Publications by authors named "Dirk Redecker"

33 Publications

Survival of Suillus pungens and Amanita francheti ectomycorrhizal genets was rare or absent after a stand-replacing wildfire.

New Phytol 2002 Sep;155(3):517-523

Institute of Botany, University of Basel, Hebelstrasse 1, CH-4056 Basel Switzerland.

•  We looked for evidence of mycelial survival by Suillus pungens and Amanita francheti following a stand-replacing wildfire. These species were selected because we had previously mapped and genotyped their fruiting bodies in the pre-fire forest. •  Mycelial survival was investigated in two ways. First, we sampled seedlings in areas where these species had fruited abundantly before the fire, and second, we collected and genotyped mushrooms of S. pungens . •  Neither species was detected on seedlings within the areas sampled, and A. francheti was not detected in any above- or below-ground samples after the fire. Genetic evidence from S. pungens revealed that post-fire genets were small and numerous, and none were found to be identical to the genets sampled prior to the fire. •  From these results we conclude that A. francheti was not a common survivor or an early colonist of the post-fire forest, and that spores are the primary means by which S. pungens recolonized. If mycelial survival occurred in either species, it must have been relatively rare.
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http://dx.doi.org/10.1046/j.1469-8137.2002.00468.xDOI Listing
September 2002

Single-Spore Extraction for Genetic Analyses of Arbuscular Mycorrhizal Fungi.

Authors:
Dirk Redecker

Methods Mol Biol 2020 ;2146:93-97

Agroécologie, Université de Bourgogne, Université de Bourgogne Franche-Comté, INRAE, AgroSup Dijon, CNRS, Dijon, France.

Biomass of arbuscular mycorrhizal fungi (AMF, Glomeromycota) is often only available in small quantities as these fungi are obligate biotrophs and many species are difficult to cultivate under controlled conditions. Here, I describe a simple, efficient approach to produce crude extracts from single or a small number of spores that can be used for genotyping AMF.
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http://dx.doi.org/10.1007/978-1-0716-0603-2_8DOI Listing
March 2021

Correction to: Tracing Rhizophagus irregularis isolate IR27 in Ziziphus mauritiana roots under field conditions.

Mycorrhiza 2020 01;30(1):171

Laboratoire des Symbioses Tropicales et Méditerranéennes UMR113 INRA/AGRO-M/CIRAD/IRD/UM2-TA10/J, Campus International de Baillarguet, 34398, Montpellier, France.

The authors of the above-mentioned published article inadvertently omitted Dirk Redecker, Dioumacor Fall and Diaminatou Sanogo from the list of authors. The names and their affiliations presented in this paper.
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http://dx.doi.org/10.1007/s00572-020-00935-1DOI Listing
January 2020

Is a mixture of arbuscular mycorrhizal fungi better for plant growth than single-species inoculants?

Mycorrhiza 2019 Jul 15;29(4):325-339. Epub 2019 Jun 15.

Institut des Sciences Exactes et Appliquées (ISEA), Université de la Nouvelle-Calédonie, BP R4, 98851, Nouméa Cedex, New Caledonia.

Inoculation of arbuscular mycorrhizal fungi (AMF) as plant growth promoters has mostly been conducted using single-species inoculum. In this study, we investigated whether co-inoculation of different native AMF species induced an improvement of plant growth in an ultramafic soil. We analyzed the effects of six species of AMF from a New Caledonian ultramafic soil on plant growth and nutrition, using mono-inoculations and mixtures comprising different numbers of AMF species, in a greenhouse experiment. The endemic Metrosideros laurifolia was used as a host plant. Our results suggest that, when the plant faced multiple abiotic stress factors (nutrient deficiencies and high concentrations of different heavy metals), co-inoculation of AMF belonging to different families was more efficient than mono-inoculation in improving biomass, mineral nutrition, Ca/Mg ratio, and tolerance to heavy metals of plants in ultramafic soil. This performance suggested functional complementarity between distantly related AMF. Our findings will have important implications for restoration ecology and mycorrhizal biotechnology applied to ultramafic soils.
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http://dx.doi.org/10.1007/s00572-019-00898-yDOI Listing
July 2019

A new genus, Planticonsortium (Mucoromycotina), and new combination (P. tenue), for the fine root endophyte, Glomus tenue (basionym Rhizophagus tenuis).

Mycorrhiza 2018 Apr 15;28(3):213-219. Epub 2018 Jan 15.

Agroécologie, INRA, Université de Bourgogne Franche-Comté, AgroSup Dijon, CNRS, 17 rue Sully, 21000, Dijon, France.

In 1977, the fine root endophyte, originally named Rhizophagus tenuis, was transferred into the genus Glomus as G. tenue, thus positioning the species with all other known arbuscular mycorrhizal fungi (Glomeromycota, Glomeromycotina). Recent molecular evidence, however, places it in a different subphylum, Mucoromycotina in the Mucoromycota. No suitable genus exists in the Mucoromycotina to accommodate G. tenue, so it is moved to Planticonsortium gen. nov. as P. tenue comb. nov.
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http://dx.doi.org/10.1007/s00572-017-0815-7DOI Listing
April 2018

Glomeromycotina: what is a species and why should we care?

New Phytol 2018 12 22;220(4):963-967. Epub 2017 Nov 22.

University of Tartu, 40 Lai Street, 51005, Tartu, Estonia.

