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Plett KL, Wojtalewicz D, Anderson IC, Plett JM. Fungal metabolism and free amino acid content may predict nitrogen transfer to the host plant in the ectomycorrhizal relationship between Pisolithus spp. and Eucalyptus grandis. THE NEW PHYTOLOGIST 2024; 242:1589-1602. [PMID: 37974494 DOI: 10.1111/nph.19400] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 10/16/2023] [Indexed: 11/19/2023]
Abstract
Ectomycorrhizal (ECM) fungi are crucial for tree nitrogen (N) nutrition; however, mechanisms governing N transfer from fungal tissues to the host plant are not well understood. ECM fungal isolates, even from the same species, vary considerably in their ability to support tree N nutrition, resulting in a range of often unpredictable symbiotic outcomes. In this study, we used isotopic labelling to quantify the transfer of N to the plant host by isolates from the ECM genus Pisolithus, known to have significant variability in colonisation and transfer of nutrients to a host. We considered the metabolic fate of N acquired by the fungi and found that the percentage of plant N acquired through symbiosis significantly correlated to the concentration of free amino acids in ECM extra-radical mycelium. Transcriptomic analyses complemented these findings with isolates having high amino acid content and N transfer showing increased expression of genes related to amino acid transport and catabolic pathways. These results suggest that fungal N metabolism impacts N transfer to the host plant in this interaction and that relative N transfer may be possible to predict through basic biochemical analyses.
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Affiliation(s)
- Krista L Plett
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, NSW, 2568, Australia
| | - Dominika Wojtalewicz
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, 2753, Australia
| | - Ian C Anderson
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, 2753, Australia
| | - Jonathan M Plett
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, 2753, Australia
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2
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Sebastiana M, Serrazina S, Monteiro F, Wipf D, Fromentin J, Teixeira R, Malhó R, Courty PE. Nitrogen Acquisition and Transport in the Ectomycorrhizal Symbiosis-Insights from the Interaction between an Oak Tree and Pisolithus tinctorius. PLANTS (BASEL, SWITZERLAND) 2022; 12:10. [PMID: 36616139 PMCID: PMC9823632 DOI: 10.3390/plants12010010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 12/04/2022] [Accepted: 12/16/2022] [Indexed: 06/17/2023]
Abstract
In temperate forests, the roots of various tree species are colonized by ectomycorrhizal fungi, which have a key role in the nitrogen nutrition of their hosts. However, not much is known about the molecular mechanisms related to nitrogen metabolism in ectomycorrhizal plants. This study aimed to evaluate the nitrogen metabolic response of oak plants when inoculated with the ectomycorrhizal fungus Pisolithus tinctorius. The expression of candidate genes encoding proteins involved in nitrogen uptake and assimilation was investigated in ectomycorrhizal roots. We found that three oak ammonium transporters were over-expressed in root tissues after inoculation, while the expression of amino acid transporters was not modified, suggesting that inorganic nitrogen is the main form of nitrogen transferred by the symbiotic fungus into the roots of the host plant. Analysis by heterologous complementation of a yeast mutant defective in ammonium uptake and GFP subcellular protein localization clearly confirmed that two of these genes encode functional ammonium transporters. Structural similarities between the proteins encoded by these ectomycorrhizal upregulated ammonium transporters, and a well-characterized ammonium transporter from E. coli, suggest a similar transport mechanism, involving deprotonation of NH4+, followed by diffusion of uncharged NH3 into the cytosol. This view is supported by the lack of induction of NH4+ detoxifying mechanisms, such as the GS/GOGAT pathway, in the oak mycorrhizal roots.
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Affiliation(s)
- Mónica Sebastiana
- BioISI—Instituto de Biosistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Susana Serrazina
- BioISI—Instituto de Biosistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Filipa Monteiro
- Linking Landscape, Environment, Agriculture and Food (LEAF), Associated Laboratory TERRA, Instituto Superior de Agronomia (ISA), Universidade de Lisboa, 1349-017 Lisbon, Portugal
- Centre for Ecology, Evolution and Environmental Changes (cE3c) & CHANGE—Global Change and Sustainability Institute, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | - Daniel Wipf
- Agroécologie, INRAE, Institut Agro, University Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Jérome Fromentin
- Agroécologie, INRAE, Institut Agro, University Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Rita Teixeira
- BioISI—Instituto de Biosistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Rui Malhó
- BioISI—Instituto de Biosistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Pierre-Emmanuel Courty
- Agroécologie, INRAE, Institut Agro, University Bourgogne Franche-Comté, F-21000 Dijon, France
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Qiao Z, Yates TB, Shrestha HK, Engle NL, Flanagan A, Morrell‐Falvey JL, Sun Y, Tschaplinski TJ, Abraham PE, Labbé J, Wang Z, Hettich RL, Tuskan GA, Muchero W, Chen J. Towards engineering ectomycorrhization into switchgrass bioenergy crops via a lectin receptor-like kinase. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:2454-2468. [PMID: 34272801 PMCID: PMC8633507 DOI: 10.1111/pbi.13671] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 06/24/2021] [Accepted: 07/09/2021] [Indexed: 05/22/2023]
Abstract
Soil-borne microbes can establish compatible relationships with host plants, providing a large variety of nutritive and protective compounds in exchange for photosynthesized sugars. However, the molecular mechanisms mediating the establishment of these beneficial relationships remain unclear. Our previous genetic mapping and whole-genome resequencing studies identified a gene deletion event of a Populus trichocarpa lectin receptor-like kinase gene PtLecRLK1 in Populus deltoides that was associated with poor-root colonization by the ectomycorrhizal fungus Laccaria bicolor. By introducing PtLecRLK1 into a perennial grass known to be a non-host of L. bicolor, switchgrass (Panicum virgatum L.), we found that L. bicolor colonizes ZmUbipro-PtLecRLK1 transgenic switchgrass roots, which illustrates that the introduction of PtLecRLK1 has the potential to convert a non-host to a host of L. bicolor. Furthermore, transcriptomic and proteomic analyses on inoculated-transgenic switchgrass roots revealed genes/proteins overrepresented in the compatible interaction and underrepresented in the pathogenic defence pathway, consistent with the view that pathogenic defence response is down-regulated during compatible interaction. Metabolomic profiling revealed that root colonization in the transgenic switchgrass was associated with an increase in N-containing metabolites and a decrease in organic acids, sugars, and aromatic hydroxycinnamate conjugates, which are often seen in the early steps of establishing compatible interactions. These studies illustrate that PtLecRLK1 is able to render a plant susceptible to colonization by the ectomycorrhizal fungus L. bicolor and shed light on engineering mycorrhizal symbiosis into a non-host to enhance plant productivity and fitness on marginal lands.
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Affiliation(s)
- Zhenzhen Qiao
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTNUSA
| | - Timothy B. Yates
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTNUSA
- Bredesen Center for Interdisciplinary Research and Graduate EducationUniversity of TennesseeKnoxvilleTNUSA
| | - Him K. Shrestha
- Genome Science and TechnologyUniversity of TennesseeKnoxvilleTNUSA
- Chemical Science DivisionOak Ridge National LaboratoryOak RidgeTNUSA
| | - Nancy L. Engle
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTNUSA
| | | | | | - Yali Sun
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTNUSA
| | | | - Paul E. Abraham
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTNUSA
- Chemical Science DivisionOak Ridge National LaboratoryOak RidgeTNUSA
| | - Jessy Labbé
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTNUSA
| | | | - Robert L. Hettich
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTNUSA
- Chemical Science DivisionOak Ridge National LaboratoryOak RidgeTNUSA
| | | | | | - Jin‐Gui Chen
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTNUSA
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4
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Sharma M, Sudheer S, Usmani Z, Rani R, Gupta P. Deciphering the Omics of Plant-Microbe Interaction: Perspectives and New Insights. Curr Genomics 2020; 21:343-362. [PMID: 33093798 PMCID: PMC7536805 DOI: 10.2174/1389202921999200515140420] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 03/29/2020] [Accepted: 04/17/2020] [Indexed: 12/19/2022] Open
Abstract
Introduction Plants do not grow in isolation, rather they are hosts to a variety of microbes in their natural environments. While, few thrive in the plants for their own benefit, others may have a direct impact on plants in a symbiotic manner. Unraveling plant-microbe interactions is a critical component in recognizing the positive and negative impacts of microbes on plants. Also, by affecting the environment around plants, microbes may indirectly influence plants. The progress in sequencing technologies in the genomics era and several omics tools has accelerated in biological science. Studying the complex nature of plant-microbe interactions can offer several strategies to increase the productivity of plants in an environmentally friendly manner by providing better insights. This review brings forward the recent works performed in building omics strategies that decipher the interactions between plant-microbiome. At the same time, it further explores other associated mutually beneficial aspects of plant-microbe interactions such as plant growth promotion, nitrogen fixation, stress suppressions in crops and bioremediation; as well as provides better insights on metabolic interactions between microbes and plants through omics approaches. It also aims to explore advances in the study of Arabidopsis as an important avenue to serve as a baseline tool to create models that help in scrutinizing various factors that contribute to the elaborate relationship between plants and microbes. Causal relationships between plants and microbes can be established through systematic gnotobiotic experimental studies to test hypotheses on biologically derived interactions. Conclusion This review will cover recent advances in the study of plant-microbe interactions keeping in view the advantages of these interactions in improving nutrient uptake and plant health.
