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Due to its insulating and draining role, assessing ground vegetation cover properties is important for high-resolution hydrological modeling of permafrost regions. In this study, morphological and effective hydraulic properties of Western Siberian Lowland ground vegetation samples (lichens, Sphagnum mosses, peat) are numerically studied based on tomography scans. Porosity is estimated through a void voxels counting algorithm, showing the existence of representative elementary volumes (REVs) of porosity for most samples. Then, two methods are used to estimate hydraulic conductivity depending on the sample's homogeneity. For homogeneous samples, direct numerical simulations of a single-phase flow are performed, leading to a definition of hydraulic conductivity related to a REV, which is larger than those obtained for porosity. For heterogeneous samples, no adequate REV may be defined. To bypass this issue, a pore network representation is created from computerized scans. Morphological and hydraulic properties are then estimated through this simplified representation. Both methods converged on similar results for porosity. Some discrepancies are observed for a specific surface area. Hydraulic conductivity fluctuates by 2 orders of magnitude, depending on the method used. Porosity values are in line with previous values found in the literature, showing that arctic cryptogamic cover can be considered an open and well-connected porous medium (over 99 % of overall porosity is open porosity). Meanwhile, digitally estimated hydraulic conductivity is higher compared to previously obtained results based on field and laboratory experiments. However, the uncertainty is less than in experimental studies available in the literature. Therefore, biological and sampling artifacts are predominant over numerical biases. This could be related to compressibility effects occurring during field or laboratory measurements. These numerical methods lay a solid foundation for interpreting the homogeneity of any type of sample and processing some quantitative properties' assessment, either with image processing or with a pore network model. The main observed limitation is the input data quality (e.g., the tomographic scans' resolution) and its pre-processing scheme. Thus, some supplementary studies are compulsory for assessing syn-sampling and syn-measurement perturbations in experimentally estimated, effective hydraulic properties of such a biological porous medium.

Despite recent progress in the understanding of the carbon (C) cycle of Siberian permafrost-affected rivers, spatial and seasonal dynamics of C export and emission from medium-sized rivers (50 000–300 000 km2 watershed area) remain poorly known. Here we studied one of the largest tributaries of the Ob River, the Ket River (watershed = 94 000 km2), which drains through pristine taiga forest of the boreal zone in the West Siberian Lowland (WSL). We combined continuous and discrete measurements of carbon dioxide (CO2) concentration using submersible CO2 sensor and floating chamber flux (FCO2), with methane (CH4), dissolved organic and inorganic C (DOC and DIC, respectively), particulate organic C and total bacterial concentrations over an 800 km transect of the Ket River main stem and its 26 tributaries during spring flood (May 2019) and 12 tributaries during summer baseflow (end of August–beginning of September 2019). The partial pressure of CO2 (pCO2) was lower and less variable in the main stem (2000 to 2500 µatm) compared to that in the tributaries (2000 to 5000 µatm). In the tributaries, the pCO2 was 40 % higher during baseflow compared to spring flood, whereas in the main stem, it did not vary significantly across the seasons. The methane concentration in the main stem and tributaries was a factor of 300 to 1900 (flood period) and 100 to 150 times lower than that of CO2 and ranged from 0.05 to 2.0 µmol L−1. The FCO2 ranged from 0.4 to 2.4 g C m−2 d−1 in the main channel and from 0.5 to 5.0 g C m−2 d−1 in the tributaries, being highest during August in the tributaries and weakly dependent on the season in the main channel. During summer baseflow, the DOC aromaticity, bacterial number, and needleleaf forest coverage of the watershed positively affected CO2 concentrations and fluxes. We hypothesize that relatively low spatial and seasonal variability in FCO2 of the Ket River is due to a flat homogeneous landscape (bogs and taiga forest) that results in long water residence times and stable input of allochthonous dissolved organic matter (DOM), which dominate the FCO2. The open water period (May to October) C emission from the fluvial network (main stem and tributaries) of the Ket River was estimated to 127 ± 11 Gg C yr−1, which is lower than the downstream dissolved and particulate C export during the same period. The estimated fluvial C emissions are highly conservative and contain uncertainties linked to ignoring hotspots and hot moments of emissions, notably in the floodplain zone. This stresses the need to improve the temporal resolution of FCO2 and water coverage across seasons and emphasizes the important role of WSL rivers in the release of CO2 into the atmosphere.

