Dissertations / Theses on the topic 'Trophic guild and community structure'

The emerald ash borer (EAB, Agrilus planipennis Fairmaire) (Coleoptera: Buprestidae) is a non-native wood boring beetle that is causing extensive ash (Fraxinus spp.) mortality in eastern North America, affecting both urban and wildland forests and drastically altering forest structure and composition. As EAB-induced ash mortality progresses, native arthropod associates of ash forests are impacted by the effects of rapid and broad scale tree mortality. These include loss of food source, increased canopy gap formation, alterations in litter inputs causing shifting temperature and moisture regimes on the forest floor, and significant accumulation of coarse woody debris. I assessed the sub-canopy arthropod community in five forests, all in different stages of the invasion process, from introduction through impact. Additionally, I assessed the ground level arthropod community in a post EAB-invaded forest with 100% mature ash mortality. Arthropod communities were assessed at the ordinal level, and with a focus on coleopterans, they were further classified to families and trophic guilds to analyze abundance, richness, and diversity. Due to their overwhelming abundance, I identified scolytines collected in the post EAB-invaded forest to species to see if the EAB-invasion was part of a greater invasional meltdown. My results indicate that the EAB-invasion in North America is affecting the native coleopteran communities associated with these forests.

Entre les fleuves Amazone et Orénoque, la frange côtière atlantique de l’Amérique du Sud (1500 km) est considérée comme la plus vaseuse au monde, conséquence des apports de sédiments en suspension de l’Amazone. Malgré la forte variabilité et l’instabilité de ces vasières uniques au monde, elles apparaissent comme des écosystèmes très productifs et sont des habitats clés dans l’accomplissement du cycle de vie des espèces de poissons et d’oiseaux qui les exploitent. Cependant, les connaissances sur les communautés biologiques qui y sont associées restent au niveau exploratoire. Ce travail de thèse vise donc à décrire la structure de l’endofaune benthique intertidale des vasières guyanaises et à définir son fonctionnement dans des environnements vaseux tropicaux très instables. Comme prévu, la forte instabilité des sédiments a entraîné une très faible diversité des assemblages de la macrofaune et de la méiofaune. Néanmoins, les communautés benthiques des vasières guyanaises ont montré une abondance remarquablement élevée avec la dominance d'espèces opportunistes de petites tailles. 39 taxons de la macrofaune ont été trouvés tandis que la méiofaune était moins diversifiée avec la présence de 34 taxons. Le tanaidacée Halmyrapseudes spaansi et le polychète Sigambra grubii sont les deux espèces de macrofaune les plus abondantes, largement réparties le long de la côte guyanaise. De même, le nématode Pseudochromadora spp., suceur d’épistrate, et Halomonhystera sp. 1 (non deposit feeders) étaient les deux espèces de méiofaune les plus abondantes sur chacune des stations. La distribution des communautés benthiques sont spécifiques aux sites d’étude et varie saisonnièrement. Les assemblages en zone estuarienne (Sinnamary) étaient plus diversifiées que dans la zone de vasière nue (Awala), alors que les abondances des communautés benthiques étaient toujours plus élevées en saison humide qu’en saison sèche. Les facteurs abiotiques et biotiques ont influencé significativement les communautés benthiques. Néanmoins, les changements dans la structure de la communauté benthique induits par la disponibilité des sources alimentaires (chl a) et la pression de prédation étaient tout aussi importantes que les variations des assemblages imposées par les paramètres abiotiques (teneur en eau, salinité ...). En particulier, une forte corrélation a été trouvée entre la méiofaune et le microphytobenthos. Les mesures isotopiques de différents compartiments des vasières ont non seulement révélé le rôle central du microphytobenthos dans la composition du régime alimentaire de la méiofaune, mais ont également montré l'importance écologique de la méiofaune comme principale source de nourriture pour les petits oiseaux limicoles et les poissons côtiers. La méiofaune et le microphytobenthos rentrent dans le régime alimentaire de trois poissons côtiers en grande proportion, alors que les oiseaux limicoles migrateurs présentaient une plus grande diversité de proies. Cependant, la contribution relative des tanaidacées dans le régime alimentaire des oiseaux limicoles était étonnamment faible. Le travail de thèse a permis d'améliorer notre compréhension de la structure de l’endofaune benthique intertidale des vasières guyanaises et de définir son fonctionnement dans des environnements vaseux tropicaux très instables. Ce travail a permis de construire, pour la première fois, un modèle conceptuel de réseau trophique des vasières intertidales mobiles guyanaises<br>Locating between the Amazon and Orinoco Rivers, the 1500 km-long Atlantic coastline of South America are considered as the muddiest areas in the world due to the large discharge of suspended sediment from the Amazon. Despite the extreme morphodynamics of these ecosystems, the Guianas mudflats are important feeding zones for many shorebirds and fish. However, the state of knowledge on benthic organisms associated with these highly unstable environments is still at an exploratory stage. This study, therefore, aims to describe the structure and dynamics of the intertidal benthic infauna in the Guianas mudflats and to define its functioning in such highly unstable tropical muddy environments. As expected, the high instability of the sediment resulted in very low diversity of both macrofauna and meiofauna assemblages. Nonetheless, the infauna communities of the Guianas mudflats showed remarkably high abundance with the predominance of small-sized opportunistic species. A total of 39 operational taxonomic units of macrofauna was recorded while meiofauna was less diverse with the occurrence of 34 taxa. The tanaid Halmyrapseudes spaansi and the polychaeta Sigambra grubii are the two most abundant macrofauna species, which widely distributed along the Guianas coast. Likewise, the nematodes epistrate feeder Pseudochromadora spp. and non-deposit feeders Halomonhystera sp. 1 were the principal components of meiofauna communities in every station. The distribution patterns of the infauna were both site-specific and seasonal variation. The assemblages in estuarine habitat were more diverse than in the bare mudflat habitat, while infauna abundances in the WS were always higher than in the DS. Both abiotic and biotic factors significantly influenced the benthic communities. Nevertheless, the changes in benthic community structure induced by food source availability (chl a) and predation pressure were more prominent than the assemblage variations imposed by abiotic parameters (mud content, salinity…). Particularly, the tight coupling between meiofauna and MPB was observed in both distribution patterns and trophic structures. The isotopic measurements of different intertidal compartments not only revealed the pivotal role of MPB on structuring meiofaunal coummunities, but also indicated the ecological importance of meiofauna as the main food source for the small shorebirds and coastal fish. Meiofauna and MPB entered the diet of three coastal fish in great proportion, whereas the migrating shorebirds showed a wider diet breadth. The isotopic ratios were perfectly matched with the feeding guilds assigned by morphological features. However, the relative contribution of tanaids to the top epibenthic predators were surprisingly lower than expected. The thesis has increased our understanding of the Guianas infauna communities, and revealed for the first time a conceptual food web model of these unique intertidal mudflats

Changes in macro-moth populations related to habitat creation were monitored using light-traps between 1993 and 1995 on low-lying, previously intensively managed, arable land at College Farm, Long Wittenham, Oxfordshire (grid reference SU 554 939). Research measured the effects of the establishment of set-aside and agro-forestry in farmland on macro-moth abundance, diversity, guild and seral structure. College Farm data from the newly created habitats were compared with unchanging and established ones within the Farm, a nearby Garden (500 metres away at Long Wittenham) sampled concurrently, and data from other farmland, gardens and woodland sites. Mobility was measured within College Farm and between it and the Garden at Long Wittenham. Large numbers of moths, of a comparatively small number of ubiquitous species, were found within College Farm. Abundance, which can be as high as in woodlands, indicated that the farmland environment is less hostile to moths than has been previously thought. Analyses showed rapid and large increases of abundance in the newly created habitats on College Farm related to the establishment of a more diverse and architecturally more complex ground flora. The differences in abundance between the Farm and Garden, where moths were generally more numerous but which were sampled with more effective light traps, progressively decreased throughout the research period. Changes 10 abundance were less marked in the Garden in line with regional population changes. Species richness was low on College Farm in comparison to woodlands and gardens. Within the Farm it was highest along a linear drainage Ditch but increased rapidly in a tree Plantation in association with greater diversity of the ground flora. Species richness was found to be constant between years in the Garden. Both the Farm and Garden and other sites investigated in Oxfordshire and elsewhere in Britain exhibited constant species proportions within the larger families, sub-families and genera. Alpha diversity was constant for the Farm as a whole and for the Garden (and did not increase after the first field season at either site) but was found to increase significantly in a tree Plantation in the second year after its establishment. Removal of vagrant species and individuals from analyses of the Farm and Garden totals showed that alpha diversity increased for the Farm (but not the Garden) between 1993 and 1995. Diversity, dominance, evenness and dissimilarity measures showed distinct habitat differences on the Farm and that the tree Plantation improved to a similar state to that of the permanent Ditch in its second year. These improvements were not associated with the presence of trees but were related to increased herb diversity and complexity. Intensive management in the Plantation in 1995 resulted in reductions in diversity. Analyses of guild structure showed that herb feeding individuals were most abundant in a tree Plantation, associated with the ground flora, and that grass feeders dominated the catches in a Barley-field, along a drainage Ditch and in a field of Set-aside. There were some marked changes between years with grass feeders contributing greater numbers to all habitat totals, being greatest in 1995. Abundance changed asynchronously and disproportionally for herb, grass and polyphagous guilds on the Farm in comparison to the changes in the Garden indicating that habitat creation was the cause. The proportions of herb, grass, woody-plant, polyphagous and other moth species were found to be constant on the Farm and in the Garden and in all other habitats investigated. Species represented by fewer than 10 individuals on the Farm and fewer than 100 individuals in the Garden were found to comprise the vagrant fraction of their, respective, totals. The majority of woody-plant feeding species and the guild 'others' were contained within this fraction. There was no evidence for an increase in abundance or species richness of woody-plant feeders as a consequence of tree planting on the Farm. The majority of individuals on the Farm and in the Garden were representatives from early seral communities. Almost all others were contained within the vagrant fraction of the faunas in these sites. Abundance changed asynchronously and disproportionally for early seres on the Farm in comparison to the changes in the Garden indicating that habitat creation was the cause. Species proportions within all seres were found to be constant on the Farm, in the Garden and in other habitats investigated. Mark-release-recapture studies showed that certain species arc highly mobile in farmland, others are comparatively poorly mobile, and that patterns of mobility change (mobility between Farm habitats increased each year for some species) in association with habitat creation. Moths increasingly remained within the Farm as evidenced by progressive increases in recapture proportions there, progressive decreases in recaptures of Farm marked moths in the Garden, and increasing proportions of multiple recaptures.

Management of fisheries resources is increasingly broadening its scope from single-species approaches to more holistic, ecosystem-based approaches that account for interactions of fish with a variety of ecological factors, such as predators, prey, and habitat. This ecosystem based fisheries management (EBFM) approach requires thorough biological and ecological understanding of systems pertaining to community structure, habitat suitability, and food web interactions. to strengthen the ecological underpinnings of EBFM efforts in Chesapeake Bay, the largest estuary in the USA, I conducted synoptic analyses examining the structure, function, and patterns of the bay's demersal fish community. This research relied on I0 years of data from a multi-species, bimonthly bottom trawl survey of the Chesapeake Bay mainstem. The unifying objectives of this work were to 1) synthesize basic biological and ecological information of many Chesapeake Bay fishes, and 2) examine the environmental drivers of community structure and trophic interactions in the Bay. One major hypothesis underlying the more detailed research objectives for each component was that bay-wide patterns in biomass and feeding habits of Chesapeake Bay fishes were mostly driven through bottom-up processes governed by a blend of small- and large-scale environmental factors. as food web structure and trophic interactions are governed by the presence, distribution, abundance, and behavior of species, Chapter 1 focused on evaluating patterns for these basic biological characteristics for a large suite of 50 species and investigating environmental factors that influence the community trends. Univariate and multivariate statistical modeling revealed that the demersal fish community (dominated by five species) was strongly structured along a salinity gradient, and other factors (e.g. dissolved oxygen, temperature, month, and year) helped regulate biomass and diversity trends. Chapter 2 synthesized diet information for 47 fish species, demonstrated the role of five prey groups (mysids, fishes, bivalves, polychaete worms, and crustaceans) in differentiating feeding guilds, and highlighted the importance of non-pelagic prey groups (especially the hyper-benthic mysids) in supporting the nutritional needs of fishes. Diets of 12 predator species were investigated in more detail in Chapter 3 to infer the dynamics of four important prey groups (mysids, bay anchovy, polychaetes, and bivalves) using advanced statistical modeling techniques. Results revealed generally coherent consumption trends across predators for a given prey, suggestive of prey availability driving consumptive patterns. Synchronous annual peaks in prey consumption were indicative of pulses in prey production (particularly mysids and bivalves) that were exploited by predator populations. to evaluate the population-scale effects of these bottom-up alterations in prey productivity, Chapter 4 relied on a simulation model to examine the potential effects that these annual changes in prey availability could have on consumption and production of one representative predator species. The model indicated that enhanced individual growth resulting from pulses in prey production could generate substantial gains in predator spawning stock biomass, recruitment, and fishery yield. However, the bottom-up effects on predator production had only modest effects on rebuilding times of a depleted population relative to controls on fishing mortality. This research represents one of the largest studies on community structure and trophic interactions for demersal fishes in an estuarine environment, contributing to a broader understanding of fish ecology within a complex and dynamic system. By filling research gaps identified for EBFM in Chesapeake Bay, this body of work also supports a more holistic management approach for the sustainable use of resources from the Chesapeake Bay and coastal waters of the Northwest Atlantic Ocean.

