1
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Krueger-Hadfield SA. Let's talk about sex: Why reproductive systems matter for understanding algae. JOURNAL OF PHYCOLOGY 2024. [PMID: 38743848 DOI: 10.1111/jpy.13462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 04/23/2024] [Accepted: 04/24/2024] [Indexed: 05/16/2024]
Abstract
Sex is a crucial process that has molecular, genetic, cellular, organismal, and population-level consequences for eukaryotic evolution. Eukaryotic life cycles are composed of alternating haploid and diploid phases but are constrained by the need to accommodate the phenotypes of these different phases. Critical gaps in our understanding of evolutionary drivers of the diversity in algae life cycles include how selection acts to stabilize and change features of the life cycle. Moreover, most eukaryotes are partially clonal, engaging in both sexual and asexual reproduction. Yet, our understanding of the variation in their reproductive systems is largely based on sexual reproduction in animals or angiosperms. The relative balance of sexual versus asexual reproduction not only controls but also is in turn controlled by standing genetic variability, thereby shaping evolutionary trajectories. Thus, we must quantitatively assess the consequences of the variation in life cycles on reproductive systems. Algae are a polyphyletic group spread across many of the major eukaryotic lineages, providing powerful models by which to resolve this knowledge gap. There is, however, an alarming lack of data about the population genetics of most algae and, therefore, the relative frequency of sexual versus asexual processes. For many algae, the occurrence of sexual reproduction is unknown, observations have been lost in overlooked papers, or data on population genetics do not yet exist. This greatly restricts our ability to forecast the consequences of climate change on algal populations inhabiting terrestrial, aquatic, and marine ecosystems. This perspective summarizes our extant knowledge and provides some future directions to pursue broadly across micro- and macroalgal species.
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2
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Filatov DA, Kirkpatrick M. How does evolution work in superabundant microbes? Trends Microbiol 2024:S0966-842X(24)00024-6. [PMID: 38360431 DOI: 10.1016/j.tim.2024.01.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 01/24/2024] [Accepted: 01/26/2024] [Indexed: 02/17/2024]
Abstract
Marine phytoplankton play crucial roles in the Earth's ecological, chemical, and geological processes. They are responsible for about half of global primary production and drive the ocean biological carbon pump. Understanding how plankton species may adapt to the Earth's rapidly changing environments is evidently an urgent priority. This problem requires evolutionary genetic approaches as evolution occurs at the level of allele frequency change within populations driven by genetic drift and natural selection (microevolution). Plankters such as the coccolithophore Gephyrocapsa huxleyi and the cyanobacterium Prochlorococcus 'marinus' are among Earth's most abundant organisms. In this opinion paper we discuss how evolution in astronomically large populations of superabundant microbes (SAMs) may act fundamentally differently than it does in the populations of more modest size found in well-studied organisms. This offers exciting opportunities to study evolution in the conditions that have yet to be explored and also leads to unique challenges. Exploring these opportunities and challenges is the goal of this article.
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Affiliation(s)
- Dmitry A Filatov
- Department of Biology, University of Oxford, Oxford, OX1 3RB, UK.
| | - Mark Kirkpatrick
- Department of Integrative Biology, University of Texas, Austin, TX 78712, USA
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3
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Yang P, Guo K, Yang Y, Lyu M, Liu J, Li X, Feng Y. Phylogeny and genetic variations of the three genome compartments in haptophytes shed light on the rapid evolution of coccolithophores. Gene 2023; 887:147716. [PMID: 37604324 DOI: 10.1016/j.gene.2023.147716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 08/15/2023] [Indexed: 08/23/2023]
Abstract
Haptophyte algae, including coccolithophores, play key roles in global carbon cycling and ecosystem. They exhibit exceptional morphological and functional diversity. However, their phylogeny is mostly based on short markers and genome researches are always limited to few species, hindering a better understanding about their evolution and diversification. In this study, by assembling 69 new plastid genomes, 65 new mitochondrial genomes, and 55 nuclear drafts, we systematically analyzed their genome variations and built the most comprehensive phylogenies in haptophytes and Noelaerhabdaceae, with the latter is the family of the model coccolithophore Emiliania huxleyi. The haptophyte genomes vary significantly in size, gene content, and structure. We detected phylogenetic incongruence of Prymnesiales between genome compartments. In Noelaerhabdaceae, by including Reticulofenestra sessilis and a proper outgroup, we found R. sessilis was not the basal taxon of this family. Noelaerhabdaceae strains have very similar genomic features and conserved sequences, but different gene content and dynamic structure. We speculate that was caused by DNA double-strand break repairs. Our results provide valuable genetic resources and new insights into the evolution of haptophytes, especially coccolithophores.
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Affiliation(s)
- Penghao Yang
- Fudan University, Shanghai 200433, China; Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310030, China
| | - Kangning Guo
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310030, China; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310024, China
| | - Yuqing Yang
- Fudan University, Shanghai 200433, China; Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310030, China
| | - Mingjie Lyu
- Institute of Crop Germplasm and Biotechnology, Tianjin Academy of Agricultural Sciences, Tianjin 300380, China
| | - Jingwen Liu
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen 361021, China
| | - Xiaobo Li
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310030, China; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310024, China
| | - Yanlei Feng
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310030, China; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310024, China.
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4
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Wheeler GL, Sturm D, Langer G. Gephyrocapsa huxleyi (Emiliania huxleyi) as a model system for coccolithophore biology. JOURNAL OF PHYCOLOGY 2023; 59:1123-1129. [PMID: 37983837 DOI: 10.1111/jpy.13404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 10/10/2023] [Indexed: 11/22/2023]
Abstract
Coccolithophores are the most abundant calcifying organisms in modern oceans and are important primary producers in many marine ecosystems. Their ability to generate a cellular covering of calcium carbonate plates (coccoliths) plays a major role in marine biogeochemistry and the global carbon cycle. Coccolithophores also play an important role in sulfur cycling through the production of the climate-active gas dimethyl sulfide. The primary model organism for coccolithophore research is Emiliania huxleyi, now named Gephyrocapsa huxleyi. G. huxleyi has a cosmopolitan distribution, occupying coastal and oceanic environments across the globe, and is the most abundant coccolithophore in modern oceans. Research in G. huxleyi has identified many aspects of coccolithophore biology, from cell biology to ecological interactions. In this perspective, we summarize the key advances made using G. huxleyi and examine the emerging tools for research in this model organism. We discuss the key steps that need to be taken by the research community to advance G. huxleyi as a model organism and the suitability of other species as models for specific aspects of coccolithophore biology.
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Affiliation(s)
- Glen L Wheeler
- The Marine Biological Association of the United Kingdom, The Laboratory, Plymouth, UK
| | - Daniela Sturm
- The Marine Biological Association of the United Kingdom, The Laboratory, Plymouth, UK
- School of Ocean and Earth Science, University of Southampton, Southampton, UK
| | - Gerald Langer
- Institute of Environmental Science and Technology (ICTA-UAB), Universitat Autònoma de Barcelona, Barcelona, Spain
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5
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Dobbelaere J, Su TY, Erdi B, Schleiffer A, Dammermann A. A phylogenetic profiling approach identifies novel ciliogenesis genes in Drosophila and C. elegans. EMBO J 2023; 42:e113616. [PMID: 37317646 PMCID: PMC10425847 DOI: 10.15252/embj.2023113616] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 05/22/2023] [Accepted: 06/01/2023] [Indexed: 06/16/2023] Open
Abstract
Cilia are cellular projections that perform sensory and motile functions in eukaryotic cells. A defining feature of cilia is that they are evolutionarily ancient, yet not universally conserved. In this study, we have used the resulting presence and absence pattern in the genomes of diverse eukaryotes to identify a set of 386 human genes associated with cilium assembly or motility. Comprehensive tissue-specific RNAi in Drosophila and mutant analysis in C. elegans revealed signature ciliary defects for 70-80% of novel genes, a percentage similar to that for known genes within the cluster. Further characterization identified different phenotypic classes, including a set of genes related to the cartwheel component Bld10/CEP135 and two highly conserved regulators of cilium biogenesis. We propose this dataset defines the core set of genes required for cilium assembly and motility across eukaryotes and presents a valuable resource for future studies of cilium biology and associated disorders.
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Affiliation(s)
- Jeroen Dobbelaere
- Max Perutz LabsUniversity of Vienna, Vienna Biocenter (VBC)ViennaAustria
| | - Tiffany Y Su
- Max Perutz LabsUniversity of Vienna, Vienna Biocenter (VBC)ViennaAustria
- Vienna BioCenter PhD ProgramDoctoral School of the University of Vienna and Medical University of ViennaViennaAustria
| | - Balazs Erdi
- Max Perutz LabsUniversity of Vienna, Vienna Biocenter (VBC)ViennaAustria
| | - Alexander Schleiffer
- Research Institute of Molecular Pathology, Vienna Biocenter (VBC)ViennaAustria
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna Biocenter (VBC)ViennaAustria
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6
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Skeffington A, Fischer A, Sviben S, Brzezinka M, Górka M, Bertinetti L, Woehle C, Huettel B, Graf A, Scheffel A. A joint proteomic and genomic investigation provides insights into the mechanism of calcification in coccolithophores. Nat Commun 2023; 14:3749. [PMID: 37353496 PMCID: PMC10290126 DOI: 10.1038/s41467-023-39336-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 06/05/2023] [Indexed: 06/25/2023] Open
Abstract
Coccolithophores are globally abundant, calcifying microalgae that have profound effects on marine biogeochemical cycles, the climate, and life in the oceans. They are characterized by a cell wall of CaCO3 scales called coccoliths, which may contribute to their ecological success. The intricate morphologies of coccoliths are of interest for biomimetic materials synthesis. Despite the global impact of coccolithophore calcification, we know little about the molecular machinery underpinning coccolithophore biology. Working on the model Emiliania huxleyi, a globally distributed bloom-former, we deploy a range of proteomic strategies to identify coccolithogenesis-related proteins. These analyses are supported by a new genome, with gene models derived from long-read transcriptome sequencing, which revealed many novel proteins specific to the calcifying haptophytes. Our experiments provide insights into proteins involved in various aspects of coccolithogenesis. Our improved genome, complemented with transcriptomic and proteomic data, constitutes a new resource for investigating fundamental aspects of coccolithophore biology.
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Affiliation(s)
- Alastair Skeffington
- Max-Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
- Biological and Environmental Sciences, University of Stirling, Stirling, FK9 4LA, UK
| | - Axel Fischer
- Max-Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Sanja Sviben
- Max-Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Magdalena Brzezinka
- Max-Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Michał Górka
- Max-Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Luca Bertinetti
- Max Planck Institute of Colloids and Interfaces, Potsdam-Golm, 14476, Germany
| | - Christian Woehle
- Max Planck Institute for Plant Breeding Research, Max Planck-Genome-Centre Cologne, Cologne, 50829, Germany
| | - Bruno Huettel
- Max Planck Institute for Plant Breeding Research, Max Planck-Genome-Centre Cologne, Cologne, 50829, Germany
| | - Alexander Graf
- Max-Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - André Scheffel
- Technische Universität Dresden, Faculty of Biology, 01307, Dresden, Germany.
- Max-Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany.
