Dissertations / Theses on the topic 'Seagrasse'

Seagrass meadows are highly productive, ecologically and economically valuable ecosystems. However, increased human activities along the coastal areas leading to processes such as eutrophication have resulted in the rapid loss and deterioration of seagrass ecosystems worldwide. This thesis focuses on the responses of seagrasses to increases in nutrients, subsequent increases in ephemeral algae, and changes in the physical-chemical properties of seawater induced by interaction with other marine biota. Both in situ and laboratory experiments conducted on the tropical seagrasses Cymodocea serrulata and Thalassia hemprichii revealed that increased concentrations of water column nutrients negatively affected seagrass photosynthesis by stimulating the growth of the epiphytic biomass on the seagrass leaves. Interaction between seagrasses and other marine organisms induced different responses in seagrass photosynthesis. Ulva intestinalis negatively affected the photosynthetic performance of the temperate seagrass Zostera marina both by reducing the light and by increasing the pH of the surrounding water. On the other hand, the coexistence of mussels Pinna muricata and seagrass Thalassia hemprichii enhanced the photosynthetic activity of the seagrass, but no effect on the mussels' calcification was recorded. This study demonstrates that seagrass productivity is affected by a multitude of indirect effects induced by nutrient over-enrichment, which act singly or in concert with each other. Understanding the responsive mechanisms involved is imperative to safeguard the ecosystem by providing knowledge and proposing measures to halt nutrient loading and to predict the future performance of seagrasses in response to increasing natural and human perturbations.
At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Papers 1, 3 and 4: Submitted. Paper 2: Manuscript.
Swedish Agency for Research Cooperation (Sida/SAREC) marine bilateral programme

Seagrass beds cover large intertidal and subtidal areas in coastal zones around the world and they are subjected to a wide variety of anthropogenic influences, such as nutrient enrichment due to sewage seepage. This study was undertaken to address specific questions focusing on whether near shore tropical seagrasses that receive a constant influx of groundwater nutrient inputs, would exhibit a higher productivity and to what extent epiphytic algae reflect the impacts of nutrient inputs. An additional aspect of study was to determine the prevalence of “acid zones” in tropical seagrasses. The productivity of the seagrasses Cymodocea rotundata, Thalassia hemprichii and Thalassodendron ciliatum was compared in two sites along the Kenyan coast; Nyali (a high nutrient site) and Vipingo (a low nutrient site). Of the three seagrasses T. hemprichii showed the most distinct differences with higher growth and biomass in the nutrient rich site whereas the growth of C. rotundata was similar in the two sites. A high epiphytic cover was found on the shoots of T. ciliatum found in the high nutrient site Nyali.

Morphological and genetic characterization of bacterial and cyanobacterial epiphytes showed specific associations of nitrogen fixing cyanobacteria on the seagrass C. rotundata in the low nutrient site (Vipingo). At this site, shoots of C. rotundata had a higher C:N ratio compared to shoots in the high nutrient site (Nyali) indicating that the association with nitrogen fixing cyanobacteria is a strategy, for this species, to meet its nutrient needs. Bacterial epiphytes belonging to the group Cytophaga-Flavobacteria-Bacteroides (CFB) were found on T. ciliatum and T. hemprichii from the two sites. CFB bacteria are characteristic of waste water, particularly from livestock farming areas, thereby confirming seepage of groundwater from surrounding catchment areas. These prokaryotic associations were specific for the different seagrasses and it appears that the establishment of epiphytic associations may not be a random encounter but a specific association that meets specific needs.

The seagrass T. ciliatum in the high nutrient site had an abundance of macroalgal epiphytes and the impact of the epiphytic coverage was assessed using Pulse Amplitude Modulated (PAM) fluorometry. The photosynthetic activity of seagrass parts that were covered by epiphytes was suppressed but the productivity of the whole shoot was not significantly reduced. In the nutrient rich site, epiphytes were found to contribute up to 45% of the total estimated gross productivity, during the SE monsoon season, while epiphytic contribution in the nutrient poor site, was 8%. Epiphytic abundance and contribution to productivity decreased during the NE monsoon. The photosynthetic activity of T. ciliatum shoots was similar in the two study sites with shoots in the nutrient rich site growing faster. T. ciliatum, in the low nutrient site, invested in the development of below ground root tissue which may indicate the development of a strategy to gain access to pore water nutrient pools.

Carbon uptake strategies of eight tropical seagrasses were re-evaluated to determine how common the “acid zone” mechanism is among tropical seagrasses. Six of the eight species studied showed photosynthetic inorganic carbon (Ci) acquisition based on carbonic anhydrase catalysed HCO₃^- to CO₂ conversions within an acidified diffusion boundary layer (“acid zone”). Cymodocea serrulata appeared to maintain its carbon uptake by extracellular carbonic anhydrase catalysed CO₂ formation from HCO₃^- without the need for acidic zones, whereas, Halophila ovalis appeared to have a system in which H⁺ extrusion may be followed by HCO₃^--H⁺ co-transport into the cells. These findings indicate that competition for carbon, between the host seagrass species and epiphytes, could determine seagrass-epiphyte associations.

Thesis (M.S.) -- University of Maryland, College Park, 2005.
Thesis research directed by: Marine, Estuarine, Environmental Sciences Graduate Program. Title from t.p. of PDF. Includes bibliographical references. Published by UMI Dissertation Services, Ann Arbor, Mich. Also available in paper.

[Truncated abstract] Biogeochemical processes in seagrass sediments influence growth and nutrition of seagrasses. This thesis investigates the below-ground interactions between biotic and abiotic factors that influence seagrass nutrition and growth, with focus on a small species of seagrass, Halophila ovalis (R. Br.) Hook ƒ., from the Swan River Estuary, Western Australia. Seagrass showed significantly lower growth and an increase in leaf nitrogen and phosphorus concentrations with increased organic matter loading. With maximal light reduction, lower growth rates and average leaf weights were observed, and leaf nitrogen and phosphorus concentrations were higher. Light reduction was also shown to increase bioavailability of inorganic nutrients within porewater of seagrass sediment . . . Sulphide was hypothesised to have an inhibitory effect on nutrient uptake of Halophila ovalis. Below-ground sulphide inhibits the photosynthetic efficiency of photosystem II at sulphide concentrations greater than 1 mM. Sulphide exposure enhanced phosphate uptake, with no significant effect on ammonium uptake of H. ovalis. This thesis demonstrates that biogeochemical processes both constrain the potential growth of seagrasses and influence the nutrient status of seagrass tissue. Consideration of the influence of sulphide stress on seagrasses is likely to be particularly important for anthropogenically influenced aquatic systems, where inputs of organic matter are enriched relative to pristine ecosystems. A better understanding of biogeochemical processes will allow researchers to predict how future changes in sediment chemistry will influence seagrass meadows.

Water motion has been shown to influence almost every aspect of the ecology of seagrass communities; seagrass communities have likewise been shown to significantly influence water movement around them. This thesis examines the important role of water motion on seagrass ecosystems by integrating field and laboratory studies of several aspects of seagrass ecology influenced by water motion. To facilitate the study of hydrodynamics of seagrass ecosystems, a solid state electronic current meter was designed and developed, using thermistors as flow sensing devices. Important characteristics of the meters include: no moving parts, compact size, high sensitivity (resolution better than ± 0.5 cm s-1), and high sampling rate (greater than 0.2 Hz). Deployment of the meters in field measurements provided reliable and meaningful results of flow conditions through seagrass canopies, and they show great potential for use in many studies of marine ecology. Field studies of water velocity profiles revealed significant differences between the shapes of profiles of different seagrass species, particularly between species of Posidonia and Amphibolis. Of particular note is the observation of a region of high water velocity beneath the leafy canopy of Amphibolis, which was not present in the Posidonia plants. Water velocity profile measurements, sediment grain size analyses and standing stock measurements were conducted across an exposure gradient in a Posidonia sinuosa meadow. These studies revealed that, while the exposed location experienced a higher ambient water velocity than the sheltered site, the baffling influence of the seagrass canopy reduced the water velocity to approximately the same at both sites, within the meadow, although the effects varied seasonally. It was also observed that the seagrass meadow produced apparent skimming flow under the low flow conditions measured at the sheltered location; this phenomenon reflects the capacity for flow redirection over the canopy, and has important implications for the sub-canopy ecosystem and the protective role of seagrasses on the seabed. Field and laboratory studies on the role of seagrass density on the hydrodynamic nature of seagrass ecosystems revealed that water velocity profiles through meadows of reduced densities, and different shoot arrangements, were markedly different to “natural” profiles, implying the existence of a “critical density” (approximately 25 % of natural meadow density) with regard to canopy hydraulics. The role of water motion at an individual leaf scale was investigated with a series of laboratory flume studies of photosynthetic rates of seagrass and algae. The results show that the response of photosynthetic rate to water velocity depends very much on the plant species, with the algae markedly more productive (on a unit chlorophyll basis) than the seagrasses tested. Increases in photosynthetic rate were observed at water velocities above approximately 2.5 cm s-1; negligible photosynthetic activity was observed below this velocity. Calculation of P v. I curves indicated that the Posidonia species had high Ik values at low velocities (1360 :mol quanta m-2 s-1 for P. australis and 250.8 :mol quanta m-2 s-1 for P. sinuosa at 1.58 cm s-1), which decreased with increasing water velocity (to 138.9 and 24.77 :mol quanta m-2 s-1 for P. australis and P. sinuosa respectively), while the algal species had relatively constant values of Ik across all water velocities (85.42 to 312.7 :mol quanta m-2 s-1 for Ulva lactuca and 169.7 to 573.9 :mol quanta m-2 s-1 for Laurencia cruciata). Dye visualization studies showed that the algae remained quite rigid at all the velocities tested, while the seagrass leaves compressed as velocity increased. This resulted in an increased rate of turbulence creation by the algae, which is believed to enhance photosynthetic rates, through improved nutrient exchange rates across the boundary layer adjacent to the thallus. Further dye visualization studies revealed the significance of blade morphology on the creation of microscale turbulence at the surface of seagrass leaves. Epiphytic growth on seagrass leaves was observed to play an important role in breaking up water flow across the leaf surface, thereby enhancing the creation of microscale turbulence. From these studies, it is clear that water motion influences all aspects of the functioning of all components of seagrass communities, playing a role in nutrient supply, reproduction, physical stability, temperature and metabolic functions. The influence of seagrass meadows on coastal hydrodynamics is also apparent, with potential impacts on sediment stability, recruitment of benthic species and coastal erosion. This thesis has clearly demonstrated that water motion is an important parameter in seagrass ecology, and requires serious consideration in seagrass research, conservation and rehabilitation programmes.

