Les nouvelles technologies de séquençage (NTS) offrent de nouvelles opportunités d'explorer les génomes et transcriptomes d'espèces polyploïdes. L'assemblage de transcriptomes et l'identification des copies de gènes dupliqués par allopolyploïdisation (homéologues) constituent cependant un véritable défi C ‘est plus particulièrement le cas dans un contexte de superposition de plusieurs évènements de polyploïdie et en l'absence de génome de référence diploïde. Les Spartines (Poaceae, Chloridoideae) représentent un excellent système pour étudier les conséquences à court terme des évènements d'hybridation et de polyploïdisation. En effet, S. maritima (hexaploïde) s'est hybridée à deux reprises avec S. alterniflora (hexaploïde) suite à son introduction récente en Europe, formant deux hybrides homoploïdes (S. x townsendii et S. x neyrautii). La duplication du génome de S. x townsendii a formé une nouvelle espèce allododécaploïde S. anglica (à la fin du XIXème siècle) qui a depuis envahi les marais salés de plusieurs continents. L'identification des gènes dupliqués au sein de S. anglica et de ses parents est importante pour la compréhension de son succès évolutif. Cependant, leurs niveaux de ploïdie, et l'absence d'espèce diploïde de référence chez les spartines nécessitent le développement d'outils adaptés. Dans ce contexte, nous avons développé et validé différents outils bioinformatiques permettant de détecter des polymorphismes afin d'identifier les différents haplotypes au sein de jeux de données NTS. Ces approches nous ont permis d'étudier l'hétérogénéité des domaines de l'ADN ribosomique 45S de S. maritima. Nous avons mis en évidence la perte de copies homéologues en conséquence de la diploïdisation en cours. Afin de développer les ressources transcriptomiques de ces espèces, cinq nouveaux transcriptomes de référence (110 423 contigs annotés pour les 5 espèces dont 37 867 contigs non-redondants) ont été assemblés et annotés. Les co-alignements des haplotypes parentaux et hybrides/allopolyploïdes nous ont permis d'identifier les homéo-SNPs discriminant les séquences homéologues. De plus, nous avons évalué la divergence entre les copies de gènes, identifié et confirmé les évènements de duplications récents au sein des Spartines. Au cours de cette thèse, nous avons également initié des approches de phylogénomique des spartines, qui permettront de préciser l'origine évolutive des copies dupliquées. / Next generation sequencing (NGS) technologies offer new opportunities to explore polyploid genomes and their corresponding transcriptomes. However, transcriptome assemblies and identification of homoeologous gene copies (duplicated by polyploidy) remain challenging, particularly in the context of recurrent polyploidy and the absence of diploid reference parents. Spartina species (Poaceae, Chloridoideae) represent an excellent system to study the short term consequences of hybridization and polyploidization in natural populations. The European S. maritima (hexaploid) hybridized twice with the American S. alterniflora (hexaploid) following its recent introduction to Europe, which resulted in the formation of two homoploid hybrids (S. x townsendii and S. x neyrautii). Whole genome duplication of S. x townsendii resulted in the fertile new allododecaploid S. anglica species (during the 19th century) that has now invaded saltmarshes on several continents. Identification of duplicated genes in S. anglica and its parental species is critical to understand its evolutionary success but their high ploidy levels require the development of adapted tools. In this context, we developed and validated different bioinformatics tools to detect polymorphisms and identify the different haplotypes from NGS datasets. These approaches enabled the study of the heterogeneity of the highly repeated 45S rDNA in S. maritima. In order to develop transcriptomic resources for these species, 5 new reference transcriptomes (110 423 annotated contigs for the 5 species with 37 867 non-redundant contigs) were assembled and annotated. Co-alignments of parental and hybrid/allopolyploid haplotypes allowed the identification of homoeoSNPs discriminating homoelogs. The divergence between duplicated genes was used to identify and confirm the recent duplication events in Spartina. Phylogenomic approaches on Spartina were also initiated in this thesis in the perspective of exploring the evolutionary history of the duplicated copies.

