Permafrost and gas hydrate related methane release in the Arctic and its impact on climate change - European cooperation for long-term monitoring: COST Action PERGAMON (www.cost-pergamon.eu)

The Arctic is a key area in our warming world as massive releases of terrestrial and oceanic methane could increase atmospheric methane concentrations much faster than expected. The vast Arctic shelf might become a major emitter of methane in the future. Only a few projects are engaged in research on methane seepage in this area. The exchange of information about ongoing and planned activities in the Arctic with respect to gas hydrate destabilization and permafrost thawing is low within the EU and almost non-existent at an international level. The aim of the COST Action PERGAMON is to promote networking internationally within the EU and beyond: data integration of terrestrial studies from wetlands and permafrost regions marine research on gas release from seeps due to decomposing gas hydrate and/or permafrost melting and atmospheric investigations carried out by monitoring stations and via satellite is urgently needed to achieve a better understanding of methane emission processes in high latitude areas.The “official” main objective of PERGAMON is to quantify the methane input from marine and terrestrial sources into the atmosphere in the Arctic region, and ultimately to evaluate the impact of Arctic methane seepage on the global climate. This will be achieved by studying the origin and type of occurrence (dissolved/free gas, gas hydrate) of different methane sources (both on land and in the sub-seabed) as well as methane migration mechanisms, biogeochemical turnover, release mechanisms, and finally by quantifying the flux into the atmosphere. Biannual meetings and open workshops/conferences that will be announced throughout the scientific community serve as a platform to exchange and proliferate knowledge on methane in the Arctic. At present, fourteen European countries are partners in PERGAMON, several non-COST country institutions are currently applying to participate (e.g. the US and Russia). PERGAMON aims to be open for new members, suggestions and input at any time of the Action. PERGAMON officially runs until November 2013 with a final meeting early in 2014

Environmental control on anaerobic oxidation of methane in the gassy sediments of Eckernforde Bay (German Baltic)

We investigated the effect of seasonal environmental changes on the rate and distribution of anaerobic oxidation of methane (AOM) in Eckernforde Bay sediments (German Baltic Sea) and identified organisms that are likely to be involved in the process. Surface sediments were sampled during September and March. Field rates of AOM and sulfate reduction (SR) were measured with radiotracer methods. Additional parameters were determined that potentially influence AOM, i.e., temperature, salinity, methane, sulfate, and chlorophyll a. Methanogenesis as well as potential rates of AOM and aerobic oxidation of methane were measured in vitro. AOM changed seasonally within the upper 20 cm of the sediment, with rates being between 1 and 14 nmol cm−3 d−1. Its distribution is suggested to be controlled by oxygen and sulfate penetration, temperature, as well as methane supply, leading to a shallow AOM zone during the warm productive season and to a slightly deeper AOM zone during the cold winter season. Rising methane bubbles apparently fed AOM above the sulfate‐methane transition. Methanosarcinales‐related anaerobic methanotrophs (ANME‐2), identified with fluorescence in situ hybridization, is suggested to mediate AOM in Eckernforde Bay. These archaea are known also from other marine methane‐rich locations. However, they were not directly associated with sulfate‐reducing bacteria. AOM is possibly mediated solely by these archaea that show a mesophilic physiology according to the seasonal temperature changes in Eckernforde Bay

Subsurface microbial methanotrophic mats in the Black Sea

A nodule-shaped microbial mat was found subsurface in sediments of a gas seep in the anoxic Black Sea. This mat was dominated by ANME-1 archaea and consumed methane and sulfate simultaneously. We propose that such subsurface mats represent the initial stage of previously investigated microbial reefs

Volume Comparison for Hypersurfaces in Lorentzian Manifolds and Singularity Theorems

We develop area and volume comparison theorems for the evolution of spacelike, acausal, causally complete hypersurfaces in Lorentzian manifolds, where one has a lower bound on the Ricci tensor along timelike curves, and an upper bound on the mean curvature of the hypersurface. Using these results, we give a new proof of Hawking's singularity theorem.Comment: 15 pages, LaTe

Microbial community in a sediment-hosted CO2 lake of the southern Okinawa Trough hydrothermal system

