1
|
Manyara D, Sánchez-García M, Montoliu-Nerin M, Rosling A. Detection of rare variants among nuclei populating the arbuscular mycorrhizal fungal model species Rhizophagus irregularis DAOM197198. G3 (BETHESDA, MD.) 2024; 14:jkae074. [PMID: 38656424 DOI: 10.1093/g3journal/jkae074] [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: 11/07/2023] [Accepted: 03/27/2024] [Indexed: 04/26/2024]
Abstract
Identifying genuine polymorphic variants is a significant challenge in sequence data analysis, although detecting low-frequency variants in sequence data is essential for estimating demographic parameters and investigating genetic processes, such as selection, within populations. Arbuscular mycorrhizal (AM) fungi are multinucleate organisms, in which individual nuclei collectively operate as a population, and the extent of genetic variation across nuclei has long been an area of scientific interest. In this study, we investigated the patterns of polymorphism discovery and the alternate allele frequency distribution by comparing polymorphism discovery in 2 distinct genomic sequence datasets of the AM fungus model species, Rhizophagus irregularis strain DAOM197198. The 2 datasets used in this study are publicly available and were generated either from pooled spores and hyphae or amplified single nuclei from a single spore. We also estimated the intraorganismal variation within the DAOM197198 strain. Our results showed that the 2 datasets exhibited different frequency patterns for discovered variants. The whole-organism dataset showed a distribution spanning low-, intermediate-, and high-frequency variants, whereas the single-nucleus dataset predominantly featured low-frequency variants with smaller proportions in intermediate and high frequencies. Furthermore, single nucleotide polymorphism density estimates within both the whole organism and individual nuclei confirmed the low intraorganismal variation of the DAOM197198 strain and that most variants are rare. Our study highlights the methodological challenges associated with detecting low-frequency variants in AM fungal whole-genome sequence data and demonstrates that alternate alleles can be reliably identified in single nuclei of AM fungi.
Collapse
Affiliation(s)
- David Manyara
- Department of Ecology and Genetics, Uppsala University, Uppsala 752 36, Sweden
| | - Marisol Sánchez-García
- Department of Ecology and Genetics, Uppsala University, Uppsala 752 36, Sweden
- Uppsala Biocentre, Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala 750 07, Sweden
| | - Merce Montoliu-Nerin
- Department of Ecology and Genetics, Uppsala University, Uppsala 752 36, Sweden
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM), Madrid 28223, Spain
| | - Anna Rosling
- Department of Ecology and Genetics, Uppsala University, Uppsala 752 36, Sweden
| |
Collapse
|
2
|
van Creij J, Auxier B, An J, Wijfjes RY, Bergin C, Rosling A, Bisseling T, Pan Z, Limpens E. Stochastic nuclear organization and host-dependent allele contribution in Rhizophagus irregularis. BMC Genomics 2023; 24:53. [PMID: 36709253 PMCID: PMC9883914 DOI: 10.1186/s12864-023-09126-6] [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] [Received: 11/24/2021] [Accepted: 01/10/2023] [Indexed: 01/30/2023] Open
Abstract
BACKGROUND Arbuscular mycorrhizal (AM) fungi are arguably the most important symbionts of plants, offering a range of benefits to their hosts. However, the provisioning of these benefits does not appear to be uniform among AM fungal individuals, with genetic variation between fungal symbionts having a substantial impact on plant performance. Interestingly, genetic variation has also been reported within fungal individuals, which contain millions of haploid nuclei sharing a common cytoplasm. In the model AM fungus, Rhizophagus irregularis, several isolates have been reported to be dikaryotes, containing two genetically distinct types of nuclei recognized based on their mating-type (MAT) locus identity. However, their extremely coenocytic nature and lack of a known single nucleus stage has raised questions on the origin, distribution and dynamics of this genetic variation. RESULTS Here we performed DNA and RNA sequencing at the mycelial individual, single spore and single nucleus levels to gain insight into the dynamic genetic make-up of the dikaryote-like R. irregularis C3 isolate and the effect of different host plants on its genetic variation. Our analyses reveal that parallel spore and root culture batches can have widely variable ratios of two main genotypes in C3. Additionally, numerous polymorphisms were found with frequencies that deviated significantly from the general genotype ratio, indicating a diverse population of slightly different nucleotypes. Changing host plants did not show consistent host effects on nucleotype ratio's after multiple rounds of subculturing. Instead, we found a major effect of host plant-identity on allele-specific expression in C3. CONCLUSION Our analyses indicate a highly dynamic/variable genetic organization in different isolates of R. irregularis. Seemingly random fluctuations in nucleotype ratio's upon spore formation, recombination events, high variability of non-tandemly repeated rDNA sequences and host-dependent allele expression all add levels of variation that may contribute to the evolutionary success of these widespread symbionts.
Collapse
Affiliation(s)
- Jelle van Creij
- grid.4818.50000 0001 0791 5666Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University & Research, Droevendaalsesteeg 1, Wageningen, The Netherlands
| | - Ben Auxier
- grid.4818.50000 0001 0791 5666Laboratory of Genetics, Department of Plant Sciences, Wageningen University & Research, Droevendaalsesteeg 1, Wageningen, The Netherlands
| | - Jianyong An
- grid.4818.50000 0001 0791 5666Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University & Research, Droevendaalsesteeg 1, Wageningen, The Netherlands ,grid.411626.60000 0004 1798 6793Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing, 102206 China
| | - Raúl Y. Wijfjes
- grid.4818.50000 0001 0791 5666Laboratory of Bioinformatics, Department of Plant Sciences, Wageningen University & Research, Droevendaalsesteeg 1, Wageningen, The Netherlands ,grid.5252.00000 0004 1936 973XCurrent affiliation: Faculty of Biology, Ludwig Maximilian University of Munich, Munich, Germany
| | - Claudia Bergin
- grid.8993.b0000 0004 1936 9457Department of Cell and Molecular Biology, Uppsala University, and Microbial Single Cell Genomics Facility, Science for Life Laboratory, Uppsala, Sweden
| | - Anna Rosling
- grid.8993.b0000 0004 1936 9457Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, SE-75236 Uppsala, Sweden
| | - Ton Bisseling
- grid.4818.50000 0001 0791 5666Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University & Research, Droevendaalsesteeg 1, Wageningen, The Netherlands ,grid.411626.60000 0004 1798 6793Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing, 102206 China
| | - Zhiyong Pan
- grid.35155.370000 0004 1790 4137Key Laboratory of Horticultural Plant Biology (Ministry of Education), Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region, Ministry of Agriculture), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, People’s Republic of China
| | - Erik Limpens
- grid.4818.50000 0001 0791 5666Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University & Research, Droevendaalsesteeg 1, Wageningen, The Netherlands
| |
Collapse
|
3
|
Sarma H, Narayan M, Peralta-Videa JR, Lam SS. Exploring the significance of nanomaterials and organic amendments - Prospect for phytoremediation of contaminated agroecosystem. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 308:119601. [PMID: 35709913 DOI: 10.1016/j.envpol.2022.119601] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 05/10/2022] [Accepted: 06/07/2022] [Indexed: 05/22/2023]
Abstract
Emerging micro-pollutants have rapidly contaminated the agro-ecosystem, posing serious challenges to a sustainable future. The vast majority of them have infiltrated the soil and damaged agricultural fields and crops after being released from industry. These pollutants and their transformed products are also transported in vast quantities which further exacerbate the damage. Sustainable remediation techniques are warranted for such large amounts of contaminants. As aforementioned, many of them have been detected at very high concentrations in soil and water which adversely affect crop physiology by disrupting different metabolic processes. To combat this situation, nanomaterials and other organic amendments assisted phytoremediation ware considered as a viable alternative. It is a potent synergistic activity between the biological system and the supplied organic or nanomaterial material to eliminate emerging contaminants and micropollutants from crop fields. This can be effectively be applied to degraded crop fields and could potentially embody a green technology for sustainable agriculture.
Collapse
Affiliation(s)
- Hemen Sarma
- Bioremediation Technology Research Group, Department of Botany, Bodoland University, Rangalikhata, Deborgaon, Kokrajhar(BTR), Assam, 783370, India; Institutional Biotech Hub, Department of Botany, Nanda Nath Saikia College, Titabar, Assam, 785630, India.
| | - Mahesh Narayan
- Department of Chemistry and Biochemistry, University of Texas at El Paso, 500 W. University Ave., El Paso, TX, 79968, USA
| | - Jose R Peralta-Videa
- Department of Chemistry and Biochemistry, University of Texas at El Paso, 500 W. University Ave., El Paso, TX, 79968, USA
| | - Su Shiung Lam
- Pyrolysis Technology Research Group, Higher Institution Centre of Excellence (HICoE), Institute of Tropical Aquaculture and Fisheries (AKUATROP), Universiti Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia; Sustainability Cluster, School of Engineering, University of Petroleum & Energy Studies, Dehradun, Uttarakhand, 248007, India
| |
Collapse
|
4
|
Singh PP, Srivastava D, Shukla S, Varsha. Rhizophagus proliferus genome sequence reiterates conservation of genetic traits in AM fungi, but predicts higher saprotrophic activity. Arch Microbiol 2021; 204:105. [DOI: 10.1007/s00203-021-02651-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 10/06/2021] [Accepted: 10/07/2021] [Indexed: 11/24/2022]
|
5
|
Reinhardt D, Roux C, Corradi N, Di Pietro A. Lineage-Specific Genes and Cryptic Sex: Parallels and Differences between Arbuscular Mycorrhizal Fungi and Fungal Pathogens. TRENDS IN PLANT SCIENCE 2021; 26:111-123. [PMID: 33011084 DOI: 10.1016/j.tplants.2020.09.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 08/29/2020] [Accepted: 09/08/2020] [Indexed: 05/25/2023]
Abstract
Arbuscular mycorrhizal fungi (AMF) live as obligate root symbionts on almost all land plants. They have long been regarded as ancient asexuals that have propagated clonally for millions of years. However, genomic studies in Rhizophagus irregularis and other AMF revealed many features indicative of sex. Surprisingly, comparative genomics of conspecific isolates of R. irregularis revealed an unexpected interstrain diversity, suggesting that AMF carry a high number of lineage-specific (LS) genes. Intriguingly, cryptic sex and LS genomic regions have previously been reported in a number of fungal pathogens of plants and humans. Here, we discuss these genomic similarities and highlight their potential relevance for AMF adaptation to the environment and for symbiotic functioning.
Collapse
Affiliation(s)
- Didier Reinhardt
- Department of Biology, University of Fribourg, Fribourg, Switzerland.
| | - Christophe Roux
- Laboratoire de Recherche en Sciences Végétales, UPS, CNRS, Université de Toulouse, Castanet-Tolosan 31326, France
| | - Nicolas Corradi
- Department of Biology, University of Ottawa, Ottawa, ON, Canada
| | - Antonio Di Pietro
- Departamento de Genética, Universidad de Cordoba, 14071 Cordoba, Spain
| |
Collapse
|
6
|
Masclaux FG, Wyss T, Pagni M, Rosikiewicz P, Sanders IR. Investigating unexplained genetic variation and its expression in the arbuscular mycorrhizal fungus Rhizophagus irregularis: A comparison of whole genome and RAD sequencing data. PLoS One 2019; 14:e0226497. [PMID: 31881076 PMCID: PMC6934306 DOI: 10.1371/journal.pone.0226497] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 11/27/2019] [Indexed: 12/19/2022] Open
Abstract
Arbuscular mycorrhizal fungi (AMF) are important symbionts of plants. Recently, studies of the AMF Rhizophagus irregularis recorded within-isolate genetic variation that does not completely match the proposed homokaryon or heterokaryon state (where heterokaryons comprise a population of two distinct nucleus genotypes). We re-analysed published data showing that bi-allelic sites (and their frequencies), detected in proposed homo- and heterokaryote R. irregularis isolates, were similar across independent studies using different techniques. This indicated that observed within-fungus genetic variation was not an artefact of sequencing and that such within- fungus genetic variation possibly exists. We then looked to see if bi-allelic transcripts from three R. irregularis isolates matched those observed in the genome as this would give a strong indication of whether bi-allelic sites recorded in the genome were reliable variants. In putative homokaryon isolates, very few bi-allelic transcripts matched those in the genome. In a putative heterokaryon, a large number of bi-allelic transcripts matched those in the genome. Bi-allelic transcripts also occurred in the same frequency in the putative heterokaryon as predicted from allele frequency in the genome. Our results indicate that while within-fungus genome variation in putative homokaryon and heterokaryon AMF was highly similar in 2 independent studies, there was little support that this variation is transcribed in homokaryons. In contrast, within-fungus variation thought to be segregated among two nucleus genotypes in a heterokaryon isolate was indeed transcribed in a way that is proportional to that seen in the genome.
