Global climate change has severe consequences at various trophic levels, especially tree plant species. In regions of Tropical Dry Forests (TDF) these impacts are extreme and still little studied. This work evaluated how environmental conditions (local, regional and global), imminent climate changes, influenced the dendroecology, wood anatomy and foliar ecophysiology of four tree species occurring in the TDF of two sites, Sergipe, Grota do Angico Natural Monument, and in a remnant of TDF in Fazenda São Pedro, municipality of Porto da Folha, Sergipe. Samples of wood and leaves of six individuals of each species, Aspidosperma pyrifolium, Ziziphus joazeiro, Tabebuia aurea and Libidibia ferrea were randomly collected. For each individual, three wood samples were collected, two for dendroecology and one for the anatomy of the wood. Leaves, of the same plants were collected at both sites, in the dry and rainy periods, and intended for the ecophysiological analyzes. Collection data on species distribution (SpeciesLink project) were used in the construction of ecological niche models (ENM). Historical climate datas were obtained from INMET, AGRITEMPO, state data, the WolrdClim project, and the NOAA. The results of the dendroecological analyzes showed the formation of annual growth rings in the four species, that the chronologies of all the taxa have a significant relation with rainfall events in both sites, and some taxa had the chronologies related to the surface temperature of the Atlantic Ocean (TSA) and ENSO events, indicating a decrease in plant growth accompanied by lower rainfall volumes in the last decade. The ENM showed different responses of the species niche to the environmental variables (precipitation and temperature) in the TDF, with significant correlations with the anatomical and physiological data, and showed the occurrence of distinct functional groups among the taxa, changing as a function of the changes in the climate. The present study confirmed that the four TDF species have dendroecological potential for climate response, and that ENM's in line with functional (anatomical and physiological) traits analysis may be a viable solution to evaluate the responses of these taxa To xeric environments, in addition to serving as diagnoses of future global climate change, given its high correlation with the functional modifications of the species evaluated here. / As mudanças climáticas globais geram consequências severas em diversos níveis tróficos, em especial às espécies vegetais arbóreas. Em regiões de Florestas Tropicais Secas (FTS) estes impactos são extremos e ainda pouco estudados. Este trabalho avaliou como as condições ambientais (locais, regionais e globais), iminentes as mudanças do clima, influenciaram na dendroecologia, anatomia da madeira e ecofisiologia foliar de quatro espécies arbóreas ocorrentes na FTS de dois locais em Sergipe, no Monumento Natural Grota do Angico, e em um remanescente de FTS na Fazenda São Pedro, município de Porto da Folha, Sergipe. Foram coletadas aleatoriamente amostras de madeiras e folhas de seis indivíduos de cada espécie, Aspidosperma pyrifolium, Ziziphus joazeiro, Tabebuia aurea e Libidibia ferrea. Para cada indivíduo foram coletadas três amostras de madeira, duas destinadas a dendroecologia e uma a anatomia da madeira. Folhas, das mesmas plantas foram coletadas nos dois locais, nos períodos seco e chuvoso, e destinadas às análises ecofisiológicas. Dados de coleções sobre a distribuição das espécies (projeto SpeciesLink) foram utilizados na construção de modelos de nicho ecológico (MNE). Dados climáticos históricos foram obtidos das plataformas do INMET, AGRITEMPO, estações estaduais, do projeto WolrdClim, e do NOAA. Os resultados das análises dendroecológicas mostraram formação de anéis de crescimento anuais nas quatro espécies, que as cronologias de todos os táxons possuem relação significativa com eventos de chuva em ambos os locais, e alguns táxons tiveram as cronologias relacionadas com a temperatura da superfície do Oceano Atlântico (TSA) e eventos de ENOS, indicando diminuição no crescimento das plantas acompanhando menores volumes de chuvas na última década. O MNE mostrou diferentes respostas do nicho das espécies às variáveis ambientais (precipitação e temperatura) nas FTS, com correlações significativas com os dados anatômicos e fisiológicos, e mostraram a ocorrência de grupos funcionais distintos entre os táxons, se alteram em função das mudanças no clima. O presente estudo confirmou que, as quatro espécies no FTS possuem potencial dendroecológico de resposta ao clima, bem como que MNE’s em consonância com a análise de traços funcionais (anatômicos e fisiológicos) podem ser uma solução viável para avaliação das respostas destes táxons a ambientes xéricos, além de servir como diagnósticos das mudanças climáticas globais futuras, vista sua alta correlação com as modificações funcionais das espécies aqui avaliadas.

