Дисертації з теми "Marine ecosystem functioning"

An ecosystem-based approach to the management of marine ecosystems is the goal of the recent European Integrated Maritime Policy, known as the Blue Book (2007), shortly followed by the new Marine Strategy Framework Directive (2008/56/EC). It is recognized that management should take into account the processes taking place within, and the interactions between ecological, social and economic systems to be effective and sustainable. Yet a quantitative knowledge about such processes and the interactions between marine ecosystems and socio-economic systems is often weak or lacking. The goal of this thesis is to explore how pressures exerted on large-scale marine ecosystems translate into state changes. The focus is on multiple pressures, and on both populations and ecosystems, i.e. on the integrated functioning of marine ecosystems. Both anthropogenic pressures, such as fishing or nutrient enrichment, and natural ones, such as climate and environmental variability, are taken into account, mainly based on the Northern Adriatic Sea case study. The Northern Adriatic Sea is a data-rich Mediterranean basin, eutrophic, heavily fished, strongly influenced by climate, and with a long history of human pressures acting on it. Different methodologies are used in a complementary manner, such as conceptual models, ecological network analysis applied to a static trophic network model, timeseries analysis, population models, review of historical data, and meta-analysis of macroecological patterns. Case studies include species of commercial importance such as small pelagics or crabs, or charismatic predators such as sharks and skates. Based on the study of the functioning of marine ecosystems from many different points of view, the main conclusion of this work is that an ecosystem-based approach is indeed necessary to manage marine ecosystems. The reason is that multiple interacting factors, including but not limited to external pressures, can and do influence ecosystem functioning “bottom up”, “top down”, as well as from the middle of the system.
Un approccio ecosistemico alla gestione degli ecosistemi marini è l’obiettivo della recente Politica Marittima Integrata per l’Unione Europea, nota come Blue Book (2007), seguita a breve dalla nuova Direttiva Quadro sulla Strategia per l’Ambiente Marino (2008/56/EC). Vi si riconosce che, per esercitare una gestione efficace e sostenibile, si devono considerare i processi che si svolgono all’interno dei sistemi ecologici, sociali ed economici, e le interazioni fra tali sistemi. Tuttavia, una conoscenza quantitativa di tali processi e delle interazioni fra gli ecosistemi marini e i sistemi socio-economici è spesso scarsa, se non del tutto mancante. Lo scopo di questa tesi è comprendere meglio come le pressioni agenti su ecosistemi marini a larga scala portino a cambiamenti di stato. Ci si è concentrati su pressioni multiple, e sia su popolazioni che ecosistemi, ovvero sul funzionamento integrato degli ecosistemi marini. Sono state considerate sia pressioni di origine antropica come pesca ed apporti di nutrienti, che naturali come la variabilità climatica ed ambientale, basandosi principalmente sul caso di studio dell’Adriatico Settentrionale. L’Adriatico Settentrionale è un bacino del Mar Mediterraneo caratterizzato da abbondanza di dati utilizzabili a scopo scientifico, ed è un ecosistema eutrofico, intensamente sfruttato dalla pesca, fortemente influenzato dal clima, ed è sottoposto a pressioni antropiche da lungo tempo. Si sono utilizzate in maniera complementare differenti metodiche, fra cui modelli concettuali, l’analisi di reti ecologiche (Ecological Network Analysis) applicata ad un modello statico di rete trofica, l’analisi di serie temporali, modelli di popolazione, rassegna di dati storici, e meta-analisi di regolarità macro-ecologiche. I casi di studio includono specie di importanza commerciale come pesce azzurro o granchi, e predatori famosi come squali e razze. La principale conclusione di questo lavoro, basata sullo studio del funzionamento degli ecosistemi marini da molti punti di vista diversi, è che un approccio ecosistemico è realmente necessario nella gestione degli ecosistemi marini. Il motivo è che il funzionamento degli ecosistemi può essere ed è effettivamente influenzato da fattori multipli interagenti fra di loro, che includono (senza essere limitati ad esse) le pressioni esterne, e che agiscono sia dal basso (cioè dai livelli gerarchici inferiori) verso l’alto, che dall’alto (cioè dai livelli gerarchici superiori) verso il basso, ed a partire dall’interno (ovvero, dalle gerarchie intermedie) del sistema.

Dissolved organic nitrogen (DON) represents a major pool of fixed, reactive nitrogen in marine systems. It is now recognized that this pool can support primary production and the ability of some algal species to exploit DON compounds as sources of Nitrogen (N) may indicate that specific DON components can exert selective pressure on the composition of the phytoplankton community. In this study the ability of monocultures of ecologically-relevant algal species from the English Channel (Emiliania huxleyi, Micromonas pusilla, Alexandrium minutum and Chaetoceros peruvianus) to grow with DON as the only N source was examined using different artificial media. Among the two tested artificial seawater recipes, Aquil* was preferred as it contained lower micronutrient concentrations, and gave better growth results for all used species. In order to constrain the DON uptake to algae alone, a method for bacterial removal was tested using antibiotic additions. Both Slocombe antibiotic mixture (Cefotaxime-Carbenicillin-Kanamycin-AugmentinTM) and Penicillin-Streptomycin-Neomycin used were effective and not toxic to the algae. Incubation with the antibiotic up to 48 hours and a transfer period into antibiotic-free medium after 72 hours proved to be effective. However, the treatment removed bacteria in A. minutum cultures only; further treatment would be required for the other species to be cultured axenically. The ability to use DON was tested for the above mentioned species using the amino acid L-Arginine (ARG) as the sole N source, and growth was compared with nitrate-containing cultures of the same species. All the selected species grew in both NOᴈ‾ and in ARG, reaching lower final densities when incubated with ARG, although these were not significant. This study has shown that E. huxleyi, A. minutum, M. pusilla and C. peruvianus can grow on organic N, either by direct or indirect uptake, and develop comparable biomasses to species using inorganic N. Both C. peruvianus and M. pusilla cultures contained dissolved ammonium at the end of the experimental period, indicating potential indirect use by the algae of organic N converted to inorganic N by bacteria. A. minutum grew in the presence of ARG along with the cosmopolitan E. huxleyi; N-demand estimates, based on the molar concentration of N-ARG consumed, correlated with the final cell density, indicating that the species did not develop on inorganic N produced from ARG mineralisation, but directly on the ON substrate. Since A. minimum has been linked to harmful algal blooms, and E. huxleyi contributes significantly to oceanic CaCOᴈ deposition, their ability to utilise DON has environmental consequences in addition to the oceanic N-budget. Climate change scenarios predict both episodic conditions of elevated rainfall and extended periods of dry conditions leading to variable riverine inputs to coastal areas, altered nitrogen to phosphorus (N:P) ratios, and changes in the inorganic to organic balance of the nutrient pools. Organic N can constitute up to 69 % of the total N pools, respectively, making it crucial, to understand the cycling of this fraction in coastal waters, and how changes in the composition of nutrient pools could impact on marine ecosystem function and health.

