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308 results for “fungal community”
Data from: Soil microclimate changes affect soil fungal communities in a Mediterranean pine forest
• Soil microclimate is a potentially important regulator of the composition of plant-associated fungal communities in climates with significant drought periods. Here, we investigated spatio-temporal dynamics of soil fungal communities in a Mediterranean Pinus pinaster forest in relation to soil moisture and temperature. • Fungal communities in 336 soil samples collected monthly during a year from 28 long-term experimental plots were assessed by PacBio sequencing of ITS2 amplicons. Total fungal biomass was estimated by analysing ergosterol. Community changes were analysed in the context of functional traits. • Soil fungal biomass was lowest during summer and late winter and highest during autumn, concurrent with a greater relative abundance of mycorrhizal species. Intra-annual spatio-temporal changes in community composition correlated significantly with soil moisture and temperature. Mycorrhizal fungi were less affected by summer drought than free-living fungi. In particular, mycorrhizal species of the short-distance exploration type increased in relative abundance under dry conditions, whereas species of the long-distance exploration type were more abundant under wetter conditions. • Our observations demonstrate a potential for compositional and functional shifts in fungal communities in response to changing climatic conditions. Free-living fungi and mycorrhizal species with extensive mycelia may be negatively affected by increasing drought periods in Mediterranean forest ecosystems.
Data from: Differences in the fungal communities nursed by two genetic groups of the alpine cushion plant, Silene acaulis
Foundation plants shape the composition of local biotic communities and abiotic environments, but the impact of a plant's intraspecific variations on these processes is poorly understood. We examined these links in the alpine cushion moss campion (Silene acaulis) on two neighboring mountain ranges in the French Alps. Genotyping of cushion plants revealed two genetic clusters matching known subspecies. The exscapa subspecies was found on both limestone and granite while the longiscapa one was only found on limestone. Even on similar limestone bedrock, cushion soils from the two S. acaulis subspecies deeply differed in their impact on soil abiotic conditions. They further strikingly differed from each other and from the surrounding bare soils in fungal community composition. Plant genotype variations accounted for a large part of the fungal composition variability in cushion soils, even when considering geography or soil chemistry, and particularly for the dominant molecular operational taxonomic units (MOTUs). Both saprophytic and biotrophic fungal taxa were related to the MOTUs recurrently associated with a single plant genetic cluster. Moreover, the putative phytopathogens were abundant, and within the same genus (Cladosporium) or species (Pyrenopeziza brassicae), MOTUs showing specificity for each plant subspecies were found. Our study highlights the combined influences of bedrock and plant genotype on fungal recruitment into cushion soils and suggests the coexistence of two mechanisms, an indirect selection resulting from the colonization of an engineered soil by free-living saprobes, and a direct selection resulting from direct plant-fungi interactions.
Data from: Ion Torrent PGM as tool for fungal community analysis: a case study of endophytes in Eucalyptus grandis reveals high taxonomic diversity
The Kingdom Fungi adds substantially to the diversity of life, but due to their cryptic morphology and lifestyle, tremendous diversity, paucity of formally described specimens, and the difficulty in isolating environmental strains into culture, fungal communities are difficult to characterize. This is especially true for endophytic communities of fungi living in healthy plant tissue. The developments in next generation sequencing technologies are, however, starting to reveal the true extent of fungal diversity. One of the promising new technologies, namely semiconductor sequencing, has thus far not been used in fungal diversity assessments. In this study we sequenced the internal transcribed spacer 1 (ITS1) nuclear encoded ribosomal RNA of the endophytic community of the economically important tree, Eucalyptus grandis, from South Africa using the Ion Torrent Personal Genome Machine (PGM). We determined the impact of various analysis parameters on the interpretation of the results, namely different sequence quality parameter settings, different sequence similarity cutoffs for clustering and filtering of databases for removal of sequences with insufficient taxonomy. Sequence similarity cutoff values only had a marginal effect on the identified family numbers, whereas different sequence quality filters had a large effect (89 vs. 48 families between least and most stringent filters). Database filtering had a small, but statistically significant, effect on the assignment of sequences to reference sequences. The community was dominated by Ascomycota, and particularly by families in the Dothidiomycetes that harbor well-known plant pathogens. The study demonstrates that semiconductor sequencing is an ideal strategy for environmental sequencing of fungal communities. It also highlights some potential pitfalls in subsequent data analyses when using a technology with relatively short read lengths.
Data from: 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.
