Дисертації з теми "Ecosystem structure and functioning"

Climate change is projected to increase the frequency and severity of extreme events, adding to the plethora of existing pressures that streams and rivers already face. Compound events such as drought may comprise numerous stressors that occur in concert to elicit ecological change. However the causal mechanisms of such impacts remain unknown, and research attempting to disentangle impacts of compound events, or link effects across levels of ecological organisation, remains in its infancy. This research investigates impacts of key drought stressors –sedimentation, dewatering and warming – across multiple ecological, hierarchical levels. At the individual level, macroinvertebrates displayed differential thermal sensitivity to warming which may explain idiosyncratic ecological responses reported elsewhere, whilst sedimentation intensified predator-prey interactions. Mesocosms were effective tools for studying drought stressors independently and in combination at the community and functional level. Dewatering main effects reduced the density of a common taxon and functional feeding group biomass, whilst all three stressors sometimes interacted together in complex ways. Stressors also had quantifiable effects at the whole-system level, e.g. stream metabolism. This study provides initial findings pertaining to drought impact causative mechanisms across multiple levels of ecological complexity, highlighting the importance of an experimental approach to predict future effects of compound events.

Despite the increased prominence of ecological measurement in fresh waters within recent national regulatory and legislative instruments, their assessment is still almost exclusively based on taxonomic structure. Integrated metrics of structure and function, though widely advocated, to date have not been incorporated into these bioassessment programmes. We sought to address this, by assessing community structure (macroinvertebrate assemblage composition) and ecosystem functioning (decomposition, primary production, and herbivory rates), in a series of replicated field experiments, at watercress farms on the headwaters of chalk streams, in southern England. The outfalls from watercress farms are typically of the highest chemical quality, however surveys have revealed long-term (30 years) impacts on key macroinvertebrate taxa, in particular the freshwater shrimp Gammarus pulex (L.), yet the ecosystem-level consequences remain unknown. Initial studies were at Europe’s largest watercress farm at St Mary Bourne, Hampshire, during the bioremediation of its complex wastewaters and changes to farm management practices. These widened to include larger scale spatiotemporal studies at other watercress farms. Detrimental ecological impacts at the start of the study were detected by the structural and functioning measures, but they did not respond to bioremediation. However, an increase in G. pulex abundance was detected, providing evidence of recovery in response to altered practices, which may be attributable to the cessation of chlorine use. The detrimental impacts were unique to the St Mary Bourne watercress farm and were not consistent across the other watercress farms in the study. Our results demonstrate the importance of integrated metrics of both ecosystem structure and functioning, to derive a more comprehensive view of aquatic ecosystems and highlights the difficulties associated with extrapolating from laboratory studies in response to stressors.

Many freshwater ecosystems sustain several invasive species. Here I examine multiple invasions in two highly invaded and well catalogued catchments; Lake Naivasha, Kenya and River Thames, England. New metrics, derived from stable isotope analysis, are used to provide measures of trophic diversity and to examine dietary interactions among species. I test the hypothesis that functionally similar sympatric species will occupy a smaller niche than their allopatric counterparts. Additionally, I quantify the impact of multiple invasive species on ecosystem structure and functioning in order to address the question; do interactions among species amplify or mitigate one another's impact? In Lake Naivasha, the stable isotope metrics revealed serial replacement of invasive species due to dietary interactions. Invasive red swamp crayfish were eventually excluded from the lake due to niche restriction in the presence of a more recent invader, the common carp. Now, the crayfish have migrated into the catchment where they overlap with a species of native river crab. Here, I found a novel mechanism of invasion, whereby the crayfish restricted their niche at the invasion front in order to reduce competition with crabs. Crayfish also caused significant changes in invertebrate community structure and increased decomposition rates, which indirectly resulted in displacement of the crabs. In the Thames catchment, I catalogue the non-indigenous species and show how invasion rates have increased significantly since 1800 due to globalisation. Using the four species of invasive crayfish present (red swamp, signal, Turkish and virile), I demonstrate their extensive diet plasticity using novel measures of niche width and individual specialisation based on stable isotope data. Interactions among the crayfish were examined and this revealed that each species has varying and independent impacts on invertebrate community structure, algal standing stock and decomposition rates. Hence, interactions among invaders are not expected to amplify or mitigate one another's impact and instead, the combined impact will be the sum of their allopatric impacts.

Salt marsh ecosystems are recognized as highly productive, diverse systems which provide key services to society, but are facing an increasing number of multiple human pressures resulting in global losses of these ecosystems. I aimed to assess the effects of human pressures on salt marsh status and functioning, focusing on the perennial Spartina spp. grasses across the Northern Adriatic Sea, using a combination of field observational studies, manipulation of pressures on salt marshes, and wave mesocosm experiments to measure erosion resistance. Major findings include: 1. Macrobenthos diversity and abundance in Spartina spp. patches were influenced by sediment and nutrient variables, and indirectly influenced by Spartina spp. which modified the sdiments via organic enrichment; 2. Spartina spp. below-ground biomass decreased resistance to erosion, with a more pronounced effect in sandy compared to silty sediments; 3. A heat wave that occurred in 2015 synergistically interacted with high nutrient loads to change the vegetation composition in experimentally fertilized plots, with a rapid shift from Spartina spp. grasses to Salicornia spp. succulents, and the heat wave triggered changes in sediment properties that reduced the erosion resistance of salt marsh sediments; 4. After exposure to different inundation levels through a salt marsh transplantation experiment, plant survival (indicated by % live shoot biomass) and % silt were the most significant predictors of erosion resistance. Overall, biomass and sediment properties were the main factors influencing lateral resistance to erosion in our experiments. The research in this thesis fills important knowledge gaps regarding the status of salt marshes and their functioning across lagoons of the Northern Adriatic Sea. These results help to consolidate the evidence of the important role of salt marsh vegetation in coastal protection, and demonstrate the conditions under which erosion resistance in salt marshes is most effective.

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O estudo dos efeitos que a diversidade de esp?cies pode causar nos processos ecossist?micos tem crescido vertiginosamente nas ?ltimas duas d?cadas. Diversos trabalhos experimentais realizados no mundo todo t?m demonstrado que uma maior diversidade de plantas contribui para o aumento da produtividade de ecossistemas terrestres. Al?m disso, esse efeito pode influenciar processos em diversos n?veis tr?ficos, contribuindo assim para a estabilidade dos processos ecossist?micos a longo prazo. Paralelamente com os estudos do efeito da diversidade, muita aten??o tem sido dada para desvendar o papel das caracter?sticas funcionais das esp?cies no funcionamento dos ecossistemas. Isto porque as caracter?sticas funcionais das esp?cies t?m se mostrado importantes "pe?as" no entendimento dos efeitos que esp?cies individuais podem exercer nos ecossistemas e suas respostas ao ambiente. Nesta tese de doutorado eu explorei algumas lacunas de conhecimento dentro dessa ?rea em crescente desenvolvimento conhecida na literatura ecol?gica como "biodiversidade e funcionamento dos ecossistemas". No primeiro cap?tulo, eu busquei evid?ncias para mecanismos que podem explicar a rela??o positiva entre diversidade e funcionamento com foco em cinco mecanismos relacionados ?s intera??es entre plantas, tendo como par?metro de funcionamento a produtividade prim?ria. No segundo cap?tulo, eu utilizei t?cnicas para a estimativa de padr?es de diversidade em escalas biogeogr?ficas e bases de dados de sat?lites com longa dura??o para desvendar se a biodiversidade em escalas macroecol?gicas promove a estabilidade da produtividade dos ambientes terrestres no semi?rido brasileiro. Por fim, o objetivo do terceiro cap?tulo foi entender como a perda da cobertura vegetal origin?ria do uso da terra por comunidades tradicionais no semi?rido brasileiro influenciaria os processos de intera??es entre plantas e o papel das caracter?sticas funcionais das esp?cies nessas intera??es. Acredito que a contribui??o individual de cada cap?tulo preenche lacunas de conhecimento importantes dessa ?rea da Ecologia que ainda se encontra em expans?o.

Non-trophic interactions are significant structuring agents of ecological communities. Knowledge of how this process drives ecosystem functioning and community structure either individually, or interactively with other processes, is however, limited, particularly in shallow soft- littoral ecosystems. At a local level, such systems are dominated by allogenic engineers such as the burrowing axiid sandprawn Callichirus kraussi Stebbing, which has important effects on macro- and meiobenthic assemblages. C. kraussi is distributed across the South African coastline, from the subtropical Mozambican border to the temperate west coast borders with Namibia. Bioturbation — the principal mechanism by which C. kraussi engineers influence associated biota in sedimentary systems, also has significant effects on sediment properties, biofilms, microalgal and microbial composition. However, theory suggests that ecosystem engineering effects are contextually dependent and contingent upon processes that are temporally and spatially variable. In South Africa, variations in background nutrient levels across the coastline is significant, with the West coast being dominated strong upwelling, which increases biological productivity. Within the west coast, upwelling is also seasonally variable, being strongest in summer. In view of this natural variability in nutrient levels across the coast, seasonal variability within the west coast and the fact that the sandprawn C. kraussi dominates across these conditions, the central focus of this PhD thesis was to investigate how ecosystem engineering by sandprawns C. kraussi and nutrient levels individually or interactively influence assemblages and ecological processes in coastal soft-sediment ecosystems. The study was carried out in Langebaan Lagoon, which is a marine lagoonal system on the west coast of South Africa that is dominated by sandprawns and subjected to seasonal upwelling that is a feature of the west coast. This thesis was based on the two principal approaches, viz. a field comparative study and in situ experiments. The field observational study investigated the responses of macroand meiofaunal communities to sandprawn bioturbation impacts between upwelling and non-upwelling seasons, with the aim of understanding how upwelling nutrient pulses modify these benthic assemblages. Benthic and water column chlorophyll-a (chl-a) levels were also measured, while meiofaunal communities were investigated within sandprawn burrows (burrow-walls) and at the sediment surface. It was hypothesized that chl-a levels, and community metrics would be lower in winter (non-upwelling) but increase in summer upwelling season due to nutrient pulses. It was also hypothesized that community metrics would be negatively correlated with sandprawn density due to bioturbatory effects (sediment turnover) in winter (non-upwelling) but this relationship would become neutral or positive increased in summer, due to increased productivity offsetting negative bioturbative effects. Clear, non-intuitive and ecologically interesting outcomes emerged from the field study. Firstly, benthic chl-a concentrations appeared to be lower in summer relative to winter in 2015, although, this pattern disappeared in 2016. In contrast, water column chl-a concentrations within the lagoon channel conformed to the posed hypothesis, being consistently greater in summer relative to winter. Even though both macro- and meiofaunal assemblages differed significantly between seasons, the hypothesis that community metrics would be greater in summer relative to winter season was not overwhelmingly supported by these findings. Pearson correlation analyses revealed that sandprawn effects were generally weaker within seasons but stronger when winter and summer data were combined and investigated per year. In terms of the latter, most community metrics and benthic chl-a levels were generally negatively correlated with sandprawn abundances, but this varied seasonally and spatially. Overall, results of the comparative study suggest that increases in water column chl-a levels do not necessarily translate into increases in benthic chl-a and community metric levels. One possible reason for this is that increasing bioturbation by C. kraussi overrides nutrient enrichment effects. This conclusion though is spatially dependent, given that results of correlation analyses were site-specific. The factorial field experiment employed in this dissertation manipulated nutrients (fertilizer capsules, Plantacote N: P: K) and sandprawns (C. kraussi densities) to investigate their individual and interactive effects on benthic assemblages. I hypothesized within the context of the grazer-reversal hypothesis of Proulx and Mazumder (1998) that, responses of diversity metrics should alter from a linear decrease at the ambient nutrient level to a unimodal hump-shaped response at the intermediate nutrient level and then to a linear increase at highest nutrients. Generally, emerging patterns for meiofaunal diversity metrics and individual morphotypes were inconsistent with the prediction of the grazer-reversal model. Instead, responses were of an increasing and decreasing nature. The outcomes of this investigation, however, revealed that meiofaunal community structure at the sediment surface was significantly affected by the main effect of sites and sandprawn densities, while within burrow-walls, the interaction between sites and nutrients, but also sandprawn densities alone, significantly affected meiofaunal community structure. Overall, meiofaunal results of this investigation showed limited support for the grazer-reversal hypothesis. Although the findings of this investigation also indicated limited support for the grazer-reversal hypothesis on the macrofauna community, interactive effects of nutrient enrichment and sandprawn densities emerged to influence the macrofaunal community structure and abundances of certain individual species/taxa. Generally, macrofaunal community metrics exhibited both increasing and decreasing patterns in response to experimental treatments, however, in some instances unimodal hump-shaped patterns emerged. There was evidence of macrofaunal functional groups (i.e. suspension feeders) conforming to the hypothesis posed, but this was site-specific. Overall, I conclude that an interplay between nutrients and sandprawns does not exert strong influences on the benthic communities of Langebaan Lagoon. However, sandprawn ecosystem engineering, mainly in the form of bioturbation overrides nutrient enrichment effects in regulating benthic assemblages.

