Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes

This revision of the classification of eukaryotes follows that of Adl et al., 2012 [J. Euk. Microbiol. 59(5)] and retains an emphasis on protists. Changes since have improved the resolution of many nodes in phylogenetic analyses. For some clades even families are being clearly resolved. As we had predicted, environmental sampling in the intervening years has massively increased the genetic information at hand. Consequently, we have discovered novel clades, exciting new genera, and uncovered a massive species level diversity beyond the morphological species descriptions. Several clades known from environmental samples only have found their home. Sampling soils, deeper marine waters, and the deep sea will continue to fill us with surprises. The main changes in this revision are the confirmation that eukaryotes form at least two domains, the loss of monophyly in the Exavata, robust support for the Haptista and Cryptista. We provide suggested primer sets for DNA sequences from environmental samples that are effective for each clade. We have provided a guide to trophic functional guilds in an appendix, to facilitate the interpretation of environmental samples. This revision of the classification of eukaryotes updates that of the International Society of Protistologists (Adl et al., 2012). Since then, there has been a massive increase in DNA sequence information of phylogenetic relevance from environmental samples. We now have a much better sense of the undescribed biodiversity in our environment (Pawlowski et al., 2012; de Vargas et al., 2015). While significant, it still remains a partial estimation as several continents and soils in general are poorly sampled, and the deeper ocean is hard to reach. This new data clarified phylogenetic relationships and the new information is incorporated in this revision

Diversification of unicellular eukaryotes: cryptomonad colonizations of marine and fresh waters inferred from revised 18S rRNA phylogeny

The cryptomonads is a well-defined lineage of unicellular eukaryotes, composed of several marine and freshwater groups. However, the evolutionary relationships among these groups are unclear due to conflicting inferences between morphological and molecular phylogenies. Here, we have inferred the evolutionary relationships among marine and freshwater species in order to better understand the importance of the marine-freshwater boundary on the historical diversification patterns of cryptomonads. We have constructed improved molecular phylogenies by taking into account rate variation both across sites and across sequences (covarion substitutions), and by analysing the vast majority of publicly available cryptomonad 18S rRNA sequences and related environmental phylotypes. The resulting phylogenies included 55 sequences, and revealed two novel freshwater cryptomonad clades (CRY1 and CRY2) and a large hidden diversity of cryptomonads. CRY1 was placed deeply within the cryptomonad phylogeny together with all the major freshwater lineages (i.e. Goniomonas and Cryptomonas), while CRY2 was placed within a lineage of marine species identified as Plagioselmis-like with the aid of a new sequence generated from a cultured species. The inferred phylogenies suggest only few successful marine-freshwater transitions over the history of cryptomonads. Most of the transitions seem to have occurred from marine to fresh waters, but re-colonizations of marine habitats have also taken place. This implies that the differences in the biogeophysical conditions between marine and fresh waters constitute a substantial barrier for the cross-colonization of these environments by cryptomonads

A hotspot of amoebae diversity : 8 new naked amoebae associated with the planktonic bloom-forming cyanobacterium Microcystis

The colonies of Microcystis, one of the most common bloom-forming cyanobacteria worldwide, harbor a diverse community of microorganisms. Among these, naked amoebae feeding on Microcystis cells can strongly influence natural Microcystis population dynamics. In this study, we investigated the species diversity of these amoebae based on 26 Microcystis-associated amoebae (MAA) strains from eutrophied water bodies in Belgium and elsewhere in western Europe. A detailed morphological characterization in combination with 18S rDNA (SSU) phylogenies revealed the presence of no less than 10 species. Nine of these belonged to the known genera Vannella (2 species), Korotnevella (2), Copromyxa (2), Vexillifera (1), Cochliopodium (1) and the recently described Angulamoeba (1). Only two were previously described, the others were new to science. One taxon could not be assigned to a known genus and is here described as Schoutedamoeba gen. n., representing a new variosean lineage. The discovery of so many new species from only one very specific habitat (Microcystis colonies) from a rather restricted geographical area indicates that the diversity of planktonic naked amoebae is much higher than previously appreciated and that only a tiny fraction of the total diversity of naked amoebae is currently known

