Geomicrobiology, bulk sediment characteristics and pore water chemistry of sediment cores from Laguna Potrok Aike, southern Patagonia

Authigenic minerals can form in the water column and sediments of lakes, either abiotically or mediated by biological activity. Such minerals have been used as paleosalinity and paleoproductivity indicators and reflect trophic state and early diagenetic conditions. They are also considered potential indicators of past and perhaps ongoing microbial activity within sediments. Authigenic concretions, including vivianite, were described in late glacial sediments of Laguna Potrok Aike, a maar lake in southernmost Argentina. Occurrence of iron phosphate implies specific phosphorus sorption behavior and a reducing environment, with methane present. Because organic matter content in these sediments was generally low during glacial times, there must have been alternative sources of phosphorus and biogenic methane. Identifying these sources can help define past trophic state of the lake and diagenetic processes in the sediments. We used scanning electron microscopy, phosphorus speciation in bulk sediment, pore water analyses, in situ ATP measurements, microbial cell counts, and measurements of methane content and its carbon isotope composition (d13C CH4) to identify components of and processes in the sediment. The multiple approaches indicated that volcanic materials in the catchment are important suppliers of iron, sulfur and phosphorus. These elements influence primary productivity and play a role in microbial metabolism during early diagenesis. Authigenic processes led to the formation of pyrite framboids and revealed sulfate reduction. Anaerobic oxidation of methane and shifts in pore water ion concentration indicated microbial influence with depth. This study documents the presence of active microbes within the sediments and their relationship to changing environmental conditions. It also illustrates the substantial role played by microbes in the formation of Laguna Potrok Aike concretions. Thus, authigenic minerals can be used as biosignatures in these late Pleistocene maar sediments.

Pore water and solid phase geochemistry of sediment core US5B

Studies of authigenic phosphorus (P) minerals in marine sediments typically focus on authigenic carbonate fluorapatite, which is considered to be the major sink for P in marine sediments and can easily be semi-quantitatively extracted with the SEDEX sequential extraction method. The role of other potentially important authigenic P phases, such as the reduced iron (Fe) phosphate mineral vivianite (Fe(II)3(PO4)*8H2O) has so far largely been ignored in marine systems. This is, in part, likely due to the fact that the SEDEX method does not distinguish between vivianite and P associated with Fe-oxides. Here, we show that vivianite can be quantified in marine sediments by combining the SEDEX method with microscopic and spectroscopic techniques such as micro X-ray fluorescence (µXRF) elemental mapping of resin-embedded sediments, as well as scanning electron microscope-energy dispersive spectroscopy (SEM-EDS) and powder X-ray diffraction (XRD). We further demonstrate that resin embedding of vertically intact sediment sub-cores enables the use of synchrotron-based microanalysis (X-ray absorption near-edge structure (XANES) spectroscopy) to differentiate between different P burial phases in aquatic sediments. Our results reveal that vivianite represents a major burial sink for P below a shallow sulfate/methane transition zone in Bothnian Sea sediments, accounting for 40-50% of total P burial. We further show that anaerobic oxidation of methane (AOM) drives a sink-switching from Fe-oxide bound P to vivianite by driving the release of both phosphate (AOM with sulfate and Fe-oxides) and ferrous Fe (AOM with Fe-oxides) to the pore water allowing supersaturation with respect to vivianite to be reached. The vivianite in the sediment contains significant amounts of manganese (~4-8 wt.%), similar to vivianite obtained from freshwater sediments. Our results indicate that methane dynamics play a key role in providing conditions that allow for vivianite authigenesis in coastal surface sediments. We suggest that vivianite may act as an important burial sink for P in brackish coastal environments worldwide.

Geochemistry and geomicrobiology profiles of ferruginous sediment, Lake Towuti, Indonesia

