Fungal growth and biomass development is boosted by plants in snow-covered soil

Fungal and bacterial communities and their associations in snow-free and snow covered (sub-)alpine Pinus cembra forest soils

BACKGROUND

In Europe, Pinus cembra forests cover subalpine and alpine areas and they are of high conservational and ecological relevance. These forests experience strong seasonality with alternating snow-free and snow covered periods. Although P. cembra is known for mycorrhization and mycorrhizae usually involve fungi, plants and bacteria, the community compositions of fungi and bacteria and their associations in (sub-)alpine P. cembra forests remain vastly understudied. Here, we studied the fungal and bacterial community compositions in three independent (sub-)alpine P. cembra forests and inferred their microbial associations using marker gene sequencing and network analysis. We asked about the effect of snow cover on microbial compositions and associations. In addition, we propose inferring microbial associations across a range of filtering criteria, based on which we infer well justified, concrete microbial associations with high potential for ecological relevance that are typical for P. cembra forests and depending on snow cover.

RESULTS

The overall fungal and bacterial community structure was comparable with regards to both forest locations and snow cover. However, occurrence, abundance, and diversity patterns of several microbial taxa typical for P. cembra forests differed among snow-free and snow covered soils, e.g. Russula, Tetracladium and Phenoliphera. Moreover, network properties and microbial associations were influenced by snow cover. Here, we present concrete microbial associations on genus and species level that were repeatedly found across microbial networks, thereby confirming their ecological relevance. Most importantly, ectomycorrhizal fungi, such as Basidioascus, Pseudotomentella and Rhizopogon, as well as saprobic Mortierella changed their bacterial association partners depending on snow cover.

CONCLUSION

This is the first study researching fungal-bacterial associations across several (sub-)alpine P. cembra forests. The poorly investigated influence of snow cover on soil fungi and bacteria, especially those mycorrhizing P. cembra roots, but also saprobic soil organisms, underlines the relevance of forest seasonality. Our findings highlight that the seasonal impact of snow cover has significant consequences for the ecology of the ecosystem, particularly in relation to mycorrhization and nutrient cycling. It is imperative to consider such effects for a comprehensive understanding of the functioning resilience and responsiveness of an ecosystem.

Lichen-associated microbial members are prevalent in the snow microbiome of a sub-arctic alpine tundra

Snow is the largest component of the cryosphere, with its cover and distribution rapidly decreasing over the last decade due to climate warming. It is imperative to characterize the snow (nival) microbial communities to better understand the role of microorganisms inhabiting these rapidly changing environments. Here, we investigated the core nival microbiome, the cultivable microbial members, and the microbial functional diversity of the remote Uapishka mountain range, a massif of alpine sub-arctic tundra and boreal forest. Snow samples were taken over a two-month interval along an altitude gradient with varying degree of anthropogenic traffic and vegetation cover. The core snow alpine tundra/boreal microbiome, which was present across all samples, constituted of Acetobacterales, Rhizobiales and Acidobacteriales bacterial orders, and of Mycosphaerellales and Lecanorales fungal orders, with the dominant fungal taxa being associated with lichens. The snow samples had low active functional diversity, with Richness values ranging from 0 to 19.5. The culture-based viable microbial enumeration ranged from 0 to 8.05 × 103 CFUs/mL. We isolated and whole-genome sequenced five microorganisms which included three fungi, one alga, and one potentially novel bacterium of the Lichenihabitans genus; all of which appear to be part of lichen-associated taxonomic clades.

Mortierellaceae from subalpine and alpine habitats: new species of Entomortierella, Linnemannia, Mortierella, Podila and Tyroliella gen. nov

