Long- and short-read metabarcoding technologies reveal similar spatiotemporal structures in fungal communities

Community Assembly Processes of Deadwood Mycobiome in a Tropical Forest Revealed by Long-Read Third-Generation Sequencing

Despite the importance of wood-inhabiting fungi on nutrient cycling and ecosystem functions, their ecology, especially related to their community assembly, is still highly unexplored. In this study, we analyzed the wood-inhabiting fungal richness, community composition, and phylogenetics using PacBio sequencing. Opposite to what has been expected that deterministic processes especially environmental filtering through wood-physicochemical properties controls the community assembly of wood-inhabiting fungal communities, here we showed that both deterministic and stochastic processes can highly contribute to the community assembly processes of wood-inhabiting fungi in this tropical forest. We demonstrated that the dynamics of stochastic and deterministic processes varied with wood decomposition stages. The initial stage was mainly governed by a deterministic process (homogenous selection), whereas the early and later decomposition stages were governed by the stochastic processes (ecological drift). Deterministic processes were highly contributed by wood physicochemical properties (especially macronutrients and hemicellulose) rather than soil physicochemical factors. We elucidated that fine-scale fungal-fungal interactions, especially the network topology, modularity, and keystone taxa of wood-inhabiting fungal communities, strongly differed in an initial and decomposing deadwood. This current study contributes to a better understanding of the ecological processes of wood-inhabiting fungi in tropical regions where the knowledge of wood-inhabiting fungi is highly limited.

Sporocarp nutrition of ectomycorrhizal fungi indicates an important role for endemic species in a high productivity temperate rainforest

Endemic species of ectomycorrhizal fungi (EMF) are found throughout many biomes, but it is unclear whether their localized distribution is dictated by habitat filtering or geographical barriers to dispersal. We examined community composition (via long-read metabarcoding) and differences in sporocarp nutrition between endemic and cosmopolitan EMF species across perhumid temperate rainforests of British Columbia, characterized by soils with high nitrogen (N) supply alongside low phosphorus (P) and cation availability. Endemic EMF species, representing almost half of the community, had significantly greater sporocarp N (24% higher), potassium (+16%), and magnesium (+17%) concentrations than cosmopolitan species. Sporocarp P concentrations were comparatively low and did not differ by fungal range. However, sporocarp N% and P% were well correlated, supporting evidence for linkages in N and P acquisition. Endemics were more likely to occur on Tsuga heterophylla (a disjunct host genus) than Picea sitchensis (a circumpolar genus). The Inocybaceae and Thelephoraceae families had high proportions of endemic taxa, while species in Cortinariaceae were largely cosmopolitan, indicating some niche conservatism among genera. We conclude that superior adaptive traits in relation to perhumid soils were skewed toward the endemic community, underscoring the potentially important contribution of these localized fungi to rainforest nutrition and productivity.

Using nanopore sequencing to identify fungi from clinical samples with high phylogenetic resolution

The study of microbiota has been revolutionized by the development of DNA metabarcoding. This sequence-based approach enables the direct detection of microorganisms without the need for culture and isolation, which significantly reduces analysis time and offers more comprehensive taxonomic profiles across broad phylogenetic lineages. While there has been an accumulating number of researches on bacteria, molecular phylogenetic analysis of fungi still remains challenging due to the lack of standardized tools and the incompleteness of reference databases limiting the accurate and precise identification of fungal taxa. Here, we present a DNA metabarcoding workflow for characterizing fungal microbiota with high taxonomic resolution. This method involves amplifying longer stretches of ribosomal RNA operons and sequencing them using nanopore long-read sequencing technology. The resulting reads were error-polished to generate consensus sequences with 99.5-100% accuracy, which were then aligned against reference genome assemblies. The efficacy of this method was explored using a polymicrobial mock community and patient-derived specimens, demonstrating the marked potential of long-read sequencing combined with consensus calling for accurate taxonomic classification. Our approach offers a powerful tool for the rapid identification of pathogenic fungi and has the promise to significantly improve our understanding of the role of fungi in health and disease.