Collapse
Affiliation(s)
- Frédéric G. Masclaux
- Department of Ecology and Evolution, University of Lausanne, Switzerland
- Vital-IT Group, Swiss Institute of Bioinformatics, Switzerland
| | - Tania Wyss
- Department of Ecology and Evolution, University of Lausanne, Switzerland
| | - Marco Pagni
- Vital-IT Group, Swiss Institute of Bioinformatics, Switzerland
| | - Pawel Rosikiewicz
- Department of Ecology and Evolution, University of Lausanne, Switzerland
| | - Ian R. Sanders
- Department of Ecology and Evolution, University of Lausanne, Switzerland
| |
Collapse
|
7
|
Abstract
Phosphorous is important for life but often limiting for plants. The symbiotic pathway of phosphate uptake via arbuscular mycorrhizal fungi (AMF) is evolutionarily ancient and today occurs in natural and agricultural ecosystems alike. Plants capable of this symbiosis can obtain up to all of the phosphate from symbiotic fungi, and this offers potential means to develop crops less dependent on unsustainable P fertilizers. Here, we review the mechanisms and insights gleaned from the fine-tuned signal exchanges that orchestrate the intimate mutualistic symbiosis between plants and AMF. As the currency of trade, nutrients have signaling functions beyond being the nutritional goal of mutualism. We propose that such signaling roles and metabolic reprogramming may represent commitments for a mutualistic symbiosis that act across the stages of symbiosis development.
Collapse
Affiliation(s)
- Chai Hao Chiu
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | - Uta Paszkowski
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| |
Collapse
|
8
|
Kokkoris V, Miles T, Hart MM. The role of in vitro cultivation on asymbiotic trait variation in a single species of arbuscular mycorrhizal fungus. Fungal Biol 2019; 123:307-317. [PMID: 30928039 DOI: 10.1016/j.funbio.2019.01.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 12/29/2018] [Accepted: 01/17/2019] [Indexed: 01/13/2023]
Abstract
Cultivating arbuscular mycorrhizal (AM) fungi in vitro is an efficient way to produce material for industry and research. However, such artificial growing conditions may impose selective pressure on fungi grown in vitro over many generations. We hypothesized that isolates subjected to long term propagation in vitro may develop increasingly ruderal traits. We proposed a predictive framework for the effect of in vitro cultivation on asymbiotic AM fungal traits. Using photomicrography and image processing, we analyzed morphology and growth traits for 14 isolates representing an in vitro cultivation gradient from 0 to >80 generations in vitro. We investigated the range of trait variation among asymbiotic growth of arbuscular mycorrhizal (AM) fungus isolates (Rhizoglomus irregulare). Spore dormancy was strongly associated with in vitro cultivation. We observed extremely high levels of inter-isolate variation for most fungal traits, but this was not related to time in vitro. Our results indicate that intra-specific diversity may have a strong ecological role in AM fungal communities.
Collapse
Affiliation(s)
- Vasilis Kokkoris
- Department of Biology, University of British Columbia, Okanagan Campus, 3333 University Way, Kelowna, BC V1V 1V7, Canada.
| | - Thea Miles
- Department of Biology, University of British Columbia, Okanagan Campus, 3333 University Way, Kelowna, BC V1V 1V7, Canada
| | - Miranda M Hart
- Department of Biology, University of British Columbia, Okanagan Campus, 3333 University Way, Kelowna, BC V1V 1V7, Canada
| |
Collapse
|
9
|
Scott TW, Kiers ET, Cooper GA, dos Santos M, West SA. Evolutionary maintenance of genomic diversity within arbuscular mycorrhizal fungi. Ecol Evol 2019; 9:2425-2435. [PMID: 30891190 PMCID: PMC6405528 DOI: 10.1002/ece3.4834] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 11/23/2018] [Accepted: 11/26/2018] [Indexed: 01/12/2023] Open
Abstract
Most organisms are built from a single genome. In striking contrast, arbuscular mycorrhizal fungi appear to maintain genomic variation within an individual fungal network. Arbuscular mycorrhizal fungi dwell in the soil, form mutualistic networks with plants, and bear multiple, potentially genetically diverse nuclei within a network. We explore, from a theoretical perspective, why such genetic diversity might be maintained within individuals. We consider selection acting within and between individual fungal networks. We show that genetic diversity could provide a benefit at the level of the individual, by improving growth in variable environments, and that this can stabilize genetic diversity even in the presence of nuclear conflict. Arbuscular mycorrhizal fungi complicate our understanding of organismality, but our findings offer a way of understanding such biological anomalies.
Collapse
Affiliation(s)
| | - E. Toby Kiers
- Institute of Ecological Sciences, Faculty of Earth and Life SciencesVrije UniversiteitAmsterdamThe Netherlands
| | | | - Miguel dos Santos
- Department of ZoologyUniversity of OxfordOxfordUK
- Department of Social Psychology and Social Neuroscience, Institute of PsychologyUniversity of BernBernSwitzerland
| | - Stuart A. West
- Department of ZoologyUniversity of OxfordOxfordUK
- Magdalen CollegeOxfordUK
| |
Collapse
|
10
|
Chen ECH, Mathieu S, Hoffrichter A, Sedzielewska-Toro K, Peart M, Pelin A, Ndikumana S, Ropars J, Dreissig S, Fuchs J, Brachmann A, Corradi N. Single nucleus sequencing reveals evidence of inter-nucleus recombination in arbuscular mycorrhizal fungi. eLife 2018; 7:e39813. [PMID: 30516133 PMCID: PMC6281316 DOI: 10.7554/elife.39813] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 11/16/2018] [Indexed: 12/18/2022] Open
Abstract
Eukaryotes thought to have evolved clonally for millions of years are referred to as ancient asexuals. The oldest group among these are the arbuscular mycorrhizal fungi (AMF), which are plant symbionts harboring hundreds of nuclei within one continuous cytoplasm. Some AMF strains (dikaryons) harbor two co-existing nucleotypes but there is no direct evidence that such nuclei recombine in this life-stage, as is expected for sexual fungi. Here, we show that AMF nuclei with distinct genotypes can undergo recombination. Inter-nuclear genetic exchange varies in frequency among strains, and despite recombination all nuclear genomes have an average similarity of at least 99.8%. The present study demonstrates that AMF can generate genetic diversity via meiotic-like processes in the absence of observable mating. The AMF dikaryotic life-stage is a primary source of nuclear variability in these organisms, highlighting its potential for strain enhancement of these symbionts.
Collapse
Affiliation(s)
- Eric CH Chen
- Department of BiologyUniversity of OttawaOttawaCanada
| | | | - Anne Hoffrichter
- Institute of Genetics, Faculty of BiologyLudwig Maximilian University of MunichMunichGermany
| | - Kinga Sedzielewska-Toro
- Institute of Genetics, Faculty of BiologyLudwig Maximilian University of MunichMunichGermany
| | - Max Peart
- Department of BiologyUniversity of OttawaOttawaCanada
| | - Adrian Pelin
- Department of BiologyUniversity of OttawaOttawaCanada
| | | | - Jeanne Ropars
- Department of BiologyUniversity of OttawaOttawaCanada
| | - Steven Dreissig
- Leibniz Institute of Plant Genetics and Crop Plant ResearchGaterslebenGermany
| | - Jorg Fuchs
- Leibniz Institute of Plant Genetics and Crop Plant ResearchGaterslebenGermany
| | - Andreas Brachmann
- Institute of Genetics, Faculty of BiologyLudwig Maximilian University of MunichMunichGermany
| | | |
Collapse
|
11
|
Chen ECH, Morin E, Beaudet D, Noel J, Yildirir G, Ndikumana S, Charron P, St-Onge C, Giorgi J, Krüger M, Marton T, Ropars J, Grigoriev IV, Hainaut M, Henrissat B, Roux C, Martin F, Corradi N. High intraspecific genome diversity in the model arbuscular mycorrhizal symbiont Rhizophagus irregularis. THE NEW PHYTOLOGIST 2018; 220:1161-1171. [PMID: 29355972 DOI: 10.1111/nph.14989] [Citation(s) in RCA: 126] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 12/03/2017] [Indexed: 05/20/2023]
Abstract
Arbuscular mycorrhizal fungi (AMF) are known to improve plant fitness through the establishment of mycorrhizal symbioses. Genetic and phenotypic variations among closely related AMF isolates can significantly affect plant growth, but the genomic changes underlying this variability are unclear. To address this issue, we improved the genome assembly and gene annotation of the model strain Rhizophagus irregularis DAOM197198, and compared its gene content with five isolates of R. irregularis sampled in the same field. All isolates harbor striking genome variations, with large numbers of isolate-specific genes, gene family expansions, and evidence of interisolate genetic exchange. The observed variability affects all gene ontology terms and PFAM protein domains, as well as putative mycorrhiza-induced small secreted effector-like proteins and other symbiosis differentially expressed genes. High variability is also found in active transposable elements. Overall, these findings indicate a substantial divergence in the functioning capacity of isolates harvested from the same field, and thus their genetic potential for adaptation to biotic and abiotic changes. Our data also provide a first glimpse into the genome diversity that resides within natural populations of these symbionts, and open avenues for future analyses of plant-AMF interactions that link AMF genome variation with plant phenotype and fitness.