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7
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Bendif EM, Probert I, Archontikis OA, Young JR, Beaufort L, Rickaby RE, Filatov D. Rapid diversification underlying the global dominance of a cosmopolitan phytoplankton. THE ISME JOURNAL 2023; 17:630-640. [PMID: 36747097 PMCID: PMC10030636 DOI: 10.1038/s41396-023-01365-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 01/10/2023] [Accepted: 01/11/2023] [Indexed: 02/08/2023]
Abstract
Marine phytoplankton play important roles in the global ecosystem, with a limited number of cosmopolitan keystone species driving their biomass. Recent studies have revealed that many of these phytoplankton are complexes composed of sibling species, but little is known about the evolutionary processes underlying their formation. Gephyrocapsa huxleyi, a widely distributed and abundant unicellular marine planktonic algae, produces calcified scales (coccoliths), thereby significantly affects global biogeochemical cycles via sequestration of inorganic carbon. This species is composed of morphotypes defined by differing degrees of coccolith calcification, the evolutionary ecology of which remains unclear. Here, we report an integrated morphological, ecological and genomic survey across globally distributed G. huxleyi strains to reconstruct evolutionary relationships between morphotypes in relation to their habitats. While G. huxleyi has been considered a single cosmopolitan species, our analyses demonstrate that it has evolved to comprise at least three distinct species, which led us to formally revise the taxonomy of the G. huxleyi complex. Moreover, the first speciation event occurred before the onset of the last interglacial period (~140 ka), while the second followed during this interglacial. Then, further rapid diversifications occurred during the most recent ice-sheet expansion of the last glacial period and established morphotypes as dominant populations across environmental clines. These results suggest that glacial-cycle dynamics contributed to the isolation of ocean basins and the segregations of oceans fronts as extrinsic drivers of micro-evolutionary radiations in extant marine phytoplankton.
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Affiliation(s)
- El Mahdi Bendif
- Department of Earth Sciences, University of Oxford, Oxford, UK.
- Department of Plant Sciences, University of Oxford, Oxford, UK.
- Institut des sciences de la mer de Rimouski (ISMER), Université du Québec à Rimouski, Rimouski, Canada.
| | - Ian Probert
- Sorbonne Université - CNRS, Roscoff Culture Collection, FR2424 Station Biologique de Roscoff, Roscoff, France
| | - Odysseas A Archontikis
- Department of Earth Sciences, University of Oxford, Oxford, UK
- Department of Earth Sciences, The Natural History Museum, London, UK
| | - Jeremy R Young
- Department of Earth Sciences, University College London, London, UK
| | - Luc Beaufort
- Aix Marseille Université, CNRS, IRD, INRAE, CEREGE, Aix-en-Provence, France
| | | | - Dmitry Filatov
- Department of Plant Sciences, University of Oxford, Oxford, UK
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8
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Barcytė D, Zátopková M, Němcová Y, Richtář M, Yurchenko T, Jaške K, Fawley KP, Škaloud P, Ševčíková T, Fawley MW, Eliáš M. Redefining Chlorobotryaceae as one of the principal and most diverse lineages of eustigmatophyte algae. Mol Phylogenet Evol 2022; 177:107607. [PMID: 35963589 DOI: 10.1016/j.ympev.2022.107607] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 07/11/2022] [Accepted: 08/05/2022] [Indexed: 10/15/2022]
Abstract
Eustigmatophyceae is one of the ∼17 classes of the vast algal phylum Ochrophyta. Over the last decade, the eustigmatophytes emerged as an expansive group that has grown from the initially recognized handful of species to well over 200 genetically distinct entities (potential species). Yet the majority of eustigs, remain represented by unidentified strains, or even only metabarcode sequences obtained from environmental samples. Moreover, the formal classification of the group has not yet been harmonized with the recently uncovered diversity and phylogenetic relationships within the class. Here we make a major step towards resolving this issue by addressing the diversity, phylogeny and classification of one of the most prominent eustigmatophyte clades previously informally called the "Eustigmataceae group". We obtained 18S rDNA and rbcL gene sequences from four new strains from the "Eustigmataceae group", and from several additional eustig strains, and performed the most comprehensive phylogenetic analyses of Eustigmatophyceae to date. Our results of these analyses confirm the monophyly of the "Eustigmataceae group" and define its major subclades. We also sequenced plastid genomes of five "Eustigmataceae group" strains to not only improve our understanding of the plastid gene content evolution in eustigs, but also to obtain a robustly resolved eustigmatophyte phylogeny. With this new genomic data, we have solidified the view of the "Eustigmataceae group" as a well-defined family level clade. Crucially, we also have firmly established the genus Chlorobotrys as a member of the "Eustigmataceae group". This new molecular evidence, together with a critical analysis of the literature going back to the 19th century, provided the basis to radically redefine the historical concept of the family Chlorobotryaceae as the formal taxonomic rubric corresponding to the "Eustigmataceae group". With this change, the family names Eustigmataceae and Characiopsidaceae are reduced to synonymy with the Chlorobotryaceae, with the latter having taxonomic priority. We additionally studied in detail the morphology and ultrastructure of two Chlorobotryaceae members, which we describe as Neustupella aerophytica gen. et sp. nov. and Lietzensia polymorpha gen. et sp. nov. Finally, our analyses of partial genomic data from several Chlorobotryaceae representatives identified genes for hallmark flagellar proteins in all of these strains. The presence of the flagellar proteins strongly suggests that zoosporogenesis is a common trait of the family and also occurs in the members never observed to produce flagellated stages. Altogether, our work paints a rich picture of one of the most diverse principal lineages of eustigmatophyte algae.
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Affiliation(s)
- Dovilė Barcytė
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Chittussiho 10, 710 00 Ostrava, Czech Republic.
| | - Martina Zátopková
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Chittussiho 10, 710 00 Ostrava, Czech Republic
| | - Yvonne Němcová
- Department of Botany, Faculty of Science, Charles University, Benátská 2, 128 00 Prague, Czech Republic
| | - Michal Richtář
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Chittussiho 10, 710 00 Ostrava, Czech Republic
| | - Tatiana Yurchenko
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Chittussiho 10, 710 00 Ostrava, Czech Republic
| | - Karin Jaške
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Chittussiho 10, 710 00 Ostrava, Czech Republic
| | - Karen P Fawley
- Division of Science and Mathematics, University of the Ozarks, Clarksville, AR 72830, USA
| | - Pavel Škaloud
- Department of Botany, Faculty of Science, Charles University, Benátská 2, 128 00 Prague, Czech Republic
| | - Tereza Ševčíková
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Chittussiho 10, 710 00 Ostrava, Czech Republic
| | - Marvin W Fawley
- Division of Science and Mathematics, University of the Ozarks, Clarksville, AR 72830, USA
| | - Marek Eliáš
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Chittussiho 10, 710 00 Ostrava, Czech Republic.
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9
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Kao T, Wang T, Ku C. Rampant nuclear-mitochondrial-plastid phylogenomic discordance in globally distributed calcifying microalgae. THE NEW PHYTOLOGIST 2022; 235:1394-1408. [PMID: 35556250 PMCID: PMC9539906 DOI: 10.1111/nph.18219] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 05/04/2022] [Indexed: 06/15/2023]
Abstract
Incongruent phylogenies have been widely observed between nuclear and plastid or mitochondrial genomes in terrestrial plants and animals. However, few studies have examined these patterns in microalgae or the discordance between the two organelles. Here we investigated the nuclear-mitochondrial-plastid phylogenomic incongruence in Emiliania-Gephyrocapsa, a group of cosmopolitan calcifying phytoplankton with enormous populations and recent speciations. We assembled mitochondrial and plastid genomes of 27 strains from across global oceans and temperature regimes, and analyzed the phylogenomic histories of the three compartments using concatenation and coalescence methods. Six major clades with varying morphology and distribution are well recognized in the nuclear phylogeny, but such relationships are absent in the mitochondrial and plastid phylogenies, which also differ substantially from each other. The rampant phylogenomic discordance is due to a combination of organellar capture (introgression), organellar genome recombination, and incomplete lineage sorting of ancient polymorphic organellar genomes. Hybridization can lead to replacements of whole organellar genomes without introgression of nuclear genes and the two organelles are not inherited as a single cytoplasmic unit. This study illustrates the convoluted evolution and inheritance of organellar genomes in isogamous haplodiplontic microalgae and provides a window into the phylogenomic complexity of marine unicellular eukaryotes.
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Affiliation(s)
- Tzu‐Tong Kao
- Institute of Plant and Microbial BiologyAcademia SinicaTaipei11529Taiwan
| | - Tzu‐Haw Wang
- Institute of Plant and Microbial BiologyAcademia SinicaTaipei11529Taiwan
| | - Chuan Ku
- Institute of Plant and Microbial BiologyAcademia SinicaTaipei11529Taiwan
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10
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Evolutionary Rates in the Haptophyta: Exploring Molecular and Phenotypic Diversity. JOURNAL OF MARINE SCIENCE AND ENGINEERING 2022. [DOI: 10.3390/jmse10060798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
Haptophytes are photosynthetic protists found in both freshwater and marine environments with an origin possibly dating back to the Neoproterozoic era. The most recent molecular phylogeny reveals several haptophyte “mystery clades” that await morphological verification, but it is otherwise highly consistent with morphology-based phylogenies, including that of the coccolithophores (calcifying haptophytes). The fossil coccolith record offers unique insights into extinct lineages, including the adaptive radiations that produced extant descendant species. By combining molecular data of extant coccolithophores and phenotype-based studies of their ancestral lineages, it has become possible to probe the modes and rates of speciation in more detail, although this approach is still limited to only few taxa because of the lack of whole-genome datasets. The evolution of calcification likely involved several steps, but its origin can be traced back to an early association with organic scales typical for all haptophytes. Other key haptophyte traits, including the haplo-diplontic life cycle, are herein mapped upon the coccolithophorid phylogeny to help navigate a discussion of their ecological benefits and trade-offs in a rapidly changing ocean.
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11
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Annunziata R, Mele BH, Marotta P, Volpe M, Entrambasaguas L, Mager S, Stec K, d’Alcalà MR, Sanges R, Finazzi G, Iudicone D, Montresor M, Ferrante MI. Trade-off between sex and growth in diatoms: Molecular mechanisms and demographic implications. SCIENCE ADVANCES 2022; 8:eabj9466. [PMID: 35044817 PMCID: PMC8769554 DOI: 10.1126/sciadv.abj9466] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Diatoms are fast-growing and winning competitors in aquatic environments, possibly due to optimized growth performance. However, their life cycles are complex, heteromorphic, and not fully understood. Here, we report on the fine control of cell growth and physiology during the sexual phase of the marine diatom Pseudo-nitzschia multistriata. We found that mating, under nutrient replete conditions, induces a prolonged growth arrest in parental cells. Transcriptomic analyses revealed down-regulation of genes related to major metabolic functions from the early phases of mating. Single-cell photophysiology also pinpointed an inhibition of photosynthesis and storage lipids accumulated in the arrested population, especially in gametes and zygotes. Numerical simulations revealed that growth arrest affects the balance between parental cells and their siblings, possibly favoring the new generation. Thus, in addition to resources availability, life cycle traits contribute to shaping the species ecological niches and must be considered to describe and understand the structure of plankton communities.
