Bacterioplankton dispersal and biogeochemical function across Alaskan Arctic catchments.

In Arctic catchments, bacterioplankton are dispersed through soils and streams, both of which freeze and thaw/flow in phase, seasonally. To characterize this dispersal and its potential impact on biogeochemistry, we collected bacterioplankton and measured stream physicochemistry during snowmelt and after vegetation senescence across multiple stream orders in alpine, tundra, and tundra-dominated-by-lakes catchments. In all catchments, differences in community composition were associated with seasonal thaw, then attachment status (i.e. free floating or sediment associated), and then stream order. Bacterioplankton taxonomic diversity and richness were elevated in sediment-associated fractions and in higher-order reaches during snowmelt. Families Chthonomonadaceae, Pyrinomonadaceae, and Xiphinematobacteraceae were abundantly different across seasons, while Flavobacteriaceae and Microscillaceae were abundantly different between free-floating and sediment-associated fractions. Physicochemical data suggested there was high iron (Fe+ ) production (alpine catchment); Fe+ production and chloride (Cl- ) removal (tundra catchment); and phosphorus (SRP) removal and ammonium (NH4 + ) production (lake catchment). In tundra landscapes, these 'hot spots' of Fe+ production and Cl- removal accompanied shifts in species richness, while SRP promoted the antecedent community. Our findings suggest that freshet increases bacterial dispersal from headwater catchments to receiving catchments, where bacterioplankton-mineral relations stabilized communities in free-flowing reaches, but bacterioplankton-nutrient relations stabilized those punctuated by lakes.

Microbiome assembly in thawing permafrost and its feedbacks to climate.

The physical and chemical changes that accompany permafrost thaw directly influence the microbial communities that mediate the decomposition of formerly frozen organic matter, leading to uncertainty in permafrost-climate feedbacks. Although changes to microbial metabolism and community structure are documented following thaw, the generality of post-thaw assembly patterns across permafrost soils of the world remains uncertain, limiting our ability to predict biogeochemistry and microbial community responses to climate change. Based on our review of the Arctic microbiome, permafrost microbiology, and community ecology, we propose that Assembly Theory provides a framework to better understand thaw-mediated microbiome changes and the implications for community function and climate feedbacks. This framework posits that the prevalence of deterministic or stochastic processes indicates whether the community is well-suited to thrive in changing environmental conditions. We predict that on a short timescale and following high-disturbance thaw (e.g., thermokarst), stochasticity dominates post-thaw microbiome assembly, suggesting that functional predictions will be aided by detailed information about the microbiome. At a longer timescale and lower-intensity disturbance (e.g., active layer deepening), deterministic processes likely dominate, making environmental parameters sufficient for predicting function. We propose that the contribution of stochastic and deterministic processes to post-thaw microbiome assembly depends on the characteristics of the thaw disturbance, as well as characteristics of the microbial community, such as the ecological and phylogenetic breadth of functional guilds, their functional redundancy, and biotic interactions. These propagate across space and time, potentially providing a means for predicting the microbial forcing of greenhouse gas feedbacks to global climate change.

Stratification of reactivity determines nitrate removal in groundwater.

Biogeochemical reactions occur unevenly in space and time, but this heterogeneity is often simplified as a linear average due to sparse data, especially in subsurface environments where access is limited. For example, little is known about the spatial variability of groundwater denitrification, an important process in removing nitrate originating from agriculture and land use conversion. Information about the rate, arrangement, and extent of denitrification is needed to determine sustainable limits of human activity and to predict recovery time frames. Here, we developed and validated a method for inferring the spatial organization of sequential biogeochemical reactions in an aquifer in France. We applied it to five other aquifers in different geological settings located in the United States and compared results among 44 locations across the six aquifers to assess the generality of reactivity trends. Of the sampling locations, 79% showed pronounced increases of reactivity with depth. This suggests that previous estimates of denitrification have underestimated the capacity of deep aquifers to remove nitrate, while overestimating nitrate removal in shallow flow paths. Oxygen and nitrate reduction likely increases with depth because there is relatively little organic carbon in agricultural soils and because excess nitrate input has depleted solid phase electron donors near the surface. Our findings explain the long-standing conundrum of why apparent reaction rates of oxygen in aquifers are typically smaller than those of nitrate, which is energetically less favorable. This stratified reactivity framework is promising for mapping vertical reactivity trends in aquifers, generating new understanding of subsurface ecosystems and their capacity to remove contaminants.

