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Khan MI, Cheema SA, Anum S, Niazi NK, Azam M, Bashir S, Ashraf I, Qadri R. Phytoremediation of Agricultural Pollutants. CONCEPTS AND STRATEGIES IN PLANT SCIENCES 2020. [DOI: 10.1007/978-3-030-00099-8_2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Burges A, Alkorta I, Epelde L, Garbisu C. From phytoremediation of soil contaminants to phytomanagement of ecosystem services in metal contaminated sites. INTERNATIONAL JOURNAL OF PHYTOREMEDIATION 2018; 20:384-397. [PMID: 28862473 DOI: 10.1080/15226514.2017.1365340] [Citation(s) in RCA: 100] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Since the emergence of phytoremediation, much research has focused on its development for (i) the removal of metals from soil and/or (ii) the reduction of metal bioavailability, mobility, and ecotoxicity in soil. Here, we review the lights and shades of the two main strategies (i.e., phytoextraction and phytostabilization) currently used for the phytoremediation of metal contaminated soils, irrespective of the level of such contamination. Both strategies face limitations to become successful at commercial scale and, then, often generate skepticism regarding their usefulness. Recent innovative approaches and paradigms are gradually establishing these phytoremediation strategies as suitable options for the management of metal contaminated soils. The combination of these phytotechnologies with a sustainable and profitable site use (a strategy called phytomanagement) grants value to the many benefits that can be obtained during the phytoremediation of metal contaminated sites, such as, for instance, the restoration of important ecosystem services, e.g. nutrient cycling, carbon storage, water flow regulation, erosion control, water purification, fertility maintenance, etc.
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Affiliation(s)
- Aritz Burges
- a Department of Conservation of Natural Resources , NEIKER-Tecnalia, Basque Institute of Agricultural Research and Development, Soil Microbial Ecology Group , Derio , Spain
| | - Itziar Alkorta
- b Department of Biochemistry and Molecular Biology , BIOFISIKA Institute (CSIC-UPV/EHU), University of the Basque Country , Bilbao , Spain
| | - Lur Epelde
- a Department of Conservation of Natural Resources , NEIKER-Tecnalia, Basque Institute of Agricultural Research and Development, Soil Microbial Ecology Group , Derio , Spain
| | - Carlos Garbisu
- a Department of Conservation of Natural Resources , NEIKER-Tecnalia, Basque Institute of Agricultural Research and Development, Soil Microbial Ecology Group , Derio , Spain
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Gao H, Zhu Z, Jiang X, Guo J, Song B, Zhang F. Denaturation of dsDNA Induced by Specific Major Groove Binding of Cadmium Ion to Thymine. ACS OMEGA 2017; 2:8490-8494. [PMID: 30023584 PMCID: PMC6044676 DOI: 10.1021/acsomega.7b01377] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 11/16/2017] [Indexed: 06/08/2023]
Abstract
The toxicity of cadmium causes varying degrees of risk to organisms. The underlying mechanism has been conventionally attributed to Cd2+-ion-induced oxidative stress. Here, we propose that the Cd2+ ion directly and stably binds with the thymine specifically in the major groove and causes denaturation of dsDNA. Using molecular dynamics simulations, it was found that the Cd2+ ion preferred to bind to the thymine exposed in the major groove. This then destroyed the hydrogen bonds between adenine and thymine, resulting in a mismatched structure of dsDNA. Our findings are expected to promote the understanding of cadmium-induced direct destruction of genomic stability and may also be helpful for the facilitation of the experimental detection of the binding sites.
