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Rewetted peatlands can be a significant source of methane (CH4), but in coastal ecosystems, input of sulfate-rich seawater could potentially mitigate these emissions. The presence of sulfate as an electron acceptor during organic matter decomposition is known to suppress methanogenesis by favoring the growth of sulfate reducers, which outcompete methanogens for substrate. We investigated the effects of a brackish water inflow on the microbial communities relative to CH4 production–consumption dynamics in a freshwater rewetted fen at the southern Baltic Sea coast after a storm surge in January 2019 and analyzed our data in context with the previous freshwater rewetted state (2014 serves as our baseline) and the conditions after a severe drought in 2018 (Fig. 1). We took peat cores at four previously sampled locations along a brackishness gradient to compare soil and pore water geochemistry as well as the microbial methane- and sulfate-cycling communities with the previous conditions. We used high-throughput sequencing and quantitative polymerase chain reaction (qPCR) to characterize pools of DNA and RNA targeting total and putatively active bacteria and archaea. Furthermore, we measured CH4 fluxes along the gradient and determined the concentrations and isotopic signatures of trace gases in the peat. We found that both the inflow effect of brackish water and the preceding drought increased the sulfate availability in the surface and pore water. Nevertheless, peat soil CH4 concentrations and the 13C compositions of CH4 and total dissolved inorganic carbon (DIC) indicated ongoing methanogenesis and little methane oxidation. Accordingly, we did not observe a decrease in absolute methanogenic archaea abundance or a substantial change in methanogenic community composition following the inflow but found that the methanogenic community had mainly changed during the preceding drought. In contrast, absolute abundances of aerobic methanotrophic bacteria decreased back to their pre-drought level after the inflow, while they had increased during the drought year. In line with the higher sulfate concentrations, the absolute abundances of sulfate-reducing bacteria (SRB) increased – as expected – by almost 3 orders of magnitude compared to the freshwater state and also exceeded abundances recorded during the drought by over 2 orders of magnitude. Against our expectations, methanotrophic archaea (ANME), capable of sulfate-mediated anaerobic methane oxidation, did not increase in abundance after the brackish water inflow. Altogether, we could find no microbial evidence for hampered methane production or increased methane consumption in the peat soil after the brackish water inflow. Because Koebsch et al. (2020) reported a new minimum in CH4 fluxes at this site since rewetting of the site in 2009, methane oxidation may, however, take place in the water column above the peat soil or in the loose organic litter on the ground. This highlights the importance of considering all compartments across the peat–water–atmosphere continuum to develop an in-depth understanding of inflow events in rewetted peatlands. We propose that the changes in microbial communities and greenhouse gas (GHG) fluxes relative to the previous freshwater rewetting state cannot be explained with the brackish water inflow alone but were potentially reinforced by a biogeochemical legacy effect of the preceding drought.

Rewetting of drained peatlands reduces the emissions of carbon dioxide (CO2) and nitrous oxide (N2O) substantially. However, elevated methane (CH4) emissions can occur, at least in the short-term. The impact of rewetting coastal peatlands with brackish water remains yet unclear, although beneficial effects such as lower CH4 emissions seem likely, due to high sulfate availability. Here, we compare pre- and post-rewetting greenhouse gas fluxes, biogeochemical parameters and the abundance of specific microbial groups in a coastal peatland at the German Baltic Sea coast that was formerly drained and used as an agricultural grassland and recently rewetted with brackish water. We hypothesized that flooding with brackish seawater reduces CO2 emissions despite favoring sulfate-reducers. It should also limit CH4 production and favor anaerobic methane and thus keep CH4 emissions low although aerobic methane oxidation may decrease. We measured CH4 and CO2 fluxes along a soil wetness gradient before rewetting and along a water level gradient after rewetting with brackish seawater and estimated cumulative CH4, CO2 net ecosystem exchange (NEE), and ecosystem respiration (Reco). Soil cores for biogeochemical and microbial analyses were taken at seven locations along the transect pre- and post-rewetting. We used quantitative polymerase chain reaction (qPCR) on 16S rRNA, mcrA, pmoA and dsrB genes to quantify the abundances of total prokaryotes, methanogens, aerobic methanotrophs and sulfate-reducing bacteria.After rewetting, cumulative CH4 net fluxes and NEE increased at locations that were previously dry, while Reco halved compared to before rewetting. This correlated with the absolute abundances of specific microbial groups and the surface/pore water biogeochemistry. Under the newly created water-logged conditions, the abundances of methanogenic as well as of sulfate-reducing bacteria (SRB) increased at previously dry sampling locations, but remained constant at the former ditch location. At the same time, the abundance of the aerobic methanotroph community on previously dry locations decreased, which indicates lower aerobic methane oxidation potentials. Pore water CH4 and CO2 concentrations suggest that gas production most likely increased at the former terrestrial locations and stable carbon isotope measurements support an increase of methanogenesis in the peat at some locations. Isotopic analyses also provide some support for persistent methane oxidation either through anaerobic or aerobic taxa at one location.Brackish water rewetting strongly modified the dominant methane-cycling processes but resulted in higher greenhouse gas emissions of both CO2 and CH4 in the first year after rewetting. As expected, CH4 emissions after rewetting were lower than in freshwater rewetted fens, while NEE was unexpectedly high. Since Reco strongly decreased, we assume that peat mineralization was successfully prevented and that ongoing CO2 emissions rather derived from strongly reduced CO2 uptake, supply of terminal electron acceptors (especially sulfate), and excess substrate availability from decaying vegetation. There is great potential for reduction of both, CH4 and CO2 emissions after the initial boost when readily available substrate is depleted. However, our study also reveals the complexity of peatland restoration and the possibility of transient effects upon rewetting, and therefore the value of undrained, pristine peatlands as well as their importance in sequestering carbon.

