Runnelling is a popular method of physical habitat modification employed on saltmarshes to control pest mosquito populations. The runnelling method involves linking the tidal source to isolated mosquito breeding pools via shallow channels that enable slow water movement of low amplitude tides. Increased tidal flushing inhibits mosquito development. The range of organisms which inhabit saltmarsh are likely to be influenced by altered tidal conditions as they exhibit specific physicochemical requirements for feeding, burrowing or growth. The dynamic nature of saltmarsh may mean that changes to the tidal frequency of a particular region of the saltmarsh promotes extension of marine-like conditions. Because runnels increase the frequency of flooding tidal events in specific regions of the saltmarsh this study predicted that resulting changes would be evident in the physical conditions of saltmarsh substrate, in the transport of buoyant vegetative propagules, in the population characteristics of surface grazing snails and in the density and aperture of crab burrows after flooding and non-flooding tidal events. The physical impacts of runnelling were determined at three marshes which appeared similar in terms of topography, substrate and tidal conditions. Soil water content and consolidation were measured using two sampling protocols: a) comparisons between modified and unmodified shores; and, b) comparisons with increasing lateral distance across the shore from the runnel edge. At one marsh, moisture levels were significantly higher at runnelled than at unrunnelled sites when tides filled the runnels, but this pattern was not found at the other marshes. Soil consolidation was greater at higher shore heights, but was not different between runnelled and unrunnelled shores. Measurements at different lateral distances from runnels demonstrated higher moisture levels and lower consolidation up to 5 m from the edge but not further away. Groups of marked Avicennia marina propagules were released at the three runnelled saltmarshes during flooding and non-flooding tidal events. Groups of propagules released within 10 m of a runnel were always transported significantly further from the starting position and further up the saltmarsh shore after both flooding and non-flooding tides than any other groups. In addition, the pattern of stranding on saltmarsh for significantly different groups was closely associated with the path of runnel construction so that propagules were located either in the runnel or in depressions linked to the runnel that had been isolated mosquito-breeding pools prior to runnelling. It is likely that altered physical soil conditions significantly affected the distribution and size structures of Salinator solida and Ophicardelus spp. snails recorded at the three saltmarshes. The interaction of tidal period and the presence of a runnel contributed to patterns with significant differences between runnelled and unrunnelled regions of the marsh. Generally, the runnel population of snails exhibited flood-like features even during non-flood periods. The distribution and size classes of snails did not differ with lateral distance from runnels. The burrow characteristics of the crab Helograpsus haswellianus were compared to increase the accuracy of estimating abundance from burrow counts. Including only those burrows which were obviously maintained by resident crabs significantly increased the confidence limits of estimating crab abundance using only burrow density counts. This method was applied to runnelled and unrunnelled sites to assess any changes in the density of burrows associated with the presence of runnels. Again, it is likely that physical soil conditions resulting from increased tidal frequency at the runnel did influence crab burrowing with fewer small burrows being found at the runnelled site, low on the shore. In addition, mid- and large-sized burrows tended to dominate close to the runnel edge. Site-specific soil characteristics may help to explain the lack of continuity in patterns associated with runnel effects on non-target saltmarsh resources. While the runnel may increase the soil water content of clayey substrates at some sites it could also result in de-watering of porous sandy soils at other shores. This was evident in the structure of the snail population and distribution of crab burrows which appeared to reflect altered soil physical characteristics associated with the runnel. Runnelling does affect non-target organisms in saltmarsh. However, the scale of impact was usually locally restricted (< 10 m from the runnel edge). The fact that patterns were not recorded at all sites suggests that the influence of runnels is variable and limited by substrate and some biological conditions. Given the efficiency and popularity of runnelling as a physical control method for reducing pest vector mosquito habitat, this study found no evidence to suggest that its use should be discontinued on any ecological basis measured.

