Orientador: Raoul Henry / Resumo: As lagoas marginais são habitats lênticos, laterais ao rio, que podem manter comunicação permanente ou não com o rio. Nesses ecossistemas é encontrada elevada biodiversidade aquática, inclusive de zooplâncton. O objetivo deste estudo foi verificar diferenças na estrutura da comunidade zooplanctônica em lagoas marginais com diferentes níveis de conectividade hidrológica, por meio dos atributos ecológicos (riqueza, abundância, diversidade beta e funcional). Foi analisada a influência da conectividade hidrológica na comunidade de Cladocera e Rotifera em seis lagoas marginais antes e após um pulso de inundação do rio Paranapanema. Os resultados mostram que a estrutura da comunidade de Cladocera e Rotifera tende a ser mais distinta após o pulso de inundação. A diversidade beta foi mais elevada nas lagoas isoladas e na lagoa conectada que possui alta compartimentalização. Outro tema abordado diz respeito à analise da distribuição de Rotifera em um gradiente longitudinal da zona litorânea e envolvendo também a zona pelágica de uma lagoa marginal colonizada por macrófitas, por meio da diversidade taxonômica e funcional. A diversidade taxonômica foi maior na região de ecótono (transição da zona pelágica e litorânea) enquanto a diversidade funcional foi mais elevada na zona litorânea da lagoa. Neste estudo, também foi descrito como os microcrustáceos estão distribuídos em um transecto horizontal da zona litorânea e pelágica de uma lagoa marginal. A comunidade de microcrustáceos foi div... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: The marginal lakes are lentic habitats, lateral to the river, that can maintain permanent communication or not with the river. High aquatic biodiversity is found in these ecosystems, including zooplankton. The aim of this study was to o verify differences in the structure of the zooplankton community in marginal lakes with different levels of hydrological connectivity, through ecological attributes (richness, abundance, beta and functional diversity). The influence of hydrological connectivity in the community of Cladocera and Rotifera in six marginal lakes was analyzed before and after the Paranapanema River pulse flood. The beta diversity was higher in isolated lakes and in connected lakes, which has high compartmentalization. Another topic addressed concerns the analysis of the distribution of Rotifera in a longitudinal gradient of the littoral zone and also involving the pelagic zone of a marginal lake colonized by macrophytes, through taxonomic and functional diversity. Taxonomic diversity was greater in the ecotone region (transition from the pelagic and littoral zone) while the functional diversity was higher in the littoral zone of the lake. In this study, it was also described how microcrustaceans are distributed in a horizontal transect of the littoral and pelagic zone of a marginal lake. The microcrustacean community was divided into six functional groups, with a predominance of the G2 group (bosminids) in the lake. Macrophytes had a strong influence on variations ... (Complete abstract click electronic access below) / Doutor

The number of co-flowering species, floral density and floral trait diversity can be major determinants of pollinator-mediated plant–plant interactions in a community. However, evaluation of how each one of these co-flowering components affects the pollination success of a single focal plant species, and how these effects vary at different spatial scales, is lacking. Here, we evaluated the effects of functional diversity (flower morphology and colour), taxonomic diversity (reflecting potential sampling effects) and flower density (conspecific and heterospecific), on the pollinator environment (i.e. visitation rate and pollinator diversity) and pollination success (i.e. pollen load size and number of pollen tubes per style) of Cakile edentula (Brassicaceae). We applied structural equation models (SEMs) at the floral-neighbourhood (plot level) and community-wide scales to uncover the factors that mediate co-flowering community effects on C. edentula pollination success. We found that co-flowering community effects at the community level are more important than fine-scale floral-neighbourhood differences in mediating plant pollination success in our study species. Increasing plant functional diversity decreased pollinator visitation rate but increased the diversity of pollinator functional groups visiting C. edentula flowers. Taxonomic diversity negatively affected pollinator diversity suggesting that other unmeasured floral traits may be relevant or that single-species effects (sampling effects) may be important. Overall, our results suggest that functional floral trait diversity in a community may be the most important factor influencing pollination success of species in a community. We also found evidence for intra- and interspecific pollinator competition mediated by flower density, but none of these effects seemed to have a significant impact on pollination success. This study is an important step towards understanding the complexity of co-flowering community effects on the pollination success of individual plant species at multiple spatial scales. This study further reveals the potential importance of plant functional diversity in a community in helping predict competitive and facilitative interactions in co-flowering communities. Synthesis. Floral density and taxonomic and functional co-flowering diversity are important drivers of pollination success in flowering plants. The effects of the co-flowering diversity on the pollination success of plant species can largely depend on the spatial scale being studied. Only evaluating the outcomes of pollinator-mediated plant–plant interactions at multiple stages of the pollination process can lead to a complete understanding of their ecological consequences in nature.

