A bioinformatics pipeline for sequence-based analyses of fungal biodiversity

Phosphorus Mobilizing Enzymes of Alnus-Associated Ectomycorrhizal Fungi in an Alaskan Boreal Floodplain

Because of its high phosphorus (P) demands, it is likely that the abundance, distribution, and N-fixing capacity of Alnus in boreal forests are tightly coupled with P availability and the mobilization and uptake of soil P via ectomycorrhizal fungi (EMF). We examined whether Alnus shifts EMF communities in coordination with increasingly more complex organic P forms across a 200-year-old successional sequence along the Tanana River in interior Alaska. Root-tip activities of acid phosphatase, phosphodiesterase, and phytase of A. tenuifolia-associated EMF were positively intercorrelated but did not change in a predictable manner across the shrub, to hardwood to coniferous forest successional sequence. Approximately half of all Alnus roots were colonized by Alnicola and Tomentella taxa, and ordination analysis indicated that the EMF community on Alnus is a relatively distinct, host-specific group. Despite differences in the activities of the two Alnus dominants to mobilize acid phosphatase and phosphodiesterase, the root-tip activities of P-mobilizing enzymes of the Alnus-EMF community were not dramatically different from other co-occurring boreal plant hosts. This suggests that if Alnus has a greater influence on P cycling than other plant functional types, additional factors influencing P mobilization and uptake at the root and/or whole-plant level must be involved.

Temporal Development of the Culturable, Endophytic Fungal Community in Healthy Grapevine Branches and Occurrence of GTD-Associated Fungi

Endophytic fungi play an important role in the life of grapevine, either as beneficial microorganisms or as pathogens. Many surveys concerning the fungal grapevine community have been conducted. Nevertheless, exactly how the fungal community arises within the plant and develops from young shoots to mature vines is still unknown. Therefore, it was the aim of this study to investigate the early development of endophytic fungal communities in healthy grapevine branches from 2 months to 8 years old. More than 3800 fungi belonging to 86 operational taxonomic units (OTUs) were isolated from wood samples and assigned to eight age groups. The community composition within the age groups changed and significant differences between young (≤ 1 year) and old (> 1 year) branches were found. The former were primarily dominated by ubiquitous, fast-growing fungi like Alternaria spp., Aureobasidium pullulans, Cladosporium spp., or Epicoccum nigrum, while communities of perennial branches additionally harbored many grapevine trunk disease (GTD)-associated fungi such as Diplodia seriata or Eutypa lata. This work gives an insight into the early development of fungal communities in grapevine, the nature and composition of primary settlers and core communities, as well as the emergence of GTD-associated fungi in perennial wood. This information may help grapevine growers to better estimate the risk in relation to the applied training system, producing mainly old branches or young shoots.

Multi-year assessment of coastal planktonic fungi reveals environmental drivers of diversity and abundance

Mycoplankton have so far been a neglected component of pelagic marine ecosystems, having been poorly studied relative to other plankton groups. Currently, there is a lack of understanding of how mycoplankton diversity changes through time, and the identity of controlling environmental drivers. Using Fungi-specific high-throughput sequencing and quantitative PCR analysis of plankton DNA samples collected over 6 years from the coastal biodiversity time series site Station L4 situated off Plymouth (UK), we have assessed changes in the temporal variability of mycoplankton diversity and abundance in relation to co-occurring environmental variables. Mycoplankton diversity at Station L4 was dominated by Ascomycota, Basidiomycota and Chytridiomycota, with several orders within these phyla frequently abundant and dominant in multiple years. Repeating interannual mycoplankton blooms were linked to potential controlling environmental drivers, including nitrogen availability and temperature. Specific relationships between mycoplankton and other plankton groups were also identified, with seasonal chytrid blooms matching diatom blooms in consecutive years. Mycoplankton α-diversity was greatest during periods of reduced salinity at Station L4, indicative of riverine input to the ecosystem. Mycoplankton abundance also increased during periods of reduced salinity, and when potential substrate availability was increased, including particulate organic matter. This study has identified possible controlling environmental drivers of mycoplankton diversity and abundance in a coastal sea ecosystem, and therefore sheds new light on the biology and ecology of an enigmatic marine plankton group. Mycoplankton have several potential functional roles, including saprotrophs and parasites, that should now be considered within the consensus view of pelagic ecosystem functioning and services.

Fire-severity effects on plant-fungal interactions after a novel tundra wildfire disturbance: implications for arctic shrub and tree migration

BACKGROUND

Vegetation change in high latitude tundra ecosystems is expected to accelerate due to increased wildfire activity. High-severity fires increase the availability of mineral soil seedbeds, which facilitates recruitment, yet fire also alters soil microbial composition, which could significantly impact seedling establishment.

RESULTS

We investigated the effects of fire severity on soil biota and associated effects on plant performance for two plant species predicted to expand into Arctic tundra. We inoculated seedlings in a growth chamber experiment with soils collected from the largest tundra fire recorded in the Arctic and used molecular tools to characterize root-associated fungal communities. Seedling biomass was significantly related to the composition of fungal inoculum. Biomass decreased as fire severity increased and the proportion of pathogenic fungi increased.

