Decontamination, pooling and dereplication of the 678 samples of the Marine Microbial Eukaryote Transcriptome Sequencing Project

Objectives Complex algae are photosynthetic organisms resulting from eukaryote-to-eukaryote endosymbiotic-like interactions. Yet the specific lineages and mechanisms are still under debate. That is why large scale phylogenomic studies are needed. Whereas available proteomes provide a limited diversity of complex algae, MMETSP (Marine Microbial Eukaryote Transcriptome Sequencing Project) transcriptomes represent a valuable resource for phylogenomic analyses, owing to their broad and rich taxonomic sampling, especially of photosynthetic species. Unfortunately, this sampling is unbalanced and sometimes highly redundant. Moreover, we observed contaminated sequences in some samples. In such a context, tree inference and readability are impaired. Consequently, the aim of the data processing reported here is to release a unique set of clean and non-redundant transcriptomes produced through an original protocol featuring decontamination, pooling and dereplication steps. Data description We submitted 678 MMETSP re-assembly samples to our parallel consolidation pipeline. Hence, we combined 423 samples into 110 consolidated transcriptomes, after the systematic removal of the most contaminated samples (186). This approach resulted in a total of 224 high-quality transcriptomes, easy to use and suitable to compute less contaminated, less redundant and more balanced phylogenies.

A microbial eukaryote with a unique combination of purple bacteria and green algae as endosymbionts

Oxygenic photosynthesizers (cyanobacteria and eukaryotic algae) have repeatedly become endosymbionts throughout evolution. In contrast, anoxygenic photosynthesizers (e.g., purple bacteria) are exceedingly rare as intracellular symbionts. Here, we report on the morphology, ultrastructure, lifestyle, and metagenome of the only “purple-green” eukaryote known. The ciliate Pseudoblepharisma tenue harbors green algae and hundreds of genetically reduced purple bacteria. The latter represent a new candidate species of the Chromatiaceae that lost known genes for sulfur dissimilation. The tripartite consortium is physiologically complex because of the versatile energy metabolism of each partner but appears to be ecologically specialized as it prefers hypoxic sediments. The emergent niche of this complex symbiosis is predicted to be a partial overlap of each partners’ niches and may be largely defined by anoxygenic photosynthesis and possibly phagotrophy. This purple-green ciliate thus represents an extraordinary example of how symbiosis merges disparate physiologies and allows emergent consortia to create novel ecological niches.

Parasites, Drugs and Captivity: Blastocystis-Microbiome Associations in Captive Water Voles

(1) Background: Blastocystis is a microbial eukaryote inhabiting the gastrointestinal tract of a broad range of animals including humans. Several studies have shown that the organism is associated with specific microbial profiles and bacterial taxa that have been deemed beneficial to intestinal and overall health. Nonetheless, these studies are focused almost exclusively on humans, while there is no similar information on other animals. (2) Methods: Using a combination of conventional PCR, cloning and sequencing, we investigated presence of Blastocystis along with Giardia and Cryptosporidium in 16 captive water voles sampled twice from a wildlife park. We also characterised their bacterial gut communities. (3) Results: Overall, alpha and beta diversities between water voles with and without Blastocystis did not differ significantly. Differences were noted only on individual taxa with Treponema and Kineothrix being significantly reduced in Blastocystis positive water voles. Grouping according to antiprotozoal treatment and presence of other protists did not reveal any differences in the bacterial community composition either. (4) Conclusion: Unlike human investigations, Blastocystis does not seem to be associated with specific gut microbial profiles in water voles.

Protist communities along freshwater–marine transition zones in Hudson Bay (Canada)

One of the most striking ecological divides on Earth is between marine and nearby freshwater environments, as relatively few taxa can move between the two. Microbial eukaryotes contribute to biogeochemical and energy cycling in both fresh and marine waters, with little species overlap between the two ecosystems. Arctic and sub-Arctic marine systems are relatively fresh compared to tropical and temperate systems, but details of microbial eukaryote communities along river-to-sea transitions are poorly known. To bridge this knowledge gap, we investigated three river-to-sea transitions (Nelson, Churchill, and Great Whale Rivers) in sub-Arctic Hudson Bay through 18S rRNA amplicon sequencing to identify microbial eukaryotes along the salinity and biogeochemical gradients. Salinity acted as the principal dispersal barrier preventing freshwater microorganisms from colonizing marine coastal waters, with microbial eukaryote communities of the three rivers clustering together. Just offshore, communities clustered by coastal regions associated with nutrient concentrations. Analysis of indicator species revealed that communities in the nitrate-depleted coastal water off the Churchill and Great Whale Rivers were dominated by heterotrophic taxa and small photosynthetic protists. In contrast, the Nelson offshore community was characterized by a high proportion of the diatom Rhizosolenia. A distinct community of heterotrophic protists was identified in the three estuarine transition zones, suggesting specialized estuarine communities. Such specialization was most marked in the Nelson River system that was sampled more intensely and showed estuarine circulation. The autochthonous community was composed of the bacterial grazers Katablepharis, Mataza, and Cryothecomonas, as well as brackish species of the diatoms Skeletonema and Thalassiosira. These findings suggest that flow regulation on the Nelson River that modifies estuarine circulation would affect estuarine community composition and distribution in the transition zone.

Nanoparticle-Biological Interactions in a Marine Benthic Foraminifer

The adverse effects of engineered nanomaterials (ENM) in marine environments have recently attracted great attention although their effects on marine benthic organisms such as foraminifera are still largely overlooked. Here we document the effects of three negatively charged ENM, different in size and composition, titanium dioxide (TiO2), polystyrene (PS) and silicon dioxide (SiO2), on a microbial eukaryote (the benthic foraminifera Ammonia parkinsoniana) using multiple approaches. This research clearly shows the presence, within the foraminiferal cytoplasm, of metallic (Ti) and organic (PS) ENM that promote physiological stress. Specifically, marked increases in the accumulation of neutral lipids and enhanced reactive oxygen species production occurred in ENM-treated specimens regardless of ENM type. This study indicates that ENM represent ecotoxicological risks for this microbial eukaryote and presents a new model for the neglected marine benthos by which to assess natural exposure scenarios.