Dissertations / Theses on the topic 'Seagrass meadow'

Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Civil and Environmental Engineering, 1998.
Includes bibliographical references (p. 235-239).
A laboratory study of the hydrodynamics of a seagrass meadow was conducted to investigate the effect of water depth and velocity variations during a tidal cycle on the mean and turbulent velocity fields in and above the vegetation layer. The principal goal was to characterize the turbulence structure of a depth-limited canopy, a gap that presently exists in the knowledge concerning the interaction of a unidirectional flow with an assemblage of plants. The experiments were carried out in an open channel flume with a model seagrass canopy. Proper modeling of the system for both the geometric and dynamic behavior of natural Zostera marina communities allows the results to be extrapolated to the conditions in a coastal, tidal meadow. The results also serve as an important comparative case to the characterization of turbulence within atmospheric plant canopies. The laboratory study included the measurement of the mean and turbulent velocity fields with the use of an acoustic Doppler velocimeter and a laser Doppler velocimeter. Standard turbulence parameters were evaluated including the velocity moments, the turbulence spectra. the turbulent kinetic energy budget and the quadrant distribution of the Reynolds stress. Each of these provided a means of describing the effect of submergence depth and the degree of canopy waving (monami) on the transport of momentum and mass between the canopy and its surrounding fluid environment. In addition. surface slope measurements were made with surface displacement gauges. the plant motion was quantified using video and camera images. and the canopy morphology was recorded from measurements taken from a random sampling of the model plants. The investigation showed a clear link between the shear generated eddies arising at the interface of the canopy and the surface layer and the vertical exchange of momentum. the plant motion characteristics and the turbulence time and length scales. The turbulence field within the seagrass meadow was composed of a shear-generated turbulence zone near the canopy height and a wake-generated zone near the bed In addition. a mean flow due to the pressure gradient from the water surface slope created a region of secondary maxima in the mean velocity profile near the bed. The parameter determining the seagrass turbulence structure was found to be the characteristic depth (H' h). defined such that the effective canopy height. reflects the plant deflection. Across the range of values considered for H/h. the flow characteristics showed a clear transition from a confined to an unbounded canopy flow. This transition was observed in all the principal turbulence parameters. From this analysis. a critical surface layer depth governing the transition between the two extreme canopy flow conditions was identified as half the effective canopy height. H'h = 1.50.
by Ernique Rafael Vivoni Gallart.
S.M.

The impact of increased sediment exposure on coastal marine ecosystems is one of the most important contemporary environmental issues. Sediment exposure is defined as the concentrations of sediment particles suspended in the water column and the amount of sediment depositing on the seabed. In addition to natural events, such as land erosion, rainfall, and tidal currents, anthropogenic activities such as land use, road building, logging, mining, port maintenance and dredging, contribute to the discharge of a great amount of sediment in the water column. As sessile suspension-feeder assemblages play a critical role in marine ecosystems through their active transfers of organic and inorganic between the water column and the seabed (i.e. benthic-pelagic coupling), increased sediment exposure generated by anthropogenic activities may negatively impact these organisms. This study set out to evaluate the influence of increased sediment exposure on suspension-feeder assemblages in a temperate seagrass habitat. Most of the research was conducted within Posidonia sinuosa meadows near Woodman Point (32◦7’S, 115◦44’E), south of Fremantle, Western Australia. At this location, persistent sediment plumes from a cement manufacturer’s wash plant provided an opportunity to study the mechanisms through which increased sediment exposure can affect suspension feeder assemblages. This study was examining: the relationship between sediment exposure and suspension feeder assemblage composition; the influence of increased sediment exposure on the contribution of potential food sources to suspension feeder diets; and the influence of sediment exposure on suspension-feeding mechanisms (filtration and retention rates) and strategies (food particle selection). The descriptive work, presented in Chapter 1, revealed a strong gradient in sediment exposure with decreasing sediment deposition with distance from the wash plant. There was little dissimilarity, in term of species diversity and biomass, among suspension-feeder assemblages under high sediment exposure and those experiencing natural sedimentation regimes. These findings indicated that the suspension-feeder assemblages at the study site were resistant to high sediment exposure and that some species could potentially display compensatory mechanisms. Thus, the degree to which increased sediment exposure influences suspension feeders was more likely to be species specific and depend on the resilience of their feeding mechanisms and strategies. Those findings underlined the need to test the causal parameters underlying responses to suspension-feeding activity and selectivity due to increased sediment exposure. Results presented in Chapter 2 indicated that the three most conspicuous suspension feeder in term of biomass and abundances presented distinct isotopic signatures, implying dissimilarities in their diets. Differences in δ13C and δ15N can be explained by consumption of different types of picoplanktonic particles and the degree to which sedimentary organic matter contributed to their diets. Increased sediment exposure had no influence on the natural diets of the ascidian Herdmania momus and the bivalve Pinna bicolor. For the sponge Tethya sp, the contribution of sedimentary organic matter to its diet increased at sites with high sediment exposure, suggesting a potential benefit to its diet. Overall, the influence of sediment exposure on suspension feeder diets was species specific and dependent on the nature (e.g. organically rich versus organically depleted) and concentrations of the sediment. In Chapter 3 data are presented to show that feeding mechanisms and strategies of three species of suspension feeders best representing the benthic assemblages were influenced by sediment exposure. Under high sediment exposure, the ascidian Herdmania momus had lower pumping rates, but maintained a relatively constant food retention rate, and optimised its food intake by expanding its food sources from mainly cyanobacteria (Synechococcus) to a wider range of food sources. The bivalve Pinna bicolor also had lower filtration activity with high sediment exposure, again, maintaining relatively constant total retention rates and displaying a change in particle selection from bacteria and Synechococcus to larger picoeukaryotic cells of higher carbon content. The sponge Tethya sp. appeared to benefit from elevated sediment concentrations, as filtration and retention rates increased, potentially related to a lack of food selectivity. In Chapter 4, a short-term laboratory experiment was combined with a field transplant experiment to investigate the response of suspension feeders to increased sediment exposure. Under elevated sediment exposure, Herdmania momus and Pinna bicolor modulated their particle selection to optimise food intake, while the non-selective suspension feeder Tethya sp increased its particle retention rate and efficiency. Both the laboratory and transplant experiment findings corroborated observations made in Chapters 1 and 2; compensatory adaptations associated with the feeding activity, such as the modulation of pumping rates and the optimisation of food intake by particle selection, help to explain the potential resistance of suspension feeder community structure to high sediment exposure. A major outcome of this research is that it informs shallow coastal ecosystems stakeholders of the possible consequences of anthropogenic activities that increase sediment exposure, particularly those in the order of TSS at 40 mg·l-1 and deposition rates in the order of 10 g·cm- 2·month-1. Despite this magnitude of sediment exposure had little influence on suspension feeder assemblage composition, the effects on the suspension-feeding function, including the increase of the filtration activity and transfers of carbon to the benthos, potentially influence benthicpelagic coupling and other ecosystem-scale processes. Given the variation in sensitivity to sediment exposure among suspension feeder species, meaningful criteria to limit the effects of anthropogenic sediment loading on shallow coastal ecosystems should take into account the whole species assemblage present at any given site.

Seagrass meadows are important ‘Blue Carbon’ sinks but many questions remain unaddressed in regards to the organic carbon (OC) sequestration capacity and processes leading to retention and persistence of OC in seagrass sediments. The research summarised in this dissertation examined 37 sediment cores from twelve Australian seagrass meadows (Posidonia australis and Halophila ovalis) in order to improve our understanding of OC storage and preservation in seagrass sediments. The research: quantified the OC storage in seagrass meadows and the reduction in stores after ecosystem degradation; the rates of OC accumulation; the roles of species composition and the depositional nature of the habitat as factors affecting OC storage; and, characterised the sedimentary organic matter (OM) accumulated over millennia using techniques not previously applied to seagrass sediments. In Oyster Harbour, Western Australia, P. australis had been present over the past 6000 years, as evidenced from radiocarbon analysis of sedimentary matter. Both seagrass- and nonseagrass-derived OM contributed to high sedimentary organic stores (10.79-11.42 kg OC m- 2; 150 cm sediment depth). The persistence of sedimentary OM over millennial scales indicated that the carbon was well-preserved, thus showing a link between carbon storage and its preservation. By quantifying accumulation rates, and using historical accounts of the highest areal cover (6.1 to 6.7 km2) and recent losses in cover (by 2.8-3.1 km2) due to eutrophication, it was estimated that up to 11.17 Gg OC has been lost from shallow sediments (50 cm depth) following seagrass loss. This carbon was potentially remineralisable and may, therefore, have been liberated back to the atmospheric CO2 pool. Nine Posidonia australis meadows were then investigated for the effect of the depositional environment on sedimentary OC stores. Based on hydrodynamic differences of meadows categorised as More Sheltered, Less Sheltered, and Exposed, the More Sheltered sites had OC stores 6-fold higher (4.57 ± 0.16 to 13.51 ± 0.53 kg OC m-2; 140 cm sediment depth) compared to Exposed meadows (2.24 ± 0.31 to 3.77 ± 0.85 kg OC m-2). The OC stores of Less Sheltered meadows were not significantly different to either of the other two categories. It was concluded that the depositional nature of a seagrass habitat can affect the OC stores, though the affects may be influenced by other site-specific characteristics. The effect of species composition on OC stores and accumulation rates was subsequently investigated by comparing the stores in estuarine P. australis and H. ovalis meadows. Comparisons were based on stratigraphic- (OC stores over a set depth) and temporal-based (i.e. accumulation over a set period of time, and as accumulation rates) measures. Organic carbon stores were between 2- (P. australis: 10.81 ± 2.06 kg OC m-2, H. ovalis: 5.17 ± 2.16 kg OC m-2; 150 cm depth) and 11-fold (P. australis: 10.87 ± 2.86 kg OC m-2, H. ovalis: 0.97 ± 0.47 kg OC m-2; 2500 yr accumulation) different between meadows of the two species. While the OC stores were different between species, it was also apparent that environmental factors also contributed to the variability, with some H. ovalis meadows having stores comparable to some P. australis meadows. Thus, both the species and environmental factors needs to be considered for robust predictions of OC storage in seagrass meadows. The final study reported here investigated the preservation of sedimentary OC in the P. australis meadow of Oyster Harbour. A range of biogeochemical variables (age, sediment grain size, anoxia, OM and OC contents, and _13C values) were characterised at increasing depth within a sediment core. Solid-state 13C nuclear magnetic resonance was applied to a seagrass core for the first time to characterise the biochemical constituents of the sedimentary OM. There was a 76-80% contribution of seagrass-derived organics (lignin, carbohydrate, and a black-carbon-like OM) into the sediment. The proportion of black-carbon-like material increased with age/depth, indicating that it underwent selective preservation. Carbohydrates decreased with depth/age and lignin showed no changes, indicating that they have undergone non-selective preservation. There was remarkable consistency in the biochemical makeup of the OM with depth, which accumulated over the past 1900 years, indicating a very high preservation potential within seagrass sediments. Cumulatively, the research presented in this dissertation has highlighted the variability of OC stores in seagrass meadows and how OC may be preserved. The research has indicated that any attempts to estimate regional or global carbon stores must take into account both the species of seagrass that dominate the meadows and the type of depositional environment that the meadows occur in. It is also clear that Posidonia meadows in south-western Australia have the potential to store very large amount of Blue Carbon, comparable in some instances to the highest stores recorded globally, and to preserve these stores over millennia. Modelling future Blue Carbon stores requires an understanding of the fate of the stored carbon following disturbance. It is clear that this carbon can be lost from the meadow, but much of it appears to be in highly recalcitrant forms and it is unclear whether this material is available for subsequent re-mineralisation.

Rising sea temperatures through climate change produce shifts in the distribution of tropical species to temperate regions, a process termed “tropicalisation”. The poleward expansion of tropical herbivores into temperate seagrass meadows is predicted to increase grazing pressure and alter ecosystem services and processes in these seagrass systems. This study attempted to examine the effects of tropicalisation on temperate seagrass meadows along the western coast of Australia, where the increasing abundance of tropical consumers such as the herbivorous Siganus fuscescens has already been documented. Through the assessment of fish assemblages in seagrass meadows and the grazing levels on seagrass in 2001 and 2016/17, as well as in situ and mesocosm feeding preference experiments, this study attempted to estimate the grazing rates and impact that the growing abundance of S. fuscescens may have in temperate seagrass meadows. Shifts in the grazing rates on seagrass between 2001 and 2016/17 were inconsistent, varying between seagrass species and location. Based on observational data on the bites on seagrass leaves, rates of consumption increased for Posidonia sinuosa while no similar pattern was found for Posidonia australis. This was despite an apparent greater consumption on P. australis compared to P. sinuosa in 2001, and the minimal amount of grazing on tethered seagrass. The higher observed level of P. sinuosa consumption in 2016/17 is likely explained by the changed herbivorous fish species composition, even though no fish were clearly observed feeding on seagrass in the current study. The tropical herbivore S. fuscescens was more abundant in 2016/17 that 2001, although abundances were patchy and no fish was observed feeding on seagrass. The higher level of P. sinuosa consumption in 2016/17, compared to 2001, supports the prediction that with increasing abundances in temperate seagrass ecosystems, tropical herbivores will enhance the consumption of seagrass. However, seagrass consumption is likely to be strongly influenced by the availability of macroalgae which were shown as the preferred food sources. Feeding trials in mesocosms were compromised by the large number of deaths and the limited grazing on natural food sources by S. fuscescens, suggesting that the population in the Perth region is susceptible to adverse handling and husbandry effects. To maximise the survival rate of captured fish, the fishing and handling procedures were altered to adapt to the ongoing observations in the response of fish to handling in the field or in the mesocosm facilities. Lesson learned from the capture, handling and husbandry of S. fuscescens in feeding trials in the current study will hopefully provide greater success for feeding preference experiments in the future. The sampling program initiated in 2001 and repeated in 2016/17 provides base-line data and the opportunity to monitor and track the shift in abundances of tropical herbivores and resultant increases in grazing rates to test the above predictions. The consequences of tropicalisation will depend on the variety of abiotic and biotic factors, including the fish assemblages in the area, the abundance of tropical species, the availability of food, and the feeding preferences that invading species will develop in response to the changed environmental conditions.