Fungi are incredibly diverse, but they are unexplored, especially in the subalpine and alpine zone. Mortierellaceae are certainly one of the most abundant, species-rich, and widely distributed cultivable soil fungal families in terrestrial habitats, including subalpine and alpine zones. The phylogeny of Mortierellaceae was recently resolved based on current state of the art molecular techniques, and the paraphyletic genus Mortierella sensu lato (s.l.) was divided into 13 monophyletic genera. Our extensive sampling campaigns in the Austrian Alps resulted in 139 different Mortierellaceae pure culture isolates representing 13 new species. For the definition of taxa, we applied both classical morphological criteria, as well as modern DNA-based methods. Phylogenetic relationships were resolved based on the ribosomal DNA internal transcribed spacer (rDNA ITS), the large subunit (LSU), and the DNA-directed RNA polymerase II largest subunit 1 (RPB1). In this study, we proposed a new genus and described 13 new species belonging to the genera Entomortierella, Linnemannia, Mortierella and Podila. In addition, we proposed eight new combinations, re-defined E. jenkinii at species level, defined a neotype for M. alpina and lecto- as well as epitypes for M. fatshederae, M. jenkinii, and M. longigemmata. The rDNA ITS region is generally applied as classical barcoding gene for fungi. However, the obtained phylogenetic resolution is often too low for an accurate identification of closely related species of Mortierellaceae, especially for small sampling sizes. In such cases, unambiguous identification can be obtained based on morphological characters of pure culture isolates. Therefore, we also provide dichotomous keys for species identification within phylogenetic lineages. Taxonomic novelties: new genus: Tyroliella Telagathoti, Probst & Peintner; New species: Entomortierella galaxiae Telagathoti, M. Probst & Peintner, Linnemannia bainierella Telagathoti, M. Probst & Peintner, Linnemannia stellaris Telagathoti, M. Probst & Peintner, Linnemannia nimbosa Telagathoti, M. Probst & Peintner, Linnemannia mannui Telagathoti, M. Probst & Peintner, Linnemannia friederikiana Telagathoti, M. Probst & Peintner, Linnemannia scordiella Telagathoti, M. Probst & Peintner, Linnemannia solitaria Telagathoti, M. Probst & Peintner, Mortierella triangularis Telagathoti, M. Probst & Peintner, Mortierella lapis Telagathoti, M. Probst & Peintner, Podila himami Telagathoti, M. Probst & Peintner, Podila occulta Telagathoti, M. Probst & Peintner, Tyroliella animus-liberi Telagathoti, Probst & Peintner; New combinations: Entomortierella basiparvispora (W. Gams & Grinb.) Telagathoti, M. Probst & Peintner, Entomortierella jenkinii (A.L. Sm.) Telagathoti, M. Probst & Peintner; Entomortierella sugadairana (Y. Takash. et al.) Telagathoti, M. Probst & Peintner, Linnemannia zonata (Linnem. ex W. Gams) Telagathoti, M. Probst & Peintner, Linnemannia fluviae (Hyang B. Lee et al.) Telagathoti, M. Probst & Peintner, Linnemannia biramosa (Tiegh.) Telagathoti, M. Probst & Peintner, Linnemannia cogitans (Degawa) Telagathoti, M. Probst & Peintner, Tyroliella pseudozygospora (W. Gams & Carreiro) Telagathoti, M. Probst & Peintner; Epitypifications (basionyms): Mortierella bainieri var. jenkinii A.L. Sm., Mortierella fatshederae Linnem., Mortierella longigemmata Linnem. Neotypification (basionym): Mortierella alpina Peyronel. Citation: Telagathoti A, Probst M, Mandolini E, Peintner U (2022). Mortierellaceae from subalpine and alpine habitats: new species of Entomortierella, Linnemannia, Mortierella, Podila and Tyroliella gen. nov. Studies in Mycology 103: 25-58. doi: 10.3114/sim.2022.103.02.

Seasonal Dynamics of Organic Carbon and Nitrogen in Biomasses of Microorganisms in Arable Mollisols Affected by Different Tillage Systems

Tillage has been reported to induce seasonal changes of organic carbon (Cmicro) and nitrogen (Nmicro) in the biomass of microorganisms. Soil microorganisms execute such ecosystem functions as it is an immediate sink of labile biophil elements; it is an agent of a conversion, catalysis and synthesis of humus substances; it transforms soil contaminants into nonhazardous wastes and it participates in soil aggregation and pedogenesis as a whole. However, the seasonal turnover of microorganisms on arable lands in temperate ecosystems has not been studied at a relevant level. Hence, we are aimed at studying the dynamics of such soil microbial biomass patterns as Cmicro, Nmicro, microbial index (MI = (Cmicro/CTOC)·100%) and CO2-C emissions against the background of 9 years of tillage and 22 years of abandoned (Ab) and fallow (F) usage. Our study was conducted on a long-term experimental site on a Mollisol in Northeast China. The maximum Cmicro and Nmicro contents were recorded at the beginning of the growing season at the 0–10-cm layer and mid-July at the 20–40-cm layer, while the minimum content was during August–October. The Cmicro content ranged from 577.79 to 381.79 mg−1 kg−1 using Ab in the spring to 229.53 to 272.86 mg−1 kg−1 in the autumn using CT (conventional tillage) and F in the 0–10- and 10–20-cm layers, respectively. The amplitude of Nmicro content changes were several times lower as compared with the Cmicro. The smallest quartile range (IQR0.25–0.75) of such changes was shown when using the following treatments: no till (NT) and Ab in the 0–10-, NT and F in the 10–20- and CT in the 20–40-cm layer. The widest Cmicro:Nmicro ratio was recorded at F and CT in the 0–20- and CT and rotational tillage (Rot) in the 20–40-cm layer. The MI dynamics were similar to the trends of Cmicro and Nmicro and changed from 0.72 ± 0.168 to 2.00 ± 0.030%. The highest share of Cmicro in CTOC was at Ab (1.82 ± 1.85%) and NT (1.66 ± 1.52 %) in the 0–10-, Ab (1.23 ± 1.27%) and NT (1.29 ± 1.32%) in the 10–20- and Ab (1.19 ± 1.09%) and F (1.11 ± 1.077%) in the 20–40-cm layer, correspondingly. The Pearson’s correlation coefficient between Cmicro and CTOC increased from the upper 0–10- to the lower 20–40-cm layer; it was “strong” and “high” between Cmicro and CTOC. Different uses of Mollisol affected the amplitude of the Cmicro and Nmicro seasonal changes, but it did not change their trend. Our results suggest the key role of Ab and NT technologies in Cmicro accumulation in the total organic carbon (TOC).

