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Kokkoris V, Banchini C, Paré L, Abdellatif L, Séguin S, Hubbard K, Findlay W, Dalpé Y, Dettman J, Corradi N, Stefani F. Rhizophagus irregularis, the model fungus in arbuscular mycorrhiza research, forms dimorphic spores. THE NEW PHYTOLOGIST 2024; 242:1771-1784. [PMID: 37434339 DOI: 10.1111/nph.19121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 06/10/2023] [Indexed: 07/13/2023]
Abstract
Rhizophagus irregularis is the model species for arbuscular mycorrhizal fungi (AMF) research and the most widely propagated species for commercial plant biostimulants. Using asymbiotic and symbiotic cultivation systems initiated from single spores, advanced microscopy, Sanger sequencing of the glomalin gene, and PacBio sequencing of the partial 45S rRNA gene, we show that four strains of R. irregularis produce spores of two distinct morphotypes, one corresponding to the morphotype described in the R. irregularis protologue and the other having the phenotype of R. fasciculatus. The two spore morphs are easily distinguished by spore colour, thickness of the subtending hypha, thickness of the second wall layer, lamination of the innermost layer, and the dextrinoid reaction of the two outer spore wall layers to Melzer's reagent. The glomalin gene of the two spore morphs is identical and that of the PacBio sequences of the partial SSU-ITS-LSU region (2780 bp) obtained from single spores of the R. cf fasciculatus morphotype has a median pairwise similarity of 99.8% (SD = 0.005%) to the rDNA ribotypes of R. irregularis DAOM 197198. Based on these results, we conclude that the model AMF species R. irregularis is dimorphic, which has caused taxonomic confusion in culture collections and possibly in AMF research.
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Affiliation(s)
- Vasilis Kokkoris
- Department of Biology, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, K1A 0C6, Canada
- Amsterdam Institute for Life and Environment (A-LIFE), Faculty of Science, Section Systems Ecology, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV, Amsterdam, the Netherlands
| | - Claudia Banchini
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, K1A 0C6, Canada
| | - Louis Paré
- Université Laval, Centre d'Étude de la Forêt (CEF) and Institut de Biologie Intégrative et des Systèmes (IBIS), 1030 Ave de la Médecine, Québec, QC, G1V 0A6, Canada
| | - Lobna Abdellatif
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, K1A 0C6, Canada
| | - Sylvie Séguin
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, K1A 0C6, Canada
| | - Keith Hubbard
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, K1A 0C6, Canada
| | - Wendy Findlay
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, K1A 0C6, Canada
| | - Yolande Dalpé
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, K1A 0C6, Canada
| | - Jeremy Dettman
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, K1A 0C6, Canada
| | - Nicolas Corradi
- Department of Biology, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
| | - Franck Stefani
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, K1A 0C6, Canada
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Banerjee S, Zhao C, Garland G, Edlinger A, García-Palacios P, Romdhane S, Degrune F, Pescador DS, Herzog C, Camuy-Velez LA, Bascompte J, Hallin S, Philippot L, Maestre FT, Rillig MC, van der Heijden MGA. Biotic homogenization, lower soil fungal diversity and fewer rare taxa in arable soils across Europe. Nat Commun 2024; 15:327. [PMID: 38184663 PMCID: PMC10771452 DOI: 10.1038/s41467-023-44073-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 11/29/2023] [Indexed: 01/08/2024] Open
Abstract
Soil fungi are a key constituent of global biodiversity and play a pivotal role in agroecosystems. How arable farming affects soil fungal biogeography and whether it has a disproportional impact on rare taxa is poorly understood. Here, we used the high-resolution PacBio Sequel targeting the entire ITS region to investigate the distribution of soil fungi in 217 sites across a 3000 km gradient in Europe. We found a consistently lower diversity of fungi in arable lands than grasslands, with geographic locations significantly impacting fungal community structures. Prevalent fungal groups became even more abundant, whereas rare groups became fewer or absent in arable lands, suggesting a biotic homogenization due to arable farming. The rare fungal groups were narrowly distributed and more common in grasslands. Our findings suggest that rare soil fungi are disproportionally affected by arable farming, and sustainable farming practices should protect rare taxa and the ecosystem services they support.
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Affiliation(s)
- Samiran Banerjee
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND, 58102, USA.
- Agroscope, Plant-Soil Interactions Group, 8046, Zurich, Switzerland.
| | - Cheng Zhao
- ETH Zurich, Institute for Environmental Decisions, 8092, Zurich, Switzerland
| | - Gina Garland
- Agroscope, Plant-Soil Interactions Group, 8046, Zurich, Switzerland
| | - Anna Edlinger
- Agroscope, Plant-Soil Interactions Group, 8046, Zurich, Switzerland
- Wageningen Environmental Research, Wageningen University & Research, Droevendaalsesteeg 3, 6708 PB, Wageningen, The Netherlands
| | - Pablo García-Palacios
- Instituto de Ciencias Agrarias, Consejo Superior de Investigaciones Científicas, 28006, Madrid, Spain
- University of Zurich, Department of Plant and Microbial Biology, 8057, Zurich, Switzerland
| | - Sana Romdhane
- University Bourgogne Franche Comte, INRAE, Institut Agro Dijon, Agroecologie, Dijon, France
| | - Florine Degrune
- Freie Universität Berlin, Institute of Biology, Altensteinstr. 6, 14195, Berlin, Germany
| | - David S Pescador
- Departamento de Farmacología, Farmacognosia y Botánica, Facultad de Farmacia, Universidad Complutense de Madrid, 28940, Madrid, Spain
- Departamento de Biología y Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, 28933, Móstoles, Spain
| | - Chantal Herzog
- Agroscope, Plant-Soil Interactions Group, 8046, Zurich, Switzerland
| | - Lennel A Camuy-Velez
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND, 58102, USA
| | - Jordi Bascompte
- University of Zurich, Department of Evolutionary Biology and Environmental Studies, 8057, Zurich, Switzerland
| | - Sara Hallin
- Swedish University of Agricultural Sciences, Department of Forest Mycology and Plant Pathology, Box 7026, 750 07, Uppsala, Sweden
| | - Laurent Philippot
- University Bourgogne Franche Comte, INRAE, Institut Agro Dijon, Agroecologie, Dijon, France
| | - Fernando T Maestre
- Departamento de Ecología, Universidad de Alicante, Carretera de San Vicente del Raspeig s/n, 03690, San Vicente del Raspeig, Alicante, Spain
- Instituto Multidisciplinar para el Estudio del Medio "Ramón Margalef", Universidad de Alicante, Carretera de San Vicente del Raspeig s/n, 03690, San Vicente, del Raspeig, Alicante, Spain
| | - Matthias C Rillig
- Freie Universität Berlin, Institute of Biology, Altensteinstr. 6, 14195, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), 14195, Berlin, Germany
| | - Marcel G A van der Heijden
- Agroscope, Plant-Soil Interactions Group, 8046, Zurich, Switzerland.
- University of Zurich, Department of Plant and Microbial Biology, 8057, Zurich, Switzerland.
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3
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Yurkov AP, Kryukov AA, Gorbunova AO, Kudriashova TR, Kovalchuk AI, Gorenkova AI, Bogdanova EM, Laktionov YV, Zhurbenko PM, Mikhaylova YV, Puzanskiy RK, Bagrova TN, Yakhin OI, Rodionov AV, Shishova MF. Diversity of Arbuscular Mycorrhizal Fungi in Distinct Ecosystems of the North Caucasus, a Temperate Biodiversity Hotspot. J Fungi (Basel) 2023; 10:11. [PMID: 38248921 PMCID: PMC10817546 DOI: 10.3390/jof10010011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 12/11/2023] [Accepted: 12/19/2023] [Indexed: 01/23/2024] Open
Abstract
BACKGROUND Investigations that are focused on arbuscular mycorrhizal fungus (AMF) biodiversity is still limited. The analysis of the AMF taxa in the North Caucasus, a temperate biodiversity hotspot, used to be limited to the genus level. This study aimed to define the AMF biodiversity at the species level in the North Caucasus biotopes. METHODS The molecular genetic identification of fungi was carried out with ITS1 and ITS2 regions as barcodes via sequencing using Illumina MiSeq, the analysis of phylogenetic trees for individual genera, and searches for operational taxonomic units (OTUs) with identification at the species level. Sequences from MaarjAM and NCBI GenBank were used as references. RESULTS We analyzed >10 million reads in soil samples for three biotopes to estimate fungal biodiversity. Briefly, 50 AMF species belonging to 20 genera were registered. The total number of the AM fungus OTUs for the "Subalpine Meadow" biotope was 171/131, that for "Forest" was 117/60, and that for "River Valley" was 296/221 based on ITS1/ITS2 data. The total number of the AM fungus species (except for virtual taxa) for the "Subalpine Meadow" biotope was 24/19, that for "Forest" was 22/13, and that for "River Valley" was 28/24 based on ITS1/ITS2 data. Greater AMF diversity, as well as number of OTUs and species, in comparison with that of forest biotopes, characterized valley biotopes (disturbed ecosystems; grasslands). The correlation coefficient between "Percentage of annual plants" and "Glomeromycota total reads" r = 0.76 and 0.81 for ITS1 and ITS2, respectively, and the correlation coefficient between "Percentage of annual plants" and "OTUs number (for total species)" was r = 0.67 and 0.77 for ITS1 and ITS2, respectively. CONCLUSION High AMF biodiversity for the river valley can be associated with a higher percentage of annual plants in these biotopes and the active development of restorative successional processes.
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Affiliation(s)
- Andrey P. Yurkov
- Laboratory of Ecology of Symbiotic and Associative Rhizobacteria, All-Russia Research Institute for Agricultural Microbiology, Pushkin, 196608 St. Petersburg, Russia; (A.A.K.); (A.O.G.); (T.R.K.); (A.I.K.); (A.I.G.); (E.M.B.); (Y.V.L.)
| | - Alexey A. Kryukov
- Laboratory of Ecology of Symbiotic and Associative Rhizobacteria, All-Russia Research Institute for Agricultural Microbiology, Pushkin, 196608 St. Petersburg, Russia; (A.A.K.); (A.O.G.); (T.R.K.); (A.I.K.); (A.I.G.); (E.M.B.); (Y.V.L.)
| | - Anastasiia O. Gorbunova
- Laboratory of Ecology of Symbiotic and Associative Rhizobacteria, All-Russia Research Institute for Agricultural Microbiology, Pushkin, 196608 St. Petersburg, Russia; (A.A.K.); (A.O.G.); (T.R.K.); (A.I.K.); (A.I.G.); (E.M.B.); (Y.V.L.)
| | - Tatyana R. Kudriashova
- Laboratory of Ecology of Symbiotic and Associative Rhizobacteria, All-Russia Research Institute for Agricultural Microbiology, Pushkin, 196608 St. Petersburg, Russia; (A.A.K.); (A.O.G.); (T.R.K.); (A.I.K.); (A.I.G.); (E.M.B.); (Y.V.L.)
- Graduate School of Biotechnology and Food Science, Peter the Great St. Petersburg Polytechnic University, 194064 St. Petersburg, Russia
| | - Anastasia I. Kovalchuk
- Laboratory of Ecology of Symbiotic and Associative Rhizobacteria, All-Russia Research Institute for Agricultural Microbiology, Pushkin, 196608 St. Petersburg, Russia; (A.A.K.); (A.O.G.); (T.R.K.); (A.I.K.); (A.I.G.); (E.M.B.); (Y.V.L.)
- Graduate School of Biotechnology and Food Science, Peter the Great St. Petersburg Polytechnic University, 194064 St. Petersburg, Russia
| | - Anastasia I. Gorenkova
- Laboratory of Ecology of Symbiotic and Associative Rhizobacteria, All-Russia Research Institute for Agricultural Microbiology, Pushkin, 196608 St. Petersburg, Russia; (A.A.K.); (A.O.G.); (T.R.K.); (A.I.K.); (A.I.G.); (E.M.B.); (Y.V.L.)
- Faculty of Biology, St. Petersburg State University, 199034 St. Petersburg, Russia;
| | - Ekaterina M. Bogdanova
- Laboratory of Ecology of Symbiotic and Associative Rhizobacteria, All-Russia Research Institute for Agricultural Microbiology, Pushkin, 196608 St. Petersburg, Russia; (A.A.K.); (A.O.G.); (T.R.K.); (A.I.K.); (A.I.G.); (E.M.B.); (Y.V.L.)
