Metagenomic and geochemical characterization of pockmarked sediments overlaying the Troll petroleum reservoir in the North Sea

Background Pockmarks (depressions in the seabed) have been discovered throughout the world’s oceans and are often related to hydrocarbon seepage. Although high concentrations of pockmarks are present in the seabed overlaying the Troll oil and gas reservoir in the northern North Sea, geological surveys have not detected hydrocarbon seepage in this area at the present time. In this study we have used metagenomics to characterize the prokaryotic communities inhabiting the surface sediments in the Troll area in relation to geochemical parameters, particularly related to hydrocarbon presence. We also investigated the possibility of increased potential for methane oxidation related to the pockmarks. Five metagenomes from pockmarks and plain seabed sediments were sequenced by pyrosequencing (Roche/454) technology. In addition, two metagenomes from seabed sediments geologically unlikely to be influenced by hydrocarbon seepage (the Oslofjord) were included. The taxonomic distribution and metabolic potential of the metagenomes were analyzed by multivariate analysis and statistical comparisons to reveal variation within and between the two sampling areas. Results The main difference identified between the two sampling areas was an overabundance of predominantly autotrophic nitrifiers, especially Nitrosopumilus, and oligotrophic marine Gammaproteobacteria in the Troll metagenomes compared to the Oslofjord. Increased potential for degradation of hydrocarbons, especially aromatic hydrocarbons, was detected in two of the Troll samples: one pockmark sample and one from the plain seabed. Although presence of methanotrophic organisms was indicated in all samples, no overabundance in pockmark samples compared to the Oslofjord samples supports no, or only low level, methane seepage in the Troll pockmarks at the present time. Conclusions Given the relatively low content of total organic carbon and great depths of hydrocarbon containing sediments in the Troll area, it is possible that at least part of the carbon source available for the predominantly autotrophic nitrifiers thriving in this area originates from sequential prokaryotic degradation and oxidation of hydrocarbons to CO2. By turning CO2 back into organic carbon this subcommunity could play an important environmental role in these dark oligotrophic sediments. The oxidation of ammonia to nitrite and nitrate in this process could further increase the supply of terminal electron acceptors for hydrocarbon degradation

A metagenomic study of methanotrophic microorganisms in Coal Oil Point seep sediments

Background Methane oxidizing prokaryotes in marine sediments are believed to function as a methane filter reducing the oceanic contribution to the global methane emission. In the anoxic parts of the sediments, oxidation of methane is accomplished by anaerobic methanotrophic archaea (ANME) living in syntrophy with sulphate reducing bacteria. This anaerobic oxidation of methane is assumed to be a coupling of reversed methanogenesis and dissimilatory sulphate reduction. Where oxygen is available aerobic methanotrophs take part in methane oxidation. In this study, we used metagenomics to characterize the taxonomic and metabolic potential for methane oxidation at the Tonya seep in the Coal Oil Point area, California. Two metagenomes from different sediment depth horizons (0-4 cm and 10-15 cm below sea floor) were sequenced by 454 technology. The metagenomes were analysed to characterize the distribution of aerobic and anaerobic methanotrophic taxa at the two sediment depths. To gain insight into the metabolic potential the metagenomes were searched for marker genes associated with methane oxidation. Results Blast searches followed by taxonomic binning in MEGAN revealed aerobic methanotrophs of the genus Methylococcus to be overrepresented in the 0-4 cm metagenome compared to the 10-15 cm metagenome. In the 10-15 cm metagenome, ANME of the ANME-1 clade, were identified as the most abundant methanotrophic taxon with 8.6% of the reads. Searches for particulate methane monooxygenase (pmoA) and methyl-coenzyme M reductase (mcrA), marker genes for aerobic and anaerobic oxidation of methane respectively, identified pmoA in the 0-4 cm metagenome as Methylococcaceae related. The mcrA reads from the 10-15 cm horizon were all classified as originating from the ANME-1 clade. Conclusions Most of the taxa detected were present in both metagenomes and differences in community structure and corresponding metabolic potential between the two samples were mainly due to abundance differences. The results suggests that the Tonya Seep sediment is a robust methane filter, where taxa presently dominating this process could be replaced by less abundant methanotrophic taxa in case of changed environmental conditions