Collapse
Affiliation(s)
- Eric C H Chen
- Department of Biology, University of Ottawa, Ottawa, ON, K1N9A7, Canada
| | - Emmanuelle Morin
- Institut National de la Recherche Agronomique (INRA), Unité Mixte de Recherche 1136 Interactions Arbres/Microorganismes, Laboratoire D'excellence Recherches Avancées sur la Biologie de l'Arbre et les Ecosystèmes Forestiers (ARBRE), Centre INRA-Grand Est-Nancy, Champenoux, 54280, France
| | - Denis Beaudet
- Department of Biology, University of Ottawa, Ottawa, ON, K1N9A7, Canada
| | - Jessica Noel
- Department of Biology, University of Ottawa, Ottawa, ON, K1N9A7, Canada
| | - Gokalp Yildirir
- Department of Biology, University of Ottawa, Ottawa, ON, K1N9A7, Canada
| | - Steve Ndikumana
- Department of Biology, University of Ottawa, Ottawa, ON, K1N9A7, Canada
| | - Philippe Charron
- Department of Biology, University of Ottawa, Ottawa, ON, K1N9A7, Canada
| | - Camille St-Onge
- Department of Biology, University of Ottawa, Ottawa, ON, K1N9A7, Canada
| | - John Giorgi
- Department of Biology, University of Ottawa, Ottawa, ON, K1N9A7, Canada
| | - Manuela Krüger
- Department of Biology, University of Ottawa, Ottawa, ON, K1N9A7, Canada
| | - Timea Marton
- Department of Biology, University of Ottawa, Ottawa, ON, K1N9A7, Canada
| | - Jeanne Ropars
- Department of Biology, University of Ottawa, Ottawa, ON, K1N9A7, Canada
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute (JGI), Walnut Creek, CA, 94598, USA
| | - Matthieu Hainaut
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, Marseille, 13288, France
- INRA, USC 1408 AFMB, Marseille, F-13288, France
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, Marseille, 13288, France
- INRA, USC 1408 AFMB, Marseille, F-13288, France
- Department of Biological Sciences, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Christophe Roux
- Laboratoire de Recherche en Sciences Végétales, UPS, CNRS 24 Chemin de Borde Rouge-Auzeville, Université de Toulouse, Castanet-Tolosan, 31326, France
| | - Francis Martin
- Institut National de la Recherche Agronomique (INRA), Unité Mixte de Recherche 1136 Interactions Arbres/Microorganismes, Laboratoire D'excellence Recherches Avancées sur la Biologie de l'Arbre et les Ecosystèmes Forestiers (ARBRE), Centre INRA-Grand Est-Nancy, Champenoux, 54280, France
| | - Nicolas Corradi
- Department of Biology, University of Ottawa, Ottawa, ON, K1N9A7, Canada
| |
Collapse
|
12
|
Sanders IR. Sex, plasticity, and biologically significant variation in one Glomeromycotina species. THE NEW PHYTOLOGIST 2018; 220:968-970. [PMID: 29480929 DOI: 10.1111/nph.15049] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Affiliation(s)
- Ian R Sanders
- Department of Ecology & Evolution, University of Lausanne, Biophore Building, 1015, Lausanne, Switzerland
| |
Collapse
|
13
|
Li Y, Wu X, Chen T, Wang W, Liu G, Zhang W, Li S, Wang M, Zhao C, Zhou H, Zhang G. Plant Phenotypic Traits Eventually Shape Its Microbiota: A Common Garden Test. Front Microbiol 2018; 9:2479. [PMID: 30459725 PMCID: PMC6232875 DOI: 10.3389/fmicb.2018.02479] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Accepted: 09/28/2018] [Indexed: 01/22/2023] Open
Abstract
Plant genotype drives the development of plant phenotypes and the assembly of plant microbiota. The potential influence of the plant phenotypic characters on its microbiota is not well characterized and the co-occurrence interrelations for specific microbial taxa and plant phenotypic characters are poorly understood. We established a common garden experiment, which quantifies prokaryotic and fungal communities in the phyllosphere and rhizosphere of six spruce (Picea spp.) tree species, through Illumina amplicon sequencing. We tested for relationships between bacterial/archaeal and fungal communities and for the phenotypic characters of their plant hosts. Host phenotypic characters including leaf length, leaf water content, leaf water storage capacity, leaf dry mass per area, leaf nitrogen content, leaf phosphorous content, leaf potassium content, leaf δ13C values, stomatal conductance, net photosynthetic rate, intercellular carbon dioxide concentration, and transpiration rate were significantly correlated with the diversity and composition of the bacterial/archaeal and fungal communities. These correlations between plant microbiota and suites of host plant phenotypic characters suggest that plant genotype shape its microbiota by driving the development of plant phenotypes. This will advance our understanding of plant-microbe associations and the drivers of variation in plant and ecosystem function.
Collapse
Affiliation(s)
- Yunshi Li
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources (NIEER), Chinese Academy of Sciences (CAS), Lanzhou, China.,University of Chinese Academy of Sciences, Beijing, China.,Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, China
| | - Xiukun Wu
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources (NIEER), Chinese Academy of Sciences (CAS), Lanzhou, China.,Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, China
| | - Tuo Chen
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources (NIEER), Chinese Academy of Sciences (CAS), Lanzhou, China.,Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, China.,State Key Laboratory of Cryospheric Sciences, NIEER, CAS, Lanzhou, China
| | - Wanfu Wang
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources (NIEER), Chinese Academy of Sciences (CAS), Lanzhou, China.,Conservation Institute, Dunhuang Academy, Dunhuang, China
| | - Guangxiu Liu
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources (NIEER), Chinese Academy of Sciences (CAS), Lanzhou, China.,Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, China
| | - Wei Zhang
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources (NIEER), Chinese Academy of Sciences (CAS), Lanzhou, China.,Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, China
| | - Shiweng Li
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources (NIEER), Chinese Academy of Sciences (CAS), Lanzhou, China.,School of Environmental and Municipal Engineering, Lanzhou Jiaotong University, Lanzhou, China
| | - Minghao Wang
- State Key Laboratory of Grassland Agro-Ecosystems, Lanzhou University, Lanzhou, China
| | - Changming Zhao
- State Key Laboratory of Grassland Agro-Ecosystems, Lanzhou University, Lanzhou, China
| | - Huaizhe Zhou
- College of Computer, National University of Defense Technology, Changsha, China
| | - Gaosen Zhang
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources (NIEER), Chinese Academy of Sciences (CAS), Lanzhou, China.,Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, China
| |
Collapse
|
14
|
Chen M, Arato M, Borghi L, Nouri E, Reinhardt D. Beneficial Services of Arbuscular Mycorrhizal Fungi - From Ecology to Application. FRONTIERS IN PLANT SCIENCE 2018; 9:1270. [PMID: 30233616 PMCID: PMC6132195 DOI: 10.3389/fpls.2018.01270] [Citation(s) in RCA: 148] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 08/10/2018] [Indexed: 05/12/2023]
Abstract
Arbuscular mycorrhiza (AM) is the most common symbiotic association of plants with microbes. AM fungi occur in the majority of natural habitats and they provide a range of important ecological services, in particular by improving plant nutrition, stress resistance and tolerance, soil structure and fertility. AM fungi also interact with most crop plants including cereals, vegetables, and fruit trees, therefore, they receive increasing attention for their potential use in sustainable agriculture. Basic research of the past decade has revealed the existence of a dedicated recognition and signaling pathway that is required for AM. Furthermore, recent evidence provided new insight into the exchange of nutritional benefits between the symbiotic partners. The great potential for application of AM has given rise to a thriving industry for AM-related products for agriculture, horticulture, and landscaping. Here, we discuss new developments in these fields, and we highlight future potential and limits toward the use of AM fungi for plant production.
Collapse
Affiliation(s)
- Min Chen
- Department of Biology, Rte Albert Gockel, University of Fribourg, Fribourg, Switzerland
| | | | - Lorenzo Borghi
- Institute of Plant and Molecular Biology, University of Zurich, Zurich, Switzerland
| | - Eva Nouri
- Department of Biology, Rte Albert Gockel, University of Fribourg, Fribourg, Switzerland
| | - Didier Reinhardt
- Department of Biology, Rte Albert Gockel, University of Fribourg, Fribourg, Switzerland
| |
Collapse
|
15
|
Maeda T, Kobayashi Y, Kameoka H, Okuma N, Takeda N, Yamaguchi K, Bino T, Shigenobu S, Kawaguchi M. Evidence of non-tandemly repeated rDNAs and their intragenomic heterogeneity in Rhizophagus irregularis. Commun Biol 2018; 1:87. [PMID: 30271968 PMCID: PMC6123716 DOI: 10.1038/s42003-018-0094-7] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 06/12/2018] [Indexed: 01/21/2023] Open
Abstract
Arbuscular mycorrhizal fungus (AMF) species are some of the most widespread symbionts of land plants. Our much improved reference genome assembly of a model AMF, Rhizophagus irregularis DAOM-181602 (total contigs = 210), facilitated a discovery of repetitive elements with unusual characteristics. R. irregularis has only ten or 11 copies of complete 45S rDNAs, whereas the general eukaryotic genome has tens to thousands of rDNA copies. R. irregularis rDNAs are highly heterogeneous and lack a tandem repeat structure. These findings provide evidence for the hypothesis that rDNA heterogeneity depends on the lack of tandem repeat structures. RNA-Seq analysis confirmed that all rDNA variants are actively transcribed. Observed rDNA/rRNA polymorphisms may modulate translation by using different ribosomes depending on biotic and abiotic interactions. The non-tandem repeat structure and intragenomic heterogeneity of AMF rDNA/rRNA may facilitate successful adaptation to various environmental conditions, increasing host compatibility of these symbiotic fungi.
Collapse
Affiliation(s)
- Taro Maeda
- Division of Symbiotic Systems, National Institute for Basic Biology, Myodaiji Nishigonaka, Okazaki, Aichi, 444-8585, Japan
| | - Yuuki Kobayashi
- Division of Symbiotic Systems, National Institute for Basic Biology, Myodaiji Nishigonaka, Okazaki, Aichi, 444-8585, Japan
| | - Hiromu Kameoka
- Division of Symbiotic Systems, National Institute for Basic Biology, Myodaiji Nishigonaka, Okazaki, Aichi, 444-8585, Japan
| | - Nao Okuma
- Division of Symbiotic Systems, National Institute for Basic Biology, Myodaiji Nishigonaka, Okazaki, Aichi, 444-8585, Japan
- The Graduate University for Advanced Studies [SOKENDAI], Hayama, Miura, Kanagawa, 240-0193, Japan
| | - Naoya Takeda
- School of Science and Technology, Kwansei Gakuin University, Gakuen, Mita, Hyogo, 669-1337, Japan
| | - Katsushi Yamaguchi
- Functional Genomics Facility, National Institute for Basic Biology, Myodaiji Nishigonaka, Okazaki, Aichi, 444-8585, Japan
| | - Takahiro Bino
- Functional Genomics Facility, National Institute for Basic Biology, Myodaiji Nishigonaka, Okazaki, Aichi, 444-8585, Japan
| | - Shuji Shigenobu
- The Graduate University for Advanced Studies [SOKENDAI], Hayama, Miura, Kanagawa, 240-0193, Japan.
- Functional Genomics Facility, National Institute for Basic Biology, Myodaiji Nishigonaka, Okazaki, Aichi, 444-8585, Japan.
| | - Masayoshi Kawaguchi
- Division of Symbiotic Systems, National Institute for Basic Biology, Myodaiji Nishigonaka, Okazaki, Aichi, 444-8585, Japan.
- The Graduate University for Advanced Studies [SOKENDAI], Hayama, Miura, Kanagawa, 240-0193, Japan.
| |
Collapse
|
16
|
Thomsen CN, Hart MM. Using invasion theory to predict the fate of arbuscular mycorrhizal fungal inoculants. Biol Invasions 2018. [DOI: 10.1007/s10530-018-1746-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
|
17
|
Masclaux FG, Wyss T, Mateus-Gonzalez ID, Aletti C, Sanders IR. Variation in allele frequencies at the bg112 locus reveals unequal inheritance of nuclei in a dikaryotic isolate of the fungus Rhizophagus irregularis. MYCORRHIZA 2018; 28:369-377. [PMID: 29675619 DOI: 10.1007/s00572-018-0834-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 04/05/2018] [Indexed: 05/26/2023]
Abstract
The genetic state of the arbuscular mycorrhizal fungus species Rhizophagus irregularis differs among isolates, including both homokaryotic and dikaryotic isolates. Via the production of multi-nucleate axexual spores, siblings of dikaryotic isolates may inherit unequal frequencies of nucleotypes. Using bg112, a microsatellite marker, previous studies revealed that lines deriving from single spores of the dikaryotic R. irregularis isolate C3 differed in their proportions of different alleles. A genomic study of single nuclei of R. irregularis, however, suggested that this marker was a multi-copy locus and that therefore it was inappropriate to study the inheritance of nuclei in dikaryotic isolates. In this study, we first analysed whole genome data of several R. irregularis isolates and demonstrated that bg112 is indeed a single copy locus in these genomes. Thus, the bg112 locus is a suitable marker to study the relative frequency of nucleotypes in R. irregularis. Second, by using amplicon sequencing, we confirmed the existence of one allele of bg112 in two homokaryotic isolates (DAOM197198 and C2) and two alleles in the dikaryotic isolate (C3). Finally, we found that the relative proportions of two bg112 alleles differed significantly among dikaryotic single-spore lines derived from isolate C3, indicating that genetically different nucleotypes are inherited unequally in this dikaryotic R. irregularis isolate.
