The overall aim of this thesis was to elucidate the relative importance of the bacterial and fungal energy channels within the soil food web and to differentiate and appreciate the differences in niche of the soil fauna when affected by differing land management. Feeding niche of the soil fauna is ambiguous and has been previously determined by observation, inference or biochemical studies. One method that can determine feeding preferences in situ is the use of stable isotopes. Stable isotopes trace the passage of C and N through different trophic levels, both at natural abundance and by the addition of a pulse of enrichment. The work described within this thesis describes the development of methods of culturing and labelling organisms for use in stable isotope studies. Bacteria, protozoa and fungi were cultured with stable isotopes enriched to 99 atom% and their growth and survival monitored. Utilising stable isotope enriched organisms means that empirical testing of the feeding interactions can occur and that differences between the bacterial and fungal energy channels can be explored. Two field sites were chosen to assess how management changes affect the food web, both sites were historically grassland with the same soil type, but one was converted to a willow woodland twenty years ago. The results of these studies have shown, at natural abundance a grassland and woodland habitat with very different stable isotope signatures, reflecting plant and soil composition, as well as differences in trophic niche and C drivers. The introduction of enriched bacteria illustrated that bacterial feeding was more widespread than normally portrayed in food web diagrams. The introduction of enriched protozoa highlighted that protozoan feeding by soil fauna was more prevalent in the grassland habitat; reflecting differences in linkages between trophic levels within the two habitats. Methods were also developed to “grow” enriched fungal hyphae back into soil food webs in a comparable way to the investigation of the bacterial energy channel. Different species of saprotrophic fungi were found to fractionate to differing extents when grown on the same natural abundance media and the fungus Absidia cylindrospora's growth was impacted when grown on a dually enriched medium. We can now infer that the bacterial energy channel is not as divergent from the fungal energy channel as previously hypothesised. The majority of soil fauna were found to be omnivorous through empirical results, consuming bacteria and protozoa, even when they were considered to be fungal feeders by the literature. The different habitats within the study were found to have different C drivers, with roots and soil being the primary driver in the grassland whilst litter was in the woodland, consequently favouring different food webs. This work makes a first step in measuring the contribution of the different feeding channels and feeding interactions occurring within the different trophic levels in the two habitats and shows the effect that one change in management has had over the entire faunal assemblage.

The study characterized the morphological differences among Cisco between geographic arms and depth strata, and determined the trophic positioning of various morphs, based on twelve years of capture data and specimens using morphological measurements, meristic counts, stomach contents, stable isotopes and fatty acids. Two main Cisco morpho-types were identified, a shallow water form and a deep water form that mainly differed in traits associated with swimming and feeding. These results were reinforced by the results on trophic ecology of morphs that demonstrated that each morph occupied a distinct niche. Results showed that shallow water groups had a more varied diet with a high percentage of copepods being ingested whereas deep-water groups showed preferences towards mysids. Although a consistent pattern in differences among shallow and deep morphs was observed, there was some degree of variation among arms of the lake suggesting a degree of isolation and adaptation to local conditions in each area of the lake. For example, in Smith Arm, morphological and dietary differences were found such as narrower body depth and a dietary preference towards daphnia. / February 2017