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Affiliation(s)
- Minaxi Sharma
- 1Department of Food Technology, ACA, Eternal University, Baru Sahib (173001), Himachal Pradesh, India; 2Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, Lai 40, Tartu, Estonia; 3Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn12612, Estonia; 4Applied Microbiology Laboratory, Department of Environmental Science and Engineering, Indian Institute of Technology (ISM), Dhanbad, India
| | - Surya Sudheer
- 1Department of Food Technology, ACA, Eternal University, Baru Sahib (173001), Himachal Pradesh, India; 2Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, Lai 40, Tartu, Estonia; 3Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn12612, Estonia; 4Applied Microbiology Laboratory, Department of Environmental Science and Engineering, Indian Institute of Technology (ISM), Dhanbad, India
| | - Zeba Usmani
- 1Department of Food Technology, ACA, Eternal University, Baru Sahib (173001), Himachal Pradesh, India; 2Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, Lai 40, Tartu, Estonia; 3Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn12612, Estonia; 4Applied Microbiology Laboratory, Department of Environmental Science and Engineering, Indian Institute of Technology (ISM), Dhanbad, India
| | - Rupa Rani
- 1Department of Food Technology, ACA, Eternal University, Baru Sahib (173001), Himachal Pradesh, India; 2Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, Lai 40, Tartu, Estonia; 3Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn12612, Estonia; 4Applied Microbiology Laboratory, Department of Environmental Science and Engineering, Indian Institute of Technology (ISM), Dhanbad, India
| | - Pratishtha Gupta
- 1Department of Food Technology, ACA, Eternal University, Baru Sahib (173001), Himachal Pradesh, India; 2Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, Lai 40, Tartu, Estonia; 3Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn12612, Estonia; 4Applied Microbiology Laboratory, Department of Environmental Science and Engineering, Indian Institute of Technology (ISM), Dhanbad, India
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Roy R, Reinders A, Ward JM, McDonald TR. Understanding transport processes in lichen, Azolla-cyanobacteria, ectomycorrhiza, endomycorrhiza, and rhizobia-legume symbiotic interactions. F1000Res 2020; 9. [PMID: 32047609 PMCID: PMC6979478 DOI: 10.12688/f1000research.19740.1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/16/2020] [Indexed: 12/20/2022] Open
Abstract
Intimate interactions between photosynthetic and non-photosynthetic organisms require the orchestrated transfer of ions and metabolites between species. We review recent progress in identifying and characterizing the transport proteins involved in five mutualistic symbiotic interactions: lichens,
Azolla–cyanobacteria, ectomycorrhiza, endomycorrhiza, and rhizobia–legumes. This review focuses on transporters for nitrogen and carbon and other solutes exchanged in the interactions. Their predicted functions are evaluated on the basis of their transport mechanism and prevailing transmembrane gradients of H
+ and transported substrates. The symbiotic interactions are presented in the assumed order from oldest to most recently evolved.
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Affiliation(s)
- Rahul Roy
- Department of Plant and Microbial Biology, University of Minnesota, Minnesota, USA
| | - Anke Reinders
- College of Continuing and Professional Studies, University of Minnesota, Minnesota, USA
| | - John M Ward
- Department of Plant and Microbial Biology, University of Minnesota, Minnesota, USA
| | - Tami R McDonald
- Biology Department, St. Catherine University, Minnesota, USA
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Stuart EK, Plett KL. Digging Deeper: In Search of the Mechanisms of Carbon and Nitrogen Exchange in Ectomycorrhizal Symbioses. FRONTIERS IN PLANT SCIENCE 2020; 10:1658. [PMID: 31993064 PMCID: PMC6971170 DOI: 10.3389/fpls.2019.01658] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 11/25/2019] [Indexed: 05/12/2023]
Abstract
Symbiosis with ectomycorrhizal (ECM) fungi is an advantageous partnership for trees in nutrient-limited environments. Ectomycorrhizal fungi colonize the roots of their hosts and improve their access to nutrients, usually nitrogen (N) and, in exchange, trees deliver a significant portion of their photosynthetic carbon (C) to the fungi. This nutrient exchange affects key soil processes and nutrient cycling, as well as plant health, and is therefore central to forest ecosystem functioning. Due to their ecological importance, there is a need to more accurately understand ECM fungal mediated C and N movement within forest ecosystems such that we can better model and predict their role in soil processes both now and under future climate scenarios. There are a number of hurdles that we must overcome, however, before this is achievable such as understanding how the evolutionary history of ECM fungi and their inter- and intra- species variability affect their function. Further, there is currently no generally accepted universal mechanism that appears to govern the flux of nutrients between fungal and plant partners. Here, we consider the current state of knowledge on N acquisition and transport by ECM fungi and how C and N exchange may be related or affected by environmental conditions such as N availability. We emphasize the role that modern genomic analysis, molecular biology techniques and more comprehensive and standardized experimental designs may have in bringing cohesion to the numerous ecological studies in this area and assist us in better understanding this important symbiosis. These approaches will help to build unified models of nutrient exchange and develop diagnostic tools to study these fungi at various scales and environments.
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Affiliation(s)
| | - Krista L. Plett
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, Australia
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7
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Favre-Godal Q, Gourguillon L, Lordel-Madeleine S, Gindro K, Choisy P. Orchids and their mycorrhizal fungi: an insufficiently explored relationship. MYCORRHIZA 2020; 30:5-22. [PMID: 31982950 DOI: 10.1007/s00572-020-00934-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 01/17/2020] [Indexed: 05/03/2023]
Abstract
Orchids are associated with diverse fungal taxa, including nonmycorrhizal endophytic fungi as well as mycorrhizal fungi. The orchid mycorrhizal (OM) symbiosis is an excellent model for investigating the biological interactions between plants and fungi due to their high dependency on these symbionts for growth and survival. To capture the complexity of OM interactions, significant genomic, numerous transcriptomic, and proteomic studies have been performed, unraveling partly the role of each partner. On the other hand, several papers studied the bioactive metabolites from each partner but rarely interpreted their significance in this symbiotic relationship. In this review, we focus from a biochemical viewpoint on the OM dynamics and its molecular interactions. The ecological functions of OM in plant development and stress resistance are described first, summarizing recent literature. Secondly, because only few studies have specifically looked on OM molecular interactions, the signaling pathways and compounds allowing the establishment/maintenance of mycorrhizal association involved in arbuscular mycorrhiza (AM) are discussed in parallel with OM. Based on mechanistic similarities between OM and AM, and recent findings on orchids' endophytes, a putative model representing the different molecular strategies that OM fungi might employ to establish this association is proposed. It is hypothesized here that (i) orchids would excrete plant molecule signals such as strigolactones and flavonoids but also other secondary metabolites; (ii) in response, OM fungi would secrete mycorrhizal factors (Myc factors) or similar compounds to activate the common symbiosis genes (CSGs); (iii) overcome the defense mechanism by evasion of the pathogen-associated molecular patterns (PAMPs)-triggered immunity and by secretion of effectors such as small inhibitor proteins; and (iv) finally, secrete phytohormones to help the colonization or disrupt the crosstalk of plant defense phytohormones. To challenge this putative model, targeted and untargeted metabolomics studies with special attention to each partner's contribution are finally encouraged and some technical approaches are proposed.
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Affiliation(s)
- Quentin Favre-Godal
- LVMH recherche, Innovation Matériaux Naturels et Développement Durable, 185 avenue de Verdun, 45800, St Jean de Braye, France.
