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Jeon Y, Baranwal P, Li L, Piezer K, Seo Y. Review: Current understanding on biological filtration for the removal of microcystins. CHEMOSPHERE 2023; 313:137160. [PMID: 36356807 DOI: 10.1016/j.chemosphere.2022.137160] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 10/10/2022] [Accepted: 10/30/2022] [Indexed: 06/16/2023]
Abstract
Harmful algal blooms (HABs) have become a global problem not only in aquatic habitats but also in public health and safety due to the production of cyanotoxins as their secondary metabolites. Among the various identified cyanotoxin groups, microcystins (MCs) are one of the most prevalent cyanotoxin detected during HABs. Different strategies including advanced physical and chemical treatment processes have been developed to mitigate the threat of cyanotoxins in water utilities, but these have revealed certain limitations in terms of high operational costs, low removal efficacy, and harmful by-products formation. Recently, biological filtration systems (BFS) have gained attention for safe drinking water production as they can treat various natural organic matter (NOM) and emerging contaminants through a highly efficient and environmentally sustainable process. However, limited attention has been given to understand the current research progress, research challenges, and knowledge gaps for the successful implementation of BFS for MC removal. Therefore, in this review, currently identified MC biodegradation pathways and MC-degrading microorganisms with their degradation rates are summarized, which may be pivotal for studying bioaugmented BFS to enhance the MC removal during HABs. Moreover, both laboratory and field studies on BFS for MC removal are reviewed, followed by a discussion of current challenges and future research needs for the practical application of BFS.
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Affiliation(s)
- Youchul Jeon
- Department of Civil and Environmental Engineering, University of Toledo, Mail Stop 307, 3006 Nitschke Hall, Toledo, OH, 43606, United States
| | - Parul Baranwal
- Department of Civil and Environmental Engineering, University of Toledo, Mail Stop 307, 3006 Nitschke Hall, Toledo, OH, 43606, United States
| | - Lei Li
- Department of Civil and Environmental Engineering, University of Toledo, Mail Stop 307, 3006 Nitschke Hall, Toledo, OH, 43606, United States
| | - Kayla Piezer
- Department of Civil and Environmental Engineering, University of Toledo, Mail Stop 307, 3006 Nitschke Hall, Toledo, OH, 43606, United States; Department of Chemical Engineering, University of Toledo, Mail Stop 307, 3048 Nitschke Hall, Toledo, OH, 43606, United States
| | - Youngwoo Seo
- Department of Civil and Environmental Engineering, University of Toledo, Mail Stop 307, 3006 Nitschke Hall, Toledo, OH, 43606, United States; Department of Chemical Engineering, University of Toledo, Mail Stop 307, 3048 Nitschke Hall, Toledo, OH, 43606, United States.
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Lopez Leyva L, Gonzalez E, Solomons NW, Koski KG. Human milk microbiome is shaped by breastfeeding practices. Front Microbiol 2022; 13:885588. [PMID: 36160202 PMCID: PMC9493375 DOI: 10.3389/fmicb.2022.885588] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 08/08/2022] [Indexed: 11/21/2022] Open
Abstract
There is evidence that breastfeeding practices may impact the milk microbiota diversity and differential abundance at the genera level; however, the possibility that distinct feeding practices, such as exclusive (EBF) and non-exclusive breastfeeding (non-EBF), might alter the milk microbiome at the species level has not been explored. This cross-sectional study analyzed the milk microbiome of 64 Mam-Mayan indigenous mothers from San Juan Ostuncalco in Guatemala. Two breastfeeding practices [exclusive (EBF) vs non-exclusive (non-EBF)] were analyzed at two stages of lactation [early (5–46 days post-partum) vs late (109–184 days post-partum)]. EBF was defined as offering only human milk and non-EBF was defined as feeding the infant herbal teas (agüitas) and/or complementary foods while continuing to breastfeed. Results identified four clusters with distinct microbial communities that segregated bacterial species by both breastfeeding practices and stage of lactation. Comparison among these clusters identified several notable patterns. First, during EBF, the microbiome differed by stage of lactation where there was a shift in differential abundance from Actinobacteria and Firmicutes in early to Bacteroidetes and Proteobacteria species in late lactation. Second, a similar comparison between non-EBF mothers by stage of lactation also identified a higher differential abundance of Actinobacteria and Firmicutes species in early lactation, but only Proteobacteria and not Bacteroidetes in late lactation, indicating a further shift in the milk microbial ecosystem with fewer oral bacteria present in late lactation. Third, comparisons between EBF and non-EBF mothers at both early and late lactation showed that mothers who exclusively breastfed had more differentially abundant species in early (11 vs 1) and late (13 vs 2) lactation. Fourth, EBF at early and late lactation had more commensal and lactic acid bacteria, including Lactobacillus gasseri, Granulicatella elegans, Streptococcus mitis, and Streptococcus parasanguinis, compared to those who did not exclusively breastfeed. Collectively, these results show that EBF has more differentially abundant bacteria, including commensal and lactic acid bacteria, and that the addition of agüitas (herbal teas) and/or complementary foods modify the milk microbiome composition by reducing the oral bacteria and introducing more environmentally sourced bacteria to the ecosystem.