Permafrost underlies approximately one quarter of Northern Hemisphere terrestrial surfaces and contains 25–50% of the global soil carbon (C) pool. Permafrost soils and the C stocks within are vulnerable to ongoing and future projected climate warming. The biogeography of microbial communities inhabiting permafrost has not been examined beyond a small number of sites focused on local-scale variation. Permafrost is different from other soils. Perennially frozen conditions in permafrost dictate that microbial communities do not turn over quickly, thus possibly providing strong linkages to past environments. Thus, the factors structuring the composition and function of microbial communities may differ from patterns observed in other terrestrial environments. Here, we analyzed 133 permafrost metagenomes from North America, Europe, and Asia. Permafrost biodiversity and taxonomic distribution varied in relation to pH, latitude and soil depth. The distribution of genes differed by latitude, soil depth, age, and pH. Genes that were the most highly variable across all sites were associated with energy metabolism and C-assimilation. Specifically, methanogenesis, fermentation, nitrate reduction, and replenishment of citric acid cycle intermediates. This suggests that adaptations to energy acquisition and substrate availability are among some of the strongest selective pressures shaping permafrost microbial communities. The spatial variation in metabolic potential has primed communities for specific biogeochemical processes as soils thaw due to climate change, which could cause regional- to global- scale variation in C and nitrogen processing and greenhouse gas emissions.

Permafrost regions store between 1.100 and 1.500 gigatons of organic carbon and account for about 50 % of the world’s soil carbon storage. About 10–20 % of near-surface permafrost has been lost due to increases in surface temperatures between 1960 and 2000, and between 10–65 % of near-surface permafrost is expected to disappear by the year 2100. The organic matter in permafrost is only weakly protected and most of it is therefore available for microbial degradation. Microorganisms thus play a central role for the permafrost carbon feedback.

Thermokarst lagoons represent the transition state from a freshwater lacustrine to a marine environment, and receive little attention regarding their role for greenhouse gas production and release in Arctic permafrost landscapes. We studied the fate of methane (CH4) in sediments of a thermokarst lagoon in comparison to two thermokarst lakes on the Bykovsky Peninsula in northeastern Siberia through the analysis of sediment CH4 concentrations and isotopic signature, methane-cycling microbial taxa, sediment geochemistry, lipid biomarkers, and network analysis. We assessed how differences in geochemistry between thermokarst lakes and thermokarst lagoons, caused by the infiltration of sulfate-rich marine water, altered the microbial methane-cycling community. Anaerobic sulfate-reducing ANME-2a/2b methanotrophs dominated the sulfate-rich sediments of the lagoon despite its known seasonal alternation between brackish and freshwater inflow and low sulfate concentrations compared to the usual marine ANME habitat. Non-competitive methylotrophic methanogens dominated the methanogenic community of the lakes and the lagoon, independent of differences in porewater chemistry and depth. This potentially contributed to the high CH4 concentrations observed in all sulfate-poor sediments. CH4 concentrations in the freshwater-influenced sediments averaged 1.34 ± 0.98 μmol g−1, with highly depleted δ13C-CH4 values ranging from −89‰ to −70‰. In contrast, the sulfate-affected upper 300 cm of the lagoon exhibited low average CH4 concentrations of 0.011 ± 0.005 μmol g−1 with comparatively enriched δ13C-CH4 values of −54‰ to −37‰ pointing to substantial methane oxidation. Our study shows that lagoon formation specifically supports methane oxidizers and methane oxidation through changes in pore water chemistry, especially sulfate, while methanogens are similar to lake conditions.

Since the beginning of the Anthropocene, lacustrine biodiversity has been influenced by climate change and human activities. These factors advance the spread of harmful cyanobacteria in lakes around the world, which affects water quality and impairs the aquatic food chain. In this study, we assessed changes in cyanobacterial community dynamics via sedimentary DNA (sedaDNA) from well-dated lake sediments of Lake Tiefer See, which is part of the Klocksin Lake Chain spanning the last 350 years. Our diversity and community analysis revealed that cyanobacterial communities form clusters according to the presence or absence of varves. Based on distance-based redundancy and variation partitioning analyses (dbRDA and VPA) we identified that intensified lake circulation inferred from vegetation openness reconstructions, δ13C data (a proxy for varve preservation) and total nitrogen content were abiotic factors that significantly explained the variation in the reconstructed cyanobacterial community from Lake Tiefer See sediments. Operational taxonomic units (OTUs) assigned to Microcystis sp. and Aphanizomenon sp. were identified as potential eutrophication-driven taxa of growing importance since circa common era (ca. CE) 1920 till present. This result is corroborated by a cyanobacteria lipid biomarker analysis. Furthermore, we suggest that stronger lake circulation as indicated by non-varved sediments favoured the deposition of the non-photosynthetic cyanobacteria sister clade Sericytochromatia, whereas lake bottom anoxia as indicated by subrecent- and recent varves favoured the Melainabacteria in sediments. Our findings highlight the potential of high-resolution amplicon sequencing in investigating the dynamics of past cyanobacterial communities in lake sediments and show that lake circulation, anoxic conditions, and human-induced eutrophication are main factors explaining variations in the cyanobacteria community in Lake Tiefer See during the last 350 years.

Thermokarst lagoons represent the transition state from a freshwater lacustrine to a marine environment, and receive little attention regarding their role for greenhouse gas production and release in Arctic permafrost landscapes. We studied the fate of methane (CH4) in sediments of a thermokarst lagoon in comparison to two thermokarst lakes on the Bykovsky Peninsula in northeastern Siberia through the analysis of sediment CH4 concentrations and isotopic signature, methane-cycling microbial taxa, sediment geochemistry, and lipid biomarkers. We specifically assessed whether sulfate-driven anaerobic methane oxidation (S-AOM) through anaerobic methanotrophic archaea (ANMEs), common in marine sediments with constant supply of sulfate and methane, establish after thermokarst lagoon development and whether sulfate-driven ANMEs consequently oxidize CH4 that would be emitted to the water column under thermokarst lake conditions. The marine-influenced lagoon environment had fundamentally different methane-cycling microbial communities and metabolic pathways compared to the freshwater lakes, suggesting a substantial reshaping of microbial and carbon dynamics during lagoon formation. Anaerobic sulfate-reducing ANME-2a/2b methanotrophs dominated the sulfate-rich sediments of the lagoon despite its known seasonal alternation between brackish and freshwater inflow. CH4 concentrations in the freshwater-influenced sediments averaged 1.34±0.98 µmol g−1, with highly depleted δ13C-CH4 values ranging from -89‰ to -70‰. In contrast, the sulfate-affected upper 300 cm of the lagoon exhibited low average CH4 concentrations of 0.011±0.005 µmol g−1 with comparatively enriched δ13C-CH4 values of -54‰ to -37‰ pointing to substantial methane oxidation. Non-competitive methylotrophic methanogens dominated the methanogenic community of the lakes and the lagoon, independent of porewater chemistry and depth. This potentially contributed to the high CH4 concentrations observed in all sulfate-poor sediments. Our study shows that S-AOM in lagoon sediments can effectively reduce sediment CH4 concentrations and we conclude that thermokarst lake to lagoon transitions have the potential to mitigate terrestrial methane fluxes before thermokarst lakes fully transition to a marine environment.