- Faculty of Biology, St. Petersburg State University, 199034 St. Petersburg, Russia;
| | - Yuri V. Laktionov
- Laboratory of Ecology of Symbiotic and Associative Rhizobacteria, All-Russia Research Institute for Agricultural Microbiology, Pushkin, 196608 St. Petersburg, Russia; (A.A.K.); (A.O.G.); (T.R.K.); (A.I.K.); (A.I.G.); (E.M.B.); (Y.V.L.)
| | - Peter M. Zhurbenko
- Laboratory of Biosystematics and Cytology, Komarov Botanical Institute of the Russian Academy of Sciences, 197022 St. Petersburg, Russia; (P.M.Z.); (Y.V.M.); (A.V.R.)
| | - Yulia V. Mikhaylova
- Laboratory of Biosystematics and Cytology, Komarov Botanical Institute of the Russian Academy of Sciences, 197022 St. Petersburg, Russia; (P.M.Z.); (Y.V.M.); (A.V.R.)
| | - Roman K. Puzanskiy
- Laboratory of Analytical Phytochemistry, Komarov Botanical Institute of the Russian Academy of Sciences, 197022 St. Petersburg, Russia;
- Faculty of Ecology, Russian State Hydrometeorological University, 192007 St. Petersburg, Russia;
| | - Tatyana N. Bagrova
- Faculty of Ecology, Russian State Hydrometeorological University, 192007 St. Petersburg, Russia;
| | - Oleg I. Yakhin
- Institute of Biochemistry and Genetics, The Ufa Federal Research Center of the Russian Academy of Sciences, 450054 Ufa, Russia;
| | - Alexander V. Rodionov
- Laboratory of Biosystematics and Cytology, Komarov Botanical Institute of the Russian Academy of Sciences, 197022 St. Petersburg, Russia; (P.M.Z.); (Y.V.M.); (A.V.R.)
| | - Maria F. Shishova
- Faculty of Biology, St. Petersburg State University, 199034 St. Petersburg, Russia;
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4
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Lutz S, Bodenhausen N, Hess J, Valzano-Held A, Waelchli J, Deslandes-Hérold G, Schlaeppi K, van der Heijden MGA. Soil microbiome indicators can predict crop growth response to large-scale inoculation with arbuscular mycorrhizal fungi. Nat Microbiol 2023; 8:2277-2289. [PMID: 38030903 PMCID: PMC10730404 DOI: 10.1038/s41564-023-01520-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 10/11/2023] [Indexed: 12/01/2023]
Abstract
Alternative solutions to mineral fertilizers and pesticides that reduce the environmental impact of agriculture are urgently needed. Arbuscular mycorrhizal fungi (AMF) can enhance plant nutrient uptake and reduce plant stress; yet, large-scale field inoculation trials with AMF are missing, and so far, results remain unpredictable. We conducted on-farm experiments in 54 fields in Switzerland and quantified the effects on maize growth. Growth response to AMF inoculation was highly variable, ranging from -12% to +40%. With few soil parameters and mainly soil microbiome indicators, we could successfully predict 86% of the variation in plant growth response to inoculation. The abundance of pathogenic fungi, rather than nutrient availability, best predicted (33%) AMF inoculation success. Our results indicate that soil microbiome indicators offer a sustainable biotechnological perspective to predict inoculation success at the beginning of the growing season. This predictability increases the profitability of microbiome engineering as a tool for sustainable agricultural management.
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Affiliation(s)
- Stefanie Lutz
- Plant-Soil Interactions, Department of Agroecology and Environment, Agroscope, Zurich, Switzerland
| | - Natacha Bodenhausen
- Department of Soil Sciences, Research Institute of Organic Agriculture (FiBL), Frick, Switzerland
| | - Julia Hess
- Plant-Soil Interactions, Department of Agroecology and Environment, Agroscope, Zurich, Switzerland
| | - Alain Valzano-Held
- Plant-Soil Interactions, Department of Agroecology and Environment, Agroscope, Zurich, Switzerland
| | - Jan Waelchli
- Plant Microbe Interactions, Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Gabriel Deslandes-Hérold
- Plant Microbe Interactions, Department of Environmental Sciences, University of Basel, Basel, Switzerland
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
- Plant Biochemistry, Institute of Molecular Plant Biology, ETH Zurich, Zurich, Switzerland
| | - Klaus Schlaeppi
- Plant Microbe Interactions, Department of Environmental Sciences, University of Basel, Basel, Switzerland.
| | - Marcel G A van der Heijden
- Plant-Soil Interactions, Department of Agroecology and Environment, Agroscope, Zurich, Switzerland.
- Department of Plant and Microbial Biology, University of Zürich, Zurich, Switzerland.
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5
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Silva AMM, Feiler HP, Lacerda-Júnior GV, Fernandes-Júnior PI, de Tarso Aidar S, de Araújo VAVP, Matteoli FP, de Araújo Pereira AP, de Melo IS, Cardoso EJBN. Arbuscular mycorrhizal fungi associated with the rhizosphere of an endemic terrestrial bromeliad and a grass in the Brazilian neotropical dry forest. Braz J Microbiol 2023; 54:1955-1967. [PMID: 37410249 PMCID: PMC10485230 DOI: 10.1007/s42770-023-01058-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 06/19/2023] [Indexed: 07/07/2023] Open
Abstract
Arbuscular mycorrhizal fungi form symbiotic associations with 80-90% of all known plants, allowing the fungi to acquire plant-synthesized carbon, and confer an increased capacity for nutrient uptake by plants, improving tolerance to abiotic and biotic stresses. We aimed at characterizing the mycorrhizal community in the rhizosphere of Neoglaziovia variegata (so-called `caroa`) and Tripogonella spicata (so-called resurrection plant), using high-throughput sequencing of the partial 18S rRNA gene. Both plants are currently undergoing a bioprospecting program to find microbes with the potential of helping plants tolerate water stress. Sampling was carried out in the Caatinga biome, a neotropical dry forest, located in northeastern Brazil. Illumina MiSeq sequencing of 37 rhizosphere samples (19 for N. variegata and 18 for T. spicata) revealed a distinct mycorrhizal community between the studied plants. According to alpha diversity analyses, T. spicata showed the highest richness and diversity based on the Observed ASVs and the Shannon index, respectively. On the other hand, N. variegata showed higher modularity of the mycorrhizal network compared to T. spicata. The four most abundant genera found (higher than 10%) were Glomus, Gigaspora, Acaulospora, and Scutellospora, with Glomus being the most abundant in both plants. Nonetheless, Gigaspora, Diversispora, and Ambispora were found only in the rhizosphere of N. variegata, whilst Scutellospora, Paraglomus, and Archaeospora were exclusive to the rhizosphere of T. spicata. Therefore, the community of arbuscular mycorrhizal fungi of the rhizosphere of each plant encompasses a unique composition, structure and modularity, which can differentially assist them in the hostile environment.
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Affiliation(s)
- Antonio Marcos Miranda Silva
- “Luiz de Queiroz” College of Agriculture, Soil Science Department, University of São Paulo, Piracicaba, São Paulo 13418-900 Brazil
| | | | | | | | - Saulo de Tarso Aidar
- Brazilian Agricultural Research Corporation, Embrapa Semiárido, Petrolina, , Pernambuco 56302-970 Brazil
| | | | - Filipe Pereira Matteoli
- Faculty of Sciences, Department of Biological Sciences, Laboratory of Microbial Bioinformatics, São Paulo State University, Bauru, 17033-360 Brazil
| | | | - Itamar Soares de Melo
- Brazilian Agricultural Research Corporation, Embrapa Meio Ambiente, Jaguariúna, São Paulo 13918-110 Brazil
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Zhou T, Zhao F, Xu K. Information Scale Correction for Varying Length Amplicons Improves Eukaryotic Microbiome Data Integration. Microorganisms 2023; 11:microorganisms11040949. [PMID: 37110372 PMCID: PMC10146031 DOI: 10.3390/microorganisms11040949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 04/03/2023] [Accepted: 04/04/2023] [Indexed: 04/29/2023] Open
Abstract
The integration and reanalysis of big data provide valuable insights into microbiome studies. However, the significant difference in information scale between amplicon data poses a key challenge in data analysis. Therefore, reducing batch effects is crucial to enhance data integration for large-scale molecular ecology data. To achieve this, the information scale correction (ISC) step, involving cutting different length amplicons into the same sub-region, is essential. In this study, we used the Hidden Markov model (HMM) method to extract 11 different 18S rRNA gene v4 region amplicon datasets with 578 samples in total. The length of the amplicons ranged from 344 bp to 720 bp, depending on the primer position. By comparing the information scale correction of amplicons with varying lengths, we explored the extent to which the comparability between samples decreases with increasing amplicon length. Our method was shown to be more sensitive than V-Xtractor, the most popular tool for performing ISC. We found that near-scale amplicons exhibited no significant change after ISC, while larger-scale amplicons exhibited significant changes. After the ISC treatment, the similarity among the data sets improved, especially for long amplicons. Therefore, we recommend adding ISC processing when integrating big data, which is crucial for unlocking the full potential of microbial community studies and advancing our knowledge of microbial ecology.
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Affiliation(s)
- Tong Zhou
- Laboratory of Marine Organism Taxonomy and Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Feng Zhao
- Laboratory of Marine Organism Taxonomy and Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kuidong Xu
- Laboratory of Marine Organism Taxonomy and Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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7
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Boussageon R, van Tuinen D, Lapadatescu C, Trépanier M, Vermersch E, Wipf D, Courty PE. Effects of field inoculation of potato tubers with the arbuscular mycorrhizal fungus Rhizophagus irregularis DAOM 197,198 are cultivar dependent. Symbiosis 2023. [DOI: 10.1007/s13199-023-00908-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
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8
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Quantifying Trade-Offs in the Choice of Ribosomal Barcoding Markers for Fungal Amplicon Sequencing: a Case Study on the Grapevine Trunk Mycobiome. Microbiol Spectr 2022; 10:e0251322. [PMID: 36409146 PMCID: PMC9769941 DOI: 10.1128/spectrum.02513-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The evolution of sequencing technology and multiplexing has rapidly expanded our ability to characterize fungal diversity in the environment. However, obtaining an unbiased assessment of the fungal community using ribosomal markers remains challenging. Longer amplicons were shown to improve taxonomic resolution and resolve ambiguities by reducing the risk of spurious operational taxonomic units. We examined the implications of barcoding strategies by amplifying and sequencing two ribosomal DNA fragments. We analyzed the performance of the full internal transcribed spacer (ITS) and a longer fragment including also a part of the 28S ribosomal subunit replicated on 60 grapevine trunk core samples. Grapevine trunks harbor highly diverse fungal communities with implications for disease development. Using identical handling, amplification, and sequencing procedures, we obtained higher sequencing depths for the shorter ITS amplicon. Despite the more limited access to polymorphism, the overall diversity in amplified sequence variants was higher for the shorter ITS amplicon. We detected no meaningful bias in the phylogenetic composition due to the amplicon choice across analyzed samples. Despite the increased resolution of the longer ITS-28S amplicon, the higher and more consistent yields of the shorter amplicons produced a clearer resolution of the fungal community of grapevine stem samples. Our study highlights that the choice of ribosomal amplicons should be carefully evaluated and adjusted according to specific goals. IMPORTANCE Surveying fungal communities is key to our understanding of ecological functions of diverse habitats. Fungal communities can inform about the resilience of agricultural ecosystems, risks to human health, and impacts of pathogens. Community compositions are typically analyzed using ribosomal DNA sequences. Due to technical limitations, most fungal community surveys were based on amplifying a short but highly variable fragment. Advances in sequencing technology enabled the use of longer fragments that can address some limitations of species identification. In this study, we examined the implications of choosing either a short or long ribosomal sequence fragment by replicating the analyses on 60 grapevine wood core samples. Using highly accurate long-read sequencing, we found that the shorter fragment produced substantially higher yields. The shorter fragment also revealed more sequence and species diversity. Our study highlights that the choice of ribosomal amplicons should be carefully evaluated and adjusted according to specific goals.
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9
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Alguacil MDM, Schlaeppi K, López-García Á, van der Heijden MGA, Querejeta JI. Contrasting Responses of Arbuscular Mycorrhizal Fungal Families to Simulated Climate Warming and Drying in a Semiarid Shrubland. MICROBIAL ECOLOGY 2022; 84:941-944. [PMID: 34608508 DOI: 10.1007/s00248-021-01886-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 09/27/2021] [Indexed: 06/13/2023]
Abstract
We carried out a 4-year manipulative field experiment in a semiarid shrubland in southeastern Spain to assess the impacts of experimental warming (W), rainfall reduction (RR), and their combination (W + RR) on the composition and diversity of arbuscular mycorrhizal fungal (AMF) communities in rhizosphere soil of H. syriacum and G. struthium shrubs using single-molecule real-time (SMRT) DNA sequencing. Across climate treatments, we encountered 109 AMF operational taxonomic units (OTUs) that were assigned to four families: Glomeraceae (93.94%), Gigasporaceae (2.19%), Claroideoglomeraceae (1.95%), and Diversisporaceae (1.92%). AMF community composition and diversity at OTU level were unaffected by the climate manipulation treatments, except for a significant decrease in AMF OTU richness in the W treatment relative to the control. However, we found a significant decrease of AMF family richness in all climate manipulation treatments relative to the control treatment. Members of the Gigasporaceae and Diversisporaceae families appeared to be highly vulnerable to intensification of heat and drought stress, as their abundances decreased by 67% and 77%, respectively, in the W + RR treatment relative to current ambient conditions. In contrast, the relative abundance and dominance of the Glomeraceae family within the AMF community increased significantly under the W + RR treatment, with Glomeraceae being the indicator family for the W + RR treatment. The interaction between warming and rainfall reduction had a significant effect on AMF community structure at family level. These findings provide new insights to help in the conservation of the soil biodiversity facing climate change in dryland ecosystems.
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Affiliation(s)
- María Del Mar Alguacil
- Soil Microbiology and Symbiotic Systems Department, Estación Experimental del Zaidín, CSIC, Profesor Albareda 1, 18008, Granada, Spain.
| | - Klaus Schlaeppi
- Plant-Soil-Interactions, Institute for Sustainability Sciences, Agroscope, Reckenholzstrasse 191, 8046, Zürich, Switzerland
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
- Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Álvaro López-García
- Soil Microbiology and Symbiotic Systems Department, Estación Experimental del Zaidín, CSIC, Profesor Albareda 1, 18008, Granada, Spain
| | - Marcel G A van der Heijden
- Plant-Soil-Interactions, Institute for Sustainability Sciences, Agroscope, Reckenholzstrasse 191, 8046, Zürich, Switzerland
- Plant-Microbe-Interactions, Department of Biology, Utrecht University, 3508TB, Utrecht, The Netherlands
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057, Zürich, Switzerland
| | - José Ignacio Querejeta
- Department of Soil and Water Conservation, CSIC-Centro de Edafología Y Biología Aplicada del Segura, Campus de Espinardo, P.O. Box 164, 30100, Murcia, Spain
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The Potential Applications of Commercial Arbuscular Mycorrhizal Fungal Inoculants and Their Ecological Consequences. Microorganisms 2022; 10:microorganisms10101897. [PMID: 36296173 PMCID: PMC9609176 DOI: 10.3390/microorganisms10101897] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 09/17/2022] [Accepted: 09/19/2022] [Indexed: 11/18/2022] Open
Abstract
Arbuscular mycorrhizal fungal (AMF) inoculants are sustainable biological materials that can provide several benefits to plants, especially in disturbed agroecosystems and in the context of phytomanagement interventions. However, it is difficult to predict the effectiveness of AMF inoculants and their impacts on indigenous AMF communities under field conditions. In this review, we examined the literature on the possible outcomes following the introduction of AMF-based inoculants in the field, including their establishment in soil and plant roots, persistence, and effects on the indigenous AMF community. Most studies indicate that introduced AMF can persist in the target field from a few months to several years but with declining abundance (60%) or complete exclusion (30%). Further analysis shows that AMF inoculation exerts both positive and negative impacts on native AMF species, including suppression (33%), stimulation (38%), exclusion (19%), and neutral impacts (10% of examined cases). The factors influencing the ecological fates of AMF inoculants, such as the inherent properties of the inoculum, dosage and frequency of inoculation, and soil physical and biological factors, are further discussed. While it is important to monitor the success and downstream impacts of commercial inoculants in the field, the sampling method and the molecular tools employed to resolve and quantify AMF taxa need to be improved and standardized to eliminate bias towards certain AMF strains and reduce discrepancies among studies. Lastly, inoculant producers must focus on selecting strains with a higher chance of success in the field, and having little or negligible downstream impacts.