A workshop at the recent International Conference on Mycorrhiza was focused on species recognition in Glomeromycotina and parts of their basic biology that define species. The workshop was motivated by the paradigm-shifting evidence derived from genomic data for sex and for the lack of heterokaryosis, and by published exchanges in Science that were based on different species concepts and have led to differing views of dispersal and endemism in these fungi. Although a lively discussion ensued, there was general agreement that species recognition in the group is in need of more attention, and that many basic assumptions about the biology of these important fungi including sexual or clonal reproduction, similarity or dissimilarity of nuclei within an individual, and species boundaries need to be re-examined and scrutinized with current techniques.
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http://dx.doi.org/10.1111/nph.14913DOI Listing
December 2018

New method for the identification of arbuscular mycorrhizal fungi by proteomic-based biotyping of spores using MALDI-TOF-MS.

Sci Rep 2017 10 30;7(1):14306. Epub 2017 Oct 30.

Institut des Sciences Exactes et Appliquées (EA 7484), Université de Nouvelle-Calédonie, BP R4, 98851, Nouméa, Nouvelle-Calédonie, France.

Arbuscular mycorrhizal fungi (AMF, Glomeromycota) are mutualistic symbionts associated with majority of land plants. These fungi play an important role in plant growth, but their taxonomic identification remains a challenge for academic research, culture collections and inoculum producers who need to certify their products. Identification of these fungi was traditionally performed based on their spore morphology. DNA sequence data have successfully been used to study the evolutionary relationships of AMF, develop molecular identification tools and assess their diversity in the environment. However, these methods require considerable expertise and are not well-adapted for "routine" quality control of culture collections and inoculum production. Here, we show that Matrix-Assisted Laser Desorption Ionisation Time of Flight Mass Spectrometry proteomic-based biotyping is a highly efficient approach for AMF identification. Nineteen isolates belonging to fourteen species, seven genera and five families were clearly differentiated by MALDI biotyping at the species level, and intraspecific differentiation was achieved for the majority. AMF identification by MALDI biotyping could be highly useful, not only for research but also in agricultural and environmental applications. Fast, accurate and inexpensive molecular mass determination and the possibility of automation make MALDI-TOF-MS a real alternative to conventional morphological and molecular methods for AMF identification.
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http://dx.doi.org/10.1038/s41598-017-14487-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5662746PMC
October 2017

Soil networks become more connected and take up more carbon as nature restoration progresses.

Nat Commun 2017 02 8;8:14349. Epub 2017 Feb 8.

NIOO-KNAW, Terrestrial Ecology, Droevendaalsesteeg 10, Wageningen 6708 PB, The Netherlands.

Soil organisms have an important role in aboveground community dynamics and ecosystem functioning in terrestrial ecosystems. However, most studies have considered soil biota as a black box or focussed on specific groups, whereas little is known about entire soil networks. Here we show that during the course of nature restoration on abandoned arable land a compositional shift in soil biota, preceded by tightening of the belowground networks, corresponds with enhanced efficiency of carbon uptake. In mid- and long-term abandoned field soil, carbon uptake by fungi increases without an increase in fungal biomass or shift in bacterial-to-fungal ratio. The implication of our findings is that during nature restoration the efficiency of nutrient cycling and carbon uptake can increase by a shift in fungal composition and/or fungal activity. Therefore, we propose that relationships between soil food web structure and carbon cycling in soils need to be reconsidered.
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http://dx.doi.org/10.1038/ncomms14349DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5309817PMC
February 2017

The largest subunit of RNA polymerase II as a new marker gene to study assemblages of arbuscular mycorrhizal fungi in the field.

PLoS One 2014 2;9(9):e107783. Epub 2014 Oct 2.

Université de Bourgogne, UMR1347 Agroécologie, Dijon, France.

Due to the potential of arbuscular mycorrhizal fungi (AMF, Glomeromycota) to improve plant growth and soil quality, the influence of agricultural practice on their diversity continues to be an important research question. Up to now studies of community diversity in AMF have exclusively been based on nuclear ribosomal gene regions, which in AMF show high intra-organism polymorphism, seriously complicating interpretation of these data. We designed specific PCR primers for 454 sequencing of a region of the largest subunit of RNA polymerase II gene, and established a new reference dataset comprising all major AMF lineages. This gene is known to be monomorphic within fungal isolates but shows an excellent barcode gap between species. We designed a primer set to amplify all known lineages of AMF and demonstrated its applicability in combination with high-throughput sequencing in a long-term tillage experiment. The PCR primers showed a specificity of 99.94% for glomeromycotan sequences. We found evidence of significant shifts of the AMF communities caused by soil management and showed that tillage effects on different AMF taxa are clearly more complex than previously thought. The high resolving power of high-throughput sequencing highlights the need for quantitative measurements to efficiently detect these effects.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0107783PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4183475PMC
June 2015

Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi.

Authors:
Conrad L Schoch Barbara Robbertse Vincent Robert Duong Vu Gianluigi Cardinali Laszlo Irinyi Wieland Meyer R Henrik Nilsson Karen Hughes Andrew N Miller Paul M Kirk Kessy Abarenkov M Catherine Aime Hiran A Ariyawansa Martin Bidartondo Teun Boekhout Bart Buyck Qing Cai Jie Chen Ana Crespo Pedro W Crous Ulrike Damm Z Wilhelm De Beer Bryn T M Dentinger Pradeep K Divakar Margarita Dueñas Nicolas Feau Katerina Fliegerova Miguel A García Zai-Wei Ge Gareth W Griffith Johannes Z Groenewald Marizeth Groenewald Martin Grube Marieka Gryzenhout Cécile Gueidan Liangdong Guo Sarah Hambleton Richard Hamelin Karen Hansen Valérie Hofstetter Seung-Beom Hong Jos Houbraken Kevin D Hyde Patrik Inderbitzin Peter R Johnston Samantha C Karunarathna Urmas Kõljalg Gábor M Kovács Ekaphan Kraichak Krisztina Krizsan Cletus P Kurtzman Karl-Henrik Larsson Steven Leavitt Peter M Letcher Kare Liimatainen Jian-Kui Liu D Jean Lodge Janet Jennifer Luangsa-ard H Thorsten Lumbsch Sajeewa S N Maharachchikumbura Dimuthu Manamgoda María P Martín Andrew M Minnis Jean-Marc Moncalvo Giuseppina Mulè Karen K Nakasone Tuula Niskanen Ibai Olariaga Tamás Papp Tamás Petkovits Raquel Pino-Bodas Martha J Powell Huzefa A Raja Dirk Redecker J M Sarmiento-Ramirez Keith A Seifert Bhushan Shrestha Soili Stenroos Benjamin Stielow Sung-Oui Suh Kazuaki Tanaka Leho Tedersoo M Teresa Telleria Dhanushka Udayanga Wendy A Untereiner Javier Diéguez Uribeondo Krishna V Subbarao Csaba Vágvölgyi Cobus Visagie Kerstin Voigt Donald M Walker Bevan S Weir Michael Weiß Nalin N Wijayawardene Michael J Wingfield J P Xu Zhu L Yang Ning Zhang Wen-Ying Zhuang Scott Federhen

