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Mishra S, Duarte GT, Horemans N, Ruytinx J, Gudkov D, Danchenko M. Complexity of responses to ionizing radiation in plants, and the impact on interacting biotic factors. Sci Total Environ 2024; 924:171567. [PMID: 38460702 DOI: 10.1016/j.scitotenv.2024.171567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 02/20/2024] [Accepted: 03/06/2024] [Indexed: 03/11/2024]
Abstract
In nature, plants are simultaneously exposed to different abiotic (e.g., heat, drought, and salinity) and biotic (e.g., bacteria, fungi, and insects) stresses. Climate change and anthropogenic pressure are expected to intensify the frequency of stress factors. Although plants are well equipped with unique and common defense systems protecting against stressors, they may compromise their growth and development for survival in such challenging environments. Ionizing radiation is a peculiar stress factor capable of causing clustered damage. Radionuclides are both naturally present on the planet and produced by human activities. Natural and artificial radioactivity affects plants on molecular, biochemical, cellular, physiological, populational, and transgenerational levels. Moreover, the fitness of pests, pathogens, and symbionts is concomitantly challenged in radiologically contaminated areas. Plant responses to artificial acute ionizing radiation exposure and laboratory-simulated or field chronic exposure are often discordant. Acute or chronic ionizing radiation exposure may occasionally prime the defense system of plants to better tolerate the biotic stress or could often exhaust their metabolic reserves, making plants more susceptible to pests and pathogens. Currently, these alternatives are only marginally explored. Our review summarizes the available literature on the responses of host plants, biotic factors, and their interaction to ionizing radiation exposure. Such systematic analysis contributes to improved risk assessment in radiologically contaminated areas.
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Affiliation(s)
- Shubhi Mishra
- Institute of Plant Genetics and Biotechnology, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, 950 07 Nitra, Slovakia
| | - Gustavo Turqueto Duarte
- Unit for Biosphere Impact Studies, Belgian Nuclear Research Centre SCK CEN, 2400 Mol, Belgium
| | - Nele Horemans
- Unit for Biosphere Impact Studies, Belgian Nuclear Research Centre SCK CEN, 2400 Mol, Belgium; Centre for Environmental Sciences, Hasselt University, 3590 Diepenbeek, Belgium
| | - Joske Ruytinx
- Department of Bio-engineering Sciences, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Dmitri Gudkov
- Institute of Hydrobiology, National Academy of Sciences of Ukraine, 04210 Kyiv, Ukraine
| | - Maksym Danchenko
- Institute of Plant Genetics and Biotechnology, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, 950 07 Nitra, Slovakia.
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2
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Lofgren L, Nguyen NH, Kennedy P, Pérez-Pazos E, Fletcher J, Liao HL, Wang H, Zhang K, Ruytinx J, Smith AH, Ke YH, Cotter HVT, Engwall E, Hameed KM, Vilgalys R, Branco S. Suillus: an emerging model for the study of ectomycorrhizal ecology and evolution. New Phytol 2024; 242:1448-1475. [PMID: 38581203 PMCID: PMC11045321 DOI: 10.1111/nph.19700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 03/07/2024] [Indexed: 04/08/2024]
Abstract
Research on mycorrhizal symbiosis has been slowed by a lack of established study systems. To address this challenge, we have been developing Suillus, a widespread ecologically and economically relevant fungal genus primarily associated with the plant family Pinaceae, into a model system for studying ectomycorrhizal (ECM) associations. Over the last decade, we have compiled extensive genomic resources, culture libraries, a phenotype database, and protocols for manipulating Suillus fungi with and without their tree partners. Our efforts have already resulted in a large number of publicly available genomes, transcriptomes, and respective annotations, as well as advances in our understanding of mycorrhizal partner specificity and host communication, fungal and plant nutrition, environmental adaptation, soil nutrient cycling, interspecific competition, and biological invasions. Here, we highlight the most significant recent findings enabled by Suillus, present a suite of protocols for working with the genus, and discuss how Suillus is emerging as an important model to elucidate the ecology and evolution of ECM interactions.
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Affiliation(s)
- Lotus Lofgren
- Department of Biology, Duke University, 130 Science Dr., Durham, NC 27708, USA
| | - Nhu H. Nguyen
- Department of Tropical Plant and Soil Sciences, University of Hawai‘i at Māno, 3190 Maile Way, Honolulu, HI 96822, USA
| | - Peter Kennedy
- Department of Plant and Microbial Biology, University of Minnesota, 1475 Gortner Ave, Saint Paul, MN 55108, USA
- Department of Ecology, Evolution and Behavior, University of Minnesota, 1475 Gortner Ave, Saint Paul, MN 55108, USA
| | - Eduardo Pérez-Pazos
- Department of Ecology, Evolution and Behavior, University of Minnesota, 1475 Gortner Ave, Saint Paul, MN 55108, USA
| | - Jessica Fletcher
- Department of Integrative Biology, University of Colorado Denver 1151 Arapahoe St, SI 2071, Denver, CO 80204, USA
| | - Hui-Ling Liao
- North Florida Research and Education Center, University of Florida, 155 Research Rd Quincy, FL 3235, USA
- Department of Soil, Water and Ecosystem Sciences, University of Florida, 1692 McCarty Dr, Room 2181, Building A, Gainesville, FL 32611, USA
| | - Haihua Wang
- North Florida Research and Education Center, University of Florida, 155 Research Rd Quincy, FL 3235, USA
- Department of Soil, Water and Ecosystem Sciences, University of Florida, 1692 McCarty Dr, Room 2181, Building A, Gainesville, FL 32611, USA
| | - Kaile Zhang
- North Florida Research and Education Center, University of Florida, 155 Research Rd Quincy, FL 3235, USA
| | - Joske Ruytinx
- Research Group of Microbiology and Plant Genetics, Department of Bioengineering Sciences, Vrije Universiteit Brussel, 1050 Brussels, Belgium, USA
| | - Alexander H. Smith
- Department of Integrative Biology, University of Colorado Denver 1151 Arapahoe St, SI 2071, Denver, CO 80204, USA
| | - Yi-Hong Ke
- Department of Ecology and Evolutionary Biology, University of Michigan, 1105 N University Ave, Ann Arbor, MI 48109, USA
| | - H. Van T. Cotter
- University of North Carolina at Chapel Hill Herbarium, 120 South Road, Chapel Hill, NC 27599, USA
| | - Eiona Engwall
- Department of Biology, University of North Carolina at Chapel Hill, 120 South Road, Chapel Hill, NC 27599, USA
| | - Khalid M. Hameed
- Department of Biology, Duke University, 130 Science Dr., Durham, NC 27708, USA
| | - Rytas Vilgalys
- Department of Biology, Duke University, 130 Science Dr., Durham, NC 27708, USA
| | - Sara Branco
- Department of Integrative Biology, University of Colorado Denver 1151 Arapahoe St, SI 2071, Denver, CO 80204, USA
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3
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Branco S, Schauster A, Liao HL, Ruytinx J. Mechanisms of stress tolerance and their effects on the ecology and evolution of mycorrhizal fungi. New Phytol 2022; 235:2158-2175. [PMID: 35713988 DOI: 10.1111/nph.18308] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 05/11/2022] [Indexed: 05/25/2023]
Abstract
Stress is ubiquitous and disrupts homeostasis, leading to damage, decreased fitness, and even death. Like other organisms, mycorrhizal fungi evolved mechanisms for stress tolerance that allow them to persist or even thrive under environmental stress. Such mechanisms can also protect their obligate plant partners, contributing to their health and survival under hostile conditions. Here we review the effects of stress and mechanisms of stress response in mycorrhizal fungi. We cover molecular and cellular aspects of stress and how stress impacts individual fitness, physiology, growth, reproduction, and interactions with plant partners, along with how some fungi evolved to tolerate hostile environmental conditions. We also address how stress and stress tolerance can lead to adaptation and have cascading effects on population- and community-level diversity. We argue that mycorrhizal fungal stress tolerance can strongly shape not only fungal and plant physiology, but also their ecology and evolution. We conclude by pointing out knowledge gaps and important future research directions required for both fully understanding stress tolerance in the mycorrhizal context and addressing ongoing environmental change.
