Coral reefs, the planet’s most diverse marine ecosystems, are threatened globally by climate change and locally by overfishing and pollution. The dynamic partnership between coral and their endosymbiotic algae (Symbiodinium) is the foundation of all tropical reef ecosystems. Symbiodinium provide coral with nutrients for growth, but stress can break down this symbiosis, causing coral bleaching. There are also life-history trade-offs amongst Symbiodinium types - some provide coral with more nutrition, while others are better able to cope with environmental stressors. Although these symbioses are believed to be a critical element of reef resilience, little is known about how local and global stressors alter these partnerships. In this thesis, I combine synthetic literature reviews and a meta-analysis, with field research, molecular analyses, bioinformatics, and statistical analyses to investigate environmentally-driven mechanisms of change in coral-symbiont interactions with the aim of advancing understanding of how corals will adapt to the stressors they now face. First, I conducted a review of coral-Symbiodinium interactions, from molecules to ecosystems and summarized the current state of the field and knowledge gaps. Next, I conducted a meta-analysis of coral bleaching and mortality during El Niño events and created an open-source coral heat stress data product. I found that the 2015-2016 El Niño instigated unprecedented thermal stress on reefs globally, and that, across all El Niño events, coral bleaching and mortality were greater at locations with higher long-term mean temperatures. I provided recommendations for future bleaching surveys, and in a related perspectives piece, highlighted the importance of survey timing during prolonged coral bleaching events. The latter three empirical chapters are based on my six field expeditions to Kiritimati (Christmas Island). Taking advantage of the atoll’s natural ecosystem-scale experiment, I tagged, sampled and tracked over 1,000 corals across its chronic human disturbance gradient. Since corals can uptake Symbiodinium from the surrounding environment, I first investigated the effect of local disturbance and winter storm waves on Symbiodinium communities in coral, sediment, and seawater. Greater variability in Symbiodinium communities at highly disturbed sites suggests that local disturbance destabilizes symbiont community structure. Since local disturbance influences Symbiodinium community structure and coral-associated microbial communities, I next examined the covariance of coral-associated Symbiodinium and microbial communities for six coral species across Kiritimati’s disturbance gradient. Most strikingly, I found corals on Kiritimati that recovered from globally unprecedented thermal stress, experienced during the 2015-2016 El Niño, while they were still at elevated temperatures. This is notable, because no coral has previously been documented to recover from bleaching while still under heat stress. Only corals protected from local stressors exhibited this capacity. Protected corals had distinct pre-bleaching algal symbiont communities and recovered with different algal symbionts, suggesting that Symbiodinium are the mechanism of resilience and that protection governs their communities. Together, this research provides novel evidence that local protection may be more important for coral resilience than previously thought, and that variability in symbiotic and microbial communities provides a potentially flexible mechanism for corals to respond to both local and global stressors. / Graduate / 2019-11-26

Os crustáceos estão entre os invertebrados marinhos mais diversos e tendem a se associar com outros organismos a fim de encontrar abrigo, oferta de alimento e um lugar seguro para reprodução. Aspectos reprodutivos como fecundidade, tamanho dos embriões e energia investida na reprodução são os principais parâmetros para a compreensão da história natural de uma espécie e/ou população. Assim, esse trabalho foi desenvolvido no sentido de investigar tais parâmetros e a influência do tipo de substrato ocupado. A espécie utilizada como modelo de estudo foi o caranguejo porcelanídeo Pachycheles monilifer coletado em dois substratos biológicos diferentes, no briozoário Schizoporella errata no píer do Itaguá e no poliqueto Phragmatopoma caudata na praia Grande, ambas as