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Feng JR, Ni HG. Effects of heavy metals and metalloids on the biodegradation of organic contaminants. ENVIRONMENTAL RESEARCH 2024; 246:118069. [PMID: 38160966 DOI: 10.1016/j.envres.2023.118069] [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: 09/03/2023] [Revised: 12/22/2023] [Accepted: 12/26/2023] [Indexed: 01/03/2024]
Abstract
Heavy metals and metalloids (HMMs) inhibit the biodegradation of organic pollutants. The degree of inhibition depends not only on the concentration and bioavailability of HMMs but also on additional factors, such as environmental variables (e.g., inorganic components, organic matter, pH, and redox potential), the nature of the metals, and microbial species. Based on the degradation pattern and metal concentrations causing half biodegradation rate reductions (RC50s), the inhibition of biodegradation was: Hg2+, As2O3 > Cu2+, Cd2+, Pb2+, Cr3+ > Ni2+, Co2+ > Mn2+, Zn2+ > Fe3+. Four patterns were observed: inhibition increases with increasing metal concentration; low concentrations stimulate, while high concentrations inhibit; high concentrations inhibit less; and mild inhibition remains constant. In addition, metal ion mixtures have more complex inhibitory effects on the degradation of organic pollutants, which may be greater than, similar to, or less than that of individual HMMs. Finally, the inhibitory mechanism of HMMs on biodegradation is reviewed. HMMs generally have little impact on the biodegradation pathway of organic pollutants for bacterial strains. However, when pollutants are biodegraded by the community, HMMs may activate microbial populations harbouring different transformation pathways. HMMs can affect the biodegradation efficiency of organic pollutants by changing the surface properties of microbes, interfering with degradative enzymes, and interacting with general metabolism.
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Affiliation(s)
- Jin-Ru Feng
- School of Urban Planning and Design, Shenzhen Graduate School, Peking University, Shenzhen, 518055, China
| | - Hong-Gang Ni
- School of Urban Planning and Design, Shenzhen Graduate School, Peking University, Shenzhen, 518055, China.
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2
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Marques Mendonca R, Fulton T, Blackwood C, Costello D. Sublethal nickel toxicity shuts off manganese oxidation and pellicle biofilm formation in Pseudomonas putida GB-1. Environ Microbiol 2023; 25:3639-3654. [PMID: 37875338 DOI: 10.1111/1462-2920.16529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 10/11/2023] [Indexed: 10/26/2023]
Abstract
In sediments, the bioavailability and toxicity of Ni are strongly influenced by its sorption to manganese (Mn) oxides, which largely originate from the redox metabolism of microbes. However, microbes are concurrently susceptible to the toxic effects of Ni, which establishes complex interactions between toxicity and redox processes. This study measured the effect of Ni on growth, pellicle biofilm formation and oxidation of the Mn-oxidizing bacteria Pseudomonas putida GB-1. In liquid media, Ni exposure decreased the intrinsic growth rate but allowed growth to the stationary phase in all intermediate treatments. Manganese oxidation was 67% less than control for bacteria exposed to 5 μM Ni and completely ceased in all treatments above 50 μM. Pellicle biofilm development decreased exponentially with Ni concentration (maximum 92% reduction) and was replaced by planktonic growth in higher Ni treatments. In solid media assays, growth was unaffected by Ni exposure, but Mn oxidation completely ceased in treatments above 10 μM of Ni. Our results show that sublethal Ni concentrations substantially alter Mn oxidation rates and pellicle biofilm development in P. putida GB-1, which has implications for toxic metal bioavailability to the entire benthic community and the environmental consequences of metal contamination.
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Affiliation(s)
| | - Taylor Fulton
- Department of Biological Sciences, Kent State University, Kent, Ohio, USA
- Department of Food, Agricultural and Biological Engineering, Ohio State University, Columbus, Ohio, USA
| | - Christopher Blackwood
- Department of Biological Sciences, Kent State University, Kent, Ohio, USA
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, Michigan, USA
| | - David Costello
- Department of Biological Sciences, Kent State University, Kent, Ohio, USA
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3
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Bhatt K, Suyal DC, Kumar S, Singh K, Goswami P. New insights into engineered plant-microbe interactions for pesticide removal. CHEMOSPHERE 2022; 309:136635. [PMID: 36183882 DOI: 10.1016/j.chemosphere.2022.136635] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 09/21/2022] [Accepted: 09/25/2022] [Indexed: 06/16/2023]
Abstract
Over the past decades, rapid industrialization along with the overutilization of organic pollutants/pesticides has altered the environmental circumstances. Moreover, various anthropogenic, xenobiotics and natural activities also affected plants, soil, and human health, in both direct and indirect ways. To counter this, several conventional methods are currently practiced, but are uneconomical, noxious, and is yet inefficient for large-scale application. Plant-microbe interactions are mediated naturally in an ecosystem and are practiced in several areas. Plant growth promoting rhizobacteria (PGPR) possess certain attributes affecting plant and soil consequently performing decontamination activity via a direct and indirect mechanism. PGPR also harbors indispensable genes stimulating the mineralization of several organic and inorganic compounds. This makes microbes potential candidates for contributing to sustainably remediating the harmful pesticide contaminants. There is a limited piece of information about the plant-microbe interaction pertaining predict and understand the overall interaction concerning a sustainable environment. Therefore, this review focuses on the plant-microbe interaction in the rhizosphere and inside the plant's tissues, along with the utilization augmenting the crop productivity, reduction in plant stress along with decontamination of pesticides/organic pollutants in soil for sustainable environmental management.
