Publications by authors named "Leho Tedersoo"

111 Publications

Sedimentary Ancient DNA (sedaDNA) Reveals Fungal Diversity and Environmental Drivers of Community Changes throughout the Holocene in the Present Boreal Lake Lielais Svētiņu (Eastern Latvia).

Microorganisms 2021 Mar 31;9(4). Epub 2021 Mar 31.

Institute of Technology, University of Tartu, Nooruse 1, 50411 Tartu, Estonia.

Fungi are ecologically important in several ecosystem processes, yet their community composition, ecophysiological roles, and responses to changing environmental factors in historical sediments are rarely studied. Here we explored ancient fungal DNA from lake Lielais Svētiņu sediment throughout the Holocene (10.5 kyr) using the ITS metabarcoding approach. Our data revealed diverse fungal taxa and smooth community changes during most of the Holocene with rapid changes occurring in the last few millennia. More precisely, plankton parasitic fungi became more diverse from the Late Holocene (2-4 kyr) which could be related to a shift towards a cooler climate. The Latest Holocene (~2 kyr) showed a distinct increase in the richness of plankton parasites, mycorrhizal, and plant pathogenic fungi which can be associated with an increased transfer rate of plant material into the lake and blooms of planktonic organisms influenced by increased, yet moderate, human impact. Thus, major community shifts in plankton parasites and mycorrhizal fungi could be utilized as potential paleo-variables that accompany host-substrate dynamics. Our work demonstrates that fungal aDNA with predicted ecophysiology and host specificity can be employed to reconstruct both aquatic and surrounding terrestrial ecosystems and to estimate the influence of environmental change.
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http://dx.doi.org/10.3390/microorganisms9040719DOI Listing
March 2021

Tree Species Richness and Neighborhood Effects on Ectomycorrhizal Fungal Richness and Community Structure in Boreal Forest.

Front Microbiol 2021 22;12:567961. Epub 2021 Feb 22.

Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia.

Tree species identity is one of the key factors driving ectomycorrhizal (EcM) fungal richness and community composition in boreal and temperate forest ecosystems, but little is known about the influence of tree species combinations and their neighborhood effects on EcM communities. To advance our understanding of host plant effects on EcM fungi, the roots of silver birch, Scots pine, and Norway spruce were analyzed using high-throughput sequencing across mature boreal forest exploratory plots of monocultures and two- and three-species mixtures in Finland. Our analyses revealed that tree species identity was an important determinant of EcM fungal community composition, but tree species richness had no significant influence on EcM fungal richness and community composition. We found that EcM fungal community composition associated with spruce depends on neighboring tree species. Our study suggests that at a regional-scale tree species identity is the primary factor determining community composition of root-associated EcM fungi alongside with tree species composition effects on EcM fungal community of spruce in mixed stands.
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http://dx.doi.org/10.3389/fmicb.2021.567961DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7939122PMC
February 2021

Temperature and pH define the realised niche space of arbuscular mycorrhizal fungi.

New Phytol 2021 Jan 28. Epub 2021 Jan 28.

Institute of Ecology and Earth Sciences, University of Tartu, Tartu, 51005, Estonia.

The arbuscular mycorrhizal (AM) fungi are a globally distributed group of soil organisms that play critical roles in ecosystem function. However, the ecological niches of individual AM fungal taxa are poorly understood. We collected > 300 soil samples from natural ecosystems worldwide and modelled the realised niches of AM fungal virtual taxa (VT; approximately species-level phylogroups). We found that environmental and spatial variables jointly explained VT distribution worldwide, with temperature and pH being the most important abiotic drivers, and spatial effects generally occurring at local to regional scales. While dispersal limitation could explain some variation in VT distribution, VT relative abundance was almost exclusively driven by environmental variables. Several environmental and spatial effects on VT distribution and relative abundance were correlated with phylogeny, indicating that closely related VT exhibit similar niche optima and widths. Major clades within the Glomeraceae exhibited distinct niche optima, Acaulosporaceae generally had niche optima in low pH and low temperature conditions, and Gigasporaceae generally had niche optima in high precipitation conditions. Identification of the realised niche space occupied by individual and phylogenetic groups of soil microbial taxa provides a basis for building detailed hypotheses about how soil communities respond to gradients and manipulation in ecosystems worldwide.
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http://dx.doi.org/10.1111/nph.17240DOI Listing
January 2021

The Taxon Hypothesis Paradigm-On the Unambiguous Detection and Communication of Taxa.

Microorganisms 2020 Nov 30;8(12). Epub 2020 Nov 30.

Natural History Museum, University of Tartu, 14a Ravila, 50411 Tartu, Estonia.

Here, we describe the taxon hypothesis (TH) paradigm, which covers the construction, identification, and communication of taxa as datasets. Defining taxa as datasets of individuals and their traits will make taxon identification and most importantly communication of taxa precise and reproducible. This will allow datasets with standardized and atomized traits to be used digitally in identification pipelines and communicated through persistent identifiers. Such datasets are particularly useful in the context of formally undescribed or even physically undiscovered species if data such as sequences from samples of environmental DNA (eDNA) are available. Implementing the TH paradigm will to some extent remove the impediment to hastily discover and formally describe all extant species in that the TH paradigm allows discovery and communication of new species and other taxa also in the absence of formal descriptions. The TH datasets can be connected to a taxonomic backbone providing access to the vast information associated with the tree of life. In parallel to the description of the TH paradigm, we demonstrate how it is implemented in the UNITE digital taxon communication system. UNITE TH datasets include rich data on individuals and their rDNA ITS sequences. These datasets are equipped with digital object identifiers (DOI) that serve to fix their identity in our communication. All datasets are also connected to a GBIF taxonomic backbone. Researchers processing their eDNA samples using UNITE datasets will, thus, be able to publish their findings as taxon occurrences in the GBIF data portal. UNITE species hypothesis (species level THs) datasets are increasingly utilized in taxon identification pipelines and even formally undescribed species can be identified and communicated by using UNITE. The TH paradigm seeks to achieve unambiguous, unique, and traceable communication of taxa and their properties at any level of the tree of life. It offers a rapid way to discover and communicate undescribed species in identification pipelines and data portals before they are lost to the sixth mass extinction.
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http://dx.doi.org/10.3390/microorganisms8121910DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7760934PMC
November 2020

Characterising the effect of crop species and fertilisation treatment on root fungal communities.

