Fungi in Permafrost

Mineral substrate quality determines the initial soil microbial development in front of the Nordenskiöldbreen, Svalbard

Substrate geochemistry is an important factor influencing early microbial development after glacial retreat on nutrient-poor geological substrates in the High Arctic. It is often difficult to separate substrate influence from climate because study locations are distant. Our study in the retreating Nordenskiöldbreen (Svalbard) is one of the few to investigate biogeochemical and microbial succession in two adjacent forefields, which share the same climatic conditions but differ in their underlying geology. The northern silicate forefield evolved in a classical chronosequence, where most geochemical and microbial parameters increased gradually with time. In contrast, the southern carbonate forefield exhibited high levels of nutrients and microbial biomass at the youngest sites, followed by a significant decline and then a gradual increase, which caused a rearrangement in the species and functional composition of the bacterial and fungal communities. This shuffling in the early stages of succession suggests that high nutrient availability in the bedrock could have accelerated early soil succession after deglaciation and thereby promoted more rapid stabilization of the soil and production of higher quality organic matter. Most chemical parameters and bacterial taxa converged with time, while fungi showed no clear pattern.

RNA Viruses Linked to Eukaryotic Hosts in Thawed Permafrost

Arctic permafrost is thawing due to global warming, with unknown consequences on the microbial inhabitants or associated viruses. DNA viruses have previously been shown to be abundant and active in thawing permafrost, but little is known about RNA viruses in these systems. To address this knowledge gap, we assessed the composition of RNA viruses in thawed permafrost samples that were incubated for 97 days at 4°C to simulate thaw conditions. A diverse RNA viral community was assembled from metatranscriptome data including double-stranded RNA viruses, dominated by Reoviridae and Hypoviridae, and negative and positive single-stranded RNA viruses, with relatively high representations of Rhabdoviridae and Leviviridae, respectively. Sequences corresponding to potential plant and human pathogens were also detected. The detected RNA viruses primarily targeted dominant eukaryotic taxa in the samples (e.g., fungi, Metazoa and Viridiplantae) and the viral community structures were significantly associated with predicted host populations. These results indicate that RNA viruses are linked to eukaryotic host dynamics. Several of the RNA viral sequences contained auxiliary metabolic genes encoding proteins involved in carbon utilization (e.g., polygalacturosase), implying their potential roles in carbon cycling in thawed permafrost. IMPORTANCE Permafrost is thawing at a rapid pace in the Arctic with largely unknown consequences on ecological processes that are fundamental to Arctic ecosystems. This is the first study to determine the composition of RNA viruses in thawed permafrost. Other recent studies have characterized DNA viruses in thawing permafrost, but the majority of DNA viruses are bacteriophages that target bacterial hosts. By contrast RNA viruses primarily target eukaryotic hosts and thus represent potential pathogenic threats to humans, animals, and plants. Here, we find that RNA viruses in permafrost are novel and distinct from those in other habitats studied to date. The COVID-19 pandemic has heightened awareness of the importance of potential environmental reservoirs of emerging RNA viral pathogens. We demonstrate that some potential pathogens were detected after an experimental thawing regime. These results are important for understanding critical viral-host interactions and provide a better understanding of the ecological roles that RNA viruses play as permafrost thaws.

Small-scale variation in a pristine montane cloud forest: evidence on high soil fungal diversity and biogeochemical heterogeneity

Montane cloud forests are fragile biodiversity hotspots. To attain their conservation, disentangling diversity patterns at all levels of ecosystem organization is mandatory. Biotic communities are regularly structured by environmental factors even at small spatial scales. However, studies at this scale have received less attention with respect to larger macroscale explorations, hampering the robust view of ecosystem functioning. In this sense, fungal small-scale processes remain poorly understood in montane cloud forests, despite their relevance. Herein, we analyzed soil fungal diversity and ecological patterns at the small-scale (within a 10 m triangular transect) in a pristine montane cloud forest of Mexico, using ITS rRNA gene amplicon Illumina sequencing and biogeochemical profiling. We detected a taxonomically and functionally diverse fungal community, dominated by few taxa and a large majority of rare species (81%). Undefined saprotrophs represented the most abundant trophic guild. Moreover, soil biogeochemical data showed an environmentally heterogeneous setting with patchy clustering, where enzymatic activities suggest distinctive small-scale soil patterns. Our results revealed that in this system, deterministic processes largely drive the assemblage of fungal communities at the small-scale, through multifactorial environmental filtering.