The western North American species of the genus Geranium have never been satisfactorily clarified. The perennial, indigenous species of this interesting group have been particularly confusing. One important reason for confusion in this group is the fact that the taxonomic probems of the perennial species have never been studied from the genetic point of view. A sound delimitation of specific and subspecific boundaries and phylogenetic relationships cannot be achieved without the application of cyto-genetic principles. In respect to the cytological phase of this study, the author has placed emphasis on chromosome numbers in order to show evidences for and possible origin of polyploidy. Detailed chromosome morphology has not been attempted because of the very small size of the chromosomes. This study has been limited to the Wasatch region. this area respresents a natural geographical unit which is small enough to permit a detailed field study of the group and yet provide a wide range of habitats, both ecologic and geographic. This region forms the western front of the Rocky Mountain province and extendes 200 miles south from the great bend in the Bear river at Soda springs, Idaho, to the pass south of Mt. Nebo and east of Nephi, Utah.

Seasonality estimates based on archaeological shellfish remains have been an important component of settlement pattern reconstruction. Investigations of this nature allow researchers to place prehistoric people on the landscape at points in space at different times of the year. Many of the previous seasonality studies, however, have focused on marine species from coastal sites, with little attention given to freshwater locales, especially ones in the Mississippi Delta. To address that disparity, this study examines freshwater mussel “season of capture” via analysis of stable oxygen isotope ratios in specimens recovered from two Late Woodland sites located along the Yazoo River, Mississippi. As freshwater mussel shells are composed of aragonite, a metastable form of calcium carbonate (CaCO3), they can suffer greatly from the impact of meteoric diagenesis. Because of this, samples must be evaluated for diagenesis prior to any geochemical analysis taking place. Archaeological shell samples were examined via thin-section petrography and scanning electron microscopy (SEM). Visual analysis indicated pristine aragonite microstructure and crystallography in all archaeological shell samples, and confirmed their suitability for isotope analysis. Vetted shells were then micromilled across accretionary growth bands, and analyzed for their oxygen isotope signatures. Isotope profiles were then interpreted for their individual “season of capture”, and oscillation patterns for 22 shell specimens indicated mussels were being collected in all four seasons. These data support the view that at least some portion of the human population at both sites engaged in shellfishing activities year-round, indicating sedentary populations at both locales. The shell assemblages were also investigated for the purpose of informing modern conservation efforts (i.e., “applied zooarchaeology”). Nearly 24,000 valves were analyzed taxonomically, yielding the presence of 37 species, of which 24 represented new river records for the Yazoo River. These data provide a valuable historical perspective, cataloging communities as they existed prior to extensive modern impacts, thus representing an ecological baseline to be compared with modern populations. Though modern data are extremely limited for the river, the study revealed it once supported a diverse mussel community containing numerous species currently considered rare, endangered, or extinct in Mississippi.