This doctoral dissertation was produced in a cooperation between Halmstad University (Wetland Research Centre, School of Business and Engineering) and Lund University (Limnology & Marine Biology, Department of Ecology). Abstract . Wetland creation at large, regional scales is implemented as a measure to abate the biodiversity loss in agricultural landscapes and the eutrophication of watersheds and coastal areas by non-point source nutrient pollution (mainly nitrogen). The consequences of creating many new wetlands for biodiversity conservation and nutrient reten- tion (ecosystem functioning) in agricultural landscapes are still relatively unknown, both on local (per wetland) and regional (per landscape) scales. In Sweden, wetland creation has progressed already since the 1990s, and by now larger numbers of created wetlands are present, mainly in the intensively farmed landscapes of southwestern Sweden. This thesis aimed to investigate the following aspects in these systems: (i) their large-scale effects on biodiversity, (ii) their functional diversity of bacterial denitrifiers, (iii) the abiotic and biotic influences on wetland ecosystem functioning, (iv) the potential for biodiversity-function links, and (v) the potential for functional links and joint functioning.(i) Created wetlands hosted diverse assemblages of macroinvertebrates and plants. They maintained a similar com- position and diversity as natural ponds in agricultural landscapes. The environmental conditions per wetland did hardly affect macroinvertebrate and plant assemblages, and the prerequisites for nutrient retention did neither. In landscapes were wetland creation efforts had increased the total density of small water bodies by more than 30%, macroinver- tebrate diversity of created wetlands was facilitated on both local and regional scales. (ii) Diverse communities of denitrifying bacteria with the capacity for conducting different denitrification steps (functional types) were present in all investigated wetlands. The richness of denitrifying bacteria communities was affected by nitrate concentration and hydraulic loading rate, which may potentially be relevant for the nitrogen retention function of created wetlands. The diversity across different functional types of bacterial denitrifiers increased with nitrate concentration. (iii) Both abiotic and biotic factors influenced ecosystem functions of created wetlands. Variation in nitrogen retention was associated to nitrate load, but even to vegetation parameters. In wetlands with constant nitrate load, planted emergent vegetation facilitated nitrogen retention compared to other vegetation types. In wetlands with variable loads, nitrogen retention was facilitated if nitrate load was high and many different vegetation types were present; nitrogen load could explain the majority of the variation in nitrogen retention compared to vegetation parameters. Phosporus retention of created wetlands was best explained by vegetation parameters. Litter decomposition was inhibited at high nitrate to phosphorus ratios. Methane production increased with age and decreased with plant cover. (iv) Biodiversity may facilitate wetland ecosystem functions, particularly in dynamic wetland ecosystems. Nitrogen retention increased with vegetation type diversity, phosphorus retention capacity with plant richness, and litter decomposition with macroinvertebrate diversity. (v) Created wetlands have the capacity of sustaining several parallel ecosystem services. Some wetland functions were coupled; nitrogen retention increased with fast litter decomposition. On the other hand, methane emission and nitro- gen retention were independent of each other, as were nitrogen and phosphorus retention.In conclusion, created wetlands have the potential to at least partly abate the lost biodiversity and multifunctionality caused by the past extensive destruction of natural wetlands in agricultural landscapes.

[Paper II] Milenkovski S., Thiere G., Weisner S.E.B., Berglund O. & Lindgren P.-E. Variation of eubacterial and denitrifying bacterial biofilm communities among constructed wetlands. Submitted manuscript. [Paper V] Thiere G. & Weisner S.E.B. Influence of biotic and abiotic parameters on ecosystem functioning of created wetlands. Manuscript.

Coastal seagrass ecosystems are complex habitats that are increasingly influenced by human perturbations. Disturbances that affect the strength of bottom-up (i.e. resource availability) and top-down (i.e. consumer) controls may also influence biomass distribution between trophic levels, sediment biogeochemistry, and seagrass ecosystem metabolism. Here, I experimentally tested how top-down and bottom-up perturbations interact with community structure (diversity, food chain length of epibenthic consumers) to alter sediment biogeochemistry and ecosystem metabolism in an experimental eelgrass (Zostera marina ) system. My data indicated that resource availability influenced SOM composition and ecosystem metabolism. Light availability tended to be a stronger determinant of SOM composition while nutrient enrichment affected secondary production of invertebrate grazers more strongly than primary producers or SOM. Top-down predator effects on SOM composition and ecosystem flux rates tended to be weak. However, the strength of the trophic cascade may partly be a function of grazer community composition and grazer susceptibility to predation. Finally, my results indicated that grazer species identity and community composition strongly influenced SOM composition. In addition to the main effects of light, nutrients, predators, and grazers there were a variety of interactive effects between resources and food web composition. Consequently, the effects of resource availability and food web composition on seagrass ecosystem functioning should not be considered in isolation.

