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The Arctic is considered as a focal region in the ongoing climate change debate. The currently observed and predicted climate warming is particularly pronounced in the high northern latitudes. Rising temperatures in the Arctic cause progressive deepening and duration of permafrost thawing during the arctic summer, creating an ‘active layer’ with high bioavailability of nutrients and labile carbon for microbial consumption. The microbial mineralization of permafrost carbon creates large amounts of greenhouse gases, including carbon dioxide and methane, which can be released to the atmosphere, creating a positive feedback to global warming. However, to date, the microbial communities that drive the overall carbon cycle and specifically methane production in the Arctic are poorly constrained. To assess how these microbial communities will respond to the predicted climate changes, such as an increase in atmospheric and soil temperatures causing increased bioavailability of organic carbon, it is necessary to investigate the current status of this environment, but also how these microbial communities reacted to climate changes in the past. This PhD thesis investigated three records from two different study sites in the Russian Arctic, including permafrost, lake shore and lake deposits from Siberia and Chukotka. A combined stratigraphic approach of microbial and molecular organic geochemical techniques were used to identify and quantify characteristic microbial gene and lipid biomarkers. Based on this data it was possible to characterize and identify the climate response of microbial communities involved in past carbon cycling during the Middle Pleistocene and the Late Pleistocene to Holocene. It is shown that previous warmer periods were associated with an expansion of bacterial and archaeal communities throughout the Russian Arctic, similar to present day conditions. Different from this situation, past glacial and stadial periods experienced a substantial decrease in the abundance of Bacteria and Archaea. This trend can also be confirmed for the community of methanogenic archaea that were highly abundant and diverse during warm and particularly wet conditions. For the terrestrial permafrost, a direct effect of the temperature on the microbial communities is likely. In contrast, it is suggested that the temperature rise in scope of the glacial-interglacial climate variations led to an increase of the primary production in the Arctic lake setting, as can be seen in the corresponding biogenic silica distribution. The availability of this algae-derived carbon is suggested to be a driver for the observed pattern in the microbial abundance. This work demonstrates the effect of climate changes on the community composition of methanogenic archae. Methanosarcina-related species were abundant throughout the Russian Arctic and were able to adapt to changing environmental conditions. In contrast, members of Methanocellales and Methanomicrobiales were not able to adapt to past climate changes. This PhD thesis provides first evidence that past climatic warming led to an increased abundance of microbial communities in the Arctic, closely linked to the cycling of carbon and methane production. With the predicted climate warming, it may, therefore, be anticipated that extensive amounts of microbial communities will develop. Increasing temperatures in the Arctic will affect the temperature sensitive parts of the current microbiological communities, possibly leading to a suppression of cold adapted species and the prevalence of methanogenic archaea that tolerate or adapt to increasing temperatures. These changes in the composition of methanogenic archaea will likely increase the methane production potential of high latitude terrestrial regions, changing the Arctic from a