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Affiliation(s)
- Rossella Annunziata
- Stazione Zoologica Anton Dohrn, Napoli, Italy
- Corresponding author. (R.A.); (M.I.F.)
| | | | | | | | | | | | | | | | - Remo Sanges
- International School for Advanced Studies (SISSA), Via Bonomea 265, Trieste 34136, Italy
| | - Giovanni Finazzi
- Université Grenoble Alpes (UGA), Centre National Recherche Scientifique (CNRS), Commissariat Energie Atomique, Energies Alternatives (CEA), Institut National Recherche Agriculture, Alimentation, Environnement (INRAE), Interdisciplinary Research Institute of Grenoble, IRIG-Laboratoire de Physiologie Cellulaire et Végétale, Grenoble, France
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12
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Resolving the microalgal gene landscape at the strain level: A novel hybrid transcriptome of Emiliania huxleyi CCMP3266. Appl Environ Microbiol 2021; 88:e0141821. [PMID: 34757817 DOI: 10.1128/aem.01418-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Microalgae are key ecological players with a complex evolutionary history. Genomic diversity, in addition to limited availability of high-quality genomes, challenge studies that aim to elucidate molecular mechanisms underlying microalgal ecophysiology. Here, we present a novel and comprehensive transcriptomic hybrid approach to generate a reference for genetic analyses, and resolve the microalgal gene landscape at the strain level. The approach is demonstrated for a strain of the coccolithophore microalga Emiliania huxleyi, which is a species complex with considerable genome variability. The investigated strain is commonly studied as a model for algal-bacterial interactions, and was therefore sequenced in the presence of bacteria to elicit the expression of interaction-relevant genes. We applied complementary PacBio Iso-Seq full-length cDNA, and poly(A)-independent Illumina total RNA sequencing, which resulted in a de novo assembled, near complete hybrid transcriptome. In particular, hybrid sequencing improved the reconstruction of long transcripts and increased the recovery of full-length transcript isoforms. To use the resulting hybrid transcriptome as a reference for genetic analyses, we demonstrate a method that collapses the transcriptome into a genome-like dataset, termed "synthetic genome" (sGenome). We used the sGenome as a reference to visually confirm the robustness of the CCMP3266 gene assembly, to conduct differential gene expression analysis, and to characterize novel E. huxleyi genes. The newly-identified genes contribute to our understanding of E. huxleyi genome diversification, and are predicted to play a role in microbial interactions. Our transcriptomic toolkit can be implemented in various microalgae to facilitate mechanistic studies on microalgal diversity and ecology. Importance Microalgae are key players in the ecology and biogeochemistry of our oceans. Efforts to implement genomic and transcriptomic tools in laboratory studies involving microalgae suffer from the lack of published genomes. In the case of coccolithophore microalgae, the problem has long been recognized; the model species Emiliania huxleyi is a species complex with genomes composed of a core, and a large variable portion. To study the role of the variable portion in niche adaptation, and specifically in microbial interactions, strain-specific genetic information is required. Here we present a novel transcriptomic hybrid approach, and generated strain-specific genome-like information. We demonstrate our approach on an E. huxleyi strain that is co-cultivated with bacteria. By constructing a "synthetic genome", we generated comprehensive gene annotations that enabled accurate analyses of gene expression patterns. Importantly, we unveiled novel genes in the variable portion of E. huxleyi that play putative roles in microbial interactions.
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Feldmesser E, Ben-Dor S, Vardi A. An Emiliania huxleyi pan-transcriptome reveals basal strain specificity in gene expression patterns. Sci Rep 2021; 11:20795. [PMID: 34675226 PMCID: PMC8531018 DOI: 10.1038/s41598-021-00072-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 09/08/2021] [Indexed: 11/09/2022] Open
Abstract
Emiliania huxleyi is a cosmopolitan coccolithophore widespread in temperate oceans. This unicellular photoautotroph forms massive recurring blooms that play an important role in large biogeochemical cycles of carbon and sulfur, which play a role in climate change. The mechanism of bloom formation and demise, controlled by giant viruses that routinely infect these blooms, is poorly understood. We generated a pan-transcriptome of E. huxleyi, derived from three strains with different susceptibility to viral infection. Expression profiling of E. huxleyi sensitive and resistant strains showed major basal differences, including many genes that are induced upon viral infection. This suggests that basal gene expression can affect the host metabolic state and the susceptibility of E. huxleyi to viruses. Due to its ecological importance, the pan-transcriptome and its protein translation, applicable to many E. huxleyi strains, is a powerful resource for investigation of eukaryotic microbial communities.
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Affiliation(s)
- Ester Feldmesser
- Bioinformatics Unit, Life Sciences Core Facilities, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Shifra Ben-Dor
- Bioinformatics Unit, Life Sciences Core Facilities, Weizmann Institute of Science, 7610001, Rehovot, Israel.
| | - Assaf Vardi
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, 7610001, Rehovot, Israel
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14
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Filatov DA, Bendif EM, Archontikis OA, Hagino K, Rickaby REM. The mode of speciation during a recent radiation in open-ocean phytoplankton. Curr Biol 2021; 31:5439-5449.e5. [PMID: 34687611 DOI: 10.1016/j.cub.2021.09.073] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 08/03/2021] [Accepted: 09/24/2021] [Indexed: 12/30/2022]
Abstract
Despite the enormous ecological importance of marine phytoplankton, surprisingly little is known about how new phytoplankton species originate and evolve in the open ocean, in the absence of apparent geographic barriers that typically act as isolation mechanisms in speciation. To investigate the mechanism of open-ocean speciation, we combined fossil and climatic records from the late Quaternary with genome-wide evolutionary genetic analyses of speciation in the ubiquitous and abundant pelagic coccolithophore genus Gephyrocapsa (including G. huxleyi, formerly known as Emiliania huxleyi). Based on the analysis of 43 sequenced genomes, we report that the best-fitting scenario for all speciation events analyzed included an extended period of complete isolation followed by recent (Holocene) secondary contact, supporting the role of geographic or oceanographic barriers in population divergence and speciation. Consistent with this, fossil data reveal considerable diachroneity of species first occurrence. The timing of all speciation events coincided with glacial phases of glacial-interglacial cycles, suggesting that stronger isolation between the ocean basins and increased segregation of ecological niches during glaciations are important drivers of speciation in marine phytoplankton. The similarity across multiple speciation events implies the generality of this inferred speciation scenario for marine phytoplankton.
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Affiliation(s)
- Dmitry A Filatov
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK.
| | - El Mahdi Bendif
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK; Department of Earth Sciences, University of Oxford, South Parks Road, Oxford OX1 3AN, UK
| | - Odysseas A Archontikis
- Department of Earth Sciences, University of Oxford, South Parks Road, Oxford OX1 3AN, UK
| | - Kyoko Hagino
- Centre for Advanced Marine Core Research, Kochi University, Nankoku, Kochi 783-8502, Japan
| | - Rosalind E M Rickaby
- Department of Earth Sciences, University of Oxford, South Parks Road, Oxford OX1 3AN, UK
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15
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Sandaa RA, Saltvedt MR, Dahle H, Wang H, Våge S, Blanc-Mathieu R, Steen IH, Grimsley N, Edvardsen B, Ogata H, Lawrence J. Adaptive evolution of viruses infecting marine microalgae (haptophytes), from acute infections to stable coexistence. Biol Rev Camb Philos Soc 2021; 97:179-194. [PMID: 34514703 DOI: 10.1111/brv.12795] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 08/27/2021] [Accepted: 09/01/2021] [Indexed: 12/13/2022]
Abstract
Collectively known as phytoplankton, photosynthetic microbes form the base of the marine food web, and account for up to half of the primary production on Earth. Haptophytes are key components of this phytoplankton community, playing important roles both as primary producers and as mixotrophs that graze on bacteria and protists. Viruses influence the ecology and diversity of phytoplankton in the ocean, with the majority of microalgae-virus interactions described as 'boom and bust' dynamics, which are characteristic of acute virus-host systems. Most haptophytes are, however, part of highly diverse communities and occur at low densities, decreasing their chance of being infected by viruses with high host specificity. Viruses infecting these microalgae have been isolated in the laboratory, and there are several characteristics that distinguish them from acute viruses infecting bloom-forming haptophytes. Herein we synthesise what is known of viruses infecting haptophyte hosts in the ocean, discuss the adaptive evolution of haptophyte-infecting viruses -from those that cause acute infections to those that stably coexist with their host - and identify traits of importance for successful survival in the ocean.
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Affiliation(s)
- Ruth-Anne Sandaa
- Department of Biological Sciences, University of Bergen, Postbox 7803, N-5020, Bergen, Norway
| | - Marius R Saltvedt
- Department of Biological Sciences, University of Bergen, Postbox 7803, N-5020, Bergen, Norway
| | - Håkon Dahle
- Department of Biological Sciences, University of Bergen, Postbox 7803, N-5020, Bergen, Norway
| | - Haina Wang
- Department of Biological Sciences, University of Bergen, Postbox 7803, N-5020, Bergen, Norway
| | - Selina Våge
- Department of Biological Sciences, University of Bergen, Postbox 7803, N-5020, Bergen, Norway
| | - Romain Blanc-Mathieu
- Laboratoire de Physiologie Cellulaire & Végétale, CEA, Université Grenoble Alpes, CNRS, INRA, IRIG, Grenoble, France
| | - Ida H Steen
- Department of Biological Sciences, University of Bergen, Postbox 7803, N-5020, Bergen, Norway
| | - Nigel Grimsley
- Sorbonne Université, CNRS, UMR 7232 Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, F-66650, Banyuls-sur-Mer, France
| | - Bente Edvardsen
- Department of Biosciences, University of Oslo, Postbox 1066, N-0316, Oslo, Norway
| | - Hiroyuki Ogata
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
| | - Janice Lawrence
- Biology Department, University of New Brunswick, PO Box 4400, Fredericton, NB, E3B 5A3, Canada
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16
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Sunagawa S, Acinas SG, Bork P, Bowler C, Eveillard D, Gorsky G, Guidi L, Iudicone D, Karsenti E, Lombard F, Ogata H, Pesant S, Sullivan MB, Wincker P, de Vargas C. Tara Oceans: towards global ocean ecosystems biology. Nat Rev Microbiol 2020; 18:428-445. [PMID: 32398798 DOI: 10.1038/s41579-020-0364-5] [Citation(s) in RCA: 129] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/27/2020] [Indexed: 12/14/2022]
Abstract
A planetary-scale understanding of the ocean ecosystem, particularly in light of climate change, is crucial. Here, we review the work of Tara Oceans, an international, multidisciplinary project to assess the complexity of ocean life across comprehensive taxonomic and spatial scales. Using a modified sailing boat, the team sampled plankton at 210 globally distributed sites at depths down to 1,000 m. We describe publicly available resources of molecular, morphological and environmental data, and discuss how an ecosystems biology approach has expanded our understanding of plankton diversity and ecology in the ocean as a planetary, interconnected ecosystem. These efforts illustrate how global-scale concepts and data can help to integrate biological complexity into models and serve as a baseline for assessing ecosystem changes and the future habitability of our planet in the Anthropocene epoch.
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Affiliation(s)
- Shinichi Sunagawa
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich, Switzerland.
| | - Silvia G Acinas
- Department of Marine Biology and Oceanography, Institute of Marine Sciences-CSIC, Barcelona, Spain
| | - Peer Bork
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany.,Max Delbrück Center for Molecular Medicine, Berlin, Germany.,Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
| | - Chris Bowler
- Institut de Biologie de l'ENS, Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France.,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, Paris, France
| | | | - Damien Eveillard
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, Paris, France.,Université de Nantes, CNRS, UMR6004, LS2N, Nantes, France
| | - Gabriel Gorsky
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, Paris, France.,Sorbonne Université, CNRS, Laboratoire d'Océanographie de Villefranche, Villefranche-sur-Mer, France
| | - Lionel Guidi
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, Paris, France.,Sorbonne Université, CNRS, Laboratoire d'Océanographie de Villefranche, Villefranche-sur-Mer, France
| | | | - Eric Karsenti
- Institut de Biologie de l'ENS, Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France.,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, Paris, France.,Directors' Research, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Fabien Lombard
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, Paris, France.,Sorbonne Université, CNRS, Laboratoire d'Océanographie de Villefranche, Villefranche-sur-Mer, France
| | - Hiroyuki Ogata
- Institute for Chemical Research, Kyoto University, Kyoto, Japan
| | - Stephane Pesant
- PANGAEA, University of Bremen, Bremen, Germany.,MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Matthew B Sullivan
- Department of Microbiology, The Ohio State University, Columbus, OH, USA.,Department of Civil, Environmental and Geodetic Engineering, The Ohio State University, Columbus, OH, USA.,Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - Patrick Wincker
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, Paris, France.,Génomique Métabolique, Genoscope, Institut de Biologie Francois Jacob, Commissariat à l'Énergie Atomique, CNRS, Université Evry, Université Paris-Saclay, Evry, France
| | - Colomban de Vargas
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, Paris, France. .,Sorbonne Université and CNRS, UMR 7144 (AD2M), ECOMAP, Station Biologique de Roscoff, Roscoff, France.