UniEuk: time to speak a common language in protistology

The 18th International Conference on Harmful Algae (ICHA), From ecosystems to socio-ecosystems, 21-26 October 2018, Nantes, France.-- Networking activities around HABs: GlobalHAB, Global HAB Status report, ICES-WGs and other initiatives.-- 1 pageUniversal taxonomic frameworks have been critical tools to structure the fields of botany, zoology, and bacteriology, as well as their large research communities. Animals and plants have relatively solid, stable morpho-taxonomies built over the last three centuries, while bacteria have been classified for three decades under coherent molecular taxonomic frameworks. By contrast, no such common language exists yet for microbial eukaryotes / protists, even though environmental `omics´ surveys suggest that they make up most of the genetic complexity of our planet¿s ecosystems. With the current deluge of eukaryotic molecular data, we urgently need a universal eukaryotic taxonomy bridging the `protist-omics´ age to the fragile, centuries-old body of classical knowledge linking protist taxa to morphological, physiological, and ecological information. UniEuk (www.unieuk.org) is an open, community-based and expert-driven international initiative to build a flexible, adaptive universal taxonomic framework for eukaryotes, focused primarily on protists. The UniEuk system comprises 3 complementary modules allowing direct community input: - EukRef, a standardized, open-source bioinformatics pipeline that allows taxonomic curation of publicly available phylogenetic marker sequences (starting with 18S rDNA), generating homogeneous sets of curated, aligned sequences and phylogenetic trees. - EukBank, a public repository of high-throughput metabarcoding datasets (starting with the V4 region of 18S rDNA) that allows monitoring of total eukaryotic diversity (e.g. saturation, phylogeny) across biomes, and identification of ecologically relevant new lineages. - EukMap, a user-friendly representation of the taxonomic framework in the form of a publicly navigable tree, fully editable by registered users, where each node/taxon is associated with standardized features (name, contextual data, links to pictures and literature, etc.). As a whole, the UniEuk system represents a community hub to centralize, safeguard and promote our current global knowledge on eukaryotic diversity and evolution, integrating expert knowledge on morphology and ecology with key molecular information from phylogenetic markers and environmental metabarcoding surveys. The resulting taxonomy, which will include toxic microalgae, will be implemented into the European Nucleotide Archive at EMBL-EBI and propagated to NCBI, and useable as a stand-alone resource for scientific, educational, or public outreach purposes. In this communication, we will present the project in more detail, and explain how members of the HAB community can get involved, including a EukRef workshop focusing on dinoflagellates (5-9 Nov 2018, Roscoff, France). Overall, UniEuk will contribute to advances on key taxonomic challenges crucial to ascertain the biogeographic distribution, range of expansion, ecology and links with toxin production of relevant harmful speciesPeer Reviewe

Phylogeny and Systematics of Leptomyxid Amoebae (Amoebozoa, Tubulinea, Leptomyxida)

We describe four new species of Flabellula, Leptomyxa and Rhizamoeba and publish new SSU rRNA gene and actin gene sequences of leptomyxids. Using these data we provide the most comprehensive SSU phylogeny of leptomyxids to date. Based on the analyses of morphological data and results of the SSU rRNA gene phylogeny we suggest changes in the systematics of the order Leptomyxida (Amoebozoa: Lobosa: Tubulinea). We propose to merge the genera Flabellula and Paraflabellula (the genus Flabellula remains valid by priority rule). The genus Rhizamoeba is evidently polyphyletic in all phylogenetic trees; we suggest retaining the generic name Rhizamoeba for the group unifying R. saxonica, R.matisi n. sp. and R. polyura, the latter remains the type species of the genus Rhizamoeba. Based on molecular and morphological evidence we move all remaining Rhizamoeba species to the genus Leptomyxa. New family Rhizamoebidae is established here in order to avoid paraphyly of the family Leptomyxidae. With the suggested changes both molecular and morphological systems of the order Leptomyxida are now fully congruent to each other

Phylogeny and Systematics of Leptomyxid Amoebae (Amoebozoa, Tubulinea, Leptomyxida)

