PF3_94d_Aerobic_H2OExt_run3_19Apr16_leopard_Infuse_1_01_73661
FTICR dataset of Alaska permafrost soil extractions
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FTICR dataset of Alaska permafrost soil extractions
FTICR dataset of Alaska permafrost soil extractions
FTICR dataset of Alaska permafrost soil extractions
Marinobacter spp. are cosmopolitan in saline environments, displaying a diverse set of metabolisms that allow them to competitively occupy these environments, some of which can be extreme in both salinity and temperature. Here, we introduce a distinct cluster of Marinobacter genomes, composed of novel isolates and in silico assembled genomes obtained from subzero, hypersaline cryopeg brines, relic seawater-derived liquid habitats within permafrost sampled near Utqiaġvik, Alaska. Using these new genomes and 45 representative publicly available genomes of Marinobacter spp. from other settings, we assembled a pangenome to examine how the new extremophile members fit evolutionarily and ecologically, based on genetic potential and environmental source. This first genus-wide genomic analysis revealed that Marinobacter spp. in general encode metabolic pathways that are thermodynamically favored at low temperature, cover a broad range of organic compounds, and optimize protein usage, e.g., the Entner–Doudoroff pathway, the glyoxylate shunt, and amino acid metabolism. The new isolates contributed to a distinct clade of subzero brine-dwelling Marinobacter spp. that diverged genotypically and phylogenetically from all other Marinobacter members. The subzero brine clade displays genomic characteristics that may explain competitive adaptations to the extreme environments they inhabit, including more abundant membrane transport systems (e.g., for organic substrates, compatible solutes, and ions) and stress-induced transcriptional regulatory mechanisms (e.g., for cold and salt stress) than in the other Marinobacter clades. We also identified more abundant signatures of potential horizontal transfer of genes involved in transcription, the mobilome, and a variety of metabolite exchange systems, which led to considering the importance of this evolutionary mechanism in an extreme environment where adaptation via vertical evolution is physiologically rate limited. Assessing these new extremophile genomes in a pangenomic context has provided a unique view into the ecological and evolutionary history of the genus Marinobacter , particularly with regard to its remarkable diversity and its opportunism in extremely cold and saline environments.
The order Thermoanaerobacterales currently consists of fermentative anaerobic bacteria, including the genus Caldicellulosiruptor. Caldicellulosiruptor are represented by thirteen species; all, but one, have closed genome sequences. Interest in these extreme thermophiles has been motivated not only by their high optimal growth temperatures (≥70°C), but also by their ability to hydrolyze polysaccharides including, for some species, both xylan and microcrystalline cellulose. Caldicellulosiruptor species have been isolated from geographically diverse thermal terrestrial environments located in New Zealand, China, Russia, Iceland and North America. Evidence of their presence in other terrestrial locations is apparent from metagenomic signatures, including volcanic ash in permafrost. Here, phylogeny and taxonomy of the genus Caldicellulosiruptor was re-examined in light of new genome sequences. Based on genome analysis of 15 strains, a new order, Caldicellulosiruptorales, is proposed containing the family Caldicellulosiruptoraceae, consisting of two genera, Caldicellulosiruptor and Anaerocellum. Furthermore, the order Thermoanaerobacterales also was re-assessed, using 91 genome-sequenced strains, and should now include the family Thermoanaerobacteraceae containing the genera Thermoanaerobacter, Thermoanaerobacterium, Caldanaerobacter, the family Caldanaerobiaceae containing the genus Caldanaerobius, and the family Calorimonaceae containing the genus Calorimonas. A main outcome of ANI/AAI analysis indicates the need to reclassify several previously designated species in the Thermoanaerobacterales and Caldicellulosiruptorales by condensing them into strains of single species. Comparative genomics of carbohydrate-active enzyme inventories suggested differentiating phenotypic features, even among strains of the same species, reflecting available nutrients and ecological roles in their native biotopes.