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17
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Functional Genomics Differentiate Inherent and Environmentally Influenced Traits in Dinoflagellate and Diatom Communities. Microorganisms 2020; 8:microorganisms8040567. [PMID: 32326461 PMCID: PMC7232425 DOI: 10.3390/microorganisms8040567] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 04/07/2020] [Accepted: 04/09/2020] [Indexed: 12/13/2022] Open
Abstract
Dinoflagellates and diatoms are among the most prominent microeukaryotic plankton groups, and they have evolved different functional traits reflecting their roles within ecosystems. However, links between their metabolic processes and functional traits within different environmental contexts warrant further study. The functional biodiversity of dinoflagellates and diatoms was accessed with metatranscriptomics using Pfam protein domains as proxies for functional processes. Despite the overall geographic similarity of functional responses, abiotic (i.e., temperature and salinity; ~800 Pfam domains) and biotic (i.e., taxonomic group; ~1500 Pfam domains) factors influencing particular functional responses were identified. Salinity and temperature were identified as the main drivers of community composition. Higher temperatures were associated with an increase of Pfam domains involved in energy metabolism and a decrease of processes associated with translation and the sulfur cycle. Salinity changes were correlated with the biosynthesis of secondary metabolites (e.g., terpenoids and polyketides) and signal transduction processes, indicating an overall strong effect on the biota. The abundance of dinoflagellates was positively correlated with nitrogen metabolism, vesicular transport and signal transduction, highlighting their link to biotic interactions (more so than diatoms) and suggesting the central role of species interactions in the evolution of dinoflagellates. Diatoms were associated with metabolites (e.g., isoprenoids and carotenoids), as well as lysine degradation, which highlights their ecological role as important primary producers and indicates the physiological importance of these metabolic pathways for diatoms in their natural environment. These approaches and gathered information will support ecological questions concerning the marine ecosystem state and metabolic interactions in the marine environment.
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18
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Falciatore A, Jaubert M, Bouly JP, Bailleul B, Mock T. Diatom Molecular Research Comes of Age: Model Species for Studying Phytoplankton Biology and Diversity. THE PLANT CELL 2020; 32:547-572. [PMID: 31852772 PMCID: PMC7054031 DOI: 10.1105/tpc.19.00158] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 10/18/2019] [Accepted: 12/13/2019] [Indexed: 05/08/2023]
Abstract
Diatoms are the world's most diverse group of algae, comprising at least 100,000 species. Contributing ∼20% of annual global carbon fixation, they underpin major aquatic food webs and drive global biogeochemical cycles. Over the past two decades, Thalassiosira pseudonana and Phaeodactylum tricornutum have become the most important model systems for diatom molecular research, ranging from cell biology to ecophysiology, due to their rapid growth rates, small genomes, and the cumulative wealth of associated genetic resources. To explore the evolutionary divergence of diatoms, additional model species are emerging, such as Fragilariopsis cylindrus and Pseudo-nitzschia multistriata Here, we describe how functional genomics and reverse genetics have contributed to our understanding of this important class of microalgae in the context of evolution, cell biology, and metabolic adaptations. Our review will also highlight promising areas of investigation into the diversity of these photosynthetic organisms, including the discovery of new molecular pathways governing the life of secondary plastid-bearing organisms in aquatic environments.
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Affiliation(s)
- Angela Falciatore
- Institut de Biologie Physico-Chimique, Laboratory of Chloroplast Biology and Light Sensing in Microalgae, UMR7141 Centre National de la Recherche Scientifique (CNRS), Sorbonne Université, 75005 Paris, France
- Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, UMR7238 Sorbonne Université, 75005 Paris, France
| | - Marianne Jaubert
- Institut de Biologie Physico-Chimique, Laboratory of Chloroplast Biology and Light Sensing in Microalgae, UMR7141 Centre National de la Recherche Scientifique (CNRS), Sorbonne Université, 75005 Paris, France
- Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, UMR7238 Sorbonne Université, 75005 Paris, France
| | - Jean-Pierre Bouly
- Institut de Biologie Physico-Chimique, Laboratory of Chloroplast Biology and Light Sensing in Microalgae, UMR7141 Centre National de la Recherche Scientifique (CNRS), Sorbonne Université, 75005 Paris, France
- Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, UMR7238 Sorbonne Université, 75005 Paris, France
| | - Benjamin Bailleul
- Institut de Biologie Physico-Chimique, Laboratory of Chloroplast Biology and Light Sensing in Microalgae, UMR7141 Centre National de la Recherche Scientifique (CNRS), Sorbonne Université, 75005 Paris, France
| | - Thomas Mock
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, United Kingdom
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19
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Alexander H, Rouco M, Haley ST, Dyhrman ST. Transcriptional response of
Emiliania huxleyi
under changing nutrient environments in the North Pacific Subtropical Gyre. Environ Microbiol 2020; 22:1847-1860. [DOI: 10.1111/1462-2920.14942] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 12/20/2019] [Accepted: 12/23/2019] [Indexed: 12/22/2022]
Affiliation(s)
- Harriet Alexander
- Biology Department Woods Hole Oceanographic Institution Woods Hole MA 02543 USA
| | - Mónica Rouco
- Biology and Paleo Environment Division, Lamont‐Doherty Earth Observatory Columbia University Palisades NY 10964 USA
- Department of Earth and Environmental Sciences Columbia University Palisades NY 10964 USA
| | - Sheean T. Haley
- Biology and Paleo Environment Division, Lamont‐Doherty Earth Observatory Columbia University Palisades NY 10964 USA
| | - Sonya T. Dyhrman
- Biology and Paleo Environment Division, Lamont‐Doherty Earth Observatory Columbia University Palisades NY 10964 USA
- Department of Earth and Environmental Sciences Columbia University Palisades NY 10964 USA
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20
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Exploring Molecular Signs of Sex in the Marine Diatom Skeletonema marinoi. Genes (Basel) 2019; 10:genes10070494. [PMID: 31261777 PMCID: PMC6678668 DOI: 10.3390/genes10070494] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 06/14/2019] [Accepted: 06/24/2019] [Indexed: 11/17/2022] Open
Abstract
Sexual reproduction plays a fundamental role in diatom life cycles. It contributes to increasing genetic diversity through meiotic recombination and also represents the phase where large-sized cells are produced to counteract the cell size reduction process that characterizes these microalgae. With the aim to identify genes linked to the sexual phase of the centric planktonic diatom Skeletonema marinoi, we carried out an RNA-seq experiment comparing the expression level of transcripts in sexualized cells with that of large cells not competent for sex. A set of genes involved in meiosis were found upregulated. Despite the fact that flagellate gametes were observed in the sample, we did not detect the expression of genes involved in the synthesis of flagella that were upregulated during sexual reproduction in another centric diatom. A comparison with the set of genes changing during the first phases of sexual reproduction of the pennate diatom Pseudo-nitzschia multistriata revealed the existence of commonalities, including the strong upregulation of genes with an unknown function that we named Sex Induced Genes (SIG). Our results further broadened the panel of genes that can be used as a marker for sexual reproduction of diatoms, crucial for the interpretation of metatranscriptomic datasets.
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21
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Filatov DA. Extreme Lewontin's Paradox in Ubiquitous Marine Phytoplankton Species. Mol Biol Evol 2019; 36:4-14. [PMID: 30351418 DOI: 10.1093/molbev/msy195] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Larger populations are expected to have larger genetic diversity. However, as pointed out by Lewontin in 1974, the range of population sizes exceeds the range of genetic diversity by many orders of magnitude (a.k.a. "Lewontin's paradox," LP). The reasons for LP remain obscure. Here, This paper reports an extreme case of LP in astronomically large populations of the ubiquitous unicellular marine phytoplankton species Emiliania huxleyi (Haptophyta)-the species that accounts for 10-20% of primary productivity in the oceans and its blooms are so extensive that they are visible from space. This study demonstrates that despite the wide distribution and enormous population size, the world-wide sample of E. huxleyi strains with sequenced genomes represents a single cohesive species and contains surprisingly limited genetic diversity (π ∼ 0.006 per silent site). The patterns of polymorphism reveal even larger populations in the past, and frequent recombination (ρ ∼ 0.006) throughout the genome, ruling out demographic history and asexual reproduction as possible causes of low polymorphism in E. huxleyi. Natural selection wiping out genetic diversity at linked sites (a.k.a. "genetic draft") must be strong and frequent to account for low polymorphism in E. huxleyi. This study sheds the first light on poorly understood evolutionary genetic processes in astronomically large populations of marine microplankton.
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Affiliation(s)
- Dmitry A Filatov
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, United Kingdom
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22
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Concepts of the last eukaryotic common ancestor. Nat Ecol Evol 2019; 3:338-344. [DOI: 10.1038/s41559-019-0796-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 01/03/2019] [Indexed: 12/27/2022]
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23
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D’Amario B, Ziveri P, Grelaud M, Oviedo A. Emiliania huxleyi coccolith calcite mass modulation by morphological changes and ecology in the Mediterranean Sea. PLoS One 2018; 13:e0201161. [PMID: 30040853 PMCID: PMC6057672 DOI: 10.1371/journal.pone.0201161] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 07/10/2018] [Indexed: 12/02/2022] Open
Abstract
To understand the response of marine calcifying organisms under high CO2 scenarios, it is critical to study their calcification patterns in the natural environment. This paper focuses on a major calcifying phytoplankton group, the coccolithophores, through the analysis of water samples collected along a W-E Mediterranean transect during two research cruises, in April 2011 (Meteor cruise M84/3) and May 2013 (MedSeA cruise 2013). The Mediterranean Sea is a marginal sea characterized by large biogeochemical gradients. Currently, it is undergoing both warming and ocean acidification, processes which are rapidly modifying species distribution and calcification. The species Emiliania huxleyi largely dominates the total coccolithophore production in present day oceans and marine basins, including the Mediterranean Sea. A series of morphometric measurements were performed on the coccoliths of this species to estimate their mass, length and calculate a calcification index (proxy for the size-normalized calcification degree). The most abundant morphotype of E. huxleyi in the Mediterranean Sea is Type A. Coccoliths of this morphotype were additionally analyzed based on scanning electron microscopy images: four calcification varieties were quantified, according to the relationship between slit length-tube width, and the state of the central area (open or closed). The average E. huxleyi coccolith mass along the Mediterranean oceanographic transect depended strongly on both the average coccolith length and calcification index. The variability in average coccolith length and calcification index across samples reflected oscillations in the relative abundance of the calcification varieties. We also demonstrated that the distribution of the calcification varieties followed the main environmental gradients (carbonate chemistry, salinity, temperature, nutrient concentrations). Hence, shifts in the distribution of the calcification varieties and of the average E. huxleyi coccolith mass are to be expected in the Mediterranean Sea under climate change. These physiological and ecological responses will modulate the net coccolithophore calcification and, ultimately, the regional carbonate export to the seafloor.
