Arctic Soils Research Articles

Temperature-dependent catabolic traits of cold-adapted soil yeasts Goffeauzyma gilvescens and Naganishia albidosimilis from Hornsund, Svalbard

Studies on the diversity and catabolic functionality of fungi in Arctic soils are still scarce. This knowledge gap needs to be urgently addressed, as global warming may have unpredictable effects on cold-adapted fungal species. We isolated two yeast species of the family Filobasidiaceae: Goffeauzyma gilvescens and Naganishia albidosimilis, from soil in central Spitsbergen (Svalbard) and characterised their metabolic properties at two temperatures, 4°C and 20°C, in a laboratory test using Biolog® FF plates. The results of the Biolog® test, which followed the molecular identification of the strains, confirmed that the two species differed in their functional (catabolic) characteristics. The effect of temperature was also highly significant and the metabolic characteristics of two species varied between the two temperatures tested. As expected, among other chemical guilds of substrates on Biolog® plates, carbohydrates were the most used and also the most segregating of the strains studied, especially at 20°C. However, the relative use of almost all substrate groups changed between the two temperatures for both species tested, indicating that temperature can also affect soil microorganisms indirectly by altering their metabolic pathways. As soil microorganisms form a complex trophic and non-trophic network, such changes in metabolism under increasing temperature may also alter relationships between species and between species and the environment. Our study contributes to a better understanding of the microbial ecology of the unique ecosystem of polar soils.

Plant–microbe interactions explain the surprising recovery of Arctic soil carbon stocks

Plant–microbe interactions explain the surprising recovery of Arctic soil carbon stocks

Arctic soil carbon trajectories shaped by plant–microbe interactions

Arctic soil carbon trajectories shaped by plant–microbe interactions

Investigating the resistome of haemolytic bacteria in Arctic soils.

Microorganisms inhabiting hostile Arctic environments express a variety of functional phenotypes, some of clinical interest, such as haemolytic ability and antimicrobial resistance. We studied haemolytic bacterial isolates from Arctic habitats, assessing their minimum inhibitory concentration (MIC) against antimicrobials. We then performed whole genome sequencing and analysed them for features conferring antimicrobial resistance. MIC data showed that Micromonospora spp. belong to 33% non-wild type (NWT) for erythromycin and penicillin and 22% NWT for tetracycline. Both Pseudomonas spp. belong to 43% NWT for nalidixic acid and streptomycin and 29% NWT for colistin. Finally, the Pedobacter isolate was in 80% NWT for antimicrobials tested. Whole-genome sequencing analyses revealed that fluoroquinolones, tetracyclines, macrolides and penams were the most frequent drug classes against which genotypic resistance was found. Additionally, resistance genes to heavy metals and disinfectants were identified. Our research demonstrates the presence of antimicrobial resistance in bacteria from Arctic habitats and highlights the importance of conservation efforts in these environments, where anthropogenic influence is becoming more evident. Furthermore, our data suggest the possible presence of novel resistance mechanisms, which could pose a threat if the responsible genes are transferable between species or become widespread due to environmental stress and alterations brought about by climate change.

Reduced CO2 Release from Arctic Soils Due to CO2 Binding to Calcium Forming Aragonite.

Arctic soils are the largest pool of organic carbon compared with other soils globally and serve as a main source for greenhouse gases, especially in the course of the predicted future temperature increase. With increasing temperatures, substantial thawing of the permafrost layer of soils is expected, altering the availability of calcium in those soils, with an increase by ∼5 mg Ca g-1 DW predicted for Alaska. Here we show for two representative soils in Alaska (initially Ca-poor or Ca-rich) that this increase in Ca availability will lead to decreases in CO2 release by 50% and 57%. It is already well-known that the cation bridging of Ca ions to organic carbon renders this carbon unavailable for microbial respiration and that Ca is altering the transformation of Corg by microbes. Here we show that the decrease of the soil CO2 release may be also due to enhanced aragonite formation (by 300% for Ca-poor and 90-200% for Ca-rich soils), as revealed by synchrotron-based scanning transmission X-ray microscopy. We therefore call upon field experiments for validation of this process and inclusion of this process in global and local carbon budget models.

