DOCSLIB.ORG

Fabien DUFOSSÉ

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Fabien DUFOSSÉ Université de Lille1 Sciences et Technologies Laboratoire d’Océanologie et de Géosciences Ecole doctorale des Sciences de la Matière, du Rayonnement et de L’environnement Thèse de Doctorat Présentée par Fabien DUFOSSÉ En vue de l’obtention du grade de Docteur Spécialité Géosciences, Écologie Paléontologie, Océanographie Effets de la limitation en sels nutritifs, de la température et de leurs interactions sur la réponse de cinq espèces phytoplanctoniques : Approche multifactorielle expérimentale en monoculture et en communauté Date de soutenance : 16 Décembre 2014 Devant le Jury composé de Pr. Pascal claquin Université de Caen Basse-Normandie Rapporteur Dr. Jean-Luc Mouget Université du Maine, Le Mans Rapporteur Pr. Jean-Michel Brylinski Université du Littoral Côte d’Opale Examinateur Dr. Alexandrine Pannard Université de Rennes 1 Examinateur Pr. Sébastien Lefebvre Université de Lille 1 Directeur de Thèse Dr. Valérie Gentilhomme Université de Lille 1 Responsable scientifique Résumé court Les effets de la limitation en azote et en phosphore, de la température et de leurs interactions ont été étudiés expérimentalement sur différents traits de réponse de cinq microalgues marines présentant des phénologies différentes en Manche Orientale ainsi qu’une large gamme de volumes cellulaires. Notre étude montre que le volume cellulaire est un paramètre essentiel à prendre en compte dans la définition de groupes fonctionnels car il conditionne une partie des réponses des microalgues aux différentes conditions environnementales. Une forte diminution de l’activité photosynthétique est constatée pour les petites cellules du fait d’une interaction entre les sels nutritifs et la température. De plus, l’intensité de la réponse aux différentes conditions environnementales augmente quand la taille diminue. Les sels nutritifs, la température et leur intéraction influencent la formation d’hydrates de carbone de façon spécifique, aboutissant à une augmentation d’hydrates de carbone par cellules en cas de limitation. Par ailleurs, nos résultats montrent un effet plus fort des sels nutritifs par rapport à la température sur les différents traits mesurés et des différences de réponse au sein d’un même groupe fonctionnel classique (diatomées). Enfin, des communautés expérimentales en limitation azote, phosphore et sans limitation, ont été constituées afin de comparer la productivité des communautés et des monocultures. La limitation en azote influence la composition spécifique des communautés et aucune relation claire entre diversité et productivité n’est mise en évidence. Cependant, les communautés sont plus efficaces que les monocultures pour l’absorption des sels nutritifs et de lumière traduisant un effet de complémentarité. Toutes ces observations sont essentielles pour comprendre les effets des modifications environnementales sur les microalgues dans le cadre du changement global et par extension, sur le fonctionnement des écosystèmes marins. Mots clefs : phytoplancton, approche multifactorielle, limitation en sels nutritifs, température, traits fonctionnels, photosynthèse, hydrates de carbone Short abstract The effects of nitrogen and phosphorus depletion, temperature and their interaction were studied on five microalgae which differ in terms of phenology and size. By a multifactorial experimental approach, we demonstrated that nutrient effects override temperature effects, and that species from a same classical functional group could show different responses. Our results suggest that size matters for the responses of microalgae in our different conditions. Indeed, an interactive effect of temperature and nutrients was observed leading to decrease of photosynthetic activity of the small sized algae. These species also showed a high variability in