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Affiliation(s)
- Barbara D’Amario
- Institute of Environmental Science and Technology (ICTA), Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
- * E-mail: (BD); (PZ)
| | - Patrizia Ziveri
- Institute of Environmental Science and Technology (ICTA), Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
- * E-mail: (BD); (PZ)
| | - Michaël Grelaud
- Institute of Environmental Science and Technology (ICTA), Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
| | - Angela Oviedo
- Institute of Environmental Science and Technology (ICTA), Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
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24
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Echeveste P, Croot P, von Dassow P. Differences in the sensitivity to Cu and ligand production of coastal vs offshore strains of Emiliania huxleyi. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 625:1673-1680. [PMID: 29056389 DOI: 10.1016/j.scitotenv.2017.10.050] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 09/24/2017] [Accepted: 10/06/2017] [Indexed: 06/07/2023]
Abstract
Copper is an essential trace metal for different physiological processes in phytoplankton, being either a limiting or toxic element depending on its bioavailability, which may induce local physiological adaptations. Atmospheric Cu deposition to the oceans can negatively impact phytoplankton growth, with the most Cu-sensitive phytoplankton exhibiting differences based on coastal vs oceanic origin. The goal of this work was to analyze sensitivity to Cu toxicity of the cosmopolitan marine calcifying phytoplankton, Emiliania huxleyi, exploring what factors determine intraspecific variability in sensitivity. We compared 17 strains isolated from coastal and open ocean waters of the Eastern South Pacific (ESP), the Mediterranean Sea, and the Tasman Sea. Offshore strains were as sensitive to Cu than coastal strains. Sensitivity to Cu was explained well by predicted depositional inputs of atmospheric Cu in the ESP both for coastal and offshore strains, but not when considered globally. The variability in Cu-sensitivity was also due to the production of organic Cu-ligands (CL), being the most productive strains the most tolerant to Cu at constitutive levels. When exposed to 100nM Cu, E. huxleyi produced significantly higher amounts of CL, especially coastal strains, but CL production did not correlate to observed EC50s.
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Affiliation(s)
- Pedro Echeveste
- Departamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile; Millennium Institute of Oceanography, Chile; Instituto de Ciencias Naturales Alexander von Humboldt, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile.
| | - Peter Croot
- Earth and Ocean Sciences, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Peter von Dassow
- Departamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile; Millennium Institute of Oceanography, Chile
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Miao H, Beardall J, Gao K. Calcification Moderates the Increased Susceptibility to UV Radiation of the Coccolithophorid Gephryocapsa oceanica Grown under Elevated CO 2 Concentration: Evidence Based on Calcified and Non-calcified Cells. Photochem Photobiol 2018; 94:994-1002. [PMID: 29701244 DOI: 10.1111/php.12928] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2017] [Accepted: 04/07/2018] [Indexed: 01/31/2023]
Abstract
The physiological performance of calcified and non-calcified cells of Gephyrocapsa oceanica (NIES-1318) and their short-term responses to UV radiation were compared for cultures grown under present-day (LC, 400 μatm) and high pCO2 (HC, 1000 μatm) conditions. Similar growth rates and Fv /Fm values were observed in both types of cell under LC conditions, indicating that the loss of calcification in the non-calcified cells did not lead to a competitive disadvantage under such conditions. Detrimental effects of elevated pCO2 were observed in both cell types, with the growth rate of non-calcified cells decreasing more markedly, which might reflect a negative impact of higher cytoplasmic H+ . When exposed to short-term UV radiation, similar trends in effective quantum yield were observed in both cell types acclimated to LC conditions. Elevated pCO2 and associated seawater chemical changes strongly reduced effective quantum yield in non-calcified cells but no significant influence was observed in calcified cells. Based on these findings and comparisons with previous studies, we suggest that the negative impact of elevated cytoplasmic H+ would exacerbate the detrimental effects of UV radiation while the possession of calcification attenuated this influence.
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Affiliation(s)
- Hangbin Miao
- State Key Laboratory of Marine Environmental Science/College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - John Beardall
- State Key Laboratory of Marine Environmental Science/College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.,School of Biological Sciences, Monash University, Clayton, Vic, Australia
| | - Kunshan Gao
- State Key Laboratory of Marine Environmental Science/College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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Vazač J, Füssy Z, Hladová I, Killi S, Oborník M. Ploidy and Number of Chromosomes in the Alveolate Alga Chromera velia. Protist 2017; 169:53-63. [PMID: 29367153 DOI: 10.1016/j.protis.2017.12.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Revised: 12/06/2017] [Accepted: 12/09/2017] [Indexed: 11/16/2022]
Abstract
Chromera velia is an alveolate alga which represents the closest known phototrophic relative to apicomplexan parasites. Although the nuclear, mitochondrial, and plastid genomes of this alga have been sequenced, the number of chromosomes and ploidy of C. velia are unknown. We explored ploidy in the vegetative cell, the predominant stage in cultures of Chromera, using the tyramide signal amplification-fluorescence in situ hybridization (TSA-FISH) in isolated nuclei of C. velia. Probes were derived from three single copy genes coding for 4-diphosphocytidyl-2-C-methyl-D-erythritol (CDP-ME) kinase, 2-C-methyl-D-erythritol 2,4-cyclodiphosphate (MEcPP) synthase and Topoisomerase II. Our results indicate that the vegetative cell of C. velia is haploid, as each probe produced a single fluorescent signal, although the possibility of diploidy with somatic pairing of homologous chromosomes cannot be completely excluded. Restriction analysis and hybridization with the telomere probe produced eight bands suggesting the presence of four chromosomes in haploid vegetative cells of C. velia. However, when the chromerid-specific telomere probe (TTTAGGG)4 was used for TSA-FISH, we consistently obtained a double signal. This may indicate that the four chromosomes are organized in clusters in interphase nuclei of C. velia, which is a chromosome organization similar to that of their apicomplexan relatives.
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Affiliation(s)
- Jan Vazač
- University of South Bohemia, Faculty of Science, Branišovská 31, 37005 České Budějovice, Czech Republic
| | - Zoltán Füssy
- Biology Centre, Czech Academy of Sciences, Branišovská 31, 37005 České Budějovice, Czech Republic
| | - Irena Hladová
- University of South Bohemia, Faculty of Science, Branišovská 31, 37005 České Budějovice, Czech Republic; Biology Centre, Czech Academy of Sciences, Branišovská 31, 37005 České Budějovice, Czech Republic
| | - Sireesha Killi
- University of South Bohemia, Faculty of Science, Branišovská 31, 37005 České Budějovice, Czech Republic; Biology Centre, Czech Academy of Sciences, Branišovská 31, 37005 České Budějovice, Czech Republic
| | - Miroslav Oborník
- University of South Bohemia, Faculty of Science, Branišovská 31, 37005 České Budějovice, Czech Republic; Biology Centre, Czech Academy of Sciences, Branišovská 31, 37005 České Budějovice, Czech Republic; Institute of Microbiology, Czech Academy of Sciences, Algatech, Novohradská 237, Opatovický mlýn, 37901 Třeboň, Czech Republic.
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27
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Frada MJ, Rosenwasser S, Ben-Dor S, Shemi A, Sabanay H, Vardi A. Morphological switch to a resistant subpopulation in response to viral infection in the bloom-forming coccolithophore Emiliania huxleyi. PLoS Pathog 2017; 13:e1006775. [PMID: 29244854 PMCID: PMC5756048 DOI: 10.1371/journal.ppat.1006775] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 01/05/2018] [Accepted: 11/27/2017] [Indexed: 11/18/2022] Open
Abstract
Recognizing the life cycle of an organism is key to understanding its biology and ecological impact. Emiliania huxleyi is a cosmopolitan marine microalga, which displays a poorly understood biphasic sexual life cycle comprised of a calcified diploid phase and a morphologically distinct biflagellate haploid phase. Diploid cells (2N) form large-scale blooms in the oceans, which are routinely terminated by specific lytic viruses (EhV). In contrast, haploid cells (1N) are resistant to EhV. Further evidence indicates that 1N cells may be produced during viral infection. A shift in morphology, driven by meiosis, could therefore constitute a mechanism for E. huxleyi cells to escape from EhV during blooms. This process has been metaphorically coined the 'Cheshire Cat' (CC) strategy. We tested this model in two E. huxleyi strains using a detailed assessment of morphological and ploidy-level variations as well as expression of gene markers for meiosis and the flagellate phenotype. We showed that following the CC model, production of resistant cells was triggered during infection. This led to the rise of a new subpopulation of cells in the two strains that morphologically resembled haploid cells and were resistant to EhV. However, ploidy-level analyses indicated that the new resistant cells were diploid or aneuploid. Thus, the CC strategy in E. huxleyi appears to be a life-phase switch mechanism involving morphological remodeling that is decoupled from meiosis. Our results highlight the adaptive significance of morphological plasticity mediating complex host-virus interactions in marine phytoplankton.
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Affiliation(s)
- Miguel José Frada
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Shilo Rosenwasser
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Shifra Ben-Dor
- Bioinformatics and Biological Computing Unit–Department of Biological Services, Weizmann Institute of Science, Rehovot, Israel
| | - Adva Shemi
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Helena Sabanay
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, Israel
| | - Assaf Vardi
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
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Simon N, Foulon E, Grulois D, Six C, Desdevises Y, Latimier M, Le Gall F, Tragin M, Houdan A, Derelle E, Jouenne F, Marie D, Le Panse S, Vaulot D, Marin B. Revision of the Genus Micromonas Manton et Parke (Chlorophyta, Mamiellophyceae), of the Type Species M. pusilla (Butcher) Manton & Parke and of the Species M. commoda van Baren, Bachy and Worden and Description of Two New Species Based on the Genetic and Phenotypic Characterization of Cultured Isolates. Protist 2017; 168:612-635. [PMID: 29028580 DOI: 10.1016/j.protis.2017.09.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 08/31/2017] [Accepted: 09/06/2017] [Indexed: 11/30/2022]
Abstract
The green picoalgal genus Micromonas is broadly distributed in estuaries, coastal marine habitats and open oceans, from the equator to the poles. Phylogenetic, ecological and genomic analyses of culture strains and natural populations have suggested that this cosmopolitan genus is composed of several cryptic species corresponding to genetic lineages. We performed a detailed analysis of variations in morphology, pigment content, and sequences of the nuclear-encoded small-subunit rRNA gene and the second internal transcribed spacer (ITS2) from strains isolated worldwide. A new morphological feature of the genus, the presence of tip hairs at the extremity of the hair point, was discovered and subtle differences in hair point length were detected between clades. Clear non-homoplasious synapomorphies were identified in the small-subunit rRNA gene and ITS2 spacer sequences of five genetic lineages. These findings lead us to provide emended descriptions of the genus Micromonas, of the type species M. pusilla, and of the recently described species M. commoda, as well as to describe 2 new species, M. bravo and M. polaris. By clarifying the status of the genetic lineages identified within Micromonas, these formal descriptions will facilitate further interpretations of large-scale analyses investigating ecological trends in time and space for this widespread picoplankter.