Polar-Region Soils as Novel Reservoir of Lactic Acid Bacteria from the Genus Carnobacterium.

Polar habitats offer excellent sites to isolate unique bacterial strains due to their diverse physical, geochemical, and biological factors. We hypothesize that the unique environmental conditions of polar regions select for distinct strains of lactic acid bacteria (LAB) with novel biochemical properties. In this study, we characterized ten strains of psychrotrophic LAB isolated from hitherto poorly described sources-High Arctic and maritime Antarctic soils and soil-like materials, including ornithogenic soils, cryoconites, elephant seal colonies, and postglacial moraines. We evaluated the physiological and biochemical properties of the isolates. Based on 16S rRNA and housekeeping genes, the four LAB strains were assigned to three Carnobacterium species: C. alterfunditum, C. maltaromaticum, and C. jeotgali. The remaining strains may represent three new species of the Carnobacterium genus. All isolates were neutrophilic and halophilic psychrotrophs capable of fermenting various carbohydrates, organic acids, and alcohols. The identified metabolic properties of the isolated Carnobacterium strains suggest possible syntrophic interactions with other microorganisms in polar habitats. Some showed antimicrobial activity against food pathogens such as Listeria monocytogenes and human pathogens like Staphylococcus spp. Several isolates exhibited unique metabolic traits with potential biotechnological applications that could be more effectively exploited under less stringent technological conditions compared to thermophilic LAB strains, such as lower temperatures and reduced nutrient concentrations. Analysis of extrachromosomal genetic elements revealed 13 plasmids ranging from 4.5 to 79.5 kb in five isolates, featuring unique genetic structures and high levels of previously uncharacterized genes. This work is the first comprehensive study of the biochemical properties of both known and new Carnobacterium species and enhances our understanding of bacterial communities in harsh and highly selective polar soil ecosystems.

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.

Wildfire effects on mercury fate in soils of North-Western Siberia

Arctic soils store 49 Gg mercury (Hg) – an extremely toxic heavy metal, whereas soil Hg can be released to the atmosphere by wildfires. For the first time we investigated the effects of wildfires on the fate of soil Hg in North-Western (NW) Siberia based on GIS maps of areas burned during the last 38 years and a field paired comparison of unburned and burned areas in tundra (mosses, lichens, some grasses, and shrubs) and forest-tundra (multi-layered canopy of larch trees, shrubs, mosses, and lichens). These field surveys were deepened by soil controlled burning to assess the Hg losses from organic horizon and mineral soil. The soil Hg stocks in the organic horizon and in the top 10 cm of the mineral soil were 3.3 ± 0.6 and 16 ± 3 mg Hg m−2 for unburned tundra and forest-tundra, respectively. After the burning by wildfires, the soil Hg stocks decreased to 2.4 ± 0.1 and 6.6 ± 0.2 mg Hg m−2 for tundra and forest-tundra, respectively. By the averages annual burned areas in NW Siberia 527 km2, wildfires in tundra and forest-tundra released 0.19 and 2.9 Mg soil Hg per year, respectively, corresponding to 28 % and 59 % of the initial soil Hg stocks. These direct effects of wildfires on Hg volatilization are raised by indirect post-pyrogenic consequences on Hg fate triggered by the vegetation succession and adsorption of atmospheric Hg on the surface of charred biomass. Charred lichens and trees accumulated 4–16 times more Hg compared to the living biomass. Blackened burned vegetation and soil reduced surface albedo and slowly increased soil temperatures in Arctic after wildfires. This created favorable conditions for seeding grasses and shrubs after wildfire and transformed burned high-latitude ecosystems into greener areas, increasing their capacity to trap atmospheric Hg by vegetation, which partly compensate the burning losses of soil Hg.