Phosphorus rather than nitrogen regulates ecosystem carbon dynamics after permafrost thaw.

Ecosystem carbon (C) dynamics after permafrost thaw depends on more than just climate change since soil nutrient status may also impact ecosystem C balance. It has been advocated that nitrogen (N) release upon permafrost thaw could promote plant growth and thus offset soil C loss. However, compared with the widely accepted C-N interactions, little is known about the potential role of soil phosphorus (P) availability. We combined 3-year field observations along a thaw sequence (constituted by four thaw stages, i.e., non-collapse and 5, 14, and 22 years since collapse) with an in-situ fertilization experiment (included N and P additions at the level of 10 g N m-2  year-1 and 10 g P m-2  year-1 ) to evaluate ecosystem C-nutrient interactions upon permafrost thaw. We found that changes in soil P availability rather than N availability played an important role in regulating gross primary productivity and net ecosystem productivity along the thaw sequence. The fertilization experiment confirmed that P addition had stronger effects on plant growth than N addition in this permafrost ecosystem. These two lines of evidence highlight the crucial role of soil P availability in altering the trajectory of permafrost C cycle under climate warming.

Tundra wildfire triggers sustained lateral nutrient loss in Alaskan Arctic.

Climate change is creating widespread ecosystem disturbance across the permafrost zone, including a rapid increase in the extent and severity of tundra wildfire. The expansion of this previously rare disturbance has unknown consequences for lateral nutrient flux from terrestrial to aquatic environments. Lateral loss of nutrients could reduce carbon uptake and slow recovery of already nutrient-limited tundra ecosystems. To investigate the effects of tundra wildfire on lateral nutrient export, we analyzed water chemistry in and around the 10-year-old  Anaktuvuk River fire scar in northern Alaska. We collected water samples from 21 burned and 21 unburned watersheds during snowmelt, at peak growing season, and after plant senescence in 2017 and 2018. After a decade of ecosystem recovery, aboveground biomass had recovered in burned watersheds, but overall carbon and nitrogen remained ~20% lower, and the active layer remained ~10% deeper. Despite lower organic matter stocks, dissolved organic nutrients were substantially elevated in burned watersheds, with higher flow-weighted concentrations of organic carbon (25% higher), organic nitrogen (59% higher), organic phosphorus (65% higher), and organic sulfur (47% higher). Geochemical proxies indicated greater interaction with mineral soils in watersheds with surface subsidence, but optical analysis and isotopes suggested that recent plant growth, not mineral soil, was the main source of organic nutrients in burned watersheds. Burned and unburned watersheds had similar δ15 N-NO3 - , indicating that exported nitrogen was of preburn origin (i.e., not recently fixed). Lateral nitrogen flux from burned watersheds was 2- to 10-fold higher than rates of background nitrogen fixation and atmospheric deposition estimated in this area. These findings indicate that wildfire in Arctic tundra can destabilize nitrogen, phosphorus, and sulfur previously stored in permafrost via plant uptake and leaching. This plant-mediated nutrient loss could exacerbate terrestrial nutrient limitation after disturbance or serve as an important nutrient release mechanism during succession.

Stream Dissolved Organic Matter in Permafrost Regions Shows Surprising Compositional Similarities but Negative Priming and Nutrient Effects.