Frozen Zoo: a collection of permafrost samples containing viable protists and their viruses

Background

Permafrost, frozen ground cemented with ice, occupies about a quarter of the Earth’s hard surface and reaches up to 1000 metres depth. Due to constant subzero temperatures, permafrost represents a unique record of past epochs, whenever it comes to accumulated methane, oxygen isotope ratio or stored mummies of animals. Permafrost is also a unique environment where cryptobiotic stages of different microorganisms are trapped and stored alive for up to hundreds of thousands of years. Several protist strains and two giant protist viruses isolated from permafrost cores have been already described.

New information

In this paper, we describe a collection of 35 amoeboid protist strains isolated from the samples of Holocene and Pleistocene permanently frozen sediments. These samples are stored at −18°C in the Soil Cryology Lab, Pushchino, Russia and may be used for further studies and isolation attempts. The collection strains are maintained in liquid media and may be available upon request. The paper also presents a dataset which consists of a table describing the samples and their properties (termed "Sampling events") and a table describing the isolated strains (termed "Occurrences"). The dataset is publicly available through the GBIF portal.

Intra- and inter-cores fungal diversity suggests interconnection of different habitats in an Antarctic frozen lake (Boulder Clay, Northern Victoria Land)

A perennially frozen lake at Boulder Clay site (Victoria Land, Antarctica), characterized by the presence of frost mounds, have been selected as an in situ model for ecological studies. Different samples of permafrost, glacier ice and brines have been studied as a unique habitat system. An additional sample of brines (collected in another frozen lake close to the previous one) was also considered. Alpha- and beta-diversity of fungal communities showed both intra- and inter-cores significant (p < 0.05) differences, which suggest the presence of interconnection among the habitats. Therefore, the layers of frost mound and the deep glacier could be interconnected while the brines could probably be considered as an open habitat system not interconnected with each other. Moreover, the absence of similarity between the lake ice and the underlying permafrost suggested that the lake is perennially frozen based. The predominance of positive significant (p < 0.05) co-occurrences among some fungal taxa allowed to postulate the existence of an ecological equilibrium in the habitats systems. The positive significant (p < 0.05) correlation between salt concentration, total organic carbon and pH, and some fungal taxa suggests that a few abiotic parameters could drive fungal diversity inside these ecological niches.

Functional and Structural Responses of Arctic and Alpine Soil Prokaryotic and Fungal Communities Under Freeze-Thaw Cycles of Different Frequencies

Ongoing climate change involves increasing snow scarcity, which results in more frequent freeze-thaw cycles (FTCs) in polar and alpine soils. Although repeated FTCs have been shown to alter the structure and functions of soil microbial communities, a thorough understanding on the influence of FTCs frequency on polar and especially alpine soil microbiomes is still elusive. Here, we investigated the impact of repeated weekly vs. daily FTC frequencies on the structure and functions of prokaryotic and fungal communities from north- and south-exposed soils from two mountain ridges, one in the Arctic and one in the High-Alps. FTCs affected prokaryotic communities more strongly than fungal communities, where mainly cold-tolerant and opportunistic fungi (e.g., Mrakia, Mortierella) were responsive. Prokaryotic communities were more affected by weekly FTCs than by daily FTCs. Daily FTCs favored fast-growing bacteria (e.g., Arthrobacter), while oligotrophic and largely uncultured taxa (e.g., Verrucomicrobia) benefited from weekly FTCs. FTCs negatively affected microbial respiration but had minor impacts on C-, N- and P-acquiring enzymatic activities. Plausible pre-adaptation of the microbial communities to naturally occurring frequent FTCs at their site of origin did not show a clear influence on the microbial responses to the tested FTCs. Altogether, our study provides an integrative overview on potential structural and functional changes of soil microbial communities in polar and alpine regions in response to the projected increase in FTCs; therefore advancing our understanding on the impact of climate change in these rapidly changing ecosystems.