Data from: Distribution and drivers of ectomycorrhizal fungal communities across the North American Arctic
Ectomycorrhizal fungi (EMF) form symbioses with a few plant species that comprise a large fraction of the arctic vegetation. Despite their importance, the identity, abundance and distribution of EMF in the Arctic, as well as the key drivers controlling their community composition are poorly understood. In this study, we investigated the diversity and structure of EMF communities across a bioclimatic gradient spanning much of the North American Arctic. We collected roots from two principal arctic ectomycorrhizal host plants, Salix arctica and Dryas integrifolia, typically growing intermingled, at 23 locations stratified across the five bioclimatic subzones of the Arctic. DNA was extracted from ectomycorrhizal root tips and the ITS region was sequenced and phylogenetically analyzed. A total of 242 fungal Operational Taxonomic Units (OTUs) were documented, with 203 OTUs belonging to the Basidiomycota and 39 to the Ascomycota, exceeding the number of previously morphologically described EMF in the Arctic. EMF communities were dominated by a few common and species-rich families such as Thelephoraceae, Inocybaceae, Sebacinaceae, Cortinariaceae, and Pyronemataceae. Both host plants showed similar species richness, with 176 OTUs on Salix arctica and 154 OTUs on Dryas integrifolia. Host plant identity did not affect EMF community composition. The ten most abundant OTUs had a wide geographic distribution throughout the Arctic, and were also found in boreal, temperate and Mediterranean regions, where they were associated with a variety of hosts. Species richness did not decline with increasing latitude. However, EMF community structure changed gradually across the bioclimatic gradient with the greatest similarity between neighboring bioclimatic subzones and locations. EMF community structure was correlated with environmental factors at a regional scale, corresponding to a complex of glaciation history, geology, soil properties, plant productivity and climate. This is the first large-scale study of EMF communities across all five bioclimatic subzones of the North American Arctic, accompanied by an extensive set of environmental factors analyzed to date. While our study provides baseline data to assess shifts of plant and fungi distribution in response to climate change, it also suggests that with ongoing climate warming, EMF community composition may be affected by northward shifts of some taxa.
Data from: ITS all right mama: Investigating the formation of chimeric sequences in the ITS2 region by DNA metabarcoding analyses of fungal mock communities of different complexities
The formation of chimeric sequences can create significant methodological bias in PCR-based DNA metabarcoding analyses. During mixed-template amplification of barcoding regions, chimera formation is frequent and well documented. However, profiling of fungal communities typically uses the more variable rDNA region ITS. Due to a larger research community, tools for chimera detection have been developed mainly for the 16S/18S markers. However, these tools are widely applied to the ITS region without verification of their performance. We examined the rate of chimera formation during amplification and 454 sequencing of the ITS2 region from fungal mock communities of different complexities. We evaluated the chimera detecting ability of two common chimera-checking algorithms: Perseus and UCHIME. Large proportions of the chimeras reported were false positives. No false negatives were found in the dataset. Verified chimeras accounted for only 0.2% of the total ITS2 reads, which is considerably less than what is typically reported in 16S and 18S metabarcoding analyses. Verified chimeric "parent sequences" had significantly higher percent identity to one another than to random members of the mock communities. Community complexity increased the rate of chimera formation. GC content was higher around the verified chimeric break points, potentially facilitating chimera formation through base pair mismatching in the neighboring regions of high similarity in the chimeric region. We conclude that the hypervariable nature of the ITS region seem to buffer the rate of chimera formation in comparison to other, less variable barcoding regions, due to shorter regions of high sequence similarity.
Bromus tectorum alters mycorrhizal fungal communities and disrupts mutualism
<p class="MsoNormal">Exotic plant invasions alter native plant productivity and ecosystem function. Mechanisms of plant invasions can include altered disturbance regimes or altered plant-soil feedbacks. Some important hypotheses regarding the invasion of cheatgrass in North America include pathogen spillover and mutualism disruption. Since an important mutualistic interaction in ecosystems is that of mycorrhizal fungi, here we test the mutualism disruption hypothesis by closely examining mycorrhizal allocation and community composition. We conducted a greenhouse study where we grew a native perennial grass in association with invaded and uninvaded soils. We found altered mycorrhizal communities and mycorrhizal allocation patterns associated with cheatgrass-invaded soils supporting the mutualism disruption hypothesis.</p>