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Affiliation(s)
- Kalpana Bhatt
- Department of Food Science, Purdue University, West Lafayette, IN, 47907, USA.
| | - Deep Chandra Suyal
- Department of Microbiology, Akal College of Basic Sciences, Eternal University, Baru Sahib, Sirmour, Himachal Pradesh, India.
| | - Saurabh Kumar
- ICAR-Research Complex for Eastern Region, Patna, 800014, Bihar, India
| | - Kuldeep Singh
- Department of Microbiology, Chaudhary Charan Singh Haryana Agricultural University, Hisar, 125004, India
| | - Priya Goswami
- Department of Biotechnology, Mangalayatan University, Uttar Pradesh, India
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4
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Farias P, Francisco R, Maccario L, Herschend J, Piedade AP, Sørensen S, Morais PV. Impact of Tellurite on the Metabolism of Paenibacillus pabuli AL109b With Flagellin Production Explaining High Reduction Capacity. Front Microbiol 2021; 12:718963. [PMID: 34557171 PMCID: PMC8453073 DOI: 10.3389/fmicb.2021.718963] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 08/10/2021] [Indexed: 11/25/2022] Open
Abstract
Tellurium (Te) is a metalloid with scarce and scattered abundance but with an increased interest in human activity for its uses in emerging technologies. As is seen for other metals and metalloids, the result of mining activity and improper disposal of high-tech devices will lead to niches with increased abundance of Te. This metalloid will be more available to bacteria and represent an increasing selective pressure. This environmental problem may constitute an opportunity to search for microorganisms with genetic and molecular mechanisms of microbial resistance to Te toxic anions. Organisms from Te-contaminated niches could provide tools for Te remediation and fabrication of Te-containing structures with added value. The objective of this study was to determine the ability of a high metal-resistant Paenibacillus pabuli strain ALJ109b, isolated from high metal content mining residues, to reduce tellurite ion, and to evaluate the formation of metallic tellurium by cellular reduction, isolate the protein responsible, and determine the metabolic response to tellurite during growth. P. pabuli ALJ109b demonstrated to be resistant to Te (IV) at concentrations higher than reported for its genus. It can efficiently remove soluble Te (IV) from solution, over 20% in 8 h of growth, and reduce it to elemental Te, forming monodisperse nanostructures, verified by scattering electron microscopy. Cultivation of P. pabuli ALJ109b in the presence of Te (IV) affected the general protein expression pattern, and hence the metabolism, as demonstrated by high-throughput proteomic analysis. The Te (IV)-induced metabolic shift is characterized by an activation of ROS response. Flagellin from P. pabuli ALJ109b demonstrates high Te (0) forming activity in neutral to basic conditions in a range of temperatures from 20°C to 37°C. In conclusion, the first metabolic characterization of a strain of P. pabuli response to Te (IV) reveals a highly resistant strain with a unique Te (IV) proteomic response. This strain, and its flagellin, display, all the features of potential tools for Te nanoparticle production.
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Affiliation(s)
- Pedro Farias
- Department of Life Sciences, CEMMPRE, University of Coimbra, Coimbra, Portugal
| | - Romeu Francisco
- Department of Life Sciences, CEMMPRE, University of Coimbra, Coimbra, Portugal
| | - Lorrie Maccario
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Jakob Herschend
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Ana Paula Piedade
- CEMMPRE, Department Mechanical Engineering, University of Coimbra, Coimbra, Portugal
| | - Søren Sørensen
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Paula V. Morais
- Department of Life Sciences, CEMMPRE, University of Coimbra, Coimbra, Portugal
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Pal A, Bhattacharjee S, Saha J, Sarkar M, Mandal P. Bacterial survival strategies and responses under heavy metal stress: a comprehensive overview. Crit Rev Microbiol 2021; 48:327-355. [PMID: 34473592 DOI: 10.1080/1040841x.2021.1970512] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Heavy metals bring long-term hazardous consequences and pose a serious threat to all life forms. Being non-biodegradable, they can remain in the food webs for a long period of time. Metal ions are essential for life and indispensable for almost all aspects of metabolism but can be toxic beyond threshold level to all living beings including microbes. Heavy metals are generally present in the environment, but many geogenic and anthropogenic activities has led to excess metal ion accumulation in the environment. To survive in harsh metal contaminated environments, bacteria have certain resistance mechanisms to metabolize and transform heavy metals into less hazardous forms. This also gives rise to different species of heavy metal resistant bacteria. Herein, we have tried to incorporate the different aspects of heavy metal toxicity in bacteria and provide an up-to-date and across-the-board review. The various aspects of heavy metal biology of bacteria encompassed in this review includes the biological notion of heavy metals, toxic effect of heavy metals on bacteria, the factors regulating bacterial heavy metal resistance, the diverse mechanisms governing bacterial heavy metal resistance, bacterial responses to heavy metal stress, and a brief overview of gene regulation under heavy metal stress.