La recherche d’une agriculture durable et respectueuse de l’environnement passe par une réduction de l’usage d’intrants de synthèse. L’agroécologie cherche à utiliser les interactions entre les organismes de l’agroécosystème pour optimiser son fonctionnement, comme la régulation naturelle des bioagresseurs. C’est dans cette optique que s’inscrit ce travail de thèse qui étudie l’effet de la fertilisation des cultures sur les épidémies de pathogènes foliaires fongiques des cultures. De plus, nous étudions l’évolution des pathogènes face à des scénarios de fertilisation. Cela questionne la durabilité des pratiques culturales qui participent à la régulation les épidémies. Pour répondre à ces questions, nous avons adopté une démarche de modélisation qui permet de simuler l’effet de différents scénarios de fertilisation. Le point de départ et l’originalité de notre démarche a été de considérer le système hôte-pathogène comme un système ressource-consommateur et d’y appliquer des concepts de l'écologie évolutive pour répondre à ces questions agronomiques. Dans les deux modèles construits durant cette thèse, la fertilisation influence directement la quantité de ressources disponible pour le pathogène. Nous nous y concentrons sur un trait d'histoire de vie du pathogène, la période de latence (durée séparant l'infection du début de la sporulation), qui correspond à la durée minimale d'un cycle infectieux et qui, conditionne la stratégie d'allocation des ressources du pathogène. La latence détermine en effet la quantité de ressource qui sera allouée à la croissance du mycélium (donc sa taille à maturité) et celle qui sera ensuite allouée à la sporulation (en relation avec sa taille). Les modèles développés permettent d'étudier les réponses épidémiologique et évolutive des pathogènes foliaires fongiques à la fertilisation des cultures, avec comme référence le système Blé d'hiver/Rouille brune. Nous avons considéré différentes échelles dans ce travail : depuis la lésion où le pathogène se nourrit directement sur son hôte, jusqu’à la parcelle où se développent les épidémies et au paysage où les flux de spores entre les parcelles sont source d’extension des épidémies dans l’agroécosystème. Un premier modèle, à l'intersection des modèles épidémiologiques "SEIR" et des modèles de populations structurées, couvre les échelles de la lésion à celles de l’épidémie et de la parcelle. Le second modèle, à l'intersection des modèles SEIR et des modèles spatiaux d'épidémiologie du paysage, couvre les échelles de la parcelle au paysage agricole. Nous étudions les dynamiques épidémiologiques et évolutives, en comparant des concepts de fitness empiriques et d’invasion. Nous montrons que la fertilisation des cultures, en déterminant la dynamique des ressources disponibles pour les pathogènes, impacte fortement les épidémies. Nos modèles prédisent que la latence des pathogènes évolue en réponse à des compromis écologiques variés, d’une part pour optimiser l’allocation des ressources au niveau des feuilles, mais également pour gagner la course face à la croissance du couvert. La fertilisation, en changeant les concentrations de métabolites foliaires et les dynamiques de croissance du couvert, impacte donc épidémies et réponses évolutives de la latence des pathogènes. A l’échelle du paysage, l’introduction de pratiques variées de fertilisation dans un paysage préalablement homogène pourrait permettre de réduire les épidémies. Cependant, notre modèle prédit une durée limitée de cet effet du fait de l’évolution et de la diversification des pathogènes dans un paysage hétérogène. Ce travail ouvre la voie à des travaux sur l’effet et la durabilité des pratiques pour réguler les épidémies dans l’agroécosystème. Enfin, nous montrons par un travail de méta-analyse qu’il existe une relation forte entre type trophique et latence du pathogène, suggérant que les différents types de pathogènes répondront différemment à des scénarios de réduction de fertilisation / The quest for a sustainable agriculture requires a reduction in the use of synthetic inputs. In this perspective, agroecology seeks to use interactions between organisms in the agroecosystem to replace inputs by ecosystem services, such as the natural regulation of pests and diseases. In this context, this thesis studies the effect of crop fertilization on epidemics of crop fungal foliar pathogens. We also take into account the evolution of these pathogens in response to fertilization scenarios. This allows us to study the sustainability of agricultural practices that contribute to the regulation of epidemics. To answer these questions, we adopted a modelling approach that simulates the effect of different fertilization scenarios. The starting point and originality of our approach was to consider the pathosystem as a consumer-resource system and to use concepts of evolutionary ecology to answer the abovementioned agronomic questions. In the two models developed in this thesis, fertilization directly determines the quantity of resources available for the pathogen. We focus on one of the pathogen's life history traits, the latent period (time period between infection and the onset of sporulating lesions), which corresponds to the minimum duration of an infectious cycle and constrains the pathogen's resource allocation strategy. The latent period determines the amount of resource that will be allocated to either growth of mycelium (and therefore to