Lake Towuti is a tectonic basin, surrounded by ultramafic rocks. Lateritic soils form through weathering and deliver abundant iron (oxy)hydroxides but very little sulfate to the lake and its sediment. To characterize the sediment biogeochemistry, we collected cores at three sites with increasing water depth and decreasing bottom water oxygen concentrations. Microbial cell densities were highest at the shallow site - a feature we attribute to the availability of labile organic matter and the higher abundance of electron acceptors due to oxic bottom water conditions. At the two other sites, OM degradation and reduction processes below the oxycline led to partial electron acceptor depletion. Genetic information preserved in the sediment as extracellular DNA provides information on aerobic and anaerobic heterotrophs related to Actinobacteria, Nitrospirae, Chloroflexi and Thermoplasmatales. These taxa apparently played a significant role in the degradation of sinking organic matter. However, extracellular DNA concentrations rapidly decrease with core depth. Despite very low sulfate concentrations, sulfate-reducing bacteria were present and viable in sediments at all three sites, as confirmed by measurement of potential sulfate reduction rates. Microbial community fingerprinting supported the presence of taxa related to Deltaproteobacteria and Firmicutes with demonstrated capacity for iron and sulfate reduction. Concomitantly, sequences of Ruminococcaceae, Clostridiales and Methanomicrobiales indicated potential for fermentative hydrogen and methane production. Such first insights into ferruginous sediments show that microbial populations perform successive metabolisms related to sulfur, iron and methane. In theory, iron reduction could reoxidize reduced sulfur compounds and desorb OM from iron minerals to allow remineralization to methane. Overall, we found that biogeochemical processes in the sediments can be linked to redox differences in the bottom waters of the three sites, like oxidant concentrations and the supply of labile OM. At the scale of the lacustrine record, our geomicrobiological study should provide a means to link the extant subsurface biosphere to past environments.

Geochemistry of sheeted dike complex minerals of ODP Hole 140-504B

Diabases were recovered during Legs 137 and 140 at Hole 504B from depths between 1621.5 and 2000.4 meters below seafloor in the lower sheeted dike complex. The samples contain multiple generations of millimetric to centimetric veins. The orientation of the measured veins suggests that two main vein sets exist: one characterized by shallow dipping and the other by random trend. Thermal contraction during rock cooling is considered the main mechanism responsible for fracture formation. Vein infill is related to the circulation of hydrothermal fluids near the spreading axis. Some veins are surrounded by millimeter-sized alteration halos due to fluid percolation from the fractures through the host rock. Vein-filling minerals are essentially amphibole, chlorite, and zeolites. Amphibole composition is controlled by the microstructural site of the rock. Actinolite is the main amphibole occurring in the veins and also in the groundmass away from the halos. In the alteration halos, amphibole shows composition of actinolitic hornblende and Mg-hornblende. Late-stage tension gashes and interstitial spaces in some amphibole-bearing veins are filled with zeolites, suggesting that the veins likely suffered multiple opening stages that record the cooling history of the circulating fluids. Evidence of deformation recorded by the recovered samples seems to be restricted to veins that clearly represent elements of weakness of the rock. On the basis of vein geometry and microstructure we infer structural interpretations for the formation mechanism and for deformation of veins.

Geochemical composition of minerals obtained from ODP Sites 180-1109, 180-1117 and 180-1118

During the last 8 m.y. the Papuan Peninsula region of Papua New Guinea has been affected by extension which opened the Woodlark Basin. The present-day spreading tip is located at the foot of the Moresby Seamount, a crustal block whose northern flank is an active low-angle normal fault related to this extension. During Ocean Drilling Program Leg 180 (7 June-11 August 1998), 11 sites (1108-1118) were drilled along a north-south-trending transect across the Woodlark Basin just ahead of the spreading tip. Four of these sites (1118, 1109, 1114, and 1117) reached the crystalline basement, which is composed of diabase and gabbro. Sites 1118 and 1109, located on the Woodlark Rise, belong to the hanging wall block, and Sites 1114 and 1117, located on the crest of the Moresby Seamount, belong to the footwall block and the fault zone itself. Most of the basalt, diabase, and gabbro that were recovered show a well-preserved magmatic texture. The diabase, which is the most abundant rock type, has a coarse-grained ophitic texture composed of poikilitic clinopyroxene including radiating, locally skeletal plagioclase laths with interstitial iron oxide grains. Secondary mineralogy consists of chlorite, zeolite, calcite, albite, and quartz. The gabbro shows a medium-grained granular texture. The magmatic mineralogy consists of euhedral laths of plagioclase and anhedral interstitial clinopyroxene. Secondary mineralogy consists of a magnesio to actinolitic hornblende, chlorite, clinozoisite, zeolite, quartz, and calcite. The retrograde metamorphic evolution of both gabbro and diabase occurred under low amphibolite to subgreenschist facies conditions associated mainly with brittle deformation and the development of a local low-temperature shear zone. This shows no evidence for high thermal gradient in the crust during the continental rifting.