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Affiliation(s)
- Nathalie Simon
- Sorbonne Universités, Université Pierre et Marie Curie - Paris 06 and Centre National de la recherche Scientifique (CNRS), UMR 7144, Laboratoire Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France.
| | - Elodie Foulon
- Sorbonne Universités, Université Pierre et Marie Curie - Paris 06 and Centre National de la recherche Scientifique (CNRS), UMR 7144, Laboratoire Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France
| | - Daphné Grulois
- Sorbonne Universités, Université Pierre et Marie Curie - Paris 06 and Centre National de la recherche Scientifique (CNRS), UMR 7144, Laboratoire Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France
| | - Christophe Six
- Sorbonne Universités, Université Pierre et Marie Curie - Paris 06 and Centre National de la recherche Scientifique (CNRS), UMR 7144, Laboratoire Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France
| | - Yves Desdevises
- Sorbonne Universités, Université Pierre et Marie Curie - Paris 06 and Centre National de la recherche Scientifique (CNRS), UMR 7232, BIOM, Observatoire Océanologique, 66650 Banyuls/Mer, France
| | - Marie Latimier
- Sorbonne Universités, Université Pierre et Marie Curie - Paris 06 and Centre National de la recherche Scientifique (CNRS), UMR 7144, Laboratoire Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France
| | - Florence Le Gall
- Sorbonne Universités, Université Pierre et Marie Curie - Paris 06 and Centre National de la recherche Scientifique (CNRS), UMR 7144, Laboratoire Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France
| | - Margot Tragin
- Sorbonne Universités, Université Pierre et Marie Curie - Paris 06 and Centre National de la recherche Scientifique (CNRS), UMR 7144, Laboratoire Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France
| | - Aude Houdan
- Sorbonne Universités, Université Pierre et Marie Curie - Paris 06 and Centre National de la recherche Scientifique (CNRS), UMR 7144, Laboratoire Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France
| | - Evelyne Derelle
- Sorbonne Universités, Université Pierre et Marie Curie - Paris 06 and Centre National de la recherche Scientifique (CNRS), UMR 7232, BIOM, Observatoire Océanologique, 66650 Banyuls/Mer, France
| | - Fabien Jouenne
- Sorbonne Universités, Université Pierre et Marie Curie - Paris 06 and Centre National de la recherche Scientifique (CNRS), UMR 7144, Laboratoire Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France
| | - Dominique Marie
- Sorbonne Universités, Université Pierre et Marie Curie - Paris 06 and Centre National de la recherche Scientifique (CNRS), UMR 7144, Laboratoire Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France
| | - Sophie Le Panse
- Sorbonne Universités, Université Pierre et Marie Curie - Paris 06 and Centre National de la recherche Scientifique (CNRS), FR2424, Imaging Core Facility, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France
| | - Daniel Vaulot
- Sorbonne Universités, Université Pierre et Marie Curie - Paris 06 and Centre National de la recherche Scientifique (CNRS), UMR 7144, Laboratoire Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France
| | - Birger Marin
- Botanisches Institut, Biozentrum Köln, Universität zu Köln, Zülpicher Str. 47b, 50674 Köln, Germany
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Taylor AR, Brownlee C, Wheeler G. Coccolithophore Cell Biology: Chalking Up Progress. ANNUAL REVIEW OF MARINE SCIENCE 2017; 9:283-310. [PMID: 27814031 DOI: 10.1146/annurev-marine-122414-034032] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Coccolithophores occupy a special position within the marine phytoplankton because of their production of intricate calcite scales, or coccoliths. Coccolithophores are major contributors to global ocean calcification and long-term carbon fluxes. The intracellular production of coccoliths requires modifications to cellular ultrastructure and metabolism that are surveyed here. In addition to calcification, which appears to have evolved with a diverse range of functions, several other remarkable features that likely underpin the ecological and evolutionary success of coccolithophores have recently been uncovered. These include complex and varied life cycle strategies related to abiotic and biotic interactions as well as a range of novel metabolic pathways and nutritional strategies. Together with knowledge of coccolithophore genetic and physiological variability, these findings are beginning to shed new light on species diversity, distribution, and ecological adaptation. Further advances in genetics and functional characterization at the cellular level will likely to lead to a rapid increase in this understanding.
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Affiliation(s)
- Alison R Taylor
- Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington, North Carolina 28403;
| | - Colin Brownlee
- Marine Biological Association, Plymouth PL1 2PB, United Kingdom; ,
- School of Ocean and Earth Science, National Oceanography Centre, University of Southampton, Southampton SO14 3ZH, United Kingdom
| | - Glen Wheeler
- Marine Biological Association, Plymouth PL1 2PB, United Kingdom; ,
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30
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Caron DA, Alexander H, Allen AE, Archibald JM, Armbrust EV, Bachy C, Bell CJ, Bharti A, Dyhrman ST, Guida SM, Heidelberg KB, Kaye JZ, Metzner J, Smith SR, Worden AZ. Probing the evolution, ecology and physiology of marine protists using transcriptomics. Nat Rev Microbiol 2016; 15:6-20. [DOI: 10.1038/nrmicro.2016.160] [Citation(s) in RCA: 128] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Kollmar M. Fine-Tuning Motile Cilia and Flagella: Evolution of the Dynein Motor Proteins from Plants to Humans at High Resolution. Mol Biol Evol 2016; 33:3249-3267. [PMID: 27880711 PMCID: PMC5100056 DOI: 10.1093/molbev/msw213] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The flagellum is a key innovation linked to eukaryogenesis. It provides motility by regulated cycles of bending and bend propagation, which are thought to be controlled by a complex arrangement of seven distinct dyneins in repeated patterns of outer- (OAD) and inner-arm dynein (IAD) complexes. Electron tomography showed high similarity of this axonemal repeat pattern across ciliates, algae, and animals, but the diversity of dynein sequences across the eukaryotes has not yet comprehensively been resolved and correlated with structural data. To shed light on the evolution of the axoneme I performed an exhaustive analysis of dyneins using the available sequenced genome data. Evidence from motor domain phylogeny allowed expanding the current set of nine dynein subtypes by eight additional isoforms with, however, restricted taxonomic distributions. I confirmed the presence of the nine dyneins in all eukaryotic super-groups indicating their origin predating the last eukaryotic common ancestor. The comparison of the N-terminal tail domains revealed a most likely axonemal dynein origin of the new classes, a group of chimeric dyneins in plants/algae and Stramenopiles, and the unique domain architecture and origin of the outermost OADs present in green algae and ciliates but not animals. The correlation of sequence and structural data suggests the single-headed class-8 and class-9 dyneins to localize to the distal end of the axonemal repeat and the class-7 dyneins filling the region up to the proximal heterodimeric IAD. Tracing dynein gene duplications across the eukaryotes indicated ongoing diversification and fine-tuning of flagellar functions in extant taxa and species.
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Affiliation(s)
- Martin Kollmar
- Department of NMR-Based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Goettingen, Germany
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32
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Calcification response of a key phytoplankton family to millennial-scale environmental change. Sci Rep 2016; 6:34263. [PMID: 27677230 PMCID: PMC5039703 DOI: 10.1038/srep34263] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2016] [Accepted: 08/31/2016] [Indexed: 11/25/2022] Open
Abstract
Coccolithophores are single-celled photosynthesizing marine algae, responsible for half of the calcification in the surface ocean, and exert a strong influence on the distribution of carbon among global reservoirs, and thus Earth’s climate. Calcification in the surface ocean decreases the buffering capacity of seawater for CO2, whilst photosynthetic carbon fixation has the opposite effect. Experiments in culture have suggested that coccolithophore calcification decreases under high CO2 concentrations ([CO2(aq)]) constituting a negative feedback. However, the extent to which these results are representative of natural populations, and of the response over more than a few hundred generations is unclear. Here we describe and apply a novel rationale for size-normalizing the mass of the calcite plates produced by the most abundant family of coccolithophores, the Noëlaerhabdaceae. On average, ancient populations subjected to coupled gradual increases in [CO2(aq)] and temperature over a few million generations in a natural environment become relatively more highly calcified, implying a positive climatic feedback. We hypothesize that this is the result of selection manifest in natural populations over millennial timescales, so has necessarily eluded laboratory experiments.
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Boyd PW, Cornwall CE, Davison A, Doney SC, Fourquez M, Hurd CL, Lima ID, McMinn A. Biological responses to environmental heterogeneity under future ocean conditions. GLOBAL CHANGE BIOLOGY 2016; 22:2633-50. [PMID: 27111095 DOI: 10.1111/gcb.13287] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2015] [Revised: 03/08/2016] [Accepted: 03/09/2016] [Indexed: 05/20/2023]
Abstract
Organisms are projected to face unprecedented rates of change in future ocean conditions due to anthropogenic climate-change. At present, marine life encounters a wide range of environmental heterogeneity from natural fluctuations to mean climate change. Manipulation studies suggest that biota from more variable marine environments have more phenotypic plasticity to tolerate environmental heterogeneity. Here, we consider current strategies employed by a range of representative organisms across various habitats - from short-lived phytoplankton to long-lived corals - in response to environmental heterogeneity. We then discuss how, if and when organismal responses (acclimate/migrate/adapt) may be altered by shifts in the magnitude of the mean climate-change signal relative to that for natural fluctuations projected for coming decades. The findings from both novel climate-change modelling simulations and prior biological manipulation studies, in which natural fluctuations are superimposed on those of mean change, provide valuable insights into organismal responses to environmental heterogeneity. Manipulations reveal that different experimental outcomes are evident between climate-change treatments which include natural fluctuations vs. those which do not. Modelling simulations project that the magnitude of climate variability, along with mean climate change, will increase in coming decades, and hence environmental heterogeneity will increase, illustrating the need for more realistic biological manipulation experiments that include natural fluctuations. However, simulations also strongly suggest that the timescales over which the mean climate-change signature will become dominant, relative to natural fluctuations, will vary for individual properties, being most rapid for CO2 (~10 years from present day) to 4 decades for nutrients. We conclude that the strategies used by biota to respond to shifts in environmental heterogeneity may be complex, as they will have to physiologically straddle wide-ranging timescales in the alteration of ocean conditions, including the need to adapt to rapidly rising CO2 and also acclimate to environmental heterogeneity in more slowly changing properties such as warming.
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Affiliation(s)
- Philip W Boyd
- Institute for Marine and Antarctic Studies, University of Tasmania, Private Bag 129, Hobart, Tas., 7001, Australia
- ACE CRC Antarctic Climate & Ecosystems CRC, UTAS, Private Bag 80, Hobart, Tas., 7001, Australia
| | - Christopher E Cornwall
- Institute for Marine and Antarctic Studies, University of Tasmania, Private Bag 129, Hobart, Tas., 7001, Australia
| | - Andrew Davison
- Australian Antarctic Division, Channel Highway, Kingston, Tas., 7050, Australia
| | - Scott C Doney
- Marine Chemistry & Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
| | - Marion Fourquez
- Institute for Marine and Antarctic Studies, University of Tasmania, Private Bag 129, Hobart, Tas., 7001, Australia
- ACE CRC Antarctic Climate & Ecosystems CRC, UTAS, Private Bag 80, Hobart, Tas., 7001, Australia
| | - Catriona L Hurd
- Institute for Marine and Antarctic Studies, University of Tasmania, Private Bag 129, Hobart, Tas., 7001, Australia
| | - Ivan D Lima
- Marine Chemistry & Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
| | - Andrew McMinn
- Institute for Marine and Antarctic Studies, University of Tasmania, Private Bag 129, Hobart, Tas., 7001, Australia
- ACE CRC Antarctic Climate & Ecosystems CRC, UTAS, Private Bag 80, Hobart, Tas., 7001, Australia
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Mayers TJ, Bramucci AR, Yakimovich KM, Case RJ. A Bacterial Pathogen Displaying Temperature-Enhanced Virulence of the Microalga Emiliania huxleyi. Front Microbiol 2016; 7:892. [PMID: 27379036 PMCID: PMC4904034 DOI: 10.3389/fmicb.2016.00892] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 05/26/2016] [Indexed: 01/01/2023] Open
Abstract
Emiliania huxleyi is a globally abundant microalga that plays a significant role in biogeochemical cycles. Over the next century, sea surface temperatures are predicted to increase drastically, which will likely have significant effects on the survival and ecology of E. huxleyi. In a warming ocean, this microalga may become increasingly vulnerable to pathogens, particularly those with temperature-dependent virulence. Ruegeria is a genus of Rhodobacteraceae whose population size tracks that of E. huxleyi throughout the alga’s bloom–bust lifecycle. A representative of this genus, Ruegeria sp. R11, is known to cause bleaching disease in a red macroalga at elevated temperatures. To investigate if the pathogenicity of R11 extends to microalgae, it was co-cultured with several cell types of E. huxleyi near the alga’s optimum (18°C), and at an elevated temperature (25°C) known to induce virulence in R11. The algal populations were monitored using flow cytometry and pulse-amplitude modulated fluorometry. Cultures of algae without bacteria remained healthy at 18°C, but lower cell counts in control cultures at 25°C indicated some stress at the elevated temperature. Both the C (coccolith-bearing) and S (scale-bearing swarming) cell types of E. huxleyi experienced a rapid decline resulting in apparent death when co-cultured with R11 at 25°C, but had no effect on N (naked) cell type at either temperature. R11 had no initial negative impact on C and S type E. huxleyi population size or health at 18°C, but caused death in older co-cultures. This differential effect of R11 on its host at 18 and 25°C suggest it is a temperature-enhanced opportunistic pathogen of E. huxleyi. We also detected caspase-like activity in dying C type cells co-cultured with R11, which suggests that programmed cell death plays a role in the death of E. huxleyi triggered by R11 – a mechanism induced by viruses (EhVs) and implicated in E. huxleyi bloom collapse. Given that E. huxleyi has recently been shown to have acquired resistance against EhVs at elevated temperature, bacterial pathogens with temperature-dependent virulence, such as R11, may become much more important in the ecology of E. huxleyi in a warming climate.
