Abstract The loss of tropical and subtropical rainforest biodiversity due to increasing anthropogenic pressure lends urgency to understanding the processes which drive species coexistence. Without an understanding of how species are distributed across the landscape and how species assemblages change through time, we cannot derive appropriate management regimes for their persistence. This thesis examines the role of deterministic drivers of spatial and temporal dynamics of Australian rainforests and investigates the potential impacts of a changing climate on Australian rainforests. The findings from three studies are presented in four chapters which examine floristic turnover in situ and at catchment, regional and continental scales. Compositional turnover in tropical rainforest following the passage of a category three cyclone was examined both at five years’ post-cyclone recovery and in the context of local and regional spatial turnover. After five years, the forest remained in an active state of recovery with an approximate 30% increase in stems, 5% decrease in basal area and a 16% increase in species richness. Local spatial turnover suggests differential impacts of cyclones over even short distances and overall, a high degree of temporal stability in these rainforests, despite the impact of frequent catastrophic disturbances. Compositional turnover in subtropical rainforest along steep moisture and temperature gradients was investigated and described along an altitudinal transect in subtropical rainforest. The identification of significant modelled climatic and mapped soil variables suggests that moisture stress is an important driver of floristic turnover in these forests. Existing high levels of turnover across tree assemblages from low to mid elevations in subtropical rainforest were identified. Such turnover is greatly reduced at higher elevations. With increasing atmospheric temperatures, the cloud cap is expected to rise and we predict that subtropical rainforest communities which currently sit at the level of the cloud base (800-900m) will experience increasing in situ floristic turnover. Our findings agree with predictions for cloud forests elsewhere: high elevation endemic species will face an increasing risk of extinction as mesic climatic envelopes move upslope out of reach. Baseline data from this study will be used as a benchmark against which to formulate and test hypotheses for climate induced floristic and structural shift. It is also acknowledged that monitoring floristic turnover as a surrogate of shifting climatic envelopes may be confounded both by a lack of knowledge regarding the underlying turnover rates of rainforest communities and by the disparity in temporal scales of tree community turnover and accelerating anthropogenic climate change. Finally, generalized dissimilarity modelling is utilised to combine disparate biological survey data and remotely sensed environmental data to investigate the determinants of floristic turnover at the regional scale. Generalized dissimilarity modelling identified four environmental predictors of β-diversity in subtropical rainforest, all closely linked with moisture stress: radiation of the driest quarter, precipitation of the driest period, slope and aspect. Ten land classes were identified and mapped for the Mt Warning Caldera and may act as appropriate management units for future climate change planning within the region. This thesis has identified a potential threat to the biodiversity of Australian rainforests under a changing climate. Increasing levels of evapotranspiration, moisture stress and an increased return rate and intensity of disturbance are predicted to lead to the upslope movement of species ranges, increasing levels of in situ floristic turnover, and will likely result in the emergence of novel rainforest communities not present under current conditions. The potential for anthropogenic climate change to impact upon native vegetation communities has emphasised the need for the continuation and expansion of monitoring programs and the development of dynamic management regimes.