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Affiliation(s)
| | - Emmanuel Gonzalez
- Canadian Centre for Computational Genomics (C3G), Department of Human Genetics, McGill University, Montréal, QC, Canada
- Microbiome Research Platform, McGill Interdisciplinary Initiative in Infection and Immunity (MI4), Genome Centre, McGill University, Montreal, QC, Canada
| | - Noel W. Solomons
- Center for Studies of Sensory Impairment, Aging and Metabolism (CeSSIAM), Guatemala City, Guatemala
| | - Kristine G. Koski
- School of Human Nutrition, McGill University, Montreal, QC, Canada
- *Correspondence: Kristine G. Koski,
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Navazas A, Mesa V, Thijs S, Fuente-Maqueda F, Vangronsveld J, Peláez AI, Cuypers A, González A. Bacterial inoculant-assisted phytoremediation affects trace element uptake and metabolite content in Salix atrocinerea. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 820:153088. [PMID: 35063508 DOI: 10.1016/j.scitotenv.2022.153088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 12/23/2021] [Accepted: 01/09/2022] [Indexed: 06/14/2023]
Abstract
Natural plant-associated microorganisms are of critical importance to plant growth and survival in field conditions under toxic concentrations of trace elements (TE) and these plant-microbial processes can be harnessed to enhance phytoremediation. The total bacterial diversity from grey willow (Salix atrocinerea) on a brownfield heavily-polluted with lead (Pb) and arsenic (As) was studied through pyrosequencing. Culturable bacteria were isolated and in vitro tested for plant growth-promotion (PGP) traits, arsenic (As) tolerance and impact on As speciation. Two of the most promising bacterial strains - the root endophyte Pantoea sp. AV62 and the rhizospheric strain Rhodococcus erythropolis AV96 - were inoculated in field to S. atrocinerea. This bioaugmentation resulted in higher As and Pb concentrations in both, roots and leaves of bacterial-inoculated plants as compared to non-inoculated plants. In consequence, bacterial bioaugmentation also affected parameters related to plant growth, oxidative stress, the levels of phytochelatins and phenylpropanoids, together with the differential expression of genes related to these tolerance mechanisms to TE in leaves. This study extends our understanding about plant-bacterial interactions and provides a solid basis for further bioaugmentation studies aiming to improve TE phytoremediation efficiency and predictability in the field.
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Affiliation(s)
- Alejandro Navazas
- Department of Organisms and Systems Biology, Area of Plant Physiology, University of Oviedo, Catedrático Rodrigo Uría s/n, 33006 Oviedo, Spain; Centre for Environmental Sciences, Hasselt University, Agoralaan Building D, B-3590 Diepenbeek, Belgium
| | - Victoria Mesa
- Faculty of Pharmacy, Université de Paris, UMR-S1139, F-75006 Paris, France
| | - Sofie Thijs
- Centre for Environmental Sciences, Hasselt University, Agoralaan Building D, B-3590 Diepenbeek, Belgium
| | | | - Jaco Vangronsveld
- Centre for Environmental Sciences, Hasselt University, Agoralaan Building D, B-3590 Diepenbeek, Belgium; Department of Plant Physiology and Biophysics, Institute of Biological Sciences, Faculty of Biology and Biotechnology, Maria Curie-Skłodowska University, Lublin, Poland
| | - Ana I Peláez
- Area of Microbiology, Department of Functional Biology and Environmental Biogeochemistry and Raw Materials Group, University of Oviedo, Oviedo, Spain; University Institute of Biotechnology of Asturias (IUBA), University of Oviedo, Oviedo, Spain
| | - Ann Cuypers
- Centre for Environmental Sciences, Hasselt University, Agoralaan Building D, B-3590 Diepenbeek, Belgium
| | - Aida González
- Department of Organisms and Systems Biology, Area of Plant Physiology, University of Oviedo, Catedrático Rodrigo Uría s/n, 33006 Oviedo, Spain.
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Samad A, Pelletier G, Séguin A, Degenhardt D, Muench DG, Martineau C. Understanding Willow Transcriptional Response in the Context of Oil Sands Tailings Reclamation. FRONTIERS IN PLANT SCIENCE 2022; 13:857535. [PMID: 35574135 PMCID: PMC9094116 DOI: 10.3389/fpls.2022.857535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 03/02/2022] [Indexed: 06/15/2023]
Abstract
One of the reclamation objectives for treated oil sands tailings (OST) is to establish boreal forest communities that can integrate with the surrounding area. Hence, selection of appropriate soil reclamation cover designs and plant species for revegetation are important aspects of tailings landform reclamation and closure. Research and monitoring of the long term and immediate impacts of capped OST on the growth and survival of native boreal plant species are currently underway. However, plant responses to OST-associated toxicity are not well known at the molecular level. Using RNA sequencing, we examined the effects of three types of OST on the willow transcriptome under different capping strategies. The transcriptomic data showed that some genes respond universally and others in a specific manner to different types of OST. Among the dominant and shared upregulated genes, we found some encoding protein detoxification (PD), Cytochrome P450 (CYPs), glutathione S-transferase regulatory process (GST), UDP-glycosyltransferase (UGT), and ABC transporter and regulatory process associated proteins. Moreover, genes encoding several stress-responsive transcription factors (bZIP, BHLH, ERF, MYB, NAC, WRKY) were upregulated with OST-exposure, while high numbers of transcripts related to photosynthetic activity and chloroplast structure and function were downregulated. Overall, the expression of 40 genes was found consistent across all tailings types and capping strategies. The qPCR analysis of a subset of these shared genes suggested that they could reliably distinguish plants exposed to different OST associated stress. Our results indicated that it is possible to develop OST stress exposure biosensors merely based on changes in the level of expression of a relatively small set of genes. The outcomes of this study will further guide optimization of OST capping and revegetation technology by using knowledge based plant stress adaptation strategies.