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Affiliation(s)
- Haiyang Gao
- Agriculture
Nanocenter, School of Life Science, Inner
Mongolia Agricultural University, 306 Zhaowuda Road, Hohhot 010018, P. R. China
- Terahertz
Technology Innovation Research Institute, Shanghai Key Laboratory
of Modern Optical System, Terahertz Science Cooperative Innovation
Center, University of Shanghai for Science
and Technology, 516 Jungong Road, Shanghai 200093, P. R. China
| | - Zhi Zhu
- Terahertz
Technology Innovation Research Institute, Shanghai Key Laboratory
of Modern Optical System, Terahertz Science Cooperative Innovation
Center, University of Shanghai for Science
and Technology, 516 Jungong Road, Shanghai 200093, P. R. China
| | - Xiankai Jiang
- Terahertz
Technology Innovation Research Institute, Shanghai Key Laboratory
of Modern Optical System, Terahertz Science Cooperative Innovation
Center, University of Shanghai for Science
and Technology, 516 Jungong Road, Shanghai 200093, P. R. China
| | - Jun Guo
- Department
of Biomedical Engineering, School of Basic Medical Sciences, Guangzhou Medical University, Xinzao, Panyu District, Guangzhou 511436, P. R. China
| | - Bo Song
- Terahertz
Technology Innovation Research Institute, Shanghai Key Laboratory
of Modern Optical System, Terahertz Science Cooperative Innovation
Center, University of Shanghai for Science
and Technology, 516 Jungong Road, Shanghai 200093, P. R. China
| | - Feng Zhang
- Agriculture
Nanocenter, School of Life Science, Inner
Mongolia Agricultural University, 306 Zhaowuda Road, Hohhot 010018, P. R. China
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Kidd P, Mench M, Álvarez-López V, Bert V, Dimitriou I, Friesl-Hanl W, Herzig R, Janssen JO, Kolbas A, Müller I, Neu S, Renella G, Ruttens A, Vangronsveld J, Puschenreiter M. Agronomic Practices for Improving Gentle Remediation of Trace Element-Contaminated Soils. INTERNATIONAL JOURNAL OF PHYTOREMEDIATION 2015; 17:1005-1037. [PMID: 25581041 DOI: 10.1080/15226514.2014.1003788] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The last few decades have seen the rise of Gentle soil Remediation Options (GRO), which notably include in situ contaminant stabilization ("inactivation") and plant-based (generally termed "phytoremediation") options. For trace element (TE)-contaminated sites, GRO aim to either decrease their labile pool and/or total content in the soil, thereby reducing related pollutant linkages. Much research has been dedicated to the screening and selection of TE-tolerant plant species and genotypes for application in GRO. However, the number of field trials demonstrating successful GRO remains well below the number of studies carried out at a greenhouse level. The move from greenhouse to field conditions requires incorporating agronomical knowledge into the remediation process and the ecological restoration of ecosystem services. This review summarizes agronomic practices against their demonstrated or potential positive effect on GRO performance, including plant selection, soil management practices, crop rotation, short rotation coppice, intercropping/row cropping, planting methods and plant densities, harvest and fertilization management, pest and weed control and irrigation management. Potentially negative effects of GRO, e.g., the introduction of potentially invasive species, are also discussed. Lessons learnt from long-term European field case sites are given for aiding the choice of appropriate management practices and plant species.
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Affiliation(s)
- Petra Kidd
- a Instituto de Investigaciones Agrobiológicas de Galicia (IIAG) , Consejo Superior de Investigaciones Científicas (CSIC) , Santiago de Compostela , Spain
| | - Michel Mench
- b INRA, UMR BIOGECO, Cestas , France; University of Bordeaux, UMR BIOGECO , Pessac , France , France
| | - Vanessa Álvarez-López
- a Instituto de Investigaciones Agrobiológicas de Galicia (IIAG) , Consejo Superior de Investigaciones Científicas (CSIC) , Santiago de Compostela , Spain
| | - Valérie Bert
- c INERIS, Technologies and Sustainable and Clean Processes , Verneuil en Halatte , France
| | - Ioannis Dimitriou
- d Swedish University of Agriculture Sciences , Department of Crop Production Ecology , Uppsala , Sweden
| | - Wolfgang Friesl-Hanl
- e AIT Austrian Institute of Technology GmbH , Health and Environment Department , Tulln , Austria
| | - Rolf Herzig
- f Phytotech Foundation (PT-F), and AGB-Bioindikation , Umweltbeobachtung und oekologische Planung Quartiergasse , Bern , Switzerland
| | - Jolien Olga Janssen
- g Hasselt University , Centre for Environmental Sciences , Diepenbeek , Belgium
| | - Aliaksandr Kolbas
- b INRA, UMR BIOGECO, Cestas , France; University of Bordeaux, UMR BIOGECO , Pessac , France , France
- h Brest State University named after A.S. Pushkin , Brest , Belarus
| | - Ingo Müller
- i Saxon State Office for Environment , Agriculture and Geology , Dresden , Germany
| | - Silke Neu
- i Saxon State Office for Environment , Agriculture and Geology , Dresden , Germany
| | - Giancarlo Renella