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Affiliation(s)
- Sara Branco
- Department of Integrative Biology, University of Colorado Denver, Denver, CO, 80204, USA
| | - Annie Schauster
- Department of Integrative Biology, University of Colorado Denver, Denver, CO, 80204, USA
| | - Hui-Ling Liao
- North Florida Research and Education Center, University of Florida, Quincy, FL, 32351, USA
- Soil and Water Sciences Department, University of Florida, Gainesville, FL, 32611, USA
| | - Joske Ruytinx
- Research Groups Microbiology and Plant Genetics, Vrije Universiteit Brussel, 1050, Brussels, Belgium
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4
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Zhang K, Tappero R, Ruytinx J, Branco S, Liao HL. Disentangling the role of ectomycorrhizal fungi in plant nutrient acquisition along a Zn gradient using X-ray imaging. Sci Total Environ 2021; 801:149481. [PMID: 34467922 DOI: 10.1016/j.scitotenv.2021.149481] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 08/01/2021] [Accepted: 08/01/2021] [Indexed: 06/13/2023]
Abstract
Zinc (Zn) is a plant essential micronutrient involved in a wide range of cellular processes. Ectomycorrhizal fungi (EMF) are known to play a critical role in regulating plant Zn status. However, how EMF control uptake and translocation of Zn and other nutrients in plant roots under different Zn conditions is not well known. Using X-ray fluorescence imaging, we found the EMF species Suillus luteus increased pine root Zn acquisition under low Zn concentrations and reduced its accumulation under higher Zn levels. By contrast, non-mycorrhizal pine roots exposed to high Zn indiscriminately take up and translocate Zn to root tissues, leading to Zn stress. Regardless of S. luteus inoculation, the absorption pattern of Ca and Cu was similar to Zn. Compared to Ca and Cu, effects of S. luteus on Fe acquisition were more marked, leading to a negative association between Zn addition and Fe concentration within EMF roots. Besides, higher nutrient accumulation in the fungal sheath, compared to hyphae inhabiting between intercellular space of cortex cells, implies the fungal sheath serves as a barrier to regulate nutrient transportation into fungal Hartig net. Our results demonstrate the crucial roles EMF play in plant nutrient uptake and how fungal partners ameliorate soil chemical conditions either by increasing or decreasing element uptake.
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Affiliation(s)
- Kaile Zhang
- North Florida Research and Education Center, University of Florida, Quincy, FL 32351, USA; Soil and Water Science Department, University of Florida, Gainesville, FL 32611, USA
| | - Ryan Tappero
- Brookhaven National Laboratory, NSLS-II, Upton, NY 11973, USA
| | - Joske Ruytinx
- Research Groups Microbiology and Plant Genetics, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussel, Belgium
| | - Sara Branco
- Department of Integrative Biology, University of Colorado Denver, Denver, CO 80204, USA
| | - Hui-Ling Liao
- North Florida Research and Education Center, University of Florida, Quincy, FL 32351, USA; Soil and Water Science Department, University of Florida, Gainesville, FL 32611, USA.
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5
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Lofgren LA, Nguyen NH, Vilgalys R, Ruytinx J, Liao HL, Branco S, Kuo A, LaButti K, Lipzen A, Andreopoulos W, Pangilinan J, Riley R, Hundley H, Na H, Barry K, Grigoriev IV, Stajich JE, Kennedy PG. Comparative genomics reveals dynamic genome evolution in host specialist ectomycorrhizal fungi. New Phytol 2021; 230:774-792. [PMID: 33355923 PMCID: PMC7969408 DOI: 10.1111/nph.17160] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 12/16/2020] [Indexed: 05/24/2023]
Abstract
While there has been significant progress characterizing the 'symbiotic toolkit' of ectomycorrhizal (ECM) fungi, how host specificity may be encoded into ECM fungal genomes remains poorly understood. We conducted a comparative genomic analysis of ECM fungal host specialists and generalists, focusing on the specialist genus Suillus. Global analyses of genome dynamics across 46 species were assessed, along with targeted analyses of three classes of molecules previously identified as important determinants of host specificity: small secreted proteins (SSPs), secondary metabolites (SMs) and G-protein coupled receptors (GPCRs). Relative to other ECM fungi, including other host specialists, Suillus had highly dynamic genomes including numerous rapidly evolving gene families and many domain expansions and contractions. Targeted analyses supported a role for SMs but not SSPs or GPCRs in Suillus host specificity. Phylogenomic-based ancestral state reconstruction identified Larix as the ancestral host of Suillus, with multiple independent switches between white and red pine hosts. These results suggest that like other defining characteristics of the ECM lifestyle, host specificity is a dynamic process at the genome level. In the case of Suillus, both SMs and pathways involved in the deactivation of reactive oxygen species appear to be strongly associated with enhanced host specificity.
