<div>Agricultural headwater streams in the Midwestern United States are subject to contaminants from fields, increased sedimentation, and degradation of natural habitat. Previous research has shown that physical instream habitat degradation better explained variation in fish community structure than water chemistry. However, these studies did not include total suspended solids (TSS), which are considered a major freshwater contaminant. The objective of this study is to determine whether total suspended solids better explains fish community structure than other variables in agricultural headwater streams. Mixed linear effects modeling was used to determine the set of independent variables that best predicts each of the fish response variables of species richness, Shannon diversity index, fish density, and index of biotic integrity. Standardized coefficients were used to determine which independent variable in each of the models had the largest influence on fish response metrics. The set of independent variables that best explained species richness were mean total suspended solids, imidacloprid, discharge, and substrate richness. Shannon diversity index was explained best by the combination of maximum total suspended solids, mean total suspended solids, atrazine, total nitrogen, and discharge. Fish density was explained best by the percentage of silt and clay, dissolved oxygen, the percentage of canopy cover, cover type richness, and discharge. IBI was explained best by the combination of the percentage of silt and clay, total phosphorus, mean total suspended solids, and dissolved oxygen. Total suspended solids was the most influential independent variable for fish species richness and Shannon diversity, however the percentage of silt and clay in benthic sediments was the most influential independent variable for fish density and IBI. Results also indicate discharge and total phosphorus as being influential to fish community metrics. The results from this study suggest that models containing a combination of different types of independent variables best explain fish community structure. This study supports the use of conservation and restoration practices that reduce total suspended solids and the amount of silt and clay present in bed sediments to increase fish community integrity of agricultural headwater streams of the Midwestern United States.</div>

Various types of woody vegetation are a key biodiversity refugee in intensively managed agricultural landscapes. However, the role of woodlots, representing an important type of such a vegetation, remains overlooked so far. Whereas the previous studies focused on the effect of their area, shape and isolation, consequences of variation in their habitat quality for biodiversity were not assessed up to now. This thesis is thus one of the first studies focusing on woodlots as a specific habitat for birds in agricultural landscape. My goals were: (I) to find out what is the bird community composition of woodlots in a Czech landscape, (II) to find out, what are the key habitat predictors of bird species richness and abundance in woodlots, (III) to describe differences in habitat preferences among various guilds and (IV) to formulate recommendations for conservational practice. I surveyed birds in 82 woodlots in an intensively managed landscape in Central Bohemia, Czechia, and measured variables describing woodlots' habitat quality together with woodlots' area, shape, isolation and types of surrounding land-use. I recorded numerous forest and non-forest bird species (57 in total), including some endangered farmland birds. The habitat variables showing significant relationships to bird community...

Rain forest canopies are renowned for their very high biodiversity and the critical role they play in key ecological processes and their influence on global climate. Despite that New Zealand supports one of the most diverse and extensive epiphyte flora of any temperate forest system, few studies have investigated epiphyte communities and their invertebrate fauna along with factors that influence their distribution and composition. This thesis represents the first comprehensive study of entire epiphyte communities and their resident invertebrate fauna in the canopy of New Zealand’s indigenous forests. The aim of this study was to determine spatial patterns of epiphyte and invertebrate species richness, abundance and community composition in relation to abiotic variables, and in particular, the responses of these communities to elevated temperature and rainfall. This study was carried out in coastal lowland podocarp-broadleaved forests at two sites on the West Coast of the South Island of New Zealand. Samples from 120 mat-forming epiphyte assemblages located on inner canopy branches of 40 northern rata (Metrosideros robusta) trees were studied to characterise the component flora and fauna. Additionally, biomass, branch and tree characteristics and community responses to treatments designed to elevate temperature and rainfall to simulate predicted climate change were measured. This investigation revealed astonishing diversity and functional