Upland Yedoma taliks are an unpredicted source of atmospheric methane

Landscape drying associated with permafrost thaw is expected to enhance microbial methane oxidation in arctic soils. Here we show that ice-rich, Yedoma permafrost deposits, comprising a disproportionately large fraction of pan-arctic soil carbon, present an alternate trajectory. Field and laboratory observations indicate that talik (perennially thawed soils in permafrost) development in unsaturated Yedoma uplands leads to unexpectedly large methane emissions (35–78 mg m−2 d−1 summer, 150–180 mg m−2 d−1 winter). Upland Yedoma talik emissions were nearly three times higher annually than northern-wetland emissions on an areal basis. Approximately 70% emissions occurred in winter, when surface-soil freezing abated methanotrophy, enhancing methane escape from the talik. Remote sensing and numerical modeling indicate the potential for widespread upland talik formation across the pan-arctic Yedoma domain during the 21st and 22nd centuries. Contrary to current climate model predictions, these findings imply a positive and much larger permafrost-methane-climate feedback for upland Yedoma.

Vegetation predicts soil shear strength in Arctic Soils: Ground-based and remote sensing techniques

Vegetation predicts soil shear strength in Arctic Soils: Ground-based and remote sensing techniques

Quantifying soil accumulation of atmospheric mercury using fallout radionuclide chronometry

Soils are a principal global reservoir of mercury (Hg), a neurotoxic pollutant that is accumulating through anthropogenic emissions to the atmosphere and subsequent deposition to terrestrial ecosystems. The fate of Hg in global soils remains uncertain, however, particularly to what degree Hg is re-emitted back to the atmosphere as gaseous elemental mercury (GEM). Here we use fallout radionuclide (FRN) chronometry to directly measure Hg accumulation rates in soils. By comparing these rates with measured atmospheric fluxes in a mass balance approach, we show that representative Arctic, boreal, temperate, and tropical soils are quantitatively efficient at retaining anthropogenic Hg. Potential for significant GEM re-emission appears limited to a minority of coniferous soils, calling into question global models that assume strong re-emission of legacy Hg from soils. FRN chronometry poses a powerful tool to reconstruct terrestrial Hg accumulation across larger spatial scales than previously possible, while offering insights into the susceptibility of Hg mobilization from different soil environments.

Genomic insights into redox-driven microbial processes for carbon decomposition in thawing Arctic soils and permafrost.

As the Arctic warms, thawing permafrost unlocks carbon, potentially accelerating climate change by releasing greenhouse gases. Our research delves into the underlying biogeochemical processes likely mediated by the soil microbial community in response to the wet and anaerobic conditions, akin to an Arctic summer thaw. We observed a significant shift in the microbial community post-thaw, with fermentative bacteria like Firmicutes and Bacteroidota taking over and switching to different fermentation pathways. The dominance of iron and sulfate-reducing bacteria likely constrained methane production in the thawing permafrost. Slow-growing microbes outweighed fast-growing ones, even after thaw, upending the expectation that rapid microbial responses to dominate after permafrost thaws. This research highlights the nuanced and complex interactions within Arctic soil microbial communities and underscores the challenges in predicting microbial response to environmental change.

Using Relationships Between Vegetation and Surface Soil Biogeochemical Properties to Assess Regional Soil Carbon Inventories for South Baffin Island, Nunavut, Canada

AbstractAs Arctic regions warm rapidly, it is unclear whether high‐latitude soil carbon (C) will decrease or increase. Predicting future dynamics of Arctic soil C stocks requires a better understanding of the quantities and controls of soil C. We explore the relationship between vegetation and surface soil C in an understudied region of the Arctic: Baffin Island, Nunavut, Canada. We combined soil C data for three vegetation types—polar desert, mesic tundra, and wet meadow—with a vegetation classification to upscale soil C stocks. Surface soil C differed significantly across vegetation types, and interactions existed between vegetation type and soil depth. Polar desert soils were consistently mineral, with relatively thin organic layers, low percent C, and high bulk density. Mesic soils exhibited an organic‐rich epipedon overlying mineral soil. Wet meadows were consistently organic soil with low bulk density and high percent C. For the top 20 cm, polar desert contained the least soil C (2.17 ± 0.48 kg m−2); mesic tundra had intermediate C (8.92 ± 0.74 kg m−2); wet meadow stored the most C (13.07 ± 0.69 kg m−2). Extrapolating to the top 30 cm, our results suggest that approximately 44 Tg C is stored in the study region with a mean landscape soil C stock of 2.75 kg m−2 for non‐water areas. Combining vegetation mapping with local soil C stocks considerably narrows the range of estimates from other upscaling approaches (27–189 Tg) for soil C on South Baffin Island.

