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Microbial ecology of permafrost soils: Populations, processes, and perspectives

Permafrost microbial research has flourished in the past decades, due in part to improvements in sampling and molecular techniques, but also the increased focus on the permafrost greenhouse gas feedback to climate change and other ecological processes in high latitude and alpine permafrost soils. Permafrost microorganisms are adapted to these extreme environments and remain active at low temperatures and when resources are limited. They are also an important component of global elemental cycles as they regulate organic matter turnover and greenhouse gas production, particularly as permafrost thaws. Here we review the permafrost microbiology literature coupled with an exploration of its historical aspects, with a particular focus on a new understanding advanced by molecular biology techniques. We further identify knowledge gaps and ways forward to improve our understanding of microbial contributions to ecosystem biogeochemistry of permafrost-affected systems.

Permafrost and Periglacial Processes

Thermo-hydrologic processes governing supra-permafrost talik dynamics in discontinuous permafrost near Umiujaq (Québec, Canada)

Widespread supra-permafrost talik formation is currently recognized as a critical mechanism that could accelerate permafrost thaw in the Arctic (e.g., Connon et al. 2018; Farquharson et al. 2022). However, the trajectory of permafrost dynamics following talik formation may prove difficult to predict. Physically-based cryohydrogeologic models provide a powerful tool for understanding processes and factors controlling talik dynamics and, ultimately, how permafrost will respond to climate change. Such models are typically used to represent multiple non-linear processes relevant for groundwater systems in cold regions, such as coupled heat and groundwater movement, including freeze-thaw dynamics and the effects on the surface energy balance and the subsurface thermal and hydraulic properties (Lamontagne-Hallé et al. 2020). Though cryohydrogeologic modeling advances have been made in simulating talik dynamics, few applications have been tested against robust long-term hydrometeorological and subsurface observations.

Quebec

A review of abrupt permafrost thaw: Definitions, usage, and a proposed conceptual framework

Purpose of Review We review how ‘abrupt thaw’ has been used in published studies, compare these definitions to abrupt processes in other Earth science disciplines, and provide a definitive framework for how abrupt thaw should be used in the context of permafrost science. Recent Findings We address several aspects of permafrost systems necessary for abrupt thaw to occur and propose a framework for classifying permafrost processes as abrupt thaw in the future. Based on a literature review and our collective expertise, we propose that abrupt thaw refers to thaw processes that lead to a substantial persistent environmental change within a few decades. Abrupt thaw typically occurs in ice-rich permafrost but may be initiated in ice-poor permafrost by external factors such as hydrologic change (i.e., increased streamflow, soil moisture fluctuations, altered groundwater recharge) or wildfire. Summary Permafrost thaw alters greenhouse gas emissions, soil and vegetation properties, and hydrologic flow, threatening infrastructure and the cultures and livelihoods of northern communities. The term ‘abrupt thaw’ has emerged in scientific discourse over the past two decades to differentiate processes that rapidly impact large depths of permafrost, such as thermokarst, from more gradual, top-down thaw processes that impact centimeters of near-surface permafrost over years to decades. However, there has been no formal definition for abrupt thaw and its use in the scientific literature has varied considerably. Our standardized definition of abrupt thaw offers a path forward to better understand drivers and patterns of abrupt thaw and its consequences for global greenhouse gas budgets, impacts to infrastructure and land-use, and Arctic policy- and decision-making.

Current Climate Change Reports

Metal mobilization from thawing permafrost to aquatic ecosystems is driving rusting of Arctic streams

Climate change in the Arctic is altering watershed hydrologic processes and biogeochemistry. Here, we present an emergent threat to Arctic watersheds based on observations from 75 streams in Alaska’s Brooks Range that recently turned orange, reflecting increased loading of iron and toxic metals. Using remote sensing, we constrain the timing of stream discoloration to the last 10 years, a period of rapid warming and snowfall, suggesting impairment is likely due to permafrost thaw. Thawing permafrost can foster chemical weathering of minerals, microbial reduction of soil iron, and groundwater transport of metals to streams. Compared to clear reference streams, orange streams have lower pH, higher turbidity, and higher sulfate, iron, and trace metal concentrations, supporting sulfide mineral weathering as a primary mobilization process. Stream discoloration was associated with dramatic declines in macroinvertebrate diversity and fish abundance. These findings have considerable implications for drinking water supplies and subsistence fisheries in rural Alaska.