complexity of epiphyte and invertebrate life in this ecosystem. The 30.6 kg (dry weight) of epiphyte material collected contained a total of 567 species, 170 epiphyte and 397 invertebrate (excluding immature specimens and mites) species, including at least 10 species new to science and many undescribed species Epiphyte communities were found to be dominated by non-vascular plants (80 % of the total species richness), particularly liverworts and invertebrate communities were dominated with respect to abundance (~ 80 % of the total individuals) by Acari, Collembola and Hymenoptera (primarily ants) and functionally by scavengers and ants. Epiphyte and invertebrate communities were highly variable with respect to spatial patterning of species richness, abundance and composition across sites, among trees within sites and among branches within trees. Overall, a highly significant proportion, > 75 %, of the variance could be attributed to differences at the branch level, but these differences could not be explained by the environmental factors measured. There were no consistent relationships between the spatial pattern of epiphytes and invertebrates, or between vascular and non-vascular plants. However, there were significant positive correlations between epiphyte biomass and invertebrate species richness (r = 0.472; p < 0.0001) and abundance (r = -0.395; p < 0.0001), as well as non-living epiphyte biomass and scavenger species richness (r = 0.4; p < 0.0001). Microclimatic measurements taken on epiphyte mats were also highly variable with respect to temperature and relative humidity at similar physical locations within the same tree as well as across trees within sites. There was also considerable variation in the intensity and frequency of climatic extremes, although potentially harmful climatic conditions were experienced by all the epiphyte mats for which weather variables were measured. Negative correlations existed between both epiphyte and invertebrate community composition and increased temperatures expressed as cumulative degree days above 5˚C. However, variability was such that there was no direct evidence that increased temperature and rainfall treatments had an effect on invertebrate species richness, abundance or diversity. Northern rata host trees harbour an astonishingly diverse and complex canopy flora and fauna that is characterised by high spatial variability. Such variability highlights that to determine species distribution and community dynamics in canopy habitats in response to disturbance caused either by climate change or invasive species the structure of entire communities at different taxonomic and spatial scales, along with their responses to microclimatic factors, need to be studied. If such complexities are not taken into account, inappropriate interpretation may result in poor decisions concerning the conservation status, vulnerability and subsequent management of such unique ecosystems.

Ecosystems currently face widespread biodiversity losses and other environmental disturbances, such as climate warming, related to increased anthropogenic activities. Within this context, scientists consider the effects of such changes on the biodiversity, and hence on the activity, of soil microorganisms. Indeed, soil microorganisms mediate a wide range of soil processes. Currently, knowledge on soil microbial diversity is still limited, partially due to technical limitations. The advent of molecular-based analyses now allows studying the soil microbial diversity. These advances in the study of soil microbial communities have lead to a growing evidence of the critical role played by the microbial community in ecosystem functioning. This relationship is supposed to be relevant for narrow processes, regulated by a restricted group of microorganisms, such as the nitrification process. This PhD thesis aimed at studying ammonia oxidizing bacteria (AOB) community structure and richness as an integrated part of soil functioning. This research aimed at investigating the effect of aboveground plant diversity on ammonia oxidizing bacteria diversity and function in forest and grassland soils with focus on the influence of (a) functional group identity of grassland plants (legumes, grasses, forbs), (b) grassland plant species richness and (c) tree species, on AOB diversity and function. Another objective of this research was to study the effect of a 3°C increase in air temperature on AOB diversity and function. The link between AOB diversity and function (potential nitrification) is also investigated. For grassland ecosystems, a microcosm experiment was realized. An experimental platform containing 288 assembled grassland communities was established in Wilrijk (Belgium). Grassland species were grown in 12 sunlit, climate controlled chambers. Each chamber contained 24 communities of variable species richness (S) (9 S=1, 9 S=3 and 6 S=9).The grassland species belonged to three functional groups: three species of each grasses (Dactylis glomerata L., Festuca arundinacea SCHREB., Lolium perenne L.), forbs (non-N-fixing dicots; Bellis perennis L., Rumex acetosa L., Plantagolanceolata