Collapse
Affiliation(s)
- Frédéric G Masclaux
- Department of Ecology and Evolution, Biophore Building, University of Lausanne, 1015, Lausanne, Switzerland
- Vital-IT Group, Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
| | - Tania Wyss
- Department of Ecology and Evolution, Biophore Building, University of Lausanne, 1015, Lausanne, Switzerland
| | - Ivan D Mateus-Gonzalez
- Department of Ecology and Evolution, Biophore Building, University of Lausanne, 1015, Lausanne, Switzerland
| | - Consolée Aletti
- Department of Ecology and Evolution, Biophore Building, University of Lausanne, 1015, Lausanne, Switzerland
| | - Ian R Sanders
- Department of Ecology and Evolution, Biophore Building, University of Lausanne, 1015, Lausanne, Switzerland.
| |
Collapse
|
18
|
Nieuwenhuis BPS, James TY. The frequency of sex in fungi. Philos Trans R Soc Lond B Biol Sci 2017; 371:rstb.2015.0540. [PMID: 27619703 DOI: 10.1098/rstb.2015.0540] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/15/2016] [Indexed: 12/16/2022] Open
Abstract
Fungi are a diverse group of organisms with a huge variation in reproductive strategy. While almost all species can reproduce sexually, many reproduce asexually most of the time. When sexual reproduction does occur, large variation exists in the amount of in- and out-breeding. While budding yeast is expected to outcross only once every 10 000 generations, other fungi are obligate outcrossers with well-mixed panmictic populations. In this review, we give an overview of the costs and benefits of sexual and asexual reproduction in fungi, and the mechanisms that evolved in fungi to reduce the costs of either mode. The proximate molecular mechanisms potentiating outcrossing and meiosis appear to be present in nearly all fungi, making them of little use for predicting outcrossing rates, but also suggesting the absence of true ancient asexual lineages. We review how population genetic methods can be used to estimate the frequency of sex in fungi and provide empirical data that support a mixed mode of reproduction in many species with rare to frequent sex in between rounds of mitotic reproduction. Finally, we highlight how these estimates might be affected by the fungus-specific mechanisms that evolved to reduce the costs of sexual and asexual reproduction.This article is part of the themed issue 'Weird sex: the underappreciated diversity of sexual reproduction'.
Collapse
Affiliation(s)
- Bart P S Nieuwenhuis
- Department of Evolutionary Biology, Uppsala University, Norbyvägen 18D, 752 36 Uppsala, Sweden
| | - Timothy Y James
- Department of Ecology and Evolutionary Biology, University of Michigan, 830 North University, Ann Arbor, MI 48109-1048, USA
| |
Collapse
|
19
|
Lo Presti L, Kahmann R. How filamentous plant pathogen effectors are translocated to host cells. CURRENT OPINION IN PLANT BIOLOGY 2017; 38:19-24. [PMID: 28460240 DOI: 10.1016/j.pbi.2017.04.005] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 04/05/2017] [Accepted: 04/10/2017] [Indexed: 06/07/2023]
Abstract
The interaction of microbes with "signature" plants is largely governed by secreted effector proteins, which serve to dampen plant defense responses and modulate host cell processes. Secreted effectors can function either in the apoplast or within plant cell compartments. How oomycetes and fungi translocate their effectors to plant cells is still poorly understood and controversial. While most oomycete effectors share a common 'signature' that was proposed to mediate their uptake via endocytosis, fungal effectors display no conserved motifs at the primary amino acid sequence level. Here we summarize current knowledge in the field of oomycete and fungal effector uptake and highlight emerging themes that may unite rather than set apart these unrelated filamentous pathogens.
Collapse
Affiliation(s)
- Libera Lo Presti
- Max Planck Institute for Terrestrial Microbiology, Dept. Organismic Interactions, Karl-von-Frisch-Strasse 10, 35043 Marburg, Germany
| | - Regine Kahmann
- Max Planck Institute for Terrestrial Microbiology, Dept. Organismic Interactions, Karl-von-Frisch-Strasse 10, 35043 Marburg, Germany.
| |
Collapse
|
20
|
Yuan P, Jauregui E, Du L, Tanaka K, Poovaiah BW. Calcium signatures and signaling events orchestrate plant-microbe interactions. CURRENT OPINION IN PLANT BIOLOGY 2017; 38:173-183. [PMID: 28692858 DOI: 10.1016/j.pbi.2017.06.003] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Revised: 06/07/2017] [Accepted: 06/08/2017] [Indexed: 05/20/2023]
Abstract
Calcium (Ca2+) acts as an essential second messenger connecting the perception of microbe signals to the establishment of appropriate immune and symbiotic responses in plants. Accumulating evidence suggests that plants distinguish different microorganisms through plasma membrane-localized pattern recognition receptors. The particular recognition events are encoded into Ca2+ signatures, which are sensed by diverse intracellular Ca2+ binding proteins. The Ca2+ signatures are eventually decoded to distinct downstream responses through transcriptional reprogramming of the defense or symbiosis-related genes. Recent observations further reveal that Ca2+-mediated signaling is also involved in negative regulation of plant immunity. This review is intended as an overview of Ca2+ signaling during immunity and symbiosis, including Ca2+ responses in the nucleus and cytosol.
Collapse
Affiliation(s)
- Peiguo Yuan
- Laboratory of Molecular Plant Science, Department of Horticulture, Washington State University, Pullman, WA 99164-6414, USA
| | - Edgard Jauregui
- Laboratory of Molecular Plant Science, Department of Horticulture, Washington State University, Pullman, WA 99164-6414, USA
| | - Liqun Du
- Laboratory of Molecular Plant Science, Department of Horticulture, Washington State University, Pullman, WA 99164-6414, USA; College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang 310036, China.
| | - Kiwamu Tanaka
- Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430, USA
| | - B W Poovaiah
- Laboratory of Molecular Plant Science, Department of Horticulture, Washington State University, Pullman, WA 99164-6414, USA.
| |
Collapse
|
21
|
Koch AM, Antunes PM, Maherali H, Hart MM, Klironomos JN. Evolutionary asymmetry in the arbuscular mycorrhizal symbiosis: conservatism in fungal morphology does not predict host plant growth. THE NEW PHYTOLOGIST 2017; 214:1330-1337. [PMID: 28186629 DOI: 10.1111/nph.14465] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 12/24/2016] [Indexed: 05/19/2023]
Abstract
Although arbuscular mycorrhizal (AM) fungi are obligate symbionts that can influence plant growth, the magnitude and direction of these effects are highly variable within fungal genera and even among isolates within species, as well as among plant taxa. To determine whether variability in AM fungal morphology and growth is correlated with AM fungal effects on plant growth, we established a common garden experiment with 56 AM fungal isolates comprising 17 genera and six families growing with three plant host species. Arbuscular mycorrhizal fungal morphology and growth was highly conserved among isolates of the same species and among species within a family. By contrast, plant growth response to fungal inoculation was highly variable, with the majority of variation occurring among different isolates of the same AM fungal species. Our findings show that host performance cannot be predicted from AM fungal morphology and growth traits. Divergent effects on plant growth among isolates within an AM fungal species may be caused by coevolution between co-occurring fungal and plant populations.
Collapse
Affiliation(s)
- Alexander M Koch
- Department of Biology, University of British Columbia, Okanagan Campus, Kelowna, BC, V1V 1V7, Canada
| | - Pedro M Antunes
- Department of Biology, Algoma University, Sault Ste. Marie, ON, P6B 2G4, Canada
| | - Hafiz Maherali
- Department of Integrative Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Miranda M Hart
- Department of Biology, University of British Columbia, Okanagan Campus, Kelowna, BC, V1V 1V7, Canada
| | - John N Klironomos
- Department of Biology, University of British Columbia, Okanagan Campus, Kelowna, BC, V1V 1V7, Canada
| |
Collapse
|
22
|
Corradi N, Brachmann A. Fungal Mating in the Most Widespread Plant Symbionts? TRENDS IN PLANT SCIENCE 2017; 22:175-183. [PMID: 27876487 DOI: 10.1016/j.tplants.2016.10.010] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 10/26/2016] [Accepted: 10/28/2016] [Indexed: 06/06/2023]
Abstract
Arbuscular mycorrhizal fungi (AMF) are relevant plant symbionts whose hyphae and spores carry hundreds of coexisting nuclei with supposedly divergent genomes but no sign of sexual reproduction. This unusual biology suggested that conventional fungal mating is not amendable to optimize strains for plant growth, but recent evidence of sexual-related nuclear inheritance in these organisms is now challenging this widespread notion. Here, we outline our knowledge of AMF genetics within a historical context, and discuss how past and new information in this area changed our understanding of AMF biology. We also highlight the mating-related processes in AMF, and propose new research avenues and approaches that could lead to a better application of these organisms for agricultural and environmental practices.
Collapse
Affiliation(s)
- Nicolas Corradi
- Canadian Institute for Advanced Research, Department of Biology, University of Ottawa, Ottawa, ON, Canada.
| | - Andreas Brachmann
- LMU Munich, Faculty of Biology, Genetics, D-82152 Planegg-Martinsried, Germany
| |
Collapse
|
23
|
Nadimi M, Stefani FOP, Hijri M. The large (134.9 kb) mitochondrial genome of the glomeromycete Funneliformis mosseae. MYCORRHIZA 2016; 26:747-755. [PMID: 27246226 DOI: 10.1007/s00572-016-0710-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 05/23/2016] [Indexed: 06/05/2023]
Abstract
Funneliformis mosseae is among the most ecologically and economically important glomeromycete species and occurs both in natural and disturbed areas in a wide range of habitats and climates. In this study, we report the sequencing of the complete mitochondrial (mt) genome of F. mosseae isolate FL299 using 454 pyrosequencing and Illumina HiSeq technologies. This mt genome is a full-length circular chromosome of 134,925 bp, placing it among the largest mitochondrial DNAs (mtDNAs) in the fungal kingdom. A comparative analysis with publically available arbuscular mycorrhizal fungal mtDNAs revealed that the mtDNA of F. mosseae FL299 contained a very large number of insertions contributing to its expansion. The gene synteny was completely reshuffled compared to previously published glomeromycotan mtDNAs and several genes were oriented in an anti-sense direction. Furthermore, the presence of different types of introns and insertions in rnl (14 introns) made this gene very distinctive in Glomeromycota. The presence of alternative genetic codes in both initiation (GUG) and termination (UGA) codons was another new feature in this mtDNA compared to previously published glomeromycotan mt genomes. The phylogenetic analysis inferred from the analysis of 14 protein mt genes confirmed the position of the Glomeromycota clade as a sister group of Mortierellomycotina. This mt genome is the largest observed so far in Glomeromycota and the first mt genome within the Funneliformis clade, providing new opportunities to better understand their evolution and to develop molecular markers.
