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10 results on '"marine eukaryotes"'

1. Evaluation of DNA Extraction Methods and Bioinformatic Pipelines for Marine Nano- and Pico-Eukaryotic Plankton Analysis

Author

Marta Muñoz-Colmenero, Ana Sánchez, Begoña Correa, Francisco G. Figueiras, Jose L. Garrido, and Carmen G. Sotelo

Subjects
nano-plankton, pico-plankton, marine eukaryotes, DNA extraction, next-generation sequencing, bioinformatic pipelines, Science, General. Including nature conservation, geographical distribution, QH1-199.5
Abstract

The smallest size fractions of plankton, nano- and pico-plankton, have been highlighted due to they accomplish key functions in marine ecosystems. However, the knowledge about some of them is scarce because they are difficult or impossible to be detected and identified with non-DNA-based methodologies. Here we have evaluated five DNA extraction protocols (MT1–MT5) and seven bioinformatic pipelines (P1–P7) to find the best protocol for detecting most of the eukaryotic species of nano- and pico-plankton present in an environmental sample using Ion Torrent technology. The protocol MT3 was the most reproducible methodology, showing less variation among samples, good DNA quality and sufficient quantity to amplify and sequence the eukaryote species, offering the best results after sequencing. For bioinformatic analyses, P1 and P7 resulted in the highest percentage of detection for the difficult-to-detect species in mock communities. However, only P1 avoided the confusion with other closed species during the taxonomic assignment. The final protocols, MT3-P1 (free) and MT3-P7 (private), showed good and consistent results when they were applied to an environmental sample, being a valuable tool to study the eukaryotes present in environmental samples of nano- and pico-plankton, even for the genera that are difficult to be detected by other techniques.

Published
2021
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2. Bioactive Compounds from Marine Sponges and Algae: Effects on Cancer Cell Metabolome and Chemical Structures.

Author

Esposito, Roberta, Federico, Serena, Glaviano, Francesca, Somma, Emanuele, Zupo, Valerio, and Costantini, Maria

Subjects
*MARINE algae, *SPONGES (Invertebrates), *CHEMICAL structure, *BIOACTIVE compounds, *METABOLOMICS, *DRUG discovery, *CANCER cells
Abstract

Metabolomics represent the set of small organic molecules generally called metabolites, which are located within cells, tissues or organisms. This new "omic" technology, together with other similar technologies (genomics, transcriptomics and proteomics) is becoming a widely used tool in cancer research, aiming at the understanding of global biology systems in their physiologic or altered conditions. Cancer is among the most alarming human diseases and it causes a considerable number of deaths each year. Cancer research is one of the most important fields in life sciences. In fact, several scientific advances have been made in recent years, aiming to illuminate the metabolism of cancer cells, which is different from that of healthy cells, as suggested by Otto Warburg in the 1950s. Studies on sponges and algae revealed that these organisms are the main sources of the marine bioactive compounds involved in drug discovery for cancer treatment and prevention. In this review, we analyzed these two promising groups of marine organisms to focus on new metabolomics approaches for the study of metabolic changes in cancer cell lines treated with chemical extracts from sponges and algae, and for the classification of the chemical structures of bioactive compounds that may potentially prove useful for specific biotechnological applications. [ABSTRACT FROM AUTHOR]

Published
2022
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3. Bioactive Compounds from Marine Sponges and Algae: Effects on Cancer Cell Metabolome and Chemical Structures

Author

Roberta Esposito, Serena Federico, Francesca Glaviano, Emanuele Somma, Valerio Zupo, Maria Costantini, Esposito, R., Federico, S., Glaviano, F., Somma, E., Zupo, V., and Costantini, M.

Subjects
algae, Aquatic Organisms, marine eukaryote, Plant Extracts, Organic Chemistry, General Medicine, Catalysis, Porifera, Computer Science Applications, Inorganic Chemistry, Neoplasms, Metabolome, Animals, Humans, cancer, marine eukaryotes, metabolism, sponges, Physical and Theoretical Chemistry, Molecular Biology, Spectroscopy, Biotechnology
Abstract

Metabolomics represent the set of small organic molecules generally called metabolites, which are located within cells, tissues or organisms. This new “omic” technology, together with other similar technologies (genomics, transcriptomics and proteomics) is becoming a widely used tool in cancer research, aiming at the understanding of global biology systems in their physiologic or altered conditions. Cancer is among the most alarming human diseases and it causes a considerable number of deaths each year. Cancer research is one of the most important fields in life sciences. In fact, several scientific advances have been made in recent years, aiming to illuminate the metabolism of cancer cells, which is different from that of healthy cells, as suggested by Otto Warburg in the 1950s. Studies on sponges and algae revealed that these organisms are the main sources of the marine bioactive compounds involved in drug discovery for cancer treatment and prevention. In this review, we analyzed these two promising groups of marine organisms to focus on new metabolomics approaches for the study of metabolic changes in cancer cell lines treated with chemical extracts from sponges and algae, and for the classification of the chemical structures of bioactive compounds that may potentially prove useful for specific biotechnological applications.

