published_or_final_version / Ecology and Biodiversity / Doctoral / Doctor of Philosophy

Phytoplankton produce allelochemicals; excreted chemical substances that are affecting other microorganisms in their direct environment. In my thesis, I investigated strain specific variability in the expression of allelochemicals of the harmful flagellate Prymnesium parvum, that is euryhaline but mainly bloom forming in brackish water. I found a large variation among strains, but further showed that all strains of P. parvum were more allelopathic in brackish water compared to marine water. In a marine microbial community, allelochemicals can affect prey, competitors and grazers both, directly and indirectly. For instance, in a food web where grazing controls prey abundance, the negative direct effect of allelochemicals on grazers will positive affect their prey. During my thesis, I investigated how marine microbial communities respond to the addition of allelochemicals. I performed field experiments with microbial communities from seawater collected from different places over Europe, and tested how this communities respond to the addition of allelochemicals from the dinoflagellate Alexandrium tamarense. Before I incubated the microbial communities for several days with A. tamarense algal filtrate, I evaluated the allelopathic efficiency of the algal filtrates with an algal monoculture of Rhodomonas spp. This allowed me to compare the effect of A. tamarense filtrate between the different microbial communities. In general, bacteria reached higher abundances when allelochemicals were present. As allelochemicals also inhibited nanoflagellates and ciliates, we concluded, that allelochemicals indirectly benefit bacteria by reducing grazing pressure. In microbial food webs with many heterotrophic grazers, allelochemicals further benefitted other phytoplankton by inhibiting grazers. It was also shown that bioavailable DOM is released from a microbial community when allelochemicals are present. As most DOM was released from the seawater fraction > 60 μm, we concluded, that larger microorganisms are more affected by allelochemicals than smaller microorganisms. The results can be explained by the surface to volume ratio of microorganisms: Larger organisms provide more contact surface for allelochemicals, and therefore, are probably more vulnerable towards allelochemicals. In conclusion, the effect of allelochemicals on a microbial community depends among others on the structure of the microbial food web, the amount of available DOM, the particle density in the seawater and the composition of the phytoplankton community.

Thesis (M.S.)--Oregon State University, 2011. / Printout. Includes bibliographical references (leaves 71-79). Also available on the World Wide Web.

Les relations symbiotiques entre organismes sont essentielles pour l’évolution de la bio- diversité et le fonctionnement des écosystèmes. En milieu terrestre ou en milieu marin benthique les symbioses sont assez bien décrites. Si dans le plancton marin, les relations entre hôtes hétérotrophes et symbiontes photosynthétiques sont des phénomènes observés dès le 19ème siècle, les mécanismes fonctionnels qui régissent ces symbioses restent largement inconnus. C’est le cas de la symbiose entre certaines espèces de radiolaires et leurs symbiontes dinoflagellés. Il s’agit d’un modèle symbiotique, composé de deux unicellulaires eucaryotes, sur lequel je me suis concentré au cours de cette thèse. Ces deux organismes sont connus pour être largement répandus dans les océans et pour leur importance au sein des écosystèmes marins, et il est donc important de mieux caractériser ces symbioses afin d’approfondir nos connaissances de ces organismes. Grâce aux technologies de séquençage haut-débit il est désormais possible d’obtenir, pour ces organismes non cultivables mais isolés depuis l’environnement, une quantité sans précédent d’information génomique. Ces approches représentent une opportunité de décrypter les mécanismes à l’oeuvre dans ces interactions symbiotiques. Mon travail de thèse a combiné la création d’outils bioinformatiques dédiés à l’analyse de données de transcriptomique des holobiontes de radiolaires et dinoflagellés et l’étude de ce modèle de symbiose. Ce travail de doctorat contribue à une meilleure compréhension des mécanismes d’adaptation fonctionnelle et évolutive des organismes photosymbiotiques marins. / Symbiotic associations between organisms are essentials in biodiversity evolution and ecosystems functioning. In terrestrial environments or in the benthic marine environment, the symbioses encountered are fairly well described and studied. In the marine plankton, photosymbioses are phenomena described and observed since the 19th century. However, if the actors of these associations begin to be identified, the fundamental functional mechanisms for the establishment and the maintenance of these symbioses remain largely unknown. This is particularly true for the symbiotic association between symbiotic radiolarians and their dinoflagellate photosymbionts, two unicellular eucaryotes, which I was interested in during this thesis. These two organisms are known to be widespread in the oceans and for their key role in marine ecosystems, and it is therefore important to characterize these symbiotic events in order to deepen our knowledge of these organisms. Thanks to high-throughput sequencing technologies it is now possible to obtain an unprecedented amount of data for these unicellular organisms that are not cultivable and need to be directly isolated from the environment. These new technologies represent a unique opportunity to better characterized the mechanisms involved in these intimate cellular interactions. My Ph.D. work has combined the implementation of bioinformatics protocols and tools dedicated to the assembly and analysis of RNA-seq data as well as to the study of holobiont transcriptomes of radiolarians and dinoflagellates. This thesis contributes to a better understanding of the mechanisms of functional and evolutionary adaptation of marine photosymbiotic organisms.

