Publications by authors named "József Geml"

43 Publications

Tundra Type Drives Distinct Trajectories of Functional and Taxonomic Composition of Arctic Fungal Communities in Response to Climate Change - Results From Long-Term Experimental Summer Warming and Increased Snow Depth.

Front Microbiol 2021 12;12:628746. Epub 2021 Mar 12.

Naturalis Biodiversity Center, Leiden, Netherlands.

The arctic tundra is undergoing climate-driven changes and there are serious concerns related to the future of arctic biodiversity and altered ecological processes under possible climate change scenarios. Arctic land surface temperatures and precipitation are predicted to increase further, likely causing major transformation in terrestrial ecosystems. As a response to increasing temperatures, shifts in vegetation and soil fungal communities have already been observed. Little is known, however, how long-term experimental warming coupled with increased snow depth influence the trajectories of soil fungal communities in different tundra types. We compared edaphic variables and fungal community composition in experimental plots simulating the expected increase in summer warming and winter snow depth, based on DNA metabarcoding data. Fungal communities in the sampled dry and moist acidic tundra communities differed greatly, with tundra type explaining ca. one-third of compositional variation. Furthermore, dry and moist tundra appear to have different trajectories in response to climate change. Specifically, while both warming and increased snow depth had significant effects on fungal community composition and edaphic variables in dry tundra, the effect of increased snow was greater. However, in moist tundra, fungal communities mainly were affected by summer warming, while increased snow depth had a smaller effect and only on some functional groups. In dry tundra, microorganisms generally are limited by moisture in the summer and extremely low temperatures in winter, which is in agreement with the stronger effect of increased snow depth relative to warming. On the contrary, moist tundra soils generally are saturated with water, remain cold year-round and show relatively small seasonal fluctuations in temperature. The greater observed effect of warming on fungi in moist tundra may be explained by the narrower temperature optimum compared to those in dry tundra.
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http://dx.doi.org/10.3389/fmicb.2021.628746DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7994276PMC
March 2021

Climate and seasonality drive the richness and composition of tropical fungal endophytes at a landscape scale.

Commun Biol 2021 Mar 9;4(1):313. Epub 2021 Mar 9.

School of Plant Sciences, University of Arizona, Tucson, AZ, USA.

Understanding how species-rich communities persist is a foundational question in ecology. In tropical forests, tree diversity is structured by edaphic factors, climate, and biotic interactions, with seasonality playing an essential role at landscape scales: wetter and less seasonal forests typically harbor higher tree diversity than more seasonal forests. We posited that the abiotic factors shaping tree diversity extend to hyperdiverse symbionts in leaves-fungal endophytes-that influence plant health, function, and resilience to stress. Through surveys in forests across Panama that considered climate, seasonality, and covarying biotic factors, we demonstrate that endophyte richness varies negatively with temperature seasonality. Endophyte community structure and taxonomic composition reflect both temperature seasonality and climate (mean annual temperature and precipitation). Overall our findings highlight the vital role of climate-related factors in shaping the hyperdiversity of these important and little-known symbionts of the trees that, in turn, form the foundations of tropical forest biodiversity.
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http://dx.doi.org/10.1038/s42003-021-01826-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7943826PMC
March 2021

Physico-Chemical Characteristics and Culturable Microbial Communities of Grape Berries Change Strongly during Noble Rot Development.

Plants (Basel) 2020 Dec 21;9(12). Epub 2020 Dec 21.

Food and Wine Research Institute, Eszterházy Károly University, 6 Leányka Street, H-3300 Eger, Hungary.

is a well-known pathogen of grapevine. However, under certain microclimatic conditions, infection results in noble rot, an essential process in the production of the world-known Tokaji wines in Hungary. We investigated the physico-chemical characteristics and culturable microorganisms associated with grape berries through several noble rot phases in the two main cultivars grown in Tokaj: cv. "" and "". We measured physical and analytical parameters routinely tested in viticulture and analyzed the ITS rDNA sequence data of fungi isolated from the sampled berries. We observed significant differences in the physico-chemical parameters among the noble rot phases as well as sampling dates. The greatest variation in berry texture and microbial structure was observed in the initial phases, with variables converging as the noble rot progressed. By finding a bijection between the examined chemical properties and the factorial parameters (e.g., noble rot phase, collection time, cultivar), an appropriate sweet winemaking material can be designed. Fungal community differed significantly among cultivars, with higher number of species observed in . Our results reveal that there is more to noble rot than only and other microorganisms may play important roles in the process.
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http://dx.doi.org/10.3390/plants9121809DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7766896PMC
December 2020

Expansion of shrubs could result in local loss of soil bacterial richness in Western Greenland.

FEMS Microbiol Ecol 2020 08;96(8)

Biodiversity Dynamics Research Group, Naturalis Biodiversity Center, Leiden, The Netherlands.

Climate warming in Greenland is facilitating the expansion of shrubs across wide areas of tundra. Given the close association between plants and soil microorganisms and the important role of soil bacteria in ecosystem functioning, it is of utmost importance to characterize microbial communities of arctic soil habitats and assess the influence of plant edaphic factors on their composition. We used 16S rRNA gene amplicons to explore the bacterial assemblages of three different soil habitats representative of a plant coverage gradient: bare ground, biological soil crusts dominated by mosses and lichens and vascular vegetation dominated by shrubs. We investigated how bacterial richness and community composition were affected by the vegetation coverage, and soil pH, moisture and carbon (C), nitrogen (N) and phosphorus (P) contents. Bacterial richness did not correlate with plant coverage complexity, while community structure varied between habitats. Edaphic variables affected both the taxonomic richness and community composition. The high number of Amplicon Sequence Variants (ASVs) indicators of bare ground plots suggests a risk of local bacterial diversity loss due to expansion of vascular vegetation.
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http://dx.doi.org/10.1093/femsec/fiaa089DOI Listing
August 2020

Vegetation, pH and Water Content as Main Factors for Shaping Fungal Richness, Community Composition and Functional Guilds Distribution in Soils of Western Greenland.

Front Microbiol 2019 11;10:2348. Epub 2019 Oct 11.

Biodiversity Dynamics, Naturalis Biodiversity Center, Leiden, Netherlands.

Fungi are the most abundant and one of the most diverse components of arctic soil ecosystems, where they are fundamental drivers of plant nutrient acquisition and recycling. Nevertheless, few studies have focused on the factors driving the diversity and functionality of fungal communities associated with these ecosystems, especially in the scope of global warming that is particularly affecting Greenland and is leading to shrub expansion, with expected profound changes of soil microbial communities. We used soil DNA metabarcoding to compare taxonomic and functional composition of fungal communities in three habitats [bare ground (BG), biological soil crusts (BSC), and vascular vegetation (VV) coverage] in Western Greenland. Fungal richness increased with the increasing complexity of the coverage, but BGs and BSCs samples showed the highest number of unique OTUs. Differences in both fungal community composition and distribution of functional guilds identified were correlated with edaphic factors (mainly pH and water content), in turn connected with the different type of coverage. These results suggest also possible losses of diversity connected to the expansion of VV and possible interactions among the members of different functional guilds, likely due to the nutrient limitation, with potential effects on elements recycling.
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http://dx.doi.org/10.3389/fmicb.2019.02348DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6797927PMC
October 2019

Vegetation on mesic loamy and sandy soils along a 1700-km maritime Eurasia Arctic Transect.