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Submitted by Socorro Pontes (socorrop@ufersa.edu.br) on 2017-05-18T15:15:57Z No. of bitstreams: 1 RogérioTVF_DISSERT.pdf: 779741 bytes, checksum: 9814a6c7549bf62e7bc2094c8b14cdb0 (MD5) / Made available in DSpace on 2017-05-18T15:15:57Z (GMT). No. of bitstreams: 1 RogérioTVF_DISSERT.pdf: 779741 bytes, checksum: 9814a6c7549bf62e7bc2094c8b14cdb0 (MD5) Previous issue date: 2013-12-19 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / Here, we quantified the patterns of change in the similarity of the fish fauna of the Upper Paraná ecoregion, caused by the introduction of non-native species and anthropogenic factors, such as the construction of dams and the elimination of a biogeographic barrier. Additionally, we evaluated the importance of changes in rates of turnover and richness species in homogenization/differentiation dynamics. For the study, we mapped the spatial distribution of fish species through occurrence data georeferenced of Brazilian zoological museums. To evaluate temporal changes in the composition of the fish fauna, the data with the distribution of the species were divided into two periods: historical period composed entirely of native species, and the contemporary period, consisting of historical fauna plus non-native species. Changes in similarity patterns between fish assemblages were quantified using the Jaccard dissimilarity index to the historical and contemporary periods. To evaluate the influence of the non-native richness species, number of dam and distance to the Itaipu Dam on changes of similarity, we performed simple and partial Mantel tests. The results showed that the fish fauna has become more dissimilar over time, due to increases in turnover rates and addition of species. Furthermore, factors related to the heterogeneity of the basins and propagules pressure after removal of a biogeographical barrier has determined the patterns of changes in the similarity of the fish fauna / Nesse estudo foram quantificados os padrões de mudança na similaridade da fauna de peixes da ecoregião do alto Paraná, produzidas pela introdução de espécies não-nativas e de fatores antropogênicos, como a construção de barragens e a eliminação de uma barreira biogeográfica. Adicionalmente, foi avaliada a importância de mudanças nas taxas de turnover e de riqueza nas mudanças de similaridade das assembleias de peixes. Para realizar o estudo, a distribuição espacial de espécies de peixes de dez bacias de drenagem do alto Paraná foi mapeada através de dados de ocorrência geo-espacializados tombados em museus zoológicos de instituições brasileiras. Para avaliar as mudanças temporais na composição da fauna de peixes, os dados com as distribuição das espécies foi divido em dois períodos: período histórico, composto somente por espécies nativas, e período contemporâneo, composto por espécies nativas mais não-nativas. Os padrões de similaridade entre as assembleias de peixes para os períodos histórico e contemporâneo foram quantificados através do índice de dissimilaridade de Jaccard. As mudanças na similaridade entre assembleias foi calculada através da diferença entre as similaridades contemporâneas e históricas. Para avaliar os efeitos da riqueza de espécies não-nativas, número de barragens e área das bacias, e a distância das bacias até a barragem de Itaipu foram utilizados testes de Mantel simples e parciais. Os resultados demostraram que a fauna de peixes tem se tornado mais dissimilar ao longo do tempo, em função de aumentos nas taxas de turnover e de adição de espécies. Além disso, fatores relacionados à heterogeneidade das bacias e da pressão de propágulos após a eliminação de uma barreira biogeográfica tem determinado os padrões de mudanças na similaridade da fauna de peixes / 2017-05-18

Les champignons mycorhiziens arbusculaires (CMA) appartiennent au phylum Glomeromycota. Ces champignons forment une association symbiotique (obligatoire pour les champignons) avec plus de 80 % des espèces de plantes vasculaires, incluant la plupart des plantes cultivées. Cette symbiose mycorhizienne arbusculaire, très répandue dans la nature, a été retrouvée dans presque tous les écosystèmes terrestres aussi bien dans des déserts chauds et froids que dans des forêts tropicales ou tempérées. L’emploi d’outils de biologie moléculaire et des fossiles ont permis d’estimer la date de l’origine de la symbiose mycorhizienne arbusculaire à environ 450 millions d’années avant notre ère. Cette date coïncide avec l’apparition des premières plantes terrestres primitives. Il existe plusieurs types de mycorhizes impliquant différents champignons et différentes plantes hôtes. Ces différents faits suggèrent que les plantes vasculaires et les champignons mycorhiziens à arbuscules ont co-évolué, et que les Glomeromycota ont influencé la capacité des plantes à coloniser le milieu terrestre. Plusieurs études ont montré que les contaminants organiques peuvent influer négativement cette relation