Mamiellales, Mamiellophyceae)
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Perspectives in Phycology Vol
Perspectives in Phycology Vol. 3 (2016), Issue 3, p. 141–154 Article Published online June 2016 Diversity and ecology of green microalgae in marine systems: an overview based on 18S rRNA gene sequences Margot Tragin1, Adriana Lopes dos Santos1, Richard Christen2,3 and Daniel Vaulot1* 1 Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR 7144, Station Biologique, Place Georges Teissier, 29680 Roscoff, France 2 CNRS, UMR 7138, Systématique Adaptation Evolution, Parc Valrose, BP71. F06108 Nice cedex 02, France 3 Université de Nice-Sophia Antipolis, UMR 7138, Systématique Adaptation Evolution, Parc Valrose, BP71. F06108 Nice cedex 02, France * Corresponding author: [email protected] With 5 figures in the text and an electronic supplement Abstract: Green algae (Chlorophyta) are an important group of microalgae whose diversity and ecological importance in marine systems has been little studied. In this review, we first present an overview of Chlorophyta taxonomy and detail the most important groups from the marine environment. Then, using public 18S rRNA Chlorophyta sequences from culture and natural samples retrieved from the annotated Protist Ribosomal Reference (PR²) database, we illustrate the distribution of different green algal lineages in the oceans. The largest group of sequences belongs to the class Mamiellophyceae and in particular to the three genera Micromonas, Bathycoccus and Ostreococcus. These sequences originate mostly from coastal regions. Other groups with a large number of sequences include the Trebouxiophyceae, Chlorophyceae, Chlorodendrophyceae and Pyramimonadales. Some groups, such as the undescribed prasinophytes clades VII and IX, are mostly composed of environmental sequences. The 18S rRNA sequence database we assembled and validated should be useful for the analysis of metabarcode datasets acquired using next generation sequencing. -
University of Oklahoma
UNIVERSITY OF OKLAHOMA GRADUATE COLLEGE MACRONUTRIENTS SHAPE MICROBIAL COMMUNITIES, GENE EXPRESSION AND PROTEIN EVOLUTION A DISSERTATION SUBMITTED TO THE GRADUATE FACULTY in partial fulfillment of the requirements for the Degree of DOCTOR OF PHILOSOPHY By JOSHUA THOMAS COOPER Norman, Oklahoma 2017 MACRONUTRIENTS SHAPE MICROBIAL COMMUNITIES, GENE EXPRESSION AND PROTEIN EVOLUTION A DISSERTATION APPROVED FOR THE DEPARTMENT OF MICROBIOLOGY AND PLANT BIOLOGY BY ______________________________ Dr. Boris Wawrik, Chair ______________________________ Dr. J. Phil Gibson ______________________________ Dr. Anne K. Dunn ______________________________ Dr. John Paul Masly ______________________________ Dr. K. David Hambright ii © Copyright by JOSHUA THOMAS COOPER 2017 All Rights Reserved. iii Acknowledgments I would like to thank my two advisors Dr. Boris Wawrik and Dr. J. Phil Gibson for helping me become a better scientist and better educator. I would also like to thank my committee members Dr. Anne K. Dunn, Dr. K. David Hambright, and Dr. J.P. Masly for providing valuable inputs that lead me to carefully consider my research questions. I would also like to thank Dr. J.P. Masly for the opportunity to coauthor a book chapter on the speciation of diatoms. It is still such a privilege that you believed in me and my crazy diatom ideas to form a concise chapter in addition to learn your style of writing has been a benefit to my professional development. I’m also thankful for my first undergraduate research mentor, Dr. Miriam Steinitz-Kannan, now retired from Northern Kentucky University, who was the first to show the amazing wonders of pond scum. Who knew that studying diatoms and algae as an undergraduate would lead me all the way to a Ph.D. -
The Mixed Lineage Nature of Nitrogen Transport and Assimilation in Marine Eukaryotic Phytoplankton: a Case Study of Micromonas Sarah M
