Plant and Soil

, Volume 384, Issue 1–2, pp 413–431 | Cite as

The art of isolating nitrogen-fixing bacteria from non-leguminous plants using N-free semi-solid media: a practical guide for microbiologists

  • José Ivo BaldaniEmail author
  • Veronica Massena Reis
  • Sandy Sampaio Videira
  • Lúcia Helena Boddey
  • Vera Lúcia Divan Baldani
Methods Paper


Background and aim

Nitrogen-fixing bacteria or diazotrophs have been isolated for many years using different formulations of N-free semi-solid media. However, the strategies used to isolate them, and the recipes of these media, are scattered through the published literature and in other sources that are more difficult to access and which are not always retrievable. Therefore, the aim of this work was to collate the various methods and recipes, and to provide a comprehensive methodological guide and their use by the scientific community working in the field of biological nitrogen fixation (BNF), particularly with non-leguminous plants.


Procedures used for bacterial counting and identification either from rhizosphere soil or on the surface of, or within, plant tissues (to access “endophytic” bacteria) are presented in detail, including colony and cell morphologies. More importantly, appropriate recipes available for each N-free semi-solid culture medium that are used to count and isolate various diazotrophs are presented.


It is recognized by those working in the field of BNF with non-legumes that the development of the N-free semi-solid medium has allowed a tremendous accumulation of knowledge on the ecology and physiology of their associated diazotrophs. At least 20 nitrogen-fixing species have been isolated and identified based on the enrichment method originally developed by Döbereiner, Day and collaborators in the 70’s. In spite of all the advances in molecular techniques used to detect bacteria, in most cases the initial isolation and identification of these diazotrophs still requires semi-solid media.


The introduction of the N-free semi-solid medium opened new opportunities for those working in the area of BNF with non-legumes not only for elucidating the important role played by their associated microorganisms, but also because some of these bacteria that were isolated using semi-solid media are now being recommended as plant growth-promoting inoculants for sugarcane (Saccharum sp.), maize (Zea mays) and wheat (Triticum aestivum) in Brazil and other countries. Further progress in the field could be made by using a combination of culture-independent molecular community analyses, in situ activity assessments with probe-directed enrichment, and isolation of target strains using modified or standard semi-solid media.


Nitrogen fixation Media recipes Isolation procedure Bacterial counting Phenotypic characterization 



The authors thank Embrapa Agrobiologia, the CNPq/INCT-FBN and FAPERJ for financial support and CNPq for the fellowship of the researchers of Embrapa Agrobiologia. Thanks also to our colleague Robert M. Boddey for his encouragement to write this guide and reading the manuscript. The authors thank the laboratory analist Fernanda Dourado for the bacterial photographs.


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Copyright information

© Springer International Publishing Switzerland 2014

Authors and Affiliations

  • José Ivo Baldani
    • 1
    Email author
  • Veronica Massena Reis
    • 1
  • Sandy Sampaio Videira
    • 1
    • 2
  • Lúcia Helena Boddey
    • 1
  • Vera Lúcia Divan Baldani
    • 1
  1. 1.Embrapa AgrobiologiaRio de JaneiroBrazil
  2. 2.Centro Universitário de Volta Redonda (UniFOA)Rio de JaneiroBrazil

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