Database (Oxford) 2014 30;2014. Epub 2014 Jun 30.

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA, CBS-KNAW Fungal Biodiversity Centre, P.O. Box 85167, 3508 AD Utrecht, The Netherlands, Department of Pharmaceutical Sciences - Microbiology, Università degli Studi di Perugia, Perugia, Italy, Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Marie Bashir Institute for Infectious Diseases and Biosecurity, Sydney Medical School-Westmead Hospital, The University of Sydney, Westmead Millennium Institute, Westmead, Australia, Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 405 30 Göteborg, Sweden, Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN 37920, USA, Illinois Natural History Survey, University of Illinois, 1816 South Oak Street, Champaign, IL 61820, USA, Mycology Section, Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3DS, UK, Natural History Museum, University of Tartu, 46 Vanemuise, 51014 Tartu, Estonia, Purdue University, Department of Botany and Plant Pathology, 915 W. State Street, West Lafayette, IN 47907, USA, Institute of Excellence in Fungal Research, and School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand, Imperial College London, Royal Botanic Gardens, Kew TW9 3DS, England, UK, Muséum National d'Histoire Naturelle, Dépt. Systématique et Evolution CP39, UMR7205, 12 Rue Buffon, F-75005 Paris, France, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, P. R. China, Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense de Madrid, Madrid 28040, Spain, Senckenberg Museum of Natural History Görlitz, PF 300 154, 02806 Görlitz, Germany, Department of Microbiology and Plant Pathology, Forestry Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0001, South Africa, Real Jardín Botánico, RJB-CSIC,

DNA phylogenetic comparisons have shown that morphology-based species recognition often underestimates fungal diversity. Therefore, the need for accurate DNA sequence data, tied to both correct taxonomic names and clearly annotated specimen data, has never been greater. Furthermore, the growing number of molecular ecology and microbiome projects using high-throughput sequencing require fast and effective methods for en masse species assignments. In this article, we focus on selecting and re-annotating a set of marker reference sequences that represent each currently accepted order of Fungi. The particular focus is on sequences from the internal transcribed spacer region in the nuclear ribosomal cistron, derived from type specimens and/or ex-type cultures. Re-annotated and verified sequences were deposited in a curated public database at the National Center for Biotechnology Information (NCBI), namely the RefSeq Targeted Loci (RTL) database, and will be visible during routine sequence similarity searches with NR_prefixed accession numbers. A set of standards and protocols is proposed to improve the data quality of new sequences, and we suggest how type and other reference sequences can be used to improve identification of Fungi. Database URL: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA177353.
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http://dx.doi.org/10.1093/database/bau061DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4075928PMC
February 2015

An evidence-based consensus for the classification of arbuscular mycorrhizal fungi (Glomeromycota).

Mycorrhiza 2013 Oct 5;23(7):515-31. Epub 2013 Apr 5.

Université de Bourgogne/INRA, UMR 1347 Agroécologie, 17 rue Sully, BP 86510, 21000, Dijon, France,

The publication of a large number of taxon names at all levels within the arbuscular mycorrhizal fungi (Glomeromycota) has resulted in conflicting systematic schemes and generated considerable confusion among biologists working with these important plant symbionts. A group of biologists with more than a century of collective experience in the systematics of Glomeromycota examined all available molecular-phylogenetic evidence within the framework of phylogenetic hypotheses, incorporating morphological characters when they were congruent. This study is the outcome, wherein the classification of Glomeromycota is revised by rejecting some new names on the grounds that they are founded in error and by synonymizing others that, while validly published, are not evidence-based. The proposed "consensus" will provide a framework for additional original research aimed at clarifying the evolutionary history of this important group of symbiotic fungi.
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http://dx.doi.org/10.1007/s00572-013-0486-yDOI Listing
October 2013

Importance of dispersal and thermal environment for mycorrhizal communities: lessons from Yellowstone National Park.

Ecology 2011 Jun;92(6):1292-302

Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, Montana 59717, USA.

