This thesis focuses on the investigation of reef communities of the Saint Peter and Saint Paul´s Archipelago (SPSPA) across an euphotic/mesophotic depth gradient. Sampling was performed on shallow and mesophotic areas (0 to 90 m depth) using SCUBA and a Remotely Operated Vehicle (ROV). The present work is composed of four chapters: Chapter 1 deals with the quantitative assessment of reef fish communities, which were divided in three distinct communities associated with different depth strata. Clear shifts in habitat use and in size-frequency distributions were recorded for some species. Abundance of black-corals and depth were the most important factors affecting the structure of fish communities, with a clear association of fish with branching black-corals in the mesophotic zone. Chapter 2 presents the first detailed qualitative assessment of benthic communities of the SPSPA. The influence of biotic and abiotic variables shaping the structure of the benthic communities was evaluated. A total of 77 benthic taxa belonging to six major functional groups were recorded. Macroalgae was the richest group (41 infrageneric taxa), with 17 new records for the SPSPA. Turf algae were the most abundant group on both shallow and mesophotic reefs. Two distinct communities were detected: a shallow one composed primarily by the zoanthid Palythoa caribaeorum (Duchassaing and Michelotti, 1861), the fleshy alga Caulerpa racemosa (Forsskål) J. Agardh, crustose coralline algae (CCA) and Bryopsis spp., and another deeper community dominated by CCA, bryozoans and scleractinian corals. Abiotic variables were the most important predictors of benthic community structure. Chapter 3 brings information on abundance, distribution size and associated fauna (epibionts) of black-corals. Although two species of black-corals, Tanacetipathes hirta (Gray, 1857) and T. thamnea (Warner, 1981), are known to occur in the SPSPA, they are undistinguishable underwater. Epibiosis, mainly by zoanthids and entanglement by fishing monofilament were important factors negatively affecting the health of black-coral colonies. Black-corals were intensively used as refuge by reef fish, especially by the endemic oblique butterflyfish Prognathodes obliquus (Chaetodontidae). A single black-coral colony repeatedly visited and monitored for ten years showed a decrease in vitality since the first observation, mainly related to fouling by algal detritus and entanglement by fishing monofilaments. Chapter 4 discusses the ecology (abundance, distribution and habitat preferences) of the fireworm Hermodice carunculata, a major predator on mesophotic zone of SPSPA. A total of 278 individuals of bearded fireworm were observed, with significant difference in abundance between euphotic and mesophotic zones. A direct association of H. carunculata with black-corals (Tanacetipathes spp.), the scleractinian Madracis decactis and depth was found. A final session with concluding remarks wraps up information on the ecology of Mesophotic Reef Ecosystems highlighting their possible importance for the stability and persistence of reef fish and benthic communities of the SPSPA, which are under threat of overfishing and climate change, thus requiring urgent protective measures. / O tema central desta tese é estudar a ecologia de comunidades recifais ao longo do gradiente de profundidade no Arquipélago São Pedro e São Paulo (ASPSP), com ênfase nos Ecossistemas Recifais Mesofóticos (ERMs). As amostragens foram realizadas da superfície até a zona mesofótica (0 a 90 m de profundidade), utilizando SCUBA e Veículos Submersíveis de Operação Remota (VSORs). Esta tese é composta por quatro capítulos. No Capítulo 1 foi realizado uma avaliação quantitativa das comunidades de peixes, as quais formaram três comunidades distintas associadas aos diferentes estratos de profundidade e ao uso de diferentes hábitats de acordo com mudanças ontogenéticas (tamanho do corpo). Corais-negros e profundidade foram os fatores mais importantes na estruturação das comunidades de peixes, com uso intenso dos corais-negros por peixes na zona mesofótica. O Capítulo 2 apresenta a primeira avaliação qualitativa das comunidades bentônicas do ASPSP, além de uma avaliação da influência de variáveis bióticas e abióticas na estruturação das comunidades. Foram registrados 77 táxons bentônicos pertencentes a seis grupos. Macroalgas foi o grupo mais rico (41 táxons), com 17 novos registros para o ASPSP. Algas formadoras de tufos (turf) constituíram o grupo mais abundante em ambos os ambientes, eufótico e mesofótico. Foram observadas duas comunidades distintas: uma superficial composta principalmente pelo zoantídeo Palythoa caribaeorum, a pela alga Caulerpa racemosa carnuda, algas calcárias incrustantes (CCA) e Bryopsis spp, e outra mais profunda dominada por CCA, briozoários e corais escleractíneos. As variáveis abióticas, particularmente profundidade e luz, foram mais importantes na estrutura da comunidade bentônica. O Capítulo 3 traz informações sobre a abundância, distribuição, tamanho e vitalidade de corais-negros. Duas espécies de corais-negros, Tanacetipathes hirta (Gray, 1857) e T. thamnea (Warner, 1981), foram identificadas. Epibiose por zoantídeos e estrangulamento por monofilamentos afetaram negativamente as colônias de coral negro, uma delas monitorada durante dez anos. Esta última apresentou uma diminuição da vitalidade devido principalmente à presença de algas e estrangulamento por monofilamento. Corais-negros formam um grupo-chave na zona mesofótica do ASPSP, sendo intensamente utilizados como hábitat por diversos peixes recifais, principalmente espécies endêmicas (e.g., o peixe-borboleta Prognathodes obliquus). O Capítulo 4 aborda a ecologia do principal predador de invertebrados bentônicos na zona mesofótica do ASPSP, o verme-de-fogo Hermodice carunculata, descrevendo sua abundância e distribuição batimétrica e discutindo seu potencial em impactar as comunidades bentônicas, especialmente os corais escleractínios e os corais-negros na zona mesofótica do ASPSP. Observou-se um total de 278 indivíduos, com diferença significativa na abundância entre as zonas eufótica e mesofótica. Foi encontrada uma associação direta entre H. carunculata e 1) corais-negros (Tanacetipathes spp), 2) o coral escleractíneo Madracis decactis e 3) profundidade. Sugere-se aqui que os ecossistemas mesofóticos são essenciais para a estabilidade para as comunidades recifais eufóticas do ASPSP, tornando urgente a necessidade de novos estudos, principalmente com foco no potencial impacto da pesca e mudanças climáticas.