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Affiliation(s)
- Lotus A Lofgren
- Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, CA, 92507, USA
- Department of Plant and Microbial Biology, University of Minnesota, St Paul, MN, 55108, USA
| | - Nhu H Nguyen
- Department of Tropical Plant and Soil Science, University of Hawaii, Manoa, HI, 96822, USA
| | - Rytas Vilgalys
- Department of Biology, Duke University, Durham, NC, 27708, USA
| | - Joske Ruytinx
- Research group Microbiology, Department of Bio-engineering Sciences, Vrije Universiteit Brussel, Brussel, BE1500, Belgium
| | - Hui-Ling Liao
- Department of Soil Microbial Ecology, University of Florida, Quincy, FL, 32351, USA
| | - Sara Branco
- Department of Integrative Biology, University of Colorado Denver, Denver, CO, 80204, USA
| | - Alan Kuo
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Kurt LaButti
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Anna Lipzen
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - William Andreopoulos
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Jasmyn Pangilinan
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Robert Riley
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Hope Hundley
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Hyunsoo Na
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Kerrie Barry
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, CA, 92507, USA
| | - Peter G Kennedy
- Department of Plant and Microbial Biology, University of Minnesota, St Paul, MN, 55108, USA
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6
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Bazzicalupo AL, Ruytinx J, Ke Y, Coninx L, Colpaert JV, Nguyen NH, Vilgalys R, Branco S. Fungal heavy metal adaptation through single nucleotide polymorphisms and copy‐number variation. Mol Ecol 2020; 29:4157-4169. [DOI: 10.1111/mec.15618] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 08/19/2020] [Indexed: 12/15/2022]
Affiliation(s)
- Anna L. Bazzicalupo
- Department of Microbiology and Immunology Montana State University Bozeman MT USA
| | - Joske Ruytinx
- Research Group of Microbiology Department of Bioengineering Sciences Vrije Universiteit Brussel Brussels Belgium
| | - Yi‐Hong Ke
- Biology Department Duke University Durham NC USA
| | - Laura Coninx
- Biology Department Centre for Environmental Sciences Hasselt University Diepenbeek Belgium
| | - Jan V. Colpaert
- Biology Department Centre for Environmental Sciences Hasselt University Diepenbeek Belgium
| | - Nhu H. Nguyen
- Department of Tropical Plant and Soil Sciences University of Hawai'i at Mānoa Honolulu HI USA
| | | | - Sara Branco
- Department of Integrative Biology University of Colorado Denver Denver CO USA
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7
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Elsacker E, Vandelook S, Van Wylick A, Ruytinx J, De Laet L, Peeters E. A comprehensive framework for the production of mycelium-based lignocellulosic composites. Sci Total Environ 2020; 725:138431. [PMID: 32298897 DOI: 10.1016/j.scitotenv.2020.138431] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 04/01/2020] [Accepted: 04/02/2020] [Indexed: 06/11/2023]
Abstract
Environmental pollution and scarcity of natural resources lead to an increased interest in developing more sustainable materials. For example, the traditional construction industry, which is largely based on the extraction of fossil fuels and raw materials, is called into question. A solution can be found in biologically augmented materials that are made by growing mycelium-forming fungal microorganisms on natural fibres rich in cellulose, hemicellulose and lignin. In this way, organic waste streams, such as agricultural waste, are valorised while creating a material that is biodegradable at the end of its life cycle - a process that fits in the spirit of circular economy. Mycelium-based materials have properties that are promising for a wide range of applications, including the use as construction materials. Despite this promise, the applicability and the practicality of these materials are largely unexplored and moreover, individual studies use a wide range of different experimental approaches and non-standardized procedures. In this review, we critically evaluate existing data on the composition of mycelium-based materials and process variables with the aim of providing a comprehensive framework of the production process. The framework illustrates the many input factors during the production that have an impact on the final characteristics of the material, and the unique potential to deploy more tuneable levels in the fabrications process that can serve to prototype a diversity of new unprecedented applications. Furthermore, we determine the applicability of existing data and identify knowledge gaps. This framework is valuable in identifying standardized approaches for future studies and in informing the design and process of new applications of mycelium-based materials.
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Affiliation(s)
- Elise Elsacker
- Architectural Engineering Research Group, Department of Architectural Engineering, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium; Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium.
| | - Simon Vandelook
- Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Aurélie Van Wylick
- Architectural Engineering Research Group, Department of Architectural Engineering, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium; Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Joske Ruytinx
- Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Lars De Laet
- Architectural Engineering Research Group, Department of Architectural Engineering, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Eveline Peeters
- Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium.
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Ruytinx J, Kafle A, Usman M, Coninx L, Zimmermann SD, Garcia K. Micronutrient transport in mycorrhizal symbiosis; zinc steals the show. FUNGAL BIOL REV 2020. [DOI: 10.1016/j.fbr.2019.09.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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9
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Coninx L, Smisdom N, Kohler A, Arnauts N, Ameloot M, Rineau F, Colpaert JV, Ruytinx J. SlZRT2 Encodes a ZIP Family Zn Transporter With Dual Localization in the Ectomycorrhizal Fungus Suillus luteus. Front Microbiol 2019; 10:2251. [PMID: 31681189 PMCID: PMC6797856 DOI: 10.3389/fmicb.2019.02251] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 09/17/2019] [Indexed: 11/13/2022] Open
Abstract
Ectomycorrhizal (ECM) fungi are important root symbionts of trees, as they can have significant effects on the nutrient status of plants. In polluted environments, particular ECM fungi can protect their host tree from Zn toxicity by restricting the transfer of Zn while securing supply of essential nutrients. However, mechanisms and regulation of cellular Zn homeostasis in ECM fungi are largely unknown, and it remains unclear how ECM fungi affect the Zn status of their host plants. This study focuses on the characterization of a ZIP (Zrt/IrtT-like protein) transporter, SlZRT2, in the ECM fungus Suillus luteus, a common root symbiont of young pine trees. SlZRT2 is predicted to encode a plasma membrane-located Zn importer. Heterologous expression of SlZRT2 in yeast mutants with impaired Zn uptake resulted in a minor impact on cellular Zn accumulation and growth. The SlZRT2 gene product showed a dual localization and was detected at the plasma membrane and perinuclear region. S. luteus ZIP-family Zn uptake transporters did not show the potential to induce trehalase activity in yeast and to function as Zn sensors. In response to excess environmental Zn, gene expression analysis demonstrated a rapid but minor and transient decrease in SlZRT2 transcript level. In ECM root tips, the gene is upregulated. Whether this regulation is due to limited Zn availability at the fungal-plant interface or to developmental processes is unclear. Altogether, our results suggest a function for SlZRT2 in cellular Zn redistribution from the ER next to a putative role in Zn uptake in S. luteus.
