Abstract Genetically modified potatoes exp- ressing antibacterial protein T4 lysozyme may offer effective control strategies for bacterial pathogens causing severe potato diseases. Apart from this beneficial effect, it is very important to investigate such engineered potatoes carefully for potential adverse effects on potato-associated bacteria which frequently exhibit plant beneficial functions such as plant growth promotion and antagonism towards pathogens invading the plant. Two field experiments were carried out in Spain to analyze the potential effects of conventional and genetically modified T4-lysozyme producing potatoes on shoot-associated bacteria. The first baseline field trial 2002 was performed in Meliana in which three conventional potato lines, Achir- ana Inta, Desire ´e, and Merkur, were cultivated and sampled at flowering. The second field trial was conducted in Cella in 2003 in order to com- pare the effects of a senescent transgenic, T4 lysozyme expressing potato trait, Desire ´e DL 12, with its isogenic, non-transformed parental line Desire ´e. Structural characteristics of potato shoot-associated bacteria was assayed by 16S rRNA-based terminal restriction fragment length polymorphism (T-RFLP) analysis and dominant community members within T-RFLP profiles were identified by sequence analysis of generated 16S rRNA gene libraries. Cultivable bacteria isolated from shoots of potatoes grown in the Meliana field trial were monitored for antibiosis against Ralstonia solanacearum, whereas isolates derived from shoots of potatoes cultivated in the Cella trial were screened for antagonism against Ralstonia solanacearum and Rhizoctonia solani, and for 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase production. Determined antagonists were identified by 16S rRNA gene analysis. All potato traits hosted a cultivar- specific community of bacteria with antagonism against the pathogens and/or potential to produce F. Rasche (&) Æ A. Sessitsch Department of Bioresources, ARC Seibersdorf research GmbH, A-2444 Seibersdorf, Austria e-mail: frank.rasche@arcs.ac.at E. Marco-Noales Æ M. M. Lo ´ pez Departamento de Proteccio ´ n Vegetal y Biotecnologı´a, Instituto Valenciano de Investigaciones Agrarias (IVIA), E-46113 Valencia, Spain H. Velvis Æ L. S. van Overbeek Crop and Production Ecology, Plant Research International (PRI), NL-6700AA Wageningen, The Netherlands J. D. van Elsas Microbial Ecology, Biological Center, Groningen University, NL-9751NN Haren, The Netherlands Present Address: H. Velvis HZPC Research, NL-9123JB Metslawier, The Netherlands Plant Soil (2006) 289:123–140 DOI 10.1007/s11104-006-9103-6 123 ORIGINAL PAPER Structural characteristics and plant-beneficial effects of bacteria colonizing the shoots of field grown conventional and genetically modified T4-lysozyme producing potatoes Frank Rasche Æ Ester Marco-Noales Æ Henk Velvis Æ Leo S. van Overbeek Æ Marı ´a M. Lo ´ pez Æ Jan D. van Elsas Æ Angela Sessitsch Received: 29 March 2006 / Accepted: 14 August 2006 / Published online: 31 October 2006 Ó Springer Science+Business Media B.V. 2006