Glacier Retreat Results in Loss of Fungal Diversity

Walker Glacier near the northern coast of Ellesmere Island in the Canadian High Arctic (terrestrial margin of the ‘Last Ice Area’) is undergoing rapid ice attrition in response to climate change. We applied culture and molecular methods to investigate fungal diversity at the terminus of this glacier. Analysis of the mycoflora composition showed that the Walker Glacier isolates separated into two clusters: the surface of the glacier ice and the glacier foreland. The recently exposed sediments of the foreland had a lower fungal diversity and different species from those on the ice, with the exception of five species that occurred in both habitats. This loss of glacial ice in the Arctic is therefore resulting in the loss of habitats for cold-dwelling fungal species. Fungal diversity is a potentially rich biological resource of glacial ecosystems, with unique taxa. The rapid loss of these glacial habitats underscores the urgency for genomic surveys of fungal diversity in the High Arctic, and the need for further isolation of strains as well as cryopreservation of environmental micro-biome samples for future research and conservation.

More smooth-spored species of Inocybe (Agaricales, Basidiomycota): type studies and 12 new species from Europe

Twelve new species of Inocybe (I. adorabilis, I. comis, I. demetris, I. filiana, I. galactica, I. morganae, I. othini, I. ovilla, I. proteica, I. somae, I. suryana and I. venerabilis) are described from Europe on the basis of detailed morphological and molecular investigation. A portrait of the recently described I. ianthinopes is given. All species are smooth-spored and some pruinose only in the apical part of the stipe, and some on entire length. The new species are compared to 24 type specimens (17 characterized by at least partial ITS sequence data), all of which are described and revised here. Epitypes were selected for two species, I. hirtella and I. sindonia. Based on our studies, we confirm that I. kuehneri and I. sindonia on one hand, and I. subalbidodisca and I. ochroalba on the other, are synonyms and furthermore suggest that I. abietis is synonymous with I. catalaunica, I. exilis with I. rufobrunnea, I. hirtellarum with I. mycenoides, I. lapidicola with I. deianae, I. ochraceolutea with I. sindonia, I. stangliana with I. pelargonium, I. subrubens with I. subhirtella and I. sulfovirescens with I. langei. All of the new species are supported by phylogenetic analyses. Among the 16 previously described species accepted here, 10 are represented by types in the phylogenetic analyses and five by own collections corresponding to the type. Two species, I. eutheloides (remaining doubtful) and I. pallidolutea are only treated morphologically. In summary, we describe as new or verify the taxonomic status and provide or corroborate morphological concepts for 37 smooth-spored species of Inocybe.

Fungal diversity notes 1387-1511: taxonomic and phylogenetic contributions on genera and species of fungal taxa

This article is the 13th contribution in the Fungal Diversity Notes series, wherein 125 taxa from four phyla, ten classes, 31 orders, 69 families, 92 genera and three genera incertae sedis are treated, demonstrating worldwide and geographic distribution. Fungal taxa described and illustrated in the present study include three new genera, 69 new species, one new combination, one reference specimen and 51 new records on new hosts and new geographical distributions. Three new genera, Cylindrotorula (Torulaceae), Scolecoleotia (Leotiales genus incertae sedis) and Xenovaginatispora (Lindomycetaceae) are introduced based on distinct phylogenetic lineages and unique morphologies. Newly described species are Aspergillus lannaensis, Cercophora dulciaquae, Cladophialophora aquatica, Coprinellus punjabensis, Cortinarius alutarius, C. mammillatus, C. quercoflocculosus, Coryneum fagi, Cruentomycena uttarakhandina, Cryptocoryneum rosae, Cyathus uniperidiolus, Cylindrotorula indica, Diaporthe chamaeropicola, Didymella azollae, Diplodia alanphillipsii, Dothiora coronicola, Efibula rodriguezarmasiae, Erysiphe salicicola, Fusarium queenslandicum, Geastrum gorgonicum, G. hansagiense, Helicosporium sexualis, Helminthosporium chiangraiensis, Hongkongmyces kokensis, Hydrophilomyces hydraenae, Hygrocybe boertmannii, Hyphoderma australosetigerum, Hyphodontia yunnanensis, Khaleijomyces umikazeana, Laboulbenia divisa, Laboulbenia triarthronis, Laccaria populina, Lactarius pallidozonarius, Lepidosphaeria strobelii, Longipedicellata megafusiformis, Lophiotrema lincangensis, Marasmius benghalensis, M. jinfoshanensis, M. subtropicus, Mariannaea camelliae, Melanographium smilaxii, Microbotryum polycnemoides, Mimeomyces digitatus, Minutisphaera thailandensis, Mortierella solitaria, Mucor harpali, Nigrograna jinghongensis, Odontia huanrenensis, O. parvispina, Paraconiothyrium ajrekarii, Parafuscosporella niloticus, Phaeocytostroma yomensis, Phaeoisaria synnematicus, Phanerochaete hainanensis, Pleopunctum thailandicum, Pleurotheciella dimorphospora, Pseudochaetosphaeronema chiangraiense, Pseudodactylaria albicolonia, Rhexoacrodictys nigrospora, Russula paravioleipes, Scolecoleotia eriocamporesi, Seriascoma honghense, Synandromyces makranczyi, Thyridaria aureobrunnea, Torula lancangjiangensis, Tubeufia longihelicospora, Wicklowia fusiformispora, Xenovaginatispora phichaiensis and Xylaria apiospora. One new combination, Pseudobactrodesmium stilboideus is proposed. A reference specimen of Comoclathris permunda is designated. New host or distribution records are provided for Acrocalymma fici, Aliquandostipite khaoyaiensis, Camarosporidiella laburni, Canalisporium caribense, Chaetoscutula juniperi, Chlorophyllum demangei, C. globosum, C. hortense, Cladophialophora abundans, Dendryphion hydei, Diaporthe foeniculina, D. pseudophoenicicola, D. pyracanthae, Dictyosporium pandanicola, Dyfrolomyces distoseptatus, Ernakulamia tanakae, Eutypa flavovirens, E. lata, Favolus septatus, Fusarium atrovinosum, F. clavum, Helicosporium luteosporum, Hermatomyces nabanheensis, Hermatomyces sphaericoides, Longipedicellata aquatica, Lophiostoma caudata, L. clematidis-vitalbae, Lophiotrema hydei, L. neoarundinaria, Marasmiellus palmivorus, Megacapitula villosa, Micropsalliota globocystis, M. gracilis, Montagnula thailandica, Neohelicosporium irregulare, N. parisporum, Paradictyoarthrinium diffractum, Phaeoisaria aquatica, Poaceascoma taiwanense, Saproamanita manicata, Spegazzinia camelliae, Submersispora variabilis, Thyronectria caudata, T. mackenziei, Tubeufia chiangmaiensis, T. roseohelicospora, Vaginatispora nypae, Wicklowia submersa, Xanthagaricus necopinatus and Xylaria haemorrhoidalis. The data presented herein are based on morphological examination of fresh specimens, coupled with analysis of phylogenetic sequence data to better integrate taxa into appropriate taxonomic ranks and infer their evolutionary relationships.