Rivers of the Arctic will become ever more important for the global climate, since they carry a majority of continental dissolved organic carbon flux into the rapidly changing polar ocean. Aqueous organics comprise a wide array of functional groups, several of which are likely to impact coastal and open water biophysical properties. Light attenuation, interfacial films, aerosol formation, gas release and momentum exchange can all be cited. We performed Lagrangian kinetic modeling for the evolution of riverine organic chemistry as the molecules in question make their way from the highlands to Arctic outlets. Classes as diverse as the proteins, sugars, lipids, re-condensates, humics, bio-tracers and small volatiles are all included. Our reduced framework constitutes an idealized northward flow driving a major hydrological discharge rate and primarily representing the Russian Lena. Mountainous, high solute and tundra sources are all simulated, and they meet up at several points between soil and delta process reactors. Turnover rates are parameterized beginning with extrapolated coastal values imposed along a limited tributary network, with connections between different terrestrial sub-ecologies. Temporal variation of our total dissolved matter most closely resembles the observations when we focus on the restricted removal and low initial carbon loads, suggesting relatively slow transformation along the water course. Thus, channel combinations and mixing must play a dominant role. Nevertheless, microbial and photochemical losses help determine the final concentrations for most species. Chemical evolution is distinct for the various functionalities, with special contributions from pre- and post-reactivity in soil and delta waters. Several functions are combined linearly to represent the collective chromophoric dissolved matter, characterized here by its absorption. Tributaries carry the signature of lignin phenols to segregate tundra versus taiga sources, and special attention is paid to the early then marine behaviors of low molecular weight volatiles. Heteropolycondensates comprise the largest percentage of reactive carbon in our simulations due to recombination/accumulation, and they tend to be preeminent at the mouth. Outlet concentrations of individual structures such as amino acids and absorbers lie above threshold values for biophysical influence, on the monolayer and light attenuation. The extent of coastal spreading is examined through targeted regional box modeling, relying on salinity and color for calibration. In some cases, plumes reach the scale of peripheral arctic seas, and amplification is expected during upcoming decades. Conclusions are mapped from the Lena to other boreal discharges, and future research questions are outlined regarding the bonding type versus mass release as permafrost degrades. Dynamic aqueous organic coupling is recommended for polar system models, from headwaters to coastal diluent.
One of the most studied permafrost-associated gas hydrate accumulations in Arctic Alaska is the Eileen Gas Hydrate Trend. This study provides a detailed re-examination of the Eileen Gas Hydrate Trend with a focus on the gas hydrate accumulation in the western part of the Prudhoe Bay Unit. This integrated analysis of downhole well log data and published geophysical data has provided new insight on structural, stratigraphic, and reservoir controls on the occurrence of gas hydrates in the Eileen Gas Hydrate Trend. This study revealed the relatively complex nature of the gas hydrate occurrences in the Eileen Gas Hydrate Trend, with gas hydrates present in a series of coarsening upward, laterally pervasive, mostly fine-grained sand beds exhibiting high gas hydrate saturations. Most of the gas hydrate-bearing reservoirs in the Eileen Gas Hydrate Trend are laterally segmented into distinct northwest- to southeast-trending fault blocks, occur in a combination of structural–stratigraphic traps, and are only partially hydrate filled with distinct down-dip water contacts. These findings suggest that the traditional parts of a petroleum system (i.e., reservoir, gas source, gas migration, and geologic timing of the system formation) also control the occurrence of gas hydrates in the Eileen Gas Hydrate Trend.
Land-atmosphere carbon exchange is known to be extremely heterogeneous in arctic ice-wedge polygonal tundra regions. In this study, a Kalman filter-based method was developed to estimate the spatio-temporal dynamics of daytime average net ecosystem exchange (NEEday) at 0.5-m resolution over a 550 m by 700 m study site. We integrated multi-scale, multi-type datasets, including normalized difference vegetation indices (NDVIs) obtained from a novel automated mobile sensor system (or tram system) and a greenness index map obtained from airborne imagery. We took advantage of the significant correlations between NDVI and NEEday identified based on flux chamber measurements. The weighted average of the estimated NEEday within the flux-tower footprint agreed with the flux tower data in term of its seasonal dynamics. We then evaluated the spatial variability of the growing season average NEEday, as a function of polygon geomorphic classes; i.e., the combination of polygon types—which are known to present different degradation stages associated with permafrost thaw—and microtopographic features (i.e., troughs, centers and rims). Our study suggests the importance of considering microtopographic features and their spatial coverage in computing spatially aggregated carbon exchange.