(Tables 1-3) Geochemical composition of seepage water in soils obtained in Schleswig-Holstein, Germany

Under defined laboratory and field conditions, the investigation of percolating water through soil columns (podsol, lessive and peat) down to groundwater table shows that the main factors which control the chemical characteristics of the percolates are: precipitation, evaporation, infiltration rate, soil type, depth and dissolved organic substances. Evaporation and percolation velocity influences the Na+, SO4**2- and Cl- concentrations. Low percolation velocity leads also to longer percolation times and water logging in less permeable strata, which results in lower Eh-values and higher CO2-concentrations due to low gas exchange with the atmosphere. Ca2+ and Mg2+ carbonate concentration depends on soil type and depth. Metamorphism and decomposition of organic substances involve NO3 reduction and K+, Mg2+, SO4**2-, CO2, Fe2+,3+ transport. The analytical data were evaluated with multi variate statistical methods.

Pore water measurements of sediment cores from the Helgoland mud area, North Sea

Iron reduction in subseafloor sulfate-depleted and methane-rich marine sediments is currently a subject of interest in subsurface geomicrobiology. While iron reduction and microorganisms involved have been well studied in marine surface sediments, little is known about microorganisms responsible for iron reduction in deep methanic sediments. Here, we used quantitative PCR (Q-PCR)-based 16S rRNA gene copy numbers and pyrosequencing-based relative abundances of bacteria and archaea to investigate covariance between distinct microbial populations and specific geochemical profiles in the top 5 m of sediment cores from the Helgoland mud area, North Sea. We found that gene copy numbers of bacteria and archaea were specifically higher around the peak of dissolved iron in the methanic zone (250-350 cm. The higher copy numbers at these depths were also reflected by the relative sequence abundances of members of the candidate division JS1, methanogenic and Methanohalobium/ANME-3 related archaea. The distribution of these populations was strongly correlated to the profile of pore-water Fe2+ while that of Desulfobacteraceae corresponded to the pore-water sulfate profile. Furthermore, specific JS1 populations also strongly co-varied with the distribution of Methanosaetaceae in the methanic zone. Our data suggest that the interplay among JS1 bacteria, methanogenic archaea and Methanohalobium/ANME-3-related archaea may be important for iron reduction and methane cycling in deep methanic sediments of the Helgoland mud area and perhaps in other methane-rich depositional environments. .

A Comparati ve Study of Mechanical and Tribological Properties of AISI-304 and AISI-316 Submitted to Glow Discharge Nitriding

Mechanical and tribological properties of AISI 304 and AISI 316 stainless steels submitted to glow discharge ion nitriding are reported. The atmosphere was 20:80 - N2:H2 with substrate temperatures ranging from 300 to 500 °C. Treatment at 300 °C produced expanded austenite (γN) in both steels. Increasing the temperature, the phases γ′-Fe4N and ε- Fe2+xN were present and the latter is the major phase for AISI 304. At 500 °C, the CrN phase was also identified in both steels. Hardnesses of about 13-14 GPa at near surface regions were obtained in both steels. Moreover, AISI 316 nitrided at 500 °C has the deepest hard layer. Tribological tests showed that wear can be reduced by up to a factor of six after the nitriding processes, even for a working temperature of 300 °C. The profiles during and after nanoscratch tests did not reveal significant differences after nitriding processes in both steels.

A Comparative Study of Mechanical and Tribological Properties of AISI-304 and AISI-316 Submitted to Glow Discharge Nitriding

Mechanical and tribological properties of AISI 304 and AISI 316 stainless steels submitted to glow discharge ion nitriding are reported. The atmosphere was 20:80 - N2:H2 with substrate temperatures ranging from 300 to 500 °C. Treatment at 300 °C produced expanded austenite (γN) in both steels. Increasing the temperature, the phases γ′-Fe4N and ε- Fe2+xN were present and the latter is the major phase for AISI 304. At 500 °C, the CrN phase was also identified in both steels. Hardnesses of about 13-14 GPa at near surface regions were obtained in both steels. Moreover, AISI 316 nitrided at 500 °C has the deepest hard layer. Tribological tests showed that wear can be reduced by up to a factor of six after the nitriding processes, even for a working temperature of 300 °C. The profiles during and after nanoscratch tests did not reveal significant differences after nitriding processes in both steels.