Multivariate analysis of enriched landfill soil consortia provide insight on the community structural perturbation and functioning during low-density polyethylene degradation

Plastic-enriched sites like landfills have immense potential for discovery of microbial consortia that can efficiently degrade plastics. In this study, we used a combination of culture enrichment, high-throughput PacBio sequencing of 16 S rRNA and the ITS gene, Fourier transform infrared (FTIR), and scanning electron microscopy (SEM) to examine the compositional and diversity perturbations of bacterial and fungal consortia from landfill soils and their impact on low-density polyethylene (LDPE) film biodegradation over a 90-day period. Results showed that enrichment cultures effectively utilized LDPE as a carbon source for cellular growth, resulting in significant weight reduction (22.4% and 55.6%) in the films. SEM analysis revealed marked changes in the micrometric surface characteristics (cracks, fissures, and erosion) and biofilm formation in LDPE films. FTIR analyses suggested structural and functional group modification related to C-H (2831-2943 cm⁻¹), and CH₂ (1400 cm⁻¹) stretching, CO and CC (680-950 cm⁻¹) scission, and CO incorporation (3320-3500 cm⁻¹) into the carbon backbone, indicative of LDPE polymer biodegradation. Enrichment cultures had lower diversity and richness of microbial taxa compared to soil samples, with LDPE as a carbon source having a direct influence on the structure and functioning of the microbial consortia. A total of 26 bacterial and 12 fungal OTU exhibiting high relative abundance and significant associations (IndVal > 0.7, q < 0.05) were identified in the enrichment culture. Bacterial taxa such as unclassified Parvibaculum FJ375498, Achromobacter xylosoxidans, unclassified Chitinophagaceae PAC002331, unclassified Paludisphaera and unclassified Comamonas JX898122, and six fungal species (Galactomyces candidus, Trichosporon chiropterorum, Aspergillus fumigatus, Penicillium chalabudae, Talaromyces thailandensis, and Penicillium citreosulfuratum) were identified as the putative LDPE degraders in the enrichment microbial consortium cultures. PICRUSt2 metagenomic functional profiling of taxonomic bacterial taxa abundances in both landfill soil and enrichment microbial consortia also revealed differential enrichment of energy production, stress tolerance, surface attachment and motility pathways, and xenobiotic degrading enzymes important for biofilm formation and hydrolytic/oxidative LDPE biodegradation. The findings shed light on the composition and structural changes in landfill soil microbial consortia during enrichment with LDPE as a carbon source and suggest novel LDPE-degrading bacterial and fungal taxa that could be explored for management of polyethylene pollution.

Abundant fungi dominate the complexity of microbial networks in soil of contaminated site: High-precision community analysis by full-length sequencing

During the past decade, the characterization of microbial community in soil of contaminated sites was primarily done by high-throughput short-read amplicon sequencing. However, due to the similarity of 16S rRNA and ITS genes amplicon sequences, the short-read approach often limits the microbial composition analysis at the species level. Here, we simultaneously performed full-length and short-read amplicon sequencing to clarify the community composition and ecological status of different microbial taxa in contaminated soil from a high-resolution perspective. We found that (1) full-length 16S rRNA gene sequencing gave better resolution for bacterial identification at all levels, while there were no significant differences between the two sequencing platforms for fungal identification in some samples. (2) Abundant taxa were vital for microbial co-occurrences network constructed by both full-length and short-read sequencing data, and abundant fungal species such as Mortierella alpine, Fusarium solani, Mrakia frigida, and Chaetomium homopilatum served as the keystone species. (3) Heavy metal correlated with the microbial community significantly, and bacterial community and its abundant taxa were assembled by deterministic process, while the other taxa were dominated by stochastic process. These findings contribute to the understanding of the ecological mechanisms and microbial interactions in site soil ecosystems and demonstrate that full-length sequencing has the potential to provide more details of microbial community.

