Abstract
Enterobacter radicincitans sp. nov. DSM16656T represents a new species of the genus Enterobacter which is a biological nitrogen-fixing endophytic bacterium with growth-promoting effects on a variety of crop and model plant species. The presence of genes for nitrogen fixation, phosphorous mobilization, and phytohormone production reflects this microbe's potential plant growth-promoting activity.
GENOME ANNOUNCEMENT
Plant beneficial endophytic interactions are characterized by the bacterial production of phytohormones, increased nutritional uptake, and environmental stress control (4). The diazotrophic strain Enterobacter radicincitans DSM16656T, formerly Pantoea agglomerans, was isolated from the phyllosphere of winter wheat under temperate climatic conditions and was described as a new species of the genus Enterobacter. The strain promoted the growth of roots and shoots and increased yields upon the inoculation of various plant species (2, 3, 6). While 10 genome sequences of Enterobacter strains have been published to date, only one displays plant growth-promoting characteristics similar to those of DSM16656T, i.e., Enterobacter sp. strain 638, which was isolated from a poplar stem (8). The sequence of the E. radicincitans DSM16656T genome, presented in this work, will extend the understanding of regulatory mechanisms of endophytic colonization and host plant interaction.
Bacterial DNA was isolated from 1-day cultures using an extraction kit (Gentra Puregene Yeast/Bact. Kit; Qiagen). Next-generation sequencing technology coupled Genome Sequencer FLX (Roche), HiSeq 2000 (Ilumina), and Sanger technology for long reads, short reads, and gap closure (MWG Eurofins), leading to 20.6-fold coverage depth. The draft genome sequence of E. radicincitans DSM16656T presented two chromosomes with a genome size of 6,041,938 bp and a G+C content of 53%. Genome annotation was performed using the Annotation Engine service (http://ae.igs.umaryland.edu/cgi/index.cgi) (1) and visualized using the Manatee genome curation and browsing tool (http://manatee.sourceforge.net). The analysis revealed a total of 6,124 protein-coding genes, 69 tRNAs, and 9 rRNAs, which equals ∼88% of the genome sequence.
Endophytic microorganisms assimilate plant metabolites and have developed mechanisms for their uptake or detoxification. The DSM16656T genome harbors 174 coding sequences for ABC transporters, 35 genes of the phosphotransferase system family, and 19 transporters from the resistance nodulation and cell division family.
Unlike plant growth-promoting Enterobacter sp. strain 638, DSM16656T is able to biologically fix atmospheric nitrogen (5). Besides the presence of the complete nif operon, comprising the nifUBALMVSNETKDHJ genes, the genome sequence indicates the dissimilation of nitrate (narBLXKGHJI) and nitrite (nirBD). The potential application of the strain as a biofertilizer is strengthened by the identification of genes for phosphate transporters (pstSCAB) and siderophore production (fhuFCDBE), which enhance the availability and uptake of phosphorus and iron for plant growth promotion. DSM16656T is able to produce auxin (7), and in accordance with that, we have identified genes for indole-3-acetaldehyde synthesis and an auxin efflux carrier. The genome information presented here will allow in-depth functional and comparative genome analyses to provide a better understanding of beneficial plant-bacterial associations.
Nucleotide sequence accession numbers.
This Whole-Genome Shotgun project has been deposited at DDBJ/EMBL/GenBank under accession no. AKYD00000000. The version presented in this paper is the first version, AKYD01000000.
ACKNOWLEDGMENTS
We thank Birgit Wernitz for excellent technical assistance.
Financial support from the Leibniz Institute of Vegetable and Ornamental Crops is gratefully acknowledged. We thank the Institute for Genome Sciences at the University of Maryland School of Medicine for providing automated annotation through the Annotation Engine service.
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