ABSTRACT Foraminiferal Assemblages on Sediments and Reef Rubble at Conch Reef, Florida USA Christy Stephenson Benthic foraminiferal assemblages are widely used to interpret responses of the benthic communities to environmental stresses. This study compares epibiotic foraminiferal assemblages, collected from reef rubble, with those from reef sediments. The study site, Conch Reef, is the site of the Aquarius Underwater Habitat research facility and includes protected areas used only for scientific studies. Although a number of studies have enumerated foraminiferal taxa from the Florida reef tract, no projects have focused on the assemblages that occur at Conch Reef. Sediment and reef rubbles samples were collected via SCUBA from a depth range of 13 to 26 m during October 2008. Foraminiferal assemblages were assessed and compared between the two sample types. A total of 117 foraminiferal species, representing 72 genera, 37 families, and 8 orders were identified in 13 sediment samples and 21 rubble samples. In the rubble samples, 70 genera were identified, including 12 symbiont-bearing genera representing 20% of the total assemblage, 12 stress-tolerant genera representing 6%, planktic foraminifers representing 1%, and 46 other smaller foraminiferal genera representing 73% of the total foraminiferal assemblage. The rubble samples were quite homogenous. The mean (+SD) Fisher alpha α diversity of genera in these samples was 12.9 + 1.4. Sediment samples included 60 of the same genera. The 12 symbiont-bearing genera represented 41% of the total assemblage, 10 stress-tolerant genera represented 3%, planktic taxa represented 2%, and 40 other smaller foraminiferal genera represented 54% of the total assemblage. Overall, the taxonomic assemblages were very similar between the sample types, with sediment assemblages clearly representing the local and regional reef foraminiferal assemblage. The mean (+SD) Fisher alpha α for sediment samples was 11.4 + 2.3, which is not significantly different from that found for the rubble samples. A concentration ratio comparing relative abundances in sediment vs. rubble samples revealed that shells of larger, symbiont-bearing taxa were about 2.5-5.5 times more concentrated in the sediment, indicating winnowing of smaller taxa. Shells of Siphonatera, an agglutinated miliolid, and Textularia, an agglutinated textularid, were more abundant in sediments than in rubble, indicating high preservation potential. The concentration ratio provides a new taphonomic index that reflects the size and durability of foraminiferal taxa. The mean FORAM Index (FI) for the sediment samples (5.57 + 0.83) indicates that water quality at Conch Reef is suitable for calcifying symbioses. The most abundant symbiont-bearing genera were Amphistegina, Laevipeneroplis, Asterigerina, and Archaias.

À l'interface bentho-pélagique, les herbiers marins présentent une multitude de rôles écosystémiques. Historiquement, les scientifiques et décideurs de La Réunion se sont focalisés sur l'écosystème récifal. Néanmoins, des prairies monospécifiques à Syringodium isoetifolium sont présentes de manière pérenne (3 hectares) au sein du complexe récifal de l'Ermitage / La Saline (côte ouest). L'objectif principal de cette étude était d'apporter les premières données sur l'écologie de ces herbiers marins. Ainsi, une approche pluridisciplinaire a été développée : 1. L'étude de la dynamique spatiale du paysage herbier sur 65 ans (dès 1950), et à l'échelle saisonnière (2013-2015) qui a permis de définir le rôle majeur des forçages hydrodynamiques et de l'eutrophisation. 2. L'analyse de la productivité de l'écosystème herbier et sa réponse métabolique face à des apports nutritifs, révèle des bilans métaboliques opposés (autotrophie/hétérotrophie) en fonction des conditions environnementales, ainsi qu'un rôle de tampon sur les flux de nutriments. 3. Des analyses isotopiques (δ13C et δ15N) ont permis d'identifier les sources de matière entrant dans l'écosystème et alimentant les réseaux trophiques associés aux herbiers. L'étude a permis d'établir un lien trophique entre Holothuria leucospilota et les herbiers marins ainsi qu'un rôle essentiel dans le maintien des populations de poisson herbivores récifaux. 