Coral reefs are being negatively impacted by various causes worldwide, and direct intervention is often warranted following disturbance to restore or replace lost ecosystem structure and function. An experimental coral reef restoration study involving standardized artificial reef modules (ReefballsTM) was conducted in Mexico’s Yucatan Peninsula in the towns of Puerto Morelos and Akumal. The purpose was to explore the use of artificial structure for restoration and mitigation applications in a highly diverse and dynamic Caribbean coral reef environment by applying and evaluating the performance of select experimental treatments hypothesized to accelerate development of the associated biota. The first treatment consisted of invertebrate enhancing artificial substrate padding material, which provided structurally complex refuge space for mobile epifaunal/infaunal invertebrates and other benthic organisms. The second treatment consisted of coral transplants, intended to provide additional structural complexity and kick-start development of stony coral populations. The third treatment consisted of settlement plates which were intended to provide data on coral recruitment and survival rates. Multiple hypotheses relating to the interactions between experimental treatments and the resulting macroalgal, non-coral invertebrate, stony coral, and coral reef fish assemblages were examined, and comparisons were made between natural and artificial substrates. In Puerto Morelos there were 40 modules; 10 controls and 10 of each of 3 treatments: substrate pads, coral transplants, and settlement plates. In Akumal there were 12 modules; 6 controls and 3 of each of 2 treatments: substrate pads and settlement plates. Following module deployment, 6 biannual monitoring trips were made over the course of three years to assess the development of the biota, with a final 7th trip made six years post-deployment. Divers conducted non-destructive visual surveys to evaluate total abundance, species richness, size class distribution, and assemblage structure of coral reef fishes. Other monitoring work included coral recruit surveys, mobile epifaunal invertebrate collections from substrate pads, and digital imaging of coral transplants, natural reef reference corals, and benthic quadrat areas. Hurricane Dean compromised the Akumal study site during the first year of the study, but Puerto Morelos was unaffected. There the modules developed biotic assemblages that differed from what was found on the natural reef, and the data suggests that the substrate pads may have had an effect on the development of faunal assemblages. Lobophora variegata macroaglae and Desmapsamma anchorata sponge were the major contributors to benthic community composition, and both had significantly greater coverage on the substrate pads treatment modules. Lobophora grew rapidly and peaked within the first year, while sponges increased steadily throughout the first three years of the study, surpassing the coverage of macroalgae before the end of the second year, much to the detriment of coral transplants and many coral recruits. By the end of the study, over 75% of the transplants were overgrown by D. anchorata, and density of new coral recruits on the Pads treatment modules was lower than the other treatments and controls. Coral recruitment was dominated by Porites astreoides on all treatments and controls, and the number of corals increased steadily throughout the study. The controls had consistently greater numbers of corals than the treatments, as well as lower percent coverage of macroalgae and sponges. Total abundance and species richness of reef fishes was generally unaffected by the treatments. However, at the family and species level, several differences were detected, particularly for the substrate pads treatment and to a lesser extent for the coral transplants treatment. For future restoration or mitigation efforts utilizing similar or identical treatments to artificial substrates, this study suggests that, in the absence of routine maintenance, greater success may be achieved after waiting several years post-deployment for the initial wave of unchecked growth by benthic organisms (i.e., macroalgae and sponges) to reach a balance point before a large investment of resources is devoted to coral transplanting. Further recommendations include routine monthly or quarterly on-site maintenance to enhance transplant survival, as well as a longer monitoring window to assess community development in response to experimental treatments. The results of this study suggest that the experimental treatments did indeed have an effect on the biota, but whether or not the effect was beneficial largely depends upon perspective. The Pads treatment in particular had the greatest effect on both reef fish and benthic community development, however, it was not beneficial for stony coral recruitment. Additional research is needed to fully understand the long-term performance and effects of the padding material on biotic assemblage development for future restoration or mitigation projects.