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11
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Ogaji YO, Lee RC, Sawbridge TI, Cocks BG, Daetwyler HD, Kaur S. De Novo Long-Read Whole-Genome Assemblies and the Comparative Pan-Genome Analysis of Ascochyta Blight Pathogens Affecting Field Pea. J Fungi (Basel) 2022; 8:jof8080884. [PMID: 36012871 PMCID: PMC9410150 DOI: 10.3390/jof8080884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 08/12/2022] [Accepted: 08/15/2022] [Indexed: 11/16/2022] Open
Abstract
Ascochyta Blight (AB) is a major disease of many cool-season legumes globally. In field pea, three fungal pathogens have been identified to be responsible for this disease in Australia, namely Peyronellaea pinodes, Peyronellaea pinodella and Phoma koolunga. Limited genomic resources for these pathogens have been generated, which has hampered the implementation of effective management strategies and breeding for resistant cultivars. Using Oxford Nanopore long-read sequencing, we report the first high-quality, fully annotated, near-chromosome-level nuclear and mitochondrial genome assemblies for 18 isolates from the Australian AB complex. Comparative genome analysis was performed to elucidate the differences and similarities between species and isolates using phylogenetic relationships and functional diversity. Our data indicated that P. pinodella and P. koolunga are heterothallic, while P. pinodes is homothallic. More homology and orthologous gene clusters are shared between P. pinodes and P. pinodella compared to P. koolunga. The analysis of the repetitive DNA content showed differences in the transposable repeat composition in the genomes and their expression in the transcriptomes. Significant repeat expansion in P. koolunga’s genome was seen, with strong repeat-induced point mutation (RIP) activity being evident. Phylogenetic analysis revealed that genetic diversity can be exploited for species marker development. This study provided the much-needed genetic resources and characterization of the AB species to further drive research in key areas such as disease epidemiology and host–pathogen interactions.
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Affiliation(s)
- Yvonne O. Ogaji
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring Road, Melbourne, VIC 3083, Australia
- School of Applied Systems Biology, La Trobe University, Melbourne, VIC 3086, Australia
| | - Robert C. Lee
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Perth, WA 6102, Australia
| | - Tim I. Sawbridge
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring Road, Melbourne, VIC 3083, Australia
- School of Applied Systems Biology, La Trobe University, Melbourne, VIC 3086, Australia
| | - Benjamin G. Cocks
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring Road, Melbourne, VIC 3083, Australia
- School of Applied Systems Biology, La Trobe University, Melbourne, VIC 3086, Australia
| | - Hans D. Daetwyler
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring Road, Melbourne, VIC 3083, Australia
- School of Applied Systems Biology, La Trobe University, Melbourne, VIC 3086, Australia
| | - Sukhjiwan Kaur
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring Road, Melbourne, VIC 3083, Australia
- Correspondence:
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12
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Delavaux CS, Ramos RJ, Sturmer SL, Bever JD. Environmental identification of arbuscular mycorrhizal fungi using the LSU rDNA gene region: an expanded database and improved pipeline. MYCORRHIZA 2022; 32:145-153. [PMID: 35099622 PMCID: PMC8907093 DOI: 10.1007/s00572-022-01068-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 01/18/2022] [Indexed: 05/02/2023]
Abstract
Arbuscular mycorrhizal fungi (AMF; Glomeromycota) are difficult to culture; therefore, establishing a robust amplicon-based approach to taxa identification is imperative to describe AMF diversity. Further, due to low and biased sampling of AMF taxa, molecular databases do not represent the breadth of AMF diversity, making database matching approaches suboptimal. Therefore, a full description of AMF diversity requires a tool to determine sequence-based placement in the Glomeromycota clade. Nonetheless, commonly used gene regions, including the SSU and ITS, do not enable reliable phylogenetic placement. Here, we present an improved database and pipeline for the phylogenetic determination of AMF using amplicons from the large subunit (LSU) rRNA gene. We improve our database and backbone tree by including additional outgroup sequences. We also improve an existing bioinformatics pipeline by aligning forward and reverse reads separately, using a universal alignment for all tree building, and implementing a BLAST screening prior to tree building to remove non-homologous sequences. Finally, we present a script to extract AMF belonging to 11 major families as well as an amplicon sequencing variant (ASV) version of our pipeline. We test the utility of the pipeline by testing the placement of known AMF, known non-AMF, and Acaulospora sp. spore sequences. This work represents the most comprehensive database and pipeline for phylogenetic placement of AMF LSU amplicon sequences within the Glomeromycota clade.
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Affiliation(s)
- Camille S Delavaux
- Department of Ecology and Evolutionary Biology, The University of Kansas, 2041 Haworth Hall, 1200 Sunnyside Avenue, Lawrence, KS, 66045, USA.
- Kansas Biological Survey, The University of Kansas, 106 Higuchi Hall, 2101 Constant Ave, Lawrence, KS, 66047, USA.
- Department of Environmental Systems Science, ETH Zurich, Universitätstrasse 16, 8092, Zurich, Switzerland.
| | - Robert J Ramos
- Department of Ecology and Evolutionary Biology, The University of Kansas, 2041 Haworth Hall, 1200 Sunnyside Avenue, Lawrence, KS, 66045, USA
- Kansas Biological Survey, The University of Kansas, 106 Higuchi Hall, 2101 Constant Ave, Lawrence, KS, 66047, USA
| | - Sidney L Sturmer
- Departamento de Ciências Naturais, Universidade Regional de Blumenau, R. Antônio da Veiga 140Santa Catarina, Blumenau, 89030-903, Brazil
| | - James D Bever
- Department of Ecology and Evolutionary Biology, The University of Kansas, 2041 Haworth Hall, 1200 Sunnyside Avenue, Lawrence, KS, 66045, USA
- Kansas Biological Survey, The University of Kansas, 106 Higuchi Hall, 2101 Constant Ave, Lawrence, KS, 66047, USA
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Gueidan C, Li L. A long-read amplicon approach to scaling up the metabarcoding of lichen herbarium specimens. MycoKeys 2022; 86:195-212. [PMID: 35153530 PMCID: PMC8828592 DOI: 10.3897/mycokeys.86.77431] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 01/24/2022] [Indexed: 01/04/2023] Open
Abstract
Reference sequence databases are critical to the accurate detection and identification of fungi in the environment. As repositories of large numbers of well-curated specimens, herbaria and fungal culture collections have the material resources to generate sequence data for large number of taxa, and could therefore allow filling taxonomic gaps often present in reference sequence databases. Financial resources to do that are however often lacking, so that recent efforts have focused on decreasing sequencing cost by increasing the number of multiplexed samples per sequencing run while maintaining high sequence quality. Following a previous study that aimed at decreasing sequencing cost for lichen specimens by generating fungal ITS barcodes for 96 specimens using PacBio amplicon sequencing, we present a method that further decreases lichen specimen metabarcoding costs. A total of 384 mixed DNA extracts obtained from lichen herbarium specimens, mostly from the four genera Buellia, Catillaria, Endocarpon and Parmotrema, were used to generate new fungal ITS sequences using a Sequel I sequencing platform and the PacBio M13 barcoded primers. The average success rate across all taxa was high (86.5%), with particularly high rates for the crustose saxicolous taxa (Buellia, Catillaria and others; 93.3%) and the terricolous squamulose taxa (Endocarpon and others; 96.5%). On the other hand, the success rate for the foliose genus Parmotrema was lower (60.4%). With this taxon sampling, greater specimen age did not appear to impact sequencing success. In fact, the 1966–1980 collection date category showed the highest success rate (97.3%). Compared to the previous study, the abundance-based sequence denoising method showed some limitations, but the cost of generating ITS barcodes was further decreased thanks to the higher multiplexing level. In addition to contributing new ITS barcodes for specimens of four interesting lichen genera, this study further highlights the potential and challenges of using new sequencing technologies on collection specimens to generate DNA sequences for reference databases.
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Xue Y, Chen L, Zhao Y, Feng Q, Li C, Wei Y. Shift of soil fungal communities under afforestation in Nanliu River Basin, southwest China. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 302:114130. [PMID: 34801868 DOI: 10.1016/j.jenvman.2021.114130] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 11/09/2021] [Accepted: 11/16/2021] [Indexed: 06/13/2023]
Abstract
Although soil fungi play a pivotal role in determining soil ecosystematic feedbacks to afforestation, there remains a big knowledge gap in the effects of afforestation on soil fungal communities, especially at a watershed scale. In this study, the variations of soil fungal diversity and community structures under afforestation were investigated in Nanliu River Basin, where paddy field and dry farmland were converted to eucalyptus plantation at an unprecedented speed. Spatial distance along the upper, middle and lower reaches of the Basin were also considered to analyze the dominant sources of the variations. The results demonstrated that eucalyptus afforestation had little effect on soil fungal diversity but could significantly influence fungal community structures. As paddy field and dry farmland converted to eucalyptus plantation, dominant fungal phylum shifted from Ascomycota to Ascomycota and Basidiomycota. Compared with afforestation from dry farmland, much bigger variation of fungal community structures was found in afforestation from paddy field. In addition, the significant change of fungal community structures exhibited in the upper reaches was from dry farmland, while presented in the middle reaches was from paddy field. However, afforestation comprised a larger source of variation than spatial distance within the soil fungal community structures, and Fusarium, Westerdykella,Zopfiella and Scleroderma were the most sensitive genera affected by afforestation. These results showed that afforestation did not always cause soil fungal diversity change and the heterogeneity of fungal community structures under afforestation was mainly controlled by original land use practices, while spatial distance partly decided the results.
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Affiliation(s)
- Yuanyuan Xue
- Key Laboratory of Ecohydrology of Inland River Basin, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lijuan Chen
- Key Laboratory of Ecohydrology of Inland River Basin, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China.
| | - Yinjun Zhao
- Key Laboratory of Environment Change and Resources Use in Beibu Gulf, Ministry of Education, School of Geography and Planning, Nanning Normal University, Nanning, 530001, China.
| | - Qi Feng
- Key Laboratory of Ecohydrology of Inland River Basin, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
| | - Changsheng Li
- University of Chinese Academy of Sciences, Beijing, 100049, China; Shapotou Desert Research and Experimental Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
| | - Yongping Wei
- School of Earth and Environmental Sciences, The University of Queensland, Brisbane, 4072, Australia
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15
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Walker C, Schüßler A, Vincent B, Cranenbrouck S, Declerck S. Anchoring the species Rhizophagus intraradices (formerly Glomus intraradices). Fungal Syst Evol 2022; 8:179-201. [PMID: 35005581 PMCID: PMC8687058 DOI: 10.3114/fuse.2021.08.14] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 11/06/2021] [Indexed: 11/07/2022] Open
Abstract
The nomenclatural type material of Rhizophagus intraradices (basionym Glomus intraradices) was originally described from a trap pot culture established with root fragments, subcultures of which later became registered in the INVAM culture collection as FL 208. Subcultures of FL 208 (designated as strain ATT 4) and a new strain, independently isolated from the type location (ATT 1102), were established as both pot cultures with soil-like substrate and in vitro root organ culture. Long-term sampling of these cultures shows spores of the species to have considerable morphological plasticity, not described in the original description. Size, shape and other features of the spores were much more variable than indicated in the protologue. Phylogenetic analyses confirmed earlier published evidence that sequences from all R. intraradices cultures formed a monophyletic clade, well separated from, and not representing a sister clade to, R. irregularis. Moreover, new phylogenetic analyses show that Rhizoglomus venetianum and R. irregularis are synonymous. The morphological characters used to separate these species exemplify the difficulties in species recognition due to the high phenotypic plasticity in the genus Rhizophagus. Rhizophagus intraradices is morphologically re-described, an epitype is designated from a single-spore isolate derived from ATT 4, and R. venetianum is synonymised with R. irregularis.
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Affiliation(s)
- C Walker
- Royal Botanic Garden Edinburgh, 21A Inverleith Row, Edinburgh EH3 5LR, UK.,School of Agriculture and Environment, University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
| | - A Schüßler
- SYMPLANTA GmbH & Co. KG, Graupnerweg 42, 64287 Darmstadt, Germany
| | - B Vincent
- Université catholique de Louvain, Earth and Life Institute, Mycology, Croix du Sud, 2 box L7.05.06, 1348 Louvain-la-Neuve, Belgium
| | - S Cranenbrouck
- Université catholique de Louvain, Earth and Life Institute, Mycology, Mycothèque de l'Université catholique de Louvain (MUCL), Croix du Sud, 2 Box L7.05.06, 1348 Louvain-la-Neuve, Belgium
| | - S Declerck
- Université catholique de Louvain, Earth and Life Institute, Mycology, Croix du Sud, 2 box L7.05.06, 1348 Louvain-la-Neuve, Belgium
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Sildever S, Laas P, Kolesova N, Lips I, Lips U, Nagai S. Plankton biodiversity and species co-occurrence based on environmental DNA – a multiple marker study. METABARCODING AND METAGENOMICS 2021. [DOI: 10.3897/mbmg.5.72371] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Metabarcoding in combination with high-throughput sequencing (HTS) allows simultaneous detection of multiple taxa by targeting single or several taxonomically informative gene regions from environmental DNA samples. In this study, a multiple-marker HTS approach was applied to investigate the plankton diversity and seasonal succession in the Baltic Sea from winter to autumn. Four different markers targeting the 16S, 18S, and 28S ribosomal RNA genes were employed, including a marker for more efficient dinoflagellate detection. Typical seasonal changes were observed in phyto- and bacterioplankton communities. In phytoplankton, the appearance patterns of selected common, dominant, or harmful species followed the patterns also confirmed based on 20 years of phytoplankton monitoring data. In the case of zooplankton, both macro- and microzooplankton species were detected. However, no seasonal patterns were detected in their appearance. In total, 15 and 2 new zoo- and phytoplankton species were detected from the Baltic Sea. HTS approach was especially useful for detecting microzooplankton species as well as for investigating the co-occurrence and potential interactions of different taxa. The results of this study further exemplify the efficiency of metabarcoding for biodiversity monitoring and the advantage of employing multiple markers through the detection of species not identifiable based on a single marker survey and/or by traditional morphology-based methods.