4. Des enquêtes locales ont révélé une méconnaissance de cet écosystème malgré leur potentiel économique et écologique. À la lumière de ces travaux de thèse, la prise en considération des herbiers marins dans la gestion du milieu marin réunionnais est nécessaire. / Located at the benthos-pelagos interface, seagrass beds have many ecosystemic roles such as coastal protection or biodiversity. Historically, scientists and decision-makers at Reunion Island have been focusing on reef ecosystems. However, for several decades, monospecific (Syringodium isoetifolium) seagrass beds have been observed (3 hectares – 2013) within Ermitage / La Saline reef (West coast). The main objective of this study was to give the first data on seagrass ecology at Reunion Island. Therefore, a multi-disciplinary study was developed. First, seascape ecology of seagrasses is analyzed at decadal (since 1950) and seasonal scales (2013-2015). Physical settings (swell) and eutrophication were driving factors on the spatial dynamics of seagrass beds. Second, seagrass community metabolism and response to nutrient loads (nitrate and phosphate) show variations in metabolic budget (autotrophy to heterotrophy) and make seagrass beds a nutrient sink following the environmental conditions. Third, stable isotope analysis (δ13C and δ15N) identified sources of particulate matter entering the ecosystem and fueling food webs. The trophic roles of seagrass beds are assessed for echinoderm and herbivorous fish communities. This study highlighted a trophic link between seagrass and Holothuria leucospilota, and proved some species to be heavily dependent on seagrass ecosystem (Leptoscarus vaigiensis, Siganus sutor). Finally, interviews showed a lack of knowledge about this ecosystem despite crucial economic and ecologic roles. Considering their major functions, seagrass beds have to be considered in future management of the coastal marine systems at Reunion Island.

As drivers of biogeochemical cycles and nutrient recycling, such as carbon turnover, the microbial community is essential in sustaining functioning ecosystems. Together with the metazoan community, the microbial community constitute the majority of all life in the benthos. Environmental change in biotic and abiotic factors may influence the dynamics of these communities, for example through a sorting or driving effect on the community structure through assembly processes. Environmental change, e.g. change in dissolved oxygen concentration, salinity and temperature, can directly or indirectly affect community composition. How, in what way, and to what extent, benthic bacterial and meiofaunal community composition in the eutrophied, brackish benthic environments, in the Baltic Sea sub-basin the Baltic Proper, respond to environmental change is understudied, both at local and seascape scale. This thesis aimed to study and understand the effects of environmental variation on the diversity and biogeographic patterns of Baltic Sea sediment bacterial and meiofaunal communities. A further aim was to understand the links between the different community levels by studying the interaction between meiofaunal- and macrofaunal communities in relation to environmental variation. Community diversity was analysed along a latitudinal transect of national environmental monitoring stations in the Baltic Proper using a framework of metapopulation and metacommunity theory. The analyses were based on environmental genomics, with high-throughput sequencing, bioinformatics and statistics. The total community genome was analysed using phylogenetic marker gene fragments as a proxy for taxonomic diversity, to investigate diversity, community structure and dynamics. Salinity and oxygen were found to be the main abiotic environmental drivers of benthic community composition and alpha- and beta-diversity patterns. Furthermore, macrofauna-meiofauna interactions were significantly more complex in higher salinity environments. Results also showed that both enhanced environmental gradients and dispersal following a major inflow of saline and oxygenated water from the Atlantic Ocean, influenced the composition of sediment bacterial communities at the seascape scale of the Baltic Sea, as shown by a reduced beta-diversity and increased alpha-diversity, and the development of a significant distance-decay of community similarity. This study also identified strong metapopulation dynamics of the benthic sediment bacterial communities with many satellite and a few core taxa. The outcomes from this study contribute to the understanding of how environmental variation and environmental change relate to changes in Baltic Sea benthic community diversity and composition, and important factors and processes governing community dynamics.

