On the microstructure, growth pattern and original porosity of belemnite rostra: insights from calcitic Jurassic belemnites

Calcitic belemnite rostra are usually employed to perform paleoenvironmental studies based on geochemical data. However, several questions, such as their original porosity and microstructure, remain open, despite they are essential to make accurate interpretations based on geochemical analyses.This paper revisits and enlightens some of these questions. Petrographic data demonstrate that calcite crystals of the rostrum solidum of belemnites grow from spherulites that successively develop along the apical line, resulting in a “regular spherulithic prismatic” microstructure. Radially arranged calcite crystals emerge and diverge from the spherulites: towards the apex, crystals grow until a new spherulite is formed; towards the external walls of the rostrum, the crystals become progressively bigger and prismatic. Adjacent crystals slightly vary in their c-axis orientation, resulting in undulose extinction. Concentric growth layering develops at different scales and is superimposed and traversed by a radial pattern, which results in the micro-fibrous texture that is observed in the calcite crystals in the rostra.Petrographic data demonstrate that single calcite crystals in the rostra have a composite nature, which strongly suggests that the belemnite rostra were originally porous. Single crystals consistently comprise two distinct zones or sectors in optical continuity: 1) the inner zone is fluorescent, has relatively low optical relief under transmitted light (TL) microscopy, a dark-grey color under backscatter electron microscopy (BSEM), a commonly triangular shape, a “patchy” appearance and relatively high Mg and Na contents; 2) the outer sector is non-fluorescent, has relatively high optical relief under TL, a light-grey color under BSEM and low Mg and Na contents. The inner and fluorescent sectors are interpreted to have formed first as a product of biologically controlled mineralization during belemnite skeletal growth and the non-fluorescent outer sectors as overgrowths of the former, filling the intra- and inter-crystalline porosity. This question has important implications for making paleoenvironmental and/or paleoclimatic interpretations based on geochemical analyses of belemnite rostra.Finally, the petrographic features of composite calcite crystals in the rostra also suggest the non-classical crystallization of belemnite rostra, as previously suggested by other authors.

Geochemical analysis at ODP Site 207-1261 from the Demerara Rise in the western equatorial Atlantic

A high-resolution geochemical record of a 120 cm black shale interval deposited during the Coniacian-Santonian Oceanic Anoxic Event 3 (ODP Leg 207, Site 1261, Demerara Rise) has been constructed to provide detailed insight into rapid changes in deep ocean and sediment paleo-redox conditions. High contents of organic matter, sulfur and redox-sensitive trace metals (Cd, Mo, V, Zn), as well as continuous lamination, point to deposition under consistently oxygen-free and largely sulfidic bottom water conditions. However, rapid and cyclic changes in deep ocean redox are documented by short-term (~15-20 ka) intervals with decreased total organic carbon (TOC), S and redox-sensitive trace metal contents, and in particular pronounced phosphorus peaks (up to 2.5 wt% P) associated with elevated Fe oxide contents. Sequential iron and phosphate extractions confirm that P is dominantly bound to iron oxides and incorporated into authigenic apatite. Preservation of this Fe-P coupling in an otherwise sulfidic depositional environment (as indicated by Fe speciation and high amounts of sulfurized organic matter) may be unexpected, and provides evidence for temporarily non-sulfidic bottom waters. However, there is no evidence for deposition under oxic conditions. Instead, sulfidic conditions were punctuated by periods of anoxic, non-sulfidic bottom waters. During these periods, phosphate was effectively scavenged during precipitation of iron (oxyhydr)oxides in the upper water column, and was subsequently deposited and largely preserved at the sea floor. After ~15-25 ka, sulfidic bottom water conditions were re-established, leading to the initial precipitation of CdS, ZnS and pyrite. Subsequently, increasing concentrations of H2S in the water column led to extensive formation of sulfurized organic matter, which effectively scavenged particle-reactive Mo complexes (thiomolybdates). At Site 1261, sulfidic bottom waters lasted for ?90-100 ka, followed by another period of anoxic, non-sulfidic conditions lasting for ~15-20 ka. The observed cyclicity at the lower end of the redox scale may have been triggered by repeated incursions of more oxygenated surface- to mid-waters from the South Atlantic resulting in a lowering of the oxic-anoxic chemocline in the water column. Alternatively, sea water sulfate might have been stripped by long-lasting high rates of sulfate reduction, removing the ultimate source for HS**- production.