Water motion has been shown to influence almost every aspect of the ecology of seagrass communities; seagrass communities have likewise been shown to significantly influence water movement around them. This thesis examines the important role of water motion on seagrass ecosystems by integrating field and laboratory studies of several aspects of seagrass ecology influenced by water motion. To facilitate the study of hydrodynamics of seagrass ecosystems, a solid state electronic current meter was designed and developed, using thermistors as flow sensing devices. Important characteristics of the meters include: no moving parts, compact size, high sensitivity (resolution better than plus-minus 0.5 cm s-1), and high sampling rate (greater than 0.2 Hz). Deployment of the meters in field measurements provided reliable and meaningful results of flow conditions through seagrass canopies, and they show great potential for use in many studies of marine ecology. Field studies of water velocity profiles revealed significant differences between the shapes of profiles of different seagrass species, particularly between species of Posidonia and Amphibolis. Of particular note is the observation of a region of high water velocity beneath the leafy canopy of Amphibolis, which was not present in the Posidonia plants. Water velocity profile measurements, sediment grain size analyses and standing stock measurements were conducted across an exposure gradient in a Posidonia sinuosa meadow. These studies revealed that, while the exposed location experienced a higher ambient water velocity than the sheltered site, the baffling influence of the seagrass canopy reduced the water velocity to approximately the same at both sites, within the meadow, although the effects varied seasonally. It was also observed that the seagrass meadow produced apparent skimming flow under the low flow conditions measured at the sheltered location; this phenomenon reflects the capacity for flow redirection over the canopy, and has important implications for the sub-canopy ecosystem and the protective role of seagrasses on the seabed. Field and laboratory studies on the role of seagrass density on the hydrodynamic nature of seagrass ecosystems revealed that water velocity profiles through meadows of reduced densities, and different shoot arrangements, were markedly different to 'natural' profiles, implying the existence of a 'critical density' (approximately 25 % of natural meadow density) with regard to canopy hydraulics. The role of water motion at an individual leaf scale was investigated with a series of laboratory flume studies of photosynthetic rates of seagrass and algae. The results show that the response of photosynthetic rate to water velocity depends very much on the plant species, with the algae markedly more productive (on a unit chlorophyll basis) than the seagrasses tested. Increases in photosynthetic rate were observed at water velocities above approximately 2.5 cm s-1; negligible photosynthetic activity was observed below this velocity. Calculation of P v. I curves indicated that the Posidonia species had high Ik values at low velocities (1360 :mol quanta m-2 s-1 for P. australis and 250.8 :mol quanta m-2 s-1 for P. sinuosa at 1.58 cm s-1), which decreased with increasing water velocity (to 138.9 and 24.77 :mol quanta m-2 s-1 for P. australis and P. sinuosa respectively), while the algal species had relatively constant values of Ik across all water velocities (85.42 to 312.7 :mol quanta m-2 s-1 for Ulva lactuca and 169.7 to 573.9 :mol quanta m-2 s-1 for Laurencia cruciata). Dye visualization studies showed that the algae remained quite rigid at all the velocities tested, while the seagrass leaves compressed as velocity increased. This resulted in an increased rate of turbulence creation by the algae, which is believed to enhance photosynthetic rates, through improved nutrient exchange rates across the boundary layer adjacent to the thallus. Further dye visualization studies revealed the significance of blade morphology on the creation of microscale turbulence at the surface of seagrass leaves. Epiphytic growth on seagrass leaves was observed to play an important role in breaking up water flow across the leaf surface, thereby enhancing the creation of microscale turbulence. From these studies, it is clear that water motion influences all aspects of the functioning of all components of seagrass communities, playing a role in nutrient supply, reproduction, physical stability, temperature and metabolic functions. The influence of seagrass meadows on coastal hydrodynamics is also apparent, with potential impacts on sediment stability, recruitment of benthic species and coastal erosion. This thesis has clearly demonstrated that water motion is an important parameter in seagrass ecology, and requires serious consideration in seagrass research, conservation and rehabilitation programmes.

Water motion has been shown to influence almost every aspect of the ecology of seagrass communities; seagrass communities have likewise been shown to significantly influence water movement around them. This thesis examines the important role of water motion on seagrass ecosystems by integrating field and laboratory studies of several aspects of seagrass ecology influenced by water motion. To facilitate the study of hydrodynamics of seagrass ecosystems, a solid state electronic current meter was designed and developed, using thermistors as flow sensing devices. Important characteristics of the meters include: no moving parts, compact size, high sensitivity (resolution better than plus-minus 0.5 cm s-1), and high sampling rate (greater than 0.2 Hz). Deployment of the meters in field measurements provided reliable and meaningful results of flow conditions through seagrass canopies, and they show great potential for use in many studies of marine ecology. Field studies of water velocity profiles revealed significant differences between the shapes of profiles of different seagrass species, particularly between species of Posidonia and Amphibolis. Of particular note is the observation of a region of high water velocity beneath the leafy canopy of Amphibolis, which was not present in the Posidonia plants. Water velocity profile measurements, sediment grain size analyses and standing stock measurements were conducted across an exposure gradient in a Posidonia sinuosa meadow. These studies revealed that, while the exposed location experienced a higher ambient water velocity than the sheltered site, the baffling influence of the seagrass canopy reduced the water velocity to approximately the same at both sites, within the meadow, although the effects varied seasonally. It was also observed that the seagrass meadow produced apparent skimming flow under the low flow conditions measured at the sheltered location; this phenomenon reflects the capacity for flow redirection over the canopy, and has important implications for the sub-canopy ecosystem and the protective role of seagrasses on the seabed. Field and laboratory studies on the role of seagrass density on the hydrodynamic nature of seagrass ecosystems revealed that water velocity profiles through meadows of reduced densities, and different shoot arrangements, were markedly different to 'natural' profiles, implying the existence of a 'critical density' (approximately 25 % of natural meadow density) with regard to canopy hydraulics. The role of water motion at an individual leaf scale was investigated with a series of laboratory flume studies of photosynthetic rates of seagrass and algae. The results show that the response of photosynthetic rate to water velocity depends very much on the plant species, with the algae markedly more productive (on a unit chlorophyll basis) than the seagrasses tested. Increases in photosynthetic rate were observed at water velocities above approximately 2.5 cm s-1; negligible photosynthetic activity was observed below this velocity. Calculation of P v. I curves indicated that the Posidonia species had high Ik values at low velocities (1360 :mol quanta m-2 s-1 for P. australis and 250.8 :mol quanta m-2 s-1 for P. sinuosa at 1.58 cm s-1), which decreased with increasing water velocity (to 138.9 and 24.77 :mol quanta m-2 s-1 for P. australis and P. sinuosa respectively), while the algal species had relatively constant values of Ik across all water velocities (85.42 to 312.7 :mol quanta m-2 s-1 for Ulva lactuca and 169.7 to 573.9 :mol quanta m-2 s-1 for Laurencia cruciata). Dye visualization studies showed that the algae remained quite rigid at all the velocities tested, while the seagrass leaves compressed as velocity increased. This resulted in an increased rate of turbulence creation by the algae, which is believed to enhance photosynthetic rates, through improved nutrient exchange rates across the boundary layer adjacent to the thallus. Further dye visualization studies revealed the significance of blade morphology on the creation of microscale turbulence at the surface of seagrass leaves. Epiphytic growth on seagrass leaves was observed to play an important role in breaking up water flow across the leaf surface, thereby enhancing the creation of microscale turbulence. From these studies, it is clear that water motion influences all aspects of the functioning of all components of seagrass communities, playing a role in nutrient supply, reproduction, physical stability, temperature and metabolic functions. The influence of seagrass meadows on coastal hydrodynamics is also apparent, with potential impacts on sediment stability, recruitment of benthic species and coastal erosion. This thesis has clearly demonstrated that water motion is an important parameter in seagrass ecology, and requires serious consideration in seagrass research, conservation and rehabilitation programmes.

Seagrasses play an essential role in the marine ecosystem by providing foods, nutrients, and habitat to the marine lives. They work as marine bioindicators by reflecting the health condition of aquatic environments. Seagrasses also act as a significant atmospheric carbon sink that mitigates global warming and rapid climate changes. Considering the importance, it is critical to monitor seagrasses across the coastlines which includes detection, mapping, percentage cover calculation, and health estimation. Remote sensing-based aerial and spectral images, acoustic images, underwater two-dimensional and three-dimensional digital images have so far been used to monitor seagrasses. For close monitoring, different machine learning classifiers such as the support vector machine (SVM), the maximum likelihood classifier (MLC), the logistic model tree (LMT) and the multilayer perceptron (MP) have been used for seagrass classification from two-dimensional digital images. All of these approaches used handcrafted feature extraction methods, which are semi-automatic. In recent years, deep learning-based automatic object detection and image classification have achieved tremendous success, especially in the computer vision area. However, to the best of our knowledge, no attempts have been made for using deep learning for seagrass detection from underwater digital images. Possible reasons include unavailability of enough image data to train a deep neural network. In this work, we have proposed a Faster R-CNN architecture based deep learning detector that automatically detects Halophila ovalis (a common seagrass species) from underwater digital images. To train the object detector, we have collected a total of 2,699 underwater images both from real-life shorelines, and from an experimental facility. The selected seagrass (Halophila ovalis) are labelled using LabelImg software, commonly used by the research community. An expert in seagrass reviewed the extracted labels. We have used VGG16, Resnet50, Inception V2, and NASNet in the Faster R-CNN object detection framework which were originally trained on COCO dataset. We have applied the transfer learning technique to re-train them using our collected dataset to be able to detect the seagrasses. Inception V2 based Faster R-CNN achieved the highest mean average precision (mAP) of 0.261. The detection models proposed in this dissertation can be transfer learned with labelled two-dimensional digital images of other seagrass species and can be used to detect them from underwater seabed images automatically.