paias localizadas em Ubatuba, litoral norte de SP. Somente os embriões em estágio inicial de desenvolvimento foram utilizados para os cálculos de fecundidade e investimento reprodutivo (RO). Os embriões foram contados e medidos sob esteromicroscópio. Para obtenção do RO foram utilizados os pesos secos das fêmeas ovígeras e das massas de embriões, previamente secos em estufa. Além dos aspectos reprodutivos, análises de distância genética também foram realizadas pelo sequenciamento de genes mitocôndrias (16S e COI) de exemplares de P. monilifer. A estimativa da porcentagem de variação genética intra e interespecífica, a possibilidade de fluxo gênico entre indivíduos de diferentes praias do estado de São Paulo foram verificadas. A partir desses dados confirmou-se a validade da espécie, assim como o fluxo gênico contínuo entre indivíduos dessas duas praias. A baixa divergência genética permite concluir que as diferenças reprodutivas encontradas são, portanto um reflexo das condições proporcionadas pelo ambiente. Os animais simbiontes do briozoário, assim como as fêmeas ovígeras, são maiores que os associados ao poliqueta e também possuem maior fecundidade e investimento reprodutivo, porém não foram encontradas diferenças em relação ao tamanho dos embriões. No substrato do briozoário o estresse reprodutivo parece ser menor que no substrato do poliqueto, já que aquele substrato proporciona um ambiente fisicamente mais estável para os organismos simbiontes. No substrato do poliqueto, além do alto hidrodinamismo local, o espaço disponível na colônia parece ser mais restrito e pode limitar o tamanho de seus habitantes. Os animais simbiontes do briozoário parecem não serem influenciados por fatores externos à colônia, entretanto o mesmo não foi observado nos simbiontes do poliqueto. Tais diferenças reprodutivas refletem o tipo de substrato ocupado, evidenciando a plasticidade fenotípica da espécie para uma melhor adaptação local. / The crustaceans are the most diverse of the marine invertebrates and many of them tend to associate with other organisms where they can find shelter, food supply and a safe place to reproduce. Reproductive traits as fecundity, egg size and reproductive output (RO) are the most important aspects to understand the species life history. This study aimed to investigate the reproductive traits in relation to the substrate that the organisms live. The studied species used as model was the porcellanid crab Pachycheles monilifer that was collected in two different substrates, one of them is the bryozoan Schizoporella errata at the Itaguá beach and the other is the polychaete Phragmatopoma caudata at Grande beach, both are located in Ubatuba, northern coast of São Paulo. Only the initial stage of eggs was used to estimate the crab fecundity and RO. The eggs were counted and measured in a stereomicroscope. To obtain the RO the female and the egg mass dry weight, which were previously dried in an oven, were used. Besides the reproductive aspects, the genetic distance between the organisms was valued with partial sequences of the mitochondrial genes 16S and COI. The estimate of the intra and interspecific genetic variation and the possibility of gene flow between the individuals from the beaches in SP were analyzed too. Therefore, with all these analyses it was possible to confirm that the species is valid and that there is gene flow among the populations. The low genetic divergence allowed us to conclude that the different reproductive traits found among the populations were due to the different substrates that the organisms inhabit. The bryozoan symbionts are larger than the polychaete symbionts as well as the females fecundity and the RO, but there is no difference in egg size. In the bryozoan substrate it seems like the physical stress is smaller than in polychaete and it promotes a more stable habitat for the crabs reproduce. In the polychaete substrate, beyond the high hydrodynamic location, the available space in the colony appears to be narrower, which could limit the size of its inhabitants. The bryozoan symbionts do not seem to be influenced by the external factors of the colony, though the same was not observed in the polychaete colony. Such differences in reproduction reflect the kind of substrate inhabited, highlighting the phenotypic plasticity of the species to a local better adaptation.