Census of below-ground biota associated with permafrost affected soils of western Greenland, with a focus on trophic structure

Large amounts of terrestrial organic carbon (OC) are stored in Arctic permafrost-affected soils. Through processes of cryoturbation and solifluction, the subsoils can contain subducted topsoil material, which largely contribute to the large OC storage in these soils. While the bacterial, archaeal, and fungal communities in such soils have been studied to some degree, information about protists and meso- and macrofauna is scarce, although these groups might substantially contribute to OC processing, through e.g., food web interactions. Different organic and mineral horizons, including subducted topsoil material, of Arctic soils were investigated using a metatranscriptomics three-domain community profiling approach. Soil horizons were compared in regards to their total microbial community composition including all three domains of life. Furthermore, abundances of different pro- and eukaryotic micropredators were examined and a variety of functional groups involved in the carbon (C) and the nitrogen (N) cycle were analyzed in relation to specific taxonomic groups and abiotic soil parameters. Our study showed that RNA yields positively correlated with the OC content of the horizon and that the composition of the microbial community in subducted topsoil material rather matched that of mineral subsoils instead of organic top horizons. Horizon-resolved profiling revealed heterogeneity in the associated microbiomes and showed major differences in microbiomes of topsoil and subducted topsoil. The abundance of protist and nematode micropredators decreased in subducted topsoil, while predatory myxobacteria remained remarkably constant and comprised high proportions of the total communities in all horizons. Correlations analysis between functional guilds and biotic and abiotic parameters suggest a major impact of predatory myxobacteria on carbon and nitrogen cycles of subducted topsoils. The study adds urgently needed information about the total biota structure in permafrost soils and first insights into the associated soil microbial food webs.

Soil resources vs. physicochemical soil properties as drivers of abundance and diversity of low Arctic soil mesofauna communities

Soil resources vs. physicochemical soil properties as drivers of abundance and diversity of low Arctic soil mesofauna communities

Genome analysis and description of Tunturibacter gen. nov. expands the diversity of Terriglobia in tundra soils.

Increased temperatures in Arctic tundra ecosystems are leading to higher microbial respiration rates of soil organic matter, resulting in the release of carbon dioxide and methane. To understand the effects of this microbial activity, it is important to better characterize the diverse microbial communities in Arctic soil. Our goal is to refine our understanding of the phylogenetic diversity of Terriglobia, a common but elusive group within the Acidobacteriota phylum. This will help us link this diversity to variations in carbon and nitrogen usage patterns. We used long-read Oxford Nanopore MinION sequences in combination with metagenomic short-read sequences to assemble complete Acidobacteriota genomes. This allowed us to build multi-locus phylogenies and annotate pangenome markers to distinguish Acidobacteriota strains from several tundra soil isolates. We identified a phylogenetic cluster containing four new species previously associated with Edaphobacter lichenicola. We conclude that this cluster represents a new genus, which we have named Tunturibacter. We describe four new species: Tunturibacter lichenicola comb. nov., Tunturibacter empetritectus sp. nov., Tunturibacter gelidoferens sp. nov., and Tunturibacter psychrotolerans sp. nov. By uncovering new species and strains within the Terriglobia and improving the accuracy of their phylogenetic placements, we hope to enhance our understanding of this complex phylum and shed light on the mechanisms that shape microbial communities in polar soils.