- CNRS, IPHC UMR 7178, Chimie analytique des molécules bioactives et pharmacognosie, Université de Strasbourg, F-67000, Strasbourg, France.
| | - Lorène Gourguillon
- LVMH recherche, Innovation Matériaux Naturels et Développement Durable, 185 avenue de Verdun, 45800, St Jean de Braye, France
| | - Sonia Lordel-Madeleine
- CNRS, IPHC UMR 7178, Chimie analytique des molécules bioactives et pharmacognosie, Université de Strasbourg, F-67000, Strasbourg, France
| | - Katia Gindro
- Agroscope, Swiss Federal Research Station, Plant Protection, 60 Route de Duiller, PO Box, 1260, Nyon, Switzerland
| | - Patrick Choisy
- LVMH recherche, Innovation Matériaux Naturels et Développement Durable, 185 avenue de Verdun, 45800, St Jean de Braye, France
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8
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Rodríguez-Gutiérrez I, Ramírez-Martínez D, Garibay-Orijel R, Jacob-Cervantes V, Pérez-Moreno J, Ortega-Larrocea MDP, Arellano-Torres E. Sympatric species develop more efficient ectomycorrhizae in the Pinus-Laccaria symbiosis. REV MEX BIODIVERS 2019. [DOI: 10.22201/ib.20078706e.2019.90.2868] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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9
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Li Q, Yan L, Ye L, Zhou J, Zhang B, Peng W, Zhang X, Li X. Chinese Black Truffle ( Tuber indicum) Alters the Ectomycorrhizosphere and Endoectomycosphere Microbiome and Metabolic Profiles of the Host Tree Quercus aliena. Front Microbiol 2018; 9:2202. [PMID: 30283422 PMCID: PMC6156548 DOI: 10.3389/fmicb.2018.02202] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 08/28/2018] [Indexed: 01/06/2023] Open
Abstract
Truffles are one group of the most famous ectomycorrhizal fungi in the world. There is little information on the ecological mechanisms of truffle ectomycorrhizal synthesis in vitro. In this study, we investigated the ecological effects of Tuber indicum – Quercus aliena ectomycorrhizal synthesis on microbial communities in the host plant roots and the surrounding soil using high-throughput sequencing and on the metabolic profiles of host plant roots using metabolomics approaches. We observed an increase in the diversity and richness of prokaryotic communities and a decrease in richness of fungal communities in the presence of T. indicum. The microbial community structures in the host roots and the surrounding soil were altered by ectomycorrhizal synthesis in the greenhouse. Bacterial genera Pedomicrobium, Variibacter, and Woodsholea and fungal genera Aspergillus, Phaeoacremonium, and Pochonia were significantly more abundant in ectomycorhizae and the ectomycorrhizosphere soil compared with the corresponding T. indicum-free controls (P < 0.05). Truffle-colonization reduced the abundance of some fungal genera surrounding the host tree, such as Acremonium, Aspergillus, and Penicillium. Putative prokaryotic metabolic functions and fungal functional groups (guilds) were also differentiated by ectomycorrhizal synthesis. The ectomycorrhizal synthesis had great impact on the measured soil physicochemical properties. Metabolic profiling analysis uncovered 55 named differentially abundant metabolites between the ectomycorhizae and the control roots, including 44 upregulated and 11 downregulated metabolites. Organic acids and carbohydrates were two major upregulated metabolites in ectomycorhizae, which were found formed dense interactions with other metabolites, suggesting their crucial roles in sustaining the metabolic functions in the truffle ectomycorrhization system. This study revealed the effects of truffle-colonization on the metabolites of ectomycorrhiza and illustrates an interactive network between truffles, the host plant, soil and associated microbial communities, shedding light on understanding the ecological effects of truffles.
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Affiliation(s)
- Qiang Li
- Soil and Fertilizer Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China.,Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Lijuan Yan
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Jena, Germany
| | - Lei Ye
- Soil and Fertilizer Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Jie Zhou
- Soil and Fertilizer Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Bo Zhang
- Soil and Fertilizer Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Weihong Peng
- Soil and Fertilizer Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Xiaoping Zhang
- Soil and Fertilizer Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Xiaolin Li
- Soil and Fertilizer Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
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10
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Daguerre Y, Levati E, Ruytinx J, Tisserant E, Morin E, Kohler A, Montanini B, Ottonello S, Brun A, Veneault-Fourrey C, Martin F. Regulatory networks underlying mycorrhizal development delineated by genome-wide expression profiling and functional analysis of the transcription factor repertoire of the plant symbiotic fungus Laccaria bicolor. BMC Genomics 2017; 18:737. [PMID: 28923004 PMCID: PMC5604158 DOI: 10.1186/s12864-017-4114-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 09/04/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Ectomycorrhizal (ECM) fungi develop a mutualistic symbiotic interaction with the roots of their host plants. During this process, they undergo a series of developmental transitions from the running hyphae in the rhizosphere to the coenocytic hyphae forming finger-like structures within the root apoplastic space. These transitions, which involve profound, symbiosis-associated metabolic changes, also entail a substantial transcriptome reprogramming with coordinated waves of differentially expressed genes. To date, little is known about the key transcriptional regulators driving these changes, and the aim of the present study was to delineate and functionally characterize the transcription factor (TF) repertoire of the model ECM fungus Laccaria bicolor. RESULTS We curated the L. bicolor gene models coding for transcription factors and assessed their expression and regulation in Poplar and Douglas fir ectomycorrhizae. We identified 285 TFs, 191 of which share a significant similarity with known transcriptional regulators. Expression profiling of the corresponding transcripts identified TF-encoding fungal genes differentially expressed in the ECM root tips of both host plants. The L. bicolor core set of differentially expressed TFs consists of 12 and 22 genes that are, respectively, upregulated and downregulated in symbiotic tissues. These TFs resemble known fungal regulators involved in the control of fungal invasive growth, fungal cell wall integrity, carbon and nitrogen metabolism, invasive stress response and fruiting-body development. However, this core set of mycorrhiza-regulated TFs seems to be characteristic of L. bicolor and our data suggest that each mycorrhizal fungus has evolved its own set of ECM development regulators. A subset of the above TFs was functionally validated with the use of a heterologous, transcription activation assay in yeast, which also allowed the identification of previously unknown, transcriptionally active yet secreted polypeptides designated as Secreted Transcriptional Activator Proteins (STAPs). CONCLUSIONS Transcriptional regulators required for ECM symbiosis development in L. bicolor have been uncovered and classified through genome-wide analysis. This study also identifies the STAPs as a new class of potential ECM effectors, highly expressed in mycorrhizae, which may be involved in the control of the symbiotic root transcriptome.
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Affiliation(s)
- Y Daguerre
- INRA, UMR 1136, INRA-Université de Lorraine, Interactions Arbres/Microorganismes, Laboratoire d'Excellence ARBRE, 54280, Champenoux, France
- Université de Lorraine, UMR 1136, INRA-Université de Lorraine, Interactions Arbres/Microorganismes, Laboratoire d'Excellence ARBRE, F-54500 Vandoeuvre-lès-, Nancy, France
- Present address: Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 901 83, Umea, Sweden
| | - E Levati
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Università degli Studi di Parma, Parco Area delle Scienze 23/A, 43124, Parma, Italy
| | - J Ruytinx
- INRA, UMR 1136, INRA-Université de Lorraine, Interactions Arbres/Microorganismes, Laboratoire d'Excellence ARBRE, 54280, Champenoux, France
- Université de Lorraine, UMR 1136, INRA-Université de Lorraine, Interactions Arbres/Microorganismes, Laboratoire d'Excellence ARBRE, F-54500 Vandoeuvre-lès-, Nancy, France
- Present address: Hasselt University, Centre for Environmental Sciences, Agoralaan building D, 3590, Diepenbeek, Belgium
| | - E Tisserant
- INRA, UMR 1136, INRA-Université de Lorraine, Interactions Arbres/Microorganismes, Laboratoire d'Excellence ARBRE, 54280, Champenoux, France
- Université de Lorraine, UMR 1136, INRA-Université de Lorraine, Interactions Arbres/Microorganismes, Laboratoire d'Excellence ARBRE, F-54500 Vandoeuvre-lès-, Nancy, France
| | - E Morin
- INRA, UMR 1136, INRA-Université de Lorraine, Interactions Arbres/Microorganismes, Laboratoire d'Excellence ARBRE, 54280, Champenoux, France
- Université de Lorraine, UMR 1136, INRA-Université de Lorraine, Interactions Arbres/Microorganismes, Laboratoire d'Excellence ARBRE, F-54500 Vandoeuvre-lès-, Nancy, France
| | - A Kohler
- INRA, UMR 1136, INRA-Université de Lorraine, Interactions Arbres/Microorganismes, Laboratoire d'Excellence ARBRE, 54280, Champenoux, France
- Université de Lorraine, UMR 1136, INRA-Université de Lorraine, Interactions Arbres/Microorganismes, Laboratoire d'Excellence ARBRE, F-54500 Vandoeuvre-lès-, Nancy, France
| | - B Montanini
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Università degli Studi di Parma, Parco Area delle Scienze 23/A, 43124, Parma, Italy
| | - S Ottonello
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Università degli Studi di Parma, Parco Area delle Scienze 23/A, 43124, Parma, Italy
| | - A Brun
- INRA, UMR 1136, INRA-Université de Lorraine, Interactions Arbres/Microorganismes, Laboratoire d'Excellence ARBRE, 54280, Champenoux, France
- Université de Lorraine, UMR 1136, INRA-Université de Lorraine, Interactions Arbres/Microorganismes, Laboratoire d'Excellence ARBRE, F-54500 Vandoeuvre-lès-, Nancy, France
| | - C Veneault-Fourrey
- INRA, UMR 1136, INRA-Université de Lorraine, Interactions Arbres/Microorganismes, Laboratoire d'Excellence ARBRE, 54280, Champenoux, France.
