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Silva RA, Hernández MA, Kalscheuer R, Steinbüchel A, Alvarez HM. Two protocols for the detection of oleaginous bacteria using Oil Red O. Appl Microbiol Biotechnol 2024; 108:375. [PMID: 38878165 PMCID: PMC11180012 DOI: 10.1007/s00253-024-13177-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 05/04/2024] [Accepted: 05/10/2024] [Indexed: 06/19/2024]
Abstract
The selection of oleaginous bacteria, potentially applicable to biotechnological approaches, is usually carried out by different expensive and time-consuming techniques. In this study, we used Oil Red O (ORO) as an useful dye for staining of neutral lipids (triacylglycerols and wax esters) on thin-layer chromatography plates. ORO could detect minimal quantities of both compounds (detection limit, 0.0025 mg of tripalmitin or 0.005 mg of cetylpalmitate). In addition, we developed a specific, rapid, and inexpensive screening methodology to detect triacylglycerol-accumulating microorganisms grown on the agar plate. This staining methodology detected 9/13 strains with a triacylglycerol content higher than 20% by cellular dry weight. ORO did not stain polyhydroxyalkanoates-producing bacteria. The four oleaginous strains not detected by this screening methodology exhibited a mucoid morphology of their colonies. Apparently, an extracellular polymeric substance produced by these strains hampered the entry of the lipophilic dye into cells. The utilization of the developed screening methodology would allow selecting of oleaginous bacteria in a simpler and faster way than techniques usually used nowadays, based on unspecific staining protocols and spectrophotometric or chromatographic methods. Furthermore, the use of ORO as a staining reagent would easily characterize the neutral lipids accumulated by microorganisms as reserve compounds. KEY POINTS: • Oil Red O staining is specific for triacylglycerols • Oil Red O staining is useful to detect oleaginous bacteria • Fast and inexpensive staining to isolate oleaginous bacteria from the environment.
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Affiliation(s)
- Roxana A Silva
- Instituto de Biociencias de la Patagonia (INBIOP), Universidad Nacional de la Patagonia San Juan Bosco y CONICET, Km 4-Ciudad Universitaria 9000, Comodoro Rivadavia, Chubut, Argentina
| | - Martín A Hernández
- Instituto de Biociencias de la Patagonia (INBIOP), Universidad Nacional de la Patagonia San Juan Bosco y CONICET, Km 4-Ciudad Universitaria 9000, Comodoro Rivadavia, Chubut, Argentina
| | - Rainer Kalscheuer
- Institute of Pharmaceutical Biology and Biotechnology, Heinrich Heine University, Universitätsstr. 1, 40225, Düsseldorf, Germany
| | - Alexander Steinbüchel
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität, Münster, Germany.
| | - Héctor M Alvarez
- Instituto de Biociencias de la Patagonia (INBIOP), Universidad Nacional de la Patagonia San Juan Bosco y CONICET, Km 4-Ciudad Universitaria 9000, Comodoro Rivadavia, Chubut, Argentina.
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2
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Lobo CB, Correa Deza MA, Arnau GV, Ferrero MA, Juárez Tomás MS. Dibenzothiophene removal by environmental bacteria with differential accumulation of intracellular inorganic polyphosphate. BIORESOURCE TECHNOLOGY 2023; 387:129582. [PMID: 37506945 DOI: 10.1016/j.biortech.2023.129582] [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: 06/01/2023] [Revised: 07/24/2023] [Accepted: 07/25/2023] [Indexed: 07/30/2023]
Abstract
Dibenzothiophene (DBT), which belongs to the group of polycyclic aromatic heterocycles of sulfur, is a model substance to study the removal of sulfur compounds from oil due to its recalcitrance to traditional and specific removal processes. The aim of this work was to evaluate DBT bioremoval by environmental bacteria and its relationship with polyphosphate (polyP) accumulation, cell surface characteristics and bioemulsifying activity. Pseudomonas sp. P26 achieved the highest DBT removal percentage (48%) after 7 days of incubation. Moreover, positive correlations were estimated between DBT removal and bioemulsifying activity and biofilm formation. A strain-dependent relationship between the content of intracellular polyP and the presence of DBT in the culture medium was also demonstrated. The study of these bacterial characteristics, which could promote DBT transformation, is a first approach to select DBT-removing bacteria, in order to develop bioformulations that are able to contribute to desulfurization processes of petroleum-derived pollutants in the future.
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Affiliation(s)
- Constanza Belén Lobo
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET), Av. Belgrano y Pje. Caseros, San Miguel de Tucumán (T4001MVB), Tucumán, Argentina.
| | - María Alejandra Correa Deza
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET), Av. Belgrano y Pje. Caseros, San Miguel de Tucumán (T4001MVB), Tucumán, Argentina.
| | - Gonzalo Víctor Arnau
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET), Av. Belgrano y Pje. Caseros, San Miguel de Tucumán (T4001MVB), Tucumán, Argentina.
| | - Marcela Alejandra Ferrero
- YPF Tecnología (Y-TEC), Av. del Petróleo Argentino (RP10) S/N entre 129 y 143 (1923), Berisso, Buenos Aires, Argentina.
| | - María Silvina Juárez Tomás
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET), Av. Belgrano y Pje. Caseros, San Miguel de Tucumán (T4001MVB), Tucumán, Argentina.
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3
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Lasota J, Ważny R, Kaźmierczak M, Błońska E. The effect of shrubs admixture in pine forest stands on soil bacterial and fungal communities and accumulation of polycyclic aromatic hydrocarbons. Sci Rep 2023; 13:16512. [PMID: 37783867 PMCID: PMC10545714 DOI: 10.1038/s41598-023-43925-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 09/30/2023] [Indexed: 10/04/2023] Open
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are a group of persistent toxic pollutants. The species composition of the stand is important in shaping the quality of soil organic matter and, consequently, the PAH content. The main purpose of the research was to determine the role of shrubs in shaping PAH accumulation in forest soils. The study covered the soils of the pine stands of the Rybnik Forest District, which experiences some of the highest deposition of industrial emissions in Europe. Pine stands with admixture of shrubs (alder buckthorn Frangula alnus and European hazelnut Coryllus avellana) growing in the same soil conditions were selected for the study. Samples for analyses were collected from the organic horizon (O) (from a depth of 0-7 cm) and humus mineral horizon (A) (from a depth of 7-15 cm). The organic C and total N concentrations, pH, alkaline cation content, soil enzyme activity and PAH content were determined. Additionally, the taxonomic composition of soil bacterial and fungal communities was determined. The highest activity of enzymes was noted in soils under influence of shrubs. The enzymatic activity was positively correlated with the content of total N, organic C, pH H2O and KCl and negatively with the C/N ratio. The highest PAH content was recorded in the soils of pine stands without the admixture of shrubs. Our research indicates the importance of shrubs in shaping the properties of surface horizons of forest soil and, consequently on the accumulation of PAHs. Shrubs stimulate biochemical activity of soils which results in lower PAHs accumulation by providing more easily decomposable organic matter.
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Affiliation(s)
- Jarosław Lasota
- Department of Ecology and Silviculture, Faculty of Forestry, University of Agriculture in Krakow, 29 Listopada 46 Str., 31-425, Kraków, Poland
| | - Rafał Ważny
- Małopolska Centre of Biotechnology, Jagiellonian University in Kraków, Gronostajowa 7a, 30-387, Kraków, Poland
| | - Marzena Kaźmierczak
- Department of Ecology and Silviculture, Faculty of Forestry, University of Agriculture in Krakow, 29 Listopada 46 Str., 31-425, Kraków, Poland
| | - Ewa Błońska
- Department of Ecology and Silviculture, Faculty of Forestry, University of Agriculture in Krakow, 29 Listopada 46 Str., 31-425, Kraków, Poland.