Appl Veg Sci 2019 Jan 27;22(1):150-167. Epub 2019 Feb 27.

Alaska Geobotany Center Institute of Arctic Biology & Department of Biology and Wildlife University of Alaska Fairbanks Alaska.

Questions: How do plant communities on zonal loamy vs. sandy soils vary across the full maritime Arctic bioclimate gradient? How are plant communities of these areas related to existing vegetation units of the European Vegetation Classification? What are the main environmental factors controlling transitions of vegetation along the bioclimate gradient?

Location: 1700-km Eurasia Arctic Transect (EAT), Yamal Peninsula and Franz Josef Land (FJL), Russia.

Methods: The Braun-Blanquet approach was used to sample mesic loamy and sandy plots on 14 total study sites at six locations, one in each of the five Arctic bioclimate subzones and the forest-tundra transition. Trends in soil factors, cover of plant growth forms (PGFs) and species diversity were examined along the summer warmth index (SWI) gradient and on loamy and sandy soils. Classification and ordination were used to group the plots and to test relationships between vegetation and environmental factors.

Results: Clear, mostly non-linear, trends occurred for soil factors, vegetation structure and species diversity along the climate gradient. Cluster analysis revealed seven groups with clear relationships to subzone and soil texture. Clusters at the ends of the bioclimate gradient (forest-tundra and polar desert) had many highly diagnostic taxa, whereas clusters from the Yamal Peninsula had only a few. Axis 1 of a DCA was strongly correlated with latitude and summer warmth; Axis 2 was strongly correlated with soil moisture, percentage sand and landscape age.

Conclusions: Summer temperature and soil texture have clear effects on tundra canopy structure and species composition, with consequences for ecosystem properties. Each layer of the plant canopy has a distinct region of peak abundance along the bioclimate gradient. The major vegetation types are weakly aligned with described classes of the European Vegetation Checklist, indicating a continuous floristic gradient rather than distinct subzone regions. The study provides ground-based vegetation data for satellite-based interpretations of the western maritime Eurasian Arctic, and the first vegetation data from Hayes Island, Franz Josef Land, which is strongly separated geographically and floristically from the rest of the gradient and most susceptible to on-going climate change.
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http://dx.doi.org/10.1111/avsc.12401DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6519894PMC
January 2019

Soil lead pollution modifies the structure of arbuscular mycorrhizal fungal communities.

Mycorrhiza 2019 Jul 23;29(4):363-373. Epub 2019 Apr 23.

Instituto Multidisciplinario de Biología Vegetal (IMBIV)-CONICET, Facultad de Ciencias Exactas, Físicas y Naturales, Universidad Nacional de Córdoba, Av. Vélez Sársfield, 1611, Córdoba, Argentina.

The impact of lead (Pb) pollution on native communities of arbuscular mycorrhizal fungi (AMF) was assessed in soil samples from the surroundings of an abandoned Pb smelting factory. To consider the influence of host identity, bulk soil surrounding plant roots soil samples of predominant plant species (Sorghum halepense, Bidens pilosa, and Tagetes minuta) growing in Pb-polluted soils and in an uncontaminated site were selected. Molecular diversity was assessed by sequencing the 18S rDNA region with primers specific to AMF (AMV4.5NF/AMDGR) using Illumina MiSeq. A total of 115 virtual taxa (VT) of AMF were identified in this survey. Plant species did not affect AMF diversity patterns. However, soil Pb content was negatively correlated with VT richness per sample. Paraglomeraceae and Glomeraceae were the predominant families while Acaulosporaceae, Ambisporaceae, Archaeosporaceae, Claroideoglomeraceae, Diversisporaceae, and Gigasporaceae were less abundant. Acaulosporaceae and Glomeraceae were negatively affected by soil Pb, but Paraglomeraceae relative abundance increased under increasing soil Pb content. Overall, 26 indicator taxa were identified; four of them were previously reported in Pb-polluted soils (VT060; VT222; VT004; VT380); and five corresponded to cultured spores of Scutellospora castaneae (VT041), Diversispora spp. and Tricispora nevadensis (VT060), Diversispora epigaea (VT061), Glomus proliferum (VT099), and Gl. indicum (VT222). Even though AMF were present in Pb-polluted soils, community structure was strongly altered via the differential responses of taxonomic groups of AMF to Pb pollution. These taxon-specific differences in tolerance to soil Pb content should be considered for future phytoremediation strategies based on the selection and utilization of native Glomeromycota.
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http://dx.doi.org/10.1007/s00572-019-00895-1DOI Listing
July 2019

Effect of forest fire prevention treatments on bacterial communities associated with productive Boletus edulis sites.

Microb Biotechnol 2019 11 15;12(6):1188-1198. Epub 2019 Apr 15.

Fire and Applied Mycology Laboratory, Departments of Agroforestry Sciences and Vegetal Production and Natural Resources, Sustainable Forest Management Research Institute, University of Valladolid (Palencia), Avda. Madrid 44, 34071, Palencia, Spain.

Cistus ladanifer scrublands, traditionally considered as unproductive, have nonetheless been observed to produce large quantities of king bolete (Boletus edulis) fruitbodies. These pyrophytic scrublands are prone to wildfires, which severely affect fungi, hence the need for fire prevention in producing C. ladanifer scrublands. In addition, B. edulis productions have severely decreased in the last years. A deeper understanding of the B. edulis life cycle and of biotic and abiotic factors influencing sporocarp formation is needed to implement management practices that facilitate B. edulis production. For example, some bacteria likely are involved in sporocarp production, representing a key part in the triple symbiosis (plant-fungus-bacteria). In this study, we used soil DNA metabarcoding in C. ladanifer scrublands to (i) assess the effect of site history and fire prevention treatment on bacterial richness and community composition; (ii) test if there was any correlation between various taxonomic groups of bacteria and mycelial biomass and sporocarp production of B. edulis; and to (iii) identify indicator bacteria associated with the most productive B. edulis sites. Our results show that site history drives bacterial richness and community composition, while fire prevention treatments have a weaker, but still detectable effect, particularly in the senescent plots. Sporocarp production correlated positively with genera in Verrucomicrobia. Several genera, e.g. Azospirillum and Gemmatimonas, were identified as indicators of the most productive sites, suggesting a potential biological role in B. edulis fructification. This study provides a better understanding of the triple symbiosis (plant-fungus-bacteria) involved in C. ladanifer-B. edulis systems.
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http://dx.doi.org/10.1111/1751-7915.13395DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6801156PMC
November 2019

Megaphylogeny resolves global patterns of mushroom evolution.