Ottimizzazione della reazione di Fenton mediante l’utilizzo di un sistema automatico di reazione

The research presented in this dissertation is aimed to the automation of the Fenton process. The Fenton reaction is finalized to the waste water pre-treatment in order to promote the abatement of the organic contaminants and make it more degradable. Reagents adopted are constituted by a mixture of iron ions and hydrogen peroxide and their effect is strictly influenced by several variables, such as: the reagents molar ratio and their quantities counterpoised to the substrate, temperature, pH, agitation, etc. Therefore, the optimization is far from being considered an easy procedure. The research was carried out using a batch configuration, through which the optimal [Fe2+]/[H2O2] and [substrate]/[H2O2] ratios were identified. Then, in order to improve the process, a semibatch configuration was performed. The preliminary results show that is possible to obtain a greater abatement efficiency for high organic burden using the semibatch configuration here proposed.

Évaluation de la performance des drains et des matériaux filtrants à ralentir le colmatage et l’ensablement en sol sableux et ferreux

Au Québec, les drains installés dans les sols sableux-limoneux sont sensibles au colmatage par ensablement et/ou par ocre de fer. Dans le passé, les drains avec des pertuis inférieurs à 2 mm étaient utilisés au Québec avec un filtre tissé de 110 microns ou un filtre tricoté de 450 microns. Récemment, des drains avec des pertuis supérieurs à 2 mm ainsi qu’un filtre de 250 microns ont été introduits sur le marché mais n’ont jamais été testés. Le projet avait pour objectif de déterminer les vitesses auxquelles se feront l’ensablement et le colmatage ferrique pour différentes combinaisons de drains (pertuis de 1,8 mm et de 3 mm) et de filtres (110 μm, 250 μm et 450 μm) dans un sol sableux à Bécancour. Un dispositif expérimental en blocs complets (3) aléatoires a été utilisé. Les débits ont été mesurés à la sortie des drains de chaque parcelle et les hauteurs des nappes ont été mesurées avec un bulleur dans des puits d’observation. Le suivi du pH, du potentiel d’oxydoréduction et du contenu en Fe2+ a été réalisé dans l’eau de la nappe et celle des drains. Les drains excavés 13 mois après leur installation ne montrent que des traces de sédiments et de colmatage ferrique. Les niveaux de Fe2+ sont significativement plus faibles dans l’eau à la sortie des drains que dans l’eau de la nappe. Le processus de colmatage ferrique ne semble que commencer et son impact n’est pas mesurable au niveau des débits unitaires à la sortie des drains.

An electrochemical process for the production of synthetic fuels at low temperatures [Resumo]

Following work exploring the low temperature electrolysis in alkaline media, using graphite consumable anodes, from which syngas was obtained1, laboratory studies have been conducted in acid media pursuing higher efficiency in the production of hydrogen and synthetic fuels. Experiments were conducted in an own designed undivided planar cell with 25 cm2 geometrical area electrodes using a 0.5 M H2SO4 solution with and without Fe(II) additions. Fe2+ oxidizes to Fe3+ at the anode surface. The redox couple Fe3+/ Fe2+ acts as an oxidation mediator not only oxidizing the bulk and detached graphite but also the surface functional groups. The practical experimental potential for graphite oxidation is within the range for the electroxidation of the Fe redox couple giving as a result a 4-fold increase in the amount of produced CO2 at near room temperature, when using 0.025 M FeSO4.

Glycosylation and Glycodiversification in Polyketide Antibiotics: Unraveling Biosynthetic Steps in Nogalamycin Formation

Soil-dwelling Streptomyces bacteria are known for their ability to produce biologically active compounds such as antimicrobial, immunosuppressant, antifungal and anticancer drugs. S. nogalater is the producer of nogalamycin, a potential anticancer drug exhibiting high cytotoxicity and activity against human topoisomerases I and II. Nogalamycin is an anthracycline polyketide comprising a four-ring aromatic backbone,a neutral deoxy sugar at C7, and an amino sugar attached via an O–C bond at C1 and a C–C bond between C2 and C5´´. This kind of attachment of the amino sugar is unusual thus making the structure of the compound highly interesting. The sugar is also associated with the biological activity of nogalamycin, as it facilitates binding to DNA. Furthermore, the sugar moieties of anthracyclines are often crucial for their biological activity. Together the interesting attachment of the amino sugar and the general reliance of polyketides on the sugar moieties for bioactivity have made the study of the biosynthesis of nogalamycin attractive. The sugar moieties are typically attached by glycosyltransferases, which use two substrates: the donor and the acceptor. The literature review of the thesis is focused on the glycosylation of polyketides and the possibilities to alter their glycosylation patterns. My own thesis work revolves around the biosynthesis of nogalamycin. We have elucidated the individual steps that lead to its rather unique structure. We reconstructed the whole biosynthetic pathway in the heterologous host S. albus using a cosmid and a plasmid. In the process, we were able to isolate new compounds when the cosmid, which contains the majority of the nogalamycin gene cluster, was expressed alone in the heterologous host. The new compounds included true intermediates of the pathway as well as metabolites, which were most likely altered by the endogenous enzymes of the host. The biological activity of the most interesting new products was tested against human topoisomerases I and II, and they were found to exhibit such activities. The heterologous expression system facilitated the generation of mutants with inactivated biosynthetic genes. In that process, we were able to identify the functions of the glycosyltransferases SnogE and SnogD, solve the structure of SnogD, discover a novel C1-hydroxylase system comprising SnoaW and SnoaL2, and establish that the two homologous non-heme α-ketoglutarate and Fe2+ dependent enzymes SnoK and SnoN catalyze atypical reactions on the pathway. We demonstrated that SnoK was responsible for the formation of the additional C–C bond, whereas SnoN is an epimerase. A combination of in vivo and in vitro techniques was utilized to unravel the details of these enzymes. Protein crystallography gave us an important means to understand the mechanisms. Furthermore, the solved structures serve as platforms for future rational design of the enzymes.