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Affiliation(s)
- Abdul Samad
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec City, QC, Canada
| | - Gervais Pelletier
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec City, QC, Canada
| | - Armand Séguin
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec City, QC, Canada
| | - Dani Degenhardt
- Natural Resources Canada, Canadian Forest Service, Northern Forestry Centre, Edmonton, AB, Canada
| | - Douglas G. Muench
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Christine Martineau
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec City, QC, Canada
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Rodríguez-Calcerrada J, Rodrigues AM, António C, Perdiguero P, Pita P, Collada C, Li M, Gil L. Stem metabolism under drought stress - a paradox of increasing respiratory substrates and decreasing respiratory rates. PHYSIOLOGIA PLANTARUM 2021; 172:391-404. [PMID: 32671841 DOI: 10.1111/ppl.13145] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 05/25/2020] [Accepted: 05/28/2020] [Indexed: 06/11/2023]
Abstract
Metabolic changes underpinning drought-induced variations in stem respiration (Rs ) are unknown. We measured Rs rates and metabolite and gene expression profiles in Ulmus minor Mill. and Quercus ilex L. seedlings subjected to increasing levels of drought stress to better understand how carbon, nitrogen and energy metabolism interact during drought. In both species, only plants showing extreme stress symptoms - i.e. negligible rates of leaf stomatal conductance and photosynthesis, and high stem dehydration (30-50% of maximum water storage) and contraction (50-150 μm week-1 ) - exhibited lower Rs rates than well-watered plants. Abundance of low-molecular weight sugars (e.g. glucose and fructose) and sugar alcohols (e.g. mannitol) increased with drought, at more moderate stress and to a higher extent in Q. ilex than U. minor. Abundance of amino acids increased at more severe stress, more abruptly, and to a higher extent in U. minor, coinciding with leaf senescence, which did not occur in Q. ilex. Organic acids changed less in response to drought: threonate and glycerate increased, and citrate decreased although slightly in both species. Transcripts of genes coding for enzymes of the Krebs cycle decreased in Q. ilex and increased in U. minor in conditions of extreme drought stress. The maintenance of Rs under severe growth and photosynthetic restrictions reveals the importance of stem mitochondrial activity in drought acclimation. The eventual decline in Rs diverts carbon substrates from entering the Krebs cycle that may help to cope with osmotic and oxidative stress during severe drought and to recover hydraulic functionality afterwards.
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Affiliation(s)
- Jesús Rodríguez-Calcerrada
- Grupo de Investigación Sistemas Naturales e Historia Forestal, Universidad Politécnica de Madrid, Madrid, 28040, Spain
| | - Ana M Rodrigues
- Plant Metabolomics Laboratory, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Oeiras, 2780-157, Portugal
| | - Carla António
- Plant Metabolomics Laboratory, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Oeiras, 2780-157, Portugal
| | - Pedro Perdiguero
- Animal Health Research Center, National Institute for Agriculture and Food Research and Technology (CISA-INIA), Valdeolmos, Madrid, 28130, Spain
| | - Pilar Pita
- Grupo de Investigación Sistemas Naturales e Historia Forestal, Universidad Politécnica de Madrid, Madrid, 28040, Spain
| | - Carmen Collada
- Grupo de Investigación Sistemas Naturales e Historia Forestal, Universidad Politécnica de Madrid, Madrid, 28040, Spain
| | - Meng Li
- Grupo de Investigación Sistemas Naturales e Historia Forestal, Universidad Politécnica de Madrid, Madrid, 28040, Spain
| | - Luis Gil
- Grupo de Investigación Sistemas Naturales e Historia Forestal, Universidad Politécnica de Madrid, Madrid, 28040, Spain
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Navazas A, Thijs S, Feito I, Vangronsveld J, Peláez AI, Cuypers A, González A. Arsenate-reducing bacteria affect As accumulation and tolerance in Salix atrocinerea. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 769:144648. [PMID: 33736260 DOI: 10.1016/j.scitotenv.2020.144648] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 12/18/2020] [Accepted: 12/18/2020] [Indexed: 06/12/2023]
Abstract
Arsenic (As)-reducing bacteria are able to influence As-speciation and, in this way, change As bio-availability. In consequence, this has an impact on As uptake by plants growing on polluted soil and on the effectiveness of the phytoremediation process. To be able to efficiently utilize these bacteria for As-phytoremediation in the field, a better understanding of the plant-bacterial interactions involved in As-tolerance or toxicity is needed. In this work, seedlings of a clone of Salix atrocinerea derived from a specimen naturally growing on an As-polluted brownfield were grown under gnotobiotic conditions exposed to As, and in the presence or absence of two of its field-associated and in vitro characterized plant growth-promoting (PGP) bacteria. The inoculation with Pantoea sp., induced a moderate reduction of AsV to AsIII in the exposure medium that, together with a coordinated plant response of As uptake, chelation and sequestration, increased As accumulation in roots; which is reflected into a higher phytostabilization. However, inoculation with Rhodococcus erythropolis due to a higher disproportionate reduction of AsV to AsIII in the medium caused less As accumulation in roots that non-bioaugmented plants and despite the lower As content, the concentrations of AsIII present in the medium and the damage suffered in roots and leaves, indicated that As tolerance mechanisms (such as prevention of AsIII uptake and efflux) did not occur in time to avoid physical disturbance and plants growth reduction. Interestingly, by two different metabolic pathways -coordinated by different key transporters mediating As uptake, tolerance, distribution and vacuolar accumulation at the roots- both bacteria limited As accumulation in Salix shoots. Our results provide for the first time a detailed insight in the plant-bacterial responses and physiological changes contributing to As tolerance in S. atrocinerea, that will facilitate the design of effective strategies for exploitation of plant-associated microorganisms for phytoremediation.