Nat Ecol Evol 2019 04 18;3(4):668-678. Epub 2019 Mar 18.

Synthetic and Systems Biology Unit, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary.

Mushroom-forming fungi (Agaricomycetes) have the greatest morphological diversity and complexity of any group of fungi. They have radiated into most niches and fulfil diverse roles in the ecosystem, including wood decomposers, pathogens or mycorrhizal mutualists. Despite the importance of mushroom-forming fungi, large-scale patterns of their evolutionary history are poorly known, in part due to the lack of a comprehensive and dated molecular phylogeny. Here, using multigene and genome-based data, we assemble a 5,284-species phylogenetic tree and infer ages and broad patterns of speciation/extinction and morphological innovation in mushroom-forming fungi. Agaricomycetes started a rapid class-wide radiation in the Jurassic, coinciding with the spread of (sub)tropical coniferous forests and a warming climate. A possible mass extinction, several clade-specific adaptive radiations and morphological diversification of fruiting bodies followed during the Cretaceous and the Paleogene, convergently giving rise to the classic toadstool morphology, with a cap, stalk and gills (pileate-stipitate morphology). This morphology is associated with increased rates of lineage diversification, suggesting it represents a key innovation in the evolution of mushroom-forming fungi. The increase in mushroom diversity started during the Mesozoic-Cenozoic radiation event, an era of humid climate when terrestrial communities dominated by gymnosperms and reptiles were also expanding.
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http://dx.doi.org/10.1038/s41559-019-0834-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6443077PMC
April 2019

Encroachment of shrubs into subalpine grasslands in the Pyrenees modifies the structure of soil fungal communities and soil properties.

FEMS Microbiol Ecol 2019 04;95(4)

CSIC, Global Ecology Unit, CREAF-CSIC-UAB, 08193, Cerdanyola del Vallès, Catalonia, Spain.

The encroachment of shrubs into grasslands is common in terrestrial ecosystems dominated by grass. Land abandonment and favourable climatic trends in recent decades have favoured the expansion of shrubs into subalpine grasslands in many mountainous regions across Europe. The advance of the succession from grassland to shrubland is expected to have a major impact on ecosystem functioning. We used DNA metabarcoding to assess whether the structure of soil fungal communities varied along the succession from subalpine grassland to shrubland in the Pyrenees, and investigated whether shrub encroachment was associated with changes in soil properties. The expansion of shrubs increased the soil C:N ratio and/or reduced the N, P or K contents. Plant-driven changes in soil properties were strongly associated with the compositional turnover of fungi, including arbuscular mycorrhizal, ectomycorrhizal, ericoid, root endophytic, saprotrophic, lichenised and pathogenic fungi. Total richness and the richness of most functional groups were correlated with soil P, N and the C:N or N:P ratios. We show that the interplay between abiotic factors (changes in soil properties) and biotic factors (occurrence and identity of shrubs) played a key role in the structure and uniqueness of soil fungal communities along the succession.
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http://dx.doi.org/10.1093/femsec/fiz028DOI Listing
April 2019

Can arbuscular mycorrhizal fungi from non-invaded montane ecosystems facilitate the growth of alien trees?

Mycorrhiza 2019 Jan 15;29(1):39-49. Epub 2018 Nov 15.

Instituto Multidisciplinario de Biología Vegetal (CONICET), Universidad Nacional de Córdoba, Casilla de Correo 495, X5000, Córdoba, Argentina.

It is generally assumed that recruitment and expansion of alien species along elevation gradients are constrained by climate. But, if plants are not fully constrained by climate, their expansion could be facilitated or hindered by other factors such as biotic interactions. Here, we assessed the composition of arbuscular mycorrhizal fungi (AMF) in soils along an elevation gradient (i.e. 900 m, 1600 m, 2200 m and 2700 m a.s.l.) through a fungal DNA meta-barcoding approach. In addition, we studied in the greenhouse the effects of AMF on growth and phosphorous (P) nutrition of seedlings of the alien trees Gleditsia triacanthos, Ligustrum lucidum and Pyracantha angustifolia cultivated in soils from those elevations, spanning the elevation at which they already form monospecific stands (below 1450 m a.s.l.) and higher elevations, above their current range of distribution in montane ecosystems of Central Argentina. For comparison, we also included in the experiment the dominant native tree Lithraea molleoides that historically occurs below 1300 m a.s.l. Arbuscular mycorrhizal fungal community composition showed strong community turnover with increasing elevation. The effects of these AMF communities on plant growth and nutrition differed among native and alien trees. While P nutrition in alien species' seedlings was generally enhanced by AMF along the whole gradient, the native species benefited only from AMF that occur in soils from the elevation corresponding to its current altitudinal range of distribution. These results suggest that AMF might foster upper range expansion of these invasive trees over non-invaded higher elevations.
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http://dx.doi.org/10.1007/s00572-018-0874-4DOI Listing
January 2019

Considerations and consequences of allowing DNA sequence data as types of fungal taxa.

