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Microorganisms drive many aspects of organic carbon cycling in thawing permafrost soils, but the compositional trajectory of the post-thaw microbiome and its metabolic activity remain uncertain, which limits our ability to predict permafrost–climate feedbacks in a warming world. Using quantitative metabarcoding and metagenomic sequencing, we determined relative and absolute changes in microbiome composition and functional gene abundance during thaw incubations of wet sedge tundra collected from northern Alaska, USA. Organic soils from the tundra active-layer (0–50 cm), transition-zone (50–70 cm), and permafrost (70+ cm) depths were incubated under reducing conditions at 4 °C for 30 days to mimic an extended thaw duration. Following extended thaw, we found that iron (Fe)-cycling Gammaproteobacteria, specifically the heterotrophic Fe(III)-reducing Rhodoferax sp. and chemoautotrophic Fe(II)-oxidizing Gallionella sp., increased by 3–5 orders of magnitude in absolute abundance within the transition-zone and permafrost microbiomes, accounting for 65% of community abundance. We also found that the abundance of genes for Fe(III) reduction (e.g., MtrE) and Fe(II) oxidation (e.g., Cyc1) increased concurrently with genes for benzoate degradation and pyruvate metabolism, in which pyruvate is used to generate acetate that can be oxidized, along with benzoate, to CO2 when coupled with Fe(III) reduction. Gene abundance for CH4 metabolism decreased following extended thaw, suggesting dissimilatory Fe(III) reduction suppresses acetoclastic methanogenesis under reducing conditions. Our genomic evidence indicates that microbial carbon degradation is dominated by iron redox metabolism via an increase in gene abundance associated with Fe(III) reduction and Fe(II) oxidation during initial permafrost thaw, likely increasing microbial respiration while suppressing methanogenesis in wet sedge tundra.

 

Methane and carbon dioxide effluxes from aquatic systems in the Arctic will affect and likely amplify global change. As permafrost thaws in a warming world, more dissolved organic carbon (DOC) and greenhouse gases are produced and move from soils to surface waters where the DOC can be oxidized to CO 2 and also released to the atmosphere. Our main study objective is to measure the release of carbon to the atmosphere via effluxes of methane (CH 4 ) and carbon dioxide (CO 2 ) from Toolik Lake, a deep, dimictic, low-arctic lake in northern Alaska. By combining direct eddy covariance flux measurements with continuous gas pressure measurements in the lake surface waters, we quantified the k 600 piston velocity that controls gas flux across the air–water interface. Our measured k values for CH 4 and CO 2 were substantially above predictions from several models at low to moderate wind speeds, and only converged on model predictions at the highest wind speeds. We attribute this higher flux at low wind speeds to effects on water-side turbulence resulting from how the surrounding tundra vegetation and topography increase atmospheric turbulence considerably in this lake, above the level observed over large ocean surfaces. We combine this process-level understanding of gas exchange with the trends of a climate-relevant long-term (30 + years) meteorological data set at Toolik Lake to examine short-term variations (2015 ice-free season) and interannual variability (2010–2015 ice-free seasons) of CH 4 and CO 2 fluxes. We argue that the biological processing of DOC substrate that becomes available for decomposition as the tundra soil warms is important for understanding future trends in aquatic gas fluxes, whereas the variability and long-term trends of the physical and meteorological variables primarily affect the timing of when higher or lower than average fluxes are observed. We see no evidence suggesting that a tipping point will be reached soon to change the status of the aquatic system from gas source to sink. We estimate that changes in CH 4 and CO 2 fluxes will be constrained with a range of +30% and −10% of their current values over the next 30 years. 

ABSTRACT In the oligotrophic oceans, key autotrophs depend on “helper” bacteria to reduce oxidative stress from hydrogen peroxide (H 2 O 2 ) in the extracellular environment. H 2 O 2 is also a ubiquitous stressor in freshwaters, but the effects of H 2 O 2 on autotrophs and their interactions with bacteria are less well understood in freshwaters. Naturally occurring H 2 O 2 in freshwater systems is proposed to impact the proportion of microcystin-producing (toxic) and non-microcystin-producing (nontoxic) Microcystis in blooms, which influences toxin concentrations and human health impacts. However, how different strains of Microcystis respond to naturally occurring H 2 O 2 concentrations and the microbes responsible for H 2 O 2 decomposition in freshwater cyanobacterial blooms are unknown. To address these knowledge gaps, we used metagenomics and metatranscriptomics to track the presence and expression of genes for H 2 O 2 decomposition by microbes during a cyanobacterial bloom in western Lake Erie in the summer of 2014. katG encodes the key enzyme for decomposing extracellular H 2 O 2 but was absent in most Microcystis cells. katG transcript relative abundance was dominated by heterotrophic bacteria. In axenic Microcystis cultures, an H 2 O 2 scavenger (pyruvate) significantly improved growth rates of one toxic strain while other toxic and nontoxic strains were unaffected. These results indicate that heterotrophic bacteria play a key role in H 2 O 2 decomposition in Microcystis blooms and suggest that their activity may affect the fitness of some Microcystis strains and thus the strain composition of Microcystis blooms but not along a toxic versus nontoxic dichotomy. IMPORTANCE Cyanobacterial harmful algal blooms (CHABs) threaten freshwater ecosystems globally through the production of toxins. Toxin production by cyanobacterial species and strains during CHABs varies widely over time and space, but the ecological drivers of the succession of toxin-producing species remain unclear. Hydrogen peroxide (H 2 O 2 ) is ubiquitous in natural waters, inhibits microbial growth, and may determine the relative proportions of Microcystis strains during blooms. However, the mechanisms and organismal interactions involved in H 2 O 2 decomposition are unexplored in CHABs. This study shows that some strains of bloom-forming freshwater cyanobacteria benefit from detoxification of H 2 O 2 by associated heterotrophic bacteria, which may impact bloom development. 