In estuarine and other aquatic systems, it is possible for water to transport locally produced carbon (food) across habitat boundaries, and provide nutrition for animals remote from the carbon source. In estuarine and marine systems, early work examining the movement of carbon from saltmarsh habitats in the USA suggested that carbon may move large distances from inshore to offshore environments. Upon closer examination, however, evidence did not support this paradigm of large-scale carbon movement, referred to as the outwelling hypothesis, in some estuaries. Physical characteristics of estuaries in which large-scale carbon movement did not occur, such as restricted access to the sea, were proposed as a possible explanation, and for these estuaries, movement of carbon among estuarine habitats was considered more likely. A mosaic of saltmarsh and mangrove habitats dominate the subtropical barrier estuary of southern Moreton Bay, Queensland, but there have been no studies that examine the movement of carbon among habitats within this system. Previous studies that examine the movement of carbon have mostly been done in saltmarshes in the northern hemisphere or in tropical mangrove systems. Different vegetation and tidal regimes in temperate marshes of the northern hemisphere preclude generalisations of carbon movement to tropical and subtropical systems. Our understanding of carbon movement in tropical systems may extend to subtropical waters, but the saltmarsh-mangrove mosaic in the subtropics distinguishes them from their tropical counterparts. The mosaic of saltmarsh and mangrove habitats among the barrier islands of southern Moreton Bay thus provide a unique opportunity to examine the small-scale movement of carbon among adjacent habitats in a subtropical system. Stable isotopes of carbon have been used successfully to trace the transfer of carbon from autotrophs to consumers at a range of spatial scales. This method is able to distinguish among carbon sources where autotrophs have different ratios of 13C/12C, and consumers take on the ratio of their food source. The success of stable isotopes in clarifying food web processes, however, depends on isotope ratios changing in predictable ways as elements are processed. As isotope ratios may be influenced by changes in productivity, and differences in nutrient source, they may vary across small and large spatial scales that may confound interpretation of food web processes. In this study I measured small and large-scale spatial variability of three estuarine autotrophs (the saltmarsh grass, Sporobolus virginicus, the seagrass Zostera capricorni and the algal community epiphytic on Z. capricorni) and showed the small-scale spatial variability to be negligible and insufficient to preclude the use of carbon and nitrogen isotopes in food web studies. Large-scale variability was more pronounced and may be useful for spatial correlation of food webs for more mobile species. The small-scale homogeneity and clearly distinguished isotope ratios of the dominant autotrophs in adjacent saltmarsh and mangrove habitats in southeast Queensland are therefore ideally suited to the study of small-scale carbon movement between adjacent habitats. Carbon isotopes of estuarine invertebrates were used to estimate the movement of particulate carbon between adjacent saltmarsh and mangroves at the tens-of-metre scale. Carbon isotope values of two crab species (Parasesarma erythrodactyla and Australoplax tridentata) and two snail species (Salinator solida and Ophicardelus quoyi) in saltmarsh closely match those of the saltmarsh grass, and suggest that the movement and assimilation of carbon occurs at a scale much smaller than has previously been examined. In mangroves, the results of this study indicate that microphytobenthos with some contribution of mangrove carbon is the most likely food source for P. erythrodactyla and A. tridentata, although contribution of carbon from saltmarsh is also possible. Under this latter scenario, carbon movement in mangroves would be considered to occur at a scale larger than that in saltmarsh habitat. A study that examined the movement and assimilation of carbon by crabs and an estuarine slug (Onchidina australis) at a finer resolution (i.e. metres) supported the original findings and indicated that the movement and assimilation of carbon occurs 5 - 8 m either side of the saltmarsh-mangrove interface. At this small-scale, the movement and subsequent foraging of crabs among habitats, the movement of particulate carbon among habitats, or a combination of crab and particulate carbon movement are three alternative models that provide plausible explanations for the pattern in carbon isotope values of crabs. Crab movement among these habitats was measured using an array of pitfall traps perpendicular to the saltmarsh-mangrove interface. To test for carbon movement, samples of detritus were collected at 2 m intervals across this same interface and the carbon isotopes analysed. For the majority of crabs (up to 90% for both species), movement up or down the shore was less than 1 m from the place of initial capture. Thus, crab movement cannot explain the trend in carbon isotope values of crabs. The pattern in detrital isotope values was similar to that of crabs and indicates that the movement of particulate carbon across the saltmarsh-mangrove interface is the most likely explanation for crab isotope ratios. Sources of carbon for estuarine invertebrates can also depend on the size of the saltmarsh patches. Examination of the movement and assimilation of carbon by crabs in saltmarsh patches of different sizes adjacent to mangroves indicates that saltmarshes less than 0.3 ha in area are subsidised by the import of allochthonous carbon, most likely from mangroves. These findings contribute substantially to our understanding of the food web value of estuarine habitats and provide an important link between landscape and food web ecology. They also have important implications for determining the conservation value of estuarine habitats with respect to their functional (food web) value. The scale-dependent sampling used in this thesis also provides important evidence for the fine-scale movement of estuarine carbon that has not previously been examined.