Published
2022

4. Functional repertoire convergence of distantly related eukaryotic plankton lineages revealed by genome-resolved metagenomics

Author

Emilie Villar, Corinne Cruaud, de Vargas C, Patrick Wincker, Chiara Vanni, Da Silva C, Chris Bowler, Karine Labadie, Julie Poulain, Clayssen Q, Eric Karsenti, Leo d’Agata, Guerra Af, Eric Pelletier, Olivier Jaillon, Eren Am, Kourlaiev A, Paul Frémont, Jean-Marc Aury, Morgan Gaia, Damien Daniel Hinsinger, Tom O. Delmont, Bernard Noël, Wessner M, Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), The Globe Institute, The University of Chicago Medicine [Chicago], Station biologique de Roscoff, Centre National de la Recherche Scientifique (CNRS), Institut de biologie de l'ENS Paris (IBENS), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), European Molecular Biology Laboratory (EMBL), ANR-11-BTBR-0008,OCEANOMICS,Biotechnologies et bioressources pour la valorisation des écosystèmes marins planctoniques(2011), ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), ANR-09-GENM-0032,TARA-GIRUS,Inventaire et ressources génétiques de virus géants à ADN dans les milieux marins sur Tara-Oceans(2009), ANR-14-CE23-0001,HydroGen,Metagenomique comparative comme instrument de mesure pour la biodiversité. Application à l'étude de la vie dans les océans(2014), ANR-10-LABX-0054,MEMOLIFE,Memory in living systems: an integrated approach(2010), ANR-11-IDEX-0001,Amidex,INITIATIVE D'EXCELLENCE AIX MARSEILLE UNIVERSITE(2011), ANR-10-INBS-0002,EMBRC-France,CENTRE NATIONAL DE RESSOURCES BIOLOGIQUES MARINES(2010), ANR-17-CE02-0012,ALGALVIRUS,Adaptations Génomique des Algues Marines aux Virus(2017), ANR-10-BLAN-1709,PHYTBACK,Rétroactions écologie-climat dues à l'évolution de la taille et de la forme du phytoplancton(2010), ANR-09-BLAN-0348,POSEIDON(2009), ANR-09-GENM-0031,PROMETHEUS,Approches génomiques pour l?analyse de la biodiversité fonctionnelle des protistes océaniques de l?expédition Tara-Oceans.(2009), European Project: 287589,EC:FP7:KBBE,FP7-OCEAN-2011,MICRO B3(2012), European Project: 261376,EC:FP7:HEALTH,FP7-HEALTH-2010-single-stage,IHMS(2011), Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), and Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS)

Subjects
Marine eukaryotes, Tara Oceans, single-cellgenomics, Marine life, Genomics, Biology, phylogeny, Genome, 03 medical and health sciences, 0302 clinical medicine, Phylogenetics, evolution, genomics, 14. Life underwater, 030304 developmental biology, open ocean, functions, 0303 health sciences, metagenomics, Phylogenetic tree, fungi, plankton, 15. Life on land, Plankton, Multicellular organism, Metagenomics, Evolutionary biology, [SDE]Environmental Sciences, anvi’o, ecology, 030217 neurology & neurosurgery
Abstract

Marine planktonic eukaryotes play a critical role in global biogeochemical cycles and climate. However, their poor representation in culture collections limits our understanding of the evolutionary history and genomic underpinnings of planktonic ecosystems. Here, we used 280 billion metagenomic reads from 143 Tara Oceans stations to reconstruct and manually curate more than 700 abundant and widespread eukaryotic metagenome-assembled genomes ranging from 10 Mbp to up to 1.3 Gbp. The resulting non-redundant genomic resource of 25 billion nucleotides that describe 10 million genes covers a wide range of poorly characterized unicellular and multicellular eukaryotic lineages that complement the long-standing contributions of culture efforts to survey the tree of marine life while better representing plankton from the open ocean. Phylogeny of the DNA-dependent RNA polymerase placed this genomic resource in a comprehensive evolutionary framework that provided insights into the relationships of eukaryotic supergroups. From there, classification of unicellular eukaryotic plankton based on functions encoded in their genes revealed four major groups connecting distantly related lineages such as the diatoms and green algae. There has been a recurrent problem in understanding the interplay between eukaryotes’ vertical evolution and their phenotype. By disentangling phylogenetic signals from functional trends with genomics, we found that neither the classical trophic mode of plankton nor its vertical evolutionary history could fully explain the genomic functional landscape of marine eukaryotes that coexisted for millions of years. Cover Navigating on the map of plankton genomics with Tara Oceans and anvi’o: a comprehensive genome-resolved metagenomic survey dedicated to eukaryotic plankton.