The relative importance of dispersal and niche restrictions remains a controversial topic in community ecology, especially for microorganisms that are often assumed to be ubiquitous. We investigated the impact of these factors for the community assembly of the root-symbiont arbuscular mycorrhizal fungi (AMF) by sampling roots from geothermal and nonthermal grasslands in Yellowstone National Park (YNP), followed by sequencing and RFLP of AMF ribosomal DNA. With the exception of an apparent generalist RFLP type closely related to Glomus intraradices, a distance-based redundancy analysis indicated that the AMF community composition correlated with soil pH or pH-driven changes in soil chemistry. This was unexpected, given the large differences in soil temperature and plant community composition between the geothermal and nonthermal grasslands. RFLP types were found in either the acidic geothermal grasslands or in the neutral to alkaline grasslands, one of which was geothermal. The direct effect of the soil chemical environment on the distribution of two AMF morphospecies isolated from acidic geothermal grasslands was supported in a controlled greenhouse experiment. Paraglomus occultum and Scutellospora pellucida were more beneficial to plants and formed significantly more spores when grown in acidic than in alkaline soil. Distance among grasslands, used as an estimate of dispersal limitations, was not a significant predictor of AMF community similarity within YNP, and most fungal taxa may be part of a metacommunity. The isolation of several viable AMF taxa from bison feces indicates that wide-ranging bison could be a vector for at least some RFLP types among grasslands within YNP. In support of classical niche theory and the Baas-Becking hypothesis, our results suggest that AMF are not limited by dispersal at the scale of YNP, but that the soil environment appears to be the primary factor affecting community composition and distribution.
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http://dx.doi.org/10.1890/10-1516.1DOI Listing
June 2011

Long-term tracing of Rhizophagus irregularis isolate BEG140 inoculated on Phalaris arundinacea in a coal mine spoil bank, using mitochondrial large subunit rDNA markers.

Mycorrhiza 2012 Jan 28;22(1):69-80. Epub 2011 Apr 28.

Institute of Botany, Academy of Sciences of the Czech Republic, Průhonice, Czech Republic.

During the last decade, the application of arbuscular mycorrhizal fungi (AMF) as bioenhancers has increased significantly. However, until now, it has been difficult to verify the inoculation success in terms of fungal symbiont establishment in roots of inoculated plants because specific fungal strains could not be detected within colonized roots. Using mitochondrial large subunit ribosomal DNA, we show that Rhizophagus irregularis (formerly known as Glomus intraradices) isolate BEG140 consists of two different haplotypes. We developed nested PCR assays to specifically trace each of the two haplotypes in the roots of Phalaris arundinacea from a field experiment in a spoil bank of a former coal mine, where BEG140 was used as inoculant. We revealed that despite the relatively high diversity of native R. irregularis strains, R. irregularis BEG140 survived and proliferated successfully in the field experiment and was found significantly more often in the inoculated than control plots. This work is the first one to show tracing of an inoculated AMF isolate in the roots of target plants and to verify its survival and propagation in the field. These results will have implications for basic research on the ecology of AMF at the intraspecific level as well as for commercial users of mycorrhizal inoculation.
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http://dx.doi.org/10.1007/s00572-011-0375-1DOI Listing
January 2012

Sebacinales everywhere: previously overlooked ubiquitous fungal endophytes.

PLoS One 2011 Feb 15;6(2):e16793. Epub 2011 Feb 15.

Institut für Evolution und Ökologie, Organismische Botanik, Universität Tübingen, Tübingen, Germany.

Inconspicuous basidiomycetes from the order Sebacinales are known to be involved in a puzzling variety of mutualistic plant-fungal symbioses (mycorrhizae), which presumably involve transport of mineral nutrients. Recently a few members of this fungal order not fitting this definition and commonly referred to as 'endophytes' have raised considerable interest by their ability to enhance plant growth and to increase resistance of their host plants against abiotic stress factors and fungal pathogens. Using DNA-based detection and electron microscopy, we show that Sebacinales are not only extremely versatile in their mycorrhizal associations, but are also almost universally present as symptomless endophytes. They occurred in field specimens of bryophytes, pteridophytes and all families of herbaceous angiosperms we investigated, including liverworts, wheat, maize, and the non-mycorrhizal model plant Arabidopsis thaliana. They were present in all habitats we studied on four continents. We even detected these fungi in herbarium specimens originating from pioneering field trips to North Africa in the 1830s/40s. No geographical or host patterns were detected. Our data suggest that the multitude of mycorrhizal interactions in Sebacinales may have arisen from an ancestral endophytic habit by specialization. Considering their proven beneficial influence on plant growth and their ubiquity, endophytic Sebacinales may be a previously unrecognized universal hidden force in plant ecosystems.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0016793PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3039649PMC
February 2011

Agroecology: the key role of arbuscular mycorrhizas in ecosystem services.

Mycorrhiza 2010 Nov 10;20(8):519-30. Epub 2010 Aug 10.

UMR INRA 1088/CNRS 5184/Université Bourgogne, Plante-Microbe-Environnement, INRA-CMSE, BP 86510, 21065, Dijon Cedex, France.

The beneficial effects of arbuscular mycorrhizal (AM) fungi on plant performance and soil health are essential for the sustainable management of agricultural ecosystems. Nevertheless, since the 'first green revolution', less attention has been given to beneficial soil microorganisms in general and to AM fungi in particular. Human society benefits from a multitude of resources and processes from natural and managed ecosystems, to which AM make a crucial contribution. These resources and processes, which are called ecosystem services, include products like food and processes like nutrient transfer. Many people have been under the illusion that these ecosystem services are free, invulnerable and infinitely available; taken for granted as public benefits, they lack a formal market and are traditionally absent from society's balance sheet. In 1997, a team of researchers from the USA, Argentina and the Netherlands put an average price tag of US $33 trillion a year on these fundamental ecosystem services. The present review highlights the key role that the AM symbiosis can play as an ecosystem service provider to guarantee plant productivity and quality in emerging systems of sustainable agriculture. The appropriate management of ecosystem services rendered by AM will impact on natural resource conservation and utilisation with an obvious net gain for human society.
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http://dx.doi.org/10.1007/s00572-010-0333-3DOI Listing
November 2010

Unique arbuscular mycorrhizal fungal communities uncovered in date palm plantations and surrounding desert habitats of Southern Arabia.

Mycorrhiza 2011 Apr 23;21(3):195-209. Epub 2010 Jun 23.