The Mixed Lineage Nature of Nitrogen Transport and Assimilation in Marine Eukaryotic Phytoplankton: A Case Study of Micromonas Sarah M. McDonald, Joshua N. Plant, and Alexandra Z. Worden* Monterey Bay Aquarium Research Institute, Moss Landing, California Present address: Center for Health Sciences, SRI International, 333 Ravenswood Avenue, Menlo Park, California 94025-3493. *Corresponding author: E-mail: [email protected]. Associate editor: Charles Delwiche Abstract Research article The prasinophyte order Mamiellales contains several widespread marine picophytoplankton (2 lm diameter) taxa, including Micromonas and Ostreococcus. Complete genome sequences are available for two Micromonas isolates, CCMP1545 and RCC299. We performed in silico analyses of nitrogen transporters and related assimilation genes in CCMP1545 and RCC299 and compared these with other green lineage organisms as well as Chromalveolata, fungi, bacteria, and archaea. Phylogenetic reconstructions of ammonium transporter (AMT) genes revealed divergent types contained within each Mamiellales genome. Some were affiliated with plant and green algal AMT1 genes and others with bacterial AMT2 genes. Land plant AMT2 genes were phylogenetically closer to archaeal transporters than to Mamiellales AMT2 genes. The Mamiellales represent the first green algal genomes to harbor AMT2 genes, which are not found in Chlorella and Chlamydomonas or the chromalveolate algae analyzed but are present in oomycetes. Fewer nitrate transporter (NRT) than AMT genes were identified in the Mamiellales. NRT1 was found in all but CCMP1545 and showed highest similarity to Mamiellales and proteobacterial NRTs. NRT2 genes formed a bootstrap-supported clade basal to other green lineage organisms. Several nitrogen-related genes were colocated, forming a nitrogen gene cluster. Overall, RCC299 showed the most divergent suite of nitrogen transporters within the various Mamiellales genomes, and we developed TaqMan quantitative polymerase chain reaction primer–probes targeting a subset of these, as well as housekeeping genes, in RCC299. -
Genes in Some Samples, Suggesting That the Gene Repertoire Is Modulated by Environmental Conditions
Analyses de variations génomiques liées à la biogéographie des picoalgues Mamiellales. Thèse de doctorat de l'université Paris-Saclay École doctorale n°577, Structure et dynamique des systèmes vivants (SDSV) Spécialité de doctorat : Sciences de la Vie et de la Santé Unité de recherche : Université Paris-Saclay, Univ Evry, CNRS, CEA, Génomique métabolique, 91057, Evry-Courcouronnes, France. Référent : Université d'Évry Val d’Essonne Thèse présentée et soutenue à Évry, le 28/08/2020, par Jade LECONTE Composition du Jury Christophe AMBROISE Professeur des universités, Université Examinateur & Président d’Evry Val d’Essonne (UMR 8071) François-Yves BOUGET Directeur de recherche CNRS, Sorbonne Rapporteur & Examinateur Université (UMR 7232) Frédéric PARTENSKY Directeur de recherche CNRS, Sorbonne Rapporteur & Examinateur Université (UMR 7144) Ian PROBERT Ingénieur de recherche, Sorbonne Examinateur Université Olivier JAILLON Directeur de thèse Directeur de recherche, CEA (UMR 8030) Remerciements Je souhaite remercier en premier lieu mon directeur de thèse, Olivier Jaillon, pour son encadrement, ses conseils et sa compréhension depuis mon arrivée au Genoscope. J’ai appris beaucoup à ses côtés, progressé dans de nombreux domaines, et apprécié partager l’unique bureau sans moquette du troisième étage avec lui. Merci également à Patrick Wincker pour m’avoir donné l’opportunité de travailler au sein du LAGE toutes ces années. J’ai grâce à vous deux eu l’occasion de plonger un peu plus loin dans le monde de l’écologie marine à travers le projet Tara Oceans, et j’en suis plus que reconnaissante. Je tiens également à remercier les membres de mon jury de thèse, à la fois mes rapporteurs François-Yves Bouget et Frédéric Partensky qui ont bien voulu évaluer ce manuscrit, ainsi que Christophe Ambroise et Ian Probert qui ont également volontiers accepté de participer à ma soutenance. -
Mannitol Biosynthesis in Algae : More Widespread and Diverse Than Previously Thought