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Ma J, Zhuang Y, Wang Y, Zhu N, Wang T, Xiao H, Chen J. Update on new trend and progress of the mechanism of polycyclic aromatic hydrocarbon biodegradation by Rhodococcus, based on the new understanding of relevant theories: a review. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:93345-93362. [PMID: 37548784 DOI: 10.1007/s11356-023-28894-y] [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: 03/18/2023] [Accepted: 07/17/2023] [Indexed: 08/08/2023]
Abstract
Rapid industrial and societal developments have led to substantial increases in the use and exploitation of petroleum, and petroleum hydrocarbon pollution has become a serious threat to human health and the environment. Polycyclic aromatic hydrocarbons (PAHs) are primary components of petroleum hydrocarbons. In recent years, microbial remediation of PAHs pollution has been regarded as the most promising and cost-effective treatment measure because of its low cost, robust efficacy, and lack of secondary pollution. Rhodococcus bacteria are regarded as one of main microorganisms that can effectively degrade PAHs because of their wide distribution, broad degradation spectrum, and network-like evolution of degradation gene clusters. In this review, we focus on the biological characteristics of Rhodococcus; current trends in PAHs degradation based on knowledge maps; and the cellular structural, biochemical, and enzymatic basis of degradation mechanisms, along with whole genome and transcriptional regulation. These research advances provide clues for the prospects of Rhodococcus-based applications in environmental protection.
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Affiliation(s)
- Jinglin Ma
- School of Petrochemical Engineering, Lanzhou University of Technology, Lanzhou, 730050, China
- Orthopaedics Key Laboratory of Gansu Province, Lanzhou University Second Hospital, Lanzhou, 730030, China
| | - Yan Zhuang
- School of Petrochemical Engineering, Lanzhou University of Technology, Lanzhou, 730050, China
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou, 730050, China
| | - Yonggang Wang
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou, 730050, China
| | - Ning Zhu
- School of Petrochemical Engineering, Lanzhou University of Technology, Lanzhou, 730050, China
| | - Ting Wang
- The Second Clinical Medical College, Lanzhou University, Lanzhou, 730030, China
| | - Hongbin Xiao
- The Second Clinical Medical College, Lanzhou University, Lanzhou, 730030, China
| | - Jixiang Chen
- School of Petrochemical Engineering, Lanzhou University of Technology, Lanzhou, 730050, China.
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5
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Behera S, Das S. Potential and prospects of Actinobacteria in the bioremediation of environmental pollutants: Cellular mechanisms and genetic regulations. Microbiol Res 2023; 273:127399. [PMID: 37150049 DOI: 10.1016/j.micres.2023.127399] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 04/22/2023] [Accepted: 04/30/2023] [Indexed: 05/09/2023]
Abstract
Increasing industrialization and anthropogenic activities have resulted in the release of a wide variety of pollutants into the environment including pesticides, polycyclic aromatic hydrocarbons (PAHs), and heavy metals. These pollutants pose a serious threat to human health as well as to the ecosystem. Thus, the removal of these compounds from the environment is highly important. Mitigation of the environmental pollution caused by these pollutants via bioremediation has become a promising approach nowadays. Actinobacteria are a group of eubacteria mostly known for their ability to produce secondary metabolites. The morphological features such as spore formation, filamentous growth, higher surface area to volume ratio, and cellular mechanisms like EPS secretion, and siderophore production in Actinobacteria render higher resistance and biodegradation ability. In addition, these bacteria possess several oxidoreductase systems (oxyR, catR, furA, etc.) which help in bioremediation. Actinobacteria genera including Arthrobacter, Rhodococcus, Streptomyces, Nocardia, Microbacterium, etc. have shown great potential for the bioremediation of various pollutants. In this review, the bioremediation ability of these bacteria has been discussed in detail. The utilization of various genera of Actinobacteria for the biodegradation of organic pollutants, including pesticides and PAHs, and inorganic pollutants like heavy metals has been described. In addition, the cellular mechanisms in these microbes which help to withstand oxidative stress have been discussed. Finally, this review explores the Actinobacteria mediated strategies and recent technologies such as the utilization of mixed cultures, cell immobilization, plant-microbe interaction, utilization of biosurfactants and nanoparticles, etc., to enhance the bioremediation of various environmental pollutants.
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Affiliation(s)
- Shivananda Behera
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela 769 008, Odisha, India
| | - Surajit Das
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela 769 008, Odisha, India.
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6
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Correa Deza MA, Lobo CB, Ferrero MA, Juárez Tomás MS. Polyphosphate accumulation and cell-surface properties by autochthonous bacteria from Argentinian Patagonia. Res Microbiol 2023; 174:104012. [PMID: 36473600 DOI: 10.1016/j.resmic.2022.104012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 10/26/2022] [Accepted: 11/26/2022] [Indexed: 12/12/2022]
Abstract
Bacteria persisting in environments contaminated with polycyclic aromatic hydrocarbons (PAHs) have developed physiological mechanisms to counteract environmental stress. Inorganic polyphosphate accumulation represents one of these possible mechanisms. Likewise, properties such as cell-surface hydrophobicity, auto-aggregation, biofilm formation and bioemulsifying activity could facilitate interaction of microorganisms with hydrophobic organic compounds. In this work, these physiological properties were compared in indigenous bacteria from polluted sediments from Argentinian Patagonia, which were cultivated in two culture media (LBm and JPP) as a way to improve in the next future the PAHs removal. The highest hydrophobicity values were obtained in Rhodococcus strains, while Bacillus sp. B18 showed the highest auto-aggregation percentage and emulsion index. The highest numerical values of biofilm formation were determined in Rhodococcus sp. F27, Pseudomonas sp. P26, and Gordonia sp. H19 either on hydrophilic or on hydrophobic support. The qualitative and quantitative polyP determinations confirmed the presence of this biopolymer in the strains evaluated. The highest intracellular phosphate mean values were obtained in Bacillus sp. B18 in LBm and Rhodococcus erythropolis 20 in JPP. The bacteria evaluated belonging to different genera showed significant differences in their cell-surface characteristics, bioemulsifying activity and polyP accumulation. The low-cost JPP culture medium was selected for future contaminant removal studies.
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Affiliation(s)
- María A Correa Deza
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET), Av. Belgrano y Pje. Caseros, San Miguel de Tucumán (T4001MVB), Tucumán, Argentina.
| | - Constanza B Lobo
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET), Av. Belgrano y Pje. Caseros, San Miguel de Tucumán (T4001MVB), Tucumán, Argentina.
| | - Marcela A Ferrero
- YPF Tecnología (Y-TEC), Av. del Petróleo Argentino (RP10) S/N entre 129 y 143 (1923), Berisso, Buenos Aires, Argentina.
| | - María S Juárez Tomás
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET), Av. Belgrano y Pje. Caseros, San Miguel de Tucumán (T4001MVB), Tucumán, Argentina.