Orientadores: Gláucia Maria Pastore, Rosângela dos Santos / Dissertação (mestrado) - Universidade Estadual de Campinas, Faculdade de Engenharia de Alimentos / Made available in DSpace on 2018-08-21T19:39:00Z (GMT). No. of bitstreams: 1 Adami_AngelicaAparecidaVieira_M.pdf: 12653852 bytes, checksum: a5b3e75b4c45344be161ab51a7df7f0a (MD5) Previous issue date: 2013 / Resumo: Estudos sao realizados com oligossacarideos, probioticos e a combinação deles; sao varios os fatores que envolvem os beneficios que estes em combinacao podem agregar para a saude dos consumidores. Esta pesquisa teve como objetivo avaliar o comportamento simbiotico in vitro das linhagens probioticas Bifidobacterium animalis (Bb-12) e Lactobacillus acidophillus (LA-05), em substratos enriquecidos com oligossacarideos, ou seja, avaliar se esses potencializavam a capacidade probiotica das linhagens estudadas. Os oligossacarideos utilizados no estudo foram o galactooligossacarideo (GOS) sintetizado pela ?-galactosidase de Scopulariops sp., frutooligossacarideo (FOSOrafti) e extrato bruto de Yacon. Avaliou-se o efeito bifidogenico de diferentes concentracoes de GOS, FOS e Yacon utilizando as culturas probioticas e sua capacidade de acidificacao do meio. Foi avaliado o perfil hidrofobico e acido da membrana celular dos probioticos usando meio enriquecido com GOS, FOS e controle meio MRS (Man Rogosa e Sharpe) sem fonte de dextrose; pelo método MATH (aderencia microbiana de hidrocarbonetos). Realizou-se tambem a producao, extracao e quantificacao de exopolissacarideos (EPS) por Lactobacillus acidophillus (LA-05) em meios enriquecidos com FOS e GOS, a quantificacao foi pelo metodo fenol-sulfurico seguida de leitura de absorbancia a 490nm, os resultados foram submetidos a uma curva padrao de glicose. Verificou-se ainda o antagonismo das linhagens probioticas cultivadas em meios suplementados com GOS, FOS, Yacon, MRS sem fonte de dextrose e controle MRS adicionado de NaOH, sobre linhagens patogenicas; o antagonismo foi avaliado atraves do metodo de difusao em agar. Avaliou tambem a capacidade de producao de acido latico. Na avaliacao bifidogenica os resultados revelaram que os substratos estimularam o metabolismo dos probioticos estudados. A melhor atividade para as linhagem de Lactobacillus acidophillus (LA-05) foi com o substrato GOS com atividade de 11,56 LogUFC (na concentracao de 200mg de GOS, em 12 horas de incubacao), e para e Bifidobacterium animalis (Bb12) foi com o substrato FOS com atividade de 11,3 LogUFC (na concentracao de 100mg FOS, em 12 horas de incubacao), na medida que se aumentou a concentracao dos substratos, houve a reducao da atividade bifidogenica. Os resultados revelaram que os prebioticos GOS e FOS estimularam o perfil de adesao e acidez da membrana celular das linhagens probioticas estudadas, quando comparado com o controle meio MRS sem fonte de dextrose. Quanto a producao de EPS, o maior valor (13,53 \g.mL) foi obtido apos 48 horas de cultivo em caldo MRS suplementado com GOS (25% v/v), enquanto que o FOS (25% v/v) tambem estimulou a producao (7,68 \g.mL) em 12 horas, seguida da queda de producao apos este periodo. Verificou-se que os oligossacarideos estimularam a acao antagonica dos probioticos sobre os micro-organismos patogenicos, e que esta inibicao do crescimento pode estar ligada com a producao de acidos pelos probioticos em conjunto com os oligossacarideos. Em sintese, os resultados revelaram que os oligossacarideos estimularam o potencial probiotico das linhagens estudadas / Abstract: Several studies have been conducted with oligosaccharides in general and also with probiotics, or combination of them, due to factors involving the combined benefits they can add to the health of consumers. This research aimed to evaluate in vitro the behavior of symbiotic probiotic strains Bifidobacterium animalis (Bb-12) and Lactobacillus acidophilus (LA-05), on substrates enriched with oligosaccharides in the case to assess whether the oligosaccharides intensified the ability of probiotic strains studied. The oligosaccharides used in this study were synthesized by the galactooligosaccharide ?-galactosidase Scopulariops sp., fructooligosaccharide and crude extract of yacon. We evaluated the bifidogenic effect of different concentrations of GOS, FOS and Yacon using probiotic cultures and their ability to acidification of the medium. Was evaluated the profile acid and hydrophobic cellular membrane of probiotics using medium supplemented with GOS, FOS and control MRS medium without added dextrose; MATH method (microbial adherence to hydrocarbons). Was also conducted production, extraction and quantification of exopolysaccharides (EPS) by Lactobacillus acidophilus (LA-05) media supplemented with FOS and GOS, quantification was by the phenolsulfuric method followed by absorbance reading at 490nm, the results were subjected to a standard curve of glucose. It was further antagonism of probiotic strains grown in media supplemented with GOS, FOS, yacon, MRS without dextrose and source control MRS added NaOH on pathogenic strains; antagonism was assessed by the agar diffusion method; also evaluated the ability to produce lactic acid. In evaluating