their responses compared to larger ones. Furthermore, particular and dissolved carbohydrates per cell was positively influenced by nutrient limitation, temperature or their interaction, independently of cell size but rather in a specific way. Lastly, in order to highlight the relationship between productivity and diversity three experimental communities were done under nitrogen or phosphorus depletion. Our results demonstrated a better efficiency of nutrient and light absorption of communities compared to monocultures. However these communities were overall less productive than monocultures in terms of carbohydrate and biomass formation. No clear trend between diversity and productivity was shown in our study. Our results provide useful information about the responses of phytoplankton to environmental gradients and consequently of several ecosystem processes taking into accounts the modifications expected through global change. Keywords: phytoplankton, nutrient limitation, temperature, functional response traits, diversity/productivity relationship, photosynthesis, carbohydrates Avant-propos Ce travail de recherche à été réalisé au sein de l’école doctorale des Sciences de la Matière, du Rayonnement et de l’Environnement (SMRE), attaché à l’Université des Sciences et Technologies de Lille 1, dans le Laboratoire d’Océanologie et de Géosciences de Wimereux (LOG). Cette thèse s’inscrit dans le cadre du programme « Impact des Changements Climatiques et Anthropiques sur la biodiversité des pRotistes des Ecosystèmes côtiers » (ICCARE) financé par la région Nord/Pas-de-Calais et la Fédération de Recherche sur la Biodiversité (FRB). Remerciements Trois ans se sont écoulés depuis le début de cette thèse. Trois ans durant lesquels j’ai eu la chance de rencontrer de nombreuses personnes, avec qui j’ai travaillé ou que j’ai simplement côtoyé et que j’aimerai remercier. Je tiens à remercier en tout premier lieu Pascal Claquin et Jean-Luc Mouget pour avoir accepté d’être rapporteurs de cette thèse ainsi que Jean-Michel Brylinski et Alexandrine Pannard, examinateurs de ce travail. Merci à Sébastien Lefebvre, mon directeur de thèse, et à Valérie Gentilhomme, responsable scientifique, qui m’ont permis de réaliser ce travail sans réelles contraintes matérielles. Merci à toi, Sébastien, pour m’avoir procuré ce confort de travail, pour ton suivi et ta réactivité qui ne m’ont jamais fait défaut, même pendant tes vacances. Merci également de m’avoir montré différentes méthodes de travail et de m’avoir initié, entre autres, aux analyses en fluorescence modulée et aux joies de la programmation. Merci à toi Valérie pour avoir suivi ce travail, pour m’avoir formé aux analyses de sels nutritifs et pour tous les conseils que tu as pu me procuré pendant ces trois ans. Enfin j’aimerai vous remercier tous les deux de m’avoir permis d’enseigner en tant que moniteur à l’université de Lille 1. Ce fut une expérience enrichissante. Merci à Francois Schmitt, directeur du Laboratoire d’Océanologie et de Géosciences, de m’avoir ouvert les portes de son laboratoire. Tout au long de ces trois ans j’ai eu l’occasion de collaborer avec des chercheurs que j’aimerai remercier. Tout d’abord, merci à Fabienne Goulard d’avoir contribué activement à ce travail et pour son expertise en tant que biochimiste. Réussir à rendre la biochimie intéressante n’est pas à la portée de tous ! Un grand merci à Elsa Breton pour m’avoir appris à me servir correctement d’un microscope, pour avoir fourni certaines souches algales et pour nos trop rares discussions scientifiques. Merci également à François Gevaert pour sa contribution aux analyses pigmentaires, que je n’ai malheureusement pas encore eu le temps de valoriser. Enfin, merci à Gonzalo Marquez pour m’avoir initié à la modélisation DEB, pour m’avoir familiarisé avec Matlab et pour m’avoir accueilli chez lui, à Lisbonne. Merci