The excessive deposition of fine inorganic sediment (<2 mm) is a major pathway by which agricultural land uses exert pressure on stream ecosystems. However, less well understood are the underlying mechanisms driving threshold biotic responses and the ecological consequences of community changes to sedimentation. Reviewing the literature, I found that sedimentation can affect algal and detrital pathways, and invertebrate community composition may show abrupt shifts with increased sediment. Moreover, functional changes to communities potentially leads to simpler food webs, with altered interactions and decreased ecosystem function. After identifying these knowledge gaps, I conducted survey and experimental research using agricultural streams on the Canterbury Plains of New Zealand’s South Island. Results from my survey of 30 streams along a sedimentation gradient showed that pollution-sensitive invertebrates (% EPT; Ephemeroptera, Plecoptera, Trichoptera) demonstrated threshold responses to sediment that varied with spatial scale, and change-point analysis indicated marked declines beyond 20% fine sediment covering streambed reaches. Structural equation modeling indicated that decreased habitat availability was a key mechanism contributing to these changes. To better understand the functional consequences of altered community structure, I investigated food webs in 12 streams along the gradient. The results showed a compression of community trophic niche space, suggesting that in particular, primary consumers became trophically more equivalent. The simplification of stream food webs with increasing sediment appeared to be the result of functional changes to invertebrate communities, with fewer specialised consumers, and shifts in the availability of basal resources. Using field and laboratory experiments investigating litter breakdown and invertebrate feeding, I found that the net consequence of functionally less diverse stream communities with increased sediment was impaired ecosystem function, demonstrated by a reduction in litter breakdown rates. The reduction of detrital resource availability through burial by sediment in laboratory mesocosm experiments strongly influenced detrital consumption rates, thus leading to reduced growth and survival of detritivorous caddisflies. The survey and experimental results support my postulate that sediment deposition causes environmental stress by degrading benthic habitat and making associated food resources (e.g., periphyton and leaves) less available. Overall, my results have provided new insights into sediment impacts on stream communities and have furthered our understanding of how these changes affect the structure and functioning of stream ecosystems.

Due to growing human demands for freshwater within the last century, manmade flow alterations are now a common characteristic of rivers worldwide. Alterations to the volume and timing of flows in rivers are known to negatively impact aquatic biodiversity, biological productivity and ecosystem functions such as nutrient cycling. While previous research has focused on the effects of flow reductions and spates, there is a lack of knowledge on how high flows across longer timespans (i.e. ‘enhanced flows’) impact the structure of river communities and the integrity of ecosystem functions. The Utah Reclamation, Mitigation and Conservation Commission has expressed interest in reducing enhanced flows in a central Utah river so as to benefit aquatic habitat and native game fish. With their funding support, I collected aquatic invertebrate and ecosystem function data under natural and enhanced flow conditions throughout Sixth Water Creek and Diamond Fork River. These data were supplemented with historical invertebrate data collected by BIO-West, Incorporated. For each river segment, I tested whether flow volume and variation had relationships with the density and health of streambed invertebrate communities. I also sought to determine how these flow metrics affected leaf litter breakdown, primary production and stream metabolism (i.e. the production and respiration of organic matter). Here, I demonstrate that enhanced flows impact streambed invertebrate communities differently in each river segment, in addition to suppressing stream metabolism system-wide. While streambed communities were mostly unaffected by enhanced flows in Sixth Water Creek, density and community health exhibited negative relationships with flow metrics in Diamond Fork River. In the Lower Diamond Fork mainstem, proportions of pollution-tolerant taxa increased as peak flows increased, while streambed invertebrate density decreased as mean monthly flows increased. Moreover, enhanced flows appeared to severely impact the production of organic matter in Sixth Water Creek and Lower Diamond Fork River. This disproportionate suppression of production over respiration shifted the river towards greater reliance on out-of-stream energy sources. These results demonstrate the importance of considering spatial gradients when investigating community responses to flow alterations, and also reveal how river ecosystems are threatened with losses of in-stream energy supplies under enhanced flows.

Orientador: Felipe Wanderley Amorim
Resumo: As mudanças globais mediadas pela ação antrópica estão alterando a biodiversidade e os ecossistemas em um ritmo acelerado. Um dos principais impulsionadores dessas mudanças é a introdução de espécies exóticas em ecossistemas nativos. Entre os grupos de organismos afetados por este processo, o das plantas é reconhecido um dos mais preocupantes, uma vez que a produção primária limita o tamanho e a composição das comunidades e participa através de efeitos em cascata em interações multi-tróficas. Uma das principais relações ecológicas influenciada por esse efeito é a relação entre plantas e polinizadores, cujo papel é importante para estrutura e funcionamento das comunidades biológicas, não apenas porque as plantas fornecem recursos alimentares essenciais para muitos grupos de animais que visitam flores, mas também porque o sucesso reprodutivo da maioria das plantas com flores depende dos serviços bióticos fornecidos por estes animais. Neste contexto, a introdução de espécies de plantas exóticas invasoras pode ter impactos críticos nas interações planta-polinizador ao nível da comunidade, principalmente através da competição com espécies nativas. Como as interações planta-polinizador são cruciais para determinar a estrutura da comunidade, nesse estudo nós testamos como o crescimento rápido de uma gramínea invasora altera a composição das espécies de plantas nativas em um campo cerrado, juntamente com os impactos deste processo sobre a estrutura das interações planta-polinizador. ... (Resumo completo, clicar acesso eletrônico abaixo)
Abstract: The global change mediated by anthropic action is altering biodiversity and ecosystems in a fast pace. One major driver of these changes is the introduction of alien species in native ecosystems. Among the groups of organisms that are affected by this process, plants are recognized to be one of the most concern, since primary production limit global communities’ sizes and composition, and participate through cascade effects on multitrophic interactions. One crucial type of interaction that is influenced by this effect is the plant-pollinator relationship, which have an important role in the structure and functioning of biological communities, not only because plants provide essential food resources for many groups of animals that visit flowers, but also because the reproductive success of most flowering plants depends on the biotic services provided by animals. In this context, the introduction of invasive alien plant species may have critical impacts on plant-pollinator interactions at community level, mainly through competition with native species. Since plantpollinator interactions are determinants of community structure, here we evaluated how the rising of a fast-growing invasive alien grass species changes plant species composition of a Neotropical grassland community along with its impacts on the structure of plant-pollinator interactions. For this, we analyzed the changes in community composition and plantpollinator interactions over time, through the temporal turnover... (Complete abstract click electronic access below)
Mestre

Habitat loss and fragmentation have been identified as the main drivers of biodiversity loss. These drivers increase the proportion of habitat edges and change the configuration of landscapes. Habitat edges are known to affect ecological patterns and processes, however, is still unknown how these boundaries affect the assemblage of interactions among species within a community, and particularly its structure. Food webs depict not only the composition of the community, but also the feeding links, which represent a measure of energy flow. Therefore, they can inform about the relationships among community diversity, stability, and ecosystem functions. This thesis explores the effects of habitat edges across native vs. managed forests on the food web of a tri-trophic system comprising plants, herbivores (Lepidoptera larvae) and predators (parasitoids). Particularly, it addresses three main objectives: 1) how food webs at habitat edges are assembled from the species and interactions present in the adjoining habitats; 2) how phylogenetic diversity and the coevolutionary signal among interacting species change across a habitat edge gradient; and 3) whether the mechanisms driving community-wide consumption rates and the ecosystem service of pest control are related to structural characteristics of the food webs. The key findings of this thesis are that, despite the composition of species and interactions of native and managed habitats merging at their interface, food-web structure did not arise as a simple combination of its adjacent habitat webs, potentially due to differential responses of organisms to habitat edges. Moreover, beyond taxonomic composition, the phylogenetic diversity and signal of coevolution among interacting species also change between habitat types, even though this did not translate to changes in consumption rates. Consumption rates and their stability increased with complementarity and redundancy in resource-use among predators. This reflects how environmental changes such as habitat fragmentation can have an effect beyond composition per se, affecting the assemblage of species interactions and even potentially interfering with natural evolutionary processes. Therefore, using interaction-network approaches for determining the impacts of changes may shed light on the underlying mechanisms driving such changes, and help to develop landscape management plans that reduce negative effects on species assemblages.

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.

Floodplains are amongst the most productive and biodiverse ecosystems. The structure and functioning of floodplains is controlled by the interaction of intermittent inundation with the floodplain landscape. These interactions create highly complex and dynamic ecosystems that are difficult to study at large scales. Consequently, most research of floodplains has been conducted at small spatial and temporal scales. Inundation of floodplains can extend over many square kilometres, however, which unifies the floodplain landscape into an integrated ecosystem operating at the landscape scale. The lack of data and poor understanding of the landscape-scale structure and functioning of floodplains limits the possibility of managing floodplains sustainably as pressure for exploitation of their resources increases. This thesis quantifies the landscape-scale relationship between the frequency and patterns of inundation, the composition and structure of the landscape, and the functioning of the floodplain landscape in terms of the distribution and dynamics of plant growth vigour over an area of approximately 376,000 ha on the Lower Balonne Floodplain; highly biodiverse, semi-arid floodplain ecosystem that straddles the state border between New South Wales and Queensland approximately 500 km inland from the eastern coast of Australia. Mean annual rainfall at St.George, to the north of the study area, is approximately 400�450 mm per year, and median annual evaporation is approximately 2000 mm per year. Plants and animals on the floodplain are therefore heavily dependent upon flooding for survival. This project is based on the analysis of 13 Landsat Thematic Mapper satellite images captured over a 10-year period during which land and water resource development increased substantially. There is now concern that development activities have affected the functioning of the floodplain to the detriment of the natural environment and agricultural productivity. The impacts from these activities on the functioning of the floodplain are not yet known, however. Inundation of the Lower Balonne Floodplain was mapped using a two-part process involving a band ratio to identify deep clear water, and a change detection analysis to identify areas of shallower inundation. This analysis shows that, in contrast with most floodplains, the main flowpath of the Lower Balonne Floodplain runs along its central axis away from river channels, which flow along the floodplain�s outer edges. Inundation propagates from the centre of the floodplain out towards river channels as flood discharge volumes increase. Variations in the spatial pattern of inundated patches within the inundated extent create distinctive aquatic habitat and connectivity conditions at different flow levels. These can be described in terms of three connectivity phases: (I) Disconnected, in which isolated patches of inundation occur at low flows and river channels are hydrologically dislocated from the floodplain; (II) Interaction, where increased hydrological connectivity between inundated patches, and between the floodplain and the river channels at moderate flows, may enable significant exchange of materials, organisms and energy; and (III) Integration, in which almost the entire floodplain landscape is connected by open water during large magnitude floods. There is an abrupt transition in inundation patterns as flows increase between 60,000 ML day-1 and 65,000 ML day-1 (ARI 2 to 2.3 years) in which inundation patterns transform from being relatively disconnected into a highly integrated network of patches. These patterns may have significant consequences for the structure and functioning of the floodplain. Increases in flows across this small range may therefore mark an important ecological flow threshold on this system. Water resource development impacts have changed the relative frequency of flows on the Lower Balonne Floodplain, which will probably affect the sequence of connectivity phases over time. The most likely impact of these changes will be to create a floodplain that is drier overall than under natural flow conditions, and that has a smaller and wetter area of high inundation frequency. The relationship between inundation and the structure of the floodplain landscape was examined by comparing a landcover map showing the distribution and character of 10 landcover types to the inundation frequency maps. Landcover types were mapped from a multi-date Reference Image composite of seven images captured over a period of 10 years. The Reference Image improves landcover discrimination by at least 14% over classification of a single-date image, and has an overall accuracy between 82.5% and 85% at the landscape-scale. The Reference Image shows that the landscape of the Lower Balonne Floodplain is a highly fragmented mosaic of diverse landcover types distributed in association with inundation frequency. Stratifying the floodplain into zones of frequent and rare inundation shows that frequently inundated areas have a less fragmented but less diverse landscape structure than rarely inundated areas. Assessment of the functioning of each landcover types within the floodplain ecosystem, based on landscape pattern metric analysis, indicates that the function of landcover types also changes between inundation frequency zones. Most importantly, these changes include a transformation of the matrix landcover type, which controls the character and dynamics of the ecosystem overall, from Open Grassland to Coolibah Open Woodland in the frequently inundated zone. The landscape structure of the Lower Balonne Floodplain has been affected by development impacts, which include clearing of native vegetation, isolation of parts of the floodplain from natural inundation events by the construction of levee banks and drainage channels, and grazing impacts. Changes to the inundation regime may also affect the structure of the floodplain landscape. Over the long term, these changes are likely to create a larger area of Open Grassland and a smaller area of Coolibah Open Woodland as the zone of frequent inundation becomes smaller and wetter. To examine the functioning of the floodplain ecosystem, the inundation maps were compared to remotely sensed indexes of plant growth vigour at the landscape and landcover-type scales. The dynamics of plant growth vigour over time are influenced by factors operating at the regional, landscape and patch scales. Evaporation is the major control of growth vigour levels at the landscape scale, but each landcover type has a distinctive pattern of growth vigour dynamics that is related to its composition and location, and possibly its landscape structure. The association between the spatial distribution of plant growth vigour and inundation frequency is non-linear, with the highest growth vigour occurring where inundation occurs approximately once per year. This indicates a subsidy-stress interaction with water in which plant growth vigour is limited by soil anoxia in areas of frequent or long term inundation, and by drought stress in rarely inundated areas. A landscape-scale model of growth vigour dynamics, founded on the principles of Hierarchical Patch Dynamics and Landscape Ecology, was created from growth vigour measurements of each landcover type over time. This model was used to examine possible impacts of development activities on the functioning of the floodplain ecosystem. This model shows that the response of plant growth vigour development activities can be complex and subtle, and include a change in mean long-term growth vigour and an increased susceptibility to drought. The model also indicates that periods of high growth vigour can occur in substantially altered floodplain ecosystems. The model was also used to explore the levels of landcover change that might cause a threshold change in the functioning of the ecosystem, which may substantially alter the disturbance-response characteristics of the floodplain ecosystem. The model indicates a threshold change when the extent of Open Grassland is reduced by 30% of its extent in 1993, in which plant growth vigour response to disturbance is virtually inverted from that observed in the images. The temporal variability of plant growth vigour levels increases as the extent of Open Grassland is further reduced. This thesis makes a number of important contributions to our understanding of floodplain structure and functioning. It includes the development of new techniques suited to studying large diverse and complex landscapes at the landscape scale from satellite images, and provides quantitative data describing the links between the structure of floodplain landscapes and their functioning at the landscape scale. This work improves the understanding of floodplain ecosystems by integrating models of floodplain structure and functioning, which have been developed largely from smaller-scale studies of temperate and tropical floodplains, with landscape-scale measurements of this semi-arid system. This thesis also has implications for the Lower Balonne Floodplain by improving the level of information about this important ecosystem and providing baseline data against which the condition of the floodplain can be assessed in future.