L.), and legumes (N-fixing dicots; Trifolium repens L., Medicago sativa L., Lotus corniculatus L.). Half of these chambers were exposed to ambient temperature and the other half were exposed to (ambient +3°C) temperature. One ambient and one (ambient+3°C) chambers were destructively harvested 4, 16 and 28 months after the start of the experiment. The influence of plant functional group identity on the nitrification process and on AOB community structure and richness (AOB diversity) was assessed in soils collected from the first two destructive amplings (chapter 2). The effect of plant species richness on AOB diversity and function was considered for soils sampled after 16 and 28 months (chapter 3). AOB function was determined by potential nitrification. AOB community structure and richness were assessed by polymerase chain reaction followed by denaturing gradient gel electrophoresis (DGGE) and sequencing of excised DGGE bands. I found that functional group identity can affect AOB community structure. In particular, the presence of legumes, both in monoculture or in mixture with forbs and grasses, lead to AOB community composition changes towards AOB clusters tolerating higher ammonium concentrations. This change in AOB community structure was only linked to increased potential nitrification under monocultures of legumes, when ammonium was supposed to be not limiting. This study revealed that physiological attributes of AOB and resource availability may be important factors in controlling the nitrification process. This research showed that the impact of plant species richness on the nitrification process could be mediated by the interactions between plants and AOB, through competition for substrate. A 3°C increase in air temperature did not affect AOB community structure, richness or function. In forest ecosystems, we studied the effect of tree species in forest sites located in Belgian and in the Grand-Duchy of Luxembourg covered each by several deciduous or coniferous tree species (Fagus sylvatica L., Quercus petraea (Mattuschka) Lieblein, Picea abies (L.) Karst, Pseudotsuga menziesii (Mirbel) Franco). We investigated the influence of these tree species on microbial processes (chapter 5) related to C and N cycling, particularly with emphasize on the nitrification process and on the diversity of AOB (chapter 6). The results showed that the effect of tree species on net N mineralization was likely to be mediated through their effect on soil microbial biomass, reflecting their influence on organic matter content and carbon availability. Influence of tree species on nitrification (potential and relative) might be related to the presence of ground vegetation through its influence on soil ammonium and labile C availability. AOB community structure was more site-specific than tree specific. However, within sites, AOB community structure under broadleaved trees differed from the one under coniferous trees. The effect on tree species on AOB was likely to be driven by the influence of tree species on net N mineralization, which regulates the substrate availability for AOB. The results also demonstrated that the relationship between AOB diversity and function might be related both to AOB abundance and AOB community structure and richness. This thesis showed no clear relationship between AOB community structure or richness and AOB function. However, we revealed that aboveground grassland plant richness, grassland plant functional groups and tree species influence AOB community structure and richness. Actuellement, les écosystèmes sont soumis à dimportantes pressions anthropiques et environnementales, pouvant aboutir à des pertes massives de biodiversité. Les scientifiques sinterrogent sur limpact de ces perturbations sur la diversité et, par conséquent, sur lactivité des microorganismes du sol. En effet, ceux-ci régulent de nombreux processus du sol. Actuellement, de nombreuses lacunes subsistent dans la connaissance de la diversité microbienne du sol. Celles-ci peuvent être partiellement attribuées aux difficultés méthodologiques associées à l'étude des micro-organismes du sol. Lavènement des techniques moléculaires nous permet de combler ces lacunes. Les avancées réalisées dans l'étude des communautés microbiennes du sol ont mis en évidence le rôle crucial joué par les communautés microbiennes dans le fonctionnement des écosystèmes. De plus, il semblerait que les processus régulés par un groupe restreint dorganismes, tel le processus de nitrification, soient plus sensibles à toute altération de la communauté. Lobjectif de cette thèse était détudier la structure de la communauté ainsi que la richesse (nombre de bandes DGGE) des bactéries oxydant lammoniac (AOB) comme une partie intégrante du fonctionnement des sols. Notre étude se focalisait sur linfluence de (a) différents groupes fonctionnels de plantes (graminées, légumineuses, dicotylédones), (b) communautés de plantes présentant une richesse spécifique croissante et (c) différentes essences forestières, sur la diversité (structure de la communauté et richesse des AOB) et la fonction des AOB. Cette recherche étudiait également limpact