We describe four new species of Flabellula, Leptomyxa and Rhizamoeba and publish new SSU rRNA gene and actin gene sequences of leptomyxids. Using these data we provide the most comprehensive SSU phylogeny of leptomyxids to date. Based on the analyses of morphological data and results of the SSU rRNA gene phylogeny we suggest changes in the systematics of the order Leptomyxida (Amoebozoa: Lobosa: Tubulinea). We propose to merge the genera Flabellula and Paraflabellula (the genus Flabellula remains valid by priority rule). The genus Rhizamoeba is evidently polyphyletic in all phylogenetic trees; we suggest retaining the generic name Rhizamoeba for the group unifying R. saxonica, R.matisi n. sp. and R. polyura, the latter remains the type species of the genus Rhizamoeba. Based on molecular and morphological evidence we move all remaining Rhizamoeba species to the genus Leptomyxa. New family Rhizamoebidae is established here in order to avoid paraphyly of the family Leptomyxidae. With the suggested changes both molecular and morphological systems of the order Leptomyxida are now fully congruent to each other. (C) 2016 Elsevier GmbH. All rights reserved

EukRef: Phylogenetic curation of ribosomal RNA to enhance understanding of eukaryotic diversity and distribution.

Environmental sequencing has greatly expanded our knowledge of micro-eukaryotic diversity and ecology by revealing previously unknown lineages and their distribution. However, the value of these data is critically dependent on the quality of the reference databases used to assign an identity to environmental sequences. Existing databases contain errors and struggle to keep pace with rapidly changing eukaryotic taxonomy, the influx of novel diversity, and computational challenges related to assembling the high-quality alignments and trees needed for accurate characterization of lineage diversity. EukRef (eukref.org) is an ongoing community-driven initiative that addresses these challenges by bringing together taxonomists with expertise spanning the eukaryotic tree of life and microbial ecologists, who use environmental sequence data to develop reliable reference databases across the diversity of microbial eukaryotes. EukRef organizes and facilitates rigorous mining and annotation of sequence data by providing protocols, guidelines, and tools. The EukRef pipeline and tools allow users interested in a particular group of microbial eukaryotes to retrieve all sequences belonging to that group from International Nucleotide Sequence Database Collaboration (INSDC) (GenBank, the European Nucleotide Archive [ENA], or the DNA DataBank of Japan [DDBJ]), to place those sequences in a phylogenetic tree, and to curate taxonomic and environmental information for the group. We provide guidelines to facilitate the process and to standardize taxonomic annotations. The final outputs of this process are (1) a reference tree and alignment, (2) a reference sequence database, including taxonomic and environmental information, and (3) a list of putative chimeras and other artifactual sequences. These products will be useful for the broad community as they become publicly available (at eukref.org) and are shared with existing reference databases

