Elizaveta M. Rivkina

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.

Nitrous oxide (N₂O) contributes to stratospheric ozone depletion and global warming. Knowledge about microbial formation and consumption of N₂O in old permafrost remains limited. Permafrost samples collected on the East Siberian Sea coast of Russia from a single borehole at depths of 5.4 and 16.9 m, which showed presence of nitrogen substances and nitrogen cycling genes, were used to establish microcosms supplemented with NO₃⁻- and N₂O to assess denitrification and N₂O consumption at 4 and 20°C. Rapid N₂O formation was observed in NO₃⁻-supplemented microcosms, but N₂O consumption was slow and incomplete over a 1-year incubation in all microcosms. Twenty-three qualified metagenome-assembled genomes (MAGs) harboring genes involved in NO₃⁻ and/or N₂O reduction were recovered from both NO₃⁻- and N₂O-supplemented microcosms. Twenty MAGs represent novel taxa. Four MAGs, two of each from NO₃⁻- and N₂O-supplemented microcosms, contained nosZ genes indicating N₂O consumption potential, however the complete denitrification (i.e., NO₃⁻→N₂) gene sets were not detected in these MAGs. Though, N₂O production exceeded N₂O consumption in NO₃⁻-supplemented microcosms at 4°C. Our microcosm experiments suggest N₂O formation surpasses its consumption in newly-thawed ~120 kyr old permafrost, emphasizing the importance of using integrated approaches to assess and predict N turnover in response to permafrost degradation.

Promethearchaeota (“Asgard” archaea), abundant throughout Earth's subsurface, may persist in a maintenance state over geological timescales. Testing this hypothesis is challenging due to the impracticality of long‐term experiments, yet ancient permafrost provides a natural laboratory. We reconstructed 22 Promethearchaeota MAGs from various classes from > 100 kyr marine permafrost, where brines maintain some liquid water below 0°C through geological time. Promethearchaeota cells appear intact as revealed by catalysed reporter deposition in situ hybridization. Six MAGs from the intracellular DNA fraction are > 7× more abundant, > 70% complete, and their completeness was not improved by exogenous DNA repair enzymes, suggesting that they have maintained high DNA integrity since being frozen. Other Promethearchaeota MAGs have low completeness that increases dramatically after DNA repair, indicating that other cells were highly degraded. The high DNA integrity MAGs share families or genera with non‐permafrost Promethearchaeota and share metabolic and DNA/protein repair genes with them. The protein repair genes protein‐L‐isoaspartyl (D‐aspartyl) O ‐methyltransferase and methionine sulfoxide reductase from Promethearchaeota match those of archaea and bacteria instead of eukaryotes. Therefore, diverse Promethearchaeota clades, seemingly without special genetic adaptations relative to non‐permafrost lineages of these clades, survive > 100 kyr in marine permafrost, suggesting that long‐term survivability is common in Promethearchaeota .

Permafrost 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.

Some organisms in nature have developed the ability to enter a state of suspended metabolism called cryptobiosis when environmental conditions are unfavorable. This state-transition requires execution of a combination of genetic and biochemical pathways that enable the organism to survive for prolonged periods. Recently, nematode individuals have been reanimated from Siberian permafrost after remaining in cryptobiosis. Preliminary analysis indicates that these nematodes belong to the genera Panagrolaimus and Plectus. Here, we present precise radiocarbon dating indicating that the Panagrolaimus individuals have remained in cryptobiosis since the late Pleistocene (~46,000 years). Phylogenetic inference based on our genome assembly and a detailed morphological analysis demonstrate that they belong to an undescribed species, which we named Panagrolaimus kolymaensis. Comparative genome analysis revealed that the molecular toolkit for cryptobiosis in P. kolymaensis and in C. elegans is partly orthologous. We show that biochemical mechanisms employed by these two species to survive desiccation and freezing under laboratory conditions are similar. Our experimental evidence also reveals that C. elegans dauer larvae can remain viable for longer periods in suspended animation than previously reported. Altogether, our findings demonstrate that nematodes evolved mechanisms potentially allowing them to suspend life over geological time scales.

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.

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.

Some organisms in nature have developed the ability to enter a state of suspended metabolism called cryptobiosis ¹ when environmental conditions are unfavorable. This state-transition requires execution of a combination of genetic and biochemical pathways ^1,2,3 that enable the organism to survive for prolonged periods. Recently, nematode individuals have been reanimated from Siberian permafrost after remaining in cryptobiosis. Preliminary analysis indicates that these nematodes belong to the genera Panagrolaimus and Plectus ⁴ . Here, we present precise radiocarbon dating indicating that the Panagrolaimus individuals have remained in cryptobiosis since the late Pleistocene (∼46,000 years). Phylogenetic inference based on our genome assembly and a detailed morphological analysis demonstrate that they belong to an undescribed species, which we named Panagrolaimus n. sp . Comparative genome analysis revealed that the molecular toolkit for cryptobiosis in Panagrolaimus n. sp . and in C. elegans is partly orthologous. We show that biochemical mechanisms employed by these two species to survive desiccation and freezing under laboratory conditions are similar. Our experimental evidence also reveals that C. elegans dauer larvae can remain viable for longer periods in suspended animation than previously reported. Altogether, our findings demonstrate that nematodes evolved mechanisms potentially allowing them to suspend life over geological time scales.

Permafrost around the world is thawing rapidly. Many scientists from a variety of disciplines have shown the importance of understanding what will happen to our ecosystem, commerce, and climate when permafrost thaws.

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.