Bibliography: pages 163-183. / A generic, size-based simulation model is developed to investigate the dynamics of carbon and nitrogen flows in plankton communities. All parameters in the model are determined by body size using empirically-determined relationships calculated from published data. The model is robust with respect to most parameters and assumptions. Because the model is based on general ecological principles, it can be used to simulate microplankton community interactions in any planktonic ecosystem. Two coastal ecosystems from the southern Benguela region in South Africa are simulated; one typical of the relatively stable surface waters on the Agulhas Bank and one typical of upwelling plumes, usually found off the west coast of South Africa. Simulated communities compare well with field observations in terms of standing stocks and size composition, and simulation results indicate that the small-scale structure of the two ecosystems and the processes occurring within them are relatively well understood. Consequently, the dynamic functioning of the two systems is investigated at the ecosystem level, using the simulation results. Hypothetical carbon flow networks are constructed, and the average importance of different flow pathways at different times is assessed. In both ecosystems, the vast majority of carbon flows pass through short, efficient-transfer pathways, although longer pathways are potentially possible. Simulation analyses are extended from coastal to oceanic food webs, and the model results are consistent with the hypothesis that oceanic phytoplankton have rapid rates of primary production. At-sea sampling of a phytoplankton bloom is mimicked by "sampling" from simulation output, and interpretation of the data using standard techniques is compared with the model output. The dangers of extrapolating from snapshot measurements is highlighted, and the experiment emphasizes the importance of size-fractionated sampling of phytoplankton. A hypothetical pelagic food web is described, consisting of at least five different trophic pathways from phytoplankton to pelagic fish. It is suggested that coastal waters probably have all the different pathways, and the relative importance and efficiency of the different pathways will determine the total fish production in an ecosystem.