également à Nicole Degros et Gwendoline Duong pour leur contribution aux analyses CHN et pigmentaires. Durant cette thèse j’ai encadré, au moins en partie, des stagiaires issus de formations et d’horizons différents que je tiens à remercier. Merci donc à Charlotte, Julie, Julien, Kevin, Khedidja, Marion, Noémie et Ragil pour votre contribution à ce travail. J’espère que cette expérience a été aussi enrichissante pour vous que pour moi. Je remercie également Morgane, assistant ingénieur, entre autres pour son aide concernant les prélèvements, l’étude du coefficient spécifique de la chlorophylle a, les extractions et dosages de la chlorophylle a et pour n’avoir pas trop rechigné à faire la vaisselle et à remplir les boites de cônes. Pendant ces trois ans j’ai eu la chance de côtoyer au quotidien de nombreuses personnes que j’aimerai remercier. Tout d’abord, merci aux différents chercheurs, qu’ils soient de la station marine ou du côté obscur du laboratoire (la MREN !), avec qui je n’ai pas nécessairement travaillé mais qui m’ont tous apporté un petit quelque chose, et particulièrement Dorothée (pour ses conseils, ses encouragements et son soutien sans faille), Nicolas (pour nos trop rares échanges de mails) ou encore Vincent (qui fait un super Tajine). Merci aux autres personnels du laboratoire et plus particulièrement, que les lecteurs n’y voient pas là une scission stérile (et inexistante…) entre les deux bâtiments, à tout le personnel de la station marine que j’ai davantage côtoyé. Merci donc aux BITOSS Didier, Michel, Patrick et Thierry (le cerbère de la porte également expert en chambre froide) pour leur aide et leur disponibilité. Merci également à Josette, pour avoir gardé un œil bienveillant sur ma personne, à Christelle et Christine pour le café (entre autres) et à Dominique (notre Mc Gyver local) pour son aide mais aussi pour ces petits moments du quotidien (rassure toi je
Load more

Recommended publications
  • Diversity in the Genus Skeletonema (Bacillariophyceae). Ii. an Assessment of the Taxonomy of S. Costatum-Like Species with the Description of Four New Species1
    J. Phycol. 41, 151–176 (2005) r 2005 Phycological Society of America DOI: 10.1111/j.1529-8817.2005.04067.x DIVERSITY IN THE GENUS SKELETONEMA (BACILLARIOPHYCEAE). II. AN ASSESSMENT OF THE TAXONOMY OF S. COSTATUM-LIKE SPECIES WITH THE DESCRIPTION OF FOUR NEW SPECIES1 Diana Sarno,2 Wiebe H. C. F. Kooistra Stazione Zoologica ‘‘Anthon Dohrn,’’ Villa Comunale, 80121 Naples, Italy Linda K. Medlin Alfred Wegener Institute, Am Handelshafen 12, D-27570 Bremerhaven, Germany Isabella Percopo and Adriana Zingone Stazione Zoologica ‘‘Anthon Dohrn,’’ Villa Comunale, 80121 Naples, Italy The morphology of strains of Skeletonema Grev- Abbreviations: AIC, Akaike information criterion; ille emend Sarno et Zingone was examined in LM, CCAP, Culture Collection of Algae and Protozoa; TEM, and SEM and compared with sequence data CCMP, The Provasoli-Guillard National Center for from nuclear small subunit rDNA and partial large Cultures of Marine Phytoplankton; FP,fultoportula; subunit rDNA. Eight distinct entities were identi- FPP, fultoportula process; hLRTs, hierarchical like- fied, of which four were known: S. menzelii Guillard, lihood ratio tests; IFPP, intercalary fultoportula Carpenter et Reimann; S. pseudocostatum Medlin process; IRP, intercalary rimoportula; IRPP, inter- emend. Zingone et Sarno; S. subsalsum (Cleve) Bet- calary rimoportula process; LSU, large subunit; hge; and S. tropicum Cleve. The other four species ML, maximum likelihood; MP, maximum parsimo- were new: S. dohrnii Sarno et Kooistra sp. nov., S. ny; RP, rimoportula; RPP, rimoportula process; grethae Zingone et Sarno sp. nov., S. japonicum Zin- SSU, small subunit; SZN, Stazione Zoologica ‘‘A. gone et Sarno sp. nov., and S. marinoi Sarno et Zin- Dohrn’’ of Naples; TFP, terminal fultoportula; gone sp.
