Coastal marine ecosystems are among the most impacted globally, attributable to individual and cumulative effects of human disturbance. Anthropogenic nutrient loading is one stressor that commonly affects nearshore ecosystems, including seagrass beds, and has positive and negative effects on the structure and function of coastal systems. An additional, previously unexplored mechanistic pathway through which nutrients may indirectly influence nearshore systems is by driving blooms of benthic jellyfish. My dissertation research, conducted on Abaco Island, Bahamas, focused on elucidating the role that benthic jellyfish have in structuring systems in which they are common (i.e., seagrass beds), and explored mechanistic processes that may drive blooms of this taxa. To establish that human disturbances (e.g., elevated nutrient availability) may drive increased abundance and size of benthic jellyfish, Cassiopea spp., I conducted surveys in human-impacted and unimpacted coastal sites. Jellyfish were more abundant (and larger) from human-impacted areas, positively correlated to elevated nutrient availability. In order to elucidate mechanisms linking Cassiopea spp. with elevated nutrients, I evaluated whether zooxanthellae from Cassiopea were higher from human-disturbed systems, and whether Cassiopea exhibited increased size following nutrient input. I demonstrated that zooxanthellae population densities were elevated in human-impacted sites, and that nutrients led to positive jellyfish growth. As heightened densities of Cassiopea jellyfish may exert top-down and bottom-up controls on flora and fauna in impacted seagrass beds, I sought to examine ecological responses to Cassiopea. I evaluated whether there was a relationship between high Cassiopea densities and lower benthic fauna abundance and diversity in shallow seagrass beds. I found that Cassiopea have subtle effects on benthic fauna. However, through an experiment conducted in a seagrass bed in which nutrients and Cassiopea were added, I demonstrated that Cassiopea can result in seagrass habitat modification, with negative consequences for benthic fauna. My dissertation research demonstrates that increased human-driven benthic jellyfish densities may have indirect and direct effects on flora and fauna of coastal marine systems. This knowledge will advance our understanding of how human disturbances shift species interactions in coastal ecosystems, and will be critical for effective management of jellyfish blooms.

Les zones humides (ZH) alluviales constituent des secteurs à forte valeur écologique etpatrimoniale. Pour comprendre et prédire l’évolution à long terme de ces zones, en particulierface aux changements globaux, il apparaît primordial de traduire les perturbationshydrologiques attendues en termes de perturbations biologiques, afin d'estimer lesconséquences potentielles de ces changements pour la biodiversité et le fonctionnement globalde ces écosystèmes. Cette thèse s’articule donc autour de deux objectifs: proposer un modèleconceptuel de fonctionnement écologique des ZH soumises à des assèchements saisonniers etestimer la vulnérabilité écologique de communautés faunistiques vivant dans ces ZH, enconsidérant conjointement les peuplements benthiques et interstitiels (principalementCrustacés).Nos résultats démontrent que la morphologie des ZH (eau relativement courante, eaustagnante, apports phréatique) et leurs modes d’assèchement (formation de mouilles isoléesou assec complet) sont essentiels dans la structuration des communautés microbiennes etd’invertébrés et dans la réponse saisonnière de la biodiversité et des processus écologiques.L’intensification probable des étiages et des assèchements augmentera l’hétérogénéité spatialeet temporelle des habitats et leur richesse spécifique mais réduira la biodiversité globale desplaines alluviales (disparition des espèces rares). Ces étiages plus sévères modifieront lesprocessus écologiques, diminuant le recyclage de la matière organique et la qualité des eauxsuperficielles. Les recherches futures devraient s’orientées vers des stratégies et des moyensefficaces pour garantir la durabilité écologique des ZH. / Alluvial wetlands offer many ecological goods and services. In order to evaluate thelong term impact of global changes, it appeared essential to translate the hydrological changesin term of biological perturbation, so as to estimate the consequences on biodiversity andecosystem functioning. This PhD thesis focuses on two points: to propose a conceptual modelof ecological functioning of the wetlands that are subjected to seasonal drying and to estimatethe ecological vulnerability of aquatic invertebrate communities of the wetlands facing theincreasing drought risk, by considering both the benthic and interstitial assemblages (with aparticular interest on Crustaceans).Our main results demonstrate that wetlands’ morphology (running water, groundwaterupwelling, stagnant water) and their drying modalities (formation of isolated pools orcomplete drying) influence both the microbial and invertebrate community structures andcontrol the seasonal responses of biodiversity and ecological processes. The potential increasein the low flow period and drying intensity may increase the spatial and temporalheterogeneity of habitats and their specific richness but may decrease the global biodiversityof floodplain (rarefaction of sensible species). Severe low flow periods may also disturb theirecological functioning, reducing the organic matter recycling and the surface waters quality.Future studies should develop efficient strategies to support the ecological durability ofwetlands.