[cat] [cat]Introducció L’ herbivorisme és un procés ecològic clau que regula la composició i l’estructura de les comunitats de plantes i determina la transferència d'energia de productors primaris a la resta de la cadena tròfica. Les plantes han desenvolupat diversos mecanismes de defensa per evitar o resistir l’herbivorisme. Entre ells destaquen les estratègies tolerància, que disminueixen l'efecte de l’herbivorisme en la vitalitat de la planta (ex. acumulació de reserves en teixits subterranis) i les estratègies de resistència, l’objectiu de les quals evitar el consum (ex. augment del contingut en fibra). Aquestes estratègies es basen en característiques morfològiques (ex. duresa) i químiques (ex. defenses químiques) de les plantes i poden expressar-se de forma contínua (constitutives) o en resposta al dany per herbívors (induïdes). L’herbivorisme en el medi marí pot ser major que en sistemes terrestres i pot tenir conseqüències especialment importants quan afecta a espècies formadores d’habitat Les fanerògames marines són espècies fundadores dominants en zones costaneres i que ens proporcionen múltiples i importants serveis ecosistèmics. Com a conseqüència de la seva rellevància ecològica i socioeconòmica, aprofundir en el coneixement de les interaccions planta-herbívor en aquests ecosistemes és crucial, ja que existeixen cada vegada més exemples que indiquen que canvis en les poblacions d'herbívors han suposat importants pertorbacions en aquests ecosistemes. El propòsit principal d'aquesta tesi és entendre com canvis en factors ambientals determinen la variació de les estratègies de defensa i la palatabilitat de la planta, i per tant el comportament dels herbívors. Contingut de la investigació La disponibilitat de nutrients destaca pels seus efectes sobre les característiques químiques i morfològiques de les plantes ja que augmenta el valor nutritiu i disminueix el contingut en fibres de les fulles tant en experiments de fertilització com en regions amb major disponibilitat de nutrients, la qual cosa les pot fer més vulnerables al consum per herbívors. La simulació del dany per herbívors afecta a les estratègies de defensa de les plantes de forma diferent en les dues espècies estudiades. Mentre que en Posidonia oceanica s'indueix la producció de compostos de resistència, en Zostera marina no hi ha inducció, disminuint a més la seva resistència i tolerància. Això es tradueix en què els herbívors prefereixen les fulles més nutritives repetidament retallades de Z. marina i les fulles sense retallar amb menys fibres i més nutrients de P. oceanica. Els canvis ambientals relacionats amb el canvi global analitzats en aquesta tesi (augment del CO2 i de la temperatura), tenen importants efectes en les plàntules de P. oceanica. L'augment del CO2 dissolt augmenta l'activitat fotosintètica de la planta i amb això les reserves de carbohidrats de les llavors. Tot i que l'augment de CO2 disminueix la qualitat nutricional de les fulles, van ser aquestes les preferides pels herbívors, possiblement a causa de l'augment de sacarosa o per altres característiques no analitzades en les plàntules. Contràriament als efectes observats amb l'augment de CO2, l'increment de la temperatura produeix efectes clarament negatius; augmentant la mortalitat, la respiració i l’ús de les reserves de la llavor en aquestes plàntules. A més disminueix el contingut en fibres de les fulles, reduint -se la resistència enfront de l’herbivorisme i augmentant per tant la preferència per herbívors. Aquests resultats mostren els potencials efectes additius que l’herbivorisme pot suposar en els impactes dels canvis ambientals en les poblacions de plantes marines. Conclusió La recerca presentada en aquesta tesi contribueix a entendre els mecanismes que influeixen en els canvis de les estratègies de defensa enfront de l’herbivorisme. Principalment, en com aquests mecanismes canvien sota diferents condicions ambientals i com els canvis en les característiques associades a resistència enfront d'herbívors determinen la vulnerabilitat de la planta enfront de l’herbivorisme. A més, destaca la importància d'avaluar els efectes dels canvis ambientals sobre les interaccions entre espècies.
[spa]Introducción: El herbivorismo es un proceso ecológico clave que regula la composición y estructura de las comunidades de plantas y determina la transferencia de energía de productores primarios al resto de la cadena trófica. Las plantas han desarrollado diversos mecanismos de defensa para evitar o resistir el herbivorismo. Entre ellos están las estrategias tolerancia, que disminuyen el efecto del herbivorismo en la vitalidad de la planta (ej. acumulación de reservas en tejidos subterráneos) y las estrategias de resistencia cuyo objetivo es evitar el consumo (ej. aumento del contenido en fibra). Estas estrategias se basan en características morfológicas (ej. dureza) y químicas de las plantas (ej. defensas químicas) y pueden expresarse de forma continua (constitutivas) o en respuesta al daño por herbívoros (inducidas). El herbivorismo en el medio marino puede ser mayor que en sistemas terrestres y puede tener importantes consecuenc ias cuando afecta a especies formadoras de hábitat Las fanerógamas marinas son especies fundadoras dominantes en zonas someras costeras que nos proporcionan múltiples e importantes servicios. Debido a su relevancia ecológica y socioeconómica, profundizar en el conocimiento de las interacciones planta-herbívoro en estos ecosistemas es crucial pues existen cada vez más ejemplos que indican que cambios en las poblaciones de herbívoros han supuesto importantes perturbaciones en dichos ecosistemas. El propósito principal de esta tesis es entender cómo cambios en factores ambientales determinan la variación de las estrategias de defensa y palatabilidad de la planta, y por tanto el comportamiento de los herbívoros. Contenido La disponibilidad de nutrientes destaca por sus efectos sobre las características químicas y morfológicas de las plantas ya que aumenta el valor nutritivo y disminuye el contenido en fibras de las hojas tanto en experimentos de fertilización como en regiones con mayor disponibilidad de nutrientes, lo cual las puede hacer más vulnerables al consumo por herbívoros. La simulación del daño por herbívoros afecta a las estrategias de defensa de las plantas de forma diferente en las dos especies estudiadas. Mientras que en Posidonia oceanica se induce la producción de compuestos de resistencia, en Zostera marina no hay inducción disminuyendo además su resistencia y tolerancia. Esto se traduce en que los herbívoros prefieren las hojas más nutritivas repetidamente recortadas de Z. marina y las hojas sin recortar con menos fibras y más nutrientes de P. oceanica. Los cambios ambientales relacionados con el cambio global analizados en esta tesis (aumento del CO2 y de la temperatura), tienen importantes efectos en las plántulas de P. oceanica. El aumento del CO2 disuelto aumenta la actividad fotosintética de la planta y con esto las reservas de carbohidratos de las semillas. A pesar de que el aumento de CO2 disminuye la calidad nutricional de las hojas, éstas fueron las preferidas por los herbívoros, posiblemente debido al aumento de sacarosa o por otras características no analizadas en las plántulas. Al contrario que el aumento de CO2, el incremento de la temperatura produce efectos claramente negativos aumentando la mortalidad, la respiración y uso de las reservas de la semilla en estas plántulas. Además, disminuye el contenido en fibras de las hojas reduciéndose la resistencia frente al herbivorismo y aumentando por tanto la preferencia por herbívoros. Estos resultados muestran los potenciales efectos aditivos que el herbivorismo puede suponer en los impactos de los cambios ambientales en las poblaciones de plantas marinas. Conclusión La investigación presentada en esta tesis contribuye a entender los mecanismos que influyen en los cambios de las estrategias de defensa frente al herbivorismo. Principalmente, en cómo estos mecanismos cambian bajo diferentes condiciones ambientales y como los cambios en las características asociadas a resistencia frente a herbívoros determinan la vulnerabilidad de la planta frente al herbivorismo. Además, destaca la importancia de evaluar los efectos de los cambios ambientales sobre las interacciones entre especies.
[eng]Introduction Herbivory is a key ecological process that regulates the composition and structure of plant communities and determines the energy transferred from primary producers to upper trophic levels. Plants have evolved a suite of defense strategies to avoid or resist herbivory. Tolerance strategies reduce the impact of herbivory in plant fitness (e.g., increased belowground reserves), and resistance strategies reduce preference or performance of the herbivore (e.g., low nutritional quality, high fiber content). These strategies are based on morphological (e.g., toughness) and chemical traits (e.g., phenolic compounds) and can be expressed regardless of the risk of herbivory (constitutively) or in response to herbivore damage (induced). In addition, defense strategies may shift under different environmental scenarios (e.g. higher resource availability often drives a lower investment in resistance). Herbivory in marine systems can be greater than in terrestrial ecosystems, and it can have particularly important consequences when it is exerted upon habitat-forming plants. Seagrasses are key foundation species dominating shallow coastal areas and providing numerous and critical ecosystem services to humans. Given their ecological and socioeconomic relevance, understanding plant-herbivore interactions in these systems is crucial since changes in herbivore populations can result in important disturbances in these ecosystems. The main purpose of this thesis is to understand the effect of changes in environmental factors in plant defense strategies against herbivory and how these changes affect the palatability of the plant, and thus herbivore behavior. Content Nutrient availability stands out for its effects on chemical and morphological plant defense traits. Plants under high nutrient environments in fertilization experiments and regions of higher nutrient availability (i.e. latitudinal comparison) exhibited higher nutritional quality and lower fiber content, both of which can increase their vulnerability to consumption. Interestingly, effects of nutrients on secondary compounds were absent or inconsistent. Simulated herbivory had clear effects on both morphological and chemical plant defense traits, however the two species studied differed in their responses. While in Posidonia oceanica, herbivory induced the production of resistance traits (e.g. fiber, secondary metabolites), in Zostera marina there was no induction of resistance traits, and on the contrary, simulated herbivory reduced their tolerance and resistance. As a result of the changes in traits exhibited by the plants, herbivores preferred the more nutritious repeatedly clipped leaves of Z. marina and the less chemically defended and more nutritious unclipped leaves of P. oceanica. The environmental changes related to global climate change that I analyzed in this thesis (i.e. increased CO2 and temperature), had important effects on defense strategies and susceptibility to grazers of P. oceanica seedlings. The increased pCO2 of seawater enhanced plant photosynthetic activity, leading to higher carbohydrate reserves in the seeds, which are the main storage tissue of the seedling. Although the increase in CO2 decreased leaf nutritional quality (i.e. leaf nitrogen), plants growing under high CO2 were preferred by the herbivores, possibly due to their increase in sucrose content or perhaps other chemical or structural characteristics that were not analyzed. In contrast to CO2, the increase in temperature produced clear negative effects on seedlings; increasing mortality and respiration resulting in greater use of seed reserves. Furthermore, warming reduced leaf fiber, which increased herbivore preference for warmed plants, and thus resulted in a decreased resistance to herbivory. These results illustrate the potential additive or counteractive effects that herbivory could have on determining the effects of environmental changes in seagrass ecosystems. Conclusion The research presented in this thesis contributes to identify the mechanisms that drive the changes in defense strategies against herbivory due to changes in environmental factors. Particularly, how these mechanisms change under different environmental conditions and how changes in traits associated with resistance to herbivores determine the vulnerability of plants to herbivory, highlighting the importance of assessing the effects of environmental factors on species interactions.

