Browse
Submit Data
Databases
API
Help

Dataset Information

4 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Unique chemical parameters and microbial activity lead to increased archaeological preservation at the Roman frontier site of Vindolanda, UK.

ABSTRACT: Waterlogged burial conditions impact upon artefact preservation. One major determinant of preservation is presence and behaviour of microorganisms, however, unravelling the mechanisms, especially in waterlogged conditions is challenging. In this study, we analysed elemental composition, bacterial diversity and community structure from excavation trenches at the Roman Site of Vindolanda, Northumberland, UK, using pXRF and 16S rRNA gene amplicon sequencing. Excavation trenches provide information of different occupation periods. The results indicated that microbial communities were dominated by Firmicutes, Bacteroidetes and Proteobacteria at a phylum level. Samples which also had visible vivianite presence showed that there were marked increases in Methylophilus. Methylophilus might be associated with favourable preservation in these anaerobic conditions. More research is needed to clearly link the presence of Methylophilus with vivianite production. The study emphasises the need for further integration of chemical and microbiome approaches, especially in good preservation areas, to explore microbial and chemical degradation mechanisms.

SUBMITTER: Orr CH

PROVIDER: S-EPMC8338975 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

A genetic history of the Balkans from Roman frontier to Slavic migrations.

Project description:The rise and fall of the Roman Empire was a socio-political process with enormous ramifications for human history. The Middle Danube was a crucial frontier and a crossroads for population and cultural movement. Here, we present genome-wide data from 136 Balkan individuals dated to the 1st millennium CE. Despite extensive militarization and cultural influence, we find little ancestry contribution from peoples of Italic descent. However, we trace a large-scale influx of people of Anatolian ancestry during the Imperial period. Between ∼250 and 550 CE, we detect migrants with ancestry from Central/Northern Europe and the Steppe, confirming that "barbarian" migrations were propelled by ethnically diverse confederations. Following the end of Roman control, we detect the large-scale arrival of individuals who were genetically similar to modern Eastern European Slavic-speaking populations, who contributed 30%-60% of the ancestry of Balkan people, representing one of the largest permanent demographic changes anywhere in Europe during the Migration Period.

| S-EPMC10752003 | biostudies-literature

Archaeal Communities: The Microbial Phylogenomic Frontier.

Project description:Archaea are a unique system for investigating the diversity of life. There are the most diverse group of organisms with the longest evolutionary history of life on Earth. Phylogenomic investigations reveal the complex evolutionary history of Archaea, overturning longstanding views of the history of life. They exist in the harshest environments and benign conditions, providing a system to investigate the basis for living in extreme environments. They are frequently members of microbial communities, albeit generally rare. Archaea were central in the evolution of Eukaryotes and can be used as a proxy for studying life on other planets. Future advances will depend not only upon phylogenomic studies but also on a better understanding of isolation and cultivation techniques.

| S-EPMC8826477 | biostudies-literature

Forgotten Mediterranean calving grounds of grey and North Atlantic right whales: evidence from Roman archaeological records.

Project description:Right whales (Eubalaena glacialis) were extirpated from the eastern North Atlantic by commercial whaling. Grey whales (Eschrichtius robustus) disappeared from the entire North Atlantic in still-mysterious circumstances. Here, we test the hypotheses that both species previously occurred in the Mediterranean Sea, an area not currently considered part of their historical range. We used ancient DNA barcoding and collagen fingerprinting methods to taxonomically identify a rare set of 10 presumed whale bones from Roman and pre-Roman archaeological sites in the Strait of Gibraltar region, plus an additional bone from the Asturian coast. We identified three right whales, and three grey whales, demonstrating that the ranges of both of these species historically encompassed the Gibraltar region, probably including the Mediterranean Sea as calving grounds. Our results significantly extend the known range of the Atlantic grey whale, and suggest that 2000 years ago, right and grey whales were common when compared with other whale species. The disappearance of right and grey whales from the Mediterranean region is likely to have been accompanied by broader ecosystem impacts, including the disappearance of their predators (killer whales) and a reduction in marine primary productivity. The evidence that these two coastal and highly accessible species were present along the shores of the Roman Empire raises the hypothesis that they may have formed the basis of a forgotten whaling industry.

| S-EPMC6053924 | biostudies-literature

Describing Chemical Reactivity with Frontier Molecular Orbitalets.