Sci Rep 2020 10 30;10(1):18741. Epub 2020 Oct 30.

Institute of Ecology and Earth Sciences, University of Tartu, Ravila 14a, 50411, Tartu, Estonia.

Information about the root mycobiome may improve the overall quality of the plants and contribute to a valuable strategy to enhance sustainable agriculture. Therefore, we assessed differences in fungal community diversity and composition in the roots of potato, wheat and barley grown under mineral nitrogen fertilisation at five rates, with and without farmyard manure amendment. The same factorial combination of treatments has been used since 1989. Species richness and diversity, as well as community composition, of different fungal guilds were characterised using Illumina MiSeq sequencing of the ITS2 region. Crop species was the main factor determining overall fungal richness and diversity, with wheat showing the highest, and potato the lowest, richness and diversity. Pathogen diversity indices were highest in wheat plots amended with farmyard manure, whereas the lowest values were observed for potato roots. Fertilisation treatments and the interaction between crop species and fertilisation had the strongest impact on arbuscular mycorrhiza and saprotroph diversity. Crop species also determined the composition of the overall fungal community and that of fungal guilds, whereas fertilisation treatment had only a minor effect. This study highlights crop species as the main driver in shaping root fungal diversity and composition under the same environmental conditions.
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http://dx.doi.org/10.1038/s41598-020-74952-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7603395PMC
October 2020

Large-scale genome sequencing of mycorrhizal fungi provides insights into the early evolution of symbiotic traits.

Nat Commun 2020 10 12;11(1):5125. Epub 2020 Oct 12.

Université de Lorraine, Institut national de recherche pour l'agriculture, l'alimentation et l' environnement, UMR Interactions Arbres/Microorganismes, Centre INRAE Grand Est-Nancy, 54280, Champenoux, France.

Mycorrhizal fungi are mutualists that play crucial roles in nutrient acquisition in terrestrial ecosystems. Mycorrhizal symbioses arose repeatedly across multiple lineages of Mucoromycotina, Ascomycota, and Basidiomycota. Considerable variation exists in the capacity of mycorrhizal fungi to acquire carbon from soil organic matter. Here, we present a combined analysis of 135 fungal genomes from 73 saprotrophic, endophytic and pathogenic species, and 62 mycorrhizal species, including 29 new mycorrhizal genomes. This study samples ecologically dominant fungal guilds for which there were previously no symbiotic genomes available, including ectomycorrhizal Russulales, Thelephorales and Cantharellales. Our analyses show that transitions from saprotrophy to symbiosis involve (1) widespread losses of degrading enzymes acting on lignin and cellulose, (2) co-option of genes present in saprotrophic ancestors to fulfill new symbiotic functions, (3) diversification of novel, lineage-specific symbiosis-induced genes, (4) proliferation of transposable elements and (5) divergent genetic innovations underlying the convergent origins of the ectomycorrhizal guild.
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http://dx.doi.org/10.1038/s41467-020-18795-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7550596PMC
October 2020

Regional-Scale In-Depth Analysis of Soil Fungal Diversity Reveals Strong pH and Plant Species Effects in Northern Europe.

Front Microbiol 2020 4;11:1953. Epub 2020 Sep 4.

Natural History Museum and Botanical Garden, University of Tartu, Tartu, Estonia.

Soil microbiome has a pivotal role in ecosystem functioning, yet little is known about its build-up from local to regional scales. In a multi-year regional-scale survey involving 1251 plots and long-read third-generation sequencing, we found that soil pH has the strongest effect on the diversity of fungi and its multiple taxonomic and functional groups. The pH effects were typically unimodal, usually both direct and indirect through tree species, soil nutrients or mold abundance. Individual tree species, particularly , , and , and overall ectomycorrhizal plant proportion had relatively stronger effects on the diversity of biotrophic fungi than saprotrophic fungi. We found strong temporal sampling and investigator biases for the abundance of molds, but generally all spatial, temporal and microclimatic effects were weak. Richness of fungi and several functional groups was highest in woodlands and around ruins of buildings but lowest in bogs, with marked group-specific trends. In contrast to our expectations, diversity of soil fungi tended to be higher in forest island habitats potentially due to the edge effect, but fungal richness declined with island distance and in response to forest fragmentation. Virgin forests supported somewhat higher fungal diversity than old non-pristine forests, but there were no differences in richness between natural and anthropogenic habitats such as parks and coppiced gardens. Diversity of most fungal groups suffered from management of seminatural woodlands and parks and thinning of forests, but especially for forests the results depended on fungal group and time since partial harvesting. We conclude that the positive effects of tree diversity on overall fungal richness represent a combined niche effect of soil properties and intimate associations.
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http://dx.doi.org/10.3389/fmicb.2020.01953DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7510051PMC
September 2020

The abundance of arbuscular mycorrhiza in soils is linked to the total length of roots colonized at ecosystem level.

PLoS One 2020 11;15(9):e0237256. Epub 2020 Sep 11.

Environmental Biology Department, Institute of Environmental Sciences, Leiden University, Leiden, Netherlands.

Arbuscular mycorrhizal fungi (AMF) strongly affect ecosystem functioning. To understand and quantify the mechanisms of this control, knowledge about the relationship between the actual abundance and community composition of AMF in the soil and in plant roots is needed. We collected soil and root samples in a natural dune grassland to test whether, across a plant community, the abundance of AMF in host roots (measured as the total length of roots colonized) is related to soil AMF abundance (using the neutral lipid fatty acids (NLFA) 16:1ω5 as proxy). Next-generation sequencing was used to explore the role of community composition in abundance patterns. We found a strong positive relationship between the total length of roots colonized by AMF and the amount of NLFA 16:1ω5 in the soil. We provide the first field-based evidence of proportional biomass allocation between intra-and extraradical AMF mycelium, at ecosystem level. We suggest that this phenomenon is made possible by compensatory colonization strategies of individual fungal species. Finally, our findings open the possibility of using AMF total root colonization as a proxy for soil AMF abundances, aiding further exploration of the AMF impacts on ecosystems functioning.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0237256PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7485760PMC
October 2020

The Relationship between Fungal Diversity and Invasibility of a Foliar Niche-The Case of Ash Dieback.