In this thesis I review how Sargassum muticum (Yendo) Fensholt, an invasive alga from Asia, has spread globally due to human activities and describe how this species can affect seagrass ecosystems. Abiotic factors such as nutrient and substratum availability may facilitate the spread of S. muticum into Zostera marina L. meadows, but analyses of seawater nutrients, and sediment particle size and % organic content revealed no significant differences between experimental quadrats in seagrass meadows either with, or without the presence of S. muticum. Phenolic compounds were examined because they form the basis of defensive mechanisms in plants and algae, therefore any change in phenolic content may affect the ability of Z. marina to protect itself from disease, herbivory and invasive species through allelopathic interactions. Results from a four year field study and multiple annual laboratory experiments showed significant reductions (p = 0.034 and p = 0.002, respectively) in the caffeic and tannic acids equivalents content of Z. marina when in the presence of S. muticum. As the abundance of S. muticum increases, other changes in the physiology of Z. marina may occur including variations in growth rates, nutrient partitioning and chlorophyll fluorescence, but data from multiple laboratory experiments illustrated no significant differences in growth. Chlorophyll fluorescence analyses revealed significant differences between treatments with and without S. muticum (p = 0.008), but pairwise comparisons indicated these differences only occurred in 2008 (p < 0.001). Significant differences were also found in nutrient partitioning amongst functional regions of the shoots (p = 0.024), but pairwise comparisons detected these differences between a biomass control treatment (ZZ: Zostera + Zostera) and the ZS (with S. muticum) and ZM (Z. marina on its own at a lower biomass per replicate) treatments (p = 0.013 and p = 0.019, respectively), but not between ZS and ZM. Previous in situ research has found negative effects of S. muticum presence on densities of kelp and other algae. Results from the long-term field study indicated significantly lower mean in situ Z. marina densities within the ZS treatment (p < 0.001). Epibiota found living on the blades of Z. marina provide food for organisms within seagrass ecosystems and also create microhabitats for other species to occupy. Alterations in the abundances of epibiota and microhabitats formed could further modify seagrass ecosystems through shifts in timing of food availability, food preferences and microhabitats created. The long-term field study data revealed significantly lower epibiota abundances within the ZS treatment (p = 0.019), but differences in biomass between treatments were not detected. Changes in the biochemistry, physiology, vegetative physiognomy and epibiota assemblages of Z. marina revealed during experimental manipulations are presented and considered within the context of long-term seagrass survival in light of increasing S. muticum invasion.

Seagrasses of southern Western Australia grow in coastal waters exposed to varying degrees of physical exposure from oceanic swell waves and waves created by strong seasonal wind patterns. Seagrass species have preferred niches within these exposures; however knowledge as to how a continuum of exposure effects seagrass distributions and landscape patterns is limited. This thesis examined long term and seasonal variability occurring in a seagrass landscape along a gradient of wave exposure on the North Sands platform, Warnbro Sound, Western Australia. Long term changes to the seagrass landscape were investigated over a 49 year time period. Seagrass areal extent was mapped from aerial photographs and compared through the years. Over the period, 1953 to 2002, there was a 27% loss of seagrass; from 273 ha in 1953 to 200 ha in 2002. Loss was separated into two causes anthropogenic (boat mooring/propeller scars) and natural. Boat mooring/propeller scars accounted for only 2%. The development of a large sand bar, growing from 27 ha to 89 ha, accounted for 66% of the loss. Historical records show a similar large-scale sediment event occurring in Warnbro Sound 170 years ago. Increased fragmentation of offshore seagrass meadows through time accounted for the remaining 32%. To confirm the gradient in exposure, several methods incorporating the effects of time and space were used to characterise water flow. Wind effects were characterised into exposure indices, significant wave heights, bottom flow velocities and surface flows were modelled and in situ flow velocity was measured. Modelling 4 and in-situ measurement of flow velocities showed the shape, bathymetry and topography of Warnbro Sound coupled with seasonal wind patterns, contributed to complex flow circulations within the bay. All flow velocities modelled and measured showed a reduction in flow shorewards. Modelled flows were highest during winter storms whereas wind effects were greatest in summer; due to the consistent and strong summer sea breezes. A comparison of two transects along this flow gradient revealed differences between them. Sediment grain size analyses were used to indicate longer term flow characteristics along the gradient of flow. Sediment profiles were coarser in the offshore exposed sites and finer in the inshore sheltered sites, but there was some modification by the seagrass. A comparison of sediment profiles between two transects along the gradient of flow showed differences. There was also a seasonal influence. Seagrass landscapes were investigated along the gradient. Aerial photographs showed a progressive increase in fragmentation of seagrass meadows from inshore to offshore. Two transects were used, each with five different seagrass landscapes progressing from solid through to fragmented. The two transects could be separated into three zones each. The middle zones were similar in landscape but differed in seagrass species. The inshore and offshore zones were the same, both in species and landscape. Distribution of seagrass species along the two transects was correlated to the flows measured over the transects. There was a relationship between seagrass distribution for the whole platform and wave exposure. 5 Amphibolis spp. occurred in the offshore region that had high flow velocities. Posidonia spp. occurred in the nearshore region that had low flow velocities. Distribution of seagrass species and fragmentation patterns were strongly correlated with wave exposure gradients. A strong correlation (r2 = 0.8) existed in winter between seagrass species (density and landscape) and environmental factors associated with exposure. Despite the strong winds in summer these had minimal effect on the seagrasses (low correlation). Winter flow conditions are therefore the driver of patterns in species distribution and fragmentation seen in the seagrass landscape of Warnbro Sound.

Rising carbon dioxide (CO2) concentrations in the atmosphere will increase the average pCO2 level in the world oceans, which will have a knock-on effect on the marine ecosystem. Coastal seagrass communities one of the most productive marine ecosystems are predicted to benefit from the increase in CO2 levels, but long-term effects of elevated CO2 on seagrass communities are less understood. Population reconstruction techniques was used to investigate the population dynamics of Cymodocea nodosa meadows, exposed to long term elevated CO2 at volcanic seeps off Greece and Italy. Effect of elevated CO2 was noticed on the growth, morphometry, density, biomass and age structure at CO2 seeps. Above to below ground biomass ratio of C. nodosa were higher at CO2 seeps than at reference sites. The plastochrome interval were similar at all CO2 seeps. The shoot age and shoot longevity of plants were lower at seeps than reference sites. The present recruitment (sampled year) of the seagrass were higher than long-term average recruitment of the communities near the seeps. Carbon to nitrogen ratios (%DW) of C. nodosa were higher in leaves at seeps. Annual leaf production was higher near the seeps. This study suggests increased production of C. nodosa under elevated CO2 levels, but other co-factors such as nutrients, trace metal toxicity must also be taken into consideration while predicting effects of future CO2 concentrations. Volcanic CO2 seeps are now being used as natural analogues for ocean acidification studies although these areas can be affected by trace element input and may alter ecosystem responses to gradient in carbonate chemistry. Here Fe and a range of trace elements (Cd, Co, Cu, Hg, Mn, Pb, Ni and Zn) were analysed from sediments and from the roots, rhizomes and leaves of seagrass at six CO2 seeps and reference sites off Greece and Italy. There were higher metal levels in sediment and seagrasses at all CO2 seeps than reference sites. Sediment Quality Guideline Quotient, a commonly used pollution index, indicated that some of the metals (Cd, Cu, Hg, Ni) were in high enough concentrations to have adverse biological effects, such as Cu at Ischia site and Hg at Vulcano. Higher accumulation of elements from sediments in roots and leaves at CO2 seeps were found from Bio Sediment Accumulation Factor index. There were higher levels of Cu, Fe, Mn and Zn in leaves and rhizomes for P. oceanica and higher levels of Cd, Co, Cu, Fe and Zn in C. nodosa compartments at CO2 seeps. Fe and Mn were found with positive correlation within sediment-roots and sediment-rhizomes, whereas Cd, Co and Pb were found with positive correlation in compartments of C. nodosa. In P. oceanica positive correlation were only observed for Cd within sediment-roots and plant compartments. Low pH and ocean acidification increased the concentration of elements at CO2 seeps than reference sites. Thus, caution is needed, when using volcanic seep systems as analogue for the effects of rising CO2, as metals can reach levels that are toxic to seagrass, masking any potential benefits of increased levels of carbon dioxide for seagrass productivity. Net community production (NCP) and community respiration (CR) were measured under air exposed and CO2 enriched conditions for intertidal Z. noltei meadows and unvegetated sediment communities during emersion in summer and winter seasons. Community production and respiration were measured in-situ using benthic chambers. CO2 flux under air and CO2 enriched conditions were measured over a series of short term incubations (30min) using an infra-red gas analyser. Incident photosynthetic active radiation (PAR) was recorded during the incubations covering the daily and seasonal variation. Linear regression model was used to test the effects of irradiance on net community production. NCP of Z. noltei community were higher under CO2 enriched conditions than air exposed conditions in both summer and winter seasons. There was no effect of CO2 on the CR rate of Z. noltei community in summer season. NCP of sediment community were higher in summer season and winter season under CO2 enriched conditions. Sediment CR rates were higher in winter than summer season. The light compensation point of Z. noltei and sediment community were lower in both seasons under CO2 enriched conditions. Seasonal budget of community production was higher in Z. noltei than sediment communities. A clear effect of PAR was noticed on the net community production of both communities. Higher PAR intensities resulted in higher NCP under CO2 enriched conditions for both communities. CO2 enrichment will have a positive effect on the intertidal communities during emersion.

Climate change is a reality. One of the main ecological concerns regarding climate change is the predicted increase in atmospheric and sea temperatures. The latter is expected to rise by roughly 2.5°C by the end of 2050 with dramatic impacts on marine ecosystems predicted around the world. Seagrass ecosystems are a good example of vital ecosystems that are threatened by climate change and other anthropogenic factors. A decline in global seagrass cover of 29% has been estimated over the last century, and at a local level, cover of the seagrass Zostera capensis has declined by 38% over the last 50 years in Langebaan Lagoon, with associated losses of invertebrate abundance by 70% in certain areas. Two limpets, Siphonaria compressa and Fissurella mutabilis depend on Zostera capensis for their survival in Langebaan Lagoon, feeding on epiphytic diatoms, filamentous algae and bacteria growing on blades on seagrass. Siphonaria compressa occurs exclusively in beds of Zostera capensis and is currently listed as critically endangered. Increasing sea temperatures have been found to directly and indirectly affect seagrass growth and survival. Temperature changes influence epiphytic microalgal growth on seagrass blades, thereby limiting light and nutrient availability to seagrasses. Key grazers, however, can potentially limit microalgal growth on seagrasses, but this function is dependant on how they respond to temperature change. Therefore, understanding the effects of temperature on seagrasses and their grazing limpets is vital to seagrass health and ultimately their persistence in marine ecosystems. To quantify the latter, a mesocosm experiment was conducted to assess the interactive effect of temperature changes and grazing by the limpets S. compressa and F. mutabilis on the seagrass Z. capensis. One of the main outcomes of the experiment was that Increasing temperatures significantly enhanced algae biomass fouling seagrass leaves. At the same time, limpet feeding significantly decreases algal fouling, especially at higher temperatures. S. compressa was significantly more effective at removing algae from the blades of Z. capensis than F. mutabilis, particularly at higher temperatures. Increasing temperatures and the feedback from grazer presence had no substantial impact on the growth of Z. capensis but vi significantly influenced the survival of the seagrass blades. Another important result for predicting future effects of temperature rise on seagrass ecosystems was that mortality of F. mutabilis was significantly greater than S. compressa at higher temperatures. Overall, the study demonstrates that increasing temperatures clearly impacts the dynamics of seagrass ecosystems, either directly by impacting seagrasses or indirectly, by increasing algal fouling. The presence of limpets is also vital in controlling the levels of algae, with S. compressa performing more of a beneficial role in keeping blades of seagrass free of fouling. These findings are relevant for the conservation of seagrasses in Langebaan Lagoon, as they indicate the importance of preserving populations of the endangered limpet S. compressa in order to maintain healthy functioning seagrass ecosystems under future warming scenarios.

