Biology subjects

Sand, K. K.

Publications and source records attributed to Sand, K. K..

8 recordsLinked to original sources

bioRxiv2025

Environmental DNA Reveals Reykjavik's Human and Ecological History

Iceland was among the last large islands settled by humans, with colonization (Landnam) in the late 9th century CE (Common Era) and is often portrayed as an ecological disaster driven by the Norse settlers. Here, we revisit this narrative through environmental DNA (eDNA) and multiproxy analyses of sediment cores from Lake Tjornin in central Reykjavik, one of Icelands earliest and longest-occupied settlements. Originally a marine embayment, Tjornin became a freshwater lake around 660 CE. Our record reveals a human presence decades before the long-accepted arrival date of 877 CE, marked by the Landnam volcanic tephra. Early settlement brought livestock, barley cultivation, and other introduced taxa that enhanced nutrient cycling and unexpectedly increased local biodiversity. Contrary to the conventional view of rapid deforestation, eDNA shows that birch and willow expanded during the settlement period, likely supported by deliberate management. Pronounced ecological and land use shifts occurred after 1200 CE, but these were coeval with the Little Ice Age cooling, compounded by volcanic eruptions, storm surges, and plague, rather than anthropogenic degradation. Crop cultivation ceased, arboreal taxa retracted, and grazing pressure maintained open landscapes. Even more profound ecological changes came after c. 1750 CE with urbanization and industrialization, as wastewater discharge, heavy-metal pollution, and fossil fuel use reshaped Tjornins ecosystem. These findings challenge the prevailing model of Norse-induced environmental collapse, revealing instead a dynamic human-environment relationship shaped by both cultural practices and external stressors. By applying eDNA to a long-occupied urban catchment, we demonstrate the power of genomic methods to refine settlement chronologies, reassess ecological baselines and changes, and integrate natural and cultural histories. This approach offers a model for revisiting human-environment interactions in urban centers worldwide.

genomics↗

bioRxiv2024

Reconciling the importance of minerals for propagation of antibiotic resistance genes in the environment

The role of mineral surfaces in environmental processes, particularly their influence on DNA preservation, biofilm formation, and genetic transfer, has garnered attention due to its implications for the spread of antibiotic resistance genes (ARg). Despite the recognized significance of mineral-mediated DNA transfer, this mechanism remains poorly understood. Here we investigate the intricate interplay between soil minerals, bacteria, and DNA, to better understand the mechanisms driving ARg propagation in natural environments. We here study the uptake of mineral adsorbed DNA into the natural competent bacteria b. subtilis and further explore the influence of minerals on the viability and subsequent biofilm formation of both b. subtilis and A. baylyi. We further adsorbed DNA to mineral surfaces and allowed biofilm formation while monitoring the propagation of the ARg through out the biofilms. All the results are set in context of mineral surface properties such as surface charge, charge densities and surface area. Our results showed that the surface properties of the mineral surfaces are highly influencing the transformation efficiencies, viability and biofilm formation where in particular a high number of positive charged surface sites enhance biofilm formation and viability and inhibit transformation. The influence of the mineral surfaces diminishes as the biofilm develops and propagation of mineral adsorbed ARg are seen widely across the mineral surfaces. Our results have implication for mitigations strategies and reconcile mineral surfaces as hot spots for the propagation of antibiotic resistance-which indeed can be driven by transformation in the absence of bacteria carrying the traits. In principle all it takes is one successful transfer event from a mineral adsorbed ARg.

microbiology↗

bioRxiv2023

A 2-million-year-old microbial and viral communities from the Kap Kobenhavn Formation in North Greenland

Environmental DNA (eDNA) from the 2-million-year-old Kap Kobenhavn Formation of northern Greenland has revealed an ecosystem of plants and animals with no contemporary analogue1. Here, we reconstruct the microbial (bacterial, archaeal, and viral) communities that thrived at the site during this time. By leveraging a novel analytical framework that integrates taxonomic profiling, DNA damage estimates, and functional reconstructions, we identify and distinguish pioneer microbial communities from later permafrost microbial assemblages. We show that at the time of sediment deposition, the terrestrial input at the Kap Kobenhavn site originated from a palustrine wetland, suggesting warmer, non-permafrost conditions. During this period, the detection of methanogenic archaea and signals of their carbon metabolism is consistent with Kap Kobenhavn and similar northern ecosystems contributing moderate methane emissions. Intriguingly, we discover a remarkable nucleotide sequence similarity--exceeding 98%--between pioneer methanogens and present-day analogues in thawing permafrost. This aligns with the concept of "time-traveling" microbes2 surviving across geological time and waiting for conditions to turn favourable rather than evolving to adapt to changing conditions. Importantly, in contrast to the plant and animal communities of the Kap Kobenhavn, a striking similarity in microbial composition to that of a contemporary thawing Arctic suggests that microbial communities may serve as the first indication of broader climate-driven ecosystem disruptions.

microbiology↗

bioRxiv2023

Importance of eDNA taphonomy and provenance for robust ecological inference: insights from interfacial geochemistry