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Affiliation(s)
- Teaghan J Mayers
- Department of Biological Sciences, University of Alberta, Edmonton AB, Canada
| | - Anna R Bramucci
- Department of Biological Sciences, University of Alberta, Edmonton AB, Canada
| | - Kurt M Yakimovich
- Department of Biological Sciences, University of Alberta, Edmonton AB, Canada
| | - Rebecca J Case
- Department of Biological Sciences, University of Alberta, Edmonton AB, Canada
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Bendif EM, Probert I, Díaz-Rosas F, Thomas D, van den Engh G, Young JR, von Dassow P. Recent Reticulate Evolution in the Ecologically Dominant Lineage of Coccolithophores. Front Microbiol 2016; 7:784. [PMID: 27252694 PMCID: PMC4877371 DOI: 10.3389/fmicb.2016.00784] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 05/09/2016] [Indexed: 11/13/2022] Open
Abstract
The coccolithophore family Noëlaerhabdaceae contains a number of taxa that are very abundant in modern oceans, including the cosmopolitan bloom-forming Emiliania huxleyi. Introgressive hybridization has been suggested to account for incongruences between nuclear, mitochondrial and plastidial phylogenies of morphospecies within this lineage, but the number of species cultured to date remains rather limited. Here, we present the characterization of 5 new Noëlaerhabdaceae culture strains isolated from samples collected in the south-east Pacific Ocean. These were analyzed morphologically using scanning electron microscopy and phylogenetically by sequencing 5 marker genes (nuclear 18S and 28S rDNA, plastidial tufA, and mitochondrial cox1 and cox3 genes). Morphologically, one of these strains corresponded to Gephyrocapsa ericsonii and the four others to Reticulofenestra parvula. Ribosomal gene sequences were near identical between these new strains, but divergent from G. oceanica, G. muellerae, and E. huxleyi. In contrast to the clear distinction in ribosomal phylogenies, sequences from other genomic compartments clustered with those of E. huxleyi strains with which they share an ecological range (i.e., warm temperate to tropical waters). These data provide strong support for the hypothesis of past (and potentially ongoing) introgressive hybridization within this ecologically important lineage and for the transfer of R. parvula to Gephyrocapsa. These results have important implications for understanding the role of hybridization in speciation in vast ocean meta-populations of phytoplankton.
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Affiliation(s)
| | - Ian Probert
- Université Pierre et Marie Curie (Paris VI), Roscoff Culture Collection, Station Biologique de RoscoffRoscoff, France; Centre National de la Recherche Scientifique, FR2424, Station Biologique de RoscoffRoscoff, France
| | - Francisco Díaz-Rosas
- Facultad de Ciencias Biológicas, Pontificia Universidad Católica de ChileSantiago, Chile; Instituto Milenio de OceanografíaConcepcion, Chile; UMI 3614, Evolutionary Biology and Ecology of Algae, Centre National de la Recherche Scientifique-UPMC Sorbonne Universités, PUCCh, UACH, Station Biologique de RoscoffRoscoff, France
| | - Daniela Thomas
- Facultad de Ciencias Biológicas, Pontificia Universidad Católica de ChileSantiago, Chile; Instituto Milenio de OceanografíaConcepcion, Chile; UMI 3614, Evolutionary Biology and Ecology of Algae, Centre National de la Recherche Scientifique-UPMC Sorbonne Universités, PUCCh, UACH, Station Biologique de RoscoffRoscoff, France
| | | | - Jeremy R Young
- Departments of Earth Sciences, University College London London, UK
| | - Peter von Dassow
- Facultad de Ciencias Biológicas, Pontificia Universidad Católica de ChileSantiago, Chile; Instituto Milenio de OceanografíaConcepcion, Chile; UMI 3614, Evolutionary Biology and Ecology of Algae, Centre National de la Recherche Scientifique-UPMC Sorbonne Universités, PUCCh, UACH, Station Biologique de RoscoffRoscoff, France
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Zhang X, Gamarra J, Castro S, Carrasco E, Hernandez A, Mock T, Hadaegh AR, Read BA. Characterization of the Small RNA Transcriptome of the Marine Coccolithophorid, Emiliania huxleyi. PLoS One 2016; 11:e0154279. [PMID: 27101007 PMCID: PMC4839659 DOI: 10.1371/journal.pone.0154279] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 04/11/2016] [Indexed: 12/31/2022] Open
Abstract
Small RNAs (smRNAs) control a variety of cellular processes by silencing target genes at the transcriptional or post-transcription level. While extensively studied in plants, relatively little is known about smRNAs and their targets in marine phytoplankton, such as Emiliania huxleyi (E. huxleyi). Deep sequencing was performed of smRNAs extracted at different time points as E. huxleyi cells transition from logarithmic to stationary phase growth in batch culture. Computational analyses predicted 18 E. huxleyi specific miRNAs. The 18 miRNA candidates and their precursors vary in length (18–24 nt and 71–252 nt, respectively), genome copy number (3–1,459), and the number of genes targeted (2–107). Stem-loop real time reverse transcriptase (RT) PCR was used to validate miRNA expression which varied by nearly three orders of magnitude when growth slows and cells enter stationary phase. Stem-loop RT PCR was also used to examine the expression profiles of miRNA in calcifying and non-calcifying cultures, and a small subset was found to be differentially expressed when nutrients become limiting and calcification is enhanced. In addition to miRNAs, endogenous small RNAs such as ra-siRNAs, ta-siRNAs, nat-siRNAs, and piwiRNAs were predicted along with the machinery for the biogenesis and processing of si-RNAs. This study is the first genome-wide investigation smRNAs pathways in E. huxleyi. Results provide new insights into the importance of smRNAs in regulating aspects of physiological growth and adaptation in marine phytoplankton and further challenge the notion that smRNAs evolved with multicellularity, expanding our perspective of these ancient regulatory pathways.
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Affiliation(s)
- Xiaoyu Zhang
- Department of Computer Science and Information Systems, California State University, San Marcos, CA, 92096, United States of America
| | - Jaime Gamarra
- Department of Computer Science and Information Systems, California State University, San Marcos, CA, 92096, United States of America
| | - Steven Castro
- Department of Biological Sciences, California State University, San Marcos, CA, 92096, United States of America
| | - Estela Carrasco
- Department of Biological Sciences, California State University, San Marcos, CA, 92096, United States of America
| | - Aaron Hernandez
- Department of Biological Sciences, California State University, San Marcos, CA, 92096, United States of America
| | - Thomas Mock
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk, NR4 7TJ, United Kingdom
| | - Ahmad R. Hadaegh
- Department of Computer Science and Information Systems, California State University, San Marcos, CA, 92096, United States of America
| | - Betsy A. Read
- Department of Biological Sciences, California State University, San Marcos, CA, 92096, United States of America
- * E-mail:
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Diversity and oceanic distribution of the Parmales (Bolidophyceae), a picoplanktonic group closely related to diatoms. ISME JOURNAL 2016; 10:2419-34. [PMID: 27003244 PMCID: PMC5030691 DOI: 10.1038/ismej.2016.38] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Revised: 01/27/2016] [Accepted: 01/29/2016] [Indexed: 11/28/2022]
Abstract
Bolidomonas is a genus of picoplanktonic flagellated algae that is closely related to diatoms. Triparma laevis, a species belonging to the Parmales, which are small cells with a siliceous covering, has been shown to form a monophyletic group with Bolidomonas. We isolated several novel strains of Bolidophyceae that have permitted further exploration of the diversity of this group using nuclear, plastidial and mitochondrial genes. The resulting phylogenetic data led us to formally emend the taxonomy of this group to include the Parmales within the Bolidophyceae, to combine Bolidomonas within Triparma and to define a novel species, Triparma eleuthera sp. nov. The global distribution of Bolidophyceae was then assessed using environmental sequences available in public databases, as well as a large 18S rRNA V9 metabarcode data set from the Tara Oceans expedition. Bolidophyceans appear ubiquitous throughout the sampled oceans but always constitute a minor component of the phytoplankton community, corresponding to at most ~4% of the metabarcodes from photosynthetic groups (excluding dinoflagellates). They are ~10 times more abundant in the small size fraction (0.8–5 μm) than in larger size fractions. T. eleuthera sp. nov. constitutes the most abundant and most widespread operational taxonomic unit (OTU) followed by T. pacifica, T. mediterranea and the T. laevis clade. The T. mediterranea OTU is characteristic of Mediterranean Sea surface waters and the T. laevis clade OTU is most prevalent in colder waters, in particular off Antarctica.
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Listmann L, LeRoch M, Schlüter L, Thomas MK, Reusch TBH. Swift thermal reaction norm evolution in a key marine phytoplankton species. Evol Appl 2016; 9:1156-1164. [PMID: 27695523 PMCID: PMC5039328 DOI: 10.1111/eva.12362] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2015] [Accepted: 01/19/2016] [Indexed: 01/21/2023] Open
Abstract
Temperature has a profound effect on the species composition and physiology of marine phytoplankton, a polyphyletic group of microbes responsible for half of global primary production. Here, we ask whether and how thermal reaction norms in a key calcifying species, the coccolithophore Emiliania huxleyi, change as a result of 2.5 years of experimental evolution to a temperature ≈2°C below its upper thermal limit. Replicate experimental populations derived from a single genotype isolated from Norwegian coastal waters were grown at two temperatures for 2.5 years before assessing thermal responses at 6 temperatures ranging from 15 to 26°C, with pCO 2 (400/1100/2200 μatm) as a fully factorial additional factor. The two selection temperatures (15°/26.3°C) led to a marked divergence of thermal reaction norms. Optimal growth temperatures were 0.7°C higher in experimental populations selected at 26.3°C than those selected at 15.0°C. An additional negative effect of high pCO 2 on maximal growth rate (8% decrease relative to lowest level) was observed. Finally, the maximum persistence temperature (Tmax) differed by 1-3°C between experimental treatments, as a result of an interaction between pCO 2 and the temperature selection. Taken together, we demonstrate that several attributes of thermal reaction norms in phytoplankton may change faster than the predicted progression of ocean warming.