- Université de Lorraine, UMR 1136, INRA-Université de Lorraine, Interactions Arbres/Microorganismes, Laboratoire d'Excellence ARBRE, F-54500 Vandoeuvre-lès-, Nancy, France.
| | - F Martin
- INRA, UMR 1136, INRA-Université de Lorraine, Interactions Arbres/Microorganismes, Laboratoire d'Excellence ARBRE, 54280, Champenoux, France
- Université de Lorraine, UMR 1136, INRA-Université de Lorraine, Interactions Arbres/Microorganismes, Laboratoire d'Excellence ARBRE, F-54500 Vandoeuvre-lès-, Nancy, France
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11
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Xu YG, Chai LH, Shi W, Wang DD, Zhang JY, Xiao XH. Transcriptome profiling and digital gene expression analysis of the skin of Dybowski's frog (Rana dybowskii) exposed to Aeromonas hydrophila. Appl Microbiol Biotechnol 2017. [PMID: 28647779 DOI: 10.1007/s00253-017-8385-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Recently, populations of Rana dybowskii, an important amphibian species in Northeast China, have decreased, mainly owing to the disease caused by Aeromonas hydrophila. However, effective control methods have not yet been developed. In order to explore the immune responses of R. dybowskii upon exposure to A. hydrophila infection, Illumina high-throughput transcriptome sequencing and digital gene expression (DGE) technology were employed to investigate transcriptomic changes in the skin of R. dybowskii exposed to A. hydrophila. In this work, a total of 26,244,446 transcriptome sequencing reads were obtained and assembled into 109,089 unique unigenes using de novo assembly, and a total of 37,105 unigenes (34.0%) were functionally annotated against the non-redundant (Nr), Swiss-Prot, Cluster of Orthologous Groups of Proteins (COG), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Gene Ontology (GO) databases. Gene expression changes in the skin tissue of R. dybowskii exposed to A. hydrophila were investigated by a tag-based DGE system, and a total of 1435 significantly differentially expressed genes were identified, including 460 that were up-regulated and 975 that were down-regulated, indicating a large change in the host transcriptome profile exposed to A. hydrophila. Among these, 478 genes were associated with immune-relevant pathways, metabolic pathways, cellular components, growth, migration, and muscle and hormone signaling pathways. We confirmed the differential expression of 106 immune-relevant genes associated with innate and adaptive immune responses. Our data provide a fairly comprehensive molecular biology background for the deeper understanding of the amphibian immune system following A. hydrophila infection.
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Affiliation(s)
- Yi-Gang Xu
- College of Wildlife Resources, Northeast Forestry University, Harbin, China. .,College of Veterinary Medicine, Northeast Agricultural University, Harbin, China.
| | - Long-Hui Chai
- College of Wildlife Resources, Northeast Forestry University, Harbin, China
| | - Wen Shi
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Dan-Dan Wang
- College of Wildlife Resources, Northeast Forestry University, Harbin, China
| | - Jing-Yu Zhang
- College of Wildlife Resources, Northeast Forestry University, Harbin, China
| | - Xiang-Hong Xiao
- College of Wildlife Resources, Northeast Forestry University, Harbin, China.
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12
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Victor T, Delpratt N, Cseke SB, Miller LM, Cseke LJ. Imaging Nutrient Distribution in the Rhizosphere Using FTIR Imaging. Anal Chem 2017; 89:4831-4837. [DOI: 10.1021/acs.analchem.6b04376] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Tiffany Victor
- Department
of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
| | - Natalie Delpratt
- National
Synchrotron Light Source II, Brookhaven National Laboratory, Upton, New York 11973, United States
| | - Sarah Beth Cseke
- Department
of Biological Science, University of Alabama in Huntsville, Huntsville, Alabama 35899, United States
| | - Lisa M. Miller
- Department
of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
- National
Synchrotron Light Source II, Brookhaven National Laboratory, Upton, New York 11973, United States
| | - Leland James Cseke
- Department
of Biological Science, University of Alabama in Huntsville, Huntsville, Alabama 35899, United States
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13
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Doré J, Kohler A, Dubost A, Hundley H, Singan V, Peng Y, Kuo A, Grigoriev IV, Martin F, Marmeisse R, Gay G. The ectomycorrhizal basidiomyceteHebeloma cylindrosporumundergoes early waves of transcriptional reprogramming prior to symbiotic structures differentiation. Environ Microbiol 2017; 19:1338-1354. [DOI: 10.1111/1462-2920.13670] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 01/03/2017] [Accepted: 01/04/2017] [Indexed: 01/10/2023]
Affiliation(s)
- Jeanne Doré
- Ecologie Microbienne; Université de Lyon; F-69622 Lyon France
- Université Lyon 1, CNRS, UMR5557, INRA, UMR1418; Villeurbanne France
| | - Annegret Kohler
- Interactions Arbres/Microorganismes, INRA-Nancy; INRA, UMR 1136 INRA-Université de Lorraine; Champenoux 54280 France
| | - Audrey Dubost
- Ecologie Microbienne; Université de Lyon; F-69622 Lyon France
- Université Lyon 1, CNRS, UMR5557, INRA, UMR1418; Villeurbanne France
| | - Hope Hundley
- U.S. Department of Energy Joint Genome Institute; Walnut Creek CA 94598 USA
| | - Vasanth Singan
- U.S. Department of Energy Joint Genome Institute; Walnut Creek CA 94598 USA
| | - Yi Peng
- U.S. Department of Energy Joint Genome Institute; Walnut Creek CA 94598 USA
| | - Alan Kuo
- U.S. Department of Energy Joint Genome Institute; Walnut Creek CA 94598 USA
| | - Igor V. Grigoriev
- U.S. Department of Energy Joint Genome Institute; Walnut Creek CA 94598 USA
| | - Francis Martin
- Interactions Arbres/Microorganismes, INRA-Nancy; INRA, UMR 1136 INRA-Université de Lorraine; Champenoux 54280 France
| | - Roland Marmeisse
- Ecologie Microbienne; Université de Lyon; F-69622 Lyon France
- Université Lyon 1, CNRS, UMR5557, INRA, UMR1418; Villeurbanne France
| | - Gilles Gay
- Ecologie Microbienne; Université de Lyon; F-69622 Lyon France
- Université Lyon 1, CNRS, UMR5557, INRA, UMR1418; Villeurbanne France
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14
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Garcia K, Doidy J, Zimmermann SD, Wipf D, Courty PE. Take a Trip Through the Plant and Fungal Transportome of Mycorrhiza. TRENDS IN PLANT SCIENCE 2016; 21:937-950. [PMID: 27514454 DOI: 10.1016/j.tplants.2016.07.010] [Citation(s) in RCA: 107] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 07/18/2016] [Accepted: 07/25/2016] [Indexed: 05/21/2023]
Abstract
Soil nutrient acquisition and exchanges through symbiotic plant-fungus interactions in the rhizosphere are key features for the current agricultural and environmental challenges. Improved crop yield and plant mineral nutrition through a fungal symbiont has been widely described. In return, the host plant supplies carbon substrates to its fungal partner. We review here recent progress on molecular players of membrane transport involved in nutritional exchanges between mycorrhizal plants and fungi. We cover the transportome, from the transport proteins involved in sugar fluxes from plants towards fungi, to the uptake from the soil and exchange of nitrogen, phosphate, potassium, sulfate, and water. Together, these advances in the comprehension of the mycorrhizal transportome will help in developing the future engineering of new agro-ecological systems.
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Affiliation(s)
- Kevin Garcia
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Joan Doidy
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
| | - Sabine D Zimmermann
- Biochimie et Physiologie Moléculaire des Plantes, Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA), Montpellier SupAgro, Université de Montpellier, 34060 Montpellier, France
| | - Daniel Wipf
- Agroécologie, AgroSup Dijon, CNRS, INRA, Université de Bourgogne Franche-Comté, 21000 Dijon, France
| | - Pierre-Emmanuel Courty
- University of Fribourg, Department of Biology, 3 rue Albert Gockel, 1700 Fribourg, Switzerland.