Authors:
Juan Carlos Zamora Måns Svensson Roland Kirschner Ibai Olariaga Svengunnar Ryman Luis Alberto Parra József Geml Anna Rosling Slavomír Adamčík Teuvo Ahti M Catherine Aime A Martyn Ainsworth László Albert Edgardo Albertó Alberto Altés García Dmitry Ageev Reinhard Agerer Begoña Aguirre-Hudson Joe Ammirati Harry Andersson Claudio Angelini Vladimír Antonín Takayuki Aoki André Aptroot Didier Argaud Blanca Imelda Arguello Sosa Arne Aronsen Ulf Arup Bita Asgari Boris Assyov Violeta Atienza Ditte Bandini João Luís Baptista-Ferreira Hans-Otto Baral Tim Baroni Robert Weingart Barreto Henry Beker Ann Bell Jean-Michel Bellanger Francesco Bellù Martin Bemmann Mika Bendiksby Egil Bendiksen Katriina Bendiksen Lajos Benedek Anna Bérešová-Guttová Franz Berger Reinhard Berndt Annarosa Bernicchia Alona Yu Biketova Enrico Bizio Curtis Bjork Teun Boekhout David Boertmann Tanja Böhning Florent Boittin Carlos G Boluda Menno W Boomsluiter Jan Borovička Tor Erik Brandrud Uwe Braun Irwin Brodo Tatiana Bulyonkova Harold H Burdsall Bart Buyck Ana Rosa Burgaz Vicent Calatayud Philippe Callac Emanuele Campo Massimo Candusso Brigitte Capoen Joaquim Carbó Matteo Carbone Rafael F Castañeda-Ruiz Michael A Castellano Jie Chen Philippe Clerc Giovanni Consiglio Gilles Corriol Régis Courtecuisse Ana Crespo Cathy Cripps Pedro W Crous Gladstone Alves da Silva Meiriele da Silva Marjo Dam Nico Dam Frank Dämmrich Kanad Das Linda Davies Eske De Crop Andre De Kesel Ruben De Lange Bárbara De Madrignac Bonzi Thomas Edison E Dela Cruz Lynn Delgat Vincent Demoulin Dennis E Desjardin Paul Diederich Bálint Dima Maria Martha Dios Pradeep Kumar Divakar Clovis Douanla-Meli Brian Douglas Elisandro Ricardo Drechsler-Santos Paul S Dyer Ursula Eberhardt Damien Ertz Fernando Esteve-Raventós Javier Angel Etayo Salazar Vera Evenson Guillaume Eyssartier Edit Farkas Alain Favre Anna G Fedosova Mario Filippa Péter Finy Adam Flakus Simón Fos Jacques Fournier André Fraiture Paolo Franchi Ana Esperanza Franco Molano Gernot Friebes Andreas Frisch Alan Fryday Giuliana Furci Ricardo Galán Márquez Matteo Garbelotto Joaquina María García-Martín Mónica A García Otálora Dania García Sánchez Alain Gardiennet Sigisfredo Garnica Isaac Garrido Benavent Genevieve Gates Alice da Cruz Lima Gerlach Masoomeh Ghobad-Nejhad Tatiana B Gibertoni Tine Grebenc Irmgard Greilhuber Bella Grishkan Johannes Z Groenewald Martin Grube Gérald Gruhn Cécile Gueidan Gro Gulden Luis Fp Gusmão Josef Hafellner Michel Hairaud Marek Halama Nils Hallenberg Roy E Halling Karen Hansen Christoffer Bugge Harder Jacob Heilmann-Clausen Stip Helleman Alain Henriot Margarita Hernandez-Restrepo Raphaël Herve Caroline Hobart Mascha Hoffmeister Klaus Høiland Jan Holec Håkon Holien Karen Hughes Vit Hubka Seppo Huhtinen Boris Ivančević Marian Jagers Walter Jaklitsch AnnaElise Jansen Ruvishika S Jayawardena Thomas Stjernegaard Jeppesen Mikael Jeppson Peter Johnston Per Magnus Jørgensen Ingvar Kärnefelt Liudmila B Kalinina Gintaras Kantvilas Mitko Karadelev Taiga Kasuya Ivona Kautmanová Richard W Kerrigan Martin Kirchmair Anna Kiyashko Dániel G Knapp Henning Knudsen Kerry Knudsen Tommy Knutsson Miroslav Kolařík Urmas Kõljalg Alica Košuthová Attila Koszka Heikki Kotiranta Vera Kotkova Ondřej Koukol Jiří Kout Gábor M Kovács Martin Kříž Åsa Kruys Viktor Kučera Linas Kudzma Francisco Kuhar Martin Kukwa T K Arun Kumar Vladimír Kunca Ivana Kušan Thomas W Kuyper Carlos Lado Thomas Læssøe Patrice Lainé Ewald Langer Ellen Larsson Karl-Henrik Larsson Gary Laursen Christian Lechat Serena Lee James C Lendemer Laura Levin Uwe Lindemann Håkan Lindström Xingzhong Liu Regulo Carlos Llarena Hernandez Esteve Llop Csaba Locsmándi Deborah Jean Lodge Michael Loizides László Lőkös Jennifer Luangsa-Ard Matthias Lüderitz Thorsten Lumbsch Matthias Lutz Dan Mahoney Ekaterina Malysheva Vera Malysheva Patinjareveettil Manimohan Yasmina Marin-Felix Guilhermina Marques Rubén Martínez-Gil Guy Marson Gerardo Mata P Brandon Matheny Geir Harald Mathiassen Neven Matočec Helmut Mayrhofer Mehdi Mehrabi Ireneia Melo Armin Mešić Andrew S Methven Otto Miettinen Ana M Millanes Romero Andrew N Miller James K Mitchell Roland Moberg Pierre-Arthur Moreau Gabriel Moreno Olga Morozova Asunción Morte Lucia Muggia Guillermo Muñoz González Leena Myllys István Nagy László G Nagy Maria Alice Neves Tuomo Niemelä Pier Luigi Nimis Nicolas Niveiro Machiel E Noordeloos Anders Nordin Sara Raouia Noumeur Yuri Novozhilov Jorinde Nuytinck Esteri Ohenoja Patricia Oliveira Fiuza Alan Orange Alexander Ordynets Beatriz Ortiz-Santana Leticia Pacheco Ferenc Pál-Fám Melissa Palacio Zdeněk Palice Viktor Papp Kadri Pärtel Julia Pawlowska Aurelia Paz Ursula Peintner Shaun Pennycook Olinto Liparini Pereira Pablo Pérez Daniëls Miquel À Pérez-De-Gregorio Capella Carlos Manuel Pérez Del Amo Sergio Pérez Gorjón Sergio Pérez-Ortega Israel Pérez-Vargas Brian A Perry Jens H Petersen Ronald H Petersen Donald H Pfister Chayanard Phukhamsakda Marcin Piątek Meike Piepenbring Raquel Pino-Bodas Juan Pablo 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IMA Fungus 2018 Jun 24;9(1):167-175. Epub 2018 May 24.

Museum of Evolution, Uppsala University, Norbyvägen 16, 75236 Uppsala, Sweden.

Nomenclatural type definitions are one of the most important concepts in biological nomenclature. Being physical objects that can be re-studied by other researchers, types permanently link taxonomy (an artificial agreement to classify biological diversity) with nomenclature (an artificial agreement to name biological diversity). Two proposals to amend the International Code of Nomenclature for algae, fungi, and plants (ICN), allowing DNA sequences alone (of any region and extent) to serve as types of taxon names for voucherless fungi (mainly putative taxa from environmental DNA sequences), have been submitted to be voted on at the 11 International Mycological Congress (Puerto Rico, July 2018). We consider various genetic processes affecting the distribution of alleles among taxa and find that alleles may not consistently and uniquely represent the species within which they are contained. Should the proposals be accepted, the meaning of nomenclatural types would change in a fundamental way from physical objects as sources of data to the data themselves. Such changes are conducive to irreproducible science, the potential typification on artefactual data, and massive creation of names with low information content, ultimately causing nomenclatural instability and unnecessary work for future researchers that would stall future explorations of fungal diversity. We conclude that the acceptance of DNA sequences alone as types of names of taxa, under the terms used in the current proposals, is unnecessary and would not solve the problem of naming putative taxa known only from DNA sequences in a scientifically defensible way. As an alternative, we highlight the use of formulas for naming putative taxa (candidate taxa) that do not require any modification of the ICN.
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http://dx.doi.org/10.5598/imafungus.2018.09.01.10DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6048565PMC
June 2018

Pb accumulation in spores of arbuscular mycorrhizal fungi.