Diversos estudos teóricos, experimentais e observacionais têm demonstrado que as relações entre a biodiversidade e as funções ecossistêmicas (BEF) são determinadas pela estrutura funcional da comunidade (ou seja, pela distribuição dos atributos das suas espécies constituintes). Isso pode ocorrer por meio de dois mecanismos mutuamente não exclusivos: (1) a hipótese de dominância (também denominada de efeito de relação de massa), na qual os processos ecossistêmicos são influenciados pela média ponderada na comunidade de um dado atributo funcional (CWM) considerado relevante; (2) a hipótese de complementaridade, na qual a maior variabilidade de um atributo funcional na comunidade (FD) é uma expressão da complementariedade de nicho, o que beneficia o desempenho dos processos ecossistêmicos. Embora ambos os mecanismos já tenham sido amplamente estudados em comunidades de plantas em pequenas escalas espaciais, análises globais considerando distintos biomas ainda são necessárias. Neste estudo, a relação entre biodiversidade e funcionamento dos ecossistemas foi avaliada com base na integração entre uma base de dados global de parcelas de vegetação (sPlot), uma base de dados de atributos de espécies de plantas (TRY) e dados do Índice de Vegetação por Diferença Normalizada (NDVI) obtidos por sensoriamento remoto. O objetivo foi verificar, simultaneamente, os efeitos de dominância e de complementaridade sobre a produção de biomassa vegetal em ecossistemas campestres em todo o mundo. Os dados sobre a estrutura funcional das comunidades (CWM e FD) foram obtidos a partir da base de dados sPLOT e TRY, utilizando para isso atributos funcionais de plantas ecologicamente relevantes. O NDVI, considerado como aproximação da produtividade da vegetação, representa uma medida do funcionamento do ecossistema e foi obtido a partir do produto MOD13Q do sensor MODIS, com resolução espacial de 250m. Para garantir que as medidas de NDVI fossem derivadas apenas de ecossistemas campestres, sem a interferência de outras fisionomias vegetais, foram descartadas as parcelas do sPlot com presença de paisagens heterogêneas no seu entorno mediante consulta a um mapa global de cobertura e uso da terra (Globcover2009). Para quantificar os efeitos independentes da dominância e da complementariedade sobre as variações no NDVI , com controle das variáveis climáticas, foi utilizada uma análise de regressão múltipla do tipo commonality. Os resultados demonstraram que o principal preditor da variação no NDVI correspondeu a um conjunto de atributos funcionais das espécies dominantes relacionados com o espectro de economia da comunidade vegetal (atributos fast-slow), indicando a prevalência da hipótese de dominância (R2 ajustado = 0,65). Os efeitos evidentes da dominância e os efeitos potenciais da complementariedade são discutidos no contexto da sua relação com os fatores abióticos, sendo que a precipitação pluviométrica, em particular, parece ter maior influência tanto sobre a composição de atributos quanto sobre a produtividade. Apesar de algumas limitações metodológicas, a abordagem inovadora utilizada neste trabalho pode ajudar a esclarecer as relações entre biodiversidade e funções ecossistêmicas em escala global, dentro de uma perspectiva integradora e baseada em dados.
Theoretical, experimental and observational studies show that biodiversity ecosystem functioning (BEF) relationships are determined by functional community structure (i.e. trait distributions in a community) through two mutually non-exclusive mechanisms: (1) The dominance hypothesis (a.k.a. mass ratio effect) links ecosystem processes to the community weighted mean (CWM) of a relevant effect trait. (2) The complementarity hypothesis states that higher variability of a trait value within a community (FD) reflects niche complementarity enhancing ecosystem processes. While both mechanisms have been extensively studied in plant communities at small spatial scales, there is a need for global analyses across biomes. Here, a data driven approach to the BEF question is presented integrating a global vegetation plot database with a trait database and remotely sensed NDVI. The objective of this study was to simultaneously evaluate dominance and complementarity effects in grassland systems worldwide. Data on functional community structure (CWM and FD) were obtained from the global vegetation plot database sPlot in combination with the plant trait database TRY using 18 ecologically relevant plant traits. Ecosystem functioning at the selected sPlot sites (n = 2941) was measured as NDVI at a spatial resolution of 250m using the MODIS product MOD13Q (annual peak NDVI being a proxy of productivity). The landcover map Globcover2009 was used for characterization of landscape heterogeneity and landcover at each site, and plots in heterogeneous non-grassland pixels were discarded. Multiple regression commonality analysis was used to disentangle the contributions of complementarity and dominance effects to the variation in NDVI, while controlling for climate variables (adjusted R2 = 0.65). The results show that a plant community economics spectrum referring to the “fast-slow traits” of the dominant species in the community was the strongest predictor of the NDVI values in the grassland systems (dominance effect). Both, evident dominance and potential complementarity effects are discussed against the background of their interplay with abiotic factors and it is noted that especially precipitation seems to drive trait composition and productivity. Despite methodological shortcomings, the novel approach presented in this paper is considered a step towards a more integrative data-driven BEF debate at the global scale

Les écosystèmes procurent de nombreux services essentiels aux sociétés humaines à travers les effets positifs de la biodiversité des communautés d'espèces. Par conséquent, identifier le rôle des organismes vivants et les facteurs influençant la diversité de leurs fonctions (ou diversité fonctionnelle), est indispensable pour prédire efficacement l'évolution des écosystèmes soumis aux pressions locales et globales.Cette thèse s'articule donc autour de deux axes: (i) établir un cadre méthodologique pour décrire la structure fonctionnelle locale et régionale des communautés, et (ii) améliorer la connaissance de l'impact des poissons sur la dégradation de la matière organique.Dans un premier temps, nous avons consolidé les outils méthodologiques permettant (i) d'améliorer la fiabilité des dendrogrammes fonctionnels, (ii) l'étude comparative des principaux indices de diversité fonctionnelle à l'échelle locale, et (iii) le développement d'une nouvelle décomposition de la diversité fonctionnelle en composantes locale (α), régionale (γ) et turnover (β). Appliqué aux communautés ichthyologiques échantillonnés le long d'un gradient de salinité, dans le système lagunaire de Patos-Mirim (Brésil), ce socle méthodologique nous a permis de révéler une structure fonctionnelle stable le long du gradient, en dépit d'une forte variabilité en composition d'espèces, ces communautés étant structurées majoritairement par un filtre environnemental agissant sur les capacités de locomotion des poissons.Dans un second temps, nous avons étudié l'impact des communautés ichthyologiques sur le cycle des nutriments. Plus précisément, nous avons estimé le potentiel de dégradation de la matière organique de plusieurs espèces de poissons, en étudiant la diversité fonctionnelle et génétique de leur flore bactérienne intestinale. Nous avons montré que les communautés ichthyologiques pouvaient influencer le recyclage des nutriments de façon non négligeable en raison d'un important potentiel de dégradation commun à la plupart des espèces étudiées, ce potentiel étant peu affecté par la diversité génétique ou les facteurs environnementaux
Ecosystems provide many services essential to Human societies through the positive effects of biodiversity exhibited by species communities. Therefore, identifying the role of living organisms and the factors influencing the diversity of their functions (i.e. functional diversity) is fundamental to accurately predict the evolution of ecosystems undergoing local and global pressures.This thesis is organized around two axes: (i) establishing a methodological framework to describe the functional structure of local and regional communities, and (ii) improving our knowledge of the impact of fish on the degradation of organic matter.First, we have consolidated the methodological tools through (i) the improvement of functional dendrograms reliability, (ii) the comparative study of the main indices estimating local functional diversity, and (iii) the development of a new decomposition of functional diversity into local (α) and regional (γ) components, and functional turnover (β). Applied to fish assemblages sampled along a salinity gradient in Patos-Mirim lagoons complex (Brazil), this methodological framework allowed us to reveal a steady functional structure, despite a high variability in species composition, these communities being primarily structured by environmental filtering acting on fish locomotion abilities. In a second step, we studied the impact of fish communities on nutrient cycling. More specifically, we estimated degradation of organic matter potential of several fish species by studying the genetic and functional diversity of their intestinal bacterial flora. We showed that the fish community could significantly influence nutrient cycling through an important degradation potential, common to most species studied, which is weakly affected by genetic diversity or environmental factors

Le changement climatique constitue un défi qui dépasse les échelles temporelles et spatiales de la plupart des problèmes. Il nécessite donc des approches qui reflètent la complexité du système terrestre. Cela est particulièrement vrai pour la biosphère et les écosystèmes forestiers, l'une des principales sources d'incertitude dans les projections climatiques. Les efforts concertés de collecte de données, tels que les inventaires forestiers, les bases de données des traits et les nouvelles technologies, telles que la télédétection, ont considérablement accru notre capacité à observer et à analyser l'état actuel de la végétation de la Terre. Cependant, pour estimer les développements futurs et comprendre les feedbacks entre la végétation et le changement climatique, des modèles sont nécessaires pour assimiler ces données et les traduire en dynamique des écosystèmes. Les modèles forestiers mécanistes et individu-centrés sont une approche particulièrement prometteuse, car ils simulent la dynamique forestière "bottom-up", reconstruisent les forêts arbre par arbre, et sont donc capables de prédire des patrons à différentes échelles. Cette thèse continue le développement du simulateur de dynamique forestière TROLL, rajoute la variation intraspécifique et la plasticité de la croissance des arbres, dérive une nouvelle méthode pour traduire les données de télédétection en inventaires forestiers virtuels et l'utilise pour inférer la structure forestière et la dynamique des écosystèmes dans les régions tropicales. Enfin, conformément à l'approche de TROLL, basée sur les traits, une mise à jour d'une base mondiale de traits, la base de données mondiale de la densité du bois est présentée, explorant la contribution des changements évolutives et cartographiant la densité du bois à travers le monde
Climate change presents society and science with a challenge that goes beyond the temporal and spatial scales of most practical problems. It therefore requires approaches that reflect the complexity of the Earth's system. This holds particularly true for the biosphere and forest ecosystems, one of the most important sources of uncertainty in climate projections. Concerted data collection efforts, such as forest inventories, trait data bases, and new technologies, such as remote sensing, have considerably increased our ability to observe and analyze the current state of the Earth's vegetation. However, to extrapolate findings into the future and understand the feedbacks between vegetation and climate change, models are needed that assimilate these data and translate them into ecosystem dynamics. Mechanistic and individual-based forest models are a particular promising approach, since they simulate dynamics bottom-up, reconstruct forests tree by tree, and are thus able to predict patterns across scales. This PhD further develops the trait- and individual-based forest growth simulator TROLL, including intraspecific variation and plasticity in tree growth, derives a new method to translate Airborne Lidar data into virtual forest inventories and uses it to infer forest structure and ecosystem dynamics in tropical rain forests. Finally, in line with TROLL's trait-based approach, an update to a global trait base, the Global Wood Density Database is presented, exploring the contribution of evolutionary lineages to wood density variation and mapping wood density across the globe