Collapse
Affiliation(s)
- Maryam Nadimi
- Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, Université de Montréal, 4101 Rue Sherbrooke Est, Montréal, QC, H1X 2B2, Canada
| | - Franck O P Stefani
- Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, Université de Montréal, 4101 Rue Sherbrooke Est, Montréal, QC, H1X 2B2, Canada
| | - Mohamed Hijri
- Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, Université de Montréal, 4101 Rue Sherbrooke Est, Montréal, QC, H1X 2B2, Canada.
| |
Collapse
|
24
|
Wyss T, Masclaux FG, Rosikiewicz P, Pagni M, Sanders IR. Population genomics reveals that within-fungus polymorphism is common and maintained in populations of the mycorrhizal fungus Rhizophagus irregularis. THE ISME JOURNAL 2016; 10:2514-26. [PMID: 26953600 PMCID: PMC5030683 DOI: 10.1038/ismej.2016.29] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 01/22/2016] [Accepted: 01/25/2016] [Indexed: 12/15/2022]
Abstract
Arbuscular mycorrhizal (AM) fungi are symbionts of most plants, increasing plant growth and diversity. The model AM fungus Rhizophagus irregularis (isolate DAOM 197198) exhibits low within-fungus polymorphism. In contrast, another study reported high within-fungus variability. Experiments with other R. irregularis isolates suggest that within-fungus genetic variation can affect the fungal phenotype and plant growth, highlighting the biological importance of such variation. We investigated whether there is evidence of differing levels of within-fungus polymorphism in an R. irregularis population. We genotyped 20 isolates using restriction site-associated DNA sequencing and developed novel approaches for characterizing polymorphism among haploid nuclei. All isolates exhibited higher within-isolate poly-allelic single-nucleotide polymorphism (SNP) densities than DAOM 197198 in repeated and non-repeated sites mapped to the reference genome. Poly-allelic SNPs were independently confirmed. Allele frequencies within isolates deviated from diploids or tetraploids, or that expected for a strict dikaryote. Phylogeny based on poly-allelic sites was robust and mirrored the standard phylogeny. This indicates that within-fungus genetic variation is maintained in AM fungal populations. Our results predict a heterokaryotic state in the population, considerable differences in copy number variation among isolates and divergence among the copies, or aneuploidy in some isolates. The variation may be a combination of all of these hypotheses. Within-isolate genetic variation in R. irregularis leads to large differences in plant growth. Therefore, characterizing genomic variation within AM fungal populations is of major ecological importance.
Collapse
Affiliation(s)
- Tania Wyss
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Frédéric G Masclaux
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Vital-IT, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Pawel Rosikiewicz
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Marco Pagni
- Vital-IT, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Ian R Sanders
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| |
Collapse
|
25
|
Ropars J, Toro KS, Noel J, Pelin A, Charron P, Farinelli L, Marton T, Krüger M, Fuchs J, Brachmann A, Corradi N. Evidence for the sexual origin of heterokaryosis in arbuscular mycorrhizal fungi. Nat Microbiol 2016; 1:16033. [PMID: 27572831 DOI: 10.1038/nmicrobiol.2016.33] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 02/23/2016] [Indexed: 12/30/2022]
Abstract
Sexual reproduction is ubiquitous among eukaryotes, and fully asexual lineages are extremely rare. Prominent among ancient asexual lineages are the arbuscular mycorrhizal fungi (AMF), a group of plant symbionts with a multinucleate cytoplasm. Genomic divergence among co-existing nuclei was proposed to drive the evolutionary success of AMF in the absence of sex(1), but this hypothesis has been contradicted by recent genome analyses that failed to find significant genetic diversity within an AMF isolate(2,3). Here, we set out to resolve issues surrounding the genome organization and sexual potential of AMF by exploring the genomes of five isolates of Rhizophagus irregularis, a model AMF. We find that genetic diversity in this species varies among isolates and is structured in a homo-dikaryon-like manner usually linked with the existence of a sexual life cycle. We also identify a putative AMF mating-type locus, containing two genes with structural and evolutionary similarities with the mating-type locus of some Dikarya. Our analyses suggest that this locus may be multi-allelic and that AMF could be heterothallic and bipolar. These findings reconcile opposing views on the genome organization of these ubiquitous plant symbionts and open avenues for strain improvement and environmental application of these organisms.
Collapse
Affiliation(s)
- Jeanne Ropars
- Canadian Institute for Advanced Research, Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | | | - Jessica Noel
- Canadian Institute for Advanced Research, Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Adrian Pelin
- Canadian Institute for Advanced Research, Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Philippe Charron
- Canadian Institute for Advanced Research, Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Laurent Farinelli
- FASTERIS S.A., Ch. du Pont-du-Centenaire 109, PO Box 28, CH-1228 Plan-les-Ouates, Switzerland
| | - Timea Marton
- Canadian Institute for Advanced Research, Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Manuela Krüger
- Canadian Institute for Advanced Research, Department of Biology, University of Ottawa, Ottawa, Ontario, Canada.,Institute of Botany, Academy of Sciences of the Czech Republic, Zámek 1, Průhonice, CZ-25243, Czech Republic
| | - Jörg Fuchs
- Leibniz Institute of Plant Genetics and Crop Plant Research, D-06466 Gatersleben, Germany
| | - Andreas Brachmann
- LMU Munich, Faculty of Biology, Genetics, D-82152 Planegg-Martinsried, Germany
| | - Nicolas Corradi
- Canadian Institute for Advanced Research, Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| |
Collapse
|
26
|
Tang N, San Clemente H, Roy S, Bécard G, Zhao B, Roux C. A Survey of the Gene Repertoire of Gigaspora rosea Unravels Conserved Features among Glomeromycota for Obligate Biotrophy. Front Microbiol 2016; 7:233. [PMID: 26973612 PMCID: PMC4771724 DOI: 10.3389/fmicb.2016.00233] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 02/15/2016] [Indexed: 01/22/2023] Open
Abstract
Arbuscular mycorrhizal (AM) fungi are a diverse group of soil fungi (Glomeromycota) that form the most ancient mutualistic association termed AM symbiosis with a majority of land plants, improving their nutrition uptake and resistance to stresses. In contrast to their great ecological implications, the knowledge of the molecular biological mechanisms involved is still scant, partly due to the limited genomic resources available. Here, we describe the gene repertoire of a new AM fungus Gigaspora rosea (Diversisporales). Among the 86332 non-redundant virtual transcripts assembled, 15346 presented similarities with proteins in the Refseq database and 10175 were assigned with GO terms. KOG and Interpro domain annotations clearly showed an enrichment of genes involved in signal transduction in G. rosea. KEGG pathway analysis indicates that most primary metabolic processes are active in G. rosea. However, as for Rhizophagus irregularis, several metabolic genes were not found, including the fatty acid synthase (FAS) gene. This finding supports the hypothesis that AM fungi depend on the lipids produced by their hosts. Furthermore, the presence of a large number of transporters and 100s of secreted proteins, together with the reduced number of plant cell wall degrading enzymes could be interpreted as an evolutionary adaptation to its mutualistic obligate biotrophy. The detection of meiosis-related genes suggests that G. rosea might use a cryptic sexual process. Lastly, a phylogeny of basal fungi clearly shows Glomeromycota as a sister clade to Mucoromycotina, not only to the Mucorales or Mortierellales. The characterization of the gene repertoire from an AM fungal species belonging to the order of Diversisporales and its comparison with the gene sets of R. irregularis (Glomerales) and Gigaspora margarita (Diversisporales), reveal that AM fungi share several features linked to mutualistic obligate biotrophy. This work contributes to lay the foundation for forthcoming studies into the genomics of Diversisporales, and also illuminates the utility of comparing gene repertoires of species from Diversisporales and other clades of Glomeromycota to gain more insights into the genetics and evolution of this fungal group.
Collapse
Affiliation(s)
- Nianwu Tang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural UniversityWuhan, China
- CNRS, Laboratoire de Recherche en Sciences Végétales, UMR, Université Paul Sabatier – Université de ToulouseCastanet Tolosan, France
| | - Hélène San Clemente
- CNRS, Laboratoire de Recherche en Sciences Végétales, UMR, Université Paul Sabatier – Université de ToulouseCastanet Tolosan, France
| | - Sébastien Roy
- AGRONUTRITION Laboratoire de BiotechnologiesToulouse, France
| | - Guillaume Bécard
- CNRS, Laboratoire de Recherche en Sciences Végétales, UMR, Université Paul Sabatier – Université de ToulouseCastanet Tolosan, France
| | - Bin Zhao
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural UniversityWuhan, China
| | - Christophe Roux
- CNRS, Laboratoire de Recherche en Sciences Végétales, UMR, Université Paul Sabatier – Université de ToulouseCastanet Tolosan, France
| |
Collapse
|
27
|
Encinas-Viso F, Alonso D, Klironomos JN, Etienne RS, Chang ER. Plant-mycorrhizal fungus co-occurrence network lacks substantial structure. OIKOS 2015. [DOI: 10.1111/oik.02667] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Francisco Encinas-Viso
- Groningen Inst. for Evolutionary Life Sciences, Univ. of Groningen; Box 11103, NL-9700 Groningen CC the Netherlands
- CSIRO, Centre for Australian National Biodiversity Research; GPO Box 1600, Canberra ACT 2601 Canberra Australia
| | - David Alonso
- Groningen Inst. for Evolutionary Life Sciences, Univ. of Groningen; Box 11103, NL-9700 Groningen CC the Netherlands
- Theoretical Ecology Lab, Center for Advanced Studies of Blanes, CEAB-CSIC; Spain
| | | | - Rampal S. Etienne
- Groningen Inst. for Evolutionary Life Sciences, Univ. of Groningen; Box 11103, NL-9700 Groningen CC the Netherlands
| | - Esther R. Chang
- Groningen Inst. for Evolutionary Life Sciences, Univ. of Groningen; Box 11103, NL-9700 Groningen CC the Netherlands
| |
Collapse
|
28
|
Ropars J, Corradi N. Homokaryotic vs heterokaryotic mycelium in arbuscular mycorrhizal fungi: different techniques, different results? THE NEW PHYTOLOGIST 2015; 208:638-641. [PMID: 25952991 DOI: 10.1111/nph.13448] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Affiliation(s)
- Jeanne Ropars
- Canadian Institute for Advanced Research, Department of Biology, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
| | - Nicolas Corradi
- Canadian Institute for Advanced Research, Department of Biology, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
| |
Collapse
|
29
|
Boon E, Halary S, Bapteste E, Hijri M. Studying genome heterogeneity within the arbuscular mycorrhizal fungal cytoplasm. Genome Biol Evol 2015; 7:505-21. [PMID: 25573960 PMCID: PMC4350173 DOI: 10.1093/gbe/evv002] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/05/2015] [Indexed: 11/12/2022] Open
Abstract
Although heterokaryons have been reported in nature, multicellular organisms are generally assumed genetically homogeneous. Here, we investigate the case of arbuscular mycorrhizal fungi (AMF) that form symbiosis with plant roots. The growth advantages they confer to their hosts are of great potential benefit to sustainable agricultural practices. However, measuring genetic diversity for these coenocytes is a major challenge: Within the same cytoplasm, AMF contain thousands of nuclei and show extremely high levels of genetic variation for some loci. The extent and physical location of polymorphism within and between AMF genomes is unclear. We used two complementary strategies to estimate genetic diversity in AMF, investigating polymorphism both on a genome scale and in putative single copy loci. First, we used data from whole-genome pyrosequencing of four AMF isolates to describe genetic diversity, based on a conservative network-based clustering approach. AMF isolates showed marked differences in genome-wide diversity patterns in comparison to a panel of control fungal genomes. This clustering approach further allowed us to provide conservative estimates of Rhizophagus spp. genomes sizes. Second, we designed new putative single copy genomic markers, which we investigated by massive parallel amplicon sequencing for two Rhizophagus irregularis and one Rhizophagus sp. isolates. Most loci showed high polymorphism, with up to 103 alleles per marker. This polymorphism could be distributed within or between nuclei. However, we argue that the Rhizophagus isolates under study might be heterokaryotic, at least for the putative single copy markers we studied. Considering that genetic information is the main resource for identification of AMF, we suggest that special attention is warranted for the study of these ecologically important organisms.