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.

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.

Our world is subjected to a panoply of drivers of change. In this context, the understanding on how our biosphere resists, absorbs or is altered by the changes, appears as a hot question in ecology. In this respect, two ecological concepts appear as essential, resilience and biotic interactions. Resilience is related to how ecosystems persist under stress or suffering disturbances. Interactions among species are to a large part responsible for the delivery of ecosystem functions, and form the architecture of biodiversity. Moreover, a substantial part of ecosystem resilience is founded on species interactions. This thesis is an attempt to shed some light on these issues through the deep exploration of specific case studies in seagrass ecosystems, in particular how seagrasses respond to external drivers (or how resilient they are), how these responses affect species interactions and which mechanisms allow coexistence of species linked by positive and negative interactions. Our approach is based upon field observations and field manipulative experiments. Chapter 1 shows how an increase of organic matter in sediment weakens the mutualism between the bivalve Loripes lucinalis and the seagrass Cymodocea nodosa. The mechanism implied is the effect of this increase (and, probably, the resulting anoxia) on seagrass root morphology (plant trait), which results in a lower provision of habitat for the bivalves, whose abundance decreases. The weakening of the mutualism can potentially decrease the resilience of these ecosystems to eutrophication and, therefore, compromise their persistence. Chapter 2 describes a facilitative cascade in which the seagrass C. nodosa favors the abundance of the pen shell Pinna nobilis, which positively affects the sea urchin Paracentrotus lividus, which in turn consumes the seagrass. We suggest that the persistence of this three-species assemblage rests on the very local impact of sea urchins on the seagrass, likely driven by behavioural and denso-dependent processes. Chapter 3 and 4 show that fast-growing species such as C. nodosa are highly resilient to stress or disturbances when affecting only the aboveground parts, recovering fast (within two weeks) from a single event of disturbance. C. nodosa shows several mechanisms of tolerance, such as compensatory growth, reallocation of internal resources and enhancement of the formation of new modules, when coping to repeated defoliation simulating herbivory. However, when the belowground parts are lost by disturbances, recovery is highly delayed up to two years and is dependent on the characteristics of the disturbance such as size and timing. Overall, this research has contributed to increase our understanding on how ecosystems respond to changes and how species interactions are maintained and disrupted. We have shown that environmental changes can alter the functioning of seagrass ecosystems at least in two directions. Firstly, by altering fundamental biological interactions, such as the seagrass-lucinid mutualism and, secondly, by affecting the resilience of ecosystems dominated by a foundation species, which promote species coexistence. Advances in the two complementary and interlinked directions will be crucial to better manage and preserve ecosystems and prevent their potential collapse under the increasing human-induced change the world is submitted to.
El nostre món està sotmès a un ampli ventall de forces que tendeixen a provocar canvis. En aquest context, entendre com la biosfera resisteix, absorbeix o és alterada per aquestes forces resulta una qüestió candent, especialment per l'ecologia. Al respecte, dos conceptes ecològics esdevenen essencials: la resiliència i les interaccions biològiques. La resiliència és la capacitat de persistència o recuperació que tenen els ecosistemes sotmesos a estrès o pertorbacions. Les interaccions entre espècies (efectes de l'existència d'una espècie sobre la fitness d'una altra) contribueixen al manteniment de les funcions ecosistèmiques i, en un cert sentit, constitueixen l'arquitectura de la biodiversitat. A més, la resiliència dels ecosistemes depèn , en gran part, d’aquestes interaccions. Aquesta tesi és un intent d’aprofundir en els aspectes esmentats a través d'una sèrie de casos d’estudi en ecosistemes d’angiospermes marines. Concretament, el que fem és estudiar com els ecosistemes d’angiospermes marines responen a les forces causants de canvis, com aquestes respostes vénen mitjançades per canvis en la interacció entre espècies, i provar d'esbrinar els mecanismes que permeten la coexistència d’espècies que es troben vinculades per interaccions positives i negatives. La nostra aproximació es basa tant en observacions com en experiments en el camp. El Capítol 1 mostra com un increment de matèria orgànica en el sediment debilita el mutualisme entre el bivalve Loripes lucinalis i l’angiosperma marina Cymodocea nodosa. El mecanisme implicat que es proposa per explicar-ho està relacionat amb la plasticitat morfològica de la planta. Així, un increment en la matèria orgànica del sediment (i, probablement, l’anòxia que se'n segueix), fa que la planta modifiqui la morfologia de les seves arrels, que esdevenen molt menys ramificades i fan disminuir per tant la disponibilitat d'hàbitat per als bivalves. Una debilitació del mutualisme pot, potencialment, disminuir la resiliència d’aquests ecosistemes a l’eutrofització i, per tant, comprometre la seva persistència. El Capítol 2 descriu una cascada de facilitació en la qual l’angiosperma marina C. nodosa afavoreix l’abundància del gran bivalve Pinna nobilis, que ajuda a incrementar l'abundància de la garota Paracentrotus lividus, que al seu torn consumeix l’angiosperma. Suggerim que la persistència d’aquest sistema de tres espècies, aparentment inestable (tres interaccions concatenades circularment, dues de positives i una de negativa) es basa en què la interacció negativa (l’efecte de les garotes sobre l’angiosperma) té un abast molt limitat, probablement degut tant al seu comportament alimentari com a les defenses de la planta enfront de l'herbivorisme. Els Capítols 3 i 4 mostren que les espècies de creixement ràpid, com ara C. nodosa, són altament resilients a l'estrès o a les pertorbacions quan aquestes afecten només les parts aèries de les plantes (defoliació parcial o total), recuperant-se ràpidament (dues setmanes) després d'una pertorbació puntual en el temps. C. nodosa mostra diversos mecanismes de tolerància a la defoliació, com ara el creixement compensatori, la reassignació de recursos interns i l’increment en la taxa de formació de nous mòduls. Tanmateix, quan les pertorbacions provoquen la pèrdua de les parts subterrànies (rizomes i arrels), la recuperació és molt més lenta, i triga fins a dos anys. A més, aquesta recuperació depèn de les característiques de la pertorbació com ara la mida de l'àrea afectada i l’època de l'any en què es produeix. En general, aquesta tesi ha contribuït a comprendre millor les respostes dels ecosistemes als canvis. Hem pogut documentar alguns processos que permeten la coexistència entre espècies, així com mecanismes de resiliència específics que esdevenen ecosistèmics quan es manifesten en espècies fundadores d'hàbitat. També hem demostrat com els canvis, més enllà d'afectar espècies individuals més o menys emblemàtiques, poden provocar alteracions de formes més subtils, com ara erosionant la seva resiliència mitjançant la modificació d’interaccions biològiques. Els avenços en totes aquestes direccions complementàries i interrelacionades són crucials per a gestionar i preservar els ecosistemes i evitar el seu possible col·lapse.

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.

Polychlorinated dibenzo-p-dioxins (PCDDs) and polychlorinated dibenzofurans(PCDFs) are two groups of lipophilic, persistent organic pollutants that are produced as by-products of various anthropogenic and industrial processes. Due to their relatively high toxic potencies and potential to bioaccumulate and biomagnify in organisms and through the food chain, the contemporary widespread distribution of these compounds is a concern to the health of the environment, wildlife and humans. This study determined the distribution, pathways and fate of PCDD/Fs in the coastal zone of Queensland, Australia, including the inshore marine environment of the World Heritage Great Barrier Reef Marine Park. This ecosystem supports unique fauna and flora such as the marine herbivorous mammal dugong (Dugong dugon) and its food source, seagrass. Elevated PCDD/Fs were present in soils and sediments along the entire Queensland coastline. Highest concentrations were found in soil from agricultural irrigation drains and in sediments near the mouths of major rivers. Elevated concentrations were associated with rural and urban types of land-use, and PCDD/Fs were present even in locations remote from anthropogenic activities. PCDD/F congener-specific analysis revealed an unusual profile in all samples, dominated by OCDD, with PCDFs present in low concentrations or below the limit of detection. Distinct HxCDD isomer patterns were observed, with the 1,2,3,7,8,9-HxCDD/1,2,3,4,6,7-HxCDD isomer pair dominating the 2,3,7,8-substituted HxCDDs. Similar congener and isomer characteristics were reported in sediments, soil and clay samples from other continents, but could not be attributed to any known source. Possible PCDD/F sources in Queensland were assessed using segmented estuarine sediment cores, for which radiochemical chronologies were established for each depth. Variations of PCDD/F concentrations in the sediment cores over several centuries of depositional history were relatively small. Elevated PCDD levels were still present in sediment slices from the early 17th century. PCDD/F homologue profiles in sediments deposited during the last 350 years were almost identical and correlated well to the characteristic profiles observed in surface sediments and soils from the entire Queensland coastline. These results suggested the presence of an unidentified PCDD source prior to the production of commercial organochlorine products. To investigate the formation of the unusual PCDD/F profiles, congener and isomer specific analyses were undertaken in soils, sediments and dated sediment cores. The results demonstrated that specific transformation processes in the environment have resulted in the observed PCDD profile characteristics. Dechlorination of OCDD was proposed to result in distinct 1,4-pattern characteristics (i.e. formation of isomers chlorinated in the 1,4,6,9-positions). Consequently, the environmental samples do not reflect the signatures of the original source. An alternative hypothesis to natural formation is discussed evaluating these processes and their implications for possible source contributions. This hypothesis explores the potential for the influence of anthropogenic PCDD precursors (e.g. pentachlorophenol) during the 1940s to 1990s. Transport of PCDD/Fs from the land-based source via impacted tributary river systems, and subsequent deposition processes are proposed to result in PCDD/F accumulation in the inshore marine ecosystem. The extent of the sediment PCDD/F contamination governs the concentrations in the extensive inshore marine seagrass meadows of Queensland. Partitioning processes in the sediment-seagrass system lead to increased toxic equivalency (TEQ) in the seagrass, compared to sediment.The relationship between contaminated inshore sediments, seagrass and dugongs were evaluated using six dugong habitat regions along the coastline. PCDD/F body burdens in dugongs are governed by sediment (and seagrass) PCDD/F concentrations in their habitat. High seagrass (and incidental sediment) ingestion rates, selective retention of toxicologically potent congeners and relatively low PCDD/F elimination capacities in dugongs are proposed to result in elevated PCDD/F concentrations and TEQ levels in adult animals. Transfer efficiencies of 4 and 27% of maternal TEQ levels to foetuses and calves (respectively) during gestation and lactation result in relatively high exposure potentials to offspring. Compared to no-observed-adverse-effect-levels in other mammals, and based on the results of this study, a tolerable daily intake (TDI) of 10-24 pg TEQ kg-1 day-1 was estimated for dugongs. The results of the present study found that dugongs from some regions along the coastline of Queensland exceed this TDI by up to 20 fold, suggesting that these populations may be at risk from PCDD/F contamination in their habitat. These results have important implications for the health of the environment, wildlife and humans and were used to develop a conceptual understanding of the sources, pathways and fate of dioxins in Queensland, Australia.