Intertidal wetland habitats in southeastern Australia have changed significantly during the past sixty years. Mangrove habitats have expanded both seawards and landwards, the latter being at the expense of saltmarsh habitats. This relatively common phenomenon is generally suggested to be an outcome of sea-level rise. Several factors potentially responsible for this change are examined, including changes in mean sealevel during the past 50 to 100 years, changes in climate, population growth, catchment landuse, and estuary type. A protocol for mapping estuarine habitats was developed and implemented, incorporating the application of geographic information systems. Spatial and temporal coastal wetland habitat changes at nine sites along the New South Wales coast are illustrated. These habitat dynamics were shown to not correlate between sites. The results demonstrate that sea-level rise in this region cannot solely account for the extent of change during the past sixty years. With the exception of one site (Careel Bay), there have been no correlations between contemporary mean sea-level rise and mangrove incursion of the saltmarsh habitats at the study sites, or with rainfall patterns, at the scale of observation in this study, which was largely decadal. The only correlations determined during this study have been between population growth and coastal wetland habitat dynamics in some sites. In spite of saltmarsh habitat loss being a regional phenomenon, local factors appear to have a profound bearing on the rates of change. Neither contemporary mean sea-level rise, rainfall patterns, estuary type, catchment landuse, catchment natural cover nor population pressure can account solely for the patterns in the spatial and temporal dynamics of the coastal wetlands of New South Wales. It seems apparent that regional factors create preconditions favourable for mangrove incursion, but that localised conditions have been responsible for the extent of these incursions from site to site. That is, despite higher sea-level and greater rainfall, the extent of change has been determined by the unique characteristics of each site. The results have important implications for current estuary management practices in the state of New South Wales. The lack of spatial and temporal trends in coastal wetland habitat dynamics point to the need for management to be conducted on a localised, rather than regional scale. Additionally, anthropogenic influences must be carefully managed, since the extent of mangrove habitat expansion into saltmarsh areas is unlikely to be a natural occurrence.

The Tay estuary is situated on the east coast of Scotland. The estuary is dominated by sediment biotopes, including mudflats which support sparse beds of two nationally scarce seagrass species, Zostera marina var. angustfolia (Hornem.) and Z. noltii (Hornem.). Seagrasses have been described as ecosystem engineers, shaping their sediment environment, and this may increase sediment deposition and stability. In this thesis the ecosystem engineering characteristics of seagrass habitats are explored. In 2008, the distribution of Zostera spp. in the Tay estuary was surveyed and mapped for the first time. Sediments within beds of Z. marina and Z. noltii were compared to investigate the influence of seagrasses on sediment characteristics. To explore the role of seagrass in sediment deposition and erosion, and coastal stability, sediment depth measurements were made in patches of Z. noltii, Z. marina and bare sediment over one year. The role of the root/rhizome system on sediment retention over winter was also considered. Sediment deposition in Z. noltii beds, and the influence of the plants on near-bed flow dynamics was further explored in the laboratory, using an 8 m seawater flume. In the field the retention of particles over 2 and 14 tides was measured, and the results of this experiment led to a study of the influence of leaf and sediment biofilms on particle retention, using the novel method of magnetic particle induction (MagPI). The efficacy of artificial seagrass beds and Z. noltii transplantation as habitat restoration techniques were compared over one year. During the trial, sediment deposition and changes in sediment characteristics were determined, and the protection given to saltmarsh cliffs fringing the study plots was assessed. Mechanisms underlying the results are suggested and the findings discussed. This study provides an insight into the ecology of seagrass in the Tay estuary and its role as an ecosystem manager. It may offer valuable data which could be utilised for future conservation policies, habitat restoration schemes and management planning of the area.

