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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.

This article discusses the importance of ethical and inclusive engagement between non-Indigenous researchers and Indigenous communities in Arctic research. It acknowledges the historical mistreatment of Indigenous peoples by researchers and emphasizes the need to build respectful relationships. The article provides ten rules for researchers to follow, including researching the culture and history of the research site, understanding different approaches to knowledge production, and establishing reciprocal community relationships. It highlights the value of Indigenous knowledge and the need for collaboration with Indigenous communities for high-quality research outcomes. The document offers guidelines and best practices for researchers seeking to collaborate with Arctic Indigenous communities, emphasizing the importance of recognizing shared humanity, respectful contact methods, aligning research questions with community objectives, compensating Indigenous participants, and planning for the continuation of research and scientific engagement. The paper underscores the need for ethical collaboration that centers Indigenous sovereignty, empowerment, and self-determination, while respecting Indigenous communities and their land and resources. [Extracted from the article]

In the past few decades, there has been an evolution in our understanding of soil organic matter (SOM) dynamics from one of inherent biochemical recalcitrance to one deriving from plant‐microbe‐mineral interactions. This shift in understanding has been driven, in part, by influential conceptual frameworks which put forth hypotheses about SOM dynamics. Here, we summarize several focal conceptual frameworks and derive from them six controls related to SOM formation, (de)stabilization, and loss. These include: (a) physical inaccessibility; (b) organo‐mineral and ‐metal stabilization; (c) biodegradability of plant inputs; (d) abiotic environmental factors; (e) biochemical reactivity and diversity; and (f) microbial physiology and morphology. We then review the empirical evidence for these controls, their model representation, and outstanding knowledge gaps. We find relatively strong empirical support and model representation of abiotic environmental factors but disparities between data and models for biochemical reactivity and diversity, organo‐mineral and ‐metal stabilization, and biodegradability of plant inputs, particularly with respect to SOM destabilization for the latter two controls. More empirical research on physical inaccessibility and microbial physiology and morphology is needed to deepen our understanding of these critical SOM controls and improve their model representation. The SOM controls are highly interactive and also present some inconsistencies which may be reconciled by considering methodological limitations or temporal and spatial variation. Future conceptual frameworks must simultaneously refine our understanding of these six SOM controls at various spatial and temporal scales and within a hierarchical structure, while incorporating emerging insights. This will advance our ability to accurately predict SOM dynamics. Plain Language Summary: Soil organic matter, the remains of plants, animals, and microbes in the soil, performs many important functions for humans and ecosystems, providing habitat for animals, nutrients for plants, climate change buffering, and structure for soil animals and human structures. Thus, it is important to understand how soil organic matter is formed, stabilized, and lost. Here, we review conceptual frameworks that have contributed to our understanding of soil organic matter over the past 20 years. We evaluate their support in experiments and also how well represented they are in computer models. We find the least support and representation for controls of soil organic matter associated with properties of microbes and physical barriers between microbes and soil organic matter. These and novel soil organic matter controls require more research for better understanding of soil organic matter functions. Key Points: Soil organic matter (SOM) research has been advanced by conceptual frameworksConceptual frameworks are associated with different SOM controls with variable empirical support and model representationMicrobial physiology and morphology and physical inaccessibility, as SOM controls, require more empirical work and model representation [ABSTRACT FROM AUTHOR]

Water table depth and vegetation are key controls of methane (CH4) emissions from peatlands. Microtopography integrates these factors into features called microforms. Microforms often differ in CH4 emissions, but microform‐dependent patterns of belowground CH4 cycling remain less clearly resolved. To investigate the impact of microtopography on belowground CH4 cycling, we characterized depth profiles of the community composition and activity of CH4‐cycling microbes using 16S rRNA amplicon sequencing, incubations, and measurements of porewater CH4 concentration and isotopic composition from hummocks and lawns at Sallie's Fen in NH, USA. Geochemical proxies of methanogenesis and methanotrophy indicated that microforms differ in dominant microbial CH4 cycling processes. Hummocks, where water table depth is lower, had higher porewater redox potential (Eh) and higher porewater δ13C‐CH4 values in the upper 30 cm than lawns, where water table depth is closer to the peat surface. Porewater δ13C‐CH4 and δD‐CH3D values were highest at the surface of hummocks where the ratio of methanotrophs to methanogens was also greatest. These results suggest that belowground CH4 cycling in hummocks is more strongly regulated by methanotrophy, while in lawns methanogenesis is more dominant. We also investigated controls of porewater CH4 chemistry. The ratio of the relative abundance of methanotrophs to methanogens was the strongest predictor of porewater CH4 concentration and δ13C‐CH4, while vegetation composition had minimal influence. As microbial community composition was strongly influenced by redox conditions but not vegetation, we conclude that water table depth is a stronger control of belowground CH4 cycling across microforms than vegetation. Plain Language Summary: Northern peatlands are significant sources of the greenhouse gas methane (CH4) to the atmosphere. Patterns of CH4 emissions across peatlands often mirror patterns in water table level, vegetation cover, and elevation over small spatial scales as these factors influence microbial CH4 production and consumption. We investigated microbial CH4 production and consumption across areas in a northern peatland with varying water table depth and vegetation cover using measurements of belowground CH4 chemistry and microbial DNA sequencing. We observed consistent signals in the belowground concentration and stable isotope composition of CH4, which can indicate where different microbial processes are occurring, that suggest slightly elevated areas with lower water table depth are hotspots for CH4 consumption while CH4 production is more prominent in areas that are lower and wetter. Overall, both CH4 chemistry and microbial communities were more strongly influenced by changes in moisture than vegetation. These insights are important for understanding how climate change may impact CH4 cycling, as CH4 producing and consuming microbes respond differently to changes in temperature and moisture. Better understanding of the distribution of CH4 production and consumption across the landscape may also help scale predictions of CH4 emissions across larger areas for global modeling efforts. Key Points: Surface porewater δ13C‐CH4 and δD‐CH3D values were more reflective of methanotrophy in hummocks and methanogenesis in lawnsCommunity composition of methanogens and methanotrophs was influenced by redox conditions and water table level across microtopographyVegetation cover had limited influence on microbial community composition and porewater CH4 concentration and stable isotope composition [ABSTRACT FROM AUTHOR]