pathogen size at maturity) or to sporulation (proportional to the pathogen’s size). The models we developed make it possible to study the epidemiological and evolutionary responses of fungal foliar pathogens to crop fertilization. We parameterized our models according to our biological knowledge of the wheat-rust pathosystem. Our modelling work encompasses different spatial and temporal scales: from the lesion where the pathogen feeds directly on its host, to the field and the landscape where the spores that flow between fields are the source of epidemics in the agroecosystem. The first model, at the intersection of the "SEIR" epidemiological models and structured population models, covers the scales of a lesion, the crop canopy and the field. The second model, at the intersection of SEIR and spatial landscape epidemiology models, covers the scales of the field and the agricultural landscape. We study epidemiological and evolutionary dynamics of pathogen populations by comparing empirical and invasion fitness concepts. We show that crop fertilization, by determining the dynamics of available resources for pathogens, has a strong impact on foliar fungal epidemics. Our models predict that pathogen latent period evolves in response to various ecological trade-offs; on the one hand to optimize resources allocation at the leaf scale, on the other hand to win the race against canopy growth. By changing the leaf metabolite content and the rate of canopy growth, fertilization therefore impacts both epidemics and evolutionary responses of pathogen latent period. At the landscape scale, the introduction of various fertilization practices in a previously homogeneous landscape could help to partially regulate epidemics. However, our model predicts that the beneficial effects of heterogeneity will vanish due to the evolution and diversification of pathogens in heterogeneous landscapes. This work sets the stage for further work on the effect and sustainability of agricultural practices on the regulation of crop epidemics in agroecosystems. Finally, by performing a meta-analysis, we bring out a strong relation between pathogen trophic type and latent period, suggesting that different trophic types of pathogens will respond differently to decreasing fertilization scenarios

L'objectif de cette étude était de mieux comprendre les relations entre les infections parasitaires, les réponses au stress physiologique et la condition corporelle des poissons. Nous avons pêché des crapets-soleil (Lepomis gibbosus) infectés naturellement par des douves et ténias (Apophallus sp., Uvulifer sp. et Proteocephalus ambloplitis) du lac Cromwell dans la région laurentienne du Québec et nous les avons soumis à différents traitements de stress aigu en laboratoire. Les niveaux de cortisol dans le plasma ont été mesurés à l’aide de la radio-immunoanalyse (RIA) et l’indice de condition de Fulton K ont été calculés pour chaque individu. Les individus avec une densité plus élevée d’Apophallus sp. et Uvulifer sp. présentaient une meilleure condition corporelle, tandis que ceux qui étaient plus fortement infectés par P.ambloplitis en avaient une plus pauvre. Les réponses au cortisol à la suite d’un stress aigu différaient d’un traitement à l’autre : les poissons ayant reçu le traitement d’un stress aigu unique présentaient des réponses au cortisol plasmatique significativement plus élevées, alors que tous les autres traitements montraient des niveaux de cortisol plus faibles. Cependant, ces différences de taux de cortisol n’étaient pas significativement liées à la densité parasitaire ou à la condition corporelle. Ces résultats suggèrent que, bien que la charge parasitaire influence la condition corporelle, elle ne semble pas affecter les réponses de cortisol causées par le stress. L’absence de relations significatives pourrait être liée à la présence réduite de certains phénotypes dans l’échantillon, ce qui pourrait révéler des tendances écologiques notables sur le cycle de vie des parasites. / The objective of this study was to better understand the relationships among parasite infection, physiological stress responses and the body condition of fish. We collected pumpkinseed sunfish (Lepomis gibbosus) naturally infected with helminthic flukes and tapeworms (Apophallus sp., Uvulifer sp., and Proteocephalus ambloplitis) from Lake Cromwell in the Quebec Laurentian region and subjected them to different stress treatments in the laboratory. Plasma cortisol levels were measured using radioimmunoassay (RIA), and Fulton's condition index K was calculated for each individual. Individuals with higher densities of Apophallus sp. and Uvulifer sp. had better body condition, while those more heavily infected with P. ambloplitis were in poorer condition. Cortisol responses following acute stress differed across treatments: fish that received the single acute stress treatment showed significantly higher plasma cortisol responses, whereas all other treatments showed lower cortisol levels. However, these differences in cortisol were not significantly related to parasite density or body condition. These results suggest that while parasite load influences body condition, it does not appear to directly affect stress-induced cortisol responses. The lack of significant relationships might be linked to the reduced presence of certain phenotypes in the sample, which may reveal important ecological trends on the parasite life cycle.

