2003, How roots control the flux of carbon to the rhizosphere, Ecology, 84, 827, 10.1890/0012-9658(2003)084[0827:HRCTFO]2.0.CO;2

Fierer, 2008, The influence of sex, handedness, and washing on the diversity of hand surface bacteria, Proceedings of the Natural Academy of Science of the United States of America, 105, 17994, 10.1073/pnas.0807920105

Fierer, 2003, Variations in microbial community composition through two soil depth profiles, Soil Biology and Biochemistry, 35, 167, 10.1016/S0038-0717(02)00251-1

Garbeva, 2004, Microbial diversity in soil: selection microbial populations by plant and soil type and implications for disease suppressiveness, Annual Review of Phytopathology, 42, 243, 10.1146/annurev.phyto.42.012604.135455

Invasive hawkweeds (Hieracium spp.) in Northeastern British Columbia—Invasive plant risk assessment and literature search. Prepared for: British Columbia Ministry of Forests and Range Range Branch, Invasive Plants Program, Prince George, B.C

Gottel, 2011, Distinct microbial communities within the endosphere and rhizosphere of Populus deltoides roots across contrasting soil types, Applied and Environmental Microbiology, 77, 5934, 10.1128/AEM.05255-11

Green, 2007, Contrasting patterns of seed and root colonization by bacteria from the genus Chryseobacterium and from the family Oxalobacteraceae, The ISME Journal, 1, 291, 10.1038/ismej.2007.33

Haichar, 2008, Plant host habitat and root exudates shape soil bacterial community structure, The ISME Journal, 2, 1221, 10.1038/ismej.2008.80

Hamady, 2009, Microbial community profiling for human microbiome projects: tools, techniques, and challenges, Genome Research, 19, 1141, 10.1101/gr.085464.108

Hamady, 2010, Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data, The ISME Journal, 4, 17, 10.1038/ismej.2009.97

Hartmann, 2008, Plant-driven selection of microbes, Plant and Soil, 321, 235, 10.1007/s11104-008-9814-y

Hodge, 2009, Plant root growth, architecture and function, Plant and Soil, 321, 153, 10.1007/s11104-009-9929-9

İnceoğlu, 2010, Effects of plant genotype and growth stage on the betaproteobacterial communities associated with different potato cultivars in two fields, Applied and Environmental Microbiology, 76, 3675, 10.1128/AEM.00040-10

Johnson, 1990, Janthinocins A, B and C, novel peptide lactone antibiotics produced by Janthinobacterium lividum, The Journal of Antibiotics, 43, 920, 10.7164/antibiotics.43.920

Kane, 2007, Whole-genome analysis of the methyl tert-butyl ether-degrading beta-proteobacterium Methylibium petroleiphilum PM1, Journal of Bacteriology, 189, 1931, 10.1128/JB.01259-06

Kirchman, 2002, The ecology of Cytophaga-Flavobacteria in aquatic environments, FEMS Microbiology Ecology, 39, 91, 10.1111/j.1574-6941.2002.tb00910.x

Kuczynski, 2010, Microbial community resemblance methods differ in their ability to detect biologically relevant patterns, Nature Methods, 7, 813, 10.1038/nmeth.1499

Kuske, 2002, Comparison of soil bacterial communities in rhizospheres of three plant species and the interspaces in an arid grassland, Applied and Environmental Microbiology, 68, 1854, 10.1128/AEM.68.4.1854-1863.2002

Loomis, 2009, A continent wide clone: population genetic variation of the invasive plant Hieracium aurantiacum (Orange Hawkweed; Asteraceae) in North America, International Journal of Plant Science, 170, 759, 10.1086/599241

Lozupone, 2007, Quantitative and qualitative beta diversity measures lead to different insights into factors that structure microbial communities, Applied and Environmental Microbiology, 73, 1576, 10.1128/AEM.01996-06

Lundberg, 2012, Defining the core Arabidopsis thaliana root microbiome, Nature, 488, 86, 10.1038/nature11237

Manter, 2010, Pyrosequencing reveals a highly diverse and cultivar-specific bacterial endophyte community in potato roots, Microbial Ecology, 60, 157, 10.1007/s00248-010-9658-x

