Plant Molecular Biology

, Volume 90, Issue 6, pp 589–603 | Cite as

RNA-seq transcriptional profiling of Herbaspirillum seropedicae colonizing wheat (Triticum aestivum) roots

  • V. C. S. Pankievicz
  • D. Camilios-Neto
  • P. Bonato
  • E. Balsanelli
  • M. Z. Tadra-Sfeir
  • H. Faoro
  • L. S. Chubatsu
  • L. Donatti
  • G. Wajnberg
  • F. Passetti
  • R. A. Monteiro
  • F. O. Pedrosa
  • E. M. Souza


Herbaspirillum seropedicae is a diazotrophic and endophytic bacterium that associates with economically important grasses promoting plant growth and increasing productivity. To identify genes related to bacterial ability to colonize plants, wheat seedlings growing hydroponically in Hoagland’s medium were inoculated with H. seropedicae and incubated for 3 days. Total mRNA from the bacteria present in the root surface and in the plant medium were purified, depleted from rRNA and used for RNA-seq profiling. RT-qPCR analyses were conducted to confirm regulation of selected genes. Comparison of RNA profile of root attached and planktonic bacteria revealed extensive metabolic adaptations to the epiphytic life style. These adaptations include expression of specific adhesins and cell wall re-modeling to attach to the root. Additionally, the metabolism was adapted to the microxic environment and nitrogen-fixation genes were expressed. Polyhydroxybutyrate (PHB) synthesis was activated, and PHB granules were stored as observed by microscopy. Genes related to plant growth promotion, such as auxin production were expressed. Many ABC transporter genes were regulated in the bacteria attached to the roots. The results provide new insights into the adaptation of H. seropedicae to the interaction with the plant.


Biological nitrogen fixation H. seropedicae RNA-seq profiling Rhizosphere PGPB-plant growth promoting bacteria 



The Brazilian Program of National Science and Technology Institute/INCT for BNF supported this work. We would like to acknowledge Dr. Eliane Vendrusculo (UFPR-Palotina) for kindly providing the wheat seeds. We are also thankful to Roseli Prado, Marilza D. Lamour and Valter Baura for technical assistance. V.C.S.P. was beneficiary of PhD fellowship from the Brazilian Research Council/CNPq. G.W. was supported by Vice-Presidência de Ensino, Informação e Comunicação/Pró-Reitoria–IOC/FIOCRUZ and Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES). F.P. acknowledges the support of Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro (FAPERJ), Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), Fundação do Câncer and Fundação Oswaldo Cruz.

Author’s contribution

Pankievicz, V. C. S.; Camilios-Neto, D. and Souza, E.M. Conceived and designed the experiments. Pankievicz, V. C. S. and Camilios-Neto, D. Plant assays, RNA purification and constructed the RNA-Seq libraries. Tadra-Sfeir, M.Z. and Faoro, H. RNA-Seq libraries, NGS sequencing and data acquisition. Pankievicz, V. C. S., Bonato, P. and Souza, E.M. RNA-Seq analysis and interpretation of the data. Donatti, L. Electronic microscopy. Wajnberg, G. and Passetti, F. GSEA and critical revisions on bioinformatics analysis. Pankievicz, V. C. S. and Souza, E.M. drafted the manuscript. Pankievicz, V. C. S.; Balsanelli, E.; Chubatsu, L.; Monteiro R. A.; Pedrosa F. O. and Souza, E. M. Critical revision of the manuscript.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

11103_2016_430_MOESM1_ESM.pdf (144 kb)
Supplementary material 1 (PDF 143 kb)
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Supplementary material 2 (PDF 123 kb)
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Supplementary material 3 (PDF 89 kb)
11103_2016_430_MOESM4_ESM.xlsx (414 kb)
Supplementary material 4 (XLSX 414 kb)


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Copyright information

© Springer Science+Business Media Dordrecht 2016

Authors and Affiliations

  • V. C. S. Pankievicz
    • 1
  • D. Camilios-Neto
    • 3
  • P. Bonato
    • 1
  • E. Balsanelli
    • 1
  • M. Z. Tadra-Sfeir
    • 1
  • H. Faoro
    • 1
  • L. S. Chubatsu
    • 1
  • L. Donatti
    • 2
  • G. Wajnberg
    • 4
    • 5
  • F. Passetti
    • 4
    • 5
  • R. A. Monteiro
    • 1
  • F. O. Pedrosa
    • 1
  • E. M. Souza
    • 1
  1. 1.Department of Biochemistry and Molecular BiologyUniversidade Federal do ParanáCuritibaBrazil
  2. 2.Department of Cellular BiologyUniversidade Federal do ParanáCuritibaBrazil
  3. 3.Department of Biochemistry and BiotechnologyUniversidade Estadual de LondrinaLondrinaBrazil
  4. 4.Bioinformatics Unit, Clinical Research CoordinationInstituto Nacional de CâncerRio de JaneiroBrazil
  5. 5.Laboratory of Functional Genomics and BioinformaticsOswaldo Cruz Institute, Fundação Oswaldo Cruz (Fiocruz)Rio de JaneiroBrazil

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