ENVIRONMENTAL MICROBIOLOGY Genetic Diversity of Endophytic Diazotrophs of the Wild Rice, Oryza alta and Identification of the New Diazotroph, Acinetobacter oryzae sp. nov. Hassan Javed Chaudhary & Guixiang Peng & Mei Hu & Yumei He & Lijuan Yang & Yan Luo & Zhiyuan Tan Received: 21 March 2011 /Accepted: 27 October 2011 # Springer Science+Business Media, LLC 2011 Abstract Thirty-three endophytic diazotrophs were isolated from surface-sterilized leaves, stem, and roots of wild rice Oryza alta. The SDS–PAGE profile of total protein and insertion sequence-based polymerase chain reaction (IS- PCR) fingerprinting grouped the isolates into four clusters (I–IV). The 16S rRNA gene sequence homology of the representative strains B21, B31, B1, and B23 of clusters I, II, III, and IV were assigned to Pseudomonas oleovorans (99.2% similarity), Burkholderia fungorum (99.4% similarity), Enterobacter cloacae (98.9% similarity), and Acinetobacter johnsonii (98.4% similarity), respectively. The results showed wide genetic diversity of the putative diazotrophic strains of the wild rice, O. alta, and the strains of cluster IV are the first report of nitrogen-fixing Acinetobacter species. The cell size, phenotypic charac- ters, total protein profile, genomic DNA fingerprinting, DNA–DNA hybridization, and antibiotic resistance differen- tiated strain B23 T from its closest relatives A. johnsonii LMG999 T and Acinetobacter haemolyticus LMG996 T . The DNA–DNA hybridization also distinguished the strain B23 T from the closely related Acinetobacter species. Based on these data, a novel species, Acinetobacter oryzae sp. nov., and strain B23 T (=LMG25575 T =CGMCC1.10689 T ) as the type strain were proposed. Introduction Rice (Oryza sativa) is the most important cereal crop and staple food for more than 50% of the world’ s population [1]. Nitrogen is the most frequent limiting nutrient in rice production which needs 1 kg per 15–20 kg of grain yield [2]. Therefore, exploitation of biological nitrogen fixation would significantly contribute to long-term nitrogen availability to the rice crop. A variety of endophytic bacteria live, reproduce, and perpetuate generation to generation of the plants [3], but little is known about their significance on metabolism of the plants. Some endophytes, however, fix N 2 which is used by the plants [4]. Diverse endophytes including the diazotrophs Klebsiella oxytoca, Enterobacter cloacae, Bradyrhizobium spp., Alcaligenes spp. [5], Azospirillum spp., Acetobacter diazotrophicus, Ideonella, and Herbas- pirillum [6, 7] have been isolated from different parts of the wild rice. Acinetobacter spp. was mainly isolated from clinical specimens and is one of the important nosocomial pathogens, which has been known to cause different kinds of opportunistic infections [8]. At present, the genus Acinetobacter included 26 species with validly published names and the type species is Acinetobacter calcoaceticus GenBank accession numbers: The 16S rDNA sequences of the organisms have been deposited in the GenBank database under accession numbers HQ697329, HQ697330, GU954428, and HQ697331 for strains B1, B21, B23 T , and B31, respectively. Electronic supplementary material The online version of this article (doi:10.1007/s00248-011-9978-5) contains supplementary material, which is available to authorized users. H. J. Chaudhary : Y. He : L. Yang : Y. Luo : Z. Tan (*) Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou 510642, China e-mail: zytan@scau.edu.cn G. Peng College of Resources and Environment, South China Agricultural University, Guangzhou 510642, China M. Hu Agro-Environment Protection Institute, Ministry of Agriculture, Tianjin 300191, China Microb Ecol DOI 10.1007/s00248-011-9978-5