Dissertação (mestrado) - Universidade Federal de Santa Catarina, Centro de Ciências Biológicas. Programa de Pós-Graduação em Biologia Vegetal / Made available in DSpace on 2012-10-20T18:06:06Z (GMT). No. of bitstreams: 1 200047.pdf: 5416566 bytes, checksum: 366692677a5796f5a722a5a189c5b201 (MD5) / Na Ilha de Santa Catarina são encontrados significativos ecossistemas de marismas, em especial na Enseada de Ratones, onde verificam-se densos bancos monotípicos de Spartina alterniflora Loisel. No presente trabalho foram avaliadas a variação da biomassa e da densidade da espécie neste estuário durante a primavera (2000) e outono (2001), bem como a cinética de decomposição da gramínea entre os meses de abril a novembro de 2001. Durante o período avaliado a marisma apresentou 569±128 hastes.m-2. No outono foram verificadas 648±225 hastes.m-2, sendo que destas 32,8% eram senescentes. Na primavera foram registradas 516±80 hastes.m-2, das quais 26,1% estavam em senescência. A média de fitomassa encontrada para a enseada de Ratones foi de 274±46gPS.m-2. Durante a primavera a fitomassa epígea foi de 326±25gPS.m-2 e 197±90gPS.m-2 no outono. Na primavera foi verificada a maior necromassa, tanto em termos absolutos quanto relativos. Durante o outono a fitomassa subterrânea foi muito superior à da fitomassa aérea, resultando em uma baixa relação massa hipógea/epígea. Os sedimentos da marisma de Ratones são orgânicos e de granulometria síltica-argilosa. A cinética de decomposição seguiu um modelo exponencial, e a meia-vida obtida para S. alterniflora foi de 153 dias para o peso seco, com um coeficiente de decomposição de 0,0045 e 52 dias para o peso seco sem cinzas, com um coeficiente de decomposição de 0,0068. O teor de nitrogênio agregado aos detritos, submetidos ao processo de decomposição, indica uma intensa atividade da micro e macrofauna associada a cadeia detritívora. A diversidade da macrofauna encontrada nos detritos de S. alterniflora confirmou sua importância na manutenção da biodiversidade estuarina da enseada de Ratones. Durante a colonização dos detritos de Spartina alterniflora pela macrofauna, houve decréscimo progressivo de crustáceos, paralelo ao acréscimo de outros grupos, principalmente oligoquetas. A variação percentual dos teores de carbono e nitrogênio verificados durante o processo de decomposição de S. alterniflora são indícios da importância da gramínea como fonte de compostos carbonáceos e nitrogenados para o estuário.

Phenotypic plasticity is the ability of a given genotype to exhibit different phenotypes in response to environmental variables, which can impact population level processes. Plasticity of ecologically-relevant traits is important to an organism’s environmental response; however, the underlying mechanisms of plasticity are largely unknown. Ecological epigenetics may offer mechanisms (e.g. DNA methylation) underlying phenotypic plasticity. Epigenetics can be defined as the underlying molecular mechanisms that allow one genotype to exhibit different phenotypes. Differential DNA methylation is one epigenetic mechanism that has been correlated with a number of ecologically-relevant traits; including, differential herbivory in Viola cazorlensis, spinescence in Ilex aquifolium, flower morphology in Linaria vulgaris, and fitness in Arabidopsis thaliana. The epigenetic correlations with traits found in these studies are interesting, but they are also partially confounded by a potential correlation between genetic and epigenetic variation. Teasing apart the correlation between genetic and epigenetic variation is one of the challenges within ecological epigenetics. This correlation has resulted in epigenetic variation being partitioned into three types by researchers: obligate, facilitated, and pure. Changes in obligate epigenetic variation are directly correlated with genetic variation. Changes in pure epigenetic variation are completely independent from genetic variation. Changes in facilitated epigenetic variation are partially dependent on genetic variation, but the outcome of the phenotype is context-dependent based on environmental conditions. Since our predictions about the outcome of phenotypic variation are driven largely by population genetics theories, which make no room for variation that operates in non-Mendelian ways, epigenetics research needs to utilize unique ways to tease apart the interaction between genetic and epigenetic variation where facilitated or pure epigenetic variation exists outside of the realm of population genetics theory. To address these issues, I performed a literature review and two research-based studies. In Chapter 1 I performed a literature review on the topic of population epigenetics addressing the correlation with genetic variation and recommending an extension to the Modern Synthesis to accommodate the non-Mendelian nature of DNA methylation. While population genetics has approximately 85-years of data to support it, epigenetics is beginning to show some of the limitations associated with predictions made using populations genetics models. One of these limitations is that population genetics as defined by the Modern Synthesis does not allow for violations of Mendelian genetics (i.e. random assortment and segregation of alleles). This