Microbial Ecology

, Volume 75, Issue 1, pp 183–191 | Cite as

The Microbiome of Eucalyptus Roots under Different Management Conditions and Its Potential for Biological Nitrogen Fixation

  • Eduardo da Silva Fonseca
  • Raquel Silva Peixoto
  • Alexandre Soares Rosado
  • Fabiano de Carvalho Balieiro
  • James M. Tiedje
  • Caio Tavora Coelho da Costa RachidEmail author
Plant Microbe Interactions


Eucalyptus plantations offer a cost-effective and renewable source of raw material. There is substantial interest in improving forestry production, especially through sustainable strategies such as the use of plant growth-promoting bacteria. However, little is known about Eucalyptus microbiology. In this study, the endophytic bacterial community was assessed in Eucalyptus urograndis roots using culture-dependent and culture-independent techniques with plants grown under different conditions. Three phyla accounted for approximately 95% of the community, with Actinobacteria corresponding to approximately 59%. This contrasts with previous studies in which Actinobacteria accounted for only 5 to 10%. Our data also revealed a high diversity of bacteria, with 359 different genera but a high level of dominance. Six genera, Mycobacterium, Bradyrhizobium, Streptomyces, Bacillus, Actinospica, and Burkholderia, accounted for more than 50% of the classified sequences. We observed a significant influence of the treatments on some genera, causing changes in the bacterial community structure. The obtained data also suggest that Eucalyptus may benefit from biological nitrogen fixation, with many abundant genera being closely related to nitrogen-fixing bacteria. Using N-depleted media, we also cultured 95 bacterial isolates, of which 24 tested positive for the nifH gene and were able to maintain growth without any N source in the medium.


Endophytic bacteria Eucalyptus microbiology Plant microbiome Roots microbiology Nitrogen fixing bacteria 


Compliance with Ethical Standards


This work received funding from the Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) and Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro (FAPERJ) and Fundação de Amparo à Pesquisa do Estado de São Paulo (Fapesp).

Conflict of Interests

The authors have declared that no competing interests exist.

Supplementary material

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Copyright information

© Springer Science+Business Media, LLC 2017
Corrected publication November/2017

Authors and Affiliations

  • Eduardo da Silva Fonseca
    • 1
  • Raquel Silva Peixoto
    • 2
  • Alexandre Soares Rosado
    • 2
  • Fabiano de Carvalho Balieiro
    • 3
  • James M. Tiedje
    • 4
  • Caio Tavora Coelho da Costa Rachid
    • 1
    Email author
  1. 1.LABEM—Laboratory of Biotechnology and Microbial Ecology—Institute of Microbiology Paulo de GóesFederal University of Rio de JaneiroRio de JaneiroBrazil
  2. 2.LEMM—Laboratory of Microbial Molecular Ecology—Institute of Microbiology Paulo de GóesFederal University of Rio de JaneiroRio de JaneiroBrazil
  3. 3.Embrapa SolosRio de JaneiroBrazil
  4. 4.Center for Microbial EcologyMichigan State UniversityEast LansingUSA

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