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Sportes A, Hériché M, Boussageon R, Noceto PA, van Tuinen D, Wipf D, Courty PE. A historical perspective on mycorrhizal mutualism emphasizing arbuscular mycorrhizas and their emerging challenges. MYCORRHIZA 2021; 31:637-653. [PMID: 34657204 DOI: 10.1007/s00572-021-01053-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 09/15/2021] [Indexed: 06/13/2023]
Abstract
Arbuscular mycorrhiza, one of the oldest interactions on earth (~ 450 million years old) and a first-class partner for plants to colonize emerged land, is considered one of the most pervasive ecological relationships on the globe. Despite how important and old this interaction is, its discovery was very recent compared to the long story of land plant evolution. The story of the arbuscular mycorrhiza cannot be addressed apart from the history, controversies, and speculations about mycorrhiza in its broad sense. The chronicle of mycorrhizal research is marked by multiple key milestones such as the initial description of a "persistent epiderm and pellicular wall structure" by Hartig; the introduction of the "Symbiotismus" and "Mycorrhiza" concepts by Frank; the description of diverse root-fungal morphologies; the first description of arbuscules by Gallaud; Mosse's pivotal statement of the beneficial nature of the arbuscular mycorrhizal symbiosis; the impact of molecular tools on the taxonomy of mycorrhizal fungi as well as the development of in vitro root organ cultures for producing axenic arbuscular mycorrhizal fungi (AMF). An appreciation of the story - full of twists and turns - of the arbuscular mycorrhiza, going from the roots of mycorrhiza history, along with the discovery of different mycorrhiza types such as ectomycorrhiza, can improve research to help face our days' challenge of developing sustainable agriculture that integrates the arbuscular mycorrhiza and its ecosystem services.
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Affiliation(s)
- Antoine Sportes
- Agroécologie, AgroSup Dijon, CNRS, Université de Bourgogne, INRAE, Université de Bourgogne Franche-Comté, Dijon, France
| | - Mathilde Hériché
- Agroécologie, AgroSup Dijon, CNRS, Université de Bourgogne, INRAE, Université de Bourgogne Franche-Comté, Dijon, France
| | - Raphaël Boussageon
- Agroécologie, AgroSup Dijon, CNRS, Université de Bourgogne, INRAE, Université de Bourgogne Franche-Comté, Dijon, France
| | - Pierre-Antoine Noceto
- Agroécologie, AgroSup Dijon, CNRS, Université de Bourgogne, INRAE, Université de Bourgogne Franche-Comté, Dijon, France
| | - Diederik van Tuinen
- Agroécologie, AgroSup Dijon, CNRS, Université de Bourgogne, INRAE, Université de Bourgogne Franche-Comté, Dijon, France
| | - Daniel Wipf
- Agroécologie, AgroSup Dijon, CNRS, Université de Bourgogne, INRAE, Université de Bourgogne Franche-Comté, Dijon, France
| | - Pierre Emmanuel Courty
- Agroécologie, AgroSup Dijon, CNRS, Université de Bourgogne, INRAE, Université de Bourgogne Franche-Comté, Dijon, France.
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Querejeta JI, Schlaeppi K, López-García Á, Ondoño S, Prieto I, van der Heijden MGA, Del Mar Alguacil M. Lower relative abundance of ectomycorrhizal fungi under a warmer and drier climate is linked to enhanced soil organic matter decomposition. THE NEW PHYTOLOGIST 2021; 232:1399-1413. [PMID: 34342894 DOI: 10.1111/nph.17661] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 07/23/2021] [Indexed: 06/13/2023]
Abstract
The aboveground impacts of climate change receive extensive research attention, but climate change could also alter belowground processes such as the delicate balance between free-living fungal decomposers and nutrient-scavenging mycorrhizal fungi that can inhibit decomposition through a mechanism called the Gadgil effect. We investigated how climate change-induced reductions in plant survival, photosynthesis and productivity alter soil fungal community composition in a mixed arbuscular/ectomycorrhizal (AM/EM) semiarid shrubland exposed to experimental warming (W) and/or rainfall reduction (RR). We hypothesised that increased EM host plant mortality under a warmer and drier climate might decrease ectomycorrhizal fungal (EMF) abundance, thereby favouring the proliferation and activity of fungal saprotrophs. The relative abundance of EMF sequences decreased by 57.5% under W+RR, which was accompanied by reductions in the activity of hydrolytic enzymes involved in the acquisition of organic-bound nutrients by EMF and their host plants. W+RR thereby created an enhanced potential for soil organic matter (SOM) breakdown and nitrogen mineralisation by decomposers, as revealed by 127-190% increases in dissolved organic carbon and nitrogen, respectively, and decreasing SOM content in soil. Climate aridification impacts on vegetation can cascade belowground through shifts in fungal guild structure that alter ecosystem biogeochemistry and accelerate SOM decomposition by reducing the Gadgil effect.
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Affiliation(s)
- José Ignacio Querejeta
- Department of Soil and Water Conservation (CEBAS-CSIC), CSIC-Centro de Edafología y Biología Aplicada del Segura, PO Box 164, Campus de Espinardo, 30100, Murcia, Spain
| | - Klaus Schlaeppi
- Plant-Soil-Interactions, Institute for Sustainability Sciences, Agroscope, Reckenholzstrasse 191, 8046, Zürich, Switzerland
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, 3013, Bern, Switzerland
- Department of Environmental Sciences, University of Basel, Bernoullistrasse 32, 4056, Basel, Switzerland
| | - Álvaro López-García
- Soil Microbiology and Symbiotic Systems Department, Estación Experimental del Zaidín (EEZ-CSIC), Profesor Albareda 1, Granada, 18008, Spain
| | - Sara Ondoño
- Department of Soil and Water Conservation (CEBAS-CSIC), CSIC-Centro de Edafología y Biología Aplicada del Segura, PO Box 164, Campus de Espinardo, 30100, Murcia, Spain
| | - Iván Prieto
- Department of Soil and Water Conservation (CEBAS-CSIC), CSIC-Centro de Edafología y Biología Aplicada del Segura, PO Box 164, Campus de Espinardo, 30100, Murcia, Spain
| | - Marcel G A van der Heijden
- Plant-Soil-Interactions, Institute for Sustainability Sciences, Agroscope, Reckenholzstrasse 191, 8046, Zürich, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057, Zürich, Switzerland
- Plant-Microbe-Interactions, Department of Biology, Utrecht University, 3508TB, Utrecht, the Netherlands
| | - María Del Mar Alguacil
- Soil Microbiology and Symbiotic Systems Department, Estación Experimental del Zaidín (EEZ-CSIC), Profesor Albareda 1, Granada, 18008, Spain
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Nelson JM, Hauser DA, Li FW. The diversity and community structure of symbiotic cyanobacteria in hornworts inferred from long-read amplicon sequencing. AMERICAN JOURNAL OF BOTANY 2021; 108:1731-1744. [PMID: 34533221 DOI: 10.1002/ajb2.1729] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 05/16/2021] [Accepted: 05/17/2021] [Indexed: 06/13/2023]
Abstract
PREMISE Nitrogen-fixing endosymbioses with cyanobacteria have evolved independently in five very different plant lineages. Expanding knowledge of these symbioses promises to improve the understanding of symbiosis evolution and broaden the toolkit for agricultural engineering to reduce artificial fertilizer use. Here we focused on hornworts, a bryophyte lineage in which all members host cyanobacteria, and investigated factors shaping the diversity of their cyanobiont communities. METHODS We sampled hornworts and adjacent soils in upstate New York throughout the hornwort growing season. We included all three sympatric hornwort species in the area, allowing us to directly compare partner selectivity. To profile cyanobacteria communities, we established a metabarcoding protocol targeting rbcL-X with PacBio long reads. RESULTS The hornwort cyanobionts detected were phylogenetically diverse, including clades that do not contain other known plant symbionts. We found significant overlap between hornwort cyanobionts and soil cyanobacteria, a pattern not previously reported in other plant-cyanobacteria symbioses. Cyanobiont communities differed between host plants only centimeters apart, but we did not detect an effect of sampling time or host species on the cyanobacterial community structure. CONCLUSIONS This study expands the phylogenetic diversity of known symbiotic cyanobacteria. Our analyses suggest that hornwort cyanobionts have a tight connection to the soil background, and we found no evidence that time within growing season, host species, or distance at the scale of meters strongly govern cyanobacteria community assembly. This study provides a critical foundation for further study of the ecology, evolution, and interaction dynamics of plant-cyanobacteria symbiosis.
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Affiliation(s)
| | | | - Fay-Wei Li
- Boyce Thompson Institute, Ithaca, NY, USA
- Plant Biology Section, Cornell University, Ithaca, NY, USA
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20
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Kumar V, Sarma VV, Thambugala KM, Huang JJ, Li XY, Hao GF. Ecology and Evolution of Marine Fungi With Their Adaptation to Climate Change. Front Microbiol 2021; 12:719000. [PMID: 34512597 PMCID: PMC8430337 DOI: 10.3389/fmicb.2021.719000] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 08/10/2021] [Indexed: 01/04/2023] Open
Abstract
Climate change agitates interactions between organisms and the environment and forces them to adapt, migrate, get replaced by others, or extinct. Marine environments are extremely sensitive to climate change that influences their ecological functions and microbial community including fungi. Fungi from marine habitats are engaged and adapted to perform diverse ecological functions in marine environments. Several studies focus on how complex interactions with the surrounding environment affect fungal evolution and their adaptation. However, a review addressing the adaptation of marine fungi to climate change is still lacking. Here we have discussed the adaptations of fungi in the marine environment with an example of Hortaea werneckii and Aspergillus terreus which may help to reduce the risk of climate change impacts on marine environments and organisms. We address the ecology and evolution of marine fungi and the effects of climate change on them to explain the adaptation mechanism. A review of marine fungal adaptations will show widespread effects on evolutionary biology and the mechanism responsible for it.
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Affiliation(s)
- Vinit Kumar
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang, China
| | | | - Kasun M. Thambugala
- Genetics and Molecular Biology Unit, Faculty of Applied Sciences, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
| | - Jun-Jie Huang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang, China
| | - Xiang-Yang Li
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang, China
| | - Ge-Fei Hao
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang, China
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21
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Tedersoo L, Albertsen M, Anslan S, Callahan B. Perspectives and Benefits of High-Throughput Long-Read Sequencing in Microbial Ecology. Appl Environ Microbiol 2021; 87:e0062621. [PMID: 34132589 PMCID: PMC8357291 DOI: 10.1128/aem.00626-21] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Short-read, high-throughput sequencing (HTS) methods have yielded numerous important insights into microbial ecology and function. Yet, in many instances short-read HTS techniques are suboptimal, for example, by providing insufficient phylogenetic resolution or low integrity of assembled genomes. Single-molecule and synthetic long-read (SLR) HTS methods have successfully ameliorated these limitations. In addition, nanopore sequencing has generated a number of unique analysis opportunities, such as rapid molecular diagnostics and direct RNA sequencing, and both Pacific Biosciences (PacBio) and nanopore sequencing support detection of epigenetic modifications. Although initially suffering from relatively low sequence quality, recent advances have greatly improved the accuracy of long-read sequencing technologies. In spite of great technological progress in recent years, the long-read HTS methods (PacBio and nanopore sequencing) are still relatively costly, require large amounts of high-quality starting material, and commonly need specific solutions in various analysis steps. Despite these challenges, long-read sequencing technologies offer high-quality, cutting-edge alternatives for testing hypotheses about microbiome structure and functioning as well as assembly of eukaryote genomes from complex environmental DNA samples.
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Affiliation(s)
- Leho Tedersoo
- Mycology and Microbiology Center, University of Tartu, Tartu, Estonia
| | - Mads Albertsen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Sten Anslan
- Mycology and Microbiology Center, University of Tartu, Tartu, Estonia
- Braunschweig University of Technology, Zoological Institute, Braunschweig, Germany
| | - Benjamin Callahan
- Department of Population Health and Pathobiology, College of Veterinary Medicine and Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina, USA
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22
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Kolaříková Z, Slavíková R, Krüger C, Krüger M, Kohout P. PacBio sequencing of Glomeromycota rDNA: a novel amplicon covering all widely used ribosomal barcoding regions and its applicability in taxonomy and ecology of arbuscular mycorrhizal fungi. THE NEW PHYTOLOGIST 2021; 231:490-499. [PMID: 33780549 DOI: 10.1111/nph.17372] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 03/23/2021] [Indexed: 05/02/2023]
Abstract
There is no consensus barcoding region for determination of arbuscular mycorrhizal fungal (AMF) taxa. To overcome this obstacle, we have developed an approach to sequence an AMF marker within the ribosome-encoding operon (rDNA) that covers all three widely applied variable molecular markers. Using a nested PCR approach specific to AMF, we amplified a part (c. 2.5 kb) of the rDNA spanning the majority of the small subunit rRNA (SSU) gene, the complete internal transcribed spacer (ITS) region and a part of the large subunit (LSU) rRNA gene. The PCR products were sequenced on the PacBio platform utilizing Single Molecule Real Time (SMRT) sequencing. Employing this method for selected environmental DNA samples, we were able to describe complex AMF communities consisting of various glomeromycotan lineages. We demonstrate the applicability of this new 2.5 kb approach to provide robust phylogenetic assignment of AMF lineages without known sequences from pure cultures and to consolidate information about AMF taxon distributions coming from three widely used barcoding regions into one integrative dataset.
