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Relative abundances of all microbial PiCRUST-inferred functional pathways for all samples, based on 16S rRNA amplicon sequencing data from a mire-wide survey (2015) and co-analyzed autochamber site samples (2014-2015). The 16S rRNA amplicon sequencing data is available under NCBI BioProject PRJNA1236848. The sample metadata and SRA accessions are available at https://doi.org/10.5281/zenodo.15047156. FUNDING: National Aeronautics and Space Administration, Interdisciplinary Science program: From Archaea to the Atmosphere (award # NNX17AK10G). National Science Foundation, Biology Integration Institutes Program: EMERGE Biology Integration Institute (award # 2022070). United States Department of Energy Office of Biological and Environmental Research, Genomic Science Program: The IsoGenie Project (grant #s DE-SC0004632, DE-SC0010580, and DE-SC0016440). Sequencing was performed using startup funding from the University of Arizona to Virginia Rich. We thank the Swedish Polar Research Secretariat and SITES for the support of the work done at the Abisko Scientific Research Station. SITES is supported by the Swedish Research Council's grant 4.3-2021-00164. 

Stordalen Mire microbial ASV table (mire-wide_ASV_table.tsv) and taxonomy (mire-wide_taxonomy.tsv), based on 16S rRNA amplicon sequencing data from a mire-wide survey (2015) and co-analyzed autochamber site samples (2014-2015). The 16S rRNA amplicon sequencing data is available under NCBI BioProject PRJNA1236848. The sample metadata and SRA accessions are available at https://doi.org/10.5281/zenodo.15047156. FUNDING: National Aeronautics and Space Administration, Interdisciplinary Science program: From Archaea to the Atmosphere (award # NNX17AK10G). National Science Foundation, Biology Integration Institutes Program: EMERGE Biology Integration Institute (award # 2022070). United States Department of Energy Office of Biological and Environmental Research, Genomic Science Program: The IsoGenie Project (grant #s DE-SC0004632, DE-SC0010580, and DE-SC0016440). Sequencing was performed using startup funding from the University of Arizona to Virginia Rich. We thank the Swedish Polar Research Secretariat and SITES for the support of the work done at the Abisko Scientific Research Station. SITES is supported by the Swedish Research Council's grant 4.3-2021-00164. 

Stordalen Mire sample metadata from a mire-wide survey (2015) and co-analyzed autochamber site samples (2014-2015). These samples were analyzed by 16S rRNA amplicon sequencing, and the 16S data is available under NCBI BioProject PRJNA1236848. Column descriptions for this metadata file: The first 4 columns (sample_name, SRA library_ID, SRA accession, BioSample) include sample & library names and accessions in NCBI. The sample_name column also matches the SampleID__ attribute in the EMERGE Database (EMERGE-DB; https://emerge-db.asc.ohio-state.edu/). The next 7 columns (SampleID, Habitat, Depth, Description, Source, Site, Origin) are the metadata used for the 16S data analysis (results available at https://doi.org/10.5281/zenodo.15047596 and https://doi.org/10.5281/zenodo.15047715). The final 9 columns (Latitude, Longitude, Date, Full Site Name, Core #, DepthMin (cm), DepthMax (cm), DepthAvg (cm), pH_porewater) provide other metadata, including latitude/longitude, sampling dates, full site and core names, depths, and porewater pH, standardized to match the nomenclature in the EMERGE-DB. FUNDING: National Aeronautics and Space Administration, Interdisciplinary Science program: From Archaea to the Atmosphere (award # NNX17AK10G). National Science Foundation, Biology Integration Institutes Program: EMERGE Biology Integration Institute (award # 2022070). United States Department of Energy Office of Biological and Environmental Research, Genomic Science Program: The IsoGenie Project (grant #s DE-SC0004632, DE-SC0010580, and DE-SC0016440). Sequencing was performed using startup funding from the University of Arizona to Virginia Rich. We thank the Swedish Polar Research Secretariat and SITES for the support of the work done at the Abisko Scientific Research Station. SITES is supported by the Swedish Research Council's grant 4.3-2021-00164. 