the results revealed that bifidogenic substrates stimulated metabolism studied probiotics, the best activity for the strain of Lactobacillus acidophilus (LA-05) was the substrate with GOS activity of 11.56 LogUFC (200mg in 12 hours incubation), and for and Bifidobacterium animalis (Bb-12) was with the FOS substrate with activity of 11.3 LogUFC (100mg in 12 hours incubation), as it increased the concentration of the substrates decreased the activity of microorganisms. The results revealed that prebiotic GOS and FOS stimulated acid profile of adhesion and cell membrane of probiotic strains studied, as compared to the MRS control medium without added dextrose. As for the highest production of EPS production (13.53 ?g.ml) was after 48 hours of culture in MRS broth supplemented with GOS, while also stimulated FOS production (7.68 ?g.ml) for 12 hours followed by production decrease thereafter. It was found that the oligosaccharides stimulated antagonistic action of probiotics on pathogenic microorganisms and that this growth inhibition is connected with acid production by probiotics together with the oligosaccharides. In summary, the results revealed that the oligosaccharides stimulated the potential probiotic strains studied / Mestrado / Ciência de Alimentos / Mestra em Ciência de Alimentos

A growing understanding of complex biotic interactions clarified the importance of symbioses with respect to the ecology and evolution of life. In particular, knowledge of symbioses between eukaryotes and microorganisms such as bacteria and fungi has revolutionized the fields of medicine and agriculture, and made clear the roles of microbes in fostering human and environmental sustainability. For example, diverse fungi associate with the seeds of plants following dispersal. These fungi can influence seed survival and germination in a host-specific and spatially explicit manner, thus influencing plant community dynamics in agricultural and natural systems. In species-rich tropical forests, seed-fungus interactions are emerging as one of the most important aspects of plant demography and community ecology. However, even closely related fungi can have opposing effects on seeds of particular plants, such that mechanisms influencing host-specific effects require further attention. Such mechanisms can include genomic traits of fungi and hosts, and the environmental context of interactions. However, studies have shown that many fungi also harbor endosymbionts than can influence their functional traits. In particular, fungi often harbor endohyphal bacteria that influence fungal phenotypes. This suggested the potential for similar, co-occurring microbes to influence the ecology of seed-associated fungi. Here, I explore the diversity, evolutionary relationships, and influence on fungal phenotypes of endohyphal bacteria inhabiting seed- and leaf-associated fungi with a focus that begins in tropical forest ecology and expands to include gene expression in an emerging model system from the temperate zone. To determine the occurrence, abundance, taxonomic diversity, and phylogenetic diversity of endohyphal bacteria among tropical seed-associated fungi, my coauthors and I used PCR and fluorescence microscopy to screen members of two common orders of seed-associated fungi, comparing their communities to those in closely related foliar endophytic fungi. We revealed a high frequency and diversity of endohyphal bacteria among both groups of fungi. We then used phylogenetic and community ecological analyses to show a lack of congruence between phylogenies of bacteria and fungi. Although seed-associated and foliar endophytic fungi share evolutionary histories, they harbor distinct endohyphal bacterial communities. To explore the influence of endohyphal bacteria on fungal phenotypes important for interactions with seeds, my coauthors and I examined a single fungus-bacterium pair consisting of a member of a well-known group of pathogenic fungi found to harbor an endohyphal bacterium closely related to those with known chitinolytic activity. We created fungal clones that were free of endohyphal bacteria, and carried out a phenotypic microarray assay comparing use of 95 unique carbon sources by cured and uncured clones. Across the majority of substrates, the fungal clones harboring endohyphal bacteria grew more rapidly and to a greater extent than the cured clones. Thus the endohyphal bacterium was associated with broader substrate use and more effective use of a variety of substrates relevant to plant biology, including seed germination. To assess the influence of endohyphal bacteria with respect to the outcomes of seed-fungus interactions, my coauthors and I examined six fungus-bacterium pairs and their interactions with the seeds of five tropical pioneer tree species. We showed that although endohyphal bacteria have little impact on colonization of seeds by fungi, they significantly altered the survival and germination of infected seeds. In most cases, endohyphal bacteria reduced the negative impacts of fungi on seeds: strains harboring them responded more similarly to uninoculated controls, whereas strains cured of them exhibited significantly