The δδ¹³C and δ¹⁵N composition of incremental segments of tooth dentine was used to infer infant and childhood diet in a post-medieval London population, and a hunting and gathering Mesolithic/Neolithic group from Latvia. Health was analysed using defects on the tooth enamel caused by stress, termed enamel hypoplasia. The populations, which differ markedly in their economy, diet and health, were selected because of the difference in childhood experiences between the two groups. The results were used to consider questions about childhood, including how early diet may have been influenced by social factors such as class or status, the effect this could have on population dynamics and how childhood diet and health are related. The results show that the London individuals were rarely breastfed beyond 6 months and in some instances not at all. A small isotopic difference between males and females was observed which could be caused by dietary or physiological differences. The peak incidence of hypoplasia may be related to developmental patterns, rather than stress caused by weaning. The Zvejnieki individuals had a slightly longer breastfeeding duration. Those buried with pendants consumed a different diet in childhood to those without pendants, suggesting a complex social system, possibly indicating that diet was related to the role a person had within the community. There is a suggestion diet may have shifted between the Middle Mesolithic and Late Neolithic, although not dramatically. Neither population have elevated δ¹³C often associated with breastfeeding. The early life histories of the groups are not compared directly, but general observations concerning the children’s lives are considered. It is concluded that economy is not a reliable predictor of infant feeding strategies, as hunter-gatherers provide children with solid foods at a similar time to industrial groups. Intra-population variability was found to be a feature of all socio-economic groups.

Investigations of interactions between climate change and humans suffer from the lack of climate proxies directly linked to historical or archaeological datasets that describe past environmental conditions at a particular location and time. We present a new set of pine tree-ring records (Pinus sylvestris L) developed from burial timbers excavated at the historical center of Yaroslavl city, Russia. A 171 year delta C-13 tree-ring chronology from AD 1430 to AD 1600 evidences mostly wet summers during the 15th century but exceptionally dry conditions of the 16th century at the Upper Volga catchment. According to the tree-ring record there were four major droughts (<-1.5 sigma) lasting from 9 to 26 years: 1501-1517, 1524-1533, 1542-1555 and 1570-1596, and major pluvials (>+1.5 sigma) lasting from 70 to 5 years: 1430-1500, 1518-1523, 1534-1541, and 1556-1564. We discuss a plausible contribution of these droughts to crop failures and city fires documented with historical chronicles for the Upper Volga catchment. The devastating drought regime of the 16th century corresponds to the loss of independence of the Yaroslavl principality to the Grand Duchy of Moscow and the formation of the centralized Russian State during the reign of Ivan the Terrible (1533-1584) underpinning the emergence of the Russian Empire. This study substantiates the value of archaeological timbers from the oldest Russian cities and inclusion of stable carbon isotope analysis for understanding hydroclimatic regimes across the mid latitudes of East European Plain, and their relationship to the history of Russia. (C) 2016 Elsevier GmbH. All rights reserved.