J Fungi (Basel) 2020 Aug 26;6(3). Epub 2020 Aug 26.

Norwegian Institute of Bioeconomy Research, p.b. 2609, 7734 Steinkjer, Norway.

European ash () is threatened by the invasive ascomycete originating from Asia. Ash leaf tissues serve as a route for shoot infection but also as a sporulation substrate for this pathogen. Knowledge of the leaf niche partitioning by indigenous fungi and is needed to understand the fungal community receptiveness to the invasion. We subjected DNA extracted from unwashed and washed leaflets of healthy and diseased European ash to PacBio sequencing of the fungal rDNA region. Leaflets from co-inhabiting rowan trees () served as a reference. The overlap in leaflet mycobiomes between ash and rowan was remarkably high, but unlike in rowan, in ash leaflets the sequence read proportion, and the qPCR-based DNA amount estimates of increased vigorously towards autumn, concomitant with a significant decline in overall fungal richness. The niche of ash and rowan leaves was dominated by epiphytic propagules ( yeasts, the dimorphic fungus and the dematiaceous hyphomycete and ), and endophytic thalli of biotrophs ( and ), the indigenous necrotroph and . Mycobiome comparison between healthy and symptomatic European ash leaflets revealed no significant differences in relative abundance of , but was more prevalent in symptomatic trees. The impacts of host specificity, spatiotemporal niche partitioning, species carbon utilization profiles and life cycle traits are discussed to understand the ecological success of in Europe. Further, the inherent limitations of different experimental approaches in the profiling of foliicolous fungi are addressed.
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http://dx.doi.org/10.3390/jof6030150DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7558441PMC
August 2020

Orchid epiphytes do not receive organic substances from living trees through fungi.

Mycorrhiza 2020 Nov 15;30(6):697-704. Epub 2020 Aug 15.

Lomonosov Moscow State University, 1-12 Leninskie Gory, 119991, Moscow, Russia.

Numerous studies of terrestrial orchids have demonstrated widespread partial mycoheterotrophy, particularly the possibility of obtaining organic matter from surrounding trees through a common fungal network. Fungi are also widespread in epiphytic orchid roots, but there have been no attempts to determine if epiphytes accept organic matter from the living stems of their phorophytes. We hypothesise that such transfer does not exist because epiphytes and phorophytes harbour different fungal communities. To test this hypothesis, we tagged three short Randia sp. trees with C-enriched CO and examined C transfer from the phorophyte into the epiphytic orchids Grosourdya appendiculata, Dendrobium oligophyllum and Gastrochilus sp. in Cat Tien National Park, (South Vietnam, Cat Tien National Park, plot size approx. 1 ha). The coincidence of fungal sequences in the orchid roots and in the branches on which they grew was also examined. We did not detect C label moving from phorophytes to epiphytes. Using Illumina sequencing, 162 fungal operational taxonomic units (OTUs) were detected. The fungal communities were significantly different between the roots of epiphytes and branches of phorophytes, although no strict fungal specificity at the species level was found in either epiphytes or phorophytes.
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http://dx.doi.org/10.1007/s00572-020-00980-wDOI Listing
November 2020

Advancing biodiversity assessments with environmental DNA: Long-read technologies help reveal the drivers of Amazonian fungal diversity.

Ecol Evol 2020 Jul 23;10(14):7509-7524. Epub 2020 Jun 23.

Gothenburg Global Biodiversity Centre Göteborg Sweden.

Fungi are a key component of tropical biodiversity. However, due to their inconspicuous and largely subterranean nature, they are usually neglected in biodiversity inventories. The goal of this study was to identify the key determinants of fungal richness, community composition, and turnover in tropical rainforests. We tested specifically for the effect of soil properties, habitat, and locality in Amazonia. For these analyses, we used high-throughput sequencing data of short and long reads of fungal DNA present in soil and organic litter samples, combining existing and novel genomic data. Habitat type (phytophysiognomy) emerges as the strongest factor explaining fungal community composition. Naturally open areas-campinas-are the richest habitat overall. Soil properties have different effects depending on the soil layer (litter or mineral soil) and the choice of genetic marker. We suggest that campinas could be a neglected hotspot of fungal diversity. An underlying cause for their rich diversity may be the overall low soil fertility, which increases the reliance on biotic interactions essential for nutrient absorption in these environments, notably ectomycorrhizal fungi-plant associations. Our results highlight the advantages of using both short and long DNA reads produced through high-throughput sequencing to characterize fungal diversity. While short reads can suffice for diversity and community comparison, long reads add taxonomic precision and have the potential to reveal population diversity.
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http://dx.doi.org/10.1002/ece3.6477DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7391351PMC
July 2020

Mycorrhizas transfer carbon in a mature mixed forest.

Mol Ecol 2020 07 17;29(13):2315-2317. Epub 2020 Jul 17.

Department of Mycology and Microbiology, University of Tartu, Tartu, Estonia.

Mycorrhizal fungi transfer nutrients to plants in exchange for photosynthates. Plants allocate up to 20% of their carbon to mycorrhizal structures, mycelium and fruit bodies of their fungal partners. Individuals of mycorrhizal fungi may encompass hundreds of square metres of soil and defragmented litter, linking multiple plant individuals of different species and size (Figure 1). Using a free-air CO enrichment (web-FACE) technique in a mature forest, interspecific transfer accounted for 40% of fine root carbon after 5 years of back and forth transfer between trees. In this issue of Molecular Ecology, Rog, Rosenstock, Körner, and Klein (2020) show that closely related trees shared relatively more mycorrhizal fungi than distantly related trees in the same experimental site, which correlated to increased carbon sharing.
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http://dx.doi.org/10.1111/mec.15520DOI Listing
July 2020

Alien ectomycorrhizal plants differ in their ability to interact with co-introduced and native ectomycorrhizal fungi in novel sites.

ISME J 2020 09 4;14(9):2336-2346. Epub 2020 Jun 4.

Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ-142 20, Prague, Czech Republic.