Project description:Locality in physical space is critical in understanding chemical reactivity in the analysis of various phenomena and processes in chemistry, biology, and materials science, as exemplified in the concepts of reactive functional groups and active sites. Frontier molecular orbitals (FMOs) pinpoint the locality of chemical bonds that are chemically reactive because of the associated orbital energies and thus have achieved great success in describing chemical reactivity, mainly for small systems. For large systems, however, the delocalization nature of canonical molecular orbitals makes it difficult for FMOs to highlight the locality of the chemical reactivity. To obtain localized molecular orbitals that also reflect the frontier nature of the chemical processes, we develop the concept of frontier molecular orbitalets (FMOLs) for describing the reactivity of large systems. The concept of orbitalets was developed recently in the localized orbital scaling correction method, which aims for eliminating the delocalization error in common density functional approximations. Orbitalets are localized in both physical and energy spaces and thus contain both orbital locality and energy information. The FMOLs are thus the orbitalets with energies highest among occupied orbitalets and lowest among unoccupied ones. The applications of FMOLs to hexadeca-1,3,5,7,9,11,13,15-octaene in its equilibrium geometry, inter- and intra-molecular charge-transfer systems, and two transition states of a bifurcating reaction demonstrate that FMOLs can connect quantum mechanical treatments of chemical systems and chemical reactivities by locating the reactive region of large chemical systems. Therefore, FMOLs extend the role of FMOs for small systems and describe the chemical reactivity of large systems with energy and locality insight, with potentially broad applications.

| S-EPMC9241161 | biostudies-literature

Essential Oils as Alternative Biocides for the Preservation of Waterlogged Archaeological Wood.

Project description:Waterlogged archaeological wood is exposed to a high risk of biological degradation during the post-excavation phases of storage and restoration. For this reason, often biocides must be used to preserve wooden remains. In the present work three essential oils (cinnamon, wild thyme, and common thyme) were tested as possible alternative biocides to use in the preservation of waterlogged archaeological wood. The oils were first tested in vitro to establish the minimum inhibitory concentration (MIC) and to evaluate the biocidal activity on selected fungal strains. Then, the established MIC was applied on waterlogged archaeological wood samples and during an actual restoration treatment. The effectiveness of the oils was evaluated through cultural analyses, ATP quantification, and next-generation sequencing. The results showed that the oils caused a significant decrease in the vitality of fungal mycelia grown in vitro and of the microbiota present in treated wood and storage water. Furthermore, an influence on the composition of the bacterial communities of treated wood samples was observed. Although further tests are needed to evaluate interferences with the materials used during restoration procedures, essential oils could be considered as a possible alternative to the currently used biocide.

| S-EPMC7765822 | biostudies-literature

In-place molecular preservation of cellulose in 5,000-year-old archaeological textiles.

Project description:The understanding of fossilization mechanisms at the nanoscale remains extremely challenging despite its fundamental interest and its implications for paleontology, archaeology, geoscience, and environmental and material sciences. The mineralization mechanism by which cellulosic, keratinous, and silk tissues fossilize in the vicinity of archaeological metal artifacts offers the most exquisite preservation through a mechanism unexplored on the nanoscale. It is at the center of the vast majority of ancient textiles preserved under nonextreme conditions, known through extremely valuable fragments. Here we show the reconstruction of the nanoscale mechanism leading to the preservation of an exceptional collection of ancient cellulosic textiles recovered in the ancient Near East (4,000 to 5,000 years ago). We demonstrate that even the most mineralized fibers, which contain inorganic compounds throughout their histology, enclose preserved cellulosic remains in place. We evidence a process that combines the three steps of water transport of biocidal metal cations and soil solutes, degradation and loss of crystallinity of cellulosic polysaccharides, and silicification.

| S-EPMC7443972 | biostudies-literature

Mechanisms of lipid preservation in archaeological clay ceramics revealed by mass spectrometry imaging.

