Arctic deltas are highly dynamic environments at the land-ocean interface that have acted as long-term sinks of sediment, carbon (C), and nitrogen (N). Climate impacts Arctic deltas and their upstream catchments through sea-level rise, altered river discharge, increased sediment fluxes, intensified biogeochemical cycling, and permafrost thaw. As a result, soil C and N in Arctic delta deposits are becoming more bioavailable. Here, we present a C and N inventory for Arctic delta compiled from over 1600 soil samples spanning 17 river deltas. We estimate that Arctic delta deposits store 57.5 ( + 9.2/-8.2) Pg C and 3.8 ( + 0.8/-0.7) Pg N across a combined area of nearly 100,000 km², representing large and potentially vulnerable biogeochemical pools. Our findings underscore the potentially pivotal role of Arctic deltas in the pan-Arctic carbon cycle and highlight their importance as dynamic zones of both C and N storage and release in a rapidly changing Arctic.

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.

Drilling of 5 holes between the lakes Reid and Nella in the Larsemann Hills oasis of East Antarctica revealed up to 15 m thick Neogene - Quaternary deposits above bedrock. Laboratory analyses comprise cryolithological, geochemical, and micropaleontological investigations, as well as radiocarbon (14C) dating. The lowermost sediments according to key biostratigraphical taxa are of early Pliocene age and were deposited in shallow marine conditions. This unit is overlain by sediments, which according to 14C dating were deposited ca. 48.1-29.6 ka BP. Their formation in lacustrine-marine conditions, as reflected by results of multi-proxy laboratory studies, suggests that the relative sea level during Marine Isotope Stage 3 has been at least 32 m higher than present, in order to allow lagoon-type deposition, when fresh lake water mixed with sea water during high tides, or near coastal marine sedimentation, when sea water mixed with melt water from adjacent glaciers. The sediments at the top of the record are tills, consisting of a lateral moraine and an end moraine. Their distribution marks the extend of the last glaciation in the area, with ice masses moving northward during the pre-Antarctic Cold Reversal glaciation 14 ka BP, or during a minor Holocene ice advance.

Fumarole fields on active volcanoes are habitats that host unique microbial ecosystems. However, DNA extraction from them for further analysis is rather challenging. In this study, we compared two different ways of sample homogenization for DNA extraction to further profile the microbial communities of active fumarolic fields from Elbrus and Ushkovsky volcanoes and the frozen fumarole deposits of Fujiyama. Vertical homogenizer gave significantly higher DNA concentrations for the Elbrus samples, and more archaeal amplicon sequence variants for Elbrus and Ushkovsky samples compared to the horizontal one. This suggests that vertical homogenizer might be preferable for DNA extraction from sandy and rocky soils. Independent of the homogenizer type, the dominant phyla for Elbrus were Acidobacteriota and Pseudomonadota, and Crenarchaeota for Ushkovsky. The bacterial community of Fuji was less diverse, with Actinomycetota, Pseudomonadota and Bacillota being the dominant phyla. Thus, the studied fumaroles showed distinct microbial profiles, revealing unique adaptations to their respective extreme environments. Within the fungal community, Ascomycota, Basidiomycota and Chytridiomycota were the most dominant phyla for all three volcanoes, but their abundance varied. This study offers the first comprehensive analysis of microbial and fungal communities of active and frozen fumarolic fields, and demonstrates that the choice of methodology can significantly influence the understanding of microbial diversity in extreme environments.

Nitrous oxide (N2O) emissions contribute to stratospheric ozone depletion and global warming. Climate warming causes permafrost thawing and decomposition of the dormant nitrogenous compounds, releasing N2O; however, understanding of the microbial formation and consumption of N2O in permafrost is still limited. Permafrost soils collected at two depths (5.4 m and 16.9 m) from the East Siberian Sea coast of Russia were used to establish microcosms assessing N2O formation and consumption in the presence of either nitrate (NO3-, 1 mM) or N2O (1 mM), respectively, during incubation at 4 and 20°C. Rapid N2O formation was observed in NO3--amended microcosms, but N2O consumption was slow and incomplete over a 1-year incubation period in all microcosms. Twenty-six quality-filtered metagenome-assembled genomes (MAGs) harboring genes involved in the reduction of NO3- and/or N2O were recovered from 16 metagenomes obtained from duplicate NO3-- and N2O-amended microcosms. None of the MAGs carried a complete set of genes to perform canonical denitrification (i.e., NO3-→N2) indicating N2O formation and consumption is likely driven by non-denitrifying bacteria. While coastal permafrost microbiomes harbor nosZ genes, activity monitored in the microcosms indicates N2O formation exceeds N2O consumption, emphasizing the need for integrated approaches to assess and predict N turnover in thawing permafrost. ### Competing Interest Statement The authors have declared no competing interest.