A decade of the berkeley math circle: the american experience, volume II

Many mathematicians have been drawn to mathematics through their experience with math circles. The Berkeley Math Circle (BMC) started in 1998 as one of the very first math circles in the U.S. Over the last decade and a half, 100 instructors--university professors, business tycoons, high school teachers, and more--have shared their passion for mathematics by delivering over 800 BMC sessions on the UC Berkeley campus every week during the school year. This second volume of the book series is based on a dozen of these sessions, encompassing a variety of enticing and stimulating mathematical topics, some new and some continuing from Volume I: from dismantling Rubik's Cube and randomly putting it back together to solving it with the power of group theory; from raising knot-eating machines and letting Alexander the Great cut the Gordian Knot to breaking through knot theory via the Jones polynomial; from entering a seemingly hopeless infinite raffle to becoming friendly with multiplicative functions in the land of Dirichlet, Möbius, and Euler; from leading an army of jumping fleas in an old problem from the International Mathematical Olympiads to improving our own essay-writing strategies; from searching for optimal paths on a hot summer day to questioning whether Archimedes was on his way to discovering trigonometry 2000 years ago Do some of these scenarios sound bizarre, having never before been associated with mathematics? Mathematicians love having fun while doing serious mathematics and that love is what this book intends to share with the reader. Whether at a beginner, an intermediate, or an advanced level, anyone can find a place here to be provoked to think deeply and to be inspired to create. In the interest of fostering a greater awareness and appreciation of mathematics and its connections to other disciplines and everyday life, MSRI and theAMS are publishing books in the Mathematical Circles Library series as a service to young people, their parents and teachers, and the mathematics profession

Metagenomics in CO2 Monitoring

-Leakage from CO2 storage areas is likely to affect the microbial communities in the overlaying sediments. We have conducted a baseline characterization of the microbial communities present in the surface sediments overlaying the Johansen formation, a potential site for CO2 storage, using metagenomics. We detected six abundant potentially CO2 fixing strains (e.g. Nitrosopumilus maritimus SCM1) as well as key genes for CO2 fixation pathways (e.g. the reductive tricarboxylic acid cycle and the Wood Ljungdahl pathway). Assuming this fraction of the community would increase in case of CO2 leakage; this information could be used as part of a surveillance project

Metagenomics in CO2 Monitoring

Leakage from CO2 storage areas is likely to affect the microbial communities in the overlaying sediments. We have conducted a baseline characterization of the microbial communities present in the surface sediments overlaying the Johansen formation, a potential site for CO2 storage, using metagenomics. We detected six abundant potentially CO2 fixing strains (e.g. Nitrosopumilus maritimus SCM1) as well as key genes for CO2 fixation pathways (e.g. the reductive tricarboxylic acid cycle and the Wood Ljungdahl pathway). Assuming this fraction of the community would increase in case of CO2 leakage; this information could be used as part of a surveillance project

Female mating preference functions predict sexual selection against hybrids between sibling species of cichlid fish

The evolutionary outcome of interspecific hybridization, i.e. collapse of species into a hybrid swarm, persistence or even divergence with reinforcement, depends on the balance between gene flow and selection against hybrids. If female mating preferences are open-ended but sign-inversed between species, they can theoretically be a source of such selection. Cichlid fish in African lakes have sustained high rates of speciation despite evidence for widespread hybridization, and sexual selection by female choice has been proposed as important in the origin and maintenance of species boundaries. However, it had never been tested whether hybridizing species have open-ended preference rules. Here we report the first experimental test using Pundamilia pundamilia, Pundamilia nyererei and their hybrids in three-way choice experiments. Hybrid males are phenotypically intermediate. Wild-caught females of both species have strong preferences for conspecific over heterospecific males. Their responses to F1 hybrid males are intermediate, but more similar to responses to conspecifics in one species and more similar to responses to heterospecifics in the other. We suggest that their mate choice mechanism may predispose haplochromine cichlids to maintain and perhaps undergo phenotypic diversification despite hybridization, and that species differences in female preference functions may predict the potential for adaptive trait transfer between hybridizing species