limitation does not allow for phenotypic variation that is directly due to environmental conditions; however, recent ecological epigenetics data shows that this can, indeed, occur. Within this review I propose epigenetic questions that we should focus on at the population level, and I make recommendations for how to approach these questions in future studies. In the second and third research-based chapters, I investigated whether an independent component of epigenetic variation was correlated with habitat, while controlling for a correlation with genetic variation, for Spartina alterniflora and Borrichia frutescens, respectively. Previous work has shown that there is no consistent genetic response to environment in these species. I, therefore, hypothesized that there would be a significant epigenetic correlation with habitat instead. To test this hypothesis, I collected leaf samples from five different sites for each species on Sapelo Island, GA. Within each site I established three 10m transects (n=20 for each microhabitat) in low, middle, and high marsh microhabitats, respectively. Plants of both species exhibit different phenotypes for height (tall, intermediate, short, respectively) based on their location within the marsh. I screened AFLP and methylation-sensitive AFLP (MS-AFLP) markers for genetic and epigenetic variation, respectively. I used a variety of statistical tests to attempt to tease apart a potential correlation between genetic and epigenetic variation and found that when genetic population structure is controlled for, significant epigenetic population structure persists across all populations for S. alterniflora and within 3 of 5 populations for B. frutescens. These results suggest that regulation of certain genomic elements via DNA methylation may play an important role in dealing with environmental variables. To fully determine the significance of these findings, future studies should examine the interaction between environmentally-mediated epigenetic variation and gene expression to determine its importance to phenotypic plasticity and habitat differentiation. The body of work I produced supports that epigenetics may play a role in environmental response in populations within relatively small spatial scales. I used a combination of statistical tests to control for potential correlations with genetic variation which allowed me to see patterns that may normally be hidden. These findings expand upon traditional views of evolution by suggesting that environment can play a role in phenotypic variation, and other research supports that the variation due to epigenetic mechanisms can be inherited in future generations. Much of the current epigenetic research is based upon studies involving model species in highly controlled studies. While this research is been incredibly informative about some of the mechanisms underlying epigenetics, to fully understand the role of epigenetics to environmental response and evolution we must pair these data with field studies of non-model organisms. Only then will we begin to see the full role of epigenetics in organisms.

Cette étude vise à explorer les mécanismes de tolérance des plantes aux xénobiotiques organiques de la famille des HAPs (phénanthrène), à travers l’analyse de l’impact des évènements de spéciation par hybridation et duplication génomique (allopolyploïdie). Nous avons pour cela mené une approche comparative sur un modèle de spéciation allopolyploïde récente, constitué des espèces parentales hexaploïdes S. alterniflora et S. maritima, et de l’allopolyploïde S. anglica qui résulte de la duplication du génome de leur hybride F1 S. x townsendii. Une approche intégrative basée sur des analyses physiologiques et moléculaires nous a permis de montrer que chez Spartina l’hybridation et le doublement du génome augmentent la tolérance aux xénobiotiques. Le parent paternel S. maritima se montre particulièrement sensible au phénanthrène par rapport au parent maternel S. alterniflora. Différentes analyses transcriptomiques ont permis l’identification de novo de transcrits spécifiquement exprimés en condition de stress, et l’annotation des petits ARNs (miARNs, leurs gènes cibles, et siARNs) agissant en tant que régulateurs de l’expression des gènes et la régulation des éléments transposables. Les analyses d’expression différentielle en réponse au stress ont permis de générer un modèle de régulation (miARN/gènes cibles) en réponse aux HAPs, testé par validation fonctionnelle en système hétérologue chez Arabidopsis. Un travail exploratoire de profilage du microbiome de la rhizosphère des spartines exposées au phénanthrène a été réalisé pour préciser les mécanismes de dégradation des xénobiotiques dans l’environnement en vue d’une application dans les stratégies de remédiation verte. / We explored mechanisms involved in tolerance to organic xenobiotics belonging to PAHs (phenanthrene), in the context of allopolyploid speciation (hybrid genome duplication). We developed a comparative approach, using a recent allopolyploidization model including the hexaploid parental species S. alterniflora and S. maritima, and the allopolyploid S. anglica, which resulted from genome doubling of the F1 hybrid S. x townsendii. Integrative approach based on