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Affiliation(s)
- Ayon Pal
- Microbiology and Computational Biology Laboratory, Department of Botany, Raiganj University, Raiganj, India
| | - Sukanya Bhattacharjee
- Microbiology and Computational Biology Laboratory, Department of Botany, Raiganj University, Raiganj, India
| | - Jayanti Saha
- Microbiology and Computational Biology Laboratory, Department of Botany, Raiganj University, Raiganj, India
| | - Monalisha Sarkar
- Mycology and Plant Pathology Laboratory, Department of Botany, Raiganj University, Raiganj, India
| | - Parimal Mandal
- Mycology and Plant Pathology Laboratory, Department of Botany, Raiganj University, Raiganj, India
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Kumar A, Jigyasu DK, Kumar A, Subrahmanyam G, Mondal R, Shabnam AA, Cabral-Pinto MMS, Malyan SK, Chaturvedi AK, Gupta DK, Fagodiya RK, Khan SA, Bhatia A. Nickel in terrestrial biota: Comprehensive review on contamination, toxicity, tolerance and its remediation approaches. CHEMOSPHERE 2021; 275:129996. [PMID: 33647680 DOI: 10.1016/j.chemosphere.2021.129996] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Revised: 02/12/2021] [Accepted: 02/15/2021] [Indexed: 06/12/2023]
Abstract
Nickel (Ni) has been a subject of interest for environmental, physiological, biological scientists due to its dual effect (toxicity and essentiality) in terrestrial biota. In general, the safer limit of Ni is 1.5 μg g-1 in plants and 75-150 μg g-1 in soil. Litreature review indicates that Ni concentrations have been estimated up to 26 g kg-1 in terrestrial, and 0.2 mg L-1 in aquatic resources. In case of vegetables and fruits, mean Ni content has been reported in the range of 0.08-0.26 and 0.03-0.16 mg kg-1. Considering, Ni toxicity and its potential health hazards, there is an urgent need to find out the suitable remedial approaches. Plant vascular (>80%) and cortical (<20%) tissues are the major sequestration site (cation exchange) of absorbed Ni. Deciphering molecular mechanisms in transgenic plants have immense potential for enhancing Ni phytoremediation and microbial remediation efficiency. Further, it has been suggested that integrated bioremediation approaches have a potential futuristic path for Ni decontamination in natural resources. This systematic review provides insight on Ni effects on terrestrial biota including human and further explores its transportation, bioaccumulation through food chain contamination, human health hazards, and possible Ni remediation approaches.
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Affiliation(s)
- Amit Kumar
- School of Hydrology and Water Resources, Nanjing University of Information Science and Technology, Nanjing, Jiangsu, 210044, China
| | - Dharmendra K Jigyasu
- Central Muga Eri Research and Training Institute, Central Silk Board, Jorhat, Assam, 785700, India.
| | - Amit Kumar
- Central Muga Eri Research and Training Institute, Central Silk Board, Jorhat, Assam, 785700, India.
| | - Gangavarapu Subrahmanyam
- Central Muga Eri Research and Training Institute, Central Silk Board, Jorhat, Assam, 785700, India.
| | - Raju Mondal
- Central Sericultural Germplasm Resources Centre (CSGRC), Central Silk Board, Ministry of Textiles, Thally Road, Hosur, Tamil Nadu, 635109, India.
| | - Aftab A Shabnam
- Central Muga Eri Research and Training Institute, Central Silk Board, Jorhat, Assam, 785700, India.
| | - M M S Cabral-Pinto
- Department of Geosciences, Geobiotec Research Centre, University of Aveiro, 3810-193 Aveiro, Portugal.
| | - Sandeep K Malyan
- Research Management and Outreach Division, National Institute of Hydrology, Jalvigyan Bhawan, Roorkee, Uttarakhand, 247667, India.
| | - Ashish K Chaturvedi
- Land and Water Management Research Group, Centre for Water Resources Development and Management, Kozhikode, Kerala, 673571, India.
| | - Dipak Kumar Gupta
- ICAR-Central Arid Zone Research Institute Regional Research Station Pali Marwar, Rajasthan, 342003, India.
| | - Ram Kishor Fagodiya
- Division of Irrigation and Drainage Engineering, ICAR-Central Soil Salinity Research Institute, Karnal, Haryana, 132001, India.
| | - Shakeel A Khan
- Centre for Environment Science and Climate Resilient Agriculture, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.
| | - Arti Bhatia
- Centre for Environment Science and Climate Resilient Agriculture, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.
