The studies presented in this thesis were designed to investigate the effects of reduced sea water pH on the behaviour of intertidal decapod crustaceans, both within the context of the variations occurring naturally in the pH of rock pool habitats, and in relation to predicted changes to ocean pH resulting from ocean acidification and potential carbon dioxide (CO2) leaks from carbon capture storage (CCS) sites. Recent studies on marine fish have shown behavioural disruptions as a result of increased CO2 concentrations in sea water and reduced pH, but the effects on crustaceans are as yet unknown. The first two studies investigated the effects of reduced pH upon the olfactory behaviour of the prawn Palaemon elegans and the hermit crab Pagurus bernhardus, focussing on their responses to food odours. Short-term (five day) exposures to highly reduced pH (pHNBS = 6.60, 6.80) revealed disruptions to the chemo-sensory behaviour of both species with a reduction in their ‘sniffing’ response, and the inability of P. bernhardus to locate the chemical cue. This was also accompanied by elevated haemolymph chloride ions. in In a further study P. bernhardus was subjected to a longer exposure (60 days) and to a range of pH levels (pHNBS = 8.00, 7.90, 7.70, 7.35 and 6.80) in order to detect a threshold for the behavioural disruptions observed, and to determine if there would be any sign of acclimation over a longer period. A clear gradient in the disruptions to the chemo-sensory responses and survival rates of the hermit crabs, and disruption to a physiological marker (elevated haemolymph calcium ions), was found. Possible thresholds for disruption were also identified at levels that match predictions for ocean acidification and leaks from proposed CO2 CCS sites. Some of the crabs in the lower pH treatments exhibited a recovery in their responses by day 60, possibly indicating an acclimation effect. The presence of disruption to haemolymph ion concentrations in both the short and longer term hermit crab studies suggest a mechanism for behavioural disruption. In a final study the effects of reduced sea water pH on a more complex behaviour, involving decision making, was investigated. Reduced sea water pH was shown to disrupt the shell assessment and selection behaviour of P. bernhardus affecting its decision making processes, although not all crabs were affected in the same way. The work presented here therefore demonstrates that reduced sea water pH could have disruptive effects upon both information gathering, via chemo-sensory processes, and decision making in intertidal crustaceans. The mechanism responsible is unlikely to be due to changes in the odour molecule, or physical damage to receptor organs. Rather the observed disruptions could be due (a) to ionic changes, causing metabolic depression or interference with neurotransmitter function, or (b) to disruption to chemoreception per se. Such disturbances to key behavioural processes have implications for inter and intraspecific species interactions and population dynamics in the marine environment. Changes in pH are already experienced by intertidal animals for short periods when rock pools are emersed, but future anthropogencially-induced reductions in sea water pH are likely to cause more sustained and widespread disruptions with, as yet, unpredictable consequences. The differential responses observed between individuals in these studies may warrant further investigation as such differences may provide the basis for selection and adaptation to projected changes in ocean pH.

This thesis presents the first description of the geographic and depth distributions of pelagic decapod shrimps in the area located around the Deepwater Horizon oil spill, based on the NOAA (National Oceanic and Atmospheric Administration) NRDA (National Resource Damage Assessment) trawl samples collected from April – June, 2011. This information is important in ecosystem models investigating trophic effects of the spill because pelagic decapod shrimp are consumed by a variety of organisms occupying higher trophic levels. One of the most abundant and diverse groups of decapods is the Family Oplophoridae. Their roles in pelagic food webs in the Gulf of Mexico (GOM) and other deep-sea ecosystems makes them ideal candidates for study; however, only a limited amount of research has been conducted on their distribution and reproductive biology. In the northeastern GOM, all previous studies have been conducted at Standard Station in the eastern Gulf (27°N, 86°W) (Hopkins and Lancraft, 1984; Hopkins et al., 1989; Hopkins and Gartner, 1992; Hopkins et al., 1994). The current study is unique because 1) it provides data from regions of the Gulf where oplophorids have never been studied, 2) allows for comparisons of distributions and abundances of oplophorid species in both the mesopelagic and bathypelagic zones by using a continuous data set, and 3) compares assemblages from two distinct bathymetric environments in the northeastern GOM: continental slope (200-1000 m bottom depth) and offshore (>1000 m). As the study site also encompasses the region most strongly impacted by the Deepwater Horizon oil spill, these data represent the first quantification of any component of the decapod crustacean assemblage in this location after the oil spill, and will be used for comparison with data obtained during future DEEPEND Consortium (Deep Pelagic Nekton Dynamics of the Gulf of Mexico) cruises to monitor changes, or lack thereof, in the assemblage after exposure to Deepwater Horizon oil and dispersants in the water column.

