title: Effects of site and plant species on rhizosphere community structure as revealed by molecular analysis of microbial guilds.
abstract: The bacterial and fungal rhizosphere communities of strawberry (Fragaria ananassa Duch.) and oilseed rape (Brassica napus L.) were analysed using molecular fingerprints. We aimed to determine to what extent the structure of different microbial groups in the rhizosphere is influenced by plant species and sampling site. Total community DNA was extracted from bulk and rhizosphere soil taken from three sites in Germany in two consecutive years. Bacterial, fungal and group-specific (Alphaproteobacteria, Betaproteobacteria and Actinobacteria) primers were used to PCR-amplify 16S rRNA and 18S rRNA gene fragments from community DNA prior to denaturing gradient gel electrophoresis (DGGE) analysis. Bacterial fingerprints of soil DNA revealed a high number of equally abundant faint bands, while rhizosphere fingerprints displayed a higher proportion of dominant bands and reduced richness, suggesting selection of bacterial populations in this environment. Plant specificity was detected in the rhizosphere by bacterial and group-specific DGGE profiles. Different bulk soil community fingerprints were revealed for each sampling site. The plant species was a determinant factor in shaping similar actinobacterial communities in the strawberry rhizosphere from different sites in both years. Higher heterogeneity of DGGE profiles within soil and rhizosphere replicates was observed for the fungi. Plant-specific composition of fungal communities in the rhizosphere could also be detected, but not in all cases. Cloning and sequencing of 16S rRNA gene fragments obtained from dominant DGGE bands detected in the bacterial profiles of the Rostock site revealed that Streptomyces sp. and Rhizobium sp. were among the dominant ribotypes in the strawberry rhizosphere, while sequences from Arthrobacter sp. corresponded to dominant bands from oilseed rape bacterial fingerprints.
authors.affiliation: Federal Biological Research Centre for Agriculture and Forestry, Braunschweig, Germany.
authors.forename: Rodrigo
authors.initials: R
authors.lastname: Costa
authors.forename: Monika
authors.initials: M
authors.lastname: Götz
authors.forename: Nicole
authors.initials: N
authors.lastname: Mrotzek
authors.forename: Jana
authors.initials: J
authors.lastname: Lottmann
authors.forename: Gabriele
authors.initials: G
authors.lastname: Berg
authors.forename: Kornelia
authors.initials: K
authors.lastname: Smalla
mesh_terms: D039903:Actinobacteria / Q000145:classification / Q000235:genetics; D020561:Alphaproteobacteria / Q000145:classification / Q000235:genetics; D001419:Bacteria / Q000145:classification* / Q000235:genetics; D020562:Betaproteobacteria / Q000145:classification / Q000235:genetics; D029688:Brassica napus / Q000382:microbiology*; D002980:Climate; D016000:Cluster Analysis; D017753:Ecosystem; D031985:Fragaria / Q000382:microbiology*; D005658:Fungi / Q000145:classification* / Q000235:genetics; D005858:Germany; D010572:Pest Control, Biological; D010802:Phylogeny; D012335:RNA, Ribosomal / Q000032:analysis; D017423:Sequence Analysis, RNA; D012988:Soil Microbiology
chemical_list: D012335:RNA, Ribosomal