Alien plants represent a potential threat to environment and society. Understanding the process of alien plants naturalization is therefore of primary importance. In alien plants, successful establishment can be constrained by the absence of suitable fungal partners. Here, we used 42 independent datasets of ectomycorrhizal fungal (EcMF) communities associated with alien Pinaceae and Eucalyptus spp., as the most commonly introduced tree species worldwide, to explore the strategies these plant groups utilize to establish symbioses with EcMF in the areas of introduction. We have also determined the differences in composition of EcMF communities associated with alien ectomycorrhizal plants in different regions. While alien Pinaceae introduced to new regions rely upon association with co-introduced EcMF, alien Eucalyptus often form novel interactions with EcMF species native to the region where the plant was introduced. The region of origin primarily determines species composition of EcMF communities associated with alien Pinaceae in new areas, which may largely affect invasion potential of the alien plants. Our study shows that alien ectomycorrhizal plants largely differ in their ability to interact with co-introduced and native ectomycorrhizal fungi in sites of introduction, which may potentially affect their invasive potential.
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http://dx.doi.org/10.1038/s41396-020-0692-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7608243PMC
September 2020

Plant nutrient-acquisition strategies drive topsoil microbiome structure and function.

New Phytol 2020 08 6;227(4):1189-1199. Epub 2020 May 6.

Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 40 Lai St, 51005, Tartu, Estonia.

Plant nutrient-acquisition strategies drive soil processes and vegetation performance, but their effect on the soil microbiome remains poorly understood. This knowledge is important to predict the shifts in microbial diversity and functions due to increasing changes in vegetation traits under global change. Here we documented the topsoil microbiomes of 145 boreal and temperate terrestrial sites in the Baltic region that broadly differed in vegetation type and nutritional traits, such as mycorrhizal types and symbiotic nitrogen-fixation. We found that sites dominated by arbuscular mycorrhizal (AM) vegetation harbor relatively more AM fungi, bacteria, fungal saprotrophs, and pathogens in the topsoil compared with sites dominated by ectomycorrhizal (EM) plants. These differences in microbiome composition reflect the rapid nutrient cycling and negative plant-soil feedback in AM soils. Lower fungal diversity and bacteria : fungi ratios in EM-dominated habitats are driven by monodominance of woody vegetation as well as soil acidification by EM fungi, which are associated with greater diversity and relative abundance of carbohydrate-active enzymes. Our study suggests that shifts in vegetation related to global change and land use may strongly alter the topsoil microbiome structure and function.
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http://dx.doi.org/10.1111/nph.16598DOI Listing
August 2020

FungalRoot: global online database of plant mycorrhizal associations.

New Phytol 2020 08 20;227(3):955-966. Epub 2020 May 20.

Institute of Ecology and Earth Sciences, University of Tartu, Ülikooli 18, 50090, Tartu, Estonia.

Testing of ecological, biogeographical and phylogenetic hypotheses of mycorrhizal traits requires a comprehensive reference dataset about plant mycorrhizal associations. Here we present a database, FungalRoot, which summarizes publicly available data about vascular plant mycorrhizal type and intensity of root colonization by mycorrhizal fungi, accompanied with rich metadata. We compiled and digitized data about plant mycorrhizal colonization in nine widespread languages. The present version of the FungalRoot database contains 36 303 species-by-site observations for 14 870 plant species, tripling the previously available compiled information about plant mycorrhizal associations. Based on these data, we provide a recommended list of genus-level plant mycorrhizal associations, based on the majority of data for species and careful analysis of conflicting data. The majority of ectomycorrhizal and ericoid mycorrhizal plants are trees (92%) and shrubs (85%), respectively. The majority of arbuscular and nonmycorrhizal plant species are herbaceous (50% and 70%, respectively). Our publicly available database is a powerful resource for mycorrhizal scientists and ecologists. It features possibilities for dynamic updating and addition of data about plant mycorrhizal associations. The new database will promote research on plant and fungal biogeography and evolution, and on links between above- and belowground biodiversity and ecosystem functioning.
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http://dx.doi.org/10.1111/nph.16569DOI Listing
August 2020

Early successional ectomycorrhizal fungi are more likely to naturalize outside their native range than other ectomycorrhizal fungi.

New Phytol 2020 09 18;227(5):1289-1293. Epub 2020 Apr 18.

Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, CZ-142 20, Prague, Czech Republic.

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http://dx.doi.org/10.1111/nph.16557DOI Listing
September 2020

Distinct fungal successional trajectories following wildfire between soil horizons in a cold-temperate forest.

New Phytol 2020 07 14;227(2):572-587. Epub 2020 Apr 14.

State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, East Beijing Road 71, Nanjing, 210008, China.

Soil fungi represent a major component of below-ground biodiversity that determines the succession and recovery of forests after disturbance. However, their successional trajectories and driving mechanisms following wildfire remain unclear. We examined fungal biomass, richness, composition and enzymes across three soil horizons (Oe, A1 and A2) along a near-complete fire chronosequence (1, 2, 8, 14, 30, 49 and c. 260 yr) in cold-temperate forests of the Great Khingan Mountains, China. The importance of soil properties, spatial distance and tree composition were also tested. Ectomycorrhizal fungal richness and β-glucosidase activity were strongly reduced by burning and significantly increased with 'time since fire' in the Oe horizon but not in the mineral horizons. Time since fire and soil C : N ratio were the primary drivers of fungal composition in the Oe and A1/A2 horizons, respectively. Ectomycorrhizal fungal composition was remarkably sensitive to fire history in the Oe horizon, while saprotroph community was strongly affected by time since fire in the deeper soil horizon and this effect emerged 18 years after fire in the A2 horizon. Our study demonstrates pronounced horizon-dependent successional trajectories following wildfire and indicates interactive effects of time since fire, soil stoichiometry and spatial distance in the reassembly of below-ground fungal communities in a cold and fire-prone region.
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http://dx.doi.org/10.1111/nph.16531DOI Listing
July 2020

How mycorrhizal associations drive plant population and community biology.

Science 2020 02;367(6480)

Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia.

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.
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http://dx.doi.org/10.1126/science.aba1223DOI Listing
February 2020

Plant functional groups associate with distinct arbuscular mycorrhizal fungal communities.

New Phytol 2020 05 17;226(4):1117-1128. Epub 2020 Feb 17.

Institute of Ecology and Earth Sciences, University of Tartu, Lai 40, Tartu, 51005, Estonia.