I cambiamenti climtici minacciano la biodiversità, il funzionamento degli ecosistemi e la vita umana su scala globale. Gli oceani mitigano l'impatto dei cambiamenti globali dovuti alle attività umane, ma diversi fattori di stress, come variazioni di temperatura, acidificazione, scioglimento dei ghiacci e deossigenazione, minacciano i sistemi marini. Studi recenti hanno svelato impatti negativi dovuti a singoli fattori di stress, ma gli effetti sinergici di più fattori di stress concomitanti sono largamente sconosciuti, soprattutto per i sistemi bentonici marini. Inoltre, le attuali evidenze si basano principalmente su risposte di singole specie in esperimenti a breve termine. I sistemi naturali con condizioni ambientali simili a quelle previste dai modelli di cambiamento globale possono servire a studiare i possibili effetti dei cambiamenti climatici. Nella presente tesi, sono stati condotti esperimenti di laboratorio ed in situ in sistemi naturali modello, per valutare i possibili effetti dell' acidificazione, deossigenazione, e fattori contemporanei di stress su biodiversità e funzionamento degli ecosistemi marini. Questi studi sono stati condotti su singole specie (Corallium rubrum), e su comunità (di coralligeno, meiofauna e microbiche). I risultati ottenuti evidenziano 4 messaggi chiave. Primo, livelli più elevati di biodiversità possono mitigare l'impatto dell' acidificazione oceanica sugli ecosistemi bentonici marini. Secondo, gli impatti sono evidenti sia su organismi calcificanti (coralli e alghe coralline) che non (nematodi), con significativi cambiamenti di struttura di comunità. Terzo, la deossigenazione degli oceani può alterare il funzionamento degli ecosistemi pelagici e bentonici, promuovendo processi chemioautotrofi e favorendo il controllo virale sulle comunità microbiche. Infine, i sistemi naturali mostrano che l'impatto di più fattori di stress concomitanti ma intermittenti può essere inferiore a quello di un solo, ma costante, fattore di stress.
Global climate change is threatening biodiversity, ecosystems functioning and human life. The oceans can help in moderating anthropogenic global change, but several stressors, such as temperature shifts, acidification, freshening, and hypoxia/anoxia are disrupting the good environmental status of marine systems. Scientific advances have unveiled the effects of single stressors, but the possible synergistical impacts of multiple-stressors remain largely overlooked, especially on benthic marine ecosystems. Moreover, current evidences are mostly based on the response of single species to short-term pertubation experiments. To help overcoming these limits, natural systems mimicking future climate change scenarios can be studied to understand the complex network of global change impacts. In the present work, we analyzed through laboratory experiments and in situ studies in natural model systems, the impacts of ocean acidification, deoxygenation, and multiple-stressors on the biodiversity and functioning of the marine ecosystems. Our studies were conducted from single species, such as Corallium rubrum, to complex communities such as the coralligenous, meiofauna and microbial assemblages. Our results highlight four key messages. First, higher biodiversity levels can partially mitigate ocean acidification's impact on benthic ecosystems. Second, impacts are evident either for calcifying (corals, coralline algae) and non-calcifying taxa (nematodes), with major shifts in the benthic assemblage composition. Third, seawater deoxigenation can alter the pelagic and benthic ecosystems functioning and biogeochemical cycles, by promoting chemoautotrophic processes and favouring the viral control of microbial assemblages. Fourth, the study of natural systems shows that the impact of temporary multiple stressors can be lower than that caused by one only but constant stressing factor.

The Northern Adriatic Sea summarizes all different critical elements of a ‘typical’ coastal area, such: important trawling activity in the inshore area, presence of aquaculture activities (mussels farms), widely distributed along the coast, presence of small scale fisheries activities, seaside touristic pressures, extended seaport activities. Among these pressures the project aims to investigate acquaculture and small scale fisheries activities within three miles from the coast. This would provide a better understanding of major impact sources and an identification of the processes that need to be preserved/enhanced to maintain or also increase the resilience of the system. Within this context, the main objectives of the project are: (1) to assess the role played by mussel culture farms, both in terms of negative impacts and positive feedbacks; (2) to focalize the attention on one of the main key factors presently affecting, but also structuring, the ecosystem in the NAS coastal area, in order to better understand the majors drivers also in terms of opportunities to be managed; (3) to define long term management objectives, indentifying the self-sustaining processes to be maintained or restored, in order to increase the system resilience and stimulate an adaptive management. To achieve these objectives, five issues were considered: benthic fauna; biogeochemical cycles; potential role as fish aggregating area; emergy analysis; artisanal fishery. The results of the present study show how a mussel farm located in a transitional environment near coast is a man made structure characterised by a sustainable use, with no direct impacts on bottom, acting as a fishing aggregating area also for some commercial species. Assimilating to an “extensive” acquaculture system, mussel farm is a structure characterised by the predominance of renewable inputs that, probably due to environmental factors such as currents and winds, doesn’t interfere both with benthic community and biogeochemical cycles of the area. Moreover the normal aggregating effects due to the confluence of great quantities of available food is increased by the presence, at the bottom, of some hard substrates, able to attract fishes species beyond for feeding, also for reproductive purpose. Nowadays, in a spatial planning management contest, the creation of further mussel farms even if may be encouraged by these results, at regional scale, it is not a firm economical sustainable, due to the low mussel selling price. Moving from this, modernize the production system by coupling mussel cultivations also with other incoming sources, may represent the right choice to maintain this type of sustainable acquacolture. Manage recreational fishing inside mussel farm may be among the feasible solutions. In the end, as underlined by the investigation on potential role as fish aggregating area, the farm, being off-limits to commercial fishing, may act one-sidedly also as a fish maker, for the nearby areas, where artisanal fishery is allowed. By the present, this activity is a sustainable practice, but, due to the species dependence and to the catch composition in terms of thermal affinity groups show a high potential vulnerability. Small modifications both in fleet structures and in environmental conditions could drive the situation towards unsustainability. An increase in available fishes biomass may act as buffer effect towards vulnerability causes, by supporting possible new fishermen, fronting the problem of small modification in fleet structures. Moreover some of the fish species enhanced by mussel farm are temperate or warm species. Given the dependence of local artisanal fishery from cold or temperate species, a shift of catches toward temperate and warm ones’, without affecting incomings, might, at least partially, release this type of activity from the variations of the thermal regime as forecast by IPCC.

