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Communities of yeasts from the litter and soil of temperate beech, oak and spruce forests. OTU identifications are based on the taxonomy of the most closely related yeast taxon. The data represent mean values from six sites per tree. A, Ascomycota; B, Basidiomycota.
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Fungi represent a group of soil microorganisms fulfilling important ecological functions. Although several studies have shown that yeasts represent a significant proportion of fungal communities, our current knowledge is based mainly on cultivation experiments. In this study, we used amplicon sequencing of environmental DNA to describe the composit...
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... ples were more variable and were dominated by Saitozyma (four OTUs, So. podzolica), Solicoccozyma (four OTUs, So. fuscescens and So. terricola), Apiotrichum (two OTUs, A. dulcitum, A.porosum), Fel- lozyma (six OTUs, F. inositophila), Leucosporidium (three OTUs, L. intermedium) and Curvibasidium (three OTUs, C. cygneicollum, C. pallidicorallinum; Fig. 3). In soil, no significant difference in the community composi- tion of yeasts was observed among different trees. Instead, soil pH (P = 0.0003, R = 0.6) and moisture (P = 0.01, R = 0.6) were found to have significant effects, as well as N content (P = 0.002, R = 0.7) and C content (P = 0.001, R = 0.7), but the last three of these ...
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Citations
... The genus was a yeast-like fungus and was proposed by Sampaio et al. [56]. The species of the genus Curvibasidium were widely distributed in various environments, e.g., white grapevine [57], litter of temperate forests [58], and marine sediments [59]. Curvibasidium pallidicorallinum has been shown to generate polygalacturonase, which might potentially improve the breakdown of berries' cell walls during fermentation [60]. ...
Microbes naturally inhabit bamboo-based materials in outdoor environments, sequentially contributing to their deterioration. Fungi play a significant role in deterioration, especially in environments with abundant water and favorable temperatures. Alkali treatment is often employed in the pretreatment of round bamboo to change its natural elastic and aesthetic behaviors. However, little research has investigated the structure and dynamics of fungal communities on alkali-treated round bamboo during natural deterioration. In this work, high-throughput sequencing and multiple characterization methods were used to disclose the fungal community succession and characteristic alterations of alkali-treated round bamboo in both roofed and unroofed habitats throughout a 13-week deterioration period. In total, 192 fungal amplicon sequence variants (ASVs) from six phyla were identified. The fungal community richness of roofed bamboo samples declined, whereas that of unroofed bamboo samples increased during deterioration. The phyla Ascomycota and Basidiomycota exhibited dominance during the entire deterioration process in two distinct environments, and the relative abundance of them combined was more than 99%. A distinct shift in fungal communities from Basidiomycota dominant in the early stage to Ascomycota dominant in the late stage was observed, which may be attributed to the increase of moisture and temperature during succession and the effect of alkali treatment. Among all environmental factors, temperature contributed most to the variation in the fungal community. The surface of round bamboo underwent continuous destruction from fungi and environmental factors. The total amount of cell wall components in bamboo epidermis in both roofed and unroofed conditions presented a descending trend. The content of hemicellulose declined sharply by 8.3% and 11.1% under roofed and unroofed environments after 9 weeks of deterioration. In addition, the contact angle was reduced throughout the deterioration process in both roofed and unroofed samples, which might be attributed to wax layer removal and lignin degradation. This study provides theoretical support for the protection of round bamboo under natural weathering.
... technologies have enabled the rapid acquisition of microbial community structure and composition information, allowing scientists to readily analyze microbial communi ties and address interesting hypotheses in microbial biodiversity and biogeography (13). Frequently targeted genes include both phylogenetic markers, like 16S rRNA genes (14)(15)(16)(17)(18)(19)(20), internal transcribed spacer, 28S rRNA genes (21)(22)(23)(24)(25)(26), and 18S rRNA genes (16,(27)(28)(29)(30), and functional genes, such as nifH (16,(31)(32)(33)(34)(35), nirK and nirS (36,37), nosZ (36,38), and dsrA and dsrB (39,40). ...
