ABSTRACT
Mycorrhizal fungi benefit plants by improved mineral nutrition and protection against stress, yet information about fundamental differences among mycorrhizal types in fungi and trees and ...their relative importance in biogeochemical processes is only beginning to accumulate. We critically review and synthesize the ecophysiological differences in ectomycorrhizal, ericoid mycorrhizal and arbuscular mycorrhizal symbioses and the effect of these mycorrhizal types on soil processes from local to global scales. We demonstrate that guilds of mycorrhizal fungi display substantial differences in genome‐encoded capacity for mineral nutrition, particularly acquisition of nitrogen and phosphorus from organic material. Mycorrhizal associations alter the trade‐off between allocation to roots or mycelium, ecophysiological traits such as root exudation, weathering, enzyme production, plant protection, and community assembly as well as response to climate change. Mycorrhizal types exhibit differential effects on ecosystem carbon and nutrient cycling that affect global elemental fluxes and may mediate biome shifts in response to global change. We also note that most studies performed to date have not been properly replicated and collectively suffer from strong geographical sampling bias towards temperate biomes. We advocate that combining carefully replicated field experiments and controlled laboratory experiments with isotope labelling and ‐omics techniques offers great promise towards understanding differences in ecophysiology and ecosystem services among mycorrhizal types.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SAZU, SBCE, SBMB, UL, UM, UPUK
The majority of vascular plants are mycorrhizal: 72% are arbuscular mycorrhizal (AM), 2.0% are ectomycorrhizal (EcM), 1.5% are ericoid mycorrhizal and 10% are orchid mycorrhizal. Just 8% are ...completely nonmycorrhizal (NM), whereas 7% have inconsistent NM–AM associations. Most NM and NM–AM plants are nutritional specialists (e.g. carnivores and parasites) or habitat specialists (e.g. hydrophytes and epiphytes). Mycorrhizal associations are consistent in most families, but there are exceptions with complex roots (e.g. both EcM and AM). We recognize three waves of mycorrhizal evolution, starting with AM in early land plants, continuing in the Cretaceous with multiple new NM or EcM linages, ericoid and orchid mycorrhizas. The third wave, which is recent and ongoing, has resulted in root complexity linked to rapid plant diversification in biodiversity hotspots.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NMLJ, NUK, OILJ, PNG, SAZU, SBCE, SBMB, UL, UM, UPUK
Mycorrhizal fungi provide plants with a range of benefits, including mineral nutrients and protection from stress and pathogens. Here we synthesize current information about how the presence and type ...of mycorrhizal association affect plant communities. We argue that mycorrhizal fungi regulate seedling establishment and species coexistence through stabilizing and equalizing mechanisms such as soil nutrient partitioning, feedback to soil antagonists, differential mycorrhizal benefits, and nutrient trade. Mycorrhizal fungi have strong effects on plant population and community biology, with mycorrhizal type-specific effects on seed dispersal, seedling establishment, and soil niche differentiation, as well as interspecific and intraspecific competition and hence plant diversity.
We draw attention to a worrying trend for the uncritical use of ‘recycled’ mycorrhizal data to compile host species lists that include obvious errors or undertake risky analyses that correlate ...mycorrhizal colonization levels with environmental or physiological factors despite inherent limitations in datasets. We are not suggesting that all meta-studies are wrong, only that more care should be taken to resolve what can safely be done with recycled mycorrhizal data in the future. We also recommend that mycorrhizal species lists should be checked against standard references since the majority of ectomycorrhizal hosts and nonmycorrhizal plants belong to families that are well resolved. However, additional research is required in cases where plant families have multiple root types within genera or occur inhabitats where mycorrhizal associations are often suppressed (see Brundrett & Tedersoo, 2018). We hope that the mycorrhizal science community will work together more closely in the future to develop and enforce standards for mycorrhizal diagnosis and to share carefully corrected datasets for realistic meta-studies.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NMLJ, NUK, OILJ, PNG, SAZU, SBCE, SBMB, UL, UM, UPUK
Summary
Fungi are the key players in ecosystems as well as in plant and human health. High‐throughput molecular identification of fungi has greatly progressed our understanding about the diversity of ...mutualists, saprotrophs, and pathogens. We argue that the methods promoted by the microbiome consortia are suboptimal for detection of the most important fungal pathogens and ecologically important degraders. We recommend several sets of optimized primers for analysis of fungi or all eukaryote groups based on either short or long amplicons that cover the ITS region as well as part of 18S and 28S rDNA.