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Sharma M, Sudheer S, Usmani Z, Rani R, Gupta P. Deciphering the Omics of Plant-Microbe Interaction: Perspectives and New Insights. Curr Genomics 2020; 21:343-362. [PMID: 33093798 PMCID: PMC7536805 DOI: 10.2174/1389202921999200515140420] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 03/29/2020] [Accepted: 04/17/2020] [Indexed: 12/19/2022] Open
Abstract
Introduction Plants do not grow in isolation, rather they are hosts to a variety of microbes in their natural environments. While, few thrive in the plants for their own benefit, others may have a direct impact on plants in a symbiotic manner. Unraveling plant-microbe interactions is a critical component in recognizing the positive and negative impacts of microbes on plants. Also, by affecting the environment around plants, microbes may indirectly influence plants. The progress in sequencing technologies in the genomics era and several omics tools has accelerated in biological science. Studying the complex nature of plant-microbe interactions can offer several strategies to increase the productivity of plants in an environmentally friendly manner by providing better insights. This review brings forward the recent works performed in building omics strategies that decipher the interactions between plant-microbiome. At the same time, it further explores other associated mutually beneficial aspects of plant-microbe interactions such as plant growth promotion, nitrogen fixation, stress suppressions in crops and bioremediation; as well as provides better insights on metabolic interactions between microbes and plants through omics approaches. It also aims to explore advances in the study of Arabidopsis as an important avenue to serve as a baseline tool to create models that help in scrutinizing various factors that contribute to the elaborate relationship between plants and microbes. Causal relationships between plants and microbes can be established through systematic gnotobiotic experimental studies to test hypotheses on biologically derived interactions. Conclusion This review will cover recent advances in the study of plant-microbe interactions keeping in view the advantages of these interactions in improving nutrient uptake and plant health.
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Affiliation(s)
- Minaxi Sharma
- 1Department of Food Technology, ACA, Eternal University, Baru Sahib (173001), Himachal Pradesh, India; 2Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, Lai 40, Tartu, Estonia; 3Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn12612, Estonia; 4Applied Microbiology Laboratory, Department of Environmental Science and Engineering, Indian Institute of Technology (ISM), Dhanbad, India
| | - Surya Sudheer
- 1Department of Food Technology, ACA, Eternal University, Baru Sahib (173001), Himachal Pradesh, India; 2Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, Lai 40, Tartu, Estonia; 3Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn12612, Estonia; 4Applied Microbiology Laboratory, Department of Environmental Science and Engineering, Indian Institute of Technology (ISM), Dhanbad, India
| | - Zeba Usmani
- 1Department of Food Technology, ACA, Eternal University, Baru Sahib (173001), Himachal Pradesh, India; 2Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, Lai 40, Tartu, Estonia; 3Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn12612, Estonia; 4Applied Microbiology Laboratory, Department of Environmental Science and Engineering, Indian Institute of Technology (ISM), Dhanbad, India
| | - Rupa Rani
- 1Department of Food Technology, ACA, Eternal University, Baru Sahib (173001), Himachal Pradesh, India; 2Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, Lai 40, Tartu, Estonia; 3Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn12612, Estonia; 4Applied Microbiology Laboratory, Department of Environmental Science and Engineering, Indian Institute of Technology (ISM), Dhanbad, India
| | - Pratishtha Gupta
- 1Department of Food Technology, ACA, Eternal University, Baru Sahib (173001), Himachal Pradesh, India; 2Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, Lai 40, Tartu, Estonia; 3Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn12612, Estonia; 4Applied Microbiology Laboratory, Department of Environmental Science and Engineering, Indian Institute of Technology (ISM), Dhanbad, India
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Steunou AS, Babot M, Bourbon M, Tambosi R, Durand A, Liotenberg S, Krieger‐Liszkay A, Yamaichi Y, Ouchane S. Additive effects of metal excess and superoxide, a highly toxic mixture in bacteria. Microb Biotechnol 2020; 13:1515-1529. [PMID: 32558268 PMCID: PMC7415354 DOI: 10.1111/1751-7915.13589] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 04/15/2020] [Accepted: 04/16/2020] [Indexed: 01/06/2023] Open
Abstract
Heavy metal contamination is a serious environmental problem. Understanding the toxicity mechanisms may allow to lower concentration of metals in the metal-based antimicrobial treatments of crops, and reduce metal content in soil and groundwater. Here, we investigate the interplay between metal efflux systems and the superoxide dismutase (SOD) in the purple bacterium Rubrivivax gelatinosus and other bacteria through analysis of the impact of metal accumulation. Exposure of the Cd2+ -efflux mutant ΔcadA to Cd2+ caused an increase in the amount and activity of the cytosolic Fe-Sod SodB, thereby suggesting a role of SodB in the protection against Cd2+ . In support of this conclusion, inactivation of sodB gene in the ΔcadA cells alleviated detoxification of superoxide and enhanced Cd2+ toxicity. Similar findings were described in the Cu+ -efflux mutant with Cu+ . Induction of the Mn-Sod or Fe-Sod in response to metals in other bacteria, including Escherichia coli, Pseudomonas aeruginosa, Pseudomonas putida, Vibrio cholera and Bacillus subtilis, was also shown. Both excess Cd2+ or Cu+ and superoxide can damage [4Fe-4S] clusters. The additive effect of metal and superoxide on the [4Fe-4S] could therefore explain the hypersensitive phenotype in mutants lacking SOD and the efflux ATPase. These findings underscore that ROS defence system becomes decisive for bacterial survival under metal excess.