Ecological communities are most commonly structured by a mixture of bottom-up processes such as habitat or prey, competition within the same trophic level, and top-down forces from higher trophic levels. Carnivore guilds play a vital role in the broader ecological community by stabilizing or destabilizing food webs. Consequently, factors influencing the structure of carnivore guilds can be critical to patterns in ecosystems. Coyotes (Canis latrans), bobcats (Lynx rufus), gray foxes (Urocyon cinereoargenteus), raccoons (Procyon lotor), red foxes (Vulpes vulpes), and striped skunks (Mephitis mephitis) occur sympatrically throughout much of their geographic ranges in North America and overlap in resource use, indicating potential for interspecific interactions. Although much is known about space use, habitat relationships, and activity patterns of the individual species separately, little is known about factors that facilitate coexistence and how interactions within this guild influence distribution, activity, and survival of the smaller carnivores. For example, gray fox populations appear to have declined in Illinois since the early 1990s and it is unknown if the increase in bobcat and coyote populations during the same time period is the cause. I conducted a large-scale non-invasive carnivore survey using an occupancy modeling framework to quantify factors affecting the structure of this widely-occurring carnivore guild. I used baited remote cameras during 3-week surveys to detect carnivores at 1,118 camera-points in 357 2.6-km2 sections (clusters of 3-4 cameras/section) in the 16 southernmost counties of Illinois (16,058 km2) during January-April, 2008-2010. I collected microhabitat data at each camera-point and landscape-level habitat data for each camera-cluster. In a multi-stage approach, I used information-theoretic methods to develop and evaluate models for detection, species-specific habitat occupancy, multi-species co-occupancy, and multi-season (colonization and extinction) occupancy dynamics. I developed hypotheses for each species regarding the occupancy of areas based on anthropogenic features, prey availability, landscape complexity, and vegetative landcover. I used photographic data, Poisson regression, and mixed-model logistic regression to quantify temporal activity of carnivores in the study area and how interspecific factors influence temporal patterns of activity. Of the 102,711 photographs of endothermic animals I recorded photographs of bobcats (n = 412 photographs), coyotes (n = 1,397), gray foxes (n = 546), raccoons (n = 40,029), red foxes (n = 149) and striped skunks (n = 2,467). Bobcats were active primarily during crepuscular periods, and their activity was reduced with precipitation and higher temperatures. The probability of detecting bobcats at a camera point decreased after a bobcat photograph was recorded, suggesting avoidance of remote cameras. Across southern Illinois, bobcat occupancy at the camera-point and camera-cluster scale (point = 0.24 ± 0.04, cluster = 0.75 ± 0.06) was negatively influenced by anthropogenic features and infrastructure. Bobcats had high rates of colonization (0.86) and low rates of extinction (0.07) during the study, suggesting an expanding population, but agricultural land was less likely to be colonized. The number of coyote photographs decreased with increased temperature, but increased with previous coyote photographs, suggesting an attraction to bait in cold weather. Nearly all camera clusters were occupied by coyotes (cluster = 0.95 ± 0.03) during the entire study. At the camera-point scale, coyote occupancy (overall point = 0.58 ± 0.03) was higher in hardwood forest stands with open understories than in other habitats. Similar to coyotes, gray foxes were more likely to be photographed in cold weather and after a previous detection had occurred. However, gray fox occupancy was much lower (point = 0.13 ± 0.01, cluster = 0.29 ± 0.03) at all scales. At the camera-cluster scale, with a buffer-area size that represented 20% of the estimated home-range size of gray foxes, the species selected spatially-complex areas with high proportions of forest, and low proportions of grassland and agriculture land cover. Gray fox occupancy of camera clusters was positively related to anthropogenic features within 100% estimated home-range buffers. Collectively, the results suggest gray fox occupancy was greatest near, but not in, anthropogenic developments. Red foxes occupied a similar proportion of the study area as gray foxes (point = 0.12 ± 0.02, cluster = 0.26 ± 0.04), but were more closely associated with anthropogenic features. Indeed, at all three scales of red fox occupancy analysis, anthropogenic feature models received more support than other hypotheses. Camera-cluster extinction probabilities were higher for both gray foxes (0.57) and red foxes (0.35) than their colonization rates (gray fox = 0.16, red fox = 0.06), suggesting both species may be declining in southern Illinois. I recorded more striped skunk photographs in January and February (i.e., during the breeding period) than in March and April. Striped skunks occupied a large portion of the study area (point = 0.47 ± 0.01, cluster = 0.79 ± 0.03) and were associated primarily with anthropogenic features, especially if the features were surrounded by agricultural land and not forest. Raccoons were essentially ubiquitous within the study area, being photographed in 99% of camera clusters. In some instances, the presence of other carnivores appeared to be an important factor in the occupancy of the 4 smaller species, but in general, habitat models were more supported than co-occurrence models. Habitat had a stronger influence on the occupancy of gray foxes and red foxes than did the presence of bobcats. However, the level of red fox activity, represented by the number of photographs recorded in a camera cluster, was negatively correlated with bobcat activity. Gray fox occupancy and level of activity were reduced in camera-clusters occupied by coyotes, but were not related to bobcat occupancy. When not considering the presence of coyotes, gray foxes appeared to use camera points with fewer hardwood and more conifer trees, which was counter to previous findings. However, when adding the effect of coyote presence, gray fox point models indicated a positive relationship with hardwood stands. Therefore, gray foxes were more likely to occupy camera points in hardwood stands than conifer stands if coyotes were also present; suggesting that hardwood stands may enhance gray fox-coyote coexistence. The 2 fox species appeared to co-occur with each other at the camera-point scale more frequently than expected on the basis of their individual selection of habitat. Similarly, camera-point occupancy of red foxes was higher when coyotes were present. These apparent canid associations may be a response to locally-high prey abundance or an unmeasured habitat variable. Activity levels of raccoons, bobcats, and coyotes were all positively correlated. Collectively, my results suggest that although gray foxes and red foxes currently coexist with bobcats and coyotes, the foxes have reduced activity in the areas occupied by larger carnivores, especially when bobcats and coyotes are highly active. Further, hardwood stands may contain trees with structure that enhances tree-climbing by gray foxes, a behavior that probably facilitates coexistence with coyotes. Therefore, efforts to manage gray foxes should focus on maintaining and increasing the amount of mature oak-hickory forest, which presumably provides a suitable prey base and refugia from intraguild predation. Additionally, the varying results from different scales of analyses underscore the importance of considering multiple spatial scales in carnivore community studies.

Nearshore marine environments are known to be highly productive systems with relatively high faunal diversity and abundances, but these systems are particularly vulnerable to negative impacts from anthropogenic disturbances that can result in habitat degradation. Despite these challenges, many shark species of various life stages utilize coastal shelf habitats, inshore estuaries, and bays. The inshore habitats of Cumberland and Nassau Sounds in northeast Florida have been proposed as potential nursery grounds by earlier work, but this suggestion did not satisfy all of the standard criteria of shark nursery designation. It has recently been stated that the combination of surveys inside and outside suspected nursery habitats, especially those incorporating mark-recapture studies, would provide a very comprehensive test of the nursery criteria. A primary objective of the present study was to initially describe the composition and abundance of shark populations utilizing the nearshore habitats of northeast Florida, while also comparing them to inshore communities, with emphasis on spatial and temporal variations in assemblages. Fishery-independent longline sampling was conducted across the region and while considerable overlap of species were observed, significant differences in community structure between inshore and nearshore locations were detected. Specifically, the inshore waters of the First Coast support nursery habitat designation for Atlantic sharpnose, blacktip, and sandbar sharks after satisfying the accepted criteria. Given the high amounts of spatial and temporal overlap observed along the First Coast, relative trophic niche dynamics were also investigated via stable isotope analysis of two tissue types. These results revealed varying trophic niche sizes in the long term, but suggest some degree of shared resource use when animals are present on the First Coast. The identification of factors that influence coastal shark habitat utilization, such as competition and resource use, can contribute to understanding and predicting how they may respond to future environmental changes.

Coastal ecosystems are more than microhabitats for marine species. Acting as atmospheric carbon filters, species in coastal environments are directly and/or indirectly associated with transferring organic carbon to species at higher trophic levels. However, the progressing change in global climatic conditions has created the need to assess the consequences of the shifting conditions on both direct and indirect interactions of physical and biological parameters at species and/or community levels. From these perturbations, the effects of biotic homogenization on ecosystem functioning and resilience can also be realised. Herein, I discuss the effects of temperature, nutrients, biotic interactions and habitat characteristics on community dynamics within intertidal rock pool systems on the south coast of South Africa using complementary qualitative and quantitative analytical methods. Seasonality had a significant impact on rock pool species with changes in composition and higher richness in winter than summer. The first two axes of the Canonical Correspondence Analysis (CCA) of the plant and animal communities each explained ~20% of the relationship between physico-chemical parameters and biological variables. The CCA highlighted that seasonal shifts in chlorophyll-a, conductivity, salinity, water depth, surface area and substratum type indirectly influenced species composition. For example, pools with heterogenous substratum comprising a mixture of sand and rock exhibited higher species diversity than homogenously bedded pools. Furthermore, a Bayesian analysis of community structure based on stable isotope ratios was used to assess how trophic pathways of carbon and nitrogen elements reflected community composition and richness. Isotopic biplots showed an increase in food web size, food chain length and the trophic positions of fish and some gastropods in winter compared to summer. There was greater dietary overlap among species in larger pools. In addition, while isotopic nearest neighbour distance and species evenness also showed a positive increase with pool size in summer, the same metrics were almost constant across all pool sizes in winter. These changes in food web packing and species evenness suggest seasonal preferences or migration of species in summer from small pools to larger pools with stable physico-chemical parameters. Furthermore, the presence of fish was seen to promote trophic diversity within some pools. The results from laboratory microcosm grazing experiments demonstrated significant direct and indirect effects of temperature and nutrients within plankton communities. Copepod grazing had an indirect positive influence on phytoplankton biomass and size structure while the interactive effects of temperature and nutrients had contrasting effects on both phytoplankton communities and copepod biomass. Shifts in water chemistry and nutrient treatments were also observed in the presence of copepods. Phosphate addition had a recognisable impact on plankton communities. The presented synthesis of the literature mainly highlighted that positive effects at one trophic level do not always positively cascade into the next trophic level which is evidence of complex interactive biotic, habitat and water chemistry effects within these intertidal ecosystems. Thus, to further understand cascading effects or community structure functioning in general, there may be a need to incorporate and understand species functional traits and how they contribute to trophic diversity, community restructuring and functioning in coastal habitats.