Permafrost thaw could induce substantial carbon (C) emissions to the atmosphere, and thus trigger a positive feedback to climate warming. As the engine of biogeochemical cycling, soil microorganisms exert a critical role in mediating the direction and strength of permafrost C‐climate feedback. However, our understanding about the impacts of thermokarst (abrupt permafrost thaw) on microbial structure and function remains limited. Here we employed metagenomic sequencing to analyze changes in topsoil (0–15 cm) microbial communities and functional genes along a permafrost thaw sequence (1, 10, and 16 years since permafrost collapse) on the Tibetan Plateau. By combining laboratory incubation and a two‐pool model, we then explored changes in soil labile and stable C decomposition along the thaw sequence. Our results showed that topsoil microbial α‐diversity decreased, while the community structure and functional gene abundance did not exhibit any significant change at the early stage of collapse (1 year since collapse) relative to non‐collapsed control. However, as the time since the collapse increased, both the topsoil microbial community structure and functional genes differed from the control. Abundances of functional genes involved in labile C degradation decreased while those for stable C degradation increased at the late stage of collapse (16 years since collapse), largely driven by changes in substrate properties along the thaw sequence. Accordingly, faster stable C decomposition occurred at the late stage of collapse compared to the control, which was associated with the increase in relative abundance of functional genes for stable C degradation. These results suggest that upland thermokarst alters microbial structure and function, particularly enhances soil stable C decomposition by modulating microbial functional genes, which could reinforce a warmer climate over the decadal timescale. [ABSTRACT FROM AUTHOR]

The magnitude of carbon (C) loss to the atmosphere via microbial decomposition is a function of the amount of C stored in soils, the quality of the organic matter, and physical, chemical and biological factors that comprise the environment for decomposition. The decomposability of C is commonly assessed by laboratory soil incubation studies that measure greenhouse gases mineralized from soils under controlled conditions. Here, we introduce the Soil Incubation Database (SIDb) version 1.0, a compilation of time series data from incubations, structured into a new, publicly available database of C flux (carbon dioxide, CO2, or methane, CH4). In addition to open access, the SIDb project also provides a platform for the development of tools for reading and analysis of incubation data as well as documentation for future use and development. In addition to introducing SIDb, we provide reporting guidance for database entry and the required variables that incubation studies need at minimum to be included in SIDb. A key application of this synthesis effort is to better characterize soil C processes in Earth system models, which will in turn reduce our uncertainty in predicting the response of soil C decomposition to a changing climate. We demonstrate a framework to fit curves to a number of incubation studies from diverse ecosystems, depths, and organic matter content using a built-in model development module that integrates SIDb with the existing SoilR package to estimate soil C pools from time series data. The database will help bridge the gap between site-level measurements, which are commonly used in incubation studies, and global remote-sensed data or data products derived from models aimed at assessing global-scale rates of decomposition and C turnover. [ABSTRACT FROM AUTHOR]

Permafrost thaw can alter the soil environment through changes in soil moisture, frequently resulting in soil saturation, a shift to anaerobic decomposition, and changes in the plant community. These changes, along with thawing of previously frozen organic material, can alter the form and magnitude of greenhouse gas production from permafrost ecosystems. We synthesized existing methane (CH4) and carbon dioxide (CO2) production measurements from anaerobic incubations of boreal and tundra soils from the geographic permafrost region to evaluate large-scale controls of anaerobic CO2 and CH4 production and compare the relative importance of landscape-level factors (e.g., vegetation type and landscape position), soil properties (e.g., pH, depth, and soil type), and soil environmental conditions (e.g., temperature and relative water table position). We found fivefold higher maximum CH4 production per gram soil carbon from organic soils than mineral soils. Maximum CH4 production from soils in the active layer (ground that thaws and refreezes annually) was nearly four times that of permafrost per gram soil carbon, and CH4 production per gram soil carbon was two times greater from sites without permafrost than sites with permafrost. Maximum CH4 and median anaerobic CO2 production decreased with depth, while CO2:CH4 production increased with depth. Maximum CH4 production was highest in soils with herbaceous vegetation and soils that were either consistently or periodically inundated. This synthesis identifies the need to consider biome, landscape position, and vascular/moss vegetation types when modeling CH4 production in permafrost ecosystems and suggests the need for longer-term anaerobic incubations to fully capture CH4 dynamics. Our results demonstrate that as climate warms in arctic and boreal regions, rates of anaerobic CO2 and CH4 production will increase, not only as a result of increased temperature, but also from shifts in vegetation and increased ground saturation that will accompany permafrost thaw. [ABSTRACT FROM AUTHOR]