Polychlorinated dibenzo-p-dioxins (PCDDs) and polychlorinated dibenzofurans(PCDFs) are two groups of lipophilic, persistent organic pollutants that are produced as by-products of various anthropogenic and industrial processes. Due to their relatively high toxic potencies and potential to bioaccumulate and biomagnify in organisms and through the food chain, the contemporary widespread distribution of these compounds is a concern to the health of the environment, wildlife and humans. This study determined the distribution, pathways and fate of PCDD/Fs in the coastal zone of Queensland, Australia, including the inshore marine environment of the World Heritage Great Barrier Reef Marine Park. This ecosystem supports unique fauna and flora such as the marine herbivorous mammal dugong (Dugong dugon) and its food source, seagrass. Elevated PCDD/Fs were present in soils and sediments along the entire Queensland coastline. Highest concentrations were found in soil from agricultural irrigation drains and in sediments near the mouths of major rivers. Elevated concentrations were associated with rural and urban types of land-use, and PCDD/Fs were present even in locations remote from anthropogenic activities. PCDD/F congener-specific analysis revealed an unusual profile in all samples, dominated by OCDD, with PCDFs present in low concentrations or below the limit of detection. Distinct HxCDD isomer patterns were observed, with the 1,2,3,7,8,9-HxCDD/1,2,3,4,6,7-HxCDD isomer pair dominating the 2,3,7,8-substituted HxCDDs. Similar congener and isomer characteristics were reported in sediments, soil and clay samples from other continents, but could not be attributed to any known source. Possible PCDD/F sources in Queensland were assessed using segmented estuarine sediment cores, for which radiochemical chronologies were established for each depth. Variations of PCDD/F concentrations in the sediment cores over several centuries of depositional history were relatively small. Elevated PCDD levels were still present in sediment slices from the early 17th century. PCDD/F homologue profiles in sediments deposited during the last 350 years were almost identical and correlated well to the characteristic profiles observed in surface sediments and soils from the entire Queensland coastline. These results suggested the presence of an unidentified PCDD source prior to the production of commercial organochlorine products. To investigate the formation of the unusual PCDD/F profiles, congener and isomer specific analyses were undertaken in soils, sediments and dated sediment cores. The results demonstrated that specific transformation processes in the environment have resulted in the observed PCDD profile characteristics. Dechlorination of OCDD was proposed to result in distinct 1,4-pattern characteristics (i.e. formation of isomers chlorinated in the 1,4,6,9-positions). Consequently, the environmental samples do not reflect the signatures of the original source. An alternative hypothesis to natural formation is discussed evaluating these processes and their implications for possible source contributions. This hypothesis explores the potential for the influence of anthropogenic PCDD precursors (e.g. pentachlorophenol) during the 1940s to 1990s. Transport of PCDD/Fs from the land-based source via impacted tributary river systems, and subsequent deposition processes are proposed to result in PCDD/F accumulation in the inshore marine ecosystem. The extent of the sediment PCDD/F contamination governs the concentrations in the extensive inshore marine seagrass meadows of Queensland. Partitioning processes in the sediment-seagrass system lead to increased toxic equivalency (TEQ) in the seagrass, compared to sediment.The relationship between contaminated inshore sediments, seagrass and dugongs were evaluated using six dugong habitat regions along the coastline. PCDD/F body burdens in dugongs are governed by sediment (and seagrass) PCDD/F concentrations in their habitat. High seagrass (and incidental sediment) ingestion rates, selective retention of toxicologically potent congeners and relatively low PCDD/F elimination capacities in dugongs are proposed to result in elevated PCDD/F concentrations and TEQ levels in adult animals. Transfer efficiencies of 4 and 27% of maternal TEQ levels to foetuses and calves (respectively) during gestation and lactation result in relatively high exposure potentials to offspring. Compared to no-observed-adverse-effect-levels in other mammals, and based on the results of this study, a tolerable daily intake (TDI) of 10-24 pg TEQ kg-1 day-1 was estimated for dugongs. The results of the present study found that dugongs from some regions along the coastline of Queensland exceed this TDI by up to 20 fold, suggesting that these populations may be at risk from PCDD/F contamination in their habitat. These results have important implications for the health of the environment, wildlife and humans and were used to develop a conceptual understanding of the sources, pathways and fate of dioxins in Queensland, Australia.
Thesis (PhD Doctorate)
Doctor of Philosophy (PhD)
School of Public Health
Faculty of Health Sciences
Full Text

As climate change continues, climactic extremes are predicted to become more frequent and intense, in some cases resulting in dramatic changes to ecosystems. The effects of climate change on ecosystems will be mediated, in part, by biotic interactions in those ecosystems. However, there is still considerable uncertainty about where and how such biotic interactions will be important in the context of ecosystem disturbance and climactic extremes. Here, I review the role of consumers in seagrass ecosystems and investigate the ecological impacts of an extreme climactic event (marine heat wave) and subsequent widespread seagrass die-off in Shark Bay, Western Australia. Specifically, I compare seagrass cover, shark catch rates, and encounter rates of air breathing fauna in multiple habitat types before and after the seagrass die-off to describe post-disturbance dynamics of the seagrass community, shifts in consumer abundances, and changes in risk-sensitive habitat use patterns by a variety of mesoconsumers at risk of predation from tiger sharks (Galeocerdo cuvier). Finally, I conducted a 16 month field experiment to assess whether xi loss of top predators, and predicted shifts in dugong foraging, could destabilize remaining seagrass. I found that the previously dominant temperate seagrass Amphibolis antarctica is stable, but not increasing. Conversely, an early-successional tropical seagrass, Halodule uninervis, is expanding. Following the die-off, the densities of several consumer species (cormorants, green turtles, sea snakes, and dugongs) declined, while others (Indo-Pacific bottlenose dolphins, loggerhead sea turtles, tiger sharks) remained stable. Stable tiger shark abundances following the seagrass die-off suggest that the seascape of fear remains intact in this system. However, several consumers (dolphins, cormorants) began to use dangerous but profitable seagrass banks more often following seagrass decline, suggesting a relaxation of anti-predator behavior. Experimental results suggest that a loss of tiger sharks would result in a behaviorally mediated trophic cascade (BMTC) in degraded seagrass beds, further destabilizing them and potentially resulting in a phase shift. My work shows that climactic extremes can have strong but variable impacts on ecosystems mediated in part by species identity, and that maintenance of top predator populations may by important to ecological resilience in the face of climate change.

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.

Seagrass beds are among the most ecologically important systems in the marine environment. They provide the primary production to nearby coral reef and mangrove communities, and seagrasses comprise a large component of the diets of many marine organisms including fishes, small invertebrate species, and many protected species such as manatees and sea turtles. This consumption provides a pathway for many contaminants to enter the marine food web via the seagrasses. The coastal location of seagrass beds causes them to be especially susceptible to anthropogenic pollution, including accumulation of heavy metals, which has been shown to have many adverse health effects in the seagrasses and marine organisms that feed on them. This study assessed the heavy metal concentrations of seagrasses in three regional locations in South Florida: Port of Miami, Card Sound Aquatic Preserve, and Florida Bay. Three species of seagrasses, Thalassia testudinum, Halodule wrightii, and Syringodium filiforme, which comprise the majority of South Florida seagrass beds, were collected monthly for a period of one year and analyzed for ten heavy metals: (arsenic (As), cadmium (Cd), copper (Cu), iron (Fe), mercury (Hg), manganese (Mn), nickel (Ni), lead (Pb), selenium (Se), zinc (Zn)). Concentrations were compared across locations, season, species, and plant part (leaves, shoots, roots, and rhizomes). Concentration ranges, in µg/g (ppm), found in seagrass tissues for all included locations, species, and plant parts were: As (0.02-2.95), Cd (0.09-10.72), Cu (0.38-33.68), Fe (1.52-1877.43), Pb (0.78-156.20), Mn (0.79-300.15), Hg (0.03-16.46), Ni (0.67-87.74), Se (0.01-4.79), Zn (1.48-669.44). Statistical analysis showed significant difference in concentrations among locations, season, species, and plant morphology.

The development of a successful protocol for micropropagating seagrass provides a valuable tool for seagrass-restoration programs and a facility to study their biology (especially their physiology). This work reports on some of the culture requirements of some seagrasses that are commonly found in Western Australia: Posidonia coriacea, P. sinuosa, P. australis and Halophila ovalis. The protocol developed for H. ovalis allows very rapid multiplication and sustainable growth of cultures while the protocol developed for Posidonia requires further development. The culture of Posidonia cariacea proved to be problematic however experimental media that provided insights into its culture conditions. The carbohydrate source was the most important medium component as it affected the development of roots and leaves. The presence of sucrose in the culture media enhanced leaf growth (especially glucose) but decreased the proportion of white roots. More fresh weight, roots, leaves and the proportion of white roots were observed in Posidonia when they were grown in glucose-based media than in mannitol-based media. When mannitol was present in the media, the proportion of white roots was high, which could be attributed to its osmotic effects. Similar responses to sucrose, glucose and mannitol were also observed for P. australis and P. sinuosa. Halophila ovalis was able to grow rapidly on most experimental media. Growth was enhanced by the presence of sucrose in the media and was essential for rapid and sustained growth. Other media components altered the growth of this species, in particular levels of nitrogen (most importantly NH4) influenced root growth and morphology. When H. ovalis is grown in media in moderate or high levels of NH4, root length was significantly reduced and root hair was limited. When NH4 was omitted from the medium, roots were significantly longer and root hairs were prolific. Posidonia coriacea and Halophila ovalis have different growth strategies under natural conditions. H. ovalis is an early succession species that grows rapidly and responds to increased nutrients. P. coriacea is slower growing, colonises later and is Jess responsive to environmental changes than H. ovalis. While the growth responses observed for P. coriacea were significant (in some cases), the differences between means were considerably smaller when compared with H. ovalis. This may be due to the different growth strategies of these species or a lack of fundamental requirement in the conditions under which P. coriacea was grown. Much of what is reported in this thesis for Posidonia will need repeating if the reasons for these differences are identified in the future. In summary, in this thesis I have demonstrated that in vitro propagation of these seagrass species is possible, It is necessary for species-specific protocols to be developed which take into consideration the growth strategies employed by each species. This is particularly significant as many researchers attempt to draw comparisons between species and protocols. The protocols developed in this research increase the knowledge of the biology of these seagrasses and can be incorporated into transplantation protocols in the future.