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Affiliation(s)
- Luisa Listmann
- Evolutionary Ecology of Marine Fishes GEOMAR Helmholtz-Centre for Ocean Research Kiel Kiel Germany
| | - Maxime LeRoch
- Evolutionary Ecology of Marine Fishes GEOMAR Helmholtz-Centre for Ocean Research Kiel Kiel Germany
| | - Lothar Schlüter
- Evolutionary Ecology of Marine Fishes GEOMAR Helmholtz-Centre for Ocean Research Kiel Kiel Germany
| | - Mridul K Thomas
- Department of Aquatic Ecology, -Eawag Swiss Federal Institute of Aquatic Science and Technology Dübendorf Switzerland
| | - Thorsten B H Reusch
- Evolutionary Ecology of Marine Fishes GEOMAR Helmholtz-Centre for Ocean Research Kiel Kiel Germany
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A paneukaryotic genomic analysis of the small GTPase RABL2 underscores the significance of recurrent gene loss in eukaryote evolution. Biol Direct 2016; 11:5. [PMID: 26832778 PMCID: PMC4736243 DOI: 10.1186/s13062-016-0107-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 01/27/2016] [Indexed: 12/30/2022] Open
Abstract
Background The cilium (flagellum) is a complex cellular structure inherited from the last eukaryotic common ancestor (LECA). A large number of ciliary proteins have been characterized in a few model organisms, but their evolutionary history often remains unexplored. One such protein is the small GTPase RABL2, recently implicated in the assembly of the sperm tail in mammals. Results Using the wealth of currently available genome and transcriptome sequences, including data from our on-going sequencing projects, we systematically analyzed the phylogenetic distribution and evolutionary history of RABL2 orthologs. Our dense taxonomic sampling revealed the presence of RABL2 genes in nearly all major eukaryotic lineages, including small “obscure” taxa such as breviates, ancyromonads, malawimonads, jakobids, picozoans, or palpitomonads. The phyletic pattern of RABL2 genes indicates that it was present already in the LECA. However, some organisms lack RABL2 as a result of secondary loss and our present sampling predicts well over 30 such independent events during the eukaryote evolution. The distribution of RABL2 genes correlates with the presence/absence of cilia: not a single well-established cilium-lacking species has retained a RABL2 ortholog. However, several ciliated taxa, most notably nematodes, some arthropods and platyhelminths, diplomonads, and ciliated subgroups of apicomplexans and embryophytes, lack RABL2 as well, suggesting some simplification in their cilium-associated functions. On the other hand, several algae currently unknown to form cilia, e.g., the “prasinophytes” of the genus Prasinoderma or the ochrophytes Pelagococcus subviridis and Pinguiococcus pyrenoidosus, turned out to encode not only RABL2, but also homologs of some hallmark ciliary proteins, suggesting the existence of a cryptic flagellated stage in their life cycles. We additionally obtained insights into the evolution of the RABL2 gene architecture, which seems to have ancestrally consisted of eight exons subsequently modified not only by lineage-specific intron loss and gain, but also by recurrent loss of the terminal exon encoding a poorly conserved C-terminal extension. Conclusions Our comparative analysis supports the notion that RABL2 is an ancestral component of the eukaryotic cilium and underscores the still underappreciated magnitude of recurrent gene loss, or reductive evolution in general, in the history of eukaryotic genomes and cells. Reviewers This article was reviewed by Berend Snel and James O. McInerney. Electronic supplementary material The online version of this article (doi:10.1186/s13062-016-0107-8) contains supplementary material, which is available to authorized users.
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Patil S, Moeys S, von Dassow P, Huysman MJJ, Mapleson D, De Veylder L, Sanges R, Vyverman W, Montresor M, Ferrante MI. Identification of the meiotic toolkit in diatoms and exploration of meiosis-specific SPO11 and RAD51 homologs in the sexual species Pseudo-nitzschia multistriata and Seminavis robusta. BMC Genomics 2015; 16:930. [PMID: 26572248 PMCID: PMC4647503 DOI: 10.1186/s12864-015-1983-5] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Accepted: 10/04/2015] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Sexual reproduction is an obligate phase in the life cycle of most eukaryotes. Meiosis varies among organisms, which is reflected by the variability of the gene set associated to the process. Diatoms are unicellular organisms that belong to the stramenopile clade and have unique life cycles that can include a sexual phase. RESULTS The exploration of five diatom genomes and one diatom transcriptome led to the identification of 42 genes potentially involved in meiosis. While these include the majority of known meiosis-related genes, several meiosis-specific genes, including DMC1, could not be identified. Furthermore, phylogenetic analyses supported gene identification and revealed ancestral loss and recent expansion in the RAD51 family in diatoms. The two sexual species Pseudo-nitzschia multistriata and Seminavis robusta were used to explore the expression of meiosis-related genes: RAD21, SPO11-2, RAD51-A, RAD51-B and RAD51-C were upregulated during meiosis, whereas other paralogs in these families showed no differential expression patterns, suggesting that they may play a role during vegetative divisions. An almost identical toolkit is shared among Pseudo-nitzschia multiseries and Fragilariopsis cylindrus, as well as two species for which sex has not been observed, Phaeodactylum tricornutum and Thalassiosira pseudonana, suggesting that these two may retain a facultative sexual phase. CONCLUSIONS Our results reveal the conserved meiotic toolkit in six diatom species and indicate that Stramenopiles share major modifications of canonical meiosis processes ancestral to eukaryotes, with important divergences in each Kingdom.
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Affiliation(s)
- Shrikant Patil
- Stazione Zoologica Anton Dohrn, Villa Comunale 1, 80121, Naples, Italy.
| | - Sara Moeys
- Department of Biology, Protistology and Aquatic Ecology, Ghent University, 9000, Ghent, Belgium. .,Department of Plant Systems Biology, Flanders Institute for Biotechnology (VIB), 9052, Ghent, Belgium. .,Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium.
| | - Peter von Dassow
- Facultad de Ciencias Biológicas, Instituto Milenio de Oceanografía, Pontificia Universidad Católica de Chile, Santiago, Chile. .,UMI 3614, Evolutionary Biology and Ecology of Algae, CNRS-UPMC Sorbonne Universités, PUCCh, UACH, Station Biologique de Roscoff, Roscoff, France.
| | - Marie J J Huysman
- Department of Biology, Protistology and Aquatic Ecology, Ghent University, 9000, Ghent, Belgium. .,Department of Plant Systems Biology, Flanders Institute for Biotechnology (VIB), 9052, Ghent, Belgium. .,Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium.
| | - Daniel Mapleson
- The Genome Analysis Centre (TGAC), Norwich Research Park, Norwich, NR4 7UH, UK.
| | - Lieven De Veylder
- Department of Plant Systems Biology, Flanders Institute for Biotechnology (VIB), 9052, Ghent, Belgium. .,Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium.
| | - Remo Sanges
- Stazione Zoologica Anton Dohrn, Villa Comunale 1, 80121, Naples, Italy.
| | - Wim Vyverman
- Department of Biology, Protistology and Aquatic Ecology, Ghent University, 9000, Ghent, Belgium.
| | - Marina Montresor
- Stazione Zoologica Anton Dohrn, Villa Comunale 1, 80121, Naples, Italy.
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Hovde BT, Deodato CR, Hunsperger HM, Ryken SA, Yost W, Jha RK, Patterson J, Monnat RJ, Barlow SB, Starkenburg SR, Cattolico RA. Genome Sequence and Transcriptome Analyses of Chrysochromulina tobin: Metabolic Tools for Enhanced Algal Fitness in the Prominent Order Prymnesiales (Haptophyceae). PLoS Genet 2015; 11:e1005469. [PMID: 26397803 PMCID: PMC4580454 DOI: 10.1371/journal.pgen.1005469] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 07/27/2015] [Indexed: 12/11/2022] Open
Abstract
Haptophytes are recognized as seminal players in aquatic ecosystem function. These algae are important in global carbon sequestration, form destructive harmful blooms, and given their rich fatty acid content, serve as a highly nutritive food source to a broad range of eco-cohorts. Haptophyte dominance in both fresh and marine waters is supported by the mixotrophic nature of many taxa. Despite their importance the nuclear genome sequence of only one haptophyte, Emiliania huxleyi (Isochrysidales), is available. Here we report the draft genome sequence of Chrysochromulina tobin (Prymnesiales), and transcriptome data collected at seven time points over a 24-hour light/dark cycle. The nuclear genome of C. tobin is small (59 Mb), compact (∼40% of the genome is protein coding) and encodes approximately 16,777 genes. Genes important to fatty acid synthesis, modification, and catabolism show distinct patterns of expression when monitored over the circadian photoperiod. The C. tobin genome harbors the first hybrid polyketide synthase/non-ribosomal peptide synthase gene complex reported for an algal species, and encodes potential anti-microbial peptides and proteins involved in multidrug and toxic compound extrusion. A new haptophyte xanthorhodopsin was also identified, together with two “red” RuBisCO activases that are shared across many algal lineages. The Chrysochromulina tobin genome sequence provides new information on the evolutionary history, ecology and economic importance of haptophytes. Microalgae are important contributors to global ecological balance, and process nearly half of the world’s carbon each year. Additionally, these organisms are deeply rooted in the earths’ evolutionary history. To better understand why algae are such strong survivors in aquatic environments and to better understand their contribution to global ecology, we sequenced the genome of a microalga that is abundant in both fresh and salt water environments, but poorly represented by current genomic information. We identify protein-coding genes responsible for the synthesis of potential toxins as well as those that produce antibiotics, and describe gene products that enhanced the ability of the alga to use light energy. We observed that a day-night cycle, similar to that found in natural environments, significantly impacts the expression of algal genes whose products are responsible for synthesizing fats—a rich source of nutrition for many other organisms.
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Affiliation(s)
- Blake T. Hovde
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
- * E-mail: (BTH); (RAC)
| | - Chloe R. Deodato
- Department of Biology, University of Washington, Seattle, Washington, United States of America
| | - Heather M. Hunsperger
- Department of Biology, University of Washington, Seattle, Washington, United States of America
| | - Scott A. Ryken
- Department of Biology, University of Washington, Seattle, Washington, United States of America
| | - Will Yost
- Department of Biology, University of Washington, Seattle, Washington, United States of America
| | - Ramesh K. Jha
- Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Johnathan Patterson
- Department of Biology, University of Washington, Seattle, Washington, United States of America
| | - Raymond J. Monnat
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
- University of Washington, Department of Pathology, Seattle, Washington, United States of America
| | - Steven B. Barlow
- Electron Microscope Facility, San Diego State University, San Diego, California, United States of America
| | - Shawn R. Starkenburg
- Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Rose Ann Cattolico
- Department of Biology, University of Washington, Seattle, Washington, United States of America
- * E-mail: (BTH); (RAC)
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Speijer D, Lukeš J, Eliáš M. Sex is a ubiquitous, ancient, and inherent attribute of eukaryotic life. Proc Natl Acad Sci U S A 2015; 112:8827-34. [PMID: 26195746 PMCID: PMC4517231 DOI: 10.1073/pnas.1501725112] [Citation(s) in RCA: 198] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Sexual reproduction and clonality in eukaryotes are mostly seen as exclusive, the latter being rather exceptional. This view might be biased by focusing almost exclusively on metazoans. We analyze and discuss reproduction in the context of extant eukaryotic diversity, paying special attention to protists. We present results of phylogenetically extended searches for homologs of two proteins functioning in cell and nuclear fusion, respectively (HAP2 and GEX1), providing indirect evidence for these processes in several eukaryotic lineages where sex has not been observed yet. We argue that (i) the debate on the relative significance of sex and clonality in eukaryotes is confounded by not appropriately distinguishing multicellular and unicellular organisms; (ii) eukaryotic sex is extremely widespread and already present in the last eukaryotic common ancestor; and (iii) the general mode of existence of eukaryotes is best described by clonally propagating cell lines with episodic sex triggered by external or internal clues. However, important questions concern the relative longevity of true clonal species (i.e., species not able to return to sexual procreation anymore). Long-lived clonal species seem strikingly rare. We analyze their properties in the light of meiotic sex development from existing prokaryotic repair mechanisms. Based on these considerations, we speculate that eukaryotic sex likely developed as a cellular survival strategy, possibly in the context of internal reactive oxygen species stress generated by a (proto) mitochondrion. Thus, in the context of the symbiogenic model of eukaryotic origin, sex might directly result from the very evolutionary mode by which eukaryotic cells arose.
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Affiliation(s)
- Dave Speijer
- Department of Medical Biochemistry, Academic Medical Center, University of Amsterdam, 1105 AZ, Amsterdam, The Netherlands;
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, and Faculty of Sciences, University of South Bohemia, 370 05 České Budějovice, Czech Republic; Canadian Institute for Advanced Research, Toronto, ON, Canada M5G 1Z8
| | - Marek Eliáš
- Department of Biology and Ecology, University of Ostrava, 710 00 Ostrava, Czech Republic
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