Permafrost degradation is delivering bioavailable dissolved organic matter (DOM) and inorganic nutrients to surface water networks. While these permafrost subsidies represent a small portion of total fluvial DOM and nutrient fluxes, they could influence food webs and net ecosystem carbon balance via priming or nutrient effects that destabilize background DOM. We investigated how addition of biolabile carbon (acetate) and inorganic nutrients (nitrogen and phosphorus) affected DOM decomposition with 28-day incubations. We incubated late-summer stream water from 23 locations nested in seven northern or high-altitude regions in Asia, Europe, and North America. DOM loss ranged from 3% to 52%, showing a variety of longitudinal patterns within stream networks. DOM optical properties varied widely, but DOM showed compositional similarity based on Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) analysis. Addition of acetate and nutrients decreased bulk DOM mineralization (i.e., negative priming), with more negative effects on biodegradable DOM but neutral or positive effects on stable DOM. Unexpectedly, acetate and nutrients triggered breakdown of colored DOM (CDOM), with median decreases of 1.6% in the control and 22% in the amended treatment. Additionally, the uptake of added acetate was strongly limited by nutrient availability across sites. These findings suggest that biolabile DOM and nutrients released from degrading permafrost may decrease background DOM mineralization but alter stoichiometry and light conditions in receiving waterbodies. We conclude that priming and nutrient effects are coupled in northern aquatic ecosystems and that quantifying two-way interactions between DOM properties and environmental conditions could resolve conflicting observations about the drivers of DOM in permafrost zone waterways.

Unexpected spatial stability of water chemistry in headwater stream networks.

Understanding how water and solutes enter and propagate through freshwater landscapes in the Anthropocene is critical to protecting and restoring aquatic ecosystems and ensuring human water security. However, high hydrochemical variability in headwater streams, where most carbon and nutrients enter river networks, has hindered effective modelling and management. We developed an analytical framework informed by landscape ecology and catchment hydrology to quantify spatiotemporal variability across scales, which we tested in 56 headwater catchments, sampled periodically over 12 years in western France. Unexpectedly, temporal variability in dissolved carbon, nutrients and major ions was preserved moving downstream and spatial patterns of water chemistry were stable on annual to decadal timescales, partly because of synchronous variation in solute concentrations. These findings suggest that while concentration and flux cannot be extrapolated among subcatchments, periodic sampling of headwaters provides valuable information about solute sources and subcatchment resilience to disturbance.

Genome Modeling System: A Knowledge Management Platform for Genomics.

In this work, we present the Genome Modeling System (GMS), an analysis information management system capable of executing automated genome analysis pipelines at a massive scale. The GMS framework provides detailed tracking of samples and data coupled with reliable and repeatable analysis pipelines. The GMS also serves as a platform for bioinformatics development, allowing a large team to collaborate on data analysis, or an individual researcher to leverage the work of others effectively within its data management system. Rather than separating ad-hoc analysis from rigorous, reproducible pipelines, the GMS promotes systematic integration between the two. As a demonstration of the GMS, we performed an integrated analysis of whole genome, exome and transcriptome sequencing data from a breast cancer cell line (HCC1395) and matched lymphoblastoid line (HCC1395BL). These data are available for users to test the software, complete tutorials and develop novel GMS pipeline configurations. The GMS is available at https://github.com/genome/gms.

Overview of Advanced LIGO adaptive optics.

This is an overview of the adaptive optics used in Advanced LIGO (aLIGO), known as the thermal compensation system (TCS). The TCS was designed to minimize thermally induced spatial distortions in the interferometer optical modes and to provide some correction for static curvature errors in the core optics of aLIGO. The TCS is comprised of ring heater actuators, spatially tunable CO2 laser projectors, and Hartmann wavefront sensors. The system meets the requirements of correcting for nominal distortion in aLIGO to a maximum residual error of 5.4 nm rms, weighted across the laser beam, for up to 125 W of laser input power into the interferometer.

Permafrost collapse alters soil carbon stocks, respiration, CH4 , and N2O in upland tundra.