Thesis (MScAgric)--Stellenbosch University, 2012. / ENGLISH ABSTRACT: The grain chinch bug, Macchiademus diplopterus, is an endemic pest of cultivated grain crops and wild grasses in the south-western Cape region of South Africa. In early summer when host plants dry out, adult grain chinch bugs aggregate in large numbers in shelter sites in surrounding areas and enter into aestivation. These shelter sites sometimes include the stalk or calyx ends of fruit, and shelter-seeking bugs can also contaminate export fruit cartons, consequently posing a phytosanitary/quarantine risk to importing countries. Presently, there are no feasible pre- or post-harvest control measures to manage this quarantine risk. The aggregating behaviour of grain chinch bugs suggests the involvement of pheromones. Therefore, investigating the chemical ecology of grain chinch bugs for potential use in control measures is the focus of the first research chapter of this study. Gas chromatography-mass spectrometry (GC-MS) was used to identify headspace volatiles collected from aggregating bugs. Olfactometer bioassays were conducted to assess the attractiveness of each gender to separate sexes, individual compounds and a mixture of the compounds as a formulated lure. The lure was tested in field trapping trials with delta and bucket traps. In the bioassays with the live insects the response of each gender to live females was greater than the responses of each gender to live males, suggesting that females may disseminate the pheromones more efficiently than males. The following eight volatile compounds were indentified from the GC-MS analysis: hexanal, (E)-2-hexenal, (E)-2-hexenol, (E)-2-hexenyl acetate, (E)-2-octenal, (E)-2-octenol, (E)-2-octenyl acetate and tridecane. In the bioassays with individual compounds, three of these eight compounds, hexanal, (E)-2-hexenal, and tridecane, elicited attraction of both females and males. The formulated lure was attractive to both males and females in the laboratory bioassay, but this attraction was not evident in the field. In the field, there was only one occasion when a significantly higher number of bugs were caught in baited traps compared to unbaited traps. Trap catches were very low compared to the actual level of infestation in the field which was evident from corrugated cardboard bands tied around tree trunks which contained many sheltering bugs. The low trap catches seen in the field were partly due to competition between the synthetic pheromone lure and the natural pheromones emitted by aggregating live insects. Also, the characteristic shelter-seeking behaviour of grain chinch bugs influenced trap catches, as more bugs were found in places that provide shelter, like cardboard bands and walls of the delta traps. This behavior of aestivating bugs could be used to the advantage of trapping bugs by integrating sheltering sites into traps in future trials. Also, the lure needs to be improved for optimum efficiency in the field. The second research chapter also addresses the quarantine risk posed by grain chinch bugs, by investigating the thermal biology of bugs to ultimately facilitate the development of effective post-harvest treatments. Critical thermal minimum and maximum temperatures (CTmin and CTmax) of both active and aestivating bugs were subjected to critical thermal limits analysis. The CTmin and CTmax of aestivating bugs were not affected by gender (p > 0.05). There was a decrease in CTmin from the active period into aestivation for both males (2.8°C to 1.0°C (± 0.1)) and females (2.1°C to 0.6°C (± 0.1)). Also, for CTmax there was an increase in tolerance from the active period into the aestivation period for both males (49.9°C to 51.0°C (± 0.1)) and females (49.9°C to 51.5°C (± 0.1)). To determine the plasticity of grain chinch bug thermal tolerance, aestivating bugs at 27 weeks into aestivation, were acclimated at different temperatures and photoperiods [18°C (10L:14D) and 26°C (16L:8D)] for a period of seven days. Both low (18°C) and high (26°C) acclimation temperatures and photoperiods increased CTmin of aestivating grain chinch bugs at 14 weeks from 0.8°C to -1.2°C and -0.1°C (± 0.1) respectively. However, CTmax was not altered by acclimation temperatures (p > 0.82). Field temperatures at collection sites were recorded to compare to grain chinch bugs thermal tolerance levels exhibited in the laboratory. These results, as well as the effects of acclimation treatments on the CTmin of bugs, have implications for post-harvest treatments, and understanding the quarantine risk posed to importing countries. The information generated from this study can be used to further advance the development of both effective pre-harvest and post-harvest control measures to reduce grain chinch bug quarantine risk. / AFRIKAANSE OPSOMMING: Die graanstinkluis, Macchiademus diplopterus, is 'n endemiese plaag van aangeplante graangewasse en wilde grasse in die Suidwes Kaap-provinsie van