Alaska

Arctic speleothems reveal nearly permafrost-free Northern Hemisphere in the Late Miocene

Arctic warming is happening at nearly four times the global average rate. Long-term trends of permafrost dynamics cannot be estimated directly from monitoring of present-day thaw processes, requiring paleoclimate-proxy information. Here we use cave carbonates (speleothems) from a northern Siberian cave to determine when the Northern Hemisphere was mostly permafrost-free. At present, thick continuous permafrost in this region prevents speleothem growth. In a series of partially eroded caves, speleothems grew during the late Tortonian stage (8.68 ± 0.09 Ma), a time when the geographic position of this site was already similar to today. Paleotemperatures reconstructed from speleothems show that mean annual air temperatures (MAAT) in the region were + 6.6°C to + 11.1°C, when contemporary global MAAT were ~ 4.5 °C higher than modern. Our findings provide direct evidence that warming to Tortonian-like temperatures would leave most of the Northern Hemisphere permafrost-free. This may release up to ~ 130 petagrams of carbon, enhancing further warming.

Siberia

Linking permafrost to the abundance, biomass, and energy density of fish in Arctic headwater streams

Permafrost thaw alters groundwater flow, river hydrology, stream-catchment interactions, and the availability of carbon and nutrients in headwater streams. The impact of permafrost on watershed hydrology and biogeochemistry of headwater streams has been demonstrated, but there is little understanding of how permafrost influences fish in these ecosystems. We examined relations among permafrost characteristics, the resulting changes in water temperature, stream hydrology (e.g., discharge flashiness), and macroinvertebrates, with the abundance, biomass, and energy density of juvenile Dolly Varden ( Salvelinus malma ) and Arctic Grayling ( Thymallus arcticus ) across 10 headwater streams in northwestern Alaska. Macroinvertebrate density was driven by concentrations of dissolved carbon and nutrients supporting stream food webs. Dolly Varden abundance was primarily related to water temperature with fewer fish in warmer streams, whereas Dolly Varden energy density decreased with the flashiness of the headwater streams. Dolly Varden biomass was related to both temperature and bottom-up food web effects. The energy density of Arctic Grayling decreased with warmer temperatures and discharge flashiness. These relations demonstrate the importance of terrestrial–aquatic connections in permafrost landscapes and indicate the complexity of landscape effects on fish. Because permafrost thaw is one of the most impactful changes occurring as the Arctic warms, an improved understanding of how stream temperature, hydrology, and bottom-up food web processes influence fish populations can aid forecasting of future conditions across the Arctic.

Alaska

Permafrost–wildfire interactions: active layer thickness estimates for paired burned and unburned sites in northern high latitudes

As the northern high-latitude permafrost zone experiences accelerated warming, permafrost has become vulnerable to widespread thaw. Simultaneously, wildfire activity across northern boreal forest and Arctic/subarctic tundra regions impacts permafrost stability through the combustion of insulating organic matter, vegetation, and post-fire changes in albedo. Efforts to synthesis the impacts of wildfire on permafrost are limited and are typically reliant on antecedent pre-fire conditions. To address this, we created the FireALT dataset by soliciting data contributions that included thaw depth measurements, site conditions, and fire event details with paired measurements at environmentally comparable burned and unburned sites. The solicitation resulted in 52 466 thaw depth measurements from 18 contributors across North America and Russia. Because thaw depths were taken at various times throughout the thawing season, we also estimated end-of-season active layer thickness (ALT) for each measurement using a modified version of the Stefan equation. Here, we describe our methods for collecting and quality-checking the data, estimating ALT, the data structure, strengths and limitations, and future research opportunities. The final dataset includes 48 669 ALT estimates with 32 attributes across 9446 plots and 157 burned–unburned pairs spanning Canada, Russia, and the United States. The data span fire events from 1900 to 2022 with measurements collected from 2001 to 2023. The time since fire ranges from 0 to 114 years. The FireALT dataset addresses a key challenge: the ability to assess impacts of wildfire on ALT when measurements are taken at various times throughout the thaw season depending on the time of field campaigns (typically June through August) by estimating ALT at the end-of-season maximum. This dataset can be used to address understudied research areas, particularly algorithm development, calibration, and validation for evolving process-based models as well as extrapolating across space and time, which could elucidate permafrost–wildfire interactions under accelerated warming across the high-northern-latitude permafrost zone. The FireALT dataset is available through the Arctic Data Center ( https://doi.org/10.18739/A2RN3092P , Talucci et al., 2024).

Arctic

Cooling perspectives on the risk of pathogenic viruses from thawing permafrost

Climate change is inducing wide-scale permafrost thaw in the Arctic and subarctic, triggering concerns that long-dormant pathogens could reemerge from the thawing ground and initiate epidemics or pandemics. Viruses, as opposed to bacterial pathogens, garner particular interest because outbreaks cannot be controlled with antibiotics, though the effects can be mitigated by vaccines and newer antiviral drugs. To evaluate the potential hazards posed by viral pathogens emerging from thawing permafrost, we review information from a diverse range of disciplines. This includes efforts to recover infectious virus from human remains, studies on disease occurrence in polar animal populations, investigations into viral persistence and infectivity in permafrost, and assessments of human exposure to the enormous viral diversity present in the environment. Based on currently available knowledge, we conclude that the risk posed by viruses from thawing permafrost is no greater than viruses in other environments such as temperate soils and aquatic systems.