carbon sink to a source. / Die Arktis ist in den gegenwärtigen Diskussionen zum Klimawandel von besonderem Interesse. Die derzeitig beobachtete globale Erwärmung ist in den hohen nördlichen Breiten besonders ausgeprägt. Dies führt dazu, dass ehemals gefrorene Böden zunehmend tiefer auftauen und daher im Boden enthaltene Kohlenstoffquellen für die mikrobielle Umsetzung und Mineralisierung zur Verfügung stehen. Aufgrund dieser Prozesse entstehen klimarelevant Gase, darunter Kohlendioxid und Methan, die aus den Böden und Sedimenten freigesetzt werden können. Wenn man bedenkt, dass in den nördlichen Permafrostgebieten die Hälfte des weltweit unter der Bodenoberfläche gelagerten Kohlenstoffs gelagert ist, wird die Bedeutung dieser Region für das Verständnis des globalen Kohlenstoffkreislaufes und der möglichen Treibhaus-gasemissionen sichtbar. Trotz dieser Relevanz, sind die am Kohlenstoffumsatz beteiligten Mikroorganismen in der Arktis wenig untersucht und ihre Anpassungsfähigkeit an die gegenwärtigen Klimaveränderungen unbekannt. Die vorliegende Arbeit untersucht daher, wie sich Klimaveränderungen in der Vergangenheit auf die Anzahl und Zusammensetzung der mikrobiellen Gemeinschaften ausgewirkt haben. Dabei liegt ein besonderer Fokus auf die methanbildenden Archaeen, um das Verständnis der mikrobiellen Methandynamik zu vertiefen. Im Rahmen dieser Arbeit wurden drei Bohrkerne aus zwei verschiedenen Standorten in der russischen Arktis untersucht, darunter terrestrischer Permafrost und Seesedimente aus Sibirien und Chukotka, Russland. Mittels der Identifikation und Quantifizierung von mikrobiellen Genen und charakteristischen Bestandteilen der mikrobiellen Zellmembran war es möglich, fossile mikrobielle Gemeinschaften in Seesedimenten mit einem Alter von bis zu 480 000 Jahren und in Permafrostablagerungen mit einem Alter von bis zu 42 000 Jahren zu rekonstruieren. Es wurde gezeigt, dass es während vergangener warmen Perioden zu einem Wachstum von Bakterien und Archaeen in allen untersuchten Standorten gekommen ist. Dieser Trend konnte auch für die Gemeinschaft der methanogenen Archaeen gezeigt werden, die während warmen und insbesondere feuchten Klimabedingungen in großer Anzahl und Diversität vorhanden waren, was wiederrum Rückschlüsse auf mögliche Methanemissionen erlaubt. In den terrestrischen Permafroststandorten wird der Temperaturanstieg als direkte Ursache für die gefundene Reaktion der mikrobiellen Gemeinschaft vermutet. Im Gegenzug dazu, führte der Temperaturanstieg im untersuchten arktischen See wahrscheinlich zu einer erhöhten Primärproduktion von organischem Kohlenstoff, die wiederum das Wachstum der Mikroorganismen antrieb. Weiterhin konnte im Rahmen dieser Arbeit gezeigt werden, dass Methanosarcina-verwandte Spezies in der Russischen Arktis weit verbreitet sind und sich an veränderte Umweltbedingungen gut anpassen können. Im Gegensatz dazu stehen Vertreter von Methanocellales und Methano-microbiales, die nicht in der Lage sich an veränderte Lebensbedingungen anzupassen. Im Rahmen dieser Arbeit konnte erstmalig gezeigt werden, dass es in früheren Warmphasen zu einem vermehrten Wachstum der an der Umsetzung des organischen Kohlenstoffs beteiligten Mikroorganismen in der Russischen Arktis gekommen ist. Im Zusammenhang mit der zukünftigen Erwärmung der Arktis kann also von einer Veränderung der am Kohlenstoffkreislauf beteiligten Mikroorganismen ausgegangen werden kann. Mit den steigenden Temperaturen werden sich einige Vertreter der methanproduzierenden Mikroorganismen an die veränderten Bedingungen anpassen können, während Temperatur-empfindliche Vertreter aus dem Habitat verdrängt werden. Diese Veränderungen in der mikrobiellen Gemeinschaft können die Methanproduktion der hohen noerdlichen Breiten erhoehen und dazu beitragen, dass aus der Arktis als eine Kohlenstoffsenke eine Kohlenstoffquelle wird.