Release of greenhouse gases from thawing permafrost is potentially the largest terrestrial feedback to climate change and one of the most likely to occur; however, estimates of its strength vary by a factor of thirty. Some of this uncertainty stems from abrupt thaw processes known as thermokarst (permafrost collapse due to ground ice melt), which alter controls on carbon and nitrogen cycling and expose organic matter from meters below the surface. Thermokarst may affect 20-50% of tundra uplands by the end of the century; however, little is known about the effect of different thermokarst morphologies on carbon and nitrogen release. We measured soil organic matter displacement, ecosystem respiration, and soil gas concentrations at 26 upland thermokarst features on the North Slope of Alaska. Features included the three most common upland thermokarst morphologies: active-layer detachment slides, thermo-erosion gullies, and retrogressive thaw slumps. We found that thermokarst morphology interacted with landscape parameters to determine both the initial displacement of organic matter and subsequent carbon and nitrogen cycling. The large proportion of ecosystem carbon exported off-site by slumps and slides resulted in decreased ecosystem respiration postfailure, while gullies removed a smaller portion of ecosystem carbon but strongly increased respiration and N2 O concentration. Elevated N2 O in gully soils persisted through most of the growing season, indicating sustained nitrification and denitrification in disturbed soils, representing a potential noncarbon permafrost climate feedback. While upland thermokarst formation did not substantially alter redox conditions within features, it redistributed organic matter into both oxic and anoxic environments. Across morphologies, residual organic matter cover, and predisturbance respiration explained 83% of the variation in respiration response. Consistent differences between upland thermokarst types may contribute to the incorporation of this nonlinear process into projections of carbon and nitrogen release from degrading permafrost.

Soil temperature and moisture as key controls of phosphorus export in mountain watersheds.

Oligotrophic mountain lakes act as sensitive indicators of landscape-scale changes in mountain regions due to their low nutrient concentration and remote, relatively undisturbed watersheds. Recent research shows that phosphorus (P) concentrations are increasing in mountain lakes around the world, creating more mesotrophic states and altering lake ecosystem structure and function. The relative importance of atmospheric deposition and climate-driven changes to local biogeochemistry in driving these shifts is not well established. In this study, we test whether increasing temperatures in watershed soils may be contributing to the observed increases in mountain lake P loading. Specifically, we test whether higher soil temperatures increase P mobilization from mountain soils by accelerating the rate of geochemical weathering and soil organic matter decomposition. We used paired soil incubation (lab) and soil transplant (field) experiments with mountain soils from around the western United States to test the effects of warming on rain-leachable P concentration, soil P mobilization, and soil respiration. Our results show that while higher temperature can increase soil P mobilization, low soil moisture can limit the effects of warming in some situations. Soils with lower bulk densities, higher pH, lower aluminum oxide contents, and lower ratios of carbon to nitrogen had much higher rain-leachable P concentration across all sites and experimental treatments. Together, these results suggest that mountain watersheds with high-P soils and relatively high soil moisture could have the largest increases in P mobilization with warming. Consequently, lakes and streams in such watersheds could become especially susceptible to soil-driven eutrophication as temperatures rise.

Characteristics of methane emissions from alpine thermokarst lakes on the Tibetan Plateau.

Understanding methane (CH4) emission from thermokarst lakes is crucial for predicting the impacts of abrupt thaw on the permafrost carbon-climate feedback. However, observational evidence, especially from high-altitude permafrost regions, is still scarce. Here, by combining field surveys, radio- and stable-carbon isotopic analyses, and metagenomic sequencing, we present multiple characteristics of CH4 emissions from 120 thermokarst lakes in 30 clusters along a 1100 km transect on the Tibetan Plateau. We find that thermokarst lakes have high CH4 emissions during the ice-free period (13.4 ± 1.5 mmol m-2 d-1; mean ± standard error) across this alpine permafrost region. Ebullition constitutes 84% of CH4 emissions, which are fueled primarily by young carbon decomposition through the hydrogenotrophic pathway. The relative abundances of methanogenic genes correspond to the observed CH4 fluxes. Overall, multiple parameters obtained in this study provide benchmarks for better predicting the strength of permafrost carbon-climate feedback in high-altitude permafrost regions.

Deep denitrification: Stream and groundwater biogeochemistry reveal contrasted but connected worlds above and below.