Из образцов тундровых почв (п-ов Быковский, Северная Якутия) были получены накопительные культуры психрофильных и психротолерантных бактерий, восстанавливающие трехвалентное железо при температурах 6-15 °С. Установлено, что самые высокие концентрации ионов Fe(II) наблюдались в накопительных культурах, выращенных с использованием растворимой соли трехвалентного железа в виде цитрата Fe(III). Анаэробные сообщества двух накопительных культур, полученные из проб мерзлотных почв урочища Мамонтовый Хайата и культивируемые при 15 °С, использовали в качестве акцептора электронов нерастворимый оксид Fe(III), а в качестве донора электронов - ацетат и формиат. С применением методов молекулярной биологии и биоинформатики были получены экспериментальные данные о составе микробных сообществ, населяющих почвы криолитозоны. Впервые было проведено сравнение состава природного микробного сообщества, сформированного в течение длительного времени в естественных условиях при низких температурах, и микробного сообщества, культивируемого в лаборатории. Показано, что, несмотря на холодные и олиготрофные условия, прокариотные сообщества арктических экосистем Северной Якутии филогенетически разнообразны. В природных образцах доминируют представители филумов Proteobacteria и Actinobacteria (~30-50 %). Однако основную массу культивируемого микробного сообщества, полученного в лабораторных условиях, составляли Firmicutes (38 %) Enrichment cultures of psychrophilic and psychrotolerant bacteria capable of reducing ferric iron at temperatures of 6 to 15 °C were obtained from samples of two tundra soils from the Bykovsky Peninsula (Northern Yakutia, eastern sector of Russian Arctic). The highest concentrations of Fe(II) ions were observed in enrichment cultures grown with the use of a soluble ferric salt in the form of Fe(III) citrate. Furthermore, anaerobic communities from two enrichment cultures derived from permafrost soil samples of the Mammoth Khayata tract and cultivated at 15 °C demonstrated a preference for insoluble Fe(III) oxide as an electron acceptor while utilizing acetate and formate as electron donors. Experimental data on the composition of microbial communities inhabiting permafrost soils were obtained through molecular biology and bioinformatics methods. Notably, this study presents a novel comparison between the composition of a naturally occurring microbial community that developed over an extended period under natural conditions at low temperatures, and a laboratory-cultivated microbial community. The results demonstrate that prokaryotic communities of the soils of Arctic ecosystems of Yakutia are phylogenetically diverse despite the cold and oligotrophic (nutrient-poor) conditions. While representatives of Proteobacteria and Actinobacteria phyla dominate in natural samples of tundra soil (~30-50 %), the cultivated microbial community obtained in vitro from natural samples was dominated by Firmicutes (38 %).

A new strain of methanogenic archaea, designated VTT, was isolated from a sample of Spitsbergen permafrost. The cells were nonmotile curved rods, 2.7–5.3 × 0.3 µm. The optimal conditions for growth were 20°C, pH 6.6, and NaCl concentrations 0.03–0.05 M. The H2/CO2 gas mixture was the only substrate used. In the presence of H2/CO2, growth was stimulated by addition of yeast extract or rumen fluid. Phylogenetic analysis of the 16S rRNA gene sequences indicated that strain VTT belonged to the genus Methanobacterium and was most closely related to M. lacus 17A1T (97.02

Приведены новые сведения о видовом разнообразии и метаболическом потенциале малоизученных микробных сообществ криопэгов полуострова Ямал. Подсчет общей численности микроорганизмов, населяющих криопэги, показал достаточно высокую плотность, составившую 106-108 кл/мл. При этом сульфатвосстанавливающие бактерии были обнаружены только в двух из трех криопэгах в численности, не превышающей 103 кл/мл. Из криопэгов впервые выделены представители бактериальных родов Acetobaсterium (штаммы K1/0, K1/6 =ВКМ B-3638, K1/7, K1/8), Labilibaculum (K2SТ, =ВКМ B-3650Т) и Trichococcus (K1TrТ, =ВКМ B-3651Т). Все изоляты являлись психроактивными и были способны расти при температуре 6 °С. New data on the species diversity and metabolic potential of insufficiently studied microbial communities in cryopegs of the Yamal Peninsula are presented. The total number of microorganisms inhabiting cryopegs is high and reaches 106-108 cells/mL. At the same time, sulfate-reducing bacteria have only been found in two out of three studied cryopegs in numbers not exceeding 103 cells/mL. Representatives of the bacterial genera Acetobacterium (strains K1/0, K1/6 =VKM B-3638, K1/7, K1/8), Labilibaculum (K2ST, =VKM B-3650T), and Trichococcus (K1TrT, =VKM B-3651Т) have been isolated from cryopegs for the first time. All isolates are psychroactive and are able to grow at 6°C.