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Affiliation(s)
- Alejandro Navazas
- Department of Organisms and Systems Biology, Area of Plant Physiology-IUBA, University of Oviedo, Catedrático Rodrigo Uría s/n, 33006 Oviedo, Spain; Centre for Environmental Sciences, Hasselt University, Agoralaan Building D, 3590 Diepenbeek, Belgium
| | - Sofie Thijs
- Centre for Environmental Sciences, Hasselt University, Agoralaan Building D, 3590 Diepenbeek, Belgium
| | - Isabel Feito
- Agri-Food Research and Development Service, Forestry Program, La Mata s/n, 33825 Grado, Spain
| | - Jaco Vangronsveld
- Centre for Environmental Sciences, Hasselt University, Agoralaan Building D, 3590 Diepenbeek, Belgium; Department of Plant Physiology, Faculty of Biology and Biotechnology, Maria Curie-Skłodowska University, Lublin, Poland
| | - Ana I Peláez
- Department of Functional Biology - Area of Microbiology-IUBA, University of Oviedo, Oviedo, Spain
| | - Ann Cuypers
- Centre for Environmental Sciences, Hasselt University, Agoralaan Building D, 3590 Diepenbeek, Belgium
| | - Aida González
- Department of Organisms and Systems Biology, Area of Plant Physiology-IUBA, University of Oviedo, Catedrático Rodrigo Uría s/n, 33006 Oviedo, Spain.
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7
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Lopez Leyva L, Gonzalez E, Li C, Ajeeb T, Solomons NW, Agellon LB, Scott ME, Koski KG. Human Milk Microbiota in an Indigenous Population Is Associated with Maternal Factors, Stage of Lactation, and Breastfeeding Practices. Curr Dev Nutr 2021; 5:nzab013. [PMID: 33898919 PMCID: PMC8053399 DOI: 10.1093/cdn/nzab013] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 01/29/2021] [Accepted: 02/17/2021] [Indexed: 01/30/2023] Open
Abstract
BACKGROUND Human milk contains a diverse community of bacteria that are modified by maternal factors, but whether these or other factors are similar in developing countries has not been explored. Our objective was to determine whether the milk microbiota was modified by maternal age, BMI, parity, lactation stage, subclinical mastitis (SCM), and breastfeeding practices in the first 6 mo of lactation in an indigenous population from Guatemala. METHODS For this cross-sectional study, Mam-Mayan indigenous mothers nursing infants aged <6 mo were recruited. Unilateral human milk samples were collected (n = 86) and processed for 16S rRNA sequencing at the genus level. Microbial diversity and relative abundance were compared with maternal factors [age, BMI, parity, stage of lactation, SCM, and 3 breastfeeding practices (exclusive, predominant, mixed)] obtained through questionnaires. RESULTS Streptococcus was the most abundant genus (33.8%), followed by Pseudomonas (18.7%) and Sphingobium (10.7%) but relative abundance was associated with maternal factors. First, Lactobacillus and Streptococcus were more abundant in early lactation whereas the common oral (Leptotrichia) and environmental (Comamonas) bacteria were more abundant in established lactation. Second, Streptococcus,Lactobacillus,Lactococcus,Leuconostoc, and Micrococcus had a higher abundance in multiparous mothers compared with primiparous mothers. Third, a more diverse microbiota characterized by a higher abundance of lactic acid bacteria (Lactobacillus,Leuconostoc, and Lactococcus), Leucobacter, and Micrococcus was found in mothers with a healthy BMI. Finally, distinct microbial communities differed by stage of lactation and by exclusive, predominant, or mixed breastfeeding practices. CONCLUSION Milk bacterial communities in an indigenous community were associated with maternal factors. Higher microbial diversity was supported by having a healthy BMI, the absence of SCM, and by breastfeeding. Interestingly, breastfeeding practices when assessed by lactation stage were associated with distinct microbiota profiles.
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Affiliation(s)
- Lilian Lopez Leyva
- School of Human Nutrition, McGill University, Ste-Anne-de-Bellevue, QC, Canada
| | - Emmanuel Gonzalez
- Canadian Centre for Computational Genomics (C3G), Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, Montréal, QC, Canada
- Microbiome Research Platform, McGill Interdisciplinary Initiative in Infection and Immunity (MI4), Genome Centre, McGill University, Montréal, QC, Canada
| | - Chen Li
- School of Human Nutrition, McGill University, Ste-Anne-de-Bellevue, QC, Canada
| | - Tamara Ajeeb
- School of Human Nutrition, McGill University, Ste-Anne-de-Bellevue, QC, Canada
| | - Noel W Solomons
- Center for Studies of Sensory Impairment, Aging and Metabolism (CeSSIAM), Guatemala City, Guatemala
| | - Luis B Agellon
- School of Human Nutrition, McGill University, Ste-Anne-de-Bellevue, QC, Canada
| | - Marilyn E Scott
- Institute of Parasitology, McGill University, Ste-Anne-de-Bellevue, QC, Canada
| | - Kristine G Koski
- School of Human Nutrition, McGill University, Ste-Anne-de-Bellevue, QC, Canada
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Shaheen S, Ahmad R, Mahmood Q, Pervez A, Maroof Shah M, Hafeez F. Gene expression and biochemical response of giant reed under Ni and Cu stress. INTERNATIONAL JOURNAL OF PHYTOREMEDIATION 2019; 21:1474-1485. [PMID: 31264465 DOI: 10.1080/15226514.2019.1633269] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Giant reed (Arundo donax) has proved to be effective in detoxification, accumulation and tolerance of toxic metals. The present study explored the stress response of giant reed against Cu and Ni stress. The effect of metal stress was studied on dry weight, chlorophyll pigments antioxidant enzymes production and selected genes expression. The accumulation of heavy metals increased in a concentration-dependent manner and depicted toxicity symptoms in leaves beyond 75 mg/L of Cu or Ni. Oxidative stress was evident in giant reed under highest exposure of Ni and Cu which increased antioxidants activities (SOD, POD and CAT). It was observed that metal transport and detoxification were possible due to the expression of glutathione reductase, Natural Resistance-Associated Macrophage Protein (NRAMP) and Yellow Stripe-Like (YSL) genes. These insights into the genetic basis of a successful remediating plant species will be useful in understanding heavy metals tolerance in giant reed.