Targeted amplicon sequencing is widely used in microbial ecology studies. However, sequencing artifacts and amplification biases are of great concern. To identify sources of these artifacts, a systematic analysis was performed using mock communities comprised of 16S rRNA genes from 33 bacterial strains. Our results indicated that while sequencing errors were generally isolated to low-abundance operational taxonomic units, chimeric sequences were a major source of artifacts. Singleton and doubleton sequences were primarily chimeras. Formation of chimeric sequences was significantly correlated with the GC content of the targeted sequences. Low-GC-content mock community members exhibited lower rates of chimeric sequence formation. GC content also had a large impact on sequence recovery. The quantitative capacity was notably limited, with substantial recovery variations and weak correlation between anticipated and observed strain abundances. The mock community strains with higher GC content had higher recovery rates than strains with lower GC content. Amplification bias was also observed due to the differences in primer affinity. A two-step PCR strategy reduced the number of chimeric sequences by half. In addition, comparative analyses based on the mock communities showed that several widely used sequence processing pipelines/methods, including DADA2, Deblur, UCLUST, UNOISE, and UPARSE, had different advantages and disadvantages in artifact removal and rare species detection. These results are important for improving sequencing quality and reliability and developing new algorithms to process targeted amplicon sequences.
IMPORTANCE
Amplicon sequencing of targeted genes is the predominant approach to estimate the membership and structure of microbial communities. However, accurate reconstruction of community composition is difficult due to sequencing errors, and other methodological biases and effective approaches to overcome these challenges are essential. Using a mock community of 33 phylogenetically diverse strains, this study evaluated the effect of GC content on sequencing results and tested different approaches to improve overall sequencing accuracy while characterizing the pros and cons of popular amplicon sequence data processing approaches. The sequencing results from this study can serve as a benchmarking data set for future algorithmic improvements. Furthermore, the new insights on sequencing error, chimera formation, and GC bias from this study will help enhance the quality of amplicon sequencing studies and support the development of new data analysis approaches.
... Although yeast cells could be mistaken for bacteria due to their similar morphology, we believe this is mostly insignificant in our experimental system. Yeasts typically account for only 0 to 10% of total soil fungal communities Mašínová et al. (2017), and the amount of fungal colonies forming units is consistently two to three orders of magnitude lower than that of bacterial cells in soilsKacergius and Sivojiene (2023); Kwiatkowska et al. (2022); Sofo et al. (2020). For these reasons, we consider the potential skewing of our bacterial results by yeast contamination to be negligible. ...
Soil microbes play an important role in governing global processes such as carbon cycling, but it is challenging to study them embedded in their natural environment and at the single cell level due to the opaque nature of the soil. Nonetheless, progress has been achieved in recent years towards visualizing microbial activities and organo-mineral interaction at the pore scale, especially thanks to the development of microfluidic 'soil chips' creating transparent soil model habitats. Image-based analyses come with new challenges as manual counting of bacteria in thousands of digital images taken from the soil chips is excessively time-consuming, while simple thresholding cannot be applied due to the background of soil minerals and debris. Here, we adopt the well-developed deep learning algorithm Mask-RCNN to quantitatively analyse the bacterial communities in soil samples from different locations in the world. This work demonstrates analysis of bacterial abundance from three contrasting locations (Greenland, Sweden and Kenya) using deep learning in microfluidic soil chips in order to characterize population and community dynamics. We additionally quantified cell- and colony morphology including cell size, shape and the cell aggregation level via calculation of the distance to the nearest neighbor. This approach allows for the first time an automated visual investigation of soil bacterial communities, and a crude biodiversity measure based on phenotypic cell morphology, which could become a valuable complement to molecular studies.