Natural and anthropogenic mercury (Hg) emissions are sequestered in terrestrial soils over short, annual to long, millennial timescales before Hg mobilization and run-off impact wetland and coastal ocean ecosystems. Recent studies have used Hg-to-carbon (C) ratios (RHgC's) measured in Alaskan permafrost mineral and peat soils together with a northern circumpolar permafrost soil carbon inventory to estimate that these soils contain large amounts of Hg (between 184 and 755 Gg) in the upper 1 m. However, measurements of RHgC on Siberian permafrost peatlands are largely missing, leaving the size of the estimated northern soil Hg budget and its fate under Arctic warming scenarios uncertain. Here we present Hg and carbon data for six peat cores down to mineral horizons at 1.5–4 m depth, across a 1700 km latitudinal (56 to 67∘ N) permafrost gradient in the Western Siberian Lowland (WSL). Mercury concentrations increase from south to north in all soil horizons, reflecting a higher stability of sequestered Hg with respect to re-emission. The RHgC in the WSL peat horizons decreases with depth, from 0.38 Gg Pg−1 in the active layer to 0.23 Gg Pg−1 in continuously frozen peat of the WSL. We estimate the Hg pool (0–1 m) in the permafrost-affected part of the WSL peatlands to be 9.3±2.7 Gg. We review and estimate pan-Arctic organic and mineral soil RHgC to be 0.19 and 0.63 Gg Pg−1, respectively, and use a soil carbon budget to revise the pan-Arctic permafrost soil Hg pool to be 72 Gg (39–91 Gg; interquartile range, IQR) in the upper 30 cm, 240 Gg (110–336 Gg) in the upper 1 m, and 597 Gg (384–750 Gg) in the upper 3 m. Using the same RHgC approach, we revise the upper 30 cm of the global soil Hg pool to contain 1086 Gg of Hg (852–1265 Gg, IQR), of which 7 % (72 Gg) resides in northern permafrost soils. Additional soil and river studies in eastern and northern Siberia are needed to lower the uncertainty on these estimates and assess the timing of Hg release to the atmosphere and rivers.

The Western Siberia Lowland (WSL) is the world’s largest frozen peatland complex, however carbon emissions (CO2+CH4) from lakes in this region remain unknown. Here, the authors sample 76 lakes and show high carbon emissions from lakes across all permafrost zones in the WSL.

In contrast to numerous studies on the dynamics of dissolved ( 0.45 µm) matter (RSM) in these regions. In order to test the effect of climate, permafrost and physio-geographical landscape parameters (bogs, forest and lake coverage of the watershed) on RSM and particulate C, N and P concentrations in river water, we sampled 33 small and medium-sized rivers (10–100 000 km2 watershed) along a 1700 km N–S transect including both permafrost-affected and permafrost-free zones of the Western Siberian Lowland (WSL). The concentrations of C and N in RSM decreased with the increase in river watershed size, illustrating (i) the importance of organic debris in small rivers which drain peatlands and (ii) the role of mineral matter from bank abrasion in larger rivers. The presence of lakes in the watershed increased C and N but decreased P concentrations in the RSM. The C : N ratio in the RSM reflected the source from the deep soil horizon rather than surface soil horizon, similar to that of other Arctic rivers. This suggests the export of peat and mineral particles through suprapermafrost flow occurring at the base of the active layer. There was a maximum of both particulate C and N concentrations and export fluxes at the beginning of permafrost appearance, in the sporadic and discontinuous zone (62–64° N). This presumably reflected the organic matter mobilization from newly thawed organic horizons in soils at the active latitudinal thawing front. The results suggest that a northward shift of permafrost boundaries and an increase in active layer thickness may increase particulate C and N export by WSL rivers to the Arctic Ocean by a factor of 2, while P export may remain unchanged. In contrast, within a long-term climate warming scenario, the disappearance of permafrost in the north, the drainage of lakes and transformation of bogs to forest may decrease C and N concentrations in RSM by 2 to 3 times.

