<p>Natural and constructed rocky reef habitats constitute important areas for lithophilic spawning fishes and their embryonic and larval offspring. Interstitial spaces created by the structure of rocky reefs create micro-environments where incubating embryos and juvenile fishes are potentially protected from predators. However, if interstitial spaces are filled or blocked by sediment deposition or biofouling, the reef structure may lose the protective benefits for embryonic and larval fish survival. Lake whitefish (<i>Coregonus clupeaformis</i>) and walleye (<i>Sander vitreus</i>) are native Great Lake lithophilic broadcast spawning fish that use rocky spawning habitats that are vulnerable to degradation caused by deposition of suspended sediments. To restore degraded rocky reef habitat, common practices include addition of material to existing reef structures or construction of new reefs, but both of these practices can be costly and time intensive. In this study, we measured the effect of different types and amounts of sediment cover on hatching success of walleye eggs and assessed if differences in female walleye (female length and egg size) account for tolerance to sediment cover. Additionally, we explored an alternative approach for reef restoration, custodial maintenance, in which we created two novel devices to potentially clean rocky reef habitat. We carried out two laboratory experiments in 2018 and 2019 to test the effect of sediment cover on hatching success of walleye eggs (2018) and to test how female identity and female length or egg size may interact with sediment cover to influence hatching success (2019). We exposed walleye eggs to instantaneous sediment cover (0 mm – 7mm) of either sand (course) or silt (fine) sediments from fertilization until day 15 of incubation. Our results indicated that walleye eggs were sensitive to silt cover (71% mortality- 2 mm cover silt) but not sand (47% mortality- 7mm cover sand). While there was an indication that hatching success was marginally related to female length and egg size, we concluded that sediment cover seemed to have similar effects on eggs, regardless of female length or egg size. The susceptibility of walleye eggs to mortality caused by sediment cover underscores the need for non-degraded spawning habitat. Our two cleaning devices used either propulsion or pressurized water jets to clean sediments from the rocky structure as they were towed behind a small vessel (i.e., did not require the use of SCUBA divers). We used devices to clean two natural rocky reefs in Saginaw Bay, Lake Huron in 2018 and 2019. We measured relative hardness before and after use of devices on cleaned and uncleaned study plots to determine effectiveness of devices. In addition, we measured egg deposition by fall (lake whitefish) and spring (walleye) lithophilic spawners on study plots to determine potential differences in fish usage of cleaned and uncleaned areas. We found that cleaning devices contributed to changes in relative hardness among study plots. Egg deposition was also variable on study plots but in general, egg deposition was consistently highest on treatment plots cleaned by our device that used propulsion. The practicality of cleaning devices was seemingly related to the magnitude of degradation of rocky reefs, nevertheless, our results show that the use of these or similar devices may potentially increase egg deposition by creating areas of higher-quality habitat. While more testing is necessary to fully understand the potential of our reef cleaning devices, this two-year study suggests that these devices may be capable of restoring degraded rocky spawning habitat which could potentially minimize the negative effects associated with sediment degradation on lithophilic spawning fish.</p>

Coral reefs have one of the highest levels of biodiversity of all ecosystems in the world and are important for both human livelihood and food security throughout many tropical countries. However, due to increased anthropogenic pressure on marine ecosystems, especially during the last couple of decades, coral reefs have become critically over-fished, and many reefs are now in a degraded state and are facing additional future threats due to further over-exploitation, chemical pollution, sedimentation, and effects of climate change. The main aim of this PhD thesis was to understand effects of anthropogenic disturbances on tropical coastal ecosystems and fish connectivity for coastal management purposes. Therefore, linkages between anthropogenic disturbance and corals were investigated (Paper I), as well as interactions between coral reef habitat and associated fish assemblage (Paper II). Furthermore, connectivity between coral reefs and other tropical coastal ecosystems was explored (Paper III), as well as fish migration to reproduction sites (Paper IV), and evaluations of spatial ecology methods (Paper V). The result showed that coral reefs that are already exposed to disturbances, such as freshwater and nutrient run-offs, may be more sensitive to climate change, in terms of increased sea surface temperatures (Paper I). In addition, there were also clear linkages between coral reef quality, in terms of coral coverage, and fish assemblages, which displayed high spatial variability and suggesting patchy recovery after the 1997/1998 bleaching and subsequent coral mass mortality event (Paper II). This highlights the importance of understanding effects of disturbances on corals, especially in terms of synergistic effects between increased water temperatures and other coastal stressors such as decreased salinity and increased nutrients; and the indirect effects of habitat degradation on the fish community. Linkages between fish and different coastal habitats were further explored. The results showed that coral reefs were strongly connected with mangrove and seagrass beds, through ontogenetic migration of fish (Paper III). Migrations to spawning sites of groupers were related to lunar activities when thousands of fish gather for reproduction purposes during new moon, which increases the risk of over-exploitation (Paper IV). The results emphasises the importance of protecting key areas such as nursing grounds and reproduction sites. Furthermore, acoustic telemetry has become an increasingly common method in studies of fish movement, and the results showed that efficiency of acoustic arrays may increase depending on deployment strategies and habitat characteristics (Paper V). In conclusion, the results from this PhD thesis emphasises the importance of protecting coral reef habitats, as well as identifying related susceptible tropical coastal areas, such as nursing grounds and reproduction sites. Indeed, a better scientific understanding of coral reef ecology and indirect and direct effects on fish assemblages are needed for efficient and accurate coastal management decisions. / <p>At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 5: Manuscript.</p>

