The Rhodotorula mucilaginosa strain AIRLRB09-2 is a laboratory isolate with proven capability of polyurethane and volatile organic compounds (e.g., acetone and styrene, degradation). Here, we report the draft genome sequence of this yeast isolated from airlift, the bioreactor for waste gas treatment containing acetone and styrene.

Permafrost degradation creates hydrologically distinct landscapes, including dry soils with enhanced drainage and wet soils with poor drainage. In Fairbanks (Alaska, USA), we compared the active layer of dry and wet degraded permafrost landscapes with that of a non-degraded intact permafrost landscape to assess how hydrological conditions shape microbial community composition, extracellular enzyme activities, and microbial extracellular polymeric substances (EPS). Based on 16S rRNA sequencing, the alpha diversity of the prokaryotic community was significantly lower in the dry site compared to the wet and intact sites, with soil organic carbon (SOC) and pH identified as the primary environmental drivers. The active layer of the dry site was dominated by Thermoleophilia and Acidobacteriae, whereas the wet site was dominated by Gammaproteobacteria and Gemmatimonadetes. The relative proportions of most bacterial classes differed significantly across depths in the dry and wet sites, while the intact site exhibited less vertical variation. Hydrolytic enzyme activities were significantly higher in the topsoil across all sites, whereas oxidative enzyme activities showed relatively uniform patterns with depth but generally exceeded hydrolytic activities. EPS content varied among sites and depths, with the highest EPS-sugar content observed in the wet site overall, whereas topsoil EPS-sugar and EPS-protein contents were highest in the wet site, followed by the dry and intact sites, and subsoil EPS content was highest in the intact site. This study demonstrates that hydrological shifts in degraded permafrost soils shape microbial community structure, enzymatic activity patterns, and EPS content, with potential implications for SOC loss and stabilization.

BACKGROUND:Foliar endophytes contribute to plant nutrient acquisition, stress tolerance, and pathogen resistance, yet their responses to ecosystem-level processes remain poorly understood. Using a space-for-time substitution design, we investigated bacterial and fungal community dynamics in the foliar endosphere of four phylogenetically distinct plant hosts across a well-characterized successional chronosequence. RESULTS:Amplicon sequencing revealed that the ecosystem development stage (site age) significantly influenced endophyte community composition, particularly among fungi, but explained only a small proportion of the total variation. Host plant identity and associated leaf stoichiometry were stronger predictors of community structure, with sampling time within the growing season also contributing significantly. Together, these deterministic factors explained 10% and 11% of bacterial and fungal compositional variation, respectively, and 27% of predicted bacterial functional potential. Null model analyses indicated that remaining variation was mostly consistent with stochastic assembly processes, particularly ecological drift. Endophytic communities were characterized by a few persistent dominant taxa and many rare, transient members with overlapping functional potential, including N2 fixation, methylotrophy, and denitrification. CONCLUSIONS:Our findings demonstrate that host identity outweighs ecosystem age in structuring foliar endophyte communities and that stochastic processes play a central role in community assembly. The coexistence of stable dominant taxa and a dynamic rare biosphere may enhance plant responsiveness to environmental changes, while the functional potential of endophytes may remain largely consistent across seasons and successional stages.