    [Show full text]
  • Community Composition of the Morphologically Cryptic Diatom Genus Skeletonema in Narragansett Bay
    University of Rhode Island DigitalCommons@URI Open Access Master's Theses 2015 COMMUNITY COMPOSITION OF THE MORPHOLOGICALLY CRYPTIC DIATOM GENUS SKELETONEMA IN NARRAGANSETT BAY Kelly Canesi University of Rhode Island, [email protected] Follow this and additional works at: https://digitalcommons.uri.edu/theses Recommended Citation Canesi, Kelly, "COMMUNITY COMPOSITION OF THE MORPHOLOGICALLY CRYPTIC DIATOM GENUS SKELETONEMA IN NARRAGANSETT BAY" (2015). Open Access Master's Theses. Paper 549. https://digitalcommons.uri.edu/theses/549 This Thesis is brought to you for free and open access by DigitalCommons@URI. It has been accepted for inclusion in Open Access Master's Theses by an authorized administrator of DigitalCommons@URI. For more information, please contact [email protected]. COMMUNITY COMPOSITION OF THE MORPHOLOGICALLY CRYPTIC DIATOM GENUS SKELETONEMA IN NARRAGANSETT BAY BY KELLY CANESI A THESIS SUBMITTED IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF MASTER OF SCIENCE IN OCEANOGRAPHY UNIVERSITY OF RHODE ISLAND 2015 MASTER OF SCIENCE THESIS OF KELLY CANESI APPROVED: Thesis Committee: Major Professor: Tatiana Rynearson Candace Oviatt Christopher Lane Nasser H. Zawia DEAN OF THE GRADUATE SCHOOL UNIVERSITY OF RHODE ISLAND 2015 ABSTRACT It is well known that morphologically cryptic species are routinely present in planktonic communities but their role in important ecological and biogeochemical processes is poorly understood. I investigated the presence of cryptic species in the genus Skeletonema, an important bloom-forming diatom, using high-throughput genetic sequencing and examined the ecological dynamics of communities relative to environmental conditions. Samples were obtained from the Narragansett Bay Long-Term Plankton Time Series, where Skeletonema spp.
    [Show full text]
  • Insights Into Global Planktonic Diatom Diversity: Comparisons Between Phylogenetically Meaningful Units That Account for Time
    bioRxiv preprint doi: https://doi.org/10.1101/167809; this version posted July 24, 2017. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-ND 4.0 International license. Insights into global planktonic diatom diversity: Comparisons between phylogenetically meaningful units that account for time Teofil Nakov, Jeremy M. Beaulieu, and Andrew J. Alverson Department of Biological Sciences University of Arkansas 1 University of Arkansas, SCEN 601 Fayetteville, AR 72701 Abstract Metabarcoding has offered unprecedented insights into microbial diversity. In many studies, short DNA sequences are binned into consecutively higher Linnaean ranks, and ranked groups (e.g., genera) are the units of biodiver- sity analyses. These analyses assume that Linnaean ranks are biologically meaningful and that identically ranked groups are comparable. We used a meta-barcode dataset for marine planktonic diatoms to illustrate the limits of this approach. We found that the 20 most abundant marine planktonic diatom genera ranged in age from 4 to 134 million years, indicating the non- equivalence of genera because some had more time to diversify than others. Still, species richness was only weakly correlated with genus age, highlighting variation in rates of speciation and/or extinction. Taxonomic classifications often do not reflect phylogeny, so genus-level analyses can include phylogenet- ically nested genera, further confounding rank-based analyses. These results underscore the indispensable role of phylogeny in understanding patterns of microbial diversity. Keywords: diversification, metabarcoding, microbes, phylogeny Preprint submitted to Bioarxiv July 24, 2017 bioRxiv preprint doi: https://doi.org/10.1101/167809; this version posted July 24, 2017.
    [Show full text]
  • Impacts of Microbial Chemical Interactions on Marine Plankton Physiology
    AN ABSTRACT OF THE DISSERTATION OF Eric R. Moore for the degree of Doctor of Philosophy in Microbiology presented on December 12, 2019. Title: Impacts of Microbial Chemical Interactions on Marine Plankton Physiology Abstract approved: ______________________________________________________ Kimberly H. Halsey The bioavailability of chemical compounds in the marine environment fundamentally influences the growth and physiology of microorganisms. Organic and inorganic chemicals that are produced by some marine plankton can be consumed by other plankton for energy production, growth, or to initiate essential physiological processes. Cultures of the diatom Thalassiosira pseudonana, a model phytoplankton species, and Pelagibacter ubique, the most abundant heterotrophic bacteria in the ocean, were used to study how microbial chemical interactions influence the physiology of these two groups of co-occurring marine plankton that have substantial roles in the carbon cycle. Specifically, the production and consumption of volatile organic compounds (VOCs) were studied in monocultures and co-cultures of these plankton. In co-culture, Pelagibacter benefited from a wide variety of VOCs produced by T. pseudonana, and heterotrophic consumption of VOCs taxed carbon fixation in the diatom by promoting the loss of diffusible VOCs from the primary producer. In this interaction, VOCs were shown to be a large fraction (ca. 20%) of fixed carbon that is transferred to heterotrophic bacteria, suggesting that VOC cycling by phytoplankton and bacteria is a significant component of the global carbon cycle. Acetone and isoprene, VOCs with important roles in atmospheric processes, were two of the VOCs utilized by Pelagibacter in co-culture. Pelagibacter metabolized acetone and isoprene at rates sufficient to explain discrepancies in measured fluxes of these compounds between the ocean and atmosphere, demonstrating that heterotrophic bacteria have significant control over the emission of VOCs from the ocean.