Shallow seagrass ecosystems frequently experience physical disturbance from vessel groundings. Specific restoration methods that modify physical, chemical, and biological aspects of disturbances are used to accelerate recovery. This study evaluated loss and recovery of ecosystem structure in disturbed seagrass meadows through plant and soil properties used as proxies for primary and secondary production, habitat quality, benthic metabolism, remineralization, and nutrient storage and exchange. The efficacy of common seagrass restoration techniques in accelerating recovery was also assessed. Beyond removal of macrophyte biomass, disturbance to seagrass sediments resulted in loss of organic matter and stored nutrients, and altered microbial and infaunal communities. Evidence of the effectiveness of restoration actions was variable. Fill placement prevented additional erosion, but the resulting sediment matrix had different physical properties, low organic matter content and nutrient pools, reduced benthic metabolism, and less primary and secondary production relative to the undisturbed ecosystem. Fertilization was effective in increasing nitrogen and phosphorus availability in the sediments, but concurrent enhancement of seagrass production was not detected. Seagrass herbivores removed substantial seagrass biomass via direct grazing, suggesting that leaf loss to seagrass herbivores is a spatially variable but critically important determinant of seagrass transplanting success. Convergence of plant and sediment response variables with levels in undisturbed seagrass meadows was not detected via natural recovery of disturbed sites, or through filling and fertilizing restoration sites. However, several indicators of ecosystem development related to primary production and nutrient accumulation suggest that early stages of ecosystem development have begun at these sites. This research suggests that vessel grounding disturbances in seagrass ecosystems create more complex and persistent resource losses than previously understood by resource managers. While the mechanics of implementing common seagrass restoration actions have been successfully developed by the restoration community, expectations of consistent or rapid recovery trajectories following restoration remain elusive.

One central challenge in the study of seagrass meadows is explaining the abundance and diversity of nekton associated with these productive habitats. While many models have been proposed to explain fish use of seagrass habitats, mainly focusing on their nursery and predator-avoidance values based on the complex habitat structure, most empirical studies were conducted on relatively large patches using catch data collected from invasive capture methods. Seagrass meadows on peri-urban coasts, however, continually being threatened and fragmented, while invasive surveying techniques could bias fish abundance data. This thesis aims to determine if small remnant Zostera capricorni patches in a peri-urban estuary provide small mobile fish with a flow-refuge within a strong tidal flow environment, using non-invasive video surveying techniques to monitor fish abundance and behaviour. The hydrodynamic characteristics of three small patches of Z. capricorni were measured using in situ deployment of Acoustic Doppler Current Profilers (ADCP) at the front and rear of the patches during tidal current flow between 20 and 30 cm/s. Seagrass canopies of densities and morphologies covered by these patches significantly baffled the free-stream flow (X), creating a near-zero, turbulent free, within-canopy hydraulic environment 0.25m from the canopy’s leading edge. Flows were deflected over the canopy surface causing the leaves to bend, compressing the canopy and thereby reducing the vertical flux under high flows. While lower flows were still significantly reduced, a small vertical flux occurred, with large turbulent eddies generating from the canopy friction. The hydraulic environment behind the patch was significantly different to that at the patch’s front – characterised by near zero flows and turbulent fluctuations (at 0m), and flow velocities increasing with downstream distance. This effect was noticeable due to the velocity above the canopy being significantly reduced from flows above the canopy (fast). This difference diminished with downstream distance, gradually resembling the front profile. The rear environment close to the patch edge matched those of other flow-refuges.
Thesis (Masters)
Master of Philosophy (MPhil)
Griffith School of Environment
Science, Environment, Engineering and Technology
Full Text

Seagrasses are considered highly important CO2 sinks, with the capacity to store substantial quantities of organic carbon in the living biomass and sediments, and thereby acting as a buffer against climate change. In this thesis, I have studied carbon storage variability in temperate and tropical seagrass habitats and identified factors influencing this variation. In addition, as seagrass areas are decreasing worldwide, I have assessed effects of different anthropogenic disturbances on carbon sequestration processes. The result from this thesis showed that there was a large variation in carbon storage within and among temperate, tropical and subtropical regions. The highest organic carbon stocks were found in temperate Zostera marina meadows, which also showed a larger carbon storage variability than the subtropical and tropical seagrass habitats. The tropical and subtropical seagrass meadows had inorganic carbon pools exceeding the organic carbon accumulation, which could potentially weakens the carbon sink function. The variability in organic carbon stocks was generally strongly related to the sediment characteristics of the seagrass habitats. In Z. marina meadows, the strength of the carbon sink function was mainly driven by the settings of the local environment, which in turn indicates that depositional areas will likely have higher organic carbon stocks than more exposed meadows, while in the tropics seagrass biomass was also influencing sedimentary carbon levels. Furthermore, locations with large areas of seagrass were associated with higher carbon storage in tropical and subtropical regions, which could be related to increased accumulation of both autochthonous and allochthonous carbon. In an in situ experiment, impacts on carbon sequestration processes from two types of disturbances (with two levels of intensity) were tested by simulating reduced water quality (by shading) and high grazing pressure (through removal of shoot biomass). At high disturbance intensity, reductions in the net community production and seagrass biomass carbon were observed, which negatively affected carbon sequestration and could impact the sedimentary organic carbon stocks over time. In the treatments with simulated grazing, erosion was also seen, likely due to an increase in near-bed hydrodynamics. When experimentally testing effects of increased current flow on organic carbon suspension in Z. marina sediment, a ten-fold release of organic carbon with higher current flow velocities was measured, which resulted in an increase in the proportion of suspended organic carbon by three times in relation to other sediment particles. Therefore, periods with enhanced hydrodynamic activity could result in a removal of organic carbon and thereby likely reduce the seagrass meadows’ capacity to store carbon. The findings of this thesis add to the emerging picture that there is a large natural variability in seagrasses’ capacity to store carbon, and highlight how human-induced disturbances could negatively affect the carbon sink function in seagrass meadows.

At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 4: Manuscript.

Seagrass meadows, or submerged aquatic vegetation, constitute an ecosystem with great importance to the coastal zone, and may be characterized as the most productive ecosystem on Earth. In addition to the provision of habitat for a wide variety of species, protection of the coastal zone and production of organic matter base for the marine trophic web, these environments have been recognized for their great capacity to store organic carbon in their soils and are, therefore, a priority area for the mitigation of increased carbon in the atmosphere. In spite of the great importance of these areas, there is little information about the soils of these ecosystems, mainly using an approach based on the genesis of its soils. Thus, this thesis covers 4 chapters aiming to: (i) evaluate changes in the characteristics of seagrass meadows publications in the last 50 years, identify knowledge gaps and priorities for future studies; (ii) to discuss the paradoxical lack of information on Brazilian seagrass meadows soils, stimulate studies to understand their characteristics and contribute to the correct inclusion of seagrass meadows soils in the Brazilian System for Soil Classification; (iii) characterize and investigate soils of seagrass meadows along the Brazilian coast, in order to understand the pedogenetic processes within these soils; and (iv) identify variations in the biogeochemical processes related to the dynamics of Fe, Mn and S along the Brazilian coast, aiming to provide an improved basis for the understanding of this ecosystem and subsidies for the use and protection policies of these coastal areas.
As pradarias marinhas (seagrasses), ou vegetação aquática submersa, constituem um ecossistema de grande importância para a zona costeira, caracterizando-se como o ecossistema mais produtivo da Terra. Além de fornecer habitat para uma grande variedade de espécies, favorecer a estabilidade costeira e produzir matéria orgânica base para a teia trófica marinha, estes ambientes têm sido reconhecidos pela grande capacidade de armazenar carbono orgânico em seus solos e são, portanto, prioritários para as medidas de mitigação do aumento de carbono na atmosfera. Apesar da grande importância desse ecossitema, há pouca informação a respeito dos solos onde estes ecossistemas estão inseridos, principalmente utilizando uma abordagem baseada na gênese dos solos. Esta tese contempla 4 capítulos cujos objetivos visam avaliar as mudanças nas características das publicações sobre pradarias marinhas nos últimos 50 anos, identificando lacunas de conhecimentos e prioridades para estudos futuros; discutir a paradoxal ausência de informação sobre os solos das pradarias marinhas do Brasil, estimulando estudos para o entendimento de suas características e contribuindo para a correta inclusão de solos de pradarias marinhas no Sistema Brasileiro de Classificação de solos; caracterizar e investigar os solos das pradarias marinhas ao longo da costa brasileira, com vistas a entender os processos pedogenéticos atuantes nestes solos; e Identificar variações nos processos biogeoquímicos relacionados à dinâmica de Fe, Mn e S ao longo da costa brasileira, com a finalidade de fornecer base para o entendimento deste ecossistema e subsídios para as políticas de proteção e de uso destas áreas costeiras.

Though often suggested in seagrass literature, interactions between abundant rhizophytic macroalgae and coexisting tropical seagrasses have not been directly examined. Based on a competitive interaction hypothesis, I first tested for negative correlations between species densities over large and small spatial scales. After finding negative correlations, I tested experimentally for a competitive interaction by manipulating the relative densities of the locally dominant seagrass and a representative macroalga. Based on significant growth responses to density manipulations, I demonstrated that these species are likely competing for some limiting resource, possibly nitrogen. This study contributes to a better understanding of processes that dictate community composition in these systems.

Seagrass restoration programmes are becoming increasingly important in helping to maintain the biodiversity of coastal systems in many parts of the world, due to large areas of seagrass being lost over the last 50 years. The success of any restoration programme should ultimately be based on transplanted seagrass meadows acting in a similur ecological manner as the meadows they are replacing. However, success has generally been measured by examining survivorship and increases in physical structure of transplanted meadows. Few programmes have incorporated other ecological functions in establishing goals and objectives. The purpose of this research was to determine how ecological functions establish in transplanted Posidonia australis meadows of Oyster Harbour, Western Australia, and to determine how transplanting factors (e.g. planting density, patch size and patch shape) may influence these processes. The study has also determined whether monitoring the return of structural variables of seagrass represents the establishment of ecological functions, or whether monitoring ecological functions is required in determining the overall success of a restoration programme.

Microorganisms play a key role in facilitating the cycling of several elements in coastal environments, including nitrogen (N). N is a key component for maintaining high seagrass productivity and is often the limiting nutrient in marine environments. Seagrasses harbour an abundant and diverse microbial community (the ‘microbiome’), however their ecological and functional roles related to the seagrass host are still poorly understood, in particular regarding N cycling. Microorganisms capable of mineralising dissolved organic nitrogen (DON) may play a pivotal role in enhancing N availability in coastal environments such as seagrass meadows. Thus, the overall aim of my thesis was to enhance current understanding of abundance and diversity of the microbial community associated with seagrass meadows and their ecological role, with specific focus on N cycling. This was achieved by using molecular techniques together with 15N-enrichment experiments and nanoscale imaging techniques. Firstly, I reviewed the literature on the potential effects that microorganisms associated with both the above- and belowground seagrass tissue may have on plant fitness and the relevance of the seagrass microbiome and I have highlighted literature gaps. For my second chapter, I determined the abundance and community composition of bacteria and archaea associated with seagrass Posidonia sinuosa meadows in Marmion Marine Park, southwestern Australia. Data were collected from different seagrass meadows and meadow ‘microenvironments’, i.e. seagrass leaf surface, sediment and water column. I performed the quantitative polymerase chain reaction (q-PCR) targeting a series of bacterial and archaeal genes: 16S rRNA, ammonia oxidation genes (amoA) and genes involved in mineralisation of DON, via the urease enzyme (ureC). High-throughput sequencing was applied to 16S rRNA and amoA genes, to explore the diversity of these microbial assemblages related to P. sinuosa meadow microenvironments. Results from this chapter show that the P. sinuosa leaf biofilm represents a favourable habitat for microorganisms, as it hosts a significantly higher microbial abundance compared to the sediment and water. Moreover, 16S rRNA and amoA sequencing data indicate a high degree of compartmentalisation of functional microbial communities between the microenvironments of the seagrass meadow (leaf, sediment and water column), pointing towards the existence of a core seagrass leaf microbiome that could have specific interactions with the plant. For my third chapter I determined the role that microorganisms inhabiting P. sinuosa seagrass leaves may play in the recycling of DON, and subsequent transfer of inorganic N (DIN) into plant tissues. To achieve this, I performed an experiment whereby seagrass leaves with and without microorganisms were incubated with DO15N, and I traced the fine-scale uptake and assimilation of microbially processed N into seagrass cells, using nanoscale secondary ion mass spectrometry (NanoSIMS). Results from this chapter show for the first time that seagrass leaf epiphytic microorganisms facilitated the uptake of 15N from DON, which was unavailable to the plant in the absence of epiphytes. This indicates that seagrass leaves have limited to no ability to take up DON, and the seagrass leaf microbiome could therefore play a much more significant role than previously thought in enhancing plant health and productivity. Finally, I determined the net nitrification rates associated with ammoniaoxidising microorganisms (AOM) inhabiting P. sinuosa leaf surfaces, and explored whether AOM facilitated, or competed for, the plant’s N uptake. My findings show that AOM may compete with seagrasses for NH4 + uptake, but that their potential to outcompete seagrass epiphytic algae for DIN uptake indicates that AOM on seagrass leaves may serve as a ‘biocontrol’ over excess epiphytic algal growth. In summary, the present thesis represents a significant advance in our understanding of the seagrass leaf-microbiome relationship and transformations of N within seagrass meadows. Moreover, it opens up new questions for future research not only on seagrass-microbiome interactions but other macrophytes in aquatic systems that may benefit from the presence of specific N-cycling microorganisms.

