Downloaded from www.microbiologyresearch.org by IP: 54.70.40.11 On: Sun, 04 Nov 2018 02:26:10 Ochrobactrum oryzae sp. nov., an endophytic bacterial species isolated from deep-water rice in India Anil K. Tripathi, 1 Subhash C. Verma, 1 Soumitra Paul Chowdhury, 1 Michael Lebuhn, 2 Andreas Gattinger 3 and Michael Schloter 3 Correspondence Michael Schloter schloter@gsf.de 1 School of Biotechnology, Faculty of Science, Banaras Hindu University, Varanasi – 221005, India 2 Institute of Water Quality Control and Waste Management, Technical University of Munich, Am Coulombwall, 85748 Garching, Germany 3 GSF–National Centre for Environment and Health, Institute of Soil Ecology, Ingolstaedter Landstrasse 1, 85764 Neuherberg, Germany A non-pigmented, motile, Gram-negative bacterium designated MTCC 4195 T was isolated from surface-sterilized seeds and plant tissue from deep-water rice (Oryza sativa) cultivated in Suraha Tal Lake in northern India. This isolate was shown to reinfect and colonize deep-water rice endophytically. The highest level of 16S rRNA sequence similarity (96?8 %) to strain MTCC 4195 T was shown by Ochrobactrum gallinifaecis DSM 15295 T . Strain MTCC 4195 T utilized c-hydroxybutyric acid, adonitol, D-glucosaminic acid and arabinose as carbon sources, but failed to use gentiobiose or citrate. The cell-wall fatty acids of strain MTCC 4195 T were characterized by the presence of a relatively large proportion of C 18 : 1 v7c and a relative small proportion of C 16 : 0 in comparison with Ochrobactrum species. DNA–DNA relatedness studies showed less than 52 % binding with the DNAs of type strains of other species of the genus Ochrobactrum. On the basis of phenotypic and genotypic characteristics and the results of 16S rRNA gene sequence analysis, the novel species Ochrobactrum oryzae sp. nov. is proposed, with MTCC 4195 T (=DSM 17471 T ) as the type strain. A search for endophytic plant-growth-promoting bacteria in rice demonstrated the ability of some strains of Herba- spirillum, Acetobacter, Azoarcus, Serratia and Pantoea to colonize rice tissues endophytically (Cocking, 2003). Endo- phytes of rice include diverse types of nitrogen-fixing and non-nitrogen-fixing bacteria, which are found mainly in the roots, culms and seeds of various wild, traditional and cultivated varieties of rice (Barraquio et al., 1997). The diversity of the endophytic bacteria associated with five varieties of deep-water rice has been characterized (Verma et al., 2001). Analysis of the genotypic diversity of the endophytic bacterial communities present inside the seeds and other tissues of five varieties of deep-water rice revealed that seven different ARDRA (amplified ribosomal DNA restriction analysis) types were present in each rice variety. On the basis of the carbon-utilization pattern obtained, one of these seven ARDRA types showed greatest similarity to members of the genus Ochrobactrum (Ka ¨mpfer et al., 2003). Two other recent reports have described the isolation of Ochrobactrum strains from nodules of Acacia mangium (Ngom et al., 2004) and Lupinus albus (Trujillo et al., 2005). Comparison of the 16S rRNA gene sequences of Ochro- bactrum isolates from A. mangium showed 98 % sequence similarity with Ochrobactrum intermedium and Ochrobac- trum anthropi (Ngom et al., 2004), whereas the 16S rRNA gene sequence of the proposed type strain of ‘Ochrobactrum lupini’ showed 100 % similarity with that of O. anthropi, and further investigations are necessary to confirm the status of ‘O. lupini’ as a distinct species (Trujillo et al., 2005). Interestingly, analysis of the plasmid profile of ‘O. lupini’ showed the presence of three plasmids carrying nodD and nifH genes. The aim of the present study was to characterize the taxo- nomic position of strain MTCC 4195 T , isolated as an endophyte from samples taken from five varieties of deep- water rice, with respect to the type strains of species of Ochrobactrum with validly published names. Seeds from deep-water rice (Oryza sativa varieties Jaisurya, Kariyawa, Supankhi, Tudihiwa and Sigra) were surface- sterilized by treatment with 1 % chloramine T for 15 min Abbreviation: ARDRA, amplified ribosomal DNA restriction analysis. The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of strain MTCC 4195 T is AM041247. 63934 G 2006 IUMS Printed in Great Britain 1677 International Journal of Systematic and Evolutionary Microbiology (2006), 56, 1677–1680 DOI 10.1099/ijs.0.63934-0