Context for and purposeRetrieval of modern and ancient environmental DNA (eDNA) from sediments has revolutionized our ability to reconstruct present and past ecosystems. Little emphasis has been placed, however, on the fundamentals of the DNA-sediment associations and, consequently, our understanding of taphonomy and provenance of eDNA in sediments remains extremely limited. If we are to be able to accurately infer community dynamics across time and space from eDNA data, we need to understand how depositional processes and sedimentary associations of DNA molecules in different settings influence our interpretation. Approach and methodsHere, we introduce interfacial geochemical principles to the field of eDNA and discuss current interpretational biases. We outline a way to increase the scope and resolution of ecological interpretations from eDNA by combining mineralogic composition with experimental adsorption data. We apply distribution coefficients to assess the relationship between the DNA fraction in water columns and DNA fraction sequestered by suspended sediment particles. We further evaluate the challenges with drawing ecological inference using eDNA from sedimentary systems that receive input from different ecosystem types as a consequence of sedimentary processes. Main results: We show thatO_LIThe retention of DNA in aqueous environments depends on the mineralogy of sediment particles and on the number of particles loaded in the water column. C_LIO_LIDNA attached to sediment particles from distal systems can be deposited in proximal systems and skew the interpretation of the proximal sediment samples. C_LIO_LIHigh particle loading in the water column can deplete suspended DNA and cause inaccurate interpretation of aqueous DNA samples. C_LIO_LIHigh particle loading in surface sediment pore waters enhances sequestration of DNA from benthic communities relative to that of water column communities, resulting in skewed estimates of species richness and abundance from sedimentary DNA. C_LI We discuss how to integrate taphonomy and provenance knowledge into the reconstruction of modern and past ecosystems, and ecosystem monitoring from eDNA data. Conclusions and the wider implicationsOur findings demonstrate that integrating information about eDNA taphonomy and provenance into modern and past ecosystem reconstruction from eDNA data can enhance the scope, resolution and accuracy of our interpretations.

biochemistry↗

bioRxiv2023

Sedimentary DNA can influence evolution:Establishing mineral facilitated horizontal gene transfer as a route to bacterial fitness

Horizontal gene transfer is one of the most important drivers of bacterial evolution. Transformation by uptake of extracellular DNA is traditionally not considered to be an effective mode of gene acquisition, simply because extracellular DNA is degraded in a matter of days when it is suspended in e.g. seawater. Mineral surfaces are, however, known to preserve DNA in the environment, and sedimentary ancient DNA studies have solidified that there are considerable amounts of fragmented DNA stored in sediments world-wide. Recently the age span of stored DNA was increased to at least 2 Ma. Here, we highlight that fragmented ancient DNA can be fueling the evolution of contemporary bacteria and advocate to consider this route for genetic variation in evolutionary history. We show that Acinetobacter baylyi can incorporate 60 bp DNA fragments adsorbed to a wide range of common sedimentary minerals and that the transformation frequencies scale with the mineral surface properties. Further, our results point to interfacial geochemical and sedimentologic processes as facilitators of evolutionary innovation where DNA-molecules are specific to the environment and the processes providing new DNA molecules may also provide the need to evolve. In contrast to heritable stochastic mutations as proposed by Darwin, the access by which bacteria acquire new genomic material at times with increased stress and also needs, would indicate a non-random mechanism that may propel evolution in a non-stochastic manner.

evolutionary biology↗

bioRxiv2020

Efficient long-range conduction in cable bacteria through nickel protein wires

Filamentous cable bacteria display unrivalled long-range electron transport, generating electrical currents over centimeter distances through a highly ordered network of fibers embedded in their cell envelope. The conductivity of these periplasmic wires is exceptionally high for a biological material, but their chemical structure and underlying electron transport mechanism remain unresolved. Here, we combine high-resolution microscopy, spectroscopy, and chemical imaging on individual cable bacterium filaments to demonstrate that the periplasmic wires consist of a conductive protein core surrounded by an insulating shell layer. The core proteins contain a sulfur-ligated nickel cofactor, and conductivity decreases when nickel is oxidized or selectively removed. The involvement of nickel as the active metal in biological conduction is remarkable, and suggests a hitherto unknown form of electron transport that enables efficient conduction in centimeter-long protein structures.

microbiology↗

bioRxiv2020

Survival of environmental DNA in natural environments: Surface charge and topography of minerals as driver for DNA storage

Extraction of environmental DNA (eDNA) from sediments are providing ground-breaking views of the past ecosystems and biodiversity. Despite this rich source of information, it is still unclear which sediments favour preservation and why. Here we used atomic force microscopy and molecular dynamics simulations to explore the DNA-mineral interaction to assess how mineralogy and interfacial geochemistry play a role in the preservation of environmental DNA on mineral substrates. We demonstrate that mineral composition, surface topography and surface charge influence DNA adsorption behavior as well as preservation. Modeling and experimental data show that DNA damage can be induced by mineral binding if there is a strong driving force for adsorption. The study shows that knowledge of the mineralogical composition of a sediment and the environmental conditions can be useful for assessing if a deposit is capable of storing extracellular DNA and to what extent the DNA would be preserved. Our data adds to the understanding of eDNA taphonomy and highlights that, for some mineral systems, fragmented DNA may not represent old DNA.

biochemistry↗

bioRxiv2017

Mineral facilitated horizontal gene transfer: A new principle for evolution of life?

A number of studies have highlighted that adsorption to minerals increases DNA longevity in the environment. Such DNA-mineral associations can essentially serve as pools of genes that can be stored across time. Importantly, this DNA is available for incorporation into alien organisms through the process of horizontal gene transfer. Here we argue that minerals hold an unrecognized potential for successfully transferring genetic material across environments and timescales to distant organisms and hypothesize that this process has significantly influenced the evolution of life. Our hypothesis is illustrated in the context of the evolution of early microbial life and the oxygenation of the Earths atmosphere and offers an explanation for observed outbursts of evolutionary events caused by horizontal gene transfer.

evolutionary biology↗