Supplementary material 6 from: Ceballos-Escalera A, Richards J, Arias MB, Inward DJG, Vogler AP (2022) Metabarcoding of insect-associated fungal communities: a comparison of internal transcribed spacer (ITS) and large-subunit (LSU) rRNA markers. MycoKeys 88: 1-33. https://doi.org/10.3897/mycokeys.88.77106
Table S2. Class level identification of OTUs showing the number of OTUs produced with ITS2 and LSU and the proportion of the total OTU set on the rarefied data
Supplementary material 5 from: Ceballos-Escalera A, Richards J, Arias MB, Inward DJG, Vogler AP (2022) Metabarcoding of insect-associated fungal communities: a comparison of internal transcribed spacer (ITS) and large-subunit (LSU) rRNA markers. MycoKeys 88: 1-33. https://doi.org/10.3897/mycokeys.88.77106
Table S1. Accession numbers corresponding with the reference sequences used to build the phylogenetic trees
Supplementary material 3 from: Ceballos-Escalera A, Richards J, Arias MB, Inward DJG, Vogler AP (2022) Metabarcoding of insect-associated fungal communities: a comparison of internal transcribed spacer (ITS) and large-subunit (LSU) rRNA markers. MycoKeys 88: 1-33. https://doi.org/10.3897/mycokeys.88.77106
Figure S3. Maximum-likelihood tree constructed in IQ-Tree2 based on three-gene (LSU D1-D2, SSU, ITS2) reference sequence alignments and OTUs for both markers (clustering thresholds: 99% LSU D1-D2 and 98% ITS2)
Supplementary material 2 from: Ceballos-Escalera A, Richards J, Arias MB, Inward DJG, Vogler AP (2022) Metabarcoding of insect-associated fungal communities: a comparison of internal transcribed spacer (ITS) and large-subunit (LSU) rRNA markers. MycoKeys 88: 1-33. https://doi.org/10.3897/mycokeys.88.77106
Figure S2. Species accumulation curves of the OTUs generated from the ITS (panel right) and LSU (panel left) metabarcodes
Archive data supporting the results in the paper: Long-term soil warming alters fine root dynamics and morphology, and their ectomycorrhizal fungal community in a temperate forest soil"
<p><span>Climate warming is predicted to affect temperate forests severely, but the response of fine roots, key to plant nutrition, water uptake, soil carbon and nutrient cycling is unclear. Understanding how fine roots will respond to increasing temperature is a prerequisite for predicting the functioning of forests in a warmer climate. We studied the response of fine roots and their ectomycorrhizal (EcM) fungal and root-associated bacterial communities to soil warming by 4 °C in a mixed spruce-beech forest in the Austrian Limestone Alps after 8 and 14 years of soil warming, respectively. Fine root biomass (FRB) and fine root production were 17% and 128% higher in the warmed plots, respectively, after 14 years. The increase in FRB (13%) was not significant after 8 years of treatment, whereas specific root length, specific root area, and root tip density were significantly higher in warmed plots at both sampling occasions. Soil warming did not affect EcM exploration types and diversity, but changed their community composition, with an increase in the relative abundance of <em>Cenoccocum</em> at 0 – 10 cm soil depth, a drought-stress tolerant genus, and an increase in short and long-distance exploration types like <em>Sebacina </em>and <em>Boletus </em>at 10 – 20 cm soil depth. Warming increased the root-associated bacterial diversity but did not affect their community composition. Soil warming did not affect nutrient concentrations of fine roots, though we found indications of limited soil phosphorus (P) and potassium (K) availability. </span><span>Our findings suggest that, in the studied ecosystem, global warming could persistently increase soil carbon inputs due to accelerated fine root growth and turnover, and could simultaneously alter fine root morphology and EcM fungal community composition towards improved nutrient foraging. </span></p>
Supplementary material 7 from: Wurzbacher C, Warthmann N, Bourne EC, Attermeyer K, Allgaier M, Powell JR, Detering H, Mbedi S, Grossart H-P, Monaghan MT (2016) High habitat-specificity in fungal communities in oligo-mesotrophic, temperate Lake Stechlin (North-East Germany). MycoKeys 16: 17-44. https://doi.org/10.3897/mycokeys.16.9646
Comprehensive Blast analysis : Explanation note: Blast results against the NCBI nt database (June 2015) for all eukaryotes presented in a Megan5 plot.
Supplementary material 6 from: Wurzbacher C, Warthmann N, Bourne EC, Attermeyer K, Allgaier M, Powell JR, Detering H, Mbedi S, Grossart H-P, Monaghan MT (2016) High habitat-specificity in fungal communities in oligo-mesotrophic, temperate Lake Stechlin (North-East Germany). MycoKeys 16: 17-44. https://doi.org/10.3897/mycokeys.16.9646
Alternative ordinations based on binary data and taxonomy : Explanation note: Two alternative NMDS accompanied by corresponding PERMANOVA statistics based on a) the presence/absence of OTUs (left panel) and the Jaccard index, and b) the taxonomic classification of SILVA NGS and the Cao index. The ellipses (coloured to POM type) are based on standard deviations around centroids with a confidence level of 0.95.
Supplementary material 5 from: Wurzbacher C, Warthmann N, Bourne EC, Attermeyer K, Allgaier M, Powell JR, Detering H, Mbedi S, Grossart H-P, Monaghan MT (2016) High habitat-specificity in fungal communities in oligo-mesotrophic, temperate Lake Stechlin (North-East Germany). MycoKeys 16: 17-44. https://doi.org/10.3897/mycokeys.16.9646
Rarefaction analysis : Explanation note: Rarefaction curves based on the OTU table without OTU singletons for all eukaryotes (left panel) and for fungal OTUs (right panel).