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Affiliation(s)
- Shahida Shaheen
- Department of Environmental Sciences, COMSATS University Islamabad, Abbottabad Campus, Pakistan
| | - Rafiq Ahmad
- Department of Environmental Sciences, COMSATS University Islamabad, Abbottabad Campus, Pakistan
| | - Qaisar Mahmood
- Department of Environmental Sciences, COMSATS University Islamabad, Abbottabad Campus, Pakistan
| | - Arshid Pervez
- Department of Environmental Sciences, COMSATS University Islamabad, Abbottabad Campus, Pakistan
| | - Mohammad Maroof Shah
- Department of Environmental Sciences, COMSATS University Islamabad, Abbottabad Campus, Pakistan
| | - Farhan Hafeez
- Department of Environmental Sciences, COMSATS University Islamabad, Abbottabad Campus, Pakistan
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Gonzalez E, Pitre FE, Brereton NJB. ANCHOR: a 16S rRNA gene amplicon pipeline for microbial analysis of multiple environmental samples. Environ Microbiol 2019; 21:2440-2468. [PMID: 30990927 PMCID: PMC6851558 DOI: 10.1111/1462-2920.14632] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 04/07/2019] [Accepted: 04/15/2019] [Indexed: 01/04/2023]
Abstract
Analysis of 16S ribosomal RNA (rRNA) gene amplification data for microbial barcoding can be inaccurate across complex environmental samples. A method, ANCHOR, is presented and designed for improved species‐level microbial identification using paired‐end sequences directly, multiple high‐complexity samples and multiple reference databases. A standard operating procedure (SOP) is reported alongside benchmarking against artificial, single sample and replicated mock data sets. The method is then directly tested using a real‐world data set from surface swabs of the International Space Station (ISS). Simple mock community analysis identified 100% of the expected species and 99% of expected gene copy variants (100% identical). A replicated mock community revealed similar or better numbers of expected species than MetaAmp, DADA2, Mothur and QIIME1. Analysis of the ISS microbiome identified 714 putative unique species/strains and differential abundance analysis distinguished significant differences between the Destiny module (U.S. laboratory) and Harmony module (sleeping quarters). Harmony was remarkably dominated by human gastrointestinal tract bacteria, similar to enclosed environments on earth; however, Destiny module bacteria also derived from nonhuman microbiome carriers present on the ISS, the laboratory's research animals. ANCHOR can help substantially improve sequence resolution of 16S rRNA gene amplification data within biologically replicated environmental experiments and integrated multidatabase annotation enhances interpretation of complex, nonreference microbiomes.
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Affiliation(s)
- Emmanuel Gonzalez
- Canadian Centre for Computational Genomics, McGill University and Genome Quebec Innovation Centre, Montréal, QC, H3A 0G1, Canada.,Department of Human Genetics, McGill University, Montreal, H3A 1B1, Canada
| | - Frederic E Pitre
- Institut de Recherche en Biologie Végétale, University of Montreal, Montreal, QC, H1X 2B2, Canada.,Montreal Botanical Garden, Montreal, QC, H1X 2B2, Canada
| | - Nicholas J B Brereton
- Institut de Recherche en Biologie Végétale, University of Montreal, Montreal, QC, H1X 2B2, Canada
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10
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Cevher-Keskin B, Selçukcan-Erol Ç, Yüksel B, Ertekin Ö, Yıldızhan Y, Onarıcı S, Kulen O, Memon AR. Comparative transcriptome analysis of Zea mays in response to petroleum hydrocarbon stress. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:32660-32674. [PMID: 30242659 DOI: 10.1007/s11356-018-3078-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 08/27/2018] [Indexed: 06/08/2023]
Abstract
The use of plants for the improvement of soils contaminated with hydrocarbons has been a primary research focus in phytoremediation studies. Obtaining insights regarding genes that are differentially induced by petroleum hydrocarbon stress and understanding plant response mechanisms against petroleum hydrocarbons at molecular level is essential for developing better phytoremediation strategies to remove these hazardous contaminants. The purpose of this study was to analyze the transcriptomal profile changes under hydrocarbon stress in maize plants and identify the genes associated with the phytoremediative capacity. Zea mays GeneChips were used to analyze the global transcriptome profiles of maize treated with different concentrations of petroleum hydrocarbons. In total, 883, 1281, and 2162 genes were differentially induced or suppressed in the comparisons of 0 (control) vs. 1% crude petroleum, 1 vs. 5% crude petroleum, and 0 vs. 5% crude petroleum, respectively. The differentially expressed genes were functionally associated with the osmotic stress response mechanism, likely preventing the uptake of water from the roots, and the phytoremediative capacity of plants, e.g., secretory pathway genes. The results presented here show the regulatory mechanisms in the response to petroleum hydrocarbon pollution in soil. Our study provides global gene expression data of Z. mays in response to petroleum hydrocarbon stress that could be useful for further studies investigating the biodegradation mechanism in maize and other plants.