La biodiversité est de plus en plus modifiée par les activités humaines, ce qui a conduit à des recherches considérables sur l'effet de la biodiversité sur le fonctionnement des écosystèmes. Ces recherches ont cependant rarement inclu le stress anthropogénique qui cause la perte de biodiversité. Cette thèse analyse l'impact du stress (pesticides et métaux lourds) sur la relation entre la biodiversité et le fonctionnement des écosystèmes à la base de la chaîne alimentaire marine, avec des producteurs marins primaires (diatomées) et leurs principaux consommateurs (copépodes). Le premier résultat est que la pollution chimique altère la régularité plutôt que la richesse des espèces, avec un effet disproportionné sur le fonctionnement si un stress sélectif provoque la domination par des espèces tolérantes avec une faible contribution fonctionnelle. L'effet du stress sur le fonctionnement est prévisible sur la base d'une corrélation des traits biologiques prédisant l'abondance des espèces et des traits prédisant leur effet sur le fonctionnement. L'effet de la biodiversité sur le fonctionnement augmente sous l'effet du stress dû à une augmentation d'interactions facilitatrices entre les espèces (effet de complémentarité). L'effet du stress sur la qualité alimentaire des producteurs primaires réduit le transfert d'énergie au niveau des consommateurs, soulignant la pertinence du changement de biodiversité dans un contexte trophique. La thèse se termine par un cadre synthétique présentant les trois principaux effets (stress sélectif, stress physiologique, complémentarité) déterminant l'effet du stress sur la relation entre la biodiversité et le fonctionnement des écosystèmes
Biodiversity is increasingly altered by human activities, which has led to considerable research on the consequences of biodiversity loss for ecosystem functioning. The anthropogenic stressors driving the ongoing biodiversity loss are however rarely included into biodiversity-ecosystem functioning experiments. The present thesis analyses the impact of anthropogenic stressors (pesticides, heavy metals) on the biodiversity-ecosystem functioning relation in marine primary producers (diatoms) and consumers (copepods). It was shown that chemical stress alters species evenness rather richness, with a disproportionate effect on functioning if stress causes dominance by tolerant species with a low functional contribution. Stress tolerance and the functional contribution were predictable based on the species’ biological traits, and the effects of stress on ecosystem functioning depended on the correlation of traits predicting species abundance and traits predicting the species’ effect on ecosystem functioning. The biodiversity effect on primary producer biomass production increased under stress due to facilitative interactions (complementarity effect). Stressor-induced biodiversity loss reduced the food quality of primary producers and impaired the energy transfer to the consumer level, highlighting the relevance of stressor-induced biodiversity changers in a trophic context. The thesis ends with a synthetic framework which puts forward the three main effects (selective stress, physiological stress, complementarity) through which anthropogenic stress affects biodiversity-ecosystem functioning relations at the basis of marine food webs

La biodiversité est de plus en plus modifiée par les activités humaines, ce qui a conduit à des recherches considérables sur l'effet de la biodiversité sur le fonctionnement des écosystèmes. Ces recherches ont cependant rarement inclu le stress anthropogénique qui cause la perte de biodiversité. Cette thèse analyse l'impact du stress (pesticides et métaux lourds) sur la relation entre la biodiversité et le fonctionnement des écosystèmes à la base de la chaîne alimentaire marine, avec des producteurs marins primaires (diatomées) et leurs principaux consommateurs (copépodes). Le premier résultat est que la pollution chimique altère la régularité plutôt que la richesse des espèces, avec un effet disproportionné sur le fonctionnement si un stress sélectif provoque la domination par des espèces tolérantes avec une faible contribution fonctionnelle. L'effet du stress sur le fonctionnement est prévisible sur la base d'une corrélation des traits biologiques prédisant l'abondance des espèces et des traits prédisant leur effet sur le fonctionnement. L'effet de la biodiversité sur le fonctionnement augmente sous l'effet du stress dû à une augmentation d'interactions facilitatrices entre les espèces (effet de complémentarité). L'effet du stress sur la qualité alimentaire des producteurs primaires réduit le transfert d'énergie au niveau des consommateurs, soulignant la pertinence du changement de biodiversité dans un contexte trophique. La thèse se termine par un cadre synthétique présentant les trois principaux effets (stress sélectif, stress physiologique, complémentarité) déterminant l'effet du stress sur la relation entre la biodiversité et le fonctionnement des écosystèmes
Biodiversity is increasingly altered by human activities, which has led to considerable research on the consequences of biodiversity loss for ecosystem functioning. The anthropogenic stressors driving the ongoing biodiversity loss are however rarely included into biodiversity-ecosystem functioning experiments. The present thesis analyses the impact of anthropogenic stressors (pesticides, heavy metals) on the biodiversity-ecosystem functioning relation in marine primary producers (diatoms) and consumers (copepods). It was shown that chemical stress alters species evenness rather richness, with a disproportionate effect on functioning if stress causes dominance by tolerant species with a low functional contribution. Stress tolerance and the functional contribution were predictable based on the species’ biological traits, and the effects of stress on ecosystem functioning depended on the correlation of traits predicting species abundance and traits predicting the species’ effect on ecosystem functioning. The biodiversity effect on primary producer biomass production increased under stress due to facilitative interactions (complementarity effect). Stressor-induced biodiversity loss reduced the food quality of primary producers and impaired the energy transfer to the consumer level, highlighting the relevance of stressor-induced biodiversity changers in a trophic context. The thesis ends with a synthetic framework which puts forward the three main effects (selective stress, physiological stress, complementarity) through which anthropogenic stress affects biodiversity-ecosystem functioning relations at the basis of marine food webs