Seagrasses constitute the basis for diverse and productive ecosystems worldwide. In East Africa, they provide important ecosystem services (e.g. fisheries) but are potentially threatened by increasing resource use and lack of enforced management regulations. The major aim of this PhD thesis was to investigate effects of anthropogenic distur-bances, primarily seaweed farming and coastal fishery, in East African seagrass beds. Seaweed farming, often depicted as a sustainable form of aquaculture, had short- and long-term effects on seagrass growth and abundance that cascaded up through the food web to the level of fishery catches. The coastal fishery, a major subsistence activity in the region, can by removing urchin predators indirectly increase densities of the sea urchin Tripneustes gratilla, which has overgrazed seagrasses in several areas. A study using simulated grazing showed that high magnitude leaf removal – typical of grazing urchins – affected seagrasses more than low magnitude removal, typical of fish grazing. Different responses in two co-occurring seagrass species furthermore indicate that high seagrass diversity in tropical seagrass beds could buffer overgrazing effects in the long run. Finally, a literature synthesis suggests that anthropogenic disturbances could drive shifts in seagrass ecosystems to an array of alternative regimes dominated by other or-ganisms (macroalgae, bivalves, burrowing shrimp, polychaetes, etc.). The formation of novel feedback mechanisms makes these regimes resilient to disturbances like seagrass recovery and transplantation projects. Overall, this suggests that resource use activities linked to seagrasses can have large-scale implications if the scale exceeds critical levels. This emphasizes the need for holistic and adaptive management at the seascape level, specifically involving improved techniques for seaweed farming and fisheries, protection of keystone species, and ecosystem-based management approaches.

Anthropogenic disturbances are ubiquitous in coastal marine ecosystems. As such, more intensive monitoring efforts are necessary to conserve these valuable habitats. Bioindicators, organisms that predictably respond to changes in environmental variables, may be utilized in monitoring efforts to assess ecosystem functioning. To incorporate organisms into monitoring programs as bioindicators managers need to first understand the difference between the natural phenology of the focal organisms and their responses to different forms of anthropogenic disturbance. To determine if gammaridean amphipods could be used as indicators of changes in environmental quality in sub-tropical seagrass ecosystems, I conducted spatial and temporal surveys of amphipod communities in south Florida. Amphipod community structure varied significantly across sites and seasons. Variation in community structure was largely driven by macrophyte biomass, food availability, seasonally variable factors (epiphyte abundance, dissolved oxygen, salinity, and temperature), water-column nitrogen concentration, and factors related to freshwater input, including low Thalassia testudinum and high Halodule wrightii densities, and salinity. Amphipods are also susceptible to mechanical damage in seagrass habitats and could be used as indicators of ecological functioning of a region. A major source of mechanical damage in seagrass ecosystems is caused by boat propellers. I simulated propeller scars in continuous seagrass beds to investigate the effects of scarring on seagrass ecosystem functioning. Seagrasses located adjacent to propeller scars experienced a shift in the limiting resource from light to phosphorus. Amphipod community structure, however, was not impacted by scarring, but amphipod density was reduced in fragmented patches. To determine if plant-herbivore interactions were impacted by propeller scarring, we removed amphipods from half of the experimental plots and measured epiphyte biomass and community composition. Top-down control on epiphyte biomass or community composition by amphipods was not affected by fragmentation, despite reduced amphipod densities. My dissertation research demonstrates that amphipods could be incorporated into existing management programs in sub-tropical seagrass ecosystems as environmental indicators. Reduced amphipod densities in fragmented seagrass beds suggests that amphipods could also be used as ecological indicators, but more research is needed to determine the extent of the impacts of fragmentation on higher trophic levels.

Coastline communities have experienced a marked increase in human populations over the last few decades. This increase in population places disproportionate pressure on coastal ecosystems to provide economic services to support local economies. At the same time, overuse of these services can aid in the destruction of the ecosystems responsible for them. Seagrass ecosystems are mainly found near coastlines, and are typically a chief provider of some of these economic goods and services. Many previous studies have documented the ecological functions of this seagrasses. Unfortunately, our increasing knowledge of seagrass structure and function has not been fully incorporated into economic models estimating their value. In this dissertation, I focus on the seagrass ecosystem in southern Biscayne Bay, and simultaneously study the ecological dynamics of the seagrass beds, and estimate its economic value. This value is based on recent ecological models in the literature as well as data I collected from the system. I focused on Biscayne Bay due to, 1) the relevance that this question had to the relationship between Biscayne Bay and the Miami metropolis, and 2) the lack of existing reliable models that explore this relationship in this area. More specifically, I became very interested in this question while working for Biscayne National Park, where such a model would have improved seagrass restoration work taking place there. I found that southern Biscayne Bay is dominated by Thalassia testudinum, with other seagrasses following a spatial pattern primarily determined by salinity and water column nutrient distribution. Syringodium filiforme was mostly found east of the islands, Halodule wrightii was mostly found near the shoreline, and Halophila engelmenii was spotted at only two of the 190 sites visited. T. testudinum distribution was largely unaffected by nutrient enrichment at all sites, but it appeared to induce severe herbivory further from the coastline. For the calendar year 2004, we deduced using a Total Ecosystems Valuation (TEV) model that seagrass ecosystems potentially contributed over $198 million US dollars to the local economy. We argue that a simultaneous understanding and use of both ecological and economic models is important for future conservation efforts of seagrass ecosystems.

Laboratory experiments determined the effects of two levels of habitat complexity upon pipefish (Syngnathus fuscus) foraging for amphipods. Habitats were composed of equal densities of either narrow (low complexity) or wide (high complexity) leafed artificial seagrass. The response to habitat, as measured by rate of encounter with amphipods, probability of attack after encounter, probability of success after attack, and overall rate of amphipod consumption, was determined for combinations of two fish size classes and three amphipod size classes. Small fish did not experience visually inhibitive effects in either habitat, while large fish had their visual fields impinged upon in the wide leaf habitat and encountered fewer amphipods. There was a general trend for encounter rate to increase with amphipod size. Large fish attack probability was positively related to amphipod size in the narrow leaf habitat, but negatively related to amphipod size in the wide leaf habitat. Small fish attack probability was negatively related to amphipod size in both habitats. Success was negatively related to a ratio of prey size to fish size, and showed no overall effect of habitat. Pipefish have flexible behaviors, allowing them to minimize unsuccessful attacks. Due to their position in the structure of vegetation, amphipods have a distribution of vulnerabilities; a criterion by which pipefish select prey. Size-selective predation on gammarid amphipods by pipefish was examined utilizing simulation modeling and laboratory experimentation. Three computer simulation models were developed: (1) a mechanistic model based on empirically derived size-dependent mechanisms of pipefish-amphipod interaction, (2) an optimal diet breadth model in which the rate of energy intake is maximized, and (3) an optimal diet breadth model where switching from energy maximization to time minimization occurs as consumption becomes limited by gastric processing (i.e. satiation). None of these models successfully accounted for the observed pattern of prey size selection. Pipefish concentrated their feeding upon smaller, energetically more profitable amphipods, in excess of what was predicted by either the mechanistic or optimal diet breadth models. This pattern of selection was evident through out 4 hour feeding bouts, indicating that diet breadth compression did not occur.

The seagrass Zostera japonica Aschers. and Graebn. occurs as pure populations and in mixture with Zostera marina L. along the intertidal regions of southwest British Columbia. At the Roberts Bank study area seed and seedling dynamics were studied in three vegetation zones: a landward monospecific zone of Z. japonica, a zone of co-existing Z. japonica and Z. marina, and a seaward monospecific zone of Z. marina. Many more seeds were produced than were found in the sediment, and even fewer germinated. Zostera japonica seeds were most abundant in the seed bank in the upper zones where there is high Z. japonica density. Even though seeds remained in the water column for up to two months, very few seeds dispersed into the lower zone populated by Z. marina. thus limiting Z. japonica's colonization of the lower zones. It is unclear what limits the dispersal of Z. japonica seeds. Of the seeds that were incorporated into the sediment few germinated (5% or less). When seeds were planted in buckets placed into the sediment, with and without Z. marina, Z. japonica was able to germinate, grow, and reproduce in one year throughout the study area. Seedlings that emerged earliest (in April) either did not establish or did not survive as long as those seedlings that emerged later in May and June. Seedlings were often found uprooted, floating in the water. The rim of the buckets and the presence of Z. marina shoots appeared to protect the Z. japonica seedlings, preventing uprooting, but the results were not conclusive. Once seedlings became established, they spread vegetatively at a rapid rate and can persist throughout the winter, either as reduced shoots or as overwintering rhizomes. These overwintering plants contribute greatly to the following year's population.
Science, Faculty of
Botany, Department of
Graduate

Many recent studies have sought to monitor health characteristics of seagrasses, including changes in aerial extent, biomass and fish community structure. While these studies have provided important information on the ecology of seagrass communities on southeast Australia, little attempt has been made to subject these sampling procedures to rigorous experimental testing and review. This study employed commonly-used standard methods for sampling seagrass community characteristics in two sites in New South Wales. Where possible, sampling protocols were tested for accuracy and efficiency at a range of temporal and spatial scales. The ARCView Geographic Information System was used to construct vegetation polygons of seagrass distribution on the Tweed River, and in the Ukerebagh Channel annually over a 5-year period. For one year (2000), distributions from identical photographs were mapped twice to identify procedural errors. In general, errors relating to incorrect boundary identification were low compared to inter-annual variability. Inter-annual variability in seagrass beds was higher than for adjacent mangrove and saltmarsh. Estimates of biomass were derived from standard replicate 0.25m x 0.25m quadrats. The experiment contrasted two sites of similar geomorphic setting. Ukerebagh Channel on the Tweed River, and Woolooware Bay with Botany Bay are both shallow, sandy marine deltaic settings supporting stands of Zostera capricorni. Significant differences were found in the degree of replication required to identify significant changes in seagrass biomass at the two sites. Ukerebagh Channel supported relatively dense stands of Z. capricorni with low intra-site variability. Here 8 replicates were sufficient to detect 10 percent change. Towra Point presented a contrast, in which 15 replicates were required to detect a similar level of change. Woolooware Bay at Towra Point has suffered from increased sedimentation relating to alterations in current velocities at Towra Point, and the result highlights the greater degree of replication required to determine significance changes in disturbed systems. The fish populations in the seagrass at Towra Point were sampled using buoyant pop nets. Fish communities differed significantly from those sampled in adjacent mangrove and saltmarsh. Differences in fish assemblages between spring high tides, neap high tides and low tides are attributed to movements of fish between seagrass and adjacent mangrove and saltmarsh. This mosaic of habitats is utilized by a number of species over a tidal cycle, with seagrass providing an important low-tide refuge for many species utilizing mangrove and saltmarsh at high tide. Limitations in the efficiency of buoyant pop nets were exposed in a novel experiment which demonstrated differences in escape rates between species. Flat-tailed mullet (Liza argenta) are likely to be under-represented in experiments using this technique. Recommendations are made regarding optimal sampling protocols for monitoring seagrass in the region. All techniques tested are suitable, though some require modification. Some texts have under-estimated the degree of replication required to appropriately monitor changes in seagrass biomass in disturbed systems, where density is lower and intra-site variability higher. The buoyant pop-nets may require modification in open-water seagrass situations where escape by Liza argenta and Acanthopagrus australis were at unacceptable levels.