Stable carbon isotope ratios and accumulation rates of organic carbon and nutrients of DSDP Hole 79-545 (Appendix A)

Future warming is predicted to shift the Earth system into a mode with progressive increase and vigour of extreme climate events possibly stimulating other mechanisms that invigorate global warming. This study provides new data and modelling investigating climatic consequences and biogeochemical feedbacks that happened in a warmer world ~112 Myr ago. Our study focuses on the Cretaceous Oceanic Anoxic Event (OAE) 1b and explores how the Earth system responded to a moderate ~25,000 yr lasting climate perturbation that is modelled to be less than 1 °C in global average temperature. Using a new chronological model for OAE 1b we present high-resolution elemental and bulk carbon isotope records from DSDP Site 545 from Mazagan Plateau off NW Africa and combine this information with a coupled atmosphere-land-ocean model. The simulations suggest that a perturbation at the onset of OAE 1b caused almost instantaneous warming of the atmosphere on the order of 0.3 °C followed by a longer (~45,000 yr) period of ~0.8 °C cooling. The marine records from DSDP Site 545 support that these moderate swings in global climate had immediate consequences for African continental supply of mineral matter and nutrients (phosphorous), subsequent oxygen availability, and organic carbon burial in the eastern subtropical Atlantic, however, without turning the ocean anoxic. The match between modelling results and stratigraphic isotopic data support previous studies [summarized in Jenkyns 2003, doi:10.1098/rsta.2003.1240] in that methane emission from marine hydrates, albeit moderate in dimension, may have been the trigger for OAE 1b, though we can not finally rule out alternative mechanisms. Following the hydrate mechanism a total of 1.15 * 10**18 g methane carbon (delta13C=-60 ?), equivalent to about 10% to the total modern gas hydrate inventory, generated the delta13Ccarb profile recorded in the section. Modelling suggests a combination of moderate-scale methane pulses supplemented by continuous methane emission at elevated levels over ~25,000 yr. The proposed mechanism, though difficult to finally confirm in the geological past, is arguably more likely to occur in a warmer world and apparently perturbs global climate and ocean chemistry almost instantaneously. This study shows that, once set-off, this mechanism can maintain Earth's climate in a perturbed mode over geological time leading to pronounced changes in regional climate.

Treatment of phenanthrene and benzene using microbial fuel cells operated continuously for possible in situ and ex situ applications

Bioelectrochemical systems could have potential for bioremediation of contaminants either in situ or ex situ. The treatment of a mixture of phenanthrene and benzene using two different tubular microbial fuel cells (MFCs) designed for either in situ and ex situ applications in aqueous systems was investigated over long operational periods (up to 155 days). For in situ deployments, simultaneous removal of the petroleum hydrocarbons (>90% in term of degradation efficiency) and bromate, used as catholyte, (up to 79%) with concomitant biogenic electricity generation (peak power density up to 6.75 mWm−2) were obtained at a hydraulic retention time (HRT) of 10 days. The tubular MFC could be operated successfully at copiotrophic (100 ppm phenanthrene, 2000 ppm benzene at HRT 30 days) and oligotrophic (phenanthrene and benzene, 50 ppb each, HRT 10 days) substrate conditions suggesting its effectiveness and robustness at extreme substrate concentrations in anoxic environments. In the MFC designed for ex situ deployments, optimum MFC performance was obtained at HRT of 30 h giving COD removal and maximum power output of approximately 77% and 6.75 mWm−2 respectively. The MFC exhibited the ability to resist organic shock loadings and could maintain stable MFC performance. Results of this study suggest the potential use of MFC technology for possible in situ/ex situ hydrocarbon-contaminated groundwater treatment or refinery effluents clean-up, even at extreme contaminant level conditions.