    [Show full text]
  • Diversity in the Genus Skeletonema (Bacillariophyceae): Iii
    /. Phycol. 43, 156-170 (2007) © 2007 by the Phycological Society of America DOI: 10.111 l/j.l529-8817.2006.00305.x DIVERSITY IN THE GENUS SKELETONEMA (BACILLARIOPHYCEAE): III. PHYLOGENETIC POSITION AND MORPHOLOGICAL VARIABILITY OF SKELETONEMA COSTATUM AND SKELETONEMA GREVILLEI, WITH THE DESCRIPTION OF SKELETONEMA ARDENS SP NOV.1 Diana Sarno2, Wiebe H. C. F. Kooistra, Sergio Balzano Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy Paul E. Hargraves Graduate School of Oceanography, University of Rhode Island, Narragansett, Rhode Island 02882-1197, USA Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy Skeletonema costatum (Grev.) Cleve emend. tional Center for Cultures of Marine Phytoplankton; Zingone et Sarno and S. grevillei Sarno et Zingone CSIRO, Commonwealth Scientific and Industrial were known only from the type material collected Research Organisation; FPP, fultoportula process; from Hong Kong waters more than a century ago. GTR, general time reversible; I FPP, intercalary ful- Both species have now been collected as live mate- toportula process; IRP, intercalary rimoportula; rial, and their morphology and phylogenetic posi- IRPP, intercalary rimoportula process; ML, maxi- tion are investigated in this study. Eight Skeletonema mum likelihood; MP, maximum parsimony; NJ, strains isolated from Florida, USA; Uruguay; and neighbor joining; RELL, resampling of estimated Brazil are attributed to S. costatum, while one In likelihood; SZN, Stazione Zoologica A. Dohrn of strain from Oman is ascribed to S. grevillei based Naples; TFPP, terminal fultoportula process; TRP, on morphological similarity to the type material of terminal rimoportula; TRPP, terminal rimoportula these species. In addition, a new Skeletonema spe- process cies, S. ardens Sarno et Zingone, is described for a strain from Singapore and two from northern Aus- tralian waters.
    [Show full text]
  • Phd Thesis the Taxa Are Listed Alphabetically Within the Bacteriastrum Genera and Each of the Chaetoceros Generic Subdivision (Subgenera)
    FACULTY OF SCIENCE DEPARTMENT OF GEOLOGY INTERDISCIPLINARY DOCTORAL STUDY IN OCEANOLOGY Sunčica Bosak TAXONOMY AND ECOLOGY OF THE PLANKTONIC DIATOM FAMILY CHAETOCEROTACEAE (BACILLARIOPHYTA) FROM THE ADRIATIC SEA DOCTORAL THESIS Zagreb, 2013 PRIRODOSLOVNO-MATEMATIČKI FAKULTET GEOLOŠKI ODSJEK INTERDISCIPLINARNI DOKTORSKI STUDIJ IZ OCEANOLOGIJE Sunčica Bosak TAKSONOMIJA I EKOLOGIJA PLANKTONSKIH DIJATOMEJA IZ PORODICE CHAETOCEROTACEAE (BACILLARIOPHYTA) U JADRANSKOM MORU DOKTORSKI RAD Zagreb, 2013 FACULTY OF SCIENCE DEPARTMENT OF GEOLOGY INTERDISCIPLINARY DOCTORAL STUDY IN OCEANOLOGY Sunčica Bosak TAXONOMY AND ECOLOGY OF THE PLANKTONIC DIATOM FAMILY CHAETOCEROTACEAE (BACILLARIOPHYTA) FROM THE ADRIATIC SEA DOCTORAL THESIS Supervisors: Dr. Diana Sarno Prof. Damir Viličić Zagreb, 2013 PRIRODOSLOVNO-MATEMATIČKI FAKULTET GEOLOŠKI ODSJEK INTERDISCIPLINARNI DOKTORSKI STUDIJ IZ OCEANOLOGIJE Sunčica Bosak TAKSONOMIJA I EKOLOGIJA PLANKTONSKIH DIJATOMEJA IZ PORODICE CHAETOCEROTACEAE (BACILLARIOPHYTA) U JADRANSKOM MORU DOKTORSKI RAD Mentori: Dr. Diana Sarno Prof. dr. sc. Damir Viličić Zagreb, 2013 This doctoral thesis was made in the Division of Biology, Faculty of Science, University of Zagreb under the supervision of Prof. Damir Viličić and in one part in Stazione Zoologica Anton Dohrn in Naples, Italy under the supervision of Diana Sarno. The doctoral thesis was made within the University interdisciplinary doctoral study in Oceanology at the Department of Geology, Faculty of Science, University of Zagreb. The presented research was mainly funded by the Ministry of Science, Education and Sport of the Republic of Croatia Project No. 119-1191189-1228 and partially by the two transnational access projects (BIOMARDI and NOTCH) funded by the European Community – Research Infrastructure Action under the FP7 ‘‘Capacities’’ Specific Programme (Ref. ASSEMBLE grant agreement no. 227799). ACKNOWLEDGEMENTS ... to my Croatian supervisor and my boss, Prof.