The reconstruction of past environmental conditions is a fascinating research area that attracts the interest of many individuals in various geological disciplines. Paleoenvironmental reconstruction studies can shed light on the understanding of past climates and are a key to the prediction of future climate changes and their consequences. These studies take on special significance when focused on areas sensitive to climate change. The Arctic region, which is experiencing dramatic changes today in its peatlands and in its ocean, is prime example. The entire region plays a major role in global climate changes and has recently received considerable interest because of the potential feedbacks to climate change and its importance in the global carbon cycle. For a better understanding of the role of Arctic peatlands and the Arctic Ocean to global climate changes, more records of past conditions and changes in the region are needed. This work applies different geochemical proxies, with special emphasis on lipid biomarkers, to the study of a permafrost peat deposit collected from the Eastern European Russian Arctic and a marine core retrieved from the Lomonosov Ridge in the central Arctic Ocean. The results reported of this study show that molecular stratigraphy obtained from the analysis of lipid biomarkers in both peat and marine profiles, combined with other environmental proxies, can contribute significantly to the study of Arctic ecosystems of the past. / <p>At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 2: Manuscript. Paper 3: Manuscript. Paper 4: Manuscript.</p>

This study deploys compound-specific multi-proxy isotopic study of lipid biomarkers to understand Neogene climatic and ecological variabilities in the Himalayan foreland. The investigation of compound-specific carbon and hydrogen isotopes along with glycerol dialkyl glycerol tetraether (GDGT) is the first of its kind for the Nepalese Siwalik. A total of 49 mudstone (and some paleosol) samples were collected from the paleomagnetically age-constrained Siwalik strata in the Surai Khola and Karnali River sections. δ13C results suggest a domination of C3 trees between 12 and 8.5 Ma, and a stepwise expansion of C4 grasses starting gradually at 8.5 Ma and culminating rapidly around 5.5 Ma. δD results show an overall gradual increase in rainfall since 12 Ma, with a rapid intensification around 5.5 Ma. The negative correlation between rainfall and GDGT-derived paleotemperature prior to 5.5 Ma indicates that the region experienced higher rainfalls during colder periods and vice versa. We propose that this negative correlation could be related to the strong presence of mid-latitude westerlies in the region because of the subdued Himalayas, when summer monsoon winds were weaker, that brought enhanced winter-precipitation particularly during colder periods. After 5.5 Ma, our data show a conspicuous positive correlation between rainfall and annual temperature, indicating the onset of modern-style seasonality in rainfall in the Indian subcontinent, which generates more rainfall during summer than during winter. Notably, this initiation of the Indian monsoon around 5.5 Ma favored the dominance of C4 grasses over C3 trees that is reflected in our δ13C data.

Compound specific isotope analysis of lake sediments is a powerful tool in deciphering evidence of changing climatic and paleoenvironmental conditions through time. Isotopic analysis of Lake El’gygytgyn pilot sediment cores, PG1351 and LZ1029, have contributed increased insight into paleoenvironmental interpretations regarding conditions of permanent ice cover and water column anoxia at the lake over the past 250 kyr. Bulk sediment δ15N was measured as a proxy for denitrification and a possible indicator for water column anoxia intensity. However, it appears that insufficient quantities of water column nitrate to fuel denitrification make its correlation with anoxia intensity ineffective. In pilot core LZ1029, compound-specific δ13C of alkanes, fatty acids, and alcohols were analyzed to determine the changing sources of organic matter as well as the source of a strong negative isotopic shift in the bulk sediment δ13C (-26‰ to -33‰) over the past 50 kyr. Results indicate that the majority of alkanes, fatty acids, and alcohols are long chain compounds consistent with a terrestrial plant origin, with increased aquatic contribution during the local last glacial maximum (LLGM). Among the compound classes examined, only the mid chain fatty acids display a strong LLGM depletion (δ13C = -43‰). Short chain fatty acids exhibit an LLGM depletion (δ13C = -35‰) similar to bulk sediment δ13C, while the δ13C trend of long chain alkanes, fatty acids, and alcohols differ from the bulk sediment δ13C trend, suggesting an autochthonous source of bulk isotope depletion. Evidence of methane cycling exists only in the presence and isotopic value of diplopterol (LLGM δ13C = -93.4‰), a biomarker for aerobic oxidation of methane. Two compounds indicative of archaeal lipids were present at considerable concentrations during the LLGM (394 and 668 µg/g TOC), but without the extreme negative δ13C associated with methanogenesis and methanotrophy. These results suggest insufficient generation of methane in the lake to have derived from such a large anaerobic archaeal methanogen community suggesting that archaea are not acting entirely as methanogens. Furthermore, it appears unlikely that a significant anoxic layer existed in the water column of Lake El’gygytgyn during the past ~50kyr. The results of this work will be applied to ongoing investigations on the newest cores from Lake El’gygytgyn, which represent the past 3.5 Myr.