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Affiliation(s)
- Anne Soisig Steunou
- Institute for Integrative Biology of the Cell (I2BC)CEACNRSUniversité Paris‐Saclay91198Gif‐sur‐YvetteFrance
| | - Marion Babot
- Institute for Integrative Biology of the Cell (I2BC)CEACNRSUniversité Paris‐Saclay91198Gif‐sur‐YvetteFrance
| | - Marie‐Line Bourbon
- Institute for Integrative Biology of the Cell (I2BC)CEACNRSUniversité Paris‐Saclay91198Gif‐sur‐YvetteFrance
| | - Reem Tambosi
- Institute for Integrative Biology of the Cell (I2BC)CEACNRSUniversité Paris‐Saclay91198Gif‐sur‐YvetteFrance
| | - Anne Durand
- Institute for Integrative Biology of the Cell (I2BC)CEACNRSUniversité Paris‐Saclay91198Gif‐sur‐YvetteFrance
| | - Sylviane Liotenberg
- Institute for Integrative Biology of the Cell (I2BC)CEACNRSUniversité Paris‐Saclay91198Gif‐sur‐YvetteFrance
| | - Anja Krieger‐Liszkay
- Institute for Integrative Biology of the Cell (I2BC)CEACNRSUniversité Paris‐Saclay91198Gif‐sur‐YvetteFrance
| | - Yoshiharu Yamaichi
- Institute for Integrative Biology of the Cell (I2BC)CEACNRSUniversité Paris‐Saclay91198Gif‐sur‐YvetteFrance
| | - Soufian Ouchane
- Institute for Integrative Biology of the Cell (I2BC)CEACNRSUniversité Paris‐Saclay91198Gif‐sur‐YvetteFrance
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9
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Kong Z, Wu Z, Glick BR, He S, Huang C, Wu L. Co-occurrence patterns of microbial communities affected by inoculants of plant growth-promoting bacteria during phytoremediation of heavy metal-contaminated soils. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2019; 183:109504. [PMID: 31421537 DOI: 10.1016/j.ecoenv.2019.109504] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 07/16/2019] [Accepted: 07/30/2019] [Indexed: 05/03/2023]
Abstract
Phytoremediation assisted by plant growth-promoting bacteria (PGPB) is an alternative method of cleaning up toxic metals from soil. However, the interactions among indigenous soil microorganisms following PGPB inoculation are far from fully understood, although these interactions are conducive to evaluate the effectiveness of PGPB. Here, we used Illumina Miseq sequencing and network analysis to decipher the co-occurrence patterns of bacterial communities following PGPB inoculation during phytoremediation of heavy metal contaminated soil. Miseq sequencing revealed that PGPB inoculation changed the bacterial community composition one day after inoculation, with minor changes continuing to be observed ten days after inoculation. This suggested that PGPB inoculants did not proliferate extensively in a new environment. Network analysis showed that PGPB inoculation altered the co-occurrence patterns, dominant modules and topological roles of individual OTUs. In the presence of PGPB inoculants the bacterial community had more complex and compact associations. Moreover, PGPB inoculation increased the percentage of connectors, indicating that PGPB may contribute to more intensified interactions among OTUs from different modules; consequently, the microbial community would be more ordered and efficient. The enhanced co-occurrence associations in the PGPB-inoculated bacterial network may contribute to the plant growth-promoting effects of PGPB during phytoremediation of heavy metal-contaminated soil.
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Affiliation(s)
- Zhaoyu Kong
- School of Life Science, Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, Nanchang University, Nanchang, 330022, China
| | - Zijun Wu
- School of Life Science, Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, Nanchang University, Nanchang, 330022, China
| | - Bernard R Glick
- Department of Biology, University of Waterloo, Waterloo, ON, N2L 3G1, Canada
| | - Shiyao He
- School of Life Science, Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, Nanchang University, Nanchang, 330022, China
| | - Cheng Huang
- School of Life Science, Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, Nanchang University, Nanchang, 330022, China
| | - Lan Wu
- School of Life Science, Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, Nanchang University, Nanchang, 330022, China.
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10
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Khanna K, Jamwal VL, Kohli SK, Gandhi SG, Ohri P, Bhardwaj R, Abd Allah EF, Hashem A, Ahmad P. Plant growth promoting rhizobacteria induced Cd tolerance in Lycopersicon esculentum through altered antioxidative defense expression. CHEMOSPHERE 2019; 217:463-474. [PMID: 30445394 DOI: 10.1016/j.chemosphere.2018.11.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 10/24/2018] [Accepted: 11/01/2018] [Indexed: 05/08/2023]
Abstract
The present study was designed to determine the role of plant growth-promoting rhizobacteria (Pseudomonas aeruginosa &Burkholderia gladioli) in alleviating Cd stress in Lycopersicon esculentum. Cd concentration of 0.4 mM enhanced superoxide anions, MDA and H2O2 by 136%, 378% and 137% that also caused nuclear and cell viability damage. Cd enhanced the activities of enzymatic antioxidants such as CAT, GST, GPOX, DHAR, and GR by 64%, 126%, 265%, 25% and 93% respectively. However, SOD, POD and PPO was decreased by Cd and enhanced by 119%, 198% and 42% by inoculation of P. aeruginosa and 65%, 119% and 33% by B. gladioli. The contents of non-enzymatic antioxidants and total antioxidants (WSA, LSA) were also enhanced in response to metal stress and reduced by supplementation with PGPR. Confocal microscopy revealed improved cell viability and decreased nuclear damage in Cd-treated L. esculentum roots supplemented with PGPRs. Gene expression studies conducted through qRT-PCR revealed that expression levels of the SOD, POD, and PPO genes were enhanced by 478%, 830% and 253%, while the expression of CAT, GR, GST, GPOX, and APOX genes decreased by 97%, 87%, 75%, 82%, 88% in P. aeruginosa-inoculated Cd-treated seedlings. Also, B. gladioli elevated the expression of SOD, POD and PPO genes and reduced the expression of CAT, GR, GPOX, APOX and GST genes respectively. Therefore, the results suggest that Cd induced oxidative stress in L. esculentum seedlings was reduced by PGPRs through modulation of antioxidative defence expression as demonstrated in terms of antioxidants both quantitatively as well as qualitatively.