Travail réalisé en cotutelle avec l'université du Littoral côte d'opale, France / Afin de réduire l’usage des fertilisants chimiques et leurs empreintes environnementales, la production de bioinoculants à base de bactéries rhizosphériques solubilisatrices de Phosphore (PSB) est une biotechnologie prometteuse. Lorsque celle-ci est associée à l’apport de phosphate de roche (RP), elle pourrait constituer une alternative écoresponsable d’amélioration de la fertilité des sols rhizosphériques, notamment à travers l’augmentation du phosphore (P) biodisponible. Pour répondre à cet enjeu environnemental majeur, il est indispensable d’étudier la biodiversité microbienne des sols en interaction avec le RP. Ainsi, ce travail de thèse a pour objectif de caractériser, d’un point de vue taxonomique, les communautés bactériennes et fongiques associées aux compartiments racinaires et rhizosphériques de plantes natives d’environnements singuliers, peu explorés, que sont d’anciens sites miniers riches en RP. Le séquençage Illumina MiSeq d’amplicons de gènes ribosomiques des différents groupes microbiens et l’assignation taxonomique des séquences regroupées en ASV, nous ont permis de mettre en évidence des valeurs de richesse et de diversité microbiennes comparables malgré la différence des teneurs en RP et en P des sols étudiés. De même, une grande similarité entre les profils des communautés a été identifiée à haut niveau taxonomique, avec une prévalence marquée des phyla Actinobacteriota et Ascomycota, et de l’ordre Glomerales pour les communautés de champignons mycorhiziens arbusculaires (CMA). À un niveau taxonomique plus bas, un core microbien de 26 ASV mycorhiziennes, persistantes à travers le gradient de RP et de P, a également été mis en évidence. Toutefois, l’analyse statistique des données environnementales nous a permis d’identifier des ASV indicatrices des habitats enrichis versus non enrichis en RP, pour chaque communauté microbienne étudiée. La synthèse de ces résultats originaux montre une influence mineure des teneurs en RP et en P sur le profil des communautés microbiennes des sites étudiés et questionne la signification écologique de la prévalence de certains taxa en lien avec l’histoire minière du site, sa restauration écologique et sa résilience, ainsi que les stratégies de vie et les attributs fonctionnels des taxa dominants. Par ailleurs, une collection de PSB a été réalisée à partir d’isolats racinaires issus des sites miniers étudiés, ou à partir d’isolats issus de spores et d’hyphes mycorhiziens piégés au contact d’apports en RP déposés dans la rhizosphère de plantes d’intérêt agronomique. Ces PSB racinaires ou hyphosphériques, testés par ailleurs pour plusieurs traits additionnels promoteurs de la croissance des plantes, ont été assignés à trois phyla : Proteobacteria, Firmicutes et, dans une moindre mesure, Actinobacteria ; Bacillus et Pseudomonas étaient les genres prédominants. Enfin, à partir de ces isolats, deux consortia bactériens avec différent traits promoteurs de la croissance des plantes (PGP), ont été constitués et testés seuls ou en combinaison avec l’apport de RP et/ou l’ajout d’un inoculum mycorhizien à base de Rhizophagus irregularis, sur la croissance de la tomate, espèce d’intérêt agronomique. Une augmentation du taux de germination, un accroissement de la hauteur des jeunes plantules et des modifications au niveau du système racinaire des plants adultes, en particulier des variations de la densité du tissu racinaire, ont été observés en réponse à l’inoculation simple par les consortia ou à leur interaction double ou tripartite avec le RP et/ou le CMA. Le profil taxonomique du microbiote natif avant et après apport des inoculants et du RP a été caractérisé. En conclusion, l’ensemble de nos travaux s’appuyant sur l’analyse des données environnementales, combinées aux données de laboratoire sur l’inoculation de plantes par des isolats bactériens, notamment d’origine minière, soulignent l’intérêt mais aussi la complexité de l’élaboration d’inoculants microbiens promoteurs de la croissance des plantes, solubilisateurs de P. / In order to reduce the use of chemical fertilizers and their environmental footprint, the production of bioinoculants based on phosphorus solubilizing rhizospheric bacteria (PSB) is a promising biotechnology. When combined with rock phosphate (RP), it could be an eco-responsible alternative to improve rhizospheric soil fertility, especially by increasing bioavailable phosphorus (P). To address this major environmental issue, studying soil microbial biodiversity and its interactions with RP is required. Thus, the objective of this thesis is to characterize, from a taxonomic point of view, the bacterial and fungal communities associated with the root and rhizospheric compartments of native plants in singular, little explored environments, located in former mining sites rich in RP. Illumina MiSeq sequencing of ribosomal gene amplicons of the different microbial groups, then taxonomic assignment of the sequences grouped in ASV, allowed us to highlight comparable microbial richness and diversity indexes of soils despite their differences in RP and P contents. As well, a high degree of similarity between the community profiles was identified at a high taxonomic level, with a marked prevalence of the phyla Actinobacteriota and Ascomycota, and of the order Glomerales for the arbuscular mycorrhizal fungi (AMF) community. At a lower taxonomic level, a microbial core of 26 mycorrhizal ASV, persistent across the RP and P gradient, was also documented. However, statistical analysis of the environmental data allowed us to identify indicator ASV for PR-enriched versus non-rich habitats for each microbial community studied. All together, these original results contributed to rule on a minor influence of RP and P levels on the microbial community’s profiles across the studied sites, and raised the questions of the ecological significance of the prevalence of certain taxa regarding the site’s mining history, its ecological restoration, as well as the life strategies and functional attributes of the dominant taxa. In addition, a collection of PSB was made from mine site root isolates, or from isolates associated with spores and mycorrhizal hyphae trapped in contact with PR inputs deposited in the rhizosphere of agronomic plants. These root or hyphospheric PSB, tested elsewhere for several additional plant growth-promoting traits, were assigned to three phyla: Proteobacteria, Firmicutes, and, to a lesser extent, Actinobacteria; Bacillus and Pseudomonas were the predominant genera. Finally, from these isolates, two bacterial consortia with different plant growth promoting (PGP) traits were constituted and tested, alone or in combination with RP inputs and/or a mycorrhizal inoculum based on Rhizophagus irregularis, on the growth of tomato, a species with an agronomic interest. An increase in germination rate or height of young seedlings, and changes in the root system of adult plants, particularly changes in root tissue density, were observed in response to single inoculation by the consortia or to their dual or tripartite interaction with RP and/or AMF. The taxonomic profile of the native microbiota before and after inoculants and RP input was characterized. In conclusion, our work based on the analysis of environmental data, combined with laboratory data from plant inoculation experiments by bacterial isolates, especially of mining origin, underlines the interest but also the complexity of the development of microbial inoculants promoting plant growth, solubilizers of P.

