Bouziane Moumen

Hosts represent complex environments where different tissues may act as distinct ecological niches, imposing different constraints that may shape parasite ecology and evolution. Such within‐host heterogeneity can generate phenotypic diversity with consequences for virulence and transmission. Our aim was to determine whether the constraints associated with infecting different host tissues lead to the coexistence of multiple parasite sub‐populations with distinct phenotypes. We tested this hypothesis using the widespread bacterial endosymbiont Wolbachia . We injected bacteria isolated from three tissues of the common pill‐bug into uninfected individuals and tracked temporal changes in Wolbachia load in the recipient host tissues, as well as the virulence associated with each bacterial source. Our results show that colonisation success depends on the tissue of origin of the injected Wolbachia . Genome resequencing did not detect any genetic variation associated with variation in bacterial replication rate, which thus likely results from phenotypic plasticity. Indeed, no recurrent tissue‐specific variants were detected, and our conservative filtering pipeline retained only one substitution and one gene conversion event. These findings highlight the genomic stability of Wolbachia across host environments while demonstrating that within‐host diversification can occur without genetic divergence. More broadly, they underscore how microenvironmental variation within hosts can shape parasite ecology.

By regulating gene expression to maintain homeostasis and enabling rapid responses to environmental change, epigenetic mechanisms can provide valuable insights into how populations respond to external pressures. Here, we examined genome-wide DNA methylation in natural populations of the mayfly Andesiops torrens from a semi-arid watershed of northern Chile exposed to intense climatic and anthropogenic stress. We analyzed 285 individuals from 30 sites using methylRAD sequencing and assembled a draft reference genome to map methylated loci and determine their associated gene functions. Discriminant analyses of principal components revealed a methylation structure among sampling sites, identifying five groups, and the coexistence within localities of individuals with distinct methylation profiles. Non-CpG methylRAD loci accounted for most methylation divergence, consistent with environmental effects. The five groups shared a broad functional spectrum dominated by regulatory processes related to cellular processes, gene regulation, morphogenesis, neurogenesis, and metabolism, and formed a continuum from core cellular regulation in small groups to more integrated developmental and adaptive stress-related control in larger groups. While the drivers of these patterns remain to be clarified, our study suggests that DNA methylation contributes to local responses in A. torrens and also reveals the potential of DNA methylation analyses as an initial approach for exploring ecological pressures in natural populations.

Pea is a model organism in biology and an agronomic crop, entering the genomics era. Although RNA‐sequencing (RNA‐seq) has become the main transcriptomic approach in biology, there is currently no genome‐wide expression atlas covering a wide range of biological conditions for this species. Here, we generate a transcriptomic atlas in Pisum sativum by integrating 149 publicly available RNA‐seq libraries, covering 10 cultivars, and a comprehensive collection of plant organs and several environmental stress conditions (heat, low temperature, nutrient, and water deficit). As proof of concept, we first verified the expression profiles of key gene families, such as sugar transporters and transcription factors (TF), across this transcriptomic atlas. Using a systems biology approach, we then inferred a regulatory network of genes responsive to water deficit, from which we predicted putative TF‐target interactions, including genes encoding monosaccharide transporter PsSTP13.2 and sugar facilitator PsSWEET6 . Finally, we exploited our meta‐analysis to identify new reference genes with stable expression based on their coefficient of variation. Ten reference genes were validated by quantitative PCR across various biological samples, including different pea varieties, organs, and stress conditions (water deficit and fungal pathogen infection). Three reference genes ( Psat6g102320 , Psat6g163160 , and Psat7g253080 ) outperformed the expression stability of common housekeeping genes ( TFIIA , PPIIA , and β‐tubulin ). Altogether, this atlas opens new avenues of integrative research in the genomics and systems biology era of legume crops.