Increasing human pressure combined with sea level rise and increased storminess is threatening coastal ecosystems around the world. Among these ecosystems, saltmarshes are particularly endangered due to their position in temperate areas with low wave action where human density is often high (e.g. estuaries). Around the UK, centuries of land reclamation have led to a substantial decrease of the area of saltmarsh. Over the past decades, restoration schemes have been implemented in numerous coastal locations in an attempt to counteract this loss. Such schemes involve allowing sea water to inundate a previously embanked area and letting the vegetation develop naturally, thereby reverting to saltmarsh through natural colonisation. However, surveys of restored areas that have looked at the recovery of plant species diversity or functional characteristics often show that restored saltmarshes do not reach the state of a natural saltmarsh ecosystem. While there is much data at the species level, recovery of plant intra-specific diversity (genetic diversity) has not been assessed in restored saltmarsh although this component of biodiversity is receiving increasing attention for its effect on ecosystem function. This thesis represents the first attempt to (1) characterize the nation-wide genetic structure of two important north-west European saltmarsh plant species, the common saltmarsh grass (Puccinellia maritima) and the sea arrowgrass (Triglochin maritima) and (2) compare levels of genetic diversity and structure between restored and natural ecosystems. Microsatellite molecular markers were developed for both species. Using innovative methods to analyse the genetic data obtained for these two polyploid species, this thesis highlights that genetic diversity at the national scale is organised regionally for both species, although gene-flow is still restricted between populations within the same region. Gene-flow between populations is determined by different processes depending on the species. While coastal processes mainly influence gene dispersal in P. maritima, overland routes of dispersal are involved for T. maritima. These differences are believed to be due to differences in dispersal ecology between the two species. Although gene-flow exists between distant saltmarshes, the genetic analysis of P. maritima and T. maritima colonists arriving on restored sites highlighted their local origin and reaffirmed that it is preferable to restore saltmarsh where a nearby natural saltmarsh can act as a source of colonists. A multiple paired-site comparison identified similar genetic diversity between restored and natural saltmarshes indicating that restoration of local genetic diversity is rapid for both species. A single site comparison at Skinflats in the Forth estuary compared fine-scale spatial genetic structure between the restored and natural saltmarsh. Interestingly, no structure was detected for T. maritima either in restored or natural saltmarsh. In contrast, a strong genetic structure organised along the elevation gradient was observed in the natural saltmarsh for P. maritima but was absent in the restored saltmarsh. The origin of this structure is not clear but could be due to restricted gene-flow between individuals from different elevations due to strong post-zygotic selection, as suggested in previous work. In any case, this lack of structure in the restored saltmarsh indicates that genetic recovery is incomplete in this respect for P. maritima. This thesis introduces the growing field of restoration genetics to saltmarsh ecology and identifies the principal population genetic trends in two of the species dominating the vegetation of north-west European saltmarshes community. The information given here will be useful for restoration practitioners and provides a strong foundation for future work characterizing the importance of genetic diversity for saltmarsh function.

Conservation of intertidal habitats in the UK is vital in order to continue to support nationally and internationally important populations of non-breeding waterbirds. Historic reclamation for agriculture and industry has resulted in the loss and degradation of large areas of these intertidal habitats in estuaries and they continue to be threatened by sea-level rise. Managed realignment is one method which is increasingly being used to restore intertidal habitats. As managed realignment is a relatively new restoration technique, the extent to which knowledge of the biology of estuaries is applicable to managed realignment sites is unclear. Habitat restoration is often unsuccessful or incomplete, so a detailed knowledge of both the natural system and the characteristics of restored systems will usually be necessary to recreate fully-functional estuarine habitats. This thesis focuses on Nigg Bay Managed Realignment Site (Nigg Bay MRS), the first managed realignment site in Scotland, and follows the first four years of ecological development to gain an understanding of how breached realignment can be used to restore intertidal habitats to support non-breeding waterbirds. This thesis has six major aims: (i) to describe the development of saltmarsh, (ii) to describe the development of intertidal flat, (iii) to describe the colonisation by non-breeding waterbirds (iv) to determine how tidal cycle and weather affect patterns of waterbird use, (v) to determine which factors affect the spatial distribution of waders and finally (vi) to determine the patterns of use by individual birds. Four summers after the re-establishment of tidal conditions, almost all of the saltmarsh species recorded on the nearby saltmarsh had colonised Nigg Bay MRS, although recognisable communities had yet to establish. Three winters after the re- establishment of tidal conditions in Nigg Bay MRS, the sediments had a significantly smaller particle size and higher organic matter content compared to the fine sands of the adjacent intertidal flats. The intertidal invertebrate community also differed from the adjacent intertidal flats. Nigg Bay MRS attracted large numbers of non-breeding waterbirds and supported each of the most common wader and wildfowl species present in the wider estuary. Nigg Bay MRS performs a number of important functions for non-breeding waterbirds by: (i) providing a foraging and resting habitat when the tide is absent and intertidal sediments in Nigg Bay are exposed; (ii) providing a foraging resource as the tide passes over the intertidal sediments within the site once the intertidal flats in Nigg Bay are inundated; and (iii) providing a high tide roosting site. On days with low temperatures and high wind speeds, more waterbirds use Nigg Bay MRS, suggesting that it is likely to be providing sheltering benefits. Nigg Bay MRS also provides top-up feeding habitat. The factors that often influence the spatial distributions of waders in estuaries appear to be operating within Nigg Bay MRS. Wader densities are greater on the intertidal flats when they are accessible than on the saltmarsh. Wader densities are also greatest close to creeks and drainage channels, possibly due to higher invertebrate densities, more accessible prey or sheltering benefits. Colour-ringing and radio-tracking of Common Redshank established that Nigg Bay MRS has a subset of regular users, including both adults and juveniles, and the wader assemblage at night may differ from the assemblage during the day. These findings are discussed in terms of the implications for locating, designing and managing future managed realignment projects.