physiological and molecular analyses highlights that hybridization and genome doubling enhance tolerance to xenobiotics in Spartina. The paternal parent S. maritima exhibits higher sensitivity compared to the maternal parent S. alterniflora. Various transcriptomic analyses were performed, to identify de novo stress responsive transcripts, and to annotate small RNAs (miRNAs, their target genes, and siRNAs) involved in gene expression and transposable element regulations. Differential expression analyses in response to stress allowed us to develop a putative miRNA regulatory network (miRNA/target genes) in response to PAH, functionally validated in Arabidopsis as heterologous system. An exploratory profiling of Spartina rhizosphere microbiome exposed to phenanthrene was also performed to characterize environmental degradation abilities, in the perspective of optimizing green remediation strategies.

Herbivores and pathogens pose a consistent threat to plant productivity. In response, plants invest in structural and/or chemical defenses that minimize damage caused by these biotic stressors. In salt marshes along the Atlantic coast of the United States, a facultative mutualism between snails (Littoraria irrorata) and multiple species of fungi exert intense top-down control of the foundation grass species Spartina alterniflora. Since exposure to herbivores and pathogens are tightly coupled in this system, I investigated whether S. alterniflora utilizes chemical and/or structural defenses to deter both snails and fungi, and examined how plant defenses varied among S. alterniflora individuals and populations. I also assessed how other marsh plants prevent snails from establishing farms, and considered whether interspecific variation in plant chemical defenses influences marsh community structure. Initial experiments revealed that S. alterniflora chemical defenses inhibited L. irrorata and two fungi that snails commonly farm. A caging experiment determined that production of chemical defenses could not be induced in the presence of snails and fungi, nor relaxed in their absence. Through separations chemistry guided by ecological assays, I isolated two distinct classes of chemical defenses from short form S. alterniflora, one of which inhibited fungal growth and the other decreased plant palatability. In a community context, the chemical defenses produced by S. alterniflora were relatively weak compared to those of four other salt marsh plant species, which produced compounds that completely inhibited L. irrorata grazing and strongly hindered fungal growth in lab assays. Nutritional and structural differences among marsh plants did not influence feeding preferences, suggesting that plant secondary chemistry was the primary driver for food selection by snails. It appears that S. alterniflora produces weak chemical defenses that slow down or limit fungal growth and snail herbivory, and may compensate for tissue losses by producing new growth. In contrast, less abundant marsh plants express chemical defenses that completely inhibit fungal farming and deter snail grazing, but doing so may come at a cost to growth or competitive ability. As marsh dieback continues with rising herbivore densities and compounding abiotic stressors, the ecosystem services that salt marshes provide may be lost. Therefore, understanding how and under what conditions salt marsh plants resist losses to herbivores and pathogens will help predict which marsh communities are most likely to be threatened in the future. Initial experiments revealed that S. alterniflora chemical defenses inhibited L. irrorata and two fungi that snails commonly farm. A caging experiment determined that production of chemical defenses could not be induced in the presence of snails and fungi, nor relaxed in their absence. Through separations chemistry guided by ecological assays, I isolated two distinct classes of chemical defenses from short form S. alterniflora, one of which inhibited fungal growth and the other decreased plant palatability. In a community context, the chemical defenses produced by S. alterniflora were relatively weak compared to those of four other salt marsh plant species, which produced compounds that completely inhibited L. irrorata grazing and strongly hindered fungal growth in lab assays. Nutritional and structural differences among marsh plants did not influence feeding preferences, suggesting that differences in plant chemistry were the primary driver for food selection by snails. It appears that S. alterniflora produces weak chemical defenses that slow down or limit fungal growth and snail herbivory, and may compensate for tissue losses by producing new growth. In contrast, less abundant marsh plants express chemical defenses that completely inhibit fungal farming and deter snail grazing, but doing so may come at a cost to growth or competitive ability against S. alterniflora. As marsh dieback continues with rising herbivore densities and compounding abiotic stressors, the ecosystem services that salt marshes provide may be lost. Therefore, understanding how and under what conditions salt marsh plants resist losses to herbivores and pathogens will help predict which marsh communities are most likely to be threatened in the future.