Identificação dos produtos de oxidação de glicosfingolípidos por espectrometria de massa

O stress oxidativo está associado ao envelhecimento e a inúmeras patologias, nomeadamente a doenças neurodegenerativas e cardiovasculares, e a diversos outros fatores. O stress oxidativo leva à oxidação de importantes biomoléculas como os lípidos e, ao contrário da maior parte dos produtos de oxidação de fosfolípidos e ácidos gordos insaturados (PUFAS), os produtos de oxidação de glicosfingolípidos (GSLs) têm sido escassamente estudados. Os glicosfingolípidos são moléculas muito diversificadas estruturalmente e com importantes funções, essencialmente no sistema nervoso central (SNC) onde estão localizados maioritariamente. Deste modo, alterações na estrutura dos GSLs conduzirão a consequente comprometimento das suas funções e ao possível desenvolvimento de patologias. Assim para identificar as modificações oxidativas que ocorrem em glicosfingolípidos e pressupor consequentes efeitos biológicos nas células sob stress oxidativo, prepararamse sistemas modelo biomiméticos com diferentes GSLs os quais foram expostos a radicais hidroxilo gerados sob condições da reação de Fenton (H2O2 e Fe2+) e as reações foram monitorizadas por diferentes metodologia utilizando a espectrometria de massa. Os resultados obtidos com este estudo permitiram-nos identificar vários produtos de oxidação produzidos durante a oxidação desta classe de lípidos. Os produtos de oxidação observados em comum, em todos os GSLs estudados (C16:0GalCer, C24:1GalCer, C24:1LacCer e GM1) foram as suas correspondentes ceramidas. Estas atuam como agentes pro-apoptóticos e podem in vivo promover a neurodegeneração nas células sob stress oxidativo. Também foi possível observar produtos com inserção de oxigénio junto às duplas ligações ou na cadeia de esfingosina (no caso do GM1) ou na cadeia de ácido gordo monoinsaturada (no caso da C24:1GalCer, C24:1LacCer), corroborando o facto de que ácidos gordos saturados não são susceptíveis à oxidação por radicais. Interessantemente em ambos os GSLs de cadeias glicosiladas compostas com mais de um açúcar (C24:1LacCer e GM1) observou-se a despolimerização oxidativa da porção glicosilada por quebra das correspondentes ligações glicosídicas. Esta degradação leva à formação de GlcCer no caso de oxidação de LacCer ou na formação de outros gangliósidos (GM2, GM3, asialoGM1 e asialoGM2) e glicolípidos (LacCer e GlcCer), no caso de oxidação de GM1. A formação por via radicalar não enzimática destes GSLs leva a distúrbios no perfil lipídico. Previamente, em certas doenças, foram observadas variações na concentração do perfil de gangliósidos e de ceramidas. Estes dados permitem sugerir que em células em condições de stress oxidativo, a acumulação de gangliósidos mais simples e ceramidas poderá ter uma contribuição de produtos da degradação oxidativa dos gangliósidos e GSLs mais complexos. Este trabalho contribui assim para uma melhor compreensão das modificações estruturais que ocorrem em alguns glicosfingolípidos em condições de stress oxidativo. Os produtos de oxidação aqui identificados suportam a sua possível futura deteção em sistemas biológicos.