Published
2021

6. Evaluation of DNA extraction methods and bioinformatic pipelines for marine nano- and pico-eukaryotic plankton analysis

Author

Ministerio de Ciencia e Innovación (España), Ministerio de Educación (España), Muñoz-Colmenero, Marta, Sánchez, Ana Cristina, Correa, Begoña, Figueiras, F. G., Garrido, J. L., González Sotelo, Carmen, Ministerio de Ciencia e Innovación (España), Ministerio de Educación (España), Muñoz-Colmenero, Marta, Sánchez, Ana Cristina, Correa, Begoña, Figueiras, F. G., Garrido, J. L., and González Sotelo, Carmen

Abstract

The smallest size fractions of plankton, nano- and pico-plankton, have been highlighted due to they accomplish key functions in marine ecosystems. However, the knowledge about some of them is scarce because they are difficult or impossible to be detected and identified with non-DNA-based methodologies. Here we have evaluated five DNA extraction protocols (MT1–MT5) and seven bioinformatic pipelines (P1–P7) to find the best protocol for detecting most of the eukaryotic species of nano- and pico-plankton present in an environmental sample using Ion Torrent technology. The protocol MT3 was the most reproducible methodology, showing less variation among samples, good DNA quality and sufficient quantity to amplify and sequence the eukaryote species, offering the best results after sequencing. For bioinformatic analyses, P1 and P7 resulted in the highest percentage of detection for the difficult-to-detect species in mock communities. However, only P1 avoided the confusion with other closed species during the taxonomic assignment. The final protocols, MT3-P1 (free) and MT3-P7 (private), showed good and consistent results when they were applied to an environmental sample, being a valuable tool to study the eukaryotes present in environmental samples of nano -and pico-plankton, even for the genera that are difficult to be detected by other techniques.

Published
2021

7. Metagenetic analysis of patterns of distribution and diversity of marine meiobenthic eukaryotes.

Author

Fonseca, Vera G., Carvalho, Gary R., Nichols, Ben, Quince, Christopher, Johnson, Harriet F., Neill, Simon P., Lambshead, John D., Thomas, W. Kelley, Power, Deborah M., and Creer, Simon

Subjects
*EUKARYOTES, *MARINE ecology, *BENTHOS, *AQUATIC biology, *MACROECOLOGY, *ANIMAL morphology, REPRODUCTIVE isolation
Abstract

Aim Meiofaunal communities that inhabit the marine benthos offer unique opportunities to simultaneously study the macroecology of numerous phyla that exhibit different life-history strategies. Here, we ask: (1) if the macroecology of meiobenthic communities is explained mainly by dispersal constraints or by environmental conditions; and (2) if levels of meiofaunal diversity surpass existing estimates based on morphological taxonomy. Location UK and mainland European coast. Methods Next-generation sequencing techniques ( NGS; Roche 454 FLX platform) using 18S nuclear small subunit ribosomal DNA ( rDNA) gene. Pyrosequences were analysed using A mplicon N oise followed by chimera removal using P erseus. Results Rarefaction curves revealed that sampling saturation was only reached at 15% of sites, highlighting that the bulk of meiofaunal diversity is yet to be discovered. Overall, 1353 OTUs were recovered and assigned to 23 different phyla. The majority of sampled sites had c. 60-70 unique operational taxonomic units ( OTUs) per site, indicating high levels of beta diversity. The environmental parameters that best explained community structure were seawater temperature, geographical distance and sediment size, but most of the variability ( R2 = 70%-80%) remains unexplained. Main conclusions High percentages of endemic OTUs suggest that meiobenthic community composition is partly niche-driven, as observed in larger organisms, but also shares macroecological features of microorganisms by showing high levels of cosmopolitanism (albeit on a much smaller scale). Meiobenthic communities exhibited patterns of isolation by distance as well as associations between niche, latitude and temperature, indicating that meiobenthic communities result from a combination of niche assembly and dispersal processes. Conversely, isolation-by-distance patterns were not identified in the featured protists, suggesting that animals and protists adhere to radically different macroecological processes, linked to life-history strategies. [ABSTRACT FROM AUTHOR]