- j University of Florence , Department of Agrifood Production and Environmental Sciences , Florence , Italy
| | - Ann Ruttens
- g Hasselt University , Centre for Environmental Sciences , Diepenbeek , Belgium
| | - Jaco Vangronsveld
- g Hasselt University , Centre for Environmental Sciences , Diepenbeek , Belgium
| | - Markus Puschenreiter
- k University of Natural Resources and Life Sciences Vienna - BOKU , Department of Forest and Soil Sciences , Tulln , Austria
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Cocozza C, Vitullo D, Lima G, Maiuro L, Marchetti M, Tognetti R. Enhancing phytoextraction of Cd by combining poplar (clone "I-214") with Pseudomonas fluorescens and microbial consortia. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2014; 21:1796-1808. [PMID: 23979851 DOI: 10.1007/s11356-013-2073-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Accepted: 08/12/2013] [Indexed: 05/18/2023]
Abstract
The plant-microorganism combinations may contribute to the success of phytoextraction of heavy metal-polluted soil. The purpose of this study was to investigate the effects of cadmium (Cd) soil concentration on selected physiological parameters of the poplar clone "I-214" inoculated at root level with a strain (BT4) of Pseudomonas fluorescens and a commercial product based on microbial consortia (Micosat F Fito®). Plants were subjected to Cd treatment of 40 mg kg(-1) in greenhouse. The effects of plant-microbe interactions, plant growth, leaf physiology, and microbial activity were periodically monitored. Metal concentration and translocation factors in plant tissues proved enhanced Cd uptake in roots of plants inoculated with P. fluorescens and transfer to shoots in plants inoculated with Micosat F Fito®, suggesting a promising strategy for using microbes in support of Cd uptake. Plant-microbe integration increased total removal of Cd, without interfering with plant growth, while improving the photosynthetic capacity. Two major mechanisms of metal phytoextraction inducted by microbial inoculation may be suggested: improved Cd accumulation in roots inoculated with P. fluorescens, implying phytostabilization prospective and high Cd transfer to shoots of inoculated plants, outlining enhanced metal translocation.
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Affiliation(s)
- Claudia Cocozza
- Dipartimento di Bioscienze e Territorio, Università degli Studi del Molise, 86090, Pesche, Italy.
| | - Domenico Vitullo
- Dipartimento Agricoltura, Ambiente e Alimenti, Università degli Studi del Molise, 86100, Campobasso, Italy
| | - Giuseppe Lima
- Dipartimento Agricoltura, Ambiente e Alimenti, Università degli Studi del Molise, 86100, Campobasso, Italy
| | - Lucia Maiuro
- Dipartimento Agricoltura, Ambiente e Alimenti, Università degli Studi del Molise, 86100, Campobasso, Italy
| | - Marco Marchetti
- Dipartimento di Bioscienze e Territorio, Università degli Studi del Molise, 86090, Pesche, Italy
| | - Roberto Tognetti
- Dipartimento di Bioscienze e Territorio, Università degli Studi del Molise, 86090, Pesche, Italy
- The EFI Project Centre on Mountain Forests (MOUNTFOR), Edmund Mach Foundation, 38010, San Michele all'Adige, Italy
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Cicatelli A, Todeschini V, Lingua G, Biondi S, Torrigiani P, Castiglione S. Epigenetic control of heavy metal stress response in mycorrhizal versus non-mycorrhizal poplar plants. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2014; 21:1723-1737. [PMID: 23975714 DOI: 10.1007/s11356-013-2072-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Accepted: 08/12/2013] [Indexed: 06/02/2023]
Abstract
It was previously shown that arbuscular mycorrhizal fungi (AMF) exert a significant improvement of growth in a tolerant white poplar (Populus alba L.) clone (AL35) grown on Cu- and Zn-polluted soil via foliar alterations in the levels of defence/stress-related transcripts and molecules. However, nothing is known about the epigenetic changes which occur during tolerance acquisition in response to heavy metals (HMs) in the same mycorrhizal vs. non-mycorrhizal poplar plants. In order to analyse the epigenome in leaves of AL35 plants inoculated or not with AMF and grown in a greenhouse on multimetal polluted or unpolluted soil, the Methylation Sensitive Amplification Polymorphism (MSAP) approach was adopted to detect cytosine DNA methylation. Modest changes in cytosine methylation patterns were detected at first sampling (4 months from planting), whereas extensive alterations (hypomethylation) occurred at second sampling (after 6 months) in mycorrhizal plants grown in the presence of HMs. The sequencing of MSAP fragments led to the identification of genes belonging to several Gene Ontology categories. Seven MSAP fragments, selected on the basis of DNA methylation status in treated vs control AL35 leaves at the end of the experiment, were analysed for their transcript levels by means of qRT-PCR. Gene expression varied in treated samples relative to controls in response to HMs and/or AMF inoculation; in particular, transcripts of genes involved in RNA processing, cell wall and amino acid metabolism were upregulated in the presence of AMF with or without HMs.