2012/2013<br>Heterotrophic nanoflagellate (HNF) grazing is one of the major source of prokaryotic mortality in marine ecosystems, acting as a strong selection pressure on communities. Protozoans may thus affect prokaryotic abundance and alter the diversity and the taxonomic composition of the prey community, as individual prokaryotes can develop distinct grazing-resistant mechanisms. Moreover, the microbial loop is well known to regulate carbon fluxes in surface marine environments but few studies have quantified the impact of HNF predation on prokaryotes in the dark ocean. The present work was aimed to: (1) quantify the impact of HNF predation on the deep prokaryotes biomass; (2) investigate if and how prey diversity varies in response to different predation pressure; (3) define taxonomic community composition in studied areas and identify most affected prokaryotic phylotypes by HNF grazing (4) evaluate the effects of small HNF (<3 µm), which are known to dominate nano-sized compartment and represent the main bacterivores in aquatic ecosystems, being an important link between bacteria and larger protists; (5) evidence differences in community sensitivity to grazing between surface and mesopelagic ecosystems (6) identify the main environmental drivers shaping microbial community diversity. Predation experiments were performed with surface and mesopelagic water samples collected from the Southern Adriatic and Northern Ionian basins. An additional predation experiment was set up in the North-eastern Adriatic Sea. We coupled the traditional ‘dilution method’ with high-throughput molecular analysis (ARISA and Ion Torrent/454 sequencing) to provide a quantitatively and qualitatively evaluation of the grazing process occurring in marine microbial communities. The present work is structured by four manuscripts in preparation and one manuscript already submitted. 1. Heterotrophic nanoflagellate grazing on picoplankton in deep waters (manuscript in preparation) 2. Effects of heterotrophic flagellate predation on bacterial community diversity (manuscript in preparation) 3. HNF grazing impact on taxonomic composition of marine prokaryotic community (manuscript in preparation) 4. Environmental drivers structuring surface and deep bacterial communities in Adriatic and Ionian Seas (manuscript in preparation) 5. Biodiversity changes of bacterial community under predation pressure analyzed by 16S rRNA pyrosequencing (manuscript submitted) My PhD research led to important progresses in the comprehension of microbial dynamics regulating carbon cycles and bacterial diversity in the Adriatic and Ionian basins. Prokaryotic abundance and biomass were one order of magnitude higher in the photic than in the aphotic layers of Southern Adriatic and Ionian Seas (surface biomass 1.68 ± 1.76 µC L-1, deep biomass 9.00 ± 2.11 µC L-1). The Northern Adriatic community presented the highest biomass value (57.46 µC L-1), according to its richer trophic status. All in situ communities displayed the same evenness, being dominated by rare phylotypes. Rare taxa were confirmed to represent the major contributors of microbial communities, with only a few phylotypes dominant. Mesopelagic bacterial communities were as rich and variable as surface assemblages, despite the significant biomass decrease along the water column. Natural archaeal assemblages were characterized by very low richness as we recovered only two genera (Cenarchaeum and Nitrosopumilus), while in situ bacterial communities were composed by the six major marine phyla (Proteobacteria, Cyanobacteria, Bacteroidetes, Actinobacteria, Firmicutes and Deinococcus-Thermus), whose contribution varied according to sampling depth. Flagellates were demonstrated to efficiently control their preys (ingestion rates: 7.86-22.26 µg C L-1 in surface experiments, 0.53-10.61 µg C L-1 in deep experiments), causing important losses in the potentially produced prokaryotic biomass. Despite picoplankton and HNF abundance reduction with depth contrasts with the hypothesis that at least 108 picoplanktonic cells L-1 are necessary to sustain HNF community, our data confirm that also in mesopelagic waters prey and predator concentrations are sufficient to sustain efficient microbial food webs. HNF grazing modified bacterial community diversity in both surface and deep marine systems but with different strength. Mesopelagic communities were more sensitive to grazing impact, evidencing a bell-shaped response to the increasing ingestion rates. Moderate-high top-down control preserved or enhanced bacterial diversity, that fell at low predation. In upper communities grazing did not induce wide variations of bacterial richness and evenness, revealing to be more stable. Small HNF (<3 µm) were the dominant size fraction within flagellate communities and likely constituted the main bacterivores. After the removal of large HNF, a higher fraction of prokaryotic phylotypes was affected. Larger protists partially reduced small flagellate impact on their preys. Larger HNF had a more important role in photic systems compared to mesopelagic waters. The fraction of bacterial taxa favored or affected by predation when small HNF were the only predators more markedly varied in surface experiments, while few phylotypes changes their behavior between the two size treatments in deep experiments. Some taxa were consumed mainly by larger HNF (3-10 µm), while others were grazed by smaller ones (<3 µm). Over 50% of the predated phylotypes belonged to the rare biosphere, mainly in the surface experiments. Rare bacteria are thus not only a dormant ‘seed bank’ but constitute a fundamental component of microbial food webs and actively vector the carbon transfer toward higher trophic levels, being as important as dominant organisms. Although general patterns applicable to all communities were not found, trends of selectivity over different phylotypes were highlighted within sampling layer along the water column and between different systems. While the majority of predator-prey interactions were characteristic to specific environments, some can be considered common to different systems (e.g. Burkholderiaceae and Pseudomonadaceae were exclusively selected in all mesopelagic sites, Bacterivoracaceae were subjected to small HNF predation independently from sampling site or depth). The Southern Adriatic and Ionian basins were significantly distinguished by both the physicochemical water characteristics and the prokaryotes and protists abundance distributions. Cluster analysis based on Jaccard and Bray-Curtis metrics evidenced that depth and geographical location of sampling sites influenced bacterial community similarity. The Southern Adriatic Sea was clearly distinguished from the Ionian Sea. The Northern Adriatic samples were always separated from the others, coherently with different biotic and abiotic characteristics of the sub-basin. Additionally, temperature, chl a and O2 concentration represented important environmental drivers shaping biodiversity of bacterial communities that inhabit Adriatic and Ionian basins. In conclusion, we evidenced that heterotrophic flagellates control bacterial biomass and select certain taxa among all possible preys, grazing also on the rare ones. HNF predation thus shapes bacterial community structures, which in turn influence the ecosystem functioning. Despite the cell abundance decrease of both predators and preys reduces encounter probabilities, the dark ocean hosts complex microbial food webs, structured around three trophic levels (i.e. prokaryotes, small and large heterotrophic flagellates).<br>I nanoflagellati eterotrofi (HNF) costituiscono una delle principali cause di mortalità dei procarioti in ambiente marino, esercitando una forte selezione sulle comunità predate. Possono modificarne l’abbondanza cellulare e alterarne la diversità e la composizione tassonomica, in quanto le diverse specie procariotiche possono sviluppare distintivi meccanismi di resistenza alla predazione. Mentre l’impatto degli HNF sui procarioti degli acque marine superficiali è ben noto, pochi studi si sono focalizzati sullo studio degli ambienti profondi. Il presenta lavoro di dottorato è stato finalizzato a: (1) quantificare l’impatto della predazione da parte degli HNF sulla biomassa procariotica profonda; (2) capire se e come la biodiversità della comunità predata vari in risposta alla diversa pressione di predazione; (3) definire la composizione tassonomica delle comunità presenti nell’area di studio e identificare i filotipi maggiormente colpiti dalla predazione da parte degli HNF; (4) valutare il contributo dei piccolo flagellati (<3 µm), i quali costituiscono la più abbondante frazione nanoplanctonica e rappresentano i principali organismi batterivori negli ambienti acquatici; (5) evidenziare possibili differenze nella risposta alla predazione tra comunità procariotiche che vivono in acque superficiali e profonde; (6) identificare i principali fattori ambientali che modulano la diversità delle comunità microbiche. Esperimenti di predazione sono stati condotti su campioni di acqua superficiale e mesopelagica raccolti nel Mar Adriatico meridionale e nel Mar Ionio settentrionale. Un ulteriore esperimento è stato condotto nel Mar Adriatico nord-orientale. Il tradizionale metodo delle diluizioni è stato abbinato ad analisi molecolari quali elettroforesi capillare (ARISA) e sequenziamento (Ion Torrent e 454) per consentire una valutazione quali-quantitativa degli effetti della predazione sulle comunità microbiche marine. La presente tesi è costituita da quattro articoli in preparazione e un articolo già sottomesso: 1. Heterotrophic nanoflagellate grazing on picoplankton in deep waters (articolo in preparazione) 2. Effects of heterotrophic flagellate predation on bacterial community diversity (articolo in preparazione) 3. HNF grazing impact on taxonomic composition of marine prokaryotic community (articolo in preparazione) 4. Environmental drivers structuring surface and deep bacterial communities in Adriatic and Ionian Seas (articolo in preparazione) 5. Biodiversity changes of bacterial community under predation pressure analyzed by 16S rRNA pyrosequencing (articolo sottomesso) La ricerca condotta durante il mio dottorato ha portato a interessanti progressi nella comprensione delle dinamiche microbiche che regolano i cicli del carbonio e la diversità batterica nei bacini adriatico e ionico. L’abbondanza e la biomassa delle comunità procariotiche superficiali è risultata un ordine di grandezza superiore rispetto alle comunità profonde in Mar Adriatico meridionale e Mar Ionio (biomassa superficiale 9.00 ± 2.11 µC L-1, biomassa profonda 1.68 ± 1.76 µC L-1). La comunità descritta nel Mar Adriatico settentrionale è caratterizzata dai valori più elevati di biomassa (57.46 µC L-1), coerentemente con l’eutrofia del bacino. I flagellati eterotrofi hanno causando perdite significative nella biomassa procariotica in tutti gli esperimenti condotti, con tassi di ingestione pari a 7.86-22.26 µgC L-1 negli esperimenti superficiali e 0.53-10.61 µgC L-1 negli esperimenti profondi. Un’abbondanza picoplanctonica di 108 cellule L-1 è stata ipotizzata come necessaria per sostenere la comunità degli flagellati. Nonostante l’aumento della profondità comporti una riduzione dell’abbondanza del picoplancton tale da non raggiungere questa soglia, i nostri dati confermano che anche negli ambienti profondi si instaurano interazione preda-predatore sufficienti a sostenere le reti trofiche microbiche. Tutte le comunità in situ hanno mostrato la medesima distribuzione, con prevalenza di filotipi rari e pochi gruppi dominanti. Le comunità mesopelagiche presentano diversità e variabilità analoghe a quelle superficiali, nonostante il decremento in biomassa lungo la colonna d’acqua. Una bassa diversità è stata osservata nelle comunità naturali di Archea, dove sono stati rilevati due soli generi (Cenarchaeum e Nitrosopumilus), mentre le comunità batteriche sono composte dai sei principali phyla marini (Proteobacteria, Cyanobacteria, Bacteroidetes, Actinobacteria, Firmicutes e Deinococcus-Thermus), la cui frequenza varia in base alla profondità di campionamento. La predazione esercitata dagli HNF ha modificato la diversità delle comunità sia superficiali che profonde ma con diversi effetti. Le comunità profonde si sono dimostrate più suscettibili alla diversa intensità della predazione. Un controllo top-down medio-alto ha preservato o incrementato la diversità batterica, che invece è risultata fortemente ridotta con bassa pressione di predazione. Al contrario, le comunità superficiali hanno subito solo leggere variazioni nella biodiversità batterica in risposta ai diversi tassi di ingestione, dimostrandosi più stabili. I piccoli flagellati (<3 µm) costituiscono la frazione dominante delle comunità nanoplanctoniche. In seguito alla rimozione dei predatori >3 µm, variazione significative dell’abbondanza sono state riscontrate in una maggiore percentuale di filotipi procariotici. Flagellati di maggiori dimensioni possono quindi mitigare l’impatto dei piccoli predatori sulle prede, con una maggior influenza nei sistemi fotici. Alcuni taxa batterici sono stati consumati prevalentemente dal grandi HNF (3-10 µm), mentre altri sono stati selezionati dai piccoli flagellati (<3 µm). Oltre il 50% dei filotipi predati apparteneva alla biosfera rara, soprattutto negli esperimenti condotti in superficie. I batteri rari (0.1-1% dell’abbondanza totale) non rappresentano quindi una frazione ‘dormiente’ il cui contributo varia in seguito a cambiamenti delle condizioni ambientali, come inizialmente ipotizzato. Costituiscono invece una componente fondamentale delle reti trofiche microbiche e contribuiscono attivamente al trasferimento di carbonio verso i livelli trofici superiori, così come gli organismi dominanti. Nonostante ciascuna comunità risponda in maniera distintiva alla predazione, in funzione della composizione tassonomica delle comunità stesse e dello stato trofico del sistema, alcuni indizi di selettività sono stati individuati. Alcune interazioni preda-predatore si sono rivelate tipiche delle comunità profonde o superficiali, mentre altre erano comuni ad entrambi i sistemi (es. Burkholderiaceae e Pseudomonadaceae sono stati selezionati sono in ambiente pelagico, Bacterivoracaceae sono stati sottoposti a predazione da parte di piccolo flagellati in tutti gli esperimenti, indipendentemente dalla profondità e dal sito di campionamento). I bacini Adriatico meridionale e Ionio settentrionale sono significativamente distinti sia per le caratteristiche chimico-fisiche della colonna d’acqua, sia per l’abbondanza di pico- e nanoplancton. La cluster analisi basata sugli indici di Jaccard e Bray-Curtis ha evidenziato che profondità di campionamento e localizzazione geografica sono i principali fattori che determinano la similarità tra le comunità batteriche. Il Mar Adriatico settentrionale è risultato sempre separato dagli altri campioni, coerentemente con le diverse caratteristiche biotiche e abiotiche del bacino. Oltre a profondità e sito geografico, temperatura, concentrazione di chl a e ossigeno contribuiscono a determinare la biodiversità batterica adriatica e ionica. In conclusione, il presente lavoro ha evidenziato come i flagellati eterotrofi controllino la biomassa procariotica e mostrino preferenza per determinati taxa, selezionando anche quelli rari. La predazione influenza la struttura delle comunità e di conseguenza il funzionamento degli ecosistemi. Anche gli ambienti marini profondi ospitano complesse reti trofiche, strutturate attorno a tre livelli principali (procarioti, piccoli e grandi flagellati eterotrofi) così come le acque superficiali.<br>XXVI Ciclo<br>1986