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Affiliation(s)
- Zuzana Kolaříková
- Institute of Botany of the Czech Academy of Sciences, Průhonice, CZ-252 43, Czech Republic
| | - Renata Slavíková
- Institute of Botany of the Czech Academy of Sciences, Průhonice, CZ-252 43, Czech Republic
| | - Claudia Krüger
- Institute of Botany of the Czech Academy of Sciences, Průhonice, CZ-252 43, Czech Republic
| | - Manuela Krüger
- Institute of Botany of the Czech Academy of Sciences, Průhonice, CZ-252 43, Czech Republic
| | - Petr Kohout
- Institute of Botany of the Czech Academy of Sciences, Průhonice, CZ-252 43, Czech Republic
- Faculty of Science, Charles University in Prague, Prague, CZ-128 44, Czech Republic
- Institute of Microbiology of the Czech Academy of Sciences, Prague, CZ-142 20, Czech Republic
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23
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Alaux PL, Mison C, Senés-Guerrero C, Moreau V, Manssens G, Foucart G, Cranenbrouck S, Declerck S. Diversity and species composition of arbuscular mycorrhizal fungi across maize fields in the southern part of Belgium. MYCORRHIZA 2021; 31:265-272. [PMID: 33211191 DOI: 10.1007/s00572-020-01007-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 11/11/2020] [Indexed: 06/11/2023]
Abstract
Arbuscular mycorrhizal fungi (AMF) are key actors among soil microbial inhabitants, forming beneficial associations with most horticultural plants and crops (e.g., maize). For maize, the world most cultivated cereal, data on AMF species diversity in fields is sparse and even totally nonexistent in the southern part of Belgium where maize represents 8% of the cultivated area. In the present study, 14 maize fields in South Belgium under conventional, conversion, or organic management were analyzed for AMF diversity and species composition using 454 pyrosequencing. A large part (54%) of the 49 AMF species observed were unknown or have not been described in the literature. AMF diversity highly varied among fields, with the number of species ranging between 1 and 37 according to the field. A statistically significant effect of management was measured on AMF diversity, with the highest Hill index values (diversity and richness) under the organic management system compared with conventional management or conversion. Our results suggest a positive effects of organic management on AMF diversity in maize. They also highlight the rather high diversity or richness of AMF and the large portion of sequences not yet ascribed to species, thereby emphasizing a need to intensify AMF identification in cropping systems.
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Affiliation(s)
- Pierre-Louis Alaux
- Earth and Life Institute, Applied Microbiology, Mycology, Université Catholique de Louvain, Croix du Sud 2, box L7.05.06, 1348, Louvain-la-Neuve, Belgium
| | - Coralie Mison
- Earth and Life Institute, Applied Microbiology, Mycology, Université Catholique de Louvain, Croix du Sud 2, box L7.05.06, 1348, Louvain-la-Neuve, Belgium
| | - Carolina Senés-Guerrero
- Escuela de Ingeniería Y Ciencias, Tecnológico de Monterrey, General Ramón Corona 2514, 45138, Zapopan, Jalisco, Mexico
| | - Virginie Moreau
- Earth and Life Institute, Applied Microbiology, Mycology, Université Catholique de Louvain, Croix du Sud 2, box L7.05.06, 1348, Louvain-la-Neuve, Belgium
| | - Gilles Manssens
- Centre Indépendant de Promotion Fourragère (CIPF), Croix du Sud, 2 L7.05.11, Louvain-la-Neuve, Belgium
| | - Guy Foucart
- Centre Indépendant de Promotion Fourragère (CIPF), Croix du Sud, 2 L7.05.11, Louvain-la-Neuve, Belgium
| | - Sylvie Cranenbrouck
- Earth and Life Institute, Applied Microbiology, Mycology, Mycothèque de L'Université Catholique de Louvain (BCCM/MUCL), Université Catholique de Louvain, Croix du Sud 2, box L7.05.06, 1348, Louvain-la-Neuve, Belgium
| | - Stéphane Declerck
- Earth and Life Institute, Applied Microbiology, Mycology, Université Catholique de Louvain, Croix du Sud 2, box L7.05.06, 1348, Louvain-la-Neuve, Belgium.
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Delavaux CS, Sturmer SL, Wagner MR, Schütte U, Morton JB, Bever JD. Utility of large subunit for environmental sequencing of arbuscular mycorrhizal fungi: a new reference database and pipeline. THE NEW PHYTOLOGIST 2021; 229:3048-3052. [PMID: 33190292 DOI: 10.1111/nph.17080] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Affiliation(s)
- Camille S Delavaux
- Department of Ecology and Evolutionary Biology, The University of Kansas, 2041 Haworth Hall, 1200 Sunnyside Avenue, Lawrence, KS, 66045, USA
- Kansas Biological Survey, The University of Kansas, 106 Higuchi Hall, 2101 Constant Ave, Lawrence, KS, 66047, USA
| | - Sidney L Sturmer
- Departamento de Ciências Naturais, Universidade Regional de Blumenau, R. Antônio da Veiga 140, Blumenau, Santa Catarina, 89030-903, Brazil
| | - Maggie R Wagner
- Department of Ecology and Evolutionary Biology, The University of Kansas, 2041 Haworth Hall, 1200 Sunnyside Avenue, Lawrence, KS, 66045, USA
- Kansas Biological Survey, The University of Kansas, 106 Higuchi Hall, 2101 Constant Ave, Lawrence, KS, 66047, USA
| | - Ursel Schütte
- Institute of Arctic Biology, University of Alaska Fairbanks, 2140 Koyukuk Drive, Fairbanks, AK, 99775, USA
| | - Joseph B Morton
- West Virginia University, 6 Alegre Pass, Santa Fe, Morgantown, NM, 87508, USA
| | - James D Bever
- Department of Ecology and Evolutionary Biology, The University of Kansas, 2041 Haworth Hall, 1200 Sunnyside Avenue, Lawrence, KS, 66045, USA
- Kansas Biological Survey, The University of Kansas, 106 Higuchi Hall, 2101 Constant Ave, Lawrence, KS, 66047, USA
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25
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Bodenhausen N, Deslandes-Hérold G, Waelchli J, Held A, van der Heijden MGA, Schlaeppi K. Relative qPCR to quantify colonization of plant roots by arbuscular mycorrhizal fungi. MYCORRHIZA 2021; 31:137-148. [PMID: 33475800 PMCID: PMC7910240 DOI: 10.1007/s00572-020-01014-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 12/15/2020] [Indexed: 05/13/2023]
Abstract
Arbuscular mycorrhiza fungi (AMF) are beneficial soil fungi that can promote the growth of their host plants. Accurate quantification of AMF in plant roots is important because the level of colonization is often indicative of the activity of these fungi. Root colonization is traditionally measured with microscopy methods which visualize fungal structures inside roots. Microscopy methods are labor-intensive, and results depend on the observer. In this study, we present a relative qPCR method to quantify AMF in which we normalized the AMF qPCR signal relative to a plant gene. First, we validated the primer pair AMG1F and AM1 in silico, and we show that these primers cover most AMF species present in plant roots without amplifying host DNA. Next, we compared the relative qPCR method with traditional microscopy based on a greenhouse experiment with Petunia plants that ranged from very high to very low levels of AMF root colonization. Finally, by sequencing the qPCR amplicons with MiSeq, we experimentally confirmed that the primer pair excludes plant DNA while amplifying mostly AMF. Most importantly, our relative qPCR approach was capable of discriminating quantitative differences in AMF root colonization and it strongly correlated (Spearman Rho = 0.875) with quantifications by traditional microscopy. Finally, we provide a balanced discussion about the strengths and weaknesses of microscopy and qPCR methods. In conclusion, the tested approach of relative qPCR presents a reliable alternative method to quantify AMF root colonization that is less operator-dependent than traditional microscopy and offers scalability to high-throughput analyses.
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Affiliation(s)
- Natacha Bodenhausen
- Plant Soil Interactions, Department of Agroecology and Environment, Agroscope, Zurich, Switzerland
- Department of Soil Sciences, Research Institute of Organic Agriculture FiBL, Frick, Switzerland
| | - Gabriel Deslandes-Hérold
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
- Plant Microbe Interactions, Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Jan Waelchli
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
- Plant Microbe Interactions, Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Alain Held
- Plant Soil Interactions, Department of Agroecology and Environment, Agroscope, Zurich, Switzerland
| | - Marcel G A van der Heijden
- Plant Soil Interactions, Department of Agroecology and Environment, Agroscope, Zurich, Switzerland
- Department of Plant and Microbial Biology, University of Zürich, Zurich, Switzerland
| | - Klaus Schlaeppi
- Plant Soil Interactions, Department of Agroecology and Environment, Agroscope, Zurich, Switzerland.
- Institute of Plant Sciences, University of Bern, Bern, Switzerland.
- Plant Microbe Interactions, Department of Environmental Sciences, University of Basel, Basel, Switzerland.
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26
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Piombo E, Abdelfattah A, Droby S, Wisniewski M, Spadaro D, Schena L. Metagenomics Approaches for the Detection and Surveillance of Emerging and Recurrent Plant Pathogens. Microorganisms 2021; 9:188. [PMID: 33467169 PMCID: PMC7830299 DOI: 10.3390/microorganisms9010188] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 01/09/2021] [Accepted: 01/12/2021] [Indexed: 12/28/2022] Open
Abstract
Globalization has a dramatic effect on the trade and movement of seeds, fruits and vegetables, with a corresponding increase in economic losses caused by the introduction of transboundary plant pathogens. Current diagnostic techniques provide a useful and precise tool to enact surveillance protocols regarding specific organisms, but this approach is strictly targeted, while metabarcoding and shotgun metagenomics could be used to simultaneously detect all known pathogens and potentially new ones. This review aims to present the current status of high-throughput sequencing (HTS) diagnostics of fungal and bacterial plant pathogens, discuss the challenges that need to be addressed, and provide direction for the development of methods for the detection of a restricted number of related taxa (specific surveillance) or all of the microorganisms present in a sample (general surveillance). HTS techniques, particularly metabarcoding, could be useful for the surveillance of soilborne, seedborne and airborne pathogens, as well as for identifying new pathogens and determining the origin of outbreaks. Metabarcoding and shotgun metagenomics still suffer from low precision, but this issue can be limited by carefully choosing primers and bioinformatic algorithms. Advances in bioinformatics will greatly accelerate the use of metagenomics to address critical aspects related to the detection and surveillance of plant pathogens in plant material and foodstuffs.
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Affiliation(s)
- Edoardo Piombo
- Department of Agricultural, Forest and Food Sciences (DISAFA), University of Torino, 10095 Grugliasco, Italy;
- Department of Forest Mycology and Plant Pathology, Uppsala Biocenter, Swedish University of Agricultural Sciences, P.O. Box 7026, 75007 Uppsala, Sweden
| | - Ahmed Abdelfattah
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, Graz 8010, Austria;
- Department of Ecology, Environment and Plant Sciences, University of Stockholm, Svante Arrhenius väg 20A, Stockholm 11418, Sweden
| | - Samir Droby
- Department of Postharvest Science, Agricultural Research Organization (ARO), The Volcani Center, Rishon LeZion 7505101, Israel;
| | - Michael Wisniewski
- U.S. Department of Agriculture—Agricultural Research Service (USDA-ARS), Kearneysville, WV 25430, USA;
- Department of Biological Sciences, Virginia Technical University, Blacksburg, VA 24061, USA
| | - Davide Spadaro
- Department of Agricultural, Forest and Food Sciences (DISAFA), University of Torino, 10095 Grugliasco, Italy;
- AGROINNOVA—Centre of Competence for the Innovation in the Agroenvironmental Sector, University of Torino, 10095 Grugliasco, Italy
| | - Leonardo Schena
- Department of Agriculture, Università Mediterranea, 89122 Reggio Calabria, Italy;
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Giovannini L, Sbrana C, Avio L, Turrini A. Diversity of a phosphate transporter gene among species and isolates of arbuscular mycorrhizal fungi. FEMS Microbiol Lett 2021; 367:5733160. [PMID: 32043113 DOI: 10.1093/femsle/fnaa024] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 02/10/2020] [Indexed: 11/14/2022] Open
Abstract
Arbuscular mycorrhizal fungi (AMF) are a key group of beneficial obligate biotrophs, establishing a mutualistic symbiosis with the roots of most land plants. The molecular markers generally used for their characterization are mainly based on informative regions of nuclear rDNA (SSU-ITS-LSU), although protein-encoding genes have also been proposed. Within functional genes, those encoding for phosphate transporters (PT) are particularly important in AMF, given their primary ability to take up Pi from soil, and to differentially affect plant phosphate nutrition. In this work, we investigated the genetic diversity of PT1 gene sequences and sequences of the taxonomically relevant SSU-ITS-LSU region in two isolates of the species Funneliformis coronatus, three isolates of the species Funneliformis mosseae and two species of the genus Rhizoglomus, originated from geographically distant areas and cultured in vivo. Our results showed that partial PT1 sequences not only successfully differentiated AMF genera and species like ribosomal gene sequences but also highlighted intraspecific diversity among F. mosseae and F. coronatus isolates. The study of functional genes related to the uptake of key mineral nutrients for the assessment of AMF diversity represents a key step in the selection of efficient isolates to be used as inocula in sustainable agriculture.