Saltmarshes provide a diverse range of ecosystem services and are protected under a number of international designations. Nevertheless they are generally declining in extent in the United Kingdom and North West Europe. The drivers of this decline are complex and poorly understood. When considering mitigation and management for future ecosystem service provision it will be important to understand why, where, and to what extent decline is likely to occur. Few studies have attempted to forecast saltmarsh morphodynamics at a system level over decadal time scales. There is no synthesis of existing knowledge available for specific site predictions nor is there a formalised framework for individual site assessment and management. This project evaluates the extent to which machine learning model approaches (boosted regression trees, neural networks and Bayesian networks) can facilitate synthesis of information and prediction of decadal-scale morphological tendencies of saltmarshes. Importantly, data-driven predictions are independent of the assumptions underlying physically-based models, and therefore offer an additional opportunity to crossvalidate between two paradigms. Marsh margins and interiors are both considered but are treated separately since they are regarded as being sensitive to different process suites. The study therefore identifies factors likely to control morphological trajectories and develops geospatial methodologies to derive proxy measures relating to controls or processes. These metrics are developed at a high spatial density in the order of tens of metres allowing for the resolution of fine-scale behavioural differences. Conventional statistical approaches, as have been previously adopted, are applied to the dataset to assess consistency with previous findings, with some agreement being found. The data are subsequently used to train and compare three types of machine learning model. Boosted regression trees outperform the other two methods in this context. The resulting models are able to explain more than 95% of the variance in marginal changes and 91% for internal dynamics. Models are selected based on validation performance and are then queried with realistic future scenarios which represent altered input conditions that may arise as a consequence of future environmental change. Responses to these scenarios are evaluated, suggesting system sensitivity to all scenarios tested and offering a high degree of spatial detail in responses. While mechanistic interpretation of some responses is challenging, process-based justifications are offered for many of the observed behaviours, providing confidence that the results are realistic. The work demonstrates a potentially powerful alternative (and complement) to current morphodynamic models that can be applied over large areas with relative ease, compared to numerical implementations. Powerful analyses with broad scope are now available to the field of coastal geomorphology through the combination of spatial data streams and machine learning. Such methods are shown to be of great potential value in support of applied management and monitoring interventions.

Previous research into bottom-up processes on saltmarshes has mainly focused on the influence of plant succession on herbivores. This study will present original research exploring the influence of bottom-up processes in a saltmarsh ecosystem between three trophic levels: Orchestia, redshanks, and sparrowhawks. Density dependence, may be the dominant top-down effect when higher numbers of sparrowhawks and redshanks are present, and may mask top-down and bottom-up trait effects which are constant. Bottom-up effects begin to emerge when cold conditions force redshanks from muddy creeks onto the saltmarsh to forage for Orchestia, because their primary prey, Corophium become less available. Larger flocks form and feeding on Orchestia requires them to balance a need to profit from the best available feeding patches and to be vigilant to sparrowhawk attack. Redshank vulnerability is compounded, because Orchestia hide in cold temperatures, so probing in the soil with their heads down makes them more vulnerable to sparrowhawk attack. Larger flocks may be able to exploit areas closer to sparrowhawk-concealing cover at the terrestrial boundary because they feel safer in greater numbers. Warmer temperatures make Orchestia more active which attracts redshanks, which can simultaneously feed and be vigilant because they peck and catch crawling and jumping Orchestia with their heads up. Consequently, increased flock size may temporarily depress Orchestia abundance, so that redshanks become spaced, leaving isolated individuals more vulnerable to attack. Therefore, it is a temperature-dependent bottom-up process which impacts upon both Orchestia and redshank behaviour, which then may influence the hunting success of sparrowhawks. Whether the characteristics of this saltmarsh ecosystem and the trophic dynamics can be compared to other examples is questionable. Saltmarshes probably differ in their topography and the way in which environmental conditions affect them that then defines which species are present and how these species interact.