Recovered microbial community structure is known to be influenced by sample storage conditions and nucleic acid extraction methods, and the impact varies by sample type. Peat soils store a large portion of soil carbon and their microbiomes mediate climate feedbacks. Here, we tested three storage conditions and five extraction protocols on peat soils from three physicochemically distinct habitats in Stordalen Mire, Sweden, revealing significant methodological impacts on microbial (here, meaning bacteria and archaea) community structure. Initial preservation method impacted alpha but not beta diversity, with in-field storage in LifeGuard buffer yielding roughly two-thirds the richness of in-field flash-freezing or transport from the field on ice (all samples were stored at −80 °C after return from the field). Nucleic acid extraction method impacted both alpha and beta diversity; one method (the PowerSoil Total RNA Isolation kit with DNA Elution Accessory kit) diverged from the others (PowerMax Soil DNA Isolation kit-High Humic Acid Protocol, and three variations of a modifiedPowerMax Soil DNA/RNA isolation kit), capturing more diverse microbial taxa, with divergent community structures. Although habitat and sample depth still consistently dominated community variation, method-based biases in microbiome recovery for these climatologically-relevant soils are significant, and underscore the importance of methodological consistency for accurate inter-study comparisons, long-term monitoring, and consistent ecological interpretations. 

Abstract The dynamics of methane (CH₄) cycling in high-latitude peatlands through different pathways of methanogenesis and methanotrophy are still poorly understood due to the spatiotemporal complexity of microbial activities and biogeochemical processes. Additionally, long-termin situmeasurements within soil columns are limited and associated with large uncertainties in microbial substrates (e.g. dissolved organic carbon, acetate, hydrogen). To better understand CH₄cycling dynamics, we first applied an advanced biogeochemical model,ecosys, to explicitly simulate methanogenesis, methanotrophy, and CH₄transport in a high-latitude fen (within the Stordalen Mire, northern Sweden). Next, to explore the vertical heterogeneity in CH₄cycling, we applied the PCMCI/PCMCI+ causal detection framework with a bootstrap aggregation method to the modeling results, characterizing causal relationships among regulating factors (e.g. temperature, microbial biomass, soil substrate concentrations) through acetoclastic methanogenesis, hydrogenotrophic methanogenesis, and methanotrophy, across three depth intervals (0–10 cm, 10–20 cm, 20–30 cm). Our results indicate that temperature, microbial biomass, and methanogenesis and methanotrophy substrates exhibit significant vertical variations within the soil column. Soil temperature demonstrates strong causal relationships with both biomass and substrate concentrations at the shallower depth (0–10 cm), while these causal relationships decrease significantly at the deeper depth within the two methanogenesis pathways. In contrast, soil substrate concentrations show significantly greater causal relationships with depth, suggesting the substantial influence of substrates on CH₄cycling. CH₄production is found to peak in August, while CH₄oxidation peaks predominantly in October, showing a lag response between production and oxidation. Overall, this research provides important insights into the causal mechanisms modulating CH₄cycling across different depths, which will improve carbon cycling predictions, and guide the future field measurement strategies. 

Abstract Soil microorganisms are pivotal in the global carbon cycle, but the viruses that affect them and their impact on ecosystems are less understood. In this study, we explored the diversity, dynamics, and ecology of soil viruses through 379 metagenomes collected annually from 2010 to 2017. These samples spanned the seasonally thawed active layer of a permafrost thaw gradient, which included palsa, bog, and fen habitats. We identified 5051 virus operational taxonomic units (vOTUs), doubling the known viruses for this site. These vOTUs were largely ephemeral within habitats, suggesting a turnover at the vOTU level from year to year. While the diversity varied by thaw stage and depth‐related patterns were specific to each habitat, the virus communities did not significantly change over time. The abundance ratios of virus to host at the phylum level did not show consistent trends across the thaw gradient, depth, or time. To assess potential ecosystem impacts, we predicted hostsin silicoand found viruses linked to microbial lineages involved in the carbon cycle, such as methanotrophy and methanogenesis. This included the identification of viruses ofCandidatusMethanoflorens, a significant global methane contributor. We also detected a variety of potential auxiliary metabolic genes, including 24 carbon‐degrading glycoside hydrolases, six of which are uniquely terrestrial. In conclusion, these long‐term observations enhance our understanding of soil viruses in the context of climate‐relevant processes and provide opportunities to explore their role in terrestrial carbon cycling.