Nearshore marine ecosystems like seagrass meadows face a wide range of anthropogenic influences, impacting the system at different spatial and temporal scales. Managing these systems in the face of these pressures requires detailed knowledge of how seagrass habitats respond to these various threats. A plethora of useful indicators have been developed to help managers and policy makers track seagrass meadow health and status, detect environmental impacts or measure the effectiveness of management interventions. However, choosing between these indicators can often be a daunting task since they vary considerably in their overall behaviour in relation to ecosystem and environmental changes. This thesis assesses the most commonly employed seagrass indicators to determine if they are adequate and appropriate to the specific needs of coastal ecosystem management. This assessment is based on evaluating three fundamental characteristics of each indicator – the robustness of its response, the specificity or generality of its response, and the time of response. We use a variety of complementary approaches to explore indicator behaviour. In Chapter 3, we use field-based studies to assess how seagrass indicators respond to the construction of a breakwater in the vicinity of a Posidonia oceanica seagrass meadow. Chapters 4 and 5 examine long-term trends in seagrass indicators to improving water quality conditions after significant regional management interventions. In addition, in Chapter 6, we comprehensively review seagrass indicator responses to multiple stressors. Chapters 3, 4 and 5 focus largely on the Catalan Coast in the Mediterranean with Posidonia oceanica as a target species. Chapter 6 in contrast is a broad review of a wide range of indicators used across several seagrass species worldwide. A central learning across these studies was that the level of biological organisation of the indicator (i.e. Physiological, biochemical, growth, morphological, structural or demographic) is critical in determining the specificity or generality of response: the lower the level (e.g. biochemical), the most specific the response, while the higher the level (e.g. population, community), the wider the response. Thus, biochemical indicators are ideal to determine the identity or even the origin of a pressure while structural indicators, in contrast, are useful as generic indicators of declining conditions. Response times are also heavily determined by the level of organisation, particularly in the detection of improving environmental quality along the Catalan coast. Biochemical indicators responded unequivocally to water quality improvements observed both in the experimental field study (Chapter 3) as well as in the analysis of the long-term data series (Chapters 4 and 5). The meta-analysis confirmed that these trends in specificity and response time were not unique to Posidonia oceanica or the Catalan coast and highlighted the critical role of plant size in determining indicator time responses. Large species take considerably longer to register a response to environmental degradation as well as improvement – a critical factor that needs to be accounted for in designing monitoring programmes and interpreting ecosystem trends. Taken together, these results suggest that differences in the behaviour of seagrass indicators require that they should be carefully selected to match the objectives of management. Based on the results reported in this thesis, where different sets of indicators have been proven successful for given management objectives, we finally develop a simple decision tree to help managers chose the most reliable sets of indicators matching their objectives. Understanding the diversity of responses that seagrass indicators display can make them a powerful set of tools in the ecosystem manager’s toolkit. Carefully employed, they can serve as bespoke solutions to a wide range of management objectives as we seek to monitor and protect these vital ecosystems and coastal water quality in the face of increasing coastal pressures.
Entendre com responen les fanerògames marines a les pressions, és clau per a poder gestionar tant els herbeis com les aigües costaneres. Actualment, disposem d’un gran nombre d’indicadors basats en fanerògames marines. Però, la manca d’informació sobre com responen als canvis ambientals, fa que no sigui fàcil escollir quins indicadors són els més adients per a cada tipus i objectiu de gestió. Aquesta tesi avalua les tres característiques bàsiques de la resposta dels indicadors més utilitzats als canvis ambientals: la robustesa de la resposta, la especificitat dels indicadors a diferents pressions i el temps de resposta. Per analitzar aquestes tres característiques, fem servir diferents aproximacions complementàries. Al capítol 3, analitzem la resposta de diferents indicadors a les obres d’ampliació del port de Blanes, situat just al costat d’un herbei de Posidonia oceanica. Als capítols 4 i 5, estudiem com responen els indicadors a la millora de la qualitat de l’aigua a la costa catalana. Finalment, al capítol 6, presentem una metaanàlisi que estudia com responen els indicadors a diferents factors d’estrès. De totes tres aproximacions, hem pogut comprovar que el nivell d’organització dels indicadors (i.e. bioquímic, estructural) és clau a l’hora de determinar el grau d’especificitat de la resposta dels indicadors a les pressions: generalment, a més baix nivell d’organització (e.g. bioquímic), més específica és la resposta i com més alt (e.g. demogràfic), més ampli és el rang de pressions que un indicador pot detectar. El temps de resposta dels indicadors varia també en funció del nivell d’organització dels indicadors, especialment, quan es tracta de la detecció de millores ambientals. A més a més, la metaanàlisi destaca la importància de la mida de les plantes per determinar el temps de resposta. Les espècies grans triguen més a detectar la degradació de les condicions ambientals i, molt més, a detectar la millora, especialment, si s’utilitzen indicadors estructurals o demogràfics. Basant-nos en els resultats d’aquesta tesi, hem elaborat un esquema per ajudar els gestors a escollir el conjunt d’indicadors que més s’ajusti a cada objectiu de gestió. Utilitzats correctament, aquests indicadors són molt útils per fer el seguiment, tant de l’estat de salut dels herbeis, com de la qualitat del medi.

In this thesis, the distribution and state of Posidonia oceanica meadows along the Turkish coast of the north eastern Mediterranean was investigated. The study area was a unique site due to the presence of eastern geographical limit of Posidonia oceanica meadows in Mediterranean Sea. It was aimed to assess the possible reasons of the absence and/or regression in relation to environmental changes. The study was conducted from September 2004 to January 2007 in 5 main regions between Anamur/Mersin and Samandag/Hatay. The regions were determined according to the presence/absence of Posidonia oceanica meadows
1 region including the boundary meadow at the geographical distribution limit, 1 region western and 3 regions eastern to that boundary meadow. To describe the hydrological characteristics of the study area temperature, salinity and light were measured as abiotic descriptors. Additionally sedimentological analysis was carried out to check the suitability of the substrate type for Posidonia oceanica colonization. The main differences between the regions were found in temperature and light conditions. Both, the recordings of temperature loggers at 10 and 15 meter depths and the sea surface temperature retrieved from satellite (NOAA-AVHRR) showed that the eastern stations with no Posidonia oceanica meadows were warmer than the western stations. Consequently in this study the maximum tolerable temperature limit for Posidonia oceanica growth was determined as 28.4°
C from the data collected by the temperature loggers placed to natural meadows near to the boundary meadow. Generally, the whole study area had a limiting light condition for seagrass growth due to low penetration depths of the 10% of surface irradiation. This was a generalized minimum light requirement for growth of seagrasses. Especially in Mersin and Iskenderun bays the minimum required light level did not reached deeper than 10 meter depths in coastal stations. The biological parameters of the Posidonia oceanica meadows were investigated under 3 complementary methods in the first two regions. The structural descriptors were measured in-situ. The lowest shoot density and leaf lengths were found to be in boundary meadow. This meadow had also the lowest depth limit among other stations. The functional descriptors were examined by the lepidochronological and phenological analysis in laboratory. Most of the measurements varied either with respect to depth or among stations according to the abiotic factors of the stations. The lepidochronological cycles obtained from sheath thicknesses were further correlated with abiotic descriptors via a mathematical model. Finally, the first transplantation experiment of Posidonia oceanica along Turkish coasts has been conducted in 2 regions where presently no meadows exist. The survival of cuttings in one station indicated the success of the methodology, while the failure in other stations provided information on the possible reasons of absence/degradation of natural meadows in the area. These included the destructive impact of bottom trawling, the high pressure of grazing (the potential causes of Lessepsian migration) and the long term changes in climate resulting in alterations of environmental conditions such as increasing temperature and reduced light penetration.

Seagrass meadows play a primary role in supporting ecosystem services in coastal lagoons. Still, their importance as habitat for fish in transitional waters is poorly understood. Moreover, the persistent loss of seagrass beds during the last decades requires conservationists to provide scientifically sound plans to enhance their preservation. The objectives of this work are i) to investigate the influence of environmental factors, including habitat characteristics, on seagrass fish assemblages in the Venice lagoon (northern Adriatic Sea, Italy); ii) to evaluate the suitability of fish fauna as indicator of the effectiveness of seagrass restoration. Ultimately, this work aims at presenting approaches for planning seagrass conservation efforts and assessing their outcomes. This work features three main sections. Firstly, the role of different floristic composition and habitat structure of seagrass beds was linked to distribution of pipefishes and seahorses (Syngnathidae), highlighting the importance of enhancing conservation of Zostera marina meadows in shallow coastal lagoon waters. Secondly, the role of seagrass fish and other nekton fauna as indicator of the success of conservation actions was investigated. A seagrass restoration scheme that recently started in the Venice lagoon allowed to test a model-based method, to predict reference conditions for nekton fauna in Z. marina and Z. noltei transplantation sites, and provide an assessment of the progress of restoration towards designed goals. Thirdly, the potential role of habitat mosaic structure in influencing seagrass fish in the Venice lagoon was evaluated. The study highlighted the importance of conservation of seagrass habitat quality at multiple spatial scales for the preservation of the associated fish assemblages, and the need for including seascape ecology in seagrass restoration projects. On the whole, this thesis provides some new insights into the critical role of seagrass conservation for the maintenance of biodiversity, and suggestions for more successful management strategies in coastal lagoons.

Diss. (sammanfattning) Stockholm : Stockholms universitet, 2010.
At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 3: Manuscript. Paper 4: Manuscript.

Thesis (Honors paper)--Florida State University, 2009.
Advisor: Dean Joseph Travis, Florida State University, College of Arts and Sciences, Dept. of Biological Sciences. Includes bibliographical references.

Seagrass meadows offshore Ras Ghanada, as elsewhere, are an important component to the ecosystem providing numerous benefits to both aquatic and human life. This work focused on mapping the spatial and temporal distribution of seagrass meadows offshore Ras Ghanada using aerial photography acquired in 1996 and high-resolution satellite images captured in 2006 and 2012. The movements of sand shoals were also tracked, so as to further explain the dynamics of this ecosystem, as it is the area between the shoal crests that hosts the best developed seagrass meadows. The natural limiting factor for seagrass on the Ras Ghanada coastal shelf seems to be the fact that they cannot inhabit the (mobile) crests of the sand shoals, but rather, are restricted to the (more stable) sands of the shoal troughs. In the considered time period, both sand shoals and seagrass meadows migrated predominantly in a southeastern direction. The changes of seagrass that occurred in this study occurred on a fairly rapid timescale, in such that they were able to come back when there was disturbance as long as they had available habitat to move into. Furthermore, although seagrass cover declined by 3.4% from 1996 – 2012, there was a greater increase than decline in the areal coverage of seagrass post-Khalifa port construction in 2010. If sediments offshore Ras Ghanada can remain stable and the waters are not polluted by further construction, seagrasses should continue to thrive in the future.

Overall, this thesis is an attempt at approaching seagrass ecosystems from a landscape perspective, with the aim of increasing knowledge about the processes generating patterns at large spatial scales, and understanding how these patterns interact with other drivers of seagrass function. Specifically, we focus on (i) understanding the dynamics of habitat fragmentation (Chapter 1), (ii) how this fragmentation interact with other seagrass disturbances, such as hydrodynamism, sedimentation and herbivory (Chapter 2 and 3) and which are the consequences of such fragmentation to biodiversity and ecosystem processes (Chapter 4). The thesis is structured in five chapters, the first four focus on the different objectives outlined above. Additionally we have included another chapter (Chapter 5) that relates seagrass quality with photosynthetic performances. All chapters originated from field observations (Chapter 1, 2, 4 and 5) or experimental manipulative experiments (Chapter 3) that posed individual questions and general hypothesis within the frame of the dynamics of habitat fragmentation at patch-size and landscape scale. For the two first chapters, we take advantage of extreme storm events and in one of them we exploit long-term data series (15-20 years). Thus, we will first aim to integrate the different results related to the effects of habitat fragmentation and the interactions with external and internal disturbances. In this thesis we have observed how storms can be an important agent of fragmentation in shallow Posidonia oceanica meadows. One of the main causes is the limited capacity of this slowgrowing seagrass species to resist and recover from extreme storm events. This has been observed either by the response of the plant to a specific storm event (Chapter 1) than by the observed responses to storms in a long-term series (Chapter 2). Once the process of fragmentation was identified, we attempted to evaluate the resilience of the meadows to external and internal disturbances. In the case of the external disturbances we compared the storms effects on continuous and fragmented meadows in two congeneric species of Posidonia. The effect was much stronger in the fragmented meadows pointing out that fragmentation makes seagrass meadows less resilient and that the Mediterranean P. oceanica is particularly vulnerable due to its limited recovery potential. Evident limitation in this study was the low level of replication. This was not due to a design error, but to the rarity of the occurrence of extreme storm events and the limited availability of long data series. In spite of this, our results are consistent in stressing that fragmentation can be a critical factor for shallow seagrass maintenance. When we add to this disturbance the natural processes that ecosystems are facing, such as herbivory, fragmentation becomes even more critical as both factors are interacting in a combined way (Chapter 3). Consequently as both factors (fragmentation and herbivory) affect additively the same processes small fragmented patches tend to have lowest canopy height (i.e. less structure), less nutrient retention and lowest primary production. Interestingly, the influence of fragmentation on biodiversity and abundance of low mobility species, which was tested in chapter 4, showed opposite effects than expected. Specifically small fragments presented a much higher biodiversity of decapods, used as a model group, although it is not fully generalizable as the observed effect was site-specific. The apparently contradictory result could be in part explained by the low habitat use by predators observed in these small fragments. This final result points out the importance that small seagrass patches might have, as potential hotspots, for the maintenance of biodiversity. Finally we discuss the potential scenario that P. oceanica fragmented meadows might face under climate change. One of the clearest effects of climate change in several regions is that atmospheric and ocean regional conditions are expected to be modified, increasing the frequency of high-intensity cyclonic formations that can even strengthen the role of disturbances on these systems.
En general, la tesis pretende acercarse a los ecosistemas de fanerógamas marinas desde el punto de vista del paisaje, con el objetivo final de incrementar el conocimiento acerca de los procesos que generan los patrones a gran escala espacial, y entender como estos patrones interactúan con otros procesos funcionales de las fanerógamas marinas. Específicamente, a lo largo de la tesis nos hemos centrado en: (i) entender las dinámicas de la fragmentación del hábitat (capítulo 1), (ii) como esta fragmentación interactúa con otras perturbaciones, como el hidrodinamismo, la sedimentación y el herbivorismo (capítulos 2 y 3), y (iii) cual pueden ser las consecuencias de dicha fragmentación en la biodiversidad y los procesos del ecosistema (capítulo 4). Además de estos cuatro capítulos, se incluye un capítulo final (capítulo 5) que relaciona el estado de las praderas de fanerógamas marinas con las características fotosintéticas. Todos los capítulos se han redactado partiendo desde observaciones de campo (cap. 1, 2, 4 y 5) o experimentos manipulativos (cap. 3), y plantean tanto preguntas individuales como hipótesis generales en el marco de las dinámicas de fragmentación del hábitat a escala de manchas y de paisaje.

Small-scale fisheries employ many millions of people around the world, and are particularly important in developing countries, where the dependency on marine resources is high and livelihood diversification options are scarce. In many areas of the world however, small-scale fisheries are at risk which threatens the food security and wellbeing of coastal people. Small-scale fisheries management has in many cases been insufficient and new comprehensive approaches are recommended to achieve social-ecological sustainability in the long-term. The aim of this thesis is to analyze empirically how social-ecological elements of seagrass-associated small-scale fisheries in the Western Indian Ocean region can be addressed for a transformation from the current mostly degraded state to more sustainable social-ecological systems and secure future livelihoods. The main method used was semi-structured interviews with local fishers. The main findings show the crucial contributions seagrass-associated small-scale fisheries make to food security and income generation and highlight the need to acknowledge the social-ecological importance of seagrasses in the seascape (Paper I). A discrepancy between low societal gains of the fishing of sea urchin predator fish species and their crucial importance in the food web (in controlling sea urchin populations and the associated grazing pressure on seagrasses) was identified (Paper II). These results suggest catch-and-release practice of sea urchin predator fish species, which could contribute to more balanced predator – sea urchin – seagrass food webs in the long run. The use of illegal dragnets was identified as a major threat to local seagrass meadows (Paper IV). Institutional elements influencing the use of such destructive dragnet were identified to be normative, cultural-cognitive and economic, which constitutes an institutional misfit to the current emphasis on regulative elements in a hierarchical manner (Paper III). Concerning future co-management initiatives, gear restrictions and education were the favoured management measures among all fishers (Paper IV). A majority of fishers were willing to participate in monitoring and controls, and most fishers thought they themselves and their communities would benefit most from seagrass-specific management. These findings highlight the need for actions on multiple scales, being the local-, management-, policy- and governance levels. The suggested actions include: education and exchange of ecological and scientific knowledge, gear management including the cessation of dragnet fishing, strengthening of local institutions, an active participation of fishers in enforcement of existing rules and regulations and an introduction of adequate alternative livelihood options.