Plasmids have the potential to transfer genetic traits within bacterial communities and thereby serve as a crucial tool for the rapid adaptation of bacteria in response to changing environmental conditions. Our knowledge of the environmental pool of plasmids (the metaplasmidome) and encoded functions is still limited due to a lack of sufficient extraction methods and tools for identifying and assembling plasmids from metagenomic datasets. Here, we present the first insights into the functional potential of the metaplasmidome of permafrost-affected active-layer soil—an environment with a relatively low biomass and seasonal freeze–thaw cycles that is strongly affected by global warming. The obtained results were compared with plasmid-derived sequences extracted from polar metagenomes. Metaplasmidomes from the Siberian active layer were enriched via cultivation, which resulted in a longer contig length as compared with plasmids that had been directly retrieved from the metagenomes of polar environments. The predicted hosts of plasmids belonged toMoraxellaceae,Pseudomonadaceae,Enterobacteriaceae,Pectobacteriaceae, Burkholderiaceae, andFirmicutes. Analysis of their genetic content revealed the presence of stress-response genes, including antibiotic and metal resistance determinants, as well as genes encoding protectants against the cold.

Permafrost (PF)-affected soils are widespread in the Arctic and store about half the global soil organic carbon. This large carbon pool becomes vulnerable to microbial decomposition through PF warming and deepening of the seasonal thaw layer (active layer [AL]). Here we combined greenhouse gas (GHG) production rate measurements with a metagenome-based assessment of the microbial taxonomic and metabolic potential before and after 5 years of incubation under anoxic conditions at a constant temperature of 4°C in the AL, PF transition layer, and intact PF. Warming led to a rapid initial release of CO₂ and, to a lesser extent, CH₄ in all layers. After the initial pulse, especially in CO₂ production, GHG production rates declined and conditions became more methanogenic. Functional gene-based analyses indicated a decrease in carbon- and nitrogen-cycling genes and a community shift to the degradation of less-labile organic matter. This study reveals low but continuous GHG production in long-term warming scenarios, which coincides with a decrease in the relative abundance of major metabolic pathway genes and an increase in carbohydrate-active enzyme classes. in press

Northern peatlands typically develop through succession from fens dominated by the moss family Amblystegiaceae to bogs dominated by the moss genus Sphagnum. How the different plants and abiotic environmental conditions provided in Amblystegiaceae and Sphagnum peat shape the respective moss associated microbial communities is unknown. Through a large-scale molecular and biogeochemical study spanning Arctic, sub-Arctic and temperate regions we assessed how the endo- and epiphytic microbial communities of natural northern peatland mosses relate to peatland type (Sphagnum and Amblystegiaceae), location, moss taxa and abiotic environmental variables. Microbial diversity and community structure were distinctly different between Amblystegiaceae and Sphagnum peatlands, and within each of these two peatland types moss taxon explained the largest part of microbial community variation. Sphagnum and Amblystegiaceae shared few (Sphagnum-specific core-community. Thus, the most abundant microorganisms in Sphagnum that are also found in all the Sphagnum plants studied, are the same OTUs as those few shared with Amblystegiaceae. Finally, we could confirm that these highly abundant OTUs were endophytes in Sphagnum, but epiphytes on Amblystegiaceae. We conclude that moss taxa and abiotic environmental variables associate with particular microbial communities. While moss taxon was the most influential parameter, hydrology, pH and temperature also had significant effects on the microbial communities. A small though highly abundant core community is shared between Sphagnum and Amblystegiaceae.

With ongoing climate warming, ice-rich permafrost, such as late Pleistocene Yedoma permafrost, is especially vulnerable to rapid and deep thaw processes. Such permafrost sediments contain a large organic matter storage that becomes increasingly accessible to microbes upon thaw. Only a few studies analysed organic matter in deep (>10 m) permafrost and thawed permafrost sediments. We studied Yedoma sediments from four sites in Yakutia in the Russian Federation: at the Arctic Ocean (Bykovsky Peninsula), inside the Lena Delta (Sobo-Sise Cliff), close to the northern hemisphere’s cold pole (Batagay) and in central Yakutia (Yukechi Alas). We measured biomarker concentrations of sediment cores taken from below thermokarst lakes and sediment samples taken from the headwall of a coastal bluff and a retrogressive thaw slump. In addition, we carried out incubation experiments to quantify greenhouse gas production in thawing permafrost. Here, we present the first molecular biomarker distributions (alkanes and fatty acids) and organic carbon turnover (anaerobic CO2 and CH4 production) data as well as insights in organic matter decomposition processes in deep frozen and thawed Yedoma sediments. We show that biomarker proxies are useful to assess the source and degree of degradation of permafrost organic matter. Furthermore, the organic matter in frozen Pleistocene Yedoma sediments was better preserved than in thawed Holocene sediments. These findings show the relevance of studying organic matter in deep permafrost sediments.