The benefits of the arbuscular mycorrhizal (AM) symbiosis between plants and fungi are modulated by the functional characteristics of both partners. However, it is unknown to what extent functionally distinct groups of plants naturally associate with different AM fungi. We reanalysed 14 high-throughput sequencing data sets describing AM fungal communities associating with plant individuals (2427) belonging to 297 species. We examined how root-associating AM fungal communities varied between plants with different growth forms, photosynthetic pathways, CSR (competitor, stress-tolerator, ruderal) strategies, mycorrhizal statuses and N-fixing statuses. AM fungal community composition differed in relation to all studied plant functional groups. Grasses, C and nonruderal plants were characterised by high AM fungal alpha diversity, while C , ruderal and obligately mycorrhizal plants were characterised by high beta diversity. The phylogenetic diversity of AM fungi, a potential surrogate for functional diversity, was higher among forbs than other plant growth forms. Putatively ruderal (previously cultured) AM fungi were disproportionately associated with forbs and ruderal plants. There was phylogenetic correlation among AM fungi in the degree of association with different plant growth forms and photosynthetic pathways. Associated AM fungal communities constitute an important component of plant ecological strategies. Functionally different plants associate with distinct AM fungal communities, linking mycorrhizal associations with functional diversity in ecosystems.
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http://dx.doi.org/10.1111/nph.16423DOI Listing
May 2020

TRY plant trait database - enhanced coverage and open access.