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Affiliation(s)
- Kanika Khanna
- Department of Botanical and Environmental Sciences, Guru Nanak Dev University, Amritsar, 143005, India
| | - Vijay Lakshmi Jamwal
- Indian Institute of Integrative Medicine (CSIR-IIIM), Council of Scientific and Industrial Research, Canal Road, Jammu, 180 001, India
| | - Sukhmeen Kaur Kohli
- Department of Botanical and Environmental Sciences, Guru Nanak Dev University, Amritsar, 143005, India
| | - Sumit G Gandhi
- Indian Institute of Integrative Medicine (CSIR-IIIM), Council of Scientific and Industrial Research, Canal Road, Jammu, 180 001, India
| | - Puja Ohri
- Department of Zoology, Guru Nanak Dev University, Amritsar, 143005, India
| | - Renu Bhardwaj
- Department of Botanical and Environmental Sciences, Guru Nanak Dev University, Amritsar, 143005, India.
| | - Elsayed Fathi Abd Allah
- Plant Production Department, College of Food and Agricultural Sciences, King Saud University, P.O. Box. 2460, Riyadh, 11451, Saudi Arabia
| | - Abeer Hashem
- Botany and Microbiology Department, College of Science, King Saud University, P.O. Box. 2460, Riyadh, 11451, Saudi Arabia; Mycology and Plant Disease Survey Department, Plant Pathology Research Institute, Agricultural Research Center, Giza, Egypt
| | - Parvaiz Ahmad
- Botany and Microbiology Department, College of Science, King Saud University, P.O. Box. 2460, Riyadh, 11451, Saudi Arabia; Department of Botany, S.P. College Srinagar, Jammu and Kashmir, India.
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11
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Brunetto G, Bastos de Melo GW, Terzano R, Del Buono D, Astolfi S, Tomasi N, Pii Y, Mimmo T, Cesco S. Copper accumulation in vineyard soils: Rhizosphere processes and agronomic practices to limit its toxicity. CHEMOSPHERE 2016; 162:293-307. [PMID: 27513550 DOI: 10.1016/j.chemosphere.2016.07.104] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 07/28/2016] [Accepted: 07/31/2016] [Indexed: 05/23/2023]
Abstract
Viticulture represents an important agricultural practice in many countries worldwide. Yet, the continuous use of fungicides has caused copper (Cu) accumulation in soils, which represent a major environmental and toxicological concern. Despite being an important micronutrient, Cu can be a potential toxicant at high concentrations since it may cause morphological, anatomical and physiological changes in plants, decreasing both food productivity and quality. Rhizosphere processes can, however, actively control the uptake and translocation of Cu in plants. In particular, root exudates affecting the chemical, physical and biological characteristics of the rhizosphere, might reduce the availability of Cu in the soil and hence its absorption. In addition, this review will aim at discussing the advantages and disadvantages of agronomic practices, such as liming, the use of pesticides, the application of organic matter, biochar and coal fly ashes, the inoculation with bacteria and/or mycorrhizal fungi and the intercropping, in alleviating Cu toxicity symptoms.
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Affiliation(s)
- Gustavo Brunetto
- Departament of Soil Science, Federal University of Santa Maria, 97105-900, Santa Maria, Rio Grande do Sul, Brazil
| | - George Wellington Bastos de Melo
- National Research Center of Grape and Wine (Centro Nacional de Pesquisa de Uva e Vinho - CNPUV), Brazilian Agricultural Research Corporation (Empresa Brasileira de Pesquisa Agropecuária - Embrapa), Bento Gonçalves, Rio Grande do Sul, CEP: 95700-000, Brazil
| | - Roberto Terzano
- Dipartimento di Scienze del Suolo, della Pianta e degli Alimenti, University of Bari "Aldo Moro", I-70126, Bari, Italy
| | - Daniele Del Buono
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di Perugia, Borgo XX Giugno 74, 06121 Perugia, Italy
| | - Stefania Astolfi
- Department of Agricultural and Forestry Sciences (DAFNE), Università della Tuscia, Viterbo, I-01100, Italy
| | - Nicola Tomasi
- Dipartimento di Scienze Agrarie e Ambientali, University of Udine, I-33100, Udine, Italy
| | - Youry Pii
- Faculty of Science and Technology, Free University of Bolzano, Piazza Università 5, 39100, Bolzano, Italy
| | - Tanja Mimmo
- Faculty of Science and Technology, Free University of Bolzano, Piazza Università 5, 39100, Bolzano, Italy.