Rewetted peatlands can be a significant source of methane, but in coastal systems, input of sulfate-rich seawater could potentially reduce these emissions. The presence of sulfate is known to suppress methanogenesis, by encouraging the growth of sulfate-reducers, which outcompete methanogens for substrate. After a drought in 2018 and a storm surge in the following winter, we investigated the effects of the drought and the brackish water inflow on the microbial communities relative to methane exchange in a rewetted fen at the southern Baltic Sea coast.We took peat cores at four previously sampled locations along a salinity gradient to compare the soil and pore water geochemistry as well as the microbial methane and sulfate cycling communities to the common freshwater rewetting state and the drought 2018. We used high-throughput sequencing and quantitative polymerase chain reaction (qPCR) to characterize pools of DNA and cDNA targeting total and putatively active bacteria and archaea. While sequencing was done for the 16S rRNA gene, qPCR was performed on key functional genes of methane production (mcrA), methane oxidation (pmoA) and sulfate reduction (dsrB) in addition to 16S rRNA. Furthermore, we measured local methane (CH4) fluxes with closed chambers and retrieved soil plugs to determine the concentrations and isotopic signatures of dissolved gases in the pore water.The sequence of the drought and the inflow of brackish water increased the absolute abundance of sulfate reducing bacteria (SRB) by two orders of magnitude. We did not observe a decrease of absolute methanogenic archaea abundance after the inflow as we expected parallel to the increase of SBRs, but saw that changes in the methanogenic communities’ compositions already took place in the drought year 2018. After the inflow, absolute abundance of aerobic methanotrophic bacteria decreased back to their pre-drought level, following an increase during 2018 drought conditions. The expected establishment of methanotrophic archaea (ANME), which are capable of sulfate-mediated anaerobic methane oxidation, was not recorded though. While CH4 fluxes showed a strong decline of almost 90 % to a new minimum since rewetting in 2009, dissolved CH4 pore water concentrations and a strong depletion of 13C-values of CH4 and CO2 (DIC) indicated ongoing methanogenesis and lack of methane oxidation after the brackish water inflow. The observed reduction of CH4 emissions might be a result of methane oxidation and sulfate reduction in the brackish water column above the peat soil. The legacy effect of the preceding drought likely influenced the microbial communities and pore water geochemistry simultaneously suggesting a mixed effect of drought and inflow. Overall, our study revealed that the sequence of drought conditions followed by the inflow of brackish water enlarged the sulfate reducing microbial communities and substantially reduced the CH4 emissions in a rewetted fen. However, unlike drought, which is associated with a rapid and irreversible peat degradation through aerobic decomposition processes, brackish water inflow encourages peat preservation by maintaining anaerobic conditions. Still, further research is needed to directly study the complex effects of brackish water rewetting on peatlands.

Although the majority of coastal sediments consist of sandy material, in some areas marine ingression caused the submergence of terrestrial carbon‐rich peat soils. This affects the coastal carbon balance, as peat represents a potential carbon source. We performed a column experiment to better understand the coupled flow and biogeochemical processes governing carbon transformations in submerged peat under coastal fresh groundwater (GW) discharge and brackish water intrusion. The columns contained naturally layered sediments with and without peat (organic carbon content in peat 39 ± 14 wt%), alternately supplied with oxygen‐rich brackish water from above and oxygen‐poor, low‐saline GW from below. The low‐saline GW discharge through the peat significantly increased the release and ascent of dissolved organic carbon (DOC) from the peat (δ13CDOC − 26.9‰ to − 27.7‰), which was accompanied by the production of dissolved inorganic carbon (DIC) and emission of carbon dioxide (CO2), implying DOC mineralization. Oxygen respiration, sulfate (urn:x-wiley:00243590:media:lno11438:lno11438-math-0001) reduction, and methane (CH4) formation were differently pronounced in the sediments and were accompanied with higher microbial abundances in peat compared to sand with urn:x-wiley:00243590:media:lno11438:lno11438-math-0002‐reducing bacteria clearly dominating methanogens. With decreasing salinity and urn:x-wiley:00243590:media:lno11438:lno11438-math-0003 concentrations, CH4 emission rates increased from 16.5 to 77.3 μmol m−2 d−1 during a 14‐day, low‐saline GW discharge phase. In contrast, oxygenated brackish water intrusion resulted in lower DOC and DIC pore water concentrations and significantly lower CH4 and CO2 emissions. Our study illustrates the strong dependence of carbon cycling in shallow coastal areas with submerged peat deposits on the flow and mixing dynamics within the subterranean estuary.

Permafrost covers a quarter of the northern hemisphere land surface and contains twice the amount of carbon that is currently present in the atmosphere. Future climate change is expected to reduce its near-surface cover by over 90% by the end of the 21st century, leading to thermokarst lake formation. Thermokarst lakes are point sources of carbon dioxide and methane which release long-term carbon stocks into the atmosphere, thereby initiating a positive climate feedback potentially contributing up to a 0.39°C rise of surface air temperatures by 2300. This review describes the potential role of thermokarst lakes in a warming world and the microbial mechanisms that underlie their contributions to the global greenhouse gas budget.

Archaea belonging to the phylum Bathyarchaeota are the predominant archaeal species in cold, anoxic marine sediments and additionally occur in a variety of habitats, both natural and man-made. Metagenomic and single-cell sequencing studies suggest that Bathyarchaeota may have a significant impact on the emissions of greenhouse gases into the atmosphere, either through direct production of methane or through the degradation of complex organic matter that can subsequently be converted into methane. This is especially relevant in permafrost regions where climate change leads to thawing of permafrost, making high amounts of stored carbon bioavailable. Here we present the analysis of nineteen draft genomes recovered from a sediment core metagenome of the Polar Fox Lagoon, a thermokarst lake located on the Bykovsky Peninsula in Siberia, Russia, which is connected to the brackish Tiksi Bay. We show that the Bathyarchaeota in this lake are predominantly peptide degraders, producing reduced ferredoxin from the fermentation of peptides, while degradation pathways for plant-derived polymers were found to be incomplete. Several genomes encoded the potential for acetogenesis through the Wood-Ljungdahl pathway, but methanogenesis was determined to be unlikely due to the lack of genes encoding the key enzyme in methanogenesis, methyl-CoM reductase. Many genomes lacked a clear pathway for recycling reduced ferredoxin. Hydrogen metabolism was also hardly found: one type 4e [NiFe] hydrogenase was annotated in a single MAG and no [FeFe] hydrogenases were detected. Little evidence was found for syntrophy through formate or direct interspecies electron transfer, leaving a significant gap in our understanding of the metabolism of these organisms.