Abstract. Understanding ancient climate dynamics is crucial to accurately forecast future changes to Earth’s climate system. The Norwegian High-Arctic archipelago of Svalbard experiences higher-magnitude warming than the lower latitudes. Its sedimentary succession provides an important climate archive spanning much of the Phanerozoic, including several hyperthermal events and mass extinctions of global importance. These include the End-Permian Mass Extinction (EPME) and the Paleocene–Eocene Thermal Maximum (PETM). In addition, the High Arctic Large Igneous Province (HALIP) provides an opportunity to study how igneous sills interact with organic-rich shales to generate greenhouse gases during contact metamorphism. The ongoing multidisciplinary international project SvalCLIME aims to systematically study these hyperthermal events and their relationships to Phanerozoic climate evolution. SvalCLIME seeks to drill multiple shallow boreholes at four sites in Spitsbergen that will provide a semi-continuous record of Phanerozoic stratigraphy from an underexplored region. The drill cores, in conjunction with outcrops, will provide a Permian–Eocene climate record of unprecedented continuity. Here, we synthesise existing pre-Quaternary Phanerozoic (540–2.58 Ma) paleoclimate and paleoenvironmental data from Svalbard in curated data packages to complement a recently published comprehensive review article. The data packages are organised by proxy, facilitating the addition of future data sets. We present composite data coverage plots of key proxies (stable carbon isotopes [δ13C], oxygen isotopes [δ18O], pyrolysis, mercury) that illustrate data availability and current data gaps. Further, we give an overview of available geochronological constraints for Svalbard’s pre-Quaternary Phanerozoic rock record, likewise curated into two data collections of 1) various methods that provide age constraints and 2) biostratigraphy. We also discuss the integration of various data sets in four case studies to illustrate the benefit of compiling such data for both drill cores (Longyearbyen CO2 lab and Deltadalen) and outcrops (Festningen, Lusitaniadalen, Munindalen and Billefjorden).

The Svalbard archipelago, located in the Norwegian High Arctic, preserves more than 650 million years of near-continuous sedimentary rock records spanning from the Neoproterozoic to the Cenozoic. The polar paleogeographic location of Svalbard in the late Mesozoic and the Cenozoic makes sites in Svalbard unique amongst well-studied temporally equivalent successions from lower paleolatitudes, allowing investigation of the polar amplification climatic effect over geological time. The sedimentary record of Svalbard has been largely controlled by northward drift of constituent geological provinces throughout much of the Phanerozoic and evolving tectono-stratigraphic environments including the influence of several Large Igneous Provinces (LIPs) and global climate fluctuations. The SVALCLIME initiative aims to systematically drill and core the sedimentary successions in Svalbard. Two sub-projects currently being evaluated by the ICDP materialized from an international workshop held in Longyearbyen in October 2022. The first is a full ICDP proposal focused on hyperthermals from the Permian to Paleogene (SVALCLIME P2P) and an ICDP-IODP Land to Sea preproposal on hothouse to coldhouse transitions in the late Paleozoic and across the Eocene–Oligocene transition (SVALCLIME Hot2Cold).The SVALCLIME P2P project aims to investigate the high-resolution Arctic paleoclimate record from 255 to 45 Ma onshore Svalbard that encompasses several Mesozoic and Cenozoic hyperthermal events and the near-field impacts of three LIPs (the Siberian Traps, the High Arctic LIP and the North Atlantic Igneous Province). Our focus will also be on the deep biosphere to uncover the relationship between mineral substrates and taxonomic and metabolic diversity of intraterrestrial microbiomes. We propose to core seven boreholes at three locations (Nordenskiöldfjellet, Botneheia and Kropotkinfjellet), with a cumulative total cored length of ~3.4 km. The SVALCLIME Hot2Cold project aims to address global transitions from hothouse to icehouse conditions during the late Paleozoic and the Eocene to Oligocene. In the preproposal we identify suitable drill sites both onshore and offshore to characterize these periods. The Forlandsundet Graben in western Spitsbergen offers an opportunity to decipher the evolution of the Fram Strait and its impact on global oceanographic circulation during the Eocene–Oligocene transition. The Upper Carboniferous to Early Permian syn and post-rift deposits of the Billefjorden Trough will be targeted to investigate >130 cyclothems originating from glacioeustatic sea level fluctuations.In this contribution, we outline the background and motivation of the SVALCLIME initiative and present the scientific objectives and the proposed drill sites.