Le Dimethylsulfoniopropionate (DMSP) est une molécule à fort impact écologique couramment produite par le phytoplancton marin, mais très rarement chez les plantes à fleurs: seulement chez quelques genres (dont Spartina chez les Poacées). Bien que les étapes enzymatiques impliquées dans la voie de biosynthèse du DMSP soient connues chez les spartines, son origine ainsi que les gènes impliqués restent encore à découvrir chez les plantes. Cette étude s’est fixée pour objectif de contribuer à élucider les mécanismes à l’origine de cette fonction chez les spartines. Cette question a été appréhendée à travers différentes approches : biochimique, métabolomique, transcriptomique, génomique comparative et phylogénétique. Les résultats ont montré que la capacité à synthétiser le DMSP a une origine unique au sein du genre Spartina et se serait mise en place il y a 3-10 millions d’années. Cette capacité est intervenue chez l’ancêtre d’un des deux principaux clades (hexaploïde) de spartines, puis a été héritée chez toutes les espèces dérivant de ce clade (hexaploïdes à dodécaploïdes). Les espèces de l’autre clade (tétraploïde) et leurs descendants (quel que soit leur niveau de ploïdie) n’accumulent pas de DMSP. En utilisant les génomes séquencés des espèces de Poacées ainsi que les ressources génomiques et transcriptomiques disponibles chez les spartines, les gènes candidats intervenant dans les 4 étapes de la voie de biosynthèse proposée dans la littérature ont été explorés. L’identification des gènes intervenant dans les deux étapes intermédiaires, supposées spécifiques de la capacité de synthèse du DMSP représente un véritable défi dans la mesure où seules des activités enzymatiques putatives ont été proposées à ce jour (sans connaissance des enzymes spécifiques ni de leur séquence protéique). Nous avons pu identifier une série de gènes candidats pour chacune des deux fonctions concernées (décarboxylase et amine oxydase), comparer leur niveau de transcription entre les espèces DMSP+ et DMSP-, et prédire leur localisation cellulaire. De plus, des analyses d’activités enzymatiques ont permis de formuler de nouvelles hypothèses et pistes de recherches sur l’émergence de cette nouvelle voie de biosynthèse chez les spartines. / Dimethylsulfoniopropionate (DMSP) is an ecologically important molecule produced by most marine phytoplankton species, but very rarely by flowering plants: only in a few genera (including Spartina in Poaceae). Despite the different enzymatic steps involved in DMSP biosynthesis are well known, the origin of the function and the genes encoding the different enzymes are yet to be discovered. To explore the evolutionary mechanisms involved in the DMSP accumulation in Spartina, we used various approaches, including biochemical analyses, metabolomics, transcriptomics, comparative genomics and phylogenetics. Notably, we demonstrate that the ability to synthesize DMSP evolved once in the Spartina genus, sometimes 3-10 million years ago. This functional innovation occurred following the emergence of the hexaploid clade, and was inherited by all Spartina species deriving from this hexaploid ancestor. Spartina species belonging to the tetraploid clade and their deriving species do not accumulate DMSP (whatever their ploidy level). Using Poaceae sequenced genomes as well as Spartina genomic and transcriptomic resources obtained in our laboratory, candidate genes involved in the four different enzymatic steps of the DMSP biosynthesis pathway were searched. Identifying genes involved in the intermediate (2nd and 3rd) steps that are specific to this pathway was particularly challenging as only putative enzymatic activities have been proposed so far (corresponding protein sequences and genes are unknown). A set of candidate genes potentially involved in these two steps (with decarboxylase and amine oxydase activities) were identified and their transcription levels were compared among DMSP producing (DMSP+) and non-producing (DMSP-) Spartina species. Their putative cellular localization was also predicted. Moreover, enzymatic activity assays open new hypotheses and research perspectives regarding this enigmatic biosynthesis pathway in Spartina.

The Dee estuary, one of the most important British estuaries in terms of size and conservation value, has been subject to extensive colonisation and development of intertidal mudflats by salt marsh vegetation. In the last century, acceleration of this process has been attributed to the ability of Spartina anglica C.E. Hubbard to colonise bare sediment. The research in this thesis aims to investigate the ecological patterns and processes involved in the development of salt marsh vegetation. These have been examined using a large-scale approach involving remote sensing techniques and a small-scale approach to examine ecological processes at the level of the individual plant and species. Large-scale temporal patterns in the distribution were investigated by analysing a sequence of monochrome aerial photographs dating from 1955 to 1997. At the marsh apex, initial rapid colonisation was followed by a decreased rate of expansion and a reduction in the pioneer zone. This suggested a steepening of the marsh elevation gradient, which is interpreted as the marsh approaching its natural limit of expansion. The rate of salt marsh expansion was consistent across the time sequence for the second target area, a cross-section of the marsh gradient, but with S. a«g/zca-dominated colonisation of mudflats changing to colonisation by a pioneer community co-dominated by S. anglica and Salicornia europaea. Large-scale spatial distribution patterns were further investigated using multispectral remote sensing data from 1997. Radiometric data were used to define the spectral characteristics of the major types of salt marsh vegetation. Airborne Thematic Mapper data were used to classify the reflectance data from the whole marsh to determine the spatial distribution of plant communities based on their spectral characteristics. Mapping of these communities provided a baseline that will be a useful tool for future management of the salt marsh. An experimental approach was used to examine the role of abiotic and biotic factors on the growth and interactions between S. anglica and Puccinellia maritima (Huds.) Parl. In two series of competition experiments, P. maritima exerted a one¬way effect over S. anglica. The intensity of this interaction was increased in environmental conditions favourable to P. maritima, and was greater in terms of above-ground than below-ground biomass. In both experiments, S. anglica exhibited a disproportionate reduction in below-ground competitive interaction in abiotic conditions less favourable to P. maritima. A corresponding increase in rhizomes suggested that this is a potential mechanism by which S. anglica may evade competitive neighbours at low marsh elevations. An appreciation of the importance of scale has led to a multi-scaled and holistic view of the ecological process of salt marsh colonisation and development. Integration of both large and small-scale approaches has provided valuable information on the ecological patterns and processes, and has important implications for current and future management of salt marsh in the Dee estuary.