The Oxford English Dictionary defines 'omnifarious' as 'comprising or relating to all sorts or varieties', which quite accurately captures the very nature of octocorals and this thesis. The research reported here, aims to describe undocumented communities of coral reef organisms - the octocorals - which are an emergent dominant component within their threatened ecosystem of the Caribbean. Within the last four decades, coral reefs worldwide have experienced a precipitous plunge in many ecosystem services they provide, and most notably in the Caribbean. The foundation to reef resilience is structured on the ecosystem's ability to repair and restructure itself in the face of environmental shifts. These intricately complex strategies of resilience depend on repair mechanisms provided by a source of biodiversity, much of which remains poorly understood. This work explores many facets of the functioning within this potential future coral reef ecosystem. These reports are one of the most significant contributions to documenting and describing octocoral biodiversity (e.g. species, genetic, and community diversity) of the wider ecoregion of the Mesoamerican Barrier Reef System within the last three decades.

A travers le monde, les zones côtières abritent une grande diversité d’ingénieurs de l’écosystème accomplissant des fonctions clés comme le recyclage de la matière organique et des nutriments. Les habitats résultants de l’activité biologique de ces espèces sont exposés à de nombreuses perturbations comme la surpêche, le piétinement ou via l’aménagement des côtes. Dans ce contexte, il est urgent de comprendre le fonctionnement de ces habitats ingénieurés et comment ils sont affectés par des perturbations croissantes. Pendant ma thèse, j’ai utilisé l’habitat récifal construit par le polychète grégaire tubicole Sabellaria alveolata comme cas d’étude. Tout d’abord, les changements environnementaux et biotiques associés à la mise en place d’un récif à S. alveolata et à sa perturbation croissante ont été évalué, se concentrant sur les paramètres du sédiment (e.g. granulométrie, contenu en matière organique) ainsi que la diversité taxonomique et les assemblages d’espèces. De manière similaire, le troisième article se penche sur le fonctionnement trophique de la communauté récifale et d’une communauté contrôle afin de comprendre les effets de la mise en place de l’espèce ingénieur sur les transferts de carbone, s’intéressant successivement à l’ensemble de la communauté des consommateurs, aux consommateurs primaires et à l’importance des sources de nourriture autochtones (microphytobenthos et Ulva sp.) vs allochtone (phytoplancton). Dans cette partie, j’ai utilisé les isotopes stables du carbone et de l’azote ainsi que différentes approches analytiques telles que des mesures de la niche isotopique et des modèles de mélange. L’article 2 a pour but de comprendre les interactions entre complexité de l’habitat récifal, hétérogénéité des sources de nourriture autochtones et échelles spatiales dans l’explication des variations du rapport isotopique du carbone de S. alveolata et d’un suspensivore associée. Dans les deux derniers chapitres, j’ai traité la question du fonctionnement de l’habitat ingénieuré de manière directe, en utilisant des incubations de carottes benthiques pour mesurer des flux biogéochimiques (e.g. demande en oxygène), ou indirecte, en utilisant des indices de diversité fonctionnelle et isotopique intégratifs. Cette dernière partie révèle l’existence d’un optimum de densité de S. alveolata, utilisée comme proxy des perturbations, où la niche trophique et le fonctionnement biogéochimique du récif sont tous les deux maximaux. / Coastal zones worldwide are home to a large diversity of ecosystem engineers that perform key functions such as the recycling of organic matter and nutrients. The habitats resulting from the biological activity of these species are exposed to numerous disturbances such as over harvesting and trampling or via coastal modification. In this context, it is becoming key to understand the functioning of these engineered habitats and how they are affected by increasing disturbances. During my PhD, I used the reef habitat built by the gregarious tubiculous polychaete Sabellaria alveolata as a study case. First, the environmental and biotic changes associated with the establishment of a S. alveolata reef and its increasing disturbance were assessed, focusing on sediment characteristics (e.g. grain-size distribution, organic matter content) along with taxonomic diversity and species assemblage. In the same vain, the third article looks into the trophic functioning of the reef community and a control community to understand the effects of the establishment of the engineer species on carbon transfers, successively looking at the whole consumer community, the primary consumers and the importance of autochthonous (microphytobenthos and Ulva sp.) vs allochthone (phytoplankton) food sources. In this part, I used carbon and nitrogen stable isotopes and different analytical approaches such as isotopic niche metrics and mixing models. Article 2 aims towards understanding the interactions between reef habitat complexity, autochthonous food source heterogeneity and spatial scales in explaining the carbon isotopic ratio variations of S. alveolata and an associated suspension-feeder. In the last two chapters, I address the functioning of the engineered habitat either directly, using benthic core incubations to measure biogeochemical fluxes (e.g. oxygen demand) or indirectly, through the use of integrative functional and isotopic diversity indices. This last part reveals the existence of an optimum value of S. alveolata density, used as a disturbance proxy, where the trophic niche and the biogeochemical functioning of the reef are both maximal.