Parasitology Research

, Volume 116, Issue 11, pp 3151–3162 | Cite as

Diversity of free-living amoebae in soils and their associated human opportunistic bacteria

  • Elodie DenetEmail author
  • Bénédicte Coupat-Goutaland
  • Sylvie Nazaret
  • Michel Pélandakis
  • Sabine Favre-Bonté
Original Paper


Free-living amoebae (FLA) are ubiquitous protozoa found worldwide in the environment. They feed by phagocytosis on various microorganisms. However, some bacteria, i.e., amoebae-resistant bacteria (ARB) or bacterial endocytobionts, can resist phagocytosis and even multiply inside FLA. This study investigated the diversity of culturable FLA in various soils from agricultural and mining sites and their bacterial endocytobionts. FLA were cultured on non-nutrient agar with alive Escherichia coli and identified by PCR and sequencing. Amoebae were lysed and bacterial endocytobionts were cultured on TSA 1/10 and Drigalski medium. Bacterial isolates were identified by PCR and 16S rDNA sequencing and characterized for their antibiotic resistance properties. To measure bacterial virulence, the amoebal model Dictyostelium discoideum was used. The analysis of FLA diversity showed that Tetramitus was the most prevalent genus in agricultural soil from Burkina Faso (73%) and garden soil from Vietnam (42%) while Naegleria and Acanthamoeba were dominant genera in mining soil from Vietnam (55%) and French alpine soil (77%). Some genera were only present in one out of the four soils analyzed. The bacterial endocytobiont included Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteria. Human opportunistic pathogens identified as Pseudomonas aeruginosa, Stenotrophomonas maltophilia, and Burkholderia cepacia were found associated with amoebae including Micriamoeba, Tetramitus, Willaertia, or Acanthamoeba. Some of these bacteria showed various antibiotic resistance phenotypes and were virulent. Our study confirms that the occurrence of these opportunistic bacteria with FLA in soils may be important for the survival, multiplication, and spread of pathogens in the environment.


Free-living amoebae Soil Bacterial endocytobiont Human pathogen Antibiotic resistance Virulence 



We wish to thank Nicole Lloyd, a native English speaker, for reviewing this article prior to publication.

Funding information

This work was supported by the CNRS (Centre National de la Recherche Scientifique). Elodie Denet was funded by a grant from the Ministère de l’Education Nationale, de l’Enseignement Supérieur et de la Recherche.

Supplementary material

436_2017_5632_MOESM1_ESM.docx (16 kb)
ESM 1 (DOCX 15 kb)


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Copyright information

© Springer-Verlag GmbH Germany 2017

Authors and Affiliations

  1. 1.Université Lyon 1 , CNRS UMR 5557/ UMR INRA 1418 Ecologie MicrobienneVilleurbanne CEDEXFrance
  2. 2.Université Lyon 1 , CNRS UMR 5240 Microbiologie, Adaptation, PathogénieVilleurbanne CEDEXFrance
  3. 3.CIRI, Centre International de Recherche en Infectiologie, Team HoriGene, Inserm, U1111Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de LyonVilleurbanneFrance

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