... In late decay stages (DC4-DC5), taxa that were previously dominant begin to be replaced by the functionally diverse Agaricales that are often associated with wood decay, along with several ectomycorrhizal taxa (Russulales and Thelephorales) and basidiomycetous yeasts in the Trichosporonales. Members of the Trichosporonales have been shown to be abundant in both litter and soil where they likely degrade hemicelluloses and produce antifungal cellobiose lipids that can suppress the growth of other yeast species [61][62][63]. An increase in ectomycorrhizal fungi (ECM) in late decay stages is likely driven by the foraging of this guild for the N-rich substrate made available by the decomposer community [64,65]. ...
Fungal communities are primary decomposers of detritus, including coarse woody debris (CWD). We investigated the succession of fungal decomposer communities in CWD through different stages of decay in the wide-ranging and early successional tree species Populus grandidentata (bigtooth aspen). We compared shifts in fungal communities over time with concurrent changes in substrate chemistry and in bacterial community composition, the latter deriving from an earlier study of the same system. We found that fungal communities were highly dynamic during the stages of CWD decay, rapidly colonizing standing dead trees and gradually changing in composition until the late stages of decomposed wood were integrated into soil organic matter. Fungal communities were most similar to neighboring stages of decay, with fungal diversity, abundance, and enzyme activity positively related to percent nitrogen, irrespective of decay class. In contrast to other studies, we found that species diversity remained unchanged across decay classes. Differences in enzyme profiles across CWD decay stages mirrored changes in carbon recalcitrance, as B-D-xylosidase, peroxidase, and Leucyl aminopeptidase activity increased as decomposition progressed. Finally, fungal and bacterial gene abundances were stable and increased, respectively, with the extent of CWD decay, suggesting that fungal-driven decomposition was associated with shifting community composition and associated enzyme functions rather than fungal quantities.
... ECM fungi and saprotrophs have filamentous growth, can be relatively large and, similar to clonal plants, they are able to translocate resources via their mycelial cords over considerable distances (Cairney, 2005). In contrast, yeasts are unicellular organisms that share several ecological characteristics with bacteria (Mašínová et al., 2017). These physiological differences between guilds presumably lead to differences in their dispersal capacity and their responses to environmental conditions, which, in turn, lead to different spatial patterns and drivers of community composition (Liang et al., 2023;Odriozola et al., 2020Odriozola et al., , 2021Peguero et al., 2021;Soininen et al., 2007;Zinger et al., 2019). ...
... Several studies have demonstrated that ECM fungi may show biogeographic patterns similar to those of macroorganisms (Bahram et al., 2012;Peay et al., 2007Peay et al., , 2012, and their geographic distributions can be limited by dispersal (Bahram et al., 2013;Talbot et al., 2014). In contrast, yeasts have been shown to resemble bacteria more than filamentous fungi in terms of the drivers of their community composition (Mašínová et al., 2017). Correspondingly, a recent study has shown that the temporal turnover of ECM fungal communities in forest soil is highly stochastic and site-specific, whereas the temporal turnover of yeasts over different sites has more systematic patterns, more similar to those of soil bacteria than of other fungal guilds (Martinović et al., 2021). ...
... Last, many studies have shown strong covariation between the spatial distribution of ECM fungi and plant community composition, which has been attributed to their plant-associated lifestyle (Bahram et al., 2013;Liang et al., 2023;Odriozola et al., 2020;Peay et al., 2013;van der Linde et al., 2018). Yet, yeasts and saprotrophs sometimes also show associations with tree identity and plant community composition, even though they are free-living organisms not directly dependent on the association with a host plant (Mašínová et al., 2017;Odriozola et al., 2021;Urbanová et al., 2015). ...
Aim
How community composition varies in space and what governs the variation has been extensively investigated in macroorganisms. However, we have only limited knowledge of microorganisms, especially fungi, despite their ecological and economic significance. Based on previous research, we define and test a series of hypotheses regarding the composition of fungal communities, their most influential drivers and their spatial scale dependence.