Zurich Basel Plant Science Center, Institute of Botany, University of Basel, Hebelstrasse 1, 4056 Basel, Switzerland.

The main objective of this study was to shed light on the previously unknown arbuscular mycorrhizal fungal (AMF) communities in Southern Arabia. We explored AMF communities in two date palm (Phoenix dactylifera) plantations and the natural vegetation of their surrounding arid habitats. The plantations were managed traditionally in an oasis and according to conventional guidelines at an experimental station. Based on spore morphotyping, the AMF communities under the date palms appeared to be quite diverse at both plantations and more similar to each other than to the communities under the ruderal plant, Polygala erioptera, growing at the experimental station on the dry strip between the palm trees, and to the communities uncovered under the native vegetation (Zygophyllum hamiense, Salvadora persica, Prosopis cineraria, inter-plant area) of adjacent undisturbed arid habitat. AMF spore abundance and species richness were higher under date palms than under the ruderal and native plants. Sampling in a remote sand dune area under Heliotropium kotschyi yielded only two AMF morphospecies and only after trap culturing. Overall, 25 AMF morphospecies were detected encompassing all study habitats. Eighteen belonged to the genus Glomus including four undescribed species. Glomus sinuosum, a species typically found in undisturbed habitats, was the most frequently occurring morphospecies under the date palms. Using molecular tools, it was also found as a phylogenetic taxon associated with date palm roots. These roots were associated with nine phylogenetic taxa, among them eight from Glomus group A, but the majority could not be assigned to known morphospecies or to environmental sequences in public databases. Some phylogenetic taxa seemed to be site specific. Despite the use of group-specific primers and efficient trapping systems with a bait plant consortium, surprisingly, two of the globally most frequently found species, Glomus intraradices and Glomus mosseae, were not detected neither as phylogenetic taxa in the date palm roots nor as spores under the date palms, the intermediate ruderal plant, or the surrounding natural vegetation. The results highlight the uniqueness of AMF communities inhabiting these diverse habitats exposed to the harsh climatic conditions of Southern Arabia.
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http://dx.doi.org/10.1007/s00572-010-0323-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3058386PMC
April 2011

Diversity of mitochondrial large subunit rDNA haplotypes of Glomus intraradices in two agricultural field experiments and two semi-natural grasslands.

Mol Ecol 2010 Apr;19(7):1497-511

Institute of Botany, University of Basel, Hebelstrasse 1, CH-4056 Basel, Switzerland.

Glomus intraradices, an arbuscular mycorrhizal fungus (AMF), is frequently found in a surprisingly wide range of ecosystems all over the world. It is used as model organism for AMF and its genome is being sequenced. Despite the ecological importance of AMF, little has been known about their population structure, because no adequate molecular markers have been available. In the present study we analyse for the first time the intraspecific genetic structure of an AMF directly from colonized roots in the field. A recently developed PCR-RFLP approach for the mitochondrial rRNA large subunit gene (mtLSU) of these obligate symbionts was used and complemented by sequencing and primers specific for a particularly frequent mtLSU haplotype. We analysed root samples from two agricultural field experiments in Switzerland and two semi-natural grasslands in France and Switzerland. RFLP type composition of G. intraradices (phylogroup GLOM A-1) differed strongly between agricultural and semi-natural sites and the G. intraradices populations of the two agricultural sites were significantly differentiated. RFLP type richness was higher in the agricultural sites compared with the grasslands. Detailed sequence analyses which resolved multiple sequence haplotypes within some RFLP types even revealed that there was no overlap of haplotypes among any of the study sites except between the two grasslands. Our results demonstrate a surprisingly high differentiation among semi-natural and agricultural field sites for G. intraradices. These findings will have major implications on our views of processes of adaptation and specialization in these plant/fungus associations.
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http://dx.doi.org/10.1111/j.1365-294X.2010.04590.xDOI Listing
April 2010

Evolutionary dynamics of introns and homing endonuclease ORFs in a region of the large subunit of the mitochondrial rRNA in Glomus species (arbuscular mycorrhizal fungi, Glomeromycota).

Mol Phylogenet Evol 2010 May 19;55(2):599-610. Epub 2010 Feb 19.

Institute of Botany, University of Basel, Hebelstrasse 1, CH-4056 Basel, Switzerland.

The large subunit of the mitochondrial ribosomal RNA genes (mtLSU) has previously been identified as a highly sensitive molecular marker for intraspecies diversity in the arbuscular mycorrhizal fungus Glomus intraradices. In this study, the respective region was analyzed in five species of Glomus (G. mosseae, G. geosporum, G. caledonium, G. clarum, G. coronatum) from the same major clade (Glomus group A), Glomus sp. ISCB 34 from the related Glomus group B and two species of Scutellospora. Results show low level of genetic polymorphism between related morphospecies. Introns homologous to those found in G. intraradices were detected as well as new ones, some of them containing putative ORFs for homing endonucleases (HEs). Introns without ORFs for HEs seem to have been inherited strictly vertically from the ancestors of Glomus groups A and B while other introns indicate occasional horizontal transfer and possibly maintenance, degeneration and loss together with their associated HE ORFs. Overall, we provide first insights into the evolutionary dynamics of introns and HEs in this ecologically important group of fungi, which was previously not analyzed in this respect.
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http://dx.doi.org/10.1016/j.ympev.2010.02.013DOI Listing
May 2010

Unexpected vagaries of microsatellite loci in Glomus intraradices: length polymorphisms are rarely caused by variation in repeat number only.

New Phytol 2008 ;180(3):568-570

Zurich-Basel Plant Science Center, Botanisches Institut der Universität Basel, Hebelstrasse 1, CH-4056 Basel, Switzerland.

