Dataset Information

Snezna jama (Slovenia): Interdisciplinary dating of cave sediments and implication for landscape evolution.

ABSTRACT: Caves are important markers of surface evolution, since they are, as a general rule, linked with ancient valley bottoms by their springs. However, caves can only be dated indirectly by means of the sediments they contain. If the sediment is older than common dating methods, one has to use multiple dating approaches in order to get meaningful results. U/Th dating, palaeomagnetic analysis of flowstone and sediment profiles, cosmogenic dating of quartz pebbles, and mammalian dating allowed a robust estimate of speleogenesis, sediment deposition, climatic change at the surface, and uplift history on the Periadriatic fault line during the Plio-Pleistocene. Our dates indicate that Snežna jama was formed in the (Upper) Miocene, received its sedimentary deposits during the Pliocene in a rather low-lying, hilly landscape, and became inactive due to uplift along the Periadriatic and Sava faults and climatic changes at the beginning of the Quaternary. Although it is only a single cave, the information contained within it makes it an important site of the Southern Alps.

SUBMITTER: Hauselmann P

PROVIDER: S-EPMC4581040 | biostudies-literature | 2015 Oct

REPOSITORIES: biostudies-literature

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Snežna jama (Slovenia): Interdisciplinary dating of cave sediments and implication for landscape evolution.

Häuselmann Philipp P Mihevc Andrej A Pruner Petr P Horáček Ivan I Čermák Stanislav S Hercman Helena H Sahy Diana D Fiebig Markus M Hajna Nadja Zupan NZ Bosák Pavel P

Geomorphology (Amsterdam, Netherlands) 20151001

Caves are important markers of surface evolution, since they are, as a general rule, linked with ancient valley bottoms by their springs. However, caves can only be dated indirectly by means of the sediments they contain. If the sediment is older than common dating methods, one has to use multiple dating approaches in order to get meaningful results. U/Th dating, palaeomagnetic analysis of flowstone and sediment profiles, cosmogenic dating of quartz pebbles, and mammalian dating allowed a robust ...[more]

PMID: 26516294

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Project description:Intra-chain domain interactions are known to play a significant role in the function and stability of multidomain proteins. These interactions are mediated through a physical interaction at domain-domain interfaces (DDIs). With a motivation to understand evolution of interfaces, we have investigated similarities among DDIs. Even though interfaces of protein-protein interactions (PPIs) have been previously studied by structurally aligning interfaces, similar analyses have not yet been performed on DDIs of either multidomain proteins or PPIs. For studying the structural landscape of DDIs, we have used iAlign to structurally align intra-chain domain interfaces of domains. The interface alignment of spatially constrained domains (due to inter-domain linkers) showed that ~88% of these could identify a structural matching interface having similar C-alpha geometry and contact pattern despite that aligned domain pairs are not structurally related. Moreover, the mean interface similarity score (IS-score) is 0.307, which is higher compared to the average random IS-score (0.207) suggesting domain interfaces are not random. The structural space of DDIs is highly connected as ~84% of all possible directed edges among interfaces are found to have at most path length of 8 when 0.26 is IS-score threshold. At this threshold, ~83% of interfaces form the largest strongly connected component. Thus, suggesting that structural space of intra-chain domain interfaces is degenerate and highly connected, as has been found in PPI interfaces. Interestingly, searching for structural neighbors of inter-chain interfaces among intra-chain interfaces showed that ~86% could find a statistically significant match to intra-chain interface with a mean IS-score of 0.311. This implies that domain interfaces are degenerate whether formed within a protein or between proteins. The interface degeneracy is most likely due to limited possible ways of packing secondary structures. In principle, interface similarities can be exploited to accurately model domain interfaces in structure prediction of multidomain proteins.

Project description:BackgroundMovile Cave (SE Romania) is a chemoautotrophically-based ecosystem fed by hydrogen sulfide-rich groundwater serving as a primary energy source analogous to the deep-sea hydrothermal ecosystems. Our current understanding of Movile Cave microbiology has been confined to the sulfidic water and its proximity, as most studies focused on the water-floating microbial mat and planktonic accumulations likely acting as the primary production powerhouse of this unique subterranean ecosystem. By employing comprehensive genomic-resolved metagenomics, we questioned the spatial variation, chemoautotrophic abilities, ecological interactions and trophic roles of Movile Cave's microbiome thriving beyond the sulfidic-rich water.ResultsA customized bioinformatics pipeline led to the recovery of 106 high-quality metagenome-assembled genomes from 7 cave sediment metagenomes. Assemblies' taxonomy spanned 19 bacterial and three archaeal phyla with Acidobacteriota, Chloroflexota, Proteobacteria, Planctomycetota, Ca. Patescibacteria, Thermoproteota, Methylomirabilota, and Ca. Zixibacteria as prevalent phyla. Functional gene analyses predicted the presence of CO2 fixation, methanotrophy, sulfur and ammonia oxidation in the explored sediments. Species Metabolic Coupling Analysis of metagenome-scale metabolic models revealed the highest competition-cooperation interactions in the sediments collected away from the water. Simulated metabolic interactions indicated autotrophs and methanotrophs as major donors of metabolites in the sediment communities. Cross-feeding dependencies were assumed only towards 'currency' molecules and inorganic compounds (O2, PO43-, H+, Fe2+, Cu2+) in the water proximity sediment, whereas hydrogen sulfide and methanol were assumedly traded exclusively among distant gallery communities.ConclusionsThese findings suggest that the primary production potential of Movile Cave expands way beyond its hydrothermal waters, enhancing our understanding of the functioning and ecological interactions within chemolithoautotrophically-based subterranean ecosystems.

Dataset Information

Snezna jama (Slovenia): Interdisciplinary dating of cave sediments and implication for landscape evolution.

Publications

Snežna jama (Slovenia): Interdisciplinary dating of cave sediments and implication for landscape evolution.

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