The mechanisms underlying within-host diversification in parasite populations are poorly understood. Yet, phenotypic and genotypic variation in parasites can shape their evolutionary trajectories and have important epidemiological consequences. Our aim was to determine whether the constraints associated with infecting different host tissues lead to the emergence and coexistence of multiple parasite sub-populations with distinct phenotypes. We tested this hypothesis using the most widespread bacterial endosymbiont, Wolbachia . We injected Wolbachia bacteria isolated from three tissues of the common pill-bug ( Armadillidium vulgare ) into uninfected individuals and monitored the growth rate and virulence of each bacterial sub-population in the new hosts. Our results highlight that within-host tissue heterogeneity leads to diverse Wolbachia phenotypes. High-depth genome re-resequencing of Wolbachia sub-populations revealed that this polymorphism was not due to genomic variation but was more likely a result of phenotypic plasticity. Indeed, we found no recurrent tissue-specific genomic variation among infected individuals. Our single nucleotide polymorphism (SNP) filtration pipeline, developed to ensure SNP validity, detected only one substitution. This Wolbachia variant, observed in one female, was present in all three bacterial sub-populations, with frequencies ranging from 24% to 58% depending on the tissue. Overall, our results support the stability of the Wolbachia genome with respect to the rarity of point mutations, in agreement with reports from other symbiotic systems. From a methodological perspective, our study highlights the need for considerable caution when detecting variants in endosymbiont populations, as our conservative approach led us to exclude more than 99.5% of the initially called variants.

Encystment is a common stress response of most protists, including free-living amoebae. Cyst formation protects the amoebae from eradication and can increase virulence of the bacteria they harbor. Here, we mapped the global molecular changes that occur in the facultatively pathogenic amoeba Acanthamoeba castellanii during the early steps of the poorly understood process of encystment. By performing transcriptomic, proteomic, and phosphoproteomic experiments during encystment, we identified more than 150,000 previously undescribed transcripts and thousands of protein sequences absent from the reference genome. These results provide molecular details to the regulation of expected biological processes, such as cell proliferation shutdown, and reveal new insights such as a rapid phospho-regulation of sites involved in cytoskeleton remodeling and translation regulation. This work constitutes the first time-resolved molecular atlas of an encysting organism and a useful resource for further investigation of amoebae encystment to allow for a better control of pathogenic amoebae.

The crucial role of microbes in the evolution, development, health, and ecological interactions of multicellular organisms is now widely recognized in the holobiont concept. However, the structure and stability of microbiota are highly dependent on abiotic and biotic factors, especially in the gut, which can be colonized by transient bacteria depending on the host’s diet. We studied these impacts by manipulating the digestive microbiota of the detritivore Armadillidium vulgare and analyzing the consequences on its structure and function. Hosts were exposed to initial starvation and then were fed diets that varied the different components of lignocellulose. A total of 72 digestive microbiota were analyzed according to the type of the diet (standard or enriched in cellulose, lignin, or hemicellulose) and the period following dysbiosis. The results showed that microbiota from the hepatopancreas were very stable and resilient, while the most diverse and labile over time were found in the hindgut. Dysbiosis and selective diets may have affected the host fitness by altering the structure of the microbiota and its predicted functions. Overall, these modifications can therefore have effects not only on the holobiont, but also on the “eco-holobiont” conceptualization of macroorganisms.