    [Show full text]
  • Thalassiosira Community Composition and Diversity in Narragansett Bay
    University of Rhode Island DigitalCommons@URI Open Access Master's Theses 2016 Thalassiosira Community Composition and Diversity in Narragansett Bay Sarah Flickinger University of Rhode Island, [email protected] Follow this and additional works at: https://digitalcommons.uri.edu/theses Recommended Citation Flickinger, Sarah, "Thalassiosira Community Composition and Diversity in Narragansett Bay" (2016). Open Access Master's Theses. Paper 880. https://digitalcommons.uri.edu/theses/880 This Thesis is brought to you for free and open access by DigitalCommons@URI. It has been accepted for inclusion in Open Access Master's Theses by an authorized administrator of DigitalCommons@URI. For more information, please contact [email protected]. THALASSIOSIRA COMMUNITY COMPOSITION AND DIVERSITY IN NARRAGANSETT BAY BY SARAH FLICKINGER A THESIS SUBMITTED IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF MASTER OF SCIENCE IN OCEANOGRAPHY UNIVERSITY OF RHODE ISLAND 2016 MASTER OF SCIENCE THESIS OF SARAH FLICKINGER APPROVED: Thesis Committee: Major Professor Tatiana Rynearson Candace Oviatt Bethany Jenkins Nasser H. Zawia DEAN OF THE GRADUATE SCHOOL UNIVERSITY OF RHODE ISLAND 2016 ABSTRACT Diatoms contribute 40-45% of marine primary production. Understanding the contributions of individual species to diatom communities is important in light of warming ocean waters and changing food webs. Here, the diatom genus Thalassiosira, which exhibits irregular pulses in abundance in Narragansett Bay, is examined using data from the Narragansett Bay Long Term Phytoplankton Time Series. High-throughput sequencing (HTS) at the highly-variable V4 region of the 18S ribosomal gene identified fourteen Thalassiosira taxa in monthly samples over a six- year time period (December 2008-December 2014), seven of which had not previously been identified in this time series.
    [Show full text]
  • Temporal Variation of Skeletonema Community Composition from a Long-Term Time Series in Narragansett Bay Identified Using High-Throughput DNA Sequencing
    Vol. 556: 1–16, 2016 MARINE ECOLOGY PROGRESS SERIES Published September 8 doi: 10.3354/meps11843 Mar Ecol Prog Ser OPENPEN FEATURE ARTICLE ACCESSCCESS Temporal variation of Skeletonema community composition from a long-term time series in Narragansett Bay identified using high-throughput DNA sequencing Kelly L. Canesi1,2, Tatiana A. Rynearson1,* 1Graduate School of Oceanography, University of Rhode Island, Narragansett, RI 02882, USA 2Present Address: Gordon and Betty Moore Foundation, Palo Alto, CA 94304, USA ABSTRACT: Phytoplankton species cannot always be identified by their morphology using light microscopy, which makes inferring the ecological and biogeochem- ical importance of individual species a difficult task. Here, a combination of microscopy and high-through- put DNA sequencing was used to examine morphologi- cally cryptic and pseudo-cryptic species in the diatom genus Skeletonema from the Long-Term Plankton Time Series in Narragansett Bay (NBay), where Skele- tonema is ecologically important, comprising up to 99% of microplankton cells in surface waters. The 28S rDNA from mock phytoplankton communities compris- ing known species was amplified and sequenced using newly developed Skeletonema-specific primers. The relative abundances of species in the sequence data did not match expected abundances, suggesting that 28S copy number can vary greatly, even among closely related diatom species. The 28S rDNA was also ampli- fied from 75 field samples collected from 2008 to 2013. High-throughout DNA sequencing revealed seasonal varia- A total of 7 Skeletonema species were identified, in- tion (2008–2013) in morphologically cryptic species diversity cluding 5 newly detected species from NBay. Skele- (line, 4-point moving average) in the ecologically important diatom genus (percent composition among tonema species composition was highly seasonal and Skeletonema species shown in different colors).