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Affiliation(s)
- Birsen Cevher-Keskin
- Marmara Research Center, Genetic Engineering and Biotechnology Institute, Plant Molecular Biology & Genetics Laboratory, The Scientific and Technological Research Council of Turkey (TUBITAK) , P O Box, 21, 41470, Gebze, Kocaeli, Turkey.
| | - Çiğdem Selçukcan-Erol
- Faculty of Science, Department of Informatics, Istanbul University, Beyazıt/Fatih, Istanbul, Turkey
| | - Bayram Yüksel
- Marmara Research Center, Genetic Engineering and Biotechnology Institute, Plant Molecular Biology & Genetics Laboratory, The Scientific and Technological Research Council of Turkey (TUBITAK) , P O Box, 21, 41470, Gebze, Kocaeli, Turkey
| | - Özlem Ertekin
- Marmara Research Center, Genetic Engineering and Biotechnology Institute, Plant Molecular Biology & Genetics Laboratory, The Scientific and Technological Research Council of Turkey (TUBITAK) , P O Box, 21, 41470, Gebze, Kocaeli, Turkey
| | - Yasemin Yıldızhan
- Marmara Research Center, Genetic Engineering and Biotechnology Institute, Plant Molecular Biology & Genetics Laboratory, The Scientific and Technological Research Council of Turkey (TUBITAK) , P O Box, 21, 41470, Gebze, Kocaeli, Turkey
| | - Selma Onarıcı
- Marmara Research Center, Genetic Engineering and Biotechnology Institute, Plant Molecular Biology & Genetics Laboratory, The Scientific and Technological Research Council of Turkey (TUBITAK) , P O Box, 21, 41470, Gebze, Kocaeli, Turkey
| | - Oktay Kulen
- Marmara Research Center, Genetic Engineering and Biotechnology Institute, Plant Molecular Biology & Genetics Laboratory, The Scientific and Technological Research Council of Turkey (TUBITAK) , P O Box, 21, 41470, Gebze, Kocaeli, Turkey
| | - Abdul Razaque Memon
- Faculty of Science and Arts, Department of Molecular Biology and Genetics, Uşak University, Bir Eylul Kampus, 64200, Uşak, Turkey
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11
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Gonzalez E, Pitre FE, Pagé AP, Marleau J, Guidi Nissim W, St-Arnaud M, Labrecque M, Joly S, Yergeau E, Brereton NJB. Trees, fungi and bacteria: tripartite metatranscriptomics of a root microbiome responding to soil contamination. MICROBIOME 2018; 6:53. [PMID: 29562928 PMCID: PMC5863371 DOI: 10.1186/s40168-018-0432-5] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 03/02/2018] [Indexed: 05/05/2023]
Abstract
BACKGROUND One method for rejuvenating land polluted with anthropogenic contaminants is through phytoremediation, the reclamation of land through the cultivation of specific crops. The capacity for phytoremediation crops, such as Salix spp., to tolerate and even flourish in contaminated soils relies on a highly complex and predominantly cryptic interacting community of microbial life. METHODS Here, Illumina HiSeq 2500 sequencing and de novo transcriptome assembly were used to observe gene expression in washed Salix purpurea cv. 'Fish Creek' roots from trees pot grown in petroleum hydrocarbon-contaminated or non-contaminated soil. All 189,849 assembled contigs were annotated without a priori assumption as to sequence origin and differential expression was assessed. RESULTS The 839 contigs differentially expressed (DE) and annotated from S. purpurea revealed substantial increases in transcripts encoding abiotic stress response equipment, such as glutathione S-transferases, in roots of contaminated trees as well as the hallmarks of fungal interaction, such as SWEET2 (Sugars Will Eventually Be Exported Transporter). A total of 8252 DE transcripts were fungal in origin, with contamination conditions resulting in a community shift from Ascomycota to Basidiomycota genera. In response to contamination, 1745 Basidiomycota transcripts increased in abundance (the majority uniquely expressed in contaminated soil) including major monosaccharide transporter MST1, primary cell wall and lamella CAZy enzymes, and an ectomycorrhiza-upregulated exo-β-1,3-glucanase (GH5). Additionally, 639 DE polycistronic transcripts from an uncharacterised Enterobacteriaceae species were uniformly in higher abundance in contamination conditions and comprised a wide spectrum of genes cryptic under laboratory conditions but considered putatively involved in eukaryotic interaction, biofilm formation and dioxygenase hydrocarbon degradation. CONCLUSIONS Fungal gene expression, representing the majority of contigs assembled, suggests out-competition of white rot Ascomycota genera (dominated by Pyronema), a sometimes ectomycorrhizal (ECM) Ascomycota (Tuber) and ECM Basidiomycota (Hebeloma) by a poorly characterised putative ECM Basidiomycota due to contamination. Root and fungal expression involved transcripts encoding carbohydrate/amino acid (C/N) dialogue whereas bacterial gene expression included the apparatus necessary for biofilm interaction and direct reduction of contamination stress, a potential bacterial currency for a role in tripartite mutualism. Unmistakable within the metatranscriptome is the degree to which the landscape of rhizospheric biology, particularly the important but predominantly uncharacterised fungal genetics, is yet to be discovered.
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Affiliation(s)
- E Gonzalez
- Canadian Center for Computational Genomics, McGill University and Genome Quebec Innovation Center, Montréal, H3A 1A4, Canada
- Department of Human Genetics, McGill University, Montreal, H3A 1B1, Canada
| | - F E Pitre
- Institut de recherche en biologie végétale, University of Montreal, Montreal, QC, H1X 2B2, Canada
- Montreal Botanical Garden, Montreal, QC, H1X 2B2, Canada
| | - A P Pagé
- Aquatic and Crop Resource Development (ACRD), National Research Council Canada, Montréal, QC, H4P 2R2, Canada
| | - J Marleau
- Institut de recherche en biologie végétale, University of Montreal, Montreal, QC, H1X 2B2, Canada
| | - W Guidi Nissim
- Department of Agri-food and Environmental Science, University of Florence, Viale delle Idee, Sesto Fiorentino, FI, Italy
| | - M St-Arnaud
- Institut de recherche en biologie végétale, University of Montreal, Montreal, QC, H1X 2B2, Canada
- Montreal Botanical Garden, Montreal, QC, H1X 2B2, Canada
| | - M Labrecque
- Institut de recherche en biologie végétale, University of Montreal, Montreal, QC, H1X 2B2, Canada
- Montreal Botanical Garden, Montreal, QC, H1X 2B2, Canada
| | - S Joly
- Institut de recherche en biologie végétale, University of Montreal, Montreal, QC, H1X 2B2, Canada
- Montreal Botanical Garden, Montreal, QC, H1X 2B2, Canada
| | - E Yergeau
- Institut National de la Recherche Scientifique, Centre INRS-Institut Armand-Frappier, Laval, QC, Canada
| | - N J B Brereton
- Institut de recherche en biologie végétale, University of Montreal, Montreal, QC, H1X 2B2, Canada.