Intermittent rivers and ephemeral streams (IRES) are watercourses that naturally and periodically cease to flow. They represent more than half of the global river network and are expanding due to global change. In this thesis, I investigate the mechanisms linking flow intermittence with biodiversity and ecosystem functioning, which sustain biogeochemical cycles and energy transfer in the system. Chapter 1 analyzes the effects of hydrology, micro-habitat (surface and subsurface zones) and biotic features on organic matter decomposition and fungal biomass, in 20 streams. In Chapter 2, I assess the effect of different flow intermittence metrics (i.e., annual intermittence regime and recent aquatic status) on aquatic biodiversity, including both taxonomic and functional-trait-based metrics, in 33 streams. Chapter 3 analyzes how aquatic hyphomycete richness and composition (beta diversity and its turnover and nestedness components) are affected by a flow intermittence gradient and how these community changes affect organic matter decomposition, in 15 streams and in a microcosm approach. Finally, in Chapter 4, I explore how changes in both leaf litter quality and quantity determine the feeding preferences and growth of an invertebrate shredder. The results of Chapter 1 show that the subsurface zone contributes to maintaining microbial decomposition during non-flow periods in IRES, mainly because of the levels of fungal biomass present in the subsurface zone. In Chapter 2, I conclude that a combination of flow intermittence metrics are needed to explain the high dynamism of the invertebrate community in IRES and potentially ecosystem functioning. Moreover, this chapter shows that hydrological variables outweigh non-hydrological factors in explaining invertebrate community variation, thereby supporting the use of the former in IRES classification and bio-monitoring routines. Chapter 3 reveals that the reduction of aquatic hyphomycete richness and species turnover as a result of flow intermittence, could have negative effects on organic matter decomposition. Finally, in Chapter 4, I provide evidence on how flow intermittence reduces the quality of leaf litter, in terms of fungal richness and composition, fungal biomass and lipid content. These changes in food quality influence the consumption rates and growth of shredders, which are able to feed selectively on higher quality leaves, even though its availability is lower. Taken together, these results will help to improve the biomonitoring and management of IRES and to a better prediction of ecosystem trajectories in response to global change.

Rising temperature caused by global warming alters physiology, phenology and/or distribution in a wide array of plant and animal species, which has dramatic knock-on effects at different levels of organisation. This study investigates the individual and interactive effects of temperature (18ᵒC, 22ᵒC and 30ᵒC) and additions of the macroalga Gracilaria gracilis (high and low) on the performance of the seagrass Zostera capensis, which occurs in Langebaan Lagoon, South Africa over a seven-week period. Results from the laboratory experiment revealed that G. gracilis did not significantly affect the performance of Z. capensis although temperature did result in greater leaf width, fouling and senescent biomass, as well as marginally greater leaf area and lower below-ground biomass at 30ᵒC. Increasing temperature also increased G. gracilis biomass, percent cover and fouling by microalgae. In addition, there was no interaction between temperature and the additions of Gracilaria. The overall findings of this study indicate that Z. capensis abundance is likely to decrease while G. gracilis will conversely increase in abundance in response to warming. Changes in abundance of those two ecosystem engineers highlight the possibility of a phase shift from a seagrass- to macroalgal-dominated state in Langebaan Lagoon.

La compréhension du fonctionnement des écosystèmes est important pour prédire, gérer et protéger les écosystèmes dans lesquels nous vivons et dont nous dépendons. Cette thèse y apporte une contribution en scrutant le compartiment zooplanctonique, qui joue un rôle crucial - quoiqu'encore largement méconnu - dans le fonctionnement des écosystèmes marins, et plus particulièrement les cycles biogéochimiques et le transfert trophique. La présente thèse propose trois perspectives différentes sur le fonctionnement du zooplancton, centrées sur la composition taxonomique (chapitre 1), la structuration en taille (chapitre 2) et la composition biochimique (chapitre 3), en utilisant une approche intégrée qui prend en compte les niveaux trophiques inférieurs et supérieurs dans le contexte du Multitrophic Biodiversity Ecosystem Functioning. Le chapitre 1 a révélé l'existence de cinq assemblages de zooplancton dans le sud de la mer du Nord et l'est de la Manche (EEC) pendant l'hiver, qui variaient en terme de productivité, d'abondance des taxons et de composition. La composition et la distribution des assemblages étaient déterminées par des variables abiotiques (nutriments dissous, salinité, profondeur, température, matière organique en suspension, chlorophylle a) et biotiques (composition du phyto- et du microplancton), des masses d'eau et des frayères de poissons. Le chapitre 2 a révélé une faible structuration de la taille du plancton entre 20 et 500 µm en ce qui concerne leur signature isotopique. Cela indique que l'omnivorie est la stratégie alimentaire dominante de cette classe de taille de plancton en hiver. Les larves de hareng (Clupea harengus) et de plie (Pleuronectes platessa) présentaient des signatures isotopiques spécifiques et différentes préférences de taille de proie. Des différences spatiales ont ainsi été observées dans la composition de la taille des proies des larves de plie échantillonnées dans les stations influencées par les rivières et dans les stations situées au centre de la Manche orientale. Le profil en acide gras (AG) du zooplancton et de la sardine différait entre la partie ouest et est de la Manche, ainsi que des différences dans la composition taxonomique du phytoplancton et du zooplancton, indiquant un contrôle ascendant du transfert trophique de ces nutriments essentiels. Tous les chapitres ont révélé une structuration spatiale dans le fonctionnement de l'écosystème, car la variabilité spatiale des caractéristiques du zooplancton semblait être liée aux niveaux trophiques inférieurs et supérieurs. L'étude combinée de la taxonomie et des traits du zooplancton (taille et composition en AG) en relation avec les niveaux trophiques inférieurs et supérieurs a révélé des caractéristiques supplémentaires du zooplancton liées à la stratégie trophique, à la reproduction et à la survie reliant le zooplancton à l'écosystème. Ainsi, l'étude du zooplancton dans un contexte multitrophique prenant en compte différents aspects de sa diversité a contribué à une compréhension plus mécaniste du zooplancton en tant que partie et en relation avec d'autres composants de l'écosystème et a facilité l'élaboration d'hypothèses pour expliquer les schémas et les relations observés. Par conséquent, l'approche utilisée dans cette thèse semble prometteuse pour acquérir les informations nécessaires pour améliorer la représentation du zooplancton dans les modèles écosystémiques et la gestion écosystémique
Understanding ecosystem functioning is important to predict, manage and protect the ecosystems in which we live and on which we depend. Intending to contribute to a better ecosystem understanding the present thesis focused on zooplankton that play a crucial role in the functioning of marine ecosystems with regard to biogeochemical cycles and trophic transfer. Despite their central role, zooplankton are to-date not adequately represented in ecosystem-models, potentially affecting ecosystem-management. The present thesis explores three different perspectives on zooplankton functioning namely taxonomical composition (chapter 1), size-structure (chapter 2) and biochemical composition (chapter 3) using an integrated approach that considers both lower and higher trophic levels within the context of Multitrophic Biodiversity Ecosystem Functioning. Chapter 1 revealed the existence of five zooplankton assemblages in the Southern North Sea and Eastern English Channel (EEC) during winter that varied with regard to productivity, taxa abundance and composition. Assemblage composition and distribution was driven by abiotic (e.g., dissolved nutrients, salinity, depth, temperature) and biotic variables (e.g., phyto- and microplankton composition), including water masses anf fish spawning grounds. Chapter 2 revealed a weak size structuration of plankton between 20 and 500 µm regarding their isotopic signature indicating omnivory was the dominant feeding strategy of this plankton size class during winter. Herring (Clupea harengus) and plaice (Pleuronectes platessa) larvae displayed species-specific isotopic signatures and different prey size preferences. Additionally, spatial differences in prey size composition were observed among plaice larvae sampled at river influenced stations compared to those collected at stations in the center of the EEC. The fatty acid (FA) profile of zooplankton and sardine (Sardina pilchardus) differed between the western and the eastern side of the English Channel alongside with differences in the taxonomical composition of phytoplankton and zooplankton, indicating a bottom-up control of the trophic transfer of these essential nutrients. Independent of the perspective, all chapters revealed spatial patterns in ecosystem functioning, as spatial variability in zooplankton characteristics seemed to be related to both lower and higher trophic levels. The combined investigation of zooplankton taxonomy and traits (size and FA composition) in relation to lower and higher trophic levels revealed additional zooplankton characteristics related to trophic strategy, reproduction and survival further connecting zooplankton to ecosystem functioning. Thus, investigating zooplankton in a multitrophic context considering different aspects to their diversity contributed to a more mechanistic understanding of zooplankton as part of, and in relation to the ecosystem. It further facilitated the development of hypotheses to explain the observed patterns and relationships. Consequently, the approach used in the present study appears promising to acquire information needed to enhance the representation of zooplankton in ecosystem models and ecosystem-based management