Mixoplankton are protist plankton that are capable of phototrophy and phagotrophy. These organismsare increasingly recognised not just as freaks of nature, but as a substantial part of marineplankton. Most existing plankton models still assume a strict dichotomy between phototrophsand heterotrophs. Few models consider mixoplanktonic activity as a synergism of the two trophicmodes. Many different mixoplankton functional types exist on a gradient between heterotrophy andphototrophy. The cryptophyte (Teleaulax)-Mesodinium-Dinophysis (TMD) complex is a specificpredator-prey interaction of different types of mixoplankton and a good example of the complexityof mixoplankton interaction and trophodynamics. The specialist non-constitutive mixoplankton(SNCM) Mesodinium acquires its chloroplasts strictly from a specific constitutive mixoplankton(CM) cryptophyte, while the harmful algal bloom (HAB) species Dinophysis acquires its third-handchloroplasts exclusively from Mesodinium.The generic NPZ-style protist model developed here shows that mixoplankton displays dynamicsthat are distinctly different from strict heterotrophs and autotrophs in terms of growth and theway they shape their environment. In addition, there is a clear niche separation between differentmixoplankton types (general non-constitutive mixoplankton (GNCM), SNCM and CM) according tonutrient, prey and light resource availabilities indicating a niche separation of each type. Thus,considering the different mixoplankton functional types in specialised multi-organism relationshipsas they are found in the TMD-complex may be important for their understanding and accurateprediction of growth and biomass development. Currently, none of the many models of Dinophysiscapture the biological dependencies. Results from a nitrogen-based TMD model suggest thatthe timing and quantity of prey availability is crucial for the bloom dynamics of Mesodinium andDinophysis. Some CMs may only feed when phosphate is the limiting nutrient. The results ofthe variable stoichiometric “Perfect Beast” model that was configured as Teleaulax amphioxeia incombination with experimental data strongly suggest that the cryptophyte feeds on bacteria tocompensate for phosphate limitation.This work shows the importance of considering mixoplankton in ecosystem models alongsidestrict heterotrophs and autotrophs and that distinction between different mixoplankton functionaltypes matters. Mixoplankton distinctly differ in their nutrient utilisation and growth dynamics.Predator-prey interactions have different implications for mixoplankton than for heterotrophs andtheir inclusion in models could improve our understanding of the formation of harmful mixoplanktonblooms. The unique physiology of mixoplankton and their nutrient utilisation and trophic levelsneed consideration in species specific models. / Le mixoplancton inclut les protistes planctoniques capables de phototrophie et de phagotrophie.Ces organismes sont de plus en plus reconnus comme une partie importante du plancton marin.Toutefois, la plupart des modèles mathématiques planctoniques existants supposent encoreune stricte dichotomie entre les organismes phototrophes et hétérotrophes et peu de modèlesconsidèrent l’activité mixoplanctonique comme une synergie entre les deux modes trophiques.De nombreux types fonctionnels mixoplanctoniques différents existent dans un gradient entrel’hétérotrophie et la phototrophie. Le complexe cryptophyte (Teleaulax)-Mesodinium-Dinophysis(TMD) est une interaction prédateur-proie spécifique entre différents types de mixoplancton et unbon exemple de la complexité des interactions et des relations trophodynamiques du mixoplancton.Mesodinium, mixoplancton spécialiste non constitutif (SNCM), ne peut acquérir ses chloroplastesque de cryptophytes (mixoplancton constitutif (CM)) spécifiques (tel que Teleaulax), tandis quel’espèce Dinophysis, responsable d’efflorescences algales nuisibles, acquiert ses chloroplastesexclusivement de Mesodinium. Le modèle générique de protistes, de type NPZ, développé dansce travail montre que le mixoplancton présente une dynamique nettement différente de celle deshétérotrophes et autotrophes strictes en termes de croissance et de la façon dont ils façonnentleur environnement. En outre, il existe une séparation de niches claire entre les différents typesde mixoplancton (mixoplancton généraliste non-constitutif (GNCM), SNCM et CM) en fonction dela disponibilité en lumière, en nutriments et en proies. En conséquence, la prise en compte desdifférents types fonctionnels du mixoplancton dans des relations multi-organismes spécialisées,telles qu’on les trouve dans le complexe TMD, peut être importante pour leur compréhension et laprédiction précise de leur croissance et biomasse. Actuellement, aucun des modèles existants deDinophysis ne rend compte de ces dépendances biologiques. Les résultats d’un modèle TMD basésur l’azote suggèrent que le moment et la quantité de proies disponibles sont des facteurs cruciauxpour la dynamique de Mesodinium et de Dinophysis. Certains CM peuvent se nourrir uniquementlorsque le phosphate est le nutriment limitant. Les résultats du modèle à stoechiométrie variable"Perfect Beast", qui a été configuré pour représenter Teleaulax amphioxeia sur base de donnéesexpérimentales, suggèrent fortement que le cryptophyte se nourrit de bactéries pour compenserla limitation en phosphate. Ce travail montre l’importance de prendre en compte le mixoplanctondans les modèles d’écosystème en plus des hétérotrophes et des autotrophes stricts et que ladistinction entre les différents types fonctionnels de mixoplancton est importante. Le mixoplanctonse distingue par son utilisation des nutriments et sa dynamique de croissance. Les interactionsprédateur-proie n’ont pas les mêmes implications pour le mixoplancton que pour les hétérotropheset leur prise en compte dans les modèles pourrait améliorer notre compréhension de la formationdes efflorescences nuisibles de mixoplancton. La physiologie unique du mixoplancton, sonutilisation des nutriments et ses niveaux trophiques doivent être pris en compte dans les modèlesspécifiques aux espèces. / Doctorat en Sciences agronomiques et ingénierie biologique / info:eu-repo/semantics/nonPublished

Bibliography: pages 112-138. / The large volume of seawater used for cooling at Koeberg Nuclear Power Station contains many planktonic organisms which are exposed to heat, chlorine and physical stress during their passage through the system. Phytoplankton biomass, measured as chlorophyll a, was reduced by an average of 55.32% due to entrainment, and productivity was decreased by 38.30% on average, mainly due to chlorination. Zooplankton mortality averaged 22.34% for all species and 30.52% for copepods, the dominant group. The copepod Paracartia africana was used in laboratory experiments designed to simulate entrainment. Latent mortality was monitored up to 60 hours after a 30-minute application of stress factors (physical stress was not simulated), and approximately 75% of the total mortality occurred within the 30-minute period. Male Paracartia experienced higher mortalities than females. Extrapolation of these results predicts an overall entrainment mortality (including latent mortality) of 40% for copepods and 29.04% for total zooplankton, although the latter cannot be substantiated. Plankton entrainment at Koeberg was not considered to be overly detrimental to the marine environment because of the very localised area affected, rapid dispersion of heat and chlorine, rapid regeneration times of phytoplankton and some zooplankton, low abundance of commercially important species and potential recruitment from the surrounding productive Benguela upwelling region.