Colonization by pioneer plants, among which the arctic willow (Salix polaris) is one of the most important, accelerates soil development after deglaciation. This is achieved through the increased input of organic matter from plant biomass and the exudation of low molecular mass organic compounds (LMMOA), predominantly organic acids, which facilitate mineral dissolution and nutrient release. These exudates support microbial activity and contribute to the formation of soil organic matter. While there is quite a lot of data on the exudation and acceleration of microbial activity in the rhizosphere of various plants, similar data concerning arctic plants, including willow, are scarce. Furthermore, there is a lack of data on the effect of C, N, P root stoichiometry on nutrient content in exudates and the rhizosphere microbiome during soil succession after deglaciation. In this study, we analysed various habitats of high-arctic tundra in Petuniabukta (Billefjorden, Svalbard), representing different stages of vegetation development. Our objectives were (i) to assess soil and rhizosphere carbon and nutrient content and availability, as well as microbial biomass CNP; (ii) to evaluate the rhizosphere effect on nutrient availability and the microbiome of arctic willow; and (iii) to measure root and exudation CNP and quality, primarily LMMOA, in arctic willow from the studied habitats. The exudates released to deionised water were analysed for LMMOA and inorganic anions (ion chromatography) as well as the total content of C and N. The plants roots were analysed for CNP content. Soil chemical properties (e.g. pH, organic C, total and exchangeable content of elements, water extractable PO43−) and microbial parameters (microbial biomass and quantity of bacteria and fungi) were assessed in both rhizosphere and bulk soils, with the rhizosphere effect calculated accordingly. The most abundant LMMOA species in willow exudates were lactate, acetate, formate, malate and citrate, followed by pyruvate, quinate and oxalate, collectively representing approximately 2

The methane-cycling microbiomes play crucial roles in methane dynamics. However, little is known about their distributions on a pan-Arctic scale as well as their responses to the widespread permafrost degradation. Based on 621 datasets of 16S rRNA gene amplicons from intact permafrost soils across the pan-Arctic, we identified only 22 methanogen and 26 methanotroph phylotypes. Their relative abundances varied significantly between sites and soil horizons. Only four methanogen phylotypes were detected at all locations. Remarkably, the permafrost soil methane filter was almost exclusively dominated by some obligate methanotroph (Methylobacter-like) phylotypes. However, a case study in Alaska suggests that atmospheric methane oxidizing bacteria (Methylocapsa-like phylotypes) dominated methanotrophs in a drier condition after permafrost degradation. These findings point towards a few key microbes particularly relevant for future studies on Arctic methane dynamics in a warming climate and that under future dry conditions, increased atmospheric methane uptake in Arctic upland soils may occur.

The redox status of permafrost soils is a decisive factor for their nutrient cycling, organic matter decomposition, and greenhouse gas emissions. Although being associated with a variety of processes, data availability of continuous redox measurements in permafrost soils is scarce. Here, we provide a unique dataset covering three years of soil redox potential measurements, obtained from a monitoring approach at three research sites near Fairbanks, Alaska. Redox potential pattern in the permafrost soil active layer showed large seasonal differences, with reducing conditions in the short summer/autumn to largely oxidizing conditions in winter and spring. However, conditions for methane production were at no time recorded in the three years. Especially the freezing and thawing had substantial impact on the redox status, highlighting that assessment of redox conditions in permafrost soils should be extended beyond the typical summer observation periods.

Permafrost degradation, freezing and thawing processes, and poor drainage due to underlain frozen ground have far-reaching consequences on soil hydrology and biology and, thus, on the redox dynamic in soils of the Arctic. Assessing the redox status of these soils is essential for understanding soil organic matter decomposition processes and can be done by temporal measurements in the field, analyses of redox-sensitive elements, or identification of microbial species or enzymes in redox process chains. While such approaches provide snippets of the complex redox dynamic, publications reporting long-term in-situ redox potential (EH) measurements in arctic permafrost soils are scarce. Limited accessibility to study sites and technical limitations in measuring the redox potential in a frozen environment may be two reasons for this research gap.But how does the redox potential develop in permafrost soils at different depths in the active layer during the summer? What happens during freezing and thawing? Finally, do thawing/degrading permafrost soils show different patterns compared to intact permafrost?We approached these research questions by installation of a unique soil monitoring setup at 3 sites near Fairbanks, Alaska, in August 2021. An intact permafrost soil (active layer depth about 50 cm) was equipped with 3 redox electrodes (for EH) and 3 hydra probes (for water content and soil temperature) in the topsoil and subsoil, respectively, and connected to a logger unit allowing continuous measurement of these parameters in both depths every 15 minutes. In addition, two sites with advanced permafrost degradation (permafrost level below 100 cm) were equipped in the same way. One degraded site featured large water contents, representing a wet thaw scenario, while the other site was well-drained, representing a dry thaw scenario, thus representing different endmembers of the ongoing climate-change induced permafrost thaw.Here, we present the first 2 years of soil monitoring in a discontinuous permafrost area in Interior Alaska from 09/2021 to 09/2023. Overall, pH values of all soils varied between 4.5-6.3. The dry thaw scenario showed oxic conditions (i.e., EH >600 mV) in top- and subsoil, while water contents were low. The wet thaw scenario exhibited high topsoil redox potentials (i.e., EH >500 mV), while subsoil redox potential was lower (i.e., EH 400 mV in the summer period (August to October), suggesting less oxygen consumption in this recently thawed permafrost subsoil.