Le changement climatique affecte de plus en plus la vie marine. Les vagues de chaleur marines (MHWs), liées au réchauffement, devraient augmenter en durée, intensité et fréquence, amplifiant leurs impacts sur les écosystèmes marins au 21e siècle. Cette thèse explore les effets du changement climatique et des MHWs sur les flux de biomasse dans les réseaux trophiques marins et leurs conséquences sur la structure et le fonctionnement des écosystèmes. J’ai développé EcoTroph-Dyn, une version dynamique du modèle EcoTroph, représentant le fonctionnement des écosystèmes marins comme un flux de biomasse continu, des producteurs primaires aux prédateurs supérieurs. Basé sur une approche virtuelle d’EcoTroph-Dyn, j'ai mis en évidence que, les MHWs pourraient avoir impacté les flux de biomasse par la perturbation de la cinétique, de l'efficacité de transfert et induire des pertes de biomasse. Ensuite, en utilisant EcoTroph-Dyn, j’ai reconstitué les biomasses des consommateurs marins de 1998 à 2021 en intégrant les variations de température et de production primaire.La biomasse animale marine, estimée à chaque niveau trophique sur une grille mondiale de 1° x 1°, révèle des pertes significatives dues aux MHWs, avec des impacts accentués aux niveaux trophiques supérieurs. Enfin, les projections de la biomasse animale des océans de 1950 à 2100 indiquent que les altérations des flux de biomasse due aux MHWs pourrait entraîner une diminution globale supplémentaire de la biomasse des consommateurs proportionnelle au réchauffement des océans, avec des impacts plus prononcés que ceux dû au changement climatique de fond. Cette thèse démontre que le changement climatique et les MHWs perturbent conjointement les flux de biomasse, réduisant la biomasse océanique future avec des répercussions majeures sur les pêcheries
Intensifying climate change is increasingly affecting marine life in the world's oceans. Extreme events like marine heatwaves (MHWs), associated with climate change, are projected to grow in duration, intensity, and frequency, further impacting marine ecosystems throughout the 21st century. In this dissertation, I investigated the effects of climate change and MHWs on biomass flows in marine food webs and their consequences on ecosystem structure and functioning. I developed a dynamic version of the EcoTroph model, named EcoTroph-Dyn, which represents the functioning of marine ecosystems as a single flow of biomass from primary producers to top predators. To study MHW effects using EcoTroph-Dyn, I estimated MHW-induced mortality from 1982 to 2021 based on the thermal preferences of various taxa. The results reveal that MHWs may have impacted biomass flow through the perturbation of the kinetics of biomassflow and transfer efficiency and caused biomass loss through instantaneous mortality. Secondly, using EcoTroph-Dyn, I hindcasted consumer biomass in marine food webs from 1998 to 2021. By integrating changes in temperature and primary production, marine animal biomass was estimated at each trophic level on a 1° x 1° grid of the global ocean. Findings show significant biomass loss due to MHWs, with more pronounced impacts at higher trophic levels. Finally, projections from 1950 to 2100 indicate that MHW-induced changes in biomass flows could drive a global consumer biomass decline, surpassing the impacts of background climate change. Overall, this dissertation demonstrates that climate change and MHWs jointly disrupt biomass flows in marine ecosystems, leading to reduced future ocean animal biomass with direct repercussions on fisheries

