Bacteria primarily metabolize at the active layer/permafrost border in the peat core from a permafrost region in western Siberia

Depth-specific distribution of bacterial MAGs in permafrost active layer in Ny Ålesund, Svalbard (79°N)

Arctic soil microbial communities may shift with increasing temperatures and water availability from climate change. We examined temperature and volumetric liquid water content (VWC) in the upper 80 cm of permafrost-affected soil over 2 years (2018-2019) at the Bayelva monitoring station, Ny Ålesund, Svalbard. We show VWC increases with depth, whereas in situ temperature is more stable vertically, ranging from -5°C to 5 °C seasonally. Prokaryotic metagenome-assembled genomes (MAGs) were obtained at 2-4 cm vertical resolution collected while frozen in April 2018 and at 10 cm vertical resolution collected while thawed in September 2019. The most abundant MAGs were Acidobacteriota, Actinomycetota, and Chloroflexota. Actinomycetota and Chloroflexota increase with depth, while Acidobacteriota classes Thermoanaerobaculia Gp7-AA8, Blastocatellia UBA7656, and Vicinamibacteria Vicinamibacterales are found above 6 cm, below 6 cm, and below 20 cm, respectively. All MAGs have diverse carbon-degrading genes, and Actinomycetota and Chloroflexota have autotrophic genes. Genes encoding β -glucosidase, N-acetyl-β-D-glucosaminidase, and xylosidase increase with depth, indicating a greater potential for organic matter degradation with higher VWC. Acidobacteriota dominate the top 6 cm with their classes segregating by depth, whereas Actinomycetota and Chloroflexota dominate below ∼6 cm. This suggests that Acidobacteriota classes adapt to lower VWC at the surface, while Actinomycetota and Chloroflexota persist below 6 cm with higher VWC. This indicates that VWC may be as important as temperature in microbial climate change responses in Arctic mineral soils. Here we describe MAG-based Seqcode type species in the Acidobacteriota, Onstottus arcticum, Onstottus frigus, and Gilichinskyi gelida and in the Actinobacteriota, Mayfieldus profundus.

Fractionation of organic C, nutrients, metals and bacteria in peat porewater and ice after freezing and thawing

To better understand freezing - thawing cycles operating in peat soils of permafrost landscapes, we experimentally modelled bi-directional freezing and thawing of peat collected from a discontinuous permafrost zone in western Siberia. We measured translocation of microorganisms and changes in porewater chemistry (pH, UV absorbance, dissolved organic carbon (DOC), and major and trace element concentrations) after thawing and two-way freezing of the three sections of 90-cm-long peat core. We demonstrate that bi-directional freezing and thawing of a peat core is capable of strongly modifying the vertical pattern of bacteria, DOC, nutrients, and trace element concentrations. Sizeable enrichment (a factor of 2 to 5) of DOC, macro- (P, K, Ca) and micro-nutrients (Ni, Mn, Co, Rb, B), and some low-mobile trace elements in several horizons of ice and peat porewater after freeze/thaw experiment may stem from physical disintegration of peat particles, leaching of peat constituents, and opening of isolated (non-connected) pores during freezing front migration. However, due to the appearance of multiple maxima of element concentration after a freeze-thaw event, the use of peat ice chemical composition as environmental archive for paleo-reconstructions is unwarranted.

Experimental assessment of tundra fire impact on element export and storage in permafrost peatlands

Extensive studies have been performed on wildfire impact on terrestrial and aquatic ecosystems in the taiga biome, however consequences of wildfires in the tundra biome remain poorly understood. In such a biome, permafrost peatlands occupy a sizable territory in the Northern Hemisphere and present an extensive and highly vulnerable storage of organic carbon. Here we used an experimental approach to model the impact of ash produced from burning of main tundra organic constituents (i.e., moss, lichen and peat) on surrounding aquatic ecosystems. We studied the chemical composition of aqueous leachates produced during short-term (1 week) interaction of ash with distilled water and organic-rich lake water at 5 g_solid L^-1 and 20 °C. The addition of ash enriched the fluid phase in major cations (i.e., Na, Ca, Mg), macro- (i.e., P, K, Si) and micronutrients (i.e., Mn, Fe, Co, Ni, Zn, Mo). This enrichment occurred over <2 days of experiment. Among 3 studied substrates, moss ash released the largest amount of macro- and micro-components into the aqueous solution. To place the obtained results in the environmental context of a peatbog watershed, we assume a fire return interval of 56 years and that the entire 0-10 cm of upper peat is subjected to fire impact. These mass balance calculations demonstrated that maximal possible delivery of elements from ash after soil burning to the hydrological network is negligibly small (<1-2 %) compared to the annual riverine export flux and element storage in thermokarst lakes. As such, even a 5-10 fold increase in tundra wildfire frequency may not sizably modify nutrient and metal fluxes and pools in the surrounding aquatic ecosystems. This result requires revisiting the current paradigm on the importance of wildfire impact on permafrost peatlands and calls a need for experimental work on other ecosystem compartments (litter, shrubs, frozen peat) which are subjected to fire events.