Alterações antrópicas em ecossistemas aquáticos exigem medidas de recuperação dos ambientes degradados, destacando-se projetos de restauração ecológica. Uma das etapas cruciais nesses projetos é a fase de monitoramento, sendo que o uso de macroinvertebrados como bioindicadores apresenta-se como uma importante ferramenta, por eles oferecerem vantagens sobre outros métodos de avaliação. Assim, o objetivo foi verificar os efeitos do assoreamento, antes e depois do rompimento da barragem de um pequeno reservatório em um riacho tropical, sobre a assembleia de macroinvertebrados aquáticos e avaliar a resposta da estrutura da comunidade após a implementação de um projeto de restauração ecológica. A pesquisa foi conduzida no riacho da Campininha, que passou por diversas alterações antrópicas, destacando-se aqui o rompimento de uma barragem e posteriormente a todos esses distúrbios pela implementação de um projeto de restauração ecológica. Foi realizada revisões da literatura para verificação da aplicabilidade da comunidade de macroinvertebrados como bioindicadores de sedimentação e na avaliação de projetos de restauração ecológica. Foram coletados dados pré-existentes antes e após o acidente e realizadas campanhas amostrais dois anos após o início da implantação do projeto de restauração. A comunidade de macroinvertebrados foi avaliada pela aplicação de índices ecológicos estruturais e funcionais alimentares e os resultados analisados por meio de ferramentas de estatística uni e multivariada. A análise da literatura mostrou que a aplicação de índices ecológicos tradicionais, tais como riqueza e diversidade, podem não ser sensíveis o suficiente para indicar impactos relacionados à sedimentação e implementação de projetos de restauração ecológica. Sendo, assim, necessária a utilização de índices que considerem a composição da comunidade, a sensibilidade dos organismos e a utilização de grupos funcionais alimentares e suas relações. Antes do rompimento da barragem a comunidade de macroinvertebrados já apresentava-se empobrecida pelo assoreamento do trecho represado e do canal fluvial. O rompimento da estrutura implicou na perda de importantes grupos e na mudança da composição da comunidade, além da perda de grupos funcionais alimentares, com consequente perda de funções ambientais. Após a implementação do projeto de restauração houve o aparecimento de 20 famílias, no entanto, os índices ecológicos tradicionais não foram capazes de identificar mudanças na comunidade. Métricas de composição e de grupos alimentares apontaram para um processo de recuperação da área. As características do sedimento tiveram um alto poder explicativo da comunidade, mostrando que a recuperação do habitat bentônico é um dos fatores que leva à uma melhor resposta da comunidade, mesmo esse não tendo sido o foco da aplicação do projeto de restauração avaliado. O relativo curto período transcorrido após a implementação do projeto já foi suficiente para indicar melhorias na qualidade ambiental. Tais resultados contrapõe a maioria dos estudos verificados na revisão da literatura. No entanto destaca-se que os mesmos foram conduzidos principalmente em ambientes temperados, indicando que em ambientes tropicais a dinâmica de recuperação é diferente. Assim aponta-se a necessidade da intensificação da implantação de projetos e monitoramento dos mesmos para a criação de um arcabouço teórico para auxiliar gestores e projetistas na sua elaboração. / Anthropic alterations in aquatic ecosystems demand the implementation of recuperation actions, highlighting ecological restoration projects. The monitoring is an important step to these projects, and the macroinvertebrates application as bioindicators is an important tool, because they are advantageous in comparison to another assessment methods. Thus, the goal was verify the effects of silting, and dam rupture in macroinvertebrate community, in a tropical stream, and assess the answer to an ecological restoration project implementation. The research was conducted in the Campininha stream, that was impacted by anthropic alterations, featured a dam rupture and after all this disturbances was implemented an ecological restoration project. A literature review was conducted to verification of the applicability of macroinvertebrates as bioindicators of silting and in ecological restoration projects assessment. Data was collected before and after the dam rupture, and samplings were done two years after the project implementation began. The macroinvertebrates community was assessed by application of structural and functional feeding indexes and the results analyzed by univariate and multivariate statistic. The literature review showed that the traditional indexes application may be not sensible to indicate impacts related to silting and ecological restoration projects implementation, and it is necessary the utilization of indexes that consider the community composition, organisms sensibility and functional feeding groups and your relations. Before the dam rupture, the macroinvertebrate community was already poor by the silting of the lake and fluvial channel. The dam rupture leaded to the loss of important groups and in the change of the macroinvertebrate community composition, also loss of functional feeding groups and consequently environmental functions. After the ecological restoration project implementation were found another 20 families, however, the traditional indexes were not sensible to indicate changes in macroinvertebrates community. Composition and functional feeding groups indexes showed the stream recuperation process. The sediment characteristics had a community high explanative power showing that the benthic habitat recovery is a factor that guide to a better community answer, even this was not the goal of the restoration project application. The relative short time after the project implementation was enough to point a environmental quality recovery, in contrast with the literature review. However the most studies analyzed was conducted in temperate environments, showing that in tropical environments the recovery dynamics is different. Thus, is necessary a intensification of restoration projects implementation and monitoring to a creation of data bases to guide managers and professionals responsible by the projects elaboration in decision make.