Increasing levels of CO2 in the atmosphere are expected to cause climatic change with negative effects on the earth's ecosystems and human society. Consequently, a variety of CO2 disposal options are discussed, including injection into the deep ocean. Because the dissolution of CO2 in seawater will decrease ambient pH considerably, negative consequences for deep-water ecosystems have been predicted. Hence, ecosystems associated with natural CO2 reservoirs in the deep sea, and the dynamics of gaseous, liquid, and solid CO2 in such environments, are of great interest to science and society. We report here a biogeochemical and microbiological characterization of a microbial community inhabiting deep-sea sediments overlying a natural CO2 lake at the Yonaguni Knoll IV hydrothermal field, southern Okinawa Trough. We found high abundances (>109 cm−3) of microbial cells in sediment pavements above the CO2 lake, decreasing to strikingly low cell numbers (107 cm−3) at the liquid CO2/CO2-hydrate interface. The key groups in these sediments were as follows: (i) the anaerobic methanotrophic archaea ANME-2c and the Eel-2 group of Deltaproteobacteria and (ii) sulfur-metabolizing chemolithotrophs within the Gamma- and Epsilonproteobacteria. The detection of functional genes related to one-carbon assimilation and the presence of highly 13C-depleted archaeal and bacterial lipid biomarkers suggest that microorganisms assimilating CO2 and/or CH4 dominate the liquid CO2 and CO2-hydrate-bearing sediments. Clearly, the Yonaguni Knoll is an exceptional natural laboratory for the study of consequences of CO2 disposal as well as of natural CO2 reservoirs as potential microbial habitats on early Earth and other celestial bodies

Giving Back: Contributions Congruent to Library Dependency Changes in a Software Ecosystem

The widespread adoption of third-party libraries for contemporary software development has led to the creation of large inter-dependency networks, where sustainability issues of a single library can have widespread network effects. Maintainers of these libraries are often overworked, relying on the contributions of volunteers to sustain these libraries. To understand these contributions, in this work, we leverage socio-technical techniques to introduce and formalise dependency-contribution congruence (DC congruence) at both ecosystem and library level, i.e., to understand the degree and origins of contributions congruent to dependency changes, analyze whether they contribute to library dormancy (i.e., a lack of activity), and investigate similarities between these congruent contributions compared to typical contributions. We conduct a large-scale empirical study to measure the DC congruence for the npm ecosystem using 1.7 million issues, 970 thousand pull requests (PRs), and over 5.3 million commits belonging to 107,242 npm libraries. We find that the most congruent contributions originate from contributors who can only submit (not commit) to both a client and a library. At the project level, we find that DC congruence shares an inverse relationship with the likelihood that a library becomes dormant. Specifically, a library is less likely to become dormant if the contributions are congruent with upgrading dependencies. Finally, by comparing the source code of contributions, we find statistical differences in the file path and added lines in the source code of congruent contributions when compared to typical contributions. Our work has implications to encourage dependency contributions, especially to support library maintainers in sustaining their projects.Supatsara Wattanakriengkrai, Dong Wang, Raula Gaikovina Kula, Christoph Treude, Patanamon Thongtanunam, Takashi Ishio, and Kenichi Matsumot

Ecological succession of a Jurassic shallow-water ichthyosaur fall.

After the discovery of whale fall communities in modern oceans, it has been hypothesized that during the Mesozoic the carcasses of marine reptiles created similar habitats supporting long-lived and specialized animal communities. Here, we report a fully documented ichthyosaur fall community, from a Late Jurassic shelf setting, and reconstruct the ecological succession of its micro- and macrofauna. The early 'mobile-scavenger' and 'enrichment-opportunist' stages were not succeeded by a 'sulphophilic stage' characterized by chemosynthetic molluscs, but instead the bones were colonized by microbial mats that attracted echinoids and other mat-grazing invertebrates. Abundant cemented suspension feeders indicate a well-developed 'reef stage' with prolonged exposure and colonization of the bones prior to final burial, unlike in modern whale falls where organisms such as the ubiquitous bone-eating worm Osedax rapidly destroy the skeleton. Shallow-water ichthyosaur falls thus fulfilled similar ecological roles to shallow whale falls, and did not support specialized chemosynthetic communities

Anaerobic Microbial Degradation of Hydrocarbons: From Enzymatic Reactions to the Environment