Excess nutrients from agricultural and urban development have created a cascade of ecological crises around the globe. Nutrient pollution has triggered eutrophication in most freshwater and coastal ecosystems, contributing to a loss in biodiversity, harm to human health, and trillions in economic damage every year. Much of the research conducted on nutrient transport and retention has focused on surface environments, which are both easy to access and biologically active. However, surface characteristics of watersheds, such as land use and network configuration, often do not explain the variation in nutrient retention observed in rivers, lakes, and estuaries. Recent research suggests subsurface processes and characteristics may be more important than previously thought in determining watershed-level nutrient fluxes and removal. In a small watershed in western France, we used a multi-tracer approach to compare surface and subsurface nitrate dynamics at commensurate spatiotemporal scales. We combined 3-D hydrological modeling with a rich biogeochemical dataset from 20 wells and 15 stream locations. Water chemistry in the surface and subsurface showed high temporal variability, but groundwater was substantially more spatially variable, attributable to long transport times (10-60 years) and patchy distribution of the iron and sulfur electron donors fueling autotrophic denitrification. Isotopes of nitrate and sulfate revealed fundamentally different processes dominating the surface (heterotrophic denitrification and sulfate reduction) and subsurface (autotrophic denitrification and sulfate production). Agricultural land use was associated with elevated nitrate in surface water, but subsurface nitrate concentration was decoupled from land use. Dissolved silica and sulfate are affordable tracers of residence time and nitrogen removal that are relatively stable in surface and subsurface environments. Together, these findings reveal distinct but adjacent and connected biogeochemical worlds in the surface and subsurface. Characterizing how these worlds are linked and decoupled is critical to meeting water quality targets and addressing water issues in the Anthropocene.

Alpine permafrost could account for a quarter of thawed carbon based on Plio-Pleistocene paleoclimate analogue.

Estimates of the permafrost-climate feedback vary in magnitude and sign, partly because permafrost carbon stability in warmer-than-present conditions is not well constrained. Here we use a Plio-Pleistocene lacustrine reconstruction of mean annual air temperature (MAAT) from the Tibetan Plateau, the largest alpine permafrost region on the Earth, to constrain past and future changes in permafrost carbon storage. Clumped isotope-temperatures (Δ47-T) indicate warmer MAAT (~1.2 °C) prior to 2.7 Ma, and support a permafrost-free environment on the northern Tibetan Plateau in a warmer-than-present climate. Δ47-T indicate ~8.1 °C cooling from 2.7 Ma, coincident with Northern Hemisphere glacial intensification. Combined with climate models and global permafrost distribution, these results indicate, under conditions similar to mid-Pliocene Warm period (3.3-3.0 Ma), ~60% of alpine permafrost containing ~85 petagrams of carbon may be vulnerable to thawing compared to ~20% of circumarctic permafrost. This estimate highlights ~25% of permafrost carbon and the permafrost-climate feedback could originate in alpine areas.

A globally relevant stock of soil nitrogen in the Yedoma permafrost domain.

Nitrogen regulates multiple aspects of the permafrost climate feedback, including plant growth, organic matter decomposition, and the production of the potent greenhouse gas nitrous oxide. Despite its importance, current estimates of permafrost nitrogen are highly uncertain. Here, we compiled a dataset of >2000 samples to quantify nitrogen stocks in the Yedoma domain, a region with organic-rich permafrost that contains ~25% of all permafrost carbon. We estimate that the Yedoma domain contains 41.2 gigatons of nitrogen down to ~20 metre for the deepest unit, which increases the previous estimate for the entire permafrost zone by ~46%. Approximately 90% of this nitrogen (37 gigatons) is stored in permafrost and therefore currently immobile and frozen. Here, we show that of this amount, ¾ is stored >3 metre depth, but if partially mobilised by thaw, this large nitrogen pool could have continental-scale consequences for soil and aquatic biogeochemistry and global-scale consequences for the permafrost feedback.

Diné citizen science: Phytoremediation of uranium and arsenic in the Navajo Nation.

