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Over the past 4 decades, a number of numerical models have been developed to quantify the magnitude, investigate the spatial and temporal variations, and understand the underlying mechanisms and environmental controls of methane (CH4) fluxes within terrestrial ecosystems. These CH4 models are also used for integrating multi-scale CH4 data, such as laboratory-based incubation and molecular analysis, field observational experiments, remote sensing, and aircraft-based measurements across a variety of terrestrial ecosystems. Here we summarize 40 terrestrial CH4 models to characterize their strengths and weaknesses and to suggest a roadmap for future model improvement and application. Our key findings are that (1) the focus of CH4 models has shifted from theoretical to site- and regional-level applications over the past 4 decades, (2) large discrepancies exist among models in terms of representing CH4 processes and their environmental controls, and (3) significant data–model and model–model mismatches are partially attributed to different representations of landscape characterization and inundation dynamics. Three areas for future improvements and applications of terrestrial CH4 models are that (1) CH4 models should more explicitly represent the mechanisms underlying land–atmosphere CH4 exchange, with an emphasis on improving and validating individual CH4 processes over depth and horizontal space, (2) models should be developed that are capable of simulating CH4 emissions across highly heterogeneous spatial and temporal scales, particularly hot moments and hotspots, and (3) efforts should be invested to develop model benchmarking frameworks that can easily be used for model improvement, evaluation, and integration with data from molecular to global scales. These improvements in CH4 models would be beneficial for the Earth system models and further simulation of climate–carbon cycle feedbacks.

Microbial degradation of soil organic matter (SOM) is a key process for terrestrial carbon cycling, although the molecular details of these transformations remain unclear. This study reports the application of ultrahigh resolution mass spectrometry to profile the molecular composition of SOM and its degradation during a simulated warming experiment. A soil sample, collected near Barrow, Alaska, USA, was subjected to a 40-day incubation under anoxic conditions and analyzed before and after the incubation to determine changes of SOM composition. A CHO index based on molecular C, H, and O data was utilized to codify SOM components according to their observed degradation potentials. Compounds with a CHO index score between -1 and 0 in a water-soluble fraction (WSF) demonstrated high degradation potential, with a highest shift of CHO index occurred in the N-containing group of compounds, while similar stoichiometries in a base-soluble fraction (BSF) did not. Additionally, compared with the classical H:C vs O:C van Krevelen diagram, CHO index allowed for direct visualization of the distribution of heteroatoms such as N in the identified SOM compounds. We demonstrate that CHO index is useful not only in characterizing arctic SOM at the molecular level but also enabling quantitative description of SOM degradation, thereby facilitating incorporation of the high resolution MS datasets to future mechanistic models of SOM degradation and prediction of greenhouse gas emissions.

We demonstrate that UV-light activation of polycrystalline ZnO films on flexible polyimide (Kapton) substrates can be used to detect and differentiate between environmental changes in oxygen and water vapor. The in-plane resistive and impedance properties of ZnO films, fabricated from bacteria-derived ZnS nanoparticles, exhibit unique resistive and capacitive responses to changes in O 2 and H 2 O. We propose that the distinctive responses to O 2 and H 2 O adsorption on ZnO could be utilized to statistically discriminate between the two analytes. Molecular dynamic simulations (MD) of O 2 and H 2 O adsorption energy on ZnO surfaces were performed using the large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) with a reactive force-field (ReaxFF). These simulations suggest that the adsorption mechanisms differ for O 2 and H 2 O adsorption on ZnO, and are governed by the surface termination and the extent of surface hydroxylation. Electrical response measurements, using DC resistance, AC impedance spectroscopy, and Kelvin Probe Force Microscopy (KPFM), demonstrate differences in response to O 2 and H 2 O, confirming that different adsorption mechanisms are involved. Statistical and machine learning approaches were applied to demonstrate that by integrating the electrical and kinetic responses the flexible ZnO sensor can be used for detection and discrimination between O 2 and H 2 O at low temperature.