Diversity and Distribution Characteristics of Soil Microbes across Forest-Peatland Ecotones in the Permafrost Regions

Permafrost peatlands are a huge carbon pool that is uniquely sensitive to global warming. However, despite the importance of peatlands in global carbon sequestration and biogeochemical cycles, few studies have characterized the distribution characteristics and drivers of soil microbial community structure in forest-peatland ecotones. Here, we investigated the vertical distribution patterns of soil microbial communities in three typical peatlands along an environmental gradient using Illumina high-throughput sequencing. Our findings indicated that bacterial richness and diversity decreased with increasing soil depth in coniferous swamp (LT) and thicket swamp (HT), whereas the opposite trend was observed in a tussock swamp (NT). Additionally, these parameters decreased at 0-20 and 20-40 cm and increased at 40-60 cm along the environmental gradient (LT to NT). Principal coordinate analysis (PCoA) indicated that the soil microbial community structure was more significantly affected by peatland type than soil depth. Actinomycetota, Proteobacteria, Firmicutes, Chloroflexota, Acidobacteriota, and Bacteroidota were the predominant bacterial phyla across all soil samples. Moreover, there were no significant differences in the functional pathways between the three peatlands at each depth, except for amino acid metabolism, membrane transport, cell motility, and signal transduction. Redundancy analysis (RDA) revealed that pH and soil water content were the primary environmental factors influencing the bacterial community structure. Therefore, this study is crucial to accurately forecast potential changes in peatland ecosystems and improve our understanding of the role of peat microbes as carbon pumps in the process of permafrost degradation.

Impact of freeze-thaw cycles on organic carbon and metals in waters of permafrost peatlands

Despite the importance of soil and surface waters freezing in permafrost landscapes, the behaviour of dissolved organic carbon (DOC), nutrients and metals during periodic freeze-thaw cycles (FTC) remains poorly known. The on-going climate warming is likely to increase the frequency of FTC in continental aquatic settings, which could modify the chemical composition of waters. In this study, we conducted 9 repetitive cycles of overnight freezing (-20 °C) and 5 h thawing (4 °C) in the laboratory using representative 0.22 μm-filtered waters from NE European permafrost peatland: leachates of vegetation and soil, and natural surface waters (depression, thermokarst lake and river). Only minor (<5%-15%) changes of DOC concentrations, SUVA₂₅₄ and molecular weight were observed in all leachates and the depression water. In contrast, several trace elements (Fe, Al, P, Mn, As, and REE) exhibited sizable variations during FTC (>10%). The leachates and the depression water were enriched in trace elements, whereas the thermokarst lake and the river demonstrated a decrease in concentration of Fe (-39 and -94%, respectively), Al (-9 and -85%), and Mn (-10 and -79%) during FTC. Overall, the observations demonstrated an increase in aliphatic low molecular weight organic matter (OM), and the precipitation of Fe, Al hydroxides and organo-mineral particles. Therefore, enhanced of frequency of FTC can favour the release of metals and toxicants from acidic OM-rich surface waters and maintain stable OM-metals-colloids in large lakes and rivers, thus regulating aquatic transport of DOC and metals from soils to the Arctic Ocean.

Eight metagenome-assembled genomes provide evidence for microbial adaptation in 20,000 to 1,000,000-year-old Siberian permafrost