Habitat, Snow-Cover and Soil pH, Affect the Distribution and Diversity of Mortierellaceae Species and Their Associations to Bacteria

Mortierellaceae species are among the most frequent and globally distributed soil fungi. However, the factors shaping their diversity and distribution remain obscure. Several species have been reported to be associated to bacteria, but the kind and frequency of such associations were not addressed up to now. We hypothesized that such associations could be important for Mortierellaceae ecology. Therefore, our aim was to understand the driving factors responsible for the Mortierellaceae diversity, community composition and bacterial associations in alpine and subalpine habitats. For answering our question, we collected both snow-free and snow-covered soil at sampling sites from different habitats: bare alpine soil in a glacier forefield, alpine dwarf-willow habitats, and high-altitude Pinus cembra forests. The isolations were carried out by direct cultivation without any antibiotics to the isolation media. Altogether, we obtained 389 Mortierellaceae isolates representing 29 operational taxonomic units (OTUs). Many OTUs could be placed to the genera Mortierella sensu stricto, Dissophora, Entomortierella, Gamsiella, Linnemannia, and Podila, but others could not unambiguously be assigned to a genus. Our results demonstrate that both, the distribution as well as the diversity of the Mortierellaceae species, were significantly influenced by habitat, soil pH, and snow-cover. We noticed that >30% of our isolates were associated to a non-contaminant bacterium. The bacteria associated to our Mortierellaceae isolates belonged to seven different genera. Pseudomonas was the most frequently detected genus associated to the isolated Mortierellaceae species and it was found to be species-specific. Mortierellaceae-bacteria pairs, including those with Pseudomonas, were influenced by location, habitat, and snow-cover. The majority of the fungus-bacterium associations were potentially epihyphal, but we also detected potential endohyphal bacterial species belonging to Mycoavidus, Burkholderiaceae, and Paraburkholderia. Taken together, the non-random associations we detected suggest that fungus-bacterium associations are ecologically meaningful - an interesting path that needs to be investigated further.

High-Throughput Volatilome Fingerprint Using PTR-ToF-MS Shows Species-Specific Patterns in Mortierella and Closely Related Genera

In ecology, Volatile Organic Compounds (VOCs) have a high bioactive and signaling potential. VOCs are not only metabolic products, but are also relevant in microbial cross talk and plant interaction. Here, we report the first large-scale VOC study of 13 different species of Mortierella sensu lato (s. l.) isolated from a range of different alpine environments. Proton Transfer Reaction-Time-of-Flight Mass Spectrometry (PTR-ToF-MS) was applied for a rapid, high-throughput and non-invasive VOC fingerprinting of 72 Mortierella s. l. isolates growing under standardized conditions. Overall, we detected 139 mass peaks in the headspaces of all 13 Mortierella s. l. species studied here. Thus, Mortierella s. l. species generally produce a high number of different VOCs. Mortierella species could clearly be discriminated based on their volatilomes, even if only high-concentration mass peaks were considered. The volatilomes were partially phylogenetically conserved. There were no VOCs produced by only one species, but the relative concentrations of VOCs differed between species. From a univariate perspective, we detected mass peaks with distinctively high concentrations in single species. Here, we provide initial evidence that VOCs may provide a competitive advantage and modulate Mortierella s. l. species distribution on a global scale.