Deux facteurs principaux, une fois combinés, permettent de comprendre l’assemblage des communautés, soient i) l’environnement (abiotique et biotique), qui agit comme un filtre sélectionnant les espèces les mieux adaptées aux conditions données, et ii) les traits fonctionnels, sur lesquels s’effectue ce filtrage environnemental puisqu’ils peuvent conférer des avantages sélectifs sous diverses conditions. Il est donc essentiel d’établir des relations fiables entre les conditions environnementales et la structure fonctionnelle des communautés afin de pouvoir identifier et comprendre les mécanismes régissant l’assemblage des communautés. Cependant, plusieurs facteurs tels que les interactions entre variables à différentes échelles spatiales peuvent complexifier la situation et c’est pourquoi, malgré une quantité grandissante d’études sur le sujet, les processus d’assemblage des communautés restent difficiles à définir et à généraliser. Cette thèse vise donc à i) mieux définir et quantifier les relations trait-environnement des systèmes d’herbacées au travers de différentes échelles spatiales et ii) déterminer l’influence de ces relations sur l’assemblage des communautés et le fonctionnement des écosystèmes. Pour réaliser ces objectifs, j’ai travaillé avec les données de programmes ayant collecté des données taxonomiques et fonctionnelles sur les communautés d’herbacées à travers la France (DivHerbe et DivGrass) et, à moindre mesure, l’Europe (VISTA). Ces bases de données couvrent donc de larges gradients climatiques régionaux ainsi que des gradients environnementaux plus locaux relatifs à la qualité des sols et aux perturbations.J’ai d’abord testé l’importance de considérer à la fois des variables environnementales locales et régionales ainsi que leurs interactions pour déterminer la structure fonctionnelle et taxonomique des communautés. J’ai ensuite étudié comment l’importance relative des processus menant soit à la convergence ou à la divergence fonctionnelle peut changer le long d’une succession, puis comment ces deux types de processus influencent notre capacité à prédire l’assemblage des communautés à partir des traits fonctionnels. Finalement, j’ai présenté comment les résultats au niveau des communautés peuvent être utiles pour étudier le niveau des écosystèmes. Les résultats de cette thèse démontrent que les variables climatiques régionales interagissent fortement avec les variables environnementales locales pour influencer les processus locaux déterminant l’assemblage des communautés. Évaluer le contexte régional semble donc nécessaire afin d’éviter des interprétations erronées des patrons d’assemblage observés. Travaillant avec ces deux niveaux de variation environnementale, une dissociation important entre la variation taxonomique et fonctionnelle des communautés a été mise à jour, reflétant l’importance de considérer plusieurs facettes de biodiversité pour comprendre la dynamique des communautés. Les résultats ont aussi démontré que les processus d’assemblage menant à la convergence et à la divergence ont un impact très différent et prédictible sur les relations liant les traits et les abondances des espèces, c’est-à-dire notre capacité à prédire l’assemblage des communautés à partir des traits. Finalement, toutes ces notions, relatives aux relations trait-environnement et à l’assemblage des communautés basé sur les traits, ont été utilisées dans un contexte de biogéographie fonctionnelle. Il a été démontré qu’il était possible de construire des cartes de valeurs de traits fonctionnels dans les prairies permanentes à l’échelle de la France, à partir de variables environnementales. Certaines propriétés écosystémiques ont ensuite pu être prédites à partir de ces cartes. Ces travaux ont donc permis d’illustrer les défis à surmonter pour utiliser nos connaissances de l’écologie fonctionnelle en vue d’une conservation et d’une exploitation viables de nos écosystèmes
There are two main factors which, combined together, allow understanding community assembly : i) the environment (both abiotic and biotic), which acts as a filter selecting species according to how well-adapted they are to given conditions, and ii) functional traits, on which this environmental filtering occurs since they represent species adaptations to particular conditions. It is thus essential to establish reliable relationships between environmental conditions and the functional structure of communities in order to identify and understand the mechanisms driving community assembly. However, several factors such as cross-scale interactions between environmental variables complicate the situation. This is why, despite a growing body of studies on the subject, processes of community assembly are still poorly understood and are difficult to generalize. The purpose of this thesis is to i) better define and quantify the trait-environment relationships in herbaceous systems across different spatial scales and ii) determine the influence of those relationships on community assembly and on ecosystem functioning. To realize these objectives, I worked with data from programs which assembled taxonomic and functional data on herbaceous communities across France (DivHerbe and DivGrass) and, to a lesser extent, Europe (VISTA). These databases thus cover large regional climatic gradients, as well as more local environmental gradients related to soil quality and disturbances. I first tested the importance of simultaneously considering local and regional environmental variables as well as their interactions to determine the taxonomic and functional structure of communities. Then, I studied how the relative importance of processes leading to either functional convergence or divergence can change along a successional gradient, and how these two types of processes influence our ability to predict community assembly from functional traits. Finally, I presented how the results at the community-level can be used to study the ecosystem-level. The results of this thesis demonstrate that regional climatic variables strongly interact with local environmental variables in driving the local processes responsible for community assembly. Assessing the regional context is thus necessary in order to avoid erroneous interpretations of observed assembly patterns. Working with those two levels of environmental variation, important discrepancies were found between taxonomic and functional variations across communities, reflecting the importance of considering several aspects of biodiversity in order to understand community dynamics. The results also demonstrated that the assembly processes leading to functional convergence and divergence have a very different and predictable impact on the relationships between traits and species relative abundances, i.e. on our ability to predict community assembly from traits. Finally, these notions related to trait-environment relationships and to trait-based community assembly were used in a functional biogeography framework: It was possible to build maps of functional traits values in permanent grasslands across France using environmental variables. These maps then allowed predicting particular ecosystem properties. Thus, this work allowed illustrating some challenges that we are facing in using our knowledge in functional ecology to build sustainable conservation and exploitation plans for our ecosystems

Les activités humaines amplifient ou interfèrent régulièrement avec les forçages « top-down » et « bottom-up » sur les écosystèmes. Pourtant, la réponse des communautés à ces perturbations reste mal comprise. Ma thèse a pour objet de mesurer les effets des top-prédateurs et des nutriments sur la structure et le fonctionnement d’écosystèmes aquatiques expérimentaux. J’ai étudié dans des mésocosmes pélagiques de 9,5 m³ l’effet d’un forçage top-down induit par deux espèces de poissons. Je montre que ces changements de top-prédateurs s’accompagnent d’une réorganisation profonde de la structure du réseau trophique planctonique. Les réorganisations dépendent en partie de la taille des organismes et de leur comportement antiprédateur, mais c’est la phylogénie qui permet le plus efficacement de prédire la réponse du zooplancton aux poissons et les effets en cascade qui en découlent. J’ai également étudié la réponse à un forçage bottom-up par ajouts de phosphore et d’azote dans des macrocosmes de 750 m³ incluant une zone littorale végétalisée. Je montre que l’ajout de nutriments a eu un effet marqué sur la biomasse des producteurs primaires (biofilm, macrophytes littoraux), que les ajouts induisent une abondance plus forte de juvéniles de perche mais la biomasse du zooplancton n’est pas modifiée. La stœchiométrie des organismes et l’activité bactérienne n’ont été que peu changées par l’enrichissement. Ces résultats suggèrent que les effets des forçages bottom-up dans les milieux pélagiques sont bien prédits par la théorie des chaînes trophique mais, à l’échelle d’écosystèmes complexes, les macrophytes et le biofilm peuvent fortement atténuer la réponse à l’enrichissement
Human activities regularly amplify or interfere with top-down and bottom-up forcing on ecosystems. However, the communities' response to these disruptions remains poorly understood. My thesis aims to measure the effects of top-predators and nutrients on the structure and functioning of experimental aquatic ecosystems. I studied in 9.5 m³ pelagic mesocosms the effect of top-down forcing induced by two fish species. I show that these changes in top-predators are accompanied by a profound reorganization of the structure of the planktonic food web. Reorganizations depend in part on the size of organisms and their anti-predatory behaviour, but phylogeny is the most effective way to predict zooplankton response to fish and the resulting cascading effects. I also studied the response to bottom-up forcing by adding phosphorus and nitrogen in 750 m³ macrocosms including a vegetated littoral area. I show that the addition of nutrients has had a significant effect on the biomass of primary producers (biofilm, littoral macrophytes), that the additions induce a higher abundance of juveniles perch but the zooplankton biomass is not modified. The stoichiometry of organisms and bacterial activity were only slightly changed by enrichment. These results suggest that the effects of bottom-up forcings in pelagic environments are well predicted by food chain theory, but at the scale of complex ecosystems, macrophytes and biofilm can strongly reduce the response to enrichment

Résumé: Deux facteurs principaux, une fois combinés, permettent de comprendre l’assemblage des communautés, soient i) l’environnement (abiotique et biotique), qui agit comme un filtre sélectionnant les espèces les mieux adaptées aux conditions données, et ii) les traits fonctionnels, sur lesquels s’effectue ce filtrage environnemental puisqu’ils représentent les adaptations des espèces aux conditions données. Il est donc essentiel d’établir des relations fiables entre les conditions environnementales et la structure fonctionnelle des communautés afin de pouvoir identifier et comprendre les mécanismes régissant l’assemblage des communautés. Cependant, plusieurs facteurs tels que les interactions entre variables environnementales à différentes échelles spatiales (par exemple le climat et la fertilité des sols) peuvent complexifier la situation et c’est pourquoi, malgré une quantité grandissante d’études sur le sujet, les processus d’assemblage des communautés restent difficiles à définir et à généraliser. Cette thèse vise donc à i) mieux définir et quantifier les relations trait-environnement des systèmes d’herbacées au travers de différentes échelles spatiales et ii) déterminer l’influence de ces relations sur l’assemblage des communautés et le fonctionnement des écosystèmes. Pour réaliser ces objectifs, j’ai travaillé avec les données de programmes ayant collecté des données taxonomiques et fonctionnelles sur les communautés d’herbacées à travers la France (DivHerbe et DivGrass) et, à moindre mesure, l’Europe (VISTA). Ces bases de données couvrent donc de larges gradients climatiques régionaux ainsi que des gradients environnementaux plus locaux relatifs à la qualité des sols et aux perturbations. J’ai d’abord testé l’importance de considérer à la fois des variables environnementales locales et régionales ainsi que leurs interactions pour déterminer la structure fonctionnelle et taxonomique des communautés. J’ai ensuite étudié comment l’importance relative des processus menant soit à la convergence ou à la divergence fonctionnelle peut changer le long d’une succession, puis comment ces deux types de processus influencent notre capacité à prédire l’assemblage des communautés à partir des traits fonctionnels. Finalement, j’ai présenté comment les résultats au niveau des communautés peuvent être utiles pour étudier le niveau des écosystèmes. Les résultats de cette thèse démontrent que les variables climatiques régionales interagissent fortement avec les variables environnementales locales pour influencer les processus locaux déterminant l’assemblage des communautés. Évaluer le contexte régional semble donc nécessaire afin d’éviter des interprétations erronées des patrons d’assemblage observés. Travaillant avec ces deux niveaux de variation environnementale, une dissociation important entre la variation taxonomique et fonctionnelle des communautés a été mise à jour, reflétant l’importance de considérer plusieurs facettes de biodiversité pour comprendre la dynamique des communautés. Les résultats ont aussi démontré que les processus d’assemblage menant à la convergence et à la divergence ont un impact très différent et prédictible sur les relations liant les traits et les abondances des espèces, c’est-à-dire notre capacité à prédire l’assemblage des communautés à partir des traits. Finalement, toutes ces notions, relatives aux relations trait-environnement et à l’assemblage des communautés basé sur les traits, ont été utilisées dans un contexte de biogéographie fonctionnelle. Il a été démontré qu’il était possible de construire des cartes de valeurs de traits fonctionnels dans les prairies permanentes à l’échelle de la France, à partir de variables environnementales. Certaines propriétés écosystémiques ont ensuite pu être prédites à partir de ces cartes. Ces travaux ont donc permis d’illustrer les défis à surmonter pour utiliser nos connaissances de l’écologie fonctionnelle en vue d’une conservation et d’une exploitation viables de nos écosystèmes.
Abstract: There are two main factors which, combined together, allow understanding community assembly : i) the environment (both abiotic and biotic), which acts as a filter selecting species according to how well-adapted they are to given conditions, and ii) functional traits, on which this environmental filtering occurs since they represent species adaptations to particular conditions. It is thus essential to establish reliable relationships between environmental conditions and the functional structure of communities in order to identify and understand the mechanisms driving community assembly. However, several factors such as cross-scale interactions between environmental variables (e.g. between climate and soil fertility) complicate the situation. This is why, despite a growing body of studies on the subject, processes of community assembly are still poorly understood and are difficult to generalize. The purpose of this thesis is to i) better define and quantify the trait-environment relationships in herbaceous systems across different spatial scales and ii) determine the influence of those relationships on community assembly and on ecosystem functioning. To realize these objectives, I worked with data from programs which assembled taxonomic and functional data on herbaceous communities across France (DivHerbe and DivGrass) and, to a lesser extent, Europe (VISTA). These databases thus cover large regional climatic gradients, as well as more local environmental gradients related to soil quality and disturbances. I first tested the importance of simultaneously considering local and regional environmental variables as well as their interactions to determine the taxonomic and functional structure of communities. Then, I studied how the relative importance of processes leading to either functional convergence or divergence can change along a successional gradient, and how these two types of processes influence our ability to predict community assembly from functional traits. Finally, I presented how the results at the community-level can be used to study the ecosystem-level. The results of this thesis demonstrate that regional climatic variables strongly interact with local environmental variables in driving the local processes responsible for community assembly. Assessing the regional context is thus necessary in order to avoid erroneous interpretations of observed assembly patterns. Working with those two levels of environmental variation, important discrepancies were found between taxonomic and functional variations across communities, reflecting the importance of considering several aspects of biodiversity in order to understand community dynamics. The results also demonstrated that the assembly processes leading to functional convergence and divergence have a very different and predictable impact on the relationships between traits and species relative abundances, i.e. on our ability to predict community assembly from traits. Finally, these notions related to trait-environment relationships and to trait-based community assembly were used in a functional biogeography framework: It was possible to build maps of functional traits values in permanent grasslands across France using environmental variables. These maps then allowed predicting particular ecosystem properties. Thus, this work allowed illustrating some challenges that we are facing in using our knowledge in functional ecology to build sustainable conservation and exploitation plans for our ecosystems.

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

La compréhension des processus contrôlant le fonctionnement des mangroves est capitale au vu des services socio-économiques/écosystémiques rendus par ces écosystèmes et des menaces qu’ils subissent. En Guyane Française, les mangroves se développent rapidement en réponse aux contraintes sédimentaires récurrentes induites naturellement par les apports sédimentaires amazoniens. Cette thèse étudie la structure et la composition de trois classes de taille de communautés benthique (méso, macro, mégafaune), et les activités de bioturbation associées (remaniement sédimentaire biologique : RS, terriers) dans les jeunes stades de mangrove. 51 taxons de méso-macrofaune et 12 espèces de crabes (mégafaune) ont été identifiés. Bien que la biodiversité benthique soit spécifique à l'âge de la mangrove, des taxons tolèrent les modifications brusques du milieu, et cette persistance maintient des fonctions clés du remaniement sédimentaire tout au long du développement des mangroves. L’intensité du RS varie le long de ce gradient (21-146 g PS.m-2.cycle tidal-1). Si les crabes dominent le RS, cette thèse souligne la contribution effective de la méso-macrofaune aux transports particulaires. Les communautés benthiques montrent des capacités de bioturbation adaptées aux instabilités récurrentes du littoral. Les variations du RS au cours du temps pourraient indiquer l’état fonctionnel des mangroves. Cette étude conclut que l’hétérogénéité morpho-sédimentaire au sein des jeunes stades de mangroves influence la structuration spatiale des crabes, le remaniement sédimentaire qu’ils induisent, et la morphologie des terriers. Les microhabitats devraient être considérés lors de l'évaluation du rôle fonctionnel de la faune benthique des mangroves
Understanding the processes that control mangroves functioning is essential regarding the socioeconomic/ecosystemic services these ecosystems provide and the increasing threats they suffer. In French Guiana, mangroves grow rapidly in response to natural sedimentary perturbations caused by sediment inputs from the Amazon River. This thesis characterizes the structure and the composition of benthic fauna communities (three size classes: meso-, macro- and megafauna) and the associated bioturbation activities (biological sediment reworking: SR, burrows) in mangrove early growth stages. 51 meso- macrofaunal taxa and 12 crab (megafauna) species were identified.Despite a mangrove age specific biodiversity, some taxa tolerate abrupt environmental changes, and such persistence maintains key sediment reworking functions along mangrove development.The SR intensity varies along this gradient from 21 to 146 g DW.m-2.tidal cycle-1. Burrower crabs dominate the SR but this thesis also outlines the non-negligible contribution of smaller-sized (meso- and macrofauna) organisms to particulate transport. Benthic communities’ bioturbation capacities are adapted to recurrent environmental instabilities. Changes of the biologicallyinduced SR may be used as a proxy of the functional status of mangrove ecosystems. This study concludes that morpho-sedimentary heterogeneity of early-growth mangrove stages influences crab spatial structuration, the crab-induced sediment reworking and burrow shapes. Thus, microhabitat specificities should be considered when evaluating the role of benthic fauna in mangroves ecosystem functioning

