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Open Access Highly Accessed Research article

The new species Enterobacter oryziphilus sp. nov. and Enterobacter oryzendophyticus sp. nov. are key inhabitants of the endosphere of rice

Pablo Rodrigo Hardoim15*, Rashid Nazir1, Angela Sessitsch2, Dana Elhottová3, Elisa Korenblum1, Leonard Simon van Overbeek4 and Jan Dirk van Elsas1

Author Affiliations

1 Department of Microbial Ecology, University of Groningen, Centre for Ecological and Evolutionary Studies, Nijenborgh 7, Groningen 9747AG, The Netherlands

2 AIT Austrian Institute of Technology GmbH, Bioresources Unit, Tulln, Austria

3 Institute of Soil Biology, Biology Centre, ASCR, v.v.i., Na Sádkách 7, České Budějovice CZ 370 05, Czech Republic

4 Plant Research International, Droevendaalsesteeg 1, Wageningen 6708PB, The Netherlands

5 Current address: Centre of Marine Science, University of Algarve, Faro 8005-139, Portugal

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BMC Microbiology 2013, 13:164  doi:10.1186/1471-2180-13-164

Published: 16 July 2013

Abstract

Background

Six independent Gram-negative, facultatively anaerobic, non-spore-forming, nitrogen-fixing rod-shaped isolates were obtained from the root endosphere of rice grown at the International Rice Research Institute (IRRI) and investigated in a polyphasic taxonomic study.

Results

The strains produced fatty acid patterns typical for members of the family Enterobacteriaceae. Comparative sequence analyses of the 16S rRNA as well as rpoB genes allocated the strains to two well-defined groups within the genus Enterobacter, family Enterobacteriaceae. The analyses indicated Enterobacter radicincitans, Enterobacter arachidis and Enterobacter oryzae to be the closest related species. An RpoB (translated) protein comparison supported the placement in the genus Enterobacter and the relatedness of our isolates to the aforementioned species. Genomic DNA:DNA hybridization analyses and biochemical analyses provided further evidence that the novel strains belong to two new species within the genus Enterobacter. The two species can be differentiated from each other and from existing enteric species by acid production from L-rhamnose and D-melibiose, decarboxylation of ornithine and utilization of D-alanine, D-raffinose L-proline and L-aspartic acid, among other characteristics. Members of both species revealed capacities to colonise rice roots, including plant-growth-promoting capabilities such as an active supply of fixed nitrogen to the plant and solubilisation of inorganic phosphorus, next to traits allowing adaptation to the plant.

Conclusions

Two novel proposed enterobacterial species, denominated Enterobacter oryziphilus sp. nov. (type strain REICA_142T=LMG 26429T=NCCB 100393T) and Enterobacter oryzendophyticus sp. nov. (type strain REICA_082T=LMG 26432T =NCCB 100390T) were isolated from rice roots. Both species are capable of promoting rice growth by supplying nitrogen and phosphorus.

Keywords:
Plant growth-promoting bacteria; Endophytes; Diazotrophic bacteria; Methanotrophic bacteria; Phosphate-solubilizing bacteria; Production of indole-3-acetic acid; International Rice Research Institute