Mobilization of dissolved organic carbon (DOC) and related trace elements (TEs) from the frozen peat to surface waters in the permafrost zone is expected to enhance under ongoing permafrost thaw and active layer thickness (ALT) deepening in high-latitude regions. The interstitial soil solutions are efficient tracers of ongoing bio-geochemical processes in the critical zone and can help to decipher the intensity of carbon and metals migration from the soil to the rivers and further to the ocean. To this end, we collected, across a 640 km latitudinal transect of the sporadic to continuous permafrost zone of western Siberia peatlands, soil porewaters from 30 cm depth using suction cups and we analyzed DOC, dissolved inorganic carbon (DIC), and 40 major elements and TEs in 0.45 µm filtered fraction of 80 soil porewaters. Despite an expected decrease in the intensity of DOC and TE mobilization from the soil and vegetation litter to the interstitial fluids with the increase in the permafrost coverage and a decrease in the annual temperature and ALT, the DOC and many major and trace elements did not exhibit any distinct decrease in concentration along the latitudinal transect from 62.2 to 67.4° N. The DOC demonstrated a maximum of concentration at 66° N, on the border of the discontinuous/continuous permafrost zone, whereas the DOC concentration in peat soil solutions from the continuous permafrost zone was equal to or higher than that in the sporadic/discontinuous permafrost zone. Moreover, a number of major (Ca, Mg) and trace (Al, Ti, Sr, Ga, rare earth elements (REEs), Zr, Hf, Th) elements exhibited an increasing, not decreasing, northward concentration trend. We hypothesize that the effects of temperature and thickness of the ALT are of secondary importance relative to the leaching capacity of peat, which is in turn controlled by the water saturation of the peat core. The water residence time in peat pores also plays a role in enriching the fluids in some elements: the DOC, V, Cu, Pb, REEs, and Th were a factor of 1.5 to 2.0 higher in mounds relative to hollows. As such, it is possible that the time of reaction between the peat and downward infiltrating waters essentially controls the degree of peat porewater enrichments in DOC and other solutes. A 2° northward shift in the position of the permafrost boundaries may bring about a factor of 1.3 ± 0.2 decrease in Ca, Mg, Sr, Al, Fe, Ti, Mn, Ni, Co, V, Zr, Hf, Th, and REE porewater concentration in continuous and discontinuous permafrost zones, and a possible decrease in DOC, specific ultraviolet absorbency (SUVA), Ca, Mg, Fe, and Sr will not exceed 20 % of their current values. The projected increase in ALT and vegetation density, northward migration of the permafrost boundary, or the change of hydrological regime is unlikely to modify chemical composition of peat porewater fluids larger than their natural variations within different micro-landscapes, i.e., within a factor of 2. The decrease in DOC and metal delivery to small rivers and lakes by peat soil leachate may also decrease the overall export of dissolved components from the continuous permafrost zone to the Arctic Ocean. This challenges the current paradigm on the increase in DOC export from the land to the ocean under climate warming in high latitudes.

Summary: The high heritability of amyotrophic lateral sclerosis (ALS) contrasts with its low molecular diagnosis rate post-genetic testing, pointing to potential undiscovered genetic factors. To aid the exploration of these factors, we introduced EpiOut, an algorithm to identify chromatin accessibility outliers that are regions exhibiting divergent accessibility from the population baseline in a single or few samples. Annotation of accessible regions with histone chromatin immunoprecipitation sequencing and Hi-C indicates that outliers are concentrated in functional loci, especially among promoters interacting with active enhancers. Across different omics levels, outliers are robustly replicated, and chromatin accessibility outliers are reliable predictors of gene expression outliers and aberrant protein levels. When promoter accessibility does not align with gene expression, our results indicate that molecular aberrations are more likely to be linked to post-transcriptional regulation rather than transcriptional regulation. Our findings demonstrate that the outlier detection paradigm can uncover dysregulated regions in rare diseases. EpiOut is available at github.com/uci-cbcl/EpiOut.