The now formally adopted ecosystem approach to fisheries (EAF) considers not only commercially important species, but the entire ecosystem and the processes that support these species. A key component of EAF management is the implementation of no-take Marine Protected Areas (MPAs). Shallow water fish stocks are depleted and fishing effort is moving deeper and further offshore to keep up with demands. This situation calls for a detailed investigation of deep nearshore reefs to provide critical information relevant to policy uptake and management decisions regarding existing and new MPAs in terms of zonation and use. To address this need, the aim of this thesis was to investigate reefs that lie between 45 and 75 m and compare them in terms of community structure and function to the relatively well-studied shallow reefs that lie within SCUBA diving depth (<25 m). Ecological collections were made in the centre of a large and well-established MPA, Tsitsikamma National Park, to ensure that data represented non-anthropogenically impacted communities. Data were collected from two study sites; Rheeders Reef, (shallow reef) and Middlebank, a deep reef complex situated near the Storms River Mouth. The first step to address the aim of this study was to obtain baseline data on the distribution patterns of both the macrobenthic invertebrates and fish assemblages. Baseline data were obtained by underwater video methods and included the use of a remotely operated vehicle, baited remote underwater stereo-video systems (stereo-BRUVs) and traditional underwater camera equipment operated by SCUBA divers. To establish functional differences between the two study sites, fatty acid (FA) and stable isotope (SI) analyses were employed. These biomarker techniques provided insight into the importance of different sources of primary production, nutritional condition and species packing. From 360 photoquadrats examined for macrobenthic invertebrate distribution patterns, 161 invertebrates were identified that demonstrated a clear changeover of species along the depth gradient. Species richness was highest on the shallow reef and decreased with an increase in depth. To understand how the measured environmental variables impacted the macrobenthic assemblage data a LINKTREE analysis was performed. LINKTREEs produce hierarchical cluster analysis based on the macrobenthic assemblage data and provide a threshold of environmental variables that correspond to each cluster. The outcome of the LINKTREE analysis indicated that the changeover of species resulted in four distinct clusters, each cluster associated with a particular set of environmental variables that fell within a depth range. On the shallowest sites, the high energy environment resulting from wave action and surge prevented the settlement of suspended particles. The high energy environment of the shallow reef selected for low-growing encrusting species. High light intensities supported great abundances of benthic algae, and as light was lost with increasing depth, algal cover gradually diminished until it was completely absent on the deep reef. The reduced impact of surface wave action on the deep reef caused increased levels of settled suspended particles. The high levels of settled particles likely caused clogging of feeding parts of the encrusting species. Consequently, upright growth forms were more common in the lower energy environment of the deep reef. A total of 48 fish species were identified from 51 stereo-BRUVs samples. Fish assemblages differed significantly between the shallow and deep reefs. The shallowest sites were characterised by many small and juvenile fish species that fed at lower trophic levels. The deep reef supported the majority of the large predatory fish that fed at higher trophic levels. Many species demonstrated depth-related ontogenetic shifts in habitat use, and as such the deep reef hosted the majority of the sexually mature individuals. The fish assemblages also demonstrated a strong association with the macrobenthic clusters identified as habitat types by the LINKTREE analysis. The results from 201 FA and 191 SI samples provided information on specific feeding interactions, but more importantly shed some light on different processes that supported the shallow and deep reef communities. The shallow reef community was characterised by greater diversity of food sources, a pattern that could be explained by the presence of benthic algae and terrestrial inputs. Greater diversity of carbon sources at the bottom of the food web meant that a larger variety of species could be supported. Higher species richness increased the number of distinct taxa that performed similar functions, rendering the shallow reef more redundant and consequently more resilient to disturbance. In contrast, the deep reef demonstrated a food web supported mainly by pelagic production, which was more variable both over space and time. The deep reef was less redundant when compared to the shallow reef, as fewer species demonstrated similar trophic niches. These factors, in addition to the increased presence of sensitive calcareous macrobenthic species on the deep study site, rendered the deep reef more vulnerable to disturbance when compared to the shallow reef. Although the data presented here were from a single study area, the limitations typically associated with these inaccessible and challenging sampling environments made the dataset a significant contribution to the knowledge of reef ecosystems. The study addressed priority research questions for South Africa as identified during the National Biodiversity Assessment. The observable differences in structure, function and vulnerability point to the need for continued protection of our shallow reefs and offshore expansion of our MPA networks. Future research should determine if the patterns identified here are common throughout the Agulhas Ecoregion to provide managers with robust evidence for the extension our MPAs offshore.

Community structure in backswimmers (Hemiptera: Notonectide), was investigated via extensive sampling throughout southern Arizona, USA, and Sonora, Mexico, from 1980 through 1985. Co-occurrence and relative abundance data were collected in more than 65 ponds, and in 177 rock basin pools (tinajas) in 21 canyons in the Southwest. Eleven species were collected in Arizona and Sonora, and were divided into two groups, species found in ponds and species found in tinajas. Only two species occurred significantly in both habitats. Tinaja species are largely Southwst endemics, and pond species are widespread or tropical in distribution. Data from artificial habitats suggest that the tinaja species use relatively high topographic relief, and pond species use relatively large surface area as cues to find their respective habitats. Two body size patterns are consistent with a competition explanation of local community structure. The body sizes of co-occurring species are relatively evenly distributed among species occurring in pond and tinaja habitats, and species of similar body size tend not to co-occur (body size ratio <1.3). For example, Notonecta kirbyi and N. lobata only co-occur in tinajas at intermediate elevations; lobata is absent at high elevations and kirbyi is absent at lower elevations. N. indica occurs in ponds at lower elevations and N. unifasciata occurs at higher elevations. Buenoa hungerfordi and B. arizonis both occur in tinajas, but not at the same time of year. Predation was shown experimentally not to be important in producing the body size pattern. Notonecta spp. preyed heavily on the smaller of two Buenoa species presented, an effect that would act to reduce the community-wide body size ratio. Because notonectid communities have larger body size ratios than expected by chance, predation would seem not to be involved in producing this pattern. However, predation does appear to reinforce microhabitat partitioning between the two genera in that Buenoa occupy deeper portions of the water column in the presence of Notonecta than in their absence. This further displaces coexisting individuals of the two genera in space, and reduces overlap in foraging for aquatic insect prey and promotes coexistence.

Thesis (Ph.D.)--Boston University<br>PLEASE NOTE: Boston University Libraries did not receive an Authorization To Manage form for this thesis or dissertation. It is therefore not openly accessible, though it may be available by request. If you are the author or principal advisor of this work and would like to request open access for it, please contact us at open-help@bu.edu. Thank you.<br>A combination of overexploitation and destructive fishing practices, such as bottom trawling, have depleted native populations of groundfishes in coastal New England and reduced benthic community diversity. The Stellwagen Bank National Marine Sanctuary (SBNMS) in the southern Gulf of Maine is partially overlapped by the Western Gulf of Maine Closed Area (WGMCA). The WGMCA is closed to commercial fishing for groundfishes managed under the Northeast Multispecies complex and the use of bottom trawling fishing gear is prohibited to protect essential fish habitat. This has reduced fishing pressure and benthic disturbance levels. The area of the SBNMS outside of the WGMCA is still disturbed by intensive commercial fishing for much of the year. Key questions for this area are (1) How does the higher level of disturbance in areas outside of the WGMCA affect SBNMS groundfish communities?, (2) Is the WGMCA effective at increasing the diversity, abundance, and biomass of groundfishes in the SBNMS?, and (3) How does the decrease in disturbance impact groundfish trophic ecology? A comparison of the groundfish communities inside and outside of the WGMCA within the SBNMS was carried out via trawl sampling. Results show that groundfish communities are more diverse inside the WGMCA than outside. Additionally, several commercial groundfish species had higher abundance and/or biomass inside the WGMCA. Stable isotope analyses showed that prey items differed for some species inside and outside of the WGMCA, but trophic levels were unaffected. Finally, stable isotope analyses of five groundfish species provide evidence that groundfishes may display a high level of foraging area fidelity. Primary conclusions include: (1) the protection of groundfish habitats from trawling disturbances paired with reduced fishing pressure will result in increases in community diversity and abundances of groundfishes, (2) groundfish ecology should be considered on a small geographic scale due to apparent site fidelity, and (3) if the entire SBNMS were closed to bottom trawling and commercial fishing, it could help to rebuild overexploited groundfish populations in the southern Gulf of Maine and serve as a source population for the remainder of the Gulf of Maine and adjacent shelf environs.<br>2031-01-01

Artificial reefs (ARs) are generally created with the intention of increasing local fish populations, biodiversity and corresponding habitat productivity, most often in support of commercial and recreational uses (e.g., diving and fishing). Numerous studies have investigated the communities that develop on artificial reefs. By contrast, far less research has focused on the surrounding infaunal communities, which represent critical trophic resources for many species that populate both natural and artificial reefs, and which may be affected both by AR deployment and the organisms that subsequently recruit to them. This study compared infaunal organism abundances at four sites between the inner and middle reefs off Broward County, Florida, before deployment of a series of Florida Department of Transportation (FDOT) AR boulders in 2009 (pre-construction) and four years later in 2013 (post-construction). Samples consisted of sediment collected in hand-held core tubes taken on open sediment adjacent to the proposed ARs and along transects at distances 3 m and 7 m from the ARs post-construction. Sample depths ranged from 12.1 to 14.6 m. Analyses were carried out on organisms retained on a >0.5 mm sieve and identified to the lowest practical taxonomic level. Data consisted of abundances rather than densities, because pre-construction samples did not record sediment volume per core. A total of 163 taxa were identified, of which only 50 were identified to genus and 64 to species. Polychaete families Spionidae, Sabellidae, Syllidae, and Hesionidae, and sipunculan superfamily Phascolosomatidea dominated pre-construction samples. Polychaetes also dominated post-construction samples, with high relative abundances of Sabellidae and Hesionidae, but with increased proportions of bivalves and amphipods. Statistical analyses (PRIMER, PERMANOVA, and SIMPER) determined whether infaunal composition, richness and, diversity differed among samples by year, site and distance from AR boulders. A slight but statistically insignificant difference in species diversity appeared between 3- and 7-m distances between years. However, composition, richness, and diversity of infauna did not differ either between pre-and post-construction samples or by sample distance from the adjacent AR boulders. The increase in homogeneity among samples post-construction may reflect recovery following the disturbance created by AR deployment, or a response to different benthic conditions generated by AR deployment. As other studies have suggested that AR fauna may influence surrounding infaunal communities to distances greater than 7 m, and that conditions may not stabilize around ARs for up to ten years following deployment, additional sampling is recommended to determine the longer-term effects of the FDOT ARs on infauna and benthic habitat (e.g., sediment composition, water movement) and assist in determining best practices for future AR deployments (e.g., composition, structure, location).