Pulling Back the Veil: The Characterization and Habitability of Enshrouded Worlds

Thesis (Ph.D.)--University of Washington, 2016-08

Diversité microbienne associée au cycle du méthane dans les mares de fonte du pergélisol subarctique

La fonte et l’effondrement du pergélisol riche en glace dans la région subarctique du Québec ont donné lieu à la formation de petits lacs (mares de thermokarst) qui émettent des gaz à effet de serre dans l’atmosphère tels que du dioxyde de carbone et du méthane. Pourtant, la composition de la communauté microbienne qui est à la base des processus biogéochimiques dans les mares de fonte a été très peu étudiée, particulièrement en ce qui concerne la diversité et l’activité des micro-organismes impliqués dans le cycle du méthane. L’objectif de cette thèse est donc d’étudier la diversité phylogénétique et fonctionnelle des micro-organismes dans les mares de fonte subarctiques en lien avec les caractéristiques de l’environnement et les émissions de méthane. Pour ce faire, une dizaine de mares ont été échantillonnées dans quatre vallées situées à travers un gradient de fonte du pergélisol, et disposant de différentes propriétés physico-chimiques. Selon les vallées, les mares peuvent être issues de la fonte de palses (buttes de tourbe, à dominance organique) ou de lithalses (buttes de sol à dominance minérale) ce qui influence la nature du carbone organique disponible pour la reminéralisation microbienne. Durant l’été, les mares étaient fortement stratifiées; il y avait un fort gradient physico-chimique au sein de la colonne d’eau, avec une couche d’eau supérieure oxique et une couche d’eau profonde pauvre en oxygène ou anoxique. Pour identifier les facteurs qui influencent les communautés microbiennes, des techniques de séquençage à haut débit ont été utilisées ciblant les transcrits des gènes de l’ARNr 16S et des gènes impliqués dans le cycle du méthane : mcrA pour la méthanogenèse et pmoA pour la méthanotrophie. Pour évaluer l’activité des micro-organismes, la concentration des transcrits des gènes fonctionnels a aussi été mesurée avec des PCR quantitatives (qPCR). Les résultats montrent une forte dominance de micro-organismes impliqués dans le cycle du méthane, c’est-à-dire des archées méthanogènes et des bactéries méthanotrophes. L’analyse du gène pmoA indique que les bactéries méthanotrophes n’étaient pas seulement actives à la surface, mais aussi dans le fond de la mare où les concentrations en oxygène étaient minimales; ce qui est inattendu compte tenu de leur besoin en oxygène pour consommer le méthane. En général, la composition des communautés microbiennes était principalement influencée par l’origine de la mare (palse ou lithalse), et moins par le gradient de dégradation du pergélisol. Des variables environnementales clefs comme le pH, le phosphore et le carbone organique dissous, contribuent à la distinction des communautés microbiennes entre les mares issues de palses ou de lithalses. Avec l’intensification des effets du réchauffement climatique, ces communautés microbiennes vont faire face à des changements de conditions qui risquent de modifier leur composition taxonomique, et leurs réponses aux changements seront probablement différentes selon le type de mares. De plus, dans le futur les conditions d’oxygénation au sein des mares seront soumises à des modifications majeures associées avec un changement dans la durée des périodes de fonte de glace et de stratification. Ce type de changement aura un impact sur l’équilibre entre la méthanogenèse et la méthanotrophie, et affectera ainsi les taux d’émissions de méthane. Cependant, les résultats obtenus dans cette thèse indiquent que les archées méthanogènes et les bactéries méthanotrophes peuvent développer des stratégies pour survivre et rester actives au-delà des limites de leurs conditions d’oxygène habituelles.