This study describes the composition and potential metabolic adaptation of microbial communities in northeastern Siberia, a repository of the oldest permafrost in the Northern Hemisphere. Samples of contrasting depth (1.75 to 25.1 m below surface), age (from 10 kyr to 1.1 Myr) and salinity (from low 0.1–0.2 ppt and brackish 0.3–1.3 ppt to saline 6.1 ppt) were collected from freshwater permafrost (FP) of borehole AL1_15 on the Alazeya River, and coastal brackish permafrost (BP) overlying marine permafrost (MP) of borehole CH1_17 on the East Siberian Sea coast. To avoid the limited view provided with culturing work, we used 16S rRNA gene sequencing to show that the biodiversity decreased dramatically with permafrost age. Nonmetric multidimensional scaling (NMDS) analysis placed the samples into three groups: FP and BP together (10–100 kyr old), MP (105–120 kyr old), and FP (> 900 kyr old). Younger FP/BP deposits were distinguished by the presence of Acidobacteriota, Bacteroidota, Chloroflexota_A, and Gemmatimonadota, older FP deposits had a higher proportion of Gammaproteobacteria, and older MP deposits had much more uncultured groups within Asgardarchaeota, Crenarchaeota, Chloroflexota, Patescibacteria, and unassigned archaea. The 60 recovered metagenome-assembled genomes and un-binned metagenomic assemblies suggested that despite the large taxonomic differences between samples, they all had a wide range of taxa capable of fermentation coupled to nitrate utilization, with the exception of sulfur reduction present only in old MP deposits.

Abstract This study describes the composition and potential metabolic adaptation of microbial communities in northeastern Siberia, a repository of the oldest permafrost in the Northern Hemisphere. Samples of contrasting depth (1.75 to 25.1 m below surface) and age (from ~ 10 kyr to 1.1 Myr) were collected from freshwater permafrost (FP) of borehole AL1_15 on the Alazeya River, and freshwater coastal permafrost (FCP) overlying marine permafrost (MP) of borehole CH1_17 on the East Siberian Sea coast. Using 16S rRNA gene sequencing, we showed that the biodiversity decreased dramatically with permafrost age and separated the samples into three groups: FP and FCP together (10–100 kyr old), FP (> 900 kyr old), and MP (105–120 kyr old). Younger FP/FCP deposits were distinguished by the presence of Acidobacteriota, Bacteroidota, Chloroflexota_A, and Gemmatimonadota, older FP deposits had a higher proportion of Gammaproteobacteria, and older MP deposits had much more uncultured groups within Asgardarchaeota, Crenarchaeota, Chloroflexota, Patescibacteria, and unassigned archaea. The 60 recovered metagenome-assembled genomes (MAGs) and un-binned metagenomic assemblies suggested that despite the large taxonomic differences between samples, they all had a wide range of taxa capable of fermentation coupled to nitrate utilization, with the exception of sulfur reduction present only in old MP deposits.

Methanobacterium sp. strain VT is a psychrotolerant methanogenic archaeon that was isolated from West Spitsbergen island (Norway) permafrost. This article describes the draft genome sequence of Methanobacterium sp. strain VT.

This article describes a study of frozen volcanic deposits collected from volcanoes Tolbachik and Bezymianny on the Kamchatka Peninsula, Russia, and Deception Island volcano, Antarctica. In addition, we studied suprasnow ash layers deposited after the 2007 eruptions of volcanoes Shiveluch and Bezymianny on Kamchatka. The main objectives were to characterize the presence and survivability of thermophilic microorganisms in perennially frozen volcanic deposits. As opposed to permafrost from the polar regions, viable thermophiles were detected in volcanic permafrost by cultivation, microscopy, and sequencing. In the permafrost of Tolbachik volcano, we observed methane formation by both psychrophilic and thermophilic methanogenic archaea, while at 37°C, methane production was noticeably lower. Thermophilic bacteria isolated from volcanic permafrost from the Deception Island were 99.93% related to Geobacillus stearothermophilus. Our data showed biological sulfur reduction to sulfide at 85°C and even at 130°C, where hyperthermophilic archaea of the genus Thermoproteus were registered. Sequences of hyperthermophilic bacteria of the genus Caldicellulosiruptor were discovered in clone libraries from fresh volcanic ash deposited on snow. Microorganisms found in volcanic terrestrial permafrost may serve as a model for the alien inhabitants of Mars, a cryogenic planet with numerous volcanoes. Thermophiles and hyperthermophiles and their metabolic processes represent a guideline for the future exploration missions on Mars.