Since the Industrial Revolution, coastal pollution has increased and seagrasses, together with other vegetated coastal ecosystems (VCEs), have been identified as potentially important filters and sinks of pollutants, such as CO2 and heavy metals. VCEs can accumulate materials in their soils for millennia reducing their abundance in the surrounding environment. However, VCEs are among the most threatened ecosystems on Earth, putting at risk their ecological services. This dissertation aims to understand the role of VCEs, particularly seagrasses, as environmental archives and biogeochemical sinks. The research assessed: i) the capacity of Posidonia seagrass meadows to sequester metal pollution, through the reconstruction of metal fluxes recorded in seagrass sedimentary archives adjacent to the Port Pirie Pb-Zn smelter in South Australia (SA); and ii) the capacity of VCEs to contribute to climate change mitigation at a regional scale, through a Blue Carbon (BC) assessment for SA. This research showed that seagrass soils in a metal polluted environment can be used to reconstruct the metal contamination history. The seagrass archives at Port Pirie revealed hot-spots of spatial and temporal contamination that reflected the operation of the smelter, its pollution management strategies, wind and currents, and the behaviour of the metals in the marine system. A seagrass area of 110 km 2 has sequestered ~20% of Pb, and ~50% of both Zn and Cd cumulative emissions from the smelter since 1999, highlighting its role in removing metal pollution from the broader environment. Additionally, this work provided insights into the variability of Corg storage among VCEs in SA, an example of an arid region characterized by low productivity. Here the distribution of Corg in the VCEs’ soil reflected both abiotic (e.g. coastal settings, aridity, hydrodynamics) and biotic (habitat type) characteristics of the sampled locations. The mean (±SE) soil Corg stocks and accumulation rates (CAR) in SA for seagrasses, mangroves and tidal marshes were 6.3±0.4, 14±2 and 13±3 kg Corg m -2 and 15±2, 32±7, 30±10 g Corg m -2 -1 yr , respectively. Those estimates are lower than national and global averages, emphasizing the need for region-specific assessments to inform blue carbon (BC) policy and projects. Finally, a seagrass case study showed that while seagrasses are generally very efficient at sequestering Corg, not all sites are suited to demonstrating this. At False Bay, a lack of net sediment accumulation and hydrodynamic-driven mixing prevented the application of radionuclide methods to determine CAR, thereby preventing to demonstrate ‘additionality’ using this method. This finding highlighted the importance of selecting suitable sites and methods for seagrass BC projects. The findings demonstrate the important role that seagrasses play as biogeochemical sinks, in this case for metal pollution and atmospheric CO2, but potentially for a wide range of materials. The ability of seagrasses to sequester these materials over millennia also makes them useful as archives, revealing past environmental conditions including pollution histories. These features make seagrasses potentially useful management tools, to aid in the monitoring of coastal ecosystems and to understand past trajectories which can inform current and future management. The research also highlights the need to conserve VCEs to maintain their valuable role as biogeochemical sinks and to prevent the release of stored materials into the broader environment.

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.

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.

The loss of large-bodied herbivores and/or top predators has been associated with large-scale changes in terrestrial, freshwater, and marine ecosystems around the world. Understanding the consequences of these declines has been hampered by a lack of studies in relatively pristine systems. To fill this gap, I investigated the dynamics of the relatively pristine seagrass ecosystem of Shark Bay, Australia. I began by examining the seagrass species distributions, stoichiometry, and patterns of nutrient limitation across the whole of Shark Bay. Large areas were N-limited, P-limited, or limited by factors other than nutrients. Phosphorus-limitation was centered in areas of restricted water exchange with the ocean. Nutrient content of seagrasses varied seasonally, but the strength of seasonal responses were species-specific. Using a cafeteria-style experiment, I found that fast-growing seagrass species, which had higher nutrient content experienced higher rates of herbivory than slow-growing species that are dominant in the bay but have low nutrient content. Although removal rates correlated well with nutrient content at a broad scale, within fast-growing species removal rates were not closely tied to N or P content. Using a combination of stable isotope analysis and animal borne video, I found that green turtles (Chelonia mydas) – one of the most abundant large-bodied herbivores in Shark Bay – appear to assimilate little energy from seagrasses at the population level. There was, however, evidence of individual specialization in turtle diets with some individuals foraging largely on seagrasses and others feeding primarily on macroalgae and gelatinous macroplankton. Finally, I used exclusion cages, to examine whether predation-sensitive habitat shifts by megagrazers (green turtles, dugongs) transmitted a behavior-mediated trophic cascade (BMTC) between sharks and seagrasses. In general, data were consistent with predictions of a behavior-mediated trophic cascade. Megaherbivore impacts on seagrasses were large only in the microhabitat where megaherbivores congregate to reduce predation risk. My study highlights the importance of large herbivores in structuring seagrass communities and, more generally, suggests that roving top predators likely are important in structuring communities - and possibly ecosystems - through non-consumptive pathways.

In response to growing global impact on ecosystems, we design programs for conservation and restoration to maintain and enhance biodiversity, productivity and ecosystem resilience. To ensure the greatest return for these programs, there is an implicit requirement for identifying and understanding the complex non-linear relationships that can exist between impact gradients, ecosystem structure and the processes that mediate the two. Ecological resilience theory has developed as one of the fundamental explanations of this complexity. The application of ecological resilience theory in a local management context, however, is often hampered by a disparity between the theory and what is practical to test empirically. This thesis used seagrass ecosystems in Moreton Bay, Queensland as a model system for the development and testing of a practical framework to examine the potential for incorporating measures of feedback loops into the empirical assessment of resilience. I focussed on the behaviour of feedback processes in relation to changing levels of impact with a view to developing a generic, testable hypothesis that could be used to assess ecological resilience more broadly. A Bayesian network was used to synthesis the known relationships between impact and seagrass response to identify three key feedback processes that stabilise seagrass ecosystems in Moreton Bay......
Thesis (PhD Doctorate)
Doctor of Philosophy (PhD)
Griffith School of Environment
Science, Environment, Engineering and Technology
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Seagrasses are ephemeral, patchy habitats, under increasing risk of fragmentation due to anthropogenic changes. The ongoing and increasing loss of seagrass makes it essential that we understand the processes of movement and connectivity of the animals which rely on seagrass as a habitat. Shrimp are among the most abundant and diverse animals in seagrass habitats. Much of the published literature remains focused on one particular facet of shrimp life. Ecologists tend to generalise habitat-scale patterns of shrimp family groups where more specific studies on individual species may only focus on the biology, taxonomy or phylogeography alone. Few studies combine ecology, biology and phylogeography. This thesis attempts to achieve a comprehensive understanding of the biology, ecology, diversity, distribution, connectivity, and phylogeography of one of the most abundant shrimp taxa from Queensland seagrasses: Phycomenes zostericola. This holistic approach provides a solid foundation of information against which to compare future connectivity studies and also other seagrass species. In general, caridean shrimp are planktonic during their early life stages and will then recruit into the same habitat type which their parents occupy. Having a planktonic larval phase allows them the potential for broad dispersal. This study found that the potential for movement among P. zostericola populations is considerable; the adults were found to frequently move among seagrass patches and larvae have a planktonic phase of anywhere up to three weeks. Surprisingly, P. zostericola show a surprising amount of genetic structure for a marine species with a planktonic larval phase. The close association of adults to seagrass habitat and the reliance of P. zostericola larvae on a current to maintain suspension may be the limiting factors preventing P. zostericola from fulfilling their migration and dispersal potential. P. zostericola has a broad distribution and can be found in most seagrass habitats around Queensland. A cryptic (morphologically indistinguishable) sibling species was discovered that is sympatric throughout the northern range of the P. zostericola distribution. The discovery of the divergent taxon provided a unique opportunity for a comparative phylogeographic study. The two sibling taxa diverged between 3.2 and 4.6 million years ago and since then have been exposed to similar biogeographic influences. A mitochondrial dataset, using the gene cytochrome oxidase I (COI), describes the historical and contemporary levels of connectivity and demographic change in response to marine biogeographic boundaries, sea level changes and currents. While regional 3 genetic structure was found to be similar between the two species, demographic changes were not. The two populations of Phycomenes are also under some kind of north vs. south selective pressures. The nuclear gene, myosin heavy chain (MyHC), shows a distinct latitudinal pattern in both Phycomenes species. This genetic pattern indicates that groups north and south of far northeast Queensland are exposed to significantly different conditions resulting in different selective forces operating on the myosin gene. Both the mitochondrial gene COI and the nuclear gene MyHC were analysed for broadly distributed populations of two other seagrass caridean species; Latreutes mucronatus and Cuapetes sp. Similar to Phycomenes, both of these species contained multiple, morphologically identical, yet genetically distinct species. The deep levels of divergence indicate that speciation had occurred between 8 and 25 million years ago. The multiple cryptic taxa found in this study confirm two commonly stated hypotheses about marine taxa: firstly, cryptic speciation is common in marine taxa and this is just as true for seagrass caridean shrimp as other groups. Secondly, biodiversity estimates in shallow marine systems are currently underestimated due to high levels of unidentified cryptic taxa. A loss of statistical power is unavoidable in sampled populations which contain cryptic taxa. Although small sample numbers of Latreutes and Cuapetes species did not allow rigorous genetic statistical analysis they did provide some insight into the structure of these populations. All analysed seagrass shrimp taxa (Phycomenes, Latreutes and Cuapetes) maintained signals of demographic expansions prior to the last glacial maximum, suggesting that the vast and rapidly changing sea-levels throughout the Pleistocene did not have drastic demographic impacts on seagrass shrimp populations over broad spatial scales. Although lowered sea levels did not have dramatic demographic effects, low sea levels and strong currents probably provided the necessary conditions for long distance migration / dispersal events; this is evident in the haplotype sharing between geographically distant populations for most of the study taxa. This study provides valuable insight into the contemporary levels of connectivity and the past responses to major environmental and habitat changes. These data will hopefully contribute to the much needed baseline data used to guide future conservation efforts of inshore marine habitats.
Thesis (PhD Doctorate)
Doctor of Philosophy (PhD)
Griffith School of Environment
Science, Environment, Engineering and Technology
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