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15
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Thijs S, Sillen W, Rineau F, Weyens N, Vangronsveld J. Towards an Enhanced Understanding of Plant-Microbiome Interactions to Improve Phytoremediation: Engineering the Metaorganism. Front Microbiol 2016; 7:341. [PMID: 27014254 PMCID: PMC4792885 DOI: 10.3389/fmicb.2016.00341] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 03/03/2016] [Indexed: 11/23/2022] Open
Abstract
Phytoremediation is a promising technology to clean-up contaminated soils based on the synergistic actions of plants and microorganisms. However, to become a widely accepted, and predictable remediation alternative, a deeper understanding of the plant-microbe interactions is needed. A number of studies link the success of phytoremediation to the plant-associated microbiome functioning, though whether the microbiome can exist in alternative, functional states for soil remediation, is incompletely understood. Moreover, current approaches that target the plant host, and environment separately to improve phytoremediation, potentially overlook microbial functions and properties that are part of the multiscale complexity of the plant-environment wherein biodegradation takes place. In contrast, in situ studies of phytoremediation research at the metaorganism level (host and microbiome together) are lacking. Here, we discuss a competition-driven model, based on recent evidence from the metagenomics level, and hypotheses generated by microbial community ecology, to explain the establishment of a catabolic rhizosphere microbiome in a contaminated soil. There is evidence to ground that if the host provides the right level and mix of resources (exudates) over which the microbes can compete, then a competitive catabolic and plant-growth promoting (PGP) microbiome can be selected for as long as it provides a competitive superiority in the niche. The competition-driven model indicates four strategies to interfere with the microbiome. Specifically, the rhizosphere microbiome community can be shifted using treatments that alter the host, resources, environment, and that take advantage of prioritization in inoculation. Our model and suggestions, considering the metaorganism in its natural context, would allow to gain further knowledge on the plant-microbial functions, and facilitate translation to more effective, and predictable phytotechnologies.
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Affiliation(s)
- Sofie Thijs
- Department of Biology, Centre for Environmental Sciences, Hasselt UniversityDiepenbeek, Belgium
| | | | | | | | - Jaco Vangronsveld
- Department of Biology, Centre for Environmental Sciences, Hasselt UniversityDiepenbeek, Belgium
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16
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Larsen PE, Sreedasyam A, Trivedi G, Desai S, Dai Y, Cseke LJ, Collart FR. Multi-Omics Approach Identifies Molecular Mechanisms of Plant-Fungus Mycorrhizal Interaction. FRONTIERS IN PLANT SCIENCE 2016; 6:1061. [PMID: 26834754 PMCID: PMC4717292 DOI: 10.3389/fpls.2015.01061] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 11/16/2015] [Indexed: 05/29/2023]
Abstract
In mycorrhizal symbiosis, plant roots form close, mutually beneficial interactions with soil fungi. Before this mycorrhizal interaction can be established however, plant roots must be capable of detecting potential beneficial fungal partners and initiating the gene expression patterns necessary to begin symbiosis. To predict a plant root-mycorrhizal fungi sensor systems, we analyzed in vitro experiments of Populus tremuloides (aspen tree) and Laccaria bicolor (mycorrhizal fungi) interaction and leveraged over 200 previously published transcriptomic experimental data sets, 159 experimentally validated plant transcription factor binding motifs, and more than 120-thousand experimentally validated protein-protein interactions to generate models of pre-mycorrhizal sensor systems in aspen root. These sensor mechanisms link extracellular signaling molecules with gene regulation through a network comprised of membrane receptors, signal cascade proteins, transcription factors, and transcription factor biding DNA motifs. Modeling predicted four pre-mycorrhizal sensor complexes in aspen that interact with 15 transcription factors to regulate the expression of 1184 genes in response to extracellular signals synthesized by Laccaria. Predicted extracellular signaling molecules include common signaling molecules such as phenylpropanoids, salicylate, and jasmonic acid. This multi-omic computational modeling approach for predicting the complex sensory networks yielded specific, testable biological hypotheses for mycorrhizal interaction signaling compounds, sensor complexes, and mechanisms of gene regulation.
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Affiliation(s)
- Peter E. Larsen
- Argonne National Laboratory, Biosciences DivisionLemont, IL, USA
- Department of Bioengineering, University of Illinois at ChicagoChicago IL, USA
| | - Avinash Sreedasyam
- Department of Biological Sciences, University of Alabama in HuntsvilleHuntsville, AL, USA
| | - Geetika Trivedi
- Department of Biological Sciences, University of Alabama in HuntsvilleHuntsville, AL, USA
| | - Shalaka Desai
- Argonne National Laboratory, Biosciences DivisionLemont, IL, USA
| | - Yang Dai
- Department of Bioengineering, University of Illinois at ChicagoChicago IL, USA
| | - Leland J. Cseke
- Department of Biological Sciences, University of Alabama in HuntsvilleHuntsville, AL, USA
| | - Frank R. Collart
- Argonne National Laboratory, Biosciences DivisionLemont, IL, USA
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17
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Abstract
Chemical ecology elucidates the nature and role of natural products as mediators of organismal interactions. The emerging techniques that can be summarized under the concept of metabolomics provide new opportunities to study such environmentally relevant signaling molecules. Especially comparative tools in metabolomics enable the identification of compounds that are regulated during interaction situations and that might play a role as e.g. pheromones, allelochemicals or in induced and activated defenses. This approach helps overcoming limitations of traditional bioassay-guided structure elucidation approaches. But the power of metabolomics is not limited to the comparison of metabolic profiles of interacting partners. Especially the link to other -omics techniques helps to unravel not only the compounds in question but the entire biosynthetic and genetic re-wiring, required for an ecological response. This review comprehensively highlights successful applications of metabolomics in chemical ecology and discusses existing limitations of these novel techniques. It focuses on recent developments in comparative metabolomics and discusses the use of metabolomics in the systems biology of organismal interactions. It also outlines the potential of large metabolomics initiatives for model organisms in the field of chemical ecology.
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Affiliation(s)
- Constanze Kuhlisch
- Friedrich Schiller University, Institute of Inorganic and Analytical Chemistry, Lessingstr. 8, D-07743 Jena, Germany.
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18
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Firrincieli A, Otillar R, Salamov A, Schmutz J, Khan Z, Redman RS, Fleck ND, Lindquist E, Grigoriev IV, Doty SL. Genome sequence of the plant growth promoting endophytic yeast Rhodotorula graminis WP1. Front Microbiol 2015; 6:978. [PMID: 26441909 PMCID: PMC4585186 DOI: 10.3389/fmicb.2015.00978] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2015] [Accepted: 09/03/2015] [Indexed: 12/22/2022] Open
Affiliation(s)
- Andrea Firrincieli
- Department for Innovation Biological, Agro-Food and Forest System, University of Tuscia Tuscia, Italy
| | - Robert Otillar
- U.S. Department of Energy Joint Genome Institute Walnut Creek, CA, USA
| | - Asaf Salamov
- U.S. Department of Energy Joint Genome Institute Walnut Creek, CA, USA
| | - Jeremy Schmutz
- U.S. Department of Energy Joint Genome Institute Walnut Creek, CA, USA ; HudsonAlpha Institute for Biotechnology Huntsville, AL, USA
| | - Zareen Khan
- School of Environmental and Forest Sciences, University of Washington Seattle, WA, USA
| | | | - Neil D Fleck
- School of Environmental and Forest Sciences, University of Washington Seattle, WA, USA
| | - Erika Lindquist
- U.S. Department of Energy Joint Genome Institute Walnut Creek, CA, USA
| | - Igor V Grigoriev
- U.S. Department of Energy Joint Genome Institute Walnut Creek, CA, USA
| | - Sharon L Doty
- School of Environmental and Forest Sciences, University of Washington Seattle, WA, USA
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19
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Plett JM, Kohler A, Khachane A, Keniry K, Plett KL, Martin F, Anderson IC. The effect of elevated carbon dioxide on the interaction between Eucalyptus grandis and diverse isolates of Pisolithus sp. is associated with a complex shift in the root transcriptome. THE NEW PHYTOLOGIST 2015; 206:1423-36. [PMID: 25377589 DOI: 10.1111/nph.13103] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Accepted: 08/26/2014] [Indexed: 05/15/2023]
Abstract
Using the newly available genome for Eucalyptus grandis, we sought to determine the genome-wide traits that enable this host to form mutualistic interactions with ectomycorrhizal (ECM) Pisolithus sp. and to determine how future predicted concentrations of atmospheric carbon dioxide (CO2 ) will affect this relationship. We analyzed the physiological and transcriptomic responses of E. grandis during colonization by different Pisolithus sp. isolates under conditions of ambient (400 ppm) and elevated (650 ppm) CO2 to tease out the gene expression profiles associated with colonization status. We demonstrate that E. grandis varies in its susceptibility to colonization by different Pisolithus isolates in a manner that is not predictable by geographic origin or the internal transcribed spacer (ITS)-based phylogeny of the fungal partner. Elevated concentrations of CO2 alter the receptivity of E. grandis to Pisolithus, a change that is correlated to a dramatic shift in the transcriptomic profile of the root. These data provide a starting point for understanding how future environmental change may alter the signaling between plants and their ECM partners and is a step towards determining the mechanism behind previously observed shifts in Eucalypt-associated fungal communities exposed to elevated concentrations of atmospheric CO2 .