As áreas de várzea estão entre os ecossistemas mais ameaçados, porém no Brasil essa situação agrava-se devido à falta de uma abordagem ecológica robusta na Lei de Proteção da Vegetação Nativa, o que torna necessário a atuação do poder público municipal para salvaguardar esses sistemas. A presente pesquisa empregou uma abordagem ecológica aplicada (limnologia, macroinvertebrados, macrófitas aquáticas) para avaliar a relação do rio Sorocaba com suas várzeas no município de Sorocaba, o uso e ocupação da terra e a sua influência sobre às variáveis limnológicas, além das demandas dos serviços ambientais fornecidos pelas várzeas ao município. Duas amostragens foram realizadas durante o ano de 2017, sendo uma no período de cheia (fevereiro) e outra na estiagem (junho). Métodos padronizados foram empregados para o desenvolvimento do presente trabalho. Evidenciou-se que a poluição orgânica e o predomino de áreas antropizadas são os principais fatores responsáveis pela alteração das variáveis limnológicas analisadas. Alguns serviços ambientais (i.e. provisão de água, controle do fluxo, regulação dos processos erosivos, regulação de nutrientes, ciclagem da água, pesca voltada ao lazer e valor intrínseco da biodiversidade) prestados pelos ecossistemas de várzea do Município de Sorocaba apresentam um balanço negativo (i.e. demanda superior à oferta). As espécies de macrófitas e famílias de macroinvertebrados encontradas são espécies indicadoras de poluição orgânica. Por fim, destaca-se a contribuição da ação estratégica e o papel da gestão municipal para o manejo dos ecossistemas de várzea. / The wetlands are among the most threatened ecosystems, although in the Brazil that situation is worse because of an ecological approach lack in the Law of Native Vegetation Protection, what makes necessary the public power action to safeguard those systems. The present research employed an applied ecological approach (limnology, macroinvertebrates, aquatic macrophytes) for Sorocaba River and its wetlands assessment in Sorocaba-SP municipality, the land cover and its influence on limnological variables, as well as the environmental services demand supplied by the municipality wetlands. Two samples were performed during 2017, one during the rainy (February) season and other on the dry season (June). Patronized methods were employed in the present research. The organic pollution and the anthropic areas predominance are the mainly factors responsible for limnological variables alteration. Some environmental services (i.e. water provision, water flow control, erosive process control, nutrient control, water cycling, recreation fishing and biodiversity intrinsic value) provided by the studied wetlands showed a negative balance (i.e. demand superior to the provision capacity). The macrophyte species and macroinvertebrate families found are organic pollution indicators. Finally, stand out the strategic action contribution and the municipality governance role for wetlands ecosystem management.

