ALBERT

Description: Mixing processes of reduced hydrothermal fluids with oxygenated seawater and fluid-rock reactions contribute to the chemical signatures of diffuse venting and likely determine the geochemical constraints on microbial life. We examined the influence of fluid chemistry on microbial diversity and activity by sampling diffuse fluids emanating through mussel beds at two contrasting hydrothermal vents. The H(2) concentration was very low at the basalt-hosted Clueless site, and mixing models suggest O(2) availability throughout much of the habitat. In contrast, effluents from the ultramafic-hosted Quest site were considerably enriched in H(2) , while O(2) is likely limited to the mussel layer. Only two different hydrogenase genes were identified in clone libraries from the H(2) -poor Clueless fluids, but these fluids exhibited the highest H(2) uptake rates in H(2) -spiked incubations (oxic conditions, at 18 °C). In contrast, a phylogenetically diverse H(2) -oxidizing potential was associated with distinct thermal conditions in the H(2) -rich Quest fluids, but under oxic conditions, H(2) uptake rates were extremely low. Significant stimulation of CO(2) fixation rates by H(2) addition was solely illustrated in Quest incubations (P-value 〈0.02), but only in conjunction with anoxic conditions (at 18 °C). We conclude that the factors contributing toward differences in the diversity and activity of H(2) oxidizers at these sites include H(2) and O(2) availability.

Description: Methane hydrate, a potential future energy resource, is known to occur naturally in vast quantities beneath the ocean floor and in permafrost regions. It is important to evaluate how much methane is recoverable from these hydrate reserves. This article introduces the theoretical background of HydrateResSim, the National Energy Technology Laboratory (NETL) methane production simulator for hydrate-containing reservoirs, originally developed for NETL by Lawrence Berkeley National Laboratory (LBNL). It describes the mathematical model that governs the dissociation of methane hydrate by depressurization or thermal stimulation of the system, including the transport of multiple temperature-dependent components in multiple phases through a porous medium. The model equations are obtained by incorporating the multiphase Darcy’s law for gas and liquid into both the mass component balances and the energy conservation equations. Two submodels in HydrateResSim for hydrate dissociation are also considered: a kinetic model and a pure thermodynamic model. Contrary to more traditional reservoir simulations, the set of model unknowns or primary variables in HydrateResSim changes throughout the simulation as a result of the formation or dissociation of ice and hydrate phases during the simulation. The primary variable switch method (PVSM) is used to effectively track these phase changes. The equations are solved by utilizing the implicit time finite-difference method on the grid system, which can properly describe phase appearance or disappearance as well as the boundary conditions. The Newton-Raphson method is used to solve the linear equations after discretization and setup of the Jacobian matrix. We report here the application of HydrateResSim to a three-component, four-phase flow system in order to predict the methane produced from a laboratory-scale reservoir. The first results of HydrateResSim code in a peer-reviewed publication are presented in this article. The numerical solution was verified against the state-of-the art simulator TOUGH+Hydrate. The model was then used to compare twodissociation theories: kinetic and pure equilibrium. Generally, the kinetic model revealed a lower dissociation rate than the equilibrium model. The hydrate dissociation patterns differed significantly when the thermal boundary condition was shifted from adiabatic to constant-temperature. The surface area factor was found to have an important effect on the rate of hydrate dissociation for the kinetic model. The deviation between the kinetic and equilibrium models was found to increase with decreasing surface area factor.

Description: Phototrophic bacteria are important primary producers of salt lakes in the Salar de Atacama and at times form visible mass developments within and on top of the lake sediments. The communities of phototrophic bacteria from two of these lakes were characterized by molecular genetic approaches using key genes for the biosynthesis of the photosynthetic apparatus in phototrophic purple bacteria (pufLM) and in green sulfur bacteria (fmoA). Terminal restriction fragment length polymorphism of the pufLM genes indicated high variability of the community composition between the two lakes and subsamples thereof. The communities were characterized by the dominance of a novel, so far undescribed lineage of pufLM containing bacteria and the presence of representatives related to known halophilic Chromatiaceae and Ectothiorhodospiraceae. In addition, the presence of BChl b-containing anoxygenic phototrophic bacteria and of aerobic anoxygenic bacteria was indicated. Green sulfur bacteria were not detected in the environmental samples, although a bacterium related to Prosthecochloris indicum was identified in an enrichment culture. This is the first comprehensive description of phototrophic bacterial communities in a salt lake of South America made possible only due to the application of the functional pufLM genes.