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http://dx.doi.org/10.1111/j.1469-8137.2008.02649.xDOI Listing
March 2009

Genetic diversity of the arbuscular mycorrhizal fungus Glomus intraradices as determined by mitochondrial large subunit rRNA gene sequences is considerably higher than previously expected.

New Phytol 2008 17;180(2):452-465. Epub 2008 Jul 17.

Institute of Botany, University of Basel, Hebelstrasse 1, CH-4056 Basel, Switzerland.

Glomus intraradices is a widespread arbuscular mycorrhizal fungus (AMF), which has been found in an extremely broad range of habitats, indicating a high tolerance for environmental factors and a generalist life history strategy. Despite this ecological versatility, not much is known about the genetic diversity of this fungal species across different habitats or over large geographic scales. A nested polymerase chain reaction (PCR) approach for the mitochondrial rRNA large subunit gene (mtLSU), distinguished different haplotypes among cultivated isolates of G. intraradices and within mycorrhizal root samples from the field. From analysis of 16 isolates of this species originating from five continents, 12 mitochondrial haplotypes were distinguished. Five additional mtLSU haplotypes were detected in field-collected mycorrhizal roots. Some introns in the mtLSU region appear to be stable over years of cultivation and are ancestral to the G. intraradices clade. Genetic diversity within G. intraradices is substantially higher than previously thought, although some mtLSU haplotypes are widespread. A restriction fragment length polymorphism approach also was developed to distinguish mtLSU haplotypes without sequencing. Using this molecular tool, intraspecific genetic variation of an AMF species can be studied directly in field plants.
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http://dx.doi.org/10.1111/j.1469-8137.2008.02574.xDOI Listing
March 2009

Molecular community analysis of arbuscular mycorrhizal fungi in roots of geothermal soils in Yellowstone National Park (USA).

Microb Ecol 2008 Nov 1;56(4):649-59. Epub 2008 May 1.

Institute of Botany, University of Basel, Hebelstrasse 1, 4056 Basel, Switzerland.

To better understand adaptation of plants and their mycorrhizae to extreme environmental conditions, we analyzed the composition of communities of arbuscular mycorrhizal fungi (AMF) in roots from geothermal sites in Yellowstone National Park (YNP), USA. Arbuscular mycorrhizal fungi were identified using molecular methods including seven specific primer pairs for regions of the ribosomal DNA that amplify different subgroups of AMF. Roots of Dichanthelium lanuginosum, a grass only occurring in geothermal areas, were sampled along with thermal and nonthermal Agrostis scabra and control plants growing outside the thermally influenced sites. In addition, root samples of Agrostis stolonifera from geothermal areas of Iceland were analyzed to identify possible common mycosymbionts between these geographically isolated locations. In YNP, 16 ribosomal DNA phylotypes belonging to the genera Archaeospora, Glomus, Paraglomus, Scutellospora, and Acaulospora were detected. Eight of these phylotypes could be assigned to known morphospecies, two others have been reported previously in molecular studies from different environments, and six were new to science. The most diverse and abundant lineage was Glomus group A, with the most frequent phylotype corresponding to Glomus intraradices. Five of the seven phylotypes detected in a preliminary sampling in a geothermal area in Iceland were also found in YNP. Nonthermal vegetation was dominated by a high diversity of Glomus group A phylotypes while nonthermal plants were not. Using multivariate analyses, a subset of three phylotypes were determined to be associated with geothermal conditions in the field sites analyzed. In conclusion, AMF communities in geothermal soils are distinct in their composition, including both unique phylotypes and generalist fungi that occur across a broad range of environmental conditions.
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http://dx.doi.org/10.1007/s00248-008-9384-9DOI Listing
November 2008

Microsatellites for disentangling underground networks: strain-specific identification of Glomus intraradices, an arbuscular mycorrhizal fungus.

Fungal Genet Biol 2008 Jun 10;45(6):812-7. Epub 2008 Mar 10.

Botanical Institute, University of Basel, Hebelstrasse 1, 4056 Basel, Switzerland.

The underground network of arbuscular mycorrhizal (AM) fungi is decisive for the above-ground diversity of many plant ecosystems, but tools to investigate the population structure of AM fungi are sorely lacking. Here, we present a bioinformatics approach to identify microsatellite markers in the AM fungus Glomus intraradices. Based on 1958 contigs of this fungus, assembled from public databases, we identified 842 microsatellites. One hundred of them were subjected to closer scrutiny by designing flanking primers and performing an extensive screen to identify polymorphic loci. We obtained 18 polymorphic microsatellite markers, and we found that seven out of eight individual single-spore cultures of G. intraradices could readily be identified by at least five allelic differences, as compared to all other strains. Two single-spore cultures, however, nominally originating from completely different locations, displayed identity at all 18 loci, suggesting with 99.999999% probability that they represent a single clone.
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http://dx.doi.org/10.1016/j.fgb.2008.02.009DOI Listing
June 2008

The cultivation bias: different communities of arbuscular mycorrhizal fungi detected in roots from the field, from bait plants transplanted to the field, and from a greenhouse trap experiment.

Mycorrhiza 2007 Dec 19;18(1):1-14. Epub 2007 Sep 19.

Institute of Botany, University of Basel, Hebelstrasse 1, 4056, Basel, Switzerland.

