Extremely Acidic Soils are Dominated by Species-Poor and Highly Specific Fungal Communities

The First Comprehensive Biodiversity Study of Culturable Fungal Communities Inhabiting Cryoconite Holes in the Werenskiold Glacier on Spitsbergen (Svalbard Archipelago, Arctic)

Cryoconite holes on glacier surfaces are a source of cold-adapted microorganisms, but little is known about their fungal inhabitants. Here, we provide the first report of distinctive fungal communities in cryoconite holes in the Werenskiold Glacier on Spitsbergen (Svalbard Archipelago, Arctic). Due to a combination of two incubation temperatures (7 °C and 24 ± 0.5 °C) and two media during isolation (PDA, YPG), as well as classical and molecular identification approaches, we were able to identify 23 different fungi (21 species and 2 unassigned species). Most of the fungi cultured from cryoconite sediment were ascomycetous filamentous micromycetes. However, four representatives of macromycetes were also identified (Bjerkandera adusta, Holwaya mucida, Orbiliaceae sp., and Trametes versicolor). Some of the described fungi possess biotechnological potential (Aspergillus pseudoglaucus, A. sydowii, Penicillium expansum, P. velutinum, B. adusta, and T. versicolor), thus, we propose the Arctic region as a source of new strains for industrial applications. In addition, two phytopathogenic representatives were present (P. sumatraense, Botrytis cinerea), as well as one potentially harmful to humans (Cladosporium cladosporioides). To the best of our knowledge, we are the first to report the occurrence of A. pseudoglaucus, C. allicinum, C. ramotenellum, P. sumatraense, P. velutinum, P. cumulodentata, B. adusta, and T. versicolor in polar regions. In all likelihood, two unassigned fungus species (Orbiliaceae and Dothideomycetes spp.) might also be newly described in such environments. Additionally, due to experimenting with 10 sampling sites located at different latitudes, we were able to conclude that the number of fungal spores decreases as one moves down the glacier. Considering the prevalence and endangerment of glacial environments worldwide, such findings suggest their potential as reservoirs of fungal diversity, which should not be overlooked.

Acidophilic microorganisms enhancing geochemical dynamics in an acidic drainage system, Amarillo river in La Rioja, Argentina

The Amarillo River in La Rioja, Argentina, is a natural acidic environment that is influenced by an abandoned mine. The river is characterized by extremely low pH and high concentrations of metals and metalloids. Fe(III)-bearing neoformed precipitated minerals are widespread along the hydrological basin. This work reports the presence of different species of iron-oxidizing bacteria and demonstrates that their action has a significant role in geochemical processes of the Amarillo River, mainly by catalyzing Fe²⁺ oxidation and intensifying the Fe(III)-bearing mineral precipitation. Various iron oxidizers (i.e. Acidithiobacillus ferrivorans, Leptospirillum ferrooxidans, Ferrimicrobium acidophilum, Alicyclobacillus cycloheptanicus) were detected in enrichment cultures at different temperatures. Moreover, this is the first report confirming that Acidithiobacillus ferrivorans is able to grow at 4 °C. Other acidophilic bacteria (i.e., Acidiphilium iwatensii) and fungi (e.g., Fodinomyces uranophilus, Coniochaeta fodinicola, Acidea extrema, Penicillium sp. and Cladosporium pseudocladosporioides) were also detected. In vitro laboratory studies recreating natural Fe(III)-bearing mineral formation showed that mineral precipitation rate was higher than 350 mg L^-1 day^-1 in the presence of microorganisms whereas it was about 15 mg L^-1 day^-1 under abiotic conditions. Jarosite was the only mineral detected in the precipitates generated by microbial action and it was also identified in the Amarillo River bed sediments. Biological Fe²⁺ oxidation rates depend on temperature which range from 8 to 32 mM day^-1 at 4 and 30 °C, respectively. Finally, a conceptual model recognizing the significant microbial role is proposed to gain a better understanding of the biogeochemistry dynamics of the Amarillo River.

Fungal and bacterial outbreak in the wine vinification area in the Saint-Marcel show cave

In the Saint-Marcel cave (France), wood barrels and thousands of bottles containing red wine were stored for vinification. After storage began, a fungal and bacterial outbreak occurred, and the area was invaded by numerous types of mold colonizing the cave ceilings and all objects related to human activities (the stairwell and oenological materials). In this study, using the metabarcoding approach, we have studied the microbial outbreak and have linked the identified microorganisms to oenological activity. Both 16S and ITS primers were used to sequence the samples collected from the cave. The results showed that the dominant microorganisms proliferating in the cave were related to wine vinification. For instance, Zasmidium cellare, a strain known for living in dark and ethanol-rich environments, was the dominant fungus on the cave stairwell. Furthermore, Guehomyces pullulans, a cold-adapted yeast used for juice clarification, was recorded as the major species on the blackened limestone ceilings. These findings reveal a complex community structure in the studied cave based on the assembly of bacteria and fungi. Finally, our results demonstrate that oenological activities could seriously affect cave preservation, changing the natural microbial communities populating cave environments.

