Archives of Microbiology

, Volume 198, Issue 9, pp 847–860 | Cite as

Transcriptomic analysis of the process of biofilm formation in Rhizobium etli CFN42

  • Agustín Reyes-Pérez
  • María del Carmen Vargas
  • Magdalena Hernández
  • Eneas Aguirre-von-Wobeser
  • Ernesto Pérez-Rueda
  • Sergio EncarnacionEmail author
Original Paper


Organisms belonging to the genus Rhizobium colonize leguminous plant roots and establish a mutually beneficial symbiosis. Biofilms are structured ecosystems in which microbes are embedded in a matrix of extracellular polymeric substances, and their development is a multistep process. The biofilm formation processes of R. etli CFN42 were analyzed at an early (24-h incubation) and mature stage (72 h), comparing cells in the biofilm with cells remaining in the planktonic stage. A genome-wide microarray analysis identified 498 differentially regulated genes, implying that expression of ~8.3 % of the total R. etli gene content was altered during biofilm formation. In biofilms-attached cells, genes encoding proteins with diverse functions were overexpressed including genes involved in membrane synthesis, transport and chemotaxis, repression of flagellin synthesis, as well as surface components (particularly exopolysaccharides and lipopolysaccharides), in combination with the presence of activators or stimulators of N-acyl-homoserine lactone synthesis This suggests that R. etli is able to sense surrounding environmental conditions and accordingly regulate the transition from planktonic and biofilm growth. In contrast, planktonic cells differentially expressed genes associated with transport, motility (flagellar and twitching) and inhibition of exopolysaccharide synthesis. To our knowledge, this is the first report of nodulation and nitrogen assimilation-related genes being involved in biofilm formation in R. etli. These results contribute to the understanding of the physiological changes involved in biofilm formation by bacteria.


Sessile Planktonic Biofilm Microarrays Rhizobium etli 



Part of this work was supported by CONACyT Grant 220790 and DGAPA-PAPIIT Grant IN213216. We are grateful to the Posgrado en Ciencias Biológicas de la Facultad de Ciencias, Universidad Nacional Autónoma de México, México; ARP was a recipient of a PhD Studentship from CONACyT. We thanks to Mario Ramírez Yáñez and Victor Bustos Zagal for technical assistance, to Rubén Paul Gaytán Colín and Eugenio López Bustos from Unidad de Síntesis, Instituto de Biotecnología-UNAM, and to Andrés Saraleguí Amaro and Xochitl Alvarado Affantranger from Unidad Laboratorio Nacional de Microscopía Avanzada-UNAM. Thanks also to Michael Dunn for comments on the manuscript and Enrique Reynaud and Veronica Narvaez for technical assistance in qPCR experiments.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

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© Springer-Verlag Berlin Heidelberg 2016

Authors and Affiliations

  1. 1.Programa de Genómica Funcional de Procariotes, Centro de Ciencias GenómicasUniversidad Nacional Autónoma de MéxicoCuernavacaMexico
  2. 2.Facultad de Ciencias, Posgrado en Ciencias BiológicasUniversidad Nacional Autónoma de MéxicoCuernavacaMexico
  3. 3.Red de Estudios Moleculares AvanzadosInstituto de EcologíaXalapaMexico
  4. 4.Departamento de Ingeniería Celular y BiocatálisisInstituto de Biotecnología, UNAMCuernavacaMexico
  5. 5.Centro de Investigación en Dinámica CelularUniversidad Autónoma del Estado de MorelosCuernavacaMexico

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