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Affiliation(s)
- Laura Coninx
- Centre for Environmental Sciences, Environmental Biology, Hasselt University, Diepenbeek, Belgium
| | - Nick Smisdom
- Biomedical Research Institute, Hasselt University, Diepenbeek, Belgium
| | - Annegret Kohler
- Laboratoire d’Excellence ARBRE, Institut National de la Recherche Agronomique, UMR 1136 INRA/Université de Lorraine Interactions Arbres/Microorganismes, Champenoux, France
| | - Natascha Arnauts
- Centre for Environmental Sciences, Environmental Biology, Hasselt University, Diepenbeek, Belgium
| | - Marcel Ameloot
- Biomedical Research Institute, Hasselt University, Diepenbeek, Belgium
| | - François Rineau
- Centre for Environmental Sciences, Environmental Biology, Hasselt University, Diepenbeek, Belgium
| | - Jan V. Colpaert
- Centre for Environmental Sciences, Environmental Biology, Hasselt University, Diepenbeek, Belgium
| | - Joske Ruytinx
- Centre for Environmental Sciences, Environmental Biology, Hasselt University, Diepenbeek, Belgium
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Pellegrin C, Daguerre Y, Ruytinx J, Guinet F, Kemppainen M, Frey NFD, Puech‐Pagès V, Hecker A, Pardo AG, Martin FM, Veneault‐Fourrey C. Laccaria bicolor
MiSSP8 is a small‐secreted protein decisive for the establishment of the ectomycorrhizal symbiosis. Environ Microbiol 2019; 21:3765-3779. [DOI: 10.1111/1462-2920.14727] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 06/18/2019] [Accepted: 06/27/2019] [Indexed: 11/29/2022]
Affiliation(s)
- Clément Pellegrin
- INRA, UMR1136Interactions Arbres/microorganismes Centre Grand‐Est Champenoux France
- UMR 1136, Interactions Arbres/Microorganismes (IAM), Faculté des Sciences et TechnologiesUniversité de Lorraine Vandœuvre lès Nancy France
| | - Yohann Daguerre
- INRA, UMR1136Interactions Arbres/microorganismes Centre Grand‐Est Champenoux France
- UMR 1136, Interactions Arbres/Microorganismes (IAM), Faculté des Sciences et TechnologiesUniversité de Lorraine Vandœuvre lès Nancy France
| | - Joske Ruytinx
- INRA, UMR1136Interactions Arbres/microorganismes Centre Grand‐Est Champenoux France
- UMR 1136, Interactions Arbres/Microorganismes (IAM), Faculté des Sciences et TechnologiesUniversité de Lorraine Vandœuvre lès Nancy France
| | - Frédéric Guinet
- INRA, UMR1136Interactions Arbres/microorganismes Centre Grand‐Est Champenoux France
- UMR 1136, Interactions Arbres/Microorganismes (IAM), Faculté des Sciences et TechnologiesUniversité de Lorraine Vandœuvre lès Nancy France
| | - Minna Kemppainen
- Laboratorio de Micología Molecular, Departamento de Ciencia y TecnologıaUniversidad Nacional de Quilmes and CONICET Roque Sáenz Peña 352 B1876 Bernal Provincia de Buenos Aires Argentina
| | - Nicolas Frei dit Frey
- Laboratoire de Recherche en Sciences VégétalesUniversité de Toulouse, CNRS, UPS 24 chemin de Borde Rouge, Auzeville, BP42617 31326 Castanet Tolosan France
| | - Virginie Puech‐Pagès
- Laboratoire de Recherche en Sciences VégétalesUniversité de Toulouse, CNRS, UPS 24 chemin de Borde Rouge, Auzeville, BP42617 31326 Castanet Tolosan France
| | - Arnaud Hecker
- INRA, UMR1136Interactions Arbres/microorganismes Centre Grand‐Est Champenoux France
- UMR 1136, Interactions Arbres/Microorganismes (IAM), Faculté des Sciences et TechnologiesUniversité de Lorraine Vandœuvre lès Nancy France
| | - Alejandro G. Pardo
- Laboratorio de Micología Molecular, Departamento de Ciencia y TecnologıaUniversidad Nacional de Quilmes and CONICET Roque Sáenz Peña 352 B1876 Bernal Provincia de Buenos Aires Argentina
| | - Francis M. Martin
- INRA, UMR1136Interactions Arbres/microorganismes Centre Grand‐Est Champenoux France
- UMR 1136, Interactions Arbres/Microorganismes (IAM), Faculté des Sciences et TechnologiesUniversité de Lorraine Vandœuvre lès Nancy France
| | - Claire Veneault‐Fourrey
- INRA, UMR1136Interactions Arbres/microorganismes Centre Grand‐Est Champenoux France
- UMR 1136, Interactions Arbres/Microorganismes (IAM), Faculté des Sciences et TechnologiesUniversité de Lorraine Vandœuvre lès Nancy France
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11
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Coninx L, Thoonen A, Slenders E, Morin E, Arnauts N, Op De Beeck M, Kohler A, Ruytinx J, Colpaert JV. The SlZRT1 Gene Encodes a Plasma Membrane-Located ZIP (Zrt-, Irt-Like Protein) Transporter in the Ectomycorrhizal Fungus Suillus luteus. Front Microbiol 2017; 8:2320. [PMID: 29234311 PMCID: PMC5712335 DOI: 10.3389/fmicb.2017.02320] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 11/10/2017] [Indexed: 11/18/2022] Open
Abstract
Zinc (Zn) is an essential micronutrient but may become toxic when present in excess. In Zn-contaminated environments, trees can be protected from Zn toxicity by their root-associated micro-organisms, in particular ectomycorrhizal fungi. The mechanisms of cellular Zn homeostasis in ectomycorrhizal fungi and their contribution to the host tree's Zn status are however not yet fully understood. The aim of this study was to identify and characterize transporters involved in Zn uptake in the ectomycorrhizal fungus Suillus luteus, a cosmopolitan pine mycobiont. Zn uptake in fungi is known to be predominantly governed by members of the ZIP (Zrt/IrtT-like protein) family of Zn transporters. Four ZIP transporter encoding genes were identified in the S. luteus genome. By in silico and phylogenetic analysis, one of these proteins, SlZRT1, was predicted to be a plasma membrane located Zn importer. Heterologous expression in yeast confirmed the predicted function and localization of the protein. A gene expression analysis via RT-qPCR was performed in S. luteus to establish whether SlZRT1 expression is affected by external Zn concentrations. SlZRT1 transcripts accumulated almost immediately, though transiently upon growth in the absence of Zn. Exposure to elevated concentrations of Zn resulted in a significant reduction of SlZRT1 transcripts within the first hour after initiation of the exposure. Altogether, the data support a role as cellular Zn importer for SlZRT1 and indicate a key role in cellular Zn uptake of S. luteus. Further research is needed to understand the eventual contribution of SlZRT1 to the Zn status of the host plant.