Yeast communities before and after spontaneous fermentation of wine grapes: a case study from Nova Scotia

Wine fermentations are generally completed by the domestic yeast Saccharomyces cerevisiae, but many indigenous vineyard yeasts also influence wine flavour and aroma. Despite the flourishing wine industry in Nova Scotia, there has yet to be any systematic evaluation of these yeasts in Atlantic Canada. The yeast communities of pressed L'Acadie blanc grapes sampled from an organic vineyard in the Annapolis Valley in 2018 and 2019 were characterized before and after spontaneous fermentation by both Illumina and PacBio sequencing, to address and compare potential platform biases. Chemical and sensory evaluations were also conducted. Basidiomycete yeasts, including Vishniacozyma carnescens, Filobasidium globisporum, and Curvibasidium cygneicollum, dominated pre-fermentation diversity. Species of Saccharomyces made up ∼0.04% of sequences prior to fermentation, but 85%-100% after fermentation, with some replicates dominated by S. cerevisiae and some by S. uvarum. PacBio sequencing detected high proportions of Hanseniaspora uvarum, while Illumina sequencing did not. A better understanding of Nova Scotia vineyard yeast communities will allow local wine makers to make better use of non-traditional yeasts and spontaneous fermentations to produce high-quality wines unique to the region.

Global patterns and rates of habitat transitions across the eukaryotic tree of life

The successful colonization of new habitats has played a fundamental role during the evolution of life. Salinity is one of the strongest barriers for organisms to cross, which has resulted in the evolution of distinct marine and non-marine (including both freshwater and soil) communities. Although microbes represent by far the vast majority of eukaryote diversity, the role of the salt barrier in shaping the diversity across the eukaryotic tree is poorly known. Traditional views suggest rare and ancient marine/non-marine transitions but this view is being challenged by the discovery of several recently transitioned lineages. Here, we investigate habitat evolution across the tree of eukaryotes using a unique set of taxon-rich phylogenies inferred from a combination of long-read and short-read environmental metabarcoding data spanning the ribosomal DNA operon. Our results show that, overall, marine and non-marine microbial communities are phylogenetically distinct but transitions have occurred in both directions in almost all major eukaryotic lineages, with hundreds of transition events detected. Some groups have experienced relatively high rates of transitions, most notably fungi for which crossing the salt barrier has probably been an important aspect of their successful diversification. At the deepest phylogenetic levels, ancestral habitat reconstruction analyses suggest that eukaryotes may have first evolved in non-marine habitats and that the two largest known eukaryotic assemblages (TSAR and Amorphea) arose in different habitats. Overall, our findings indicate that the salt barrier has played an important role during eukaryote evolution and provide a global perspective on habitat transitions in this domain of life.

A roadmap to understanding diversity and function of coral reef-associated fungi

Tropical coral reefs are hotspots of marine productivity, owing to the association of reef-building corals with endosymbiotic algae and metabolically diverse bacterial communities. However, the functional importance of fungi, well-known for their contribution to shaping terrestrial ecosystems and global nutrient cycles, remains underexplored on coral reefs. We here conceptualize how fungal functional traits may have facilitated the spread, diversification, and ecological adaptation of marine fungi on coral reefs. We propose that functions of reef-associated fungi may be diverse and go beyond their hitherto described roles of pathogens and bioeroders, including but not limited to reef-scale biogeochemical cycles and the structuring of coral-associated and environmental microbiomes via chemical mediation. Recent technological and conceptual advances will allow the elucidation of the physiological, ecological, and chemical contributions of understudied marine fungi to coral holobiont and reef ecosystem functioning and health and may help provide an outlook for reef management actions.

Best practices in metabarcoding of fungi: From experimental design to results

The development of high-throughput sequencing (HTS) technologies has greatly improved our capacity to identify fungi and unveil their ecological roles across a variety of ecosystems. Here we provide an overview of current best practices in metabarcoding analysis of fungal communities, from experimental design through molecular and computational analyses. By reanalysing published data sets, we demonstrate that operational taxonomic units (OTUs) outperform amplified sequence variants (ASVs) in recovering fungal diversity, a finding that is particularly evident for long markers. Additionally, analysis of the full-length ITS region allows more accurate taxonomic placement of fungi and other eukaryotes compared to the ITS2 subregion. Finally, we show that specific methods for compositional data analyses provide more reliable estimates of shifts in community structure. We conclude that metabarcoding analyses of fungi are especially promising for integrating fungi into the full microbiome and broader ecosystem functioning context, recovery of novel fungal lineages and ancient organisms as well as barcoding of old specimens including type material.