Spartina anglica est une espèce exotique hybride qui peuple les zones humides littorales. Elle s’est installée dans le Bassin d’Arcachon au cours des années 1980, envahissant fortement les prés salés et les platiers vaseux préalablement occupés par, respectivement, Spartina maritima et Zostera noltei. Face aux inquiétudes suscitées par cette installation, cette thèse vise à comprendre, par une approche pluridisciplinaire, les mécanismes d’invasion et ses conséquences sur le milieu physique et sur les espèces végétales natives. L’objectif de ce travail est d’étudier l’occupation de niche par S. anglica et ses interactions avec deux espèces intertidales natives : S. maritima et Z. noltei.L’analyse d’images aériennes et satellitales a montré que, 30 ans après l’invasion, dans une zone densément peuplée par la Spartine native, la zone haute des prés salés a peu changé : la Spartine anglaise a occupé des niches vides et n’a pas remplacé la végétation native. Une expérience de transplantation réciproque et de mesures de biomasses confirment ce résultat, en montrant que l’espèce native offre une résistance à la colonisation de l’espèce exotique. L’expansion de la Spartine anglaise vers les replats de marée de l’intérieur du Bassin serait ainsi liée à sa capacité à tolérer les perturbations physiques, à sa forte plasticité de croissance en milieu oxygéné et riche en nutriments et à son comportement auto-facilitateur. Sa forte capacité d’ingénieur d’écosystèmes semble être liée à son système racinaire très développé, qui améliore l’aération des sols fortement anoxiques.Les effets de la colonisation par l’espèce exotique des zones intertidales basses à subtidales sur la Zostère naine sont importants sur le long-terme (dizaines d’années). En tant qu’ingénieur d’écosystèmes, la Spartine exotique favorise l’élévation du sol par sédimentation, entrainant une dessiccation du sédiment, peu favorable à la Zostère. Des mesures physiques au sein de patchs de l’espèce exotique suggèrent que l’élévation du sédiment est toutefois lente, surtout liée à une allocation de biomasse spécifique aux racines ainsi qu’à des rhizomes qui permettent de résister à l’érosion.En termes de gestion et de conservation des prés salés du Bassin d’Arcachon, ces résultats indiquent l’importance de limiter les perturbations physiques et les apports nutritifs qui pourraient rompre la résistance à l’invasion de la Spartine native. Ils supportent aussi l’idée que la Spartine anglaise pourrait être un allié robuste face à l’élévation du niveau de la mer. / Spartina anglica is a hybrid exotic cordgrass that inhabits coastal salt marshes. This species arrived in the Bay of Arcachon in the 1980s and since has importantly colonized the salt marshes and tidal flats formerly only occupied by the native Spartina maritima and Zostera noltei, respectively. This work aims at understanding, with an interdisciplinary perspective, the invasion mechanisms of this exotic cordgrass and the outcoming changes of its introduction in the Bay, both to the physical environment and to the native vegetation. Different approaches were considered in order to assess the niche occupancy by the exotic Spartina and its interactions with the native intertidal species, Spartina maritima and Zostera noltei.The analysis of aerial and satellite images has shown that, in about 30 years after the invasion, within a zone densely populated by the native Spartina, the global high marsh zone did not suffer significant changes with the arrival of the invasive species. Spartina anglica did not replace the existent marsh vegetation, it occupied empty niches along the intertidal area instead. Additionally, experimental works of cross transplantation and biomass measurements have corroborated that the native Spartina maritima offers resistance to the colonization by the exotic Spartina. It was also shown that the invasive occupies the same intertidal niche along the elevation and anoxic gradient than the native. The successful extension of Spartina anglica into the mudflat towards the inner Bay was related to its likely ability to tolerate physical disturbances, its strong growth plasticity in nutrient- and oxygen- rich patches and its self-facilitator behaviour. This latter trait is related to its strong ecosystem-engineering ability due to its prominent root system and consequent ability to ameliorate the oxygenation of highly anoxic soils.The main effect of the exotic Spartina species on the seagrass is related to its stronger ecosystem-engineering ability, favouring bed accretion up to levels that are not favourable to Z. noltei through enhancement of desiccation stress. However, hydrodynamic and altimetry measurements have shown that the process of bed accretion is slow and, due to the cordgrass’ specific preferential biomass allocation to roots, its efficiency is more linked to its resistance to erosion rather than sediment trapping.The results of this study provide relevant information for the definition of appropriate action and conservation strategies of marsh zones in the Bay of Arcachon, and in particular the importance of limiting physical disturbance and nutrient pollution that could disrupt the biotic resistance of the native cord grass. They also suggest a potentially important role of the exotic species in facing increasing Sea Level Rise.