Suid-Afrika. In die vroeë somer wanneer gasheerplante uitdroog, soek groot getalle volwasse graanstinkluise skuiling in die omliggende gebiede en gaan in ʼn somerrusperiode. Hierdie skuilplekke sluit soms die stam of kelk eindes van vrugte in en graanstinkluise kan ook uitvoer-vrugte kartonne kontamineer. Gevolglik word lande wat vrugte uit Suid-Afrika invoer, aan die fitosanitêre kwarantynrisiko van stinkluisbesmetting blootgestel. Tans is daar nie haalbare voor- of na-oes beheermaatreëls om hierdie kwarantyn risiko te bestuur nie. Die aggregasiegedrag van graanstinkluise dui op die betrokkenheid van ʼn feromoon. ‘n Ondersoek van die chemiese ekologie van die graanstinkluis vir moontlike gebruik in beheermaatreëls is die fokus van die eerste gedeelte van hierdie studie. Gaschromatografie-massaspektrometrie (GC-MS) is gebruik om die vlugtige organiese verbindings in die bodamp van die saamgetrosde stinkluise te identifiseer. Olfaktometriese biotoetse is uitgevoer om die aantreklikheid van die insekte vir die teenoorgestelde geslag te bepaal, asook van die individuele verbindings en 'n mengsel van die verbindings as 'n geformuleerde lokmiddel in lokvalle. Die lokmiddel is getoets in veldproewe met deltatipe en emmertipe lokvalle. In die olfaktometriese biotoetse met die lewende insekte is die reaksie van beide geslagte teenoor lewende wyfies groter as die reaksie van die geslagte teenoor mannetjies, wat daarop dui dat wyfies die feromoon meer doeltreffend as mannetjies versprei. Die volgende agt verbindings is geïdentifiseer met behulp van GC-MS-analise: heksanaal, (E)-2-heksenaal, (E)-2-heksenol, (E)-2-heksenielasetaat, (E)-2-oktenaal, (E)-2-oktenol, (E)-2-oktenielasetaat en tridekaan. In die biotoetse met individuele verbindings het drie van die agt verbindings, hexanal, (E)-2-hexenal, en tridecane, lokaktiwiteit vir beide geslagte getoon. Die geformuleerde lokmiddel was aantreklik vir beide geslagte in laboratorium toetse, maar soortgelyke lok is nie in die veld gevind nie, waar daar net een keer 'n aansienlike groter getal graanstinkluise met lokmiddel gevang is in vergelyking met lokvalle sonder lokmiddel. Die getal graanstinkluise in lokvalle was baie laag in vergelyking met die werklike vlak van besmetting in die veld, wat duidelik geblyk het uit die getalle graanstinkluise wat skuiling gesoek het in die geriffelde karton bande wat om boomstamme vasgemaak was. Die lae lokvalvangste in die veld was deels te wyte aan die kompetisie tussen sintetiese feromoon en die natuurlike feromoon van saamgetrosde insekte. Die kenmerkende aggregasiegedrag van graanstinkluise het lokvalvangste beïnvloed, aangesien meer stinkluise gevind is in plekke wat skuiling bied, soos die kartonbande en die binnekant van die delta-lokvalle. Hierdie skuilings van graanstinkluise kan in toekomstige proewe uitgebuit word deur vir meer skuilplek in lokvalle voorsiening te maak. Die formulering en die aanbieding van die lokmiddle moet ook verbeter word vir 'n optimale doeltreffendheid in die veld. In die tweede hoofstuk word die kwarantynrisiko van die graanstinkluis aangespreek deur die ondersoek van die termiese biologie van stinkluise om uiteindelik die ontwikkeling van doeltreffende na-oes behandelings te fasiliteer. Kritiese termiese minimum en maksimum temperature (CTmin en CTmax) van beide aktiewe en rustende graanstinkluise is bepaal deur analise van die kritiese termiese beperkings van die insek. Die CTmin en CTmax van rustende graanstinkluise is nie geraak deur geslag nie (p > 0.05). Daar was 'n afname in CTmin van die aktiewe tydperk tot in rus, vir beide manlike (2.8°C tot 1.0°C (± 0.1)) en vroulike insekte (2.1°C tot 0.6°C (± 0.1)). Ook vir die CTmax was daar 'n verbetering in toleransie vanaf die aktiewe tydperk tot in die rusperiode vir beide manlike (49.9°C tot 51.0°C (± 0.1)) en vroulike insekte (49.9°C tot 51.5°C (± 0.1)). Om die aanpasbaarheid van die termiese toleransie van die graanstinkluis te bepaal, is graanstinkluise 27 weke na aanvang van die rusperiode geakklimatiseer by verskillende temperature en fotoperiodes [18°C (10L: 14D) en 26°C (16L: 8D)] vir 'n tydperk van sewe dae. Beide lae (18°C) en hoë (26°C) akklimatiseringstemperature en fotoperiodes het onderskeidelik die CTmin van rustende graanstinkluise op 14 weke verhoog van 0.8°C tot -1.2°C en -0.1°C (± 0.1). Daar is egter geen effek op CTmax deur akklimasie temperature nie (p > 0.82). Veldtemperature is ook bepaal om te vergelyk met graanstinkluis termiese toleransie vlakke wat in die laboratorium bepaal is. Hierdie resultate, sowel as die gevolge van die akklimasie behandelings op die CTmin van graanstinkluise, het implikasies vir na-oes behandelings, en begrip van die kwarantyngevaar wat dit inhou vir vrugte-invoerlande. Die inligting wat uit hierdie studie voortvloei, kan gebruik word om die ontwikkeling van beide effektiewe voor-oes en na-oes beheermaatreëls te bevorder en om die kwarantynrisiko wat graanstinkluise inhou, te verminder.