Diversity, distribution, and ecology of viable fungi in permafrost and active layer of Maritime Antarctica

We evaluated the diversity and distribution of viable fungi present in permafrost and active layers obtained from three islands of Maritime Antarctica. A total of 213 fungal isolates were recovered from the permafrost, and 351 from the active layer, which were identified in 58 taxa; 27 from permafrost and 31 from the active layer. Oidiodendron, Penicillium, and Pseudogymnoascus taxa were the most abundant in permafrost. Bionectriaceae, Helotiales, Mortierellaceae, and Pseudeurotium were the most abundant in the active layer. Only five shared both substrates. The yeast Mrakia blollopis represented is the first reported on Antarctic permafrost. The fungal diversity detected was moderate to high, and composed of cosmopolitan, cold-adapted, and endemic taxa, reported as saprobic, mutualistic, and parasitic species. Our results demonstrate that permafrost shelters viable fungi across the Maritime Antarctica, and that they are contrasting to the overlying active layer. We detected important fungal taxa represented by potential new species, particularly, those genetically close to Pseudogymnoascus destructans, which can cause extinction of bats in North America and Eurasia. The detection of viable fungi trapped in permafrost deserves further studies on the extension of its fungal diversity and its capability to expand from permafrost to other habitats in Antarctica, and elsewhere.

The role of changing temperature in microbial metabolic processes during permafrost thaw

Approximately one fourth of the Earth's Northern Hemisphere is underlain by permafrost, earth materials (soil, organic matter, or bedrock), that has been continuously frozen for at least two consecutive years. Numerous studies point to evidence of accelerated climate warming in the Arctic and sub-Arctic where permafrost is located. Changes to permafrost biochemical processes may critically impact ecosystem processes at the landscape scale. Here, we sought to understand how the permafrost metabolome responds to thaw and how this response differs based on location (i.e. chronosequence of permafrost formation constituting diverse permafrost types). We analyzed metabolites from microbial cells originating from Alaskan permafrost. Overall, permafrost thaw induced a shift in microbial metabolic processes. Of note were the dissimilarities in biochemical structure between frozen and thawed samples. The thawed permafrost metabolomes from different locations were highly similar. In the intact permafrost, several metabolites with antagonist properties were identified, illustrating the competitive survival strategy required to survive a frozen state. Interestingly, the intensity of these antagonistic metabolites decreased with warmer temperature, indicating a shift in ecological strategies in thawed permafrost. These findings illustrate the impact of change in temperature and spatial variability as permafrost undergoes thaw, knowledge that will become crucial for predicting permafrost biogeochemical dynamics as the Arctic and Antarctic landscapes continue to warm.

Extreme environments: microbiology leading to specialized metabolites

The prevalence of multidrug-resistant microbial pathogens due to the continued misuse and overuse of antibiotics in agriculture and medicine is raising the prospect of a return to the preantibiotic days of medicine at the time of diminishing numbers of drug leads. The good news is that an increased understanding of the nature and extent of microbial diversity in natural habitats coupled with the application of new technologies in microbiology and chemistry is opening up new strategies in the search for new specialized products with therapeutic properties. This review explores the premise that harsh environmental conditions in extreme biomes, notably in deserts, permafrost soils and deep-sea sediments select for micro-organisms, especially actinobacteria, cyanobacteria and fungi, with the potential to synthesize new druggable molecules. There is evidence over the past decade that micro-organisms adapted to life in extreme habitats are a rich source of new specialized metabolites. Extreme habitats by their very nature tend to be fragile hence there is a need to conserve those known to be hot-spots of novel gifted micro-organisms needed to drive drug discovery campaigns and innovative biotechnology. This review also provides an overview of microbial-derived molecules and their biological activities focusing on the period from 2010 until 2018, over this time 186 novel structures were isolated from 129 representatives of microbial taxa recovered from extreme habitats.

High-Alpine Permafrost and Active-Layer Soil Microbiomes Differ in Their Response to Elevated Temperatures