mutuellement bénéfique qu'entretiennent la plante et le champignon conduisant à une diminution de la croissance du CMA mais aussi à une modification des interactions au sein de la communauté de CMA elle-même. Ainsi, mon projet de maîtrise vise à quantifier la diversité mycorhizienne arbusculaire de deux espèces de plante Eleocharis obtusa et Panicum capillare qui poussent dans un bassin hautement contaminé par des hydrocarbures pétroliers de façon très hétérogène et étudier les structures des communautés des CMA dans des échantillons de sol rhizosphérique et de racines de celles-ci. L'un des résultats important de mon étude est la découverte d’une très grande diversité des CMA associés à E. obtusa et P. capillare dans ce milieu contaminé. En effet, pas moins de 26 unités taxonomiques opérationnelles (OTU) de champignons mycorhiziens à arbuscules ont été recensés. La quasi-totalité des familles de Glomeroycota sont représentées à l'exception de Ambisporaceae, Geosiphonaceae et Pacisporaceae. Ainsi, le genre Diversispora domine la communauté des CMA par son abondance relative, cependant le genre Claroideoglomus est le plus abondant des genres des CMA. Ensuite, mon projet a déterminé l'influence de la plante hôte sur la composition de la communauté de CMA. D'après l'analyse de la diversité alpha, les plantes présentent une structure de diversité différente. Les valeurs de Local Contributions to beta Diveristy (LCBD) élevées étaient souvent liées à un site avec un grand nombre de taxons de CMA. En utilisant une analyse en composante principale (ACP), j’ai constaté que les échantillons récoltés en 2011 auraient sensiblement la même composition en OTU. J’ai pu observer également une variation de la communauté des OTU de CMA d'une année à l'autre pour les plantes. La rhizosphère des plantes récoltées la même année avait une communauté d'OTU similaire globalement, pourtant au niveau racinaire, j’ai observé une spécificité chez des certains OTU. Cette étude fournit une vue d’ensemble de la diversité des CMA associés à des végétaux localisés dans les sédiments très polluées. Elle suggère aussi que les CMA peuvent être des candidats microbiens potentiellement importants dans la restauration des sols contaminés par le pétrole. / The arbuscular mycorrhizal fungi (AMF) belong to phylum Glomeromycota, a group of early divergent fungal lineage. These fungi form a mutualistic symbiotic association with more than 80% of vascular plant species, including most important crops. The arbuscular mycorrhizal symbiosis is widespread and has been found in almost all terestrial ecosystems on earth such as hot and cold deserts, as well as tropical and temperate forests. The use of molecular biology tools and fossil records dated back the origin of arbuscular mycorrhizal symbiosis to 460 million years ago, which coincides with the emergence of terrestrial plants. There are several types of mycorrhizas depending on fungal groups and host plants. It has been suggested that vascular plants and AMF have co-evolved and that Glomeromycota helped plant ancestors to colonize the land. It has been reported that organic contaminants can negatively impact this mutually beneficial symbiosis between plant and fungi reducing the growth of the AMF and changing the structure of AMF communities. The objective of my master project was to determine the diversity of arbuscular mycorrhizal fungi associated with two plant species, Eleocharis obtusa and Panicum capillare, which spontaneously growing a highly petroleum hydrocarbons contaminated basin with an heterogeneous pattern of contamination, and to describe the structures of their communities in their rhizosphere soils and roots. My results revealed an unexpected high diversity of AMF OTUs associated with two plant species. Indeed, we identified 26 OTUs of AMF. This diversity covered the most important families of Glomeroycota except Ambisporaceae, Geosiphonaceae and Pacisporaceae. Genus Diversispora dominated the AMF community by its relative abundance, however the genus Claroideoglomus was the most represented in the samples. My study determined the influence of the host plant on the composition of the AMF community. Based on the analysis of the α diversity, we found that the rhizospheric soil and root samples showed different community structures between the two plants species. β diversity analysis showed that high Local Contributions to β Diveristy (LCBD) values (high uniqueness of species composition) were often linked to the sample with a large number of AMF taxa. Using a principal component analysis (PCA), we found that the samples collected in 2011 have approximately the same composition of OTUs. It is likely that a turnover of AMF OTU and 4 plants may occur from one year to another. This study provides an overview of the diversity of AMF associated with plants located in heavily polluted sediments. It also suggests that AMF may be potentially important microbial candidates in the remediation of oil-contaminated soils.