Thawing Arctic permafrost can induce hydrologic change and alter redox conditions, shifting the balance of soil organic matter (SOM) decomposition. There remains uncertainty about how soil saturation and redox transitions impact dissolved and gas phase carbon fluxes, and efforts to link hydrobiogeochemical processes to ecosystem-scale models are limited. This study evaluates SOM decomposition of Arctic tundra soils using column experiments, water chemistry measurements, microbial community analysis, and a PFLOTRAN reactive transport model. Soil columns from a thermokarst channel (TC) and an upland tundra (UC) were exposed to cycles of saturation and drainage, which controlled carbon emissions. During saturation, an outflow of dissolved organic carbon from the UC soil correlated with elevated reduced iron and decreased pH; during drainage, UC carbon dioxide fluxes were 70% higher than TC fluxes. Intermittent methane release was observed for TC, consistent with higher methanogen abundance. Slower drainage in the TC soil correlated with more subtle biogeochemical changes. PFLOTRAN simulations captured experimental trends in soil carbon fluxes, oxygen concentrations, and water contents. The model was then used to evaluate additional soil water drainage rates. This study emphasizes the importance of considering hydrologic change when evaluating and simulating SOM decomposition in dynamic Arctic tundra environments.

Glycoside hydrolase (GH) enzymes apply acid/base chemistry to catalyze the decomposition of complex carbohydrates. These ubiquitous enzymes accept protons from solvent and donate them to substrates at close to neutral pH by modulating the pKₐ values of key side chains during catalysis. However, it is not known how the catalytic acid residue acquires a proton and transfers it efficiently to the substrate. To better understand GH chemistry, we used macromolecular neutron crystallography to directly determine protonation and ionization states of the active site residues of a family 11 GH at multiple pD (pD = pH + 0.4) values. The general acid glutamate (Glu) cycles between two conformations, upward and downward, but is protonated only in the downward orientation. We performed continuum electrostatics calculations to estimate the pKₐ values of the catalytic Glu residues in both the apo- and substrate-bound states of the enzyme. The calculated pKₐ of the Glu increases substantially when the side chain moves down. The energy barrier required to rotate the catalytic Glu residue back to the upward conformation, where it can protonate the glycosidic oxygen of the substrate, is 4.3 kcal/mol according to free energy simulations. These findings shed light on the initial stage of the glycoside hydrolysis reaction in which molecular motion enables the general acid catalyst to obtain a proton from the bulk solvent and deliver it to the glycosidic oxygen.

CRISPR/Cas9 has been widely applied to various plant species accelerating the pace of plant genome editing and precision breeding in crops. Unintended effects beyond off-target nucleotide mutations are still somewhat unexplored. We investigated the degree and patterns of epigenetic changes after gene editing. We examined changes in DNA methylation in genome-edited promoters of naturally hypermethylated genes (AT1G72350 and AT1G09970) and hypomethylated genes (AT3G17320 and AT5G28770) from . Transgenic plants were developed via -mediated floral dip transformation. Homozygous edited lines were selected from segregated T plants by an digestion assay using ribonucleoprotein complex. Bisulfite sequencing comparisons were made between paired groups of edited and non-edited plants to identify changes in DNA methylation of the targeted loci. We found that directed mutagenesis via CRISPR/Cas9 resulted in no unintended morphological or epigenetic alterations. Phenotypes of wild-type, transgenic empty vector, and transgenic edited plants were similar. Epigenetic profiles revealed that methylation patterns of promoter regions flanking target sequences were identical among wild-type, transgenic empty vector, and transgenic edited plants. There was no effect of mutation type on epigenetic status. We also evaluated off-target mutagenesis effects in the edited plants. Potential off-target sites containing up to 4-bp mismatch of each target were sequenced. No off-target mutations were detected in candidate sites. Our results showed that CRISPR/Cas9 did not leave an epigenetic footprint on either the immediate gene-edited DNA and flanking DNA or introduce off-target mutations.

Climate change is warming tundra ecosystems in the Arctic, resulting in the decomposition of previously-frozen soil organic matter (SOM) and release of carbon (C) to the atmosphere; however, the processes that control SOM decomposition and C emissions remain highly uncertain. In this study, we evaluate geochemical factors that influence microbial production of carbon dioxide (CO₂) and methane (CH₄) in the seasonally-thawed active layer of interstitial polygonal tundra near Barrow, Alaska. We report spatial and seasonal patterns of dissolved gases in relation to the geochemical properties of Fe and organic C in soil and soil solution, as determined using spectroscopic and chromatographic techniques. The chemical composition of soil water collected during the annual thaw season varied significantly with depth. Soil water in the middle of the active layer contained abundant Fe(III), and aromatic-C and low-molecular-weight organic acids derived from SOM decomposition. At these depths, CH₄ was positively correlated with the ratio of Fe(III) to total Fe in waterlogged transitional and low-centered polygons but negatively correlated in the drier flat- and high-centered polygons. These observations contradict the expectation that CH₄ would be uniformly low where Fe(III) was high due to inhibition of methanogenesis by Fe(III)-reduction reactions. Our results suggest that vertically-stratified Fe redox reactions influence respiration/fermentation of SOM and production of substrates (e.g., low-molecular-weight organic acids) for methanogenesis, but that these effects vary with soil moisture. We infer that geochemical differences induced by water saturation dictate microbial products of SOM decomposition, and Fe geochemistry is an important factor regulating methanogenesis in anoxic tundra soils.