Isopods constitute a particular group of crustaceans that has successfully colonized all environments including marine, freshwater and terrestrial habitats. Their ability to use various food sources, especially plant biomass, might be one of the reasons of their successful spread. All isopods, which feed on plants and their by-products, must be capable of lignocellulose degradation. This complex composite is the main component of plants and is therefore an important nutrient source for many living organisms. Its degradation requires a large repertoire of highly specialized Carbohydrate-Active enZymes (called CAZymes) which are produced by the organism itself and in some cases, by its associated microbiota. The acquisition of highly diversified CAZymes could have helped isopods to adapt to their diet and to their environment, especially during land colonization. To test this hypothesis, isopod host CAZomes (i.e. the entire CAZyme repertoire) were characterized in marine, freshwater and terrestrial species through a transcriptomic approach. Many CAZymes were identified in 64 isopod transcriptomes, comprising 27 de novo datasets. Our results show that marine, freshwater and terrestrial isopods exhibit different CAZomes, illustrating different strategies for lignocellulose degradation. The analysis of variations of the size of CAZy families shows these are expanded in terrestrial isopods while they are contracted in aquatic isopods; this pattern is probably resulting from the evolution of the host CAZomes during the terrestrial adaptation of isopods. We show that CAZyme gene duplications and horizontal transfers can be involved in adaptive divergence between isopod CAZomes. Our characterization of the CAZomes in 64 isopods species provides new insights into the evolutionary processes that enabled isopods to conquer various environments, especially terrestrial ones.

Woodlice are recognized as keystone species in terrestrial ecosystems due to their role in the decomposition of organic matter. Thus, they contribute to lignocellulose degradation and nutrient cycling in the environment together with other macroarthropods. Lignocellulose is the main component of plants and is composed of cellulose, lignin and hemicellulose. Its digestion requires the action of multiple Carbohydrate-Active enZymes (called CAZymes), typically acting together as a cocktail with complementary, synergistic activities and modes of action. Some invertebrates express a few endogenous lignocellulose-degrading enzymes but in most species, an efficient degradation and digestion of lignocellulose can only be achieved through mutualistic associations with endosymbionts. Similar to termites, it has been suspected that several bacterial symbionts may be involved in lignocellulose degradation in terrestrial isopods, by completing the CAZyme repertoire of their hosts. To test this hypothesis, host transcriptomic and microbiome shotgun metagenomic datasets were obtained and investigated from the pill bug Armadillidium vulgare. Many genes of bacterial and archaeal origin coding for CAZymes were identified in the metagenomes of several host tissues and the gut content of specimens from both laboratory lineages and a natural population of A. vulgare. Some of them may be involved in the degradation of cellulose, hemicellulose, and lignin. Reconstructing a lignocellulose-degrading microbial community based on the prokaryotic taxa contributing relevant CAZymes revealed two taxonomically distinct but functionally redundant microbial communities depending on host origin. In parallel, endogenous CAZymes were identified from the transcriptome of the host and their expression in digestive tissues was demonstrated by RT-qPCR, demonstrating a complementary enzyme repertoire for lignocellulose degradation from both the host and the microbiome in A. vulgare. Our results provide new insights into the role of the microbiome in the evolution of terrestrial isopods and their adaptive radiation in terrestrial habitats.

In animals, sexual differences between males and females are usually determined by sex chromosomes. Alternatively, sex may also be determined by vertically transmitted intracellular microbial endosymbionts. The best known cytoplasmic sex manipulative endosymbiont is Wolbachia which can, for instance, feminize genetic males into phenotypic females in the terrestrial isopod Armadillidium vulgare. However, the molecular genetic basis of cytoplasmic sex determination is unknown. To identify candidate genes of feminization induced by Wolbachia strain wVulC from A. vulgare, we sequenced the genome of Wolbachia strain wCon from Cylisticus convexus, the most closely related known Wolbachia strain to wVulC that does not induce feminization, and compared it to the wVulC genome. Then, we performed gene expression profiling of the 216 resulting wVulC candidate genes throughout host developmental stages in A. vulgare and the heterologous host C. convexus. We identified a set of 35 feminization candidate genes showing differential expression during host sexual development. Interestingly, 27 of the 35 genes are present in the f element, which is a piece of a feminizing Wolbachia genome horizontally transferred into the nuclear genome of A. vulgare and involved in female sex determination. Assuming that the molecular genetic basis of feminization by Wolbachia and the f element is the same, the 27 genes are candidates for acting as master sex determination genes in A. vulgare females carrying the f element.