Natural cycles of environmental variability and long-term deoxygenation in the ocean impose oxygen deficiency (hypoxia) on marine communities. My research exploits a naturally occurring hypoxia cycle in Saanich Inlet, British Columbia, Canada where I combined spatial surveys with remotely operated vehicles, ecological time-series from the subsea cabled observatory VENUS, and lab-based respirometry experiments to examine the influence of seasonally variable oxygen conditions on epibenthic communities. In situ oxygen thresholds established for dozens of fish and invertebrate species in this system show they naturally occur in lower oxygen levels than what general lethal and sublethal thresholds would predict. Expansion of hypoxic waters induced a loss of community structure which was previously characterized by disjunct distributions among species. Communities in variable hypoxia also have scale-dependent structure across a range of time scales but are primarily synchronized to a seasonal oscillation between two phases. Time-series revealed timing of diurnal movement in the slender sole Lyopsetta exilis and reproductive behavior of squat lobster Munida quadrispina in the hypoxia cycle. Hypoxia-induced mortality of sessile species slowed the rate of community recovery after deoxygenation. The 10-year oxygen time-series from VENUS, revealed a significant increase in the annual low-oxygen period in Saanich Inlet and that deoxygenation has occurred in this system since 2006. Differences in the critical oxygen thresholds (O2crit) and standard metabolic rates of key species (spot prawn Pandalus platyceros, slender sole, and squat lobster) determined the lowest in situ oxygen at which populations occurred and explained disproportionate shifts in distributions and community respiration. Finally, a meta-analysis on global O2crit reported for crustaceans showed that hypoxia tolerance differs among major ocean basins. Long-term trends of deoxygenation suggest a future regime shift may occur when the duration at which a system remains below critical oxygen levels exceeds the time needed for communities to recover. Species-specific traits will determine the critical threshold and the nature of the community response in systems influenced by variable states of oxygen deficiency. However, oceanographic and evolutionary history provides context when determining the regional response of benthic communities influenced by rapidly changing environments. / Graduate / 0329 / 0416 / 0433 / jwfchu@gmail.com

[Truncated abstract. Please see the pdf format for the complete text. Also, formulae and special characters can only be approximated here. Please see the pdf version for an accurate reproduction.] This thesis examines the water use, ecophysiology and hydraulic architecture of Eucalyptus marginata (jarrah) growing on bauxite mine rehabilitation sites in the jarrah forest of south-western Australia. The principal objective was to characterise the key environment and plant-based influences on tree water use, and to better understand the dynamics of water use over a range of spatial and temporal scales in this drought-prone ecosystem. A novel sap flow measurement system (based on the use of the heat pulse method) was developed so that a large number of trees could be monitored concurrently in the field. A validation experiment using potted jarrah saplings showed that rates of sap flow (transpiration) obtained using this system agreed with those obtained gravimetrically. Notably, diurnal patterns of transpiration were measured accurately and with precision using the newly developed heat ratio method. Field studies showed that water stress and water use by jarrah saplings on rehabilitation sites were strongly seasonal: being greatest in summer when it was warm and dry, and least in winter when it was cool and wet. At different times, water use was influenced by soil water availability, vapour pressure deficit (VPD) and plant hydraulic conductance. In some areas, there was evidence of a rapid decline in transpiration in response to dry soil conditions. At the end of summer, most saplings on rehabilitation sites were not water stressed, whereas water status in the forest was poor for small saplings but improved with increasing size. It has been recognised that mature jarrah trees avoid drought by having deep root systems, however, it appears that saplings on rehabilitation sites may have not yet developed functional deep roots, and as such, they may be heavily reliant on moisture stored in surface soil horizons. Simple predictive models of tree water use revealed that stand water use was 74 % of annual rainfall at a high density (leaf area index, LAI = 3.1), high rainfall (1200 mm yr-1) site, and 12 % of rainfall at a low density (LAI = 0.4), low rainfall (600 mm yr-1) site, and that water use increased with stand growth. A controlled field experiment confirmed that: (1) sapling transpiration was restricted as root-zone water availability declined, irrespective of VPD; (2) transpiration was correlated with VPD when water was abundant; and (3) transpiration was limited by soil-to-leaf hydraulic conductance when water was abundant and VPD was high (> 2 kPa). Specifically, transpiration was regulated by stomatal conductance. Large stomatal apertures could sustain high transpiration rates, but stomata were sensitive to hydraulic perturbations caused by soil water deficits and/or high evaporative demand. No other physiological mechanisms conferred immediate resistance to drought. Empirical observations were agreeably linked with a current theory suggesting that stomata regulate transpiration and plant water potential in order to prevent hydraulic dysfunction following a reduction in soil-to-leaf hydraulic conductance. Moreover, it was clear that plant hydraulic capacity determined the pattern and extent of stomatal regulation. Differences in hydraulic capacity across a gradient in water availability were a reflection of differences in root-to-leaf hydraulic conductance, and were possibly related to differences in xylem structure. Saplings on rehabilitation sites had greater hydraulic conductance (by 50 %) and greater leaf-specific rates of transpiration at the high rainfall site (1.5 kg m-2 day1) than at the low rainfall site (0.8 kg m-2 day1) under near optimal conditions. Also, rehabilitation-grown saplings had significantly greater leaf area, leaf area to sapwood area ratios and hydraulic conductance (by 30-50 %) compared to forest-grown saplings, a strong indication that soils in rehabilitation sites contained more water than soils in the forest. Results suggested that: (1) the hydraulic structure and function of saplings growing under the same climatic conditions was determined by soil water availability; (2) drought reduced stomatal conductance and transpiration by reducing whole-tree hydraulic conductance; and (3) saplings growing on open rehabilitation sites utilised more abundant water, light and nutrients than saplings growing in the forest understorey. These findings support a paradigm that trees evolve hydraulic equipment and physiological characteristics suited to the most efficient use of water from a particular spatial and temporal niche in the soil environment.