dune augmentation de température de 3°C sur ces paramètres. Létablissement dun lien éventuel entre la diversité et la fonction (nitrification potentielle) des AOB a aussi été envisagé. Concernant les écosystèmes prairiaux, nous avons réalisé une étude en microcosmes. Une plateforme expérimentale comprenant 288 communautés artificielles de plantes a été établie à Wilrijk (Belgique). Cette plateforme consistait en 12 chambres, dont une moitié était à température ambiante et la seconde était à température ambiante augmentée de 3°C. Chaque chambre contient 24 communautés de plantes de richesse spécifique variable (9 S=1, 9 S=3 et 6 S=9). Les communautés de plantes sont créées avec 9 espèces de plantes appartenant à trois groupes fonctionnels : 3 espèces de graminées (Dactylis glomerata L., Festuca arundinacea SCHREB., Lolium perenne L.), de légumineuses (dicotylédones fixatrices dazote ;Trifolim repens L., Medicago sativa L., Lotus corniculatus L.), et de dicotylédones non fixatrices dazote (Bellis perennis L., Rumex acetosa L., Plantago lanceolata L.). Les sols issus dune chambre à température ambiante et dune chambre à température ambiante augmentée de 3°C ont été échantillonnés, respectivement, 4, 16 et 28 mois après le début de lexpérimentation. Linfluence des groupes fonctionnels de plantes sur le processus de nitrification ainsi que sur la structure de la communauté et la richesse des AOB a été mesuré sur les sols issus des deux premiers échantillonnages (chapitre 2). Nous avons mesuré leffet de la richesse croissante en plantes sur la diversité et lactivité des AOB sur les sols échantillonnés après 16 et 28 mois dexpérimentation (chapitre 3). La structure de la communauté ainsi que la richesse des AOB ont été évaluées à laide dune amplification spécifique par réaction de polymérisation en chaîne (PCR) de lADN génomique extrait du sol suivie par une séparation par électrophorèse sur gel dacrylamide en présence dun gradient dénaturant (DGGE). Nous avons identifié les différentes AOB présentes par séquençage des bandes DGGE excisées. Nos résultats ont montré que les différents groupes fonctionnels peuvent affecter la structure de la communauté des AOB. En particulier, la présence de légumineuses, aussi bien en monoculture quen mélange avec des graminées ou des dicotylédones non fixatrices dazote, provoque des changements au sein de la structure de la communauté des AOB, favorisant la présence de clusters tolérants des concentrations en ammonium plus élevées. Ces changements de la structure de la communauté des AOB sont liés à des augmentations de la production potentielle de nitrates (nitrification potentielle) quand lammonium est supposé être non limitant. Cette étude révèle que la physiologie des AOB ainsi que la disponibilité en substrat peuvent être des facteurs majeurs intervenant dans le contrôle du processus de nitrification. Cette recherche montre que linfluence de la richesse spécifique des plantes sur la nitrification pourrait dépendre des interactions entre les plantes et les AOB via la compétition pour le substrat. Une augmentation de la température de lair de 3°C na pas influencé les richesse, structure de la communauté ou les fonctions des AOB. Pour les écosystèmes forestiers, nous aborderons leffet de différentes essences forestières (Picea abies (L.) KARST, Fagus sylvatica L., Quercus petraea LIEBLEIN ; Pseudotsuga menziezii (MIRB.) FRANCO) dans différents peuplements au Grand Duché du Luxembourg et en Belgique. Nous avons étudié l'influence de ces essences forestières sur les processus microbiens (chapitre 5) liés aux cycles du carbone et de lazote, en particulier leur effet sur le processus de nitrification et la diversité des AOB (chapitre 6). Notre étude révèle que linfluence des essences forestières sur la minéralisation nette de lazote pourrait être attribuable à leur effet sur la biomasse microbienne, reflétant ainsi leur effet sur la teneur en matière organique et la disponibilité en carbone. Limpact des essences forestières sur la nitrification (à la fois sur la nitrification relative et sur la nitrification potentielle) serait conditionné par la présence de végétation au sol, en raison de linfluence de celle-ci sur la disponibilité en ammonium et en carbone labile. Nous avons observé que la structure de la communauté des AOB était plus spécifique aux sites quaux essences forestières. Cependant, au sein dun site, elle différait sous feuillus et sous conifères. Les essences forestières influenceraient la structure de la communauté des AOB au travers de limpact quelles ont sur la minéralisation nette de lazote qui régule, quant à elle, la disponibilité en ammonium. Cette recherche démontre que le lien observé entre la diversité et la fonction dépendrait la fois de labondance, de la structure de la communauté et de la richesse des AOB. Cette thèse na révélé aucune relation claire entre la structure de la communauté ou la richesse des AOB et leur fonction. Par contre, nous avons observé que la richesse spécifique et les groupes fonctionnels de plantes prairiales et les essences forestières affectent la structure de la communauté et la richesse des AOB.