Permafrost microbes may be metabolically active in microscopic layers of liquid brines, even in ancient soil. Metagenomics can help discern whether permafrost microbes show adaptations to this environment. Thirty-three metagenome-assembled genomes (MAGs) were obtained from six depths (3.5 m to 20 m) of freshly-cored permafrost from the Siberia Kolyma-Indigirka Lowland region. These soils have been continuously frozen for ∼20,000 to 1,000,000 years. Eight of these MAGs were ≥80% complete with <10% contamination and were taxonomically identified as Aminicenantes, Atribacteria, Chloroflexi, and Actinobacteria within bacteria and Thermoprofundales within archaea. MAGs from these taxa have previously been obtained from non-permafrost environments and have been suggested to show adaptations to long-term energy-starvation, but they have never been explored in ancient permafrost. The permafrost MAGs had higher proportions of clusters of orthologous genes (COGs) from 'Energy production and conversion' and 'Carbohydrate transport and metabolism' than their non-permafrost counterparts. They also contained genes for trehalose synthesis, thymine metabolism, mevalonate biosynthesis and cellulose degradation that were less prevalent in non-permafrost genomes. Many of these genes are involved in membrane stabilization and osmotic stress responses, consistent with adaptation to the anoxic, high ionic strength, cold environments of permafrost brine films. Our results suggest that this ancient permafrost contains DNA in high enough quality to assemble MAGs from microorganisms with adaptations to subsist long-term freezing in this extreme environment. Importance 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. The fate of permafrost microorganisms is connected to these predicted rapid environmental changes. Studying ancient permafrost with culture independent techniques can give a glimpse into how these microorganisms function in these extreme low temperature and energy conditions. This will aid understanding of how they will change with the environment. This study presents genomic data from this unique environment aged ∼20,000 to 1,000,000-years-old.

Bacterial Number and Genetic Diversity in a Permafrost Peatland (Western Siberia): Testing a Link with Organic Matter Quality and Elementary Composition of a Peat Soil Profile

Permafrost peatlands, containing a sizable amount of soil organic carbon (OC), play a pivotal role in soil (peat) OC transformation into soluble and volatile forms and greatly contribute to overall natural CO2 and CH4 emissions to the atmosphere under ongoing permafrost thaw and soil OC degradation. Peat microorganisms are largely responsible for the processing of this OC, yet coupled studies of chemical and bacterial parameters in permafrost peatlands are rather limited and geographically biased. Towards testing the possible impact of peat and peat pore water chemical composition on microbial population and diversity, here we present results of a preliminary study of the western Siberia permafrost peatland discontinuous permafrost zone. The quantitative evaluation of microorganisms and determination of microbial diversity along a 100 cm thick peat soil column, which included thawed and frozen peat and bottom mineral horizon, was performed by RT-PCR and 16S rRNA gene-based metagenomic analysis, respectively. Bacteria (mainly Proteobacteria, Acidobacteria, Actinobacteria) strongly dominated the microbial diversity (99% sequences), with a negligible proportion of archaea (0.3–0.5%). There was a systematic evolution of main taxa according to depth, with a maximum of 65% (Acidobacteria) encountered in the active layer, or permafrost boundary (50–60 cm). We also measured C, N, nutrients and ~50 major and trace elements in peat (19 samples) as well as its pore water and dispersed ice (10 samples), sampled over the same core, and we analyzed organic matter quality in six organic and one mineral horizon of this core. Using multiparametric statistics (PCA), we tested the links between the total microbial number and 16S rRNA diversity and chemical composition of both the solid and fluid phase harboring the microorganisms. Under climate warming and permafrost thaw, one can expect a downward movement of the layer of maximal genetic diversity following the active layer thickening. Given a one to two orders of magnitude higher microbial number in the upper (thawed) layers compared to bottom (frozen) layers, an additional 50 cm of peat thawing in western Siberia may sizably increase the total microbial population and biodiversity of active cells.

Shotgun metagenomics reveals distinct functional diversity and metabolic capabilities between 12 000-year-old permafrost and active layers on Muot da Barba Peider (Swiss Alps)

The warming-induced thawing of permafrost promotes microbial activity, often resulting in enhanced greenhouse gas emissions. The ability of permafrost microorganisms to survive the in situ sub-zero temperatures, their energetic strategies and their metabolic versatility in using soil organic materials determine their growth and functionality upon thawing. Hence, functional characterization of the permafrost microbiome, particularly in the underexplored mid-latitudinal alpine regions, is a crucial first step in predicting its responses to the changing climate, and the consequences for soil-climate feedbacks. In this study, for the first time, the functional potential and metabolic capabilities of a temperate mountain permafrost microbiome from central Europe has been analysed using shotgun metagenomics. Permafrost and active layers from the summit of Muot da Barba Peider (MBP) [Swiss Alps, 2979 m above sea level (a.s.l.)] revealed a strikingly high functional diversity in the permafrost (north-facing soils at a depth of 160 cm). Permafrost metagenomes were enriched in stress-response genes (e.g. cold-shock genes, chaperones), as well as in genes involved in cell defence and competition (e.g. antiviral proteins, antibiotics, motility, nutrient-uptake ABC transporters), compared with active-layer metagenomes. Permafrost also showed a higher potential for the synthesis of carbohydrate-active enzymes, and an overrepresentation of genes involved in fermentation, carbon fixation, denitrification and nitrogen reduction reactions. Collectively, these findings demonstrate the potential capabilities of permafrost microorganisms to thrive in cold and oligotrophic conditions, and highlight their metabolic versatility in carbon and nitrogen cycling. Our study provides a first insight into the high functional gene diversity of the central European mountain permafrost microbiome. Our findings extend our understanding of the microbial ecology of permafrost and represent a baseline for future investigations comparing the functional profiles of permafrost microbial communities at different latitudes.