The interactions of sulfate-reducing bacteria and Spartina alterniflora marsh grass have been established using a simulated salt marsh system and these interactions have been quantified using geochemical and molecular tools. Plant activities have a direct influence on mercury methylators and therefore control mercury transformation in the environment. Biogeochemical data show that sulfate and sulfide profiles change seasonally due to plant growth and senescence. Spartina alterniflora impact the two drivers for sulfate and sulfide transformation. The community of sulfate-reducing bacteria serve as the anaerobic driver and transform sulfate to sulfide (sulfate reduction). Sulfate-reducing bacteria have been identified as the principal methylators of mercury (Andersson, et al., 1990; Compeau and Bartha, 1985; Compeau and Bartha, 1984; Blum and Bartha, 1980; Gilmour and Capone). The aerobic driver is dissolved oxygen present in both porewater and plant root exudates, which transform sulfide back to sulfate (sulfide oxidation). Sulfate is not limiting in the vegetated sediment, even at the lower depths. Therefore, although sulfate reduction rates were high when plant activity was high, oxidative processes were also significant in the upper 4-cm of the sediment. In addition, demethylation of methylmercury to ionic Hg(II) in the porewater can occur through oxidative processes (Oremland et al., 1991). Therefore, the significance of sulfide oxidation may have strong implications for methylmercury demethylation in our marsh system.

Thesis (M.S.)--University of North Carolina at Wilmington, 2003. / Includes bibliographical references (leaves : [26]-29).

Thesis (M.E.S.)--Evergreen State College, 2006. / Title from title screen viewed (3/30/2009). Includes bibliographical references (leaves 40-45).

The primary production of Spartina maritima, the dominant macrophyte of the intertidal salt marshes of the Swartkops estuary, was determined for inclusion into the proposed ecosystem model. Several methods for measuring net production devised for North temperate Spartina species were used, as no single method was considered reliable for the local species. In addition, a new method was devised to take into account the aseasonal growth behaviour of S. maritima . Most energy for growth appears to be directed into leaf production, rather than shoot growth. Live net production values were 523-680 g m⁻²‚ yr ⁻¹, which are generally lower than estimates of N. American Spartina species. Total Live production of S. maritima for the whole Swartkops estuary was 495,6 x I0³kg yr ⁻¹, which is an estimation of potential food resources. Formation of S. maritima detritus by decomposition was significantly related to air and water temperatures. Thus detritus production showed a wide seasonal variation about a mean of 374 g m⁻² yr⁻¹. The total S. maritima detritus production of 307,5 x I0³kg for the whole Swartkops estuary was determined as an estimate of available food resources. Export of detrital material from Spartina marshes to estuarine waters was negligible. Even during a maximal Equinoctial tide, only 6,26 dry g m⁻² detritus was exported from the creek catchment area of Spartina stands. This study has shown that concepts evolved for North temperate estuaries should be carefully considered before being applied to local situations, particularly in view of the relatively low, aseasonal production of S. maritima and the negligible contribution of its detritus to estuarine waters. Furthermore, it is essential that utilisation of primary production by secondary producers be determined before the function of the estuarine ecosystem may be understood