Whole‐ecosystem interactions and feedbacks constrain ecosystem responses to environmental change. The effects of these constraints on responses to climate trends and extreme weather events have been well studied. Here we examine how these constraints respond to changes in day‐to‐day weather variability without changing the long‐term mean weather. Although environmental variability is recognized as a critical factor affecting ecological function, the effects of climate change on day‐to‐day weather variability and the resultant impacts on ecosystem function are still poorly understood. Changes in weather variability can alter the mean rates of individual ecological processes because many processes respond non‐linearly to environmental drivers. We assessed how these individual‐process responses to changes in day‐to‐day weather variability interact with one another at an ecosystem level. We examine responses of arctic tundra to changes in weather variability using stochastic simulations of daily temperature, precipitation, and light to drive a biogeochemical model. Changes in weather variability altered ecosystem carbon, nitrogen, and phosphorus stocks and cycling rates in our model. However, responses of some processes (e.g., respiration) were inconsistent with expectations because ecosystem feedbacks can moderate, or even reverse, direct process responses to weather variability. More weather variability led to greater carbon losses from land to atmosphere; less variability led to higher carbon sequestration on land. The magnitude of modeled ecosystem response to weather variability was comparable to that predicted for the effects of climate mean trends by the end of the century.

 

Climate warming has increased permafrost thaw in arctic tundra and extended the duration of annual thaw (number of thaw days in summer) along soil profiles. Predicting the microbial response to permafrost thaw depends largely on knowing how increased thaw duration affects the composition of the soil microbiome. Here, we determined soil microbiome composition from the annually thawed surface active layer down through permafrost from two tundra types at each of three sites on the North Slope of Alaska, USA. Variations in soil microbial taxa were found between sites up to ~90 km apart, between tundra types, and between soil depths. Microbiome differences at a site were greatest across transitions from thawed to permafrost depths. Results from correlation analysis based on multi‐decadal thaw surveys show that differences in thaw duration by depth were significantly, positively correlated with the abundance of dominant taxa in the active layer and negatively correlated with dominant taxa in the permafrost. Microbiome composition within the transition zone was statistically similar to that in the permafrost, indicating that recent decades of intermittent thaw have not yet induced a shift from permafrost to active‐layer microbes. We suggest that thaw duration rather than thaw frequency has a greater impact on the composition of microbial taxa within arctic soils.

 

Abstract. The TGS 2600 was the first low-cost solid-state sensor that shows a response to ambient levels of CH4 (e.g., range ≈1.8–2.7 µmol mol−1). Here we present an empirical function to correct the TGS 2600 signal for temperature and (absolute) humidity effects and address the long-term reliability of two identical sensors deployed from 2012 to 2018. We assess the performance of the sensors at 30 min resolution and aggregated to weekly medians. Over the entire period the agreement between TGS-derived and reference CH4 mole fractions measured by a high-precision Los Gatos Research instrument was R2=0.42, with better results during summer (R2=0.65 in summer 2012). Using absolute instead of relative humidity for the correction of the TGS 2600 sensor signals reduced the typical deviation from the reference to less than ±0.1 µmol mol−1 over the full range of temperatures from −41 to 27 ∘C. At weekly resolution the two sensors showed a downward drift of signal voltages indicating that after 10–13 years a TGS 2600 may have reached its end of life. While the true trend in CH4 mole fractions measured by the high-quality reference instrument was 10.1 nmolmol-1yr-1 (2012–2018), part of the downward trend in sensor signal (ca. 40 %–60 %) may be due to the increase in CH4 mole fraction because the sensor voltage decreases with increasing CH4 mole fraction. Weekly median diel cycles tend to agree surprisingly well between the TGS 2600 and reference measurements during the snow-free season, but in winter the agreement is lower. We suggest developing separate functions for deducing CH4 mole fractions from TGS 2600 measurements under cold and warm conditions. We conclude that the TGS 2600 sensor can provide data of research-grade quality if it is adequately calibrated and placed in a suitable environment where cross-sensitivities to gases other than CH4 are of no concern. 

