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

Abstract

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.

The all-intracellular order Legionellales is unexpectedly diverse, globally distributed and lowly abundant

“…In general, Proteobacteria were within the most common bacteria in soils and aquatic environments in different countries (Denet et al . 2017 ; Hosen et al . 2017 ; Naghoni et al .…”

“…Many of the predominant amoebae in those soils are Tetramitus , Acanthamoeba and Naegleria (Denet et al . 2017 ; Peabody et al . 2017 ) known to be hosts for Legionellales .…”

Survival and growth of Stenotrophomonas maltophilia in free-living amoebae (FLA) and bacterial virulence properties

“…Two strains (MEEB-Am6.1 and MEEB-Am6.2) were isolated by a culturable method from two different amoebal genera i.e. Micriamoeba and Tetramitus and two different soils, Vietnam and Burkina Faso, respectively [ 17 ]. Two reference strains of S .…”

“…Recently, we showed that S . maltophilia is also part of the microbiome of several free-living amoebal genera from soils collected in Burkina Faso and Vietnam [ 17 ]. However, its role in the context of amoebal interactions is poorly known.…”

Estudio del papel de las amebas de vida libre como reservorio de Helicobacter pylori y otras bacterias patógenas en aguas y alimentos mediante técnicas moleculares

“…Las FLA son organismos ubicuos que se han aislado en el medio ambiente del suelo (Reyes-Batlle et al, 2014, Denet et al, 2017, del agua (García et al, 2013;Montalbano Di Filippo et al, 2015) y del aire (Rivera et al, 1994). Además se han aislado de otros ambientes, como lentillas y estuches para guardarlas (Martín-Navarro et al, 2008;Gomes et al, 2016), aires acondicionados (Astorga et al, 2011) e incluso vegetales (Chavatte et al, 2016).…”