The response of microbial communities to the predicted rising temperatures in alpine regions might be an important part of the ability of these ecosystems to deal with climate change. Soil microbial communities might be significantly affected by elevated temperatures, which influence the functioning of soils within high-alpine ecosystems. To evaluate the potential of the permafrost microbiome to adapt to short-term moderate and extreme warming, we set up an incubation experiment with permafrost and active soil layers from northern and southern slopes of a high-alpine mountain ridge on Muot da Barba Peider in the Swiss Alps. Soils were acclimated to increasing temperatures (4–40°C) for 26 days before being exposed to a heat shock treatment of 40°C for 4 days. Alpha-diversity in all soils increased slightly under gradual warming, from 4 to 25°C, but then dropped considerably at 40°C. Similarly, heat shock induced strong changes in microbial community structures and functioning in the active layer of soils from both northern and southern slope aspects. In contrast, permafrost soils showed only minor changes in their microbial community structures and no changes in their functioning, except regarding specific respiration activity. Shifts in microbial community structures with increasing temperature were significantly more pronounced for bacteria than for fungi, regardless of the soil origin, suggesting higher resistance of high-alpine fungi to short-term warming. Firmicutes, mainly represented by Tumebacillus and Alicyclobacillaceae OTUs, increased strongly at 40°C in active layer soils, reaching almost 50% of the total abundance. In contrast, Saccharibacteria decreased significantly with increasing temperature across all soil samples. Overall, our study highlights the divergent responses of fungal and bacterial communities to increased temperature. Fungi were highly resistant to increased temperatures compared to bacteria, and permafrost communities showed surprisingly low response to rising temperature. The unique responses were related to both site aspect and soil origin indicating that distinct differences within high-alpine soils may be driven by substrate limitation and legacy effects of soil temperatures at the field site.

Alpine soil microbial ecology in a changing world

Climate change has a disproportionally large impact on alpine soil ecosystems, leading to pronounced changes in soil microbial diversity and function associated with effects on biogeochemical processes at the local and supraregional scales. However, due to restricted accessibility, high-altitude soils remain largely understudied and a considerable heterogeneity hampers the comparability of different alpine studies. Here, we highlight differences and similarities between alpine and arctic ecosystems, and we discuss the impact of climatic variables and associated vegetation and soil properties on microbial ecology. We consider how microbial alpha-diversity, community structures and function change along altitudinal gradients and with other topographic features such as slope aspect. In addition, we focus on alpine permafrost soils, harboring a surprisingly large unknown microbial diversity and on microbial succession along glacier forefield chronosequences constituting the most thoroughly studied alpine habitat. Finally, highlighting experimental approaches, we present climate change studies showing shifts in microbial community structures and function in response to warming and altered moisture, interestingly with some contradiction. Collectively, despite harsh environmental conditions, many specially adapted microorganisms are able to thrive in alpine environments. Their community structures strongly correlate with climatic, vegetation and soil properties and thus closely mirror the complexity and small-scale heterogeneity of alpine soils.

Living strategy of cold-adapted fungi with the reference to several representative species

Our planet is dominant with cold environments that harbour enormously diverse cold-adapted fungi comprising representatives of all phyla. Investigation based on culture-dependent and independent methods has demonstrated that cold-adapted fungi are cosmopolitan and occur in diverse habitants and substrates. They live as saprobes, symbionts, plant and animal parasites and pathogens to perform crucial functions in different ecosystems. Pseudogymnoascus destructans caused bat white-nose syndrome and Ophiocordyceps sinensis as Chinese medicine are the representative species that have significantly ecological and economic significance. Adaptation to cold niches has made this group of fungi a fascinating resource for the discovery of novel enzymes and secondary metabolites for biotechnological and pharmaceutical uses. This review provides the current understanding of living strategy and ecological functions of cold-adapted fungi, with particular emphasis on how those fungi overcome the extreme low temperature and perform their ecological function.

[Biosynthesis of biologically active low-molecular weight compounds by fungi of the genus Penicillium (review)]

The recent data on exometabolite biosynthesis in fungi of the genus Penicillium is summarized. The study of creative species, as well as those isolated from extreme ecotopes, resulted in the identification of a number of novel, biologically active compounds. Alkaloid biosynthesis has been shown to begin on.the first day of fungus cultivation and to proceed throughout the cultivation period. Idiophase kinetics was observed for the biosynthesis of polyketide metabolites. The mechanisms of regulation of biosynthesis of promising bioactive compounds are discussed.

The microbial diversity, distribution, and ecology of permafrost in China: a review

Permafrost in China mainly located in high-altitude areas. It represents a unique and suitable ecological niche that can be colonized by abundant microbes. Permafrost microbial community varies across geographically separated locations in China, and some lineages are novel and possible endemic. Besides, Chinese permafrost is a reservoir of functional microbial groups involved in key biogeochemical cycling processes. In future, more work is necessary to determine if these phylogenetic groups detected by DNA-based methods are part of the viable microbial community, and their functional roles and how they potentially respond to climate change. This review summaries recent studies describing microbial biodiversity found in permafrost and associated environments in China, and provides a framework for better understanding the microbial ecology of permafrost.