Marschner, 2005, Microbial community composition and functioning in the rhizosphere of three Banksia species in native woodland in Western Australia, Applied Soil Ecology, 28, 191, 10.1016/j.apsoil.2004.09.001

Marschner, 2001, Soil and plant specific effects on bacterial community composition in the rhizosphere, Soil Biology and Biochemistry, 33, 1437, 10.1016/S0038-0717(01)00052-9

Masson-Boivin, 2009, Establishing nitrogen-fixing symbiosis with legumes: how many rhizobium recipes?, Trends in Microbiology, 17, 458, 10.1016/j.tim.2009.07.004

Micallef, 2009, Plant age and genotype impact the progression of bacterial community succession in the Arabidopsis rhizosphere, Plant Signaling and Behavior, 4, 777, 10.4161/psb.4.8.9229

Opelt, 2007, Investigations of the structure and function of bacterial communities associated with Sphagnum mosses, Environmental microbiology, 9, 2795, 10.1111/j.1462-2920.2007.01391.x

Osanai, 2012, Co-occurring grass species differ in their associated microbial community composition in a temperate native grassland, Plant and Soil, 368, 419, 10.1007/s11104-012-1529-4

Ottesen, 2013, Baseline survey of the anatomical microbial ecology of an important food plant: solanum lycopersicum (tomato), BMC Microbiology, 13, 114, 10.1186/1471-2180-13-114

Peiffer, 2013, Diversity and heritability of the maize rhizosphere microbiome under field conditions, Proceedings of the Natural Acadademy of Science of the United States of America, 110, 6548, 10.1073/pnas.1302837110

Redford, 2010, The ecology of the phyllosphere: geographic and phylogenetic variability in the distribution of bacteria on tree leaves, Environmental Microbiology, 12, 2885, 10.1111/j.1462-2920.2010.02258.x

Reysenbach, 1995, Reliable amplification of hyperthermophilic Archaeal 16s rRNAgenes by the polymerase chain reaction, Archaea: a laboratory manual, 101

Roumet, 2006, Suites of root traits differ between annual and perennial species growing in the field, The New Phytologist, 170, 357, 10.1111/j.1469-8137.2006.01667.x

Schmid, 2006, The genus Herbaspirillum, The prokaryotes, 141, 10.1007/0-387-30745-1_7

Schweitzer, 2008, Plant–soil–microorganism interactions: heritable relationship between plant genotype and associated soil microorganisms, Ecology, 89, 773, 10.1890/07-0337.1

Shivaji, 1991, Identification of Janthinobacterium lividum from the soils of the islands of Scotia Ridge and from Antarctic peninsula, Polar Biology, 11, 267, 10.1007/BF00238461

Simek, 2010, Broad habitat range of the phylogenetically narrow R-BT065 cluster, representing a core group of the Betaproteobacterial genus Limnohabitans, Applied and Environmental Microbiology, 76, 631, 10.1128/AEM.02203-09

Singh, 2007, Influence of grass species and soil type on rhizosphere microbial community structure in grassland soils, Applied Soil Ecology, 36, 147, 10.1016/j.apsoil.2007.01.004

Smalla, 2001, Bulk and rhizosphere soil bacterial communities studied by denaturing gradient gel electrophoresis: plant-dependent enrichment and seasonal shifts revealed, Applied and Environmental Microbiology, 67, 4742, 10.1128/AEM.67.10.4742-4751.2001

Van Overbeek, 2008, Effects of plant genotype and growth stage on the structure of bacterial communities associated with potato (Solanum tuberosum L.), FEMS Microbiology Ecology, 64, 283, 10.1111/j.1574-6941.2008.00469.x

Weinert, 2009, Rhizosphere communities of genetically modified zeaxanthin-accumulating potato plants and their parent cultivar differ less than those of different potato cultivars, Applied and Environmental Microbiology, 75, 3859, 10.1128/AEM.00414-09

Wieland, 2001, Variation of microbial communities in soil, rhizosphere, and rhizoplane in response to crop species, soil type, and crop development, Applied and Environmental Microbiology, 67, 5849, 10.1128/AEM.67.12.5849-5854.2001