    [Show full text]
  • Variability Approaching the Thermal Limits Can Drive Diatom Community Dynamics
    University of Rhode Island DigitalCommons@URI Graduate School of Oceanography Faculty Publications Graduate School of Oceanography 3-2-2020 Variability approaching the thermal limits can drive diatom community dynamics Stephanie Anderson Tatiana A. Rynearson Follow this and additional works at: https://digitalcommons.uri.edu/gsofacpubs Limnol. Oceanogr. 9999, 2020, 1–13 © 2020 The Authors. Limnology and Oceanography published by Wiley Periodicals, Inc. on behalf of Association for the Sciences of Limnology and Oceanography. doi: 10.1002/lno.11430 Variability approaching the thermal limits can drive diatom community dynamics Stephanie I. Anderson , Tatiana A. Rynearson * Graduate School of Oceanography, University of Rhode Island, Narragansett, Rhode Island Abstract Organismal distributions are largely mediated by temperature, suggesting thermal trait variability plays a key role in defining species’ niches. We employed a trait-based approach to better understand how inter- and intra- specific thermal trait variability could explain diatom community dynamics using 24 strains from 5 species in the diatom genus Skeletonema, isolated from Narragansett Bay (NBay), where this genus can comprise up to 99% of the microplankton. Strain-specific thermal reaction norms were generated using growth rates obtained at temperatures ranging from −2Cto36C. Comparison of thermal reaction norms revealed inter- and intraspe- cific similarities in the thermal optima, but significant differences approaching the thermal limits. Cellular ele- mental composition was determined for two thermally differentiated species and again, the most variation occurred approaching the thermal limits. To determine the potential impact of interspecific variability on com- munity composition, a species succession model was formulated utilizing each species’ empirically determined thermal reaction norm and historical temperature data from NBay.
    [Show full text]
  • Diversity and Seasonal Occurrence of Skeletonema (Bacillariophyta) Species in Xiamen Harbour and Surrounding Seas, China
    Cryptogamie, Algologie, 2012, 33 (3): 245-263 ©2012 Adac. Tous droits réservés Diversity and seasonal occurrence of Skeletonema (Bacillariophyta) species in Xiamen Harbour and surrounding seas, China Haifeng GU a*,Xiaodong ZHANG b,c,jun SUN b &Zhaohe LUO a a Third Institute of Oceanography, Xiamen, 361005, P. R. China b Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, P. R. China c Graduate School of the Chinese Academy of Sciences, Beijing, 100039, P. R. China Summary – Skeletonema costatum like cells are recorded globally and often generate ahuge biomass when blooming. In the present study we performed ataxonomic and geographic survey of the species diversity in Skeletonema along the Chinese coastline. We concentrated our efforts on Xiamen Harbour, where we followed the annual cycle of the generic diversity by collecting 51 water samples from 2006 to 2010. Atotal of 687 strains of Skeletonema were established and they were identified as S. ardens, S. costatum, S. dohrnii, S. grevillei, S. menzelii,and S. tropicum. S. dohrnii is awinter-spring species, whereas other species tend to appear in summer and autumn. S. costatum is the single species present throughout the year. To assess how the species overcome the period in which they are not detectable in the water column we also sampled the surface sediments and either isolated resting stages and incubated them into cultures, or we generated monoclonal strains by incubating the sediment and isolated whatever emerged from it. The above six species except S. grevillei, and S. pseudocostatum as well, were detected this way, implying that the species produce resting stages.