Dynamique de l'oxygène et l'activité microbienne dans les lacs de fonte du pergélisol subarctique

Les lacs de thermokarst (lacs peu profonds créés par le dégel et l’érosion du pergélisol riche en glace) sont un type unique d’écosystèmes aquatiques reconnus comme étant de grands émetteurs de gaz à effet de serre vers l’atmosphère. Ils sont abondants dans le Québec subarctique et ils jouent un rôle important à l’échelle de la planète. Dans certaines régions, les lacs de thermokarst se transforment rapidement et deviennent plus grands et plus profonds. L’objectif de cette étude était d’améliorer la compréhension et d’évaluer quelles variables sont déterminantes pour la dynamique de l’oxygène dans ces lacs. C’est pourquoi j’ai examiné les possibles changements futurs de la dynamique de l’oxygène dans ces lacs dans un contexte de réchauffement climatique. Une grande variété de méthodes ont été utilisées afin de réaliser cette recherche, dont des analyses in situ et en laboratoire, ainsi que la modélisation. Des capteurs automatisés déployés dans cinq lacs ont mesuré l’oxygène, la conductivité et la température de la colonne d’eau en continu de l’été 2012 jusqu’à l’été 2015, à des intervalles compris entre 10 à 60 minutes. Des analyses en laboratoire ont permis de déterminer la respiration et les taux de production bactériens, les variables géochimiques limnologiques, ainsi que la distribution de la production bactérienne entre les différentes fractions de taille des communautés. La température de l’eau et les concentrations d’oxygène dissous d’un lac de thermokarst ont été modélisées avec des données du passé récent (1971) au climat futur (2095), en utilisant un scénario modéré (RCP 4.5) et un scénario plus extrême (RCP 8.5) de réchauffement climatique. Cette recherche doctorale a mis en évidence les conditions anoxiques fréquentes et persistantes présentes dans de nombreux lacs de thermokarst. Aussi, ces lacs sont stratifiés pendant l’hiver comme des concentrations élevées d’ions s’accumulent dans leurs hypolimnions à cause de la formation du couvert de glace (cryoconcentration) et de la libération des ions avec la respiration bactérienne. Les différences de température contribuent également à la stabilité de la stratification. La dynamique de mélange des lacs de thermokarst étudiés était contrastée : la colonne d’eau de certains lacs se mélangeait entièrement deux fois par année, d’autres lacs se mélangeaient qu’une seule fois en automne, alors que certains lacs ne se mélangeaient jamais entièrement. Les populations bactériennes étaient abondantes et très actives, avec des taux respiratoires comparables à ceux mesurés dans des écosystèmes méso-eutrophes ou eutrophes des zones tempérées de l’hémisphère nord. L’érosion des matériaux contenus dans le sol des tourbières pergélisolées procure un substrat riche en carbone et en éléments nutritifs aux populations bactériennes, et ils constituent des habitats propices à la colonisation par des populations de bactéries associées aux particules. Le modèle de la concentration d’oxygène dissous dans un lac a révélé que le réchauffement des températures de l’air pourrait amincir le couvert de glace et diminuer sa durée, intensifiant le transfert de l’oxygène atmosphérique vers les eaux de surface. Ainsi, la concentration en oxygène dissous dans la colonne d’eau de ce lac augmenterait et les périodes de conditions anoxiques pourraient devenir plus courtes. Finalement, cette thèse doctorale insiste sur le rôle des lacs de thermokarst comme des réacteurs biogéochimiques pour la dégradation du carbone organique, qui était retenu dans les sols gelés, en gaz à effet de serre libérés dans l’atmosphère. L’oxygène est un indicateur sensible du mélange de la colonne d’eau et de la dynamique chimique des lacs, en plus d’être une variable clé des processus métaboliques.