Authors:
Jens Kattge Gerhard Bönisch Sandra Díaz Sandra Lavorel Iain Colin Prentice Paul Leadley Susanne Tautenhahn Gijsbert D A Werner Tuomas Aakala Mehdi Abedi Alicia T R Acosta George C Adamidis Kairi Adamson Masahiro Aiba Cécile H Albert Julio M Alcántara Carolina Alcázar C Izabela Aleixo Hamada Ali Bernard Amiaud Christian Ammer Mariano M Amoroso Madhur Anand Carolyn Anderson Niels Anten Joseph Antos Deborah Mattos Guimarães Apgaua Tia-Lynn Ashman Degi Harja Asmara Gregory P Asner Michael Aspinwall Owen Atkin Isabelle Aubin Lars Baastrup-Spohr Khadijeh Bahalkeh Michael Bahn Timothy Baker William J Baker Jan P Bakker Dennis Baldocchi Jennifer Baltzer Arindam Banerjee Anne Baranger Jos Barlow Diego R Barneche Zdravko Baruch Denis Bastianelli John Battles William Bauerle Marijn Bauters Erika Bazzato Michael Beckmann Hans Beeckman Carl Beierkuhnlein Renee Bekker Gavin Belfry Michael Belluau Mirela Beloiu Raquel Benavides Lahcen Benomar Mary Lee Berdugo-Lattke Erika Berenguer Rodrigo Bergamin Joana Bergmann Marcos Bergmann Carlucci Logan Berner Markus Bernhardt-Römermann Christof Bigler Anne D Bjorkman Chris Blackman Carolina Blanco Benjamin Blonder Dana Blumenthal Kelly T Bocanegra-González Pascal Boeckx Stephanie Bohlman Katrin Böhning-Gaese Laura Boisvert-Marsh William Bond Ben Bond-Lamberty Arnoud Boom Coline C F Boonman Kauane Bordin Elizabeth H Boughton Vanessa Boukili David M J S Bowman Sandra Bravo Marco Richard Brendel Martin R Broadley Kerry A Brown Helge Bruelheide Federico Brumnich Hans Henrik Bruun David Bruy Serra W Buchanan Solveig Franziska Bucher Nina Buchmann Robert Buitenwerf Daniel E Bunker Jana Bürger Sabina Burrascano David F R P Burslem Bradley J Butterfield Chaeho Byun Marcia Marques Marina C Scalon Marco Caccianiga Marc Cadotte Maxime Cailleret James Camac Jesús Julio Camarero Courtney Campany Giandiego Campetella Juan Antonio Campos Laura Cano-Arboleda Roberto Canullo Michele Carbognani Fabio Carvalho Fernando Casanoves Bastien Castagneyrol Jane A Catford Jeannine Cavender-Bares Bruno E L Cerabolini Marco Cervellini Eduardo Chacón-Madrigal Kenneth Chapin F Stuart Chapin Stefano Chelli Si-Chong Chen Anping Chen Paolo Cherubini Francesco Chianucci Brendan Choat Kyong-Sook Chung Milan Chytrý Daniela Ciccarelli Lluís Coll Courtney G Collins Luisa Conti David Coomes Johannes H C Cornelissen William K Cornwell Piermaria Corona Marie Coyea Joseph Craine Dylan Craven Joris P G M Cromsigt Anikó Csecserits Katarina Cufar Matthias Cuntz Ana Carolina da Silva Kyla M Dahlin Matteo Dainese Igor Dalke Michele Dalle Fratte Anh Tuan Dang-Le Jirí Danihelka Masako Dannoura Samantha Dawson Arend Jacobus de Beer Angel De Frutos Jonathan R De Long Benjamin Dechant Sylvain Delagrange Nicolas Delpierre Géraldine Derroire Arildo S Dias Milton Hugo Diaz-Toribio Panayiotis G Dimitrakopoulos Mark Dobrowolski Daniel Doktor Pavel Dřevojan Ning Dong John Dransfield Stefan Dressler Leandro Duarte Emilie Ducouret Stefan Dullinger Walter Durka Remko Duursma Olga Dymova Anna E-Vojtkó Rolf Lutz Eckstein Hamid Ejtehadi James Elser Thaise Emilio Kristine Engemann Mohammad Bagher Erfanian Alexandra Erfmeier Adriane Esquivel-Muelbert Gerd Esser Marc Estiarte Tomas F Domingues William F Fagan Jaime Fagúndez Daniel S Falster Ying Fan Jingyun Fang Emmanuele Farris Fatih Fazlioglu Yanhao Feng Fernando Fernandez-Mendez Carlotta Ferrara Joice Ferreira Alessandra Fidelis Bryan Finegan Jennifer Firn Timothy J Flowers Dan F B Flynn Veronika Fontana Estelle Forey Cristiane Forgiarini Louis François Marcelo Frangipani Dorothea Frank Cedric Frenette-Dussault Grégoire T Freschet Ellen L Fry Nikolaos M Fyllas Guilherme G Mazzochini Sophie Gachet Rachael Gallagher Gislene Ganade Francesca Ganga Pablo García-Palacios Verónica Gargaglione Eric Garnier Jose Luis Garrido André Luís de Gasper Guillermo Gea-Izquierdo David Gibson Andrew N Gillison Aelton Giroldo Mary-Claire Glasenhardt Sean Gleason Mariana Gliesch Emma Goldberg Bastian Göldel Erika Gonzalez-Akre Jose L Gonzalez-Andujar Andrés González-Melo Ana González-Robles Bente Jessen Graae Elena Granda Sarah Graves Walton A Green Thomas Gregor Nicolas Gross Greg R Guerin Angela Günther Alvaro G Gutiérrez Lillie Haddock Anna Haines Jefferson Hall Alain Hambuckers Wenxuan Han Sandy P Harrison Wesley Hattingh Joseph E Hawes Tianhua He Pengcheng He Jacob Mason Heberling Aveliina Helm Stefan Hempel Jörn Hentschel Bruno Hérault Ana-Maria Hereş Katharina Herz Myriam Heuertz Thomas Hickler Peter Hietz Pedro Higuchi Andrew L Hipp Andrew Hirons Maria Hock James Aaron Hogan Karen Holl Olivier Honnay Daniel Hornstein Enqing Hou Nate Hough-Snee Knut Anders Hovstad Tomoaki Ichie Boris Igić Estela Illa Marney Isaac Masae Ishihara Leonid Ivanov Larissa Ivanova Colleen M Iversen Jordi Izquierdo Robert B Jackson Benjamin Jackson Hervé Jactel Andrzej M Jagodzinski Ute Jandt Steven Jansen Thomas Jenkins Anke Jentsch Jens Rasmus Plantener Jespersen Guo-Feng Jiang Jesper Liengaard Johansen David Johnson Eric J Jokela Carlos Alfredo Joly Gregory J Jordan Grant Stuart Joseph Decky Junaedi Robert R Junker Eric Justes Richard Kabzems Jeffrey Kane Zdenek Kaplan Teja Kattenborn Lyudmila Kavelenova Elizabeth Kearsley Anne Kempel Tanaka Kenzo Andrew Kerkhoff Mohammed I Khalil Nicole L Kinlock Wilm Daniel Kissling Kaoru Kitajima Thomas Kitzberger Rasmus Kjøller Tamir Klein Michael Kleyer Jitka Klimešová Joice Klipel Brian Kloeppel Stefan Klotz Johannes M H Knops Takashi Kohyama Fumito Koike Johannes Kollmann Benjamin Komac Kimberly Komatsu Christian König Nathan J B Kraft Koen Kramer Holger Kreft Ingolf Kühn Dushan Kumarathunge Jonas Kuppler Hiroko Kurokawa Yoko Kurosawa Shem Kuyah Jean-Paul Laclau Benoit Lafleur Erik Lallai Eric Lamb Andrea Lamprecht Daniel J Larkin Daniel Laughlin Yoann Le Bagousse-Pinguet Guerric le Maire Peter C le Roux Elizabeth le Roux Tali Lee Frederic Lens Simon L Lewis