Les lagunes côtières Méditerranéennes constituent des zones de nourrissage pour les juvéniles de plusieurs espèces de poissons côtiers. C’est sur cet apport constant en juvéniles ainsi que sur les ressources trophiques du milieu que s’appuie l’aquaculture extensive dans la lagune Vassova (Préfecture de Kavala, Grèce). Afin d’optimiser la production piscicole, il apparaît important d’identifier les processus favorisant la survie et la croissance des jeunes poissons.Ce travail s’est focalisé sur une espèce communément exploitée dans les lagunes Méditerranéennes : le mulet sauteur Liza saliens (Mugilidae). Notre étude s’est attachée à identifier les ressources trophiques soutenant la croissance des juvéniles de L. saliens (15 - 50 mm, longueur totale / LT) et à préciser leur qualité nutritionnelle en termes d’apports en acides gras polyinsaturés (AGPI). Ainsi, pendant la période de colonisation de la lagune Vassova par L. saliens (Juin - Novembre), des prélèvements mensuels de poissons (juvéniles de L.saliens et principales espèces piscicoles sédentaires), de leurs proies potentielles, et des différentes sources de matière organique ont été effectués sur deux stations de la lagune. Une approche combinant l’analyse des biomarqueurs lipidiques, l’analyse isotopique et l’analyse des contenus stomacaux a été adoptée afin d’identifier les sources de carbone soutenant la croissance des jeunes L. saliens. Les analyses lipidiques ont également permis de suivre l’évolution de la composition en AG des lipides membranaires (lipides polaires : LP) et destockage (lipides neutres : LN) des juvéniles de L. saliens durant leur premiers mois de vie lagunaire. Enfin, en déterminant par GC-C-IR-MS la composition isotopique des AGPI assimilés par L. saliens, il a été possible d’identifier l’origine de ces composés essentiels. Nos résultats montrent qu’à leur arrivée dans la lagune, les juvéniles (~15 mm, LT) se nourrissent exclusivement d’organismes planctoniques. Lorsque les juvéniles atteignent les 20 mm (LT), ils passent progressivement vers une alimentation principalement basée sur des proies benthiques. Ce changement de régime alimentaire se traduit par une diminution importante des apports alimentaires en 22:6ω3. A cet égard, les résultats obtenus en GC-C-IRMS montrent que chez L. saliens cet AGPI a comme toute première origine, les microorganismes du compartiment planctonique. Il apparaît donc qu’au cours de leur transition du milieu planctonique marin vers le milieu benthique lagunaire, les juvéniles de L. saliens sont confrontés à une diminution de la qualité nutritionnelle. Néanmoins, le 22 :6ω3, mais également le 20:4ω6 semblent être activement retenus dans les lipides membranaires des jeunes poissons. Plus généralement, nos résultats montrent que le 20:4ω6 est fortement retenu par les principales espèces pisciaires de la lagune, suggérant l’importance pour les poissons estuariens, de ce composé essentiel impliqué dans la résistance des poissons aux stress environnementaux. / Mediterranean coastal lagoons are considered as major nursery areas for several coastal fish species. In Vassova lagoon (Kavala Prefecture, Greece), this continuous input of juveniles, along with the lagoons’ naturalfood resources, sustain local extensive aquaculture. Therefore, in order to optimise the fisheries’ yield, thefactors affecting juveniles’ growth and survival in the lagoon need to be assessed. The objectives of this research work are to identify the organic matter sources sustaining growth of a common commercial Mediterranean species (Liza saliens, Mugilidae) juveniles’ (15 – 50 mm, total length / TL) and to assess their nutritional quality in terms of polyunsaturated fatty acids (PUFAs). In that aim, fish (L.saliens juveniles and principal resident fish species), their potential preys, and basal organic matter sources where sampled monthly during L. saliens settlement in Vassova lagoon (June - November). The origin of carbon assimilated by L. saliens was assessed using lipid and isotopic biomarker approaches as well as stomach content analysis. Moreover, lipid analyses allowed understanding the influence of diet on the fatty acid (FA) composition of L. saliens storage (neutral lipids : NLs) and membrane lipids (polar lipids: PLs) during early life in the lagoon. Finally, the isotopic composition of the PUFAs assimilated by L. saliens juveniles was determined by GC-C-IRMS and allowed the assessment of the sources of these compounds in the ecosystem. Results indicate that at their arrival at the lagoons’ mouth L. saliens juveniles (~15 mm, TL) feed on planktonic organisms. When juveniles reach the size of 20 mm (TL), they progressively shift towards benthic prey. This dietary shift is followed by an important decrease of the dietary levels of DHA. Indeed, in Vassova lagoon, this PUFA seems to be mainly produced by planktonic microorganisms. Therefore, during the transition from the marine planktonic environment towards the lagoons’ demersal habitat, L. saliens juveniles probably experience a decrease in the nutritional quality of their food. However, 22:6ω3 as well as 20:4ω6 appear to be actively retained in L.saliens membrane lipids (PLs). More interestingly, 20:4ω6 seems also to be retained by other fish species found in the lagoon. The latter suggests that this essential compound, which in fish is implicated in resistance processes to environmental stressors, has an important physiological role for fish in estuarine environments.