Nutrient fluxes on an intertidal mudflat in Marennes-Oleron Bay, and influence of the emersion period

Fluxes of nutrients (NH sub(4) super(+), NO sub(3) super(-), PO sub(4) super(3-) and Si(OH) sub(4)) were studied on an intertidal mudflat in Marennes-Oleron Bay, France, at two different seasons and at different times of the emersion period. Fluxes through the sediment-water interface were both calculated from vertical profiles of nutrient concentration in pore-water (diffusive fluxes, JD) and measured in light and dark benthic mini-chambers (measured fluxes, J sub(0)). Results indicate that ammonia was mainly released in summer while nitrate was mainly taken up in late winter. This uptake from the overlying water was probably due to the coupling of nitrification-denitrification within the sediment. The J sub(0) /J sub(D) ratio further indicates that bioturbation likely enhanced ammonia release in summer. Concerning phosphate, the comparison of diffusive and measured fluxes suggests that PO sub(4) super(3-) could be assimilated by the biofilm in winter while it was released in summer at a high rate due to both bioturbation and desorption because of the relative summer anoxic conditions. Silica was always released by the sediment, but at a higher rate in summer. Statistically significant differences in measured fluxes were detected in dark chambers at different times of low tide, thus suggesting a short-term variability of fluxes. Microphytobenthos preferred ammonia to nitrate, but assimilated nitrate when ammonia was not available. It also turned out that benthic cells could be limited in nitrogen during low tide in late winter. In summer, ammonia was not limiting and microphytobenthic activity significantly decreased the measured flux of NH sub(4) super(+) in the middle of low tide when its photosynthetic capacity was highest.

Assessment of heavy metals' bonding with various sedimentary phases in Shefa-Rud river (Guilan Province)

In the present investigation, bulk and chemical partitioning of elements in the Shefa-Rud riverbed sediments are studied. Higher concentrations of elemental concentrations have been observed in estuarine zone when compared with riverine sediments (except for Al, Fe, Pb and Mn). Manganese is mobilized under anoxic conditions prevailing in the Caspian Sea. Lithogenous materials are greatly diluted in the estuarine zone by various pollutants present in the Caspian Sea. Organic metallic bonds are not significantly present in the area of study. Geological units of the area of study have resulted in the lower concentrations of elemental concentrations of riverbed sediments when compared with published values for mean crust and world sediments ones. Though, cluster analysis has clearly shown the importance of alumina-silicates in controlling the distribution of Fe and Mn in riverbed sediments but it could not depict controlling mechanism for other studied elements. Geochemical Index (Igeo) and Enrichment Factor (EF) values are indicative of a clean environment throughout the river course. These values are in a well agreement with results of chemical partitioning data. Quantification of EF values is not logically possible and therefore Igeo values can be used more effectively.

Quantification of microbial communities in subsurface marine sediments of the Black Sea and off Namibia

Organic-rich subsurface marine sediments were taken by gravity coring up to a depth of 10 m below seafloor at six stations from the anoxic Black Sea and the Benguela upwelling system off Namibia during the research cruises Meteor 72-5 and 76-1, respectively. The quantitative microbial community composition at various sediment depths was analyzed using total cell counting, catalyzed reporter deposition fluorescence in situ hybridization (CARD FISH) and quantitative real-time PCR (Q-PCR). Total cell counts decreased with depths from 10(9) to 10(10) cells/mL at the sediment surface to 10(7)-10(9) cells/mL below one meter depth. Based on CARD FISH and Q-PCR analyses overall similar proportions of Bacteria and Archaea were found. The down-core distribution of prokaryotic and eukaryotic small subunit ribosomal RNA genes (16S and 18S rRNA) as well as functional genes involved in different biogeochemical processes was quantified using Q-PCR. Crenarchaeota and the bacterial candidate division JS-1 as well as the classes Anaerolineae and Caldilineae of the phylum Chloroflexi were highly abundant. Less abundant but detectable in most of the samples were Eukarya as well as the metal and sulfate-reducing Geobacteraceae (only in the Benguela upwelling influenced sediments). The functional genes cbbL, encoding for the large subunit of RuBisCO, the genes dsrA and aprA, indicative of sulfate-reducers as well as the mcrA gene of methanogens were detected in the Benguela upwelling and Black Sea sediments. Overall, the high organic carbon content of the sediments goes along with high cell counts and high gene copy numbers, as well as an equal abundance of Bacteria and Archaea.