Description: Analyses of clone libraries from water and sediments of different sites from Salar de Huasco, a high-altitude athalassohaline wetland in the Chilean Altiplano, revealed the presence of five unique clusters of uncultured Archaea that have not been previously reported or specifically assigned. These sequences were distantly related (83–96% sequence identity) to a limited number of other clone sequences and revealed no identity to cultured Archaea. The abundance of Archaea and Bacteria was estimated using qPCR and community composition was examined through the construction of clone libraries of archaeal 16S rRNA gene. Archaea were found to be dominant over Bacteria in sediments from two saline sites (sites H4: 6.31 × 104 and site H6: 1.37 × 104 μS cm−1) and in one of the water samples (freshwater from site H0: 607 μS cm−1). Euryarchaeotal sequences were more abundant than crenarchaeotal sequences. Many of the clone sequences (52%) were similar to uncultured archaeal groups found in marine ecosystems having identity values between 99% and 97%. A major fraction of the sequences (40%) were members of Methanobacteria, while others were included in the Marine Benthic Groups B and D, the Miscellaneous Crenarchaeotic Group, the Terrestrial Miscellaneous Euryarchaeotal Group, Marine Group I and Halobacteria. The presence of uncultured archaeal groups in Salar de Huasco extends their known distribution in inland waters, providing new clues about their possible function in the environment.

Description: Life at deep-sea hydrothermal vents depends on chemolithoautotrophic microorganisms as primary producers mediating the transfer of energy from hydrothermal fluids to higher trophic levels. A comprehensive molecular survey was performed with microbial communities in a mussel patch at the Irina II site of the Logatchev hydrothermal field by combining the analysis of 16S rRNA gene sequences with studies of functional key genes involved in biochemical pathways of sulfur oxidation–reduction (soxB, aprA) and autotrophic carbon fixation (aclB, cbbM, cbbL). Most significantly, major groups of chemoautotrophic sulfur oxidizers in the diffuse fluids differed in their biosynthetic pathways of both carbon fixation and sulfur oxidation. One important component of the community, the Epsilonproteobacteria, has the potential to grow chemoautotrophically by means of the reductive tricarboxylic acid cycle and to gain energy through the oxidation of reduced sulfur compounds using the Sox pathway. The majority of soxB and all retrieved aclB gene sequences were assigned to this group. Another important group in this habitat, the Gammaproteobacteria, may use the adenosine 5'-phosphosulfate pathway and the Calvin–Benson–Bassham cycle, deduced from the presence of aprA and cbbM genes. Hence, two important groups of primary producers at the investigated site might use different pathways for sulfur oxidation and carbon fixation.

Description: The chemical composition of the Caribbean sponge Pandaros acanthifolium was reinvestigated and led to the isolation of 12 new steroidal glycosides, namely, pandarosides E-J (1-6) and their methyl esters (7-12). Their structures were determined on the basis of extensive spectroscopic analyses, including two-dimensional NMR and HRESIMS data. Like the previously isolated pandarosides A-D (13-16), the new compounds 1-12 share an unusual oxidized D-ring and a cis C/D ring junction. The absolute configurations of the aglycones were assigned by interpretation of CD spectra, whereas the absolute configurations of the monosaccharide units were determined by chiral GC analyses of the acid methanolysates. The majority of the metabolites showed in vitro activity against three or four parasitic protozoa. Particularly active were the compounds 3 (pandaroside G) and its methyl ester (9), which potently inhibited the growth of Trypanosoma brucei rhodesiense (IC(50) values 0.78 and 0.038 mu M, respectively) and Leishmania donovani (IC(50)'s 1.3 and 0.051 mu M, respectively).