The microbial ecology of permafrost

Permafrost constitutes a major portion of the terrestrial cryosphere of the Earth and is a unique ecological niche for cold-adapted microorganisms. There is a relatively high microbial diversity in permafrost, although there is some variation in community composition across different permafrost features and between sites. Some microorganisms are even active at subzero temperatures in permafrost. An emerging concern is the impact of climate change and the possibility of subsequent permafrost thaw promoting microbial activity in permafrost, resulting in increased potential for greenhouse-gas emissions. This Review describes new data on the microbial ecology of permafrost and provides a platform for understanding microbial life strategies in frozen soil as well as the impact of climate change on permafrost microorganisms and their functional roles.

Commercial DNA extraction kits impact observed microbial community composition in permafrost samples

The total community genomic DNA (gDNA) from permafrost was extracted using four commercial DNA extraction kits. The gDNAs were compared using quantitative real-time PCR (qPCR) targeting 16S rRNA genes and bacterial diversity analyses obtained via 454 pyrosequencing of the 16S rRNA (V3 region) amplified in single or nested PCR. The FastDNA(®) SPIN (FDS) Kit provided the highest gDNA yields and 16S rRNA gene concentrations, followed by MoBio PowerSoil(®) (PS) and MoBio PowerLyzer™ (PL) kits. The lowest gDNA yields and 16S rRNA gene concentrations were from the Meta-G-Nome™ (MGN) DNA Isolation Kit. Bacterial phyla identified in all DNA extracts were similar to that found in other soils and were dominated by Actinobacteria, Firmicutes, Gemmatimonadetes, Proteobacteria, and Acidobacteria. Weighted UniFrac and statistical analyses indicated that bacterial community compositions derived from FDS, PS, and PL extracts were similar to each other. However, the bacterial community structure from the MGN extracts differed from other kits exhibiting higher proportions of easily lysed β- and γ-Proteobacteria and lower proportions of Actinobacteria and Methylocystaceae important in carbon cycling. These results indicate that gDNA yields differ between the extraction kits, but reproducible bacterial community structure analysis may be accomplished using gDNAs from the three bead-beating lysis extraction kits.

New environmental metabarcodes for analysing soil DNA: potential for studying past and present ecosystems

Metabarcoding approaches use total and typically degraded DNA from environmental samples to analyse biotic assemblages and can potentially be carried out for any kinds of organisms in an ecosystem. These analyses rely on specific markers, here called metabarcodes, which should be optimized for taxonomic resolution, minimal bias in amplification of the target organism group and short sequence length. Using bioinformatic tools, we developed metabarcodes for several groups of organisms: fungi, bryophytes, enchytraeids, beetles and birds. The ability of these metabarcodes to amplify the target groups was systematically evaluated by (i) in silico PCRs using all standard sequences in the EMBL public database as templates, (ii) in vitro PCRs of DNA extracts from surface soil samples from a site in Varanger, northern Norway and (iii) in vitro PCRs of DNA extracts from permanently frozen sediment samples of late-Pleistocene age (~16,000-50,000 years bp) from two Siberian sites, Duvanny Yar and Main River. Comparison of the results from the in silico PCR with those obtained in vitro showed that the in silico approach offered a reliable estimate of the suitability of a marker. All target groups were detected in the environmental DNA, but we found large variation in the level of detection among the groups and between modern and ancient samples. Success rates for the Pleistocene samples were highest for fungal DNA, whereas bryophyte, beetle and bird sequences could also be retrieved, but to a much lesser degree. The metabarcoding approach has considerable potential for biodiversity screening of modern samples and also as a palaeoecological tool.

Ancient fungi in Antarctic permafrost environments

Filamentous fungi in 36 samples of Antarctic permafrost sediments were studied. The samples collected during the Russian Antarctic expedition of 2007-2009 within the framework of the Antarctic Permafrost Age Project (ANTPAGE) were recovered from different depths in ice-free oases located along the perimeter of the continent. Fungal diversity was determined by conventional microbiological techniques combined with a culture-independent method based on the analysis of internal transcribed spacer (ITS2) sequences in total DNA of the samples. The study revealed a rather low fungal population density in permafrost, although the diversity found was appreciable, representing more than 26 genera. Comparison of the data obtained by different techniques showed that the culture-independent method enabled the detection of ascomycetous and basidiomycetous fungi not found by culturing. The molecular method failed to detect members of the genera Penicillium and Cladosporium that possess small-sized spores known to have a high resistance to environmental changes.