reduced survival and germination. Seeds infected by fungi of the same genotype that differ with respect to the identity of their endohyphal bacteria exhibited differences, but so did seeds infected by strains of those isolates not harboring bacteria, suggesting that factors in addition to the presence of endohyphal bacteria can drive variation in the outcomes of seed-fungus interactions. Together these analyses suggest intricate interactions between fungi and bacteria that result in context-dependent outcomes. This turned our focus to gene expression as a means to understand mechanisms of interactions between endohyphal bacteria and their fungal hosts. Last, my coauthors and I describe methods we developed to co-culture fungi and their endohyphal bacteria for downstream analysis of differences in gene expression among a fungus-bacterium pair and axenic cultures of each symbiont. We focused on an emerging model system: a foliar endophytic strain of Pestalotiopsis aff. neglecta (Ascomycota) known to harbor an endohyphal bacterium in the genus Luteibacter (Xanthomonadaceae). The focal bacterium is in part reliant on its host fungus for acquisition of certain sulfur-containing compounds such as sulfate. We showed that inoculating a low-methionine growth medium with bacteria recovered in exponential phase from a high-methionine medium supports growth suitable for comparing axenic growth with that in co-culture with its host fungus. Although bacterial cell density in co-cultures was significantly greater than that in axenic cultures, the opposite was true for the host fungus. We expect results from transcriptomics analyses to reflect partial reliance on– and antagonism of Pestalotiopsis by Luteibacter, and here present the first pipeline of methods for examining gene expression for a facultatively symbiotic endohyphal bacterium and its host, a member of the most species-rich and economically important fungal phylum.

Philosophiae Doctor - PhD / Frankia is one of two partners in the globally distributed N2-fixing actinorhizal symbiosis between this filamentous soil-dwelling actinomycete and almost 300 species of host plants from eight diverse angiosperm families. The actinorhizal symbiosis is a major contributor to nitrogen reservoirs in terrestrial ecosystems, and allows actinorhizal plants to perform the role of pioneers in newly formed and nitrogen-poor soils. Frankia are differentiated into four main host-infection groups (1: Alnus/Comptonia/Myrica-infective, 2: Rosaceae/Datisca/Coriaria-infective, 3: Elaeagnaceae/Gymnostoma-infective and 4: Casuarina-infective), and there is a large degree of phylogenetic clustering within these HIGs. Of these host lineages, species from the genus Morella, from the family Myricaceae, are notable as they have the ability to establish effective partnerships with Frankia from more than one host-infection group. Africa houses 16 of the world’s 33 currently accepted Morella species, and Morella is the continents only genus containing endemic actinorhizal species. Despite this, the diversity of Frankia in symbiosis with African Morella has never been explored. To address this lack of knowledge I investigated Frankia in root nodules of six Morella species from the Cape flora of Southern Africa, as well as in rhizosphere soils from selected hosts. Partial nif H gene fragments recovered from 202 root nodules yielded 26 unique sequences, which phylogenetic analysis assigned to Frankia Cluster I (the Alnus host infection group) and Frankia Cluster III (the Elaeagnus host infection group)1. Nineteen nif H sequences were assigned to three sub-clusters within Frankia Cluster III (CC-3, CC-4 and CC-5), and the remaining seven sequences to two sub-clusters within Cluster I (CC-1 and CC-2), one of which (CC-1) is novel to the current study. Identical sequences were recovered from nodules collected at geographically distant locations, suggesting a cosmopolitan distribution within the region for some subgroups from both clusters, but more localized distribution (or tighter host-specificity) for others. Soil pH correlated with strain presence in nodules, with Cluster I sequences being associated with hosts growing in acidic soils exclusively. Furthermore, three Morella species from the Cape flora of southern Africa are promiscuous in their natural habitats, with host infection group influenced by habitat edaphic conditions. In order to explore the correlation between soil characteristics and Frankia presence in nodules, nif H soil libraries were created from selected host rhizospheres. While Cluster III sequences from these libraries corresponded closely to sequences found in nodules from the same sites, the dominant Cape Cluster I group (CC-1) was absent from all six libraries, even when present in nodules recovered from the same soils. Whether this was due to low abundance of -but strong selection for- these strains by hosts under particular conditions, or due to the absence in soil of hyphal forms of these strains could not be determined. Cluster III strains are known to be better able to persist saprophytically than their relatives from other host-infection groups. A second group of Cluster I