Simulação de um sistema de tratamento de águas residuais de lamas ativadas

A modelação matemática de Estações de Tratamento de Águas Residuais (ETAR) tem sido uma ferramenta de enorme utilidade nas fases de projeto e de exploração destas estruturas de tratamento. O presente estudo teve por objetivo principal construir um modelo matemático da ETAR de Bragança, em particular do seu tratamento biológico de lamas ativadas, com vista a avaliar, compreender e otimizar o seu desempenho. A construção do modelo foi efetuada com recurso ao ambiente de simulação WRc STOAT 5.0. O processo de lamas ativadas foi descrito pelo modelo de referência ASAL3. O modelo construído foi calibrado e validado com base em dados experimentais de 2015, obtidos no âmbito do programa de controlo analítico da ETAR. O modelo foi ainda utilizado para avaliar a qualidade do efluente em resposta a alterações do caudal e composição do afluente, a alterações de condições operacionais e a outras alternativas de tratamento. O modelo mostrou-se bastante adequado na descrição da evolução mensal da qualidade do efluente final da ETAR relativamente aos parâmetros Sólidos Suspensos Totais (SST) e Carência Bioquímica de Oxigénio (CBO5), embora apresente uma tendência para os subestimar em 1,5 e 3,5 mg/L, respetivamente. Em relação ao azoto total, os valores simulados aproximaram-se dos valores reais, quando se aumentaram as taxas de recirculação interna para 400%, um fator de cerca de 4 vezes superior. Os resultados do modelo e dos cenários mostram e reforçam o bom desempenho e a operação otimizada da ETAR em relação a remoção de SST e CBO5. Em relação ao azoto total, a ETAR não assegura de forma sistemática uma eficiência elevada, mas apresenta um bom desempenho, face ao que o modelo consegue explicar para as mesmas condições operacionais. Através do estudo de cenários procurou-se encontrar alternativas de tratamento eficientes e viáveis de remoção de azoto total, mas não se identificaram soluções que assegurassem decargas de azoto abaixo dos limites legais. Os melhores resultados que se alcançaram para a remoção deste contaminante estão associados ao aumento das taxas de recirculação interna do sistema pré-anóxico existente e a uma configuração do tipo Bardenpho de quatro estágios com alimentação distribuída, em proporções iguais, pelos dois estágios anóxicos. Outras soluções que envolvam tecnologias distintas podem e devem ser equacionadas em projetos futuros que visem a melhoria de eficiência de remoção de azoto da ETAR.

Biostratigraphy and average linear sedimentation rate and accumulation rate of ODP Site 159-959 (Table 1)