CONCLUSIONS

Our results suggest that effects of fire severity on soil biota reduces seedling performance and thus we hypothesize that in certain ecological contexts fire-severity effects on plant-fungal interactions may dampen the expected increases in tree and shrub establishment after tundra fire.

Ectomycorrhizal fungi mediate indirect effects of a bark beetle outbreak on secondary chemistry and establishment of pine seedlings

Dendroctonus ponderosae has killed millions of Pinus contorta in western North America with subsequent effects on stand conditions, including changes in light intensity, needle deposition, and the composition of fungal community mutualists, namely ectomycorrhizal fungi. It is unknown whether these changes in stand conditions will have cascading consequences for the next generation of pine seedlings. To test for transgenerational cascades on pine seedlings, we tested the effects of fungal inoculum origin (beetle-killed or undisturbed stands), light intensity and litter (origin and presence) on seedling secondary chemistry and growth in a glasshouse. We also tracked survival of seedlings over two growing seasons in the same stands from which fungi and litter were collected. Fungal communities differed by inoculum origin. Seedlings grown with fungi collected from beetle-killed stands had lower monoterpene concentrations and fewer monoterpene compounds present compared with seedlings grown with fungi collected from undisturbed stands. Litter affected neither monoterpenes nor seedling growth. Seedling survival in the field was lower in beetle-killed than in undisturbed stands. We demonstrate that stand mortality caused by prior beetle attacks of mature pines have cascading effects on seedling secondary chemistry, growth and survival, probably mediated through effects on below-ground mutualisms.

Rich and cold: diversity, distribution and drivers of fungal communities in patterned-ground ecosystems of the North American Arctic

Fungi are abundant and functionally important in the Arctic, yet comprehensive studies of their diversity in relation to geography and environment are not available. We sampled soils in paired plots along the North American Arctic Transect (NAAT), which spans all five bioclimatic subzones of the Arctic. Each pair of plots contrasted relatively bare, cryoturbated patterned-ground features (PGFs) and adjacent vegetated between patterned-ground features (bPGFs). Fungal communities were analysed via sequencing of 7834 ITS-LSU clones. We recorded 1834 OTUs - nearly half the fungal richness previously reported for the entire Arctic. These OTUs spanned eight phyla, 24 classes, 75 orders and 120 families, but were dominated by Ascomycota, with one-fifth belonging to lichens. Species richness did not decline with increasing latitude, although there was a decline in mycorrhizal taxa that was offset by an increase in lichen taxa. The dominant OTUs were widespread even beyond the Arctic, demonstrating no dispersal limitation. Yet fungal communities were distinct in each subzone and were correlated with soil pH, climate and vegetation. Communities in subzone E were distinct from the other subzones, but similar to those of the boreal forest. Fungal communities on disturbed PGFs differed significantly from those of paired stable areas in bPGFs. Indicator species for PGFs included lichens and saprotrophic fungi, while bPGFs were characterized by ectomycorrhizal and pathogenic fungi. Our results suggest that the Arctic does not host a unique mycoflora, while Arctic fungi are highly sensitive to climate and vegetation, with potential to migrate rapidly as global change unfolds.

Redefining the human oral mycobiome with improved practices in amplicon-based taxonomy: discovery of Malassezia as a prominent commensal

Fungi are a large, complex group, increasingly recognized as emerging threats. Their roles as modifiers of health mandate accurate portrayals of fungal communities in humans. As an entry point into the airways and gastrointestinal tract, fungi in the mouth are relevant to several biocompartments. We have revised current practices in sequence-based taxonomy assignments and employed the improvements to address the question of the fungal genera present in the healthy human mouth. The human oral mycobiome was surveyed using massively parallel, high throughput sequencing of internal transcribed spacer 1 (ITS1) amplicons from saliva following robust extraction methods. Taxonomy was assigned by comparison to a curated reference dataset, followed by filtering with an empirically determined BLAST E-value match statistic (10⁻⁴²). Nomenclature corrections further refined results by conjoining redundant names for a single fungal genus. Following these curation steps, about two-thirds of the initially identified genera were eliminated. In comparison with the one similar metagenomic study and several earlier culture-based ones, our findings change the current conception of the oral mycobiome, especially with the discovery of the high prevalence and abundance of the genus Malassezia. Previously identified as an important pathogen of the skin, and recently reported as the predominant fungal genus at the nostril and backs of the head and ear, this is the first account of Malassezia in the human mouth. Findings from this study were in good agreement with others on the existence of many consensus members of the core mycobiome, and on unique patterns for individual subjects. This research offered a cautionary note about unconditional acceptance of lengthy lists of community members produced by automated assignments, provided a roadmap for enhancing the likely biological relevance of sequence-based fungal surveys, and built the foundation for understanding the role of fungi in health and disease of the oral cavity.