The nature and extent of microbial biodiversity remain controversial with persistent debates over patterns of distributions (i.e. cosmopolitanism vs. endemism) and the processes that structure these patterns (neutrality vs. selection). We used culture-independent approaches to address these issues focusing on two groups of ciliates, the Oligotrichia (Spirotrichea) and Choreotrichea (Spirotrichea). To assess the diversity of these ciliates, we designed primers specific to SSU rDNA of ciliates within these clades, and investigated (1) geographic and temporal distributions along three coastal sites in the Northwest Atlantic; (2) the relationship between ciliate communities in the benthos and the plankton along the New England coast; and (3) diversity in ciliate communities across an environmental gradient at six stations in Long Island Sound spanning the frontal region that separates the fresher Connecticut River outflow plume from the open Sound. Each collection had its own distinct assemblage of rare and abundant ciliate haplotypes, and genealogical analyses of our samples combined with published sequences from identified morphospecies reveal that haplotype diversity at these sites is greatest within the genus Strombidium, in the Oligotrichia. Clustering of phylogenetic types indicates that benthic assemblages of oligotrichs and choreotrichs appear to be more like those from spatially distinct benthic communities than the ciliate communities sampled in the water above them. Neither ciliate diversity nor species composition showed any clear relationship to measured environmental parameters (temperature, salinity, accessory pigment composition, and chorophyll), although we observed that diversity decreased moving from nearshore to offshore. We find no strong fit of our communities to log series, geometric, or log normal distributions, though one of the 3 clusters is most consistent with a log series distribution. These analyses suggest that Oligotrich and Choreotrich communities in coastal environments may be distributed in a neutral manner. We investigated the effectiveness of molecular approaches in characterizing ciliate diversity in our samples. Estimates of diversity based on molecular markers are similar to estimates from morphological observations for Choreotrich ciliates, but much greater for Oligotrich ciliates. Sediment and plankton subsamples differed in their robustness to repeated subsampling. Sediment gave variable estimates of diversity while plankton subsamples produced consistent results.

Bibliography: leaves 254-267. / Microfiche. / xiii, 267 leaves, bound ill. 29 cm

Marine microorganisms play a significant role in the cycling of nutrients in the open ocean through production, consumption, and degradation of organic matter (OM). Carbon (C), nitrogen (N), and phosphorus (P) are essential ingredients in every known recipe for life. However, the cycling of each of these elements proceeds at different rates such that the ratio of C:N:P can vary widely between particulate, dissolved, organic, and inorganic pools. To better understand the mechanisms controlling these transformations, this study investigated the bacterial remineralization of photosynthetically-derived organic matter derived from cultures of Trichodesmium IMS101, Thalassiosira weissflogii, Prochlorococcus MED4, and particulate material collected from the surface waters of an upwelling regime. Experiments were conducted at sea for a short duration (<6d) and in the laboratory for longer periods (<150 days). In all treatments, across experiments, we observed rapid and selective P remineralization independent of the type of organic material added. Full solubilization and remineralization of P typically occurred within a week. Conversely, N remineralization was slower, with only 39-45% of particulate N (PN) remineralized in shorter (6d) experiments and 55-75% of PN remineralized in <150d experiments. Nitrification was observed after 70-98 days depending on the remineralizing bacteria (isolated from either the Oregon coastal upwelling regime or the North Pacific Subtropical Gyre (NPSG). Notably, these events did not transform the full complement of ammonium to nitrate. This differential lability between N and P led to rapid changes in the N:P ratio of inorganic pools as organic matter was depolymerized by varying bacterial populations. The variable input of potentially limiting elements could have consequences for primary productivity and particle export. Finally, we observed that in short-term experiments with heterotrophic bacteria collected from the NPSG, the N:P ratio of remineralization (11 ± 2.2) was independent of the N:P of added organic material (5-23). This uniformity of inorganic ratios implies differential lability and N:P composition of residual semi-labile and refractory organic matter. Formation of refractory C and N rich organic matter, often termed the microbial pump, is a significant pathway for the transport and sequestration of elements in the aphotic zone of the ocean interior. The experimental results reported here suggest that differential supply of POM leads to rapid and preferential P remineralization, N:P remineralization independent of the N:P of added substrates, and variable N:P of residual organic matter. These findings help constrain our knowledge of elemental cycling in the marine environment. / Graduation date: 2013