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La Sindrome da Affaticamento Cronico/Encefalomielite Mialgica (CFS/ME), è una grave malattia multisistemica caratterizzata da anomalie immunologiche e disfunzioni del metabolismo energetico. Recenti evidenze suggeriscono l’esistenza di una forte correlazione tra disbiosi e condizione patologica. La presente ricerca ha analizzato la composizione del microbiota intestinale ed orale in pazienti con CFS/ME rispetto a controlli sani e ha determinato se eventuali differenze osservate potrebbero essere utili in futuro per l'identificazione di biomarcatori diagnostici. La composizione batterica fecale e salivare dei pazienti con CFS/ME è stata studiata mediante sequenziamento Illumina degli ampliconi del gene 16S rRNA. Il microbiota fecale dei pazienti con CFS/ME ha mostrato una significativa riduzione di Lachnospiraceae, in particolare di Anaerostipes, rispetto ai gruppi di soggetti senza CFS/ME e un incremento di Phascolarctobacterium faecium e unclassified Ruminococcus. Bacteroides vulgatus, unclassified Bacteroides, Bacteroides uniformis e unclassified Barnesiella sono risultati significativamente più abbondanti nei pazienti con CFS/ME. Il microbiota orale dei pazienti con CFS/ME ha mostrato un aumento significativo di Rothia dentocariosa. Il profilo metabolico fecale di un sottogruppo di pazienti con CFS/ME ha mostrato un aumento complessivo di SCFA e di derivati dell'indolo rispetto ai gruppi non CFS/ME, suggerendo un aumento dei processi di fermentazione. I nostri risultati supportano l'ipotesi autoimmune per la CFS/ME e se saranno confermati da studi più ampi, le differenze rilevate nei profili microbici dei pazienti CFS/ME potrebbero essere utilizzate come markers per una diagnosi più accurata e per lo sviluppo di strategie terapeutiche specifiche. / The Chronic Fatigue Syndrome/Myalgic Encephalomyelitis (CFS/ME), is a severe multisystemic disease characterized by immunological abnormalities and dysfunction of energy metabolism. Recent evidence suggest that there is a strong correlation between dysbiosis and pathological condition. The present research investigated the composition of the intestinal and oral microbiota in CFS/ME patients in comparison to healthy controls and determined whether any observed differences could be useful for the identification of diagnostic biomarkers. The fecal and salivary bacterial composition in CFS/ME patients was investigated by Illumina sequencing of 16S rRNA gene amplicons. The fecal microbiota of CFS/ME patients showed a significant reduction of Lachnospiraceae, particularly Anaerostipes, compared to the non-CFS/ME groups, and an increase of Phascolarctobacterium faecium and unclassified Ruminococcus. Bacteroides vulgatus, unclassified Bacteroides, Bacteroides uniformis and unclassified Barnesiella resulted significantly more abundant in CFS/ME patients. The oral microbiota of CFS/ME patients showed a significant increase of Rothia dentocariosa. The fecal metabolic profile of a subgroup of CFS/ME patients revealed an overall increase of SCFAs and indole derivatives compared to the non-CFS/ME groups, suggesting an increase in the fermentation processes. Our results support the autoimmune hypothesis for CFS/ME condition and if confirmed by larger studies, the differences detected in the microbial profiles of CFS/ME patients may be used as markers for a more accurate diagnosis and for the development of specific therapeutic strategies.