Strain NGK65T, a novel hexadecane degrading, non-motile, Gram-positive, rod-to-coccus shaped, aerobic bacterium, was isolated from plastic polluted soil sampled at a landfill. Strain NGK65T hydrolysed casein, gelatin, urea and was catalase-positive. It optimally grew at 28 °C, in 0–1% NaCl and at pH 7.5–8.0. Glycerol, d-glucose, arbutin, aesculin, salicin, potassium 5-ketogluconate, sucrose, acetate, pyruvate and hexadecane were used as sole carbon sources. The predominant membrane fatty acids were iso-C16:0 followed by iso-C17:0 and C18:1 ω9c. The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and hydroxyphosphatidylinositol. The cell-wall peptidoglycan type was A3γ, with ll-diaminopimelic acid and glycine as the diagnostic amino acids. MK 8 (H4) was the predominant menaquinone. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain NGK65T belongs to the genus Nocardioides (phylum Actinobacteria ), appearing most closely related to Nocardioides daejeonensis MJ31T (98.6%) and Nocardioides dubius KSL-104T (98.3%). The genomic DNA G+C content of strain NGK65T was 68.2%. Strain NGK65T and the type strains of species involved in the analysis had average nucleotide identity values of 78.3–71.9% as well as digital DNA–DNA hybridization values between 22.5 and 19.7%, which clearly indicated that the isolate represents a novel species within the genus Nocardioides . Based on phenotypic and molecular characterization, strain NGK65T can clearly be differentiated from its phylogenetic neighbours to establish a novel species, for which the name Nocardioides alcanivorans sp. nov. is proposed. The type strain is NGK65T (=DSM 113112T=NCCB 100846T).

The decomposition of thawing permafrost organic matter (OM) to the greenhouse gases (GHG) carbon dioxide (CO2) and methane forms a positive feedback to global climate change. Data on in situ GHG fluxes from thawing permafrost OM are scarce and OM degradability is largely unknown, causing high uncertainties in the permafrost‐carbon climate feedback. We combined in situ CO2 and methane flux measurements at an abrupt permafrost thaw feature with laboratory incubations and dynamic modeling to quantify annual CO2 release from thawing permafrost OM, estimate its in situ degradability and evaluate the explanatory power of incubation experiments. In July 2016 and 2019, CO2 fluxes ranged between 0.24 and 2.6 g CO2‐C m−2 d−1. Methane fluxes were low, which coincided with the absence of active methanogens in the Pleistocene permafrost. CO2 fluxes were lower three years after initial thaw after normalizing these fluxes to thawed carbon, indicating the depletion of labile carbon. Higher CO2 fluxes from thawing Pleistocene permafrost than from Holocene permafrost indicate OM preservation for millennia and give evidence that microbial activity in the permafrost was not substantial. Short‐term incubations overestimated in situ CO2 fluxes but underestimated methane fluxes. Two independent models simulated median annual CO2 fluxes of 160 and 184 g CO2‐C m−2 from the thaw slump, which include 25%–31% CO2 emissions during winter. Annual CO2 fluxes represent 0.8% of the carbon pool thawed in the surface soil. Our results demonstrate the potential of abrupt thaw processes to transform the tundra from carbon neutral into a substantial GHG source., Plain Language Summary: Thawing of permanently frozen soils (permafrost) in the northern hemisphere forms a threat to global climate since these soils contain large amounts of frozen organic carbon, which might be decomposed to the greenhouse gases (GHGs) carbon dioxide (CO2) and methane upon thaw. How fast these GHGs are produced is largely unknown, since field observations of greenhouse gas fluxes from thawing permafrost are too sparse. Consequently, simulations on the effect of thawing permafrost soils on future climate are highly uncertain. We measured CO2 and methane fluxes from soils affected by abrupt permafrost thaw in Siberia during two summer seasons. We used these field observations and long‐term incubation data to calibrate two models that simulate the CO2 release over a whole year. We found that greenhouse gas fluxes were dominated by CO2 and that the minor importance of methane was due to the absence of methane producing microorganisms in the Pleistocene permafrost. The CO2 release in the first year accounted for 0.8% of thawed permafrost carbon but decomposition rates decreased after the depletion of the rapidly decomposable organic matter. Abrupt permafrost thaw turned the tundra into a substantial source of CO2, of which 25%–31% was released in the non‐growing season., Key Points: Abrupt permafrost thaw turned the tundra into a substantial annual source of CO2 of which 25%–31% were released in the non‐growing season. About 0.8% of thawed permafrost carbon was decomposed to CO2 in one year but decomposition rates declined after the loss of labile carbon. Methane contributed a minor fraction to total greenhouse gas fluxes also because of a low methanogen abundance in Pleistocene permafrost., German Ministry for Education and Research, German Research Foundation, https://doi.org/10.5281/zenodo.5584710

Sedimentary ancient DNA-based studies have been used to probe centuries of climate and environmental changes and how they affected cyanobacterial assemblages in temperate lakes. Due to cyanobacteria containing potential bloom-forming and toxin-producing taxa, their approximate reconstruction from sediments is crucial, especially in lakes lacking long-term monitoring data. To extend the resolution of sediment record interpretation, we used high-throughput sequencing, amplicon sequence variant (ASV) analysis, and quantitative PCR to compare pelagic cyanobacterial composition to that in sediment traps (collected monthly) and surface sediments in Lake Tiefer See. Cyanobacterial composition, species richness, and evenness was not significantly different among the pelagic depths, sediment traps and surface sediments (p &gt, 0.05), indicating that the cyanobacteria in the sediments reflected the cyanobacterial assemblage in the water column. However, total cyanobacterial abundances (qPCR) decreased from the metalimnion down the water column. The aggregate-forming (Aphanizomenon) and colony-forming taxa (Snowella) showed pronounced sedimentation. In contrast, Planktothrix was only very poorly represented in sediment traps (meta- and hypolimnion) and surface sediments, despite its highest relative abundance at the thermocline (10 m water depth) during periods of lake stratification (May–October). We conclude that this skewed representation in taxonomic abundances reflects taphonomic processes, which should be considered in future DNA-based paleolimnological investigations.