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Affiliation(s)
- Jonathan M Plett
- Hawkesbury Institute for the Environment, University of Western Sydney, Richmond, NSW, 2753, Australia
| | - Annegret Kohler
- INRA, UMR 1136 INRA-University of Lorraine, Interactions Arbres/Microorganismes, Laboratory of Excellence ARBRE, INRA-Nancy, 54280, Champenoux, France
| | - Amit Khachane
- Hawkesbury Institute for the Environment, University of Western Sydney, Richmond, NSW, 2753, Australia
| | - Kerry Keniry
- Hawkesbury Institute for the Environment, University of Western Sydney, Richmond, NSW, 2753, Australia
| | - Krista L Plett
- Hawkesbury Institute for the Environment, University of Western Sydney, Richmond, NSW, 2753, Australia
| | - Francis Martin
- INRA, UMR 1136 INRA-University of Lorraine, Interactions Arbres/Microorganismes, Laboratory of Excellence ARBRE, INRA-Nancy, 54280, Champenoux, France
| | - Ian C Anderson
- Hawkesbury Institute for the Environment, University of Western Sydney, Richmond, NSW, 2753, Australia
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20
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Kuske CR, Hesse CN, Challacombe JF, Cullen D, Herr JR, Mueller RC, Tsang A, Vilgalys R. Prospects and challenges for fungal metatranscriptomics of complex communities. FUNGAL ECOL 2015. [DOI: 10.1016/j.funeco.2014.12.005] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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21
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Plett JM, Tisserant E, Brun A, Morin E, Grigoriev IV, Kuo A, Martin F, Kohler A. The Mutualist Laccaria bicolor Expresses a Core Gene Regulon During the Colonization of Diverse Host Plants and a Variable Regulon to Counteract Host-Specific Defenses. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2015; 28:261-73. [PMID: 25338146 DOI: 10.1094/mpmi-05-14-0129-fi] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The coordinated transcriptomic responses of both mutualistic ectomycorrhizal (ECM) fungi and their hosts during the establishment of symbiosis are not well-understood. This study characterizes the transcriptomic alterations of the ECM fungus Laccaria bicolor during different colonization stages on two hosts (Populus trichocarpa and Pseudotsuga menziesii) and compares this to the transcriptomic variations of P. trichocarpa across the same time-points. A large number of L. bicolor genes (≥ 8,000) were significantly regulated at the transcriptional level in at least one stage of colonization. From our data, we identify 1,249 genes that we hypothesize is the 'core' gene regulon necessary for the mutualistic interaction between L. bicolor and its host plants. We further identify a group of 1,210 genes that are regulated in a host-specific manner. This variable regulon encodes a number of genes coding for proteases and xenobiotic efflux transporters that we hypothesize act to counter chemical-based defenses simultaneously activated at the transcriptomic level in P. trichocarpa. The transcriptional response of the host plant P. trichocarpa consisted of differential waves of gene regulation related to signaling perception and transduction, defense response, and the induction of nutrient transfer in P. trichocarpa tissues. This study, therefore, gives fresh insight into the shifting transcriptomic landscape in both the colonizing fungus and its host and the different strategies employed by both partners in orchestrating a mutualistic interaction.
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22
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Kuo A, Kohler A, Martin FM, Grigoriev IV. Expanding genomics of mycorrhizal symbiosis. Front Microbiol 2014; 5:582. [PMID: 25408690 PMCID: PMC4219462 DOI: 10.3389/fmicb.2014.00582] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Accepted: 10/15/2014] [Indexed: 12/11/2022] Open
Abstract
The mycorrhizal symbiosis between soil fungi and plant roots is a ubiquitous mutualism that plays key roles in plant nutrition, soil health, and carbon cycling. The symbiosis evolved repeatedly and independently as multiple morphotypes [e.g., arbuscular mycorrhizae (AM), ectomycorrhizal (ECM)] in multiple fungal clades (e.g., phyla Glomeromycota, Ascomycota, Basidiomycota). The accessibility and cultivability of many mycorrhizal partners make them ideal models for symbiosis studies. Alongside molecular, physiological, and ecological investigations, sequencing led to the first three mycorrhizal fungal genomes, representing two morphotypes and three phyla. The genome of the ECM basidiomycete Laccaria bicolor showed that the mycorrhizal lifestyle can evolve through loss of plant cell wall-degrading enzymes (PCWDEs) and expansion of lineage-specific gene families such as short secreted protein (SSP) effectors. The genome of the ECM ascomycete Tuber melanosporum showed that the ECM type can evolve without expansion of families as in Laccaria, and thus a different set of symbiosis genes. The genome of the AM glomeromycete Rhizophagus irregularis showed that despite enormous phylogenetic distance and morphological difference from the other two fungi, symbiosis can involve similar solutions as symbiosis-induced SSPs and loss of PCWDEs. The three genomes provide a solid base for addressing fundamental questions about the nature and role of a vital mutualism.
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Affiliation(s)
- Alan Kuo
- United States Department of Energy Joint Genome InstituteWalnut Creek, CA, USA
| | - Annegret Kohler
- UMR, Lab of Excellence for Advanced Research on the Biology of TRee and Forest Ecosystems, Tree-Microbe Interactions, Institut National de la Recherche Agronomique, Université de LorraineNancy, France
| | - Francis M. Martin
- UMR, Lab of Excellence for Advanced Research on the Biology of TRee and Forest Ecosystems, Tree-Microbe Interactions, Institut National de la Recherche Agronomique, Université de LorraineNancy, France
| | - Igor V. Grigoriev
- United States Department of Energy Joint Genome InstituteWalnut Creek, CA, USA
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23
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Larsen PE, Cseke LJ, Miller RM, Collart FR. Modeling forest ecosystem responses to elevated carbon dioxide and ozone using artificial neural networks. J Theor Biol 2014; 359:61-71. [PMID: 24928153 DOI: 10.1016/j.jtbi.2014.05.047] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Revised: 05/23/2014] [Accepted: 05/31/2014] [Indexed: 11/26/2022]
Abstract
Rising atmospheric levels of carbon dioxide and ozone will impact productivity and carbon sequestration in forest ecosystems. The scale of this process and the potential economic consequences provide an incentive for the development of models to predict the types and rates of ecosystem responses and feedbacks that result from and influence of climate change. In this paper, we use phenotypic and molecular data derived from the Aspen Free Air CO2 Enrichment site (Aspen-FACE) to evaluate modeling approaches for ecosystem responses to changing conditions. At FACE, it was observed that different aspen clones exhibit clone-specific responses to elevated atmospheric levels of carbon dioxide and ozone. To identify the molecular basis for these observations, we used artificial neural networks (ANN) to examine above and below-ground community phenotype responses to elevated carbon dioxide, elevated ozone and gene expression profiles. The aspen community models generated using this approach identified specific genes and subnetworks of genes associated with variable sensitivities for aspen clones. The ANN model also predicts specific co-regulated gene clusters associated with differential sensitivity to elevated carbon dioxide and ozone in aspen species. The results suggest ANN is an effective approach to predict relevant gene expression changes resulting from environmental perturbation and provides useful information for the rational design of future biological experiments.
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Affiliation(s)
- Peter E Larsen
- Argonne National Laboratory, Biosciences Division, 9700 South Cass Avenue, Argonne, IL 60439, USA.
| | - Leland J Cseke
- Department of Biological Sciences, University of Alabama in Huntsville, Huntsville, AL 35899, USA.
| | - R Michael Miller
- Argonne National Laboratory, Biosciences Division, 9700 South Cass Avenue, Argonne, IL 60439, USA.
| | - Frank R Collart
- Argonne National Laboratory, Biosciences Division, 9700 South Cass Avenue, Argonne, IL 60439, USA.