Resurrection of inactive microbes and resistome present in the natural frozen world: Reality or myth?

The present world faces a new threat of ancient microbes and resistomes that are locked in the cryosphere and now releasing upon thawing due to climate change and anthropogenic activities. The cryosphere act as the best preserving place for these microbes and resistomes that stay alive for millions of years. Current reviews extensively discussed whether the resurrection of microbes and resistomes existing in these pristine environments is true or just a hype. Release of these ancient microorganisms and naked DNA is of great concern for society as these microbes can either cause infections directly or they can interact with contemporary microorganisms and affect their fitness, survival, and mutation rate. Moreover, the contemporary microorganisms may uptake the unlocked naked DNA, which might transform non-pathogenic microorganisms into deadly antibiotic-resistant microbes. Additionally, the resurrection of glacial microorganisms can cause adverse effects on ecosystems downstream. The release of glacial pathogens and naked DNA is real and can lead to fatal outbreaks; therefore, we must prepare ourselves for the possible reemergence of diseases caused by these microbes. This study provides a scientific base for the adoption of actions by international cooperation to develop preventive measures.

Metagenomic insights into the fungal assemblages of the northwest Himalayan cold desert

Psychrophilic fungi are a critical biotic component in cold deserts that serves a central role in nutrient recycling and biogeochemical cycles. Despite their ecological significance, culture-independent studies on psychrophilic mycobiome are limited. In the present study, the fungal diversity patterns across the Drass, an Indian cold desert in the Himalaya, were indexed by targeted amplicon pyrosequencing (ITS). In the Drass dataset, Ascomycota was represented by 92 genera, while 22 genera represented Basidiomycota. The most abundant genus was Conocybe (20.46%). Most of the identified genera were reported in the literature to be prolific extracellular hydrolytic enzyme producers. To identify whether the Drass fungal assemblages share similarities to other cold deserts, these were further compared to Antarctic and Arctic cold deserts. Comparative analysis across the three cold deserts indicated the dominance of Dikarya (Ascomycota and Basidiomycota). The observed alpha diversity, Shannon index as well as Pielou's evenness was highest in the Antarctic followed by Drass and Arctic datasets. The genera Malassezia, Preussia, Pseudogymnoascus, Cadophora, Geopora, Monodictys, Tetracladium, Titaea, Mortierella, and Cladosporium were common to all the cold deserts. Furthermore, Conocybe was represented predominantly in Drass. Interestingly, the genus Conocybe has not been previously reported from any other studies on Antarctic or Arctic biomes. To the best of our knowledge, this is the first fungal metagenome study in Drass soil. Our analysis shows that despite the similarities of low temperature among the cold deserts, a significant differential abundance of fungal communities prevails in the global cold deserts.

The Snowmelt Niche Differentiates Three Microbial Life Strategies That Influence Soil Nitrogen Availability During and After Winter

Soil microbial biomass can reach its annual maximum pool size beneath the winter snowpack and is known to decline abruptly following snowmelt in seasonally snow-covered ecosystems. Observed differences in winter versus summer microbial taxonomic composition also suggests that phylogenetically conserved traits may permit winter- versus summer-adapted microorganisms to occupy distinct niches. In this study, we sought to identify archaea, bacteria, and fungi that are associated with the soil microbial bloom overwinter and the subsequent biomass collapse following snowmelt at a high-altitude watershed in central Colorado, United States. Archaea, bacteria, and fungi were categorized into three life strategies (Winter-Adapted, Snowmelt-Specialist, Spring-Adapted) based upon changes in abundance during winter, the snowmelt period, and after snowmelt in spring. We calculated indices of phylogenetic relatedness (archaea and bacteria) or assigned functional attributes (fungi) to organisms within life strategies to infer whether phylogenetically conserved traits differentiate Winter-Adapted, Snowmelt-Specialist, and Spring-Adapted groups. We observed that the soil microbial bloom was correlated in time with a pulse of snowmelt infiltration, which commenced 65 days prior to soils becoming snow-free. A pulse of nitrogen (N, as nitrate) occurred after snowmelt, along with a collapse in the microbial biomass pool size, and an increased abundance of nitrifying archaea and bacteria (e.g., Thaumarchaeota, Nitrospirae). Winter- and Spring-Adapted archaea and bacteria were phylogenetically clustered, suggesting that phylogenetically conserved traits allow Winter- and Spring-Adapted archaea and bacteria to occupy distinct niches. In contrast, Snowmelt-Specialist archaea and bacteria were phylogenetically overdispersed, suggesting that the key mechanism(s) of the microbial biomass crash are likely to be density-dependent (e.g., trophic interactions, competitive exclusion) and affect organisms across a broad phylogenetic spectrum. Saprotrophic fungi were the dominant functional group across fungal life strategies, however, ectomycorrhizal fungi experienced a large increase in abundance in spring. If well-coupled plant-mycorrhizal phenology currently buffers ecosystem N losses in spring, then changes in snowmelt timing may alter ecosystem N retention potential. Overall, we observed that snowmelt separates three distinct soil niches that are occupied by ecologically distinct groups of microorganisms. This ecological differentiation is of biogeochemical importance, particularly with respect to the mobilization of nitrogen during winter, before and after snowmelt.