Greenhouse gas (GHG) emissions from abrupt thaw beneath thermokarst lakes were projected to at least double radiative forcing from circumpolar permafrost-soil carbon fluxes by the end of this century, primarily through the release of methane, a much stronger GHG than CO2. Thermokarst lagoons represent the first stage of a thermokarst lake transition to a marine setting with so far neglected consequences for GHG production and release. We expected that along the transition from a thermokarst lake to a thermokarst lagoon, sediment concentrations of terminal electron acceptors like sulfate increase with an associated drop in methanogenic activity, a shift towards non-competitive methylotrophic methanogenesis, and the occurrence of sulfate-driven anaerobic methane oxidation (AOM). To explore this, we targeted a variety of geochemical and microbial parameters including sediment methane and CO2 concentrations, gaseous carbon isotopic signatures, hydrochemistry, GHG production rates, ratios of CH4/CO2, and occurrence of methane-cycling microbial taxa in sediments of two thermokarst lakes and a thermokarst lagoon on the Bykovsky Peninsula located in northeastern Siberia adjacent to Tiksi Bay. We found multiple lines of evidence that AOM in sediment layers influenced by Tiksi Bay water (i.e. the lagoon) functions as effective microbial methane filter. Annually, the lagoon is decoupled from Tiksi Bay for more than six months, resulting in more saline conditions below the ice cover compared to Tiksi Bay. Despite sub-zero near-surface sediment temperatures for approximately nine months per year, we show that, at least in early spring, AOM led to near-surface sediment methane concentrations approximating only about 1% of those measured in near-surface thermokarst lake sediments. Structural equation modelling stresses pore-water chemistry and increases in anaerobic methanotrophic abundance as main controls for the drop of in-situ methane concentrations and the corresponding increase in carbon isotopic signature. Shallow sediment layers (i.e. younger carbon) corresponded with higher rates of potential methane production, especially in the non-lagoon settings but even in the lagoon, potential methane production rates in the surface sediment layers were relatively unaffected by the marine influence. We propose that this reflects the overall dominance of non-competitive methylotrophic methanogenesis independent of pore-water chemistry and sediment depth. Overall, our study suggests that thermokarst lake to lagoon transitions have the potential to offset atmospheric methane fluxes from abrupt thaw lake structures long before thermokarst lakes fully transgress onto the Arctic shelf.

Permafrost describes the condition of earth material (sand, ground, organic matter, etc.) cemented by ice when its temperature remains at or below 0°C continuously for longer than 2 years. Evidently, permafrost is as old as the time passed from freezing of the earth material. Permafrost is a unique phenomenon and may preserve life forms it encloses. Therefore, in order to talk confidently about the preservation of paleo-objects in permafrost, knowledge about the geological age of sediments, i.e. when the sediments were formed, and permafrost age, when those sediments became permanently frozen, is essential. There are two types of permafrost-syngenetic and epigenetic. The age of syngenetic permafrost corresponds to the geological age of its sediments, whereas the age of epigenetic permafrost is less than the geological age of its sediments. Both of these formations preserve microorganisms and their metabolic products; however, the interpretations of the microbiological and molecular-biological data are inconsistent. This paper reviews the current knowledge of time-temperature history and age of permafrost in relation to available microbiological and metagenomic data.

This paper presents results of the micropaleontological study of permafrost sediments exposed by CHUK 1/17 borehole at Cape Maly Chukochy, on the coast of the East Siberian Sea (Kolyma Lowland). Micropaleontological analysis, together with the lithological structure and the main physicochemical characteristics, enabled reconstructing sedimentation conditions during transition from nearshore marine to continental environments in the Middle and Late Neopleistocene. The existence of a tundra-steppe biome was confirmed for this region, which shows its significant advancement to the north. This study, using the example of this territory, shows the importance of studying microfossils for understanding the history of the region in the Quaternary and lays the basis for further microbiological and metagenomic studies of the sediments exposed by the borehole.

