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ABSTRACT Aerobes require dioxygen (O₂) to grow; anaerobes do not. However, nearly all microbes—aerobes, anaerobes, and facultative organisms alike—express enzymes whose substrates include O₂, if only for detoxification. This presents a challenge when trying to assess which organisms are aerobic from genomic data alone. This challenge can be overcome by noting that O₂utilization has wide-ranging effects on microbes: aerobes typically have larger genomes encoding distinctive O₂-utilizing enzymes, for example. These effects permit high-quality prediction of O₂utilization from annotated genome sequences, with several models displaying ≈80% accuracy on a ternary classification task for which blind guessing is only 33% accurate. Since genome annotation is compute-intensive and relies on many assumptions, we asked if annotation-free methods also perform well. We discovered that simple and efficient models based entirely on genomic sequence content—e.g., triplets of amino acids—perform as well as intensive annotation-based classifiers, enabling rapid processing of genomes. We further show that amino acid trimers are useful because they encode information about protein composition and phylogeny. To showcase the utility of rapid prediction, we estimated the prevalence of aerobes and anaerobes in diverse natural environments cataloged in the Earth Microbiome Project. Focusing on a well-studied O₂gradient in the Black Sea, we found quantitative correspondence between local chemistry (O₂:sulfide concentration ratio) and the composition of microbial communities. We, therefore, suggest that statistical methods like ours might be used to estimate, or “sense,” pivotal features of the chemical environment using DNA sequencing data.IMPORTANCEWe now have access to sequence data from a wide variety of natural environments. These data document a bewildering diversity of microbes, many known only from their genomes. Physiology—an organism’s capacity to engage metabolically with its environment—may provide a more useful lens than taxonomy for understanding microbial communities. As an example of this broader principle, we developed algorithms that accurately predict microbial dioxygen utilization directly from genome sequences without annotating genes, e.g., by considering only the amino acids in protein sequences. Annotation-free algorithms enable rapid characterization of natural samples, highlighting quantitative correspondence between sequences and local O₂levels in a data set from the Black Sea. This example suggests that DNA sequencing might be repurposed as a multi-pronged chemical sensor, estimating concentrations of O₂and other key facets of complex natural settings. 

Abstract Permafrost influences 25% of land in the Northern Hemisphere, where it stabilizes the ground beneath communities and infrastructure and sequesters carbon. However, the coevolution of permafrost, river dynamics, and vegetation in Arctic environments remains poorly understood. As rivers meander, they erode the floodplain at cutbanks and build new land through bar deposition, creating sequences of landforms with distinct formation ages. Here we mapped these sequences along the Koyukuk River floodplain, Alaska, analyzing permafrost occurrence, and landform and vegetation types. We used radiocarbon and optically stimulated luminescence (OSL) dating to develop a floodplain age map. Deposit ages ranged from modern to 10 ka, with more younger deposits near the modern channel. Permafrost rapidly reached 50% areal extent in all deposits older than 200 years then gradually increased up to ∼85% extent for deposits greater than 4 Kyr old. Permafrost extent correlated with increases in black spruce and wetland abundance, as well as increases in permafrost extent within wetland, and shrub and scrub vegetation classes. We developed an inverse model to constrain permafrost formation rate as a function of air temperature. Permafrost extent initially increased by ∼25% per century, in pace with vegetation succession, before decelerating to <10% per millennia as insulating overbank mud and moss slowly accumulated. Modern permafrost extent on the Koyukuk floodplain therefore reflects a dynamic balance between widespread, time‐varying permafrost formation and rapid, localized degradation due to cutbank erosion that might trigger a rapid loss of permafrost with climatic warming. 