Permafrost region subsurface organic carbon (OC) pools are a major component of the terrestrial carbon cycle and vulnerable to a warming climate. Thermokarst lagoons are an important transition stage with complex depositional histories during which permafrost and lacustrine carbon pools are transformed along eroding Arctic coasts. The effects of temperature and salinity changes during thermokarst lake to lagoon transitions on thaw history and lagoon deposits are understudied. We analyzed two 30-m-long sediment cores from two thermokarst lagoons on the Bykovsky Peninsula, Northeast Siberia, using sedimentological, geochronological, hydrochemical, and biogeochemical techniques. Using remote sensing we distinguished between a semi-closed and a nearly closed lagoon. We (1) characterized the depositional history, (2) studied the impact of marine inundation on ice-bearing permafrost and taliks, and (3) quantified the OC pools for different stages of thermokarst lagoons. Fluvial and former Yedoma deposits were found at depth between 30 and 8.5 m, while lake and lagoon deposits formed the upper layers. The electrical conductivity of the pore water indicated hypersaline conditions for the semi-closed lagoon (max: 108 mS/cm), while fresh to brackish conditions were observed beneath a 5 m-thick surface saline layer at the nearly closed lagoon. The deposits had a mean OC content of 15 ± 2 kg/m3, with higher values in the semi-closed lagoon. Based on the cores we estimated a total OC pool of 5.7 Mt-C for the first 30 m of sediment below five mapped lagoons on the Bykovsky Peninsula. Our results suggest that paleo river branches shaped the middle Pleistocene landscape followed by late Pleistocene Yedoma permafrost accumulation and early Holocene lake development. Afterward, lake drainage, marine flooding, and bedfast ice formation caused the saline enrichment of pore water, which led to cryotic talik development. We find that the OC-pool of Arctic lagoons may comprise a substantial inventory of partially thawed and partially refrozen OC, which is available for microbial degradation processes at the Arctic terrestrial-marine interface. Climate change in the Arctic leading to sea level rise, permafrost thaw, coastal erosion, and sea ice loss may increase the rate of thermokarst lagoon formation and thus increase the importance of lagoons as biogeochemical processors of former permafrost OC.

Drainage of peatlands for intensive and long-term agricultural use leads to higher mineralization rates of the organic material and thus, increased carbon dioxide (CO2) emissions. However, when degraded peatlands are rewetted, high methane (CH4) emissions are frequently observed, that may offset the reductions in CO2 emissions. The created anaerobic conditions are favorable for methanogenic microorganisms and lead to the production of CH4. The presence of sulfate in marine waters typically inhibits methanogenesis because methanogens are outcompeted by sulfate reducers. Therefore, the rewetting of coastal peatlands with marine waters is assumed to keep CH4 emissions low. Flooding of coastal wetlands as a consequence of higher sea levels could strengthen the carbon sink function of these systems if the peatlands are able to grow their surface on par with the sea level. We used the January 2019 storm surge in the southern Baltic Sea to investigate the effects of brackish water intrusion on microbial abundance and community data along with CO2 and CH4 exchange data on a rewetted minerotrophic fen. Previous studies showed that despite the proximity to the Baltic Sea, the fen’s marine sulfate pool was substantially exhausted, and the microbial community was dominated by acetotrophic methanogens and high CH4 emission characteristic for freshwater environments. We took parallel soil cores to compare the microbial methane-cycling community to the former freshwater rewetted state from four locations along a brackish water gradient. We used high-throughput sequencing and quantitative polymerase chain reaction (qPCR) on pools of DNA and cDNA targeting total and putatively active bacteria and archaea (16S rRNA gene), methanogens (mcrA), methanotrophs (pmoA) and sulfate-reducing bacteria (dsrB). Greenhouse gas (GHG) fluxes along the salinity transect were measured locally with closed-chambers and in addition on the ecosystem level using the eddy covariance approach. Chamber measurements along the transect imply lower CH4 emissions at plots with higher salinity post-intrusion. This coincides with a drop in ecosystem CH4 fluxes and with shifts from methane-cycling to sulfate-reducing microorganisms. We expect that organisms involved in anaerobic CH4 oxidation with sulfate as terminal electron acceptor will be more prominent after the saltwater intrusion.Moreover, the effect of rewetting with saltwater on GHG fluxes and microbial communities in degraded fens will be discussed relative to the effects of freshwater inundation and seasonal droughts which were assessed in the same location before.

Temperature is an important factor governing microbe-mediated carbon feedback from permafrost soils. The link between taxonomic and functional microbial responses to temperature change remains elusive due to the lack of studies assessing both aspects of microbial ecology. Our previous study reported microbial metabolic and trophic shifts in response to short-term temperature increases in Arctic peat soil, and linked these shifts to higher CH4 and CO2 production rates (Proceedings of the National Academy of Sciences of the United States of America, 112, E2507–E2516). Here, we studied the taxonomic composition and functional potential of samples from the same experiment. We see that along a high-resolution temperature gradient (1–30°C), microbial communities change discretely, but not continuously or stochastically, in response to rising temperatures. The taxonomic variability may thus in part reflect the varied temperature responses of individual taxa and the competition between these taxa for resources. These taxonomic responses contrast the stable functional potential (metagenomic-based) across all temperatures or the previously observed metabolic or trophic shifts at key temperatures. Furthermore, with rising temperatures we observed a progressive decrease in species diversity (Shannon Index) and increased dispersion of greenhouse gas (GHG) production rates. We conclude that the taxonomic variation is decoupled from both the functional potential of the community and the previously observed temperature-dependent changes in microbial function. However, the reduced diversity at higher temperatures might help explain the higher variability in GHG production at higher temperatures.