This is a repository copy of Mannitol biosynthesis in algae : more widespread and diverse than previously thought. White Rose Research Online URL for this paper: https://eprints.whiterose.ac.uk/113250/ Version: Accepted Version Article: Tonon, Thierry orcid.org/0000-0002-1454-6018, McQueen Mason, Simon John orcid.org/0000-0002-6781-4768 and Li, Yi (2017) Mannitol biosynthesis in algae : more widespread and diverse than previously thought. New Phytologist. pp. 1573-1579. ISSN 1469-8137 https://doi.org/10.1111/nph.14358 Reuse Items deposited in White Rose Research Online are protected by copyright, with all rights reserved unless indicated otherwise. They may be downloaded and/or printed for private study, or other acts as permitted by national copyright laws. The publisher or other rights holders may allow further reproduction and re-use of the full text version. This is indicated by the licence information on the White Rose Research Online record for the item. Takedown If you consider content in White Rose Research Online to be in breach of UK law, please notify us by emailing [email protected] including the URL of the record and the reason for the withdrawal request. [email protected] https://eprints.whiterose.ac.uk/ 1 Mannitol biosynthesis in algae: more widespread and diverse than previously thought. Thierry Tonon1,*, Yi Li1 and Simon McQueen-Mason1 1 Department of Biology, Centre for Novel Agricultural Products, University of York, Heslington, York, YO10 5DD, UK. * Author for correspondence: tel +44 1904328785; email [email protected] Key words: Algae, primary metabolism, mannitol biosynthesis, mannitol-1-phosphate dehydrogenase, mannitol-1-phosphatase, haloacid dehalogenase, histidine phosphatase, evolution of metabolic pathways. -
Lateral Gene Transfer of Anion-Conducting Channelrhodopsins Between Green Algae and Giant Viruses
bioRxiv preprint doi: https://doi.org/10.1101/2020.04.15.042127; this version posted April 23, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 5 Lateral gene transfer of anion-conducting channelrhodopsins between green algae and giant viruses Andrey Rozenberg 1,5, Johannes Oppermann 2,5, Jonas Wietek 2,3, Rodrigo Gaston Fernandez Lahore 2, Ruth-Anne Sandaa 4, Gunnar Bratbak 4, Peter Hegemann 2,6, and Oded 10 Béjà 1,6 1Faculty of Biology, Technion - Israel Institute of Technology, Haifa 32000, Israel. 2Institute for Biology, Experimental Biophysics, Humboldt-Universität zu Berlin, Invalidenstraße 42, Berlin 10115, Germany. 3Present address: Department of Neurobiology, Weizmann 15 Institute of Science, Rehovot 7610001, Israel. 4Department of Biological Sciences, University of Bergen, N-5020 Bergen, Norway. 5These authors contributed equally: Andrey Rozenberg, Johannes Oppermann. 6These authors jointly supervised this work: Peter Hegemann, Oded Béjà. e-mail: [email protected] ; [email protected] 20 ABSTRACT Channelrhodopsins (ChRs) are algal light-gated ion channels widely used as optogenetic tools for manipulating neuronal activity 1,2. Four ChR families are currently known. Green algal 3–5 and cryptophyte 6 cation-conducting ChRs (CCRs), cryptophyte anion-conducting ChRs (ACRs) 7, and the MerMAID ChRs 8. Here we 25 report the discovery of a new family of phylogenetically distinct ChRs encoded by marine giant viruses and acquired from their unicellular green algal prasinophyte hosts. -
The Genome of Prasinoderma Coloniale Unveils the Existence of a Third Phylum Within Green Plants
Downloaded from orbit.dtu.dk on: Oct 10, 2021 The genome of Prasinoderma coloniale unveils the existence of a third phylum within green plants Li, Linzhou; Wang, Sibo; Wang, Hongli; Sahu, Sunil Kumar; Marin, Birger; Li, Haoyuan; Xu, Yan; Liang, Hongping; Li, Zhen; Cheng, Shifeng Total number of authors: 24 Published in: Nature Ecology & Evolution Link to article, DOI: 10.1038/s41559-020-1221-7 Publication date: 2020 Document Version Publisher's PDF, also known as Version of record Link back to DTU Orbit Citation (APA): Li, L., Wang, S., Wang, H., Sahu, S. K., Marin, B., Li, H., Xu, Y., Liang, H., Li, Z., Cheng, S., Reder, T., Çebi, Z., Wittek, S., Petersen, M., Melkonian, B., Du, H., Yang, H., Wang, J., Wong, G. K. S., ... Liu, H. (2020). The genome of Prasinoderma coloniale unveils the existence of a third phylum within green plants. Nature Ecology & Evolution, 4, 1220-1231. https://doi.org/10.1038/s41559-020-1221-7 General rights Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. Users may download and print one copy of any publication from the public portal for the purpose of private study or research. You may not further distribute the material or use it for any profit-making activity or commercial gain You may freely distribute the URL identifying the publication in the public portal If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. -
Protist Diversity Along a Salinity Gradient in a Coastal Lagoon