The impact of wildfire on terrestrial and aquatic ecosystems in permafrost-affected regions is a major and still poorly understood consequence of climate warming in high latitudes. Towards better characterization of processes controlling post-fire nutrient migration and to establish the relationship between forest litter and aquatic systems during a fire event, we studied organic and inorganic solute leaching from ash that was produced via burning organic litter (topsoil) collected in permafrost-affected forest in western Siberia. Litter samples were burned at 300, 450 and 600 °C and dissolved organic carbon (DOC), major elements (Ca, Mg, Cl, SO4, Na, N, P, K, Si), carboxylic organic acids, and ∼ 40 trace elements were analyzed in leachates (

Abstract People with substance use disorders (SUD) have a high prevalence of chronic hepatitis C virus (HCV) infection and mental health disorders. We aimed to assess the impact of integrated HCV treatment on psychological distress measured by Hopkins-symptom-checklist-10 (SCL-10). This multi-center randomized controlled trial evaluated psychological distress as a secondary outcome of integrated HCV treatment (INTRO-HCV trial). From 2017 to 2019, 289 participants were randomly assigned to receive either integrated or standard HCV treatment with direct-acting antiviral therapy. Integrated HCV treatment was delivered in eight decentralized outpatient opioid agonist therapy clinics and two community care centers; standard treatment was delivered in internal medicine outpatient clinics at centralized hospitals. Participants in the integrated treatment arm had a sustained virologic response of 93% compared to 73% for those in standard treatment arm. Psychological distress was assessed using SCL-10 prior to initiation of HCV treatment and 12 weeks after treatment completion. The mean SCL-10 score prior to HCV treatment was 2.2 (standard deviation [SD]: 0.7) for patients receiving integrated HCV treatment and 2.2 (SD: 0.8) for those receiving standard HCV treatment. Twelve weeks after the end of treatment, the mean SCL-10 score change was − 0.1 (− 0.3;0.0) in the integrated compared to the standard arm. Psychological distress did not substantially change during the treatment period and was not significantly different between the treatment arms.

Objective: To better understand the microbial profile of complicated parapneumonic effusions and empyema, and to evaluate whether antimicrobial selection would differ if guided by targeted metagenomic sequencing (tMGS) vs conventional cultures (CCs) alone. Patients and Methods: We analyzed the pleural fluid of a cohort of 47 patients undergoing thoracentesis from January 1, 2017 to August 31, 2019, to characterize their microbial profile. All samples underwent 16S ribosomal ribonucleic acid gene polymerase chain reaction, followed by tMGS. Results: Pleural space infection was deemed clinically present in 20 of the 47 (43%) participants. Of those, n=7 (35%) had positive pleural fluid cultures and n=14 (70%) had positive tMGS results. The organisms identified by tMGS were concordant with CCs; however, tMGS detected additional bacterial species over CCs alone. Streptococcus and Staphylococcus species were the most common organisms identified, with Streptococcus intermedius/constellatus identified in 5 patients. Polymicrobial infections were found in 6 of the 20 patients, with anaerobes being the most common organisms identified in these cases. Conclusion: Streptococci and staphylococci were the most common organisms identified in infected pleural fluid. Anaerobes were common in polymicrobial infections. When compared with CCs, tMGS had higher sensitivity than CCs. Targeted metagenomic sequencing identified additional organisms, not identified by CCs, with associated potential management implications.

[This corrects the article DOI: 10.1371/journal.pmed.1003818.].