Discovery of Novel Serum Biomarkers for Diagnosing and Staging Alzheimer’s DiseaseDipti Jigar ShahDepartment of Chemistry and Biochemistry, BYUDoctor of PhilosophyAlzheimer’s disease (AD) is an untreatable neurologic disease affecting more than 5 million Americans, most over 60 years of age. Protein plaques and neurofibrillary tangles typify AD brain pathology and are thought to cause the progressive dementia and brain shrinkage observed in AD. Currently there are no methods to diagnose the disease at a time before damage becomes irreversible.Biochemical tests for AD using cerebrospinal fluid analysis or neuroimaging are not yet sufficiently sensitive and specific, and they are invasive. This points to a need for a more easily applied and more sensitive diagnostic test. Although the gross anatomical changes are localized to the brain, AD is likely to involve changes throughout the body. As a result of this, changes in the abundance of certain biomolecules present in the circulation system are likely to occur. Consequently, a serum proteomics approach able to measure such changes, when applied to AD, would likely find quantitative changes in relevant molecules that can help diagnose the disease correctly, ideally early in the disease process. The goal of this work was to discover and validate novel diagnostic serum biomarkers for AD. For biomarker discovery and validation, we used a novel serum proteomics approach involving reversed phase capillary-liquid chromatography-electrospray ionization-quadrupole-time of flight mass spectrometry. Our samples were protein depleted, which helped us survey low molecular weight species in the serum without ion suppression from larger proteins like albumin. We were able to observe more than 8000 molecular species in a single run. The overall project was comprised of four studies: (i) discovery of novel potential serum AD markers, (ii) blinded validation of diagnostically promising biomarkers found in the initial study, with their further chemical identification, (iii) exploring gender-based serum AD biomarkers, and (v) discovery of biomarkers that distinguish early versus moderate stage AD. In the first study, the approach found 38 significant (p < 0.05) biomarkers and 21 near significant (p = 0.05 to 0.099) biomarkers. On using the forward selection approach, we built multi-marker panels with specificities and sensitivities higher than 80%.The second study reports on a blinded validation study that was performed on a new set of serum samples. We focused on the 13 most promising AD biomarkers found as part of the initial study. We successfully validated 4 of these biomarkers that showed highly significant statistical p-values. As part of this study, research was conducted to identify these 4 biomarkers, which was accomplished using tandem mass spectrometry with fragmentation experiments. The third study used data from the initial study but looked at gender specific biomarkers. We found 31 significant and near significant serum AD biomarkers for women, 16 for men, and 25 that were gender independent. Multi-marker panels of AD biomarkers for women or men had sensitivities of >60% and specificities >85%.In the fourth study, cases with moderate AD were compared to cases with very mild or mild AD to find novel biomarkers that could be used for staging. We found 44 significant and near significant biomarkers that were quantitatively different between mild and severe AD. In conclusion, we were successful in accomplishing the goal of this work of finding, validating and identifying novel serum biomarkers that diagnose AD.

The investigation presented in this thesis examined the microbial and functional diversity of the meltwater ponds Fresh, Orange and Salt Ponds on the McMurdo Ice Shelf, near Bratina Island, Antarctica. These sites were chosen because of the ecological importance and absence of detailed characterisations of their diversity and function as part of Antarctica?s largest wetland. Particular focus was on cyanobacterial diversity, nitrogen fixation and secondary metabolite production. Using 16S rRNA gene and morphological analysis a large diversity of cyanobacteria (more than 22 phylotypes) was identified with high phylogenetic similarities (up to 99% sequence identity) to cyanobacteria from mats in other regions of Antarctica. In addition biogeographical distributions were identified including potentially endemic and cosmopolitan cyanobacteria. High salinities were also connected to the change and reduction of diversity. Lipid marker analyses were performed targeting hydrocarbons, ether-linked hydrocarbons, methylated fatty acid esters (FAME), wax esters, hopanols and sterols. Lipid biomarker profiles were similar to typical cyanobacteria dominated mats with major input from microorganisms including oxygenic and anoxygenic phototrophs, obligate aerobic and anaerobic heterotrophs that conduct the metabolic processes of fermentation, sulphate reduction, sulphate and iron-oxidation, methanogeneses. Signature lipids indicative of Chloroflexus and archaea, as well as branched aliphatic alkanes with quaternary substituted carbon atoms (BAQCs), were identified for the first time in Fresh, Orange and Salt Ponds. Based on nifH gene analysis, the nitrogen fixing diversity characterised in Orange Pond consisted of cyanobacterial Nostoc sp. as well as firmicutes, beta-, gamma- and delta-proteobacteria. Acetylene reduction assays and nifH gene RNA transcript diversity identified Nostoc sp. as a main contributor of nitrogenase activity in these ponds. Furthermore, analytical methods were used to identify the cyanobacterial secondary metabolites microcystins, although the genetic basis for this production and the toxin producer could not been identified. However non-ribosomal peptide synthetases (NRPS) and polyketide synthases (PKS) genes were identified which could be the genetic basis for novel bioactives. The use of a multi-disciplinary approach synthesis and subsequent results significantly increased our understanding of the diversity and function of microbial mat communities in the unique meltwater ponds of the McMurdo Ice shelf, Antarctica.