The main aim of this doctoral research project was to assess the benthic ecosystem functioning in areas subjected to multiple and diffuse impacts. The Aeolian Islands, originated by the volcanic activity and characterised by continuous gas emissions and presence of thermal vents on the surrounding seabed, represent a good natural laboratory for global warming and carbon capture and storage (CCS) leakage studies. The aim of this work was to investigate to what extend the high CO2 alone and in combination with the high temperature affects the microphytobenthic abundance and its community composition (Chapter 1). A further objective was to detect a possible change in the primary production rate in relation with these two variables. Higher microphytobenthic densities were recorded at the vent stations and values were even more pronounced in relation with high temperature. On the other hand, high microphytobenthic abundances were coupled with low community richness and diversity. The gross primary production estimates were strongly coupled with the microphytobentic abundance values. We observed several diatoms with morphological deformities, The Port of Trieste represents an area with a diffuse sediment contamination as it is subjected to diverse impacts: the shipbuilding activities, the iron and steel plant, the petroleum industry and the port activities. The aim of this study (Chapter 2) was to detect any variation in the structure of the microbenthic community, both as active phototrophic and resting microbenthos, and the possible differences in the primary production and respiration at stations subjected to different anthropogenic impacts. The total microbenthic abundance did not vary among stations. On the other hand, the structure of the community gave more information. In particular, the analysis based on the active and resting microbenthic community structure highlighted a clear separation among stations close to the productive activities from the more distant ones and the reference station, indicating a contamination effect on those communities. As an example of an area severely contaminated by heavy metals and synthetic organic compounds, the Mar Piccolo of Taranto was chosen. Firstly, the microphyto- and macrozoobenthic communities were investigated and a marked influence of contamination on the abundance and biodiversity of those two communities was detected (Chapter 3). To further asses the overall trophic status of the benthic ecosystem, an integrated study of the active phototrophic and resting microbenthic stages, combined with the main photoautotrophic pathways, was conducted (Chapter 4). Furthermore, although the Mar Piccolo is very shallow, the benthic system was scarcely productive, likely as a consequence of the accumulated contaminants in the surface sediments that probably interfere with the proper functioning of the benthic ecosystem. Contrary to the benthic ecosystem, the pelagic one was very productive and a clear seasonal succession of different sized plankton phototrophs was observed (Chapter 5). To have a better overall view and provide some insights into the benthic-pelagic coupling, the primary production and heterotrophic prokaryotic production in the water column were integrated with those in the sediments and related to the origin of the organic matter pools based on the analysis of stable isotopes (Chapter 6).

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

O presente estudo abrange questões relevantes sobre o funcionamento de rios temporários. São abordados diferentes tópicos tais como a problemática da escassez de água particularmente na bacia Mediterrânica, a biodiversidade aquática e ripícola, a dinâmica de nutrientes e fatores fundamentais para a gestão e conservação de rios temporários Mediterrânicos. O principal objetivo é estudar alguns dos processos que ocorrem ao nível da bacia de drenagem e galeria ripícola associada, fazendo sempre a ligação dos resultados obtidos com a importância de uma correta gestão da bacia hidrográfica. Os resultados obtidos demonstraram uma necessidade urgente de implementação de estratégias de gestão adequadas ao nível das bacias hidrográficas de forma a reduzir a vulnerabilidade dos rios temporários. A tese pretende acima de tudo adicionar informação sobre rios temporários dada a sua importante representatividade a nível mundial; ### Ecosystem functioning of temporary rivers Abstract: This research intended to address some relevant issues concerning the functioning of temporary rivers. It will be approached different topics such as water scarcity particularly in the Mediterranean basin, aquatic and riparian biodiversity, nutrients dynamics and key factors in the management and conservation of temporary Mediterranean streams. The main aim is to study some of the processes that occur within the river basin and subjacent riparian gallery, always linking the obtained data with the importance of a correct river basin management. The results showed an urgent need to implement suitable management strategies at river basin level to reduce the vulnerability of temporary rivers. This thesis intends most of all to increase the knowledge on temporary rivers given their important worldwide representativity.

Globally land use change (LUC) with increasing in land use intensity has led to a decrease in soil organic matter (SOM). The reduction of soil C stock across LUC has been accompanied by a destabilization of soil structure and increases the soil erosion susceptibility. The destabilized soil structure is also concomitant with a loss of soil biodiversity and in particular, soil macroinvertebrate community. The focus of this dissertation is the effect of LUC with increasing in land use intensity on soil macrofauna, aggregation and SOM allocation. We hypothesized that LUC reduces soil macrofaunal biodiversity and consequently decreases soil engineering processes, resulting in destabilization of soil structure and impairing the ability of soil to physically protect SOM from decomposition inside stable aggregates, finally leading to depleted SOC stocks across LUC. In order to test these hypotheses, we conducted a field survey in 3 chronosequences of land use comprising native vegetation (NV), pasture (PA), and sugarcane crop (SC) in Central-Southern Brazil. This land use sequence provides a gradient of land use intensity and is projected to add 6.4 Mha of new sugarcane areas in Brazil by 2021. At each sampling point soil blocks of 25 X 25 cm and 5 x 5 cm to 10 cm depth were simultaneously collected from 0-10 cm, 10-20 cm, and 20-30 cm soil layers, for macrofauna isolation and aggregate fractionation, respectively. Within a radius of 6 meters around each sampling point, 12 subsamples were also collected from the same soil layers, and combined for total soil C and N concentration. An average reduction of 89% in the density of the soil macrofaunal community was observed when SC replaces PA, and a loss of 39% in the diversity of macrofauna groups. Our findings showed that, over a range of soil textures (16 - 66% clay), such biodiversity loss was strongly correlated with the destabilization of soil structure across LUC, whereas soil texture was not so. These observations consistently indicate that the abundance of detritivore soil animals, especially earthworms and termites, may be a significant predictor of soil structure transformations across LUC in tropical environments. Moreover, the sharp reduction in the abundance of earthworms was strongly positively correlated with the decrease in intra macroaggregate-associated C. As a result, after more than 20 years of sugarcane crop there were losses of 40 and 35% of C and N stocks, respectively, resulting in a rate of C emission of 1.3 Mg ha-1 yr-1. This C loss primarily occurred in the macroaggregate-associated C, as a result of the faster macroaggregate turnover under SC. In summary, the results presented here provide a mechanistic explanation as to why there is soil C depletion when increasing land use intensity in tropical soils: the huge reduction in the abundance of soil engineering invertebrates after LUC impair the ability of soil to physically protect SOM from decomposition inside stable aggregates, and therefore it is a primary mechanism controlling the soil C stocks\' depletion across LUC.
Globalmente mudanças no uso da terra (MUT) com o aumento da intensidade de uso do solo têm levado a uma diminuição da matéria orgânica do solo (MOS). A redução do estoque de C do solo após MUT tem sido acompanhada por uma desestabilização da estrutura do solo e aumento da susceptibilidade a erosão. A desestabilização da estrutura também é concomitante com a perda da biodiversidade do solo e, em particular, da comunidade de macroinvertebrados do solo. O foco deste trabalho é o efeito de MUT com aumento na intensidade de uso do solo sobre a macrofauna do solo, agregação e alocação da MOS. Nossa hipótese é que MUT reduz a diversidade da macrofauna do solo e, conseqüentemente, diminui os processos de engenharia de solo, resultando na desestabilização da estrutura do solo e prejudicando a capacidade do solo para proteger fisicamente a MOS da decomposição dentro de agregados estáveis, finalmente levando a redução dos estoques de C após MUT. Foi realizada uma pesquisa em 3 cronosseqüências de uso da terra que compreendem vegetação nativa (NV), pastagem (PA), e cana-de-açúcar (CA) na região Centro-Sul do Brasil. Esta MUT fornece um gradiente de intensidade de uso do solo e é projetada para adicionar 6,4 Mha de novas áreas de CA no Brasil até 2021. Em cada ponto de amostragem de solo blocos de 25 x 25 cm e 5 x 5 cm a 10 cm de profundidade foram coletados simultaneamente das camadas 0-10 cm, 10-20 cm e 20-30 cm de solo, para isolamento da macrofauna e fracionamento de agregados, respectivamente. Foi observada uma redução média de 89% na densidade da comunidade da macrofauna quando CA substitui PA, e uma perda de 39% da diversidade de grupos. Nossos resultados mostraram que, em um intervalo de texturas do solo (16-66% de argila), tal perda de biodiversidade foi fortemente correlacionada com a desestabilização da estrutura do solo após MUT. Estas observações indicam consistentemente que a abundância de animais detritívoros, especialmente minhocas e cupins, pode ser um preditor significativo de transformações da estrutura do solo em MUT. Além disso, a forte redução na abundância de minhocas foi fortemente e positivamente correlacionada com a diminuição do C alocado intra macroagregados. Como resultado, após mais de 20 anos de cultura de CA houve perdas de 40 e 35% dos estoques de C e N, respectivamente, resultando em uma taxa de emissão de C de 1,3 Mg ha-1 ano-1. Esta perda de C ocorreu principalmente no C associado aos macroagregados, como um resultado da reciclagem mais rápida dos macroagregados sob CA. Em resumo, os resultados aqui apresentados fornecem uma explicação mecanicista a respeito de porque há esgotamento do C do solo quando aumenta-se a intensidade de uso do solo em ambientes tropicais: a enorme redução na abundância de invertebrados \"engenheiros do solo\" após MUT prejudica a capacidade do solo para proteger fisicamente a MOS da decomposição dentro de agregados estáveis, e, portanto, é um mecanismo primário controlando a redução dos estoques de C no solo relacionada a MUT.

The central theme of this thesis was the search for ecologically meaningful ways to quantify the relationships between the biota and ecosystem processes. This thesis investigated whether a "functional group" approach, that characterised the fauna according to similarities in their activities, could be successfully employed to quantifiably link species' performance to important ecosystem processes. Initially the abilities of traditional "trophic" and "bioturbatory" categories to characterise the estuarine macrobenthic fauna and discriminate between estuarine sites were examined. This thesis determined that the perceived inter-site similarity within an estuary varied according to the function being investigated and that the apparent associations between abiotic factors and biotic assemblages were also heavily influenced by the choice of functional classification. This study provided strong evidence that links between the macrobenthos and abiotic factors were most easily detected if the species were grouped according to their bioturbatory abilities. Thus, attempts to model the contribution of the estuarine macrofauna to sediment mixing throughout an estuary were pursued in preference to modelling trophic group distribution. This thesis identified limitations of existing "bioturbation" categories and hence, developed a novel classification system that incorporated species' activity rates, magnitude and location within the sediment. Strong evidence was found that estuarine macrobenthic communities should be treated as two separate assemblages: one shallow assemblage occupying surface and near surface layers, and one deep assemblage with the ability to exploit the sediment at greater depths. The two separate assemblages displayed different associations with the environmental factors examined in this study. By developing new functional groupings of species' behaviour, and treating shallow and deep assemblages as separate entities, this thesis was able to estimate the contribution of the biota to sediment mixing and successfully develop and validate generic predictive models of functional group distribution within the Tamar/Plym estuarine system. Since the functional groups themselves convey information about the magnitude of their effect and the sediment horizons impacted, this thesis represents an important advance in our ability to predict biological contribution to sediment mixing processes in estuarine ecosystems.

The Great Salt Lake (GSL) wetlands account for ~75% of all Utah wetlands and provide not only critical habitat for millions of migratory birds, but also provide valuable ecosystem functions and services as well as economic benefits to Utahns. However, these wetlands are facing an aggressive invader, Phragmites australis, that has spreading across the GSL wetlands and replacing native wetland habitats. Wetland managers have spent countless resources and time trying to control the spread of P. australis and restore GSL wetlands. However, we do not fully understand how these wetlands functions and services are being altered with this habitat homogenization because functional data for our wetland species have not been well documented. This lack of knowledge may hinder wetland restoration efforts. To create baseline functional data for the GSL wetland species and better understand how the spread of P. australis might be affecting the overall health of the system, I measured eight individual ecosystem functions for seven dominant habitat types found across the GSL wetlands. I compared these individual functions across habitat types as well as created two different multifunctionality indices using an averaging and a thresholds approach. With these comparisons, I was able to determine the distinct functional strengths of different wetland habitat types and their overall functional abilities. I found that functional abilities varied greatly by habitat type and that not one single habitat could support every function even at the lowest threshold measured. I found that Typha latifolia, Schoenoplectus acutus, and P. australis, had the highest multifunctional values. However, I also found that some habitats offered unique functions, such as Salicornia rubra and playa, and that these functions were lacking in other habitats, including the most multifunctional habitats. These findings suggest that maintaining habitat heterogeneity will be critical in ensuring a fully functioning wetland system that can provide a multitude of ecosystems services that benefit both humans and wildlife. The findings of this study will supply wetland managers with a better understanding of the functional strengths of different wetland habitats. This data will aid in ongoing restoration efforts by enabling managers to target certain functions and create more efficient and effective management plans.