Reconstructing the long-term evolution of organic sedimentation in the eastern Equatorial Atlantic (ODP Leg 159) provides information about the history of the climate/ocean system, sediment accumulation, and deposition of hydrocarbon-prone rocks. The recovery of a continuous, 1200 m long sequence at ODP Site 959 covering sediments from Albian (?) to the present day (about 120 Ma) makes this position a key location to study these aspects in a tropical oceanic setting. New high resolution carbon and pyrolysis records identify three main periods of enhanced organic carbon accumulation in the eastern tropical Atlantic, i.e. the late Cretaceous, the Eocene-Oligocene, and the Pliocene-Pleistocene. Formation of Upper Cretaceous black shales off West Africa was closely related to the tectonosedimentary evolution of the semi-isolated Deep Ivorian Basin north of the Côte d'Ivoire-Ghana Transform Margin. Their deposition was confined to certain intervals of the last two Cretaceous anoxic events, the early Turonian OAE2 and the Coniacian-Santonian OAE3. Organic geochemical characteristics of laminated Coniacian-Santonian shales reveal peak organic carbon concentrations of up to 17% and kerogen type I/II organic matter, which qualify them as excellent hydrocarbon source rocks, similar to those reported from other marginal and deep sea basins. A middle to late Eocene high productivity period occurred off equatorial West Africa. Porcellanites deposited during that interval show enhanced total organic carbon (TOC) accumulation and a good hydrocarbon potential associated with oil-prone kerogen. Deposition of these TOC-rich beds was likely related to a reversal in the deep-water circulation in the adjacent Sierra Leone Basin. Accordingly, outflow of old deep waters of Southern Ocean origin from the Sierra Leone Basin into the northern Gulf of Guinea favored upwelling of nutrient-enriched waters and simultaneously enhanced the preservation potential of sedimentary organic matter along the West African continental margin. A pronounced cyclicity in the carbon record of Oligocene-lower Miocene diatomite-chalk interbeds indicates orbital forcing of paleoceanographic conditions in the eastern Equatorial Atlantic since the Oligocene-Miocene transition. A similar control may date back to the early Oligocene but has to be confirmed by further studies. Latest Miocene-early Pliocene organic carbon deposition was closely linked to the evolution of the African trade winds, continental upwelling in the eastern Equatorial Atlantic, ocean chemistry and eustatic sea level fluctuations. Reduction in carbonate carbon preservation associated with enhanced carbon dissolution is recorded in the uppermost Miocene (5.82-5.2 Ma) section and suggests that the latest Miocene carbon record of Site 959 documents the influence of corrosive deep waters which formed in response to the Messinian Salinity Crisis. Furthermore, sea level-related displacement of higher productive areas towards the West African shelf edge is indicated at 5.65, 5.6, 5.55, 5.2, 4.8 Ma. In view of humid conditions in tropical Africa and a strong West African monsoonal system around the Miocene-Pliocene transition, the onset of pronounced TOC cycles at about 5.6 Ma marks the first establishment of upwelling cycles in the northern Gulf of Guinea. An amplification in organic carbon deposition at 3.3 Ma and 2.45 Ma links organic sedimentation in the tropical eastern Equatorial Atlantic to the main steps of northern hemisphere glaciation and testifies to the late Pliocene transition from humid to arid conditions in central and western African climate. Aridification of central Africa around 2.8 Ma is not clearly recorded at Site 959. However, decreased and highly fluctuating carbonate carbon concentrations are observed from 2.85 Ma on that may relate to enhanced terrigenous (eolian) dilution from Africa.

Bioorthogonal Noncanonical Amino Acid Tagging for Selective Analysis of the Pseudomonas aeruginosa Proteome

In natural environments, bacterial physiology is frequently characterized by slow metabolic rates and complex cellular heterogeneities. The opportunistic pathogen Pseudomonas aeruginosa provides one such example; P. aeruginosa forms untreatable chronic biofilm infections of the cystic fibrosis lung, where oxygen limitation can lead to states of metabolic dormancy. To better understand the biology of these states, in vitro experiments must be adapted to better recapitulate natural settings. However, low rates of protein turnover and cellular or phenotypic complexity make these systems difficult to study using established methods. Here we adapt the bioorthogonal noncanonical amino acid tagging (BONCAT) method for time- and cell-selective proteomic analysis to the study of P. aeruginosa. Analysis of proteins synthesized in an anoxic dormancy state led to the discovery of a new type of transcriptional regulator which we designated SutA. We performed detailed analyses of SutA’s role in transcription under slow growth states and we elucidated the structural basis for its regulatory behavior. Additionally, we used cell-selective targeting of BONCAT labeling to measure the dynamic proteomic response of an antibiotic-tolerant biofilm subpopulation. Overall this work shows the utility of selective proteomics as applied to bacterial physiology and describes the broad biological insight obtained from that application.