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Affiliation(s)
- Luca Giovannini
- Dipartimento di Scienze Agrarie, Alimentari e Agro-ambientali, Università di Pisa, 56124 Pisa, Italy
| | - Cristiana Sbrana
- CNR, Istituto di Biologia e Biotecnologia Agraria, 56124 Pisa, Italy
| | - Luciano Avio
- Dipartimento di Scienze Agrarie, Alimentari e Agro-ambientali, Università di Pisa, 56124 Pisa, Italy
| | - Alessandra Turrini
- Dipartimento di Scienze Agrarie, Alimentari e Agro-ambientali, Università di Pisa, 56124 Pisa, Italy
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28
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Kundel D, Bodenhausen N, Jørgensen HB, Truu J, Birkhofer K, Hedlund K, Mäder P, Fliessbach A. Effects of simulated drought on biological soil quality, microbial diversity and yields under long-term conventional and organic agriculture. FEMS Microbiol Ecol 2020; 96:fiaa205. [PMID: 33016314 PMCID: PMC7705324 DOI: 10.1093/femsec/fiaa205] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 10/02/2020] [Indexed: 11/12/2022] Open
Abstract
Drought and agricultural management influence soil microorganisms with unknown consequences for the functioning of agroecosystems. We simulated drought periods in organic (biodynamic) and conventional wheat fields and monitored effects on soil water content, microorganisms and crops. Above the wilting point, water content and microbial respiration were higher under biodynamic than conventional farming. Highest bacterial and fungal abundances were found in biodynamically managed soils, and distinct microbial communities characterised the farming systems. Most biological soil quality parameters and crop yields were only marginally affected by the experimental drought, except for arbuscular mycorrhizal fungi (AMF), which increased in abundance under the experimental drought in both farming systems. AMF were further strongly promoted by biodynamic farming resulting in almost three times higher AMF abundance under experimental drought in the biodynamic compared with the conventional farming system. Our data suggest an improved water storage capacity under biodynamic farming and confirms positive effects of biodynamic farming on biological soil quality. The interactive effects of the farming system and drought may further be investigated under more substantial droughts. Given the importance of AMF for the plant's water supply, more in-depth studies on AMF may help to clarify their role for yields under conditions predicted by future climate scenarios.
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Affiliation(s)
- Dominika Kundel
- Department of Soil Sciences, Research Institute of Organic Agriculture (FiBL), 5070 Frick, Switzerland
- Ecology, Department of Biology, University of Konstanz, 78464 Konstanz, Germany
| | - Natacha Bodenhausen
- Department of Soil Sciences, Research Institute of Organic Agriculture (FiBL), 5070 Frick, Switzerland
| | | | - Jaak Truu
- Institute of Molecular and Cell Biology, University of Tartu, 51010 Tartu, Estonia
| | - Klaus Birkhofer
- Department of Ecology, Brandenburg University of Technology, 03046 Cottbus, Germany
| | | | - Paul Mäder
- Department of Soil Sciences, Research Institute of Organic Agriculture (FiBL), 5070 Frick, Switzerland
| | - Andreas Fliessbach
- Department of Soil Sciences, Research Institute of Organic Agriculture (FiBL), 5070 Frick, Switzerland
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Community Structure of Arbuscular Mycorrhizal Fungi in Soils of Switchgrass Harvested for Bioenergy. Appl Environ Microbiol 2020; 86:AEM.00880-20. [PMID: 32709729 PMCID: PMC7499029 DOI: 10.1128/aem.00880-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 07/20/2020] [Indexed: 01/08/2023] Open
Abstract
Learning more about the biodiversity and composition of arbuscular mycorrhizal fungi (AMF) under alternative agricultural management scenarios may be important to the sustainable intensification of switchgrass grown as a bioenergy crop. Using PacBio single-molecule sequencing and taxonomic resolution to the level of amplicon sequence variant (ASV), we assessed the effects of nitrogen amendment on AMF associating with switchgrass and explored relationships between AMF and switchgrass yield across three sites of various productivities in Wisconsin. Nitrogen amendment had little effect on AMF diversity metrics or community composition. While AMF ASV diversity was not correlated with switchgrass yield, AMF family richness and switchgrass yield had a strong, positive relationship at one of our three sites. Each of our sites was dominated by unique ASVs of the species Paraglomus brasilianum, indicating regional segregation of AMF at the intraspecific level. Our molecular biodiversity survey identified putative core members of the switchgrass microbiome, as well as novel clades of AMF, especially in the order Paraglomerales and the genus Nanoglomus Furthermore, our phylogenies unite the cosmopolitan, soil-inhabiting clade deemed GS24 with Pervetustaceae, an enigmatic family prevalent in stressful environments. Future studies should isolate and characterize the novel genetic diversity found in switchgrass agroecosystems and explore the potential yield benefits of AMF richness.IMPORTANCE We assessed the different species of beneficial fungi living in agricultural fields of switchgrass, a large grass grown for biofuels, using high-resolution DNA sequencing. Contrary to our expectations, the fungi were not greatly affected by fertilization. However, we found a positive relationship between plant productivity and the number of families of beneficial fungi at one site. Furthermore, we sequenced many species that could not be identified with existing reference databases. One group of fungi was highlighted in an earlier study for being widely distributed but of unknown taxonomy. We discovered that this group belonged to a family called Pervetustaceae, which may benefit switchgrass in stressful environments. To produce higher-yielding switchgrass in a more sustainable manner, it could help to study these undescribed fungi and the ways in which they may contribute to greater switchgrass yield in the absence of fertilization.
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El-Gazzar N, Almaary K, Ismail A, Polizzi G. Influence of Funneliformis mosseae enhanced with titanium dioxide nanoparticles (TiO2NPs) on Phaseolus vulgaris L. under salinity stress. PLoS One 2020; 15:e0235355. [PMID: 32817671 PMCID: PMC7446817 DOI: 10.1371/journal.pone.0235355] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 06/14/2020] [Indexed: 11/18/2022] Open
Abstract
The Arbuscular mycorrhizal fungi (AMF) (Funneliformis mosseae), are the most widely distributed symbiont assisting plants to overcome counteractive environmental conditions. In order to improve the sustainability and the activity of AMF, the use of nanotechnology was important. The main objective of this study was to investigate the effect of titanium dioxide nanoparticles (TiO2NPs) on the activity of AMF in common bean roots as well as its activity under salinity stress using morphological and molecular methods. The activity of AMF colonization has increased in the presence of TiO2NPs especially for arbuscule activity (A%), which increased three times with the presence of TiO2NPs. The improvement rate of Funneliformis mosseae on plant growth increased from 180% to 224% of control at the lowest level of salinity and increased from 48% to 130% at higher salinity level, respectively. The AMF dependencies for plant dry biomass increased in the presence of TiO2NPs from 277% in the absence of salinity to 465 and 883% % at low and high salinity levels, respectively. The presence of AMF co-inoculated with TiO2NPs resulted in increasing the salinity tolerance of plants at all levels and reached 110% at salinity level of 100 mM NaCl. Quantitative colonization methods showed that the molecular intensity ratio and the relative density of paired inocula AMF Nest (NS) or chitin synthases gene (Chs) with TiO2NPs were higher significantly P.>0.05 than single inoculants of AMF gene in roots under the presence or the absence of salinity by about two folds and about 40%. Hence, the positive effect of TiO2NPs was confined to its effect on AMF not on bean plants itself.
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Affiliation(s)
- Nashwa El-Gazzar
- Botany and Microbiology Department, Faculty of Science, Zagazig University, Zagazig, Egypt
- * E-mail:
| | - Khalid Almaary
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Ahmed Ismail
- Plant Pathology Research Institute, Agricultural Research Center, Giza, Egypt
| | - Giancarlo Polizzi
- Dipartimento di Gestionedei Sistemi Agroalimentari e Ambientali, Sezione di Patologia Vegetale, Catania, Italy
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31
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Stefani F, Dupont S, Laterrière M, Knox R, Ruan Y, Hamel C, Hijri M. Similar Arbuscular Mycorrhizal Fungal Communities in 31 Durum Wheat Cultivars ( Triticum turgidum L. var. durum) Under Field Conditions in Eastern Canada. FRONTIERS IN PLANT SCIENCE 2020; 11:1206. [PMID: 32849748 PMCID: PMC7431883 DOI: 10.3389/fpls.2020.01206] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 07/24/2020] [Indexed: 06/11/2023]
Abstract
Wheat is among the important crops harnessed by humans whose breeding efforts resulted in a diversity of genotypes with contrasting traits. The goal of this study was to determine whether different old and new cultivars of durum wheat (Triticum turgidum L. var. durum) recruit specific arbuscular mycorrhizal (AM) fungal communities from indigenous AM fungal populations of soil under field conditions. A historical set of five landraces and 26 durum wheat cultivars were field cultivated in a humid climate in Eastern Canada, under phosphorus-limiting conditions. To characterize the community of AMF inhabiting bulk soil, rhizosphere, and roots, MiSeq amplicon sequencing targeting the 18S rRNA gene (SSU) was performed on total DNAs using a nested PCR approach. Mycorrhizal colonization was estimated using root staining and microscope observations. A total of 317 amplicon sequence variants (ASVs) were identified as belonging to Glomeromycota. The core AM fungal community (i.e., ASVs present in > 50% of the samples) in the soil, rhizosphere, and root included 29, 30, and 29 ASVs, respectively. ASVs from the genera Funneliformis, Claroideoglomus, and Rhizophagus represented 37%, 18.6%, and 14.7% of the sequences recovered in the rarefied dataset, respectively. The two most abundant ASVs had sequence homology with the 18S sequences from well-identified herbarium cultures of Funneliformis mosseae BEG12 and Rhizophagus irregularis DAOM 197198, while the third most abundant ASV was assigned to the genus Paraglomus. Cultivars showed no significant difference of the percentage of root colonization ranging from 57.8% in Arnautka to 84.0% in AC Navigator. Cultivars were generally associated with similar soil, rhizosphere, and root communities, but the abundance of F. mosseae, R. irregularis, and Claroideoglomus sp. sequences varied in Eurostar, Golden Ball, and Wakooma. Although these results were obtained in one field trial using a non-restricted pool of durum wheat and at the time of sampling, that may have filtered the community in biotopes. The low genetic variation between durum wheat cultivars for the diversity of AM symbiosis at the species level suggests breeding resources need not be committed to leveraging plant selective influence through the use of traditional methods for genotype development.
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Affiliation(s)
- Franck Stefani
- Ottawa Research and Development Centre of Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Sarah Dupont
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, QC, Canada
| | - Mario Laterrière
- Quebec Research and Development Centre of Agriculture and Agri-Food Canada, Quebec, QC, Canada
| | - Ron Knox
- Swift Current Research and Development Centre of Agriculture and Agri-Food Canada, Swift Current, SK, Canada
| | - Yuefeng Ruan
- Swift Current Research and Development Centre of Agriculture and Agri-Food Canada, Swift Current, SK, Canada
| | - Chantal Hamel
- Quebec Research and Development Centre of Agriculture and Agri-Food Canada, Quebec, QC, Canada
| | - Mohamed Hijri
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, QC, Canada
- AgroBioSciences, Mohammed VI Polytechnic University, Ben Guerir, Morocco
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32
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Hanafy RA, Johnson B, Youssef NH, Elshahed MS. Assessing anaerobic gut fungal diversity in herbivores using D1/D2 large ribosomal subunit sequencing and multi-year isolation. Environ Microbiol 2020; 22:3883-3908. [PMID: 32656919 DOI: 10.1111/1462-2920.15164] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 05/22/2020] [Accepted: 07/10/2020] [Indexed: 11/30/2022]
Abstract
The anaerobic gut fungi (AGF, Neocallimastigomycota) reside in the alimentary tracts of herbivores where they play a central role in the breakdown of plant material. Here, we report on the development of the hypervariable domains D1/D2 of the large ribosomal subunit (D1/D2 LSU) as a barcoding marker for the AGF. We generated a reference D1/D2 LSU database for all cultured AGF genera, as well as the majority of candidate genera encountered in prior internal transcribed spacer 1 (ITS1)-based surveys. Subsequently, a D1/D2 LSU-based diversity survey using long read PacBio SMRT sequencing was conducted on faecal samples from 21 wild and domesticated herbivores. Twenty-eight genera and candidate genera were identified, including multiple novel lineages that were predominantly, but not exclusively, identified in wild herbivores. Association between certain AGF genera and animal lifestyles, or animal host family was observed. Finally, to address the current paucity of AGF isolates, concurrent isolation efforts utilizing multiple approaches to maximize recovery yielded 216 isolates belonging to 12 different genera, several of which have no prior cultured-representatives. Our results establish the utility of D1/D2 LSU and PacBio sequencing for AGF diversity surveys, the culturability of multiple AGF taxa, and demonstrate that wild herbivores represent a yet-untapped reservoir of AGF diversity.
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Affiliation(s)
- Radwa A Hanafy
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Britny Johnson
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Noha H Youssef
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Mostafa S Elshahed
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
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33
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New MiSeq based strategy exposed plant-preferential arbuscular mycorrhizal fungal communities in arid soils of Mexico. Symbiosis 2020. [DOI: 10.1007/s13199-020-00698-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
AbstractArbuscular mycorrhizal fungi (AMF) are obligate symbionts of c. 80% of land plants, having enormous ecological and economic impact, as they often improve crop plant nutrition and yield. DNA-based identification with molecular markers is used to analyze AM fungal communities in the field, but reaching species level taxonomic resolution remains challenging. Thus, currently there is no consensus on how to analyze high-throughput sequences and assign them into species. Here, a new sequencing strategy combined with taxonomic affiliations implemented with an evolutionary placement algorithm (EPA) was established. It is based on sequencing a c. 450 bp region of the large subunit (LSU) ribosomal rRNA gene with the MiSeq-Illumina platform. The method is suitable for the discrimination of closely related AMF species and was used to study host-AMF preferences in roots of Pequin pepper, soybean and orange at one location in the arid northeast of Mexico. Twenty AM fungal species from 13 genera were detected. Phylogenetic affiliation of reads to species revealed crop preferential associations. In Pequin pepper roots, several Rhizophagus species represented most of the community, Rhizophagus clarus being the most abundant. The soybean AM fungal community was dominated by Rhizophagus irregularis and Funneliformis mosseae and that of orange by several species of Dominikia, some of them only found in this crop. Unraveling the AMF-plant preferences of important crops by an affordable and robust sequencing method, combined with phylotaxonomic AMF species resolution, is an important tool to obtain taxonomic units that are meaningful in both biological and ecological studies.