Currently, global change is promoting the spatiotemporal occurrence of temporary streams, altering fluvial ecosystem function and structure, and the ecosystem services they provide. To effectively protect fluvial ecosystems, a detailed understanding of the effects of hydrological regime changes on their biodiversity and functioning is needed. Organisms inhabiting temporary streams are directly affected by their hydrological regime, including the stream biofilm. Biofilms are associations of microorganisms and they are of particular relevance in temporary streams because of their diversity, abundance, and key role in ecosystem processes. Therefore, understanding biofilm response to hydrological regime variability is key to understand the implications of increasing non-flow periods on fluvial ecosystems. The results of this thesis demonstrate the non-flow duration as a key influence on the structure and functioning of river biofilms, the importance of maintaining photoautotrophic stream biodiversity to preserve stream ecosystems functioning and the protective role of canopy cover to protect these communities
El canvi global està promovent l’aparició de rius intermitents, alterant funcionament, estructura i serveis ecosistèmics dels sistemes fluvials. Per a protegir efectivament els ecosistemes fluvials, es necessita un coneixement detallat dels efectes del canvi de règim hidrològic sobre la seva biodiversitat i funcionament. Els organismes que habiten els rius temporals estan directament afectats pels canvis hidrològics, inclòs el biofilm. Els biofilms són associacions de microorganismes i particularment rellevants als rius temporals per la seva diversitat, abundància i paper en processos ecosistèmics. Així, entendre la resposta del biofilm a la variabilitat del règim hidrològic és clau per entendre les implicacions del increment del període sec als ecosistemes fluvials. Els resultats d'aquesta tesi demostren la duració del període sec com a vector d'estructura i funcionament del biofilm, la importància de mantenir la biodiversitat fotoautòtrofa per preservar el funcionament ecosistèmic i el paper protector de la coberta vegetal sobre aquestes comunitats

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.

Headwater streams are important habitats, unique in their heterogeneity and biodiversity. they are considered significant for the functioning of whole river systems. Many headwater systems. such as those in the temperate and sub arctic northern hemisphere, drain peat dominated catchments, a habitat that is increasingly threatened by climate change, acidification and pressures from an array of land management practices. Together these impacts are resulting in the widespread degradation of peatlands and it is hypothesised that stressors could severely impact streams draining these systems, causing shifts in macro invertebrate community composition and alterations to functional process rates. However, there is a lack of information on the exact impacts of these stressors to peatland streams and, furthermore, limited knowledge of these ecosystems in their intact state. Thus, the overarching aim of this work is to improve understanding surrounding the impacts of stressors to peatland streams and to contextualise this research with an improved knowledge of the dynamics of intact peatland streams. This work focused on streams originating from blanket peats in the UK, which form important headwaters of many major UK rivers, and had four main objectives. 1) Develop a holistic understanding of an intact peatland stream through intensive assessment of physico chemistry, macroinvertebrate communities and three functional processes (algae accrual, plant litter decomposition and whole stream metabolism) using both a longitudinal survey and intense seasonal monitoring. 2) Assess the impacts of two catchment-scale drivers of change in peatland habitats (rotational heather burning and erosion) on stream ecosystems, examining physicochemistry, macroinvertebrates and ecosystem functioning across fifteen streams. 3) Examine gradients of sedimentation associated with environmental change and land management using streamside mesocosm and reach experiments. 4) Consider the mechanisms that elicit a change in physicochemisty, macroinvertebrates and ecosystem function by considering interrelationships and advancement of conceptual models. The interdisciplinary approach used in this thesis allowed a novel assessment of the spatiotemporal variability of peatland stream ecosystems and for the first time hig~lighted alterations in both macroinvertebrate communities and ecosystem functioning along the stream length and across seasons in an intact peatland stream. Increases in macroinvertebrate abundance, primary production and community vi j b respiration were observed with increasing distance downstream and with increasing catchment size. These parameters, along with algae accrual and leaf litter decomposition rates, also showed strong seasonal patterns, decreasing in winter and amplifying in summer. Variations in these parameters were driven predominantly by increases in temperature, photosynthetically active radiation (PAR), suspended sediment concentrations (SSC), discharge and dissolved organic carbon (DOC). Erosion, and to some degree rotational heather burning, were found to impact physicochemical variables, with total oxidised nitrogen (TON) and SSC displaying increased concentration.s in impacted catchments. Associated shifts were found in macroinvertebrate communities, with amplified abundance in eroded catchments driven by increases in ' more sediment tolerate taxa, such as Chironomidae and Oligo chaeta. Streams draining eroded and burnt catchments also displayed lower numbers of sensitive Ephemeroptera, Plecoptera and Trichoptera taxa. Functional parameters did not reflect these changes in chemistry and biota, but there were clear differences between the fifteen individual streams. Experiments undertaken in streamside mesocosms and stream reaches showed impacts of organic sedimentation across several levels of ecological organisation. Increased benthic sedimentation led to declines in macroinvertebrate abundance, shifts in - species composition and increased sediment respiration rates. Short term influx of organic sediment in reach based experiments caused significant increases in the downstream drift of macroinvertebrates during nocturnal periods, however, these streams were quick to recover to pre-experiment drift rates and benthic communities were not affected over the period of the experiment. These influx events produced a rapid and severe decline in GPP measured though whole stream metabolism rates, This body of research highlights peatland streams as unique and heterogenic systems but also as systems that are sensitive to anthropogenic stressors at both the catchment and reach scale, These habitats have intrinsic importance, supporting diverse macroinvertebrate communities, are significant for the modulation of carbon and are good indicators of the condition of the surrounding catchment. Thus, this work emphasises the need for restorative measures and sustainable management in peatland habitats that considers the streams they support. In addition, this work furthers knowledge of the baseline conditions in these systems and increases understanding of the use of functional processes as ecological indicators in peatland..streams.

Conversion of forests to pasture has been extensive throughout the tropics and subtropics, and these forests continue to experience deforestation at high levels. Such clearing can alter plant-animal dynamics and thereby degrade ecosystem functioning. It is often assumed that re-establishment of vegetation will recover forest-like communities of animals such as invertebrates, together with the roles they play in important ecosystem processes. However, there has so far been little empirical evidence to support this. This thesis investigated the impact of deforestation on invertebrate-mediated ecosystem functioning, and its recovery during regeneration of rainforests on former pasture. Specifically, it focused on two key ecosystem processes which underly forest regeneration dynamics, while also comparing two different reforestation pathways. The two processes were leaf litter decomposition rates and insect seedling herbivory. For decomposition, functional associations with decomposer invertebrates as well as vegetation structure and floristics were also investigated. Both these ecosystem processes were examined across 25 sites representing different phases of rainforest deforestation and subsequent reforestation. The study area was the Numinbah Conservation Area and surrounds on the Gold Coast Hinterland, in the eastern Australian subtropics. Here the local council had begun restoration management on disused pasture approximately 10 years prior to the beginning of this thesis. Five study sites were placed in each of five vegetation types, consisting of two reference states of grazed pasture and old-growth rainforest (to represent the deforestation process and to indicate the target of restoration), together with three types of regenerating vegetation: unassisted woody regrowth aged 20-50 years on former pasture, and assisted regeneration aged 1-4 and 5-11 years after human interventions that aimed to accelerate natural regeneration within previously-unassisted regrowth. To measure decomposition rates (mass loss % per unit time), open and closed mesh litter bags (to exclude macro-invertebrates >1mm length and width) were deployed across the 25 sites filled with leaves of five local tree species for five and eight months. Most of the decomposition had already occurred by five months, as only a further 3% decomposition occurred in the following three months. Macro-invertebrates did contribute to mass loss, but their exclusion from litter bags only marginally decreased decomposition rates, by 3%. Decomposer community composition at a broad taxonomic level differed strongly between pasture and all other vegetation types. Decomposition rates in open bags were about 50% slower in pasture than in old-growth forest, but had recovered to 83% of old-growth values in all types of regenerating vegetation. Samples of decomposer invertebrates were also collected from ground litter within each of the 25 sites. Abundances of macro- and meso-decomposer invertebrates decreased by 95% and 77% respectively in pasture. Abundances of invertebrate decomposers had recovered to old-growth forest levels in all restoration types of recovering vegetation. However, decomposition rates in open-bags were significantly correlated (across sites) with abundances of both macro- and meso-decomposers, most strongly so for meso-decomposers. Investigations were also made into how vegetation structure and floristic composition of trees differed among the five vegetation types, and associations between these differences and variations in decomposition differed among sites. The main changes in vegetation were: (1) after 5-10 years of interventions to assist natural regeneration, abundance and species richness of trees (>1 m height) with stem sizes <10 cm dbh and 10-50 cm dbh had recovered, (2) also after 5-10 years of interventions to assist natural regeneration, canopy cover had recovered, and (3) tree species composition (all stem sizes) differed between old-growth and regenerating areas, and between unassisted and assisted natural regeneration (respectively dominated by Lantana camara and various pioneer tree species). There was a large step-change in decomposition rates associated with the transition from pasture to regenerating woody vegetation (33% difference), during which canopy cover (from 0% in pasture to 51-69% in regenerating areas) was both most important for describing differences in vegetation, and a good predictor of decomposition rates. A second step-change of decomposition rates was associated with the transition from regenerating woody vegetation (of all types) to old-growth rainforest (17% difference), during which both canopy cover and tree species composition were most important in describing differences in vegetation. However, canopy cover no longer explained variation in decomposition rates among woody regeneration areas and old-growth rainforest; in these cases, tree species composition was the better predictor. To investigate seedling herbivory, 200 seedlings of two tree species (100 Glochidion ferdinandi and 100 Toona ciliata) were planted across the 25 sites (eight seedlings of each species per site), and leaf area loss (%) and the types of damage were recorded on immature and mature tagged leaves at four times during seven months. The percentage of leaf area lost due to herbivory accumulated in leaves over time for both species and at seven months was 25% and 37% respectively for G. ferdinandi and T. ciliata. There was no difference in the accumulated amount of herbivory between leaves which were immature or mature when first tagged, and there was no effect of vegetation type on herbivory rates in either species. Leaf start age (immature vs mature) also had no effect on the type of herbivory. Vegetation type did have an effect on the type of herbivory, which was mostly driven by differences in pasture, but more so for T. ciliata than G. ferdinandi. However, the damage types were driven by relatively uncommon types of leaf damage. On the other hand, the damage types which occurred most frequently, and caused the greatest amount of damage, occurred consistently throughout all the vegetation types. Most leaf damage was caused by various types of Lepidoptera larvae. The results of this study showed that conversion of forest to pasture halved decomposition rates but had little effect on seedling herbivory. The reduction in decomposition was associated with an effect of deforestation on important drivers of decomposition rates, including the abundance and composition of decomposer invertebrates, and amount and composition of canopy cover. During regeneration, decomposition rates partially recovered, associated with a full recovery of decomposer invertebrates. However, a full recovery of decomposition rates was likely restricted by a difference in litter layer quality, because tree species composition in old-growth rainforest differed greatly from that in all types of regenerating vegetation. Seedling herbivory was unaffected by deforestation, most likely because adults of the most common type of insect herbivores, Lepidoptera, can detect suitable host plants through the volatile chemicals that they emit, and because they are also capable of flying the distances (<2 km) from source populations. Since seedling herbivory was little effected by deforestation, the concept of recovery during regeneration did not apply, and neither did it change during regeneration. Overall, both types of invertebrate-mediated ecosystem functioning were resilient to deforestation as any decline in functioning quickly recovered (or partially recovered) during reforestation. These results occurred irrespective of whether interventions to assist natural regeneration were used. Decomposition rates had already substantially recovered before the woody regrowth reached 20-50 years of age, and seedling herbivory was unaffected by the types of vegetation within which the host plant was located. Therefore, it is unlikely that any types of interventions used to assist natural regeneration would have a significant effect on invertebrate-mediated ecosystem functioning subsequent to regeneration of regrowth aged 20-50 years. Further, the recovery of the invertebrate communities was likely facilitated by the proximity to an old-growth rainforest source, together with extensive surrounding forest cover of several types. Therefore, a reduced supply of source invertebrate populations in the landscapes that surround regenerating areas may, in poorly forested regions, lead to lower functional resilience. Nevertheless, in moderately forested landscapes (such as in the present study), simply removing barriers to natural regeneration may be all that is required to achieve successful recovery of invertebrate-mediated ecosystem functioning during regeneration.
Thesis (PhD Doctorate)
Doctor of Philosophy (PhD)
School of Environment and Sc
Full Text

Once regarded as little more than simple model systems, microbial communities are now understood to drive major earth processes and patterns of biodiversity. In order to more fully understand them, there is a need to investigate the mechanisms that determine the structure and function of microbial systems. Predator-prey interactions have been studied for a long time in macroecological systems and are known for their role in determining community structure and dynamics. Functional diversity has come to the fore of ecology to take a central role in understanding what links species to biodiversity and ecosystem function. In this thesis I investigated the biodiversity and ecosystem functioning of microbial predator-prey communities. I used naturally occurring bacterial communities in combination with co-occurring heterotrophic protists to perform manipulative experiments to investigate: a) the functional diversity of heterotrophic protists and their interactive contributions to ecosystem functioning; b) the effects of bacterial prey community diversity and composition on these attributes of protists; and c) the role of functional diversity in maintaining protist community diversity. I found that not only is it possible to classify functional diversity by species interactions, but that the effects of prey community diversity and composition highlight the flexible nature of this property, particularly in predators. I also found evidence of negative biodiversity-functioning relationships and strong competitive interactions among heterotrophic protists. However, their functional diversity allowed them to maintain higher diversity in disturbed environments. Taken together, my thesis has advanced the understanding of the role of predator-prey interactions and functional diversity in regulating interactions and ecosystem functioning in microbial systems.

