The diversity of archaea and bacteria in association with the roots of Zeamays L.

The diversity of bacteria and archaea associating on the surface and interi or of maize roots (Zea mays L.) was investigated. A bacterial 16S rDNA prim er was designed to amplify bacterial sequences directly from maize roots by PCR to the exclusion of eukaryotic and chloroplast DNA. The mitochondrial sequence from maize was easily separated from the PCR-amplified bacterial s equences by size fractionation. The culturable component of the bacterial c ommunity was also assessed, reflecting a community composition different fr om that of the clone library. The phylogenetic overlap between organisms ob tained by cultivation and those identified by direct PCR amplification of 1 6S rDNA was 48%. Only 4 bacterial divisions were found in the culture colle ction, which represented 27 phylotypes, whereas 6 divisions were identified in the clonal analysis, comprising 74 phylotypes, including a member of th e OP10 candidate division originally described as a novel division level li neage in a Yellowstone hot spring. The predominant group in the culture col lection was the actinobacteria and within the clone library, the oc-proteob acteria predominated. The population of maize-associated proteobacteria res embled the proteobacterial population of a typical soil community within wh ich resided a subset of specific plant-associated bacteria, such as Rhizobi um- and Herbaspirillum-related phylotypes. The representation of phylotypes within other divisions (OP10 and Acidobacterium) suggests that maize roots support a distinct bacterial community. The diversity within the archaeal domain was low. Of the 50 clones screened, 6 unique sequence types were ide ntified, and 5 of these were highly related to each other (sharing 98%, seq uence identity). The archaeal sequences clustered with good bootstrap suppo rt near Marine group I (crenarchaea) and with Marine group II (euryarchaea) uncultured archaea. The results suggest that maize supports a diverse root -associated microbial community composed of species that for the first time have been described as inhabitants of a plant-root environment.