Methane (CH 4 ) is a powerful greenhouse gas that is produced by a diverse set of natural and anthropogenic emission sources. Biogenic methane sources generally involve anaerobic decay processes such as those occurring in wetlands, melting permafrost, or the digestion of organic matter in the guts of ruminant animals. Thermogenic CH 4 sources originate from the breakdown of organic material at high temperatures and pressure within the Earth's crust, a process which also produces more complex trace hydrocarbons such as ethane (C 2 H 6 ). Here, we present the development and deployment of an uncrewed aerial system (UAS) that employs a fast (1 Hz) and sensitive (1–0.5 ppb s -1 ) CH 4 and C 2 H 6 sensor and ultrasonic anemometer. The UAS platform is a vertical-takeoff, hexarotor drone (DJI Matrice 600 Pro, M600P) capable of vertical profiling to 120 m altitude and plume sampling across scales up to 1 km. Simultaneous measurements of CH 4 and C 2 H 6 concentrations, vector winds, and positional data allow for source classification (biogenic versus thermogenic), differentiation, and emission rates without the need for modeling or a priori assumptions about winds, vertical mixing, or other environmental conditions. The system has been used for direct quantification of methane point sources, such as orphan wells, and distributed emitters, such as landfills and wastewater treatment facilities. With detectable source rates as low as 0.04 and up to ~1500 kg h -1 , this UAS offers a direct and repeatable method of horizontal and vertical profiling of emission plumes at scales that are complementary to regional aerial surveys and localized ground-based monitoring.
Abstract. Large changes in the Arctic carbon balance are expected as warming linked to climate change threatens to destabilize ancient permafrost carbon stocks. The eddy covariance (EC) method is an established technique to quantify net losses and gains of carbon between the biosphere and atmosphere at high spatiotemporal resolution. Over the past decades, a growing network of terrestrial EC tower sites has been established across the Arctic, but a comprehensive assessment of the network's representativeness within the heterogeneous Arctic region is still lacking. This creates additional uncertainties when integrating flux data across sites, for example when upscaling fluxes to constrain pan-Arctic carbon budgets and changes therein. This study provides an inventory of Arctic (here > = 60∘ N) EC sites, which has also been made available online (https://cosima.nceas.ucsb.edu/carbon-flux-sites/, last access: 25 January 2022). Our database currently comprises 120 EC sites, but only 83 are listed as active, and just 25 of these active sites remain operational throughout the winter. To map the representativeness of this EC network, we evaluated the similarity between environmental conditions observed at the tower locations and those within the larger Arctic study domain based on 18 bioclimatic and edaphic variables. This allows us to assess a general level of similarity between ecosystem conditions within the domain, while not necessarily reflecting changes in greenhouse gas flux rates directly. We define two metrics based on this representativeness score: one that measures whether a location is represented by an EC tower with similar characteristics (ER1) and a second for which we assess if a minimum level of representation for statistically rigorous extrapolation is met (ER4). We find that while half of the domain is represented by at least one tower, only a third has enough towers in similar locations to allow reliable extrapolation. When we consider methane measurements or year-round (including wintertime) measurements, the values drop to about 1/5 and 1/10 of the domain, respectively. With the majority of sites located in Fennoscandia and Alaska, these regions were assigned the highest level of network representativeness, while large parts of Siberia and patches of Canada were classified as underrepresented. Across the Arctic, mountainous regions were particularly poorly represented by the current EC observation network. We tested three different strategies to identify new site locations or upgrades of existing sites that optimally enhance the representativeness of the current EC network. While 15 new sites can improve the representativeness of the pan-Arctic network by 20 %, upgrading as few as 10 existing sites to capture methane fluxes or remain active during wintertime can improve their respective ER1 network coverage by 28 % to 33 %. This targeted network improvement could be shown to be clearly superior to an unguided selection of new sites, therefore leading to substantial improvements in network coverage based on relatively small investments.