Project description:Traces of lipids, absorbed and preserved for millennia within the inorganic matrix of ceramic vessels, act as molecular fossils and provide manifold information about past people's subsistence, diet, and rituals. It is widely assumed that lipids become preserved after adsorption into nano- to micrometer-sized pores, but to this day the distribution of these lipids in the ceramics was virtually unknown, which severely limits our understanding about the process of lipid preservation. Here we use secondary ion mass spectrometry (SIMS) imaging for direct in situ analysis of lipids absorbed in 700- to 2,000-y-old archaeological pottery. After sectioning from larger sherds, wall cross-sections of smaller fragments were used for SIMS analysis. Lipids were found in relatively large zones of 5- to 400-µm diameter, which does not support the notion of absorption only into individual nanometer-scale pores but indicates that more macroscopic structures in the ceramics are involved in lipid preservation as well. Furthermore, lipids were found concentrated on calcium carbonate inclusions in the ceramics, which suggests that precipitation of fatty acids as calcium salts is an important aspect of lipid preservation in archaeological samples. This has important implications for analytical methods based on extraction of lipids from archaeological ceramics and needs to be considered to maximize the yield and available information from each unique sample.

| S-EPMC7334506 | biostudies-literature

Chemical and archaeological evidence for the earliest cacao beverages.

Project description:Chemical analyses of residues extracted from pottery vessels from Puerto Escondido in what is now Honduras show that cacao beverages were being made there before 1000 B.C., extending the confirmed use of cacao back at least 500 years. The famous chocolate beverage served on special occasions in later times in Mesoamerica, especially by elites, was made from cacao seeds. The earliest cacao beverages consumed at Puerto Escondido were likely produced by fermenting the sweet pulp surrounding the seeds.

| S-EPMC2141886 | biostudies-other

Long-Term Effectiveness, under a Mountain Environment, of a Novel Conservation Nanomaterial Applied on Limestone from a Roman Archaeological Site.

Project description:A novel alkoxysilane-based product was applied on limestone samples from a Roman archaeological site. The study consisted of an initial phase to evaluate site environmental conditions in order to choose the most suitable product type to be applied. The decay that was produced in the site is mainly caused by natural action, with water being the main vehicle for the decay agents. Thus, the effectiveness of an innovative product with hydrophobic/consolidant properties and two commercial products (consolidant and hydrophobic agent) were evaluated on limestone from Acinipo site, under laboratory conditions. Next, the long-term effectiveness of the three products under study was evaluated by the exposure of limestone samples in the archaeological site for a period of three years. Since the recognized incompatibility between alkoxysilanes and pure carbonate stones, the interaction between the products and the limestones was widely investigated. The results that were obtained allow for it to be concluded that the innovative product presents adequate compatibility and adherence to the limestone under study, producing a long-term effective, homogeneous, and continuous coating with a depth of penetration of up to 10 mm. However, the commercial products produced discontinuous aggregates on the limestone surface, did not penetrate into its porous structure and it did not produce long-lasting effects.

| S-EPMC5978071 | biostudies-literature

Characterization of structural changes in modern and archaeological burnt bone: Implications for differential preservation bias.

Project description:Structural and thermodynamic factors which may influence burnt bone survivorship in archaeological contexts have not been fully described. A highly controlled experimental reference collection of fresh, modern bone burned in temperature increments 100-1200˚C is presented here to document the changes to bone tissue relevant to preservation using Fourier transform infrared spectroscopy and X-ray diffraction. Specific parameters investigated here include the rate of organic loss, amount of bone mineral recrystallization, and average growth in bone mineral crystallite size. An archaeological faunal assemblage ca. 30,000 years ago from Tolbor-17 (Mongolia) is additionally considered to confirm visibility of changes seen in the modern reference sample and to relate structural changes to commonly used zooarchaeological scales of burning intensity. The timing of our results indicates that the loss of organic components in both modern and archaeological bone burnt to temperatures up to 700˚C are not accompanied by growth changes in the average crystallite size of bone mineral bioapatite, leaving the small and reactive bioapatite crystals of charred and carbonized bone exposed to diagenetic agents in depositional contexts. For bones burnt to temperatures of 700˚C and above, two major increases in average crystallite size are noted which effectively decrease the available surface area of bone mineral crystals, decreasing reactivity and offering greater thermodynamic stability despite the mechanical fragility of calcined bone. We discuss the archaeological implications of these observations within the context of Tolbor-17 and the challenges of identifying anthropogenic fire.

| S-EPMC8318310 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data