FicD genes in invertebrates: A tale of transposons, pathogenic and integrated viruses

Many gene families are shared across the tree of life between distantly related species because of horizontal gene transfers (HGTs). However, the frequency of HGTs varies strongly between gene families and biotic realms suggesting differential selection pressures and functional bias. One gene family with a wide distribution are FIC-domain containing enzymes (FicDs). FicDs catalyze AMPylation, a post-translational protein modification consisting in the addition of adenosine monophosphate to accessible residues of target proteins. Beside the well-known conservation of FicDs in deuterostomes, we report the presence of a conserved FicD gene ortholog in a large number of protostomes and microbial eukaryotes. We also reported additional FicD gene copies in the genomes of some rotifers, parasitic worms and bivalves. A few dsDNA viruses of these invertebrates, including White spot syndrome virus, Cherax quadricarinatus iridovirus, Ostreid herpesvirus-1 and the beetle nudivirus, carry copies of FicDs, with phylogenetic analysis suggesting a common origin of these FicD copies and the duplicated FicDs of their invertebrate hosts. HGTs and gene duplications possibly mediated by endogenous viruses or genetic mobile elements seem to have contributed to the transfer of AMPylation ability from bacteria and eukaryotes to pathogenic viruses, where this pathway could have been hijacked to promote viral infection

Selective Sorting and Degradation of Permafrost Organic Matter in the Nearshore Zone of Herschel Island (Yukon, Canada)

AbstractErosion of permafrost coasts due to climate warming releases large quantities of organic carbon (OC) into the Arctic Ocean. While burial of permafrost OC in marine sediments potentially limits degradation, resuspension of sediments in the nearshore zone potentially enhances degradation and greenhouse gas production, adding to the “permafrost carbon feedback.” Recent studies, focusing on bulk sediments, suggest that permafrost OC derived from coastal erosion is predominantly deposited close to shore. However, bulk approaches disregard sorting processes in the coastal zone, which strongly influence the OC distribution and fate. We studied soils and sediments along a transect from the fast‐eroding shoreline of Herschel Island—Qikiqtaruk (Yukon, Canada) to a depositional basin offshore. Sample material was fractionated by density (1.8 g cm−3) and size (63 μm), separating loose OC from mineral‐associated OC. Each fraction was analyzed for element content (TOC, TN), carbon isotopes (δ13C, Δ14C), molecular biomarkers (n‐alkanes, n‐alkanoic acids, lignin phenols, cutin acids), and mineral surface area. The OC partitioning between fractions changes considerably along the transect, highlighting the importance of hydrodynamic sorting in the nearshore zone. Additionally, OC and biomarker loadings decrease along the land‐ocean transect, indicating significant loss of OC during transport. However, molecular proxies for degradation show contrasting trends, suggesting that OC losses are not always well reflected in its degradation state. This study, using fraction partitioning that crosses land‐ocean boundaries in a way not done before, aids to disentangle sorting processes from degradation patterns, and provides quantitative insight into losses of thawed and eroded permafrost OC.</jats:p

Visualizing data on permafrost degradation in a pan-arctic pilot service aiming at a non-scientific audience

Climate change has led to an increase in permafrost warming and thaw at global scale. Land surface change associated with permafrost thaw include the acceleration of Arctic coastal erosion, increased thaw slumping in hillslope regions, the drainage and formation of lakes, as well as an intensification of disturbances on land, such as forest fires and droughts. Thermo-erosion threatens infrastructure and leads to gullying, slumping, and even landslides. Arctic communities living on frozen ground are strongly affected by these processes and are increasingly forced to adapt their livelihoods. In some areas, the relocation of settlements has become the last resort and is already actively planned for several communities in Alaska. Remote sensing analyses can be applied to detect and map permafrost disturbances at high spatial resolution across large regions to quantify landscape change, hydrological dynamics, and permafrost vulnerability. In the ERC PETA-CARB, ESA CCI Permafrost, and NSF Permafrost Discovery Gateway projects, a pan-arctic time series covering twenty years was produced using Landsat TM, ETM+, and OLI imagery. Following good scientific practice, this data is published via a digital data library and also available through a cloud-based analysis platform to facilitate re-use by other scientists. However, the data is not readily designed and presented to be interpreted by non-scientists and non-experts. In order to make the scientific findings more easily accessible, within the EU Arctic PASSION project we designed a tailored web-based portal specifically targeting non-scientific user communities, stakeholders, and rightsholders as part of the projects Permafrost Pilot Service. With the new portal, the Arctic Landscape EXplorer (ALEX), we provide interactive maps for recent information on land surface changes, hot spots of disturbances, and potential areas of active permafrost thaw and erosion. While focusing on the local to regional scale relevant for private users, as well as local, regional, and state-level decision makers, exploring the data up to the pan-arctic scale may open new avenues for understanding permafrost change for the general public. Recent consultations with local representatives and stakeholders from Alaska aimed to ensure that their actual information needs are met. Having received positive feedback and strong interest in the tool encouraged us to continue our work

Severe 21st-century ocean acidification in Antarctic Marine Protected Areas

Antarctic coastal waters are home to several established or proposed Marine Protected Areas (MPAs) supporting exceptional biodiversity. Despite being threatened by anthropogenic climate change, uncertainties remain surrounding the future ocean acidification (OA) of these waters. Here we present 21st-century projections of OA in Antarctic MPAs under four emission scenarios using a high-resolution ocean–sea ice–biogeochemistry model with realistic ice-shelf geometry. By 2100, we project pH declines of up to 0.36 (total scale) for the top 200 m. Vigorous vertical mixing of anthropogenic carbon produces severe OA throughout the water column in coastal waters of proposed and existing MPAs. Consequently, end-of-century aragonite undersaturation is ubiquitous under the three highest emission scenarios. Given the cumulative threat to marine ecosystems by environmental change and activities such as fishing, our findings call for strong emission-mitigation efforts and further management strategies to reduce pressures on ecosystems, such as the continuation and expansion of Antarctic MPAs