Published
2014
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8. Evaluation of DNA extraction methods and bioinformatic pipelines for marine nano- and pico-eukaryotic plankton analysis

Author

Francisco G. Figueiras, Begoña Correa, Ana Sánchez, Carmen G. Sotelo, Marta Muñoz-Colmenero, José L. Garrido, Ministerio de Ciencia e Innovación (España), and Ministerio de Educación (España)

Subjects
0106 biological sciences, lcsh:QH1-199.5, Sample (material), Marine eukaryotes, Ocean Engineering, Computational biology, lcsh:General. Including nature conservation, geographical distribution, Aquatic Science, Biology, Oceanography, 01 natural sciences, DNA sequencing, 03 medical and health sciences, Nano, Size fractions, Pico-plankton, lcsh:Science, DNA extraction, 030304 developmental biology, Water Science and Technology, Protocol (science), 0303 health sciences, Global and Planetary Change, 010604 marine biology & hydrobiology, fungi, Bioinformatic pipelines, Nano-plankton, Ion semiconductor sequencing, Plankton, Next-generation sequencing, lcsh:Q
Abstract

16 pages, 6 figures, 2 tables, The smallest size fractions of plankton, nano- and pico-plankton, have been highlighted due to they accomplish key functions in marine ecosystems. However, the knowledge about some of them is scarce because they are difficult or impossible to be detected and identified with non-DNA-based methodologies. Here we have evaluated five DNA extraction protocols (MT1–MT5) and seven bioinformatic pipelines (P1–P7) to find the best protocol for detecting most of the eukaryotic species of nano- and pico-plankton present in an environmental sample using Ion Torrent technology. The protocol MT3 was the most reproducible methodology, showing less variation among samples, good DNA quality and sufficient quantity to amplify and sequence the eukaryote species, offering the best results after sequencing. For bioinformatic analyses, P1 and P7 resulted in the highest percentage of detection for the difficult-to-detect species in mock communities. However, only P1 avoided the confusion with other closed species during the taxonomic assignment. The final protocols, MT3-P1 (free) and MT3-P7 (private), showed good and consistent results when they were applied to an environmental sample, being a valuable tool to study the eukaryotes present in environmental samples of nano -and pico-plankton, even for the genera that are difficult to be detected by other techniques., This study was funded by the Spanish Ministry of Science and Innovation, Grant CTM2014-56119-R (i-SMALL project). MM-C holds a “Juan de la Cierva Formación” postdoctoral fellowship from the Spanish Ministry of Education with reference code FJCI-2017-32722.

Published
2020

9. Energetic coupling between plastids and mitochondria drives CO2 assimilation in diatoms

Author

Judit Prihoda, Fabrice Rappaport, Denis Falconet, Stefano Santabarbara, Pierre Joliot, Benjamin Bailleul, Atsuko Tanaka, Pierre Cardol, Richard Bligny, Omer Murik, Chris Bowler, Paul G. Falkowski, Serena Flori, Dimitris Petroutsos, Leila Tirichine, Nicolas Berne, Anja Krieger-Liszkay, Giovanni Finazzi, Valeria Villanova, Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Physiologie membranaire et moléculaire du chloroplaste (PMMC), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Institute of Marine and Coastal Sciences, Rutgers, The State University of New Jersey [New Brunswick] (RU), Rutgers University System (Rutgers)-Rutgers University System (Rutgers), Génétique et Physiologie des Microalgues, Université de Liège, Laboratoire de physiologie cellulaire végétale (LPCV), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Recherche Agronomique (INRA)-Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS), Fermentalg, Serv Bioenerget Biol Struct & Mécanisme, Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Istituto di Biofisica, Consiglio Nazionale delle Ricerch, Collège de France (CdF (institution)), Region Rhone-Alpes (Cible project)- Marie Curie Initial Training Network Accliphot (FP7-PEPOPLE-2012-ITN, 316427)- CNRS Defi (ENRS 2013)- CEA Bioenergies program- Belgian Fonds de la Recherche Scientifique- Incentive Grant for Scientific Research F 4520- COSI ITN project, ANR-12-BIME-0005,DiaDomOil,Domestication des diatomées pour la production de biocarburants(2012), ANR-09-BLAN-0139,PhytAdapt,Adaptation du phytoplancton(2009), ANR-11-LABX-0011,DYNAMO,Dynamique des membranes transductrices d'énergie : biogénèse et organisation supramoléculaire.(2011), ANR-11-IDEX-0001,Amidex,INITIATIVE D'EXCELLENCE AIX MARSEILLE UNIVERSITE(2011), ANR-10-IDEX-0001,PSL,Paris Sciences et Lettres(2010), European Project: 294823,EC:FP7:ERC,ERC-2011-ADG_20110310,DIATOMITE(2012), European Project: 287589,EC:FP7:KBBE,FP7-OCEAN-2011,MICRO B3(2012), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris)-École normale supérieure - Paris (ENS Paris)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC), Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), ANR: NT09_567009,Phytadapt,Phytadapt, ANR-11-LABX-0011/11-LABX-0011,DYNAMO,Dynamique des membranes transductrices d'énergie : biogénèse et organisation supramoléculaire.(2011), ANR: ANR-11-IDEX-0001-02,ANR-11-IDEX-0001-02, ANR-10-IDEX-0001-02/10-LABX-0054,MEMOLIFE,Memory in living systems: an integrated approach(2010), Institut de biologie de l'ENS Paris (IBENS), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université de Liège, Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Bailleul B., Berne N., Murik O., Petroutsos D., Prihoda J., Tanaka A., Villanova V., Bligny R., Flori S., Falconet D., Krieger-Liszkay A., Santabarbara S., Rappaport F., Joliot P., Tirichine L., Falkowski P.G., Cardol P., Bowler C., Finazzi G., and Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris

Subjects
Aquatic Organisms, chemistry.chemical_compound, Adenosine Triphosphate, Settore BIO/04 - Fisiologia Vegetale, CYCLIC ELECTRON FLOW, Plastids, Photosynthesis, PHAEODACTYLUM-TRICORNUTUM, Plant Proteins, chemistry.chemical_classification, Multidisciplinary, microalgae, Respiration, Carbon fixation, Energetic interactions, Proton-Motive Force, Mitochondria, metabolic mutant, Phenotype, ATP/NADPH ratio, OXYGEN PHOTOREDUCTION, Carbon dioxide, Oxidoreductases, Oxidation-Reduction, Ocean, Oceans and Seas, Electron flow, Marine eukaryotes, Biology, CHLAMYDOMONAS-REINHARDTII, Carbon cycle, Carbon Cycle, Mitochondrial Proteins, Energetic exchanges, Botany, Organic matter, Ecosystem, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, 14. Life underwater, Plastid, Diatoms, Chemiosmosis, fungi, ECS, Carbon Dioxide, chemistry, 13. Climate action, NADP
Abstract

International audience; Diatoms are one of the most ecologically successful classes of photosynthetic marine eukaryotes in the contemporary oceans. Over the past 30 million years, they have helped to moderate Earth's climate by absorbing carbon dioxide from the atmosphere, sequestering it via the biological carbon pump and ultimately burying organic carbon in the lithosphere. The proportion of planetary primary production by diatoms in the modern oceans is roughly equivalent to that of terrestrial rainforests. In photosynthesis, the efficient conversion of carbon dioxide into organic matter requires a tight control of the ATP/NADPH ratio which, in other photosynthetic organisms, relies principally on a range of plastid-localized ATP generating processes. Here we show that diatoms regulate ATP/NADPH through extensive energetic exchanges between plastids and mitochondria. This interaction comprises the re-routing of reducing power generated in the plastid towards mitochondria and the import of mitochondrial ATP into the plastid, and is mandatory for optimized carbon fixation and growth. We propose that the process may have contributed to the ecological success of diatoms in the ocean.

Published
2015
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10. Metabarcoding Marine Sediments: Preparation of Amplicon Libraries.

Author

Fonseca VG and Lallias D

Subjects
Biodiversity, DNA Primers genetics, High-Throughput Nucleotide Sequencing, Polymerase Chain Reaction, DNA Barcoding, Taxonomic methods, Geologic Sediments analysis
Abstract

The accurate assessment of community composition and ultimately species identification is of utmost importance in any ecological and evolutionary study. Advances in sequencing technologies have allowed the unraveling of levels of biodiversity never imagined before when applied to large-scale environmental DNA studies (also termed metabarcoding/metagenetics/metasystematics/environmental barcoding). Here, we describe a detailed protocol to assess eukaryotic biodiversity in marine sediments, identifying key steps that should not be neglected when preparing Next-Generation Sequencing (NGS) amplicon libraries: DNA extraction, multiple PCR amplification of DNA barcode markers with index/ tag-primers, and final Illumina MiSeq sequencing library preparation.

Published
2016
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