REGULAR ARTICLE Transcriptome and proteome profiles of the diazotroph Nitrospirillum amazonense strain CBAmC in response to the sugarcane apoplast fluid Leonardo A. Terra & Cleiton P. de Soares & Carlos H. S. G. Meneses & Michelle Z. Tadra Sfeir & Emanuel M. de Souza & Vanildo Silveira & Márcia S. Vidal & José I. Baldani & Stefan Schwab Received: 30 January 2019 /Accepted: 1 July 2019 # Springer Nature Switzerland AG 2019 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 proteo- mic 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 pro- files 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 assim- ilative metabolism of iron. In contrast, active trans- porters of organic compounds, chemotaxis system and flagellum structure were underexpressed. Conclusions The bacterial metabolic pathways / func- tions 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 per- haps be involved in the previously observed effect of promoting plant growth. Keywords Transcripts . Proteins . Bacteria-plant interaction . Saccharum spp. Introduction Sugarcane is an important agricultural crop in Brazil for producing sugar, ethanol, and, more recently, electric power (Alves et al. 2015). Ethanol and electricity, in particular, are considered to be clean energy sources (bioenergy) because they are renewable, and thus Plant Soil https://doi.org/10.1007/s11104-019-04201-y Responsible Editor: Jerri Edson Zilli Electronic supplementary material The online version of this article (https://doi.org/10.1007/s11104-019-04201-y) contains supplementary material, which is available to authorized users. L. A. Terra Pró-Reitoria de Pesquisa e Pós-Graduação, Universidade Federal Rural do Rio de Janeiro, Seropédica, Brazil L. A. Terra : M. S. Vidal : J. I. Baldani : S. Schwab (*) Embrapa Agrobiologia, Seropédica, Brazil e-mail: stefan.schwab@embrapa.br C. P. de Soares : V. Silveira Centro de Biociências e Biotecnologia, Universidade Estadual Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil C. H. S. G. Meneses Departamento de Biologia, Universidade Estadual da Paraíba, Campina Grande, Brazil M. Z. Tadra Sfeir : E. M. de Souza Departmento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, Brazil