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34
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Ontivero RE, Voyron S, Allione LVR, Bianco P, Bianciotto V, Iriarte HJ, Lugo MA, Lumini E. Impact of land use history on the arbuscular mycorrhizal fungal diversity in arid soils of Argentinean farming fields. FEMS Microbiol Lett 2020; 367:5869666. [PMID: 32648900 DOI: 10.1093/femsle/fnaa114] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 07/08/2020] [Indexed: 12/20/2022] Open
Abstract
Arbuscular mycorrhizal fungi (AMF) are a key soil functional group, with an important potential to increase crop productivity and sustainable agriculture including food security. However, there is clear evidence that land uses, crop rotations and soil features affect the AMF diversity and their community functioning in many agroecosystems. So far, the information related to AMF biodiversity in ecosystems like the Argentinean Puna, an arid high plateau where plants experience high abiotic stresses, is still scarce. In this work, we investigated morphological and molecular AMF diversity in soils of native corn, bean and native potato Andean crops, under a familiar land use, in Chaupi Rodeo (Jujuy, Argentina), without agrochemical supplements but with different histories of crop rotation. Our results showed that AMF morphological diversity was not only high and variable among the three different crop soils but also complemented by Illumina MiSeq data. The multivariate analyses highlighted that total fungal diversity is significantly affected by the preceding crop plants and the rotation histories, more than from the present crop species, while AMF communities are significantly affected by preceding crop only in combination with the effect of nitrogen and calcium soil concentration. This knowledge will give useful information on appropriate familiar farming.
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Affiliation(s)
- R Emanuel Ontivero
- Grupo de Micología, Diversidad e Interacciones Fúngicas (MICODIF), Área Ecología, Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis (UNSL), Ejército de los Andes 950, D5700ANW San Luis, Argentina.,Instituto Multidisciplinario de Investigaciones Biológicas (IMIBIO)-Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), UNSL, Almirante Brown 907, D5700ANW San Luis, Argentina
| | - Samuele Voyron
- Institute for Sustainable Plant Protection (IPSP-CNR) and Department of Life Sciences and Systems Biology, University of Turin (DiBIOS), Viale P.A. Mattioli, 25, I-10125 Turin, Italy
| | - Lucía V Risio Allione
- Grupo de Micología, Diversidad e Interacciones Fúngicas (MICODIF), Área Ecología, Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis (UNSL), Ejército de los Andes 950, D5700ANW San Luis, Argentina.,Laboratorio de Dasonomía, Facultad de Ingeniería en Cs. Agropecuarias (FICA), Universidad Nacional de San Luis (UNSL), Ruta Provincial 55. D5730 Villa Mercedes, San Luis, Argentina
| | - Paolo Bianco
- Institute for Sustainable Plant Protection (IPSP-CNR) and Department of Life Sciences and Systems Biology, University of Turin (DiBIOS), Viale P.A. Mattioli, 25, I-10125 Turin, Italy
| | - Valeria Bianciotto
- Institute for Sustainable Plant Protection (IPSP-CNR) and Department of Life Sciences and Systems Biology, University of Turin (DiBIOS), Viale P.A. Mattioli, 25, I-10125 Turin, Italy
| | - Hebe J Iriarte
- Grupo de Micología, Diversidad e Interacciones Fúngicas (MICODIF), Área Ecología, Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis (UNSL), Ejército de los Andes 950, D5700ANW San Luis, Argentina.,Instituto Multidisciplinario de Investigaciones Biológicas (IMIBIO)-Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), UNSL, Almirante Brown 907, D5700ANW San Luis, Argentina
| | - Mónica A Lugo
- Grupo de Micología, Diversidad e Interacciones Fúngicas (MICODIF), Área Ecología, Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis (UNSL), Ejército de los Andes 950, D5700ANW San Luis, Argentina.,Instituto Multidisciplinario de Investigaciones Biológicas (IMIBIO)-Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), UNSL, Almirante Brown 907, D5700ANW San Luis, Argentina
| | - Erica Lumini
- Institute for Sustainable Plant Protection (IPSP-CNR) and Department of Life Sciences and Systems Biology, University of Turin (DiBIOS), Viale P.A. Mattioli, 25, I-10125 Turin, Italy
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35
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House GL, Bever JD. Biochar soil amendments in prairie restorations do not interfere with benefits from inoculation with native arbuscular mycorrhizal fungi. Restor Ecol 2020. [DOI: 10.1111/rec.12924] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Geoffrey L. House
- Department of Biology Indiana University 1001 East Third Street Bloomington IN 47405 U.S.A
| | - James D. Bever
- Department of Ecology and Evolutionary Biology and Kansas Biological Survey The University of Kansas 2041 Haworth Hall, 1200 Sunnyside Avenue Lawrence KS 66045 U.S.A
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36
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Stefani F, Bencherif K, Sabourin S, Hadj-Sahraoui AL, Banchini C, Séguin S, Dalpé Y. Taxonomic assignment of arbuscular mycorrhizal fungi in an 18S metagenomic dataset: a case study with saltcedar (Tamarix aphylla). MYCORRHIZA 2020; 30:243-255. [PMID: 32180012 DOI: 10.1007/s00572-020-00946-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 03/06/2020] [Indexed: 06/10/2023]
Affiliation(s)
- Franck Stefani
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, ON, K1A 0C6, Canada.
| | - Karima Bencherif
- Faculté des Sciences de la Nature et de la Vie, Université de Djelfa, Route de Moudjbara, BP 3117, 17000, Djelfa, Algeria
| | - Stéphanie Sabourin
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, ON, K1A 0C6, Canada
| | - Anissa Lounès Hadj-Sahraoui
- UR 4492 - UCEIV - Unité de Chimie Environnementale et Interactions sur le Vivant, SFR Condorcet FR CNRS 3417, Université Littoral Côte d'Opale, F-62228, Calais Cedex, France
| | - Claudia Banchini
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, ON, K1A 0C6, Canada
| | - Sylvie Séguin
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, ON, K1A 0C6, Canada
| | - Yolande Dalpé
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, ON, K1A 0C6, Canada
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37
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Inoculation with Rhizophagus Irregularis Does Not Alter Arbuscular Mycorrhizal Fungal Community Structure within the Roots of Corn, Wheat, and Soybean Crops. Microorganisms 2020; 8:microorganisms8010083. [PMID: 31936180 PMCID: PMC7023141 DOI: 10.3390/microorganisms8010083] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 12/31/2019] [Accepted: 01/03/2020] [Indexed: 01/02/2023] Open
Abstract
Little is known about establishment success of the arbuscular mycorrhizal fungal (AMF) inocula and their effects on a soil-indigenous community of AMF. In this study, we assessed the effect of introducing Rhizophagus irregularis DAOM-197198 in soil under field condition on the community composition of indigenous AMF in the roots of corn (Zea mays), soybean (Glycine max), and wheat (Triticum aestivum). Three field trials were conducted with inoculated and non-inoculated plots. Four to ten roots and their rhizosphere soil samples of two growth stages for corn and wheat, and one growing stage of soybean, were collected, totalling 122 root and soil samples. Root colonization was measured microscopically, and the fungal communities were determined by paired-end Illumina MiSeq amplicon sequencing using 18S rDNA marker. After quality trimming and merging of paired ends, 6.7 million sequences could be assigned to 414 different operational taxonomic units. These could be assigned to 68 virtual taxa (VT) using the AMF reference sequence database MaarjAM. The most abundant VT corresponded to R. irregularis. The inoculation treatment did not influence the presence of R. irregularis, or AMF community diversity in roots. This seems to indicate that inoculation with R. irregularis DAOM-197198 does not change the indigenous AMF community composition, probably because it is already present in high abundance naturally.
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38
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Nilsson RH, Anslan S, Bahram M, Wurzbacher C, Baldrian P, Tedersoo L. Mycobiome diversity: high-throughput sequencing and identification of fungi. Nat Rev Microbiol 2020; 17:95-109. [PMID: 30442909 DOI: 10.1038/s41579-018-0116-y] [Citation(s) in RCA: 390] [Impact Index Per Article: 97.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Fungi are major ecological players in both terrestrial and aquatic environments by cycling organic matter and channelling nutrients across trophic levels. High-throughput sequencing (HTS) studies of fungal communities are redrawing the map of the fungal kingdom by hinting at its enormous - and largely uncharted - taxonomic and functional diversity. However, HTS approaches come with a range of pitfalls and potential biases, cautioning against unwary application and interpretation of HTS technologies and results. In this Review, we provide an overview and practical recommendations for aspects of HTS studies ranging from sampling and laboratory practices to data processing and analysis. We also discuss upcoming trends and techniques in the field and summarize recent and noteworthy results from HTS studies targeting fungal communities and guilds. Our Review highlights the need for reproducibility and public data availability in the study of fungal communities. If the associated challenges and conceptual barriers are overcome, HTS offers immense possibilities in mycology and elsewhere.
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Affiliation(s)
- R Henrik Nilsson
- Gothenburg Global Biodiversity Centre, Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden.
| | - Sten Anslan
- Zoological Institute, Braunschweig University of Technology, Braunschweig, Germany
| | - Mohammad Bahram
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Christian Wurzbacher
- Chair of Urban Water Systems Engineering, Technical University of Munich, Garching, Germany
| | - Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Praha, Czech Republic
| | - Leho Tedersoo
- Natural History Museum of Tartu University, Tartu, Estonia
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39
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Callahan BJ, Wong J, Heiner C, Oh S, Theriot CM, Gulati AS, McGill SK, Dougherty MK. High-throughput amplicon sequencing of the full-length 16S rRNA gene with single-nucleotide resolution. Nucleic Acids Res 2019; 47:e103. [PMID: 31269198 PMCID: PMC6765137 DOI: 10.1093/nar/gkz569] [Citation(s) in RCA: 270] [Impact Index Per Article: 54.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 06/08/2019] [Accepted: 06/20/2019] [Indexed: 12/24/2022] Open
Abstract
Targeted PCR amplification and high-throughput sequencing (amplicon sequencing) of 16S rRNA gene fragments is widely used to profile microbial communities. New long-read sequencing technologies can sequence the entire 16S rRNA gene, but higher error rates have limited their attractiveness when accuracy is important. Here we present a high-throughput amplicon sequencing methodology based on PacBio circular consensus sequencing and the DADA2 sample inference method that measures the full-length 16S rRNA gene with single-nucleotide resolution and a near-zero error rate. In two artificial communities of known composition, our method recovered the full complement of full-length 16S sequence variants from expected community members without residual errors. The measured abundances of intra-genomic sequence variants were in the integral ratios expected from the genuine allelic variants within a genome. The full-length 16S gene sequences recovered by our approach allowed Escherichia coli strains to be correctly classified to the O157:H7 and K12 sub-species clades. In human fecal samples, our method showed strong technical replication and was able to recover the full complement of 16S rRNA alleles in several E. coli strains. There are likely many applications beyond microbial profiling for which high-throughput amplicon sequencing of complete genes with single-nucleotide resolution will be of use.
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Affiliation(s)
- Benjamin J Callahan
- Department of Population Health & Pathobiology, North Carolina State University, Raleigh, NC 27607, USA.,Bioinformatics Research Center, North Carolina State University, Raleigh, NC 27695, USA
| | - Joan Wong
- Pacific Biosciences of California, Inc., Menlo Park, CA 94025, USA
| | - Cheryl Heiner
- Pacific Biosciences of California, Inc., Menlo Park, CA 94025, USA
| | - Steve Oh
- Pacific Biosciences of California, Inc., Menlo Park, CA 94025, USA
| | - Casey M Theriot
- Department of Population Health & Pathobiology, North Carolina State University, Raleigh, NC 27607, USA
| | - Ajay S Gulati
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.,Department of Pediatrics, Division of Gastroenterology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.,Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Sarah K McGill
- Department of Medicine, Division of Gastroenterology and Hepatology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Michael K Dougherty
- Department of Medicine, Division of Gastroenterology and Hepatology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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40
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Tedersoo L, Anslan S. Towards PacBio-based pan-eukaryote metabarcoding using full-length ITS sequences. ENVIRONMENTAL MICROBIOLOGY REPORTS 2019; 11:659-668. [PMID: 31219680 DOI: 10.1111/1758-2229.12776] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 06/14/2019] [Indexed: 05/03/2023]
Abstract
Development of high-throughput sequencing techniques has greatly benefited our understanding about microbial ecology, yet the methods producing short reads suffer from species-level resolution and uncertainty of identification. Here, we optimize Pacific Biosciences-based metabarcoding protocols covering the internal transcribed spacer (ITS region) and partial small subunit of the rRNA gene for species-level identification of all eukaryotes, with a specific focus on Fungi (including Glomeromycota) and Stramenopila (particularly Oomycota). Based on tests on composite soil samples and mock communities, we propose best suitable degenerate primers, ITS9munngs + ITS4ngsUni for eukaryotes and selected groups therein and discuss the pros and cons of long read-based identification of eukaryotes.