Location
Czech Republic.
Time period
Present.
Taxa studied
Fungi.
Methods
We analysed the distance decay relationships, community composition and its drivers (physical distance, litter and soil chemistry, tree composition and climate) in fungi using multivariate analyses. We compared the results across three fungal ecological guilds (ectomycorrhizal fungi, saprotrophs and yeasts), two forest microhabitats (litter and bulk soil) and six spatial scales (from 5 m to 80 km) that comprehensively cover the Czech Republic.
Results
We found that, similar to macroorganisms, the ectomycorrhizal fungi and saprotrophs showed marked distance–decay relationships, and their community composition was driven mainly by vegetation and dispersal at local scales but, at regional scales, by environmental effects. In contrast, the third fungal guild, the unicellular yeasts, showed little distance decay, suggesting extraordinary spatial homogeneity, as often seen in microorganisms, such as bacteria.
Main conclusions
Our results underscore the remarkable variation in the community ecology of fungi, which seems to range well‐known patterns both from the macro‐ and the microworld. Knowledge of these patterns advances our understanding of the ecology of fungi, rather understudied organisms of significant ecological and economic importance, which our findings identify as a potentially suitable model for bridging the gaps between the biogeography of micro‐ and macroorganisms.
... The drivers of yeast community assembly in soils are more complex and mainly include the effects of environmental conditions and vegetation (Mašínová et al., 2017), among which soil physicochemical properties are the key factors. Because the soil physical and chemical properties reflect both the growth state of plants and the survival conditions of yeast in the soil. ...
Shihezi Reclamation Area is located at the southern edge of the Junggar Basin, with natural, soil, and climatic conditions unique to the production of peaches. In turn, peach orchards have accumulated rich microbial resources. As an important taxon of soil fungi, the diversity and community structure changes of yeast in the soil of peach orchards on spatial and temporal scales are still unknown. Here, we aimed to investigate the changes in yeast diversity and community structure in non-rhizosphere and rhizosphere soils of peach trees of different ages in the peach orchard and the factors affecting them, as well as the changes in the yeast co-occurrence network in the peach orchard at spatial and temporal scales. High-through put sequencing results showed that a total of 114 yeast genera were detected in all soil samples, belonging to Ascomycota (60 genera) and Basidiomycota (54 genera). The most dominant genus, Cryptococcus, was present in greater than 10% abundance in each sample. Overall, the differences in yeast diversity between non-rhizosphere and rhizosphere soil of peach trees at 3, 8 and 15 years were not significant. Principal coordinate analysis (PCoA) showed that differences in yeast community structure were more pronounced at the temporal scale compared to the spatial scale. The results of soil physical and chemical analysis showed that the 15-year-old peach rhizosphere soil had the lowest pH, while the OM, TN, and TP contents increased significantly. Redundancy analysis showed that soil pH and CO were key factors contributing to changes in soil yeast community structure in the peach orchard at both spatial and temporal scales. The results of co-occurrence network analysis showed that the peach orchard soil yeast network showed synergistic effects as a whole, and the degree of interactions and connection tightness of the 15-year-old peach orchard soil yeast network were significantly higher than the 3- and 8-year-old ones on the time scale. The results reveal the distribution pattern and mechanism of action of yeast communities in peach orchard soils, which can help to develop effective soil management strategies and improve the stability of soil microecology, thus promoting crop growth.
... Nevertheless, the substantial differences in genus dominance between uncrusted and biocrust soils were diluted under mulch. The highest response to mulch corresponds to the Basidiomycota yeasts (Tremellomycetes), in particular Naganishia, described as being able to utilize a wide spectrum of C sources materials (Mašínová et al., 2017). The initial degradation of wood mulch increased the abundance of yeasts and saprotrophs in soils. ...