The eastern tropical north Pacific (ETNP) is characterized by one of the ocean's most severe midwater oxygen minimum zones (OMZs), where oxygen levels are often less than 5 µM. The copepod family Eucalanidae is a numerically abundant and diverse zooplankton group in the ETNP, and displays a wide range of vertical distributions related to environmental oxygen concentrations. The goal of this dissertation was to develop a better understanding of the ecology, physiology, and biochemistry of closely related copepod species (family Eucalanidae) that inhabit the ETNP OMZ system. This was accomplished through examining different parameters relating to (1) metabolic rates, (2) detailed lipid composition and biomarkers, and (3) body composition, enzyme activity and survivorship in low oxygen water. Oxygen consumption, ammonium, urea, and phosphate excretion rates were generally highest in Subeucalanus subtenuis, a copepod primarily residing in the upper euphotic zone. Eucalanus inermis, typically found in the lowest oxygen environment of the species examined, showed significantly lower metabolic rates largely due to high water content. Rhincalanus rostrifrons, residing primarily in the upper oxycline, showed intermediate rates, likely relating to its higher reliance on lipid catabolism than S. subtenuis and E. inermis. Urea excretion rates showed a complicated relationship with temperature and oxygen, which calls for further study. Knowledge of such interactions is necessary for accurate modeling of nitrogen cycles in OMZ and other oceanic regions. Lipid biomarkers suggested that S. subtenuis, E. inermis and Pareucalanus attenuatus all fed primarily on particulates near the chlorophyll maximum region, while R. rostrifrons and R. nasutus likely fed on sinking particulates at depth. These results also emphasized the difference in lipid composition between wax esters and triacylglycerol components of storage lipids. This study suggested a much larger role of phylogeny in characterizing lipid contents than previously thought. Body composition, enzyme assays and survivorship studies suggested that E. inermis, S. subtenuis, P. attenuatus, R. nasutus and R. rostrifrons formed four separate ecological groups based on genus. E. inermis had low organic matter, moderate lactate dehydrogenase (LDH) activity, and high survivorship at oxygen concentrations < 20 µM. Rhincalanus spp. also had moderate LDH activity and high survivorship in low oxygen, but were unique in particularly low protein and high lipid content. S. subtenuis was characterized by high protein content, no measurable LDH activity and low survivorship in < 20 µM O2. P. attenuatus was similar to S. subtenuis in many respects, but had lower protein content and a different lipid accumulation strategy. In conclusion, eucalanoid copepods utilized many different ecological strategies in the ETNP OMZ system. Features of different ecological groups fit well with their observed vertical distributions in the water column. Understanding the ecology of organisms in OMZ systems will allow us better predictive capability for the effects of expanding OMZs in other regions.