2011/2012
Molte attività antropiche sono localizzate lungo le coste e poggiano sui molteplici servizi offerti da questi particolari ecosistemi. Con l’aumentare della vulnerabilità e del sempre più accentuato stato di degrado di queste aree, diverse politiche ambientali sono state sviluppate con lo scopo di promuovere una gestione sostenibile delle risorse naturali, tra cui la Direttiva Quadro sulla Strategia per l’Ambiente Marino (2008/56/EC) in Europa. Le realtà economiche e sociali sono strettamente connesse tra loro e con i sistemi ecologici su cui poggiano. Per comprendere come l’uomo interagisce con l’ambiente, il modello concettuale DPSIR viene ampiamente adottato. Inoltre, sul piano strettamente ecologico, una solida conoscenza del funzionamento dell’ecosistema costiero costituisce un prerequisito fondamentale. Questa tematica complessa deriva dall’integrazione di parametri sia strutturali (caratterizzazione chimica e delle comunità biologiche) che funzionali (quali i principali processi di produzione primaria, respirazione e degradazione della sostanza organica), che nell’insieme descrivono come le varie forme di carbonio sono stoccate e come si realizza il fluire di carbonio ed energia attraverso il sistema. Lo studio del funzionamento dell’ecosistema bentonico costituisce uno strumento particolarmente utile nello sviluppare forme sostenibili di gestione ambientale dal momento che il dominio bentonico funge da deposito di ciò che avviene nella colonna d’acqua. I casi di studio presentati descrivono la parte PSI del modello concettuale DPSIR: come le Pressioni inducono cambiamenti nello Stato dell’ecosistema determinando di conseguenza alterazioni ambientali ed eventuali influenze negative sulle attività umane (Impatti). Lo scopo della tesi consiste nel contribuire a promuovere una gestione basata sull’ecosistema e sul suo funzionamento in aree costiere mediante una miglior conoscenza della sua funzionalità in presenza di specifici stress. I casi di studio vengono presentati secondo un ordine dettato dell’aumentare della complessità dell’approccio seguito: dal più semplice, caratterizzato solo da parametri strutturali, al più complesso, in cui sono stati indagati anche diversi parametri funzionali. La risposta della comunità microalgale bentonica (microfitobenthos - MPB) alle biodeposizioni derivanti dalle mitilicolture è stata studiata non solo paragonando una mitilicoltura con un controllo ma anche considerando le caratteristiche della comunità sotto ad un impianto più recente e in un’area dove l’attività è stata rimossa (Capitolo 2). Questo approccio innovativo permette di indagare l’evoluzione temporale dell’impatto e se è possibile un ripristino. Comparando le quattro aree, la comunità è caratterizzata da una maggiore proliferazione dei taxa tolleranti a condizioni di arricchimento organico sotto alle mitilicolture attive rispetto agli altri due siti. L’area dismessa, inoltre, presenta un popolamento microalgale simile a quello del controllo suggerendo la resilienza del sistema e, di conseguenza, una certa sostenibilità dell’attività di mitilicoltura. Tre comunità bentoniche sono state studiate sinotticamente in un’area costiera soggetta a stress multipli, come l’influenza del Po, la presenza di piattaforme per l’estrazione del gas e il prelievo/scarico di sedimenti (Capitolo3). Insieme alla caratterizzazione chimica, lo studio del MPB, della meiofauna e della macrofauna forniscono una descrizione dello stato dell’ecosistema bentonico in un esempio di monitoraggio che costituisce una base di dati a cui fare riferimento prima di qualsiasi intervento nell’area d’interesse. Lo studio di mesocosmo (Capitolo 4) è focalizzato sulla risposta della comunità microbica bentonica ad un abbassamento di pH dovuto alla fuoriuscita di CO2 da un suo sito di stoccaggio CCS (Carbon dioxide Capture and Storage). Costituisce un esempio di esperimento condotto in laboratorio con lo scopo di simulare eventuali scenari futuri derivanti da un intervento antropico in ambiente naturale prima della sua realizzazione. Relativamente a questo focus, sia i parametri strutturali (abbondanze picobentoniche, densità e composizione del MPB) che i funzionali relativi alla comunità microbica bentonica (attività enzimatiche, Produzione Procariotica di C e respirazione) sono stati studiati per la prima volta. I risultati suggeriscono che la comunità microbica è scarsamente sensibile anche ad un considerevole abbassamento di pH, probabilmente a causa di un effetto buffer esercitato dalla matrice sedimentaria. L’azione sinergica di idrocarburi e metalli pesanti sul funzionamento dell’ecosistema bentonico è stata studiata in un sistema fluviale-lagunare severamente contaminato (Capitolo 5). Numerosi parametri sono stati considerati e dalla loro integrazione deriva un’accurata descrizione del fluire di carbonio attraverso il sistema. I risultati relativi ai parametri microbici come le attività degradative, le produzioni primaria e secondaria e l’analisi del MPB, delineano una situazione inaspettata nel sito considerato più impattato. Il sedimento di tale stazione ospita infatti una comunità microbica bentonica estremamente attiva sia in termini di produttori primari che di procarioti volti al recupero della sostanza organica e conseguente conversione in nuova biomassa. Gli studi presentati in questa tesi non hanno la pretesa di costituire una descrizione esaustiva e completa del funzionamento dell’ecosistema bentonico, ma sottolineano l’importanza di questo approccio innovativo nel contribuire a sviluppare forme sostenibili di gestione delle risorse costiere.
Several human activities are settled along the coasts and rely on the ecosystem services provided by nature. The growing concern about the vulnerability of these areas promotes the development of environmental policies aimed at the sustainable management of the marine resources, such as the Marine Strategy Framework Directive (2008/56/CE) in Europe. Economic, societal and ecological systems are closely interlinked. For understanding how man interacts with the environment, the DPSIR conceptual model is largely adopted. Moreover, a robust knowledge on the coastal ecosystem functioning is needed as a prerequisite. This complex task derives by the integration of both structural (chemical and biological communities) and functional (processes as primary production, respiration and mineralisation) parameters which together describe the forms of carbon storage (organic and inorganic) and the flows of carbon and energy through the system. The study of the benthic ecosystem functioning is a tool particularly useful in developing sustainable management of coastal environments because the benthic domain acts as a repository of what happens in the overlying water. The four case-studies of my thesis focus on the PSI part of the DIPSIR conceptual model, i.e. on how Pressures translate into State changes which may, in turn, negatively affect the environment and the human activities (Impacts). The goal is to contribute in achieving an operational ecosystem-based management of coastal and shallow environments by improving the scientific knowledge on the functioning of shallow benthic ecosystems under specific pressures. The order of the papers is from the simplest to the most complex approach by adding the structural parameters first and then the functional ones. The response of the benthic microalgal community (microphytobenthos - MPB) to the mussel farm biodeposition has been investigated not only comparing the sediment beneath a mussel farm with a control site but also considering a relatively recent mussel farm and a disused one (Chapter 2). This innovative approach in the experimental design allows to study the temporal evolution of the mussel farming impact and the potential recovery of microphytobenthos. The community changes among the four areas with a more pronounced proliferation of those taxa that are tolerant to organic enrichment under the active mussel farms than in the other two sites. The disused farm is characterised by an assemblage similar to that of the control suggesting a resilience of the system and consequently the sustainability of this productive activity. Three benthic communities have been synoptically investigated in a shallow area subjected to multiple-stressor impacts such as the Po River influence, the presence of gas platforms, sediment dumping and sand extraction (Chapter 3). Together with some chemical parameters (Total Organic Carbon, Total Nitrogen, etc.), the synoptic study of different communities (MPB, meiofauna and macrofauna) gives a description of the state of the benthic ecosystem as an example of monitoring survey which represents the reference point for decision-makers prior to any kind of intervention. The mesocosm study (Chapter 4) focuses on the response of shallow benthic microbial communities to a decrease of pH due to the leakage of CO2 from a Carbon dioxide Capture and Storage (CCS) site. This is an example of a laboratory experiment aimed to simulate and predict the possible scenarios derived by an anthropogenic intervention in the natural environment before its actual execution. Benthic microbial structural (prokaryote abundance, MPB densities and composition) and functional parameters (exoenzymatic activities, Prokaryotic C Production and benthic respiration) have been investigated for the first time within this focus. Overall, the findings suggest a microbial community slightly sensitive to consistent pH decrease probably due to a buffer effect exerted by the sedimentary matrix. The synergistic impact of hydrocarbons and heavy metals on the benthic ecosystem functioning has been investigated in a severely contaminated Adriatic lagoon (Chapter 5). Several parameters have been considered in order to describe the overall flow of C through the system. The exoenzymatic activities, the Prokaryotic C Production, MPB composition and the Primary Production suggest an unexpected situation in the site that is considered the most impacted. The sediments at this station are inhabited by a microalgal community that is extremely active in fixing inorganic C through the Primary Production process. In addition, the occurrence of an efficient prokaryotic community in transforming the sedimentary organic C in new biomass, suggests a solid benthic microbial loop. These studies have not the pretence to describe exhaustively the benthic ecosystem functioning. Nevertheless they highlight the importance of this innovative approach in contributing to the development of a sustainable management of coastal resources.
XXV Ciclo
1984

Confined coastal lagoons are shallow and dynamic water bodies that play an important ecological role. Considering the severe degradation they have been facing in the last years, understanding the functioning of these habitats for their proper management and conservation is essential. Nowadays, one of the most important descriptors of ecosystem functioning is the metabolism, the use of which has increased with the application of the free dissolved oxygen (DO) technique and the development of more affordable and reliable sensors. Quantifying metabolic rates as well as identifying the factors that contribute to their temporal and spatial variation are very important in assessing these ecosystems behaviour and their response to future changes. Thus, the aim of the thesis was to estimate the ecosystem metabolism of a set of Mediterranean confined coastal lagoons in La Pletera salt marsh identifying the main drivers of its variation and its application to study phytoplankton
Les llacunes costaneres mediterrànies de tipus confinat són cossos d’aigua poc profunds i dinàmics, amb un paper ecològic molt important. Davant la regressió que han patit durant els darrers anys, entendre el funcionament d’aquests habitats per una correcta gestió i conservació esdevé fonamental. Avui dia, un dels descriptors més importants del funcionament ecosistèmic és el metabolisme, l’ús del qual s’ha incrementat amb l’aplicació de la tècnica de l’oxigen lliure i el desenvolupament de sensors cada cop més assequibles i fiables. La quantificació de les taxes metabòliques i la identificació dels factors que contribueixen a la seua variació temporal i espacial són molt importants per avaluar el comportament dels ecosistemes i la seua resposta a futurs canvis. Així, l’objectiu d’aquesta tesi va ser estimar el metabolisme ecosistèmic d’un conjunt de llacunes costaneres mediterrànies confinades a la maresma de la Pletera, identificar els seus principals factors de variació i la seua aplicació per estudiar el fitoplàncton
Programa de Doctorat en Ciència i Tecnologia de l'Aigua

Agricultural expansion and logging are resulting in habitat degradation and fragmentation, especially in tropical regions. In Southeast Asia oil palm agriculture and commercial logging are the main threats to rainforest biodiversity, and I assessed the impacts of forest disturbance and land-use change on species composition and ecosystem functioning. I explored the role of the High Conservation Value (HCV) approach for biodiversity conservation in tropical agricultural landscapes and concluded that better knowledge exchange between scientists and HCV users is needed to improve biodiversity conservation in managed landscapes. I carried out a meta-analysis to examine the responses of birds, ants and beetles to the conversion of rainforest to oil palm which revealed that species in plantations were generally small-bodied species from lower trophic levels that had low abundances in forest. I collected new field data from Sabah(Malaysian Borneo) on dung beetle diversity and ecosystem functioning in undisturbed forest, selectively logged forest and forest fragments (5-3,529 ha). Dung beetle diversity was adversely affected by forest fragmentation, but not by selective logging. Larger fragments with better quality forest supported similar species assemblages to continuous forest, including functionally important dung beetle species. Dung removal, seed burial and seed dispersal were maintained in selectively logged forest, but were reduced by >50% in forest fragments. Dung removal in forest fragments was dependent on a few large, disturbance-tolerant species, which resulted in highly variable rates of functioning in fragments. Consistently high rates of dung removal and seed dispersal required high species richness as well as high biomass of dung beetles. Overall, forest fragmentation adversely affected diversity and ecosystem functioning, although fragments >100 ha maintained some dung beetle diversity and ecosystem functions. By contrast, degraded logged forest was functionally similar to undisturbed forest and thus should receive higher protection.

Many of the processes on earth which are essential for sustaining life are driven by biological systems and it is functional diversity aswell as species richness which determines the health and sustainability of ecosystems. Ecosystem functions, from primary production to decomposition, are determined by the interactions both between organisms and between organisms and their environment. As such, there has long been an appeal in classifying species by their roles in ecological communities rather than by taxonomic groupings. However, there is often a disconnect between the criteria used to classify species into functional groups, often common morphological attributes, and the effect that the organisms within those groups have on specific ecosystem functions as the appropriateness of the classification criteria is rarely empirically tested. This thesis investigates inter- and intra-species variation in benthic invertebrates with respect to their effects on ecosystem processes (particle reworking and bioirrigation) and functions (nutrient cycling) and considers whether species can be grouped for single and multiple ecosystem functions in different environmental contexts. Overall the results show that species can be grouped by their effects on specific single ecosystem functions, but that these groups cannot be applied across multiple functions and processes. Further they show that species’ contributions to ecosystem functions change with environmental context (salinity, organic enrichment, seawater acidification and temperature), and that changes in the ecosystem processes known to mediate functions do not necessarily reflect a change in functioning. In addition intra-species variation in functional activity indicates that it may not be appropriate for all members of a population to be ascribed to the same functional group. This thesis highlights a need to test that different functional groups reflect different effects on ecosystem functioning. Further it shows that functional groups are not constant, individuals within populations are not necessarily functional equivalents, and that individuals have the capacity to change their contributions to ecosystem functions and processes. Future research needs to acknowledge and incorporate both biotic and abiotic sources of variability in species effects on ecosystem functions and processes.