Barbara Lhotsky Yuanzhi Li Xine Li Jeremy W Lichstein Mario Liebergesell Jun Ying Lim Yan-Shih Lin Juan Carlos Linares Chunjiang Liu Daijun Liu Udayangani Liu Stuart Livingstone Joan Llusià Madelon Lohbeck Álvaro López-García Gabriela Lopez-Gonzalez Zdeňka Lososová Frédérique Louault Balázs A Lukács Petr Lukeš Yunjian Luo Michele Lussu Siyan Ma Camilla Maciel Rabelo Pereira Michelle Mack Vincent Maire Annikki Mäkelä Harri Mäkinen Ana Claudia Mendes Malhado Azim Mallik Peter Manning Stefano Manzoni Zuleica Marchetti Luca Marchino Vinicius Marcilio-Silva Eric Marcon Michela Marignani Lars Markesteijn Adam Martin Cristina Martínez-Garza Jordi Martínez-Vilalta Tereza Mašková Kelly Mason Norman Mason Tara Joy Massad Jacynthe Masse Itay Mayrose James McCarthy M Luke McCormack Katherine McCulloh Ian R McFadden Brian J McGill Mara Y McPartland Juliana S Medeiros Belinda Medlyn Pierre Meerts Zia Mehrabi Patrick Meir Felipe P L Melo Maurizio Mencuccini Céline Meredieu Julie Messier Ilona Mészáros Juha Metsaranta Sean T Michaletz Chrysanthi Michelaki Svetlana Migalina Ruben Milla Jesse E D Miller Vanessa Minden Ray Ming Karel Mokany Angela T Moles Attila Molnár Jane Molofsky Martin Molz Rebecca A Montgomery Arnaud Monty Lenka Moravcová Alvaro Moreno-Martínez Marco Moretti Akira S Mori Shigeta Mori Dave Morris Jane Morrison Ladislav Mucina Sandra Mueller Christopher D Muir Sandra Cristina Müller François Munoz Isla H Myers-Smith Randall W Myster Masahiro Nagano Shawna Naidu Ayyappan Narayanan Balachandran Natesan Luka Negoita Andrew S Nelson Eike Lena Neuschulz Jian Ni Georg Niedrist Jhon Nieto Ülo Niinemets Rachael Nolan Henning Nottebrock Yann Nouvellon Alexander Novakovskiy Kristin Odden Nystuen Anthony O'Grady Kevin O'Hara Andrew O'Reilly-Nugent Simon Oakley Walter Oberhuber Toshiyuki Ohtsuka Ricardo Oliveira Kinga Öllerer Mark E Olson Vladimir Onipchenko Yusuke Onoda Renske E Onstein Jenny C Ordonez Noriyuki Osada Ivika Ostonen Gianluigi Ottaviani Sarah Otto Gerhard E Overbeck Wim A Ozinga Anna T Pahl C E Timothy Paine Robin J Pakeman Aristotelis C Papageorgiou Evgeniya Parfionova Meelis Pärtel Marco Patacca Susana Paula Juraj Paule Harald Pauli Juli G Pausas Begoña Peco Josep Penuelas Antonio Perea Pablo Luis Peri Ana Carolina Petisco-Souza Alessandro Petraglia Any Mary Petritan Oliver L Phillips Simon Pierce Valério D Pillar Jan Pisek Alexandr Pomogaybin Hendrik Poorter Angelika Portsmuth Peter Poschlod Catherine Potvin Devon Pounds A Shafer Powell Sally A Power Andreas Prinzing Giacomo Puglielli Petr Pyšek Valerie Raevel Anja Rammig Johannes Ransijn Courtenay A Ray Peter B Reich Markus Reichstein Douglas E B Reid Maxime Réjou-Méchain Victor Resco de Dios Sabina Ribeiro Sarah Richardson Kersti Riibak Matthias C Rillig Fiamma Riviera Elisabeth M R Robert Scott Roberts Bjorn Robroek Adam Roddy Arthur Vinicius Rodrigues Alistair Rogers Emily Rollinson Victor Rolo Christine Römermann Dina Ronzhina Christiane Roscher Julieta A Rosell Milena Fermina Rosenfield Christian Rossi David B Roy Samuel Royer-Tardif Nadja Rüger Ricardo Ruiz-Peinado Sabine B Rumpf Graciela M Rusch Masahiro Ryo Lawren Sack Angela Saldaña Beatriz Salgado-Negret Roberto Salguero-Gomez Ignacio Santa-Regina Ana Carolina Santacruz-García Joaquim Santos Jordi Sardans Brandon Schamp Michael Scherer-Lorenzen Matthias Schleuning Bernhard Schmid Marco Schmidt Sylvain Schmitt Julio V Schneider Simon D Schowanek Julian Schrader Franziska Schrodt Bernhard Schuldt Frank Schurr Galia Selaya Garvizu Marina Semchenko Colleen Seymour Julia C Sfair Joanne M Sharpe Christine S Sheppard Serge Sheremetiev Satomi Shiodera Bill Shipley Tanvir Ahmed Shovon Alrun Siebenkäs Carlos Sierra Vasco Silva Mateus Silva Tommaso Sitzia Henrik Sjöman Martijn Slot Nicholas G Smith Darwin Sodhi Pamela Soltis Douglas Soltis Ben Somers Grégory Sonnier Mia Vedel Sørensen Enio Egon Sosinski Nadejda A Soudzilovskaia Alexandre F Souza Marko Spasojevic Marta Gaia Sperandii Amanda B Stan James Stegen Klaus Steinbauer Jörg G Stephan Frank Sterck Dejan B Stojanovic Tanya Strydom Maria Laura Suarez Jens-Christian Svenning Ivana Svitková Marek Svitok Miroslav Svoboda Emily Swaine Nathan Swenson Marcelo Tabarelli Kentaro Takagi Ulrike Tappeiner Rubén Tarifa Simon Tauugourdeau Cagatay Tavsanoglu Mariska Te Beest Leho Tedersoo Nelson Thiffault Dominik Thom Evert Thomas Ken Thompson Peter E Thornton Wilfried Thuiller Lubomír Tichý David Tissue Mark G Tjoelker David Yue Phin Tng Joseph Tobias Péter Török Tonantzin Tarin José M Torres-Ruiz Béla Tóthmérész Martina Treurnicht Valeria Trivellone Franck Trolliet Volodymyr Trotsiuk James L Tsakalos Ioannis Tsiripidis Niklas Tysklind Toru Umehara Vladimir Usoltsev Matthew Vadeboncoeur Jamil Vaezi Fernando Valladares Jana Vamosi Peter M van Bodegom Michiel van Breugel Elisa Van Cleemput Martine van de Weg Stephni van der Merwe Fons van der Plas Masha T van der Sande Mark van Kleunen Koenraad Van Meerbeek Mark Vanderwel Kim André Vanselow Angelica Vårhammar Laura Varone Maribel Yesenia Vasquez Valderrama Kiril Vassilev Mark Vellend Erik J Veneklaas Hans Verbeeck Kris Verheyen Alexander Vibrans Ima Vieira Jaime Villacís Cyrille Violle Pandi Vivek Katrin Wagner Matthew Waldram Anthony Waldron Anthony P Walker Martyn Waller Gabriel Walther Han Wang Feng Wang Weiqi Wang Harry Watkins James Watkins Ulrich Weber James T Weedon Liping Wei Patrick Weigelt Evan Weiher Aidan W Wells Camilla Wellstein Elizabeth Wenk Mark Westoby Alana Westwood Philip John White Mark Whitten Mathew Williams Daniel E Winkler Klaus Winter Chevonne Womack Ian J Wright S Joseph Wright Justin Wright Bruno X Pinho Fabiano Ximenes Toshihiro Yamada Keiko Yamaji Ruth Yanai Nikolay Yankov Benjamin Yguel Kátia Janaina Zanini Amy E Zanne David Zelený Yun-Peng Zhao Jingming Zheng Ji Zheng Kasia Ziemińska Chad R Zirbel Georg Zizka Irié Casimir Zo-Bi Gerhard Zotz Christian Wirth