Le mésozooplancton joue un rôle clé dans les écosystèmes pélagiques méditerranéens, comme intermédiaire entre les niveaux trophiques inférieurs et supérieurs. Dans cette thèse, nous avons recherché la meilleure combinaison de mailles de filets de prélèvement et de techniques d'analyse des échantillons (FlowCAM et ZOOSCAN) pour délivrer la plus complète estimation de l’abondance, la structure de taille et les taux trophiques et métaboliques associés. Cette étude a été réalisée à partir d'échantillons prélevés à deux stations JULIO et ANTARES de Méditerranée nord-ouest.Ensuite, nous avons appliqué cette méthodologie pour étudier la communauté du mésozooplancton (1) en Méditerranée du Nord-Ouest (campagne MOOSE GE 2017), région à productivité printanière et estivale dépendante du processus de convection hivernale, et (2) dans le sud de la Méditerranée (campagne PEACETIME 2017), dont les régions oligotrophes sont épisodiquement fertilisées par des événements de poussières sahariennes.Des analyses multivariées et des diagrammes rang-fréquence, ont montré des différences d’assemblages marquées entre les deux campagnes, mais légères entre les sous-bassins visités. En général, le mésozooplancton total a montré des variations réduites en abondance et biomasse sur l'ensemble de la zone, avec une contribution notable de la fraction des petites tailles, notamment pour les flux associés (demande en carbone, pression de broutage, respiration et excrétion).Nos résultats mettent en évidence que la structure de la communauté du mésozooplancton de Méditerranée est fortement réactive à diverses de forçages externes typiques, dont les événements de dépôts de poussières sahariennes<br>Mesozooplankton plays a key role in Mediterranean pelagic ecosystems, acting as intermediate link between lower and higher trophic levels. In this thesis, we firstly used samples collected at two time-series stations in the North Western Mediterranean Sea to obtain a large combination of mesh size nets and sample analysis treatments (FlowCAM and ZOOSCAN) allowing to deliver the most complete estimations of its abundance, size structure and trophic and metabolic functions. Then, we applied the optimized methodology to study the mesozooplankton community in two areas: (1) the North Western Mediterranean Sea (during the MOOSE-GE 2017 cruise), a region of which the spring and summer productivity is strongly dependent on the winter deep-water convection process, and (2) the Southern Mediterranean Sea (during PEACETIME cruise 2017), including oligotrophic regions episodically fertilized by Saharan nutrient-rich dust deposition events. The zooplankton taxa assemblages, analyzed using multivariate analysis and rank frequency diagrams, showed marked differences between the two surveys, but slightly differed between sub-basins within each survey. In general, total mesozooplankton showed reduced variations in abundance and biomass values over the whole area, with a noticeable contribution from the small size fraction both for abundance and biomass, and consequently for the zooplankton fluxes (carbon demand, grazing pressure, respiration, and excretion). Our results highlight that the mesozooplankton community structure is strongly reactive to various time-scale external forcings typical of the Mediterranean Sea, including episodic dust deposition events

Food web structure is of underlying importance to ecological functions and processes. Whilst it is understood that a range of biotic and abiotic factors affect structure, relatively little is known of the role of biodiversity per se in structuring food webs. In this thesis I utilise novel multi-dimensional estimates of food web structure based on stable isotope ratios of nitrogen (δ15N) and carbon (δ13C) to quantify structural responses to changing community diversity. I additionally investigate methodological aspects of sample preparation and stable isotope quantifications of food chains. Using an arthropod prey-predator system, in chapter 2 I demonstrate that tissue selection and lipid extraction are important methodological procedures for deriving accurate δ15N and δ13C signatures. In chapter 3 I test the utility of δ15N to quantify food chain length, and δ13C to trace primary energy sources through to end consumers. Bayesian resampling of variance in sample means for plant and arthropod food chains produces robust isotopic estimates that match known food chain length well despite some error variance, and estimates of δ13C-range that trace trophic transfers. Chapter 4 represents a change in system from lab to field as I determine δ15N and δ13C signatures for plant and invertebrate species within three grassland communities representing a gradient of biodiversity. Quantifications of community bivariate isotopic space using isotopic metrics revealed that greater taxonomic richness increased both diversity of resource space exploited and overlap in resource space. These results therefore suggest that loss of diversity affected structure through altering relative patterns of niche partitioning in resource exploitation amongst community members. In chapter 5, I additionally find evidence that grassland management mediated changes in food web compartmental structure that were associated with differences in generalist invertebrate predator feeding habits. Taken together, these findings develop and demonstrate the utility of isotopic approaches to quantifying food web structure, and provide evidence of important mechanisms by which biodiversity affects food web structure. I conclude that the preservation of natural food web structure and trophic dynamics are further reasons for halting loss of biodiversity.

The dark kangaroo mouse, Microdipodops megacephalus, is a sensitive species in the Great Basin Desert. This thesis explores the structure of desert rodent communities of the Great Basin to better understand M. megacephalus' place in the community and the conditions that promote large and stable populations. To determine community structure, I used nestedness analysis to evaluate 99 communities of nocturnal granivorous rodents. I found that the community structure was non-random, indicating the existence of assembly rules and ecological constraints. I also found that M. megacephalus was the second most vulnerable species in the community. To explore the correlation between species diversity and relative abundance, I performed regression analyses on M. megacephalus and five commonly co-occurring species of the nocturnal granivore guild: Perognathus longimembris (little pocket mouse), Perognathus parvus (Great Basin pocket mouse), Dipodomys ordii (Ord's kangaroo rat), Dipodomys microps (chisel-toothed kangaroo rat), and Peromyscus maniculatus (deer mouse). Results showed a positive correlation between rodent species diversity and relative abundance for M. megacephalus, P. longimembris, P. parvus, and D. microps, and a negative correlation for D. ordii and P. maniculatus. To further understand community composition, I ran interspecific association analyses based on presence-absence data for the six species using chi-square to determine strength of interspecific associations. I found positive interspecific associations between M. megacephalus and P. parvus, between P. longimembris and P. parvus, between P. longimembris and D. microps, and between D. microps and P. maniculatus, and a negative association between P. longimembris and P. maniculatus. A species cluster dendogram with respect to sites in common further supports the interspecific association results. A site cluster dendogram with respect to species abundances implies that dune habitat promotes diversity but not uniformity. All results indicate that M. megacephalus is more abundant and stable at sites with high species richness. The results also provide evidence for the existence of assembly rules, competition, and niche partitioning in desert rodent communities.

Le concept de réseau d'interactions est central en Écologie et différents modèles et méthodes ont été utilisés. Ce travail de thèse met en relation deux approches développées par des courants séparés : l'étude des matrices de communauté et les analyses entrée-sortie. Il confronte leurs hypothèses aux propriétés fondamentales des écosystèmes estuariens. Il précise explicitement les liens entre les différentes matrices, ainsi que la signification des mixed trophic impacts. Les matrices de la storage et de la throughflowanalyses sont reliées à des jacobiennes de modèles à compartiments dont les flux sont contrôlés par les compartiments donneurs ou receveurs. Contrairement à ce qui est le plus souvent présenté dans la littérature, l'analyse des mixed trophic impacts est ici interprétée en terme de présence-absence du compartiment considéré. Avec les données disponibles sur les réseaux trophiques de cinq estuaires européens, des matrices qualitatives et quantitatives sont construites afin de réaliser des analyses de sensibilité. Ces premières explorations montrent des niveaux d'incertitudes très élevés, et ceci même pour le signe des prédictions. Par ailleurs, ce travail de thèse approfondit les possibilités d'étude de dynamiques transitoires à partir de la matrice de communauté. Il souligne des éléments importants qu'il est nécessaire de prendre en compte lorsque ces approches sont choisies<br>Networks are a key concept in ecology and a number of models and methods have been used. This PhD dissertation links two approaches, the community matrix and input-output analyses, which have been developed by separate streams of theory. It compares their assumptions with important features of estuarine systems. It explicitly analyses the links between the matrices and the significance of the mixed trophic impacts analysis. Matrices of storage and throughflow analyses are linked to Jacobian matrices of donor or recipient controlled compartment models. Unlike most of what can be seen in the litterature, here the mixed trophic impacts are interpreted as the effects of a compartment being present or absent. Using available data in the case of five European estuaries, qualitative and quantitative matrices are built in the aim of performing sensitivity analyses. First explorations reveal high levels of uncertainties, even in the sign of the predictions. Furthermore, this work examines in more details the possibilities to explore transient dynamics from the community matrix. This PhD dissertation emphasises important features which are necessary to consider when choosing such approaches

L'objectif principal de cette thèse était d'étudier la dynamique spatiale et temporelle de la structure des communautés de poissons du fleuve Mékong en aval et du grand lac Tonlé Sap au Cambodge. Les deux systèmes sont fortement liés et caractérisés par les systèmes d'inondation pulsés. À l'aide d'approches multivariées sur des bases de données piscicoles, environnementales et des traits fonctionnels des taxons étudiés, j'ai pu mettre en évidence : * les gradients longitudinaux des caractéristiques physicochimiques des eaux et l'importance relative des facteurs environnementaux dans la structuration des communautés de poissons à large échelle ; * la structure temporelle des communautés de poissons qui est fortement liée aux traits fonctionnels des taxons et déclenchée par les crues occasionnées du système * la structure de base du réseau trophique et l'état écologique du système d'inondation pulsé qui est perturbé par la pression anthropique. Ces résultats ont démontré leurs valeurs quant à leurs potentiels de transferts vers la compréhension écologique et la gestion durable des ressources de pêches dans le système d'inondation pulsé en Asie tropicale en relevant que : * la connectivité entre le fleuve Mékong et le lac Tonlé Sap est indispensable pour les poissons pour compléter leurs cycles de vie, et la conservation devrait prioritairement s'effectuer au milieu du Mékong où se trouve la plus forte diversité. * dans le système d'inondation pulsé, la structure temporelle des communautés dépend des dynamiques des crues, donc l'aménagement des cours d'eau est à éviter au maximum. * la compréhension bioécologique complète des communautés et leurs relations trophiques sont primordiales pour la mise en place des plans de gestion et de conservation à long terme<br>The main objective of the thesis was to study the spatial and temporal dynamics of fish community structure in Lower Mekong river basin and Tonle Sap Great Lake in Cambodia. These two systems are strongly connected to each other and characterised by flood pulse system. By using the multivariate approaches on the fish, environmental and fish functional traits data sets, I am able to highlight: * the longitudinal gradients of physicochemical characteristics of water and the relative importance of environmental factors in explaining the large scale patterns of fish community; * the temporal structure of fish community, which is strongly linked to functional traits of fish and trigged by the pulse dynamics of the system; * the baseline trophic structure model and ecological health assessment of flood pulse system, which is disturbed by anthropogenic pressure. These results have demonstrated their values as well as their potentials to transfers toward an ecological understanding and sustainable fisheries resource management of the flood pulse system in tropical Asia by suggesting: * the connectivity between Mekong river and Tonle Sap lek is essential for fish to complete their life cycle and also the conservation should be done in the middle part of Lower Mekong river where containing the highest diversity; * in flood pulse system, the temporal structure of fish community strongly depend on the dynamics of pulses; therefore any river development must be strictly prohibited; * complete bio-ecological understanding of communities and their trophic relationships are crucial to the establishment of long-term management and conservation plans