Populations of many species of migratory birds are declining, and an understanding of how populations are linked between the breeding and nonbreeding grounds is necessary in order to determine drivers of declines. While all current tracking technologies to study the movements of small songbirds are limited by their coarse resolution, tracking birds by measuring stable isotopes in keratin offers an advantage because it requires only a single capture and is cost-effective, which leads to robust sample sizes. While this tracking method is accurate, stable hydrogen isotope values measured in feathers (δ2Hf) are known to be variable within a site, and may be influenced by the hydrology of a site. In this study, we assessed sources of variation in δ2Hf values in a wetland-associated Neotropical migratory bird, the prothonotary warbler (Protonotaria citrea), by comparing δ2Hf values among ages, sexes, years and feather type. We found that age and year significantly influence δ2Hf values, and that differences between primaries and rectrices are statistically significant but generally small. We also tested the accuracy and precision of models to assign prothonotary warblers to their breeding origin using known-origin feathers. We assigned birds in a spatially-explicit manner using an interpolated surface of stable hydrogen values measured in precipitation (δ2Hp), and developed a species-specific calibration equation to account for the offset between δ2Hf and δ2Hp, which explained 51% of the variation in δ2Hf values. We incorporated breeding bird abundance as prior information in our assignment model, and compared two sources of abundance data: the Breeding Bird Survey and a spatio-temporal exploratory model developed with eBird data. The assignment model with no prior information was accurate (83% of birds correctly assigned to their true location of origin), but imprecise (50% of grid cells assigned as likely locations of origin). Incorporating abundance as prior information led to a decrease in accuracy (9-14% of birds correctly assigned) but higher precision (1% of grid cells assigned as likely). We also assigned prothonotary warblers to their breeding origin using feathers collected from across the nonbreeding range. We found that all nonbreeding sampling locations contained a mixture of birds whose origins spanned the majority of the breeding range, with no evidence of strong connectivity between the seasons. In the absence of strong connectivity, the influence of events occurring at one nonbreeding location will be widespread and diffuse across the breeding range. For prothonotary warblers, understanding connectivity can help conservation planners understand how nonbreeding season habitat destruction and other processes influence population dynamics. We recommend that future studies account for age and year variation in δ2Hf values when possible, and continue to examine the trade-off between precision gained and accuracy lost when using abundance as prior information.

Springs in the Middle Atlas Mountains of Morocco are significant sources for public water supply. From March 2014 to May 2015, water temperatures were measured hourly at three springs (Ribaa, Sidi Rached, and Zerouka); water levels were measured hourly at Sidi Rached and Zerouka; and daily turbidity data were obtained from Ribaa. From March 2014 to March 2015, daily water samples were taken at Zerouka for analyses of the stable isotopes deuterium and oxygen-18. Hourly weather data (precipitation and air temperature) were available from March 2014 to May 2015 from Ifrane, near Zerouka. Temperature responses varied between the springs, showing a time-lagged seasonal signal at Sidi Rached, near-constant values at Zerouka, and relatively stable dry-season values followed by flashy wet-season behavior at Ribaa. Stage at Sidi Rached and Zerouka tracked together, with a broad minimum in late summer and responses to individual storms superposed on the signal. Stable isotopes fluctuated daily but were frequently out of phase with each other. Autocorrelation analyses of spring parameters indicate that Sidi Rached and Zerouka have greater inertia than Ribaa. Cross-correlation analyses show characteristic time lags between (1) precipitation and stage, (2) air temperature and water isotopes, and (3) air and water temperatures. However, as shown in previous work, there is a broad range of time lags between precipitation and turbidity. The variety of spring behaviors is consistent with differences in hydraulic connectivity within each spring basin.