Grasslands are one of the most important ecosystems on Earth, covering approximately one-third of the Earth’s surface. Grassland biodiversity is important as many services provided by such ecosystems are crucial for the human economy and well-being. Given the importance of grasslands ecosystems, in recent years research has been carried out on the potential to monitor them with novel remote sensing techniques. Improved detectors technology and novel sensors providing fine-scale hyperspectral imagery have been enabling new methods to monitor plant traits (PTs) and biodiversity. The aims of the work were to study different approaches to monitor key grassland PTs such as Leaf Area Index (LAI) and biodiversity-related traits. The thesis consists of 3 parts: 1) Evaluating the performance of remote sensing methods to estimate LAI in grassland ecosystems, 2) Estimating plant biodiversity by using the optical diversity approach in grassland ecosystems, and 3) Investigating the relationship between PTs variability with alpha and beta diversity for the applicability of the optical diversity approach in a subalpine grassland of the Italian Alps To evaluate the performance of remote sensing methods to estimate LAI, temporal and spatial observations of hyperspectral reflectance and LAI were analyzed at a grassland site in Monte Bondone, Italy (IT-MBo). In 2018, ground temporal observations of hyperspectral reflectance and LAI were carried out at a grassland site in Neustift, Austria (AT-NEU). To estimate biodiversity, in 2018 and 2019 a floristics survey was conducted to determine species composition and hyperspectral data were acquired at two grassland sites: IT-MBo and University of Padova’s Experimental Farm, Legnaro, Padua, Italy (IT-PD) respectively. Furthermore, in 2018, biochemistry analysis of the biomass samples collected from the grassland site IT-MBo was carried out to determine the foliar biochemical PTs variability. The results of the thesis demonstrated that the grassland spectral response across different spectral regions (Visible: VIS, red-edge: RE, Near-infrared: NIR) showed to be both site-specific and scale-dependent. In the first part of the thesis, the performance of spectral vegetation indices (SVIs) based on visible, red-edge (RE), and NIR bands alongside SVIs solely based or NIR-shoulder bands (wavelengths 750 - 900 nm) was evaluated. A strong correlation (R2 > 0.8) was observed between grassland LAI and both RE and NIR-shoulder SVIs on a temporal basis, but not on a spatial basis. Using the PROSAIL Radiative Transfer Model (RTM), it was demonstrated that grassland structural heterogeneity strongly affects the ability to retrieve LAI, with high uncertainties due to structural and biochemical PTs co-variation. In the second part, the applicability of the spectral variability hypothesis (SVH) was questioned and highlighted the challenges to use high-resolution hyperspectral images to estimate biodiversity in complex grassland ecosystems. It was reported that the relationship between biodiversity (Shannon, Richness, Simpson, and Evenness) and optical diversity metrics (Coefficient of variation (CV) and Standard deviation (SD)) is not consistent across plant communities. The results of the second part suggested that biodiversity in terms of species richness could be estimated by optical diversity metrics with an R2 = 0.4 at the IT-PD site where the grassland plots were artificially established and are showing a lower structure and complexity from the natural grassland plant communities. On the other hand, in the natural ecosystems at IT-MBo, it was more difficult to estimate biodiversity indices, probably due to structural and biochemical PTs co-variation. The effects of canopy non-vegetative elements (flowers and dead material), shadow pixels, and overexposed pixels on the relationship between optical diversity metrics and biodiversity indices were highlighted. In the third part, we examined the relationship between PTs variability (at both local and community scales, measured by standard deviation and by the Euclidean distances of the biochemical and biophysical PTs respectively) and taxonomic diversity (both α-diversity and β-diversity, measured by Shannon’s index and by Jaccard dissimilarity index of the species, families, and functional groups percent cover respectively) in Monte Bondone, Trentino province, Italy. The results of the study showed that the PTs variability metrics at alpha scale were not correlated with α-diversity. However, the results at the community scale (β-diversity) showed that some of the investigated biochemical and biophysical PTs variations metrics were associated with β-diversity. The SVH approach was also tested to estimate β-diversity and we found that spectral diversity calculated by spectral angular mapper (SAM) showed to be a better proxy of biodiversity in the same ecosystem where the spectral diversity failed to estimate alpha diversity, this leading to the conclusion that the link between functional and species diversity may be an indicator of the applicability of optical sampling methods to estimate biodiversity. The findings of the thesis highlighted that grassland structural heterogeneity strongly affects the ability to retrieve both LAI and biodiversity, with high uncertainties due to structural and biochemical PTs co-variation at complex grassland ecosystems. In this context, the uncertainties of satellite-based products (e.g., LAI) in monitoring grassland canopies characterized by either spatially or temporally varying structure need to be carefully taken into account. The results of the study highlighted that the poor performance of optical diversity proxies in estimating biodiversity in structurally heterogeneous grasslands might be due to the complex relationships between functional diversity and biodiversity, rather than the impossibility to detect functional diversity with spectral proxies.