Aplicación de musicomovigramas en la educación de niños con TEA

Con el paso de los años, la sociedad en la que vivimos y, por tanto, la educación, han ido evolucionando. En la enseñanza tradicional, eran los docentes los que tomaban todas y cada una de las decisiones, es decir, tenían un papel totalmente activo. Sin embargo, poco a poco, y debido a los múltiples cambios que se han ido produciendo, los alumnos, han ido cobrando un papel mucho menos pasivo, siendo ahora, los únicos protagonistas de su proceso de enseñanza-aprendizaje. Por otra parte, los docentes, se han convertido en guías y mediadores de las aulas. Como consecuencia de esto, los métodos de enseñanza, también se han visto sometidos a un gran cambio y en este sentido, numerosos estudios demuestran los múltiples beneficios que tanto la música, como las TIC, están teniendo en la sociedad que nos rodea. A lo largo del presente Trabajo Fin de Grado (TFG) se hará una revisión exhaustiva de diferentes autores, gracias a los cuales, es posible asegurar la necesidad de incorporar en las aulas ambos recursos desde edades muy tempranas. Vivimos en un mundo en el que continuamente estamos en contacto con ruidos y sonidos. Son muchas las personas que recomiendan hablar al feto, y poner música junto al vientre de la madre durante los meses de gestación. Además, desde el día de nuestro nacimiento, comenzamos a estar en contacto con ruidos que poco a poco se irán convirtiendo en algo muy familiar para nosotros. En cuanto a las TIC, actualmente están presentes en todas nuestras actividades diarias, nos encontramos en la era digital en la que las nuevas tecnologías cobran un papel fundamental. Frecuentemente, escuchamos la expresión “hoy en día los niños nacen con una Tablet debajo del brazo”, sin embargo, ¿es adecuado el uso que se está dando a este tipo de recursos? Tal y como se indicará en el apartado siguiente, la música nos permite desarrollarnos de manera holística a nivel social, cognitivo y emocional. También, incide en nuestro estado de ánimo, nuestro desarrollo físico, etc. Además, en el caso de los Alumnos con Necesidades Educativas Especiales (ACNEE), como son aquellos que presentan Trastorno del Espectro Autista (TEA), la música los permite sentirse seguros, cómodos y tranquilos. Por otra parte, los niños con TEA se verán muy beneficiados a nivel social y en el desarrollo de la comunicación, gracias a las TIC. Sin embargo, se ha podido comprobar que, en la etapa de Educación Infantil, no existe un momento específico dedicado a la educación musical, lo que nos lleva pensar cómo poder transmitir diferentes contenidos del currículum, a través de recursos didáctico-musicales que, a su vez, incorporen las TIC, como son los musicomovigramas. A lo largo de este TFG, nos centraremos en la influencia tan positiva que tanto la música como las TIC, tienen en todos los niños desde edades muy tempranas y de forma más concreta, en cómo afectan a los niños que presentan TEA. Además, se plasmarán una serie de objetivos que pretenden ser conseguidos, mediante la elaboración del presente documento, así como la metodología que se seguirá para alcanzarlos. Igualmente, se elaborará una programación didáctica que contará con un apartado de justificación, en el que se señalarán los motivos por los que se ha creado este musicomovigrama en concreto. Del mismo modo, habrá una sección de objetivos (generales y específicos), contenidos (conceptuales, procedimentales y aptitudinales), competencias, metodología, recursos materiales y evaluación (del alumno y docente). A continuación, nos centraremos en cómo elaborar un musicomovigrama, para lo que se creará un videotutorial, así como en los programas que se han utilizado para la creación de este, sus ventajas y sus inconvenientes. El paso siguiente, será la puesta en práctica y, por tanto, en el punto 8, se enmarcarán los resultados obtenidos tras la aplicación del musicomovigrama, así como las conclusiones. Por último, habrá un apartado de referencias bibliográficas en el que quedarán reflejados, todos y cada uno de los artículos, libros, programas, videos, etc. que se han consultado para la elaboración del TFG, así como los anexos, donde que recogerá todo aquello que no se haya considerado oportuno incluir en los puntos anteriores

Genomic evidence for global ocean plankton biogeography shaped by large-scale current systems

International audienceBiogeographical studies have traditionally focused on readily visible organisms, but recent technological advances are enabling analyses of the large-scale distribution of microscopic organisms, whose biogeographical patterns have long been debated1,2. The most prominent global biogeography of marine plankton was derived by Longhurst3 based on parameters principally associated with photosynthetic plankton. Localized studies of selected plankton taxa or specific organismal sizes1,4–7 have mapped community structure and begun to assess the roles of environment and ocean current transport in shaping these patterns2,8. Here we assess global plankton biogeography and its relation to the biological, chemical and physical context of the ocean (the ‘seascape’) by analyzing 24 terabases of metagenomic sequence data and 739 million metabarcodes from the Tara Oceans expedition in light of environmental data and simulated ocean current transport. In addition to significant local heterogeneity, viral, prokaryotic and eukaryotic plankton communities all display near steady-state, large-scale, size-dependent biogeographical patterns. Correlation analyses between plankto transport time and metagenomic or environmental dissimilarity reveal the existence of basin-scale biological and environmental continua emerging within the main current systems. Across oceans, there is a measurable, continuous change within communities and environmental factors up to an average of 1.5 years of travel time. Modulation of plankton communities during transport varies with organismal size, such that the distribution of smaller plankton best matches Longhurst biogeochemical provinces, whereas larger plankton group into larger provinces. Together these findings provide an integrated framework to interpret plankton community organization in its physico-chemical context, paving the way to a better understanding of oceanic ecosystem functioning in a changing global environment