Emerging from the ice-fungal communities are diverse and dynamic in earliest soil developmental stages of a receding glacier

We used amplicon sequencing and isolation of fungi from in-growth mesh bags to identify active fungi in three earliest stages of soil development (SSD) at a glacier forefield (0-3, 9-14, 18-25 years after retreat of glacial ice). Soil organic matter and nutrient concentrations were extremely low, but the fungal diversity was high [220 operational taxonomic units (OTUs)/138 cultivated OTUs]. A clear successional trend was observed along SSDs, and species richness increased with time. Distinct changes in fungal community composition occurred with the advent of vascular plants. Fungal communities of recently deglaciated soil are most distinctive and rather similar to communities typical for cryoconite or ice. This indicates melting water as an important inoculum for native soil. Moreover, distinct seasonal differences were detected in fungal communities. Some fungal taxa, especially of the class Microbotryomycetes, showed a clear preference for winter and early SSD. Our results provide insight into new facets regarding the ecology of fungal taxa, for example, by showing that many fungal taxa might have an alternative, saprobial lifestyle in snow-covered, as supposed for a few biotrophic plant pathogens of class Pucciniomycetes. The isolated fungi include a high proportion of unknown species, which can be formally described and used for experimental approaches.

Ligninolytic Activity at 0 °C of Fungi on Oak Leaves Under Snow Cover in a Mixed Forest in Japan

Despite the importance of litter decomposition under snow cover in boreal forests and tundra, very little is known regarding the characteristics and functions of litter-decomposing fungi adapted to the cold climate. We investigated the decomposition of oak leaves in a heavy snowfall forest region of Japan. The rate of litter weight loss reached 26.5% during the snow cover period for 7 months and accounted for 64.6% of the annual loss (41.1%). Although no statistically significant lignin loss was detected, decolourization portions of oak leaf litter, which was attributable to the activities of ligninolytic fungi, were observed during snow cover period. This suggests that fungi involved in litter decomposition can produce extracellular enzymes to degrade lignin that remain active at 0 °C. Fungi were isolated from oak leaves collected from the forest floor under the snow layer. One hundred and sixty-six strains were isolated and classified into 33 operational taxonomic units (OTUs) based on culture characteristics and nuclear rDNA internal transcribed spacer (ITS) region sequences. To test the ability to degrade lignin, the production of extracellular phenoloxidases by isolates was quantified at 0 °C. Ten OTUs (9 Ascomycota and 1 Basidiomycota) of fungi exhibited mycelial growth and ligninolytic activity. These results suggested that some litter-decomposing fungi that had the potential to degrade lignin at 0 °C significantly contribute to litter decomposition under snow cover.

Phylogenetic systematics of Syncephalis (Zoopagales, Zoopagomycotina), a genus of ubiquitous mycoparasites

We examined phylogenetic relationships among species of the mycoparasite genus Syncephalis using sequences from three nuclear ribsosomal DNA genes (18S, 5.8S, and 28S nuc rDNA) and a gene encoding the largest subunit of RNA polymerase II (RPB1). Our data set included 88 Syncephalis isolates comprising 23 named species and several unnamed taxa. We also revived a culturing technique using beef liver and cellophane to grow several Syncephalis isolates without their host fungi to obtain pure parasite DNA. Most isolates, however, were grown in co-cultures with their host fungi, so we designed Syncephalis-specific primers to obtain sequence data. Individual and combined data sets were analyzed by maximum likelihood (ML) and Bayesian methods. We recovered 20 well-supported lineages and 38 operational taxonomic units (OTUs). Most major clades contained isolates from distant localities on multiple continents. There were taxonomic and nomenclature issues within several clades, probably due to high phenotypic plasticity or species dimorphism. We also conducted an analysis of Syncephalis nuc rDNA internal transcribed spacer (ITS) sequences for 31 phylogenetically diverse isolates, and we determined that most Syncephalis species have long ITS sequences relative to other fungi. Although commonly employed eukaryotic and fungal primers are compatible with diverse Syncephalis species, the ITS sequences of Syncepahlis are nonetheless rarely recovered in environmental molecular diversity surveys.

Colony-PCR Is a Rapid Method for DNA Amplification of Hyphomycetes

Fungal pure cultures identified with both classical morphological methods and through barcoding sequences are a basic requirement for reliable reference sequences in public databases. Improved techniques for an accelerated DNA barcode reference library construction will result in considerably improved sequence databases covering a wider taxonomic range. Fast, cheap, and reliable methods for obtaining DNA sequences from fungal isolates are, therefore, a valuable tool for the scientific community. Direct colony PCR was already successfully established for yeasts, but has not been evaluated for a wide range of anamorphic soil fungi up to now, and a direct amplification protocol for hyphomycetes without tissue pre-treatment has not been published so far. Here, we present a colony PCR technique directly from fungal hyphae without previous DNA extraction or other prior manipulation. Seven hundred eighty-eight fungal strains from 48 genera were tested with a success rate of 86%. PCR success varied considerably: DNA of fungi belonging to the genera Cladosporium, Geomyces, Fusarium, and Mortierella could be amplified with high success. DNA of soil-borne yeasts was always successfully amplified. Absidia, Mucor, Trichoderma, and Penicillium isolates had noticeably lower PCR success.