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7
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Applied of actinobacteria consortia-based bioremediation to restore co-contaminated systems. Res Microbiol 2023; 174:104028. [PMID: 36638934 DOI: 10.1016/j.resmic.2023.104028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 11/04/2022] [Accepted: 01/05/2023] [Indexed: 01/12/2023]
Abstract
Global industrialization and natural resources extraction have left cocktails of environmental pollutants. Thus, this work focuses on developing a defined actinobacteria consortium able to restore systems co-contaminated with pollutants occurring in Argentinian environments. In this context, five actinobacteria were tested in solid medium to evaluate antagonistic interactions and tolerance against lindane (LIN), Reactive Black B-V (RBV), phenanthrene (Ph) and Cr(VI). The strains showed absence of antagonism, and most of them tolerated the presence of individual pollutants and their mixtures, except Micromonospora sp. A10. Thus, a quadruple consortium constituted by Streptomyces sp. A5, M7, MC1, and Amycolatopsis tucumanensis DSM 45259T, was tested in liquid systems with individual contaminants. The best microbial growth was observed in the presence of RBV and the lowest on Cr(VI). Removals detected were 83.3%, 65.0% and 52.4% for Ph, RBV and LIN, respectively, with absence of Cr(VI) dissipation. Consequently, the consortium performance was tested against the organic mixture, and a microbial growth similar to the biotic control and a LIN removal increase (61.2%) were observed. Moreover, the four actinobacteria of the consortium survived the mixture bioremediation process. These results demonstrate the potential of the defined actinobacteria consortium as a tool to restore environments co-contaminated with organic pollutants.
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8
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Nelson AR, Narrowe AB, Rhoades CC, Fegel TS, Daly RA, Roth HK, Chu RK, Amundson KK, Young RB, Steindorff AS, Mondo SJ, Grigoriev IV, Salamov A, Borch T, Wilkins MJ. Wildfire-dependent changes in soil microbiome diversity and function. Nat Microbiol 2022; 7:1419-1430. [PMID: 36008619 PMCID: PMC9418001 DOI: 10.1038/s41564-022-01203-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 07/18/2022] [Indexed: 12/13/2022]
Abstract
Forest soil microbiomes have crucial roles in carbon storage, biogeochemical cycling and rhizosphere processes. Wildfire season length, and the frequency and size of severe fires have increased owing to climate change. Fires affect ecosystem recovery and modify soil microbiomes and microbially mediated biogeochemical processes. To study wildfire-dependent changes in soil microbiomes, we characterized functional shifts in the soil microbiota (bacteria, fungi and viruses) across burn severity gradients (low, moderate and high severity) 1 yr post fire in coniferous forests in Colorado and Wyoming, USA. We found severity-dependent increases of Actinobacteria encoding genes for heat resistance, fast growth, and pyrogenic carbon utilization that might enhance post-fire survival. We report that increased burn severity led to the loss of ectomycorrhizal fungi and less tolerant microbial taxa. Viruses remained active in post-fire soils and probably influenced carbon cycling and biogeochemistry via turnover of biomass and ecosystem-relevant auxiliary metabolic genes. Our genome-resolved analyses link post-fire soil microbial taxonomy to functions and reveal the complexity of post-fire soil microbiome activity.
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Affiliation(s)
- Amelia R Nelson
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA
| | - Adrienne B Narrowe
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA
- Eastern Regional Research Center, Agricultural Research Service, Wyndmoor, PA, USA
| | - Charles C Rhoades
- Rocky Mountain Research Station, U.S. Forest Service, Fort Collins, CO, USA
| | - Timothy S Fegel
- Rocky Mountain Research Station, U.S. Forest Service, Fort Collins, CO, USA
| | - Rebecca A Daly
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA
| | - Holly K Roth
- Department of Chemistry, Colorado State University, Fort Collins, CO, USA
| | - Rosalie K Chu
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Kaela K Amundson
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA
| | - Robert B Young
- Chemical Analysis and Instrumentation Laboratory, New Mexico State University, Las Cruces, NM, USA
| | - Andrei S Steindorff
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Stephen J Mondo
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, USA
| | - Igor V Grigoriev
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
| | - Asaf Salamov
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Thomas Borch
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA
- Department of Chemistry, Colorado State University, Fort Collins, CO, USA
- Department of Civil and Environmental Engineering, Colorado State University, Fort Collins, CO, USA
| | - Michael J Wilkins
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA.
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9
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Bourguignon N, Alessandrello M, Booth R, Lobo CB, Juárez Tomás MS, Cumbal L, Perez M, Bhansali S, Ferrero M, Lerner B. Bioremediation on a chip: A portable microfluidic device for efficient screening of bacterial biofilm with polycyclic aromatic hydrocarbon removal capacity. CHEMOSPHERE 2022; 303:135001. [PMID: 35605730 DOI: 10.1016/j.chemosphere.2022.135001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 04/11/2022] [Accepted: 05/14/2022] [Indexed: 06/15/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are pollutants of critical environmental and public health concern and their elimination from contaminated sites is significant for the environment. Biodegradation studies have demonstrated the ability of bacteria in biofilm conformation to enhance the biodegradation of pollutants. In this study, we used our newly developed microfluidic platform to explore biofilm development, properties, and applications of fluid flow, as a new technique for screening PAHs-degrading biofilms. The optimization and evaluation of the flow condition in the microchannels were performed through computational fluid dynamics (CFD). The formation of biofilms by PAHs-degrading bacteria Pseudomonas sp. P26 and Gordonia sp. H19, as pure cultures and co-culture, was obtained in the developed microchips. The removal efficiencies of acenaphthene, fluoranthene and pyrene were determined by HPLC. All the biofilms formed in the microchips removed all tested PAHs, with the higher removal percentages observed with the Pseudomonas sp. P26 biofilm (57.4% of acenaphthene, 40.9% of fluoranthene, and 28.9% of pyrene). Pseudomonas sp. P26 biofilm removed these compounds more efficiently than planktonic cultures. This work proved that the conformation of biofilms enhances the removal rate. It also provided a new tool to rapid and low-cost screen for effective pollutant-degrading biofilms.
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Affiliation(s)
- Natalia Bourguignon
- IREN Center, National Technological University, Buenos Aires, 1706, Argentina; Department of Electrical and Computer Engineering, Florida International University, Miami, FL, 33174, USA
| | - Mauricio Alessandrello
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI, CONICET), Tucumán, Argentina
| | - Ross Booth
- Roche Sequencing Solutions, Inc., 4300 Hacienda Dr, Pleasanton, CA, 94588, USA
| | - Constanza Belén Lobo
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI, CONICET), Tucumán, Argentina
| | | | - Luis Cumbal
- Centro de Nanociencia y Nanotecnologia, Universidad de Las Fuerzas Armadas ESPE, Av. Gral. Rumiñahui s/n, Sangolqui, P.O. BOX 171-5-231B, Ecuador
| | - Maximiliano Perez
- IREN Center, National Technological University, Buenos Aires, 1706, Argentina; Department of Electrical and Computer Engineering, Florida International University, Miami, FL, 33174, USA
| | - Shekhar Bhansali
- Department of Electrical and Computer Engineering, Florida International University, Miami, FL, 33174, USA
| | - Marcela Ferrero
- YPF Tecnologia, Av. del Petróleo Argentino, 900-1198, Berisso, Buenos Aires, Argentina.
| | - Betiana Lerner
- IREN Center, National Technological University, Buenos Aires, 1706, Argentina; Department of Electrical and Computer Engineering, Florida International University, Miami, FL, 33174, USA.