Many regional and local factors can influence the distribution of native and exotic species in ecological communities. I examined the regional- and local-scale determinants of native and exotic vascular plant species richness and composition in a highly fragmented oak savanna ecosystem on southeastern Vancouver Island. In sharp contrast to most reported results, I found a negative relationship between native and exotic richness at the regional scale, and no relationship at the local scale. Two extrinsic factors, surrounding road density and climate, best explained the regional-scale relationship by each affecting natives and exotics in opposite ways. Road density and climate were also the dominant predictors of native and exotic composition at the regional scale. Patterns in the patch occupancy of individual species confirmed the importance of these factors but I found that low surrounding road densities and cool, wet conditions predicted the presence of many natives and the absence of many exotics. Environmental factors explained variation in richness and composition at the local scale, but these factors were different for natives and exotics. My results suggest that natives and exotics respond to roads and climate in fundamentally different ways. Roads increase both exotic propagule pressure and disturbance, which may facilitate exotic invasion. In contrast, disturbance from roads may increase the likelihood of local extinction for particular natives. Differing climatic preferences within the native and exotic species pools may also partially explain the observed patterns. There was no evidence that native diversity directly affects exotic diversity (or vice versa). Surprisingly, I found that connectivity was not an important predictor of richness or composition despite the high degree of habitat fragmentation in this ecosystem.

The aim of this thesis was to increase knowledge about metapopulation and metacommunity processes in patchy, dynamic landscapes, using epiphytic bryophytes as a model system. Host trees and deciduous forest stands in the coniferous landscape are patchy, temporal and undergo changes in habitat quality during succession. Epiphytes must track this dynamic habitat network for their long-term survival. Community patterns at different spatial scales were explored and linked to regional metapopulation processes and local population dynamics. Spatial structuring in species richness both at a local and regional scale indicated stronger dispersal limitation but lower sensitivity to habitat quality in species with large asexual than in species with small sexual diaspores. In sexually dispersed species, a strong rescue effect was indicated by a bimodal frequency distribution of the species and by increasing local abundance with increasing patch connectivity. Present connectivity to other deciduous forest patches had positive effects on richness of asexually dispersed species, whereas richness of sexually dispersed species was instead related to the landscape connectivity 30 years ago. A study of local growth and reproduction suggested that this is caused by delayed sexual, but not asexual, reproduction. Habitat conditions affected the production of sporophytes, but not of asexual diaspores. No differences in either growth rates or competitive abilities among species with different dispersal and life-history strategies were found. In vitro experiments showed that establishment is higher from large asexual diaspores than from small sexual. Establishment of all diaspore types was limited by pH. There were indications of trade-offs between high germination and protonemal growth rates, desiccation tolerance and a rapid development of shoots from protonema. The results indicated that the epiphyte metacommunity is structured by two main trade-offs: dispersal distance (diaspore size) versus age at first reproduction, and dispersal distance versus sensitivity to habitat quality. Trade-offs in species traits may have evolved as a consequence of conflicting selection pressures imposed by habitat turnover, connectivity and irregular water supply rather than by species interactions. Syndromes of interrelated species traits imply that fairly small changes in habitat conditions can lead to distinct changes in metacommunity diversity: the results indicate that increasing distances among patches cause most harm to asexually dispersed species, whereas cuttings of forests of high age and quality as well as increasing patch dynamics are most harmful to sexually dispersed species. / Senarelagd disputation från: 2009-09-26, Lindahlsalen, EBC, Villavägen 9, 75236 Uppsala, Uppsala, 10:00

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Many regional and local factors can influence the distribution of native and exotic species in ecological communities. I examined the regional- and local-scale determinants of native and exotic vascular plant species richness and composition in a highly fragmented oak savanna ecosystem on southeastern Vancouver Island. In sharp contrast to most reported results, I found a negative relationship between native and exotic richness at the regional scale, and no relationship at the local scale. Two extrinsic factors, surrounding road density and climate, best explained the regional-scale relationship by each affecting natives and exotics in opposite ways. Road density and climate were also the dominant predictors of native and exotic composition at the regional scale. Patterns in the patch occupancy of individual species confirmed the importance of these factors but I found that low surrounding road densities and cool, wet conditions predicted the presence of many natives and the absence of many exotics. Environmental factors explained variation in richness and composition at the local scale, but these factors were different for natives and exotics. My results suggest that natives and exotics respond to roads and climate in fundamentally different ways. Roads increase both exotic propagule pressure and disturbance, which may facilitate exotic invasion. In contrast, disturbance from roads may increase the likelihood of local extinction for particular natives. Differing climatic preferences within the native and exotic species pools may also partially explain the observed patterns. There was no evidence that native diversity directly affects exotic diversity (or vice versa). Surprisingly, I found that connectivity was not an important predictor of richness or composition despite the high degree of habitat fragmentation in this ecosystem.