Supplementary material 8 from: Wurzbacher C, Warthmann N, Bourne EC, Attermeyer K, Allgaier M, Powell JR, Detering H, Mbedi S, Grossart H-P, Monaghan MT (2016) High habitat-specificity in fungal communities in oligo-mesotrophic, temperate Lake Stechlin (North-East Germany). MycoKeys 16: 17-44. https://doi.org/10.3897/mycokeys.16.9646
Phylogenetic tree of Neocallimastigales sequences : Explanation note: Phylogenetic bayesian tree based on 10 million generations. Sequences that were classified as Neocallimastigales in the manuscript are coloured in red with the frequency of sequences in the dataset in black. The name corresponds to the representative read identifier in the dataset (accessible at ENA nucleotide archive: PRJEB14236). Node labels are posterior probabilities above 0.8. Statistically supported branches have an probability of 0.95-1.
Supplementary material 4 from: Wurzbacher C, Warthmann N, Bourne EC, Attermeyer K, Allgaier M, Powell JR, Detering H, Mbedi S, Grossart H-P, Monaghan MT (2016) High habitat-specificity in fungal communities in oligo-mesotrophic, temperate Lake Stechlin (North-East Germany). MycoKeys 16: 17-44. https://doi.org/10.3897/mycokeys.16.9646
Krona charts of classified OTUs (RDP) and sequences (SILVA NGS). : Explanation note: File archive in "zip" format. Decompress with e.g., "unzip" for inspecting individual html files. Open html files with an internet browser (network connection must be enabled). Krona charts presenting the classified sequences based on a) OTUs classified by the RDP classifier, and b) based clipped reads processed by the SILVA NGS pipeline.
Supplementary material 3 from: Wurzbacher C, Warthmann N, Bourne EC, Attermeyer K, Allgaier M, Powell JR, Detering H, Mbedi S, Grossart H-P, Monaghan MT (2016) High habitat-specificity in fungal communities in oligo-mesotrophic, temperate Lake Stechlin (North-East Germany). MycoKeys 16: 17-44. https://doi.org/10.3897/mycokeys.16.9646
Detailed results of the clipping procedure : Explanation note: File archive in "zip" format. Decompress with e.g., "unzip" for inspecting individual files. Files describing the bioinformatic processing and the effects of the clipping procedure.
Supplementary material 1 from: Wurzbacher C, Warthmann N, Bourne EC, Attermeyer K, Allgaier M, Powell JR, Detering H, Mbedi S, Grossart H-P, Monaghan MT (2016) High habitat-specificity in fungal communities in oligo-mesotrophic, temperate Lake Stechlin (North-East Germany). MycoKeys 16: 17-44. https://doi.org/10.3897/mycokeys.16.9646
Accompanying data tables : Explanation note: Two additional tables stating 1) the physicochemistry of the lake during the sampled time span, 2) the proportions of fungal-like organism and terrestrial fungi ("forest fungi", see main text).
Data from: Human disturbance increases functional but not structural variability of stream fungal communities
Temporal stability of ecosystem functions is often regulated by the same environmental factors that also shape diversity. Therefore, species diversity, ecosystem functions and their environmental regulators should be considered together to understand and predict the consequences of anthropogenic disturbances on ecosystems. We studied the influence of land-use disturbance (agriculture) and a natural stressor (low pH due to specific geology) on the temporal variability (variability among successive years) of fungal decomposer communities and leaf decomposition rates in streams. We used next-generation sequencing techniques (pyrosequencing) to determine the composition of fungal assemblages. Temporal variability of leaf decomposition was higher in human-disturbed streams than in circumneutral reference or naturally acidic sites, whereas the latter two did not differ. Fungal operational taxonomic unit (OTU) richness and evenness were lower in human-impacted sites than in circumneutral reference sites. However, there were no significant differences between stream types in the temporal variability of fungal community composition. Fungal OTU evenness was negatively and among-year variability of water chemistry positively related to temporal variability in leaf decomposition. Partial regressions showed that these two factors had independent effects on decomposition rates. Although the dominant OTUs in the disturbed streams were temporally stable, they did not maintain stable ecosystem functions, suggesting that variability in decomposition was driven mainly by changes in the metabolic responses of dominant taxa to environmental fluctuations. Our results show that leaf decomposition rates in reference sites vary little through time, supporting the use of leaf decomposition assays in bioassessment. Our results also highlight the importance of measuring not only the mean rates, but also temporal variability of process rates when assessing the influence of human disturbance on ecosystem functioning.
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International Brain Laboratory public data
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OpenNeuro
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