Faced with the global overexploitation of marine resources and the rapid degradation of ecosystems’ integrity, many states agreed to the principle of an ecosystem approach to fisheries (EAF). In fact, overfishing induces strong decrease of targeted species biomass, which impact predators, their competitors, prey, and ultimately the ecosystems’ trophic networks. Thus, it is an important challenge to understand the trophic functioning of marine ecosystems and the related impacts of fisheries. In this spirit, my thesis was developed to address concerns about the potential impacts of fisheries on the underlying trophic functioning, and to better understand this trophic functioning and its variability through ecosystems. Two well-known trophodynamic models were used : Ecopath with Ecosim (EwE) and EcoTroph (ET). First, I developed EcoBase, i.e., an online repository to gather and communicate information from EwE models, which enabled to give a global overview of the applications of the EwE modeling approach. Then, the ET model was corrected and standardized through the creation of a software package in R. A new trophic control, i.e., foraging arena (FA) trophic control, was integrated to study its impacts on trophic flows and fishing effects on aquatic ecosystem trophic networks. I showed that that making ecosystem behavior more realistic by incorporating FA controls into EcoTroph decreased the resistance and the production of modeled ecosystems facing increasing fishing mortality. An analysis of case studies focusing on marine protected areas (MPAs) was then performed using EwE and ET. I analyzed the potential spillover effect from three MPAs, and showed that their potential exports were at the same order of magnitude as the amount of catch that could have been obtained inside the reserve. Finally, a meta-analysis of marine ecosystem trophic functioning was conducted using 127 EwE models, which showed that ecosystem types were distinguished by different biomass trophic spectra and associated trophic indices. These differences were mainly driven by different production, but also kinetic for some ecosystem types. In conclusion, trophodynamic models, as EwE and ET, appeared to be useful tools to better understand the trophic functioning of marine ecosystems, its variability through ecosystems, and the associated impacts of fisheries.
Science, Faculty of
Zoology, Department of
Graduate

Multiple dimensions of biodiversity within and across producer and consumer guilds in the food web affect an ecosystem’s functionality and stability. Tropical and subtropical aquatic ecosystems, which are extremely diverse, have received much less attention than terrestrial ecosystems in regards to the effects of biodiversity on ecosystem functioning. We conducted a field experiment that tested for effects of macrophyte functional diversity on diversity and stability of associated fish assemblages in floodplain lakes of the Upper Paraná River floodplain, Brazil. Three levels of macrophyte functional diversity were maintained through time in five floodplain lakes and response variables included various components of fish taxonomic and functional diversity and stability. Components of functional diversity of fish assemblages were quantified using a suite of ecomorphological traits that relate to foraging and habitat use. Response variables primarily distinguished macrophyte treatments from the control. Macrophyte treatments had, on average, double the number of species and total abundance than the control treatment, but only limited effects on stability. The high diversity treatment was essentially nested within the low diversity for assemblage structure and had similar or even slightly lower levels of species richness and abundance in most cases. Gymnotiformes and young-of-year were diverse and relatively abundant in macrophyte treatments contributing to the large differences in diversity between macrophyte and control treatments. Higher fish diversity in structured habitats compared to more homogenous habitats is likely associated with increased ecomorphological diversity to exploit heterogeneous microhabitats and resources provided by the macrophytes.

Les écosystèmes côtiers, interface entre terre et mer, sont soumis au changement climatique ainsi qu’à de fortes pressions anthropiques. Par conséquent, les eaux côtières sont sujettes à eutrophisation. Le phytoplancton demande une attention particulière dû à son rôle de producteur primaire des écosystèmes marins. Récemment, l’efflorescence des algues nuisibles est devenue mondialement, une inquiétude croissante. Le but de la thèse a été de décrire et de mesurer les réponses temporelles et les causalités de la structure de communauté phytoplanctonique sous impact des changements globaux, en présence d’une algue nuisible. Pour ce faire, le concept de niche écologique et une méthode statistique, ont été adaptés. Les "Within Outlying Mean Indexes" ont été proposés pour affiner l’analyse "Outlying Mean Index" en combinant ses propriétés avec la décomposition de la marginalité de l’analyse "K-select". Les dynamiques des sous-niches de la communauté d’espèce ont été étudiées dans des conditions environnementales d’ abondances basses (L) ou fortes (H) de Phaeocystis spp. Le sous-ensemble H était caractérisé par une large niche de Phaeocystis spp. ainsi qu’une forte diversité de diatomées. Dans le sous-ensemble L, Phaeocystis spp. a subit une forte contrainte biologique probablement induite par la compétition des diatomées pour les ressources. La relation diversité-productivité du phytoplancton s’est avérée plus forte à l’échelle saisonnière que sur le long-terme. Le déséquilibre des ressources n’a pas eu de lien direct avec la productivité à long terme. Le succès à long terme de l’espèce invasive et de son impact sur la productivité, est favorisé par une suite d’années froides avec des ressources élevées et déséquilibrées, augmentant le nombre de petites espèces de diatomées et donc son efflorescence. Enfin, je discute des améliorations méthodologiques, du potentiel d’utilisation de l’approche par traits, et d’éventuelles montages expérimentaux pour supporter les résultats de la thèse
Coastal ecosystems, the interfaces between land and sea, are subject to climate change and high anthropogenic pressure. Consequently, most coastal waters are prone to eutrophication. The phytoplankton require a special attention because of its role of primary producer in marine ecosystems. Recently, Harmful Algae Bloom outbreaks has raised concern worldwide. The thesis aim was to describe and to measure the temporal responses and causalities of the phytoplankton community structure, with the occurrence of a harmful algae, under global changes. To do so, the ecological niche concept and a statistical method were adapted. The Within Outlying Mean Indexes was proposed to refine the Outlying Mean Index analysis by combining its properties with the K-select analysis species marginality decomposition. The subniche dynamics of the species composing the community were studied under environmental conditions hosting low (L) and high (H) Phaeocystis spp. abundance. Subset H was characterized by a large Phaeocystis spp. niche and a high diatom diversity. In subset L, Phaeocystis spp. was subject to great biological constrain suspected to be caused by diatom competition for resources. The phytoplankton diversity productivity was stronger at a seasonal scale than on the long-term. The resource imbalance had no direct link with productivity in the long-term. The long-term invasive species success and its impact on productivity is favored by successive cold years with high resource imbalance which rise the number of small species and its bloom. I finally discussed on the methodological improvements, the potential use of the trait-based approach, and possible experimental set-ups to support the thesis results