Abstract Rapid warming in the Arctic threatens to destabilize mercury (Hg) deposits contained within soils in permafrost regions. Yet current estimates of the amount of Hg in permafrost vary by ∼4 times. Moreover, how Hg will be released to the environment as permafrost thaws remains poorly known, despite threats to water quality, human health, and the environment. Here we present new measurements of total mercury (THg) contents in discontinuous permafrost in the Yukon River Basin in Alaska. We collected riverbank and floodplain sediments from exposed banks and bars near the villages of Huslia and Beaver. Median THg contents were 49⁺¹³/₋₂₁ng THg g sediment⁻¹and 39⁺¹⁶/₋₁₈ng THg g sediment⁻¹for Huslia and Beaver, respectively (uncertainties as 15th and 85th percentiles). Corresponding THg:organic carbon ratios were 5.4^+2.0/_−2.4Gg THg Pg C⁻¹and 4.2^+2.4/_−2.9Gg THg Pg C⁻¹. To constrain floodplain THg stocks, we combined measured THg contents with floodplain stratigraphy. Trends of THg increasing with smaller sediment size and calculated stocks in the upper 1 m and 3 m are similar to those suggested for this region by prior pan-Arctic studies. We combined THg stocks and river migration rates derived from remote sensing to estimate particulate THg erosional and depositional fluxes as river channels migrate across the floodplain. Results show similar fluxes within uncertainty into the river from erosion at both sites (95⁺¹²/₋₄₇kg THg yr⁻¹and 26⁺¹⁵⁴/₋₁₃kg THg yr⁻¹at Huslia and Beaver, respectively), but different fluxes out of the river via deposition in aggrading bars (60⁺⁴⁰/₋₂₉kg THg yr⁻¹and 10^+5.3/_−1.7kg THg yr⁻¹). Thus, a significant amount of THg is liberated from permafrost during bank erosion, while a variable but generally lesser portion is subsequently redeposited by migrating rivers. 

Abstract How will bank erosion rates in Arctic rivers respond to a warming climate? Existing physical models predict that bank erosion rates should increase with water temperature as permafrost thaws more rapidly. However, the same theory predicts much faster erosion than is typically observed. We propose that these models are missing a key component: a layer of thawed sediment on the bank that buffers heat transfer and slows erosion. We developed a 1D model for this thawed layer, which reveals three regimes for permafrost riverbank erosion. Thaw‐limited erosion occurs in the absence of a thawed layer, such that rapid pore‐ice melting sets the pace of erosion, consistent with existing models. Entrainment‐limited erosion occurs when pore‐ice melting outpaces bank erosion, resulting in a thawed layer, and the relatively slow entrainment of sediment sets the pace of erosion similar to non‐permafrost rivers. Third, the intermediate regime occurs when the thawed layer goes through cycles of thickening and failure, leading to a transient thermal buffer that slows thaw rates. Distinguishing between these regimes is important because thaw‐limited erosion is highly sensitive to water temperature, whereas entrainment‐limited erosion is not. Interestingly, the buffered regime produces a thawed layer and relatively slow erosion rates like the entrainment‐limited regime, but erosion rates are temperature sensitive like the thaw‐limited regime. The results suggest the potential for accelerating erosion in a warming Arctic where bank erosion is presently thaw‐limited or buffered. Moreover, rivers can experience all regimes annually and transition between regimes with warming, altering their sensitivity to climate change. 

Abstract Climatic warming and permafrost thaw are predicted to increase Arctic riverbank erosion, threatening communities and accelerating sediment, carbon and nutrient cycling between rivers and floodplains. Existing theory assumes that pore‐ice thaw sets riverbank erosion rates, but overpredicts observed erosion rates by orders of magnitude. Here, we developed a simple model that predicts more modest rates due to a sediment‐entrainment limitation and riverbank armoring by slump blocks. Results show that during times of thaw‐limited erosion, the river rapidly erodes permafrost and undercuts its banks, consistent with previous work. However, overhanging banks generate slump blocks that must thaw and erode by sediment entrainment. Sediment entrainment can limit bank and slump block erosion rates, producing seasonally averaged rates more consistent with observations. Importantly, entrainment‐limited riverbank erosion does not depend on water temperature, indicating that decadal erosion rates may be less sensitive to warming than predicted previously. 

Abstract Permafrost thaw is hypothesized to increase riverbank erosion rates, which threatens Arctic communities and infrastructure. However, existing erosion models have not been tested against controlled flume experiments with open‐channel flow past an erodible, hydraulically rough permafrost bank. We conducted temperature‐controlled flume experiments where turbulent water eroded laterally into riverbanks consisting of sand and pore ice. The experiments were designed to produce ablation‐limited erosion such that any thawed sediment was quickly transported away from the bank. Bank erosion rates increased linearly with water temperature, decreased with pore ice content, and were insensitive to changes in bank temperature, consistent with theory. However, erosion rates were approximately a factor of three greater than expected. The heightened erosion rates were due to a greater coefficient of heat transfer from the turbulent water to the permafrost bank caused by bank grain roughness. A revised ablation‐limited bank erosion model with a heat transfer coefficient that includes bank roughness matched our experimental results well. Results indicate that bank erosion along Arctic rivers can accelerate under scenarios of warming river water temperatures for cases where the cadence of bank erosion is set by pore‐ice melting rather than sediment entrainment. 