Sci Total Environ 2018 Dec 21;643:238-246. Epub 2018 Jun 21.

IMBIV-CONICET, Universidad Nacional de Córdoba, Av. Vélez Sársfield 1611, X5016CGA Córdoba, Argentina.

Heavy metal (HM) pollution of soils is one of the most important and unsolved environmental problems affecting the world, with alternative solutions currently being investigated through different approaches. Arbuscular mycorrhizal fungi (AMF) are soil inhabitants that form symbiotic relationships with plants. This alleviates HM toxicity in the host plant, thereby enhancing tolerance. However, the few investigations that have addressed the presence of metals in the fungus structures were performed under experimental conditions, with there being no results reported for Pb. The current study represents a first approximation concerning the capability of spores to accumulate Pb in the AMF community present in a Pb polluted soil under field conditions. Micro X-ray fluorescence was utilized to obtain a direct observation of Pb in spores, and the innovation of total reflection X-ray fluorescence was applied to obtain Pb quantification in spores. The AMF community included species of Ambisporaceae, Archaeosporaceae, Gigasporacea, Glomeraceae and Paraglomeraceae, and was tolerant to high Pb concentrations in soil. Pb accumulation in AMF spores was demonstrated at the community level and corroborated by direct observation of the most abundant spores, which belonged to the Gigasporaceae group. Spore Pb accumulation is possibly dependent on the AMF and host plant species.
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http://dx.doi.org/10.1016/j.scitotenv.2018.06.199DOI Listing
December 2018

Dispatch from the field II: the mystery of the red and blue male (Araneae, Tetragnathidae, ).

Biodivers Data J 2018 3(6):e24777. Epub 2018 Apr 3.

Danau Girang Field Centre, Sabah, Malaysia.

Background: Males of are difficult to associate with conspecific females, and sex-matching errors may persist in the taxonomic literature. Recommended best practices for definitive sex matching in this genus suggest finding a male in the web of a female, or better yet, mating pairs.

New Information: A male was observed hanging on a frame line of the web of a female , a species for which the male was previously undescribed. This occurred during a tropical ecology field course held at the Danau Girang Field Centre in Sabah, Malaysia. A taxonomic description was completed as a course activity.
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http://dx.doi.org/10.3897/BDJ.6.e24777DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5904518PMC
April 2018

Taxonomy based on science is necessary for global conservation.

Authors:
Scott A Thomson Richard L Pyle Shane T Ahyong Miguel Alonso-Zarazaga Joe Ammirati Juan Francisco Araya John S Ascher Tracy Lynn Audisio Valter M Azevedo-Santos Nicolas Bailly William J Baker Michael Balke Maxwell V L Barclay Russell L Barrett Ricardo C Benine James R M Bickerstaff Patrice Bouchard Roger Bour Thierry Bourgoin Christopher B Boyko Abraham S H Breure Denis J Brothers James W Byng David Campbell Luis M P Ceríaco István Cernák Pierfilippo Cerretti Chih-Han Chang Soowon Cho Joshua M Copus Mark J Costello Andras Cseh Csaba Csuzdi Alastair Culham Guillermo D'Elía Cédric d'Udekem d'Acoz Mikhail E Daneliya René Dekker Edward C Dickinson Timothy A Dickinson Peter Paul van Dijk Klaas-Douwe B Dijkstra Bálint Dima Dmitry A Dmitriev Leni Duistermaat John P Dumbacher Wolf L Eiserhardt Torbjørn Ekrem Neal L Evenhuis Arnaud Faille José L Fernández-Triana Emile Fiesler Mark Fishbein Barry G Fordham André V L Freitas Natália R Friol Uwe Fritz Tobias Frøslev Vicki A Funk Stephen D Gaimari Guilherme S T Garbino André R S Garraffoni József Geml Anthony C Gill Alan Gray Felipe G Grazziotin Penelope Greenslade Eliécer E Gutiérrez Mark S Harvey Cornelis J Hazevoet Kai He Xiaolan He Stephan Helfer Kristofer M Helgen Anneke H van Heteren Francisco Hita Garcia Norbert Holstein Margit K Horváth Peter H Hovenkamp Wei Song Hwang Jaakko Hyvönen Melissa B Islam John B Iverson Michael A Ivie Zeehan Jaafar Morgan D Jackson J Pablo Jayat Norman F Johnson Hinrich Kaiser Bente B Klitgård Dániel G Knapp Jun-Ichi Kojima Urmas Kõljalg Jenő Kontschán Frank-Thorsten Krell Irmgard Krisai-Greilhuber Sven Kullander Leonardo Latella John E Lattke Valeria Lencioni Gwilym P Lewis Marcos G Lhano Nathan K Lujan Jolanda A Luksenburg Jean Mariaux Jader Marinho-Filho Christopher J Marshall Jason F Mate Molly M McDonough Ellinor Michel Vitor F O Miranda Mircea-Dan Mitroiu Jesús Molinari Scott Monks Abigail J Moore Ricardo Moratelli Dávid Murányi Takafumi Nakano Svetlana Nikolaeva John Noyes Michael Ohl Nora H Oleas Thomas Orrell Barna Páll-Gergely Thomas Pape Viktor Papp Lynne R Parenti David Patterson Igor Ya Pavlinov Ronald H Pine Péter Poczai Jefferson Prado Divakaran Prathapan Richard K Rabeler John E Randall Frank E Rheindt Anders G J Rhodin Sara M Rodríguez D Christopher Rogers Fabio de O Roque Kevin C Rowe Luis A Ruedas Jorge Salazar-Bravo Rodrigo B Salvador George Sangster Carlos E Sarmiento Dmitry S Schigel Stefan Schmidt Frederick W Schueler Hendrik Segers Neil Snow Pedro G B Souza-Dias Riaan Stals Soili Stenroos R Douglas Stone Charles F Sturm Pavel Štys Pablo Teta Daniel C Thomas Robert M Timm Brian J Tindall Jonathan A Todd Dagmar Triebel Antonio G Valdecasas Alfredo Vizzini Maria S Vorontsova Jurriaan M de Vos Philipp Wagner Les Watling Alan Weakley Francisco Welter-Schultes Daniel Whitmore Nicholas Wilding Kipling Will Jason Williams Karen Wilson Judith E Winston Wolfgang Wüster Douglas Yanega David K Yeates Hussam Zaher Guanyang Zhang Zhi-Qiang Zhang Hong-Zhang Zhou

PLoS Biol 2018 03 14;16(3):e2005075. Epub 2018 Mar 14.

International Commission on Zoological Nomenclature, Singapore.