The investigation presented in this thesis examined the microbial and functional diversity of the meltwater ponds Fresh, Orange and Salt Ponds on the McMurdo Ice Shelf, near Bratina Island, Antarctica. These sites were chosen because of the ecological importance and absence of detailed characterisations of their diversity and function as part of Antarctica?s largest wetland. Particular focus was on cyanobacterial diversity, nitrogen fixation and secondary metabolite production. Using 16S rRNA gene and morphological analysis a large diversity of cyanobacteria (more than 22 phylotypes) was identified with high phylogenetic similarities (up to 99% sequence identity) to cyanobacteria from mats in other regions of Antarctica. In addition biogeographical distributions were identified including potentially endemic and cosmopolitan cyanobacteria. High salinities were also connected to the change and reduction of diversity. Lipid marker analyses were performed targeting hydrocarbons, ether-linked hydrocarbons, methylated fatty acid esters (FAME), wax esters, hopanols and sterols. Lipid biomarker profiles were similar to typical cyanobacteria dominated mats with major input from microorganisms including oxygenic and anoxygenic phototrophs, obligate aerobic and anaerobic heterotrophs that conduct the metabolic processes of fermentation, sulphate reduction, sulphate and iron-oxidation, methanogeneses. Signature lipids indicative of Chloroflexus and archaea, as well as branched aliphatic alkanes with quaternary substituted carbon atoms (BAQCs), were identified for the first time in Fresh, Orange and Salt Ponds. Based on nifH gene analysis, the nitrogen fixing diversity characterised in Orange Pond consisted of cyanobacterial Nostoc sp. as well as firmicutes, beta-, gamma- and delta-proteobacteria. Acetylene reduction assays and nifH gene RNA transcript diversity identified Nostoc sp. as a main contributor of nitrogenase activity in these ponds. Furthermore, analytical methods were used to identify the cyanobacterial secondary metabolites microcystins, although the genetic basis for this production and the toxin producer could not been identified. However non-ribosomal peptide synthetases (NRPS) and polyketide synthases (PKS) genes were identified which could be the genetic basis for novel bioactives. The use of a multi-disciplinary approach synthesis and subsequent results significantly increased our understanding of the diversity and function of microbial mat communities in the unique meltwater ponds of the McMurdo Ice shelf, Antarctica.

Ces travaux d'archéométrie concernent l’étude moléculaire par GC-MS de marqueurs lipidiques (biomarqueurs) préservés au sein de sols archéologiques et de substances végétales impliquées en tant qu'ingrédients dans la confection d’artefacts. Des analyses complémentaires en isotopie du carbone de composés individuels et des mesures de datation au 14C (AMS MICADAS) de la matière organique totale des sols, d'extraits lipidiques et d'un composé individuel (miliacine) ont également été effectuées. Cette approche a permis:- de montrer l’existence de la culture de millet dès l’âge du Bronze en Alsace, les sols associés à cette culture et leur contenu organique ayant été piégés et préservés dans des silos à grains enterrés datés de l’âge du Fer.- d'identifier la nature de structures archéologiques comme étant d'anciennes latrines et une aire de stabulation de bétail via l'identification de stéroïdes fécaux.- d'établir des critères chimiotaxonomiques fiables basés sur l'analyse des lipides pour l’authentification de résines de styrax et de liquidambars.- d'identifier la nature d'une résine issue de Styrax officinalis ayant été incorporée dans l’enduit organique ornant un crâne décoré (IXème millénaire av. J.-C., site de Nahal Hemar, Israël).- de mettre en évidence l’emploi de brai de bouleau comme agent collant lors de la confection d’un bijou daté du Premier âge du Fer. / In this archaeometric study, lipid biomarkers from archaeological soils and organic substances originating from plants found on artefacts were investigated by GC-MS. In addition, the stable carbon isotopic composition of individual lipids and the 14C age (AMS MICADAS) of soil organic matter, lipid extracts and one isolated compound (miliacin) were determined. Such an archaeometric approach allowed:- the existence of a millet cultivation during the Bronze Age in Alsace to be unveiled for the first time based on preserved molecular remains of this cereal in agricultural soils trapped within grain silos dated from the Iron Age.- the function of uncharacterized archaeological structures to be identified as ancient latrines and a stall area based on the identification of faecal steroidal markers.- reliable chemotaxonomic criteria for the authentication of styrax resins and liquidambar gums to be established using specific organic markers (triterpenoids, notably).- the vegetal component of an organic coating decorating a skull from the 9th millennium BC (Nahal Hemar site, Israel) to be identified as a resin from Styrax officinalis.- the use of birch bark tar as adhesive for the making of a jewellery dated from the Iron Age to be discovered.