From genus to phylum: large-subunit and internal transcribed spacer rRNA operon regions show similar classification accuracies influenced by database composition

We compared the classification accuracy of two sections of the fungal internal transcribed spacer (ITS) region, individually and combined, and the 5' section (about 600 bp) of the large-subunit rRNA (LSU), using a naive Bayesian classifier and BLASTN. A hand-curated ITS-LSU training set of 1,091 sequences and a larger training set of 8,967 ITS region sequences were used. Of the factors evaluated, database composition and quality had the largest effect on classification accuracy, followed by fragment size and use of a bootstrap cutoff to improve classification confidence. The naive Bayesian classifier and BLASTN gave similar results at higher taxonomic levels, but the classifier was faster and more accurate at the genus level when a bootstrap cutoff was used. All of the ITS and LSU sections performed well (>97.7% accuracy) at higher taxonomic ranks from kingdom to family, and differences between them were small at the genus level (within 0.66 to 1.23%). When full-length sequence sections were used, the LSU outperformed the ITS1 and ITS2 fragments at the genus level, but the ITS1 and ITS2 showed higher accuracy when smaller fragment sizes of the same length and a 50% bootstrap cutoff were used. In a comparison using the larger ITS training set, ITS1 and ITS2 had very similar accuracy classification for fragments between 100 and 200 bp. Collectively, the results show that any of the ITS or LSU sections we tested provided comparable classification accuracy to the genus level and underscore the need for larger and more diverse classification training sets.

Fungal high-throughput taxonomic identification tool for use with next-generation sequencing (FHiTINGS)

Improvements in DNA sequencing technology provide unprecedented opportunities to explore fungal diversity, but also present challenges in data analysis due to the large number of sequences generated. Here, we describe an open source software program "FHiTINGS" that utilizes the output of a BLASTn (blastall) search to rapidly identify, classify, and parse internal transcribed spacer (ITS) DNA sequences produced in fungal ecology studies that utilize next-generation DNA sequencing. This tool was designed for use with 454 pyrosequencing and is also appropriate for use with any sequencing platform that allows for BLAST searches against the indicated ITS database. For each sequence, FHiTINGS uses the lowest common ancestor method (LCA) to produce a single identification from BLAST output results, and then assigns taxonomic ranks from species through kingdom when possible for each sequence based on the Index Fungorum database. The program then sums and sorts this data into tabular form to enable rapid analysis of the sample, including α-diversity measures or richness. In silico testing demonstrates the time required to analyze and classify 1000 sequences is reduced from over 2 h by manual sorting to <1 min of computational time when using FHiTINGS, and that the classification output from the software is consistent with that derived from manual sorting of the data.

Fungal endophytic communities in grapevines (Vitis vinifera L.) respond to crop management

We studied the distribution of fungal endophytes of grapevine (Vitis vinifera L.) plants in a subalpine area of northern Italy, where viticulture is of high economic relevance. We adopted both cultivation-based and cultivation-independent approaches to address how various anthropic and nonanthropic factors shape microbial communities. Grapevine stems were harvested from several locations considering organic and integrated pest management (IPM) and from the cultivars Merlot and Chardonnay. Cultivable fungi were isolated and identified by internal-transcribed-spacer sequence analysis, using a novel colony-PCR method, to amplify DNA from fungal specimens. The composition of fungal communities was assessed using a cultivation-independent approach, automated ribosomal intergenic spacer analysis (ARISA). Multivariate statistical analysis of both culture-dependent and culture-independent data sets was convergent and indicated that fungal endophytic communities in grapevines from organically managed farms were different from those from farms utilizing IPM. Fungal communities in plants of cv. Merlot and cv. Chardonnay overlapped when analyzed using culture-dependent approaches but could be partially resolved using ARISA fingerprinting.

Are similarity- or phylogeny-based methods more appropriate for classifying internal transcribed spacer (ITS) metagenomic amplicons?

• The internal transcribed spacer (ITS) of the nuclear ribosomal DNA region is a widely used species marker for plants and fungi. Recent metagenomic studies using next-generation sequencing, however, generate only partial ITS sequences. Here we compare the performance of partial and full-length ITS sequences with several classification methods. • We compiled a full-length ITS data set and created short fragments to simulate the read lengths commonly recovered from current next-generation sequencing platforms. We compared recovery, erroneous recovery, and coverage for the following methods: best BLAST hit classification, MEGAN classification, and automated phylogenetic assignment using the Statistical Assignment Program (SAP). • We found that summarizing results with more inclusive taxonomic ranks increased recovery and reduced erroneous recovery. The similarity-based methods BLAST and MEGAN performed consistently across most fragment lengths. Using a phylogeny-based method, SAP runs with queries 400 bp or longer worked best. Overall, BLAST had the highest recovery rates and MEGAN had the lowest erroneous recovery rates. • A high-throughput ITS classification method should be selected, taking into consideration read length, an acceptable tradeoff between maximizing the total number of classifications and minimizing the number of erroneous classifications, and the computational speed of the assignment method.