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12
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Yergeau E, Tremblay J, Joly S, Labrecque M, Maynard C, Pitre FE, St-Arnaud M, Greer CW. Soil contamination alters the willow root and rhizosphere metatranscriptome and the root-rhizosphere interactome. THE ISME JOURNAL 2018; 12:869-884. [PMID: 29330533 PMCID: PMC5864237 DOI: 10.1038/s41396-017-0018-4] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Revised: 10/10/2017] [Accepted: 11/03/2017] [Indexed: 11/09/2022]
Abstract
Phytoremediation using willows is thought to be a sustainable alternative to traditional remediation techniques involving excavation, transport, and landfilling. However, the complexity of the interaction between the willow and its associated highly diverse microbial communities makes the optimization of phytoremediation very difficult. Here, we have sequenced the rhizosphere metatranscriptome of four willow species and the plant root metatranscriptome for two willow species growing in petroleum hydrocarbon-contaminated and non-contaminated soils on a former petroleum refinery site. Significant differences in the abundance of transcripts related to different bacterial and fungal taxa were observed between willow species, mostly in contaminated soils. When comparing transcript abundance in contaminated vs. non-contaminated soil for each willow species individually, transcripts for many microbial taxa and functions were significantly more abundant in contaminated rhizosphere soil for Salix eriocephala, S. miyabeana and S. purpurea, in contrast to what was observed in the rhizosphere of S. caprea. This agrees with the previously reported sensitivity of S. caprea to contamination, and the superior tolerance of S. miyabeana and S. purpurea to soil contamination at that site. The root metatranscriptomes of two species were compared and revealed that plants transcripts are mainly influenced by willow species, while microbial transcripts mainly responded to contamination. A comparison of the rhizosphere and root metatranscriptomes in the S. purpurea species revealed a complete reorganization of the linkages between root and rhizosphere pathways when comparing willows growing in contaminated and non-contaminated soils, mainly because of large shifts in the rhizosphere metatranscriptome.
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Affiliation(s)
- Etienne Yergeau
- Centre INRS-Institut Armand-Frappier, Institut National de la Recherche Scientifique, Université du Québec, Laval, QC, Canada.
| | - Julien Tremblay
- National Research Council Canada, Energy, Mining and Environment, Montréal, QC, Canada
| | - Simon Joly
- Institut de recherche en biologie végétale, Jardin botanique de Montréal et Université de Montréal, Montréal, QC, Canada
| | - Michel Labrecque
- Institut de recherche en biologie végétale, Jardin botanique de Montréal et Université de Montréal, Montréal, QC, Canada
| | - Christine Maynard
- National Research Council Canada, Energy, Mining and Environment, Montréal, QC, Canada
| | - Frederic E Pitre
- Institut de recherche en biologie végétale, Jardin botanique de Montréal et Université de Montréal, Montréal, QC, Canada
| | - Marc St-Arnaud
- Institut de recherche en biologie végétale, Jardin botanique de Montréal et Université de Montréal, Montréal, QC, Canada
| | - Charles W Greer
- National Research Council Canada, Energy, Mining and Environment, Montréal, QC, Canada
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Yanitch A, Brereton NJB, Gonzalez E, Labrecque M, Joly S, Pitre FE. Transcriptomic Response of Purple Willow ( Salix purpurea) to Arsenic Stress. FRONTIERS IN PLANT SCIENCE 2017; 8:1115. [PMID: 28702037 PMCID: PMC5487440 DOI: 10.3389/fpls.2017.01115] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 06/09/2017] [Indexed: 05/25/2023]
Abstract
Arsenic (As) is a toxic element for plants and one of the most common anthropogenic pollutants found at contaminated sites. Despite its severe effects on plant metabolism, several species can accumulate substantial amounts of arsenic and endure the associated stress. However, the genetic mechanisms involved in arsenic tolerance remains obscure in many model plant species used for land decontamination (phytoremediation), including willows. The present study assesses the potential of Salix purpurea cv. 'Fish Creek' for arsenic phytoextraction and reveals the genetic responses behind arsenic tolerance, phytoextraction and metabolism. Four weeks of hydroponic exposure to 0, 5, 30 and 100 mg/L revealed that plants were able to tolerate up to 5 mg/L arsenic. Concentrations of 0 and 5 mg/L of arsenic treatment were then used to compare alterations in gene expression of roots, stems and leaves using RNA sequencing. Differential gene expression revealed transcripts encoding proteins putatively involved in entry of arsenic into the roots, storage in vacuoles and potential transport through the plant as well as primary and secondary (indirect) toxicity tolerance mechanisms. A major role for tannin as a compound used to relieve cellular toxicity is implicated as well as unexpected expression of the cadmium transporter CAX2, providing a potential means for internal arsenic mobility. These insights into the underpinning genetics of a successful phytoremediating species present novel opportunities for selection of dedicated arsenic tolerant crops as well as the potential to integrate such tolerances into a wider Salix ideotype alongside traits including biomass yield, biomass quality, low agricultural inputs and phytochemical production.