Marsh vegetation is widely considered to offer protection against coastal storm damage, and vegetated flow has thus become a key area of hydrodynamic research. This study investigates the utility of simulated Spartina alterniora marsh vegetation as storm protection using an ADV measurement technique, and is the first to apply jet self-similarity analysis to characterize the overall mean and turbulent flow properties of a three-dimensional axisymmetric jet through a vegetated array. The mean axial flow of a horizontal axisymmetric turbulent jet is obstructed by three configurations of staggered arrays of vertical rigid plant stems. The entire experiment is repeated over five sufficiently high jet Reynolds number conditions to ensure normalization and subsequent collapse of data by nozzle velocity so that experimental error is obtained. All self-similarity parameters for the unobstructed free jet correspond to typical published values: the axial decay coefficient B is 5:8 +/- 0:2, the Gaussian spreading coefficient c is 85 +/- 5, and the halfwidth spreading rate eta_(1/2) is 0:093 +/- 0:003. Upon the introduction of vegetation, from partially obstructed to fully obstructed, B falls from 5:1+/- 0:2 to 4:2 +/- 0:2 and finally 3:7 +/-0:1 for the fully obstructed case, indicating that vegetation reduces axial jet velocity. Cross-sectionally averaged momentum for the unobstructed free jet is M=M0 = 1:05 +/- 0:07, confirming conservation of momentum. Failure of conservation of momentum is most pronounced in the fully obstructed scenario – M=M0 = 0:54 +/- 0:05. The introduction of vegetation increases spreading of the impinging jet. The entrainment coefficient alpha for the free jet case is 0.0575; in the fully obstructed case, alpha = 0:0631. Mean advection of mean and turbulent kinetic energy demonstrates an expected reduction in turbulence intensity within the vegetated array. In general, turbulent production decreases as axial depth of vegetation increases, though retains the bimodal profile of the free jet case; the fully vegetated case, however, exhibits clear peaks behind plant stems. Turbulent transport was shown to be unaffected by vegetation and appears to be primarily a function of axial distance from the jet nozzle. An analysis of rate of dissipation revealed that not only does the cumulative effect of upstream wakes overall depress the magnitude of spectral energy density across all wavenumbers but also that plant stems dissipate large anisotropic eddies in centerline streamwise jet flow. This study, thus, indicates that sparse emergent vegetation both reduces axial flow velocity and has a dissipative effect on jet flow. Typically, however, storm surge does not exhibit the lateral spreading demonstrated by an axisymmetric jet; therefore, the results of this study cannot conclusively support the claim that coastal vegetation reduces storm surge axial velocity.

Epiphytes are organisms attached to plants and are responsible for the majority of primary productivity in many aquatic systems. While epiphytes serve as a valuable food resource to herbivores, they may prove deleterious to the host plant by competing for light and nutrients, as well as increasing sheer stress. This study evaluated the impacts of nutrient additions, nitrogen and phosphorus, on the epiphytic algal community on Spartina alterniflora over the course of two growing seasons. Three nutrient treatments (N, P, and N+P) and one control treatment were placed in a salt marsh in the Tolomato River during the growing seasons of 2011 and 2012. To assess community development, we examined biomass, ash-free dry mass (AFDM), chlorophyll-a levels, cell counts, and community diversity by algal division. The nutrient additions did not significantly alter any of the measured parameters in either sampling year. However, the sampling month did have a significant (pa, and community composition. A total of 155 infrageneric taxa were identified. Biomass tended to be dominated by diatoms and red algae, while cyanobacteria were most abundant. In both years, biomass was highest in the spring with a second smaller pulse in the fall. Conversely, chlorophyll-a levels varied between the years and did not show the same monthly patterns as AFDM. A laboratory study subjecting S. alterniflora to the same nutrient additions also found no significant effects of increased nutrients, but did observe temporal changes in biomass and chlorophyll-a levels. Overall, epiphytic growth was not influenced by nutrient additions in this study suggesting that this and other similar salt marsh systems may be resilient to anthropogenic eutrophication. Instead, other factors, such as light and herbivory, likely played a key role in determining epiphytic algal growth and community composition.

