Shedding light on microbial dark matter: a TM6 bacterium as natural endosymbiont of a free‐living amoeba

Abstract

The TM6 phylum belongs to the so-called microbial dark matter that gathers uncultivated bacteria detected only via DNA sequencing. Recently, the genome sequence of a TM6 bacterium (TM6SC1) has led to suggest that this bacterium would adopt an endosymbiotic life. In the present paper, free-living amoebae bearing a TM6 strain were isolated from a water network. The amoebae were identified as Vermamoeba vermiformis and the presence of a TM6 strain was detected by polymerase chain reaction and microscopy. The partial sequence of its 16S rRNA gene showed this strain to be closely related to the sequenced TM6SC1 strain. These bacteria displayed a pyriform shape and were found within V. vermiformis. Therefore, these bacteria were named Vermiphilus pyriformis. Interactions studies showed that V. pyriformis was highly infectious and that its relation with V. vermiformis was specific and highly stable. Finally, it was found that V. pyriformis inhibited the encystment of V. vermiformis. Overall, this study describes for the first time an endosymbiotic relationship between a TM6 bacterium and a free-living amoeba in the environment. It suggests that other bacteria of the TM6 phylum might also be endosymbiotic bacteria and may be found in other free-living amoebae or other organisms.

Chromulinavorax destructans, a pathogenic TM6 bacterium with an unusual replication strategy targeting protist mitochondrion

“…nov.) is proposed. This family also contains the original MAG of JCVI_TM6SC1 and might also harbour Vermiphilus pyriformis, based on a partial 16S sequence [5]. The basal nodes in the 16S rDNA ML tree are poorly supported, likely due to undersampling, and similar to previous analysis ( Figure 8A) [4].…”

“…The genomic complement, enriched in conserved gene functions found in endosymbionts or parasites of eukaryotes such as Chlamydia, Wolbachia, and Rickettsia, further suggested that TM6 was associated with eukaryotic hosts [3,4]. Indeed, two representatives of the TM6 phylum were since isolated in amoebae, competent hosts to a vast array of bacterial, eukaryotic, and viral symbionts and pathogens [5,6]. The first isolate, Babela massiliensis, is an obligate pathogen that causes lysis of its host, Acanthamoeba castellanii, while the other, Vermiphilus pyriformis, maintains a stable relationship with its host Vermamoeba vermiformis, suggesting that different TM6 bacteria might employ different life history strategies [5,6].…”

“…Indeed, two representatives of the TM6 phylum were since isolated in amoebae, competent hosts to a vast array of bacterial, eukaryotic, and viral symbionts and pathogens [5,6]. The first isolate, Babela massiliensis, is an obligate pathogen that causes lysis of its host, Acanthamoeba castellanii, while the other, Vermiphilus pyriformis, maintains a stable relationship with its host Vermamoeba vermiformis, suggesting that different TM6 bacteria might employ different life history strategies [5,6]. Since only the sequence for Babela massiliensis is available, a detailed comparison of the genomic complement involved in the different lifestyles is not possible.…”

‘Candidatus Cochliophilus cryoturris’ (Coxiellaceae), a symbiont of the testate amoeba Cochliopodium minus

“…The number of symbionts per amoeba cell varied and ranged from a few to over 100. The infection did not compromise the host’s capability to encyst as described for some other symbionts 16, 42 , nor did we observe pronounced lysis of the amoeba at room temperature or at 28 °C. Over a period of two years, the amoebae remained infected, demonstrating that this symbiont-amoeba relationship is a stable long-term association.…”

The multi-omics promise in context: from sequence to microbial isolate

“…This first isolated geothermal nanoarchaeon, proposed as "Candidatus Nanopusillus acidilobi" represents the smallest cultured organism to date (100-300 nm cell size), and available cultures now allow experimentation to reveal its particular metabolism and adaptation features. Many more ultra-small bacteria and archaea with similar ectosymbiotic or ectoparasitic lifestyles might await discovery and identification of their hosts, something that -apart from single cell genomics -is only feasible by direct cultivation (Delafont et al 2015;He et al 2015;Wurch et al 2016). We conclude that genomic information of microbes derived from low diversity environments can often be obtained relatively easily and that individual genome reconstructions are often feasible (Figure 3).…”