    [Show full text]
  • Morphology and Phylogeny of Picoeukaryotes and Planktonic Pennate Diatoms in the Middle and South Adriatic Sea
    University of Zagreb FACULTY OF SCIENCE DEPARTMENT OF BIOLOGY Maja Mucko MORPHOLOGY AND PHYLOGENY OF PICOEUKARYOTES AND PLANKTONIC PENNATE DIATOMS IN THE MIDDLE AND SOUTH ADRIATIC SEA DOCTORAL THESIS Zagreb, 2018 Sveučilište u Zagrebu PRIRODOSLOVNO-MATEMATIČKI FAKULTET BIOLOŠKI ODSJEK Maja Mucko MORFOLOGIJA I FILOGENIJA PIKOEUKARIOTA I PENATNIH PLANKTONSKIH DIJATOMEJA U SREDNJEM I JUŽNOM JADRANU DOKTORSKI RAD Zagreb, 2018 This doctoral dissertation was carried out as a part of the postgraduate programme at University of Zagreb, Faculty of Science, Department of Biology – Botany, under the supervision of dr.sc. Zrinka Ljubešić. The research was performed in the frame of the Bio-tracing Adriatic Water Masses (BIOTA) project, supported by the Croatian Science Foundation (project number UIP- 2013-11-6433); project leader dr.sc. Zrinka Ljubešić). The experimental part of the research was carried out in part at Ruđer Bošković Institute, Zagreb, Croatia, while part of the bioinformatic analyses was carried out at University of Arkansas, Fayeteville, USA. Acknowledgments Firstly, I would like to express my sincere gratitude to my supervisor Dr Zrinka Ljubešić for the continuous support of my Ph.D. study and related research, for her patience, guidance, motivation, and immense knowledge. She helped me in all phases of research and writing of this thesis. I could not have imagined having a better supervisor for my Ph.D. study. In addition to my supervisor, I would like to thank my thesis committee: Dr Daniela Marić Pfannkuchen, Dr Sunčica Bosak and Dr Regine Jahn, for their insightful comments and encouragement, but also for the hard questions, which motivated me to widen my research from various perspectives.
    [Show full text]
  • Distance and Character-Based Evaluation of the V4 Region of the 18S Rrna Gene for the Identification of Diatoms (Bacillariophyceae)
    Distance and Character-Based Evaluation of the V4 Region of the 18S rRNA Gene for the Identification of Diatoms (Bacillariophyceae) Ian A. Luddington1*, Irena Kaczmarska1, Connie Lovejoy2 1 Department of Biology, Mount Allison University, Sackville, Canada, 2 Que´bec-Oce´an, De´partement de Biologie and Institut de Biologie Inte´grative et des Syste`mes, Universite´ Laval, Que´bec, Canada Abstract DNA barcoding is a molecular tool that exploits a unique DNA sequence of a standardized gene or non-coding region for the species identification of unknown individuals. The investigation into a suitable barcode for diatoms is ongoing and there are several promising candidates including mitochondrial, plastidial and nuclear markers. We analyzed 272 sequences from 76 diatoms species in the orders Thalassiosirales, Lithodesmiales and Cymatosirales, using distance and character based approaches, to assess the applicability of a DNA barcode based on the hypervariable V4 region of the nuclear 18S rRNA gene. We show that the proposed V4 barcode separated ca. 97% of all centric diatom taxa tested using a threshold p- distance of 0.02 and that many problem pairs were further separated using a character based approach. The reliability of amplification, extensive reference library and variability seen in the V4 region make it the most promising candidate to date for a barcode marker for diatoms particularly when combined with DNA character analysis. Citation: Luddington IA, Kaczmarska I, Lovejoy C (2012) Distance and Character-Based Evaluation of the V4 Region of the 18S rRNA Gene for the Identification of Diatoms (Bacillariophyceae). PLoS ONE 7(9): e45664. doi:10.1371/journal.pone.0045664 Editor: Rodolfo Paranhos, Instituto de Biologia, Brazil Received June 23, 2012; Accepted August 21, 2012; Published September 21, 2012 Copyright: ß 2012 Luddington et al.
    [Show full text]