The continued warming of the Arctic could release vast stores of carbon into the atmosphere from high-latitude ecosystems, especially from thawing permafrost. Increasing uptake of carbon dioxide (CO 2 ) by vegetation during longer growing seasons may partially offset such release of carbon. However, evidence of significant net annual release of carbon from site-level observations and model simulations across tundra ecosystems has been inconclusive. To address this knowledge gap, we combined top-down observations of atmospheric CO 2 concentration enhancements from aircraft and a tall tower, which integrate ecosystem exchange over large regions, with bottom-up observed CO 2 fluxes from tundra environments and found that the Alaska North Slope is not a consistent net source nor net sink of CO 2 to the atmosphere (ranging from ₋6 to +6 Tg C yr -1 for 2012–2017). Our analysis suggests that significant biogenic CO 2 fluxes from unfrozen terrestrial soils, and likely inland waters, during the early cold season (September–December) are major factors in determining the net annual carbon balance of the North Slope, implying strong sensitivity to the rapidly warming freeze-up period. At the regional level, we find no evidence of the previously reported large late-cold-season (January–April) CO 2 emissions to the atmosphere during the study period. Despite the importance of the cold-season CO 2 emissions to the annual total, the interannual variability in the net CO 2 flux is driven by the variability in growing season fluxes. During the growing season, the regional net CO 2 flux is also highly sensitive to the distribution of tundra vegetation types throughout the North Slope. This study shows that quantification and characterization of year-round CO 2 fluxes from the heterogeneous terrestrial and aquatic ecosystems in the Arctic using both site-level and atmospheric observations are important to accurately project the Earth system response to future warming.
Methane (CH 4 ) emissions from the boreal and arctic region are globally significant and highly sensitive to climate change. There is currently a wide range in estimates of high-latitude annual CH 4 fluxes, where estimates based on land cover inventories and empirical CH 4 flux data or process models (bottom-up approaches) generally are greater than atmospheric inversions (top-down approaches). A limitation of bottom-up approaches has been the lack of harmonization between inventories of site-level CH 4 flux data and the land cover classes present in high-latitude spatial datasets. Here we present a comprehensive dataset of small-scale, surface CH 4 flux data from 540 terrestrial sites (wetland and non-wetland) and 1247 aquatic sites (lakes and ponds), compiled from 189 studies. The Boreal–Arctic Wetland and Lake Methane Dataset (BAWLD-CH 4 ) was constructed in parallel with a compatible land cover dataset, sharing the same land cover classes to enable refined bottom-up assessments. BAWLD-CH 4 includes information on site-level CH 4 fluxes but also on study design (measurement method, timing, and frequency) and site characteristics (vegetation, climate, hydrology, soil, and sediment types, permafrost conditions, lake size and depth, and our determination of land cover class). The different land cover classes had distinct CH 4 fluxes, resulting from definitions that were either based on or co-varied with key environmental controls. Fluxes of CH 4 from terrestrial ecosystems were primarily influenced by water table position, soil temperature, and vegetation composition, while CH 4 fluxes from aquatic ecosystems were primarily influenced by water temperature, lake size, and lake genesis. Models could explain more of the between-site variability in CH 4 fluxes for terrestrial than aquatic ecosystems, likely due to both less precise assessments of lake CH 4 fluxes and fewer consistently reported lake site characteristics. Analysis of BAWLD-CH 4 identified both land cover classes and regions within the boreal and arctic domain, where future studies should be focused, alongside methodological approaches. Overall, BAWLD-CH 4 provides a comprehensive dataset of CH 4 emissions from high-latitude ecosystems that are useful for identifying research opportunities, for comparison against new field data, and model parameterization or validation.
Abstract. Hector is an open-source reduced-complexity climate–carbon cycle model that models critical Earth system processes on a global and annual basis. Here, we present an updated version of the model, Hector V3.2.0 (hereafter Hector V3), and document its new features, implementation of new science, and performance. Significant new features include permafrost thaw, a reworked energy balance submodel, and updated parameterizations throughout. Hector V3 results are in good general agreement with historical observations of atmospheric CO2 concentrations and global mean surface temperature, and the future temperature projections from Hector V3 are consistent with more complex Earth system model output data from the sixth phase of the Coupled Model Intercomparison Project. We show that Hector V3 is a flexible, performant, robust, and fully open-source simulator of global climate changes. We also note its limitations and discuss future areas for improvement and research with respect to the model's scientific, stakeholder, and educational priorities.
Abstract. A significant portion of the Arctic coastal plain is classified as polygonal tundra and plays a vital role in soil carbon cycling. Recent research suggests that lateral transport of dissolved carbon could exceed vertical carbon releases to the atmosphere. However, the details of lateral subsurface flow in polygonal tundra have not been well studied. We incorporated a subsurface transport process into an existing state-of-the-art hydrothermal model. The model captures the physical effects of freeze–thaw cycles on lateral flow in polygonal tundra. The new modeling capability enables non-reactive tracer movement within subsurface. We utilized this new capability to investigate the impact of freeze–thaw cycles on lateral flow in the polygonal tundra. Our study indicates the important role of freeze–thaw cycles and the freeze-up effect in lateral tracer transport, suggesting that dissolved species could be transported from the middle of the polygon to the sides within a couple of thaw seasons. Introducing lateral carbon transport into the climate models could substantially reduce the uncertainty associated with the impact of thawing permafrost.