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10
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Vaksmaa A, Egger M, Lüke C, Martins PD, Rosselli R, Asbun AA, Niemann H. Microbial communities on plastic particles in surface waters differ from subsurface waters of the North Pacific Subtropical Gyre. MARINE POLLUTION BULLETIN 2022; 182:113949. [PMID: 35932724 DOI: 10.1016/j.marpolbul.2022.113949] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 07/08/2022] [Accepted: 07/11/2022] [Indexed: 06/15/2023]
Abstract
The long-term fate of plastics in the ocean and their interactions with marine microorganisms remain poorly understood. In particular, the role of sinking plastic particles as a transport vector for surface microbes towards the deep sea has not been investigated. Here, we present the first data on the composition of microbial communities on floating and suspended plastic particles recovered from the surface to the bathypelagic water column (0-2000 m water depth) of the North Pacific Subtropical Gyre. Microbial community composition of suspended plastic particles differed from that of plastic particles afloat at the sea surface. However, in both compartments, a diversity of hydrocarbon-degrading bacteria was identified. These findings indicate that microbial community members initially present on floating plastics are quickly replaced by microorganisms acquired from deeper water layers, thus suggesting a limited efficiency of sinking plastic particles to vertically transport microorganisms in the North Pacific Subtropical Gyre.
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Affiliation(s)
- Annika Vaksmaa
- Department of Marine Microbiology & Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, 't Horntje, the Netherlands.
| | - Matthias Egger
- The Ocean Cleanup, Rotterdam, the Netherlands; Egger Research and Consulting, St. Gallen, Switzerland
| | - Claudia Lüke
- Radboud University, Department of Microbiology, Nijmegen, the Netherlands
| | | | - Riccardo Rosselli
- Departamento de Fisiología, Genética y Microbiología, Facultad de Ciencias, Universidad de Alicante, Spain; LABAQUA S.A.U, C/Dracma 16-18, Pol. Ind. Las Atalayas, 03114 Alicante, Spain
| | - Alejandro Abdala Asbun
- Department of Marine Microbiology & Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, 't Horntje, the Netherlands
| | - Helge Niemann
- Department of Marine Microbiology & Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, 't Horntje, the Netherlands; Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, the Netherlands
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11
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Alfaify AM, Mir MA, Alrumman SA. Klebsiella oxytoca: an efficient pyrene-degrading bacterial strain isolated from petroleum-contaminated soil. Arch Microbiol 2022; 204:248. [PMID: 35397012 DOI: 10.1007/s00203-022-02850-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Revised: 02/21/2022] [Accepted: 03/15/2022] [Indexed: 11/26/2022]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are the hazardous xenobiotic agents of oil production. One of the methods to eliminate hazardous compounds is bioremediation, which is the most efficient and cost-effective method to eliminate the harmful byproducts of crude petroleum processing. In this study, five pure bacterial isolates were isolated from petroleum-contaminated soil, four of which showed a robust growth on the PAH pyrene, as a sole carbon source. Various methods viz mass spectroscopy, biochemical assays, and 16S RNA sequencing employed to identify the isolates ascertained the consistent identification of Klebsiella oxytoca by all three methods. Scanning electron microscopy and Gram staining further demonstrated the characterization of the K. oxytoca. High-performance liquid chromatography of the culture supernatant of K. oxytoca grown in pyrene containing media showed that the cells started utilizing pyrene from the 6th day onwards and by the 12th day of growth, 70% of the pyrene was completely degraded. A genome search for the genes predicted to be involved in pyrene degradation using Kyoto Encyclopedia of Genes and Genomes (KEGG) confirmed their presence in the genome of K. oxytoca. These results suggest that K. oxytoca would be a suitable candidate for removing soil aromatic hydrocarbons.
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Affiliation(s)
- Abdulkhaleg M Alfaify
- Department of Biology, College of Science, King Khalid University, Abha, Saudi Arabia
| | - Mushtaq Ahmad Mir
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, P. O. Box 3665, Abha, 61421, Saudi Arabia.
| | - Sulaiman A Alrumman
- Department of Biology, College of Science, King Khalid University, Abha, Saudi Arabia
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Hu J, Bao Y, Huang H, Zhang Z, Chen F, Li L, Wu Q. The preliminary investigation of potential response biomarkers to PAHs exposure on childhood asthma. JOURNAL OF EXPOSURE SCIENCE & ENVIRONMENTAL EPIDEMIOLOGY 2022; 32:82-93. [PMID: 33972693 DOI: 10.1038/s41370-021-00334-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 04/14/2021] [Accepted: 04/22/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Exposure to polycyclic aromatic hydrocarbons (PAHs) is a potential risk factor for asthma prevalence. This study aims to explore whether PAHs exposure is associated with childhood asthma by altering microbial diversity and metabolic profiles. METHODS Thirty children with asthma and 30 children as control in Nanjing, China were recruited. Urinary 1-hydroxypyrene (1-OHPyr) level was determined by UPLC-Orbitrap-MS as a PAHs exposure biomarker. Logistic regression was conducted to investigate the association between 1-OHPyr and childhood asthma. Microbial diversity was analyzed by 16S rRNA gene sequencing. Metabolic profiles were obtained by UPLC-Orbitrap-MS methods. Differential microbiota and metabolites were screened and selected as response biomarkers or intermediates. Mediation analysis was conducted to assess the association between PAHs and asthma mediated by intermediates. RESULTS Participating children with and without asthma aged 6.43 ± 2.23 years. The urinary 1-OHPyr level ranged from 0.10 to 1.51 μmol/mol (creatinine corrected) in the participants. The urinary 1-OHPyr level was associated with childhood asthma (OR = 7.21, 95% CI: 1.03-50.42 per 1 μmol/mol unit). Microbial diversity was decreased in the group with asthma and there was a significant shift in the abundance of Proteobacteria (at the phylum level), Veillonella and Prevotella (at the genus level). The enrichment pathway analysis showed that differentially expressed metabolites were involved in purine metabolism, amino acid metabolism, and lipid and fatty acid metabolism. The urinary 1-OHPyr level was associated with the abundance of Actinomyces sp. oral clone IO076 and 7-methylguanine that showed a mediation effect on the association between urinary 1-OHPyr levels and childhood asthma by mediation analysis. CONCLUSIONS Urinary 1-OHPyr exposure was associated with childhood asthma, microbial diversity, and metabolic profiles. Microbial diversity and metabolic profiles may be intermediates as response biomarkers to PAHs exposure in childhood asthma. Further research is needed to confirm these study results and determine the underlying mechanism.
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Affiliation(s)
- Jinye Hu
- The Key Laboratory of Modern Toxicology of Ministry of Education and Department of Health Inspection and Quarantine, Nanjing Medical University, Nanjing, China
| | - Yuling Bao
- Department of Respiratory, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Hui Huang
- Department of Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Zhan Zhang
- The Key Laboratory of Modern Toxicology of Ministry of Education and Department of Health Inspection and Quarantine, Nanjing Medical University, Nanjing, China
| | - Feng Chen
- Department of Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Lei Li
- The Key Laboratory of Modern Toxicology of Ministry of Education and Department of Health Inspection and Quarantine, Nanjing Medical University, Nanjing, China.
| | - Qian Wu
- The Key Laboratory of Modern Toxicology of Ministry of Education and Department of Health Inspection and Quarantine, Nanjing Medical University, Nanjing, China.
