Facilitating accessible, rapid, and appropriate processing of ancient metagenomic data with AMDirT [version 1; peer review: 1 approved, 1 approved with reservations]

Background: Access to sample-level metadata is important when selecting public metagenomic sequencing datasets for reuse in new biological analyses. The Standards, Precautions, and Advances in Ancient Metagenomics community (SPAAM, https://spaam-community.github.io) has previously published AncientMetagenomeDir, a collection of curated and standardised sample metadata tables for metagenomic and microbial genome datasets generated from ancient samples. However, while sample-level information is useful for identifying relevant samples for inclusion in new projects, Next Generation Sequencing (NGS) library construction and sequencing metadata are also essential for appropriately reprocessing ancient metagenomic data. Currently, recovering information for downloading and preparing such data is difficult when laboratory and bioinformatic metadata is heterogeneously recorded in prose-based publications. Methods: Through a series of community-based hackathon events, AncientMetagenomeDir was updated to provide standardised library-level metadata of existing and new ancient metagenomic samples. In tandem, the companion tool 'AMDirT' was developed to facilitate automated metadata curation and data validation, as well as rapid data filtering and downloading. Results: AncientMetagenomeDir was extended to include standardised metadata of over 5000 ancient metagenomic libraries. The companion tool 'AMDirT' provides both graphical- and command-line interface based access to such metadata for users from a wide range of computational backgrounds. We also report on errors with metadata reporting that appear to commonly occur during data upload and provide suggestions on how to improve the quality of data sharing by the community.Conclusions: Together, both standardised metadata and tooling will help towards easier incorporation and reuse of public ancient metagenomic datasets into future analyses.Bioarchaeolog

Climate variability on the Adriatic seaboard during the last glacial inception and MIS 5c from Frasassi Cave stalagmite record

A stalagmite (FR16) from Frasassi Cave, located near the Adriatic coast of the Italian peninsula, offers a 16 kyr petrographic and stable isotope record spanning from 112.8 ± 1.5 ka to 96.6 ± 1.0 ka, corresponding to the interval from marine isotope stage (MIS) 5c to MIS 5d. The physical characteristics of FR16 calcite, allowed for a thorough understanding of the processes controlling isotopic changes, because fabrics as well are controlled by the environmental parameters within the cave that reflect external climate forcing. The FR16 δ13C profile matches fabric changes where columnar fabric usually corresponds to more negative values and micrite/microsparite layers to less negative δ13C values, and with the North Greenland Ice-core Project (NGRIP) δ18O record with more negative δ13C values during interstadials GI24 and GI23. This suggests a hydrological sensitivity for the two proxies, and their variability can be linked to recharge changes. On the other hand, the response to Greenland events appears subdued in the δ18O record and the trend mimics instead the Northern Hemisphere (NH) summer insolation with more negative δ18O values corresponding to the maximum insolation centred at ca. 105 ka. This behaviour can be explained by the higher sensitivity of δ18O to rainfall seasonality, moisture source and trajectories, whose combined effect attenuated the stadials/intersadials signal in the stalagmite

Climate variability on the Adriatic seaboard during the last glacial inception and MIS 5c from Frasassi Cave stalagmite record

International audienceA stalagmite (FR16) from Frasassi Cave, located near the Adriatic coast of the Italian peninsula, offers a 16 kyr petrographic and stable isotope record spanning from 112.8 ± 1.5 ka to 96.6 ± 1.0 ka, corresponding to the interval from marine isotope stage (MIS) 5c to MIS 5d. The physical characteristics of FR16 calcite, allowed for a thorough understanding of the processes controlling isotopic changes, because fabrics as well are controlled by the environmental parameters within the cave that reflect external climate forcing. The FR16 δ13C profile matches fabric changes where columnar fabric usually corresponds to more negative values and micrite/microsparite layers to less negative δ13C values, and with the North Greenland Ice-core Project (NGRIP) δ18O record with more negative δ13C values during interstadials GI24 and GI23. This suggests a hydrological sensitivity for the two proxies, and their variability can be linked to recharge changes. On the other hand, the response to Greenland events appears subdued in the δ18O record and the trend mimics instead the Northern Hemisphere (NH) summer insolation with more negative δ18O values corresponding to the maximum insolation centred at ca. 105 ka. This behaviour can be explained by the higher sensitivity of δ18O to rainfall seasonality, moisture source and trajectories, whose combined effect attenuated the stadials/intersadials signal in the stalagmit

High‐resolution synchrotron X‐ray fluorescence investigation of calcite coralloid speleothems: Elemental incorporation and their potential as environmental archives

Synchrotron high-resolution and micro-X-ray fluorescence elemental mapping of two coeval coralloid speleothems from Lamalunga Cave (Italy) are complemented with petrographic, morphological and microstratigraphic studies. The importance of these speleothems relies on their direct and indirect association with a complete Neanderthal skeleton (‘Altamura Man’) found inside the cave. The coralloids grew discontinuously between 64.6 ka and the Holocene and reveal exceptionally high concentrations of Mg, Sr and Si, particularly on convex surfaces, where evaporation is more intense. The incorporation of trace elements depends on several factors including location, shape and geometrical evolution during their growth, as well as climate and environmental parameters. This resulted in calcite precipitation with Sr compositions from 100 to 1200 ppm and an average concentration of 7000 ppm Mg. An unusually high Si content (up to 16%) is possibly derived from volcanic ash transported as particulate and in solution inside the cave. The most common fabrics observed consist of non-fluorescent elongated columnar calcite forming clean isopachous bands and fluorescent fibre-like crystals associated with laminated, lenticular bands high in Sr, Mg and Si. Variability in Sr, Mg and Si concentrations appears to induce fabric changes in the coralloids. Elongation and lattice distortion of the crystals was found to coincide with high Mg concentrations. The transition from compact elongated to open to fibre-like, is here interpreted as due to high concentrations of Si and Sr, which are preferentially incorporated in the speleothem at crystal boundaries and intra-laminae. It is here inferred that coralloid fabric changes and their elemental content potentially record local rainfall variations through time, with the clean compact calcite marking high infiltration and open fibre-like and micrite fabrics recording dry periods