Collapse
Affiliation(s)
- Eva Boon
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, Quebec, Canada
| | - Sébastien Halary
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, Quebec, Canada
| | - Eric Bapteste
- CNRS, UMR7138, Institut de Biologie Paris-Seine, Paris, France Sorbonne Universités, UPMC Univ Paris 06, Institut de Biologie Paris-Seine (IBPS), Paris, France
| | - Mohamed Hijri
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, Quebec, Canada
| |
Collapse
|
30
|
Beaudet D, de la Providencia IE, Labridy M, Roy-Bolduc A, Daubois L, Hijri M. Intraisolate mitochondrial genetic polymorphism and gene variants coexpression in arbuscular mycorrhizal fungi. Genome Biol Evol 2014; 7:218-27. [PMID: 25527836 PMCID: PMC4316628 DOI: 10.1093/gbe/evu275] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/06/2014] [Indexed: 11/13/2022] Open
Abstract
Arbuscular mycorrhizal fungi (AMF) are multinucleated and coenocytic organisms, in which the extent of the intraisolate nuclear genetic variation has been a source of debate. Conversely, their mitochondrial genomes (mtDNAs) have appeared to be homogeneous within isolates in all next generation sequencing (NGS)-based studies. Although several lines of evidence have challenged mtDNA homogeneity in AMF, extensive survey to investigate intraisolate allelic diversity has not previously been undertaken. In this study, we used a conventional polymerase chain reaction -based approach on selected mitochondrial regions with a high-fidelity DNA polymerase, followed by cloning and Sanger sequencing. Two isolates of Rhizophagus irregularis were used, one cultivated in vitro for several generations (DAOM-197198) and the other recently isolated from the field (DAOM-242422). At different loci in both isolates, we found intraisolate allelic variation within the mtDNA and in a single copy nuclear marker, which highlighted the presence of several nonsynonymous mutations in protein coding genes. We confirmed that some of this variation persisted in the transcriptome, giving rise to at least four distinct nad4 transcripts in DAOM-197198. We also detected the presence of numerous mitochondrial DNA copies within nuclear genomes (numts), providing insights to understand this important evolutionary process in AMF. Our study reveals that genetic variation in Glomeromycota is higher than what had been previously assumed and also suggests that it could have been grossly underestimated in most NGS-based AMF studies, both in mitochondrial and nuclear genomes, due to the presence of low-level mutations.
Collapse
Affiliation(s)
- Denis Beaudet
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 Rue Sherbrooke Est, Montréal, QC H1X 2B2, Canada
| | - Ivan Enrique de la Providencia
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 Rue Sherbrooke Est, Montréal, QC H1X 2B2, Canada
| | - Manuel Labridy
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 Rue Sherbrooke Est, Montréal, QC H1X 2B2, Canada
| | - Alice Roy-Bolduc
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 Rue Sherbrooke Est, Montréal, QC H1X 2B2, Canada
| | - Laurence Daubois
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 Rue Sherbrooke Est, Montréal, QC H1X 2B2, Canada
| | - Mohamed Hijri
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 Rue Sherbrooke Est, Montréal, QC H1X 2B2, Canada
| |
Collapse
|
31
|
Limpens E, Geurts R. Plant-driven genome selection of arbuscular mycorrhizal fungi. MOLECULAR PLANT PATHOLOGY 2014; 15:531-534. [PMID: 25041428 PMCID: PMC6638801 DOI: 10.1111/mpp.12149] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Affiliation(s)
- Erik Limpens
- Plant Science - Laboratory of Molecular Biology, Wageningen University, Droevendaalsesteeg 1, Wageningen, 6708PB, the Netherlands
| | | |
Collapse
|
32
|
Moscatiello R, Sello S, Novero M, Negro A, Bonfante P, Navazio L. The intracellular delivery of TAT-aequorin reveals calcium-mediated sensing of environmental and symbiotic signals by the arbuscular mycorrhizal fungus Gigaspora margarita. THE NEW PHYTOLOGIST 2014; 203:1012-1020. [PMID: 24845011 DOI: 10.1111/nph.12849] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Accepted: 04/10/2014] [Indexed: 06/03/2023]
Abstract
Arbuscular mycorrhiza (AM) is an ecologically relevant symbiosis between most land plants and Glomeromycota fungi. The peculiar traits of AM fungi have so far limited traditional approaches such as genetic transformation. The aim of this work was to investigate whether the protein transduction domain of the HIV-1 transactivator of transcription (TAT) protein, previously shown to act as a potent nanocarrier for macromolecule delivery in both animal and plant cells, may translocate protein cargoes into AM fungi. We evaluated the internalization into germinated spores of Gigaspora margarita of two recombinant TAT fusion proteins consisting of either a fluorescent (GFP) or a luminescent (aequorin) reporter linked to the TAT peptide. Both TAT-fused proteins were found to enter AM fungal mycelia after a short incubation period (5-10 min). Ca2+ measurements in G. margarita mycelia pre-incubated with TAT-aequorin demonstrated the occurrence of changes in the intracellular free Ca2+ concentration in response to relevant stimuli, such as touch, cold, salinity, and strigolactones, symbiosis-related plant signals. These data indicate that the cell-penetrating properties of the TAT peptide can be used as an effective strategy for intracellularly delivering proteins of interest and shed new light on Ca2+ homeostasis and signalling in AM fungi.
Collapse
Affiliation(s)
- Roberto Moscatiello
- Department of Biology, University of Padova, Via U. Bassi 58/B, 35131, Padova, Italy
| | | | | | | | | | | |
Collapse
|
33
|
Abstract
Trade-offs between individual fitness and the collective performance of crop and below-ground symbiont communities are common in agriculture. Plant competitiveness for light and soil resources is key to individual fitness, but higher investments in stems and roots by a plant community to compete for those resources ultimately reduce crop yields. Similarly, rhizobia and mycorrhizal fungi may increase their individual fitness by diverting resources to their own reproduction, even if they could have benefited collectively by providing their shared crop host with more nitrogen and phosphorus, respectively. Past selection for inclusive fitness (benefits to others, weighted by their relatedness) is unlikely to have favoured community performance over individual fitness. The limited evidence for kin recognition in plants and microbes changes this conclusion only slightly. We therefore argue that there is still ample opportunity for human-imposed selection to improve cooperation among crop plants and their symbionts so that they use limited resources more efficiently. This evolutionarily informed approach will require a better understanding of how interactions among crops, and interactions with their symbionts, affected their inclusive fitness in the past and what that implies for current interactions.
Collapse
Affiliation(s)
- E. Toby Kiers
- Institute of Ecological Sciences, Faculty of Earth and Life Sciences, Vrije Universiteit, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
| | - R. Ford Denison
- Ecology Evolution and Behavior, University of Minnesota, St Paul, MN 55108, USA
| |
Collapse
|
34
|
Chagnon PL. Ecological and evolutionary implications of hyphal anastomosis in arbuscular mycorrhizal fungi. FEMS Microbiol Ecol 2014; 88:437-44. [DOI: 10.1111/1574-6941.12321] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Revised: 03/05/2014] [Accepted: 03/06/2014] [Indexed: 01/10/2023] Open
|
35
|
Angelard C, Tanner CJ, Fontanillas P, Niculita-Hirzel H, Masclaux F, Sanders IR. Rapid genotypic change and plasticity in arbuscular mycorrhizal fungi is caused by a host shift and enhanced by segregation. THE ISME JOURNAL 2014; 8:284-94. [PMID: 24030596 PMCID: PMC3906815 DOI: 10.1038/ismej.2013.154] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Revised: 07/22/2013] [Accepted: 08/05/2013] [Indexed: 11/09/2022]
Abstract
Arbuscular mycorrhizal fungi (AMF) are among the most abundant symbionts of plants, improving plant productivity and diversity. They are thought to mostly grow vegetatively, a trait assumed to limit adaptability. However, AMF can also harbor genetically different nuclei (nucleotypes). It has been shown that one AMF can produce genotypically novel offspring with proportions of different nucleotypes. We hypothesized that (1) AMF respond rapidly to a change of environment (plant host) through changes in the frequency of nucleotypes; (2) genotypically novel offspring exhibit different genetic responses to environmental change than the parent; and (3) genotypically novel offspring exhibit a wide range of phenotypic plasticity to a change of environment. We subjected AMF parents and offspring to a host shift. We observed rapid and large genotypic changes in all AMF lines that were not random. Genotypic and phenotypic responses were different among offspring and their parents. Even though growing vegetatively, AMF offspring display a broad range of genotypic and phenotypic changes in response to host shift. We conclude that AMF have the ability to rapidly produce variable progeny, increasing their probability to produce offspring with different fitness than their parents and, consequently, their potential adaptability to new environmental conditions. Such genotypic and phenotypic flexibility could be a fast alternative to sexual reproduction and is likely to be a key to the ecological success of AMF.
Collapse
Affiliation(s)
- Caroline Angelard
- Department of Ecology and Evolution,
University of Lausanne, Lausanne, Switzerland
| | | | | | | | - Frédéric Masclaux
- Department of Ecology and Evolution,
University of Lausanne, Lausanne, Switzerland
- Vital-IT Group, Swiss Institute for
Bioinformatics, University of Lausanne, Lausanne,
Switzerland
| | - Ian R Sanders
- Department of Ecology and Evolution,
University of Lausanne, Lausanne, Switzerland
| |
Collapse
|
36
|
Lin K, Limpens E, Zhang Z, Ivanov S, Saunders DGO, Mu D, Pang E, Cao H, Cha H, Lin T, Zhou Q, Shang Y, Li Y, Sharma T, van Velzen R, de Ruijter N, Aanen DK, Win J, Kamoun S, Bisseling T, Geurts R, Huang S. Single nucleus genome sequencing reveals high similarity among nuclei of an endomycorrhizal fungus. PLoS Genet 2014; 10:e1004078. [PMID: 24415955 PMCID: PMC3886924 DOI: 10.1371/journal.pgen.1004078] [Citation(s) in RCA: 172] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Accepted: 11/18/2013] [Indexed: 12/03/2022] Open
Abstract
Nuclei of arbuscular endomycorrhizal fungi have been described as highly diverse due to their asexual nature and absence of a single cell stage with only one nucleus. This has raised fundamental questions concerning speciation, selection and transmission of the genetic make-up to next generations. Although this concept has become textbook knowledge, it is only based on studying a few loci, including 45S rDNA. To provide a more comprehensive insight into the genetic makeup of arbuscular endomycorrhizal fungi, we applied de novo genome sequencing of individual nuclei of Rhizophagus irregularis. This revealed a surprisingly low level of polymorphism between nuclei. In contrast, within a nucleus, the 45S rDNA repeat unit turned out to be highly diverged. This finding demystifies a long-lasting hypothesis on the complex genetic makeup of arbuscular endomycorrhizal fungi. Subsequent genome assembly resulted in the first draft reference genome sequence of an arbuscular endomycorrhizal fungus. Its length is 141 Mbps, representing over 27,000 protein-coding gene models. We used the genomic sequence to reinvestigate the phylogenetic relationships of Rhizophagus irregularis with other fungal phyla. This unambiguously demonstrated that Glomeromycota are more closely related to Mucoromycotina than to its postulated sister Dikarya.