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http://dx.doi.org/10.1371/journal.pbio.2005075DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5851535PMC
March 2018

Spatio-temporal dynamics of soil bacterial communities as a function of Amazon forest phenology.

Sci Rep 2018 03 12;8(1):4382. Epub 2018 Mar 12.

Department of Plant Biology, University of Campinas, Campinas, Brazil.

Most tropical evergreen rain forests are characterised by varying degrees of precipitation seasonality that influence plant phenology and litterfall dynamics. Soil microbes are sensitive to soil water:air ratio and to nutrient availability. We studied if within-year seasonality in precipitation and litterfall-derived nutrient input resulted in predictable seasonal variation in soil bacterial diversity/microbial functional groups in an Amazonian forest. We characterised the spatio-temporal dynamics of microbial communities from the plot to the stand scales and related them to precipitation seasonality and spatial variability in soil characteristics. Community composition and functional diversity showed high spatial heterogeneity and was related to variability in soil chemistry at the stand level. Large species turnover characterised plot level changes over time, reflecting precipitation seasonality-related changes in soil nutrient and moisture regimes. The abundance of decomposers was highest during the rainy season, characterised also by anaerobic saprophytes and N-fixers adapted to fluctuating redox conditions. In contrast, Beijerinckiaceae, likely derived from the phyllosphere, were found at higher abundances when litter inputs and accumulation were highest. We showed that in a mildly seasonal rain forest, the composition of soil microbial communities appears to be following canopy phenology patterns and the two are interlinked and drive soil nutrient availability.
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http://dx.doi.org/10.1038/s41598-018-22380-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5847513PMC
March 2018

Out of sight, but no longer out of mind - towards an increased recognition of the role of soil microbes in plant speciation.

New Phytol 2018 02;217(3):965-967

Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695, USA.

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http://dx.doi.org/10.1111/nph.14979DOI Listing
February 2018

Abrupt changes in the composition and function of fungal communities along an environmental gradient in the high Arctic.

Mol Ecol 2017 Sep 12;26(18):4798-4810. Epub 2017 Aug 12.

CSIC, Global Ecology Unit, CREAF-CSIC-UAB, Cerdanyola del Vallès, Catalonia, Spain.

Fungi play a key role in soil-plant interactions, nutrient cycling and carbon flow and are essential for the functioning of arctic terrestrial ecosystems. Some studies have shown that the composition of fungal communities is highly sensitive to variations in environmental conditions, but little is known about how the conditions control the role of fungal communities (i.e., their ecosystem function). We used DNA metabarcoding to compare taxonomic and functional composition of fungal communities along a gradient of environmental severity in Northeast Greenland. We analysed soil samples from fell fields, heaths and snowbeds, three habitats with very contrasting abiotic conditions. We also assessed within-habitat differences by comparing three widespread microhabitats (patches with high cover of Dryas, Salix, or bare soil). The data suggest that, along the sampled mesotopographic gradient, the greatest differences in both fungal richness and community composition are observed amongst habitats, while the effect of microhabitat is weaker, although still significant. Furthermore, we found that richness and community composition of fungi are shaped primarily by abiotic factors and to a lesser, though still significant extent, by floristic composition. Along this mesotopographic gradient, environmental severity is strongly correlated with richness in all fungal functional groups: positively in saprotrophic, pathogenic and lichenised fungi, and negatively in ectomycorrhizal and root endophytic fungi. Our results suggest complex interactions amongst functional groups, possibly due to nutrient limitation or competitive exclusion, with potential implications on soil carbon stocks. These findings are important in the light of the environmental changes predicted for the Arctic.
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http://dx.doi.org/10.1111/mec.14227DOI Listing
September 2017

Changes in richness and community composition of ectomycorrhizal fungi among altitudinal vegetation types on Mount Kinabalu in Borneo.

New Phytol 2017 Jul 12;215(1):454-468. Epub 2017 Apr 12.

Biodiversity Dynamics Research Group, Naturalis Biodiversity Center, Vondellaan 55, PO Box 9517, 2300 RA, Leiden, the Netherlands.

The distribution patterns of tropical ectomycorrhizal (ECM) fungi along altitudinal gradients remain largely unknown. Furthermore, despite being an iconic site for biodiversity research, virtually nothing is known about the diversity and spatial patterns of fungi on Mt Kinabalu and neighbouring mountain ranges. We carried out deep DNA sequencing of soil samples collected between 425 and 4000 m above sea level to compare richness and community composition of ECM fungi among altitudinal forest types in Borneo. In addition, we tested whether the observed patterns are driven by habitat or by geometric effect of overlapping ranges of species (mid-domain effect). Community composition of ECM fungi was strongly correlated with elevation. In most genera, richness peaked in the mid-elevation montane forest zone, with the exception of tomentelloid fungi, which showed monotonal decrease in richness with increasing altitude. Richness in lower-mid- and mid-elevations was significantly greater than predicted under the mid-domain effect model. We provide the first insight into the composition of ECM fungal communities and their strong altitudinal turnover in Borneo. The high richness and restricted distribution of many ECM fungi in the montane forests suggest that mid-elevation peak richness is primarily driven by environmental characteristics of this habitat and not by the mid-domain effect.
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http://dx.doi.org/10.1111/nph.14566DOI Listing
July 2017

Changes in composition and abundance of functional groups of arctic fungi in response to long-term summer warming.

Biol Lett 2016 Nov;12(11)

Department of Biological Sciences, University of Alaska Anchorage, Anchorage, AK 99508, USA.

We characterized fungal communities in dry and moist tundra and investigated the effect of long-term experimental summer warming on three aspects of functional groups of arctic fungi: richness, community composition and species abundance. Warming had profound effects on community composition, abundance, and, to a lesser extent, on richness of fungal functional groups. In addition, our data show that even within functional groups, the direction and extent of response to warming tend to be species-specific and we recommend that studies on fungal communities and their roles in nutrient cycling take into account species-level responses.
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http://dx.doi.org/10.1098/rsbl.2016.0503DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5134034PMC
November 2016

Long-term increase in snow depth leads to compositional changes in arctic ectomycorrhizal fungal communities.

Glob Chang Biol 2016 09 8;22(9):3080-96. Epub 2016 Jun 8.

Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA, Leiden, The Netherlands.