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Affiliation(s)
- Laura Coninx
- Environmental Biology, Centre for Environmental Sciences, Hasselt University, Hasselt, Belgium
| | - Anneleen Thoonen
- Environmental Biology, Centre for Environmental Sciences, Hasselt University, Hasselt, Belgium
| | - Eli Slenders
- Biomedical Research Institute, Hasselt University, Hasselt, Belgium
| | - Emmanuelle Morin
- Institut National de la Recherche Agronomique, Laboratoire d’Excellence ARBRE, UMR 1136, Université de Lorraine Interactions Arbres/Microorganismes, Champenoux, France
| | - Natascha Arnauts
- Environmental Biology, Centre for Environmental Sciences, Hasselt University, Hasselt, Belgium
| | - Michiel Op De Beeck
- Environmental Biology, Centre for Environmental Sciences, Hasselt University, Hasselt, Belgium
| | - Annegret Kohler
- Institut National de la Recherche Agronomique, Laboratoire d’Excellence ARBRE, UMR 1136, Université de Lorraine Interactions Arbres/Microorganismes, Champenoux, France
| | - Joske Ruytinx
- Environmental Biology, Centre for Environmental Sciences, Hasselt University, Hasselt, Belgium
| | - Jan V. Colpaert
- Environmental Biology, Centre for Environmental Sciences, Hasselt University, Hasselt, Belgium
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12
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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13
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Ruytinx J, Coninx L, Nguyen H, Smisdom N, Morin E, Kohler A, Cuypers A, Colpaert JV. Identification, evolution and functional characterization of two Zn CDF-family transporters of the ectomycorrhizal fungus Suillus luteus. Environ Microbiol Rep 2017; 9:419-427. [PMID: 28557335 DOI: 10.1111/1758-2229.12551] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Revised: 05/22/2017] [Accepted: 05/22/2017] [Indexed: 06/07/2023]
Abstract
Two genes, SlZnT1 and SlZnT2, encoding Cation Diffusion Facilitator (CDF) family transporters were isolated from Suillus luteus mycelium by genome walking. Both gene models are very similar and phylogenetic analysis indicates that they are most likely the result of a recent gene duplication event. Comparative sequence analysis of the deduced proteins predicts them to be Zn transporters. This function was confirmed by functional analysis in yeast for SlZnT1. SlZnT1 was able to restore growth of the highly Zn sensitive yeast mutant Δzrc1 and localized to the vacuolar membrane. Transformation of Δzrc1 yeast cells with SlZnT1 resulted in an increased accumulation of Zn compared to empty vector transformed Δzrc1 yeast cells and equals Zn accumulation in wild type yeast cells. We were not able to express functional SlZnT2 in yeast. In S. luteus, both SlZnT genes are constitutively expressed whatever the external Zn concentrations. A labile Zn pool was detected in the vacuoles of S. luteus free-living mycelium. Therefore we conclude that SlZnT1 is indispensable for maintenance of Zn homeostasis by transporting excess Zn into the vacuole.
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Affiliation(s)
- Joske Ruytinx
- Centre for Environmental Sciences, Environmental Biology, Hasselt University, Agoralaan building D, Diepenbeek, 3590, Belgium
| | - Laura Coninx
- Centre for Environmental Sciences, Environmental Biology, Hasselt University, Agoralaan building D, Diepenbeek, 3590, Belgium
| | - Hoai Nguyen
- Centre for Environmental Sciences, Environmental Biology, Hasselt University, Agoralaan building D, Diepenbeek, 3590, Belgium
| | - Nick Smisdom
- Biomedical Research Institute, Hasselt University, Agoralaan building C, Diepenbeek, 3590, Belgium
| | - Emmanuelle Morin
- Institut National de la Recherche Agronomique, UMR1136 INRA-Université de Lorraine Interactions Arbres/Microorganismes, Laboratoire d'Excellence ARBRE, Champenoux, 54280, France
| | - Annegret Kohler
- Institut National de la Recherche Agronomique, UMR1136 INRA-Université de Lorraine Interactions Arbres/Microorganismes, Laboratoire d'Excellence ARBRE, Champenoux, 54280, France
| | - Ann Cuypers
- Centre for Environmental Sciences, Environmental Biology, Hasselt University, Agoralaan building D, Diepenbeek, 3590, Belgium
| | - Jan V Colpaert
- Centre for Environmental Sciences, Environmental Biology, Hasselt University, Agoralaan building D, Diepenbeek, 3590, Belgium
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14
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Ruytinx J, Martin F. Chapter 2 Comparative and Functional Genomics of Ectomycorrhizal Symbiosis. Mycology 2017. [DOI: 10.1201/9781315119496-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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15
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Rineau F, Lmalem H, Ahren D, Shah F, Johansson T, Coninx L, Ruytinx J, Nguyen H, Grigoriev I, Kuo A, Kohler A, Morin E, Vangronsveld J, Martin F, Colpaert JV. Comparative genomics and expression levels of hydrophobins from eight mycorrhizal genomes. Mycorrhiza 2017; 27:383-396. [PMID: 28066872 DOI: 10.1007/s00572-016-0758-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 12/22/2016] [Indexed: 06/06/2023]
Abstract
Hydrophobins are small secreted proteins that are present as several gene copies in most fungal genomes. Their properties are now well understood: they are amphiphilic and assemble at hydrophilic/hydrophobic interfaces. However, their physiological functions remain largely unexplored, especially within mycorrhizal fungi. In this study, we identified hydrophobin genes and analysed their distribution in eight mycorrhizal genomes. We then measured their expression levels in three different biological conditions (mycorrhizal tissue vs. free-living mycelium, organic vs. mineral growth medium and aerial vs. submerged growth). Results confirmed that the size of the hydrophobin repertoire increased in the terminal orders of the fungal evolutionary tree. Reconciliation analysis predicted that in 41% of the cases, hydrophobins evolved from duplication events. Whatever the treatment and the fungal species, the pattern of expression of hydrophobins followed a reciprocal function, with one gene much more expressed than others from the same repertoire. These most-expressed hydrophobin genes were also among the most expressed of the whole genome, which suggests that they play a role as structural proteins. The fine-tuning of the expression of hydrophobin genes in each condition appeared complex because it differed considerably between species, in a way that could not be explained by simple ecological traits. Hydrophobin gene regulation in mycorrhizal tissue as compared with free-living mycelium, however, was significantly associated with a calculated high exposure of hydrophilic residues.