Myrmecridium hiemale sp. nov. from snow-covered alpine soil is the first eurypsychrophile in this genus of anamorphic fungi

Myrmecridium hiemale sp. nov. was isolated from snow-covered alpine bare soil and is described as the first eurypsychrophilic species of this genus of filamentous fungi. Colony growth temperature experiments were carried out in the range 4-37 °C. Morphological characteristics and colony appearance were in accordance with characteristics typical for Myrmecridium, but M. hiemale does not grow at temperatures of 25 °C and above. Sequence analyses of the internal transcribed spacer and LSU rRNA D1/D2 regions indicated that the strain in question represents a distinct taxon within the genus Myrmecridium (Myrmecridiaceae, Sordariomycetes, Ascomycota). The type strain of M. hiemale is CBS 141017^T(=JMRC 12083^T). A morphological description is provided, and a key is presented for the currently known taxa of Myrmecridium, a group of interesting fungi that are either saprobes or plant endophytes.

Spatial Distribution of Fungal Communities in an Arable Soil

Fungi are prominent drivers of ecological processes in soils, so that fungal communities across different soil ecosystems have been well investigated. However, for arable soils taxonomically resolved fine-scale studies including vertical itemization of fungal communities are still missing. Here, we combined a cloning/Sanger sequencing approach of the ITS/LSU region as marker for general fungi and of the partial SSU region for arbuscular mycorrhizal fungi (AMF) to characterize the microbiome in different maize soil habitats. Four compartments were analyzed over two annual cycles 2009 and 2010: a) ploughed soil in 0–10 cm, b) rooted soil in 40–50 cm, c) root-free soil in 60–70 cm soil depth and d) maize roots. Ascomycota was the most dominant phylum across all compartments. Fungal communities including yeasts and AMF differed strongly between compartments. Inter alia, Tetracladium, the overall largest MOTU (molecular operational taxonomic unit), occurred in all compartments, whereas Trichosporon dominated all soil compartments. Sequences belonging to unclassified Helotiales were forming the most abundant MOTUs exclusively present in roots. This study gives new insights on spatial distribution of fungi and helps to link fungal communities to specific ecological properties such as varying resources, which characterize particular niches of the heterogeneous soil environment.

Temporal variation of Bistorta vivipara-associated ectomycorrhizal fungal communities in the High Arctic

Ectomycorrhizal (ECM) fungi are important for efficient nutrient uptake of several widespread arctic plant species. Knowledge of temporal variation of ECM fungi, and the relationship of these patterns to environmental variables, is essential to understand energy and nutrient cycling in Arctic ecosystems. We sampled roots of Bistorta vivipara ten times over two years; three times during the growing-season (June, July and September) and twice during winter (November and April) of both years. We found 668 ECM OTUs belonging to 25 different ECM lineages, whereof 157 OTUs persisted throughout all sampling time-points. Overall, ECM fungal richness peaked in winter and species belonging to Cortinarius, Serendipita and Sebacina were more frequent in winter than during summer. Structure of ECM fungal communities was primarily affected by spatial factors. However, after accounting for spatial effects, significant seasonal variation was evident revealing correspondence with seasonal changes in environmental conditions. We demonstrate that arctic ECM richness and community structure differ between summer (growing-season) and winter, possibly due to reduced activity of the core community, and addition of fungi adapted for winter conditions forming a winter-active fungal community. Significant month × year interactions were observed both for fungal richness and community composition, indicating unpredictable between-year variation. Our study indicates that addressing seasonal changes requires replication over several years.

Psychrophilic fungi from the world's roof

During a survey of cold-adapted fungi in alpine glaciers on the Qinghai-Tibet Plateau, 1 428 fungal isolates were obtained of which 150 species were preliminary identified. Phoma sclerotioides and Pseudogymnoascus pannorum were the most dominant species. Psychrotolerant species in Helotiales (Leotiomycetes, Ascomycota) were studied in more detail as they represented the most commonly encountered group during this investigation. Two phylogenetic trees were constructed based on the partial large subunit nrDNA (LSU) to infer the taxonomic placements of these strains. Our strains nested in two well-supported major clades, which represented Tetracladium and a previously unknown lineage. The unknown lineage is distant to any other currently known genera in Helotiales. Psychrophila gen. nov. was therefore established to accommodate these strains which are characterised by globose or subglobose conidia formed from phialides on short or reduced conidiophores. Our analysis also showed that an LSU-based phylogeny is insufficient in differentiating strains at species level. Additional analyses using combined sequences of ITS+TEF1+TUB regions were employed to further investigate the phylogenetic relationships of these strains. Together with the recognisable morphological distinctions, six new species (i.e. P. antarctica, P. lutea, P. olivacea, T. ellipsoideum, T. globosum and T. psychrophilum) were described. Our preliminary investigation indicates a high diversity of cold-adapted species in nature, and many of them may represent unknown species.