Mid-20th century mining in Naabeehó Bináhásdzo (Navajo Nation) polluted soil and groundwater with uranium and arsenic. The Diné and other indigenous residents of this region use groundwater for drinking, livestock, and irrigation, creating a serious environmental health risk. Currently, many individuals and communities on the Navajo Nation must purchase and transport treated water from hours away. Sunflowers (Helianthus annuus) preferentially take up uranium and arsenic, potentially representing a tool to remove these contaminants through on-site, low-cost phytoremediation. This study reports the results of a collaboration among researchers, high school students, teachers, and tribal leaders to analyze water chemistry and perform a phytoremediation experiment. In 2018 and 2019, we compiled existing data from the Navajo Nation Environmental Protection Agency (NNEPA) and collected samples from surface and groundwater. We then used sunflower seedlings grown in local soil to assess whether phytoremediation could be effective at removing arsenic and uranium. For the NNEPA-sampled wells, 9.5% exceeded the maximum contaminant level for uranium (30 µg per liter) and 16% for arsenic (10 µg per liter). For the new samples, uranium was highest in surface pools, suggesting leaching from local soil. Unlike studies from humid regions, sunflowers did not decrease uranium and arsenic in soil water. Instead, there was no change in arsenic concentration and an increase in uranium concentration in both planted and control treatments, attributable to weathering of uranium-bearing minerals in the desert soil. Because much of global uranium mining occurs in arid and semiarid regions, the ineffectiveness of phytoremediation on the Navajo Nation emphasizes the importance of prevention and conventional remediation. More generally, the participatory science approach created meaningful relationships and an important collaboration between a tribal chapter and a university, providing both cultural and scientific experiential learning opportunities for Diné high school students, undergraduate researchers, and senior personnel.

Limited progress in nutrient pollution in the U.S. caused by spatially persistent nutrient sources.

Human agriculture, wastewater, and use of fossil fuels have saturated ecosystems with nitrogen and phosphorus, threatening biodiversity and human water security at a global scale. Despite efforts to reduce nutrient pollution, carbon and nutrient concentrations have increased or remained high in many regions. Here, we applied a new ecohydrological framework to ~12,000 water samples collected by the U.S. Environmental Protection Agency from streams and lakes across the contiguous U.S. to identify spatial and temporal patterns in nutrient concentrations and leverage (an indicator of flux). For the contiguous U.S. and within ecoregions, we quantified trends for sites sampled repeatedly from 2000 to 2019, the persistence of spatial patterns over that period, and the patch size of nutrient sources and sinks. While we observed various temporal trends across ecoregions, the spatial patterns of nutrient and carbon concentrations in streams were persistent across and within ecoregions, potentially because of historical nutrient legacies, consistent nutrient sources, and inherent differences in nutrient removal capacity for various ecosystems. Watersheds showed strong critical source area dynamics in that 2-8% of the land area accounted for 75% of the estimated flux. Variability in nutrient contribution was greatest in catchments smaller than 250 km2 for most parameters. An ensemble of four machine learning models confirmed previously observed relationships between nutrient concentrations and a combination of land use and land cover, demonstrating how human activity and inherent nutrient removal capacity interactively determine nutrient balance. These findings suggest that targeted nutrient interventions in a small portion of the landscape could substantially improve water quality at continental scales. We recommend a dual approach of first prioritizing the reduction of nutrient inputs in catchments that exert disproportionate influence on downstream water chemistry, and second, enhancing nutrient removal capacity by restoring hydrological connectivity both laterally and vertically in stream networks.

What do we need to predict groundwater nitrate recovery trajectories?

Nitrate contamination affects many of the Earth's aquifers and surface waters. Large-scale predictions of groundwater nitrate trends normally require the characterization of multiple anthropic and natural factors. To assess different approaches for upscaling estimates of nitrate recovery, we tested the influence of hydrological, historical, and biological factors on predictions of future nitrate concentration in aquifers. We tested the factors with a rich hydrogeological dataset from a fractured bedrock catchment in western France (Brittany). A sensitivity analysis performed on a calibrated model of groundwater flow, denitrification, and nitrogen inputs revealed that trends in nitrate concentration can effectively be approximated with a limited number of key parameters. The total mass of nitrate that entered the aquifer since the beginning of the industrial period needs to be characterized, but the shape of the historical nitrogen input time series can be largely simplified without substantially altering the predictions. Aquifer flow and transport processes can be represented by the mean and standard deviation of the residence time distribution, offering a tractable tool to make reasonable predictions at watershed to regional scales. Apparent sensitivity to denitrification rate was primarily attributable to time lags in oxygen depletion, meaning that denitrification can be simplified to an on/off process, defined only by the time needed for nitrate to reach the hypoxic reactive layer. Obtaining these key parameters at large scales is still challenging with currently available information, but the results are promising regarding our future ability to predict nitrate concentration with integrated monitoring and modeling approaches.