The effect of cattle grazing on the abundance and distribution of vegetation, burrowing crabs (Uca rapax, Uca pugnax, and Sesarma cinereum), marsh periwinkles (Littoraria irrorata), horn snails (Cerithidea pliculosa), and salt marsh snails (Melampus bidentatus) was evaluated over four seasons (summer 2000, fall 2000, winter 2001, and spring 2001) in grazed and ungrazed treatments. A Galveston Island salt marsh adjacent to Snake Island Cove was sampled at five elevations, from the water's edge to the high tidal flats. Data were analyzed for statistical differences using a two-way ANOVA in SAS. Cattle grazing may affect the vegetation and macroinvertebrate communities in salt marshes through trampling and herbivory. Vegetation resources available to other herbivores are decreased by the direct consumption of plant material by cattle. Spartina alterniflora and Salicornia virginica heights were significantly greater in ungrazed treatments than grazed for every season in the edge, upper, and middle elevation zones. Total aerial vegetative cover was also reduced significantly in grazed treatments, with the greatest impact in the edge and upper marsh. In the ungrazed treatments, S. alterniflora stem density was significantly greater in edge elevations, while both S. virginica percent cover and stem density in the edge elevation was greater. Burrowing crab populations were greater in the upper marsh and edge habitat of ungrazed treatments, while significantly greater in most of the middle marsh habitats of the grazed treatment. Size of burrowing crabs was generally significantly greater in ungrazed treatments. Cerithidea pliculosa size decreased in grazed treatments, but population had an overall increase in grazed treatments. Littoraria irrorata had very few differences between treatments, although few specimens were found. Melampus bidentatus populations were too small to evaluate thoroughly. Macroinvertebrate populations could be used to assess the overall health of grazed salt marshes.

The effect of cattle grazing on the abundance and distribution of vegetation, burrowing crabs (Uca rapax, Uca pugnax, and Sesarma cinereum), marsh periwinkles (Littoraria irrorata), horn snails (Cerithidea pliculosa), and salt marsh snails (Melampus bidentatus) was evaluated over four seasons (summer 2000, fall 2000, winter 2001, and spring 2001) in grazed and ungrazed treatments. A Galveston Island salt marsh adjacent to Snake Island Cove was sampled at five elevations, from the water's edge to the high tidal flats. Data were analyzed for statistical differences using a two-way ANOVA in SAS. Cattle grazing may affect the vegetation and macroinvertebrate communities in salt marshes through trampling and herbivory. Vegetation resources available to other herbivores are decreased by the direct consumption of plant material by cattle. Spartina alterniflora and Salicornia virginica heights were significantly greater in ungrazed treatments than grazed for every season in the edge, upper, and middle elevation zones. Total aerial vegetative cover was also reduced significantly in grazed treatments, with the greatest impact in the edge and upper marsh. In the ungrazed treatments, S. alterniflora stem density was significantly greater in edge elevations, while both S. virginica percent cover and stem density in the edge elevation was greater. Burrowing crab populations were greater in the upper marsh and edge habitat of ungrazed treatments, while significantly greater in most of the middle marsh habitats of the grazed treatment. Size of burrowing crabs was generally significantly greater in ungrazed treatments. Cerithidea pliculosa size decreased in grazed treatments, but population had an overall increase in grazed treatments. Littoraria irrorata had very few differences between treatments, although few specimens were found. Melampus bidentatus populations were too small to evaluate thoroughly. Macroinvertebrate populations could be used to assess the overall health of grazed salt marshes.