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24
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Meijueiro ML, Santoyo F, Ramirez L, Pisabarro AG. Transcriptome characteristics of filamentous fungi deduced using high-throughput analytical technologies. Brief Funct Genomics 2014; 13:440-50. [DOI: 10.1093/bfgp/elu033] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
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Tschaplinski TJ, Plett JM, Engle NL, Deveau A, Cushman KC, Martin MZ, Doktycz MJ, Tuskan GA, Brun A, Kohler A, Martin F. Populus trichocarpa and Populus deltoides exhibit different metabolomic responses to colonization by the symbiotic fungus Laccaria bicolor. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2014; 27:546-56. [PMID: 24548064 DOI: 10.1094/mpmi-09-13-0286-r] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Within boreal and temperate forest ecosystems, the majority of trees and shrubs form beneficial relationships with mutualistic ectomycorrhizal (ECM) fungi that support plant health through increased access to nutrients as well as aiding in stress and pest tolerance. The intimate interaction between fungal hyphae and plant roots results in a new symbiotic "organ" called the ECM root tip. Little is understood concerning the metabolic reprogramming that favors the formation of this hybrid tissue in compatible interactions and what prevents the formation of ECM root tips in incompatible interactions. We show here that the metabolic changes during favorable colonization between the ECM fungus Laccaria bicolor and its compatible host, Populus trichocarpa, are characterized by shifts in aromatic acid, organic acid, and fatty acid metabolism. We demonstrate that this extensive metabolic reprogramming is repressed in incompatible interactions and that more defensive compounds are produced or retained. We also demonstrate that L. bicolor can metabolize a number of secreted defensive compounds and that the degradation of some of these compounds produces immune response metabolites (e.g., salicylic acid from salicin). Therefore, our results suggest that the metabolic responsiveness of plant roots to L. bicolor is a determinant factor in fungus-host interactions.
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Sebastiana M, Vieira B, Lino-Neto T, Monteiro F, Figueiredo A, Sousa L, Pais MS, Tavares R, Paulo OS. Oak root response to ectomycorrhizal symbiosis establishment: RNA-Seq derived transcript identification and expression profiling. PLoS One 2014; 9:e98376. [PMID: 24859293 PMCID: PMC4032270 DOI: 10.1371/journal.pone.0098376] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Accepted: 05/01/2014] [Indexed: 11/19/2022] Open
Abstract
Ectomycorrhizal symbiosis is essential for the life and health of trees in temperate and boreal forests where it plays a major role in nutrient cycling and in functioning of the forest ecosystem. Trees with ectomycorrhizal root tips are more tolerant to environmental stresses, such as drought, and biotic stresses such as root pathogens. Detailed information on these molecular processes is essential for the understanding of symbiotic tissue development in order to optimize the benefits of this natural phenomenon. Next generation sequencing tools allow the analysis of non model ectomycorrhizal plant-fungal interactions that can contribute to find the "symbiosis toolkits" and better define the role of each partner in the mutualistic interaction. By using 454 pyrosequencing we compared ectomycorrhizal cork oak roots with non-symbiotic roots. From the two cDNA libraries sequenced, over 2 million reads were obtained that generated 19,552 cork oak root unique transcripts. A total of 2238 transcripts were found to be differentially expressed when ECM roots were compared with non-symbiotic roots. Identification of up- and down-regulated gens in ectomycorrhizal roots lead to a number of insights into the molecular mechanisms governing this important symbiosis. In cork oak roots, ectomycorrhizal colonization resulted in extensive cell wall remodelling, activation of the secretory pathway, alterations in flavonoid biosynthesis, and expression of genes involved in the recognition of fungal effectors. In addition, we identified genes with putative roles in symbiotic processes such as nutrient exchange with the fungal partner, lateral root formation or root hair decay. These findings provide a global overview of the transcriptome of an ectomycorrhizal host root, and constitute a foundation for future studies on the molecular events controlling this important symbiosis.
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Affiliation(s)
- Mónica Sebastiana
- Plant Systems Biology Lab, Center for Biodiversity, Functional and Integrative Genomics, Faculty of Sciences, University of Lisbon, Lisbon, Portugal
| | - Bruno Vieira
- Center for Environmental Biology, Faculty of Sciences, University of Lisbon, Lisbon, Portugal
| | - Teresa Lino-Neto
- Plant Functional Biology Centre, Center for Biodiversity, Functional and Integrative Genomics, University of Minho, Braga, Portugal
| | - Filipa Monteiro
- Plant Systems Biology Lab, Center for Biodiversity, Functional and Integrative Genomics, Faculty of Sciences, University of Lisbon, Lisbon, Portugal
| | - Andreia Figueiredo
- Plant Systems Biology Lab, Center for Biodiversity, Functional and Integrative Genomics, Faculty of Sciences, University of Lisbon, Lisbon, Portugal
| | - Lisete Sousa
- Department of Statistics and Operational Research, Center of Statistics and Applications from Lisbon University, Faculty of Sciences, University of Lisbon, Lisbon, Portugal
| | - Maria Salomé Pais
- Plant Systems Biology Lab, Center for Biodiversity, Functional and Integrative Genomics, Faculty of Sciences, University of Lisbon, Lisbon, Portugal
| | - Rui Tavares
- Plant Functional Biology Centre, Center for Biodiversity, Functional and Integrative Genomics, University of Minho, Braga, Portugal
| | - Octávio S. Paulo
- Center for Environmental Biology, Faculty of Sciences, University of Lisbon, Lisbon, Portugal
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Casieri L, Ait Lahmidi N, Doidy J, Veneault-Fourrey C, Migeon A, Bonneau L, Courty PE, Garcia K, Charbonnier M, Delteil A, Brun A, Zimmermann S, Plassard C, Wipf D. Biotrophic transportome in mutualistic plant-fungal interactions. MYCORRHIZA 2013; 23:597-625. [PMID: 23572325 DOI: 10.1007/s00572-013-0496-9] [Citation(s) in RCA: 95] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2012] [Accepted: 03/13/2013] [Indexed: 05/08/2023]
Abstract
Understanding the mechanisms that underlie nutrient use efficiency and carbon allocation along with mycorrhizal interactions is critical for managing croplands and forests soundly. Indeed, nutrient availability, uptake and exchange in biotrophic interactions drive plant growth and modulate biomass allocation. These parameters are crucial for plant yield, a major issue in the context of high biomass production. Transport processes across the polarized membrane interfaces are of major importance in the functioning of the established mycorrhizal association as the symbiotic relationship is based on a 'fair trade' between the fungus and the host plant. Nutrient and/or metabolite uptake and exchanges, at biotrophic interfaces, are controlled by membrane transporters whose regulation patterns are essential for determining the outcome of plant-fungus interactions and adapting to changes in soil nutrient quantity and/or quality. In the present review, we summarize the current state of the art regarding transport systems in the two major forms of mycorrhiza, namely ecto- and arbuscular mycorrhiza.
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Affiliation(s)
- Leonardo Casieri
- UMR Agroécologie INRA 1347/Agrosup/Université de Bourgogne, Pôle Interactions Plantes Microorganismes ERL 6300 CNRS, BP 86510, 21065, Dijon Cedex, France,
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Tarkka MT, Herrmann S, Wubet T, Feldhahn L, Recht S, Kurth F, Mailänder S, Bönn M, Neef M, Angay O, Bacht M, Graf M, Maboreke H, Fleischmann F, Grams TEE, Ruess L, Schädler M, Brandl R, Scheu S, Schrey SD, Grosse I, Buscot F. OakContigDF159.1, a reference library for studying differential gene expression in Quercus robur during controlled biotic interactions: use for quantitative transcriptomic profiling of oak roots in ectomycorrhizal symbiosis. THE NEW PHYTOLOGIST 2013; 199:529-540. [PMID: 23672230 DOI: 10.1111/nph.12317] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Accepted: 04/02/2013] [Indexed: 05/09/2023]
Abstract
Oaks (Quercus spp.), which are major forest trees in the northern hemisphere, host many biotic interactions, but molecular investigation of these interactions is limited by fragmentary genome data. To date, only 75 oak expressed sequence tags (ESTs) have been characterized in ectomycorrhizal (EM) symbioses. We synthesized seven beneficial and detrimental biotic interactions between microorganisms and animals and a clone (DF159) of Quercus robur. Sixteen 454 and eight Illumina cDNA libraries from leaves and roots were prepared and merged to establish a reference for RNA-Seq transcriptomic analysis of oak EMs with Piloderma croceum. Using the Mimicking Intelligent Read Assembly (MIRA) and Trinity assembler, the OakContigDF159.1 hybrid assembly, containing 65 712 contigs with a mean length of 1003 bp, was constructed, giving broad coverage of metabolic pathways. This allowed us to identify 3018 oak contigs that were differentially expressed in EMs, with genes encoding proline-rich cell wall proteins and ethylene signalling-related transcription factors showing up-regulation while auxin and defence-related genes were down-regulated. In addition to the first report of remorin expression in EMs, the extensive coverage provided by the study permitted detection of differential regulation within large gene families (nitrogen, phosphorus and sugar transporters, aquaporins). This might indicate specific mechanisms of genome regulation in oak EMs compared with other trees.