Flaviviruses cause some of the most detrimental vertebrate diseases, yet little is known of their impacts on invertebrates. Microbial activities at the animal-water interface are hypothesized to influence viral replication and possibly contribute to pathology of echinoderm wasting diseases due to hypoxic stress. We assessed the impacts of enhanced microbial production and suboxic stress on Apostichopus californicus associated flavivirus (PcaFV) load in a mesocosm experiment. Organic matter amendment and suboxic stress resulted in lower PcaFV load, which also correlated negatively with animal mass loss and microbial activity at the animal-water interface. These data suggest that PcaFV replication and persistence was best supported in healthier specimens. Our results do not support the hypothesis that suboxic stress or microbial activity promote PcaFV replication, but rather that PcaFV appears to be a neutral or beneficial symbiont of Apostichopus californicus.

The paper analyzed the number of ecological-trophic groups of microorganisms and the elemental composition of the active, permafrost and thawed layers of a typical flat mount frozen peatlands (plateau palsa) in the Nadym-Pur interfluves, Western Siberia, with part of it affected by fire. The number of ecological-trophic groups was found to change after permafrost thaw. The study revealed a relationship between the number of microorganisms and the content of some chemical elements in the soil profile of the plateau palsa in the Nadym-Pur interfluve. A statistically significant relationship was found between the most probable number of microorganisms (CFU/g) in different peat layers and the pH, the ash content and the content of calcium, magnesium, strontium, and iron.

Predicting the impacts of predatory invasive species is important for prioritising conservation interventions. Functional response experiments, which examine consumption by predators in relation to prey density, are a useful way to assess the potential strength of novel predator-prey relationships. However, such experiments are often conducted without consideration of sex or only with males to reduce invasion risk. Here, we compared the functional responses of male and female European green crabs (Carcinus maenas), a global invader, feeding on varnish clams (Nuttallia obscurata) to test whether the two sexes have similar potential for impact. We also examined potential correlates of predation behaviour by measuring sex-specific movement and prey choice. Both sexes displayed a Type II hyperbolic functional response, which can destabilise prey populations at low prey densities. However, males and females exhibited some differences in foraging behaviour. Female green crabs had slightly lower attack rates, which were not linked to sex differences in movement, and slightly longer handling times, which were not linked to sex differences in prey choice. These small, non-significant differences nevertheless translated into significantly greater functional response ratios, which are used to predict the ecological impact of invasive species, for males than females. There was no difference in the proportion of clams consumed between males and females with similar crusher claw heights, but females have smaller crusher claws on average, hence they consumed a smaller proportion of clams. Repeated surveys of four populations of European green crabs established in British Columbia, Canada, showed that sex ratio is highly variable. Taken together, these results and population-level modelling suggest that trying to evaluate the potential impact of European green crabs on clam populations by sampling only males could result in overestimation, even in populations that have male-biased sex-ratios. Consumer sex might generally be an important feature to consider when using functional response experiments to forecast the impact of new invasive species, especially those with marked sexual dimorphism that affect foraging.

Oceanic heatwaves have significant impacts on disease dynamics in marine ecosystems. Following an extreme heatwave in Nanoose Bay, British Columbia, Canada, a severe sea cucumber wasting event occurred that resulted in the mass mortality of Apostichopus californicus. Here, we sought to determine if heat stress in isolation could trigger wasting symptoms in A. californicus. We exposed sea cucumbers to (i) a simulated marine heatwave (22 °C), (ii) an elevated temperature treatment (17 °C), or (iii) control conditions (12 °C). We measured the presence of skin lesions, mortality, posture maintenance, antipredator defences, spawning, and organ evisceration during the 79-hour thermal exposure, as well as 7-days post-exposure. Both the 22 °C and 17 °C treatments elicited stress responses where individuals exhibited a reduced ability to maintain posture and an increase in stress spawning. The 22 °C heatwave was particularly stressful, as it was the only treatment where mortality was observed. However, none of the treatments induced wasting symptoms as observed in the Nanoose Bay event. This study provides evidence that sea cucumber wasting may not be triggered by heat stress in isolation, leaving the cause of the mass mortality event observed in Nanoose unknown.