Diversity and structure of soil microbiota of the Jinsha earthen relic

In order to define the diversity and composition of the microbial communities colonizing of the soil microbiome of the Jinsha earthen relic, we used high-throughput sequencing technology to identify and characterize the microbiota in 22 samples collected from the Jinsha earthen relic in China during 2017 and 2018. We compared the taxonomy of the microbial communities from samples taken at different times and different sites. Our results showed that the identity of the dominant bacterial phyla differed among the samples. Proteobacteria (23–86.2%) were the predominant bacterial phylum in all samples taken from site A in both 2017 and 2018. However, Actinobacteria (21–92.3%) were the most popular bacterial phylum in samples from sites B and C in 2017 and 2018. Ascomycota were identified as the only fungal phyla in samples in 2017. However, the group varied drastically in relative abundance between 2017 and 2018. Functional analysis of the soil bacterial community suggested that abundant members of the microbiota may be associated with metabolism and the specific environment. This report was the first high-throughput sequencing study of the soil of the Jinsha earthen relic microbiome. Since soil microbiota can damage soil and archeological structures, comprehensive analyses of the microbiomes at archeological sites may contribute to the understand of the influence of microorganisms on the degradation of soil, as well as to the identification of potentially beneficial or undesirable members of these microbial communities in archeological sites. The study will be helpful to provide effective data and guidance for the prevention and control of microbial corrosion of the Jinsha earthen relic.

Biofilm and planktonic microbial communities in highly acidic soil (pH < 3) in the Soos National Nature Reserve, Czech Republic

Biofilm formation is a typical life strategy used by microorganisms populating acidic water systems. The same strategy might be used by microbes in highly acidic soils that are, however, neglected in this regard. In the present study, the microbial community in such highly acidic soil in the Soos National Nature Reserve (Czech Republic) has been investigated using high-throughput DNA sequencing and the organisms associated with biofilm life mode and those preferring planktonic life were distinguished using the biofilm trap technique. Our data show the differences between biofilm and planktonic microbiota fraction, although the majority of the organisms were capable of using both life modes. The by far most abundant prokaryotic genus was Acidiphilium and fungi were identified among the most abundant eukaryotic elements in biofilm formations. On the other hand, small flagellates from diverse taxonomical groups predominated in plankton. The application of cellulose amendment as well as the depth of sampling significantly influenced the composition of the detected microbial community.

Fungi, a neglected component of acidophilic biofilms: do they have a potential for biotechnology?

Fungi from extreme environments, including acidophilic ones, belong to biotechnologically most attractive organisms. They can serve as a source of enzymes and metabolites with potentially uncommon properties and may actively participate within bioremediation processes. In respect of their biotechnological potential, extremophilic fungi are mostly studied as individual species. Nevertheless, microorganisms rarely live separately and they form biofilms instead. Living in biofilms is the most successful life strategy on the Earth and the biofilm is the most abundant form of life in extreme environments including highly acidic ones. Compared to bacterial fraction, fungal part of acidophilic biofilms represents a largely unexplored source of organisms with possible use in biotechnology and especially data on biofilms of highly acidic soils are missing. The functioning of the biofilm results from interactions between organisms whose metabolic capabilities are efficiently combined. When we look on acidophilic fungi and their biotechnological potential we should take this fact into account as well. The practical problem to be resolved in connection with extensive studies of exploitable properties and abilities of acidophilic fungi is the methodology of isolation of strains from the nature. In this respect, novel isolation techniques should be developed.

Isolation, Characterization, and Metal Response of Novel, Acid-Tolerant Penicillium spp. from Extremely Metal-Rich Waters at a Mining Site in Transbaikal (Siberia, Russia)

The role of fungi in metal cycling in acidic environments has been little explored to date. In this study, two acid-tolerant and metal-resistant Penicillium isolates, strains ShG4B and ShG4C, were isolated from a mine site in the Transbaikal area of Siberia (Russia). Waters at the mine site were characterized by extremely high metal concentrations: up to 18 g l^-1 Fe and > 2 g l^-1 each of Cu, Zn, Al, and As. Both isolates were identified as Penicillium spp. by phylogenetic analyses and they grew well in Czapek medium acidified to pH 2.5. Resistance to Cu, Cd, Ni, Co, and arsenate was in the range of 1-10 g l^-1. Further experiments with Penicillium strain ShG4C demonstrated that growth in Cu-containing media was accompanied by the precipitation of Cu-oxalate (moolooite) and the formation of extracellular vesicles enriched in Cu on the mycelia. Vesicles were greatly reduced in size in Cd-containing media and were not formed in the presence of Ni or Co. Cd-oxalate was detected as a crystalline solid phase in Cd-exposed mycelia. Hydrated Ni-sulfate (retgersite) and Co-sulfate (bieberite) were detected in mycelia grown in the presence of Ni and Co, respectively. The results demonstrated that acid-tolerant and metal-resistant Penicillium constitute a component in extremophilic microbiomes, contributing to organic matter breakdown and formation of secondary solid phases at pH ranges found in acid rock drainage.

Talaromyces sayulitensis, Acidiella bohemica and Penicillium citrinum in Brazilian oil shale by-products

Fine shale particles and retorted shale are waste products generated during the oil shale retorting process. These by-products are small fragments of mined shale rock, are high in silicon and also contain organic matter, micronutrients, hydrocarbons and other elements. The aims of this study were to isolate and to evaluate fungal diversity present in fine shale particles and retorted shale samples collected at the Schist Industrialization Business Unit (Six)-Petrobras in São Mateus do Sul, State of Paraná, Brazil. Combining morphology and internal transcribed spacer (ITS) sequence, a total of seven fungal genera were identified, including Acidiella, Aspergillus, Cladosporium, Ochroconis, Penicillium, Talaromyces and Trichoderma. Acidiella was the most predominant genus found in the samples of fine shale particles, which are a highly acidic substrate (pH 2.4-3.6), while Talaromyces was the main genus in retorted shale (pH 5.20-6.20). Talaromyces sayulitensis was the species most frequently found in retorted shale, and Acidiella bohemica in fine shale particles. The presence of T. sayulitensis, T. diversus and T. stolli in oil shale is described herein for the first time. In conclusion, we have described for the first time a snapshot of the diversity of filamentous fungi colonizing solid oil shale by-products from the Irati Formation in Brazil.