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Affiliation(s)
- Aymeric Yanitch
- Institut de Recherche en Biologie Végétale, University of MontrealMontréal, QC, Canada
| | | | - Emmanuel Gonzalez
- Canadian Centre for Computational Genomics, C3G Montreal Node, McGill University and Genome Quebec Innovation CentreMontréal, QC, Canada
| | - Michel Labrecque
- Institut de Recherche en Biologie Végétale, University of MontrealMontréal, QC, Canada
- Montreal Botanical GardenMontréal, QC, Canada
| | - Simon Joly
- Institut de Recherche en Biologie Végétale, University of MontrealMontréal, QC, Canada
- Montreal Botanical GardenMontréal, QC, Canada
| | - Frederic E. Pitre
- Institut de Recherche en Biologie Végétale, University of MontrealMontréal, QC, Canada
- Montreal Botanical GardenMontréal, QC, Canada
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Aydin S, Karaçay HA, Shahi A, Gökçe S, Ince B, Ince O. Aerobic and anaerobic fungal metabolism and Omics insights for increasing polycyclic aromatic hydrocarbons biodegradation. FUNGAL BIOL REV 2017. [DOI: 10.1016/j.fbr.2016.12.001] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Brereton NJB, Gonzalez E, Marleau J, Nissim WG, Labrecque M, Joly S, Pitre FE. Comparative Transcriptomic Approaches Exploring Contamination Stress Tolerance in Salix sp. Reveal the Importance for a Metaorganismal de Novo Assembly Approach for Nonmodel Plants. PLANT PHYSIOLOGY 2016; 171:3-24. [PMID: 27002060 PMCID: PMC4854704 DOI: 10.1104/pp.16.00090] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 03/20/2016] [Indexed: 05/09/2023]
Abstract
Metatranscriptomic study of nonmodel organisms requires strategies that retain the highly resolved genetic information generated from model organisms while allowing for identification of the unexpected. A real-world biological application of phytoremediation, the field growth of 10 Salix cultivars on polluted soils, was used as an exemplar nonmodel and multifaceted crop response well-disposed to the study of gene expression. Sequence reads were assembled de novo to create 10 independent transcriptomes, a global transcriptome, and were mapped against the Salix purpurea 94006 reference genome. Annotation of assembled contigs was performed without a priori assumption of the originating organism. Global transcriptome construction from 3.03 billion paired-end reads revealed 606,880 unique contigs annotated from 1588 species, often common in all 10 cultivars. Comparisons between transcriptomic and metatranscriptomic methodologies provide clear evidence that nonnative RNA can mistakenly map to reference genomes, especially to conserved regions of common housekeeping genes, such as actin, α/β-tubulin, and elongation factor 1-α. In Salix, Rubisco activase transcripts were down-regulated in contaminated trees across all 10 cultivars, whereas thiamine thizole synthase and CP12, a Calvin Cycle master regulator, were uniformly up-regulated. De novo assembly approaches, with unconstrained annotation, can improve data quality; care should be taken when exploring such plant genetics to reduce de facto data exclusion by mapping to a single reference genome alone. Salix gene expression patterns strongly suggest cultivar-wide alteration of specific photosynthetic apparatus and protection of the antenna complexes from oxidation damage in contaminated trees, providing an insight into common stress tolerance strategies in a real-world phytoremediation system.
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Affiliation(s)
- Nicholas J B Brereton
- Institut de recherche en biologie végétale, University of Montreal, Montreal QC H1X 2B2, Canada (N.J.B.B., E.G., J.M., M.L., S.J., F.E.P.); andMontreal Botanical Garden, Montreal, QC H1X 2B2, Canada (W.G.N., M.L., S.J., F.E.P.)
| | - Emmanuel Gonzalez
- Institut de recherche en biologie végétale, University of Montreal, Montreal QC H1X 2B2, Canada (N.J.B.B., E.G., J.M., M.L., S.J., F.E.P.); andMontreal Botanical Garden, Montreal, QC H1X 2B2, Canada (W.G.N., M.L., S.J., F.E.P.)
| | - Julie Marleau
- Institut de recherche en biologie végétale, University of Montreal, Montreal QC H1X 2B2, Canada (N.J.B.B., E.G., J.M., M.L., S.J., F.E.P.); andMontreal Botanical Garden, Montreal, QC H1X 2B2, Canada (W.G.N., M.L., S.J., F.E.P.)
| | - Werther Guidi Nissim
- Institut de recherche en biologie végétale, University of Montreal, Montreal QC H1X 2B2, Canada (N.J.B.B., E.G., J.M., M.L., S.J., F.E.P.); andMontreal Botanical Garden, Montreal, QC H1X 2B2, Canada (W.G.N., M.L., S.J., F.E.P.)
| | - Michel Labrecque
- Institut de recherche en biologie végétale, University of Montreal, Montreal QC H1X 2B2, Canada (N.J.B.B., E.G., J.M., M.L., S.J., F.E.P.); andMontreal Botanical Garden, Montreal, QC H1X 2B2, Canada (W.G.N., M.L., S.J., F.E.P.)
| | - Simon Joly
- Institut de recherche en biologie végétale, University of Montreal, Montreal QC H1X 2B2, Canada (N.J.B.B., E.G., J.M., M.L., S.J., F.E.P.); andMontreal Botanical Garden, Montreal, QC H1X 2B2, Canada (W.G.N., M.L., S.J., F.E.P.)
| | - Frederic E Pitre
- Institut de recherche en biologie végétale, University of Montreal, Montreal QC H1X 2B2, Canada (N.J.B.B., E.G., J.M., M.L., S.J., F.E.P.); andMontreal Botanical Garden, Montreal, QC H1X 2B2, Canada (W.G.N., M.L., S.J., F.E.P.)
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