When considering the large amount of work done on dune ecology, and that a number of the classical ecological theories originate from work on dunes, it is apparent that there remains a need for physiological and mechanistic explanations of dune plant phenomena. This thesis demonstrated that in the extreme coastal environment dune plants must survive both high rates of burial (disturbance), and low nutrient availability (stress). The ability of four species to respond to these two factors corresponded with their position in a vegetation gradient on the dunes. A low stem tissue density was shown to enhance the potential stem elongation rate of buried plants, but reduced the maximum height to which a plant could grow. Such a tradeoff implies that tall light-competitive plants are able to survive only in stable areas, while burial responsive mobile-dune plants are limited to areas of low vegetation height. This stem tissue density tradeoff was suggested as the mechanism determining the zonation that species show within the dune vegetation gradient present at various sites in South Africa. Finally, detailed investigations of dune plant ecophysiology found that: 1) The resources used in the response to burial derive from external sources of carbon and nitrogen, as well as simple physiological and physical mechanisms of resource allocation. 2) The leaves of dune plants were found to be operating at one extreme of the photosynthetic continuum; viz efficient use of leaf nitrogen at the expense of water loss. 3) Contrary to other ecosystems, the environmental characteristics of dunes may allow plants to occupy a high disturbance, high stress niche, through the maintenance of lowered competition. 4) At least two mobile-dune species form steep dunes, and are able to optimise growth, on steeper dunes, such that they have to grow less in response to burial than plants that form more shallow dunes. In this thesis, it was shown that the link between the carbon and nitrogen economies of dune plants was pivotal in determining species distributions and survival under extreme environmental conditions. As vast areas of the world’s surface are covered by sand dunes these observations are not just of passing interest.

Les communautés végétales constituent des systèmes complexes au sein desquels de nombreuses espèces, pouvant présenter une large variété de traits fonctionnels, interagissent entre elles et avec leur environnement. En raison de la quantité et de la diversité de ces interactions les mécanismes qui gouvernent les dynamiques des ces communautés sont encore mal connus. Les approches basées sur la modélisation permettent de relier de manière mécaniste les processus gouvernant les dynamiques des individus ou des populations aux dynamiques des communautés qu'ils forment. L'objectif de cette thèse était de développer de telles approches et de les mettre en oeuvre pour étudier les mécanismes sous-jacents aux dynamiques des communautés. Nous avons ainsi développés deux approches de modélisation. La première s'appuie sur un cadre de modélisation stochastique permettant de relier les dynamiques de populations aux dynamiques des communautés en tenant compte des interactions intra- et interspécifiques et de l'impact des variations environnementale et démographique. Cette approche peut-être aisément appliquée à des systèmes réels et permet de caractériser les populations végétales à l'aide d'un petit nombre de paramètres démographiques. Cependant nos travaux suggèrent qu'il n'existe pas de relation simple entre ces paramètres et les traits fonctionnels des espèces, qui gouvernent pourtant leur réponse aux facteurs externes. La seconde approche a été développée pour dépasser cette limite et s'appuie sur le modèle individu-centré Nemossos qui représente de manière explicite le lien entre le fonctionnement des individus et les dynamiques de la communauté qu'ils forment. Afin d'assurer un grand potentiel d'application à Nemossos, nous avons apportés une grande attention au compromis entre réalisme et coût de paramétrisation. Nemossos a ainsi pu être entièrement paramétré à partir de valeur de traits issues de la littérature , son réalisme a été démontré, et il a été utilisé pour mener des expériences de simulations numériques sur l'importance de la variabilité temporelle des conditions environnementales pour la coexistence d'espèces fonctionnellement différentes. La complémentarité des deux approches nous a permis de proposer des éléments de réponse à divers questions fondamentales de l'écologie des communautés incluant le rôle de la compétition dans les dynamiques des communautés, l'effet du filtrage environnementale sur leur composition fonctionnel ou encore les mécanismes favorisant la coexistence des espèces végétales. Ici ces approches ont été utilisées séparément mais leur couplage peut offrir des perspectives intéressantes telles que l'étude du lien entre le fonctionnement des plantes et les dynamiques des populations. Par ailleurs chacune des approches peut être utilisée dans une grande variété d'expériences de simulation susceptible d'améliorer notre compréhension des mécanismes gouvernant les communautés végétales. / Plant communities are complex systems in which multiple species differing by their functional attributes interact with their environment and with each other. Because of the number and the diversity of these interactions the mechanisms that drive the dynamics of theses communities are still poorly understood. Modelling approaches enable to link in a mechanistic fashion the process driving individual plant or population dynamics to the resulting community dynamics. This PhD thesis aims at developing such approaches and to use them to investigate the mechanisms underlying community dynamics. We therefore developed two modelling approaches. The first one is based on a stochastic modelling framework allowing to link the population dynamics to the community dynamics whilst taking account of intra- and interspecific interactions as well as environmental and demographic variations. This approach is easily applicable to real systems and enables to describe the properties of plant population through a small number of demographic parameters. However our work suggests that there is no simple relationship between these parameters and plant functional traits, while they are known to drive their response to extrinsic factors. The second approach has been developed to overcome this limitation and rely on the individual-based model Nemossos that explicitly describes the link between plant functioning and community dynamics. In order to ensure that Nemossos has a large application potential, a strong emphasis has been placed on the tradeoff between realism and parametrization cost. Nemossos has then been successfully parameterized from trait values found in the literature, its realism has been demonstrated and it has been used to investigate the importance of temporal environmental variability for the coexistence of functionally differing species. The complementarity of the two approaches allows us to explore various fundamental questions of community ecology including the impact of competitive interactions on community dynamics, the effect of environmental filtering on their functional composition, or the mechanisms favoring the coexistence of plant species. In this work, the two approaches have been used separately but their coupling might offer interesting perspectives such as the investigation of the relationships between plant functioning and population dynamics. Moreover each of the approaches might be used to run various simulation experiments likely to improve our understanding of mechanisms underlying community dynamics.