Abstract Whether permafrost systematically alters the rate of riverbank erosion is a fundamental geomorphic question with significant importance to infrastructure, water quality, and biogeochemistry of high‐latitude watersheds. For over four decades, this question has remained unanswered due to a lack of data. Using remotely sensed imagery, we addressed this knowledge gap by quantifying riverbank erosion rates across the Arctic and subarctic. To compare these rates to non‐permafrost rivers, we assembled a global data set of published riverbank erosion rates. We found that erosion rates in rivers influenced by permafrost are on average nine times lower than non‐permafrost systems; erosion rate differences increase up to 40 times for the largest rivers. To test alternative hypotheses for the observed erosion rate difference, we examined differences in total water yield and erosional efficiency between these rivers and non‐permafrost rivers. Neither of these factors nor differences in river sediment loads provided compelling alternative explanations, leading us to conclude that permafrost limits riverbank erosion rates. This conclusion was supported by field investigations of rates and patterns of erosion along three rivers flowing through discontinuous permafrost in Alaska. Our results show that permafrost limits maximum bank erosion rates on rivers with stream powers greater than 900 Wm⁻¹. On smaller rivers, however, hydrology rather than thaw rate may be the dominant control on bank erosion. Our findings suggest that Arctic warming and hydrological changes should increase bank erosion rates on large rivers but may reduce rates on rivers with drainage areas less than a few thousand km². 

Abstract Permafrost degradation is altering biogeochemical processes throughout the Arctic. Thaw‐induced changes in organic matter transformations and mineral weathering reactions are impacting fluxes of inorganic carbon (IC) and alkalinity (ALK) in Arctic rivers. However, the net impact of these changing fluxes on the concentration of carbon dioxide in the atmosphere (pCO₂) is relatively unconstrained. Resolving this uncertainty is important as thaw‐driven changes in the fluxes of IC and ALK could produce feedbacks in the global carbon cycle. Enhanced production of sulfuric acid through sulfide oxidation is particularly poorly quantified despite its potential to remove ALK from the ocean‐atmosphere system and increasepCO₂, producing a positive feedback leading to more warming and permafrost degradation. In this work, we quantified weathering in the Koyukuk River, a major tributary of the Yukon River draining discontinuous permafrost in central Alaska, based on water and sediment samples collected near the village of Huslia in summer 2018. Using measurements of major ion abundances and sulfate () sulfur (³⁴S/³²S) and oxygen (¹⁸O/¹⁶O) isotope ratios, we employed the MEANDIR inversion model to quantify the relative importance of a suite of weathering processes and their net impact onpCO₂. Calculations found that approximately 80% of in mainstem samples derived from sulfide oxidation with the remainder from evaporite dissolution. Moreover,³⁴S/³²S ratios,¹³C/¹²C ratios of dissolved IC, and sulfur X‐ray absorption spectra of mainstem, secondary channel, and floodplain pore fluid and sediment samples revealed modest degrees of microbial sulfate reduction within the floodplain. Weathering fluxes of ALK and IC result in lower values ofpCO₂over timescales shorter than carbonate compensation (∼10⁴ yr) and, for mainstem samples, higher values ofpCO₂over timescales longer than carbonate compensation but shorter than the residence time of marine (∼10⁷ yr). Furthermore, the absolute concentrations of and Mg²⁺in the Koyukuk River, as well as the ratios of and Mg²⁺to other dissolved weathering products, have increased over the past 50 years. Through analogy to similar trends in the Yukon River, we interpret these changes as reflecting enhanced sulfide oxidation due to ongoing exposure of previously frozen sediment and changes in the contributions of shallow and deep flow paths to the active channel. Overall, these findings confirm that sulfide oxidation is a substantial outcome of permafrost degradation and that the sulfur cycle responds to permafrost thaw with a timescale‐dependent feedback on warming. 

This document describes geomorphic relative age mapping and radiocarbon (14C) measurements used to construct floodplain age models for three locations within the Yukon River Watershed: Huslia, Alaska (65.700 N, 156.387 W), Alakanuk, Alaska (62.685 N, 164.644 W), and Beaver, Alaska (66.362 N, 147.398 W). We describe the field sampling protocols, geomorphic mapping of cross-cutting relationships (aided by digital elevation models (DEMs) and high-resolution satellite imagery), 14C and optically stimulated luminescence (OSL) lab analyses, Markov Chain Monte Carlo (MCMC) interpolation through the geomorphic–radiogenic age constraints, and the resulting floodplain terrain age models.