Vol. 74: 263–277, 2015 AQUATIC MICROBIAL ECOLOGY Published online March 25 doi: 10.3354/ame01740 Aquat Microb Ecol Protist diversity along a salinity gradient in a coastal lagoon Sergio Balzano1,2,*, Elsa Abs1, Sophie C. Leterme1 1School of Biological Sciences, Flinders University, GPO Box 2100, Adelaide 5001, South Australia 2Present address: Department of Marine Organic Biogeochemistry, Royal Netherlands Institute for Sea Research, PO Box 59, 1790AB Den Burg, The Netherlands ABSTRACT: The importance of microbial eukaryotes to aquatic systems has been widely acknowledged in the last decade, and the application of high-throughput sequencing techniques has revealed an astonishing diversity and high proportions of novel taxa. Most studies have focused either on marine or freshwater ecosystems; thus, information on estuarine communities is either incomplete or missing. We assessed the composition of microbial eukaryotes along a South Australian coastal lagoon affected by a broad (7 to 65 PSU) salinity gradient, the Coorong Lagoon. This lagoon extends for over 170 km from the mouth of the River Murray (Murray Mouth) south- wards, where the salinity increases up to hypersaline values. We sampled 5 stations during the austral summer and winter and sequenced the amplified V4 region of the 18S rRNA gene using Ion Torrent. Genetic libraries were mostly represented by reads from 5 phyla, with Chlorophyta prevailing in summer, diatoms in winter and Haptophyta in the southernmost sampling sites. In spite of the broad spatial and temporal salinity changes observed, the communities of small eukaryotes clustered in 2 groups reflecting the sample location. Moreover, dissimilarities between samples were unaffected by differences in salinity, but increased with increasing geographic dis- tances. -
Marine Algae and Land Plants Share Conserved Phytochrome Signaling Systems
Marine algae and land plants share conserved phytochrome signaling systems Deqiang Duanmua,1, Charles Bachyb,1, Sebastian Sudekb, Chee-Hong Wongc, Valeria Jiménezb, Nathan C. Rockwella, Shelley S. Martina, Chew Yee Nganc, Emily N. Reistetterb, Marijke J. van Barenb, Dana C. Priced, Chia-Lin Weic, Adrian Reyes-Prietoe,f, J. Clark Lagariasa,2, and Alexandra Z. Wordenb,f,2 aDepartment of Molecular and Cellular Biology, University of California, Davis, CA 95616; bMonterey Bay Aquarium Research Institute, Moss Landing, CA 95039; cSequencing Technology Group, Joint Genome Institute, Lawrence Berkeley National Laboratory, Walnut Creek, CA 94598; dDepartment of Ecology, Evolution, and Natural Resources, Institute of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ 08903; eBiology Department, University of New Brunswick, Fredericton, NB, Canada E3B5A3; and fIntegrated Microbial Biodiversity Program, Canadian Institute for Advanced Research, Toronto, ON, Canada M5G 1Z8 Contributed by J. Clark Lagarias, September 3, 2014 (sent for review June 18, 2014) Phytochrome photosensors control a vast gene network in duce light signals into biochemical outputs that shape overall streptophyte plants, acting as master regulators of diverse growth organismal responses (1, 13). and developmental processes throughout the life cycle. In contrast Although plant phytochromes control vast, complicated gene with their absence in known chlorophyte algal genomes and most networks, their origin, evolution, and ancestral signaling mech- sequenced prasinophyte -
Simplified Transformation of Ostreococcus Tauri Using
G C A T T A C G G C A T genes Technical Note Simplified Transformation of Ostreococcus tauri Using Polyethylene Glycol Frédéric Sanchez 1, Solène Geffroy 2, Manon Norest 1, Sheree Yau 1, Hervé Moreau 1 and Nigel Grimsley 1,* 1 CNRS UMR7232 BIOM (Biologie Intégrative des Organismes Marin) Sorbonne University, 66650 Banyuls sur Mer, France; [email protected] (F.S.); [email protected] (M.N.); [email protected] (S.Y.); [email protected] (H.M.) 2 IFREMER, Centre Atlantique, 44331 Nantes CEDEX 03, France; solene.geff[email protected] * Correspondence: [email protected] Received: 15 March 2019; Accepted: 21 May 2019; Published: 26 May 2019 Abstract: Ostreococcus tauri is an easily cultured representative of unicellular algae (class Mamiellophyceae) that abound in oceans worldwide. Eight complete 13–22 Mb genomes of phylogenetically divergent species within