Altered Weddell Sea warm- and dense-water pathways in response to 21st-century climate change

Abstract. The transport of water masses with ocean circulation is a key component of the global climate system. In this context, the Filchner Trough in the southern Weddell Sea is critical, as it is a hotspot for the cross-shelf-break exchange of Dense Shelf Water and Warm Deep Water. We present results from Lagrangian particle tracking experiments in a global-ocean–sea-ice model (FESOM-1.4) which includes ice-shelf cavities and has eddy-permitting resolution on the southern Weddell Sea continental shelf. With backward and forward experiments, we assess changes between a present-day and a future (SSP5-8.5) time slice in the origin of waters reaching the Filchner Ice Shelf front and the fate of waters leaving it. We show that particles reaching the ice-shelf front from the open ocean originate from 173 % greater depths by 2100 (median; 776 m as compared to 284 m for the present day), while waters leaving the cavity towards the open ocean end up at 35 % shallower depths (550 m as compared to 850 m for the present day). Pathways of water leaving the continental shelf increasingly occur in the upper ocean, while the on-shelf flow of waters that might reach the ice-shelf cavity, i.e., at deeper layers, becomes more important by 2100. Simultaneously, median transit times between the Filchner Ice Shelf front and the continental shelf break decrease (increase) by 6 (9.5) months in the backward (forward) experiments. In conclusion, our study demonstrates the sensitivity of regional circulation patterns in the southern Weddell Sea to ongoing climate change, with direct implications for ice-shelf basal melt rates and local ecosystems. </jats:p

Carbon Stocks and Potential Greenhouse Gas Production of Permafrost-Affected Active Floodplains in the Lena River Delta

Arctic warming increases the degradation of permafrost soils but little is known about floodplain soils in the permafrost region. This study quantifies soil organic carbon (SOC) and soil nitrogen stocks, and the potential CH4 and CO2 production from seven cores in the active floodplains in the Lena River Delta, Russia. The soils were sandy but highly heterogeneous, containing deep, organic rich deposits with >60% SOC stored below 30 cm. The mean SOC stocks in the top 1 m were 12.9 ± 6.0 kg C m−2. Grain size analysis and radiocarbon ages indicated highly dynamic environments with sediment re-working. Potential CH4 and CO2 production from active floodplains was assessed using a 1-year incubation at 20°C under aerobic and anaerobic conditions. Cumulative aerobic CO2 production mineralized a mean 4.6 ± 2.8% of initial SOC. The mean cumulative aerobic:anaerobic C production ratio was 2.3 ± 0.9. Anaerobic CH4 production comprised 50 ± 9% of anaerobic C mineralization; rates were comparable or exceeded those for permafrost region organic soils. Potential C production from the incubations was correlated with total organic carbon and varied strongly over space (among cores) and depth (active layer vs. permafrost). This study provides valuable information on the carbon cycle dynamics from active floodplains in the Lena River Delta and highlights the key spatial variability, both among sites and with depth, and the need to include these dynamic permafrost environments in future estimates of the permafrost carbon-climate feedback

Impact of increased resolution on Arctic Ocean simulations in Ocean Model Intercomparison Project phase 2 (OMIP-2)

Abstract. This study evaluates the impact of increasing resolution on Arctic Ocean simulations using five pairs of matched low- and high-resolution models within the OMIP-2 (Ocean Model Intercomparison Project phase 2) framework. The primary objective is to assess whether a higher resolution can mitigate typical biases in low-resolution models and improve the representation of key climate-relevant variables. We reveal that increasing the horizontal resolution contributes to a reduction in biases in mean temperature and salinity and improves the simulation of the Atlantic water layer and its decadal warming events. A higher resolution also leads to better agreement with observed surface mixed-layer depth, cold halocline base depth and Arctic gateway transports in the Fram and Davis straits. However, the simulation of the mean state and temporal changes in Arctic freshwater content does not show improvement with increased resolution. Not all models achieve improvements for all analyzed ocean variables when spatial resolution is increased so it is crucial to recognize that model numerics and parameterizations also play an important role in faithful simulations. Overall, a higher resolution shows promise in improving the simulation of key Arctic Ocean features and processes, but efforts in model development are required to achieve more accurate representations across all climate-relevant variables. </jats:p

A universal tool for marine metazoan species identification: towards best practices in proteomic fingerprinting

AbstractProteomic fingerprinting using MALDI-TOF mass spectrometry is a well-established tool for identifying microorganisms and has shown promising results for identification of animal species, particularly disease vectors and marine organisms. And thus can be a vital tool for biodiversity assessments in ecological studies. However, few studies have tested species identification across different orders and classes. In this study, we collected data from 1246 specimens and 198 species to test species identification in a diverse dataset. We also evaluated different specimen preparation and data processing approaches for machine learning and developed a workflow to optimize classification using random forest. Our results showed high success rates of over 90%, but we also found that the size of the reference library affects classification error. Additionally, we demonstrated the ability of the method to differentiate marine cryptic-species complexes and to distinguish sexes within species.</jats:p