Applied Microbiology and Biotechnology

, Volume 97, Issue 23, pp 10117–10134 | Cite as

Diversity of sporadic symbionts and nonsymbiotic endophytic bacteria isolated from nodules of woody, shrub, and food legumes in Ethiopia

  • Aregu Amsalu Aserse
  • Leena A. Räsänen
  • Fassil Aseffa
  • Asfaw Hailemariam
  • Kristina Lindström
Applied microbial and cell physiology


Fifty-five bacterial isolates were obtained from surface-sterilized nodules of woody and shrub legumes growing in Ethiopia: Crotalaria spp., Indigofera spp., and Erythrina brucei, and the food legumes soybean and common bean. Based on partial 16S rRNA gene sequence analysis, the majority of the isolates were identified as Gram-negative bacteria belonging to the genera Achromobacter, Agrobacterium, Burkholderia, Cronobacter, Enterobacter, Mesorhizobium, Novosphingobium, Pantoea, Pseudomonas, Rahnella, Rhizobium, Serratia, and Variovorax. Seven isolates were Gram-positive bacteria belonging to the genera Bacillus, Paenibacillus, Planomicrobium, and Rhodococcus. Amplified fragment length polymorphism (AFLP) fingerprinting showed that each strain was genetically distinct. According to phylogenetic analysis of recA, glnII, rpoB, and 16S rRNA gene sequences, Rhizobium, Mesorhizobium, and Agrobacterium were further classified into six different genospecies: Agrobacterium spp., Agrobacterium radiobacter, Rhizobium sp., Rhizobium phaseoli, Mesorhizobium sp., and putative new Rhizobium species. The strains from R. phaseoli, Rhizobium sp. IAR30, and Mesorhizobium sp. ERR6 induced nodules on their host plants. The other strains did not form nodules on their original host. Nine endophytic bacterial strains representing seven genera, Agrobacterium, Burkholderia, Paenibacillus, Pantoea, Pseudomonas, Rhizobium, and Serratia, were found to colonize nodules of Crotalaria incana and common bean on co-inoculation with symbiotic rhizobia. Four endophytic Rhizobium and two Agrobacterium strains had identical nifH gene sequences with symbiotic Rhizobium strains, suggesting horizontal gene transfer. Most symbiotic and nonsymbiotic endophytic bacteria showed plant growth-promoting properties in vitro, which indicate their potential role in the promotion of plant growth when colonizing plant roots and the rhizosphere.


Endophytic bacteria Diversity Phylogeny Nodulation Co-inoculation Plant growth promoting 



We thank to the Ethiopian Agricultural Research Institute and National Meteorology Agency of Ethiopia for providing annual mean rainfall and temperature data of the sampling sites. This work was supported by the Academy of Finland and the University of Helsinki. We appreciate the Ella and Georg Ehrnrooth Foundation for granting stipends for PhD student Aregu Amsalu Aserse.

Supplementary material

253_2013_5248_MOESM1_ESM.doc (1.2 mb)
ESM 1 (DOC 1216 kb)


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Copyright information

© Springer-Verlag Berlin Heidelberg 2013

Authors and Affiliations

  • Aregu Amsalu Aserse
    • 1
  • Leena A. Räsänen
    • 1
    • 2
  • Fassil Aseffa
    • 3
  • Asfaw Hailemariam
    • 4
    • 5
  • Kristina Lindström
    • 1
    • 6
  1. 1.Department of Food and Environmental SciencesUniversity of HelsinkiHelsinkiFinland
  2. 2.Institute of Soil Science and Plant CultivationPulawyPoland
  3. 3.Cellular, Microbial and Molecular Biology Program UnitAddis Ababa UniversityAddis AbabaEthiopia
  4. 4.Ministry of Agriculture and Rural Development, National Soil Testing CentreAddis AbabaEthiopia
  5. 5.Menagesha Biotech Industry P L CAddis AbabaEthiopia
  6. 6.Department of Environmental SciencesUniversity of HelsinkiHelsinkiFinland

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