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Affiliation(s)
- Angela Cicatelli
- Dipartimento di Chimica e Biologia, Università di Salerno, 84084, Fisciano, SA, Italy
| | - Valeria Todeschini
- Dipartimento di Scienze e Innovazione Tecnologica, Università del Piemonte Orientale, 15121, Alessandria, Italy
| | - Guido Lingua
- Dipartimento di Scienze e Innovazione Tecnologica, Università del Piemonte Orientale, 15121, Alessandria, Italy
| | - Stefania Biondi
- Dipartimento BiGeA, Università di Bologna, 40126, Bologna, Italy
| | - Patrizia Torrigiani
- Dipartimento di Scienze Agrarie, Università di Bologna, 40127, Bologna, Italy
| | - Stefano Castiglione
- Dipartimento di Chimica e Biologia, Università di Salerno, 84084, Fisciano, SA, Italy.
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Ciurli A, Lenzi L, Alpi A, Pardossi A. Arsenic uptake and translocation by plants in pot and field experiments. INTERNATIONAL JOURNAL OF PHYTOREMEDIATION 2014; 16:804-23. [PMID: 24933886 DOI: 10.1080/15226514.2013.856850] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
A work undertaken by pot and field experiments to assess the suitability of poplars and ferns for the in-situ, phytoextraction, of a dumping site with residues from the roasting process of arseno-pyrite is reported. The main characteristic of this site is the high content of both the As metalloid and heavy metals (e.g., Al, Fe, Cu, Co, Cr, Pb). Two poplar clones (Populus deltoides 'Dvina' and Populus x canadensis 'Orion') and Pteris vittata (Chinese brake fern) were planted in the contaminated soil both ex situ in pots and in situ. Plant survival, As accumulation in plant tissues, leaf content of pigments, soluble proteins, activity of catalase and SH-groups in both roots and leaves were evaluated during a 24-month study period. Both poplar and fern plants exhibited an increase in the activity of catalase and SH group contents when grown in the presence of pyrite ashes. The results showed that the co-planting system (arsenic-hyperaccumulator fern Pteris vittata and Populus clones) was suitable for phytoextraction of multi-contaminated dumping sites. Agronomic measures such as irrigation, soil tillage and amendments also seem to be necessary for the successful establishment of poplar trees and ferns in contaminated soils in order to enhance plant growth through the improvement of soil conditions.
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Marmiroli M, Imperiale D, Maestri E, Marmiroli N. The response of Populus spp. to cadmium stress: chemical, morphological and proteomics study. CHEMOSPHERE 2013; 93:1333-44. [PMID: 23981839 DOI: 10.1016/j.chemosphere.2013.07.065] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Revised: 07/24/2013] [Accepted: 07/27/2013] [Indexed: 05/08/2023]
Abstract
Poplar (Populus) species are seen as candidates for removing heavy metal contamination from polluted soil. A bottom-up multidisciplinary approach was utilized to compare the performances of clones 58-861 and Poli (Populus nigra) and A4A, a Populus nigra × Populus deltoides hybrid to Cd toxicity. Qualitative and quantitative differences in their tolerance to Cd exposure and the uptake, accumulation and translocation of Cd were noted following the hydroponic exposure of rooted cuttings to 20 μM CdSO₄ for either 48 h or 14 d. Cadmium was less toxic for the hybrid clone A4A as compared to Poli and 58-861. Cd uptake and root to shoot translocation were determined by AAS, and its compartmentation was analyzed using SEM/EDX. A comparative proteomic approach was utilized to identify changes in proteins expression according to dose and time of exposure. Toxicity to Cd mainly influenced proteins related to general defense, stress response and carbohydrate metabolism.
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Affiliation(s)
- Marta Marmiroli
- Department of Life Sciences, University of Parma, Parco Area delle Scienze 33/A, 43124 Parma, Italy.