Herbivory by barnacle geese (Branta leucopsis) alters the vegetation cover and reduces ecosystem productivity in high-Arctic peatlands, limiting the carbon sink strength of these ecosystems. Here we investigate how herbivory-induced vegetation changes affect the activities of peat soil microbiota using metagenomics, metatranscriptomics and targeted metabolomics in a comparison of fenced exclosures and nearby grazed sites. Our results show that a different vegetation with a high proportion of vascular plants developed due to reduced herbivory, resulting in a larger and more diverse input of polysaccharides to the soil at exclosed study sites. This coincided with higher sugar and amino acid concentrations in the soil at this site as well as the establishment of a more abundant and active microbiota, including saprotrophic fungi with broad substrate ranges, like Helotiales (Ascomycota) and Agaricales (Basidiomycota). A detailed description of fungal transcriptional profiles revealed higher gene expression for cellulose, hemicellulose, pectin, lignin and chitin degradation at herbivory-exclosed sites. Furthermore, we observed an increase in the number of genes and transcripts for predatory eukaryotes such as Entomobryomorpha (Arthropoda). We conclude that in the absence of herbivory, the development of a vascular vegetation alters the soil polysaccharide composition and supports larger and more active populations of fungi and predatory eukaryotes.

Although peatlands cover only about 3% of the land surface of the Earth they store approx. 42% of all soil carbon, if not considerably more, as newest model approaches suggest. Only a minor fraction of all peatlands (5%) is drained, making up a total of 0.15% of the land surface. However from this small land area approx. 5.5% of the global anthropogenic CO2 emissions derive. Therefore, rewetting peatlands on a massive scale is seen as a viable option to decrease greenhouse gas (GHG) emissions and to create GHG sinks in the long run. Our understanding of the ecological and biogeochemical functioning of rewetted peatlands is limited, and especially limited when regarding fen peatlands, which are not even well understood in the pristine state. Thus, there is strong demand to investigate the ecological functioning of these ecosystems.All peatlands that are not pristine anymore, are managed peatlands, regardless of wether they are still used, abandoned, or rewetted/restored. To ask the right questions regarding the ecological functioning of these systems, it is essential to acknowledge managed peatlands as novel ecosystems. The „novel ecosystem“ approach has been developed primarily to address the effect of invasive species or climate change on biodiversity and ecological functioning. „Novel“ ecosystems result as a consequence of human activity but don’t need ongoing human intervention to maintain the novel state. In my talk I will argue that understanding managed peatlands as novel ecosystems is essential to a proper investigation of their ecological and biogeochemical functioning. The argument will be based on the results of several recent research projects in managed temperate peatlands focussing on, inter alia, short-term and long-term vegetation development, GHG emissions and microbial community development.

The thermokarst lakes of permafrost regions play a major role in the global carbon cycle. These lakes are sources of methane to the atmosphere but the methane flux is restricted by an ice cover for most of the year. We provide insights into the methane pathways in the winter ice cover on three different water bodies in a continuous permafrost region in Siberia. The first is a bay underlain by submarine permafrost (Tiksi Bay, TB), the second a shallow thermokarst lagoon (Polar Fox, PF) and the third a land-locked, freshwater thermokarst lake (Goltsovoye Lake, GL). In total, 11 ice cores were analyzed as records of the freezing process and methane pathways during the winter season. In TB, the hydrochemical parameters indicate an open system freezing. In contrast, PF was classified as a semi-closed system, where ice growth eventually cuts off exchange between the lagoon and the ocean. The GL is a closed system without connections to other water bodies. Ice on all water bodies was mostly methane-supersaturated with respect to the atmospheric equilibrium concentration, except of three cores from the lake. Generally, the TB ice had low methane concentrations (3.48–8.44 nM) compared to maximum concentrations of the PF ice (2.59–539 nM) and widely varying concentrations in the GL ice (0.02–14817 nM). Stable delta13CCH4 isotope signatures indicate that methane above the ice-water interface was oxidized to concentrations close to or below the calculated atmospheric equilibrium concentration in the ice of PF. We conclude that methane oxidation in ice may decrease methane concentrations during winter. Therefore, understanding seasonal effects to methane pathways in Arctic saline influenced or freshwater systems is critical to anticipate permafrost carbon feedbacks in course of global warming.

As the Arctic coast erodes, it drains thermokarst lakes, transforming them into lagoons, and, eventually,integrates them into subsea permafrost. Lagoons represent the rst stage of a thermokarst lake transition to amarine setting and possibly more saline and colder upper boundary conditions. In this research,borehole data, electrical resistivity surveying, and modeling of heat and salt diffusion were carried out atPolar Fox Lagoon on the Bykovsky Peninsula, Siberia. Polar Fox Lagoon is a seasonally isolated waterbody connected to Tiksi Bay through a channel, leading to hypersaline waters under the ice cover.The boreholes in the center of the lagoon revealed oating ice and a saline cryotic bed underlain by asaline cryotic talik, a thin icebearing permafrost layer, and unfrozen ground. The bathymetry showedthat most of the lagoon had bedfast ice in spring. In bedfast ice areas, the electrical resistivity profilessuggested that an unfrozen saline layer was underlain by a thick layer of refrozen talik. The modelingshowed that thermokarst lake taliks can refreeze when submerged in saltwater with mean annual bottomwater temperatures below or slightly above 0°C. This occurs, because the top-down chemical degradationof newly formed icebearing permafrost is slower than the refreezing of the talik. Hence, lagoons mayprecondition taliks with a layer of ice-bearing permafrost before encroachment by the sea, and this frozenlayer may act as a cap on gas migration out of the underlying talik.