| | - Stefano Cesco
- Faculty of Science and Technology, Free University of Bolzano, Piazza Università 5, 39100, Bolzano, Italy
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12
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Dourado MN, Franco MR, Peters LP, Martins PF, Souza LA, Piotto FA, Azevedo RA. Antioxidant enzymes activities of Burkholderia spp. strains-oxidative responses to Ni toxicity. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2015; 22:19922-32. [PMID: 26289332 DOI: 10.1007/s11356-015-5204-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2015] [Accepted: 08/10/2015] [Indexed: 05/23/2023]
Abstract
Increased agriculture production associated with intense application of herbicides, pesticides, and fungicides leads to soil contamination worldwide. Nickel (Ni), due to its high mobility in soils and groundwater, constitutes one of the greatest problems in terms of environmental pollution. Metals, including Ni, in high concentrations are toxic to cells by imposing a condition of oxidative stress due to the induction of reactive oxygen species (ROS), which damage lipids, proteins, and DNA. This study aimed to characterize the Ni antioxidant response of two tolerant Burkholderia strains (one isolated from noncontaminated soil, SNMS32, and the other from contaminated soil, SCMS54), by measuring superoxide dismutase (SOD), catalase (CAT), glutathione reductase (GR), and glutathione S-transferase (GST) activities. Ni accumulation and bacterial growth in the presence of the metal were also analyzed. The results showed that both strains exhibited different trends of Ni accumulation and distinct antioxidant enzymes responses. The strain from contaminated soil (SCMS54) exhibited a higher Ni biosorption and exhibited an increase in SOD and GST activities after 5 and 12 h of Ni exposure. The analysis of SOD, CAT, and GR by nondenaturing PAGE revealed the appearance of an extra isoenzyme in strain SCMS54 for each enzyme. The results suggest that the strain SCMS54 isolated from contaminated soil present more plasticity with potential to be used in soil and water bioremediation.
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Affiliation(s)
- M N Dourado
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo (USP), 13400-970, Piracicaba, SP, Brazil
| | - M R Franco
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo (USP), 13400-970, Piracicaba, SP, Brazil
| | - L P Peters
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo (USP), 13400-970, Piracicaba, SP, Brazil
| | - P F Martins
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo (USP), 13400-970, Piracicaba, SP, Brazil
| | - L A Souza
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo (USP), 13400-970, Piracicaba, SP, Brazil
| | - F A Piotto
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo (USP), 13400-970, Piracicaba, SP, Brazil
| | - R A Azevedo
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo (USP), 13400-970, Piracicaba, SP, Brazil.
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San Martin-Uriz P, Mirete S, Alcolea PJ, Gomez MJ, Amils R, Gonzalez-Pastor JE. Nickel-resistance determinants in Acidiphilium sp. PM identified by genome-wide functional screening. PLoS One 2014; 9:e95041. [PMID: 24740277 PMCID: PMC3989265 DOI: 10.1371/journal.pone.0095041] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Accepted: 03/23/2014] [Indexed: 11/18/2022] Open
Abstract
Acidiphilium spp. are conspicuous dwellers of acidic, metal-rich environments. Indeed, they are among the most metal-resistant organisms; yet little is known about the mechanisms behind the metal tolerance in this genus. Acidiphilium sp. PM is an environmental isolate from Rio Tinto, an acidic, metal-laden river located in southwestern Spain. The characterization of its metal resistance revealed a remarkable ability to tolerate high Ni concentrations. Here we report the screening of a genomic library of Acidiphilium sp. PM to identify genes involved in Ni resistance. This approach revealed seven different genes conferring Ni resistance to E. coli, two of which form an operon encoding the ATP-dependent protease HslVU (ClpQY). This protease was found to enhance resistance to both Ni and Co in E. coli, a function not previously reported. Other Ni-resistance determinants include genes involved in lipopolysaccharide biosynthesis and the synthesis of branched amino acids. The diversity of molecular functions of the genes recovered in the screening suggests that Ni resistance in Acidiphilium sp. PM probably relies on different molecular mechanisms.