strains, detected at only one sampling site, was present in that site's corresponding soil library. An Alnus-infective subgroup, cluster AI, which has been detected in soils collected on five continents, was also detected in the of the Cape soil libraries but never in nodules, raising questions as to this group’s ability to persist in soil in the absence of known suitable hosts. Ten Frankia strains representing all three of the numerically dominant subgroups (CC-1, CC-3 and CC-4, found in 186 of 202 root nodules) were isolated from four Morella species. These isolates represent six of the most abundant unique nodular nif H sequences found in the field survey, and display morphological and cultural characteristics typical of Frankia. Phylogenetic analysis confirmed their identity as Frankia, and multilocus analysis revealed that the isolates belong to three genospecies. Two of these genospecies fall into existing groups within the Elaeagnus-infective Cluster III, while the remaining genospecies is a novel addition to the otherwise well-described Alnus-infective Cluster I. Whole genome sequencing of a representative from each of the Cape genospecies allowed for basic annotation and genome descriptions, which agreed in each case with what has been previously found for strains from the Elaeagnus and Alnus host-infection groups, respectively. Similarly, the organization of nitrogenase gene clusters in each of the sequenced strains mirrors that found in other strains from their respective host-infection groups, indicating that this gene cluster is highly conserved in different Frankia lineages. For the first time the diversity of Frankia nodulating endemic African Morella, and present in root-associated soils of these species, has been explored. This is also the first study to report isolation and description of Frankia strains from actinorhizal plants endemic to Africa.

Les symbioses ont un role majeur dans le fonctionnement et l'equilibre des ecosystemes. Dans les oceans, qui couvrent pres de 70 % de la surface de la planete, vivent une multitude d'organismes incapables de lutter contre les courants et la plupart sont microscopiques, il s'agit du plancton. Les organismes du plancton, comme ceux d'autres ecosystemes, entretiennent des symbioses, mais la nature et l'ampleur de ces interactions sont encore mal connues dans le plancton du fait la petite taille de ces organismes et de la difficulte d'echantillonnage des ecosystemes planctoniques, surtout dans les zones les plus eloignees des cotes. Les principaux objectifs de cette these sont de donner un apercu global de la place occupee par ces symbioses dans le plancton et de proposer des methodes originales permettant leur detection. Les travaux presentes dans ce manuscrit s'appuient sur l'analyse des donnees generees lors de l'expedition Tara Oceans (2009-2013) pendant laquelle 210 stations oceaniques ont ete echantillonnees a travers le monde. Ils concernent plus precisement le jeu de donnees environnemental obtenu grace au sequencage a haut debit (Illumina) de la region hypervariable V9 (130 nucleotides) de la sousunite 18S de l'ADN ribosomique des organismes eucaryotes (metabarcoding). Dans un premier temps, un etat des lieux de la diversite et de la structure des communautes du pico-nano-micro-mesoplancton (0,8-2000 μm) eucaryote de la zone photique des oceans temperes a tropicaux est realise. Il met en evidence la place importante occupee par les symbiotes au sein de ces communautes. Ensuite, l'etude de deux cas de symbiose (Blastodinium- Copepodes et Symbiodinium-Tiarina) montre les difficultes inherentes a la detection de couples symbiotiques a partir d’un jeu de donnees issue d'etudes par metabarcoding du plancton (flexibilite de la specificite des symbioses dans le plancton), mais aussi la possibilite de distinguer les differentes phases de vie des symbiotes (libres et symbiotiques) lorsque les echantillons etudies ont ete fractionnes. Enfin, un ensemble de methodes est propose afin d'ameliorer l'efficacite de la detection de symbioses dans le cadre d'etudes par reseau de cooccurrences des communautes planctoniques. L'analyse de la distribution des metabarcodes le long des fractions de taille (piconano- (0.8-5 μm), nano- (5-20 μm), micro- (20-180 μm), et meso-plancton (180-2000 μm)) permet de differencier ceux provenant d'organismes symbiotiques de ceux d'organismes libres, sans a priori. De plus la comparaison de l'abondance de groupes genetiques definis a differents niveaux de resolution permet de detecter des associations symbiotiques peu specifiques et d'apprecier leur niveau de specificite. / The oceans, which cover nearly 70 % of the earth's surface, is host to a myriad of mostly microscopic organisms that drift with the currents and are collectively called plankton. As in other ecosystems, symbioses play a major role in the functioning and equilibrium of the plankton. But the exact nature and strength of those symbiotic interactions are still poorly known, not only due to the small size of most planktonic organisms, but also because of the inherent difficulty of sampling planktonic ecosystems, especially in the high-seas. The main goals of this thesis