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Affiliation(s)
- F Rineau
- Centre for Environmental Sciences, Environmental Biology group, UHasselt, Hasselt, Belgium.
| | - H Lmalem
- Centre for Environmental Sciences, Environmental Biology group, UHasselt, Hasselt, Belgium
| | - D Ahren
- Department of Biology, Microbial Ecology Group, Lund University, Ecology Building, 223 62, Lund, SE, Sweden
| | - F Shah
- Department of food and environmental sciences, University of Helsinki, Helsinki, Finland
| | - T Johansson
- Department of Biology, Microbial Ecology Group, Lund University, Ecology Building, 223 62, Lund, SE, Sweden
| | - L Coninx
- Centre for Environmental Sciences, Environmental Biology group, UHasselt, Hasselt, Belgium
| | - J Ruytinx
- Centre for Environmental Sciences, Environmental Biology group, UHasselt, Hasselt, Belgium
| | - H Nguyen
- Centre for Environmental Sciences, Environmental Biology group, UHasselt, Hasselt, Belgium
| | - I Grigoriev
- US Department of Energy Joint Genome Institute (JGI), Walnut Creek, CA, USA
| | - A Kuo
- US Department of Energy Joint Genome Institute (JGI), Walnut Creek, CA, USA
| | - A Kohler
- Laboratory of Excellence Advanced Research on the Biology of Tree and Forest Ecosystems (ARBRE), Institut National de la Recherche Agronomique (INRA), UMR 1136, Champenoux, France
- Laboratory of Excellence ARBRE, University of Lorraine, UMR 1136, Champenoux, France
| | - E Morin
- Laboratory of Excellence Advanced Research on the Biology of Tree and Forest Ecosystems (ARBRE), Institut National de la Recherche Agronomique (INRA), UMR 1136, Champenoux, France
- Laboratory of Excellence ARBRE, University of Lorraine, UMR 1136, Champenoux, France
| | - J Vangronsveld
- Centre for Environmental Sciences, Environmental Biology group, UHasselt, Hasselt, Belgium
| | - F Martin
- Laboratory of Excellence Advanced Research on the Biology of Tree and Forest Ecosystems (ARBRE), Institut National de la Recherche Agronomique (INRA), UMR 1136, Champenoux, France
- Laboratory of Excellence ARBRE, University of Lorraine, UMR 1136, Champenoux, France
| | - J V Colpaert
- Centre for Environmental Sciences, Environmental Biology group, UHasselt, Hasselt, Belgium
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16
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Nguyen H, Rineau F, Vangronsveld J, Cuypers A, Colpaert JV, Ruytinx J. A novel, highly conserved metallothionein family in basidiomycete fungi and characterization of two representative SlMTa
and SlMTb
genes in the ectomycorrhizal fungus Suillus luteus. Environ Microbiol 2017; 19:2577-2587. [DOI: 10.1111/1462-2920.13729] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Revised: 03/03/2017] [Accepted: 03/04/2017] [Indexed: 12/11/2022]
Affiliation(s)
- Hoai Nguyen
- Centre for Environmental Sciences, Environmental Biology; Hasselt University; Agoralaan Building D Diepenbeek 3590 Belgium
| | - François Rineau
- Centre for Environmental Sciences, Environmental Biology; Hasselt University; Agoralaan Building D Diepenbeek 3590 Belgium
| | - Jaco Vangronsveld
- Centre for Environmental Sciences, Environmental Biology; Hasselt University; Agoralaan Building D Diepenbeek 3590 Belgium
| | - Ann Cuypers
- Centre for Environmental Sciences, Environmental Biology; Hasselt University; Agoralaan Building D Diepenbeek 3590 Belgium
| | - Jan V. Colpaert
- Centre for Environmental Sciences, Environmental Biology; Hasselt University; Agoralaan Building D Diepenbeek 3590 Belgium
| | - Joske Ruytinx
- Centre for Environmental Sciences, Environmental Biology; Hasselt University; Agoralaan Building D Diepenbeek 3590 Belgium
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17
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Kohler A, Kuo A, Nagy LG, Morin E, Barry KW, Buscot F, Canbäck B, Choi C, Cichocki N, Clum A, Colpaert J, Copeland A, Costa MD, Doré J, Floudas D, Gay G, Girlanda M, Henrissat B, Herrmann S, Hess J, Högberg N, Johansson T, Khouja HR, LaButti K, Lahrmann U, Levasseur A, Lindquist EA, Lipzen A, Marmeisse R, Martino E, Murat C, Ngan CY, Nehls U, Plett JM, Pringle A, Ohm RA, Perotto S, Peter M, Riley R, Rineau F, Ruytinx J, Salamov A, Shah F, Sun H, Tarkka M, Tritt A, Veneault-Fourrey C, Zuccaro A, Tunlid A, Grigoriev IV, Hibbett DS, Martin F. Convergent losses of decay mechanisms and rapid turnover of symbiosis genes in mycorrhizal mutualists. Nat Genet 2015; 47:410-415. [PMID: 25706625 DOI: 10.1038/ng3223] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Accepted: 01/28/2015] [Indexed: 05/26/2023]
Abstract
To elucidate the genetic bases of mycorrhizal lifestyle evolution, we sequenced new fungal genomes, including 13 ectomycorrhizal (ECM), orchid (ORM) and ericoid (ERM) species, and five saprotrophs, which we analyzed along with other fungal genomes. Ectomycorrhizal fungi have a reduced complement of genes encoding plant cell wall-degrading enzymes (PCWDEs), as compared to their ancestral wood decayers. Nevertheless, they have retained a unique array of PCWDEs, thus suggesting that they possess diverse abilities to decompose lignocellulose. Similar functional categories of nonorthologous genes are induced in symbiosis. Of induced genes, 7-38% are orphan genes, including genes that encode secreted effector-like proteins. Convergent evolution of the mycorrhizal habit in fungi occurred via the repeated evolution of a 'symbiosis toolkit', with reduced numbers of PCWDEs and lineage-specific suites of mycorrhiza-induced genes.