Host-Specialist Dominated Ectomycorrhizal Communities of Pinus cembra are not Affected by Temperature Manipulation

Ectomycorrhizae (EM) are important for the survival of seedlings and trees, but how they will react to global warming or changes in soil fertility is still in question. We tested the effect of soil temperature manipulation and nitrogen fertilization on EM communities in a high-altitude Pinus cembra afforestation. The trees had been inoculated in the 1960s in a nursery with a mixture of Suillus placidus, S. plorans and S. sibircus. Sampling was performed during the third year of temperature manipulation in June and October 2013. Root tips were counted, sorted into morphotypes, and sequenced. Fungal biomass was measured as ergosterol and hyphal length. The EM potential of the soil was assessed with internal transcribed spacers (ITS) clone libraries from in-growth mesh bags (MB). Temperature manipulation of ± 1 °C had no effect on the EM community. A total of 33 operational taxonomic units (OTUs) were identified, 20 from the roots, 13 from MB. The inoculated Suillus spp. colonized 82% of the root tips, thus demonstrating that the inoculation was sustainable. Nitrogen fertilization had no impact on the EM community, but promoted depletion in soil organic matter, and caused a reduction in soil fungal biomass.

Arctic fungal communities associated with roots of Bistorta vivipara do not respond to the same fine-scale edaphic gradients as the aboveground vegetation

Soil conditions and microclimate are important determinants of the fine-scale distribution of plant species in the Arctic, creating locally heterogeneous vegetation. We hypothesize that root-associated fungal (RAF) communities respond to the same fine-scale environmental gradients as the aboveground vegetation, creating a coherent pattern between aboveground vegetation and RAF. We explored how RAF communities of the ectomycorrhizal (ECM) plant Bistorta vivipara and aboveground vegetation structure of arctic plants were affected by biotic and abiotic variables at 0.3-3.0-m scales. RAF communities were determined using pyrosequencing. Composition and spatial structure of RAF and aboveground vegetation in relation to collected biotic and abiotic variables were analysed by ordination and semi-variance analyses. The vegetation was spatially structured along soil C and N gradients, whereas RAF lacked significant spatial structure. A weak relationship between RAF community composition and the cover of two ECM plants, B. vivipara and S. polaris, was found, and RAF richness increased with host root length and root weight. Results suggest that the fine-scale spatial structure of RAF communities of B. vivipara and the aboveground vegetation are driven by different factors. At fine spatial scales, neighbouring ECM plants may affect RAF community composition, whereas soil nutrients gradients structure the vegetation.

Gromochytrium mamkaevae gen. & sp. nov. and two new orders: Gromochytriales and Mesochytriales (Chytridiomycetes)

During the last decade several new orders were established in the class Chytridiomycetes on the basis of zoospore ultrastructure and molecular phylogeny. Here we present the ultrastructure and molecular phylogeny of strain x-51 CALU – a parasite of the alga Tribonema gayanum, originally described as Rhizophydium sp. based on light microscopy. Detailed investigation revealed that the zoospore ultrastructure of this strain has unique characters not found in any order of Chytridiomycetes: posterior ribosomal core unbounded by the endoplasmic reticulum and detached from the nucleus or microbody-lipid complex, and kinetosome composed of microtubular doublets. An isolated phylogenetic position of x-51 is further confirmed by the analysis of 18S and 28S rRNA sequences, and motivates the description of a new genus and species Gromochytrium mamkaevae. The sister position of G. mamkaevae branch relative to Mesochytrium and a cluster of environmental sequences, as well as the ultrastructural differences between Gromochytrium and Mesochytrium zoospores prompted us to establish two new orders: Gromochytriales and Mesochytriales.

Substantial compositional turnover of fungal communities in an alpine ridge-to-snowbed gradient

The main gradient in vascular plant, bryophyte and lichen species composition in alpine areas, structured by the topographic gradient from wind-exposed ridges to snowbeds, has been extensively studied. Tolerance to environmental stress, resulting from wind abrasion and desiccation towards windswept ridges or reduced growing season due to prolonged snow cover towards snowbeds, is an important ecological mechanism in this gradient. The extent to which belowground fungal communities are structured by the same topographic gradient and the eventual mechanisms involved are less well known. In this study, we analysed variation in fungal diversity and community composition associated with roots of the ectomycorrhizal plant Bistorta vivipara along the ridge-to-snowbed gradient. We collected root samples from fifty B. vivipara plants in ten plots in an alpine area in central Norway. The fungal communities were analysed using 454 pyrosequencing analyses of tag-encoded ITS1 amplicons. A distinct gradient in the fungal community composition was found that coincided with variation from ridge to snowbeds. This gradient was paralleled by change in soil content of carbon, nitrogen and phosphorus. A large proportion (66%) of the detected 801 nonsingleton operational taxonomic units (OTUs) were ascomycetes, while basidiomycetes dominated quantitatively (i.e. with respect to number of reads). Numerous fungal OTUs, many with taxonomic affinity to Sebacinales, Cortinarius and Meliniomyces, showed distinct affinities either to ridge or to snowbed plots, indicating habitat specialization. The compositional turnover of fungal communities along the gradient was not paralleled by a gradient in species richness.