Structure and functioning of Cystoseira (Fucales) populations. An applicative study to assess their relevance for marine coastal ecosystems and for human well-being, in a conservation and restoration perspective

An increase in cephalopod abundance worldwide has been observed over recent decades, possibly a function of cephalopods’ response to the effects of climate change and the reduction in predation by human exploitation on predators of marine systems. Additionally, there has been a renewal of fisheries interest due to the development of markets for cephalopod products and the reduction of finfish stocks. Assessing their role in food webs is thus essential for understanding and anticipating upcoming changes in ecosystem functioning and services. From this perspective, ecosystem models can be used as powerful tools to understand the impact of a group of species on the system, and to anticipate future developments and foresee the future dynamics. However, these models generally fail to represent cephalopods ecology adequately. This thesis thus aimed to tackle the issue of representing cephalopods ecology in ecosystem models and to use these new methods to assess their role in ecosystems and the potential changing of this role under climate change: Identifying the limits of ecosystem models when it comes to representing cephalopods ecology; Tackling the issue by improving the existing features of the Atlantis modelling framework and developing additional tools to represent the particularity of cephalopods ecology; Testing the sensitivity of the resulting model to various ecological processes and cephalopod life-history; Subjecting the model to an environmental change scenario and analysing the implications for cephalopods and other groups. A preliminary investigation into the representation of cephalopod ecology in ecosystem models around the world asserts the limitations of our understanding of their impact on the system. I find that despite the frequent lack of data on cephalopod ecology, structural improvements to models could already bring valuable additional insights on their role in the ecosystem. I then focused on an ecosystem model of the South East of Australia region to investigate the role of cephalopods in the food web. New features were added to the Atlantis modelling framework and many mechanisms disregarded until now were used to adequately represent the life-history traits of cephalopods; their exponential growth, their opportunistic and voracious feeding, their predation on relatively large prey; their ontogenic ecological shifts. The model was then subjected to a series of sensitivity tests to cephalopod parameters to identify the key ecological processes of this group and their impact on the structure and functioning of marine food web. This exercise revealed the potential of ecosystem models to adequately simulate cephalopod life-history traits, and pointed to the key importance of the growth capacity of squid species to drive their role in the ecosystem. The ecosystem model is also used to assess the impact of climate change on cephalopod ecology and on ecosystem functioning. An increase in temperature over 50 years, following one of the IPCC scenarios, is forced on the model. Results indicate that upcoming changes will benefit squid species as they take advantage of food-web changes better than many forage fishes that are both their competitors and their prey. The abundance of arrow squid, an oceanic squid, increases by about 15%, and the abundance of calamari, a neritic squid, increases by about 9% by the end of the climate change scenario. This leads to a substantial ecosystem change that could impact many species of interest for fisheries, and should therefore be taken in to consideration for the future of marine exploitation.

River inflow is one of the most important factors influencing the density and biomass of estuarine biotic communities. The aim of this study was to obtain an understanding of the ecosystem functioning of selected estuaries on the east coast of South Africa and to represent their dynamics through ecosystem models. The responses of water column nutrients, plankton density and biomass to inlet phase changes for 16 temporarily open/closed estuaries (TOCEs) in South Africa were first determined. This analysis demonstrated that inlet phase and the duration of mouth closure were the most important factors determining plankton density and biomass of the analysed TOCEs. Estimates of planktonic standing stocks for four of these estuaries revealed that stocks can be from 26 to 10 000 times higher during the closed compared to the open phase. Also, slightly higher variability of planktonic density and biomass was recorded during the closed phase of TOCEs. The second major thrust of this study was to analyse the variability and temporal stability of planktonic and macrobenthic invertebrate density and biomass in two KwaZulu-Natal estuaries over a dry/wet cycle. The results suggest that “stable” variability and species synchronization could be the mechanisms whereby the estuarine biota of these systems compensate for environmental changes and attain a degree of environmental homeostasis. The third major thrust involved an assessment of the spatio-temporal variations in the elemental composition and stoichiometry of suspended and sediment detritus, zooplankton and macrobenthic taxa from two estuaries over a dry/wet cycle. Significant seasonal variations in the elemental composition of detritus, zooplankton and macrobenthic species were found, with the variations in the elemental content of sediment and suspended detritus being related to the seasonal changes in river inflow, while the among-taxa variability was mainly explained by feeding mode. Finally, static seasonal carbon and nitrogen ecosystem network models were developed for the East Kleinemonde, Mlalazi and Mpenjati estuaries to investigate their nutrient dynamics and ecosystem functioning. The results indicated that the East Kleinemonde and Mpenjati estuaries were mainly dependent on primary producers during the dry season, especially the high standing stocks of phytoplankton and microphytobenthos. Similarly, the dependency on detritus was higher during the wet season due to the high riverine imports during this season. Consequently, higher detritivory was recorded in all three study systems during the wet season. Cycling of nitrogen was higher than of carbon on a seasonal basis, with higher recycling of nitrogen during the dry season implying a lower availability of this element due to reduced freshwater inflow and nutrient input during the low rainfall period. System indices indicated that the organization of these systems was higher during the dry season, while the overheads on imports and exports peaked during the wet season. The ecosystem models analysed here provide an initial insight into the overall carbon and nitrogen dynamics of estuaries on the east coast of South Africa.
M.Sc. University of KwaZulu-Natal, Durban 2013.