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13
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Aparicio JD, Espíndola D, Montesinos VN, Litter MI, Donati E, Benimeli CS, Polti MA. Evaluation of the sequential coupling of a bacterial treatment with a physicochemical process for the remediation of wastewater containing Cr and organic pollutants. JOURNAL OF HAZARDOUS MATERIALS 2021; 418:126307. [PMID: 34130164 DOI: 10.1016/j.jhazmat.2021.126307] [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: 02/26/2021] [Revised: 05/31/2021] [Accepted: 06/01/2021] [Indexed: 06/12/2023]
Abstract
A restoration strategy was developed for the treatment of two artificial liquid systems (Minimal Medium, MM, and Water Carbon Nitrogen, WCN) contaminated with Cr(VI), lindane (γ-HCH), phenanthrene (Phe), and reactive black 5 (RB5), through the use of an actinobacteria consortium, coupled with a physicochemical treatment using a column filled with nano-scale zero valent iron particles immobilized on dried Macrocystis pyrifera algae biomass. The Sequential Treatment A (STA: physicochemical followed by biological method) removed the three organic compounds with different effectiveness; however, it was very ineffective for Cr(VI) removal. The Sequential Treatment B (STB: biological followed by the physicochemical method) removed the four compounds with variable efficiencies. The removal of γ-HCH, Phe, and RB5 in both effluents did not present significant differences, regardless of the sequential treatment used. The highest removal of Cr(VI) and total Cr was observed in MM and WCN, respectively. Ecotoxicity tests (L. sativa) of the effluents treated with both methodological couplings demonstrated that the toxicity of WCN only decreased at the end of STA, while that of MM decreased at all stages of both sequential treatments. Therefore, MM would be more appropriate to perform both treatments.
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Affiliation(s)
- Juan Daniel Aparicio
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI), CONICET, Av. Belgrano y Pasaje Caseros, 4000 Tucumán, Argentina; Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán, Ayacucho 491, 4000 Tucumán, Argentina
| | - Diego Espíndola
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI), CONICET, Av. Belgrano y Pasaje Caseros, 4000 Tucumán, Argentina; Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán, Ayacucho 491, 4000 Tucumán, Argentina
| | - Víctor Nahuel Montesinos
- Gerencia Química, Centro Atómico Constituyentes, CNEA, Av. Gral. Paz 1499, 1650 San Martín, Prov. de Buenos Aires, Argentina
| | - Marta Irene Litter
- IIIA (CONICET-UNSAM), Universidad Nacional de General San Martín, Campus Miguelete, Av. 25 de Mayo y Francia, 1650 San Martín, Prov. de Buenos Aires, Argentina
| | - Edgardo Donati
- CINDEFI (CONICET, UNLP), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina
| | - Claudia Susana Benimeli
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI), CONICET, Av. Belgrano y Pasaje Caseros, 4000 Tucumán, Argentina; Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Catamarca, Av. Belgrano 300, 4700 Catamarca, Argentina.
| | - Marta Alejandra Polti
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI), CONICET, Av. Belgrano y Pasaje Caseros, 4000 Tucumán, Argentina; Facultad de Ciencias Naturales e Instituto Miguel Lillo, Universidad Nacional de Tucumán, Miguel Lillo 205, 4000 Tucumán, Argentina.
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Mohapatra M, Yadav R, Rajput V, Dharne MS, Rastogi G. Metagenomic analysis reveals genetic insights on biogeochemical cycling, xenobiotic degradation, and stress resistance in mudflat microbiome. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2021; 292:112738. [PMID: 34020306 DOI: 10.1016/j.jenvman.2021.112738] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 04/05/2021] [Accepted: 04/29/2021] [Indexed: 05/22/2023]
Abstract
Mudflats are highly productive coastal ecosystems that are dominated by halophytic vegetation. In this study, the mudflat sediment microbiome was investigated from Nalabana Island, located in a brackish water coastal wetland of India; Chilika, based on the MinION shotgun metagenomic analysis. Bacterial, archaeal, and fungal communities were mostly composed of Proteobacteria (38.3%), Actinobacteria (20.7%), Euryarchaeota (76.1%), Candidatus Bathyarchaeota (6.8%), Ascomycota (47.2%), and Basidiomycota (22.0%). Bacterial and archaeal community composition differed significantly between vegetated mudflat and un-vegetated bulk sediments. Carbon, nitrogen, sulfur metabolisms, oxidative phosphorylation, and xenobiotic biodegradation were the most common microbial functionalities in the mudflat metagenomes. Furthermore, genes involved in oxidative stresses, osmotolerance, secondary metabolite synthesis, and extracellular polymeric substance synthesis revealed adaptive mechanisms of the microbiome in mudflat habitat. Mudflat metagenome also revealed genes involved in the plant growth and development, suggesting that microbial communities could aid halophytic vegetation by providing tolerance to the abiotic stresses in a harsh mudflat environment. Canonical correspondence analysis and co-occurrence network revealed that both biotic (vegetation and microbial interactions) and abiotic factors played important role in shaping the mudflat microbiome composition. Among abiotic factors, pH accounted for the highest variance (20.10%) followed by available phosphorus (19.73%), total organic carbon (9.94%), salinity (8.28%), sediment texture (sand) (6.37%) and available nitrogen (5.53%) in the mudflat microbial communities. Overall, this first metagenomic study provided a comprehensive insight on the community structure, potential ecological interactions, and genetic potential of the mudflat microbiome in context to the cycling of organic matter, xenobiotic biodegradation, stress resistance, and in providing the ecological fitness to halophytes. These ecosystem services of the mudflat microbiome must be considered in the conservation and management plan of coastal wetlands. This study also advanced our understanding of fungal diversity which is understudied from the coastal lagoon ecosystems.
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Affiliation(s)
- Madhusmita Mohapatra
- Wetland Research and Training Centre, Chilika Development Authority, Balugaon, 752030, Odisha, India; School of Biotechnology, KIIT University, Bhubaneswar, Odisha, 751024, India
| | - Rakeshkumar Yadav
- National Collection of Industrial Microorganisms (NCIM), Biochemical Sciences, CSIR-National Chemical Laboratory (NCL), Pune, 411008, India; Academic of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Vinay Rajput
- National Collection of Industrial Microorganisms (NCIM), Biochemical Sciences, CSIR-National Chemical Laboratory (NCL), Pune, 411008, India
| | - Mahesh S Dharne
- National Collection of Industrial Microorganisms (NCIM), Biochemical Sciences, CSIR-National Chemical Laboratory (NCL), Pune, 411008, India; Academic of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Gurdeep Rastogi
- Wetland Research and Training Centre, Chilika Development Authority, Balugaon, 752030, Odisha, India.
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Pandya DK, Kumar MA. Chemo-metric engineering designs for deciphering the biodegradation of polycyclic aromatic hydrocarbons. JOURNAL OF HAZARDOUS MATERIALS 2021; 411:125154. [PMID: 33858107 DOI: 10.1016/j.jhazmat.2021.125154] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 01/07/2021] [Accepted: 01/13/2021] [Indexed: 06/12/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are non-polar organic compounds that are omnipresent in the environment and released due to anthropogenic activities through emissions and discharges. PAHs, being xenobiotic and exerts health impacts, thus they attract serious concern by the environmentalists. The stringent regulations and the need of sustainable development urges the hunt for a technically feasible and cost-effective wastewater treatment. Although the conventional physico-chemical treatment are widely preferred, they cause secondary pollution problems and demand subsequent treatment options. This comprehensive review intends to address the (a) different PAHs and their associated toxicity, (b) the remedial strategies, particularly biodegradation. The biological wastewater treatment techniques that involve microbial systems are highly influenced by the different physio-chemical and environmental parameters. Therefore, suitable optimization techniques are prerequisite for effective functioning of the biological treatment that sustains judiciously and interpreted in a lesser time. Here we have aimed to discuss (a) different chemo-metric tools involved in the design of experiments (DoE), (b) design equations and models, (c) tools for evaluating the model's adequacy and (d) plots for graphically interpreting the chemo-metric designs. However, to best of our knowledge, this is a first review to discuss the PAHs biodegradation that are tailored by chemo-metric designs. The associated challenges, available opportunities and techno-economic aspects of PAHs degradation using chemo-metric engineering designs are explained. Additionally, the review highlights how well these DoE tools can be suited for the sustainable socio-industrial sectors. Concomitantly, the futuristic scope and prospects to undertake new areas of research exploration were emphasized to unravel the least explored chemo-metric designs.