Wet grasslands are highly productive wetland ecosystems that provide many important ecosystem services, including nutrient removal for water purification, carbon (C) sequestration, local climate regulation, water retention, and flood attenuation. Like other ecosystems, wet grasslands are affected by multiple biotic and abiotic factors, the interactions of which may affect their functionality. We conducted a fully factorial mesocosm experiment to disentangle the importance of soil type (mineral or organic), water (high vs low) and nutrient level (NPK fertilized or unfertilized) effects on plant and soil parameters and how these affect ecosystem respiration (RECO) and greenhouse gas (GHG) emissions. In the fifth year of the experiment, we measured plant biomass and production, soil biological and chemical parameters, and GHG fluxes four times during the year, once before the start of the growing season and then in the beginning, peak and end of the growing season. We found that plant, soil and GHG parameters showed distinct seasonality and were influenced by all tested factors, both singly and interactively, affecting many aspects of wet grassland ecosystems by acting through several plant-soil feedbacks. Soil type, both primarily and in several interactions with water and nutrient levels, controlled soil properties, microbial biomass, and bacterial and fungal abundances. Plant presence, the productivity of which was stimulated by nutrient addition, together with some plant-soil feedbacks, were the main drivers of RECO and GHG emissions (relevant only for CH4 because N2O was not emitted in any sampling occasion). As a result, CO2 and CH4 emissions were 12 and 3 times greater, respectively, in vegetated compared to un-vegetated samples. In addition, water level and nutrient addition interactions influenced gas emissions, with CO2 emissions being greater in low water, fertilized conditions, while CH4 emissions increased under high water, unfertilized conditions. When correcting for the greater global warming potential (GWP) of CH4, it still accounted for only a maximum of 18 % of the GHG fluxes. We showed that multiple environmental factors interact to impact wet grassland functions. Managers should focus their activities on managing the factors that most allow for wet grasslands to maintain their structure and functions to future disturbances.

ABSTRACTPermafrost microbial research has flourished in the past decades, due in part to improvements in sampling and molecular techniques, but also the increased focus on the permafrost greenhouse gas feedback to climate change and other ecological processes in high latitude and alpine permafrost soils. Permafrost microorganisms are adapted to these extreme environments and remain active at low temperatures and when resources are limited. They are also an important component of global elemental cycles as they regulate organic matter turnover and greenhouse gas production, particularly as permafrost thaws. Here we review the permafrost microbiology literature coupled with an exploration of its historical aspects, with a particular focus on a new understanding advanced by molecular biology techniques. We further identify knowledge gaps and ways forward to improve our understanding of microbial contributions to ecosystem biogeochemistry of permafrost‐affected systems.

