Morphology, ultrastructure, genomics, and phylogeny of Euplotes vanleeuwenhoeki sp. nov. and its ultra-reduced endosymbiont “Candidatus Pinguicoccus supinus” sp. nov.

Abstract

Taxonomy is the science of defining and naming groups of biological organisms based on shared characteristics and, more recently, on evolutionary relationships. With the birth of novel genomics/bioinformatics techniques and the increasing interest in microbiome studies, a further advance of taxonomic discipline appears not only possible but highly desirable. The present work proposes a new approach to modern taxonomy, consisting in the inclusion of novel descriptors in the organism characterization: (1) the presence of associated microorganisms (e.g.: symbionts, microbiome), (2) the mitochondrial genome of the host, (3) the symbiont genome. This approach aims to provide a deeper comprehension of the evolutionary/ecological dimensions of organisms since their very first description. Particularly interesting, are those complexes formed by the host plus associated microorganisms, that in the present study we refer to as “holobionts”. We illustrate this approach through the description of the ciliate Euplotes vanleeuwenhoeki sp. nov. and its bacterial endosymbiont “Candidatus Pinguicoccus supinus” gen. nov., sp. nov. The endosymbiont possesses an extremely reduced genome (~ 163 kbp); intriguingly, this suggests a high integration between host and symbiont.

‘Candidatus Sarmatiella mevalonica’ endosymbiont of the ciliate Paramecium provides insights on evolutionary plasticity among Rickettsiales

“…In order to get DNA with minimal proportion of contaminants in a sufficient amount for genome sequencing, a whole genome amplification (WGA) was performed using QIAGEN Repli‐G single‐cell kit from around five Paramecium cells as previously described (Serra et al ., 2020), and sequenced with Illumina HiSeq X by Admera Health (South Plainfield, NJ, USA), obtaining 44 434 254 2 × 150 bp read pairs. After a preliminary assembly of total reads with SPAdes 3.6.0 (Bankevich et al ., 2012), the contigs belonging to the endosymbiont were selected using the blobology pipeline (https://github.com/blaxterlab/blobology) (Kumar et al ., 2013), as described previously (e.g.…”

The neotypification of Frontonia vernalis (Ehrenberg, 1833) Ehrenberg, 1838 and the description of Frontonia paravernalis sp. nov. trigger a critical revision of frontoniid systematics

“…Small transparent drops spread over the cells of F. vernalis and F. leucas are, apparently, trichocysts. The image is not copyrighted due to the age of the work found and described by means of a multimethod study [16,36,37] a novel species of green frontoniid, F. paravernalis sp. nov., closely related to the F. vernalis group.…”

Genome Analysis of a Verrucomicrobial Endosymbiont With a Tiny Genome Discovered in an Antarctic Lake

“…Here, we describe Candidatus Organicella extenuata, a member of the Verrucomicrobia with a highly reduced genome, recovered as a metagenomeassembled genome with genetic code 4 (UGA-to-Trp recoding) from Organic Lake. It is closely related to Candidatus Pinguicocccus supinus (163,218 bp, 205 genes), a newly described cytoplasmic endosymbiont of the freshwater ciliate Euplotes vanleeuwenhoeki (Serra et al, 2020). At 158,228 bp (encoding 194 genes), the genome of Ca.…”