At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 1: Manuscript. Paper 4: Manuscript.

During the last decade, the academic interest for Earth’s natural carbon sinks and their role concerning climate change has increased. Today, many scientists around the world are trying to calculate different ecosystem’s potential to sequester and store carbon dioxide from the atmosphere. As a newcomer to the scientific arena, the term ‘blue carbon’ has been well received by scientists in the field. ‘Blue carbon’ highlights the carbon captured and stored by productive ecosystems along the world’s coasts. The term refers to coastal wetlands – such as mangrove forests, salt marshes and seagrass meadows – and it came to life as the scientific community recognized these ecosystems’ significant potential as effective carbon sinks. New research indicates that these ecosystems’ complex and vertical root systems can store much larger amounts of carbon in the soil than any other terrestrial ecosystem. By studying this subject, scientists are trying to understand how these ecosystems can help us in the quest of removing excessive carbon dioxide from the atmosphere. The goal of this thesis is to conduct a literature review, aiming to analyse and compile the new research on ‘blue carbon’ that has been published during the last 10 years. The paper aims to investigate whether the ecosystem’s potential as carbon sinks differ from each other, and what threats they will face in the future. It will additionally review if scientists have been able to unite around any predictions about what the future for ‘blue carbon’ – and its role in mitigating climate change – will look like.
Under det senaste decenniet har intresset kring naturliga kolsänkors potential och roll i att mildra klimatförändringar ökat. Idag är det många forskare som arbetar med att beräkna mängden kol som olika ekosystem runt om världen kan lagra i sin biomassa och i jorden under dess rötter. Som en nykomling på den vetenskapliga arenan, har termen ’blue carbon’ blivit väl mottaget av forskare inom området. ’Blue carbon’ syftar på det kol som fixeras och lagras av de produktiva ekosystemen längs världens kuster. Termen refererar till kustbelägna våtmarker – så som mangroveskogar, saltträsk och sjögräsbäddar – och introducerades efter att den vetenskapliga världen erkänt deras imponerande potential som kolsänkor. Ny forskning tyder på att deras avancerade och vertikala rotsystem kan lagra mer koldioxid i marken än vad vanliga terrestra skogar kan. Genom att studera detta ämne försöker forskare att förstå hur dessa ekosystem kan hjälpa oss att avlägsna överskottet av koldioxid från atmosfären. Målet med denna uppsats är att utföra en litteraturstudie och analysera, samt sammanställa den nya forskningen om ’blue carbon’ som publicerats de senaste 10 åren. Uppsatsen kommer undersöka hur stor skillnad det är mellan de olika ekosystemen och vilka hot de står inför i framtiden. Dessutom kommer den undersöka ifall forskare kommit närmre i att enas kring förutsägelser om framtiden för ’blue carbon’, och hur dess roll i att mildra klimatförändringarna kommer se ut.

Seagrass ecosystems are some of the most productive in the world and provide a variety of ecosystem services but are facing global decline chiefly due to anthropogenic disturbance. Mechanical disturbances to seagrass meadows from anchoring, propeller scars, and mooring scars result in losses or damage to both shoots and the underlying rhizome. I conducted a literature synthesis on the extent of, recovery from, and ecological impacts of these mechanical disturbances to seagrass meadows. The literature suggests that anchoring damage tends to be worst in deeper water where larger vessels anchor and can cause large (>100m²) loss per anchoring and recovery may take decades to over a century. Propeller damage is of largest concern in shallow (<2m) areas experiencing heavy boat traffic because propeller damage can only occur where the propeller can come close to the seagrass. Mooring damage is highly variable depending on the type of mooring used (<10m² to >1000m² scoured per mooring). Seagrass patches experiencing these mechanical disturbances have, in some studies, been found to have lower seagrass percent cover and shoot density than reference areas. This indicates scars can have ‘halos’ of impacted seagrass meadow. Some seagrass systems cannot recover within a century (e.g. Posidonia oceanica meadows at the extent of their depth tolerance) while others recover annually from some disturbances (e.g., anchor scars <1m²). Systems face altered species composition when scars are preferentially recolonized by certain species and patterns of recovery are affected by altered biogeochemical conditions following disturbances. Additionally, mooring, anchoring, and propeller scarring frequently alter meadow density, cover, patch size, patch shape, patch isolation, edge area, and ratios of edge to interior meadow leading to changes in faunal community structure. Correlations between these disturbances and faunal abundances, densities, and richness in seagrass ecosystems are complex, vary temporally (sometimes on the scale of days), and may result in species showing positive, negative, or no responses to a wide range of disturbance regimes.

To explore the connections between mooring scarring, the surrounding seagrass meadow condition and epifaunal community, in the second part of this thesis I measured 30 mooring scars to determine average scar size. To explore any potential ‘halo’ effect around mooring scars for seagrass or epifauna and to seek any difference in epifaunal community between mooring and reference sites I also sampled paired sites at eight locations in Nantucket Harbor, Massachusetts three times each in the summer of 2015. Each location consisted of a meadow site actively experiencing mooring scarring and a reference site without moorings. My conservative sampling methods of the 30 sampled mooring scars found scars to average 21.1m². Across my paired sites, seagrass was found to have lower cover and lower canopy height in mooring versus reference sites. Seagrass cover and canopy height were lower in the first few meters (typically 2-3m) surrounding each scar in comparison to paired reference quadrats indicating a ‘halo’ effect of each scar. I did not detect a difference in epifaunal community composition or density per blade between mooring and reference sites; however, the relatively constant per blade concentration of epifauna combined with the differences in seagrass biomass between the mooring versus reference sites indicate an overall increase in the total amount of epifauna in areas with less disturbance. Epifaunal community composition was different and between locations and sampling dates indicating these factors are more important than proximity to mooring scarring in determining epifaunal abundance and richness. When considering scar area and the ‘halo’ of each scar I estimate that at least 32ha (2%) of Nantucket Harbor was impacted by mooring scarring. Given that the estimates of seagrass do not include areas previously denuded of this plant and that my measurements were conservative, likely a larger portion of this harbor’s potential seagrass habitat is impacted. Combined with the findings of loss due to these direct boat-related physical disturbances of seagrass meadows worldwide across regions, this halo effect is likely to also be found for moorings globally. I encourage management of the issue by employing and fine-tuning mooring methods (such as deploying moorings with anchor connections that do not drag on the sea floor) to minimize these unintentional but strong effects of mooring on the recipient habitat.

Les écosystèmes côtiers présentent une forte production biologique, soutenue par une grande diversité de sources de matière organique particulaire (autochtones : phytoplancton, microphytobenthos, phanérogames marines, macroalgues, épiphytes ; allochtones : apports continentaux), pouvant contribuer à la production secondaire. La diversité de ces sources complexifie de manière considérable le fonctionnement écologique des systèmes côtiers — e.g. cycles biogéochimiques, réseaux trophiques — et en rend sa compréhension difficile.Une étude spatio-temporelle réalisée en 2009 dans le Bassin d’Arcachon, une lagune semi-fermée qui abrite le plus grand herbier à Zostera noltii d’Europe, a été menée afin d'estimer l’origine et la composition des matières organiques particulaire en suspension (MOPS) et sédimentaire (MOS) et d'appréhender le devenir des différentes sources de matière organique dans le réseau trophique macrobenthique. Cette approche quantitative a été effectuée principalement à l’aide des rapports isotopiques et élémentaires (δ15N, δ13C et C/N) et/ ou des acides grasA l’échelle annuelle et en moyenne pour les trois stations étudiées, la MOPS est composée principalement de phytoplancton (48 ± 2%) mais aussi de matériel continental (19 ± 4%) et de microphytobenthos (16 ± 2%), les macroalgues et les phanérogames ne contribuant que peu (8 ± 1% et 5 ± 1%, respectivement). Cette composition, qui présente une saisonnalité (faible contribution du phytoplancton en hiver au profit des apports continentaux), est principalement dépendante du climat (température) et de l’hydrodynamique / hydrodynamique sédimentaire (apports continentaux, remise en suspension du sédiment). A l’échelle annuelle et en moyenne pour les six stations ayant fait l’objet du suivi annuel, la MOS est composée principalement de sources benthiques (phanérogames : 23 ± 3% ; microphytobenthos : 19 ± 1% ; macroalgues : 19 ± 5%), mais également de matériel continental (27 ± 8%) et de phytoplancton (11 ± 2%). A l’échelle de l’écosystème (étude printanière) la composition de la MOS est similaire — avec toutefois une plus forte contribution du phytoplancton, au dépend de la matière continentale. Elle est géographiquement homogène, ce que semble favoriser l’hydrodynamique du bassin d’Arcachon associée à sa faible profondeur. La principale différence spatiale apparaît entre le sédiment subtidal (faible contribution des macrophytes au profit du matériel continental) et le sédiment de l’herbier intertidal. L’étude des voies de transfert trophique de la matière organique particulaire a mis en évidence une organisation trophique complexe avec l’existence de sous-groupes au sein des déposivores d’interface et des brouteurs. A l’échelle annuelle et à l’échelle du Bassin d’Arcachon, le microphytobenthos et les phanérogames (incluant leurs épiphytes) soutiennent 90% de la production macrozoobenthique. Cette production secondaire est principalement effectuée par les déposivores (60%). Une forte bactérivorie a été mise en évidence notamment chez les déposivores et chez le suspensivore invasif Crepidula fornicata. Les bactéries représentent ainsi un intermédiaire important dans le transfert de MOP des producteurs primaires vers les consommateurs primaires. Toutefois la pression trophique qu’exercent les consommateurs primaires de la macrofaune benthique sur les producteurs primaires est relativement modeste puisque le macrozoobenthos n’absorbe que 10% de la production primaire totale du système, ce qui rend cette dernière potentiellement disponible pour d’autres compartiments biologiques. Malgré cela l’herbier à Zostera noltii représente une ressource importante pour la macrofaune benthique. Dans le contexte de sa régression, une disparition de l’herbier engendrerait une diminution de la biomasse du macrozoobenthos
Abstract

The aim of this study was to develop and examine the use of backscatter data collected with multibeam sonar (MBS) systems for benthic habitat mapping. Backscatter data were collected from six sites around the Australian coastal zone using the Reson SeaBat 8125 MBS system operating at 455 kHz. Benthic habitats surveyed in this study included: seagrass meadows, rhodolith beds, coral reef, rock, gravel, sand, muddy sand, and mixtures of those habitats. Methods for processing MBS backscatter data were developed for the Coastal Water Habitat Mapping (CWHM) project by a team from the Centre for Marine Science and Technology (CMST). The CMST algorithm calculates the seafloor backscatter strength derived from the peak and integral (or average) intensity of backscattered signals for each beam. The seafloor backscatter strength estimated from the mean value of the integral backscatter intensity was shown in this study to provide an accurate measurement of the actual backscatter strength of the seafloor and its angular dependence. However, the seafloor backscatter strength derived from the peak intensity was found to be overestimated when the sonar insonification area is significantly smaller than the footprint of receive beams, which occurs primarily at oblique angles. The angular dependence of the mean backscatter strength showed distinct differences between hard rough substrates (such as rock and coral reef), seagrass, coarse sediments and fine sediments. The highest backscatter strength was observed not only for the hard and rough substrate, but also for marine vegetation, such as rhodolith and seagrass. The main difference in acoustic backscatter from the different habitats was the mean level, or angle-average backscatter strength. However, additional information can also be obtained from the slope of the angular dependence of backscatter strength.It was shown that the distribution of the backscatter. The shape parameter was shown to relate to the ratio of the insonification area (which can be interpreted as an elementary scattering cell) to the footprint size rather than to the angular dependence of backscatter strength. When this ratio is less than 5, the gamma shape parameter is very similar for different habitats and is nearly linearly proportional to the ratio. Above a ratio of 5, the gamma shape parameter is not significantly dependent on the ratio and there is a noticeable difference in this parameter between different seafloor types. A new approach to producing images of backscatter properties, introduced and referred to as the angle cube method, was developed. The angle cube method uses spatial interpolation to construct a three-dimensional array of backscatter data that is a function of X-Y coordinates and the incidence angle. This allows the spatial visualisation of backscatter properties to be free from artefacts of the angular dependence and provides satisfactory estimates of the backscatter characteristics.Using the angle-average backscatter strength and slope of the angular dependence, derived by the angle cube method, in addition to seafloor terrain parameters, habitat probability and classification maps were produced to show distributions of sand, marine vegetation (e.g. seagrass and rhodolith) and hard substrate (e.g. coral and bedrock) for five different survey areas. Ultimately, this study demonstrated that the combination of high-resolution bathymetry and backscatter strength data, as collected by MBS, is an efficient and cost-effective tool for benthic habitat mapping in costal zones.

Les herbiers marins constituent des habitats remarquables et diversifiés des eaux côtières des territoires ultramarins français. Une meilleure compréhension de leur état écologique sous l’influence des perturbations multiples auxquels ils sont soumis est nécessaire pour répondre aux enjeux des politiques publiques environnementales s’appliquant à l’échelle de ces territoires. Divers paramètres représentant la plupart des compartiments biologiques, allant de la physiologie des phanérogames marines à l’écosystème ont été testés in situ dans des conditions environnementales contrastées. Ces expérimentations ont permis d’évaluer les relations pressions-état des herbiers de différents territoires dans les trois océans et de sélectionner les descripteurs les plus pertinents selon les principaux objectifs de gestion. Sur la base des données collectées, une première version d’indicateurs intégrés combinant des indicateurs d'alerte précoce et de diagnostic (nutriments et certains métaux traces) et des paramètres de réponse à long terme (densité des plants et recouvrement) adaptés aux échelles de temps de la gestion ont été développés. Une première classification de l’état des herbiers étudiés est ainsi proposée. Ces outils intégrés devraient permettre de renforcer l’efficacité des mesures de gestion, tout en facilitant une mise en oeuvre mutualisée des différentes politiques publiques. L'évaluation de l'état de santé des herbiers marins et de leur environnement est essentielle afin de déployer des mesures de gestion et de préservation appropriées pour améliorer de manière durable l’état et la résilience de cet écosystème menacé
Seagrass meadows forms remarkable and diversified habitats in the coastal waters of the French overseas territories. A better understanding of their ecological status under multiple disturbances to which they are subjected is necessary to respond to environmental public policy issues applying to these territories. In situ experiments were conducted on the three oceans, in which parameters representing most biological compartments, ranging from the physiology of seagrass to the ecosystem, were tested under contrasting environmental conditions. These experiments lead to assess the pressure-state relationships of seagrass beds in different territories and to select the most relevant descriptors according to the main management objectives. On the basis of the data collected, the first databases of integrated indicators combining early warning indicators (nutrients and trace metals) and long-term response parameters (plant density and cover) adapted to management time scales were developed. A first classification the health status of studied seagrass meadows is thus proposed. These integrated tools will make it possible to improve the effectiveness of the management of this threatened ecosystem, while facilitating the sharing of the implementation of the various public policies. The assessment of seagrass beds health status and their associated environment is essential to deployed appropriate management actions and improve ecosystem quality and long term resilience