Bacterial exopolysaccharides (EPS) act as natural biopolymers that bind soil particles together, promoting structural stability and creating protective microenvironments for microbial survival. This study aimed to isolate and characterize potential EPS-producing bacteria from the active layer of two degraded permafrost soils with different hydrological landscapes, and from non-degraded permafrost soil. A total of 64 bacterial isolates were obtained, representing three phyla: Firmicutes, Actinomycetota, and Pseudomonadota. EPS production was assessed by determining the polysaccharide content measured as glucose equivalent, and 26 bacterial isolates were identified as potential EPS producers. Among the bacterial isolates, Curtobacterium oceanosedimentum, Frigoribacterium faeni, Streptomyces strains, Neobacillus bataviensis, and Mesobacillus subterraneus exhibited high polysaccharide concentrations. Uronic acids were present in EPS produced by C. oceanosedimentum and N. bataviensis, while amino sugars were identified in EPS from isolates of Bacillus, Streptomyces, Luteimonas, and Phyllobacterium. Based on 16S rRNA gene sequence similarities, the relative proportion of taxa associated with EPS-producing bacterial isolates such as Bacillus, Peribacillus, and Streptomyces was higher in the dry site, while Neobacillus, Pseudarthrobacter, and Microbacterium were more abundant in the wet and intact sites. This study suggests that EPS production with diverse carbohydrate compositions primarily promotes structural stability in degrading permafrost soils by binding soil particles together and forming protective microenvironments. Additionally, EPS may contribute to nutrient retention and microbial protection under fluctuating environmental conditions, complementing their primary role in soil stability.

The methane-cycling microbiomes in Arctic permafrost-affected soils play crucial roles in the production and consumption of this important greenhouse gas. However, little is known about the distributions of Arctic methanogens and methanotrophs across the regional scale and along the vertical soil profile, as well as their responses to the widespread permafrost thaw. Using a unique sample set from nine different locations across the pan-Arctic, we identified methanogen and methanotroph phylotypes in 729 datasets of 16S rRNA gene amplicons. In 621 samples of intact permafrost soils across the pan-Arctic, only 22 methanogen and 26 methanotroph phylotypes were identified. Relative abundances of both functional groups varied significantly between sites and soil horizons. Only four methanogen phylotypes were detected at all locations, with the hydrogenotrophic Methanobacterium lacus dominating. Remarkably, the permafrost soil methane filter was almost exclusively comprised of a few phylotypes closely related to the obligate methanotrophic species Methylobacter tundripaludum. In degraded permafrost sites in Alaska, M. tundripaludum also dominated the methanotroph microbiome in the wet site. However, in dry, water-drained former permafrost site, Methylocapsa phylotypes, closely related with the atmospheric methane oxidizing bacteria, were exclusively found and dominant, indicating a massive restructuring of the methanotroph guild that consequently resulted in functional changes from a soil methane filter to an atmospheric methane sink. This study provides first insights into the identity and intricate spatial distribution of methanotrophs and methanogens in permafrost soils at a pan-Arctic scale and their responses to different water status after permafrost degradation. These findings point towards a few key microbes particularly relevant for future studies on Arctic CH4 dynamics in a warming climate and that under future dry conditions more atmospheric CH4 uptake in Arctic upland soils might happen. ### Competing Interest Statement The authors have declared no competing interest.

Changes in organic matter accumulation in wetlands are critical for climate dynamics. Different nitrogen (N) inputs in Sphagnum-dominated peat bogs can lead to varying rates of carbon (C) and N accumulation, influencing greenhouse gas emissions. We investigated how contrasting N deposition shapes microbial communities in two Czech peat bogs, focusing on biological N2 fixation (BNF) as a key N input in pristine wetlands. Higher N deposition resulted in a more active microbial community with increased enzyme activity and C acquisition, potentially accelerating decomposition and reducing C storage. Enhanced denitrification, indicated by active nosZ Clade I genes, suggests that higher N inputs may increase N losses through denitrification. In contrast, the lower N site showed a less active microbial community with slower decomposition, beneficial for C sequestration, though potentially less adaptable to future N increases. Experimental BNF rates were 70 times higher at the high N site, consistent with elevated diazotroph activity indicated by active nifH gene. Phosphorus (P) availability and NH4+/NO3− ratios appeared to drive BNF differences, emphasizing the need for managed N inputs to maintain peatland ecological functions.