In der vorliegenden Arbeit werden für ein stark anthropogen beeinflusstes Einzugsgebiet die komplexen Zusammenhänge zwischen Witterung, Landnutzung, Erosion, Gerinneabfluss, Stofffrachten und Makrozoobenthos analysiert. Dafür wurde eine Messstation eingerichtet, an der Fließgeschwindigkeit, Trübung, pH Wert und Leitfähigkeit kontinuierlich gemessen wurden. Mit Hilfe eines durchflussgesteuerten Probennehmers wurden Wasserproben entnommen und im Labor auf verschiedene Inhaltsstoffe (Nährstoffe, Schwermetalle) analysiert sowie die Konzentration von Feinsediment bestimmt. Es konnte eine Beziehung zwischen Trübung und Sedimentkonzentration abgeleitet werden. Die chemischen Analysen zeigten einen komplexen Zusammenhang zwischen der Erosion von landwirtschaftlichen Flächen, dem Stoffeintrag von versiegelten Arealen (Verkehrsflächen, Dächer) aber auch witterungs- und vegetationsbedingte saisonale Effekte. Ein Vergleich der Eigenschaften der Schwebstoffe/Feinsediment im Landwasser mit denen von Ackerboden (Maisfelder) zeigte, dass diese die „chemische Handschrift“ der Ackerböden trugen. Mit Hilfe der Modelle EROSION 3D und ICECREAM wurden die abgetragenen Bodenmengen für das Einzugsgebiet bzw. für ausgewählte Hänge quantifiziert. EROSION 3D überschätzt den Bodenaustrag aus dem Untersuchungsgebiet deutlich. Das Modell ist ungeeignet, um für das Einzugsgebiet reale Abtragswerte mit den zur Verfügung stehenden flächenhaften Eingangsdaten zu berechnen. Bereits für Einzelhänge werden zu große Bodenabträge berechnet. Verstärkend kommt hinzu, dass auf Grund der Modellannahme jeder Partikel, der das Gewässer erreicht auch aus dem Einzugsgebiet heraustransportiert wird. Das Modell kann empfohlen werden, um erosionsgefährdete Flächen auszuweisen. In der Untersuchungsperiode von 2009 bis Juli 2011 wurde an Hand von 57 Driftfängen mit unterschiedlichen hydrologischen Randbedingungen die Wirkung der Fließgeschwindigkeit auf den Übergang benthischer Invertebraten in die freie Welle identifiziert. Aus Uferbereichen gelangen zufällig terrestrische Invertebraten in das Gewässer, deren Anteil sich durch gewässernahen Oberflächenabfluss in Folge von Niederschlagsereignissen erhöht. Die Driftdichte nimmt ab Fließgeschwindigkeiten von 0,3 m/s deutlich zu. Oligochaeta, Cyclopoida und Dipolstraca driften verstärkt bei Fließgeschwindigkeiten >0,6 m/s.

Benthic filter feeders (BFF) can reduce phytoplankton concentration (abundance) thereby controlling eutrophication in several ecosystems, including rivers. However, experiments suggest warming can alter the relationship between BFF grazing rate and the growth rate of (heterotrophic) planktonic prey. To investigate how eutrophication control by grazers is altered with temperature under the influence of other important abiotic (water depth, and speed, light, and turbidity) and biotic factors (initial phytoplankton concentration [hereafter: Pin value], BFF density and spatial BFF distribution), we developed a spatially-explicit computer simulation model. This model simulates the dynamics of a phytoplankton population traveling through a simplified river channel while being grazed by BFF. Our model includes the thermal responses of BFF grazing and phytoplankton growth. The results show that BFF grazing can qualitatively alter and, in some circumstances, even reverse the response of phytoplankton to warming. Moreover, the response of grazer-controlled phytoplankton to warming, water depth and Pin value is non-linear and phytoplankton can increase steeply with slight changes within some ranges of these variables. In addition, these variables can interact causing their combined effects on eutrophication to differ from what is expected considering their isolated effects. Generally, the effect of most variables, including temperature, Pin value and BFF density and spatial distribution, is larger at shallow waters. Moreover, our study shows that phytoplankton control can be substantially improved by heterogeneous BFF distributions where the BFF are located at the extremes of the river either upstream or downstream instead of homogenously distributed along the whole river. However, warming can cause a switch between these two optimal distributions or even can cause differences among the spatial distributions to disappear. In general, the homogeneous BFF distribution can be used as conservative estimate of eutrophication control. In conclusion, this work shows that trophic control can qualitatively alter the response of eutrophication to warming, supporting previous studies suggesting that the prediction of global warming effects requires considering not only the thermal responses of organisms but also their trophic interactions. In addition to these biotic variables, this thesis reveals that considering the interactions between abiotic and biotic variables and including their spatial distribution are important for eutrophication control. Especially, the detection of thresholds in the response of grazer-controlled phytoplankton to temperature, water depth, Pin value, and spatial BFF distribution indicates that one should be careful with predictions because of potential abrupt changes. Although further studies are needed to make specific recommendations for water quality management, our work provides preliminary suggestions on the conditions where grazers or Pin reductions can be more efficient to control eutrophication.