Hydrocarbons are abundant in anoxic environments and pose biochemical challenges to their anaerobic degradation by microorganisms. Within the framework of the Priority Program 1319, investigations funded by the Deutsche Forschungsgemeinschaft on the anaerobic microbial degradation of hydrocarbons ranged from isolation and enrichment of hitherto unknown hydrocarbon-degrading anaerobic microorganisms, discovery of novel reactions, detailed studies of enzyme mechanisms and structures to process-oriented in situ studies. Selected highlights from this program are collected in this synopsis, with more detailed information provided by theme-focused reviews of the special topic issue on 'Anaerobic biodegradation of hydrocarbons' [this issue, pp. 1-244]. The interdisciplinary character of the program, involving microbiologists, biochemists, organic chemists and environmental scientists, is best exemplified by the studies on alkyl-/arylalkylsuccinate synthases. Here, research topics ranged from in-depth mechanistic studies of archetypical toluene-activating benzylsuccinate synthase, substrate-specific phylogenetic clustering of alkyl-/arylalkylsuccinate synthases (toluene plus xylenes, p-cymene, p-cresol, 2-methylnaphthalene, n-alkanes), stereochemical and co-metabolic insights into n-alkane-activating (methylalkyl) succinate synthases to the discovery of bacterial groups previously unknown to possess alkyl-/arylalkylsuccinate synthases by means of functional gene markers and in situ field studies enabled by state-of-the-art stable isotope probing and fractionation approaches. Other topics are Mo-cofactor-dependent dehydrogenases performing O-2-independent hydroxylation of hydrocarbons and alkyl side chains (ethylbenzene, p-cymene, cholesterol, n-hexadecane), degradation of p-alkylated benzoates and toluenes, glycyl radical-bearing 4-hydroxyphenylacetate decarboxylase, novel types of carboxylation reactions (for acetophenone, acetone, and potentially also benzene and naphthalene), W-cofactor-containing enzymes for reductive dearomatization of benzoyl-CoA (class II benzoyl-CoA reductase) in obligate anaerobes and addition of water to acetylene, fermentative formation of cyclohexanecarboxylate from benzoate, and methanogenic degradation of hydrocarbons

Evaluation and optimization of PCR primers for selective and quantitative detection of marine ANME subclusters involved in sulfate-dependent anaerobic methane oxidation

Since the discovery that anaerobic methanotrophic archaea (ANME) are involved in the anaerobic oxidation of methane coupled to sulfate reduction in marine sediments, different primers and probes specifically targeting the 16S rRNA gene of these archaea have been developed. Microbial investigation of the different ANME subtypes (ANME-1; ANME-2a, b, and c; and ANME-3) was mainly done in sediments where specific subtypes of ANME were highly enriched and methanogenic cell numbers were low. In different sediments with higher archaeal diversity and abundance, it is important that primers and probes targeting different ANME subtypes are very specific and do not detect other ANME subtypes or methanogens that are also present. In this study, primers and probes that were regularly used in AOM studies were tested in silico on coverage and specificity. Most of the previously developed primers and probes were not specific for the ANME subtypes, thereby not reflecting the actual ANME population in complex samples. Selected primers that showed good coverage and high specificity for the subclades ANME-1, ANME-2a/b, and ANME-2c were thoroughly validated using quantitative polymerase chain reaction (qPCR). From these qPCR tests, only certain combinations seemed suitable for selective amplification. After optimization of these primer sets, we obtained valid primer combinations for the selective detection and quantification of ANME-1, ANME-2a/b, and ANME-2c in samples where different ANME subtypes and possibly methanogens could be present. As a result of this work, we propose a standard workflow to facilitate selection of suitable primers for qPCR experiments on novel environmental samples.This research is supported by the Dutch Technology Foundation STW (project 10711), which is part of the Netherlands Organization for Scientific Research (NWO), and which is partly funded by the Ministry of Economic Affairs. Research of AJMS is supported by ERC grant (project 323009). Research of PHATand AJMS is supported by the SIAM Gravitation grant (project 024.002.002) of the Netherlands Ministry of Education, Culture and Science and the Netherlands Science Foundation (NWO).info:eu-repo/semantics/publishedVersio

Ocean currents shape the microbiome of Arctic marine sediments

Prokaryote communities were investigated on the seasonally stratified Alaska Beaufort Shelf (ABS). Water and sediment directly underlying water with origin in the Arctic, Pacific or Atlantic oceans were analyzed by pyrosequencing and length heterogeneity-PCR in conjunction with physicochemical and geographic distance data to determine what features structure ABS microbiomes. Distinct bacterial communities were evident in all water masses. Alphaproteobacteria explained similarity in Arctic surface water and Pacific derived water. Deltaproteobacteria were abundant in Atlantic origin water and drove similarity among samples. Most archaeal sequences in water were related to unclassified marine Euryarchaeota. Sediment communities influenced by Pacific and Atlantic water were distinct from each other and pelagic communities. Firmicutes and Chloroflexi were abundant in sediment, although their distribution varied in Atlantic and Pacific influenced sites. Thermoprotei dominated archaea in Pacific influenced sediments and Methanomicrobia dominated in methane-containing Atlantic influenced sediments. Length heterogeneity-PCR data from this study were analyzed with data from methane-containing sediments in other regions. Pacific influenced ABS sediments clustered with Pacific sites from New Zealand and Chilean coastal margins. Atlantic influenced ABS sediments formed another distinct cluster. Density and salinity were significant structuring features on pelagic communities. Porosity co-varied with benthic community structure across sites and methane did not. This study indicates that the origin of water overlying sediments shapes benthic communities locally and globally and that hydrography exerts greater influence on microbial community structure than the availability of methane