Symbionts of the ciliate Euplotes: diversity, patterns and potential as models for bacteria-eukaryote endosymbioses

Abstract

Endosymbioses between bacteria and eukaryotes are enormously important in ecology and evolution, and as such are intensely studied. Despite this, the range of investigated hosts is narrow in the context of the whole eukaryotic tree of life: most of the information pertains to animal hosts, while most of the diversity is found in unicellular protists. A prominent case study is the ciliate Euplotes, which has repeatedly taken up the bacterium Polynucleobacter from the environment, triggering its transformation into obligate endosymbiont. This multiple origin makes the relationship an excellent model to understand recent symbioses, but Euplotes may host bacteria other than Polynucleobacter, and a more detailed knowledge of these additional interactions is needed in order to correctly interpret the system. Here, we present the first systematic survey of Euplotes endosymbionts, adopting a classical as well as a metagenomic approach, and review the state of knowledge. The emerging picture is indeed quite complex, with some Euplotes harbouring rich, stable prokaryotic communities not unlike those of multicellular animals. We provide insights into the distribution, evolution and diversity of these symbionts (including the establishment of six novel bacterial taxa), and outline differences and similarities with the most well-understood group of eukaryotic hosts: insects.

Keywords: Devosia; Euplotes; Francisellaceae; Holosporales; Rickettsiales; prokaryote–eukaryote symbioses.

Figure 1.

FISHs with species-specific oligonucleotide probes for the six novel endosymbiotic taxa. (a) ‘Ca. Finniella dimorpha’ in E. daidaleos Eda1. (b) ‘Ca. Fujishimia apicalis' in E. octocarinatus Eoc1/2. (c) ‘Ca. Anadelfobacter sociabilis’ in E. octocarinatus Eoc1/2. (d) ‘Ca. Euplotella sexta’ in E. octocarinatus Eoc1/2. (e) ‘Ca. Bandiella numerosa’ in E. woodruffi Ewo1 (the asterisk marks autofluorescence signal from an undigested alga). (f) ‘Ca. Parafinniella ignota’ in Euplotes sp. EMP. Grey outlines represent Euplotes cells and were drawn based on the corresponding bright field pictures. Bars represent 10 µm. (Online version in colour.)

Figure 2.

16S rRNA-based phylogenetic affiliations of bacterial endosymbionts of Euplotes. (a) Phylogenetic tree of family Burkholderiaceae (Betaproteobacteria), including symbiotic Polynucleobacter forming a polyphyletic group in the otherwise free-living clade ‘PnecC’, and the exclusively symbiotic genus ‘Ca. Protistobacter’. (b) Phylogenetic tree of orders Rickettsiales and Holosporales (Alphaproteobacteria), entirely composed of intracellular bacteria harboured by diverse hosts. (c) Phylogenetic tree of the closely related families Francisellaceae and Fastidiosibacteraceae, including obligate and opportunistic endosymbionts as well as free-living bacteria. (d) Phylogenetic tree of Devosia (Alphaproteobacteria) and closely related genera. Euplotes endosymbionts are highlighted, and colour-coded according to their host species. Numbers in square brackets represent the number of sequences in collapsed nodes. Standard bootstrap supports, when at or above 70%, are provided close to the corresponding node. Bars stand for an estimated sequence divergence of 0.1.

Figure 3.

Synopsis of all Euplotes strains and populations screened for the presence of bacterial endosymbionts with molecular techniques. On the left, a simplified phylogeny of the Euplotes species investigated is presented. On columns, symbionts are organized first by their characterization as ‘essential’ or ‘accessory’, and then by taxonomy. Asterisks mark bacterial species found in hosts other than Euplotes. The ‘absence’ status is employed for negative FISH or negative metagenomic screening results. Black dots represent presences inferred by the recovery of 16S rRNA gene sequences (through Sanger or high-throughput sequencing) but not confirmed by FISH. (Online version in colour.)