Mulches are highly effective in mitigating the risk of erosion generated after wildfires in fire-prone ecosystems. Despite being a technique commonly used, it remains completely unexplored how mulches interact with the positive effects of the emergent moss biocrust on the recovery and resilience of soils and their microbial communities. For this purpose, the effects of wood-based mulch were assayed on the soil stability and moisture improvement, the nutrient inputs, and the response of microbial biomass, activity, composition, and diversity. Soils were studied after one year of wood mulch application at two rates representing possible scenarios, "Rate 1" (65 % of soil cover), and "Rate 2" (100 % of cover), and "Control" soils without mulch. The biocrust development had a positive impact on soil aggregate stability and moisture retention before mulch application. However, one year after the mulch application the biocrust cover was drastically inhibited, especially at the highest rate of mulch. Independently of the biocrust presence, soils at Rate 1 registered a tendency to higher nitrogen content, available phosphorous, basal respiration, and microbial biomass carbon, suggesting an incipient recovery of soil conditions and soil functionality. However, the microbial community composition became more homogeneous and less diverse under the mulch presence (regardless of the application rate), and the positive effect of moss biocrust emergence on the microbial diversity was diluted after one year. The fungal community was particularly sensitive to the wood mulch presence, increasing in richness in response to fresh wood incorporation to soils, in particular saprotrophs and yeasts. The fungal and bacterial compositional shifts after the mulch application reveal an incipient wood decomposition stage, but the transitory loss in beta diversity after the moss biocrust suppression warns about the necessity of including the microbial diversity information into post-fire management planning. Studying the effects of forest management on the above and belowground soil communities is essential to understanding the resistance and resilience of semi-arid forests to the increasing intensity and severity of wildfires.
... Besides rodents, the species was also reported from human clinical material in Switzerland (isolate bM 128, ITS sequence accession JX122382) (De Respinis et al. 2013). Based on metabarcoding data, the species is rather common in temperate Europe: Czech Republic (Baldrian et al. 2016, Mašínová et al. 2017, Denmark (Frøslev et al. 2019), Estonia (Oja et al. 2017, Bahram et al. 2020, Hungary (Geml 2019), Germany (Purahong et al. 2018) and Poland (Prada-Salcedo et al. 2021). It was also detected in the forest soil in Kansas and Massachusetts (Anthony et al. 2017). ...
Arthroderma is the most diverse genus of dermatophytes, and its natural reservoir is considered to be soil enriched by keratin sources. During a study on the diversity of dermatophytes in wild small rodents in the Czech Republic, we isolated several strains of Arthroderma . To explore the diversity and ecological significance of these isolates from rodents (n = 29), we characterised the strains genetically (i.e., sequenced ITS, tubb and tef1α ), morphologically, physiologically, and by conducting mating experiments. We then compared the rodent-derived strains to existing ITS sequence data from GenBank and the GlobalFungi Database to further investigate biogeography and the association of Arthroderma species with different types of environments. In total, eight Arthroderma species were isolated from rodents, including four previously described species ( A. crocatum , A. cuniculi , A. curreyi , A. quadrifidum ) and four new species proposed herein, i.e., A. rodenticum , A. simile , A. zoogenum and A. psychrophilum . The geographical distribution of these newly described species was not restricted to the Czech Republic nor rodents. Additional isolates were obtained from bats and other mammals, reptiles, and soil from Europe, North America, and Asia. Data mining showed that the genus has a diverse ecology, with some lineages occurring relatively frequently in soil, whereas others appeared to be more closely associated with live animals, as we observed in A. rodenticum . Low numbers of sequence reads ascribed to Arthroderma in soil show that the genus is rare in this environment, which supports the hypothesis that Arthroderma spp. are not soil generalists but rather strongly associated with animals and keratin debris. This is the first study to utilise existing metabarcoding data to assess biogeographical, ecological, and diversity patterns in dermatophytes.
