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Transcriptome and proteome profiles of the diazotroph Nitrospirillum amazonense strain CBAmC in response to the sugarcane apoplast fluid

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Abstract

Background and aims

The endophytic diazotrophic strain CBAmC of Nitrospirillum amazonense has been reported as a plant growth promoter of sugarcane variety RB867515 when grown under field conditions. The present work aimed to assess the influence of apoplast fluid from RB867515 on the transcriptomic and proteomic profiles of CBAmC cultured in vitro.

Methods

RNA-Seq in Ion Proton™ and ESI-LC-MS/MS peptide analysis were used to evaluate the transcriptomic and proteomic profiles, respectively, of CBAmC exposed for 2 h to the sugarcane apoplast fluid.

Results

The bacterial transcriptomic and proteomic profiles were well correlated. The overall response of CBAmC to the apoplast fluid included overexpression of defense systems against reactive oxygen species (ROS) and osmotic stress, RND efflux pumps for toxic compounds, Sec and Tat secretory systems, and assimilative metabolism of iron. In contrast, active transporters of organic compounds, chemotaxis system and flagellum structure were underexpressed.

Conclusions

The bacterial metabolic pathways / functions activated in response to the sugarcane apoplast fluid are most likely related to its adaptation to the peculiar characteristics of the fluid. The activation of some of those functions could be determinant for its adaptation to the sugarcane apoplastic niche, and perhaps be involved in the previously observed effect of promoting plant growth.

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Data availability

RNA-Seq data have been deposited to the NCBI’s Gene Expression Omnibus (GEO) database (Edgar et al. 2002) under the serial accession number GSE130321. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE (Perez-Riverol et al. 2019) partner repository with the dataset identifier PXD013518.

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Acknowledgements

The authors thank Alexandre C. Baraúna for helping in the apoplast fluid preparation. This study was partially supported by the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES-L.A.T. doctorate fellowship, call CAPES/Embrapa no. 015/2014), and Brazilian Agricultural Research Corporation (Embrapa) project code 02.13.08.006.00.00.

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Authors and Affiliations

  1. Pró-Reitoria de Pesquisa e Pós-Graduação, Universidade Federal Rural do Rio de Janeiro, Seropédica, Brazil

    Leonardo A. Terra

  2. Embrapa Agrobiologia, Seropédica, Brazil

    Leonardo A. Terra, Márcia S. Vidal, José I. Baldani & Stefan Schwab

  3. Centro de Biociências e Biotecnologia, Universidade Estadual Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil

    Cleiton P. de Soares & Vanildo Silveira

  4. Departamento de Biologia, Universidade Estadual da Paraíba, Campina Grande, Brazil

    Carlos H. S. G. Meneses

  5. Departmento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, Brazil

    Michelle Z. Tadra Sfeir & Emanuel M. de Souza

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  1. Leonardo A. Terra
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Correspondence to Stefan Schwab.

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Terra, L.A., de Soares, C.P., Meneses, C.H.S.G. et al. Transcriptome and proteome profiles of the diazotroph Nitrospirillum amazonense strain CBAmC in response to the sugarcane apoplast fluid. Plant Soil 451, 145–168 (2020). https://doi.org/10.1007/s11104-019-04201-y

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