Description: The prasinophyte order Mamiellales contains several widespread marine picophytoplankton (≤2 μm diameter) taxa, including Micromonas and Ostreococcus. Complete genome sequences are available for two Micromonas isolates, CCMP1545 and RCC299. We performed in silico analyses of nitrogen transporters and related assimilation genes in CCMP1545 and RCC299 and compared these with other green lineage organisms as well as Chromalveolata, fungi, bacteria, and archaea. Phylogenetic reconstructions of ammonium transporter (AMT) genes revealed divergent types contained within each Mamiellales genome. Some were affiliated with plant and green algal AMT1 genes and others with bacterial AMT2 genes. Land plant AMT2 genes were phylogenetically closer to archaeal transporters than to Mamiellales AMT2 genes. The Mamiellales represent the first green algal genomes to harbor AMT2 genes, which are not found in Chlorella and Chlamydomonas or the chromalveolate algae analyzed but are present in oomycetes. Fewer nitrate transporter (NRT) than AMT genes were identified in the Mamiellales. NRT1 was found in all but CCMP1545 and showed highest similarity to Mamiellales and proteobacterial NRTs. NRT2 genes formed a bootstrap-supported clade basal to other green lineage organisms. Several nitrogen-related genes were colocated, forming a nitrogen gene cluster. Overall, RCC299 showed the most divergent suite of nitrogen transporters within the various Mamiellales genomes, and we developed TaqMan quantitative polymerase chain reaction primer-probes targeting a subset of these, as well as housekeeping genes, in RCC299. All those investigated showed expression either under standard growth conditions or under nitrogen depletion. Like other recent publications, our findings show a higher degree of "mixed lineage gene affiliations" among eukaryotes than anticipated, and even the most phylogenetically anomalous versions appear to be functional. Nitrogen is often considered a regulating factor for phytoplankton populations. This study provides a springboard for exploring the use and functional diversification of inorganic nitrogen transporters and related genes in eukaryotic phytoplankton. © 2010 The Author.

Description: The metabolic demands of a rare paper nautilus, Argonauta nouryi, in the eastern tropical Pacific (ETP) are evaluated. After adjusting for temperature and size, the rates of oxygen consumption and of aerobic and anaerobic metabolic potential (as evidenced by citrate synthase and octopine dehydrogenase activities, respectively) of A. nouryi were much higher than those in holopelagic octopods that exhibit float-and-wait predation strategies. In fact, the rates were similar to those found in small epipelagic squids and benthic octopods. The critical oxygen partial pressure was 4.9 kPa at 20°C, suggesting that the strong oxygen minimum layer found at intermediate depths in the ETP may constrain the vertical distribution of A. nouryi to the upper few metres of the water column. We also report the occurrence of a chain of shelled females at the surface, in which each animal was attached, as if on the benthos, to the next individual in the chain. Although it may constitute an effective strategy to increase the rates of mate encounter in the vast open ocean, there may be an important ecological trade-off for such behaviour, namely the increase in visibility at the surface with concomitant attraction of predators.

Description: The distribution of paralarvae and small juvenile cephalopods sampled by a rectangular midwater trawl (opening area 8 m2) over the continental shelf off Cape Santa Marta Grande, southern Brazil (28°09′S–29°56′S) during spring 1989 is discussed. An intrusion of Brazil Current Tropical Water (22°C; 36.5) separates warm, less-saline water (22°C; 35.2) from cooler, more-saline water (15°C; 36.4). Prevailing northeasterly winds led to upwelling of South Atlantic Central Water over the shelf, promoting high Chl a concentrations. Three species constituted 99% of the 628 cephalopods collected: Illex argentinus (n = 540; 4–40 mm mantle length, ML), Argonauta nodosa (n = 46; 2–19 mm ML), and Loligo sanpaulensis (n = 42, 2–21 mm ML). Segregation of I. argentinus juveniles of similar size suggests school formation as small as 10 mm ML. The presence of mature males along with fertilized female A. nodosa indicates mating early in life. There was a consistent and direct link between high plankton production and high densities of juvenile cephalopods through a short and ecologically efficient food chain. The relationship between production, pycnocline intensity, and the density of paralarvae and juveniles revealed suitable conditions for survival and growth during the upwelling season.