Three strains of methanotrophic bacteria (EbAT, EbBT and Eb1) were isolated from the River Elbe, Germany. These Gram-negative, rod-shaped or coccoid cells contain intracytoplasmic membranes perpendicular to the cell surface. Colonies and liquid cultures appeared bright-pink. The major cellular fatty acids were 12:0 and 14:0, in addition in Eb1 the FA 16:1ω5t was also dominant. Methane and methanol were utilized as sole carbon sources by EbBT and Eb1, while EbAT could not use methanol. All strains oxidize methane using the particulate methane monooxygenase. Both strains contain an additional soluble methane monooxygenase. The strains grew optimally at 15–25 °C and at pH 6 and 8. Based on 16S rRNA gene analysis recovered from the full genome, the phylogenetic position of EbAT is robustly outside any species clade with its closest relatives being Methylomonas sp. MK1 (98.24%) and Methylomonas sp. 11b (98.11%). Its closest type strain is Methylomonas methanica NCIMB11130 (97.91%). The 16S rRNA genes of EbBT are highly similar to Methylomonas methanica strains with Methylomonas methanica R-45371 as the closest relative (99.87% sequence identity). However, average nucleotide identity (ANI) and digital DNA-DNA-hybridization (dDDH) values reveal it as distinct species. The DNA G + C contents were 51.07 mol% and 51.5 mol% for EbAT and EbBT, and 50.7 mol% for Eb1, respectively. Strains EbAT and EbBT are representing two novel species within the genus Methylomonas. For strain EbAT we propose the name Methylomonas albis sp. nov (LMG 29958, JCM 32282) and for EbBT, we propose the name Methylomonas fluvii sp. nov (LMG 29959, JCM 32283). Eco-physiological descriptions for both strains are provided. Strain Eb1 (LMG 30323, JCM 32281) is a member of the species Methylovulum psychrotolerans. This genus is so far only represented by two isolates but Eb1 is the first isolate from a temperate environment; so, an emended description of the species is given.

The concept of a ‘plastisphere microbial community’ arose from research on aquatic plastic debris, while the effect of plastics on microbial communities in soils remains poorly understood. Therefore, we examined the inhabiting microbial communities of two plastic debris ecosystems with regard to their diversity and composition relative to plastic-free soils from the same area using 16S rRNA amplicon sequencing. Furthermore, we studied the plastic-colonizing potential of bacteria originating from both study sites as a measure of surface adhesion to UV-weathered polyethylene (PE) using high-magnification field emission scanning electron microscopy (FESEM). The high plastic content of the soils was associated with a reduced alpha diversity and a significantly different structure of the microbial communities. The presence of plastic debris in soils did not specifically enrich bacteria known to degrade plastic, as suggested by earlier studies, but rather shifted the microbial community towards highly abundant autotrophic bacteria potentially tolerant to hydrophobic environments and known to be important for biocrust formation. The bacterial inoculates from both sites formed dense biofilms on the surface and in micrometer-scale surface cracks of the UV-weathered PE chips after 100 days of in vitro incubation with visible threadlike EPS structures and cross-connections enabling surface adhesion. High-resolution FESEM imaging further indicates that the microbial colonization catalyzed some of the surface degradation of PE. In essence, this study suggests the concept of a ‘terrestrial plastisphere’ as a diverse consortium of microorganisms including autotrophs and other pioneering species paving the way for those members of the consortium that may eventually break down the plastic compounds.

Both the frequency and intensity of drought events are expected to increase, with unresolved alterations to peatland methane cycling and the involved microbial communities. While existing studies have assessed drought effects via experimental approaches under controlled conditions, to our knowledge, no studies have examined the in-situ effects of natural drought in restored temperate fens. In this study, we used quantitative polymerase chain reaction (qPCR) and high throughput 16S rRNA gene amplicon sequencing of DNA and complementary DNA (cDNA) to determine the abundances and community structure of total and putatively active microbial communities following the 2018 European summer drought. Together with geochemical and methane flux data, we compared these results to a non-drought reference dataset. During drought, water level and methane flux rates decreased to a new recent minimum in both fens. This corresponded with pronounced shifts in porewater geochemistry. Microbial community composition in the drought year differed markedly, and was characterized by a greater relative and total abundance of aerobic methanotrophs, and, in one of the two sites, by a decrease in total methanogen abundance. In contrast to the non-drought reference years, type I methanotrophs were clearly more dominant than type II methanotrophs in both fens. cDNA sequencing confirmed the activity of type I methanotrophs during drought, with Methylomonaceae having the highest average relative abundance of bacterial cDNA transcripts. We show that changes in microbial community dynamics, porewater geochemistry, and ecosystem methane fluxes can be substantial following natural drought in restored fens, and provide the first in-situ evidence from a natural drought which suggests type I methanotroph populations are more active than type II methanotrophs in response to drought effects. Type I methanotrophs may represent a key microbial control over methane emissions in restored temperate fens subject to natural drought.

Submarine permafrost is more vulnerable to thawing than permafrost on land. Besides increased heat transfer from the ocean water, the penetration of salt lowers the freezing temperature and accelerates permafrost degradation. Microbial communities in thawing permafrost are expected to be stimulated by warming but how they develop under submarine conditions is completely unknown. We used the unique records of two submarine permafrost cores from the Laptev Sea on the East Siberian Arctic Shelf, inundated about 540 and 2500 years ago, to trace how bacterial communities develop depending on duration of the marine influence and pore water chemistry. Combined with geochemical analysis, we quantified total cell numbers and bacterial gene copies, and determined the community structure of bacteria using deep sequencing of the bacterial 16S rRNA gene. We show that submarine permafrost is an extreme habitat for microbial life deep below the seafloor with changing thermal and chemical conditions. Pore water chemistry revealed different pore water units reflecting the degree of marine influence and stages of permafrost thaw. Millennia after inundation by sea water, bacteria stratify into communities in permafrost, marine-affected permafrost, and seabed sediments. In contrast to pore water chemistry, the development of bacterial community structure, diversity and abundance in submarine permafrost appears site-specific, showing that both sedimentation and permafrost thaw histories strongly affect bacteria. Finally, highest microbial abundance was observed in the ice-bonded seawater unaffected but warmed permafrost of the longer inundated core, suggesting that permafrost bacterial communities exposed to submarine conditions start to proliferate millennia after warming.