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Affiliation(s)
- Mika T Tarkka
- Department of Soil Ecology, UFZ - Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, 06120, Halle/Saale, Germany
| | - Sylvie Herrmann
- Department of Soil Ecology, UFZ - Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, 06120, Halle/Saale, Germany
- Department of Community Ecology, UFZ - Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, 06120, Halle/Saale, Germany
| | - Tesfaye Wubet
- Department of Soil Ecology, UFZ - Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, 06120, Halle/Saale, Germany
| | - Lasse Feldhahn
- Department of Soil Ecology, UFZ - Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, 06120, Halle/Saale, Germany
- Institute of Computer Science, Martin-Luther University, Von-Seckendorff-Platz 1, 06120, Halle/Saale, Germany
| | - Sabine Recht
- Department of Soil Ecology, UFZ - Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, 06120, Halle/Saale, Germany
| | - Florence Kurth
- Department of Soil Ecology, UFZ - Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, 06120, Halle/Saale, Germany
| | - Sarah Mailänder
- IMIT-Physiological Ecology of Plants, Auf der Morgenstelle 1, 72076, Tübingen, Germany
| | - Markus Bönn
- Department of Soil Ecology, UFZ - Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, 06120, Halle/Saale, Germany
- Institute of Computer Science, Martin-Luther University, Von-Seckendorff-Platz 1, 06120, Halle/Saale, Germany
| | - Maren Neef
- IMIT-Physiological Ecology of Plants, Auf der Morgenstelle 1, 72076, Tübingen, Germany
| | - Oguzhan Angay
- Section Pathology of Woody Plants, Technische Universität München, Hans-Carl-von-Carlowitz-Platz 2, 85354, Freising, Germany
- TEEG: Ecophysiology of Plants, Technische Universität München, Hans-Carl-von-Carlowitz-Platz 2, 85354, Freising, Germany
| | - Michael Bacht
- Animal Ecology, Department of Ecology, Faculty of Biology, Philipps-Universität Marburg, Karl-von-Frisch Str. 8, 35032, Marburg, Germany
| | - Marcel Graf
- J.F. Blumenbach Institute of Zoology and Anthropology, Georg August University Göttingen, Berliner Str. 28, 37073, Göttingen, Germany
| | - Hazel Maboreke
- Ecology Group, Institute of Biology, Humboldt-Universität zu Berlin, Philippstr. 13, 10115, Berlin, Germany
| | - Frank Fleischmann
- Section Pathology of Woody Plants, Technische Universität München, Hans-Carl-von-Carlowitz-Platz 2, 85354, Freising, Germany
| | - Thorsten E E Grams
- TEEG: Ecophysiology of Plants, Technische Universität München, Hans-Carl-von-Carlowitz-Platz 2, 85354, Freising, Germany
| | - Liliane Ruess
- Ecology Group, Institute of Biology, Humboldt-Universität zu Berlin, Philippstr. 13, 10115, Berlin, Germany
| | - Martin Schädler
- Department of Community Ecology, UFZ - Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, 06120, Halle/Saale, Germany
- Animal Ecology, Department of Ecology, Faculty of Biology, Philipps-Universität Marburg, Karl-von-Frisch Str. 8, 35032, Marburg, Germany
| | - Roland Brandl
- Animal Ecology, Department of Ecology, Faculty of Biology, Philipps-Universität Marburg, Karl-von-Frisch Str. 8, 35032, Marburg, Germany
| | - Stefan Scheu
- J.F. Blumenbach Institute of Zoology and Anthropology, Georg August University Göttingen, Berliner Str. 28, 37073, Göttingen, Germany
| | - Silvia D Schrey
- IMIT-Physiological Ecology of Plants, Auf der Morgenstelle 1, 72076, Tübingen, Germany
| | - Ivo Grosse
- Institute of Computer Science, Martin-Luther University, Von-Seckendorff-Platz 1, 06120, Halle/Saale, Germany
| | - François Buscot
- Department of Soil Ecology, UFZ - Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, 06120, Halle/Saale, Germany
- Institute of Biology, Leipzig University, Johannisallee 21-23, 04103, Leipzig, Germany
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Hacquard S, Tisserant E, Brun A, Legué V, Martin F, Kohler A. Laser microdissection and microarray analysis of Tuber melanosporum ectomycorrhizas reveal functional heterogeneity between mantle and Hartig net compartments. Environ Microbiol 2013; 15:1853-69. [PMID: 23379715 DOI: 10.1111/1462-2920.12080] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Accepted: 12/27/2012] [Indexed: 02/02/2023]
Abstract
The ectomycorrhizal (ECM) symbiosis, a mutualistic plant-fungus association, plays a fundamental role in forest ecosystems by enhancing plant growth and by providing host protection from root diseases. The cellular complexity of the symbiotic organ, characterized by the differentiation of structurally specialized tissues (i.e. the fungal mantle and the Hartig net), is the major limitation to study fungal gene expression in such specific compartments. We investigated the transcriptional landscape of the ECM fungus Tuber melanosporum during the major stages of its life cycle and we particularly focused on the complex symbiotic stage by combining the use of laser capture microdissection and microarray gene expression analysis. We isolated the fungal/soil (i.e. the mantle) and the fungal/plant (i.e. the Hartig net) interfaces from transverse sections of T. melanosporum/Corylus avellana ectomycorrhizas and identified the distinct genetic programmes associated with each compartment. Particularly, nitrogen and water acquisition from soil, synthesis of secondary metabolites and detoxification mechanisms appear to be important processes in the fungal mantle. In contrast, transport activity is enhanced in the Hartig net and we identified carbohydrate and nitrogen-derived transporters that might play a key role in the reciprocal resources' transfer between the host and the symbiont.
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Affiliation(s)
- Stéphane Hacquard
- UMR 1136 INRA/Université de Lorraine, Interactions Arbres/Micro-organismes, INRA, Institut National de la Recherche Agronomique, Centre INRA de Nancy, 54280 Champenoux, France
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30
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Larsen PE, Collart FR. BowStrap v1.0: Assigning statistical significance to expressed genes using short-read transcriptome data. BMC Res Notes 2012; 5:275. [PMID: 22676709 PMCID: PMC3494516 DOI: 10.1186/1756-0500-5-275] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2012] [Accepted: 05/25/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Background: Deep RNA sequencing, the application of Next Generation sequencing technology to generate a comprehensive profile of the message RNA present in a set of biological samples, provides unprecedented resolution into the molecular foundations of biological processes. By aligning short read RNA sequence data to a set of gene models, expression patterns for all of the genes and gene variants in a biological sample can be calculated. However, accurate determination of gene model expression from deep RNA sequencing is hindered by the presence of ambiguously aligning short read sequences. FINDINGS BowStrap, a program for implementing the sequence alignment tool 'Bowtie' in a bootstrap-style approach, accommodates multiply-aligning short read sequences and reports gene model expression as an averaged aligned reads per Kb of gene model sequence per million aligned deep RNA sequence reads with a confidence interval, suitable for calculating statistical significance of presence/absence of detected gene model expression. BowStrap v1.0 was validated against a simulated metatranscriptome. Results were compared with two alternate 'Bowtie'-based calculations of gene model expression. BowStrap is better at accurately identifying expressed gene models in a dataset and provides a more accurate estimate of gene model expression level than methods that do not incorporate a boot-strap style approach. CONCLUSIONS BowStrap v1.0 is superior in ability to detect significant gene model expression and calculate accurate determination of gene model expression levels compared to other alignment-based methods of determining patterns of gene expression. BowStrap v1.0 also can utilize multiple processors as has decreased run time compared to the previous version, BowStrap 0.5. We anticipate that BowStrap will be a highly useful addition to the available set of Next Generation RNA sequence analysis tools.
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Affiliation(s)
- Peter E Larsen
- Biosciences Division, Argonne National Laboratory, Lemont, IL, 60490, USA.
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31
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Unraveling plant-microbe interactions: can multi-species transcriptomics help? Trends Biotechnol 2011; 30:177-84. [PMID: 22209623 DOI: 10.1016/j.tibtech.2011.11.002] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2011] [Revised: 11/04/2011] [Accepted: 11/04/2011] [Indexed: 01/17/2023]
Abstract
Plants in their natural habitats are surrounded by a large number of microorganisms. Some microbes directly interact with plants in a mutually beneficial manner whereas others colonize the plant only for their own benefit. In addition, microbes can indirectly affect plants by drastically altering their environments. Understanding the complex nature of plant-microbe interactions can potentially offer new strategies to enhance plant productivity in an environmentally friendly manner. As briefly reviewed here, the emerging area of multi-species transcriptomics holds the promise to provide knowledge on how this can be achieved. We discuss key aspects of how transcriptome analysis can be used to provide a more comprehensive picture of the complex interactions of plants with their biotic and abiotic environments.
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