Metabarcoding of insect-associated fungal communities: a comparison of internal transcribed spacer (ITS) and large-subunit (LSU) rRNA markers

Full taxonomic characterisation of fungal communities is necessary for establishing ecological associations and early detection of pathogens and invasive species. Complex communities of fungi are regularly characterised by metabarcoding using the Internal Transcribed Spacer (ITS) and the Large-Subunit (LSU) gene of the rRNA locus, but reliance on a single short sequence fragment limits the confidence of identification. Here we link metabarcoding from the ITS2 and LSU D1-D2 regions to characterise fungal communities associated with bark beetles (Scolytinae), the likely vectors of several tree pathogens. Both markers revealed similar patterns of overall species richness and response to key variables (beetle species, forest type), but identification against the respective reference databases using various taxonomic classifiers revealed poor resolution towards lower taxonomic levels, especially the species level. Thus, Operational Taxonomic Units (OTUs) could not be linked via taxonomic classifiers across ITS and LSU fragments. However, using phylogenetic trees (focused on the epidemiologically important Sordariomycetes) we placed OTUs obtained with either marker relative to reference sequences of the entire rRNA cistron that includes both loci and demonstrated the largely similar phylogenetic distribution of ITS and LSU-derived OTUs. Sensitivity analysis of congruence in both markers suggested the biologically most defensible threshold values for OTU delimitation in Sordariomycetes to be 98% for ITS2 and 99% for LSU D1-D2. Studies of fungal communities using the canonical ITS barcode require corroboration across additional loci. Phylogenetic analysis of OTU sequences aligned to the full rRNA cistron shows higher success rate and greater accuracy of species identification compared to probabilistic taxonomic classifiers.

Effects of operational taxonomic unit inference methods on soil microeukaryote community analysis using long-read metabarcoding

Long amplicon metabarcoding has opened the door for phylogenetic analysis of the largely unknown communities of microeukaryotes in soil. Here, we amplified and sequenced the ITS and LSU regions of the rDNA operon (around 1500 bp) from grassland soils using PacBio SMRT sequencing. We tested how three different methods for generation of operational taxonomic units (OTUs) effected estimated richness and identified taxa, and how well large-scale ecological patterns associated with shifting environmental conditions were recovered in data from the three methods. The field site at Kungsängen Nature Reserve has drawn frequent visitors since Linnaeus's time, and its species rich vegetation includes the largest population of Fritillaria meleagris in Sweden. To test the effect of different OTU generation methods, we sampled soils across an abrupt moisture transition that divides the meadow community into a Carex acuta dominated plant community with low species richness in the wetter part, which is visually distinct from the mesic-dry part that has a species rich grass-dominated plant community including a high frequency of F. meleagris. We used the moisture and plant community transition as a framework to investigate how detected belowground microeukaryotic community composition was influenced by OTU generation methods. Soil communities in both moisture regimes were dominated by protists, a large fraction of which were taxonomically assigned to Ciliophora (Alveolata) while 30%-40% of all reads were assigned to kingdom Fungi. Ecological patterns were consistently recovered irrespective of OTU generation method used. However, different methods strongly affect richness estimates and the taxonomic and phylogenetic resolution of the characterized community with implications for how well members of the microeukaryotic communities can be recognized in the data.

Long- and short-read metabarcoding technologies reveal similar spatiotemporal structures in fungal communities

Fungi form diverse communities and play essential roles in many terrestrial ecosystems, yet there are methodological challenges in taxonomic and phylogenetic placement of fungi from environmental sequences. To address such challenges, we investigated spatiotemporal structure of a fungal community using soil metabarcoding with four different sequencing strategies: short-amplicon sequencing of the ITS2 region (300-400 bp) with Illumina MiSeq, Ion Torrent Ion S5 and PacBio RS II, all from the same PCR library, as well as long-amplicon sequencing of the full ITS and partial LSU regions (1200-1600 bp) with PacBio RS II. Resulting community structure and diversity depended more on statistical method than sequencing technology. The use of long-amplicon sequencing enables construction of a phylogenetic tree from metabarcoding reads, which facilitates taxonomic identification of sequences. However, long reads present issues for denoising algorithms in diverse communities. We present a solution that splits the reads into shorter homologous regions prior to denoising, and then reconstructs the full denoised reads. In the choice between short and long amplicons, we suggest a hybrid approach using short amplicons for sampling breadth and depth, and long amplicons to characterize the local species pool for improved identification and phylogenetic analyses.