Dispersed ground ice of permafrost peatlands: Potential unaccounted carbon, nutrient and metal sources

The physical and chemical consequences of massive ground ice (wedges) melt upon permafrost thaw is one of the central issues of environmental research linked to climate warming in the Arctic. Little is known about the chemical properties of dispersed ground ice abundant throughout permafrost peatlands that can easily melt with increasing active layer thickness (ALT). This is especially pertinent in continental lowlands, that account for sizeable areas of the Arctic, and contain high amount of organic carbon in both solid (peat) and liquid (porewater) phases. Here we studied 8 peat cores (0-130 cm depth)-comprised of porewater from the active layer (0-45 cm) as well as ice dispersed in frozen peat (40-130 cm)-across a latitudinal profile of Western Siberia Lowland (WSL) extending from discontinuous into continuous permafrost zones. Dissolved Organic Carbon (DOC), alkali and alkaline-earth metals (Ca, Mg, Sr, Ba, Li, Rb, Cs), sulfate, phosphorus, some trace elements (Al, Fe, Mn, Zn, Ni, Co, V, As, Y, REE, Zr, Hf, U) were sizably [more than 3 times] enriched in peat ice compared to peat porewaters from the active layer. In most sampled cores, there was a local maximum of strong enrichment (up to factors between 14 and 58) in DOC, P, Ca, Mg, Mn, Fe, Sr, As located 30-50 cm below the active layer. This maximum likely occurred due to solute concentration during full freezing of the soil column during winter. There was a sizable correlation between DOC, Al, Fe and other major and trace element concentrations that suggests strong control of organic complexes and organo-mineral (Al, Fe) colloids on element migration throughout the peat profile. The pool of C, major cations and trace metals in peat ice (40-130 cm) was approximately 3-55 times higher than the pool of these elements in porewaters from the active layer (0-40 cm). A 1-m increase of the ALT over the next 100 years is capable of mobilizing 58 ± 38 Tg of DOC from soil ice into the rivers and lakes of the WSL latitudinal belt (63-67 °N). This fast lateral export of C (3.7 ± 2.7 t C km^-2 y^-1) may double current C yields in WSL rivers (3.4 ± 1.3 t C km^-2 y^-1). A strong increase (150-200%) in riverine export of Zn, P and Cs may also occur while other micronutrients (Fe, Ni, Co, Ba, Mo, Rb) and toxicants (Cd, As, Al) may be affected to a lesser degree (20-30% increase). We propose a global peat ice inventory in permafrost regions is essential for assessing the consequences of permafrost thaw on surface aquatic systems.

Composition and photo-reactivity of organic matter from permafrost soils and surface waters in interior Alaska

Yedoma permafrost soils are especially susceptible to abrupt thaw due to their exceptional thickness and high ice content. Compared to other mineral soils, yedoma has a high organic carbon content, which has shown to be particularly biolabile. The organic carbon in these deposits needs to be characterised to provide an identification toolkit for detecting and monitoring the thaw, mobilisation and mineralisation of yedoma permafrost. This study characterised organic carbon isolates from thermokarst lakes (either receiving inputs from thaw of original yedoma or refrozen-thermokarst deposits, or lacking recent thaw) during winter and summer seasons within the Goldstream Creek watershed, a discontinuous permafrost watershed in interior Alaska, to identify the extent to which thermokarst-lake environments are impacted by degradation of yedoma permafrost. Waters from lakes of varied age and thermokarst activity, as well as active layer and undisturbed yedoma permafrost soils were isolated and characterised by functional group abundance (multiCP-MAS ¹³C and SPR-W5-WATERGATE ¹H NMR), absorbance and fluorescence, and photobleaching ability. DOM isolated from winter and summer seasons revealed differing composition and photoreactivity, suggesting varied active layer and permafrost influence under differing ground water flow regimes. Water extractable organic matter isolates from permafrost leachates revealed variation in terms of photoreactivity and photolability, with the youngest sampled permafrost isolate being the most photoreactive and photolabile. As temperatures increase, release of permafrost organic matter is inevitable. Obtaining a holistic understanding of DOM composition and photoreactivity will allow for a better prediction of permafrost thaw impacts in the coming decades.