The community composition of arbuscular mycorrhizal fungi (AMF) was investigated in roots of four different plant species (Inula salicina, Medicago sativa, Origanum vulgare, and Bromus erectus) sampled in (1) a plant species-rich calcareous grassland, (2) a bait plant bioassay conducted directly in that grassland, and (3) a greenhouse trap experiment using soil and a transplanted whole plant from that grassland as inoculum. Roots were analyzed by AMF-specific nested polymerase chain reaction, restriction fragment length polymorphism screening, and sequence analyses of rDNA small subunit and internal transcribed spacer regions. The AMF sequences were analyzed phylogenetically and used to define monophyletic phylotypes. Overall, 16 phylotypes from several lineages of AMF were detected. The community composition was strongly influenced by the experimental approach, with additional influence of cultivation duration, substrate, and host plant species in some experiments. Some fungal phylotypes, e.g., GLOM-A3 (Glomus mosseae) and several members of Glomus group B, appeared predominantly in the greenhouse experiment or in bait plants. Thus, these phylotypes can be considered r strategists, rapidly colonizing uncolonized ruderal habitats in early successional stages of the fungal community. In the greenhouse experiment, for instance, G. mosseae was abundant after 3 months, but could not be detected anymore after 10 months. In contrast, other phylotypes as GLOM-A17 (G. badium) and GLOM-A16 were detected almost exclusively in roots sampled from plants naturally growing in the grassland or from bait plants exposed in the field, indicating that they preferentially occur in late successional stages of fungal communities and thus represent the K strategy. The only phylotype found with high frequency in all three experimental approaches was GLOM A-1 (G. intraradices), which is known to be a generalist. These results indicate that, in greenhouse trap experiments, it is difficult to establish a root-colonizing AMF community reflecting the diversity of these fungi in the field roots because fungal succession in such artificial systems may bias the results. However, the field bait plant approach might be a convenient way to study the influence of different environmental factors on AMF community composition directly under the field conditions. For a better understanding of the dynamics of AMF communities, it will be necessary to classify AMF phylotypes and species according to their life history strategies.
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http://dx.doi.org/10.1007/s00572-007-0147-0DOI Listing
December 2007

Cooccurring Gentiana verna and Gentiana acaulis and their neighboring plants in two Swiss upper montane meadows harbor distinct arbuscular mycorrhizal fungal communities.

Appl Environ Microbiol 2007 Sep 13;73(17):5426-34. Epub 2007 Jul 13.

Institute of Botany, University of Basel, Hebelstrasse 1, CH-4056 Basel, Switzerland.

The community composition of arbuscular mycorrhizal fungi (AMF) was analyzed in roots of Gentiana verna, Gentiana acaulis, and accompanying plant species from two species-rich Swiss alpine meadows located in the same area. The aim of the study was to elucidate the impact of host preference or host specificity on the AMF community in the roots. The roots were analyzed by nested PCR, restriction fragment length polymorphism screening, and sequencing of ribosomal DNA small-subunit and internal transcribed spacer regions. The AMF sequences were analyzed phylogenetically and used to define monophyletic sequence types. The AMF community composition was strongly influenced by the host plant species, but compositions did not significantly differ between the two sites. Detailed analyses of the two cooccurring gentian species G. verna and G. acaulis, as well as of neighboring Trifolium spp., revealed that their AMF communities differed significantly. All three host plant taxa harbored AMF communities comprising multiple phylotypes from different fungal lineages. A frequent fungal phylotype from Glomus group B was almost exclusively found in Trifolium spp., suggesting some degree of host preference for this fungus in this habitat. In conclusion, the results indicate that within a relatively small area with similar soil and climatic conditions, the host plant species can have a major influence on the AMF communities within the roots. No evidence was found for a narrowing of the mycosymbiont spectrum in the two green gentians, in contrast to previous findings with their achlorophyllous relatives.
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http://dx.doi.org/10.1128/AEM.00987-07DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2042084PMC
September 2007

Phylogeny of the glomeromycota (arbuscular mycorrhizal fungi): recent developments and new gene markers.

Mycologia 2006 Nov-Dec;98(6):885-95

Institute of Botany, University of Basel, Hebelstasse 1, Basel, Switzerland.

The fungal symbionts of arbuscular mycorrhiza form a monophyletic group in the true Fungi, the phylum Glomeromycota. Fewer than 200 described species currently are included in this group. The only member of this clade known to form a different type of symbiosis is Geosiphon pyriformis, which associates with cyanobacteria. Because none of these fungi has been cultivated without their plant hosts or cyanobacterial partners, progress in obtaining multigene phylogenies has been slow and the nuclear-encoded ribosomal RNA genes have remained the only widely accessible molecular markers. rDNA phylogenies have revealed considerable polyphyly of some glomeromycotan genera that has been used to reassess taxonomic concepts. Environmental studies using phylogenetic methods for molecular identification have recovered an amazing diversity of unknown phylotypes, suggesting considerable cryptic species diversity. Protein gene sequences that have become available recently have challenged the rDNA-supported sister group relationship of the Glomeromycota with Asco/Basidiomycota. However the number of taxa analyzed with these new markers is still too small to provide a comprehensive picture of intraphylum relationships. We use nuclear-encoded rDNA and rpb1 protein gene sequences to reassess the phylogeny of the Glomeromycota and discuss possible implications.
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http://dx.doi.org/10.3852/mycologia.98.6.885DOI Listing
October 2007

Acaulospora alpina, a new arbuscular mycorrhizal fungal species characteristic for high mountainous and alpine regions of the Swiss Alps.

Mycologia 2006 Mar-Apr;98(2):286-94

Zurich-Basel Plant Science Center, Institute of Botany, University of Basel, Hebelstrasse 1, CH-4056 Basel, Switzerland.