Accelerated warming in the Arctic has led to concern regarding the amount of carbon emission potential from Arctic water bodies. Yet, aquatic carbon dioxide (CO 2 ) and methane (CH 4 ) flux measurements remain scarce, particularly at high resolution and over long periods of time. Effluxes of methane (CH 4 ) and carbon dioxide (CO 2 ) from Toolik Lake, a deep glacial lake in northern Alaska, were measured for the first time with the direct eddy covariance (EC) flux technique during six ice-free lake periods (2010–2015). CO 2 flux estimates from the lake (daily average efflux of 16.7 ± 5.3 mmol m −2 d −1 ) were in good agreement with earlier estimates from 1975–1989 using different methods. CH 4 effluxes in 2010–2015 (averaging 0.13 ± 0.06 mmol m −2 d −1 ) showed an interannual variation that was 4.1 times greater than median diel variations, but mean fluxes were almost one order of magnitude lower than earlier estimates obtained from single water samples in 1990 and 2011–2012. The overall global warming potential (GWP) of Toolik Lake is thus governed mostly by CO 2 effluxes, contributing 86–93% of the ice-free period GWP of 26–90 g CO 2,eq m −2 . Diel variation in fluxes was also important, with up to a 2-fold (CH 4 ) to 4-fold (CO 2 ) difference between the highest nighttime and lowest daytime effluxes. Within the summer ice-free period, on average, CH 4 fluxes increased 2-fold during the first half of the summer, then remained almost constant, whereas CO 2 effluxes remained almost constant over the entire summer, ending with a linear increase during the last 1–2 weeks of measurements. Due to the cold bottom temperatures of this 26 m deep lake, and the absence of ebullition and episodic flux events, Toolik Lake and other deep glacial lakes are likely not hot spots for greenhouse gas emissions, but they still contribute to the overall GWP of the Arctic. 

We present a framework for assessing biogeochemical recovery of terrestrial ecosystems from disturbance. We identify three recovery phases. In Phase 1, nitrogen is redistributed from soil organic matter to vegetation, but the ecosystem continues to lose nitrogen because the recovering vegetation cannot take up nitrogen as fast as it is released from soil. In Phase 2, the ecosystem begins re-accumulating nitrogen and converges on a quasi-steady state in which vegetation and soil-microbial processes are in balance. In Phase 3, vegetation and soil-microbial processes remain in balance and the ecosystem slowly re-accumulates the remaining nitrogen. Phase 3 follows a balanced-accumulation trajectory along a continuum of quasi-steady states that approaches the true steady state asymptotically. We examine the effects of three ecosystem properties on recovery: openness of the nitrogen cycle, nitrogen distribution in and turnover between vegetation and soils, and the proportion of nitrogen losses that are in a refractory form. Openness exacerbates Phase 1 nitrogen losses but speeds recovery in Phases 2 and 3. A high fraction of ecosystem nitrogen in vegetation, resulting from nitrogen turnover that is slow in vegetation but fast in soil, exacerbates Phase 1 nitrogen losses but speeds recovery in Phases 2 and 3. A high proportion of nitrogen loss in refractory form mitigates Phase 1 nitrogen losses and speeds recovery in Phases 2 and 3. Application of our conceptual framework requires empirical recognition of the continuum of quasi-steady states constituting the balanced-accumulation trajectory and a distinction between the balanced-accumulation trajectory and the true steady state. 

Microbes and sunlight convert terrigenous dissolved organic matter (DOM) in surface waters to greenhouse gases. Prior studies show contrasting results about how biological and photochemical processes interact to contribute to the degradation of DOM. In this study, DOM leached from the organic layer of tundra soil was exposed to natural sunlight or kept in the dark, incubated in the dark with the natural microbial community, and analyzed for gene expression and DOM chemical composition. Microbial gene expression (metatranscriptomics) in light and dark treatments diverged substantially after 4 hours. Gene expression suggested that sunlight exposure of DOM initially stimulated microbial growth by (a) replacing the function of enzymes that degrade higher molecular weight DOM such as enzymes for aromatic carbon degradation, oxygenation, and decarboxylation, and (b) releasing low molecular weight compounds and inorganic nutrients from DOM. However, growth stimulation following sunlight exposure of DOM came at a cost. Sunlight depleted the pool of aromatic compounds that supported microbial growth in the dark treatment, ultimately causing slower growth in the light treatment over 5 days. These first measurements of microbial metatranscriptomic responses to photo-alteration of DOM provide a mechanistic explanation for how sunlight exposure of terrigenous DOM alters microbial processing and respiration of DOM.