The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the Functional Diversity of Eukaryotic Life in the Oceans through Transcriptome Sequencing

Microbial ecology is plagued by problems of an abstract nature. Cell sizes are so small and population sizes so large that both are virtually incomprehensible. Niches are so far from our everyday experience as to make their very definition elusive. Organisms that may be abundant and critical to our survival are little understood, seldom described and/or cultured, and sometimes yet to be even seen. One way to confront these problems is to use data of an even more abstract nature: molecular sequence data. Massive environmental nucleic acid sequencing, such as metagenomics or metatranscriptomics, promises functional analysis of microbial communities as a whole, without prior knowledge of which organisms are in the environment or exactly how they are interacting. But sequence-based ecological studies nearly always use a comparative approach, and that requires relevant reference sequences, which are an extremely limited resource when it comes to microbial eukaryotes

Vertical distribution of picoeukaryotic diversity in the Sargasso Sea

20 pages, 5 figures, 4 tables, supplementary material http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2007.01247.x/suppinfoEukaryotic molecular diversity within the picoplanktonic size-fraction has primarily been studied in marine surface waters. Here, the vertical distribution of picoeukaryotic diversity was investigated in the Sargasso Sea from euphotic to abyssal waters, using size-fractionated samples (< 2 μm). 18S rRNA gene clone libraries were used to generate sequences from euphotic zone samples (deep chlorophyll maximum to the surface); the permanent thermocline (500 m); and the pelagic deep-sea (3000 m). Euphotic zone and deep-sea data contrasted strongly, the former displaying greater diversity at the first-rank taxon level, based on 232 nearly full-length sequences. Deep-sea sequences belonged almost exclusively to the Alveolata and Radiolaria, while surface samples also contained known and putative photosynthetic groups, such as unique Chlorarachniophyta and Chrysophyceae sequences. Phylogenetic analyses placed most Alveolata and Stramenopile sequences within previously reported 'environmental' clades, i.e. clades within the Novel Alveolate groups I and II (NAI and NAII), or the novel Marine Stramenopiles (MAST). However, some deep-sea NAII formed distinct, bootstrap supported clades. Stramenopiles were recovered from the euphotic zone only, although many MAST are reportedly heterotrophic, making the observed distribution a point for further investigation. An unexpectedly high proportion of radiolarian sequences were recovered. From these, five environmental radiolarian clades, RAD-I to RAD-V, were identified. RAD-IV and RAD-V were composed of Taxopodida-like sequences, with the former solely containing Sargasso Sea sequences, although from all depth zones sampled. Our findings highlight the vast diversity of these protists, most of which remain uncultured and of unknown ecological function. © 2007 The Authors; Journal compilation © 2007 Society for Applied Microbiology and Blackwell Publishing Ltd.Cruise attendance and construction of clone libraries were supported by an NSF grant (0074392) to A.Z.W. and an UCSDAcademic Senate Grant to F.A. F. Not, all sequence curation, data analyses and subsequent work were supported by a Gordon and Betty Moore Foundation Young Investigator award to A.Z.W.Peer Reviewe

Corrigendum: Assessing the Diversity and Distribution of Apicomplexans in Host and Free-Living Environments Using High-Throughput Amplicon Data and a Phylogenetically Informed Reference Framework

A Corrigendum on Assessing the Diversity and Distribution of Apicomplexans in Host and Free-Living Environments Using High-Throughput Amplicon Data and a Phylogenetically Informed Reference Framework by del Campo, J., Heger, T. J., Rodríguez-Martínez, R., Worden, A. Z., Richards, T. A., Massana, R., et al. (2019). Frontiers in Microbiology. 10:2373. doi: 10.3389/fmicb.2019.02373.-- 2 pagesIn the original article, the reference for Kotabová et al., 2012 was incorrectly written as Kotabová, E., Vancová, M., Lukeš, J., Oborník, M., Modri, D., Lukeš, M., et al. (2012). Morphology, ultrastructure and life cycle of Vitrella brassicaformis n. sp., n. gen., a novel chromerid from the great barrier reef. Protist 163, 306–323. doi: 10.1016/j.protis.2011.09.001. It should be Oborník, M., Modrý, D., Lukeš, M., Cernotíková-Stríbrná, E., Cihlár, J., Tesarová, M., et al. (2012). Morphology, ultrastructure and life cycle of Vitrella brassicaformis n. sp., n. gen., a novel chromerid from the great barrier reef. Protist 163, 306–323. doi: 10.1016/j.protis.2011.09.001 Furthermore, the reference should be cited as Oborník et al. 2012. In the original article Moore, R. B., Oborník, M., Janouškovec, J., Chrudimský, T., Vancová, M., Green, D. H., et al. (2008). A photosynthetic alveolate closely related to apicomplexan parasites. Nature 451, 959–963. doi: 10.1038/nature06635 was not cited in the article. The citation has now been inserted in INTRODUCTION, Paragraph 3 and should read: Understanding what this diversity and distribution means requires a more detailed dissection of which apicomplexans appear in which environments. This is currently not possible because we lack a robust phylogenetic framework (e.g., a reference tree) upon which to base such inferences. Moreover, it has5 recently been shown that the apicomplexans are the sister group to another odd collection of microbial predators (colpodellids) and putatively symbiotic algae (chromerids), collectively known as chrompodellids or “Apicomplexan-related lineages” (ARLs) (Leander et al., 2003; Moore et al., 2008; Oborník et al., 2012; Woo et al., 2015). These lineages have aided in understanding of how apicomplexans evolved to become parasites and the ecological conditions that might have led to this transition. The authors apologize for these errors and state that this does not change the scientific conclusions of the article in any way. The original article has been updatedPeer reviewe

Phylogeny, Evidence for a Cryptic Plastid, and Distribution of Chytriodinium Parasites (Dinophyceae) Infecting Copepods

8 pages, 3 figures, supporting information https://doi.org/10.1111/jeu.12701Spores of the dinoflagellate Chytriodinium are known to infest copepod eggs causing their lethality. Despite the potential to control the population of such an ecologically important host, knowledge about Chytriodinium parasites is limited: we know little about phylogeny, parasitism, abundance, or geographical distribution. We carried out genome sequence surveys on four manually isolated sporocytes from the same sporangium, which seemed to be attached to a copepod nauplius, to analyze the phylogenetic position of Chytriodinium based on SSU and concatenated SSU/LSU rRNA gene sequences, and also characterize two genes related to the plastidial heme pathway, hemL and hemY. The results suggest the presence of a cryptic plastid in Chytriodinium and a photosynthetic ancestral state of the parasitic Chytriodinium/Dissodinium clade. Finally, by mapping Tara Oceans V9 SSU amplicon data to the recovered SSU rRNA gene sequences from the sporocytes, we show that globally, Chytriodinium parasites are most abundant within the pico/nano‐ and mesoplankton of the surface ocean and almost absent within microplankton, a distribution indicating that they generally exist either as free‐living spores or host‐associated sporangiaThis work was supported by a grant from the Gordon and Betty Moore Foundation (GBMF3307) to P.J.K., T.A.R., A.Z.W., and A.E.S., and from NSERC (RGPIN‐2014–03994) to P.J.K. Ship time was supported by a grant from the David and Lucile Packard Foundation through MBARI and GBMF3788 to A.Z.W. J.dC. was supported by a Marie Curie International Outgoing Fellowship grant (FP7‐PEOPLE‐2012‐IOF-331450 CAARL), and N.O., M.K., and J.dC. were supported by a grant from the Tula Foundation to the Centre for Microbial Biodiversity and Evolution at UBCPeer Reviewe