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Wang X, Zou M, Huang H, Ren Y, Li L, Yang X, Li N. Gold nanoparticle enhanced fluorescence anisotropy for the assay of single nucleotide polymorphisms (SNPs) based on toehold-mediated strand-displacement reaction. Biosens Bioelectron 2013; 41:569-75. [DOI: 10.1016/j.bios.2012.09.023] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2012] [Accepted: 09/15/2012] [Indexed: 10/27/2022]
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Tognetti R, Cocozza C, Marchetti M. Shaping the multifunctional tree: the use of Salicaceae in environmental restoration. IFOREST - BIOGEOSCIENCES AND FORESTRY 2013. [PMID: 0 DOI: 10.3832/ifor0920-006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
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He J, Ma C, Ma Y, Li H, Kang J, Liu T, Polle A, Peng C, Luo ZB. Cadmium tolerance in six poplar species. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2013; 20:163-74. [PMID: 22669564 DOI: 10.1007/s11356-012-1008-8] [Citation(s) in RCA: 106] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2012] [Accepted: 05/23/2012] [Indexed: 05/21/2023]
Abstract
Selection of poplar species with greater Cd tolerance and exploiting the physiological mechanisms involved in Cd tolerance are crucial for application of these species to phyto-remediation. The aim of this study is to investigate variation in Cd tolerance among the six poplar species and its underlying physiological mechanisms. Cuttings of six Populus species were cultivated for 10 weeks before exposure to either 0 or 200 μM CdSO(4) for 20 days. Gas exchange in mature leaves was determined by a portable photosynthesis system. Cd concentrations in tissues were analyzed by a flame atomic absorbance spectrometry. Subsequently, Cd amount per plant, bio-concentration factor (BCF) and translocation factor (T (f)) were calculated. Nonenzymatic compounds and activities of antioxidative enzymes in tissues were analyzed spectrophotometrically. Cd exposure caused decline in photosynthesis in four poplar species including Populus cathayana (zhonghua 1). Among the six species, P. cathayana (zhonghua 1) displayed the highest Cd concentrations in tissues, the largest Cd amount in aerial parts, the highest BCF in aerial parts and T (f) under Cd exposure. Under Cd stress, increases in total soluble sugars in roots but decreases in starch in roots, wood, and leaves of P. cathayana (zhonghua 1) were found. Induced O (2) (•-) and H(2)O(2) production in roots and leaves, and increases in free proline, soluble phenolics, and activities of antioxidative enzymes were observed in P. cathayana (zhonghua 1). Based on results of this pot experiment, it is concluded that P. cathayana (zhonghua 1) is superior to other five species for Cd phyto-remediation, and its well-coordinated physiological changes under Cd exposure confer the great Cd tolerance of this species.
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Affiliation(s)
- Jiali He
- College of Life Sciences, Northwest Agriculture & Forestry University, Yangling, Shaanxi 712100, People's Republic of China
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Visioli G, Marmiroli N. The proteomics of heavy metal hyperaccumulation by plants. J Proteomics 2012; 79:133-45. [PMID: 23268120 DOI: 10.1016/j.jprot.2012.12.006] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Revised: 12/06/2012] [Accepted: 12/07/2012] [Indexed: 10/27/2022]
Abstract
Hyperaccumulators are distinguished from non-hyperaccumulators on the basis of their capacity to extract heavy metal ions from the soil, their more efficient root-to-shoot translocation of these ions and their greater ability to detoxify and sequester heavy metals in the shoot. The understanding of the mechanisms underlying metal ion accumulation has progressed beyond the relevant biochemistry and physiology to encompass the genetic and molecular regulatory systems which differentiate hyperaccumulators from non-hyperaccumulators. This paper reviews the literature surrounding the application of proteomics technology to plant metal hyperaccumulation, in particular involving the elements As, Cd, Cu, Ni, Pb and Zn. The hyperaccumulation process across a number of unrelated plant species appears to be associated with proteins involved in energy metabolism, the oxidative stress response and abiotic and biotic stress. The relevance of transducers of the metal stress response to the phenomenon of hyperaccumulation is summarized. Proteomic data complement the more voluminous genomic and transcriptomic data sets in providing a more nuanced picture of the process, and should therefore help in the identification of the major genetic determinants of the hyperaccumulation phenomenon.