Collapse
Affiliation(s)
- Kui Lin
- Laboratory of Computational Molecular Biology, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Erik Limpens
- Laboratory of Molecular Biology, Department of Plant Science, Wageningen University, Wageningen, The Netherlands
| | - Zhonghua Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of Ministry of Agriculture, Sino-Dutch Joint Lab of Horticultural Genomics, Beijing, China
| | - Sergey Ivanov
- Laboratory of Molecular Biology, Department of Plant Science, Wageningen University, Wageningen, The Netherlands
| | | | - Desheng Mu
- Novome Biotech Inc., Zhongguancun Life Science Park, Beijing, China
| | - Erli Pang
- Laboratory of Computational Molecular Biology, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Huifen Cao
- Laboratory of Computational Molecular Biology, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Hwangho Cha
- Laboratory of Computational Molecular Biology, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Tao Lin
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of Ministry of Agriculture, Sino-Dutch Joint Lab of Horticultural Genomics, Beijing, China
| | - Qian Zhou
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of Ministry of Agriculture, Sino-Dutch Joint Lab of Horticultural Genomics, Beijing, China
| | - Yi Shang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of Ministry of Agriculture, Sino-Dutch Joint Lab of Horticultural Genomics, Beijing, China
| | - Ying Li
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of Ministry of Agriculture, Sino-Dutch Joint Lab of Horticultural Genomics, Beijing, China
| | - Trupti Sharma
- Laboratory of Molecular Biology, Department of Plant Science, Wageningen University, Wageningen, The Netherlands
| | - Robin van Velzen
- Laboratory of Molecular Biology, Department of Plant Science, Wageningen University, Wageningen, The Netherlands
| | - Norbert de Ruijter
- Laboratory of Cell Biology, Department of Plant Science, Wageningen University, Wageningen, The Netherlands
| | - Duur K. Aanen
- Laboratory of Genetics, Department of Plant Science, Wageningen University, Wageningen, The Netherlands
| | - Joe Win
- The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
| | - Sophien Kamoun
- The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
| | - Ton Bisseling
- Laboratory of Molecular Biology, Department of Plant Science, Wageningen University, Wageningen, The Netherlands
- College of Science, King Saud University, Riyadh, Saudi Arabia
| | - René Geurts
- Laboratory of Molecular Biology, Department of Plant Science, Wageningen University, Wageningen, The Netherlands
| | - Sanwen Huang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of Ministry of Agriculture, Sino-Dutch Joint Lab of Horticultural Genomics, Beijing, China
- Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| |
Collapse
|
37
|
Boon E, Zimmerman E, St-Arnaud M, Hijri M. Allelic differences within and among sister spores of the arbuscular mycorrhizal fungus Glomus etunicatum suggest segregation at sporulation. PLoS One 2013; 8:e83301. [PMID: 24386173 PMCID: PMC3873462 DOI: 10.1371/journal.pone.0083301] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2012] [Accepted: 11/10/2013] [Indexed: 01/08/2023] Open
Abstract
Arbuscular mycorrhizal fungi (AMF) are root-inhabiting fungi that form mutualistic symbioses with their host plants. AMF are made up of coenocytic networks of hyphae through which nuclei and organelles can freely migrate. In this study, we investigated the possibility of a genetic bottleneck and segregation of allelic variation at sporulation for a low-copy Polymerase1-like gene, PLS. Specifically, our objectives were (1) to estimate what allelic diversity is passed on to a single spore (2) to determine whether this diversity is less than the total amount of variation found in all spores (3) to investigate whether there is any differential segregation of allelic variation. We inoculated three tomato plants with a single spore of Glomus etunicatum each and after six months sampled between two and three daughter spores per tomato plant. Pyrosequencing PLS amplicons in eight spores revealed high levels of allelic diversity; between 43 and 152 alleles per spore. We corroborated the spore pyrosequencing results with Sanger- and pyrosequenced allele distributions from the original parent isolate. Both sequencing methods retrieved the most abundant alleles from the offspring spore allele distributions. Our results indicate that individual spores contain only a subset of the total allelic variation from the pooled spores and parent isolate. Patterns of allele diversity between spores suggest the possibility for segregation of PLS alleles among spores. We conclude that a genetic bottleneck could potentially occur during sporulation in AMF, with resulting differences in genetic variation among sister spores. We suggest that the effects of this bottleneck may be countered by anastomosis (hyphal fusion) between related hyphae.
Collapse
Affiliation(s)
- Eva Boon
- Institut de recherche en biologie végétale, Département de sciences biologiques, Université de Montréal, Montreal, Quebec, Canada
| | - Erin Zimmerman
- Institut de recherche en biologie végétale, Département de sciences biologiques, Université de Montréal, Montreal, Quebec, Canada
| | - Marc St-Arnaud
- Institut de recherche en biologie végétale, Département de sciences biologiques, Université de Montréal, Montreal, Quebec, Canada
| | - Mohamed Hijri
- Institut de recherche en biologie végétale, Département de sciences biologiques, Université de Montréal, Montreal, Quebec, Canada
| |
Collapse
|
38
|
Abstract
The default mineral nutrient acquisition strategy of land plants is the symbiosis with arbuscular mycorrhiza (AM) fungi. Research into the cell and developmental biology of AM revealed fascinating insights into the plasticity of plant cell development and of interorganismic communication. It is driven by the prospect of increased exploitation of AM benefits for sustainable agriculture. The plant cell developmental program for intracellular accommodation of AM fungi is activated by a genetically defined signaling pathway involving calcium spiking in the nucleus as second messenger. Calcium spiking is triggered by chitooligosaccharides released by AM fungi that are probably perceived via LysM domain receptor kinases. Fungal infection and calcium spiking are spatiotemporally coordinated, and only cells committed to accommodating the fungus undergo high-frequency spiking. Delivery of mineral nutrients by AM fungi occurs at tree-shaped hyphal structures, the arbuscules, in plant cortical cells. Nutrients are taken up at a plant-derived periarbuscular membrane, which surrounds fungal hyphae and carries a specific transporter composition that is of direct importance for symbiotic efficiency. An elegant study has unveiled a new and unexpected mechanism for specific protein localization to the periarbuscular membrane, which relies on the timing of gene expression to synchronize protein biosynthesis with a redirection of secretion. The control of AM development by phytohormones is currently subject to active investigation and has led to the rediscovery of strigolactones. Nearly all tested phytohormones regulate AM development, and major insights into the mechanisms of this regulation are expected in the near future.
Collapse
Affiliation(s)
- Caroline Gutjahr
- Institute of Genetics, Faculty of Biology, University of Munich, 82152 Martinsried, Germany; ,
| | | |
Collapse
|
39
|
Genome of an arbuscular mycorrhizal fungus provides insight into the oldest plant symbiosis. Proc Natl Acad Sci U S A 2013; 110:20117-22. [PMID: 24277808 DOI: 10.1073/pnas.1313452110] [Citation(s) in RCA: 444] [Impact Index Per Article: 40.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The mutualistic symbiosis involving Glomeromycota, a distinctive phylum of early diverging Fungi, is widely hypothesized to have promoted the evolution of land plants during the middle Paleozoic. These arbuscular mycorrhizal fungi (AMF) perform vital functions in the phosphorus cycle that are fundamental to sustainable crop plant productivity. The unusual biological features of AMF have long fascinated evolutionary biologists. The coenocytic hyphae host a community of hundreds of nuclei and reproduce clonally through large multinucleated spores. It has been suggested that the AMF maintain a stable assemblage of several different genomes during the life cycle, but this genomic organization has been questioned. Here we introduce the 153-Mb haploid genome of Rhizophagus irregularis and its repertoire of 28,232 genes. The observed low level of genome polymorphism (0.43 SNP per kb) is not consistent with the occurrence of multiple, highly diverged genomes. The expansion of mating-related genes suggests the existence of cryptic sex-related processes. A comparison of gene categories confirms that R. irregularis is close to the Mucoromycotina. The AMF obligate biotrophy is not explained by genome erosion or any related loss of metabolic complexity in central metabolism, but is marked by a lack of genes encoding plant cell wall-degrading enzymes and of genes involved in toxin and thiamine synthesis. A battery of mycorrhiza-induced secreted proteins is expressed in symbiotic tissues. The present comprehensive repertoire of R. irregularis genes provides a basis for future research on symbiosis-related mechanisms in Glomeromycota.
Collapse
|
40
|
Roger A, Colard A, Angelard C, Sanders IR. Relatedness among arbuscular mycorrhizal fungi drives plant growth and intraspecific fungal coexistence. THE ISME JOURNAL 2013; 7:2137-46. [PMID: 23823490 PMCID: PMC3806264 DOI: 10.1038/ismej.2013.112] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2013] [Revised: 05/29/2013] [Accepted: 05/31/2013] [Indexed: 11/09/2022]
Abstract
Arbuscular mycorrhizal fungi (AMF) form symbioses with most plant species. They are ecologically important determinants of plant growth and diversity. Considerable genetic variation occurs in AMF populations. Thus, plants are exposed to AMF of varying relatedness to each other. Very little is known about either the effects of coexisting AMF on plant growth or which factors influence intraspecific AMF coexistence within roots. No studies have addressed whether the genetics of coexisting AMF, and more specifically their relatedness, influences plant growth and AMF coexistence. Relatedness is expected to influence coexistence between individuals, and it has been suggested that decreasing ability of symbionts to coexist can have negative effects on the growth of the host. We tested the effect of a gradient of AMF genetic relatedness on the growth of two plant species. Increasing relatedness between AMFs lead to markedly greater plant growth (27% biomass increase with closely related compared to distantly related AMF). In one plant species, closely related AMF coexisted in fairly equal proportions but decreasing relatedness lead to a very strong disequilibrium between AMF in roots, indicating much stronger competition. Given the strength of the effects with such a shallow relatedness gradient and the fact that in the field plants are exposed to a steeper gradient, we consider that AMF relatedness can have a strong role in plant growth and the ability of AMF to coexist. We conclude that AMF relatedness is a driver of plant growth and that relatedness is also a strong driver of intraspecific coexistence of these ecologically important symbionts.
Collapse
Affiliation(s)
- Aurélien Roger
- University of Lausanne, Department of Ecology and Evolution, Lausanne, Switzerland
| | - Alexandre Colard
- University of Lausanne, Department of Ecology and Evolution, Lausanne, Switzerland
| | - Caroline Angelard
- University of Lausanne, Department of Ecology and Evolution, Lausanne, Switzerland
| | - Ian R Sanders
- University of Lausanne, Department of Ecology and Evolution, Lausanne, Switzerland
| |
Collapse
|
41
|
Ceballos I, Ruiz M, Fernández C, Peña R, Rodríguez A, Sanders IR. The in vitro mass-produced model mycorrhizal fungus, Rhizophagus irregularis, significantly increases yields of the globally important food security crop cassava. PLoS One 2013; 8:e70633. [PMID: 23950975 PMCID: PMC3737348 DOI: 10.1371/journal.pone.0070633] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Accepted: 06/26/2013] [Indexed: 11/22/2022] Open
Abstract
The arbuscular mycorrhizal symbiosis is formed between arbuscular mycorrhizal fungi (AMF) and plant roots. The fungi provide the plant with inorganic phosphate (P). The symbiosis can result in increased plant growth. Although most global food crops naturally form this symbiosis, very few studies have shown that their practical application can lead to large-scale increases in food production. Application of AMF to crops in the tropics is potentially effective for improving yields. However, a main problem of using AMF on a large-scale is producing cheap inoculum in a clean sterile carrier and sufficiently concentrated to cheaply transport. Recently, mass-produced in vitro inoculum of the model mycorrhizal fungus Rhizophagus irregularis became available, potentially making its use viable in tropical agriculture. One of the most globally important food plants in the tropics is cassava. We evaluated the effect of in vitro mass-produced R. irregularis inoculum on the yield of cassava crops at two locations in Colombia. A significant effect of R. irregularis inoculation on yield occurred at both sites. At one site, yield increases were observed irrespective of P fertilization. At the other site, inoculation with AMF and 50% of the normally applied P gave the highest yield. Despite that AMF inoculation resulted in greater food production, economic analyses revealed that AMF inoculation did not give greater return on investment than with conventional cultivation. However, the amount of AMF inoculum used was double the recommended dose and was calculated with European, not Colombian, inoculum prices. R. irregularis can also be manipulated genetically in vitro, leading to improved plant growth. We conclude that application of in vitro R. irregularis is currently a way of increasing cassava yields, that there is a strong potential for it to be economically profitable and that there is enormous potential to improve this efficiency further in the future.
