Is diversification history of maize influencing selection of soil bacteria by roots? MARIE-LARA BOUFFAUD,*†‡ MARTINA KYSELKOVA ´ ,*†‡§ BRIGITTE GOUESNARD, – GENEVIEVE GRUNDMANN,*†‡ DANIEL MULLER*†‡ and YVAN MOE ¨ NNE-LOCCOZ*†‡ *Universite ´ de Lyon, F-69622, Lyon, France, †Universite ´ Lyon 1, Villeurbanne, France, ‡CNRS, UMR5557, Ecologie Microbienne, Villeurbanne, France, §Biology Centre AS CR, Institute of Soil Biology, C ˇ eske ´ Bude ˇjovice, Czech Republic, –INRA, UMR 1334 AGAP, F- 34398 Montpellier, France Abstract A wide range of plant lines has been propagated by farmers during crop selection and dissemination, but consequences of this crop diversification on plant-microbe interac- tions have been neglected. Our hypothesis was that crop evolutionary history shaped the way the resulting lines interact with soil bacteria in their rhizospheres. Here, the significance of maize diversification as a factor influencing selection of soil bacteria by seedling roots was assessed by comparing rhizobacterial community composition of inbred lines representing the five main genetic groups of maize, cultivated in a same European soil. Rhizobacterial community composition of 21-day-old seedlings was analysed using a 16S rRNA taxonomic microarray targeting 19 bacterial phyla. Rhizobacterial community composition of inbred lines depended on the maize genetic group. Differences were largely due to the prevalence of certain Betaproteobacteria and especially Burkholderia, as confirmed by quantitative PCR and cloning ⁄ sequencing. However, these differences in bacterial root colonization did not correlate with plant microsatellite genetic distances between maize genetic groups or individual lines. Therefore, the genetic structure of maize that arose during crop diversification (resulting in five main groups), but not the extent of maize diversification itself (as determined by maize genetic distances), was a significant factor shaping rhizobacterial community composition of seedlings. Keywords: bacterial community, plant diversity, rhizosphere, taxonomic microarray, Zea mays Received 25 February 2011; revision received 26 August 2011; accepted 26 September 2011 Introduction Soil microbial community displays high taxonomic and functional diversity, and plays key roles in nutrient cycling and biotic interactions, especially with plants (Raaijmakers et al. 2009). Plant roots are colonized by a wide range of microorganisms, which use organic exu- dates and other rhizodeposits as growth susbtrates (Berg & Smalla 2009). These microorganisms may have neutral, detrimental or beneficial effects on growth and functioning of the host plant (Escobar & Dandekar 2003; Alabouvette et al. 2006; Tyler & Triplett 2008; Aroca & Ruiz-Lozano 2009; Raaijmakers et al. 2009). Therefore, understanding how plant roots select soil microbes to form the microbial community of the rhizo- sphere is an important scientific issue when considering plant growth and health, and this information may be useful to better exploit plant germplasm stemming from crop diversification (Den Herder et al. 2010). A high number of studies have dealt with the diver- sity of the microbial community of the rhizosphere, especially in the case of cultivated plants (Kandeler et al. 2002; Smalla et al. 2001; Sun et al. 2008). Most cul- tivated plants are characterized by evolutionarily recent (i.e. within the last 12 000 years) events of domestica- tion and man-driven selection (Purugganan & Fuller 2009). The latter have accompanied their dissemination to different regions of the world, leading to different species or subspecies according to local environmental Correspondence: Yvan Moe ¨nne-Loccoz, Fax: (33) 472 431223; E-mail: yvan.moenne-loccoz@univ-lyon1.fr Ó 2011 Blackwell Publishing Ltd Molecular Ecology (2011) doi: 10.1111/j.1365-294X.2011.05359.x