are to give a global view of the importance of planktonic symbioses and to propose novel methods for their detection. The work presented in this manuscript is based on analyses of data generated during the Tara Oceans expedition (2009-2013), during which sea water was collected and size fractionated by filtration at 210 sampling locations distributed across the world's oceans. The data analyses presented herein mostly focus on an environmental metabarcoding dataset obtained from next-generation sequencing (Illumina) of the V9 hypervariable region (~130 nucleotides long) of the 18S small ribosomal subunit of eukaryotic organisms. We begin by assessing the diversity and structure of pico-, nano-, micro and meso-planktonic eukaryotic communities (0.8-2000 μm) in the photic zone of tropical to temperate sea regions. Then, we present two cases of symbioses (Blastodinium-Copepods and Symbiodinium-Tiarina) to illustrate both the difficulties encountered when trying to detect symbiotic relationships using metabarcoding data due to varying specificities of symbiotic relationships, but also the potential solutions offered by size-fractionated sampling to distinguish between the different stages of the life cycle of symbiotic organisms (free living and symbiotic stages). Finally, we propose a set of methods to improve the detection of symbioses by studying the co-occurrence of organisms in planktonic communities: we use the distribution of metabarcodes along size fractions ((piconano- (0.8-5 μm), nano- (5-20 μm), micro- (20-180 μm), and meso-plancton (180-2000 μm)) to distinguish likely free living organisms from those that have a symbiotic life style, and we compare the abundance of genetic groups constructed by clustering metabarcodes at different resolution levels, which allows us to detect interactions occurring above the species level and to evaluate their level of specificity.

Le succès évolutif des Cnidaires symbiotiques réside en grande partie dans leurs échanges trophiques établis avec les Dinoflagellés du genre Symbiodinium. Cependant, le réchauffement climatique global ainsi que les pollutions ont un impact fort sur les écosystèmes coralliens, notamment en conduisant à la rupture de la symbiose, phénomène appelé blanchissement. La compréhension des mécanismes qui régissent l’établissement, le maintien et la rupture de la symbiose est essentielle à la prévention des épisodes de blanchissement massif. Dans ce contexte, les objectifs de mon projet de thèse sont de caractériser les médiateurs chimiques de l’anémone de mer Anemonia viridis, de les localiser, et d’analyser leur réponse face à un stress. Parmi les composés caractérisés, les lipides et les bétaïnes sont les plus abondants et présentent une grande diversité. Certains sont transférés des symbiotes vers l’hôte. Des anémones de mer ont ensuite été traitées en laboratoire afin de provoquer la rupture de la symbiose et le blanchissement des individus. Une étude cinétique a été menée par une approche globale comparative identique à celle réalisée sur l’anémone symbiotique. Par ailleurs, une cartographie de l’évolution de composés clé a été réalisée par MALDI-MSI. La réponse au stress a été évaluée et a permis d’identifier des lipides de bétaïne et trois indicateurs lipidiques comme marqueurs de réponse précoce au stress. L’ensemble de ces résultats apporte de nouveaux éléments de réponse concernant le rôle des médiateurs chimiques clés dans le maintien de la symbiose, ainsi que leur influence sur sa rupture. / The ecological success of cnidarian-dinoflagellate symbiosis mainly relies on nutrient recycling. Environmental changes, such as global warming or pollution, often result to symbiosis breakdown, also called cnidarian bleaching. The understanding of mechanisms regulating the symbiosis establishment, maintenance and breakdown is essential to prevent massive bleaching phenomena. In this respect, my PhD project focused on the characterization of chemical mediators expressed in the sea anemone Anemonia viridis, their localization and their modulation by stress conditions. A comparative study was first conducted to characterize the chemical mediators and analyze their distribution within the symbiotic sea anemone. We described a great abundance and diversity of lipids in A. viridis tissues. From these results, we proposed possible transfers of FAs between the symbiotic partners. A thermal stress and a chemical stress have also been applied in laboratory-controlled conditions in order to induce symbiosis breakdown and bleaching of the sea anemones, in order to correlate A. viridis metabolome to its symbiotic status. A mapping of these metabolites has been performed by MALDI-MSI of tentacle cross-sections, as well as their evolution following stress. Some betaine lipids have thus been proposed as short-term indicators of stress. A. viridis stress response has also been evaluated with a lipidomic approach, and allowed to identify 3 lipid indicators of early stress response based on membrane fluidity markers. Overall, this study provides insight on key chemical mediators that may regulate the symbiosis maintenance, and may contribute to the symbiosis breakdown.