Collapse
Affiliation(s)
- Isabel Ceballos
- Soil Microbiology, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Michael Ruiz
- Soil Microbiology, Universidad Nacional de Colombia, Bogotá, Colombia
| | | | - Ricardo Peña
- Utopía, Universidad de La Salle, Yopal, Colombia
| | - Alia Rodríguez
- Soil Microbiology, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Ian R. Sanders
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- * E-mail:
| |
Collapse
|
42
|
Lindahl BD, Nilsson RH, Tedersoo L, Abarenkov K, Carlsen T, Kjøller R, Kõljalg U, Pennanen T, Rosendahl S, Stenlid J, Kauserud H. Fungal community analysis by high-throughput sequencing of amplified markers--a user's guide. THE NEW PHYTOLOGIST 2013; 199:288-299. [PMID: 23534863 PMCID: PMC3712477 DOI: 10.1111/nph.12243] [Citation(s) in RCA: 515] [Impact Index Per Article: 46.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2013] [Accepted: 02/18/2013] [Indexed: 05/17/2023]
Abstract
Novel high-throughput sequencing methods outperform earlier approaches in terms of resolution and magnitude. They enable identification and relative quantification of community members and offer new insights into fungal community ecology. These methods are currently taking over as the primary tool to assess fungal communities of plant-associated endophytes, pathogens, and mycorrhizal symbionts, as well as free-living saprotrophs. Taking advantage of the collective experience of six research groups, we here review the different stages involved in fungal community analysis, from field sampling via laboratory procedures to bioinformatics and data interpretation. We discuss potential pitfalls, alternatives, and solutions. Highlighted topics are challenges involved in: obtaining representative DNA/RNA samples and replicates that encompass the targeted variation in community composition, selection of marker regions and primers, options for amplification and multiplexing, handling of sequencing errors, and taxonomic identification. Without awareness of methodological biases, limitations of markers, and bioinformatics challenges, large-scale sequencing projects risk yielding artificial results and misleading conclusions.
Collapse
Affiliation(s)
- Björn D Lindahl
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Box 7026, SE-750 07, Uppsala, Sweden
| | - R Henrik Nilsson
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, SE-405 30, Gothenburg, Sweden
| | - Leho Tedersoo
- Institute of Ecology and Earth Sciences/Natural History Museum, University of Tartu, 46 Vanemuise St., 51014, Tartu, Estonia
| | - Kessy Abarenkov
- Institute of Ecology and Earth Sciences/Natural History Museum, University of Tartu, 46 Vanemuise St., 51014, Tartu, Estonia
| | - Tor Carlsen
- Department of Biology, University of Oslo, PO Box 1066, Blindern, N-0316, Oslo, Norway
| | - Rasmus Kjøller
- Department of Biology, University of Copenhagen, Øster Farimagsgade 2D, 1353, Copenhagen, Denmark
| | - Urmas Kõljalg
- Institute of Ecology and Earth Sciences/Natural History Museum, University of Tartu, 46 Vanemuise St., 51014, Tartu, Estonia
| | - Taina Pennanen
- The Finnish Forest Research Institute, PL 18, FI-01301, Vantaa, Finland
| | - Søren Rosendahl
- Department of Biology, University of Copenhagen, Øster Farimagsgade 2D, 1353, Copenhagen, Denmark
| | - Jan Stenlid
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Box 7026, SE-750 07, Uppsala, Sweden
| | - Håvard Kauserud
- Department of Biology, University of Oslo, PO Box 1066, Blindern, N-0316, Oslo, Norway
| |
Collapse
|
43
|
Riley R, Corradi N. Searching for clues of sexual reproduction in the genomes of arbuscular mycorrhizal fungi. FUNGAL ECOL 2013. [DOI: 10.1016/j.funeco.2012.01.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
|
44
|
Root Allies: Arbuscular Mycorrhizal Fungi Help Plants to Cope with Biotic Stresses. SOIL BIOLOGY 2013. [DOI: 10.1007/978-3-642-39317-4_15] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
|
45
|
Li T, Hu YJ, Hao ZP, Li H, Wang YS, Chen BD. First cloning and characterization of two functional aquaporin genes from an arbuscular mycorrhizal fungus Glomus intraradices. THE NEW PHYTOLOGIST 2013; 197:617-630. [PMID: 23157494 DOI: 10.1111/nph.12011] [Citation(s) in RCA: 111] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Accepted: 09/22/2012] [Indexed: 05/09/2023]
Abstract
Arbuscular mycorrhizal (AM) symbiosis is known to stimulate plant drought tolerance. However, the molecular basis for the direct involvement of AM fungi (AMF) in plant water relations has not been established. Two full-length aquaporin genes, namely GintAQPF1 and GintAQPF2, were cloned by rapid amplification of cDNA 5'- and 3'-ends from an AMF, Glomus intraradices. Aquaporin localization, activities and water permeability were examined by heterologous expression in yeast. Gene expression during symbiosis was also analyzed by quantitative real-time polymerase chain reaction. GintAQPF1 was localized to the plasma membrane of yeast, whereas GintAQPF2 was localized to both plasma and intracellular membranes. Transformed yeast cells exhibited a significant decrease in cell volume on hyperosmotic shock and faster protoplast bursting on hypo-osmotic shock. Polyethylene glycol (PEG) stimulated, but glycerol inhibited, the aquaporin activities. Furthermore, the expression of the two genes in arbuscule-enriched cortical cells and extraradical mycelia of maize roots was also enhanced significantly under drought stress. GintAQPF1 and GintAQPF2 are the first two functional aquaporin genes from AMF reported to date. Our data strongly support potential water transport via AMF to host plants, which leads to a better understanding of the important role of AMF in plant drought tolerance.
Collapse
Affiliation(s)
- Tao Li
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Ya-Jun Hu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Zhi-Peng Hao
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Hong Li
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - You-Shan Wang
- Institute of Plant Nutrition and Resources, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Bao-Dong Chen
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| |
Collapse
|
46
|
Thiéry O, Moora M, Vasar M, Zobel M, Öpik M. Inter- and intrasporal nuclear ribosomal gene sequence variation within one isolate of arbuscular mycorrhizal fungus, Diversispora sp. Symbiosis 2012. [DOI: 10.1007/s13199-012-0212-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
47
|
Ehinger MO, Croll D, Koch AM, Sanders IR. Significant genetic and phenotypic changes arising from clonal growth of a single spore of an arbuscular mycorrhizal fungus over multiple generations. THE NEW PHYTOLOGIST 2012; 196:853-861. [PMID: 22931497 DOI: 10.1111/j.1469-8137.2012.04278.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Accepted: 07/11/2012] [Indexed: 05/26/2023]
Abstract
Arbuscular mycorrhizal fungi (AMF) are highly successful plant symbionts. They reproduce clonally producing multinucleate spores. It has been suggested that some AMF harbor genetically different nuclei. However, recent advances in sequencing the Glomus irregulare genome have indicated very low within-fungus polymorphism. We tested the null hypothesis that, with no genetic differences among nuclei, no significant genetic or phenotypic variation would occur among clonal single spore lines generated from one initial AMF spore. Furthermore, no additional variation would be expected in the following generations of single spore lines. Genetic diversity contained in one initial spore repeatedly gave rise to genetically different variants of the fungus with novel phenotypes. The genetic changes represented quantitative changes in allele frequencies, most probably as a result of changes in the frequency of genetic variation partitioned on different nuclei. The genetic and phenotypic variation is remarkable, given that it arose repeatedly from one clonal individual. Our results highlight the dynamic nature of AMF genetics. Even though within-fungus genetic variation is low, some is probably partitioned among nuclei and potentially causes changes in the phenotype. Our results are important for understanding AMF genetics, as well as for researchers and biotechnologists hoping to use AMF genetic diversity for the improvement of AMF inoculum.
Collapse
Affiliation(s)
- Martine O Ehinger
- Department of Ecology & Evolution, University of Lausanne, 1015, Lausanne, Switzerland
| | - Daniel Croll
- Department of Ecology & Evolution, University of Lausanne, 1015, Lausanne, Switzerland
- Plant Pathology, Institute of Integrative Biology, ETH Zürich, 8092, Zürich, Switzerland
| | - Alexander M Koch
- Department of Ecology & Evolution, University of Lausanne, 1015, Lausanne, Switzerland
- Irving K. Barber School of Arts and Sciences, University of British Columbia at Okanagan, Okanagan, Kelowna, BC, V1V 1V7 Canada
| | - Ian R Sanders
- Department of Ecology & Evolution, University of Lausanne, 1015, Lausanne, Switzerland
| |
Collapse
|
48
|
Helgason T. Keeping it in the family: segregation of genetic variation in Glomus irregulare. THE NEW PHYTOLOGIST 2012; 196:655-656. [PMID: 23043587 DOI: 10.1111/j.1469-8137.2012.04360.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
|
49
|
Abstract
The arbuscular mycorrhizal fungi (AMF) are important symbionts of land plants, which are known for their tremendous positive effects on terrestrial ecosystems, their peculiar cellular features, and their very old evolutionary history. To date, no sexual stage or apparatus have ever been observed in these organisms; a remarkable absence for a eukaryotic lineage. For this reason, AMF have long been considered an evolutionary oddity, having evolved for over 500 millions of years in the absence of sexual reproduction and meiosis. Here, we discuss the recent identification across a number of AMF genomes, of many genes that are known to be involved in the process of meiosis in several eukaryotic model species. The presence of these genes in AMF is a previously unsuspected and highly intriguing finding, which suggests the presence of a “hidden” sexual (or parasexual) reproduction that awaits formal observation in these poorly studied fungi.
Collapse
Affiliation(s)
- Nicolas Corradi
- Canadian Institute for Advanced Research; Department of Biology; University of Ottawa; Ottawa, ON Canada
| | | |
Collapse
|
50
|
Baluška F, Volkmann D, Menzel D, Barlow P. Strasburger's legacy to mitosis and cytokinesis and its relevance for the Cell Theory. PROTOPLASMA 2012; 249:1151-1162. [PMID: 22526203 DOI: 10.1007/s00709-012-0404-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2012] [Accepted: 03/22/2012] [Indexed: 05/31/2023]
Abstract
Eduard Strasburger was one of the most prominent biologists contributing to the development of the Cell Theory during the nineteenth century. His major contribution related to the characterization of mitosis and cytokinesis and especially to the discovery of the discrete stages of mitosis, which he termed prophase, metaphase and anaphase. Besides his observations on uninucleate plant and animal cells, he also investigated division processes in multinucleate cells. Here, he emphasised the independent nature of mitosis and cytokinesis. We discuss these issues from the perspective of new discoveries in the field of cell division and conclude that Strasburger's legacy will in the future lead to a reformulation of the Cell Theory and that this will accommodate the independent and primary nature of the nucleus, together with its complement of perinuclear microtubules, for the organisation of the eukaryotic cell.
Collapse
|