Total DNA (intracellular, iDNA and extracellular, eDNA) from ancient permafrost records the mixed genetic repository of the past and present microbial populations through geological time. Given the exceptional preservation of eDNA under perennial frozen conditions, typical metagenomic sequencing of total DNA precludes the discrimination between fossil and living microorganisms in ancient cryogenic environments. DNA repair protocols were combined with high throughput sequencing (HTS) of separate iDNA and eDNA fraction to reconstruct metagenome-assembled genomes (MAGs) from ancient microbial DNA entrapped in Siberian coastal permafrost. Despite the severe DNA damage in ancient permafrost, the coupling of DNA repair and HTS resulted in a total of 52 MAGs from sediments across a chronosequence (26–120 kyr). These MAGs were compared with those derived from the same samples but without utilizing DNA repair protocols. The MAGs from the youngest stratum showed minimal DNA damage and thus likely originated from viable, active microbial species. Many MAGs from the older and deeper sediment appear related to past aerobic microbial populations that had died upon freezing. MAGs from anaerobic lineages, including Asgard archaea, however exhibited minimal DNA damage and likely represent extant living microorganisms that have become adapted to the cryogenic and anoxic environments. The integration of aspartic acid racemization modeling and metaproteomics further constrained the metabolic status of the living microbial populations. Collectively, combining DNA repair protocols with HTS unveiled the adaptive strategies of microbes to long-term survivability in ancient permafrost. Our results indicated that coupling of DNA repair protocols with simultaneous sequencing of iDNA and eDNA fractions enabled the assembly of MAGs from past and living microorganisms in ancient permafrost. The genomic reconstruction from the past and extant microbial populations expanded our understanding about the microbial successions and biogeochemical alterations from the past paleoenvironment to the present-day frozen state. Furthermore, we provided genomic insights into long-term survival mechanisms of microorganisms under cryogenic conditions through geological time. The combined strategies in this study can be extrapolated to examine other ancient non-permafrost environments and constrain the search for past and extant extraterrestrial life in permafrost and ice deposits on Mars.

A gene coding for a novel putative amylase, oligo-1,6-glucosidase from a psychrotrophic bacterium Exiguobacterium sibiricum from Siberian permafrost soil was cloned and expressed in Escherichia coli. The amino acid sequence of the predicted protein EsOgl and its 3D model displayed several features characteristic for the cold-active enzymes while possessing an unusually high number of proline residues in the loops-a typical feature of thermophilic enzymes. The activity of the purified recombinant protein was tested with p-nitrophenyl α-D-glucopyranoside as a substrate. The enzyme displayed a plateau-shaped temperature-activity profile with the optimum at 25 °C and a pronounced activity at low temperatures (50% of maximum activity at 5 °C). To improve the thermal stability at temperatures above 40 °C, we have introduced proline residues into four positions of EsOgl by site-directed mutagenesis according to "the proline rule". Two of the mutants, S130P and A109P demonstrated a three- and two-fold increased half-life at 45 °C. Moreover, S130P mutation led to a 60% increase in the catalytic rate constant. Combining the mutations resulted in a further increase in stability transforming the temperature-activity profile to a typical mesophilic pattern. In the most thermostable variant A109P/S130P/E176P, the half-life at 45 °C was increased from 11 min (wild-type) to 129 min.

In natural, permanently frozen habitats, some organisms may be preserved for hundreds to tens of thousands of years. For example, stems of Antarctic moss were successfully regrown from an over millennium-old sample covered by ice for about 400 years1. Likewise, whole campion plants were regenerated from seed tissue preserved in relict 32,000-year-old permafrost2, and nematodes were revived from the permafrost of two localities in northeastern Siberia, with source sediments dated over 30,000 years BP3. Bdelloid rotifers, microscopic multicellular animals, are known for their ability to survive extremely low temperatures4. Previous reports suggest survival after six to ten years when frozen between -20° to 0°C4-6. Here, we report the survival of an obligate parthenogenetic bdelloid rotifer, recovered from northeastern Siberian permafrost radiocarbon-dated to ∼24,000 years BP. This constitutes the longest reported case of rotifer survival in a frozen state. We confirmed the finding by identifying rotifer actin gene sequences in a metagenome obtained from the same sample. By morphological and molecular markers, the discovered rotifer belongs to the genus Adineta, and aligns with a contemporary Adineta vaga isolate collected in Belgium. Experiments demonstrated that the ancient rotifer withstands slow cooling and freezing (∼1°C min-1) for at least seven days. We also show that a clonal culture can continuously reproduce in the laboratory by parthenogenesis.