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Comparative genomics reveal a flagellar system, a type VI secretion system and plant growth-promoting gene clusters unique to the endophytic bacterium Kosakonia radicincitans

Affiliation
Leibniz Institute of Vegetable and Ornamental Crops, Grossbeeren, Germany
Becker, Matthias;
Affiliation
Leibniz Institute of Vegetable and Ornamental Crops, Grossbeeren, Germany ; Algorithms in Bioinformatics, Center for Bioinformatics, University of Tübingen, Tübingen, Germany
Patz, Sascha;
GND
1170372171
Affiliation
Leibniz Institute of Vegetable and Ornamental Crops, Grossbeeren, Germany ; Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institute–Federal Research Centre for Cultivated Plants, Braunschweig
Becker, Yvonne;
GND
1175986992
Affiliation
Leibniz Institute of Vegetable and Ornamental Crops, Grossbeeren, Germany ; Julius Kuehn Institute, Institute for national and international plant health, Braunschweig, Germany
Berger, Beatrice;
Affiliation
Leibniz Institute of Vegetable and Ornamental Crops, Grossbeeren, Germany
Drungowski, Mario;
Affiliation
Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
Bunk, Boyke;
Affiliation
Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
Overmann, Jörg;
Affiliation
Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
Spröer, Cathrin;
Affiliation
Federal Institute for Risk Assessment, Berlin, Germany
Reetz, Jochen;
Affiliation
Leibniz Institute of Vegetable and Ornamental Crops, Grossbeeren, Germany
Tchuisseu Tchakounte, Gylaine V.;
Affiliation
Leibniz Institute of Vegetable and Ornamental Crops, Grossbeeren, Germany
Ruppel, Silke

The recent worldwide discovery of plant growth-promoting (PGP) Kosakonia radicincitans in a large variety of crop plants suggests that this species confers significant influence on plants, both in terms of yield increase and product quality improvement. We provide a comparative genome analysis which helps to unravel the genetic basis for K. radicincitans' motility, competitiveness and plant growth-promoting capacities. We discovered that K. radicincitans carries multiple copies of complex gene clusters, among them two flagellar systems and three type VI secretion systems (T6SSs). We speculate that host invasion may be facilitated by different flagella, and bacterial competitor suppression by effector proteins ejected via T6SSs. We found a large plasmid in K. radicincitans DSM 16656T, the species type strain, that confers the potential to exploit plant-derived carbon sources. We propose that multiple copies of complex gene clusters in K. radicincitans are metabolically expensive but provide competitive advantage over other bacterial strains in nutrient-rich environments. The comparison of the DSM 16656T genome to genomes of other genera of enteric plant growth-promoting bacteria (PGPB) exhibits traits unique to DSM 16656T and K. radicincitans, respectively, and traits shared between genera. We used the output of the in silico analysis for predicting the purpose of genomic features unique to K. radicincitans and performed microarray, PhyloChip, and microscopical analyses to gain deeper insight into the interaction of DSM 16656T, plants and associated microbiota. The comparative genome analysis will facilitate the future search for promising candidates of PGPB for sustainable crop production.

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License Holder: 2018 Becker, Patz, Becker, Berger, Drungowski, Bunk, Overmann, Spröer, Reetz, Tchuisseu Tchakounte and Ruppel.

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