The aim of this study was to develop and examine the use of backscatter data collected with multibeam sonar (MBS) systems for benthic habitat mapping. Backscatter data were collected from six sites around the Australian coastal zone using the Reson SeaBat 8125 MBS system operating at 455 kHz. Benthic habitats surveyed in this study included: seagrass meadows, rhodolith beds, coral reef, rock, gravel, sand, muddy sand, and mixtures of those habitats. Methods for processing MBS backscatter data were developed for the Coastal Water Habitat Mapping (CWHM) project by a team from the Centre for Marine Science and Technology (CMST). The CMST algorithm calculates the seafloor backscatter strength derived from the peak and integral (or average) intensity of backscattered signals for each beam. The seafloor backscatter strength estimated from the mean value of the integral backscatter intensity was shown in this study to provide an accurate measurement of the actual backscatter strength of the seafloor and its angular dependence. However, the seafloor backscatter strength derived from the peak intensity was found to be overestimated when the sonar insonification area is significantly smaller than the footprint of receive beams, which occurs primarily at oblique angles. The angular dependence of the mean backscatter strength showed distinct differences between hard rough substrates (such as rock and coral reef), seagrass, coarse sediments and fine sediments. The highest backscatter strength was observed not only for the hard and rough substrate, but also for marine vegetation, such as rhodolith and seagrass. The main difference in acoustic backscatter from the different habitats was the mean level, or angle-average backscatter strength. However, additional information can also be obtained from the slope of the angular dependence of backscatter strength.
It was shown that the distribution of the backscatter. The shape parameter was shown to relate to the ratio of the insonification area (which can be interpreted as an elementary scattering cell) to the footprint size rather than to the angular dependence of backscatter strength. When this ratio is less than 5, the gamma shape parameter is very similar for different habitats and is nearly linearly proportional to the ratio. Above a ratio of 5, the gamma shape parameter is not significantly dependent on the ratio and there is a noticeable difference in this parameter between different seafloor types. A new approach to producing images of backscatter properties, introduced and referred to as the angle cube method, was developed. The angle cube method uses spatial interpolation to construct a three-dimensional array of backscatter data that is a function of X-Y coordinates and the incidence angle. This allows the spatial visualisation of backscatter properties to be free from artefacts of the angular dependence and provides satisfactory estimates of the backscatter characteristics.
Using the angle-average backscatter strength and slope of the angular dependence, derived by the angle cube method, in addition to seafloor terrain parameters, habitat probability and classification maps were produced to show distributions of sand, marine vegetation (e.g. seagrass and rhodolith) and hard substrate (e.g. coral and bedrock) for five different survey areas. Ultimately, this study demonstrated that the combination of high-resolution bathymetry and backscatter strength data, as collected by MBS, is an efficient and cost-effective tool for benthic habitat mapping in costal zones.

Les phanérogames marines sont un compartiment biologique fondamental au bon maintien des environnements côtiers grâce aux nombreux services écosystémiques qu’elles fournissent. Au cours des dernières décennies, leur surface a été considérablement réduite à l’échelle mondiale, entraînant la perte de leurs fonctions régulatrices, notamment des conditions hydrodynamiques et des flux sédimentaires. Dans ce contexte, cette thèse s’attache à mieux comprendre la réponse des processus hydro-sédimentaires des lagunes côtières peu profondes au déclin d’espèces intertidales, à travers l’étude régionale de l’effet de la régression des herbiers de zostères (Zostera noltei et Zostera marina) du Bassin d’Arcachon. Cette analyse a été menée grâce à de la modélisation numérique, qui a nécessité de développer et mettre en place une plateforme de modélisation bio-hydro-sédimentaire, constituée de quatre modèles couplés (modèle hydrodynamique, modèle de vagues, modèle de transport sédimentaire et modèle de croissance des zostères), prenant tous en compte l’influence de la végétation. Une attention particulière a été portée à l’implémentation de la végétation dans le modèle de vague et le modèle de transport, en utilisant des approches combinant expériences en laboratoire, de terrain et de la modélisation numérique. Dans un premier temps, l’influence de la régression des herbiers de zostères a été étudiée sur les conditions hydrodynamiques et a révélé d’importantes modifications de l’hydrodynamique tidale et des conditions de vagues, notamment l’intensification des vitesses sur le fond de l’ordre de 100 % et de la hauteur de vagues de 50 % sur les estrans où les herbiers ont le plus décliné. Ensuite, la contribution de la régression des herbiers sur la modification de l’hydrodynamique tidale a été comparée à celle induite par la reconfiguration des Passes, montrant que le déclin des herbiers a été le principal responsable de la modification des vitesses sur les estrans et chenaux à l’intérieur du Bassin. En réponse au déclin de Zostera spp., ainsi qu’à l’intensification des conditions hydrodynamiques qui en a résulté, cet environnement a subi d’importantes modifications de la dynamique sédimentaire. Les flux d’érosion et de dépôt ont été particulièrement impactés par le déclin, générant des concentrations en matières en suspension de 2 à 6 fois plus importantes. La régression des herbiers a également perturbé les échanges sédimentaires entre la lagune et l’océan ouvert, ainsi qu’entre les différentes zones du Bassin, donnant lieu à une redistribution des différentes classes sédimentaires et à la modification de la composition du sédiment superficiel. Les estrans situés le long des côtes ont eu tendance à s’accréter et à s’envaser, alors que les estrans plus centraux ont eu tendance à s’éroder et devenir plus sableux. En particulier, nous avons montré que la régression des herbiers est le principal responsable des évolutions bathymétriques observées à l’intérieur du Bassin. Enfin, l’évolution potentielle des herbiers de zostères a été étudiée à travers différentes conséquences du changement climatique que sont la hausse du niveau marin et l’évolution des températures de l’air et de l’eau. Une attention particulière a été portée à la génération de forçages environnementaux futurs, reproduisant les éventuelles températures et le niveau marin à l’horizon 2050. La biomasse des herbiers a témoigné de réponses contrastées à ces deux processus, très dépendantes de plusieurs facteurs environnementaux (profondeur, exposition à l’hydrodynamique, temps de renouvellement). Nous avons également montré que, plus que l’augmentation des températures moyennes, c’est l’augmentation de la fréquence et de l’intensité des événements extrêmes de température qui devrait être le principal facteur de contrôle des évolutions de biomasse dans le Bassin d’Arcachon
Seagrass meadows provide numerous ecosystem services and constitute a fundamental biological component for the sustainability of coastal environments. Over the past decades, the surface colonized by seagrasses has drastically declined globally, reducing their capacity to regulate hydrodynamic conditions and sediment fluxes. In this context, this work aims to better understand the response of hydro-sedimentary processes to the decline of intertidal seagrass in a shallow coastal lagoon. For this purpose, the Arcachon lagoon (France), extensively colonized by seagrass meadows (Zostera noltei and Zostera marina), was used as a study area. This analysis was conducted through a numerical modeling approach that required the preliminary development and implementation of a hydro-bio-sedimentary modeling platform, consisting of four coupled models (flow model, wave model, sediment transport model, and seagrass growth model), all accounting for the effect of vegetation. Specific attention was paid to the implementation of vegetation in the wave and sediment models, utilizing combined numerical, field, and laboratory experiments. The impact of seagrass decline was first studied on hydrodynamics, revealing significant changes in tidal hydrodynamics and the wave regime, especially an intensification in bottom current velocities by 100% and wave height by 50% on the tidal flats. Further investigation into the relative influence of seagrass decline and morphological evolutions of the inlet on tidal hydrodynamics showed that vegetation loss was the main factor influencing the modification of current velocities inside the lagoon. In response to the decline of Zostera spp. and the subsequent intensification of hydrodynamic conditions, this environment underwent significant changes in sediment dynamics. Modification of erosion and deposition fluxes resulted in suspended sediment concentrations 3 to 6 times higher in the areas where vegetation decreased the most. Seagrass decline also impacted sediment transport between the lagoon and the open ocean, as well as among different areas of the lagoon, leading to the redistribution of the different sediment classes and altering the composition of the seabed sediment. The tidal flats located along the coastlines accreted and became siltier, while those in the center of the lagoon eroded and became sandier. In particular, our results demonstrated that seagrass decline was the primary contributor to the observed bathymetric changes in the lagoon. Finally, potential evolutions of marine phanerogams were investigated, considering various consequences of climate change such as sea level rise and increase of temperature. For this analysis, special consideration was given to generating environmental forcing that reproduces potential temperature and water level conditions by 2050. Seagrass biomass exhibited contrasting responses to these processes, clearly dependent on multiple environmental factors (depth, hydrodynamic exposure, renewal time). We also showed that, beyond global warming, it is the increase in frequency and intensity of extreme temperature events that are expected to induce the most significant changes in seagrass biomass

Les écosystèmes marins côtiers subissent de nombreuses perturbations naturelles et anthropiques. Dans le contexte socio-économique actuel, mieux comprendre le fonctionnement et transfert des contaminants dans ces écosystèmes est primordial. L’étude du transfert de la matière organique et des contaminants aux interfaces, constitue un enjeu crucial. Les principaux objectifs sont de caractériser l’ichtyofaune des herbiers de posidonie et comprendre les relations trophiques ; d’établir les niveaux et variabilité spatiale de la contamination en éléments traces ETs et polluants organiques persistants POPs dans les compartiments de l’écosystème ; et d’identifier les sources et les processus influençant les niveaux de contamination le long du réseau trophique à Marseille et Hyères. La caractérisation du peuplement de poissons et des relations trophiques au sein de l’écosystème est nécessaire pour comprendre les niveaux de contamination. Chez les poissons, le phénomène de bioaccumulation des ETs est difficile à mettre en évidence, excepté pour le mercure. L’influence du régime alimentaire, taille et besoins physiologiques et métaboliques est manifeste. La grande stabilité et la rémanence des POPs leur confèrent des propriétés de bioconcentration et de bioamplification importantes. Les concentrations en contaminants mesurées, ainsi que la détection de pesticides toxiques interdits, attestent de la nécessité de considérer cette pollution avec attention, plus forte à Marseille
The marine ecosystems undergo frequent disturbances. In the current socio-economic context characterized by intensive urban development and industrialization, it is of primordial importance for the management of the environment to achieve a better understanding of the functioning and the transfer of contaminants within these ecosystems. The study of the transfer of organic matter and contaminants to the interfaces is thus a crucial issue. The main objectives are to characterize the fish fauna and to determine the food webs; to establish the levels and patterns of spatial variability of contamination by trace elements TEs and persistent organic pollutants POPs; and to identify the sources and the processes having an influence on the levels of contamination throughout the food webs. The characterization of the fish populations and the trophic relations between the compartments of the ecosystem is necessary in order to understand the levels of contamination in TEs and POPs. For the fishes, it is difficult to provide evidence of the phenomenon of bioaccumulation of TEs, except for mercury, but the influence of diet, size and physiological and metabolic requirements is obvious. The great stability, liposolubility and persistence of the POPs confer on them significant bioconcentration and bioamplification capabilities. The concentrations in TEs and POPs recorded, and the detection of banned toxic pesticides, attest to the necessity of paying close attention to this pollution

碩士
國立中山大學
海洋生物研究所
97
Fluctuation of the seagrass ecosystem may be informative to the impacts of environmental changes. This study focuses on a small, inconspicuous triplefin blenny, Enneapterygius minutus, found in a specific tide pool of seagrass meadow on Gui Wan Bi, Green Island, Taiwan. Its high abundance and stable residence make this species a suitable candidate to monitor the condition of the seagrass ecosystem. Monthly collections were made during low tide from April 2007 to July 2008. The otolith microstructure was examined to study their age and growth circumstance. Developmental stages of the ovaries based on histological characteristics together with data of batch fecundity and GSI value were applied to estimate size at maturation and the spawning seasonality of the individual assemblages in the tide pool. A length-frequency analysis was made by using the monthly data. Enneapterygius minutus is a kind of short life species. It has a quite low batch fecundity and a year-long breeding ability with a seasonal high peak mainly from late winter to late spring. The recruitment of juvenile individuals began about a month after breeding had occurred. These data show that Enneapterygius minutus uses seagrass meadows as a hatching and nursing habitat. According to the close relationship between Enneapterygius minutus and seagrass meadow, it would be possible to monitor this ecosystem by using this species as an indicator when it is under environmental stress.

Seagrasses are key coastal ecosystems, providing many ecosystem services. Seagrasses increase biodiversity as they provide habitat for a large set of organisms. In addition, their structure provides hiding places to avoid predation. Seagrasses can grow in shallow marine coastal areas, but several factors regulate their growth and distribution. Seagrasses can uptake different kinds of organic and inorganic nutrients through their leaves and roots. Nitrogen and phosphorous are the most important nutrients for seagrass growth. Biological nitrogen fixation is the conversion of atmospheric nitrogen into ammonia by diazotrophic bacteria. This process provides a significant source of nitrogen for seagrass growth. The nitrogen fixation is controlled by the nif genes which are found in diazotrophs. The main goal of the project is to measure nitrogen fixation rates on seagrass sediments, in order to compare among various seagrass species from the Red Sea. Moreover, we will compare the fixing rates of the Vegetated areas with the bare sediments. This project will help to ascertain the role of nitrogen fixing bacteria in the development of seagrass meadows.