Several studies have found separation of biogeographic provinces on the West Florida Shelf (WFS), but the location of this separation differs depending on different organisms with faunal boundaries proposed at Apalachicola, Cedar Key, Anclote Key. Tampa Bay, Charlotte Harbor, Cape Romano, or Cape Sable. Biogeographic boundaries can be gradual over a given space and are often species-specific. Analyses of marine benthic mapping and community characterization of Florida’s West-central coast shallow water (depth) hardbottom habitats indicate a major shift in the benthos across Tampa Bay. Quantitative benthic surveys of 29 sites yielded a total of 4,079 individuals of nine stony coral species and 1,918 soft coral colonies. Populations were dominated by four species of corals: Siderastrea radians, Oculina robusta, Solenastrea hyades, and Cladacora arbuscula. Most corals were less than 10 cm in diameter. Cluster analyses of coral density and major functional group percent cover showed distinct differences in hard and soft coral densities and species demographics from south to north with clear spatial patterns between regions. These benthic hardbottom coral communities change over a relatively small spatial scale (10’s of km), indicating a biogeographical province or ecosystem region boundary in marine benthic communities at, or very near, the mouth of Tampa Bay. Broader studies are needed to identify the shifts in benthic community biogeography along the West Florida Shelf.

Recent technological advances in unmanned observational platforms, including remotely operated vehicles (ROVs) and small unmanned aerial systems (sUAS), have made them highly effective tools for research and monitoring within marine and coastal environments. One of the primary types of data collected by these systems is video imagery, which is often captured at an angle oblique to the Earth’s surface, rather than normal to it (e.g., downward looking). This thesis presents a newly developed suite of tools designed to digitally map oblique imagery data collected with ROV and sUAS in coastal and marine environments and quantitatively evaluates the accuracy of the resultant maps. Results indicate that maps generated from oblique imagery collected with unmanned vehicles have highly variable accuracy relative to maps generated with imagery data collected with conventional mapping platforms. These results suggest that resultant maps have the potential to match or even surpass the accuracy of maps generated with imagery data collected with conventional mapping platforms but realizing that potential is largely dependent upon careful survey design.

No description available.

Analysis of foraminifera for synorogenic pelagic units of Rote and Savu Islands, Indonesia, reveals high rates of surface uplift in the past 1.5 Ma of the incipient Banda arc-continent collision. Paleodepth estimates are derived from benthonic forams and ages from planktonic forams. But estimates are complicated, however, by abundant reworking; yet several distinctive species have been found. Synorogenic deposits in western Rote yield forams of biozone Neogene (N) 18 and depths from 5000-5700 meters at the base of the section, and 3600 meters at the top of the section. Eastern Rote yields forams of N 19/20 - N 22 and depths from 5400-5700 meters. Central Rote yields N 21 and depths from 5000-5700 meters. Because all of the sections are presently about the same elevation (~200 m), long-term surface uplift rates are slightly higher (1.84-3.29 m/yr) in eastern and central Rote than those in western Rote. Forams from Savu yield ages of N19/20 - N 22. Across Savu depth estimates range from 3200-5700 meters, which yields a range of uplift rates from 1.86 mm/yr in SE Savu to 3.25 mm/yr in Central Savu. These results indicate the Banda arc-continent collision caused uplift of Rote and Savu at rates of 1-2 mm/yr over the past 3 Ma.