this class are available, and their DNA sequences are nearly always present in metagenomic data produced from marine samples. Here we describe a simplified and robust transformation protocol for the smallest of these algae (O. tauri). Polyethylene glycol (PEG) treatment was much more efficient than the previously described electroporation protocol. Short (2 min or less) incubation times in PEG gave >104 transformants per microgram DNA. The time of cell recovery after transformation could be reduced to a few hours, permitting the experiment to be done in a day rather than overnight as used in previous protocols. DNA was randomly inserted in the O. tauri genome. In our hands PEG was 20–40-fold more efficient than electroporation for the transformation of O. -
Proposal for Practical Multi-Kingdom Classification of Eukaryotes Based on Monophyly 2 and Comparable Divergence Time Criteria
bioRxiv preprint doi: https://doi.org/10.1101/240929; this version posted December 29, 2017. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 1 Proposal for practical multi-kingdom classification of eukaryotes based on monophyly 2 and comparable divergence time criteria 3 Leho Tedersoo 4 Natural History Museum, University of Tartu, 14a Ravila, 50411 Tartu, Estonia 5 Contact: email: [email protected], tel: +372 56654986, twitter: @tedersoo 6 7 Key words: Taxonomy, Eukaryotes, subdomain, phylum, phylogenetic classification, 8 monophyletic groups, divergence time 9 Summary 10 Much of the ecological, taxonomic and biodiversity research relies on understanding of 11 phylogenetic relationships among organisms. There are multiple available classification 12 systems that all suffer from differences in naming, incompleteness, presence of multiple non- 13 monophyletic entities and poor correspondence of divergence times. These issues render 14 taxonomic comparisons across the main groups of eukaryotes and all life in general difficult 15 at best. By using the monophyly criterion, roughly comparable time of divergence and 16 information from multiple phylogenetic reconstructions, I propose an alternative 17 classification system for the domain Eukarya to improve hierarchical taxonomical 18 comparability for animals, plants, fungi and multiple protist groups. Following this rationale, 19 I propose 32 kingdoms of eukaryotes that are treated in 10 subdomains. These kingdoms are 20 further separated into 43, 115, 140 and 353 taxa at the level of subkingdom, phylum, 21 subphylum and class, respectively (http://dx.doi.org/10.15156/BIO/587483). -
Diapositive 1
1 Diversity and ecology of green microalgae in marine systems: 2 an overview based on 18S rRNA sequences 3 4 Margot Tragin1, Adriana Lopes dos Santos1, Richard Christen2, 3, Daniel Vaulot1* 5 1 Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR 7144, Station Biologique, Place 6 Georges Teissier, 29680 Roscoff, France 7 2 CNRS, UMR 7138, Systématique Adaptation Evolution, Parc Valrose, BP71. F06108 Nice 8 cedex 02, France 9 3 Université de Nice-Sophia Antipolis, UMR 7138, Systématique Adaptation Evolution, Parc 10 Valrose, BP71. F06108 Nice cedex 02, France 11 12 13 * corresponding author : [email protected] 14 Revised version : 28 March 2016 15 For Perspectives in Phycology 16 17 Tragin et al. - Marine Chlorophyta diversity and distribution - p. 2 18 Abstract 19 Green algae (Chlorophyta) are an important group of microalgae whose diversity and ecological 20 importance in marine systems has been little studied. In this review, we first present an overview of 21 Chlorophyta taxonomy and detail the most important groups from the marine environment. Then, using 22 public 18S rRNA Chlorophyta sequences from culture and natural samples retrieved from the annotated 23 Protist Ribosomal Reference (PR²) database, we illustrate the distribution of different green algal 24 lineages in the oceans. The largest group of sequences belongs to the class Mamiellophyceae and in 25 particular to the three genera Micromonas, Bathycoccus and Ostreococcus. These sequences originate 26 mostly from coastal regions. Other groups with a large number of sequences include the 27 Trebouxiophyceae, Chlorophyceae, Chlorodendrophyceae and Pyramimonadales. Some groups, such as 28 the undescribed prasinophytes clades VII and IX, are mostly composed of environmental sequences.