Abstract. Temporally continuous snow depth estimates are vital for understanding changing snow patterns and impacts on permafrost in the Arctic. We trained a random forest machine learning model to predict snow depth from variability in snow–ground interface temperature. The model performed well on Alaska's Seward Peninsula where it was trained and at Arctic evaluation sites (RMSE ≤ 0.15 m). It performed poorly at temperate sites with deeper snowpacks, partially due to training data limitations. Small temperature sensors are cheap and easy to deploy, so this technique enables spatially distributed and temporally continuous snowpack monitoring at high latitudes to an extent previously infeasible.
Abstract. In ice-rich polygonal tundra, spatiotemporal heterogeneity in ground-ice melt reshapes topography, impacting infrastructure, water and carbon cycles. This study evaluates changes in topography and subsurface structure at a coastal Arctic site by comparing data from two surveys conducted a decade apart. Each survey includes electrical resistivity tomography, active layer thickness, photogrammetry, and topographic data. Results reveal subsidence and decrease in permafrost table elevation with varying intensity and spatial distribution across polygons, alongside diverse thermal-hydrological responses, such as thermokarst pool formation in high-centered-polygons and more even subsidence in flat-centered-polygons. The study also underscores the value and limitations of sporadic surveys.
This dataset represents spatially intensive thaw depth surveys with individual point measurements spaced ~0.5 m apart. The three ~10x10m grids cover an ice wedge and a portion of its two neighboring polygons. The data contain thaw depth, frost table elevation, ground surface elevation, active layer depth and surface water inundation across three seasons (2012, 2013 and 2014) at Utqiagvik (Barrow) NGEE Areas B, C and D. There are a total of 69 extracted files separated by month, year, and area. The data were originally provided in excel workbooks, these files have been preserved within the zip "Original_Files." The files were transformed for archiving with images pulled out into JPEGs, data preserved as CSV files and some methodological information preserved as TXT files. Some functions, features, and formatting were lost during the transformation. Missing data were defined with blank cells. Additional documentation can be found in files labelled with "information.txt" file endings.The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was a research effort to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy's Office of Biological and Environmental Research.The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska.Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy's Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).[2024-07-15] Renamed BEO_Thaw_Depth_Frost_Table_Area_*_*_*.csv, BEO_Thaw_Depth_Frost_Table_Area_*_*_*_Plot_1.JPEG, and BEO_Thaw_Depth_Frost_Table_Area_*_*_*_Plot_2.JPEG names that had E or L to be Early or Late. Renamed BEO_Thaw_Depth_Frost_Table_Area_*_*_*_Plot_1.JPEG, BEO_Thaw_Depth_Frost_Table_Area_*_*_*_Plot_2.JPEG, and BEO_Thaw_Depth_Frost_Table_Area_*_information_Plot_1.JPEG to BEO_Thaw_Depth_Frost_Table_Area_*_*_*_Gridpoints.JPEG, BEO_Thaw_Depth_Frost_Table_Area_*_*_*_3Dgraphic.JPEG, and BEO_Thaw_Depth_Frost_Table_Area_*_information_LiDAR_DEM.JPEG, respectively. Updated BEO_Thaw_Depth_Frost_Table_flmd.csv file to reflect above updates.
This dataset consists of field measurements of CO2 and CH4 flux, as well as soil properties made during 2013 in Areas A-D of Intensive Site 1 at the Next-Generation Ecosystem Experiments (NGEE) Arctic site near Barrow, Alaska. Included are i) measurements of CO2 and CH4 flux made from June to September (ii) Calculation of corresponding Gross Primary Productivity (GPP) and CH4 exchange (transparent minus opaque) between atmosphere and the ecosystem (ii) Measurements of Los Gatos Research (LGR) chamber air temperature made from June to September (ii) measurements of surface layer depth, type of surface layer, soil temperature and soil moisture from June to September. This data package contains two *.csv files and one *.pdf file. NGEE Arctic Project Summary: The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was a research effort to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy's Office of Biological and Environmental Research. The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska. Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy's Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).