Biology subjects

Alacid, E.

Publications and source records attributed to Alacid, E..

4 recordsLinked to original sources

bioRxiv2025

Single-cell sequencing reveals unexpected genetic diversity among Bodo spp. flagellates and their bacterial endosymbionts

Bodo is a cosmopolitan genus of free living bacterivorous single-celled flagellates in the class Kinetoplastea. Members of genus Bodo are considered the closest free-living relatives to the parasitic lineages Trypanosoma and Leishmania, the causative agents of the human diseases sleeping sickness, Chagas disease, and leishmaniasis. Currently, a single genome exists for the one formally described species in the genus, Bodo saltans. Previous studies on B. saltans have shown that it is dependent on an endosymbiotic bacterium from the order Holosporales, "Candidatus Bodocaedibacter vickermanii". Using single cell-sequencing, we isolated, sequenced, and assembled genomes for seven uncultured Bodo spp. cells from a single freshwater sample from Royal Leamington Spa, UK. By using comparative genomics, we show that these seven cells represent three potentially novel Bodo species and exhibit unexpected levels of diversity at the genome level. Our results indicate that Small Subunit (SSU) rDNA sequencing, often used to classify Bodo flagellates, is insufficient for determining species delimitation in this genus. In addition, we recovered a Holosporales bacterium genome from all seven Bodo spp. cells. Surprisingly, these seven bacterial endosymbionts also represent three potentially novel species and one novel genus of Holosporales bacteria. This diversity would be indistinguishable in routinely-used SSU ribosomal DNA (rDNA) metabarcoding or bulk sequencing pipelines, thus demonstrating the utility of using single-cell sequencing to reveal the level of genomic diversity within lineages of microbial eukaryotes and their cobionts.

microbiology↗

bioRxiv2025

Phagocytosis repurposed: infection strategies in a globalmarine diatom-parasite interaction

Microbial host-parasite interactions shape global biogeochemical cycles, yet their cellular and evolutionary mechanisms remain poorly understood. Here, we developed a novel model pathosystem to explore the interaction between the globally distributed eukaryotic microparasite, Pirsonia, and its host, the bloom-forming diatom, Coscinodiscus. Culture conditions recapitulated Pirsonias rapid life cycle in vitro and live-cell imaging enabled quantitative assessments of infection dynamics and host mortality. To investigate the genetic basis of this interaction, we assembled the Pirsonia genome and identified unique genetic innovations relative to their oomycete relatives. Time-resolved dual RNA-Seq enabled tracking of parasite gene expression through the infection cycle and revealed an upregulation of an expanded multi-gene family of integrin-like proteins in Pirsonia zoospores, analogous to the variable surface proteins in other parasitic lineages. Genes upregulated during infection were associated with cytoskeletal dynamics and drug inhibition assays confirmed that actin is required for host infection, consistent with the presence of parasitic pseudopodia on infected hosts. The dependence on both actin-based phagocytic mechanisms and parasitic-like surface proteins highlights Pirsonias intermediate state between predator and parasite, providing new insights into the evolution of parasite strategies and the complex cellular interactions controlling parasitic shunts in marine trophic networks.

evolutionary biology↗

bioRxiv2022

Identification of a Non-Canonical Ciliate Nuclear Genetic Code Where UAA and UAG Code for Different Amino Acids

The genetic code is one of the most highly conserved features across life. Only a few lineages have deviated from the "universal" genetic code. Amongst the few variants of the genetic code reported to date, the codons UAA and UAG virtually always have the same translation, suggesting that their evolution is coupled. Here, we report the genome and transcriptome sequencing of a novel ciliate, belonging to the Oligohymenophorea class, where the translation of the UAA and UAG stop codons have changed to specify different amino acids. Genomic and transcriptomic analyses revealed that UAA has been reassigned to encode lysine, while UAG has been reassigned to encode glutamic acid. We identified multiple suppressor tRNA genes with anticodons complementary to the reassigned codons. We show that the retained UGA stop codon is enriched in the 3UTR immediately downstream of the coding region of genes, suggesting that there is functional drive to maintain tandem stop codons. Using a phylogenomics approach, we reconstructed the ciliate phylogeny and mapped genetic code changes, highlighting the remarkable number of independent genetic code changes within the Ciliophora group of protists. According to our knowledge, this is the first report of a genetic code variant where UAA and UAG encode different amino acids.

genomics↗

bioRxiv2021

Host preferences of coexisting Perkinsea parasitoids during coastal dinoflagellate blooms

Parasites in aquatic systems are highly diverse and ubiquitous. In marine environments, parasite-host interactions contribute substantially to shaping microbial communities, but their nature and complexity remain poorly understood. In this study, we examined the relationship between Perkinsea parasitoids and bloom-forming dinoflagellate species. Our aim was to determine whether parasite-host species interactions are specific and whether the diversity and distribution of parasitoids are shaped by their dinoflagellate hosts. Several locations along the Catalan coast (NW Mediterranean Sea) were sampled during the blooms of five dinoflagellate species and the diversity of Perkinsea was determined by combining cultivation-based methods with metabarcoding of the V4 region of 18S rDNA. Most known species of Parviluciferaceae, and others not yet described, were detected, some of them coexisting in the same coastal location, and with a wide distribution. The specific parasite-host interactions determined for each of the studied blooms demonstrated the host preferences exhibited by parasitoids in nature. The dominance of a species within the parasitoid community is driven by the presence and abundances of its preferred host(s).The absence of parasitoid species, often associated with a low abundance of their preferred hosts, suggested that high infection rates are reached only under conditions that favour parasitoid propagation, especially dinoflagellate blooms.

molecular biology↗