Microbial Source Tracking (MST) is a field of study that attempts to identify the source of fecal contamination in waterways in order to assist with development of remediation strategies. Biologists at Cal Poly Center for Applications in Biotechnology (CAB) are developing a new MST method using microbes from the genus Bacteroides. Bacteroides species are host-specific microorganisms that can theoretically be used to trace back to a single host species. After fecal samples are collected, biologists use Next-Generation Sequencing (NGS) techniques to obtain only the genetic sequences of microorganisms belonging to the phylum Bacteroidetes. Investigators hypothesize that similar sequences belong to the same phlyogenetic group (i.e., the same genus) and can therefore be computationally clustered. Each cluster of related sequences, typically 97% similar, is called an Operational Taxonomic Unit (OTU). Theoretically, an OTU acts as a molecular signature that can be traced back to a specific host genus. This thesis presents LOTUS, the Library of OTUs, a web-based computational tool for the preliminary investigation of the use of the Bacteroides OTU library as an MST method. This work discusses the four contributions of LOTUS: a database design which accurately models OTUs and the underlying relationships necessary for source tracking, a pipeline to create OTUs from raw sequencing reads, a method of assigning taxonomy to OTUs, and a web-based user interface. In preliminary testing for a reference library of twelve samples, LOTUS produced 1,431 OTUs, of which 891 were single-source (OTUs derived from sequences from a single host species). Using these OTUs, LOTUS was able to accurately taxonomically match four of five unknown test samples, showing promise for using OTUs as an MST method.

The Dallas-Fort Worth International (DFW) Airport is located in a densely urbanized area with one of the fastest-growing populations in the U.S.A. The airport property includes a large tract of "protected" riparian forest that is unique to the urban surroundings. This dissertation explores variables that influence the benthic macroinvertebrate community structure found in urbanized prairie streams that were initially assessed by the University of North Texas (UNT) Benthic Ecology Lab during four, non-consecutive biomonitoring studies (2004, 2005, 2008, and 2014) funded by the DFW Airport. Additionally, land use analysis was performed using 5-meter resolution satellite imagery and eCognition to characterize the imperviousness of the study area watersheds at multiple scales. Overall, flow conditions and imperviousness at the watershed scale explained the most variability in the benthic stream community. Chironomidae taxa made up 20-50% of stream communities and outperformed all other taxa groups in discriminating between sites of similar flows and urban impairments. This finding highlights the need for genus level identifications of the chironomid family, especially as the dominant taxa in urban prairie streams. Over the course of these biomonitoring survey events, normal flow conditions and flows associated with supra-seasonal drought were experienced. Prevailing drought conditions of 2014 did not negatively influence stream communities, allowing this study to capture the long-term natural (temporal) variability of urban prairie stream communities. Such long-term studies are imperative for discerning between stream impairment versus natural variation, especially as droughts become more frequent and severe.

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