Many arctic ecological processes are regulated by soil temperature that is tightly interconnected with snow cover distribution and persistence. Recently, various climate-induced changes have been observed in arctic tundra ecosystems, e.g. shrub expansion, resulting in reduction in albedo and greater C fixation in aboveground vegetation as well as increased rates of soil C mobilization by microbes. Importantly, the net effects of these shifts are unknown, in part because our understanding of belowground processes is limited. Here, we focus on the effects of increased snow depth, and as a consequence, increased winter soil temperature on ectomycorrhizal (ECM) fungal communities in dry and moist tundra. We analyzed deep DNA sequence data from soil samples taken at a long-term snow fence experiment in Northern Alaska. Our results indicate that, in contrast with previously observed responses of plants to increased snow depth at the same experimental site, the ECM fungal community of the dry tundra was more affected by deeper snow than the moist tundra community. In the dry tundra, both community richness and composition were significantly altered while in the moist tundra, only community composition changed significantly while richness did not. We observed a decrease in richness of Tomentella, Inocybe and other taxa adapted to scavenge the soil for labile N forms. On the other hand, richness of Cortinarius, and species with the ability to scavenge the soil for recalcitrant N forms, did not change. We further link ECM fungal traits with C soil pools. If future warmer atmospheric conditions lead to greater winter snow fall, changes in the ECM fungal community will likely influence C emissions and C fixation through altering N plant availability, fungal biomass and soil-plant C-N dynamics, ultimately determining important future interactions between the tundra biosphere and atmosphere.
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http://dx.doi.org/10.1111/gcb.13294DOI Listing
September 2016

Evolution of endemism on a young tropical mountain.

Nature 2015 Aug 12;524(7565):347-50. Epub 2015 Aug 12.

Naturalis Biodiversity Center, Darwinweg 2, 2333 CR Leiden, The Netherlands.

Tropical mountains are hot spots of biodiversity and endemism, but the evolutionary origins of their unique biotas are poorly understood. In varying degrees, local and regional extinction, long-distance colonization, and local recruitment may all contribute to the exceptional character of these communities. Also, it is debated whether mountain endemics mostly originate from local lowland taxa, or from lineages that reach the mountain by long-range dispersal from cool localities elsewhere. Here we investigate the evolutionary routes to endemism by sampling an entire tropical mountain biota on the 4,095-metre-high Mount Kinabalu in Sabah, East Malaysia. We discover that most of its unique biodiversity is younger than the mountain itself (6 million years), and comprises a mix of immigrant pre-adapted lineages and descendants from local lowland ancestors, although substantial shifts from lower to higher vegetation zones in this latter group were rare. These insights could improve forecasts of the likelihood of extinction and 'evolutionary rescue' in montane biodiversity hot spots under climate change scenarios.
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http://dx.doi.org/10.1038/nature14949DOI Listing
August 2015

Long-term warming alters richness and composition of taxonomic and functional groups of arctic fungi.

FEMS Microbiol Ecol 2015 Aug 6;91(8):fiv095. Epub 2015 Aug 6.

Naturalis Biodiversity Center, PO Box 9517, 2300 RA Leiden, the Netherlands Faculty of Science, Leiden University, PO Box 9502, 2300 RA Leiden, the Netherlands Plant Conservation and Population Biology, KU Leuven, Kasteelpark Arenberg 31, Box 2437, 3001 Leuven, Belgium.

Fungi, including symbionts, pathogens and decomposers, play crucial roles in community dynamics and nutrient cycling in terrestrial ecosystems. Despite their ecological importance, the response of most arctic fungi to climate warming is unknown, so are their potential roles in driving the observed and predicted changes in tundra communities. We carried out deep DNA sequencing of soil samples to study the long-term effects of experimental warming on fungal communities in dry heath and moist tussock tundra in Arctic Alaska. The data presented here indicate that fungal community composition responds strongly to warming in the moist tundra, but not in the dry tundra. While total fungal richness was not significantly affected by warming, there were clear correlations among operational taxonomic unit richness of various ecological and taxonomic groups and long-term warming. Richness of ectomycorrhizal, ericoid mycorrhizal and lichenized fungi generally decreased with warming, while richness of saprotrophic, plant and animal pathogenic, and root endophytic fungi tended to increase in the warmed plots. More importantly, various taxa within these functional guilds followed opposing trends that highlight the importance of species-specific responses to warming. We recommend that species-level ecological differences be taken into account in climate change and nutrient cycling studies that involve arctic fungi.
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http://dx.doi.org/10.1093/femsec/fiv095DOI Listing
August 2015

Long-term experimental warming alters community composition of ascomycetes in Alaskan moist and dry arctic tundra.

Mol Ecol 2015 Jan 10;24(2):424-37. Epub 2015 Jan 10.

Naturalis Biodiversity Center, Darwinweg 2, P.O. Box 9517, 2300 RA, Leiden, the Netherlands; Faculty of Science, Leiden University, P.O. Box 9502, 2300 RA, Leiden, the Netherlands.

Arctic tundra regions have been responding to global warming with visible changes in plant community composition, including expansion of shrubs and declines in lichens and bryophytes. Even though it is well known that the majority of arctic plants are associated with their symbiotic fungi, how fungal community composition will be different with climate warming remains largely unknown. In this study, we addressed the effects of long-term (18 years) experimental warming on the community composition and taxonomic richness of soil ascomycetes in dry and moist tundra types. Using deep Ion Torrent sequencing, we quantified how OTU assemblage and richness of different orders of Ascomycota changed in response to summer warming. Experimental warming significantly altered ascomycete communities with stronger responses observed in the moist tundra compared with dry tundra. The proportion of several lichenized and moss-associated fungi decreased with warming, while the proportion of several plant and insect pathogens and saprotrophic species was higher in the warming treatment. The observed alterations in both taxonomic and ecological groups of ascomycetes are discussed in relation to previously reported warming-induced shifts in arctic plant communities, including decline in lichens and bryophytes and increase in coverage and biomass of shrubs.
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http://dx.doi.org/10.1111/mec.13045DOI Listing
January 2015

Fungal biogeography. Global diversity and geography of soil fungi.

Science 2014 Nov;346(6213):1256688

Natural History Museum, University of Tartu, Tartu, Estonia.

Fungi play major roles in ecosystem processes, but the determinants of fungal diversity and biogeographic patterns remain poorly understood. Using DNA metabarcoding data from hundreds of globally distributed soil samples, we demonstrate that fungal richness is decoupled from plant diversity. The plant-to-fungus richness ratio declines exponentially toward the poles. Climatic factors, followed by edaphic and spatial variables, constitute the best predictors of fungal richness and community composition at the global scale. Fungi show similar latitudinal diversity gradients to other organisms, with several notable exceptions. These findings advance our understanding of global fungal diversity patterns and permit integration of fungi into a general macroecological framework.
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http://dx.doi.org/10.1126/science.1256688DOI Listing
November 2014

Greenhouse seedlings of Alnus showed low host intrageneric specificity and a strong preference for some Tomentella ectomycorrhizal associates.

Microb Ecol 2015 May 5;69(4):813-25. Epub 2014 Nov 5.