Bacteria are immensely diverse and hold key-positions in essentially all biogeochemical cycles. In freshwater ecosystems, bacteria degrade and mineralize organic compounds, linking the pool of dissolved organic matter to higher trophic levels. Aware of the global biodiversity loss, ecologists have started identifying the relationship of diversity and ecosystem functioning. Central to this is the question if species can functionally replace other species, hence being functionally redundant. Functional redundancy might allow communities to maintain functioning when diversity is lost. Due to their large numbers and great diversity, bacterial communities have been suspected to harbor large amounts of redundancy. The central aim of this thesis is to investigate the coupling of diversity and ecosystem functioning of bacterial communities and to understand how environmental perturbation affects this relationship. I manipulated the diversity of complex communities by a dilution technique, and measured the performance of bacterioplankton and biofilm-forming communities at different diversities. Reduction of bacterial diversity differently affected different functions, and that the presence or absence of certain species might be causing this pattern. However, for ecosystems to function, the interplay of multiple functions, i.e. multifunctionality, has to be sustained over long periods of time. In bacterial biofilm communities reduced diversity affected multifunctionality, as reflected by extracellular enzyme activities. A continuous cultivation system was used to address the importance of diversity for resistance and resilience upon environmental perturbation. The analysis of co-occurrence of bacterial taxa showed that the communities form a dense network before the perturbation and that these patterns are disturbed by the environmental perturbation. The final chapter of the thesis presents experimental evidence for the positive effects of temporal and spatial refuges for bacterial communities and the functions they provide. Overall, I found several indications for a lower amount of functional redundancy as previously assumed and it becomes apparent from this thesis that a multifunctional perspective and the consideration of environmental heterogeneity is pivotal.

The Effects of Tropical Forest Management on Biodiversity and Ecosystem Functioning Eleanor M. Slade 1. Between 35 % and 50 % of all closed-canopy tropical forest has been lost, and the rate of deforestation continues to increase throughout the tropics. Despite a wealth of literature on the effects of tropical forest disturbance on the diversity and composition of a variety of taxa, there is still no clear consensus on the value of disturbed forests for biodiversity. 2. If forest management practises are to be sustainable in the long-term they should maintain both biodiversity and ecosystem functioning (the interactions and processes of the ecosystem), as well as a timber harvest. However, few studies have investigated the extent to which ecosystem functioning is reduced in logged forests. The effects of different logging intensities on a variety of taxa, and the ecosystem processes with which they are associated, were assessed in the Danum Valley Conservation Area in Sabah (Malaysian Borneo). 3. Even under high logging intensities, the forests of Sabah appear to have been managed in a way that maintains timber yields in the short-term. However, other aspects of forest structure had been affected, which could have important consequences ecologically, and for the long-term sustainability of timber harvests. 4. Combining field studies with manipulative experiments allows assessment of the impacts of species changes associated with habitat modification on measures of ecosystem functioning. Dung beetle (Coleoptera: Scarabaeidae: Scarabaeinae) functional group richness and composition were manipulated in a series of field experiments. Certain functional groups and species were found to have a greater impact on ecosystem functioning than others; nevertheless a full complement of species was needed to maintain full ecosystem functioning. 5. Dung beetles appeared to be relatively robust to changes in forest structure associated with selective logging, but species richness was reduced with high-intensity logging. There was a corresponding decrease in ecosystem functioning (dung and seed removal) with a decrease in species richness, and a decrease in the biomass of large nocturnal tunnellers, suggesting that although some species are dominant, rare species are also needed to preserve full ecosystem functioning. 6. A complex interaction between birds and ants resulted in reduced herbivory of seedlings of the important timber tree, Parashorea malaanonan, in some instances. However, this interaction was not affected by either selective or high intensity logging. Seedfall of P. malaanonan, was reduced in logged forest compared to primary forest. Despite insect seed predation being higher in primary forest, there was still successful recruitment during a non-mast year. Parasitism of insect-predated seeds was found to be inversely density dependent, and was higher in logged forest where seed predation was lower. 7. The results of this thesis suggest that the forests of Sabah appear to be being logged under a management system that is compatible with sustainable timber management, but not necessarily sustainable forest management. Low intensity selective logging seems to preserve much of the original forest structure, biodiversity and ecosystem functioning compared to logging at higher intensities. However, ecosystem processes were variable in their response to logging, suggesting that management decisions should be based on the consideration of multiple taxa and processes.

Orientador: Gustavo Quevedo Romero
Texto em português e inglês
Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia
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Resumo: Com a intensificação das transformações dos sistemas naturais pela atividade humana, o entendimento dos processos que afetam as comunidades e o funcionamento dos ecossistemas tornou-se um tema central para a ecologia contemporânea. As interações entre as espécies, bem como as interações entre as espécies e os componentes abióticos do meio ambiente, afetam tanto os padões de diversidade biológica como funções ecossistêmicas. Neste trabalho, buscou-se compreender o papel relativo das interações predador-presa e dos componentes abióticos sobre as propriedades das comunidades e funcionamento dos ecossistemas. No primeiro capítulo, investiguei o papel do tamanho do habitat sobre os efeitos de predadores terrestres na estrutura de comunidades e funcionamento de ecossistemas adjacentes. O tamanho do habitat modera cascatas tróficas dentro de ecossistemas, deste modo, esperei que efeitos similares do tamanho do habitat poderiam afetar cascatas tróficas que ocorrem através dos limites dos ecossistemas. No segundo capítulo, explorei predições relacionadas a variação no formato de pirâmides tróficas de biomassa ao longo de gradientes ambientais (tamanho do habitat, concentração de detritos e produtividade). Além disso, investiguei a contribuição relativa dos efeitos de consumo direto e do risco de predação nas interações predador-presa como mecanismos estruturadores de pirâmides tróficas de biomassa. No terceiro capítulo, tive como objetivo investigar os efeitos de dois extremos de um gradiente ambiental e os efeitos de predadores sobre os componentes da diversidade de presas detritívoras (i.e., diversidade funcional, filogenética e taxonômica). Além disso, explorei o papel relativo do ambiente, dos predadores e dos componentes da diversidade sobre o funcionamento ecossistêmico (i.e., decomposição e fluxo de nitrogênio). Os resultados encontrados nos três capítulos demonstram que fatores abióticos são cruciais na determinação das propriedades das comunidades, interações predador-presa e, consequentemente, no funcionamento ecossistêmico. O papel relativo dos efeitos cascatas de predadores é altamente dependente das condições ambientais que medeiam as interações entre predadores e presas
Abstract: In the face of the increasing transformation of environmental conditions by human activity, understanding the processes that affect communities and ecosystem functioning has become fundamental goals in ecology. The interactions between coexisting species and, their interactions with the abiotic components of environment, affect the patterns of biological diversity and functions of ecosystems. In this study, I sought to understand the relative role of predator-prey interactions and of abiotic factors on the communities¿ properties and ecosystem functioning. In the first chapter, I investigated the role of habitat size in mediating the effects of terrestrial predators on the structure of communities and the functioning of adjacent ecosystems. Habitat size mediated trophic cascades within ecosystems; therefore, I expected that similar effects of habitat size affect cross-ecosystem trophic cascades. In the second chapter, I explored predictions related to the variation of trophic pyramids of biomass across environmental gradients (i.e., habitat size, detritus concentration and productivity). Furthermore, I investigated the relative contribution of consumptive and non-consumptive effects of predators on the shape of trophic pyramids of biomass. In the third chapter, I sought to investigate the effects of two extremes of an environmental gradient and the effects of predators on the components of detritivores diversity (i.e., functional, phylogenetic and taxonomic). Moreover, I explored the relative role of environment, predators and detritivore diversity components on the functioning of ecosystems (i.e., detritus processing and nitrogen flux). The results from this study demonstrated that abiotic factors are crucial determinants of community properties, predator-prey interactions and ecosystem functioning. The relative role of the predators cascading effects are strongly dependent on the environmental conditions which mediate the interactions between predators and prey
Doutorado
Ecologia
Doutora em Ecologia

The relationship between biodiversity and ecosystem functioning is important in maintaining agroecosystem sustainability. Plant-microbe symbioses, such as exists between the grass tall fescue (Schedonorus arundinaceum) and the asexual fungal endophyte Epichloë coenophiala, can be utilized to enhance agroecosystem functions, such as herbivore resistance. “Novel” E. coenophiala strains that vary in the production of mammal- and insect-toxic compounds have been identified, inserted into tall fescue cultivars, and are planted in pastures globally. Novel fungal endophyte-tall fescue associations may have divergent ecosystem function effects. This study assessed effects of different fescue-endophyte symbiotic combinations on pasture ecosystem function, including aboveground (fescue biomass, plant species richness, alkaloid synthesis, arthropod abundance) and belowground (soil microbial biomass, soil enzyme activity, trace gas fluxes) parameters. Results showed no significant effects of increasing symbiotic diversity within a fescue stand on aboveground measurements, bar arthropod abundance and alkaloid synthesis. Most soil parameters quantified had significant symbiotic diversity effects. For example, soil microbial biomass decreased whereas soil enzyme activity increased with increasing symbiotic diversity. Overall, our results suggested that increasing symbiotic diversity had weak to moderate effects on aboveground processes and stronger effects on certain belowground processes, indicating that symbiotic diversity can impact ecosystem functions and warrants further research.

How anthropogenic changes to species composition and diversity are likely to affect the properties of the ecosystems of which they are an integral part, and by extension the goods and services humans derive from them, is a key question in ecology. Despite over a decade of vigorous empirical research and theoretical developments, there remain many unknowns. Using intertidal rockpools and laboratory marine mesocosrns, I used a variety of approaches to address several of these relatively poorly studied issues. In particular, the work presented here focused on the relative roles of species composition and richness, as well as the extent to which such effects are context-dependent. The first study (Chapter II) takes advantage of a successional gradient of macroalgal species composition and diversity resulting from the periodic addition of artificial rockpools to a coastal defense structure. The results show that the focal ecosystem properties (macroalgal biomass and productivity) were largely determined by species composition (and functional traits). Macroalgal species evenness, but not diversity, peaked at intermediate stages during the chronosequence, but no measure of diversity had a detectable influence on primary productivity. The results confirm the prediction that effects of species diversity will be outweighed by compositional changes during succession. I used an experimental approach in Chapters III to V, manipulating the composition and richness of intertidal molluscan grazers (Chapters III and V) and intertidal predatory crabs (Chapter IV) and measuring their effects on prey assemblages as focal ecosystem processes. In a 13-month field experiment (Chapter III) I found that effects on the composition and functioning of developing rockpool communities were determined by grazer composition, not the number of species. Laboratory mesocosm experiments show that the influence of species richness on ecosystem processes can be context-dependent. The effect of resource partitioning (of the multi-species prey assemblage) among predators was only detectable at high predator densities where competitive interactions between individual predators were magnified. A factorial experiment using the rate of algal consumption by molluscan grazers as a response variable, provides the first empirical test of the prediction that the balance between species richness and identity effects can be determined by the degree of spatial heterogeneity (Chapter V). Species identity had strong effects on homogeneous substrates, with the identity of the best-performing species dependent on the substrate. The strengths and limitations of the predominantly small-scale experimental approach employed here are discussed (Chapter VI).

Biological communities are changing across the globe as a result of anthropogenic pressures; abundances of individuals are declining within populations and species are becoming extinct. Biological diversity and trophic complexity in grasslands and soil food webs are positively associated with the cycling of nutrients in soil and water, primary productivity and decomposition. Since these ecosystem processes underpin a number of goods and services to society, human-driven changes in the structure of ecosystems could negatively impact upon human wellbeing. However, the majority of our knowledge of the role of biodiversity in ecosystem functioning comes from studies conducted in temperate grassland systems. Consequently, our understanding of how of higher-level organisms influence ecological processes in different ecosystems is limited. This thesis aims to address these knowledge gaps by investigating how dung beetle traits and functional diversity influence the secondary dispersal of seeds and the emergence and survival of seedlings in the northeastern Brazilian Amazon. My first research aim was to understand the importance of intraspecific variability in dung beetle traits for the accuracy of functional diversity (FD) indices (Chapter 2). This chapter demonstrates that intraspecific differences in dung beetle traits are small compared to between species differences. However, failure to include intraspecific variability resulted in large errors in the calculation of FD indices when describing small and/or species poor communities. Second, I investigated how dung beetle diversity influences secondary seed dispersal, and the role of environmental context in modulating relationships. Here I reveal positive relationships between dung beetle functional diversity and both the probability of seed burial and the dispersion of seeds throughout the soil profile. However, these patterns were dependant on soil type and thus environmental context (Chapter 3). Finally, I explored the multitrophic significance of findings from Chapter 3 by testing how dung beetle communities affect the burial of different sizes of seeds and emergence and survival of seedlings (Chapter 4). Results from this chapter demonstrate how dung beetles could influence vegetation regeneration because beetle diversity negatively affected the likelihood that experimental seeds emerged from the soil surface, but positively impacted on the likelihood that emerged seeds survived until the end of the experiment period. Furthermore, I show that large seeds could be more vulnerable to anthropogenic driven changes in dung beetle communities than smaller seeds. These research aims were realised through field-based experiments from which I sampled and identified approximately 2,650 dung beetles from 180 naturally formed communities, collected more than 17,000 morphological trait measurements and sieved approximately 11 tonnes of soil in search of 1800 seed mimics. Overall, this work demonstrates diversity in dung beetle communities is positively associated with the ecological processes they govern but that environmental context is instrumental in modulating biodiversity-ecosystem functioning relationships. I use the outcomes from this work to discuss the challenges in describing diversity-functioning relationships across trophic levels. Finally, I highlight that ecological processes are the product of complex species-specific interactions, dependent on the biotic and abiotic environment. Therefore, predicting the consequences of anthropogenic-driven species losses for the structure and functioning of natural systems is a major research challenge.