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Affiliation(s)
- Annegret Kohler
- 1] Institut National de la Recherche Agronomique (INRA), Laboratory of Excellence Advanced Research on the Biology of Tree and Forest Ecosystems (ARBRE), UMR 1136, Champenoux, France. [2] University of Lorraine, Laboratory of Excellence ARBRE, UMR 1136, Champenoux, France
| | - Alan Kuo
- US Department of Energy Joint Genome Institute (JGI), Walnut Creek, California, USA
| | - Laszlo G Nagy
- 1] Department of Biology, Clark University, Worcester, Massachusetts, USA. [2] Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Center, Hungarian Academy of Sciences, Szeged, Hungary
| | - Emmanuelle Morin
- 1] Institut National de la Recherche Agronomique (INRA), Laboratory of Excellence Advanced Research on the Biology of Tree and Forest Ecosystems (ARBRE), UMR 1136, Champenoux, France. [2] University of Lorraine, Laboratory of Excellence ARBRE, UMR 1136, Champenoux, France
| | - Kerrie W Barry
- US Department of Energy Joint Genome Institute (JGI), Walnut Creek, California, USA
| | - Francois Buscot
- 1] Department of Soil Ecology, Helmholtz Centre for Environmental Research-Helmholtz Zentrum fuer Umweltforschung, Halle, Germany. [2] German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Björn Canbäck
- Department of Biology, Microbial Ecology Group, Lund University, Lund, Sweden
| | - Cindy Choi
- US Department of Energy Joint Genome Institute (JGI), Walnut Creek, California, USA
| | - Nicolas Cichocki
- 1] Institut National de la Recherche Agronomique (INRA), Laboratory of Excellence Advanced Research on the Biology of Tree and Forest Ecosystems (ARBRE), UMR 1136, Champenoux, France. [2] University of Lorraine, Laboratory of Excellence ARBRE, UMR 1136, Champenoux, France
| | - Alicia Clum
- US Department of Energy Joint Genome Institute (JGI), Walnut Creek, California, USA
| | - Jan Colpaert
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Alex Copeland
- US Department of Energy Joint Genome Institute (JGI), Walnut Creek, California, USA
| | - Mauricio D Costa
- Departamento de Microbiologia, Bolsista do Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), Universidade Federal de Viçosa, Viçosa, Brazil
| | - Jeanne Doré
- UMR CNRS 5557, Unité Sous Contrat INRA 1364, Université de Lyon, Université Lyon 1, Villeurbanne, France
| | - Dimitrios Floudas
- Department of Biology, Clark University, Worcester, Massachusetts, USA
| | - Gilles Gay
- UMR CNRS 5557, Unité Sous Contrat INRA 1364, Université de Lyon, Université Lyon 1, Villeurbanne, France
| | - Mariangela Girlanda
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università degli Studi di Torino, Torino, Italy
| | - Bernard Henrissat
- 1] CNRS, UMR 7257, Aix-Marseille Université, Marseille, France. [2] Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, Marseille, France. [3] Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Sylvie Herrmann
- 1] Department of Soil Ecology, Helmholtz Centre for Environmental Research-Helmholtz Zentrum fuer Umweltforschung, Halle, Germany. [2] German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Jaqueline Hess
- Department of Biosciences, University of Oslo, Oslo, Norway
| | - Nils Högberg
- Department of Forest Mycology and Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Tomas Johansson
- Department of Biology, Microbial Ecology Group, Lund University, Lund, Sweden
| | - Hassine-Radhouane Khouja
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università degli Studi di Torino, Torino, Italy
| | - Kurt LaButti
- US Department of Energy Joint Genome Institute (JGI), Walnut Creek, California, USA
| | - Urs Lahrmann
- Department of Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | | | - Erika A Lindquist
- US Department of Energy Joint Genome Institute (JGI), Walnut Creek, California, USA
| | - Anna Lipzen
- US Department of Energy Joint Genome Institute (JGI), Walnut Creek, California, USA
| | - Roland Marmeisse
- UMR CNRS 5557, Unité Sous Contrat INRA 1364, Université de Lyon, Université Lyon 1, Villeurbanne, France
| | - Elena Martino
- 1] Institut National de la Recherche Agronomique (INRA), Laboratory of Excellence Advanced Research on the Biology of Tree and Forest Ecosystems (ARBRE), UMR 1136, Champenoux, France. [2] Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università degli Studi di Torino, Torino, Italy
| | - Claude Murat
- 1] Institut National de la Recherche Agronomique (INRA), Laboratory of Excellence Advanced Research on the Biology of Tree and Forest Ecosystems (ARBRE), UMR 1136, Champenoux, France. [2] University of Lorraine, Laboratory of Excellence ARBRE, UMR 1136, Champenoux, France
| | - Chew Y Ngan
- US Department of Energy Joint Genome Institute (JGI), Walnut Creek, California, USA
| | - Uwe Nehls
- Department of Ecology, Biology/Chemistry, Botany, University of Bremen, Bremen, Germany
| | - Jonathan M Plett
- 1] Institut National de la Recherche Agronomique (INRA), Laboratory of Excellence Advanced Research on the Biology of Tree and Forest Ecosystems (ARBRE), UMR 1136, Champenoux, France. [2] University of Lorraine, Laboratory of Excellence ARBRE, UMR 1136, Champenoux, France
| | - Anne Pringle
- Harvard Forest, Harvard University, Petersham, Massachusetts, USA
| | - Robin A Ohm
- US Department of Energy Joint Genome Institute (JGI), Walnut Creek, California, USA
| | - Silvia Perotto
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università degli Studi di Torino, Torino, Italy
| | - Martina Peter
- Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Forest Dynamics, Birmensdorf, Switzerland
| | - Robert Riley
- US Department of Energy Joint Genome Institute (JGI), Walnut Creek, California, USA
| | - Francois Rineau
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Joske Ruytinx
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Asaf Salamov
- US Department of Energy Joint Genome Institute (JGI), Walnut Creek, California, USA
| | - Firoz Shah
- Department of Biology, Microbial Ecology Group, Lund University, Lund, Sweden
| | - Hui Sun
- US Department of Energy Joint Genome Institute (JGI), Walnut Creek, California, USA
| | - Mika Tarkka
- 1] Department of Soil Ecology, Helmholtz Centre for Environmental Research-Helmholtz Zentrum fuer Umweltforschung, Halle, Germany. [2] German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Andrew Tritt
- US Department of Energy Joint Genome Institute (JGI), Walnut Creek, California, USA
| | - Claire Veneault-Fourrey
- 1] Institut National de la Recherche Agronomique (INRA), Laboratory of Excellence Advanced Research on the Biology of Tree and Forest Ecosystems (ARBRE), UMR 1136, Champenoux, France. [2] University of Lorraine, Laboratory of Excellence ARBRE, UMR 1136, Champenoux, France
| | - Alga Zuccaro
- 1] Department of Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany. [2] University of Cologne, Botanical Institute, Cluster of Excellence on Plant Sciences (CEPLAS), Cologne, Germany
| | - Anders Tunlid
- Department of Biology, Microbial Ecology Group, Lund University, Lund, Sweden
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute (JGI), Walnut Creek, California, USA
| | - David S Hibbett
- Department of Biology, Clark University, Worcester, Massachusetts, USA
| | - Francis Martin
- 1] Institut National de la Recherche Agronomique (INRA), Laboratory of Excellence Advanced Research on the Biology of Tree and Forest Ecosystems (ARBRE), UMR 1136, Champenoux, France. [2] University of Lorraine, Laboratory of Excellence ARBRE, UMR 1136, Champenoux, France
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Ruytinx J, Nguyen H, Van Hees M, Op De Beeck M, Vangronsveld J, Carleer R, Colpaert JV, Adriaensen K. Zinc export results in adaptive zinc tolerance in the ectomycorrhizal basidiomycete Suillus bovinus. Metallomics 2014; 5:1225-33. [PMID: 23715468 DOI: 10.1039/c3mt00061c] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
On Zn-polluted soils, populations of the ectomycorrhizal basidiomycete Suillus bovinus exhibit an elevated Zn tolerance when compared to populations on non-polluted sites. To elucidate the mechanism of Zn tolerance, the time-course of Zn uptake was studied in isolates with contrasting Zn tolerance. Unidirectional fluxes and subcellular compartmentation of Zn were investigated through radiotracer flux analyses. Fluorescence imaging was used to support the subcellular Zn compartmentation. After 2 h of exposure to 200 μM Zn, significantly more Zn was accumulated in Zn-sensitive isolates compared to tolerant isolates, despite similar short-term uptake kinetics and similar extracellular Zn sequestration in cell walls. In Zn-sensitive isolates twice as much Zn accumulated in the cytoplasm and 12 times more Zn in the vacuole. (65)Zn efflux analyses revealed a considerably faster Zn export in the Zn-tolerant isolate. The adaptive Zn tolerance in S. bovinus is therefore achieved by a preferential removal of Zn out of the cytoplasm, back into the apoplast, instead of the usual transfer of Zn into the vacuole. Zn exclusion in the fungal symbiont eventually contributes to a lower Zn influx in host plants.
