Biology subjects

Boisard, J.

Publications and source records attributed to Boisard, J..

5 recordsLinked to original sources

bioRxiv2026

Lateral gene transfer introduced the microbial anaerobiosis-related gene rquA into early animals

Lateral gene transfer (LGT) enables rapid metabolic innovation in microbes, but its evolutionary importance in animals remains debated. Among metabolic traits with major ecological consequences, adaptations to low-oxygen conditions often involve modifications of mitochondrial electron transport and the quinones that mediate electron flow. Rhodoquinone-based anaerobic metabolism occurs in several eukaryotic lineages, yet the evolutionary routes by which animals acquired this capability are poorly understood. Here we show that freshwater sponges possess a rhodoquinone biosynthesis gene, rquA, previously restricted to microbial lineages, which was acquired by lateral gene transfer and functionally integrated into sponge metabolism. Heterologous expression of rquA from the model freshwater sponge Ephydatia muelleri enables rhodoquinone production in yeast, consistent with functional conservation. In E. muelleri, the rquA gene is upregulated under hypoxia and rhodoquinone is detectable across all lifestages, however, it is most abundant in early development in the pluiripotent gemmules. Using comparative genomics, we find that the presence of rquA in freshwater sponges correlates with loss of key genes of the ubiquinone biosynthesis pathway, suggesting these animals cannot synthesize ubiquinone de novo and we show that E. muelleri can convert exogenous ubiquinone to rhodoquinone. Rhodoquinone levels were significantly higher in rquA-encoding freshwater sponges compared to marine sponges that were sampled from natural environments. This study reveals that an early animal lineage acquired a microbial metabolism-related gene via lateral gene transfer during or before the transition to freshwater environments, enabling rhodoquinone utilization and potentially enhancing tolerance to oxygen fluctuations. Thereby, demonstrating how LGT shapes energy metabolism even in multicellular organisms.

evolutionary biology↗

bioRxiv2026

Semi-permeable capsules enable parallel cultivation and live microscopic observations of microbial eukaryotes

Semi-permeable capsules (SPCs) create enclosed porous microenvironments, diffusible to only small proteins and macromolecules. This presents a powerful tool for single cell observation, isolation, and sequencing. However, their range of use for sustaining viable microbial eukaryotes is largely unexplored. Single-cell eukaryotes are often understudied, with a wealth of unknown lifecycles, culturing methods and inter-microbial interactions, which are difficult to visualize. Here, we show that eukaryotes from eight different supergroups can be captured and propagated in SPCs. Encapsulation allowed observations of cell stages, motility and growth in a traceable and parallelized manner.

microbiology↗

bioRxiv2026

CoMR: an integrative scoring pipeline for Comprehensive Mitochondrial proteome Reconstruction across eukaryotes

Mitochondrial proteome reconstruction from eukaryotic sequence data typically relies on prediction of mitochondrial targeting signals (MTSs). However, MTS predictors are primarily trained on model organisms and may perform poorly in phylogenetically divergent lineages or in organisms with atypical or reduced targeting sequences. Accurate reconstruction therefore requires integration of complementary sources of evidence beyond targeting prediction alone. We developed CoMR (Comprehensive Mitochondrial Reconstructor), an integrative workflow that combines targeting prediction, curated homology searches, large-scale similarity searches, and automated phylogenetic analysis within a unified scoring framework. Benchmarking on the model yeast Saccharomyces cerevisiae yielded strong discriminatory performance (ROC-AUC = 0.92), exceeding standalone TargetP2 prediction (ROC-AUC = 0.72). In the divergent anaerobic protist Paratrimastix pyriformis, CoMR maintained robust performance (ROC-AUC = 0.86) validated with an experimental proteome despite extreme class imbalance, achieving a precision-recall AUC of 0.183 ([~]78-fold enrichment over random expectation and [~]10-fold improvement over TargetP2). Ablation analyses demonstrate that predictive performance is robust to individual evidence-layer removal and that the relative contribution of homology sources depends on phylogenetic context. Together, these results show that integrative evidence scoring improves mitochondrial proteome reconstruction across both model and non-model eukaryotes.

bioinformatics↗

bioRxiv2025

Anaerobic protist survival in microcosms is dependent on microbiome metabolic function.

Anaerobic environments serve as habitats for diverse microorganisms, including unicellular eukaryotes (protists) and prokaryotes. To thrive in low-oxygen environments, protists and prokaryotes often establish specialized metabolic cross-feeding associations, such as syntrophy, with other microorganisms. Previous studies show that the breviate protist Lenisia limosa engages in a mutualistic association with a denitrifying Arcobacter bacterium based on hydrogen exchange. Here, we investigate if the ability to form metabolic interactions is conserved in other breviates by studying five diverse breviate microcosms and their associated bacteria We show that five laboratory microcosms of marine breviates live with multiple hydrogen-consuming prokaryotes that are predicted to have different preferences for terminal electron acceptors using genome-resolved metagenomics. Growth of the prokaryotes and protists within the microcosms respond differently to electron acceptors depending on the make-up of the prokaryotic community. We find that the metabolic capabilities of the bacteria and not their taxonomic affiliations determine protist growth and survival and present new potential protist-interacting bacteria from the Arcobacteraceae, Desulfovibrioaceae and Terasakiella lineages. This investigation uncovers potential nitrogen and sulfur cycling pathways within these bacterial populations, hinting at their roles in syntrophic interactions with the protists via hydrogen exchange.

microbiology↗

bioRxiv2021

Marine gregarine genomes illuminate current understanding of apicomplexan glideosome

Our current view of the evolutionary history, coding and adaptive capacities of Apicomplexa, protozoan parasites of a wide range of metazoan, is currently strongly biased toward species infecting humans, as data on early diverging apicomplexan lineages infecting invertebrates is extremely limited. Here, we characterized the genome of the marine eugregarine Porospora gigantea, intestinal parasite of Lobsters, remarkable for the macroscopic size of its vegetative feeding forms (trophozoites) and its gliding speed, the fastest so far recorded for Apicomplexa. Two highly syntenic genomes named A and B were assembled. Similar in size (~9 Mb) and coding capacity (~5300 genes), A and B genomes are 10.8% divergent at the nucleotide level, corresponding to 16-38 My in divergent time. Orthogroup analysis across 25 (proto)Apicomplexa species, including Gregarina niphandrodes, showed that A and B are highly divergent from all other known apicomplexan species, revealing an unexpected breadth of diversity. Phylogenetically these two species branch sister to Cephaloidophoroidea, and thus expand the known crustacean gregarine superfamily. The genomes were mined for genes encoding proteins necessary for gliding, a key feature of apicomplexans parasites, currently studied through the molecular model called glideosome. Sequence analysis shows that actin-related proteins and regulatory factors are strongly conserved within apicomplexans. In contrast, the predicted protein sequences of core glideosome proteins and adhesion proteins are highly variable among apicomplexan lineages, especially in gregarines. These results confirm the importance of studying gregarines to widen our biological and evolutionary view of apicomplexan species diversity, and to deepen our understanding of the molecular bases of key functions enabling parasitism, such as the glideosome.

genomics↗