Glob Chang Biol 2020 01 31;26(1):119-188. Epub 2019 Dec 31.

Max Planck Institute for Biogeochemistry, Jena, Germany.

Plant traits-the morphological, anatomical, physiological, biochemical and phenological characteristics of plants-determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait-based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits-almost complete coverage for 'plant growth form'. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait-environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives.
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http://dx.doi.org/10.1111/gcb.14904DOI Listing
January 2020

Global mycorrhizal plant distribution linked to terrestrial carbon stocks.

Nat Commun 2019 11 7;10(1):5077. Epub 2019 Nov 7.

Natural History Museum and Institute of Ecology and Earth Sciences, University of Tartu, 14a Ravila, 50411, Tartu, Estonia.

Vegetation impacts on ecosystem functioning are mediated by mycorrhizas, plant-fungal associations formed by most plant species. Ecosystems dominated by distinct mycorrhizal types differ strongly in their biogeochemistry. Quantitative analyses of mycorrhizal impacts on ecosystem functioning are hindered by the scarcity of information on mycorrhizal distributions. Here we present global, high-resolution maps of vegetation biomass distribution by dominant mycorrhizal associations. Arbuscular, ectomycorrhizal, and ericoid mycorrhizal vegetation store, respectively, 241 ± 15, 100 ± 17, and 7 ± 1.8 GT carbon in aboveground biomass, whereas non-mycorrhizal vegetation stores 29 ± 5.5 GT carbon. Soil carbon stocks in both topsoil and subsoil are positively related to the community-level biomass fraction of ectomycorrhizal plants, though the strength of this relationship varies across biomes. We show that human-induced transformations of Earth's ecosystems have reduced ectomycorrhizal vegetation, with potential ramifications to terrestrial carbon stocks. Our work provides a benchmark for spatially explicit and globally quantitative assessments of mycorrhizal impacts on ecosystem functioning and biogeochemical cycling.
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http://dx.doi.org/10.1038/s41467-019-13019-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6838125PMC
November 2019

Relative Performance of MinION (Oxford Nanopore Technologies) versus Sequel (Pacific Biosciences) Third-Generation Sequencing Instruments in Identification of Agricultural and Forest Fungal Pathogens.

Appl Environ Microbiol 2019 11 16;85(21). Epub 2019 Oct 16.

Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia

Culture-based molecular identification methods have revolutionized detection of pathogens, yet these methods are slow and may yield inconclusive results from environmental materials. The second-generation sequencing tools have much-improved precision and sensitivity of detection, but these analyses are costly and may take several days to months. Of the third-generation sequencing techniques, the portable MinION device (Oxford Nanopore Technologies) has received much attention because of its small size and possibility of rapid analysis at reasonable cost. Here, we compare the relative performances of two third-generation sequencing instruments, MinION and Sequel (Pacific Biosciences), in identification and diagnostics of fungal and oomycete pathogens from conifer (Pinaceae) needles and potato () leaves and tubers. We demonstrate that the Sequel instrument is efficient for metabarcoding of complex samples, whereas MinION is not suited for this purpose due to a high error rate and multiple biases. However, we find that MinION can be utilized for rapid and accurate identification of dominant pathogenic organisms and other associated organisms from plant tissues following both amplicon-based and PCR-free metagenomics approaches. Using the metagenomics approach with shortened DNA extraction and incubation times, we performed the entire MinION workflow, from sample preparation through DNA extraction, sequencing, bioinformatics, and interpretation, in 2.5 h. We advocate the use of MinION for rapid diagnostics of pathogens and potentially other organisms, but care needs to be taken to control or account for multiple potential technical biases. Microbial pathogens cause enormous losses to agriculture and forestry, but current combined culturing- and molecular identification-based detection methods are too slow for rapid identification and application of countermeasures. Here, we develop new and rapid protocols for Oxford Nanopore MinION-based third-generation diagnostics of plant pathogens that greatly improve the speed of diagnostics. However, due to high error rate and technical biases in MinION, the Pacific BioSciences Sequel platform is more useful for in-depth amplicon-based biodiversity monitoring (metabarcoding) from complex environmental samples.
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http://dx.doi.org/10.1128/AEM.01368-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6803294PMC
November 2019

Mycorrhizal types differ in ecophysiology and alter plant nutrition and soil processes.

Biol Rev Camb Philos Soc 2019 10 3;94(5):1857-1880. Epub 2019 Jul 3.

Institute of Ecology and Earth Sciences, University of Tartu, 14a Ravila, 50411 Tartu, Estonia.

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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http://dx.doi.org/10.1111/brv.12538DOI Listing
October 2019

Towards PacBio-based pan-eukaryote metabarcoding using full-length ITS sequences.

Environ Microbiol Rep 2019 10 4;11(5):659-668. Epub 2019 Jul 4.

Zoological Institute, Technische Universität Braunschweig, Mendelssohnstrasse 4, 38106, Braunschweig, Germany.

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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http://dx.doi.org/10.1111/1758-2229.12776DOI Listing
October 2019

Misallocation of mycorrhizal traits leads to misleading results.

Proc Natl Acad Sci U S A 2019 06 6;116(25):12139-12140. Epub 2019 Jun 6.

School of Biological Sciences, University of Western Australia, Crawley, WA 6009, Australia.

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http://dx.doi.org/10.1073/pnas.1903178116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6589762PMC
June 2019

Global mismatches in aboveground and belowground biodiversity.

Conserv Biol 2019 10 26;33(5):1187-1192. Epub 2019 Apr 26.

German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103, Leipzig, Germany.

Human activities are accelerating global biodiversity change and have resulted in severely threatened ecosystem services. A large proportion of terrestrial biodiversity is harbored by soil, but soil biodiversity has been omitted from many global biodiversity assessments and conservation actions, and understanding of global patterns of soil biodiversity remains limited. In particular, the extent to which hotspots and coldspots of aboveground and soil biodiversity overlap is not clear. We examined global patterns of these overlaps by mapping indices of aboveground (mammals, birds, amphibians, vascular plants) and soil (bacteria, fungi, macrofauna) biodiversity that we created using previously published data on species richness. Areas of mismatch between aboveground and soil biodiversity covered 27% of Earth's terrestrial surface. The temperate broadleaf and mixed forests biome had the highest proportion of grid cells with high aboveground biodiversity but low soil biodiversity, whereas the boreal and tundra biomes had intermediate soil biodiversity but low aboveground biodiversity. While more data on soil biodiversity are needed, both to cover geographic gaps and to include additional taxa, our results suggest that protecting aboveground biodiversity may not sufficiently reduce threats to soil biodiversity. Given the functional importance of soil biodiversity and the role of soils in human well-being, soil biodiversity should be considered further in policy agendas and conservation actions by adapting management practices to sustain soil biodiversity and considering soil biodiversity when designing protected areas.
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http://dx.doi.org/10.1111/cobi.13311DOI Listing
October 2019

Mycobiome diversity: high-throughput sequencing and identification of fungi.

Nat Rev Microbiol 2019 01;17(2):95-109

Natural History Museum of Tartu University, Tartu, Estonia.

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.
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http://dx.doi.org/10.1038/s41579-018-0116-yDOI Listing
January 2019

Corrigendum for: "Oomycete-specific ITS primers for identification and metabarcoding" published in MycoKeys, doi: 10.3897/mycokeys.14.9244.

MycoKeys 2018 5(41):119-120. Epub 2018 Nov 5.

Institute of Ecology and Earth Sciences, University of Tartu, Ravila 14a, 50411 Tartu, Estonia.

[This corrects the article DOI: 10.3897/mycokeys.14.9244.].
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http://dx.doi.org/10.3897/mycokeys.41.30558DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6232247PMC
November 2018