In this thesis, I have developed a new methodology for the accurate determination of mass-dependent variations in nickel (Ni) isotope compositions. Nickel is initially separated in a three-column ion-exchange procedure, and the purified solutions are analysed by multi-collector inductively coupled plasma mass spectrometry (MCICPMS) using a double-spike technique. Using this methodology, I have measured the first Ni isotope ratios for a wide variety of natural geological samples. Significant Ni isotope variations were observed, with an overall spread in delta 60Ni-values of -0.9 to 2.5 permil. In igneous rocks Ni isotopes appear to be largely homogeneous, with only small variations (0.2 permil) between different rock types. Weathering of silicate rocks does on the other hand appear to cause significant fractionation of Ni isotopes, probably producing an isotopically heavy riverine input to the ocean. A heavy isotope signature is also visible in hydrogenetic ferromanganese crusts, with surface scrapings from globally distributed crusts show an average delta 60Ni-value of 1.65 permil. However, the variation in these samples is over 1.5 permil, likely reflecting local sources or biological processes, or alternatively indicating a heterogeneous Ni isotopic composition of the ocean. Organic-rich sediments also show heavy isotopic compositions, which are possibly transferred to the crude oils originating in these types of sediments. The only significant reservoir of light Ni isotopes found during this project are sulphides from magmatic systems. Overall, this thesis demonstrates the potential of this system as a powerful new tracer for a variety of geochemical processes.

The arrival of the North American Monsoon System (NAMS) terminates a presummer hyperarid period in the southwestern United States (U.S.), providing summer moisture that is favorable for forest growth. Montane forests in this region rely on winter snowpack to drive much of their growth; the extent to which they use NAMS moisture is uncertain. We addressed this by studying stable carbon and oxygen isotopes in earlywood and latewood from 11 sites along a latitudinal gradient extending from Arizona and New Mexico to Utah. This study provides the first regional perspective on the relative roles of winter versus summer precipitation as an ecophysiological resource. Here we present evidence that Ponderosa pine uses NAMS moisture differentially across this gradient. C-13/C-12 ratios suggest that photosynthetic water use efficiency during latewood formation is more sensitive to summer precipitation at the northern than at the southern sites. This is likely due to the fact that NAMS moisture provides sufficiently favorable conditions for tree photosynthesis and growth during most years in the southern sites, whereas the northern sites experience larger summer moisture variability, which in some years is limiting growth. Cellulose O-18 and C-13 values revealed that photoassimilates in the southern sites were produced under higher vapor pressure deficit conditions during spring compared to summer, demonstrating a previously underappreciated effect of seasonal differences in atmospheric humidity on tree ring isotope ratios. Our findings suggest that future changes in NAMS will potentially alter productivity and photosynthetic water use dynamics differentially along latitudinal gradients in southwestern U.S. montane forests.

Northern lakes and ponds are abundant and emit large amounts of the potent climate forcer methane to the atmosphere at rates prone to change with amplified Arctic warming. In spite of being important, fluxes from surface waters are not well understood. Long-term measurements are lacking and the dominant and irregular transport mode ebullition (bubbling) is rarely quantified, which complicate the inclusion of lakes and ponds in the global methane budget. This thesis focuses on variations in emissions on both local and regional scales. A synthesis of methane fluxes from almost all studied sites constrains uncertainties and demonstrates that northern lakes and ponds are a dominant source at high latitudes. Per unit area variations in flux magnitudes among different types of water bodies are mainly linked to water depth and type of sediment. When extrapolated, total area is key and thus post-glacial lakes dominate emissions over water bodies formed by peat degradation or thermokarst processes. Further, consistent multiyear measurements in three post-glacial lakes in Stordalen, northern Sweden, reveal that seasonal ebullition, primarily driven by fermentation of acetate, can be predicted by easily measured parameters such as temperature and heat energy input over the ice-free season. Assuming that most water bodies respond similarly to warming, this thesis also suggests that northern lakes and ponds will release substantially more methane before the end of the century, primarily as a result of longer ice-free seasons. Improved uncertainty reductions of both current and future estimates rely on increased knowledge of landscape-level processes related to changes in aquatic systems and organic loading with permafrost thaw, as well as more high-quality measurements, seldom seen in contemporary data. Sampling distributed over entire ice-free seasons and across different depth zones is crucial for accurately quantifying methane emissions from northern lakes and ponds. / <p>At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 4: Manuscript.</p>