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Affiliation(s)
- Darshita Ketan Pandya
- Analytical and Environmental Science Division & Centralized Instrument Facility, CSIR-Central Salt & Marine Chemicals Research Institute, Bhavnagar 364002, Gujarat, India
| | - Madhava Anil Kumar
- Analytical and Environmental Science Division & Centralized Instrument Facility, CSIR-Central Salt & Marine Chemicals Research Institute, Bhavnagar 364002, Gujarat, India; Academy of Scientific and Innovative Research, Ghaziabad 201002, Uttar Pradesh, India.
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16
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Sineli PE, Herrera HM, Aparicio JD, Guerrero DS, Polti MA, Dávila Costa JS. Genomic analysis and proteomic response of the chromium-resistant and phenanthrene-degrading strain Streptomyces sp. MC1. J Appl Microbiol 2021; 131:719-727. [PMID: 33434397 DOI: 10.1111/jam.15002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 12/26/2020] [Accepted: 01/08/2021] [Indexed: 11/28/2022]
Abstract
AIM Chemically disparate toxic organic and/or inorganic molecules produced by anthropogenic activities often hinder the bioremediation process. This research was conducted to understand the capacity of Streptomyces sp. MC1 to remove chemically disparate toxics such as Cr(VI) or phenanthrene. METHODS AND RESULTS Genomic, metabolic modeling and proteomic approaches were used in this study. Our results demonstrated that Streptomyces sp. MC1 has the genetic determinants to remove Cr(VI) or degrade phenanthrene. Proteomics showed that these genetic determinants were expressed. Metabolic versatility of the strain was confirmed by two metabolic models in complex and minimal media. Interestingly, our results also suggested a connection between the degradation of phenanthrene and synthesis of specialized metabolites. CONCLUSIONS Streptomyces sp. MC1 has the genetic and physiological potential to remove Cr(VI) or degrade phenanthrene SIGNIFICANCE AND IMPACT OF STUDY: The probability of a microorganism to survive in the presence of different contaminants depends on its genetic potential and the ability to express it. The genetic and proteomic profiles obtained for Streptomyces sp. MC1 can be recommended as model and predict if other Streptomyces strains can be used in bioremediation processes. Our work also hypothesized that intermediates of the phenanthrene degradation serve as precursors for the specialized metabolism.
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Affiliation(s)
- P E Sineli
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET), San Miguel de Tucumán, Argentina
| | - H M Herrera
- Universidad Nacional de Tucumán, Argentina, Tucumán, Argentina
| | - J D Aparicio
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET), San Miguel de Tucumán, Argentina.,Universidad Nacional de Tucumán, Argentina, Tucumán, Argentina
| | - D S Guerrero
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET), San Miguel de Tucumán, Argentina
| | - M A Polti
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET), San Miguel de Tucumán, Argentina.,Universidad Nacional de Tucumán, Argentina, Tucumán, Argentina
| | - J S Dávila Costa
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET), San Miguel de Tucumán, Argentina
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17
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Benedek T, Szentgyörgyi F, Szabó I, Farkas M, Duran R, Kriszt B, Táncsics A. Aerobic and oxygen-limited naphthalene-amended enrichments induced the dominance of Pseudomonas spp. from a groundwater bacterial biofilm. Appl Microbiol Biotechnol 2020; 104:6023-6043. [PMID: 32415320 PMCID: PMC7306034 DOI: 10.1007/s00253-020-10668-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 04/29/2020] [Accepted: 05/04/2020] [Indexed: 12/20/2022]
Abstract
In this study, we aimed at determining the impact of naphthalene and different oxygen levels on a biofilm bacterial community originated from a petroleum hydrocarbon-contaminated groundwater. By using cultivation-dependent and cultivation-independent approaches, the enrichment, identification, and isolation of aerobic and oxygen-limited naphthalene degraders was possible. Results indicated that, regardless of the oxygenation conditions, Pseudomonas spp. became the most dominant in the naphthalene-amended selective enrichment cultures. Under low-oxygen conditions, P. veronii/P. extremaustralis lineage affiliating bacteria, and under full aerobic conditions P. laurentiana-related isolates were most probably capable of naphthalene biodegradation. A molecular biological tool has been developed for the detection of naphthalene 1,2-dioxygenase-related 2Fe-2S reductase genes of Gram-negative bacteria. The newly developed COnsensus DEgenerate Hybrid Oligonucleotide Primers (CODEHOP-PCR) technique may be used in the monitoring of the natural attenuation capacity of PAH-contaminated sites. A bacterial strain collection with prolific biofilm-producing and effective naphthalene-degrading organisms was established. The obtained strain collection may be applicable in the future for the development of biofilm-based bioremediation systems for the elimination of PAHs from groundwater (e.g., biofilm-based biobarriers).
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Affiliation(s)
- Tibor Benedek
- Regional University Centre of Excellence in Environmental Industry, Szent István University, Páter K. u. 1, Gödöllő, H-2100, Hungary.
| | - Flóra Szentgyörgyi
- Department of Environmental Protection and Safety, Szent István University, Páter K. u. 1, Gödöllő, H-2100, Hungary
| | - István Szabó
- Department of Environmental Protection and Safety, Szent István University, Páter K. u. 1, Gödöllő, H-2100, Hungary
| | - Milán Farkas
- Department of Environmental Protection and Safety, Szent István University, Páter K. u. 1, Gödöllő, H-2100, Hungary
| | - Robert Duran
- IPREM UMR CNRS 5254, Equipe Environnement et Microbiologie, MELODY Group, Université de Pau et des Pays de l'Adour, Pau, France
| | - Balázs Kriszt
- Department of Environmental Protection and Safety, Szent István University, Páter K. u. 1, Gödöllő, H-2100, Hungary
| | - András Táncsics
- Regional University Centre of Excellence in Environmental Industry, Szent István University, Páter K. u. 1, Gödöllő, H-2100, Hungary
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18
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Baoune H, Aparicio JD, Acuña A, El Hadj-Khelil AO, Sanchez L, Polti MA, Alvarez A. Effectiveness of the Zea mays-Streptomyces association for the phytoremediation of petroleum hydrocarbons impacted soils. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2019; 184:109591. [PMID: 31514081 DOI: 10.1016/j.ecoenv.2019.109591] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 08/15/2019] [Accepted: 08/19/2019] [Indexed: 06/10/2023]
Abstract
Restoring polluted sites by petroleum hydrocarbons is a challenge because of their complexity and persistence in the environment. The main objective of the present study was to investigate the performance of plant-actinobacteria system for the remediation of crude petroleum and pure-polycyclic aromatic hydrocarbons (PAHs) contaminated soils. The endophytic strain Streptomyces sp. Hlh1 was tested for its ability to degrade model PAHs (phenanthrene, pyrene and anthracene) in liquid minimal medium. Streptomyces sp. Hlh1 demonstrated the ability to grow on PAHs as sole carbon and energy source, reaching hydrocarbons removal of 63%, 93% and 83% for phenanthrene, pyrene and anthracene, respectively. Maize plant was chosen to study the impact of Streptomyces sp. Hlh1 inoculation on the dissipation of contaminants and plant growth. Thus, maize seedlings grown in soils contaminated with crude petroleum and pure-PAHs were inoculated with Streptomyces sp. Hlh1. Results showed that the endophyte inoculation increased contaminants removal. Maximum hydrocarbons removal (70%) was achieved in inoculated and planted soil contaminated with crude oil, while 61%, 59%, and 46% of hydrocarbons dissipation were registered for phenanthrene, pyrene and anthracene, respectively. These degradations rates were significantly higher compared to non-inoculated systems in all the treatments evaluated. Further, it was revealed that hydrocarbons (C8-C30) were efficiently degraded in plant-Streptomyces Hlh1 system. Moreover, the inoculation with the actinobacteria resulted significant plant development and enhanced photosynthetic pigments compared to plants grown in the other experimental conditions. The present study provide evidence that the inoculation of maize plants with Streptomyces sp. Hlh1 play a remarkable role in the removal of petroleum hydrocarbons, enhancing plant development in contaminated soils.