Permafrost soils in the northern hemisphere are known to harbor large amounts of soil organic matter (SOM). Global climate warming endangers this stable soil organic carbon (SOC) pool by triggering permafrost thaw and deepening the active layer, while at the same time progressing soil formation. But depending, e.g., on ice content or drainage, conditions in the degraded permafrost can range from water-saturated/anoxic to dry/oxic, with concomitant shifts in SOM stabilizing mechanisms. In this field study in Interior Alaska, we investigated two sites featuring degraded permafrost, one water-saturated and the other well-drained, alongside a third site with intact permafrost. Soil aggregate- and density fractions highlighted that permafrost thaw promoted macroaggregate formation, amplified by the incorporation of particulate organic matter, in topsoils of both degradation sites, thus potentially counteracting a decrease in topsoil SOC induced by the permafrost thawing. However, the subsoils were found to store notably less SOC than the intact permafrost in all fractions of both degradation sites. Our investigations revealed up to net 75

Despite rapid progress in plant–microbe interaction research within terrestrial environments, our knowledge of aquatic plant and macroalgae microbiome structure, function, and ecology remains scarce, even though these hosts are key players in structuring the lacustrine environments. Here, we used the co-occurring, fast-growing hosts Hydrilla verticillata (Hydrocharitaceae) and Cladophora spp. (Chlorophyta), which dominate the littoral zones of a nitrogen-limited, hard-water lake, Lake Atitlán (Guatemala). The aim of this study was: (1) to assess the structure of Hydrilla phyllosphere-associated and Cladophora filament-associated bacterial and fungal assemblages in the context of host specificity; (2) to predict microbial potential to contribute to biogeochemical cycling in the lake littoral; and (3) to compare the aquatic microbiome structure to available datasets from terrestrial ecosystems, using next-generation amplicon sequencing, co-occurrence network analysis, and N2-fixation activity measurements. We show that the microbiomes associated with the phyllosphere of aquatic macrophytes and macroalgal filaments are surprisingly similar, with taxonomic and functional complexity analogous to that of rhizospheric assemblages in terrestrial plants, and have a potential to efficiently recycle nutrients from organic matter. We suggest that especially the fungal associations with these hosts represent an untapped research area of microbial ecology that warrants further attention.

Permafrost degradation leads to the formation of contrasting hydrological conditions such as water-saturated anoxic and dry oxic soils, which significantly influence the bacterial community structure and abundance. To investigate the bacterial abundance and diversity under these hydrological conditions, we collected soil samples from different horizons of both dry and wet degraded permafrost soils and non-degraded intact permafrost soil for comparison. The bacterial alpha diversity, measured by the Observed and Chao1 indices, was significantly greater in wet degraded permafrost soil (wet site) and intact permafrost soil (intact site) than in dry degraded permafrost soils (dry site). Notably, the wet and intact sites exhibited similar levels of alpha diversity as well as shared greater number of zOTUs. The relative proportion of most bacterial taxa was significantly differed among the sites. At the class level, dry site was dominated mainly by K-strategic bacteria like aliphatic degraders (Thermoleophilia), acidophilic and cellulolytic (Acidobacteriae), while wet site was dominated by mainly r-strategic bacteria from class Gammaproteobacteria and anoxygenic aerobic phototrophs (Gemmatimonadetes). According to Spearman correlation analysis, the relative proportion of bacterial taxa in dry and wet sites showed significant correlation with soil physicochemical parameters, whereas fewer correlations were found in intact site. The relative proportion of Pseudomonadota classes and Acidobacteriota were positively correlated with SOC, N, and C:N ratio, but were negatively correlated with pH in both dry and wet sites. In contrast, anaerobic methylotrophs (Methylomirabilota), anoxygenic photoheterotrops (Chloroflexota), Gemmatimonadota and filamentous Actinobacteriota were negatively correlated with SOC, N, and C:N. Additionally, strong correlations were observed between bacterial taxa and extracellular enzyme activities, where Alphaproteobacteria, Gammaproteobacteria, and Acidobacteriota showed positive correlations with both hydrolytic and oxidative enzymes in dry and wet sites, except for PerOx in wet site where they showed negative correlation. Conversely, Gemmatimonadota and Actinobacteriota displayed negative correlations with enzymes in dry and wet site, except for the PerOx in wet site, where they showed positive correlation. ### Competing Interest Statement The authors have declared no competing interest.