Tese de mestrado, Ecologia Marinha, Universidade de Lisboa, Faculdade de Ciências, 2015
As pradarias de ervas marinhas, assim como muitos outros ecossistemas marinhos, estão a sofrer uma degradação sem precedentes em todo o planeta. Devido à rápida perda destes habitats, são necessárias técnicas de monitorização que permitam de forma precisa caracterizar o estado das pradarias de ervas marinhas ao longo do tempo. Adicionalmente é importante considerar o custo e logística na monitorização, assim como a sua flexibilidade em diferentes condições de amostragem e de forma não intrusiva, para um trabalho de campo periódico. Varias metodologias tem sido propostas ao longo do tempo para o estudo de ecossistemas marinhos como as pradarias de ervas marinhas. O objectivo do presente trabalho é o desenvolvimento e teste (análise comparativa) de uma nova abordagem de baixo custo, ao mapeamento dos limites e densidade de pradarias de ervas marinhas, com recurso a imagens aéreas a baixa altitude e alta definição (0.1 m ), obtidas autonomamente. Pretendeu-se assim vencer várias das limitações propostas por metodologias anteriores. Foram abrangidos 3 níveis na análise comparativa: as fases de aquisição (metodologia), a avaliação da influência das condições de aquisição das mesmas e a classificação das imagens. A análise comparativa dos diferentes resultados foi dirigida, não só à avaliação da expressão territorial das manchas – extensão e delimitação – mas também à avaliação comparativa, em termos de resultados e exequibilidade, das metodologias empregues. O trabalho de campo foi desenvolvido na península de Tróia, tendo como alvo duas áreas principais: uma no extremo NO da península de Tróia e outra entre as instalações da Marinha e o novo cais dos ferries. Para a análise comparativa ao nível da aquisição das imagens, a pradaria situada no extremo NO da península de Tróia, foi monitorizada com uma metodologia já testada e avaliada em prévios estudos, a partir de imagens oblíquas em cor verdadeira, obtidas a partir de um ponto fixo elevado na proximidade (o topo de um dos hotéis existentes). Por outro lado na pradaria situada na localização do novo cais dos ferries, foi aplicada a nova metodologia proposta, com fotografia a partir de um balão cativo, a uma altitude de aproximadamente 50 m, que foi guiado ao longo da linha de costa por um operador. Vários fatores ambientais foram inicialmente considerados para o teste das metodologias: vento, ondas, maré, etc. Sendo que o nível de maré foi o fator finalmente usado para a análise comparativa consoante as condições de aquisição. Os levantamentos fotográficos de ambas as manchas foram realizadas com uma periodicidade de base mensal, sempre em condições de baixa-mar de águas vivas. O nível de maré abrange um amplo intervalo de possibilidades, contudo, as imagens foram diferenciadas em dois grupos no contexto das condições de aquisição: emerso e submerso. Emerso refere-se a imagens em que a pradaria apresenta alguma porção emersa e submerso, refere-se às imagens com a totalidade da pradaria submersa. Assim, estes dois grupos permitiram uma clara diferenciação entre diferentes condições ambientais flutuantes e típicas dos ambientes estudados. Estas condições foram também condicionantes para a aquisição de imagens aéreas com ambas as metodologias, o que permitia avaliar a flexibilidade da aplicação da nova metodologia proposta. Em ambos as metodologias de aquisição, as imagens originais em cor verdadeira foram ortorrectificadas (georreferenciadas), com base em levantamentos de campo levados a cabo com recurso a um sistema de GPS com correcção diferencial RTK, para obter os pontos de controlo de referencia para o processo. No caso das imagens obtidas com a nova metodologia proposta, a partir do balão, foram agrupadas 2 ou 3 imagens, em mosaicos representativos de uma secção significativa da área alvo. Finalmente, estas imagens rectificadas e em cor verdadeira, foram processadas para permitir avaliar a distribuição e densidade das manchas de ervas marinhas. Para a análise comparativa ao nível de classificação da imagem, foram utilizados e comparados diferentes algoritmos de classificação, nomeadamente classificação de base pixel e classificação baseada em objectos. Todas as imagens classificadas foram reclassificadas até obter mapas binários representando as classes: Ervas marinhas; Não-ervas marinhas. A partir dos mapas binários para cada uma das imagens processadas, foram obtidos: área da classe Ervas marinhas; precisão de classificação da imagem (a través da comparação com pontos controlo na imagem em cor verdadeira); e o coeficiente kappa (comparando mapas binários). Estes parâmetros foram usados no contexto da análise comparativa para os 3 níveis propostos: • As áreas da classe Ervas marinhas foram comparadas para testar a semelhança/diferença entre a área de cobertura em cada uma das condições de amostragem (emerso/submerso) para cada uma das metodologias usadas (imagens obliquas/imagens com o balão). Assim, foi possível comparar se a situação de maré, influía nos resultados de estudos de densidade e distribuição a través das imagens aéreas. • A precisão na classificação das imagens foi comparado para cada um dos 3 níveis, por forma a avaliar semelhanças/diferenças entre o processo de aquisição das imagens (metodologias), entre condições de amostragem e entre abordagens nas classificações das imagens. • O coeficiente kappa foi obtido a partir da comparação entre mapas binários, comparando condições de amostragem (emerso/submerso) e classificação da imagem (pixel/objecto). Os resultados mostraram que as imagens obtidas com o balão apresentavam menos erros e distorções no processo de rectificação, devido a sua maior verticalidade. Contudo, tinham a limitação decorrente de uma distribuição mais limitante dos pontos de controlo de referencia obtidos com o GPS-RTK. As imagens obtidas a partir do balão a 50 m de altitude permitiram abranger a largura toda da pradaria. Por outro lado, os resultados obtidos através da análise das imagens classificadas (mapas binários), mostraram diferencias significativas (p=3.221×10-05) só ao nível de comparação entre abordagens de classificação das imagens, sendo que a classificação baseada em objectos, ofereceu resultados mais precisos que a classificação de base pixel. Este estudo demonstrou que a metodologia proposta, com o balão cativo, oferece a possibilidade de mapeamento de pradarias de ervas marinhas a baixo custo, com imagens de alta resolução e com elevada precisão. Os resultados a nível de precisão na nova metodologia usada foram semelhantes aos obtidos com a metodologia comparada de imagens obliquas, já demonstrada em estudos anteriores como uma metodologia que vencia limitações de outras abordagens. As maiores limitações para à aplicação da nova metodologia com o balão cativo foram devido as condições meteorológicas, nomeadamente o vento. Contudo, a nova metodologia com o balão ofereceu outras vantagens relativamente às fotografias obliquas além do menor error na rectificação: nomeadamente, a independência de aplicação e o maior detalhe das imagens para representar a complexidade dos ecossistemas. No contexto das condições de amostragem, foi demonstrado que o nível de maré não é um fator que influencie resultados e interpretações, desde que dentro de um limite de visibilidade mínima e para uma cota de maré máxima de 0.8 m, para permitir obter imagens desejáveis. Finalmente, a maior precisão obtida com a classificação baseada em objectos indica que este abordagem oferece uma maior capacidade para classificar as imagens destes sistemas aquáticos superando possíveis limitações p. ex., de visibilidade devida à turbidez o à presença de objectos não desejados na classificação. Este estudo demonstrou a possibilidade e interesse do mapeamento não intrusivo, de baixo custo e com elevada precisão de pradarias de ervas marinhas, mas que também pode ser aplicado noutros ecossistemas intertidais, oferecendo uma nova ferramenta para à necessária monitorização periódica de sistemas complexos.
Seagrass meadows, together with other coastal marine habitats, are facing unprecedented declines, which requires low cost methodologies for its highly frequent periodic monitoring, able to represent accurately the complexity of those ecosystems. In this context, the aim of the present study was to develop a new approach using nadir aerial photographies from low altitude – high resolution (0.1 m), with a helium balloon system. The methodology was tested (comparative analysis) at 3 levels. First, at methodology level agains an oblique terrestrial photography methodology used in previous studies at the same location. Second, at sampling conditions level for typical changing environment situations – emerged and submerged. Third, at image classification level comparing pixel- and object-based classification. Testing for each of the levels, was through the analysis of processed images taken, which include: georeferencing and, for nadir aerial photographies, a mosaicking process, and image classification. Final images data, were obtained from the binary (seagrass / non-seagrass) classified maps of each treated image, from which it was obtained: area of seagrass class for each image; classification accuracy; and kappa coefficients values from comparison between classified maps. Hence, area results were used to test for sampling conditions comparative analysis; classification accuracies were used to test for 3 levels (methodology, sampling conditions and image classification) comparative analysis; and kappa analysis to compare binary maps between pairs of images for sampling conditions and image classification comparative analysis. Results showed significance differences only at image classification level comparison (p=3.221×10-05), scoring higher accuracy values for object-based classification. The study demonstrated that highly accurate results can be obtained through the proposed low cost methodology, for different sampling conditions, overcoming some classification issues with the object-based approach. Thus, allowing to reliably represent the seagrass meadows structural complexity through low altitude-high resolution images in a nonintrusive low-cost approach.

Nearshore marine habitats provide critical nursery grounds for juvenile fishes, but their functional role requires the consideration of the impacts of spatial connectivity. This thesis examines nursery function in seagrass habitats through a marine landscape (“seascape”) lens, focusing on the spatial interactions between habitats, and their effects on population and trophic dynamics associated with nursery function to rockfish (Sebastes spp.). In the temperate Pacific Ocean, rockfish depend on nearshore habitats after an open-ocean, pelagic larval period. I investigate the role of two important spatial attributes, habitat adjacency and complexity, on rockfish recruitment to seagrass meadows, and the provision of subsidies to rockfish food webs. To test for these effects, underwater visual surveys and collections of young-of-the-year (YOY) Copper Rockfish recruitment (summer 2015) were compared across adjacent seagrass, kelp forest, and sand habitats within a nearshore seascape on the Central Coast of British Columbia. Recruitment was positively influenced by the structural complexity of seagrass and adjacency to kelp forest sites, however a negative interaction between seagrass complexity and kelp forest adjacency suggests that predation modifies Copper Rockfish recruitment densities. In addition, using δ13C and δ15N isotopes to determine the basal contributions to seagrass food webs, kelp-derived nutrients were on average 47% ± 0.4 of YOY Copper Rockfish diets, which was 3x and 67x greater than the contribution of autochthonous seagrass production (seagrass epiphyte and seagrass blades, respectively). YOY Copper Rockfish diets in seagrass adjacent to sand habitats had the greatest amounts of kelp-derived nutrients and harpacticoid copepods, and concurrently had lower body condition compared to rockfish in the seagrass kelp edges and interior, feeding predominantly on seagrass epiphytes and calanoid copepods. This thesis provides further evidence that temperate seagrasses are nurseries for rockfish and that spatial elements of seascapes, including connectivity via habitat adjacency and variability in habitat structure, alter the recruitment and diets of rockfish in seagrass habitats. These seascape nursery effects are important considerations for marine planning, especially given the global decline of nearshore habitats.
Graduate

碩士
國立中山大學
海洋環境及工程學系研究所
95
This study refers to developed ecological model abroad, and established the seagrass model with MATLAB compiler. I also took the seagrass meadows in south Taiwan-Nanwan for my studying case, and simulated the dynamic effect of seagrass and epiphyte biomass, as well as nutrient, and attempted to go on probing into the cause with northeast monsoon and typhoon. The simulating site of this study was Nanwan, which is located at Hengchun Peninsula, the southern tip of Taiwan. The dominant species in this area is Thalassia hemprichii. South Taiwan is situated at a tropical climate, and the variation of air temperature is small. Additionally, Kurshio embranchment cause the variation of water temperature smaller, about 24 (℃) to 30 (℃).The northeastern monsoonal winds, formed downhill winds, are extremely forceful from October to April, so the wind speed is greater during this period than the rest of the year. In South Taiwan, dry-wet season is clearly. The dry season is from November to April, and the wet season is from May to October. The main rainfall comes from southwest monsoon, especially summer typhoon (June to September). The wind speed is raised abruptly by typhoon and makes water agitate, which not only cause the mortality raising but also the sediment turbulence. By Lin’s research (2005), the growing area of seagrass meadow in Nanwan is a half-closed tidal pool where human makes huge effect and there is a lot of drainage of house and inn sewage. Furthermore, these seagrasses in Nanwan would be exposed to air during the period of poor tide and the emerged period is the longest of these three areas -Nanwan, Dakwan and Wanliton. The seasonal dynamic of seagrass, which is located in the high site of intertidal zone, is obvious, and the biomass is larger in summer than in winter; but that is not obvious in the low site and tidal pool. By the seasonal condition and some specially climate condition mentioned above, the analysis of simulate cases would be go on. Comparing of the modeling result and real measurement, the seasonal changing situation mostly match up. No matter high site (emerged and dried) or low site, there is the maximum of seagrass biomass (including above ground, below ground, or shoot density) in summer, and the minimum in winter. Typhoon causes the biomass losing abruptly in summer. R/S ratio (below-ground biomass division above-ground biomass) is bigger in winter than in summer. On one hand the inside nitrogen redistribution is larger in summer, because the larger growth rate occurs in summer, and the more nutrient is supplied from roots, on the other the redistribution is smaller in winter cause the less nutrient is supplied from roots. Epiphyte biomass has the maximum in summer, when the nutrient concentration of water is larger. In the section of the difference between low and high site seagrass, it is apparent that the high site seagrass would be exposed to air and dried by northeast monsoon. Although typhoon comes up, its influence is not so strong as northeast monsoon at high site. The maximum biomass still occurs in summer, and it is presumed that the living environment of high site seagrass is with more pressure by nature. The above-ground biomass of high site seagrass is smaller than low site, but the below-ground biomass is much lager at high site. Besides, shoot density is larger at high site. The biomass of epiphyte is larger at low site just opposite to shoot density. It is supposed that high site seagrass is emerged to air and limited by environment factors so above-ground biomass would be reduced and store up the sustenance to below-ground biomass. It is conjectured that the main factor with shoot density is affected by light density and below-ground biomass. In shallow water, the seagrass at high site could accept more light energy, moreover the below-ground biomass is sufficient and the recruitment rate is large, thus there are more shoots at high site. Epiphytes are also limited by water depth and wind, and the biomass of epiphyte at high site is smaller than at low site.