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Affiliation(s)
- Leho Tedersoo
- Institute of Ecology and Earth Sciences, University of Tartu, Estonia
| | - Sten Anslan
- Zoological Institute, Technische Universität Braunschweig, Mendelssohnstrasse 4, 38106, Braunschweig, Germany
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41
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Heeger F, Wurzbacher C, Bourne EC, Mazzoni CJ, Monaghan MT. Combining the 5.8S and ITS2 to improve classification of fungi. Methods Ecol Evol 2019. [DOI: 10.1111/2041-210x.13266] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Felix Heeger
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB) Berlin Germany
- Berlin Center for Genomics in Biodiversity Research Berlin Germany
| | - Christian Wurzbacher
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB) Berlin Germany
- Berlin Center for Genomics in Biodiversity Research Berlin Germany
- Chair of Urban Water Systems Engineering Technical University of Munich Garching Germany
| | - Elizabeth C. Bourne
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB) Berlin Germany
- Berlin Center for Genomics in Biodiversity Research Berlin Germany
| | - Camila J. Mazzoni
- Berlin Center for Genomics in Biodiversity Research Berlin Germany
- Department of Evolutionary Genetics Leibniz Institute of Zoo‐ and Wildlife Research (IZW) Berlin Germany
| | - Michael T. Monaghan
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB) Berlin Germany
- Berlin Center for Genomics in Biodiversity Research Berlin Germany
- Institut für Biologie Freie Universität Berlin Berlin Germany
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42
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Banerjee S, Walder F, Büchi L, Meyer M, Held AY, Gattinger A, Keller T, Charles R, van der Heijden MGA. Agricultural intensification reduces microbial network complexity and the abundance of keystone taxa in roots. THE ISME JOURNAL 2019; 13:1722-1736. [PMID: 30850707 PMCID: PMC6591126 DOI: 10.1038/s41396-019-0383-2] [Citation(s) in RCA: 383] [Impact Index Per Article: 76.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 02/04/2019] [Accepted: 02/17/2019] [Indexed: 01/28/2023]
Abstract
Root-associated microbes play a key role in plant performance and productivity, making them important players in agroecosystems. So far, very few studies have assessed the impact of different farming systems on the root microbiota and it is still unclear whether agricultural intensification influences the structure and complexity of microbial communities. We investigated the impact of conventional, no-till, and organic farming on wheat root fungal communities using PacBio SMRT sequencing on samples collected from 60 farmlands in Switzerland. Organic farming harbored a much more complex fungal network with significantly higher connectivity than conventional and no-till farming systems. The abundance of keystone taxa was the highest under organic farming where agricultural intensification was the lowest. We also found a strong negative association (R2 = 0.366; P < 0.0001) between agricultural intensification and root fungal network connectivity. The occurrence of keystone taxa was best explained by soil phosphorus levels, bulk density, pH, and mycorrhizal colonization. The majority of keystone taxa are known to form arbuscular mycorrhizal associations with plants and belong to the orders Glomerales, Paraglomerales, and Diversisporales. Supporting this, the abundance of mycorrhizal fungi in roots and soils was also significantly higher under organic farming. To our knowledge, this is the first study to report mycorrhizal keystone taxa for agroecosystems, and we demonstrate that agricultural intensification reduces network complexity and the abundance of keystone taxa in the root microbiome.
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Affiliation(s)
- Samiran Banerjee
- Agroscope, Department of Agroecology & Environment, Reckenholzstrasse 191, 8046, Zürich, Switzerland.
| | - Florian Walder
- Agroscope, Department of Agroecology & Environment, Reckenholzstrasse 191, 8046, Zürich, Switzerland.
| | - Lucie Büchi
- Agroscope, Plant Production Systems, Route de Duillier 50, 1260, Nyon, Switzerland
- Natural Resources Institute, University of Greenwich, London, UK
| | - Marcel Meyer
- Agroscope, Department of Agroecology & Environment, Reckenholzstrasse 191, 8046, Zürich, Switzerland
| | - Alain Y Held
- Agroscope, Department of Agroecology & Environment, Reckenholzstrasse 191, 8046, Zürich, Switzerland
| | - Andreas Gattinger
- Research Institute of Organic Agriculture FiBL, 5070, Frick, Switzerland
- Justus-Liebig University Giessen, Organic Farming with focus on Sustainable Soil Use, Karl-Glöckner-Str. 21C, 35394, Giessen, Germany
| | - Thomas Keller
- Agroscope, Department of Agroecology & Environment, Reckenholzstrasse 191, 8046, Zürich, Switzerland
- Swedish University of Agricultural Sciences, Department of Soil & Environment, Box 7014, 75007, Uppsala, Sweden
| | - Raphael Charles
- Agroscope, Plant Production Systems, Route de Duillier 50, 1260, Nyon, Switzerland
- Research Institute of Organic Agriculture FiBL, Jordils 3, 1001, Lausanne, Switzerland
| | - Marcel G A van der Heijden
- Agroscope, Department of Agroecology & Environment, Reckenholzstrasse 191, 8046, Zürich, Switzerland
- Department of Plant and Microbial Biology, University of Zürich, 8008, Zürich, Switzerland
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43
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Gueidan C, Elix JA, McCarthy PM, Roux C, Mallen-Cooper M, Kantvilas G. PacBio amplicon sequencing for metabarcoding of mixed DNA samples from lichen herbarium specimens. MycoKeys 2019; 53:73-91. [PMID: 31205446 PMCID: PMC6557899 DOI: 10.3897/mycokeys.53.34761] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 05/10/2019] [Indexed: 12/12/2022] Open
Abstract
The detection and identification of species of fungi in the environment using molecular methods heavily depends on reliable reference sequence databases. However, these databases are largely incomplete in terms of taxon coverage, and a significant effort is required from herbaria and living fungal collections for the mass-barcoding of well-identified and well-curated fungal specimens or strains. Here, a PacBio amplicon sequencing approach is applied to recent lichen herbarium specimens for the sequencing of the fungal ITS barcode, allowing a higher throughput sample processing than Sanger sequencing, which often required the use of cloning. Out of 96 multiplexed samples, a full-length ITS sequence of the target lichenised fungal species was recovered for 85 specimens. In addition, sequences obtained for co-amplified fungi gave an interesting insight into the diversity of endolichenic fungi. Challenges encountered at both the laboratory and bioinformatic stages are discussed, and cost and quality are compared with Sanger sequencing. With increasing data output and reducing sequencing cost, PacBio amplicon sequencing is seen as a promising approach for the generation of reference sequences for lichenised fungi as well as the characterisation of lichen-associated fungal communities.
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Affiliation(s)
- Cécile Gueidan
- Australian National Herbarium, National Research Collections Australia, CSIRO-NCMI, Canberra, ACT, 2601, Australia Australian National Herbarium Canberra Australia
| | - John A Elix
- Research School of Chemistry, Building 137, Australian National University, Canberra, ACT, 2601, Australia Australian National University Canberra Australia
| | - Patrick M McCarthy
- 64 Broadsmith St, Scullin, ACT, 2614, Australia Unaffilaited Canberra Australia
| | - Claude Roux
- 390 chemin des Vignes vieilles, 84120 Mirabeau, France Unaffilaited Mirabeau France
| | - Max Mallen-Cooper
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, University of New South Wales Sydney, Kensington, NSW, 2052, Australia University of New South Wales Sydney Sydney Australia
| | - Gintaras Kantvilas
- 64 Broadsmith St, Scullin, ACT, 2614, Australia Unaffilaited Canberra Australia
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44
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Microbial associations enabling nitrogen acquisition in plants. Curr Opin Microbiol 2019; 49:83-89. [DOI: 10.1016/j.mib.2019.10.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 10/03/2019] [Accepted: 10/11/2019] [Indexed: 01/29/2023]
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45
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Hage‐Ahmed K, Rosner K, Steinkellner S. Arbuscular mycorrhizal fungi and their response to pesticides. PEST MANAGEMENT SCIENCE 2019; 75:583-590. [PMID: 30255557 PMCID: PMC6587947 DOI: 10.1002/ps.5220] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 09/19/2018] [Accepted: 09/19/2018] [Indexed: 05/19/2023]
Abstract
Arbuscular mycorrhizal fungi (AMF) form symbioses with the majority of plant species and can provide multiple benefits to the host plant. In agro-ecosystems, the abundance and community structure of AMF are affected by agricultural management practices. This review describes and discusses current knowledge on the effects of inorganic and organic chemical pesticides on AMF in the conflicting area between agricultural use and environmental concerns. Variable effects have been reported following chemical pesticide use, ranging from neutral to positive and negative. Moreover, a species-specific reaction has been documented. The reported effects of pesticides on arbuscular mycorrhizal symbiosis are very diverse, and even when the same substance is investigated, the results are often contradictory. These effects depend on many parameters, such as the active substance, the mode of action, the mode of application and the dosage. In the field, determinants such as the physico-chemical behavior of the active substances, the soil type and other soil microorganisms contribute to the fate of pesticides and thus the amount of active substances to which AMF are exposed. This review highlights that the fate of AMF following pesticide use needs to be addressed in a broader agro-ecosystem context. © 2018 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
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Affiliation(s)
- Karin Hage‐Ahmed
- Division of Plant Protection, Department of Crop SciencesUniversity of Natural Resources and Life Sciences ViennaTullnAustria
| | - Kathrin Rosner
- Division of Plant Protection, Department of Crop SciencesUniversity of Natural Resources and Life Sciences ViennaTullnAustria
| | - Siegrid Steinkellner
- Division of Plant Protection, Department of Crop SciencesUniversity of Natural Resources and Life Sciences ViennaTullnAustria
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46
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Tedersoo L, Drenkhan R, Anslan S, Morales‐Rodriguez C, Cleary M. High-throughput identification and diagnostics of pathogens and pests: Overview and practical recommendations. Mol Ecol Resour 2019; 19:47-76. [PMID: 30358140 PMCID: PMC7379260 DOI: 10.1111/1755-0998.12959] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 08/01/2018] [Accepted: 08/28/2018] [Indexed: 12/26/2022]
Abstract
High-throughput identification technologies provide efficient tools for understanding the ecology and functioning of microorganisms. Yet, these methods have been only rarely used for monitoring and testing ecological hypotheses in plant pathogens and pests in spite of their immense importance in agriculture, forestry and plant community dynamics. The main objectives of this manuscript are the following: (a) to provide a comprehensive overview about the state-of-the-art high-throughput quantification and molecular identification methods used to address population dynamics, community ecology and host associations of microorganisms, with a specific focus on antagonists such as pathogens, viruses and pests; (b) to compile available information and provide recommendations about specific protocols and workable primers for bacteria, fungi, oomycetes and insect pests; and (c) to provide examples of novel methods used in other microbiological disciplines that are of great potential use for testing specific biological hypotheses related to pathology. Finally, we evaluate the overall perspectives of the state-of-the-art and still evolving methods for diagnostics and population- and community-level ecological research of pathogens and pests.
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Affiliation(s)
- Leho Tedersoo
- Natural History Museum and Institute of Ecology and Earth SciencesUniversity of TartuTartuEstonia
| | - Rein Drenkhan
- Institute of Forestry and Rural EngineeringEstonian University of Life SciencesTartuEstonia
| | - Sten Anslan
- Natural History Museum and Institute of Ecology and Earth SciencesUniversity of TartuTartuEstonia
| | | | - Michelle Cleary
- Southern Swedish Forest Research CentreSwedish University of Agricultural SciencesAlnarpSweden
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47
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Bruns TD, Corradi N, Redecker D, Taylor JW, Öpik M. Glomeromycotina: what is a species and why should we care? THE NEW PHYTOLOGIST 2018; 220:963-967. [PMID: 29165821 DOI: 10.1111/nph.14913] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
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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Affiliation(s)
- Thomas D Bruns
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720-3102, USA
| | - Nicolas Corradi
- Department of Biology, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
| | - Dirk Redecker
- Agroécologie, Université de Bourgogne Franche-Comté, INRA, CNRS, AgroSup Dijon, F-21000, Dijon, France
| | - John W Taylor
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720-3102, USA
| | - Maarja Öpik
- University of Tartu, 40 Lai Street, 51005, Tartu, Estonia
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48
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Bennett AE, Evans DM, Powell JR. Potentials and pitfalls in the analysis of bipartite networks to understand plant–microbe interactions in changing environments. Funct Ecol 2018. [DOI: 10.1111/1365-2435.13223] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Alison E. Bennett
- Evolution, Ecology, and Organismal Biology The Ohio State University Columbus Ohio
| | - Darren M. Evans
- School of Natural and Environmental Sciences Newcastle University Newcastle upon Tyne UK
| | - Jeff R. Powell
- Hawkesbury Institute for the Environment, Western Sydney University Penrith New South Wales Australia
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49
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Heeger F, Bourne EC, Baschien C, Yurkov A, Bunk B, Spröer C, Overmann J, Mazzoni CJ, Monaghan MT. Long-read DNA metabarcoding of ribosomal RNA in the analysis of fungi from aquatic environments. Mol Ecol Resour 2018; 18:1500-1514. [DOI: 10.1111/1755-0998.12937] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 07/05/2018] [Accepted: 07/28/2018] [Indexed: 01/06/2023]
Affiliation(s)
- Felix Heeger
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB); Berlin Germany
- Berlin Center for Genomics in Biodiversity Research; Berlin Germany
| | - Elizabeth C. Bourne
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB); Berlin Germany
- Berlin Center for Genomics in Biodiversity Research; Berlin Germany
| | - Christiane Baschien
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures; Braunschweig Germany
| | - Andrey Yurkov
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures; Braunschweig Germany
| | - Boyke Bunk
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures; Braunschweig Germany
| | - Cathrin Spröer
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures; Braunschweig Germany
| | - Jörg Overmann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures; Braunschweig Germany
| | - Camila J. Mazzoni
- Berlin Center for Genomics in Biodiversity Research; Berlin Germany
- Leibniz Institute of Zoo- and Wildlife Research (IZW); Berlin Germany
| | - Michael T. Monaghan
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB); Berlin Germany
- Berlin Center for Genomics in Biodiversity Research; Berlin Germany
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50
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Cotton TEA. Arbuscular mycorrhizal fungal communities and global change: an uncertain future. FEMS Microbiol Ecol 2018; 94:5096018. [DOI: 10.1093/femsec/fiy179] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 09/10/2018] [Indexed: 01/13/2023] Open
Affiliation(s)
- TE Anne Cotton
- Department of Animal and Plant Sciences, Alfred Denny Building, Western Bank, The University of Sheffield, Sheffield, South Yorkshire, S10 2TN, UK
- Plant Production and Protection (P3) Institute for Translational Plant and Soil Biology, Department of Animal and Plant Sciences, Alfred Denny Building, Western Bank, The University of Sheffield, Sheffield, South Yorkshire, S10 2TN, UK
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