La presente tesis "estudio de los efectos sobre el medio litoral derivados de la implantación de saneamientos integrales en la costa Cantábrica" pretende evaluar la validez de los diseños ambientales de estos saneamientos integrales como instrumentos predictivos aplicables a la gestión de la calidad de los sistemas acuáticos litorales mediante la realización de estudios dirigidos a analizar la afección que originan los vertidos de aguas tratadas a través del emisario submarino sobre el estado de las aguas costeras, sobre la calidad de los fondos sedimentarios y sobre las comunidades bentónicas establecidas; así como, mediante el análisis de la evolución de la calidad de las masas de agua estuarinas afectadas por los vertidos de tormenta. Los resultados obtenidos han servido para proponer una serie de indicaciones para el diseño de los programas de control operativo planteados en la DMA, a aplicar en las masas de agua afectadas por este tipo de vertidos. / This PhD thesis titled "Effects of coastal sanitations on Cantabrian littoral ecosystems (Bay of Biscay)" was carried out to evaluate the applicability of the environmental design of the sewer systems constructed in the north of Spain to the management of the aquatic ecosystems. This work has analysed the effects caused by the treated effluents discharged by the submarine outfall on the water and sediment quality and on the structure and composition of the hard-bottom benthic communities dwelling the outfall surroundings. On the other hand this study has analysed the recovery of the estuarine ecosystem (water, bacteriology, sediments and benthic organisms) directly affected in the past by the urban effluents and nowadays affected by storm discharges. Results obtained in both surveys have contributed to propose a guidance for the design of the Operative control of the water masses established in the EU Water Framework Directive in the north of Spain.

Orientadora: Profa. Dra. Natalia Pirani Ghilardi-Lopes / Dissertação (mestrado) - Universidade Federal do ABC, Programa de Pós-Graduação em Evolução e Diversidade, São Bernardo do Campo, 2018. / Apesar da importância do monitoramento das unidades de conservação (UCs) marinhas, problemas logísticos e orçamentários dificultam sua realização e, consequentemente, a gestão efetiva dessas áreas. Por isso, é necessária a busca por alternativas de baixo custo que possam auxiliar nessas questões. A abordagem por biótopos associada à ciência cidadã mostra-se adequada para o monitoramento de comunidades marinhas bentônicas por possibilitar extensa amostragem em curto período de tempo e com baixo custo, além de integrar cidadãos ativamente em produções de conhecimento. Essa pode ser uma ferramenta interessante para o monitoramento de UCs marinhas; porém, é importante que a elaboração do protocolo de monitoramento e sua validação sejam realizadas considerando-se as recomendações da literatura. Nesse sentido, este trabalho se propôs a (1) avaliar o status dos protocolos de ciência cidadã para bentos marinho e costeiro no mundo e (2) a propor, aplicar e validar o uso da ciência cidadã associada à abordagem por biótopos como uma ferramenta para o monitoramento de comunidades bentônicas em UCs marinhas. Para isso, realizamos o levantamento e comparação da estrutura de protocolos de ciência cidadã para bentos costeiro e marinho, incluindo o protocolo proposto no presente estudo. Apesar da maioria dos projetos encontrados apresentarem várias das características recomendadas pela literatura, seus principais interesses são a coleta de dados e os resultados oriundos destes, ficando a educação dos CCs, sua inclusão no processo de desenvolvimento do protocolo e sua avaliação em segundo plano. Sugerimos que os protocolos considerem a educação científica e ambiental dos CCs como um objetivo a ser atingido, e nosso protocolo leva tais ideias em consideração. Para embasar a elaboração do nosso protocolo, realizamos um levantamento prévio dos biótopos de um trecho do infralitoral consolidado da Ilha das Palmas (Estação Ecológica Tupinambás, Ubatuba/SP). Nesse levantamento, foram identificados 20 biótopos e três animais vágeis associados em apenas um mergulho. Também foram detectados organismos invasores e a dominância de tapetes na área de estudo. Isso é um demonstrativo de que a caracterização de comunidades marinhas bentônicas utilizando o método visual por biótopos pode agilizar a identificação de possíveis impactos negativos e a realização de planos de prevenção ou mitigação dos mesmos. Cientistas cidadãos (CCs) voluntários foram capacitados no uso do protocolo, que foi dividido em duas etapas: (1) a coleta de dados, que consistiu de registros fotográficos padronizados do costão rochoso; e (2) o processamento das fotografias, que consistiu da identificação (ID) dos biótopos nas fotos em um curso presencial. As fotos obtidas durante a Etapa 1 estão disponíveis na plataforma Zooniverse, através do projeto Monitore Tupinambás (https://www.zooniverse.org/projects/larissakawabe/monitore-tupinambas), no qual qualquer voluntário pode contribuir com as análises, seguindo o tutorial disponível. A avaliação educacional da pesquisa, realizada através de questionários pré e pós-atividade, mostrou principalmente que houve mudanças de percepção dos CCs em relação ao ambiente estudado. Para a validação dos dados da Etapa 2, comparamos as IDs dos biótopos realizadas pelas pesquisadoras (grupo controle) e CCs (grupo experimental), analisando a precisão e acurácia das respostas. Apesar das limitações inerentes do método utilizado (ID por foto) e das necessidades de modificação do protocolo identificadas por CCs e pesquisadoras; os resultados de acurácia e precisão foram comparáveis aos de outros trabalhos similares, demonstrando que esse protocolo, o primeiro a ser desenvolvido com foco em bentos marinho no Brasil, é uma ferramenta promissora para o monitoramento participativo e de longo prazo das UCs marinhas do país, auxiliando na gestão dessas áreas e na educação ambiental e científica dos cidadãos participantes. / Despite the importance of monitoring the marine protected areas (MPAs), logistical and budgetary problems make it difficult to carry out and, consequently, affect the effective management of these areas. Therefore, it is necessary to search for low-cost alternatives that could help with these issues. The biotope approach associated with citizen science could be interesting for the monitoring of marine benthic communities because it allows extensive sampling in a relatively short period of time and at low cost. At the same time, citizens are integrated as active contributors in the knowledge production. This can be an interesting tool for the MPA monitoring; however, it is important that the elaboration of the monitoring protocol and its validation consider the literature recommendations. In this sense, this work aimed to (1) evaluate the status of citizen science protocols for marine and coastal benthos in the world and (2) to propose, apply and validate the use of citizen science associated with the biotope approach as a tool for monitoring benthic communities in MPAs. For this, we conducted a survey and comparison of the structure of citizen science protocols for coastal and marine benthos, including the protocol proposed in the present study. Although most of the projects found present several of the characteristics recommended by the literature, their main interests are the data collection and their results, being the education of citizen scientists, their inclusion in the protocol development process and their evaluation in the background. We suggest that the protocols consider the scientific and environmental education of citizen scientists as a goal to be achieved, and our protocol takes such ideas into account. To support the elaboration of our protocol, we carried out a preliminary biotopes survey of a consolidated subtidal section of the Ilha das Palmas (Tupinambás Ecological Station, Ubatuba/SP). In this survey, 20 biotopes and three associated animals were identified in only one dive. Invasive organisms and carpet dominance were also detected in the study area. This is a demonstration that the benthic marine communities characterization using the biotope visual method can speed up the identification of possible negative impacts and the implementation of prevention or mitigation plans. Volunteer citizen scientists were trained in the use of the protocol, which was divided into two steps: (1) data collection, which consisted of standardized photographic records of the rocky reef; and (2) the processing of the photographs, which consisted of identification (ID) of the biotopes in the photos in a classroom course. The photos obtained during Stage 1 are available on the Zooniverse platform through the Monitore Tupinambás project (https://www.zooniverse.org/projects/larissakawabe/monitore-tupinambas), in which any volunteer can contribute to the analyzes, following the tutorial available. The educational evaluation of the research, performed through pre and post-activity questionnaires, showed mainly that there were changes in perception of citizen scientists in relation to the studied environment. For the data validation of Stage 2, we compared the biotope IDs performed by the researchers (control group) and citizen scientists (experimental group), analyzing their accuracy and precision. Despite the inherent limitations of the method used (ID per photo) and the identification by citizen scientists and researchers of protocol modification needs; the results of accuracy and precision were comparable to those of other similar studies, demonstrating that this protocol, the first developed with a focus on marine benthos in Brazil, is a promising tool for the participatory and long-term monitoring of the country's MPA, assisting in the management of these areas and in the environmental and scientific education of the citizens scientists.

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