Tese de mestrado em Ecologia Marinha, 2021, Universidade de Lisboa, Faculdade de Ciências
Desde a Revolução Industrial que o aumento significativo da concentração de dióxido de carbono (CO2) na atmosfera, resultante das atividades humanas, tem vindo a provocar grandes alterações na físico-química dos oceanos. O CO2 atmosférico é dissolvido nos oceanos causando uma diminuição do pH da água, através de um processo denominado acidificação dos oceanos. Como resultado do aumento da captação de CO2 pelo oceano, o pH da superfície oceânica poderá diminuir entre 0,13 e 0,42 unidades, até o final do século XXI. Paralelamente, o aumento do efeito de estufa contribuiu significativamente para o aquecimento global da Terra e subsequentemente dos oceanos, uma vez que estes absorvem mais de 90% da acumulação de calor atmosférico. Deste modo e em resultado da subida das temperaturas médias globais, é previsível que ocorra um aumento de 1°C a 3°C da temperatura da superfície da água do mar (SST), até 2090. Por conseguinte, os eventos climáticos extremos têm vindo a ser cada vez mais frequentes e intensos, tanto a uma escala espacial como temporal. Dentro dos eventos climáticos extremos, as ondas de calor marinhas (MHW) foram identificadas como os principais fatores de stress para os organismos marinhos, provocando efeitos prejudiciais sobre as comunidades e ecossistemas costeiros. As MHWs são classificadas de acordo com a sua intensidade, variando de moderadas (categoria I) a extremas (categoria IV) e podem resultar não só de processos da interação entre a atmosfera e o oceano, como também da influência humana que aumenta a severidade e frequência destes eventos. De acordo com o Painel Intergovernamental para as Alterações Climáticas (IPCC), a frequência de MHWs duplicou desde 1982 e tem sido também acompanhada por um aumento de intensidade ao nível mundial. Estudos anteriores revelam que as MHWs provocam efeitos deletérios na biosfera marinha, ameaçando a biodiversidade. Os ecossistemas costeiros são de particular importância uma vez que são zonas cruciais de reprodução para uma grande variedade de organismos marinhos e são dos habitats mais expostos e vulneráveis às alterações climáticas e a consequentes aumentos da temperatura da água do mar. Dentro destes ecossistemas, as pradarias marinhas desempenham um papel ecológico essencial de suporte da biodiversidade uma vez que fornecem alimento, abrigo e habitats berçários para a vida marinha, sendo assim zonas de reprodução muito importantes para peixes e invertebrados. Para além disso, diminuem a erosão costeira e servem de espécies bandeira, indicadoras de estado do sistema onde se incluem. Assim como os mangais e os sapais, as pradarias marinhas são um dos principais sumidouros de carbono azul do planeta, tendo uma elevada capacidade de sequestro de carbono nas suas raízes e rizomas, o que as torna cruciais nas estratégias de combate e mitigação das alterações climáticas. Todas estas características culminam no reconhecimento de serem um dos ecossistemas mais produtivos da biosfera estando esta função ecológica na base todos estes serviços. Deste modo, torna-se imperativo estudar os efeitos que as futuras alterações climáticas poderão provocar nestes ecossistemas. As ervas marinhas são plantas vasculares com a capacidade de produzir flores, frutos e sementes, pertencendo assim ao grupo das angiospérmicas. Podem ser encontradas nas zonas costeiras de todos os continentes, excetuando a Antártica e crescem em águas pouco profundas devido à necessidade de luz para realização da fotossíntese. Enraízam-se em substratos macios e finos de lama ou areia e em zonas intertidais e subtidais em ambientes marinhos e estuarinos. A diversidade global de espécies de ervas marinhas é baixa (existem cerca de 66 espécies em todo o mundo). No entanto as ervas marinhas podem ter faixas que se estendem por milhares de quilómetros de costa, ocupando entre 160,000 e 600,000 km2 a nível mundial. Existem pradarias mono-específicas (formadas por apenas 1 espécie) ou multiespecíficas (formadas por várias espécies). As pradarias formadas por um maior número de espécies encontram-se nas zonas dos trópicos, enquanto que nas zonas temperadas as pradarias são formadas por uma ou duas espécies. No que diz respeito ao impacto das MHWs em ervas marinhas, estudo anteriores mostraram que, quando sujeitas a estes eventos extremos de temperatura há uma diminuição da sobrevivência, do crescimento e das taxas de fotossíntese destas plantas. As pradarias marinhas têm vindo a desaparecer, não só devido às alterações climáticas, mas também devido a causas relacionadas com a ação humana como técnicas de pesca destrutivas, danos causados pela ancoragem de embarcações de pesca e também por contaminação causada pelo tratamento de resíduos e esgotos urbanos que provocam a eutrofização. Com todos estes impactos, estes habitats costeiros são por isso classificados como vulneráveis e em perigo de extinção na Lista Vermelha de Espécies Ameaçadas da União Internacional para a Conservação da Natureza (IUCN). As pradarias marinhas são conhecidas como hotspots de biodiversidade marinha, suportando e aumentando a diversidade da macrofauna associada. Os taxas dominantes da macrofauna associada a estes ecossistemas são os poliquetas, os moluscos e os crustáceos. O estudo das comunidades de macrofauna em pradarias marinhas é um complemento importante a considerar na monitorização destes ecossistemas costeiros por ser um dos elementos de qualidade biológica das águas costeiras de acordo com a Diretiva Quadro da Água da União Europeia. Zostera noltei encontra-se ao longo da região do Mediterrâneo e do Atlântico Norte Temperado. É uma espécie com um crescimento rápido e uma larga distribuição, formando extensas pradarias em zonas intertidais. Em Portugal, as pradarias de ervas marinhas estão presentes na maioria dos estuários, rias e lagoas. Z. noltei é a espécie mais abundante no estuário do Sado, seguindo-se Cymodocea nodosa e Zostera marina em zonas intertidais e subtidais. A zona de estudo do estuário do Sado é uma área com um impacto acentuado devido ao desenvolvimento agrícola, à presença de infraestruturas urbanas e atividades industriais e portuárias que tem ocorrido nas últimas décadas, tornando-o num sistema de águas poluídas e eutrofizadas com efeitos negativos nas comunidades estuarinas. A presente dissertação teve como objetivo estudar a resiliência das pradarias da erva marinha Z. noltei, e das comunidades de macroinvertebrados associada, no Estuário do Sado a cenários de MHWs de diferentes intensidades. Neste sentido, foram simulados três cenários laboratoriais (i.e. controlo, MHW de intensidade III e MHW de intensidade IV) em sistemas de suporte de vida semi-abertos adequados à manutenção ex situ de organismos marinhos e no final foram analisadas taxas de sobrevivência, perfil de pigmentos das folhas de Z. noltei, diversos parâmetros fotossintéticos e índices de biodiversidade da macrofauna associada (i.e. índice de diversidade de Shannon-Wiener, Simpson e Margalef e índice de equitabilidade de Pielou). Não foram observadas diferenças significativas entre tratamentos para qualquer um dos parâmetros analisados das plantas. O mesmo sucedeu com os índices de biodiversidade calculados para a macrofauna associada. A ausência de diferenças significativas entre os vários tratamentos demonstra que as pradarias marinhas de Z. noltei no Estuário do Sado estão adaptadas a mudanças abruptas, de curta duração, na temperatura da água. Tal deverá estar associado ao facto desta espécie existir em locais sujeitos a variações ambientais diárias (i.e. regimes de marés) nas zonas intertidais. Apesar destes resultados, o estudo do impacto destes eventos climáticos extremos em ervas marinhas continua a ser importante, não só por ser escasso e por haver uma necessidade constante de conservar estes ecossistemas, mas também para que seja possível prever a resiliência destas espécies quando expostas aos cenários futuros propostos pelo IPCC.
Extreme weather events (EWEs) are becoming more frequent and intense, both at a spatial as well as temporal scales. Within EWEs, marine heat waves (MHWs) have been identified as major stressors to marine biota, taunting detrimental effects over coastal communities and ecosystems. According to the Intergovernmental Panel on Climate Change (IPCC), the frequency of MHWs has doubled since 1982 at a worldwide level, being additionally accompanied by an intensity increase. Coastal habitats are of particular concern, and within these habitats, seagrass meadows are known to play an essential ecological role by providing food, shelter and crucial nursery habitats for a wide range of marine species. Additionally, they store staggering amounts of carbon in their roots which makes them important for the carbon cycle. They also act as ecological service providers, by promoting sea bottom stabilization, nutrient cycling, act as buffer/trophic transfer zones to sensitive habitats (i.e. coral reefs) and as “environmental status beacons” of coastal ecosystems. As a result of direct anthropogenic pressure and increasing/intensification of MHWs, these key “blue ecosystems” are experiencing a global pressure and subsequent decline. Within this context, the present dissertation aims to investigate the effect of simulated marine heat waves on Z. noltei and associated macrofauna, collected in the Sado estuary, by analyzing several endpoints including: survival, photobiological responses, pigment analyses and biodiversity indices (Shannon-Wiener, Simpson and Margalef diversity indexes, and Pielou’s evenness index). No significant effects were observed between treatments for any of the endpoints analyzed. The same happened with the biodiversity indexes calculated for the associated macrofauna. The present findings suggest that Z. noltei and associated macrofauna may be resilient to short-term extreme MHW conditions. Yet, it is worth noting that such plasticity and adaptive capacity may not suffice under long-term/chronic warming conditions expected and projected by the IPCC until the end of the century.

Habitat fragmentation is often regarded as a biodiversity threat associated with habitat degradation; however, research has also revealed beneficial effects on biodiversity as well, depending on the ecosystem and species community. This study examined the biodiversity of small nekton residing in seagrass meadows characterized by three levels of habitat fragmentation, and as a habitat gradient comprised of measures such as habitat amount, connectivity, patch shape, and proximity. Landscapes were mapped using recent advances in GPS and GIS technology, and analyzed using established methods from research in terrestrial ecosystems. Species richness was not significantly different as a function of fragmentation regardless of season, suggesting that the amount of habitat and configuration of several patches in fragmented habitats is sufficient to support comparable numbers of species in several patches compared to communities in large, continuous seagrass meadows. Species evenness declined significantly in fragmented habitats versus continuous ones in both seasons. Within fragmented landscapes, evenness progressively declined as habitat amount and connectivity decreased and patch isolation and density increased, suggesting that changes in landscape qualities can differentially impact processes supporting metapopulations such as dispersal and reproduction in certain species, thereby influencing community structure. Analyses that included measures of habitat connectivity, proximity, and patch density in addition to habitat amount accounted for more variability in species evenness than those just containing percent cover, and showed that fragmentation’s impacts can differ geographically. These data suggest that community resilience to fragmentation can differ between similar animal communities residing in separate locations, and that landscape configuration plays an important role in determining how communities respond to fragmentation after a threshold of change in habitat amount has been exceeded.
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Abigail Scott studied how herbivore grazing can modify seagrass meadows in the Great Barrier Reef. She found that herbivores act as ecosystem engineers in these seagrass meadows, particularly green turtles and dugong. Abigail's results will be used to inform seagrass monitoring on the Great Barrier Reef.

Seagrass meadows are important habitats of marine plants, adapted to the colonization of coastal and estuarine environments, which provide important functions within the ecosystem. The remarkable decline of seagrass meadows at regional/local (Ria de Aveiro) and global scales has presented however negative implications for the sustainability of the ecosystems where they follow this trend. In this context, the main objective of this work was to improve the present knowledge about seagrass dynamics in the Ria de Aveiro, from a multidisciplinary viewpoint (experimental data collection and treatment and numerical modelling), as well as to anticipate potential changes at the system level in these communities. Therefore, it is intended to contribute to the promotion of adequate management and conservation strategies to minimize its decline and enhance its recovery. From the application of a conceptual DSPIR framework (Drivers-Pressures-State-Impacts- Responses), the results pointed that gradual changes in hydrodynamic characteristics are the basis of the local decline of these communities, presently colonized by monospecific intertidal meadows of Zostera noltei. The scarce availability of seagrass models is even more prominent when dealing with intertidal communities, subject to alternating periods of exposure to air and submergence. As so, the inherent peculiarities of intertidal seagrass Z. noltei communities were investigated, showing a greater influence of the sedimentary characteristics on the relative water content of the plant, rather than the air exposure time. Afterwards, it was developed a seagrass biological model together with a desiccation model of the plant, in order to suppress the previously identified gap, both of which were later coupled to the water quality model (Delft3D-WAQ). The numerical model was calibrated using experimental data collected in the study area (Mira Channel), showing a reliable reproduction of the state variables described by means of above and belowground biomass. However, the present set up needs to be improved, namely in what regards sedimentplant interface and internal nutrient dynamics, before it can be applied to other systems with similar challenges. The performance of the numerical model was analysed through different methodologies that presented divergent results, which suggests the application of further approaches for a robust conclusion. A sensitivity analysis was computed, showing that the parameters used to describe the dependence of the ambient temperature (water and air) are the most sensitive, suggesting that these should be particularly addressed in future experimental surveys, by increasing the frequency of the in situ measurements. Two exploratory simulations of extreme event, extreme river flow and heat-wave, respectively showed a decrease in the favourable conditions for seagrass presence, according to the water velocity and salinity; and clear negative impacts on seagrass growth. Following a prospective viewpoint, different evolutionary scenarios to the future, resulting from the foreseen climate change, were set according to the more and less pessimistic projection (RCP 4.5 and RCP 8.5). The numerical model projections pointed out for a noticeable loss of colonised areas by seagrass (between around 30 and 70%, respectively) compared to the present situation. The multiple stressors analysed generally showed a synergistic effect on the loss of the relative area of seagrass, compared to the isolated sum of each of the factors, which highlights the complex and intrinsic relations established between them. The areas colonized by seagrass meadows that showed greater resilience, to the two simulated climate change scenarios, are located in the south and northwest areas of the central lagoon. The spatial distribution of the anomalies between the reference and the climate change scenarios, showed no uniform pattern of variation, occurring areas with descreased favourable conditions for seagrass presence, but also some areas that verified an improvement of these conditions. For a more effective and holistic approach to the natural evolution and modelling of these systems, a wider spatial and temporal coverage of biotic and abiotic descriptors of these communities should be performed. Moreover, the overview of the ongoing and forthcoming anthropogenic actions must also be included, in the context of the socio-economic development of the region, as well as the framework of the future scenarios in the scope of climate change (temporal scale referred to the end of the century). As so, the management actions can be implemented to promote the resilience of these habitats and assure the services provided by the ecosystem.
As pradarias marinhas constituem importantes habitats de plantas superiores, adaptadas à colonização de ambientes costeiros e estuarinos, que desempenham importantes funções nestes ecossistemas. O seu declínio acentuado verificado a escalas regionais/locais (Ria de Aveiro) e globais tem, no entanto, apresentado implicações nefastas para a sustentabilidade dos ecossistemas onde estão inseridas. Neste contexto, o objectivo principal deste trabalho consistiu em aprofundar o conhecimento presente da dinâmica das pradarias marinhas na Ria de Aveiro, sob o ponto de vista multidisciplinar (colheita e tratamento de dados experimentais e modelação numérica), bem como prever as potenciais alterações ao nível do sistema nestas comunidades. Desta forma, pretende-se contribuir para a promoção de estratégias de conservação adequadas para minimizar o seu declínio e potenciar a sua recuperação. Partindo da aplicação de um modelo conceptual DPSIR (Drivers-Pressures- State-Impacts-Responses), concluiu-se que as alterações graduais nas características hidrodinâmicas estão na base do declínio local destas comunidades, presentemente colonizadas por pradarias monoespecíficas intertidais de Zostera noltei. A escassez de modelos numéricos de pradaria é acentuada, sendo ainda mais proeminente quando se tratam de comunidades intertidais, sujeitas a períodos alternados de exposição ao ar e submersão. Desta forma, as particularidades inerentes às comunidades de pradarias intertidais foram investigadas, mostrando maior influência das características sedimentares no teor relativo de água da planta, em detrimento do tempo de exposição ao ar. Posteriormente, foi desenvolvido um modelo biológico de pradaria, juntamente com um modelo de dessecação da planta, com vista a suprimir a lacuna previamente identificada, sendo ambos posteriormente acoplados ao modelo de qualidade da água (Delft3D-WAQ). Utilizando os dados experimentais colhidos na área de estudo (Canal de Mira) calibrou-se o modelo numérico, tendo-se verificado uma reprodução fiável das variáveis-estado descritas pela biomassa aérea e subterrânea. Porém, a presente configuração requer melhorias adicionais, nomeadamente no que respeita à interface sedimento-planta e dinâmica interna de nutrientes, previamente a ser passível de ser aplicado a outros sistemas com desafios semelhantes. O desempenho do modelo numérico foi analisado por diferentes metodologias que apresentaram resultados divergentes, o que sugere a necessidade de desenvolvimento e aplicação de metodologias adicionais para uma conclusão robusta. Foi realizada uma análise de sensibilidade, que permitiu aferir que os parâmetros usados para descrever a dependência da temperatura ambiente (água e ar) são os mais sensíveis. Deste modo, salienta-se a sua potencial importância e sugere-se a sua consideração em planeamentos experimentais futuros com maior frequência de amostragem nas medições in situ. Numa abordagem exploratória, simularam-se dois eventos extremos, caudal fluvial extremo e onda de calor, tendo os resultados apresentado, respectivamente, uma diminuição das condições favoráveis para a presença de pradarias em termos de velocidade da corrente e salinidade, e um claro decréscimo no crescimento da planta. Seguindo uma abordagem prospectiva, estabeleceram-se diferentes cenários evolutivos para o futuro, resultantes das expectáveis alterações climáticas, de acordo com a projecção mais e menos pessimista (RCP 4.5 e RCP 8.5). As previsões numéricas obtidas indicam uma perda acentuada de áreas colonizadas por pradarias marinhas (entre aproximadamente 30 e 70%, respectivamente) comparativamente à situação presente. As áreas colonizadas por pradarias que mostraram uma maior resiliência, nos dois cenários de alterações climáticas, situam-se na zona sul e noroeste da laguna central. Na análise espacial da anomalia entre o cenário de referência e de alterações climáticas, não se verificou um padrão uniforme, havendo áreas que apresentam um decréscimo nas condições favoráveis para a presença de pradarias marinhas, simultaneamente à ocorrência de áreas que apontam para um melhoramento das mesmas condições. Para uma abordagem mais efectiva e holística da evolução natural e modelação destes sistemas, deve considerar-se uma maior cobertura espacial e temporal dos descritores bióticos e abióticos destas comunidades. Deve ser ainda incluído o levantamento das actividades antropogénicas decorrentes e previstas no contexto do desenvolvimento socio-económico da região (escala temporal até meio do século), e ainda, deve ser feito o enquadramento nos cenários futuros no contexto das alterações climáticas (escala temporal até final do século), para que medidas de gestão possam ser implementadas no sentido de promover a resiliência destes habitats, de forma a garantir os serviços prestados.
Projecto LAGOONS – FP7/2007-2013; Projecto AquiMap (MAR-02.01.01-FEAMP-0022)
Programa Doutoral em Biologia