Geochemical analysis at ODP Site 207-1259 from the Demerara Rise in the western equatorial Atlantic

Organic carbon-rich shales deposited during the Coniacian-Santonian Oceanic Anoxic Event 3 were drilled during ODP Leg 207 at Demerara Rise. We present integrated high-resolution geochemical records of core intervals from ODP Sites 1259 and 1261 both from nannofossil biozone CC14. Our results reveal systematic variations in marine and detrital sediment contribution, depositional processes, and bottom water redox conditions during black shale formation at two locations on Demerara Rise in different paleo-water depths. A combination of redox proxies (Fe/S, P/Al, C/P, redox-sensitive/sulfide-forming trace metals Mn, Cd, Mo, Ni, V, Zn) and other analytical approaches (bulk sediment composition, P speciation, electron microscopy, X-ray diffraction) evidence anoxic to sulfidic bottom water and sediment conditions throughout the deposition of black shale. These extreme redox conditions persisted and were periodically punctuated by short-termed periods with less reducing bottom waters irrespective of paleo-water depth. Sediment supply at both sites was generally dominated by marine material (carbonate, organic matter, opal) although relationships of detrital proxies as well as glauconitic horizons support some influence of turbidites, winnowing bottom currents and/or variable detritus sources, along with less reducing bottom water at the proposed shallower location (ODP Site 1259). At Site 1261, located at greater paleo-depth, redox fluctuations were more regular, and steady hemipelagic sedimentation sustained the development of mostly undisturbed lamination in the sedimentary record. Strong similarities of the studied deposits exist with the stratigraphic older Cenomanian-Turonian OAE2 black shale sections at Demerara Rise, suggesting that the primary mechanisms controlling continental supply and ocean redox state were time-invariant and kept the western equatorial Atlantic margin widely anoxic over millions of years.

Upper lower triassic stromatolite from Anhui, South China: geobiologic features and paleoenvironmental implications

Widespread stromatolites and other microbialite deposits characterize Lower Triassic marine successions worldwide. This study documents a stromatolite deposit, 1.1. m thick, from the upper Spathian (Lower Triassic) of the Susong area, South China. The stromatolite comprises distinct laminated domes in the basal part and columns at the upper part. Dark laminae are loosely spaced and interlayered with thicker light colored laminae. Diffusive dark colored laminae are composed of peloidal micrite that grade locally into microclotted structures, and yield copies of bacteria clump-like and coccoid-like spheroid aggregates. The former are characterized by cloudy, micrite nuclei rimmed by coarse-grained, euhedral sparry calcite crystals, while the latter are comprised of solid calcite crystal nuclei coated with rather thin micrite envelopes. The cloudy, micrite nuclei resemble bacteria clump-like structures observed in present-day travertine. Both the coccoid-like spheroids and bacteria clump-like structures are surrounded by coarse-grained euhedral calcite crystals, suggesting a similar accretion mechanism. Both spherical structures therefore could be crucial in the accretion of the Susong stromatolite. The laminated/microclotted structures are interpreted as the result of variation in timing of lithification relative to the timing of the decay of microbes. Micro-analysis also unravels the common occurrence of authigenic micro-quartz crystals in association with Fe-bearing illite clay minerals in the stromatolite columns. Their coalescing nature with each other, together with the associated pyrite grains, strongly support the formation of micro-quartz crystals from microbial reduction of an Fe-bearing smectite precursor by sulfate reducing bacteria. A comparison of the Susong stromatolite with its counterparts from the upper Lower Triassic strata in Dajiang, South China reveals many similarities in stromatolite microstructures, suggesting that a harsh, euxinic-anoxic environment resulting in the bloom of sulfate reducing bacteria most likely extended into the latest Spathian in South China.