Instituto Multidisciplinario de Biología Vegetal (IMBIV), CONICET, Universidad Nacional de Córdoba, CC 495, 5000, Córdoba, Argentina,

Ectomycorrhizal (ECM) fungal associates of Alnus are relatively few in comparison with those associated with other tree hosts. The composition of ECM assemblages associated with Alnus seems to change very little across the Northern Hemisphere. However, Alnus-associated ECM assemblages from the Western United States, Mexico, and Argentina tend to differ from those in eastern North America and Europe, presumably due to their different biogeographic histories. Alnus glutinosa is a northern European species subjected to diverse environmental conditions. To address intrageneric host preference within two distantly related Alnus species (Alnus acuminata and A. glutinosa), we tested the ECM colonization on seedlings of both species inoculated with natural soil from A. acuminata forests. Two tomentelloid ECM fungi from A. acuminata natural soils were determined from the anatomotyping and molecular analysis. Both species colonized A. glutinosa seedlings and presented similar relative abundances. Additional soil sequence data from A. acuminata sites suggest that a variety of tomentelloid taxa occur, including several unidentified Tomentella lineages. Maximum-likelihood and Bayesian inference analyses based on internal transcribed spacer (ITS) sequences from various locations do not reflect associations of taxa based on their biogeographic origin, and clades are in general constituted by sequences from diverse regions, including South America, Mexico, USA, and Europe. Results illustrate the probable role of specific tomentelloid fungi in the early colonization of seedlings in A. acuminata forests as well as their importance in the structure of the ECM propagule community at the sites.
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http://dx.doi.org/10.1007/s00248-014-0522-2DOI Listing
May 2015

Summer temperature increase has distinct effects on the ectomycorrhizal fungal communities of moist tussock and dry tundra in Arctic Alaska.

Glob Chang Biol 2015 Feb 8;21(2):959-72. Epub 2014 Oct 8.

Naturalis Biodiversity Center, P.O. Box 9517, Leiden, RA, 2300, The Netherlands.

Arctic regions are experiencing the greatest rates of climate warming on the planet and marked changes have already been observed in terrestrial arctic ecosystems. While most studies have focused on the effects of warming on arctic vegetation and nutrient cycling, little is known about how belowground communities, such as fungi root-associated, respond to warming. Here, we investigate how long-term summer warming affects ectomycorrhizal (ECM) fungal communities. We used Ion Torrent sequencing of the rDNA internal transcribed spacer 2 (ITS2) region to compare ECM fungal communities in plots with and without long-term experimental warming in both dry and moist tussock tundra. Cortinarius was the most OTU-rich genus in the moist tundra, while the most diverse genus in the dry tundra was Tomentella. On the diversity level, in the moist tundra we found significant differences in community composition, and a sharp decrease in the richness of ECM fungi due to warming. On the functional level, our results indicate that warming induces shifts in the extramatrical properties of the communities, where the species with medium-distance exploration type seem to be favored with potential implications for the mobilization of different nutrient pools in the soil. In the dry tundra, neither community richness nor community composition was significantly altered by warming, similar to what had been observed in ECM host plants. There was, however, a marginally significant increase in OTUs identified as ECM fungi with the medium-distance exploration type in the warmed plots. Linking our findings of decreasing richness with previous results of increasing ECM fungal biomass suggests that certain ECM species are favored by warming and may become more abundant, while many other species may go locally extinct due to direct or indirect effects of warming. Such compositional shifts in the community might affect nutrient cycling and soil organic C storage.
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http://dx.doi.org/10.1111/gcb.12716DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4322476PMC
February 2015

The contribution of DNA metabarcoding to fungal conservation: diversity assessment, habitat partitioning and mapping red-listed fungi in protected coastal Salix repens communities in the Netherlands.

PLoS One 2014 17;9(6):e99852. Epub 2014 Jun 17.

Naturalis Biodiversity Center, Leiden, The Netherlands.

Western European coastal sand dunes are highly important for nature conservation. Communities of the creeping willow (Salix repens) represent one of the most characteristic and diverse vegetation types in the dunes. We report here the results of the first kingdom-wide fungal diversity assessment in S. repens coastal dune vegetation. We carried out massively parallel pyrosequencing of ITS rDNA from soil samples taken at ten sites in an extended area of joined nature reserves located along the North Sea coast of the Netherlands, representing habitats with varying soil pH and moisture levels. Fungal communities in Salix repens beds are highly diverse and we detected 1211 non-singleton fungal 97% sequence similarity OTUs after analyzing 688,434 ITS2 rDNA sequences. Our comparison along a north-south transect indicated strong correlation between soil pH and fungal community composition. The total fungal richness and the number OTUs of most fungal taxonomic groups negatively correlated with higher soil pH, with some exceptions. With regard to ecological groups, dark-septate endophytic fungi were more diverse in acidic soils, ectomycorrhizal fungi were represented by more OTUs in calcareous sites, while detected arbuscular mycorrhizal genera fungi showed opposing trends regarding pH. Furthermore, we detected numerous red listed species in our samples often from previously unknown locations, indicating that some of the fungal species currently considered rare may be more abundant in Dutch S. repens communities than previously thought.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0099852PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4061046PMC
February 2015

Large-scale fungal diversity assessment in the Andean Yungas forests reveals strong community turnover among forest types along an altitudinal gradient.

Mol Ecol 2014 May;23(10):2452-72

Naturalis Biodiversity Center, Darwinweg 2, P.O. Box 9517, 2300, RA Leiden, the Netherlands; Faculty of Science, Leiden University, P.O. Box 9502, 2300, RA Leiden, the Netherlands.

The Yungas, a system of tropical and subtropical montane forests on the eastern slopes of the Andes, are extremely diverse and severely threatened by anthropogenic pressure and climate change. Previous mycological works focused on macrofungi (e.g. agarics, polypores) and mycorrhizae in Alnus acuminata forests, while fungal diversity in other parts of the Yungas has remained mostly unexplored. We carried out Ion Torrent sequencing of ITS2 rDNA from soil samples taken at 24 sites along the entire latitudinal extent of the Yungas in Argentina. The sampled sites represent the three altitudinal forest types: the piedmont (400-700 m a.s.l.), montane (700-1500 m a.s.l.) and montane cloud (1500-3000 m a.s.l.) forests. The deep sequence data presented here (i.e. 4 108 126 quality-filtered sequences) indicate that fungal community composition correlates most strongly with elevation, with many fungi showing preference for a certain altitudinal forest type. For example, ectomycorrhizal and root endophytic fungi were most diverse in the montane cloud forests, particularly at sites dominated by Alnus acuminata, while the diversity values of various saprobic groups were highest at lower elevations. Despite the strong altitudinal community turnover, fungal diversity was comparable across the different zonal forest types. Besides elevation, soil pH, N, P, and organic matter contents correlated with fungal community structure as well, although most of these variables were co-correlated with elevation. Our data provide an unprecedented insight into the high diversity and spatial distribution of fungi in the Yungas forests.
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http://dx.doi.org/10.1111/mec.12765DOI Listing
May 2014