La méiofaune joue un rôle important dans le fonctionnement des habitats benthiques à substrat meuble (ex. flux de matière) en relation avec sa production élevée, sa position trophique intermédiaire et les importants transferts d’énergie vers les niveaux trophiques supérieurs qui y sont lié. Les relations trophiques et les flux de matière organique liés à la méiofaune restent néanmoins mal connus ou peu pris en compte. Afin de mieux appréhender le rôle de la méiofaune, la structure des communautés et les relations trophiques entre les sources de nourriture et ces consommateurs ont été déterminées dans cinq habitats à substrat meuble (i.e., vasière nue, herbier, zone à sables) de la baie de Marennes-Oléron, France, et de la baie de Sylt-Rømø, Allemagne, en tenant compte des variations temporelles. Le peuplement de méiofaune s’est trouvé être dominé par les nématodes et les copépodes benthiques. Les biomasses de microphytobenthos et de matière organique du sédiment sont apparues comme étant deux facteurs structurants pour les communautés. L’utilisation combinée de différents traceurs de la matière (i.e., isotopes stables, acides gras) a démontré que le microphytobenthos et les bactéries étaient les ressources trophiques majeures de la méiofaune dans les cinq habitats étudiés. Les mesures réalisées sur la structure des communautés et les données issues des traceurs de la matière ont été implémentées dans des modèles de réseaux trophiques. Dans tous les habitats, ces modèles ont mis en évidence que le flux de carbone dominant était issu du microphytobenthos, ceci démontrant les très faibles changements de comportements alimentaires malgré les importantes différences de sources trophiques en termes de disponibilité et de production des sources de nourriture entre ces différents habitats. Tous les groupes trophiques de nématodes, à l’exception des déposivores sélectifs, étaient particulièrement sélectifs et s’alimentaient majoritairement à partir de microphytobenthos, ceci étant à l’origine d’une forte production et d’un court temps de renouvellement de la méiofaune. En conclusion, cette thèse démontre le rôle important de la méiofaune dans les habitats à substrat meuble ainsi que l’importance de la relation trophique entre le microphytobenthos et la méiofaune dans le fonctionnement de ces réseaux trophiques<br>Meiofauna play an important role in ecosystem processes in soft-bottom benthic habitats, e.g. food web dynamics, related to their highproduction, their intermediate trophic position and the energy they transfer towards higher trophic levels. The trophic linkages and flows of organic matter related to the meiofauna remain poorly known or taken into account. To better assess the role of meiofauna, the community structure and trophic relationships between food sources and meiofauna were determined in five intertidal soft-bottom habitats (i.e., mudflat, seagrass bed, sandflat) of the Marennes-Oléron Bay, France, and the Sylt-Rømø Bight, Germany, taking temporal variations into account. Meiofauna communities were dominated by nematodes and benthic copepods. Biomass of microphytobenthos and of sediment organic matter were two of the major drivers of community structure. The combination of trophic markers (i.e., stable isotopes, fatty acids) demonstrated that microphytobenthos and bacteria were the major food sources of meiofauna in the five habitats. Information from community structure assessments and trophic marker analyses were implemented in food web models. In all habitats, these models demonstrated that the main flow of carbon to meiofauna originated from microphytobenthos, highlighting negligible changes in meiofauna feeding behavior besides the large differences in availability and productivity of food sources between these habitats. All trophic groups of nematodes, except for selective deposit feeding nematodes, were highly selective and mainly fed on microphytobenthos, resulting in a high production and a short turn-over time of meiofauna. In conclusion, this thesis demonstrated the important role of meiofauna in soft-bottom habitats as well as the importance of the trophic pathway from microphytobenthos to meiofauna in the functioning of these food webs

Le concept de réseau d'interactions est central en Écologie et différents modèles et méthodes ont été utilisés. Ce travail de thèse met en relation deux approches développées par des courants séparés : l'étude des matrices de communauté et les analyses entrée-sortie. Il confronte leurs hypothèses aux propriétés fondamentales des écosystèmes estuariens. Il précise explicitement les liens entre les différentes matrices, ainsi que la signification des mixed trophic impacts. Les matrices de la storage et de la throughflowanalyses sont reliées à des jacobiennes de modèles à compartiments dont les flux sont contrôlés par les compartiments donneurs ou receveurs. Contrairement à ce qui est le plus souvent présenté dans la littérature, l'analyse des mixed trophic impacts est ici interprétée en terme de présence-absence du compartiment considéré. Avec les données disponibles sur les réseaux trophiques de cinq estuaires européens, des matrices qualitatives et quantitatives sont construites afin de réaliser des analyses de sensibilité. Ces premières explorations montrent des niveaux d'incertitudes très élevés, et ceci même pour le signe des prédictions. Par ailleurs, ce travail de thèse approfondit les possibilités d'étude de dynamiques transitoires à partir de la matrice de communauté. Il souligne des éléments importants qu'il est nécessaire de prendre en compte lorsque ces approches sont choisies<br>Networks are a key concept in ecology and a number of models and methods have been used. This PhD dissertation links two approaches, the community matrix and input-output analyses, which have been developed by separate streams of theory. It compares their assumptions with important features of estuarine systems. It explicitly analyses the links between the matrices and the significance of the mixed trophic impacts analysis. Matrices of storage and throughflow analyses are linked to Jacobian matrices of donor or recipient controlled compartment models. Unlike most of what can be seen in the litterature, here the mixed trophic impacts are interpreted as the effects of a compartment being present or absent. Using available data in the case of five European estuaries, qualitative and quantitative matrices are built in the aim of performing sensitivity analyses. First explorations reveal high levels of uncertainties, even in the sign of the predictions. Furthermore, this work examines in more details the possibilities to explore transient dynamics from the community matrix. This PhD dissertation emphasises important features which are necessary to consider when choosing such approaches

Les plages de sable sont des écosystèmes dynamiques couvrant 70% des côtes mondiales. Ces systèmes abritent un cortège spécifique unique et assurent des fonctions essentielles de nourricerie, de nurserie et d’épuration des eaux. Or à proximité des côtes, la population humaine est en développement constant ce qui accroît les multiples pressions d’origine anthropique sur les écosystèmes côtiers. L’apport en excès de nutriments constitue une menace majeure qui peut se traduire par le développement d’importantes biomasses de macroalgues opportunistes (eutrophisation). La fréquence et l’intensité de ces blooms, communément formés de chlorophycées à court cycle de vie (ulves) et appelés marées vertes (MV), s'amplifient sur les côtes françaises et dans le Monde menaçant le fonctionnement de systèmes prépondérants et uniques.La plupart des études visant à déterminer les effets des MV sur la structure et le fonctionnement d’écosystèmes sédimentaires ont été conduites dans des environnements abrités, micro- ou atidaux. Cette problématique est restée presqu’inexplorée dans des écosystèmes plus dynamiques (systèmes ouverts et macrotidaux) en raison des difficultés de mise en place d’échantillonnage et de détection des effets de stress d’origine anthropique, inhérentes à la variabilité de ces systèmes. Cette thèse a donc eu pour objectif principal de combler ce manque et produire des connaissances en étudiant les réponses in situ des communautés benthiques de plages de sable fin macrotidales en présence ou non de MV. Quatre études ont été menées à différentes échelles spatio-temporelles et en considérant différents compartiments biologiques pour répondre à cette question générale.Ce travail de thèse montre qu’à l’échelle de la région Bretagne (variabilité intégrée sur 2700km de côtes et 7 ans) les communautés benthiques d’écosystèmes dynamiques sont modifiées significativement et de manière conservative par la présence de MV. Ce travail démontre aussi que les marées vertes impactent différemment la faune benthique en fonction du type d’habitat (plages semi-exposées vs. exposées), de la profondeur (mediolittoral vs. infralittoral), et du compartiment biologique (macrofaune benthique vs. juvéniles de poissons plats). Ces comparaisons ont permis d’identifier la faune benthique de médiolittoral inférieur des plages exposées comme étant le système le plus affecté par les MV. L’étude des variations à fine échelle spatio-temporelle de ce dernier montre que les caractéristiques faunistiques (uni- et multi-variées) sont modifiées le long d’un gradient de couverture d’algues vertes. Par exemple, la β-diversité décroît significativement le long de ce gradient. Afin d’explorer les processus pouvant expliquer ces modifications, et déterminer si ces changements ont des répercussions sur le fonctionnement de l’écosystème « plage de sable », les effets de l’accumulation d’ulves sur le réseau trophique à différent(e)s niveaux/échelles ont été mesurés. Les résultats de cette étude montrent qu’une importante biomasse d’ulves induit un changement de la structure entière du réseau trophique et une modification importante du fonctionnement trophique des plages. Les expérimentations menées au cours de cette thèse montrent que les changements observés sont induits par des effets directs (consommation de débris d’ulves) et indirects (modifications d’autres sources de nourriture) de la présence des MV.Cette thèse propose un cadre de travail visant à mieux détecter les effets de stress anthropiques sur la structure et le fonctionnement d’écosystèmes dynamiques. Dans un contexte de changement global forçant les écosystèmes à faire face à de multiples stress, cette approche pourrait se révéler particulièrement utile pour démêler, comprendre et prédire les effets de perturbations induites par les activités humaines sur le fonctionnement des écosystèmes et constituer une aide à la gestion de ces environnements particuliers<br>Highly dynamic systems, often considered as resilient systems, are characterised by abiotic and biotic processes under continuous and strong changes in space and time. Because of this variability, the detection of overlapping anthropogenic stress is challenging. Coastal areas harbour dynamic ecosystems in the for of open sandy beaches, which cover the vast majority of the world’s ice-free coastline. These ecosystems are currently threatened by increasing human-induced pressure, among which mass-development of opportunistic macroalgae (mainly composed of Chlorophyta, so called green tides), resulting from the eutrophication of coastal waters. The ecological impact of opportunistic macroalgal blooms (green tides, and blooms formed by other opportunistic taxa), has long been evaluated within sheltered and non-tidal ecosystems. Little is known, however, on how more dynamic ecosystems, such as open macrotidal sandy beaches, respond to such stress. This thesis assesses the effects of anthropogenic stress on the structure and the functioning of highly dynamic ecosystems using sandy beaches impacted by green tides as a study case. The thesis is based on four field studies, which analyse natural sandy sediment benthic community dynamics over several temporal (from month to multi-year) and spatial (from local to regional) scales. In this thesis, I report long-lasting responses of sandy beach benthic invertebrate communities to green tides, across thousands of kilometres and over seven years; and highlight more pronounced responses of zoobenthos living in exposed sandy beaches compared to semi-exposed sands. Within exposed sandy sediments, and across a vertical scale (from inshore to nearshore sandy habitats), I also demonstrate that the effects of the presence of algal mats on intertidal benthic invertebrate communities is more pronounced than that on subtidal benthic invertebrate assemblages, but also than on flatfish communities. Focussing on small-scale variations in the most affected faunal group (i.e. benthic invertebrates living at low shore), this thesis reveals a decrease in overall beta-diversity along a eutrophication-gradient manifested in the form of green tides, as well as the increasing importance of biological variables in explaining ecological variability of sandy beach macrobenthic assemblages along the same gradient. To illustrate the processes associated with the structural shifts observed where green tides occurred, I investigated the effects of high biomasses of opportunistic macroalgae (Ulva spp.) on the trophic structure and functioning of sandy beaches. This work reveals a progressive simplification of sandy beach food web structure and a modification of energy pathways over time, through direct and indirect effects of Ulva mats on several trophic levels. Through this thesis I demonstrate that highly dynamic systems respond differently (e.g. shift in δ13C, not in δ15N) and more subtly (e.g. no mass-mortality in benthos was found) to anthropogenic stress compared to what has been previously shown within more sheltered and non-tidal systems. Obtaining these results would not have been possible without the approach used through this work; I thus present a framework coupling field investigations with analytical approaches to describe shifts in highly variable ecosystems under human-induced stress

