Specific Detection of Bradyrhizobium and Rhizobium Strains Colonizing Rice ( Oryza sativa ) Roots by 16S-23S Ribosomal DNA Intergenic Spacer-Targeted PCR

• DOI: 10.1128/aem.67.8.3655-3664.2001
• Publication Date: 2002-07-27T10:00:58Z
• Authors: Zhiyuan Tan; Thomas Hurek; Pablo Vinuesa; Peter Müller; Jagdish K. Ladha; Barbara Reinhold-...
• Keywords: Bradyrhizobium; Rhizobium leguminosarum; Bradyrhizobium japonicum

ABSTRACT In addition to forming symbiotic nodules on legumes, rhizobial strains are members of soil or rhizosphere communities occur as endophytes, e.g., in rice. Two which have been isolated from root the aquatic legumes Aeschynomene fluminensis (IRBG271) and Sesbania aculeata (IRBG74) were previously found promote rice growth. analyzing their phylogenetic positions, we assessed suitability 16S-23S ribosomal DNA (rDNA) intergenic spacer (IGS) sequences for differentiation closely related taxa development PCR protocols allowing specific detection environment. 16S rDNA sequence analysis (sequence identity, 99%) IGS showed that strain IRBG271 was but distinct Bradyrhizobium elkanii . Rhizobium sp. ( ) IRBG74 located - Agrobacterium cluster a novel lineage according (96.8 98.9% identity with tumefaciens; emended name, radiobacter ). Strain harbored four copies rRNA operons whose varied only slightly (2 9 nucleotides). The analyses allowed intraspecies differentiation, especially genus Bradyrhizobium, illustrated here japonicum, B. elkanii, liaoningense, Chamaecytisus BTA-1. It also clearly differentiated fast-growing species strains, albeit lower statistical significance. Moreover, high variability highly IGS-targeted nested-PCR assays. Strains specifically detected complex mixtures numerous bacteria roots gnotobiotically cultured even soil-grown plants after inoculation. Thus, is an attractive technique both microbial ecology systematics.