archives@tulane.edu / During the Deepwater Horizon (DWH) oil spill in 2010, approximately 0.5 billion liters (3.1 million barrels) of oil were released into the northern Gulf of Mexico during the largest marine oil spill in history . A significant portion of the released oil was weathered into residues by physical, photochemical, and biological processes prior to landing on 1773 km of coastline, including 754 km of marsh shoreline in Louisiana. Researchers endeavored to describe effects of oil residues in the soil on salt marsh organisms and communities. Many studies focused on two pillars of salt marsh ecology: the microbial communities through which a large portion of the salt marsh food web is connected and Spartina alterniflora, a foundational species of Gulf Coast salt marshes. In this dissertation I describe how cryptic, or difficult to observe, elements of salt marsh ecology, like microbial communities and plant genetics, respond to oil residues in the environment. Using a suite of field, growth chamber, and greenhouse experiments I show that these microbial communities are difficult to characterize and may respond to other factors more strongly than they do to oil residues. I present evidence that the plant is resilient to oil in the environment, and changes in its microbiome, but exerts a measurable influence on the biodegradation of oil residues and the microbiome in the soil. This dissertation provides a greater understanding of the complexity of the salt marsh response to an oil spill. / 1 / Stephen K. Formel

Les Spartines jouent un rôle écologique majeur sur les marais salés. Elles représentent un excellent modèle pour appréhender les conséquences écologiques de la spéciation par hybridation et polyploïdie dans le contexte d'invasion biologique. On s'intéresse plus particulièrement, à l'hybridation récente entre une espèce hexaploïde d'origine américaine Spartina alterniflora et une espèce hexaploïde européenne S. maritima ayant donnés deux hybrides F1 (S. x townsendii et S. x neyrautii) et la nouvelle espèce envahissante allododécaploïde (S. anglica). Les nouvelles technologies de séquençage haut-débit facilitent l'exploration de ces génomes peu connus. L'assemblage et l'annotation d'un transcriptome de référence ont permis d'annoter 16 753 gènes chez les spartines hexaploïdes et d'identifier des gènes d'intérêts écologique et évolutif. Une sélection de ces gènes a ensuite été analysée à travers une étude d'expression par PCR quantitative sur les populations naturelles des 5 espèces du complexe. Les résultats ont permis de mettre en évidence une expression homogène intra-populations mais une grande variabilité entre les espèces. L'analyse du génome des Spartines a ciblé prioritairement le développement de ressources génomiques concernant l'espèce S. maritima pour l'analyse des compartiments codant et répété à l'aide de séquençage d'une banque BAC et d'un run de pyroséquençage d'ADN génomique. Les analyses ont permis d'évaluer une proportion d'éléments répétés représentant près de 30% du génome. Les données générées ont alors été comparées avec les génomes séquencés phylogénétiquement proches et ont permis de premières comparaisons entre les spartines et les autres Poaceae. / Spartina species play an important ecological role on salt marshes. They represent an excellent system to study the ecological consequences of hybrid and polyploid speciation in biological invasion contexts. In this study, we examined the effects of hybridization between the hexaploid American-native species Spartina alterniflora and the European species S. maritima, that gave rise to two F1 hybrids (S. x townsendii in England et S. x neyrautii in France) and the new invasive allododecaploid species (S. anglica). Next-generation sequencing technologies offer new perspectives to explore these previously poorly known genomes. The assembly of a reference transcriptome (from 454 Roche pyrosequencing) allowed annotation of 16,753 genes in hexaploid Spartina and identification of ecologically and evolutionary important genes. Expression levels of a subset of these genes were analyzed by quantitative PCR in Spartina natural populations. The results indicate intrapopulation homogenous expression but extreme variability between species. The European S. maritima beneficiated from genomic resource development through a BAC library and one pyrosequencing run. Our analyses estimated the relative proportions of repetitive sequences as about 30% and have identified the main transposable element families Data generated were also compared to closely related sequenced species and provided the first insights into the evolution of Spartina genomes in the Poaceae family.

Aboveground plant community dynamics in the oligohaline marsh at Big Branch Marsh National Wildlife Refuge, Louisiana, USA, were assessed in response to nutrient loading (3 N x 3 P treatments) and disturbance (both planned lethal disturbance and stochastic tropical storm/hurricane disturbance). Sampling was conducted seasonally from April 2004 to September 2006. Spartina patens and Schoenoplectus americanus are co-dominant plant species in this marsh. Low N-loading additions resulted in increased S. patens cover. However, increased N loading did not result in a shift in plant community composition despite S. americanus consistently having higher leaf tissue N than S. patens. Our results indicate that S. americanus may be more resilient than S. patens to disturbances that do not increase marsh surface elevation. Hurricane Katrina deposited significant amounts of sediment into remaining plots (August 29, 2005). By 2006, this disturbance resulted in a significant increase in both species richness and S. patens cover.