Les plages de sable sont des écosystèmes dynamiques couvrant 70% des côtes mondiales. Ces systèmes abritent un cortège spécifique unique et assurent des fonctions essentielles de nourricerie, de nurserie et d’épuration des eaux. Or à proximité des côtes, la population humaine est en développement constant ce qui accroît les multiples pressions d’origine anthropique sur les écosystèmes côtiers. L’apport en excès de nutriments constitue une menace majeure qui peut se traduire par le développement d’importantes biomasses de macroalgues opportunistes (eutrophisation). La fréquence et l’intensité de ces blooms, communément formés de chlorophycées à court cycle de vie (ulves) et appelés marées vertes (MV), s'amplifient sur les côtes françaises et dans le Monde menaçant le fonctionnement de systèmes prépondérants et uniques.La plupart des études visant à déterminer les effets des MV sur la structure et le fonctionnement d’écosystèmes sédimentaires ont été conduites dans des environnements abrités, micro- ou atidaux. Cette problématique est restée presqu’inexplorée dans des écosystèmes plus dynamiques (systèmes ouverts et macrotidaux) en raison des difficultés de mise en place d’échantillonnage et de détection des effets de stress d’origine anthropique, inhérentes à la variabilité de ces systèmes. Cette thèse a donc eu pour objectif principal de combler ce manque et produire des connaissances en étudiant les réponses in situ des communautés benthiques de plages de sable fin macrotidales en présence ou non de MV. Quatre études ont été menées à différentes échelles spatio-temporelles et en considérant différents compartiments biologiques pour répondre à cette question générale.Ce travail de thèse montre qu’à l’échelle de la région Bretagne (variabilité intégrée sur 2700km de côtes et 7 ans) les communautés benthiques d’écosystèmes dynamiques sont modifiées significativement et de manière conservative par la présence de MV. Ce travail démontre aussi que les marées vertes impactent différemment la faune benthique en fonction du type d’habitat (plages semi-exposées vs. exposées), de la profondeur (mediolittoral vs. infralittoral), et du compartiment biologique (macrofaune benthique vs. juvéniles de poissons plats). Ces comparaisons ont permis d’identifier la faune benthique de médiolittoral inférieur des plages exposées comme étant le système le plus affecté par les MV. L’étude des variations à fine échelle spatio-temporelle de ce dernier montre que les caractéristiques faunistiques (uni- et multi-variées) sont modifiées le long d’un gradient de couverture d’algues vertes. Par exemple, la β-diversité décroît significativement le long de ce gradient. Afin d’explorer les processus pouvant expliquer ces modifications, et déterminer si ces changements ont des répercussions sur le fonctionnement de l’écosystème « plage de sable », les effets de l’accumulation d’ulves sur le réseau trophique à différent(e)s niveaux/échelles ont été mesurés. Les résultats de cette étude montrent qu’une importante biomasse d’ulves induit un changement de la structure entière du réseau trophique et une modification importante du fonctionnement trophique des plages. Les expérimentations menées au cours de cette thèse montrent que les changements observés sont induits par des effets directs (consommation de débris d’ulves) et indirects (modifications d’autres sources de nourriture) de la présence des MV.Cette thèse propose un cadre de travail visant à mieux détecter les effets de stress anthropiques sur la structure et le fonctionnement d’écosystèmes dynamiques. Dans un contexte de changement global forçant les écosystèmes à faire face à de multiples stress, cette approche pourrait se révéler particulièrement utile pour démêler, comprendre et prédire les effets de perturbations induites par les activités humaines sur le fonctionnement des écosystèmes et constituer une aide à la gestion de ces environnements particuliers<br>Highly dynamic systems, often considered as resilient systems, are characterised by abiotic and biotic processes under continuous and strong changes in space and time. Because of this variability, the detection of overlapping anthropogenic stress is challenging. Coastal areas harbour dynamic ecosystems in the for of open sandy beaches, which cover the vast majority of the world’s ice-free coastline. These ecosystems are currently threatened by increasing human-induced pressure, among which mass-development of opportunistic macroalgae (mainly composed of Chlorophyta, so called green tides), resulting from the eutrophication of coastal waters. The ecological impact of opportunistic macroalgal blooms (green tides, and blooms formed by other opportunistic taxa), has long been evaluated within sheltered and non-tidal ecosystems. Little is known, however, on how more dynamic ecosystems, such as open macrotidal sandy beaches, respond to such stress. This thesis assesses the effects of anthropogenic stress on the structure and the functioning of highly dynamic ecosystems using sandy beaches impacted by green tides as a study case. The thesis is based on four field studies, which analyse natural sandy sediment benthic community dynamics over several temporal (from month to multi-year) and spatial (from local to regional) scales. In this thesis, I report long-lasting responses of sandy beach benthic invertebrate communities to green tides, across thousands of kilometres and over seven years; and highlight more pronounced responses of zoobenthos living in exposed sandy beaches compared to semi-exposed sands. Within exposed sandy sediments, and across a vertical scale (from inshore to nearshore sandy habitats), I also demonstrate that the effects of the presence of algal mats on intertidal benthic invertebrate communities is more pronounced than that on subtidal benthic invertebrate assemblages, but also than on flatfish communities. Focussing on small-scale variations in the most affected faunal group (i.e. benthic invertebrates living at low shore), this thesis reveals a decrease in overall beta-diversity along a eutrophication-gradient manifested in the form of green tides, as well as the increasing importance of biological variables in explaining ecological variability of sandy beach macrobenthic assemblages along the same gradient. To illustrate the processes associated with the structural shifts observed where green tides occurred, I investigated the effects of high biomasses of opportunistic macroalgae (Ulva spp.) on the trophic structure and functioning of sandy beaches. This work reveals a progressive simplification of sandy beach food web structure and a modification of energy pathways over time, through direct and indirect effects of Ulva mats on several trophic levels. Through this thesis I demonstrate that highly dynamic systems respond differently (e.g. shift in δ13C, not in δ15N) and more subtly (e.g. no mass-mortality in benthos was found) to anthropogenic stress compared to what has been previously shown within more sheltered and non-tidal systems. Obtaining these results would not have been possible without the approach used through this work; I thus present a framework coupling field investigations with analytical approaches to describe shifts in highly variable ecosystems under human-induced stress

碩士<br>國立臺灣海洋大學<br>海洋生物研究所<br>95<br>Abstract The forth Nuclear Power Plant built at Gungliao,Taipei county. may pose potential environmental threats to the nearby Yenliao Bay coastal ecosystem due to the thermal discharge, impingement and entrainment in the water of outlet and intake areas after the plant starting to operate in the 2009. Therefore, collecting ecological data in Yenliao Bay before the operation of the 4th Nuclear Power Plant and use it as the baseline information is important for the assessment and monitoring programs for the environmental impact of the 4th Nuclear Power Plant. The purposes of this research are: 1) to demonstrate spatial and a temporal variation of fish community in Yenliao bay; 2) to assemble feeding guilds of dominate fish species using their gut contents; and 3) to construct trophic model of Yenliao bay coastal ecosystem using ECOPATH with ECOSIM. Results showed that species richness, total biomass, and abundance are all larger in the outlet station than the station near intake area. It may be due to the ecotone effect which resulted from the mixed sand and reef seabed near the outlet area and has an isolated reef located nearby. According to stomach contents examined, there were five feeding guilds: 1) benthic feeding fish; 2) piscivorous fish; 3) herbivorous fish; 4) zooplanktivorous fish; 5) polyp-feeding fish in the Yenliao Bay. Among them, benthic feeding fish account for the largest proportion (81.3%). The reef dominant species are almost belonging to the zooplanktivores. The ratio of total primary production to total respiratory is 1.0 which indicates the Yenliao bay was an autotrophic system. It was comprised of 4 trophic levels(4.03). The geometric mean of the trophic transfer efficiencies was 11.1%. The most prominent biological group in terms of biomass and energy flow in the bay was herbivorous zooplankton, its consumption was 983gWW m-2yr-1. Manipulations of the biomass of detritus and benthic feeding fish would have a distinct impact on most compartments. Trophic transfer efficiencies among the 4 trophic levels were 10.7%, 19.3%, and 6.6% respectively. Comparing cycling and ecosystem properties with other coastal ecosystems, it appeared that overall biomass of Yenliao Bay was lower than ones in Chiku and Topony lagoon ecosystems and was equivalent to Kuosheng Bay in the north coast. It is an autotrophic system and has phytoplankton-based food sources, low proportion of the recycled flow, and short food chain. In conclusion, Yenliao Bay is a developing ecosystem which was suffered from disturbances continuously.

abstract: Urban ecosystems cover less than 3% of the Earth's land surface, yet more than half of the human population lives in urban areas. The process of urbanization stresses biodiversity and other ecosystem functions within and far beyond the city. To understand the mechanisms underlying observed changes in biodiversity patterns, several observational and experimental studies were performed in the metropolitan area of Phoenix, Arizona, and the surrounding Sonoran Desert. The first study was comprised of seven years of arthropod monitoring using pitfall traps in common urban land-use types. This study revealed differences in community structure, diversity and abundance over time and between urban and wildland habitats. Urban habitats with high productivity had higher abundances of arthropods, but lower diversity compared to wildland habitats. Arthropod abundance in less-productive urban habitats was positively correlated with precipitation, but abundance in high-productivity urban habitats was completely decoupled from annual fluctuations in precipitation. This study showed the buffering capacity and the habitat heterogeneity of urban areas. To test the mechanisms controlling community diversity and structure in urban areas, a major field experiment was initiated. Productivity of the native shrub Encelia farinosa and bird predation of associated arthropods were manipulated to test whether bottom-up or top-down forces were more important in urban habitats compared to wildland habitats. Abundance, richness and similarity were monitored, revealing clear differences between urban and wildland habitats. An unusually cold and dry first season had a negative effect on plant growth and arthropod abundance. Plants in urban habitats were relatively unaffected by the low temperature. An increase in arthropod abundance with water availability indicated bottom-up forces in wildland habitats, whereas results from bird exclusions suggested that bird predation may not be as prominent in cities as previously thought. In contrast to the pitfall study, arthropod abundance was lower in urban habitats. A second field experiment testing the sheltering effect of urban structures demonstrated that reduced wind speed is an important factor facilitating plant growth in urban areas. A mathematical model incorporating wind, water and temperature demonstrated that urban habitats may be more robust than wildland habitats, supporting the empirical results.<br>Dissertation/Thesis<br>Ph.D. Biology 2010

Tese de dout., Ciências e Tecnologia das Pescas, Faculdade de Ciências do Mar e do Ambiente, Universidade do Algarve, 2005<br>A mass-balance trophic model was created to describe the coastal ecosystem of the Cape Verde Archipelago for the time period from 1981 to 1985, using available estimates on biomass and catches. This time period was characterised by predominantly artisanal fisheries and a low level of motorisation; the initial phase of a more intensive fishery development. Subsequently, a dynamic simulation model, using Ecopath with Ecosim, was used to simulate from 1986 to 2000, incorporating time series information on biomass, catches and catch per unit of effort (CPUE). Using this approach, a number of problems were detected in model specification such as incompatible biomass estimates for small pelagics and various demersal fish groups. Measures of fishing effort in fishing days or trips were found to be unreliable, in particular for the artisanal fishery. Available biomass estimates for small pelagic resources from acoustic surveys were questionable. Conventional biomass dynamic modelling was therefore applied to estimate biomass of small pelagics and provide indications for management purposes, including parameter estimation and risk assessment using the frequentist and Bayesian approaches. After a number of adjustments applied to the initial model, the approach used in simulation was to fit the model to observed catch estimates by adjusting effort, placing less emphasis on fitting to CPUE and biomass estimates. A reasonable overall fit to time series of catches was obtained for 18 fish groups, using only two overall trends for artisanal and industrial effort and three specific trends for small pelagics, yellowfin, and skipjack, which are the main targets of the indutrial fisheries. The observed decrease in abundance of important predators such as yellowfin and skipjack tuna resulted in decreased predation on neritic pelagic species and some demersal fish groups, but this was compensated by higher fishing mortality over the study period. Consequently, the model estimated an almost constant biomass of neritic fish species from 1986 to 2000. Overall fish biomass decreased by 10 percent, including pelagic migratory species. Relative fishing effort was assumed to have almost tripled over the time period from 1986 to 2000 (effort directed towards small pelagics was assumed to have increased by a factor 5), but this resulted in only a 19 per cent increase in catches. Thus, previous assessments of potential fish harvest, ranging from 25 000 to 58 000 tonnes, appear to have been overly optimistic. Alternative methodologies were applied to assess the fishery resources in Cape Verde in order to gain further understanding on the dynamics of the system and the effects of fishing over time as well as to validate the results of ecosystem modelling. This included nonparametric multidimensional scaling (MDS), generalized linear models (GLM), size spectra analysis, and a type of time series analysis (MAFA). The changes observed over time in the size structure and species composition/abundance of demersal fish communities were slight or even negligible. There was a tendency for lower abundance of demersal fish in recent years, but a decreasing trend was not apparent. It is however important to note that these iv results were based on trawl survey data, which concern a limited area of trawlable grounds in Cape Verde. In contrast, time series analysis of catch data indicates that a shift has occurred with decreasing catches of important pelagic species such as yellowfin and skipjack tuna and increasing catches of small pelagics and neritic tuna as well as some demersal species. Simulation with Ecosim gave similar results as they were based on the same catch data, but this is nevertheless reassuring as alternative methods gave consistent results. We believe that this study has been successful in taking the first steps towards an ecosystem approach to assess the effects of fishing in Cape Verde, but further research is necessary to resolve some crucial issues such as the conflicting results on demersal fish biomass and the possible over-exploitation of demersal predators and moray eels. Priority should also be given to the definition of fleet components, effort and CPUE estimation, and the study of increasing efficiency, using the available catch and effort data.<br>Fundação para a Ciência e a Tecnologia