Controls on the Respiration of Ancient Carbon Draining From Permafrost Soils Into Sunlit Arctic Surface Waters

AbstractThe thawing of ancient organic carbon stored in arctic permafrost soils, and its oxidation to carbon dioxide (CO2, a greenhouse gas), is predicted to amplify global warming. However, the extent to which organic carbon in thawing permafrost soils will be released as CO2 is uncertain. A critical unknown is the extent to which dissolved organic carbon (DOC) from thawing permafrost soils is respired to CO2 by microbes upon export of freshly thawed DOC to both dark bottom waters and sunlit surface waters. In this study, we quantified the radiocarbon age and 13C composition of CO2 produced by microbial respiration of DOC that was leached from permafrost soils and either kept in the dark or exposed to ultraviolet and visible wavelengths of light. We show that permafrost DOC most labile to microbial respiration was as old or older (ages 4,000–11,000 a BP) and more 13C‐depleted than the bulk DOC in both dark and light‐exposed treatments, likely indicating respiration of old, 13C‐depleted lignin and lipid fractions of the permafrost DOC pool. Light exposure either increased, decreased, or had no effect on the magnitude of microbial respiration of old permafrost DOC relative to respiration in the dark, depending on both the extent of DOC oxidation during exposure to light and the wavelength of light. Together, these findings suggest that photochemical changes affecting the lability of permafrost DOC during sunlight exposure are an important control on the magnitude of microbial respiration of permafrost DOC in arctic surface waters.

Draft genome sequence of Acerihabitans sp. strain TG2T, isolated from an Arctic tundra soil sample.

Acerihabitans sp. type strain TG2T (VKM B-3773T) is a gram-negative, anaerobic psychrophilic bacterium that was isolated from a tundra soil sample selected by the Bykovsky Peninsula (Russia). This report describes the generation and annotation of the 5.3 Mb draft genome sequence of Acerihabitans sp. strain TG2T.

Leakage of old carbon dioxide from a major river system in the Canadian Arctic.

The Canadian Arctic is warming at an unprecedented rate. Warming-induced permafrost thaw can lead to mobilization of aged carbon from stores in soils and rocks. Tracking the carbon pools supplied to surrounding river networks provides insight on pathways and processes of greenhouse gas release. Here, we investigated the dual-carbon isotopic characteristics of the dissolved inorganic carbon (DIC) pool in the main stem and tributaries of the Mackenzie River system. The radiocarbon (14C) activity of DIC shows export of "old" carbon (2,380 ± 1,040 14C years BP on average) occurred during summer in sampling years. The stable isotope composition of river DIC implicates degassing of aged carbon as CO2 from riverine tributaries during transport to the delta; however, information on potential drivers and fluxes are still lacking. Accounting for stable isotope fractionation during CO2 loss, we show that a large proportion of this aged carbon (60 ± 10%) may have been sourced from biospheric organic carbon oxidation, with other inputs from carbonate weathering pathways and atmospheric exchange. The findings highlight hydrologically connected waters as viable pathways for mobilization of aged carbon pools from Arctic permafrost soils.

Comparative analysis of characteristics of antibiotic resistomes between Arctic soils and representative contaminated samples using metagenomic approaches

Antibiotic resistance is one of the most concerned global health issues. However, comprehensive profiles of antibiotic resistance genes (ARGs) in various environmental settings are still needed to address modern antibiotic resistome. Here, Arctic soils and representative contaminated samples from ARG pollution sources were analyzed using metagenomic approaches. The diversity and abundance of ARGs in Arctic soils were significantly lower than those in contaminated samples (p < 0.01). ARG profiles in Arctic soils were featured with the dominance of vanF, ceoB, and bacA related to multidrug and bacitracin, whereas those from ARG pollution sources were characterized by prevalent resistance to anthropogenic antibiotics such as sulfonamides, tetracyclines, and beta-lactams. Mobile genetic elements (MGEs) were found in all samples, and their abundance and relatedness to ARGs were both lower in Arctic soils than in polluted samples. Significant relationships between bacterial communities and ARGs were observed (p < 0.01). Cultural bacteria in Arctic soils had clinically-concerned resistance to erythromycin, vancomycin, ampicillin, etc., but ARGs relevant to those antibiotics were undetectable in their genomes. Our results suggested that Arctic environment could be an important reservoir of novel ARGs, and antibiotic stresses could cause ARG pollution via horizontal gene transfer and enrichment of resistant bacteria.