... Within the Ascomycota, Cephalotrichum is a saprophytic soil fungus [72]; Myrmecridium, a plant endophytes taxon, has been reported to produce extracellular hydrolytic enzymes and cellulase [73]; Podospora are well-known cellulose degraders [74]; Nigrospora has the capacity to improve the withstand stress of host plants and produce antifungal compounds [75]; and Gibellulopsis is linked to carbohydrate content [76]. Within the Basidiomycota, members of Saitozyma are involved in the decomposition of dead plant biomass [77]; Colacogloea is a saprophytic yeast that can persist in difficult conditions [53]. Within the Mortierellomycota, Mortierella is mostly composed of saprophytic species that perform several functions, including the degradation of cellulose and lignin [78]. ...
The interaction between invasive plants and soil microbial communities is critical for plant establishment. However, little is known about the assembly and co-occurrence patterns of fungal communities in the rhizosphere soil of Amaranthus palmeri. The soil fungal communities and co-occurrence networks were investigated in 22 invaded patches and 22 native patches using high-throughput Illumina sequencing. Despite having little effect on alpha diversity, plant invasion significantly altered the composition of the soil fungal community (ANOSIM, p < 0.05). Fungal taxa associated with plant invasion were identified using linear discriminant analysis effect size (LEfSe). In the rhizosphere soil of A. palmeri, Basidiomycota was significantly enriched, while Ascomycota and Glomeromycota were significantly reduced when compared to native plants. At the genus level, the invasion of A. palmeri dramatically increased the abundance of beneficial fungi and potential antagonists such as Dioszegia, Tilletiopsis, Colacogloea, and Chaetomium, while it significantly decreased the abundance of pathogenic fungi such as Alternaria and Phaeosphaeria. Plant invasion reduced the average degree and average path length, and increased the modularity value, resulting in a less complex but more effective and stable network. Our findings improved the knowledge of the soil fungal communities, network co-occurrence patterns, and keystone taxa in A. palmeri-invaded ecosystems.
... For example, Cladosporium cladosporioides is a decomposer of organic material in soils with a worldwide distribution [46], E. nigrum is routinely isolated from plant material and air and soil [47], F. oxysporum is found throughout the world (as a soil saprophyte or plant endophyte or plant disease, depending on isolate) [48], and Sa. podzolica is a widespread soil yeast [49]. It was surprising that bacterial diversity was fairly low in the asbestos-contaminated soil samples. ...
Internal Transcribed Spacer and 16S Amplicon Sequencing Identifies Microbial Species Abstract: Inhalation of asbestos fibres can cause lung inflammation and the later development of asbestosis, lung cancer, and mesothelioma, and the use of asbestos is banned in many countries. In most countries, large amounts of asbestos exists within building stock, buried in landfills, and in contaminated soil. Mechanical, thermal, and chemical treatment options do exist, but these are expensive, and they are not effective for contaminated soil, where only small numbers of asbestos fibres may be present in a large volume of soil. Research has been underway for the last 20 years into the potential use of microbial action to remove iron and other metal cations from the surface of asbestos fibres to reduce their toxicity. To access sufficient iron for metabolism, many bacteria and fungi produce organic acids, or iron-chelating siderophores, and in a growing number of experiments these have been found to degrade asbestos fibres in vitro. This paper uses the internal transcribed spacer (ITS) and 16S amplicon sequencing to investigate the fungal and bacterial diversity found on naturally-occurring asbestos minerals, asbestos-containing building materials, and asbestos-contaminated soils with a view to later selectively culturing promising species, screening them for siderophore production, and testing them with asbestos fibres in vitro. After filtering, 895 ITS and 1265 16S amplicon sequencing variants (ASVs) were detected across the 38 samples, corresponding to a range of fungal, bacteria, cyanobacterial, and lichenized fungal species. Samples from Auckland (North Island, New Zealand) asbestos cement, Auckland asbestos-contaminated soils, and raw asbestos rocks from Kahurangi National Park (South Island, New Zealand) were comprised of very different microbial communities. Five of the fungal species detected in this study are known to produce siderophores.