Permafrost peatlands, containing a sizable amount of soil organic carbon (OC), play a pivotal role in soil (peat) OC transformation into soluble and volatile forms and greatly contribute to overall natural CO2 and CH4 emissions to the atmosphere under ongoing permafrost thaw and soil OC degradation. Peat microorganisms are largely responsible for the processing of this OC, yet coupled studies of chemical and bacterial parameters in permafrost peatlands are rather limited and geographically biased. Towards testing the possible impact of peat and peat pore water chemical composition on microbial population and diversity, here we present results of a preliminary study of the western Siberia permafrost peatland discontinuous permafrost zone. The quantitative evaluation of microorganisms and determination of microbial diversity along a 100 cm thick peat soil column, which included thawed and frozen peat and bottom mineral horizon, was performed by RT-PCR and 16S rRNA gene-based metagenomic analysis, respectively. Bacteria (mainly Proteobacteria, Acidobacteria, Actinobacteria) strongly dominated the microbial diversity (99% sequences), with a negligible proportion of archaea (0.3–0.5%). There was a systematic evolution of main taxa according to depth, with a maximum of 65% (Acidobacteria) encountered in the active layer, or permafrost boundary (50–60 cm). We also measured C, N, nutrients and ~50 major and trace elements in peat (19 samples) as well as its pore water and dispersed ice (10 samples), sampled over the same core, and we analyzed organic matter quality in six organic and one mineral horizon of this core. Using multiparametric statistics (PCA), we tested the links between the total microbial number and 16S rRNA diversity and chemical composition of both the solid and fluid phase harboring the microorganisms. Under climate warming and permafrost thaw, one can expect a downward movement of the layer of maximal genetic diversity following the active layer thickening. Given a one to two orders of magnitude higher microbial number in the upper (thawed) layers compared to bottom (frozen) layers, an additional 50 cm of peat thawing in western Siberia may sizably increase the total microbial population and biodiversity of active cells.

Snowpack exhibits properties that make it a unique natural archive of airborne pollution. The data on insoluble particles in the Ob River catchment (Western Siberia) snowpack are limited. Insoluble particles in the snowpack of Western Siberia were studied at 36 sites on a 2800 km submeridional profile from the city of Barnaul to Salekhard in February 2020. Snow samples were collected over the full depth of the snow core, from the surface of the snow cover to the boundary with soil, except for the lower 1–2 cm. After the filtration of melted snow through a 0.45-µm membrane, the particle composition was studied using a scanning electron microscope with an energy microprobe. In the background areas, the concentration of insoluble particles in the snow was below 2 mg/L. Significantly higher particle concentrations were encountered near cities and hydrocarbon production areas. Particulate matter in snow mainly consists of biogenic and lithogenic particles mixed with anthropogenic particles (ash and black carbon aggregates). The proportion of anthropogenic particles increases near cities and areas of active hydrocarbon production.

Ocean acidification (OA) is one of the most significant threats to marine life, and is predicted to drive important changes in marine communities. Although OA impacts will be the sum of direct effects mediated by alterations of physiological rates and indirect effects mediated by shifts in species interactions and biogenic habitat provision, direct and indirect effects are rarely considered together for any given species. Here, we assess the potential direct and indirect effects of OA on a ubiquitous group of crustaceans: caprellid amphipods (Caprella laeviuscula and Caprella mutica). Direct physiological effects were assessed by measuring caprellid heart rate in response to acidification in the laboratory. Indirect effects were explored by quantifying caprellid habitat dependence on the hydroid Obelia dichotoma, which has been shown to be less abundant under experimental acidification. We found that OA resulted in elevated caprellid heart rates, suggestive of increased metabolic demand. We also found a strong, positive association between caprellid population size and the availability of OA-vulnerable O. dichotoma, suggesting that future losses of biogenic habitat may be an important indirect effect of OA on caprellids. For species such as caprellid amphipods, which have strong associations with biogenic habitat, a consideration of only direct or indirect effects could potentially misestimate the full impact of ocean acidification.