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Affiliation(s)
- Hafida Baoune
- Laboratoire de Protection des écosystème en Zones Arides et Semi-arides, FNSV, Université Kasdi Merbah Ouragla, 30000, Algeria; Planta Piloto de Procesos Industriales Microbiológicos (PROIMI), CONICET. Av. Belgrano y Pasaje Casero., 4000, Tucumán, Argentina.
| | - Juan Daniel Aparicio
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI), CONICET. Av. Belgrano y Pasaje Casero., 4000, Tucumán, Argentina.
| | - Adrian Acuña
- Universidad Tecnológica Nacional, Av. de Los Inmigrantes 555, 9400, Santa Cruz, Argentina.
| | - Aminata Ould El Hadj-Khelil
- Laboratoire de Protection des écosystème en Zones Arides et Semi-arides, FNSV, Université Kasdi Merbah Ouragla, 30000, Algeria.
| | - Leandro Sanchez
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI), CONICET. Av. Belgrano y Pasaje Casero., 4000, Tucumán, Argentina.
| | - Marta Alejandra Polti
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI), CONICET. Av. Belgrano y Pasaje Casero., 4000, Tucumán, Argentina; Facultad de Ciencias Naturales e Instituto Miguel Lillo, Universidad Nacional de Tucumán (UNT), Miguel Lillo 205, 4000, Tucumán, Argentina.
| | - Analia Alvarez
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI), CONICET. Av. Belgrano y Pasaje Casero., 4000, Tucumán, Argentina; Facultad de Ciencias Naturales e Instituto Miguel Lillo, Universidad Nacional de Tucumán (UNT), Miguel Lillo 205, 4000, Tucumán, Argentina.
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Bourguignon N, Irazusta V, Isaac P, Estévez C, Maizel D, Ferrero MA. Identification of proteins induced by polycyclic aromatic hydrocarbon and proposal of the phenanthrene catabolic pathway in Amycolatopsis tucumanensis DSM 45259. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2019; 175:19-28. [PMID: 30878660 DOI: 10.1016/j.ecoenv.2019.02.071] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 02/15/2019] [Accepted: 02/22/2019] [Indexed: 06/09/2023]
Abstract
In the present study the polycyclic aromatic hydrocarbon removal and metabolic adaptation of Amycolatopsis tucumanensis DSM 45259 were investigated. Analysis of one-dimensional gel electrophoresis of crude cell extracts revealed differential synthesis of proteins which were identified by MALDI-TOF. To elucidate the phenanthrene metabolic pathway in A. tucumanensis DSM45259, two-dimensional electrophoresis and detection of phenanthrene degradation intermediates by GS-MS were performed. The presence of aromatic substrates resulted in changes in the abundance of proteins involved in the metabolism of aromatic compounds, oxidative stress response, energy production and protein synthesis. The obtained results allowed us to clarify the phenanthrene catabolic pathway, by confirming the roles of several proteins involved in the degradation process and comprehensive adaptation. This may clear the way for more efficient engineering of bacteria in the direction of more effective bioremediation applications.
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Affiliation(s)
- Natalia Bourguignon
- Universidad Tecnológica Nacional (UTN), Facultad Regional de Haédo, París 532, 1706 Haedo, Buenos Aires, Argentina.
| | - Verónica Irazusta
- Instituto de Investigaciones para la Industria Química (INIQUI), CONICET-UNSa, Argentina; Facultad de Ciencias Naturales, UNSa, Salta, Argentina
| | - Paula Isaac
- Centro de Investigaciones y Transferencia de Villa María (CIT Villa María), CONICET-Instituto de Ciencias Básicas y Aplicadas, Universidad Nacional de Villa María, Córdoba, Argentina
| | - Cristina Estévez
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI, CONICET), Tucumán, Argentina
| | - Daniela Maizel
- Instituto de Astronomía y Física del Espacio, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Buenos Aires, Intendente Güiraldes 2160, C1428EGA CABA, Argentina
| | - Marcela A Ferrero
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI, CONICET), Tucumán, Argentina
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Baoune H, Ould El Hadj-Khelil A, Pucci G, Sineli P, Loucif L, Polti MA. Petroleum degradation by endophytic Streptomyces spp. isolated from plants grown in contaminated soil of southern Algeria. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2018; 147:602-609. [PMID: 28923725 DOI: 10.1016/j.ecoenv.2017.09.013] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 09/04/2017] [Accepted: 09/07/2017] [Indexed: 06/07/2023]
Abstract
Petroleum hydrocarbons are well known by their high toxicity and recalcitrant properties. Their increasing utilization around worldwide led to environmental contamination. Phytoremediation using plant-associated microbe is an interesting approach for petroleum degradation and actinobacteria have a great potential for that. For this purpose, our study aimed to isolate, characterize, and assess the ability of endophytic actinobacteria to degrade crude petroleum, as well as to produce plant growth promoting traits. Seventeen endophytic actinobacteria were isolated from roots of plants grown naturally in sandy contaminated soil. Among them, six isolates were selected on the basis of their tolerance to petroleum on solid minimal medium and characterized by 16S rDNA gene sequencing. All petroleum-tolerant isolates belonged to the Streptomyces genus. Determination by crude oil degradation by gas chromatorgraph-flame ionization detector revealed that five strains could use petroleum as sole carbon and energy source and the petroleum removal achieved up to 98% after 7 days of incubation. These isolates displayed an important role in the degradation of the n-alkanes (C6-C30), aromatic and polycyclic aromatic hydrocarbons. All strains showed a wide range of plant growth promoting features such as siderophores, phosphate solubilization, 1-aminocyclopropane-1-carboxylate deaminase, nitrogen fixation and indole-3-acetic acid production as well as biosurfactant production. This is the first study highlighting the petroleum degradation ability and plant growth promoting attributes of endophytic Streptomyces. The finding suggests that the endophytic actinobacteria isolated are promising candidates for improving phytoremediation efficiency of petroleum contaminated soil.