mSystems

Permafrost thaw controls iron flux from wetlands and sulfide-bearing rocks to Arctic rivers and streams

Recent warming has caused widespread iron mobilization into Arctic waterbodies that degrades ecosystems and threatens natural resources. Yet, understanding where and when iron flux occurs remains limited. Here, we investigate iron loading across regional to local scales in Arctic Alaska using climate, water chemistry, and borehole data together with mapped geology and permafrost presence. We show that both anoxic microbial iron reduction and acid rock drainage from iron-sulfide oxidation mobilize iron. Iron influx is strongly associated with lowland wetlands, sulfide-rich upland bedrock, and near-surface permafrost. Acid rock drainage chemistry correlates very strongly with the depth of seasonal thaw above permafrost from the previous year, indicating a one-year lag. These findings clarify the spatial and temporal dynamics of Arctic river rusting, provide a mechanistic understanding of the phenomenon, and may allow anticipation of its occurrence and assessment of its implications for aquatic ecosystem health and subsistence resources under ongoing climate change.

Alaska

The dominance and growth of shallow groundwater resources in continuous permafrost environments

Water is a limited resource in Arctic watersheds with continuous permafrost because freezing conditions in winter and the impermeability of permafrost limit storage and connectivity between surface water and deep groundwater. However, groundwater can still be an important source of surface water in such settings, feeding springs and large aufeis fields that are abundant in cold regions and generating runoff when precipitation is rare. Whether groundwater is sourced from suprapermafrost taliks or deeper regional aquifers will impact water availability as the Arctic continues to warm and thaw. Previous research is ambiguous about the role of deep groundwater, leading to uncertainty regarding Arctic water availability and changing water resources. We analyzed chemistry and residence times of spring, stream, and river waters in the continuous permafrost zone of Alaska, spanning the mountains to the coastal plain. Water chemistry and age tracers show that surface waters are predominately sourced from recent precipitation and have short (<50 y) subsurface residence times. Remote sensing indicates trends in the areal extent of aufeis over the last 37 y, and correlations between aufeis extent and previous year summer temperature. Together, these data indicate that surface waters in continuous permafrost regions may be impacted by short flow paths and shallow suprapermafrost aquifers that are highly sensitive to climatic and hydrologic change over annual timescales. Despite the lack of connection to regional aquifers, continued warming and permafrost thaw may promote deepening of the shallow subsurface aquifers and creation of shallow taliks, providing some resilience to Arctic freshwater ecosystems.

Proceedings of the National Academy of Sciences

A history of cryohydrogeology modeling and recent advancements through the integration of solute transport

Groundwater flow systems and permafrost are interrelated because permafrost thaw enhances permeability, while groundwater flow can advect heat and accelerate permafrost thaw (McKenzie et al. 2021). Given amplified climate change in cold regions, there is renewed interest in ‘cryohydrogeology’, the study of groundwater in cold regions. Many data-driven studies have shown that permafrost thaw is leading to activated aquifers and increased baseflow across the pan-Arctic region (e.g. Walvoord and Striegl 2007, Evans et al. 2020). Empirical evidence of a subsurface ‘replumbing’ (Walvoord and Kurylyk 2016) in permafrost regions raises questions about the fate of sequestered contaminants in the North (Langer et al. 2023). We will discuss the history of and emerging opportunities in cryohydrogeological modeling, with a focus on recent contaminant transport modeling.

Conference Paper

Quantifying methane emissions from a rich fen with uncrewed aircraft systems in boreal Alaska

Thawing of permafrost in northern latitudes is accelerating, potentially releasing substantial amounts of methane (CH 4 ) as forested permafrost plateaus transition into wetlands. This ecosystem shift alters the carbon exchange between the soil and atmosphere, influencing the permafrost-carbon feedback. Monitoring these changes may require measurement platforms operating across varied spatial and temporal scales. Recent advancements in small uncrewed aircraft systems (sUAS) enable high resolution CH 4 flux quantification in remote, complex terrains; however, comparisons with established methods such as eddy covariance flux towers remain limited. We used a hexacopter sUAS to quantify CH 4 emissions from the Alaska Peatland Experiment, a wetland within the Bonanza Creek Experimental Forest. Using an ensemble of methods to define the background CH 4 concentration, along with near surface emissions from soil chambers, helped constrain our flux estimates. The sUAS method yielded an average flux of 0.0077 ± 0.0019 mol s −1 CH 4 , within a factor of two concurrent tower-derived total source flux estimates (0.0036 ± 0.00042 mol s −1 CH 4 ). To assess spatial drivers of observed fluxes, we conducted a 2D footprint analysis and overlaid the results with high-resolution hyperspectral land cover classification, quantifying vegetative contributions within each footprint. This revealed higher fen representation in sUAS measurements (73.8%) than in tower footprints (58.8%), and lower tussock meadow representation (15.6% and 30.3%, respectively). These differences were consistent with known variation in vegetation-specific CH 4 emissions. Our results highlight that combining footprint modeling with land cover characterization can enhance interpretations of CH 4 fluxes and guide cross-platform comparisons.