This study addressed the effects of salinity and pot size on the interaction between leguminous plant hosts and arbuscular mycorrhizal fungi in four pine rockland soils using a shade house trap-plant experiment. Little is known about the belowground diversity of pine rocklands and the interactions between aboveground and belowground biota – an increased understanding of these interactions could lead to improved land management decisions, conservation and restoration efforts. Following twelve weeks of growth, plants were measured for root and shoot dry biomass and percent colonization by arbuscular mycorrhizal fungi. Overall, arbuscular mycorrhizal fungi had positive fitness effects on the four legume species (Cajanus cajan, Chamaecrista fasciculata, Tephrosia angustissima and Abrus precatorius), improving their growth rate, shoot and root biomass; pot size influenced plant-fungal interactions; and percent colonization by arbuscular mycorrhizal fungi was influenced by soil type as well as salinity.

The stability of marine photosymbiotic holobionts has major implications for the future of coral reef communities. This study aims to describe the stability of the Red Sea giant clam holobiont over the duration of one year and during induced bleaching stress under laboratory thermal manipulations. Tridacnid clams of the species Tridacna maxima were sampled at three reef locations near the central Saudi coast of the Red Sea. Associated Symbiodinium of Red Sea giant clams have previously been described to be part of only Clade A, which suggests a strong specificity in the clam-algal partnership, but specific types and potential shifting of types within this clade have not been examined for giant clams. The results from this study confirm that tridacnid symbiont types shift over time and the change between three A1 types suggests a biological and functional significance of two undescribed A1 Symbiodinium types. Experimental bleaching shows that Red Sea giant clams, although exposed to rather hot temperatures naturally, will bleach at 34°C after two weeks, and severely bleached clams likely will not recover. During bleaching, Symbiodinium types shift as well, and shift more drastically than seasonal shifts during the year. This shifting may be an evolved characteristic of the giant clam to aid in surviving major changes in the environment. However, more research is needed to determine if these holobionts are capable of keeping up with the global forecast of warming in reef environments.

Coral reefs are the most diverse marine ecosystems of significant ecological and economic importance, globally. Increasing environmental stress imposed by global warming, ocean acidification and pollution has led to the continuous decline of coral reefs. For reefs to thrive and survive, they rely on the stable endosymbiosis between coral animal and photosynthetic algae. The fragile symbiotic relationship is dependent on a balanced metabolic exchange, which is easily disturbed by stress, consequently leading to the loss of the endosymbiotic algae - a process known as bleaching. Since corals energetically rely on the algae, the breakdown of symbiosis can have fatal consequences. However, the underlying molecular and cellular mechanisms of this symbiosis are thus far poorly understood. The small sea anemone Aiptasia has provided an experimentally tractable model organism, furthering our understanding on the function of symbiosis and hence, coral susceptibility and resilience to stress. Nonetheless, this model organism is comparatively young and therefore, requires innovative approaches as well as establishment and optimization of protocols. In this thesis, we applied transcriptomic, proteomic and epigenomic tools in Aiptasia, with the aim to assess the dynamics of symbiosis and thermotolerance. Heat stress studies, on Aiptasia's originating from geographically distinct regions, provided insight into the cnidarian-algae symbiosis mechanisms and the role of metabolic compatibility in symbiosis. Furthermore, findings elucidated that associating with thermotolerant algae can improve the cnidarian host's tolerance, potentially acting as a form of local adaptation. Finally, the role of epigenetic mechanisms in cnidarian symbiosis was investigated, by optimizing Chromatin Immunoprecipitation (ChIP) and establishing the genomic landscape of histone 3 lysine 9 acetylation (H3K9ac) in Aiptasia. These new results will enable progressing Aiptasia further as a model organism and thus, advance our understanding on the complex mechanisms of coral symbiosis.