Acaulospora alpina sp. nov. forms small (65-85 microm diam), dark yellow to orange-brown spores laterally on the neck of hyaline to subhyaline sporiferous saccules. The spores have a three-layered outer spore wall, a bi-layered middle wall and a three-layered inner wall. The surface of the second layer of the outer spore wall is ornamented, having regular, circular pits (1.5-2 microm diam) that are as deep as wide and truncated conical. A "beaded" wall layer as found in most other Acaulospora spp. is lacking. The spore morphology of A. alpina resembles that of A. paulinae but can be differentiated easily by the unique ornamentation with the characteristic pits and by the spore color. A key is presented summarizing the morphological differences among Acaulospora species with an ornamented outer spore wall. Partial DNA sequences of the ITS1, 5.8S subunit and ITS2 regions of ribosomal DNA show that A. alpina and A. paulinae are not closely related. Acaulospora lacunosa, which has similar color but has generally bigger spores, also has distinct rDNA sequences. Acaulospora alpina is a characteristic member of the arbuscular mycorrhizal fungal communities in soils with pH 3.5-6.5 in grasslands of the Swiss Alps at altitudes between 1800 and 2700 m above sea level. It is less frequent at 1300-1800 m above sea level, and it so far has not been found in the Alps below 1300 m or in the lowlands of Switzerland.
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http://dx.doi.org/10.3852/mycologia.98.2.286DOI Listing
September 2006

Communities of arbuscular mycorrhizal fungi in arable soils are not necessarily low in diversity.

Mol Ecol 2006 Jul;15(8):2277-89

Botanical Institute, University of Basel, Hebelstrasse, 1, CH-4056 Basel, Switzerland.

Communities of arbuscular mycorrhizal fungi (AMF) in five agricultural field sites of different management intensities were studied. Variable regions of the ribosomal RNA genes were used to detect and identify AMF directly within colonized roots. Roots from a continuous maize monoculture showed low AMF diversity, in agreement with previous reports on molecular diversity of AMF in agricultural soils. In contrast, a substantially higher diversity of AMF was found throughout the long term 'DOK' field experiment, where organic and conventional agricultural practices have been compared side by side since 1978. In this experiment, a 7-year crop rotation is performed under lower levels of inorganic fertilizer input and chemical pest control. These results are in good agreement with analyses of the spore community previously conducted in these field sites. In a third site, an organically managed leek field with soil of very high phosphate content reflecting the highly intensive conventional field history and intensive tillage, we detected a low-diversity community comparable to the maize monoculture. In addition to fungi from Glomus group A, which have previously been reported to dominate arable soils, we regularly found members of the genera Scutellospora, Paraglomus and Acaulospora. The genus Acaulospora was shown to occur more frequently early in the growing season, suggesting that the life history strategy of AMF may influence the active community at a given time. These data show that the diversity of AMF is not always low in arable soils. Furthermore, low-input agriculture involving crop rotation may provide better conditions to preserve AMF diversity, by preventing the selection for the few AMF taxa tolerating high nutrient levels.
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http://dx.doi.org/10.1111/j.1365-294X.2006.02921.xDOI Listing
July 2006

Evolution of metazoa and fungi.

Authors:
Dirk Redecker

Science 2006 Apr;312(5770):53-4; author reply 53-4

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http://dx.doi.org/10.1126/science.312.5770.53cDOI Listing
April 2006

Mitochondrial large ribosomal subunit sequences are homogeneous within isolates of Glomus (arbuscular mycorrhizal fungi, Glomeromycota).

Mycol Res 2005 Dec;109(Pt 12):1315-22

Institute of Botany, University of Basel, Hebelstr. 1, CH-4056 Basel, Switzerland.

Partial sequences of the mtLSU rDNA were obtained from the arbuscular mycorrhizal (AM) fungi Glomus proliferum (isolate DAOM 226389) and G. intraradices (isolates JJ291 and BEG75). The exon sequences of the two species showed regions of strong divergence. There was no evidence of intra-isolate sequence heterogeneity as it is found in variable regions of nuclear ribosomal genes of Glomeromycota. In G. intraradices JJ291, two introns were found in the partial LSU sequence. One of the introns contained an ORF for a putative site-specific homing endonuclease of the LAGLIDADG family. In G. intraradices BEG75, one of the introns was missing and the other had a DNA sequence distinct from JJ291. G. proliferum had no introns in the region sequenced. A PCR primer was designed to amplify the fragment of the mtLSU of a different, distinguishable G. intraradices genotype from colonized roots of a field sample. These mitochondrial gene sequences are the first reported from the phylum Glomeromycota. Our findings indicate that the intra-individual sequence heterogeneity of the Glomeromycota may be a peculiar feature of the nuclear genes. Therefore, mtLSU and its introns have the potential to be highly sensitive genetic markers for these fungi in the future.
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http://dx.doi.org/10.1017/s0953756205003977DOI Listing
December 2005

Bacteria associated with spores of the arbuscular mycorrhizal fungi Glomus geosporum and Glomus constrictum.

Appl Environ Microbiol 2005 Nov;71(11):6673-9

Laboratory of Microbiology, University of Neuchâtel, CP2, CH-2007, Neuchâtel, Switzerland.

Spores of the arbuscular mycorrhizal fungi (AMF) Glomus geosporum and Glomus constrictum were harvested from single-spore-derived pot cultures with either Plantago lanceolata or Hieracium pilosella as host plants. PCR-denaturing gradient gel electrophoresis analysis revealed that the bacterial communities associated with the spores depended more on AMF than host plant identity. The composition of the bacterial populations linked to the spores could be predominantly influenced by a specific spore wall composition or AMF exudate rather than by specific root exudates. The majority of the bacterial sequences that were common to both G. geosporum and G. constrictum spores were affiliated with taxonomic groups known to degrade biopolymers (Cellvibrio, Chondromyces, Flexibacter, Lysobacter, and Pseudomonas). Scanning electron microscopy of G. geosporum spores revealed that these bacteria are possibly feeding on the outer hyaline spore layer. The process of maturation and eventual germination of AMF spores might then benefit from the activity of the surface microorganisms degrading the outer hyaline wall layer.
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http://dx.doi.org/10.1128/AEM.71.11.6673-6679.2005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1287740PMC
November 2005