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Affiliation(s)
- Joske Ruytinx
- Hasselt University, Centre for Environmental Sciences, Environmental Biology Group, Agoralaan, Gebouw D, 3590 Diepenbeek, Belgium
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19
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Ruytinx J, Craciun AR, Verstraelen K, Vangronsveld J, Colpaert JV, Verbruggen N. Transcriptome analysis by cDNA-AFLP of Suillus luteus Cd-tolerant and Cd-sensitive isolates. Mycorrhiza 2011; 21:145-154. [PMID: 20512595 DOI: 10.1007/s00572-010-0318-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2010] [Accepted: 05/10/2010] [Indexed: 05/29/2023]
Abstract
The ectomycorrhizal basidiomycete Suillus luteus (L.:Fr.), a typical pioneer species which associates with young pine trees colonizing disturbed sites, is a common root symbiont found at heavy metal contaminated sites. Three Cd-sensitive and three Cd-tolerant isolates of S. luteus, isolated respectively from non-polluted and a heavy metal-polluted site in Limburg (Belgium), were used for a transcriptomic analysis. We identified differentially expressed genes by cDNA-AFLP analysis. The possible roles of some of the encoded proteins in heavy metal (Cd) accumulation and tolerance are discussed. Despite the high conservation of coding sequences in S. luteus, a large intraspecific variation in the transcript profiles was observed. This variation was as large in Cd-tolerant as in sensitive isolates and may help this pioneer species to adapt to novel environments.
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Affiliation(s)
- Joske Ruytinx
- Centre for Environmental Sciences, Environmental Biology Group, Universiteit Hasselt, 3590 Diepenbeek, Belgium
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20
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Smeets K, Ruytinx J, Van Belleghem F, Semane B, Lin D, Vangronsveld J, Cuypers A. Critical evaluation and statistical validation of a hydroponic culture system for Arabidopsis thaliana. Plant Physiol Biochem 2008; 46:212-218. [PMID: 18024051 DOI: 10.1016/j.plaphy.2007.09.014] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2007] [Indexed: 05/25/2023]
Abstract
Arabidopsis thaliana is one of the most widely used model organisms in plant sciences. Because of the increasing knowledge in the understanding of its molecular pathways, a reproducible and stable growth set-up for obtaining uniform plants becomes more important. In order to be able to easily harvest and study both roots and shoots, and to allow simple exposure to water-soluble toxic substances, a hydroponic system is the desired cultivation method for controlled plant growth. Based on earlier developed hydroponic cultivation protocols, a hydroponic set-up was optimized and statistically validated using linear mixed-effects models. In order to determine important components that influence the level of variability in a hydroponic set-up, stress-related indicators were examined at the biochemical as well as at the molecular level. It is highly recommended that statistical as well as biological assumptions are carried out before post-analyses are performed. Therefore, we suggest a model where factors that influence variability such as the usage of different pots and harvesting on different times are taken into account in the analyses. Furthermore, in contrast to what has been reported in earlier studies, our findings indicate that continuous aeration of the hydroponic solution is highly important.
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Affiliation(s)
- Karen Smeets
- Centre for Environmental Sciences, Hasselt University, Campus Diepenbeek, Agoralaan - Building D, B-3590 Diepenbeek, Belgium.
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21
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Muller LAH, Craciun AR, Ruytinx J, Lambaerts M, Verbruggen N, Vangronsveld J, Colpaert JV. Gene expression profiling of a Zn-tolerant and a Zn-sensitive Suillus luteus isolate exposed to increased external zinc concentrations. Mycorrhiza 2007; 17:571-580. [PMID: 17530303 DOI: 10.1007/s00572-007-0134-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2007] [Accepted: 04/27/2007] [Indexed: 05/15/2023]
Abstract
Complementary DNA (cDNA)-amplified fragment-length polymorphism (AFLP) was applied to analyze transcript profiles of a Zn-tolerant and a Zn-sensitive isolate of the ectomycorrhizal basidiomycete Suillus luteus, both cultured with and without increased external zinc concentrations. From the obtained transcript profiles that covered approximately 2% of the total expected complement of genes in S. luteus, 144 nonredundant, differentially expressed transcript-derived fragments (TDFs), falling in different classes of expression pattern, were isolated and sequenced. Thirty-six of the represented genes showed homology to function-known genes, whereas 6 matched unknown protein coding sequences, and 102 were possibly novel. Although relatively few TDFs were found to be responsive to the different zinc treatments, their modulated expression levels may suggest a different transcriptional response to zinc treatments in both isolates. Among the identified genes that could be related to heavy-metal detoxification or the tolerance trait were genes encoding for homologues of a heat-shock protein, a putative metal transporter, a hydrophobin, and several proteins involved in ubiquitin-dependent proteolysis.
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Affiliation(s)
- L A H Muller
- Environmental Biology Group, Centre for Environmental Sciences, Hasselt University, Agoralaan, Gebouw D, 3590, Diepenbeek, Belgium
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, DUMC Box 3020, Durham, NC, 27710, USA
| | - A R Craciun
- Laboratoire de Physiologie et de Génétique Moléculaire des Plantes, Université Libre de Bruxelles, 1050, Brussels, Belgium
| | - J Ruytinx
- Environmental Biology Group, Centre for Environmental Sciences, Hasselt University, Agoralaan, Gebouw D, 3590, Diepenbeek, Belgium
| | - M Lambaerts
- Environmental Biology Group, Centre for Environmental Sciences, Hasselt University, Agoralaan, Gebouw D, 3590, Diepenbeek, Belgium
| | - N Verbruggen
- Laboratoire de Physiologie et de Génétique Moléculaire des Plantes, Université Libre de Bruxelles, 1050, Brussels, Belgium
| | - J Vangronsveld
- Environmental Biology Group, Centre for Environmental Sciences, Hasselt University, Agoralaan, Gebouw D, 3590, Diepenbeek, Belgium
| | - J V Colpaert
- Environmental Biology Group, Centre for Environmental Sciences, Hasselt University, Agoralaan, Gebouw D, 3590, Diepenbeek, Belgium.
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