Linear nitramines (R–N(R′)NO 2 ; R′ = H or alkyl) are toxic compounds, some with environmental relevance, while others are rare natural product nitramines. One of these natural product nitramines is N -nitroglycine (NNG), which is produced by some Streptomyces strains and exhibits antibiotic activity towards Gram-negative bacteria. An NNG degrading heme enzyme, called NnlA, has recently been discovered in the genome of Variovorax sp. strain JS1663 ( Vs NnlA). Evidence is presented that NnlA and therefore, NNG degradation activity is widespread. To achieve this objective, we characterized and tested the NNG degradation activity of five Vs NnlA homologs originating from bacteria spanning several classes and isolated from geographically distinct locations. E. coli transformants containing all five homologs converted NNG to nitrite. Four of these five homologs were isolated and characterized. Each isolated homolog exhibited similar oligomerization and heme occupancy as Vs NnlA. Reduction of this heme was shown to be required for NnlA activity in each homolog, and each homolog degraded NNG to glyoxylate, NO 2 − and NH 4 + in accordance with observations of Vs NnlA. It was also shown that NnlA cannot degrade the NNG analog 2-nitroaminoethanol. The combined data strongly suggest that NnlA enzymes specifically degrade NNG and are found in diverse bacteria and environments. These results imply that NNG is also produced in diverse environments and NnlA may act as a detoxification enzyme to protect bacteria from exposure to NNG.

The candidate division Korarchaeota comprises a group of uncultivated microorganisms that, by their small subunit rRNA phylogeny, may have diverged early from the major archaeal phyla Crenarchaeota and EURYARCHAEOTA: Here, we report the initial characterization of a member of the Korarchaeota with the proposed name, \"Candidatus Korarchaeum cryptofilum,\" which exhibits an ultrathin filamentous morphology. To investigate possible ancestral relationships between deep-branching Korarchaeota and other phyla, we used whole-genome shotgun sequencing to construct a complete composite korarchaeal genome from enriched cells. The genome was assembled into a single contig 1.59 Mb in length with a G + C content of 49%. Of the 1,617 predicted protein-coding genes, 1,382 (85%) could be assigned to a revised set of archaeal Clusters of Orthologous Groups (COGs). The predicted gene functions suggest that the organism relies on a simple mode of peptide fermentation for carbon and energy and lacks the ability to synthesize de novo purines, CoA, and several other cofactors. Phylogenetic analyses based on conserved single genes and concatenated protein sequences positioned the korarchaeote as a deep archaeal lineage with an apparent affinity to the CRENARCHAEOTA: However, the predicted gene content revealed that several conserved cellular systems, such as cell division, DNA replication, and tRNA maturation, resemble the counterparts in the EURYARCHAEOTA: In light of the known composition of archaeal genomes, the Korarchaeota might have retained a set of cellular features that represents the ancestral archaeal form.

As the Arctic warms, thawing permafrost unlocks carbon, potentially accelerating climate change by releasing greenhouse gases. Our research delves into the underlying biogeochemical processes likely mediated by the soil microbial community in response to the wet and anaerobic conditions, akin to an Arctic summer thaw. We observed a significant shift in the microbial community post-thaw, with fermentative bacteria like Firmicutes and Bacteroidota taking over and switching to different fermentation pathways. The dominance of iron and sulfate-reducing bacteria likely constrained methane production in the thawing permafrost. Slow-growing microbes outweighed fast-growing ones, even after thaw, upending the expectation that rapid microbial responses to dominate after permafrost thaws. This research highlights the nuanced and complex interactions within Arctic soil microbial communities and underscores the challenges in predicting microbial response to environmental change.