JGR Atmospheres

Perspectives on transportable array Alaska background noise levels

Background seismic noise fundamentally sets a lower bound on our ability to record signals arising from earthquakes. The background noise spectrum at a station is a combination of cultural noise, ocean-generated microseism noise, intrinsic instrument self-noise, and the sensitivity of the instrument to nonseismic noise sources. The USArray-Transportable Array Alaska deployed 195 stations across Alaska and parts of Canada (Yukon, British Columbia, and Northwest Territories). These stations were all installed using similar techniques and made use of instruments with similar self-noise levels. As such, this network provides an opportunity to look at how geographic location influences seismic background. Using these broadband stations, we report background noise levels from 0.2 to 75 s period in six discrete bands. By constructing “noise maps,” we depict both spatial and temporal changes in the background noise field. Using these maps, combined with targeted analysis, we infer sources and contributing factors to noise levels in these different period bands. These include cultural noise, the formation of sea ice, seasonal changes in permafrost and wave activity in the Gulf of Alaska, and magnetic field variability. We use this study as an opportunity to review several previous studies examining seismic noise in Arctic regions.

Book chapter

Continental-scale prediction of hydrologic signatures and processes

Understanding how dominant hydrologic processes and their drivers vary across diverse continental-scale landscapes is critical for hydrologic modeling and water management applications. Our research addresses this question by synthesizing large-sample watershed datasets, Caravan and GAGES-II, and developing random forest models to identify patterns in hydrologic function. We assessed dominant processes by examining hydrologic signatures – summary indicators of watershed function derived from hydroclimatic time series and random forest models across 14 146 gauged United States watersheds. The results reveal clear continental-scale gradients in hydrologic processes, including baseflow, overland flow, storage, and water balance losses. Our map of dominant processes highlights, for example, the transition from baseflow to fast responses and back to baseflow along the elevation gradient from the Appalachian spine, through the Piedmont, to the Eastern Coastal Plain; a distinct outer ring around the Great Lakes region; and sharp contrasts between coastal and inland processes in the West. Variable importance analysis from random forest models show that processes in the western U.S. are primarily controlled by climate, whereas in the eastern U.S., soil, geology, and topography play larger roles, with distinct human influences apparent in urban areas. Our approach of estimating dominant processes and their drivers facilitates extending process knowledge from research watersheds to the continental scale, assessing current hydrological understanding, and evaluating hydrological model structures.

conterminous United States

High-pass corner frequency selection and review tool for use in ground-motion processing

Raw seismological waveform data contain noise from the instrument’s surroundings and the instrument itself that can dominate recordings at low and high frequencies. To use these data in ground‐motion modeling, the effects of noise on the signals must be reduced and the signals’ usable frequency range identified. We present automated procedures to efficiently reduce low‐frequency noise that are implemented in the software package gmprocess. These procedures check for, and as needed remove, low‐frequency artifacts in the displacement record using polynomial fits, which can be used in combination with existing signal‐to‐noise ratio (SNR)‐based corner‐frequency selection procedures. The automated selections are then efficiently verified and refined using a graphical user interface (GUI) that plots relevant ground‐motion time series and spectra and tracks modifications to signal processing parameters. We demonstrate these procedures using recordings from the 2020 M 5.1 Sparta, North Carolina, and the 2013 M 4.7 southern Ontario earthquakes. Data processed with the SNR‐only and polynomial criteria for these events contain displacement artifacts in 37% and 23% of processed traces, respectively. Records with remaining artifacts are corrected manually using the GUI. These processing steps illustrate the workflow for efficient data processing with quality control.

Seismological Research Letters

Automated, near real-time ground-motion processing at the U.S. Geological Survey

We describe automated ground‐motion processing software named gmprocess that has been developed at the U.S. Geological Survey (USGS) in support of near‐real‐time earthquake hazard products. Because of the open‐source development process, this software has benefitted from the involvement and contributions of a broad community and has been used for a wider range of applications than was initially envisioned. Here, we give an overview and introduction to the software, including how it has leveraged other open‐source libraries. We highlight some key features that gmprocess provides, compare response spectra calculated with the automated processing approach of gmprocess to the response spectra provided by the Next Generation Attenuation projects, and summarize projects that have utilized gmprocess. These use‐cases demonstrate that this software development effort has been successfully leveraged in earthquake research activities both within and outside the USGS.

Seismological Research Letters