In 2010, the largest oil spill in U.S history occurred off the coast of Louisiana from April 20th to September 19th, when the well was declared officially sealed by the U.S Coast Guard, after releasing more than 4.4 million barrels of crude oil into the Gulf of Mexico (GOM) (McNutt et al., 2012). This spill was unique because it occurred in deep water approximately 1500 m below the ocean surface. Virtually nothing is known about the effects of oil spills on marine life in the deep sea, and there are limited data on mesopelagic and bathypelagic animals in the GOM before the Deepwater Horizon oil spill (DWHOS). The study presented here focuses on one of the most abundant and diverse groups of pelagic decapod crustaceans in the GOM – the family Oplophoridae and also includes one species from the family Pandalidae. Past studies on pelagic decapod crustaceans have been limited on both spatial and temporal scales. This study is unique because 1) it covers a large temporal range with data collected in 2011 and from 2015-2017, allowing for a more in-depth look at crustacean assemblage patterns, 2) it allows analysis of seasonality in reproduction, about which little is known for any deep-sea species, and 3) it assesses the potential effects of the Loop Current on species distribution and abundances, about which little is known. This information is important in understanding how the DWHOS may have affected the GOM ecosystem because pelagic decapod crustacean are intermediate components of the food web, and are in turn preyed upon by higher trophic levels. Unfortunately, there were little data on the mesopelagic ecosystem from this region before the spill, with the exception of a site in the eastern GOM (Standard Station, Hopkins et al., 1989; Hopkins et al., 1994). Therefore, these data, which incorporate samples taken one, five, six and seven years after the DWHOS, were analyzed with respect to year and season to determine if any trends were present. Results indicate that both biomass and abundance were significantly higher in 2011, than in subsequent years, indicating that the ecosystem has been declining since 2011. These two parameters were also lower in Loop Current water when compared to Common Water at all depths up to 1200 m, indicating that the Loop Current does have effects on deeper waters. The information obtained from this thesis will also act as a reference state for future studies in the GOM to monitor changes, or lack thereof, in the assemblage of deep-sea oplophorid and pandalid crustaceans.

Dégradés par plusieurs siècles d’endiguement et menacés par les effets du changement climatique, les marais intertidaux européens font aujourd’hui l’objet d’un nombre croissant de restaurations par rétablissement des marées sur d’anciennes zones endiguées, suivant une tendance générale appelée dépoldérisation. Cette thèse décrit la trajectoire de restauration des marais intertidaux à partir des communautés de necton (i.e., poissons et crustacés décapodes), sur la base de deux sites dépoldérisés accidentellement dans l’estuaire de la Gironde : le marais de Mortagne et l’île Nouvelle. L’évolution du necton dans les marais dépoldérisés est caractérisée à travers une approche synchronique à l’échelle de la mosaïque des habitats estuariens. La composition du necton dans les marais dépoldérisés est en grande partie similaire à celles des milieux intertidaux naturels et se différencie nette-ment des marais endigués, où les espèces exotiques d’eau douce prospèrent. Les marais restaurés apparaissent particulièrement attractifs pour le mulet porc, Liza ramada. La distribution des traits fonctionnels au sein des communautés de poissons révèle un changement de structure fonctionnelle au cours de la dépoldérisation, le temps de restauration étant inféré à partir d’un gradient de naturalité des habitats estuariens. En particulier, la spécialisation, la dispersion et la richesse fonctionnelle augmentent au cours de la restauration. Concernant l’évolution des règles d’assemblage, aucune tendance claire ne se dégage : les patrons diffèrent selon les traits fonctionnels.La dynamique temporelle de la composition des communautés de necton dans l’un des sites dépoldérisés montre une succession de trois phases au cours des quatre années suivant la restauration. Un changement plus abrupt concernant l’abondance de certaines espèces et la structure fonctionnelle des communautés est identifié au milieude la seconde phase, moins de deux ans après la dépoldérisation. La cinétique de transformation des communautés est probablement ralentie par le drainage incomplet du site dans les premiers temps de la dépoldérisation. Les résultats de cette thèse permettent de mieux comprendre la trajectoire de restauration des marais intertidaux, sans intervention humaine, tout en soulignant les atouts et les limites de certains modèles théoriques utilisés en écologie de la restauration. / European intertidal marshes have greatly declined during the past centuries because of land claim andhave recently been threatened by the effects of climate change. In recent years, an increasing number of tidal resto-ration projects have been implemented, following a global trend termed de-embankment. This thesis describes therestoration trajectory of tidally restored marshes from the response of nekton (i.e., fish and decapod crustaceans)based on two storm-breached study sites in the Gironde estuary : the Mortagne marsh and the Nouvelle island.Nekton assemblage composition of tidally restored marshes was described through a whole-estuary approach en-compassing natural, restored and dyked habitats. Nekton assemblages of tidally restored marshes showed highcompositional similarity with natural intertidal habitats and greatly departed from dyked marshes. Dyked marsheswere characterized by high occurrence of freshwater exotic taxa. Tidally restored marshes seemed particularly at-tractive for the thin-lipped grey mullet, Liza ramada. The functional traits’ distribution within fish communities revealeda change in functional structure in the course of restoration using the naturalness state of habitats as a proxy forrestoration time. Most notably, functional specialization, dispersion and richness increased with restoration time.No clear pattern of change was observed in community assembly over time ; trends chiefly varied with respect totraits. Temporal trends in one of the restored sites revealed three phases in the first four years of tide restoration.The abundance of several species and the community functional structure changed more steeply in the midst ofthe second phase, less than two years following tide restoration. Community turnover was probably delayed dueto incomplete drainage of the site in the early stages of restoration. The results of this thesis lead to a better un-derstanding of the restoration trajectory of tidal marshes without human intervention and highlight the strengths andweaknesses of some theoretical models used in restoration ecology.