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Affiliation(s)
- Hafida Baoune
- Laboratoire de protection des écosystème en zones arides et semi-arides, FNSV, Université Kasdi Merbah Ouragla, 30000, Algeria.
| | - Aminata Ould El Hadj-Khelil
- Laboratoire de protection des écosystème en zones arides et semi-arides, FNSV, Université Kasdi Merbah Ouragla, 30000, Algeria.
| | - Graciela Pucci
- Centro de estudios e Investigación en Microbiología Aplicada (CEIMA), Universidad Nacional de la Patagonia San Juan Bosco (UNPSJB), Ruta Provincial N°1km 4, Comodoro Rivadavia, Chubut, Argentina.
| | - Pedro Sineli
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI), CONICET, Av. Belgrano y Pasaje Caseros, 4000 Tucumán, Argentina.
| | - Lotfi Loucif
- Laboratoire de biotechnologie des molécules bioactives et de la physiopathologie cellulaire (LBMBPC), Faculté des sciences de la nature et de la vie, Université de Batna 2, Batna, Algeria.
| | - Marta Alejandra Polti
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI), CONICET, Av. Belgrano y Pasaje Caseros, 4000 Tucumán, Argentina; Facultad de Ciencias Naturales e Instituto Miguel Lillo, Universidad Nacional de Tucumán (UNT), Miguel Lillo 251, 4000 Tucumán, Argentina.
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21
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Iffis B, St-Arnaud M, Hijri M. Petroleum Contamination and Plant Identity Influence Soil and Root Microbial Communities While AMF Spores Retrieved from the Same Plants Possess Markedly Different Communities. FRONTIERS IN PLANT SCIENCE 2017; 8:1381. [PMID: 28848583 PMCID: PMC5550799 DOI: 10.3389/fpls.2017.01381] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 07/25/2017] [Indexed: 05/30/2023]
Abstract
Phytoremediation is a promising in situ green technology based on the use of plants to cleanup soils from organic and inorganic pollutants. Microbes, particularly bacteria and fungi, that closely interact with plant roots play key roles in phytoremediation processes. In polluted soils, the root-associated microbes contribute to alleviation of plant stress, improve nutrient uptake and may either degrade or sequester a large range of soil pollutants. Therefore, improving the efficiency of phytoremediation requires a thorough knowledge of the microbial diversity living in the rhizosphere and in close association with plant roots in both the surface and the endosphere. This study aims to assess fungal ITS and bacterial 16S rRNA gene diversity using high-throughput sequencing in rhizospheric soils and roots of three plant species (Solidago canadensis, Populus balsamifera, and Lycopus europaeus) growing spontaneously in three petroleum hydrocarbon polluted sedimentation basins. Microbial community structures of rhizospheric soils and roots were compared with those of microbes associated with arbuscular mycorrhizal fungal (AMF) spores to determine the links between the root and rhizosphere communities and those associated with AMF. Our results showed a difference in OTU richness and community structure composition between soils and roots for both bacteria and fungi. We found that petroleum hydrocarbon pollutant (PHP) concentrations have a significant effect on fungal and bacterial community structures in both soils and roots, whereas plant species identity showed a significant effect only on the roots for bacteria and fungi. Our results also showed that the community composition of bacteria and fungi in soil and roots varied from those associated with AMF spores harvested from the same plants. This let us to speculate that in petroleum hydrocarbon contaminated soils, AMF may release chemical compounds by which they recruit beneficial microbes to tolerate or degrade the PHPs present in the soil.
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Bourguignon N, Bargiela R, Rojo D, Chernikova TN, de Rodas SAL, García-Cantalejo J, Näther DJ, Golyshin PN, Barbas C, Ferrero M, Ferrer M. Insights into the degradation capacities of Amycolatopsis tucumanensis DSM 45259 guided by microarray data. World J Microbiol Biotechnol 2016; 32:201. [PMID: 27785708 DOI: 10.1007/s11274-016-2163-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2016] [Accepted: 10/18/2016] [Indexed: 10/20/2022]
Abstract
The analysis of catabolic capacities of microorganisms is currently often achieved by cultivation approaches and by the analysis of genomic or metagenomic datasets. Recently, a microarray system designed from curated key aromatic catabolic gene families and key alkane degradation genes was designed. The collection of genes in the microarray can be exploited to indicate whether a given microbe or microbial community is likely to be functionally connected with certain degradative phenotypes, without previous knowledge of genome data. Herein, this microarray was applied to capture new insights into the catabolic capacities of copper-resistant actinomycete Amycolatopsis tucumanensis DSM 45259. The array data support the presumptive ability of the DSM 45259 strain to utilize single alkanes (n-decane and n-tetradecane) and aromatics such as benzoate, phthalate and phenol as sole carbon sources, which was experimentally validated by cultivation and mass spectrometry. Interestingly, while in strain DSM 45259 alkB gene encoding an alkane hydroxylase is most likely highly similar to that found in other actinomycetes, the genes encoding benzoate 1,2-dioxygenase, phthalate 4,5-dioxygenase and phenol hydroxylase were homologous to proteobacterial genes. This suggests that strain DSM 45259 contains catabolic genes distantly related to those found in other actinomycetes. Together, this study not only provided new insight into the catabolic abilities of strain DSM 45259, but also suggests that this strain contains genes uncommon within actinomycetes.
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Affiliation(s)
- Natalia Bourguignon
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET), Tucumán, Argentina
| | - Rafael Bargiela
- Consejo Superior de Investigaciones Científicas (CSIC), Institute of Catalysis, Madrid, Spain
| | - David Rojo
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Monteprincipe, Boadilla del Monte, Madrid, Spain
| | | | - Sara A López de Rodas
- Unidad de Genómica-Campus Moncloa, C.A.I. Genómica y Proteómica, Facultad CC. Biológicas, Universidad Complutense de Madrid, Madrid, Spain
| | - Jesús García-Cantalejo
- Unidad de Genómica-Campus Moncloa, C.A.I. Genómica y Proteómica, Facultad CC. Biológicas, Universidad Complutense de Madrid, Madrid, Spain
| | - Daniela J Näther
- Institute for Microbiology, Biocentre, Goethe University, Frankfurt, Germany
| | - Peter N Golyshin
- School of Biological Sciences, Bangor University, Gwynedd, LL57 2UW, UK
| | - Coral Barbas
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Monteprincipe, Boadilla del Monte, Madrid, Spain
| | - Marcela Ferrero
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET), Tucumán, Argentina
| | - Manuel Ferrer
- Consejo Superior de Investigaciones Científicas (CSIC), Institute of Catalysis, Madrid, Spain.
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23
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Iffis B, St-Arnaud M, Hijri M. Petroleum hydrocarbon contamination, plant identity and arbuscular mycorrhizal fungal (AMF) community determine assemblages of the AMF spore-associated microbes. Environ Microbiol 2016; 18:2689-704. [DOI: 10.1111/1462-2920.13438] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Bachir Iffis
- Institut de Recherche en Biologie Végétale, Université de Montréal and Jardin botanique de Montréal; 4101 Rue Sherbrooke Est Montréal QC H1X 2B2 Canada
| | - Marc St-Arnaud
- Institut de Recherche en Biologie Végétale, Université de Montréal and Jardin botanique de Montréal; 4101 Rue Sherbrooke Est Montréal QC H1X 2B2 Canada
| | - Mohamed Hijri
- Institut de Recherche en Biologie Végétale, Université de Montréal and Jardin botanique de Montréal; 4101 Rue Sherbrooke Est Montréal QC H1X 2B2 Canada
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