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BFBNIB, FZAB, GIS, IJS, IZUM, KILJ, NLZOH, NUK, OILJ, PILJ, PNG, SAZU, SBCE, SBMB, UL, UM, UPUK
Second-generation, high-throughput sequencing methods have greatly improved our understanding of the ecology of soil microorganisms, yet the short barcodes (< 500 bp) provide limited taxonomic and ...phylogenetic information for species discrimination and taxonomic assignment.
Here, we utilized the third-generation Pacific Biosciences (PacBio) RSII and Sequel instruments to evaluate the suitability of full-length internal transcribed spacer (ITS) barcodes and longer rRNA gene amplicons for metabarcoding Fungi, Oomycetes and other eukaryotes in soil samples.
Metabarcoding revealed multiple errors and biases: Taq polymerase substitution errors and mis-incorporating indels in sequencing homopolymers constitute major errors; sequence length biases occur during PCR, library preparation, loading to the sequencing instrument and quality filtering; primer–template mismatches bias the taxonomic profile when using regular and highly degenerate primers.
The RSII and Sequel platforms enable the sequencing of amplicons up to 3000 bp, but the sequence quality remains slightly inferior to Illumina sequencing especially in longer amplicons. The full ITS barcode and flanking rRNA small subunit gene greatly improve taxonomic identification at the species and phylum levels, respectively. We conclude that PacBio sequencing provides a viable alternative for metabarcoding of organisms that are of relatively low diversity, require > 500-bp barcode for reliable identification or when phylogenetic approaches are intended.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NMLJ, NUK, OILJ, PNG, SAZU, SBCE, SBMB, UL, UM, UPUK
Fungi are major ecological players in both terrestrial and aquatic environments by cycling organic matter and channelling nutrients across trophic levels. High-throughput sequencing (HTS) studies of ...fungal communities are redrawing the map of the fungal kingdom by hinting at its enormous - and largely uncharted - taxonomic and functional diversity. However, HTS approaches come with a range of pitfalls and potential biases, cautioning against unwary application and interpretation of HTS technologies and results. In this Review, we provide an overview and practical recommendations for aspects of HTS studies ranging from sampling and laboratory practices to data processing and analysis. We also discuss upcoming trends and techniques in the field and summarize recent and noteworthy results from HTS studies targeting fungal communities and guilds. Our Review highlights the need for reproducibility and public data availability in the study of fungal communities. If the associated challenges and conceptual barriers are overcome, HTS offers immense possibilities in mycology and elsewhere.
Summary
Development of high‐throughput sequencing techniques has greatly benefited our understanding about microbial ecology, yet the methods producing short reads suffer from species‐level ...resolution and uncertainty of identification. Here, we optimize Pacific Biosciences‐based metabarcoding protocols covering the internal transcribed spacer (ITS region) and partial small subunit of the rRNA gene for species‐level identification of all eukaryotes, with a specific focus on Fungi (including Glomeromycota) and Stramenopila (particularly Oomycota). Based on tests on composite soil samples and mock communities, we propose best suitable degenerate primers, ITS9munngs + ITS4ngsUni for eukaryotes and selected groups therein and discuss the pros and cons of long read‐based identification of eukaryotes.
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BFBNIB, FZAB, GIS, IJS, IZUM, KILJ, NLZOH, NUK, OILJ, PILJ, PNG, SAZU, SBCE, SBMB, UL, UM, UPUK
High‐throughput sequencing methods have become a routine analysis tool in environmental sciences as well as in public and private sector. These methods provide vast amount of data, which need to be ...analysed in several steps. Although the bioinformatics may be applied using several public tools, many analytical pipelines allow too few options for the optimal analysis for more complicated or customized designs. Here, we introduce PipeCraft, a flexible and handy bioinformatics pipeline with a user‐friendly graphical interface that links several public tools for analysing amplicon sequencing data. Users are able to customize the pipeline by selecting the most suitable tools and options to process raw sequences from Illumina, Pacific Biosciences, Ion Torrent and Roche 454 sequencing platforms. We described the design and options of PipeCraft and evaluated its performance by analysing the data sets from three different sequencing platforms. We demonstrated that PipeCraft is able to process large data sets within 24 hr. The graphical user interface and the automated links between various bioinformatics tools enable easy customization of the workflow. All analytical steps and options are recorded in log files and are easily traceable.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SAZU, SBCE, SBMB, UL, UM, UPUK
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