Bibliography : leaves 293-304.
xii, 304 leaves : ill., maps ; 30 cm.
Title page, contents and abstract only. The complete thesis in print form is available from the University Library.
Thesis (Ph.D.)--University of Adelaide, Dept. of Zoology, 1994

Interactions amongst invertebrates, epiphytes, and seagrasses were studied in intertidal meadows near Townsville, Australia. Data were collected to test the assumptions of the prevailing model of seagrass-epiphyte-grazer interactions. That model assumes that epiphytes have the potential to limit seagrass standing crop, but that invertebrate grazers limit epiphytes, and therefore indirectly benefit the seagrass. Furthermore, it is generally assumed that the community of epifaunal invertebrates is largely composed of epiphyte grazers, especially small gastropods and peracardian crustaceans, and that direct consumption of the seagrass is of minor importance. One intertidal plot, 100 m2 was established in each of three meadows; Shelly Beach, Cockle Bay and Picnic Bay. Samples of seagrass, invertebrates and epiphytic materials were taken at one to two month intervals over two years. Leaf samples were taken to estimate epifaunal invertebrate densities and epiphytic loads from the same leaves. The percent coverage of the leaves by epiphytic material was estimated, and the material was scraped from the leaves to estimate its ash-free dry weight (AFDW). The seagrass leaf area index (LAI), below ground dry weight (BGDW), and shoot or leaf density in each plot were estimated from core samples. In June 2002, a sudden migration of the sea hare Bursatella leachii into the plot established at Shelly Beach was associated with a rapid reduction in epiphytic loads on Halophila ovalis, but not Halodule uninervis. Unexpectedly, the LAI of H. ovalis declined by two-thirds, while that of H. uninervis remained unchanged. It was hypothesised that the reduction in H. ovalis LAI was due to the sudden exposure of the leaves to high levels of irradiance, resulting in photodamage and photoinhibition. To test that hypothesis, a shading experiment was performed. Plots, 0.5 m2, were shaded with 70% shade cloth over 29 days, to adapt the seagrass to low light conditions, and were then exposed to ambient light. Chlorophyll concentrations increased significantly under shade, then fell to control levels in 4-10 days of exposure in both H. ovalis and H. uninervis. However, the former species did not show any significant increase in chlorophyll per area of substrate under shading, but appeared to trade-off increased chlorophyll production with a decrease in LAI and leaf density. There were no significant differences directly related to the treatments other than the changes in chlorophyll concentrations and an increase in leaf length due to shading of H. uninervis. During two years of sampling, occasions of high epiphytic loads, AFDW >2.0 mg/cm2, on Halodule uninervis were followed by declines in shoot densities, BGDW, and LAI in the plots at Shelly Beach and Cockle Bay. However, within plots there were positive correlations between epiphytic cover and LAI. Those relationships suggested that H. uninervis benefited from epiphytic cover, up to a threshold, possibly because of protective effects against high irradiance. There may also have been reciprocal effects, such that increases in the seagrass canopy promoted development of epiphytic cover, which may have acted as a density-dependent limiter of H. uninervis production. The litiopid gastropod Alaba virgata was the commonest epifaunal epiphyte-grazer, especially at Shelly Beach. Its densities were negatively correlated with epiphytic cover. The positive relationship between epiphytic cover and H. uninervis LAI suggested that A. virgata was likely to have an indirect negative impact on the seagrass, contrary to the prevailing model of seagrass-epiphyte-grazer interactions. Likewise, the commonest amphipod, Ericthonius, had densities that were negatively correlated with epiphytic cover at Cockle Bay and Picnic Bay, but appeared most likely to have a negative impact on the seagrass. The epifaunal communities were numerically dominated by suspension feeders; including the amphipods Ericthonius and Podocerus; the bivalve Electroma, and Anemones. Total epifaunal abundance was negatively correlated with seagrass LAI in each plot. Those relationships likely reflected a negative impact of the seagrass canopy on water flow, and thus food resources for suspension feeders. Therefore, epifaunal abundance and epiphytic cover had inverse relationships to seagrass LAI. A path analysis showed that a bottom-up model with separate effects from seagrass LAI to total epifaunal abundance and to epiphytic cover fit the data well. That analysis used data from all plots in a multigroup design, and suggested that the same processes were occurring in each of the plots despite other major differences among them. There was conspicuous evidence of damage by invertebrate herbivores to the leaves of Halophila ovalis. The areas damaged were measured using image analysis techniques on leaf samples. Those animals found to be consuming seagrass included; a nerite gastropod, Smaragdia souverbiana; an undescribed species of sacoglossa; an amphithoid amphipod, Cymadusa sp.; and the sphaeromatid isopods Cymodoce spp. H. ovalis declined at Shelly Beach during the course of the study, and Halodule uninervis became more abundant, in a pattern suggesting successional change. However, changes in H. ovalis LAI and BGDW were correlated with measures of damage that were most likely caused by crustacean feeding. The prevailing model of seagrass-epiphyte-grazer interactions does not provide a suitable description of those interactions in the intertidal meadows studied near Townsville. There was little evidence that epiphyte grazers would benefit the seagrass by removing epiphytic cover. On the contrary, there was evidence of negative impacts by exposing the leaves to high levels of irradiance, which are commonly experienced in tropical intertidal habitats. Suspension feeders, not epiphyte grazers, dominated the epifaunal community, which therefore had a very different relationship to the seagrass and its epiphytic cover from that anticipated in the current literature. Also unanticipated, consumption of seagrass appeared to play an important role in successional development. From this study, new models are proposed that will hopefully provide a better understanding from which to test and analyse interactions amongst invertebrates, epiphytes and seagrasses in tropical intertidal meadows.

Identification, quantification and monetization of ecosystem services is key for current ecosystem management and policy making. Current estimates of global organic carbon stocks in seagrass meadows and saltmarshes suffer from overrepresentation of certain species and do not account for variation in carbon storage due to abiotic factors. Sediment cores were extracted in Zostera noltei and Spartina maritima habitats along a hydrodynamic gradient in the Ria Formosa, a location that was converted to a clam farm and an area colonized by Caulerpa prolifera. Vegetation at those locations was also described. Organic carbon storage, contribution of the main organic matter sources to the sediment and vegetation properties were analyzed. Relations to estimate organic carbon and total nitrogen using organic matter values were estimated and the possibility of using sediment color to estimate organic matter was investigated. Z. noltei and S. maritima both stored similar amounts of carbon, on average 2.2 times more than the clam farm. The effect of hydrodynamics was significant, with carbon storage capacities in Z. noltei and S. maritima increasing by a maximum factor of 2.08 and 3.44 (respectively), from the most exposed to most sheltered station. Suspended particulate organic matter and autochthonous organic matter were the major contributors to sedimentary organic matter, with a bigger contribution from the former in Z. noltei sediment. No significant differences in contributions were found along the hydrodynamic gradient. Organic carbon storage in Z. noltei and S. maritima fell below reported global means, with the difference becoming even more drastic in high hydrodynamics areas. Understanding carbon storage variation and increasing the diversity of conditions under which they are measured is a key point to increase accuracy of carbon stocks estimations both at a global and local scale.
Os serviços ecossistémicos providenciam vários benefícios à população humana. Alguns destes são úteis para o nosso bem-estar, enquanto que outros são absolutamente essenciais às populações nas áreas que estes abrangem. Atualmente, o sistema que se tem mostrado mais eficaz para a sua gestão consiste na sua monetização e entrada no mercado. Este sistema permite uma formulação e adoção de políticas ambientais baseada em valores quantitativos, através de uma análise custo-benefício entre o aumento do rigor da proteção aplicada a um ecossistema e um aumento da sua exploração. Este tipo de análise tem revelado que, por vezes, a substituição de um serviço ecossistémico tem um custo superior ao benefício económico trazido por uma atividade que o prejudicaria. A desvantagem deste sistema é a necessidade de identificar, quantificar e monetizar corretamente estes serviços, sob o risco de subestimação da importância do ecossistema. O sequestro de carbono atmosférico é um dos serviços ecossistémicos prestados por áreas costeiras vegetadas, tal como pradarias de ervas marinhas e sapais. Este carbono está incluído no chamado Carbono Azul, carbono sequestrado em áreas oceânicas. Apesar de constituírem uma pequena percentagem da área marítima, as áreas vegetais costeiras representam mais de metade dos stocks de carbono azul. O aumento da pressão internacional nos governos para gerirem as suas emissões de dióxido de carbono tem levado a um forte interesse em estimar a capacidade destes habitats em sequestrar carbono, de modo a permitir uma eficaz avaliação e monetização. Cores de sedimento foram retirados em 10 estações na Ria Formosa, Portugal. Estes foram retirados em 4 habitats diferentes: pradarias de Zostera noltei, sapais de Spartina maritima, uma zona de viveiro de amêijoas e uma zona colonizada por Caulera prolifera. Nos habitats de Z. noltei e S. maritima, quatro cores foram retirados ao longo de um gradiente hidrodinâmico. Estes cores foram analisados ao longo da sua profundidade, sendo efetuada uma descrição do perfil sedimentar e medições da cor do sedimento. Subamostras foram feitas a cada 2 cm e para análises do conteúdo de matéria orgânica, carbono orgânico, azoto total, δ13Corg, δ15Ntotal. O conteúdo de carbono orgânico foi combinado com medições de densidade aparente seca para estimar capacidade de armazenamento de carbono orgânico nos habitats amostrados até uma profundidade máxima de 1 metro de profundidade. As assinaturas isotópicas (δ13Corg e δ15Ntotal) foram analisadas com um modelo de mistura de isótopos estáveis para estimar a origem da matéria orgânica no sedimento de Z. noltei e S. maritima. Nestas estações de amostragem, os conteúdos de carbono orgânico, as capacidades de sequestração e contribuições das fontes de matéria orgânica foram comparadas ao longo do gradiente hidrodinâmico e entre habitats. A vegetação nas estações ao longo do gradiente hidrodinâmico foi descrita relativamente à densidade de rebentos, altura da vegetação, área da copa, biomassa aérea e biomassa subterrânea. As diferenças entre as propriedades da vegetação foram analisadas entre estações e espécies. Por fim, modelos para a estimativas dos conteúdos elementares (carbono orgânico e azoto total) com base no conteúdo de matéria orgânica, bem como a estimativa da matéria orgânica com base na cor de sedimento foram propostos. Os perfis sedimentares descritos nos locais suportam a importância da variação de hidrodinâmica ao longo das estações de amostragem, sendo observado um aumento progressivo da fração de argila e lodo no sedimento com a redução da hidrodinâmica à qual a estação está exposta. No sedimento da estação do viveiro de amêijoas, o sedimento era quase totalmente areia, exceto uma pequena camada de lama que possivelmente terá sido formada durante o período em que este local não foi explorado. Foram encontradas diferenças entre os armazenamentos de carbono (por área) entre as áreas vegetadas (Zostera noltei e Spartina maritima) e o viveiro de amêijoas. Esta diferença era esperada e deve-se ao distúrbio constante a que o sedimento superficial é submetido, bem como a constituição do sedimento (areia) que promove taxas de decomposição mais elevadas neste local. Os armazenamentos de carbono dos habitats Z. noltei e S. maritima não diferiram e encontraram-se abaixo das atuais estimativas globais de armazenamento nestes habitats. Os conteúdos de carbono orgânico (em percentagem de peso seco) diminuíram continuamente ao longo da profundidade nas 8 estações de Z. noltei e S. maritima, indicando degradação contínua da matéria orgânica ao longo do tempo. Nas 2 estações mais expostas à hidrodinâmica, esta diminuição foi menos acentuada e os valores de conteúdo de carbono médios foram mais baixos do que nas 2 estações mais abrigadas. Esta diferença poderá indicar diferentes taxas de degradação da matéria orgânica, ou refletir diferenças em taxas de sedimentação e sequestração de matéria orgânica. As contribuições das fontes de matéria orgânica sugerem que a origem da matéria orgânica nestes dois habitats não difere muito, sendo os principais contribuidores matéria orgânica particulada suspensa, seguido de produção primária nestes habitats (tecido vegetal de Z. noltei e S. maritima). A contribuição do tecido vegetal de Z. noltei e S. maritima nas pradarias de ervas marinhas aumentou com a diminuição da hidrodinâmica, sugerindo que existem diferenças nas taxas de exportação de produtividade primária neste habitat, em função da energia à qual a pradaria está exposta. Por fim, a matéria orgânica mostrou ser um bom estimador para conteúdos elementares (Corg e Ntotal), sendo que esta relação não variou significativamente entre habitats. Em conclusão, este trabalho reforça a importância da utilização de dados representativos ao estimar armazenamentos de carbono nestes habitats. Grandes discrepâncias são encontradas entre as espécies usadas para estimar médias globais, fazendo com que estimativas com base nestes valores tenham uma grande probabilidade de sobre/subestimar os armazenamentos. As diferenças encontradas dentro de um habitat com base na hidrodinâmica do local mostram também a importância de tentar incluir parâmetros abióticos nestas estimativas, de modo a melhorar a sua exatidão. Com variações em stock de carbono.