Phloeomyzus passerinii est un important ravageur des peupleraies en Europe. Ce puceron se développe sur les troncs de peuplier, avec un mode nutrition mal connu, et présente des performances variables selon les génotypes de peuplier. Dans une optique de gestion de cet insecte, il était nécessaire de clarifier la nature de ses interactions trophiques avec son hôte. En complément, nous avons étudié comment la résistance de l’hôte et des facteurs environnementaux, comme la fertilisation et une contrainte hydrique, pouvaient affecter ces interactions. Des approches histologiques et biochimiques ont permis de mettre en évidence l’induction par l’insecte d’un tissu organise dans l’écorce d’un génotype sensible (I-214), qualifiable de pseudo-galle, où les composés phénoliques solubles disparaissent mais ou des acides aminés s’accumulent. Des approches complémentaires ont montré que le comportement de nutrition du puceron était optimisé sur ces tissus modifiés, et son développement larvaire amélioré. Concernant les mécanismes de résistance, dans un génotype très résistant (Brenta), la formation de la pseudogalle était totalement inhibée, suite à une lignification intense et étendue des tissus, empêchant l’installation du puceron. Dans un génotype de résistance intermédiaire (I-45/51), la formation était seulement partiellement inhibée, diminuant les performances démographiques et comportementales de l’insecte, et la capacité du tissu modifié à accumuler des acides aminés. Pour étudier l’impact environnemental, nous avons considéré les effets de trois niveaux de fertilisation et de trois niveaux d’irrigation du sol. La fertilisation n’a pas modifié les performances du puceron, probablement à cause d’une accumulation d’acides aminés par la pseudogalle d’autant plus forte que la fertilisation était faible. Le déficit hydrique a affecté les interactions, notamment au travers d’un effet génotype dépendant, favorisant le développement de l’insecte lors d’une contrainte intermédiaire chez le génotype résistant seulement et affectant négativement le développement chez les génotypes sensible et résistant lors d’une contrainte élevée. / Phloeomyzus passerinii is an important pest of cultivated poplar stands in Europe. It develops onpoplar trunks, thanks to an undefined feeding mode, and exhibits variable performances depending on poplargenotypes. To develop efficient management strategies, we have investigated the trophic interactions betweenthis pest and its host. In addition, we have studied how host resistance and environmental factors, like fertilizationand water deficit, could affect these interactions. Histological and biochemical approaches highlighted theinduction by the aphid of an organized tissue in the bark of a susceptible poplar genotype (I-214), considered as apseudogall, where soluble phenolic compounds disappear but amino acids accumulate. Behavioral andphysiological approaches showed that the aphid nutrition behavior is optimized on these modified tissues, andthat its nymphal development is improved. Regarding resistance mechanisms, on a highly resistant genotype(Brenta), pseudogall formation was totally inhibited, due to an intense and extended lignification, preventing aphidsettlement. On a moderately resistant genotype (I-45/51), pseudogall formation was only partially inhibited,reducing demographic and behavioral performances of the insect, and the ability of the pseudogall to accumulateamino acids. To study environmental impacts, we considered the effects of three soil fertilization levels and threeirrigation levels. Fertilization did not modify aphid performances, probably due to an increase in amino acidsaccumulation by the pseudogall when fertilization decreased. Water deficit affected the interactions, through agenotype dependant effect, favoring insect development under an intermediate deficit on the resistant genotypeonly, and negatively affecting the development on both susceptible and resistant genotypes during a severe waterdeficit.

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