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Affiliation(s)
- Giovanna Visioli
- Department of Life Sciences, University of Parma, Parco Area delle Scienze 11/a, 43124, Parma Italy
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Martin F, Bovet L, Cordier A, Stanke M, Gunduz I, Peitsch MC, Ivanov NV. Design of a tobacco exon array with application to investigate the differential cadmium accumulation property in two tobacco varieties. BMC Genomics 2012; 13:674. [PMID: 23190529 PMCID: PMC3602038 DOI: 10.1186/1471-2164-13-674] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2012] [Accepted: 11/23/2012] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND For decades the tobacco plant has served as a model organism in plant biology to answer fundamental biological questions in the areas of plant development, physiology, and genetics. Due to the lack of sufficient coverage of genomic sequences, however, none of the expressed sequence tag (EST)-based chips developed to date cover gene expression from the whole genome. The availability of Tobacco Genome Initiative (TGI) sequences provides a useful resource to build a whole genome exon array, even if the assembled sequences are highly fragmented. Here, the design of a Tobacco Exon Array is reported and an application to improve the understanding of genes regulated by cadmium (Cd) in tobacco is described. RESULTS From the analysis and annotation of the 1,271,256 Nicotiana tabacum fasta and quality files from methyl filtered genomic survey sequences (GSS) obtained from the TGI and ~56,000 ESTs available in public databases, an exon array with 272,342 probesets was designed (four probes per exon) and tested on two selected tobacco varieties.Two tobacco varieties out of 45 accumulating low and high cadmium in leaf were identified based on the GGE biplot analysis, which is analysis of the genotype main effect (G) plus analysis of the genotype by environment interaction (GE) of eight field trials (four fields over two years) showing reproducibility across the trials. The selected varieties were grown under greenhouse conditions in two different soils and subjected to exon array analyses using root and leaf tissues to understand the genetic make-up of the Cd accumulation. CONCLUSIONS An Affymetrix Exon Array was developed to cover a large (~90%) proportion of the tobacco gene space. The Tobacco Exon Array will be available for research use through Affymetrix array catalogue. As a proof of the exon array usability, we have demonstrated that the Tobacco Exon Array is a valuable tool for studying Cd accumulation in tobacco leaves. Data from field and greenhouse experiments supported by gene expression studies strongly suggested that the difference in leaf Cd accumulation between the two specific tobacco cultivars is dependent solely on genetic factors and genetic variability rather than on the environment.
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Affiliation(s)
- Florian Martin
- Philip Morris International R&D, Philip Morris Products SA, Neuchatel, 2000, Switzerland
| | - Lucien Bovet
- Philip Morris International R&D, Philip Morris Products SA, Neuchatel, 2000, Switzerland
| | - Audrey Cordier
- Philip Morris International R&D, Philip Morris Products SA, Neuchatel, 2000, Switzerland
| | - Mario Stanke
- Institut für Mathematik und Informatik, Greifswald, D-17487, Germany
| | - Irfan Gunduz
- Philip Morris International Operations, Neuchatel, 2000, Switzerland
| | - Manuel C Peitsch
- Philip Morris International R&D, Philip Morris Products SA, Neuchatel, 2000, Switzerland
| | - Nikolai V Ivanov
- Philip Morris International R&D, Philip Morris Products SA, Neuchatel, 2000, Switzerland
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Marmiroli M, Pietrini F, Maestri E, Zacchini M, Marmiroli N, Massacci A. Growth, physiological and molecular traits in Salicaceae trees investigated for phytoremediation of heavy metals and organics. TREE PHYSIOLOGY 2011; 31:1319-1334. [PMID: 22052656 DOI: 10.1093/treephys/tpr090] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Worldwide, there are many large areas moderately contaminated with heavy metals and/or organics that have not been remediated due to the high cost and technical drawbacks of currently available technologies. Methods with a good potential for coping with these limitations are emerging from phytoremediation techniques, using, for example, specific amendments and/or plants selected from various candidates proven in several investigations to be reasonably efficient in extracting heavy metals from soil or water, or in co-metabolizing organics with bacteria flourishing or inoculated in their rhizospheres. Populus and Salix spp., two genera belonging to the Salicaceae family, include genotypes that can be considered among the candidates for this phytoremediation approach. This review shows the recent improvements in analytical tools based on the identification of useful genetic diversity associated with classical growth, physiological and biochemical traits, and the importance of plant genotype selection for enhancing phytoremediation efficiency. Particularly interesting are studies on the application of the phytoremediation of heavy metals and of chlorinated organics, in which microorganisms selected for their degradation capabilities were bioaugmented in the rhizosphere of Salicaceae planted at a high density for biomass and bioenergy production.
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Affiliation(s)
- Marta Marmiroli
- Department of Environmental Sciences, Section of Genetic and Environmental Biotechnology, Parco Area delle Scienze 11/A, Parma, Italy.
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