博士<br>國立臺灣海洋大學<br>海洋生物研究所<br>101<br>Kueishan Island (northeastern Taiwan) is an important deep-sea fishing ground and is famous for its unique hydrothermal vents that extend from shallow to deep waters. Decapod crustaceans are major components of economical species in the Kueishan Island fishing group and also the dominant species in the hydrothermal vent systems there. Multivariate analyses revealed significant differences in decapod crustacean species composition between the vent and non-vent regions. The results suggest that trawling disturbances may be the main factor causing the decapod crustacean community structure off the Kueishan Island waters being rather unstable. This is also the first report on the tropic level of the vent fauna in Taiwan. The trophic shift of Kueishan Island shallow and deep water hydrothermal vents were examined through stable C and N isotope. The deep water Kueishan Island hydrothermal vent is a chemoautotrophic system, with the vent mussel Bathymodiolus taiwanensis (associated with chemosynthetic bacteria) forms the basal part of this trophic system. Moreover, hydrothermal vents are supporting the principal food source for the deep-sea vent endemic shrimp Alvinocaris chelys and mud shrimp Nihonotrypaea thermophila. The deep-sea vent endemic crab Xenograpsus testudinatus and hermit crab Paragiopagurus ventilatus have a wide range of food source, with the latter having the major food source from general deep sea environment. The food source of the shallow-water vent X. testudinatus also varies from the vent and adjacent non-vent environment, but plankton is not its principal food source. Since Xenograpsus populations from both shallow and deep-water vents show large variations in stable isotope signatures (some individuals even with nitrogen values close to that of non-vent species), it is possible that X. testudinatus may transfer energy between the deep-sea hydrothermal vents and adjacent non-vent environment.

xvii, 175 leaves : ill. ; 29 cm Notes Typescript Thesis (Ph. D.)--University of Oregon, 2002 Includes vita and abstract Includes bibliographical references (leaves 150-175) Another copy on microfilm is located in Archives

The distribution and abundance of stream fishes are influenced by many factors operating at multiple scales. Understanding how environmental variables influence the structure of stream fish assemblages is important for habitat assessment, stream restoration, and for predicting responses to environmental change. An emerging view in community ecology is that a focus on the functional structure of species assemblages in relation to environmental gradients may reveal more general patterns applicable across geographic regions. In this study, I used functional traits related to the trophic ecology, habitat use, and life-history strategies of fishes to examine the influences of environmental factors on stream fish assemblages. The research was carried out in two large regions: the Río Grijalva basin in southern Mexico and the Brazos and Trinity basins in Central Texas. In both regions, relationships between functional structure of stream fish assemblages and environmental factors at local, landscape, and regional scales were examined. Environmental characteristics at all three scales influenced the functional attributes of assemblages studied here. At the local reach scale, stream size, substrate characteristics, the availability of riffle and pool habitats, and abundance of in-stream cover structures were related to the functional trait composition of fish assemblages in the Río Grijalva Basin and in Central Texas streams. Landscape features most strongly related to functional structure in both regions were the extent of forested area in the watershed and the amount of land developed for urban and agricultural uses. At the regional scale, broad physiographic differences between ecoregions had a large influence on the taxonomic and functional composition of stream fish assemblages in Central Texas. Along the broad-scale longitudinal fluvial gradient of the Grijalva region, pronounced changes in the species composition, functional trait diversity, and trophic structure of fish assemblages were observed.

This study investigates the distribution and functional guild structure of the bee community in hardwood stands of Algonquin Provincial Park under different logging regimes, assessing both the role of different aspects of the habitat in affecting this distribution and structure, as well as the use of different sampling techniques. The distribution of bee individuals and species was most dependent on the abundance of raspberry (Rubus strigosus), an important floral and nesting resource. Also of importance were total floral resources, microclimate, and habitat heterogeneity. The functional guild structure of the bee community, which was relatively resilient to habitat variation, was related to a greater variety of factors, reflecting wide-ranging behaviours and requirements of different guilds. Malaise traps, pan traps and nets varied in their effectiveness at collecting different bee genera and a high percentage of species were collected only with one trap type. Malaise traps performed relatively poorly in forested environments, though very well in more disturbed, open habitats. Pan traps and nets performed better in forested environments. Trap nests were an inefficient sampling technique in forests, but were effective at collecting some species of cavity-nesting bees. These findings underline the importance of raspberry for bee communities of northern hardwood forests, and the importance of heterogeneity, both of habitat types and sampling techniques, to attain the highest species richness of bees.

Climate change and anthropogenic pressure are deeply altering the global environments dramatically threating the persistence of biodiversity and ecosystems processes including the primary production, matter cycling and energy flux. However, the still scarce knowledge on the biodiversity organization in the food web structure, and not only on the species number, limits our power to predict the effects of environmental change and the possible response mechanism of biological community to environmental variations. This work aims to understand the mechanism underlying the community structure and its stability under different natural or anthropogenic pressures conditions. The food web structure and metrics, the main carbon pathways and the taxa that play a key role in the community organisation in aquatic ecosystems were identified and quantified. The extensive field sampling and stable isotope analysis of each individual collected in the study ecosystems allowed to reconstruct and compare highly detailed food webs and trophic niche at both spatio-temporal and hierarchical scale (from individuals to community). In addition, the new consideration of trophic specie based on restricted interval of two elements isotopic signals, proved to be an efficient approach to overcome the current limits of the classical food web reconstruction, that occur when the biodiversity and the possible trophic interactions between species within an ecosystem are particularly complex. Our results highlight that modifications in the availability and quality of basal resources alters the interactions among organisms at different hierarchal scale with cascade effects on the entire food web structure, complexity, and stability. In accordance with optimal foraging theory, the availability of food sources has imposed change of link density already starting from single individuals with important variation of recurring patterns in the food web structure. Specifically, the consumers diet breadth decreased with the per capita availability and quality of resources increased. This, in turn, led to a relatively simpler food web characterized by lower link density affects the stability of the community against biodiversity loss and biological invasions. Our results are of particular relevance providing the key information for understanding the mechanisms that structure the community and its possible response to the different disturbance conditions. The results support that the expected changes in the habitat physical conditions could be reflected in food web architecture and organisms with greater generalism and trophic plasticity may be able to persist after a disturb playing a key role in community stability. The structure and function of food webs could be an efficient measure to predict and mitigate the effect of induced both physical and biological change on natural communities, both in the short and medium-long term.

In a changing climate, it is increasingly important to be able to model environmental effects on food webs, and to do that, one must have appropriate dynamic models. I present a shallow lake ecosystem model where producers, grazers, carnivores, piscivores, and detritivores are coupled through resource (light, nutrients and detritus) fluxes between the benthic and pelagic habitats and through carnivore life history events (ontogenetic habitat and diet shifts). The two habitats each contain primary producers, grazers, carnivores and detritivores. Within the habitats, there is strong top-down regulation, but across habitat boundaries, bottom-up interactions drive production. In the absence of piscivores, stage-structured carnivores cause intriguing patters of alternative stable states. Notably, the model predicts a lesser dependence on benthic production with detritus presence. Model predictions are largely in agreement with empirical studies. The results have implications for management of freshwater, and for the interpretation of previous models.

Dissertação de mestrado em Ecologia<br>Os nemátodes do solo desempenham um papel essencial no funcionamento deste ecossistema e não reflectem apenas as características do solo, da vegetação e do seu modo de gestão mas traduzem, também, os efeitos de contaminantes. A composição estrutural de uma comunidade pode dar indicação da intensidade do impacto resultante de diferentes agentes stressores nessa comunidade, sendo por isso útil na avaliação do efeito ecológico e toxicológico. Recentemente tem sido avaliado este efeito de forma mais relevante e completa, baseada não apenas numa abordagem taxonómica mas, também, ao nível da estrutura da comunidade, com base nos tipos tróficos. Com o presente trabalho pretendeu-se estudar o efeito de diferentes produtos de uso corrente como fitoquímicos e, ainda, de alguns metais, sobre uma comunidade nativa de nemátodes do solo, não só sob uma perspectiva taxonómica (ao nível da família) mas, também, estrutural. Para isso foi utilizada uma comunidade de nemátodes de um solo proveniente de uma horta cultivada em modo de produção biológica, num local sem qualquer aplicação de pesticidas químicos. Com o objectivo de se detectar alterações provocadas por contaminantes na comunidade dos nemátodes, conhecer a sensibilidade dos diferentes grupos tróficos e famílias e avaliar a sua utilidade como bioindicadores do solo, analisou-se o seu efeito na abundância total destes organismos, no número de famílias e na abundância dos diferentes grupos tróficos (estrutura da comunidade). Foram utilizados três compostos de natureza diversa (óleo de verão, abamectina e fosetil) e três metais (cádmio, zinco e cobre), em três doses diferentes. Os contaminantes, na forma de solução aquosa, foram adicionados ao solo (volume de 50 cm3), previamente desfaundao e, inoculado com aproximadamente 1000 nemátodes. Após 15 dias de exposição ao contaminante, com temperatura regulada (21 C), os nemátodes foram extraídos do solo pelo método do tabuleiro de Whitehead e Hemming, identificados ao nível da família e agrupados segundo os diferentes tipos tróficos; bacteriófagos; fungívoros; parasitas das plantas e predadores-omnívoros. Os dados obtidos revelaram uma resposta dos nemátodes à toxicidade, provocada pelos contaminantes testados, que se traduziu a vários níveis e de forma diversa nesta comunidade. A abundância total dos nemátodes diminuiu significativamente após o tratamento com os metais, Cd, Zn e Cu e com os produtos fitofarmacêuticos óleo de verão e abamectina, nas concentrações mais elevadas, excepto no tratamento com abamectina que actuou mesmo na concentração mais baixa. A abamectina e o cádmio foram os contaminantes que mais afectaram significativamente o número de famílias de nemátodes nas concentrações de 0,0096 g a.i./Kg e 500 mg/Kg, respectivamente. A estrutura trófica sofreu, também, mudanças significativas por acção destes contaminantes, nas concentrações mais elevadas, excepto no tratamento com abamectina (que actuou na concentração mais baixa). O fosetil, entre os produtos fitofarmacêuticos e o zinco, entre os metais analisados, foram os contaminantes com menor efeito tóxico sobre a diversidade e estrutura da comunidade de nemátodes do solo estudado. Nos ensaios com Cd, Cu e abamectina, dominaram os nemátodes oportunistas. Os resultados obtidos neste estudo confirmam a possibilidade de utilização de uma abordagem com base nos efeitos sobre a estrutura da comunidade dos nemátodes do solo, em ecotoxicologia dos solos.<br>Soil nematodes play an essential role in soil functioning ecosystems and reflect not only the characteristics of the soil, vegetation and its management but also reflect the effects of contaminants. The structural composition of the community can give an indication of the intensity of the resulting impact of different stressors and is therefore useful for evaluating the ecological and toxicological effects. Recently this effect has been evaluated in a more complete and relevant way using not only taxonomic, but also a trait approach of the structure community. This work aimed to study the effect of different pesticides frequently used and yet, some metals on a native community of soil nematodes, not only by a taxonomic (at the family level), but also structural perspective. For this a nematode community from a soil of a vegetable garden grown under organic farming, in a field free of any chemical pesticide application. In order to detect changes in the nematode community caused by contaminants, the effect on the total abundance of organisms, number of families and abundance of different trophic groups (structure of the community) was analyzed. For the assays, three compounds of diverse nature (summer oil, abamectin and fosetyl) and the metals (cadmium, zinc and copper) were used in three different doses. Water solutions of the contaminants were added to the soil (50 cm3 volume), previously defaunated and inoculated with about 1000 nematodes. After 15 days of exposure to the contaminant, at regulated temperature (21 oC) the nematodes were extracted by the method of Whitehead and Hemming tray, identified to family level and grouped according to the different trophic traits (bacterivorous, plant-pasasitic, fungivorous and predators-omnivorous). Data obtained showed a response of the soil nematodes to the toxicity caused by the tested contaminants at different levels and ways on the community. The total abundance of the nematodes decreased significantly after treatment with all metals, Cd, Zn and Cu and with the pesticides summer oil and abamectin, in the highest concentrations, except for the treatment with abamectin which also decreased with the lowest concentration. The abamectin and cadmium were the contaminants affecting more significantly the number of families of nematodes in concentrations of 0.0096 g a.i. / kg and 500 mg / kg, respectively. The trophic structure of the community also changed significantly under these contaminants in the highest concentrations, except for treatment with abamectin (lowest concentration). Fosetyl, among the pesticides, and zinc, were the contaminants showing less toxic effect on diversity and on the structure of the nematodes community. Opportunists were the dominant nematodes in the assays with Cd, Cu and abamectin. The results obtained in this study confirm the possibility of using an approach based on the effects of stressor agents on the structure of the community of soil nematodes, in soil ecotoxicology.