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Affiliation(s)
- Patxi San Martin-Uriz
- Centro de Astrobiología (INTA-CSIC), Instituto Nacional de Técnica Aeroespacial, Torrejón de Ardoz, Madrid, Spain
| | - Salvador Mirete
- Centro de Astrobiología (INTA-CSIC), Instituto Nacional de Técnica Aeroespacial, Torrejón de Ardoz, Madrid, Spain
| | - Pedro J. Alcolea
- Centro de Investigaciones Biológicas (CSIC), Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Manuel J. Gomez
- Centro de Astrobiología (INTA-CSIC), Instituto Nacional de Técnica Aeroespacial, Torrejón de Ardoz, Madrid, Spain
| | - Ricardo Amils
- Centro de Astrobiología (INTA-CSIC), Instituto Nacional de Técnica Aeroespacial, Torrejón de Ardoz, Madrid, Spain
- Centro de Biología Molecular Severo Ochoa (UAM-CSIC), Universidad Autónoma de Madrid, Madrid, Spain
| | - Jose E. Gonzalez-Pastor
- Centro de Astrobiología (INTA-CSIC), Instituto Nacional de Técnica Aeroespacial, Torrejón de Ardoz, Madrid, Spain
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Mandalakis M, Panikov N, Dai S, Ray S, Karger BL. Comparative proteomic analysis reveals mechanistic insights into Pseudomonas putida F1 growth on benzoate and citrate. AMB Express 2013; 3:64. [PMID: 24156539 PMCID: PMC3827995 DOI: 10.1186/2191-0855-3-64] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2013] [Accepted: 10/21/2013] [Indexed: 11/10/2022] Open
Abstract
Pseudomonas species are capable to proliferate under diverse environmental conditions and thus have a significant bioremediation potential. To enhance our understanding of their metabolic versatility, this study explores the changes in the proteome and physiology of Pseudomonas putida F1 resulting from its growth on benzoate, a moderate toxic compound that can be catabolized, and citrate, a carbon source that is assimilated through central metabolic pathways. A series of repetitive batch cultivations were performed to ensure a complete adaptation of the bacteria to each of these contrasting carbon sources. After several growth cycles, cell growth stabilized at the maximum level and exhibited a reproducible growth profile. The specific growth rates measured for benzoate (1.01 ± 0.11 h-1) and citrate (1.11 ± 0.12 h-1) were similar, while a higher yield was observed for benzoate (0.6 and 0.3 g cell mass per g of benzoate and citrate, respectively), reflecting the different degrees of carbon reduction in the two substrates. Comparative proteomic analysis revealed an enrichment of several oxygenases/dehydrogenases in benzoate-grown cells, indicative of the higher carbon reduction of benzoate. Moreover, the upregulation of all 14 proteins implicated in benzoate degradation via the catechol ortho-cleavage pathway was observed, while several stress-response proteins were increased to aid cells to cope with benzoate toxicity. Unexpectedly, citrate posed more challenges than benzoate in the maintenance of pH homeostasis, as indicated by the enhancement of the Na+/H+ antiporter and carbonic anhydrase. The study provides important mechanistic insights into Pseudomonas adaptation to varying carbon sources that are of great relevance to bioremediation efforts.
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15
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Moreno R, Rojo F. The contribution of proteomics to the unveiling of the survival strategies used by Pseudomonas putida
in changing and hostile environments. Proteomics 2013; 13:2822-30. [DOI: 10.1002/pmic.201200503] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2012] [Revised: 02/26/2013] [Accepted: 03/28/2013] [Indexed: 01/14/2023]
Affiliation(s)
- Renata Moreno
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología; CSIC Madrid Spain
| | - Fernando Rojo
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología; CSIC Madrid Spain
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16
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Poirier I, Hammann P, Kuhn L, Bertrand M. Strategies developed by the marine bacterium Pseudomonas fluorescens BA3SM1 to resist metals: A proteome analysis. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2013; 128-129:215-32. [PMID: 23314334 DOI: 10.1016/j.aquatox.2012.12.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2012] [Revised: 12/05/2012] [Accepted: 12/09/2012] [Indexed: 05/17/2023]
Abstract
A global proteomic evaluation of the response of the marine bacterium Pseudomonas fluorescens BA3SM1 to Cd, Zn and Cu was performed by two dimensional gel electrophoresis followed by mass spectrometry. When stressed with Cd, the most toxic metal for P. fluorescens BA3SM1, cell growth is rapidly affected and the number of proteins up-regulated (sixteen for 0.4 mM Cd) remains low in comparison with results obtained for Zn and Cu (twenty eight for 1.5mM Zn and forty four for 1.5 mM Cu). The changes in protein expression indicate that the cell adapts to metals by inducing essentially seven defense mechanisms: cell aggregation/biofilm formation (Zn=Cu>Cd); modification of envelope properties to increase the extracellular metal biosorption and/or control the uptake of metal (Cu>Zn); metal export (Cd=Zn and probably Cu); responses to oxidative stress (Cu>Zn>Cd); intracellular metal sequestration (Zn=Cu and probably Cd); hydrolysis of abnormally folded proteins (Cd=Cu), and the over-synthesis of proteins inhibited by metal (Cd>Cu>Zn). To the best of our knowledge, this is the first report showing that a marine P. fluorescens is able to acquire a metal-resistant phenotype, making the strain BA3SM1 a promising agent for bioremediation processes.
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Affiliation(s)
- Isabelle Poirier
- Microorganismes Métaux et Toxicité, Institut National des Sciences et Techniques de la Mer, Conservatoire National des Arts et Métiers, Cherbourg-Octeville, France.
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17
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Duan J, Jiang W, Cheng Z, Heikkila JJ, Glick BR. The complete genome sequence of the plant growth-promoting bacterium Pseudomonas sp. UW4. PLoS One 2013; 8:e58640. [PMID: 23516524 PMCID: PMC3596284 DOI: 10.1371/journal.pone.0058640] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Accepted: 02/05/2013] [Indexed: 11/18/2022] Open
Abstract
The plant growth-promoting bacterium (PGPB) Pseudomonas sp. UW4, previously isolated from the rhizosphere of common reeds growing on the campus of the University of Waterloo, promotes plant growth in the presence of different environmental stresses, such as flooding, high concentrations of salt, cold, heavy metals, drought and phytopathogens. In this work, the genome sequence of UW4 was obtained by pyrosequencing and the gaps between the contigs were closed by directed PCR. The P. sp. UW4 genome contains a single circular chromosome that is 6,183,388 bp with a 60.05% G+C content. The bacterial genome contains 5,423 predicted protein-coding sequences that occupy 87.2% of the genome. Nineteen genomic islands (GIs) were predicted and thirty one complete putative insertion sequences were identified. Genes potentially involved in plant growth promotion such as indole-3-acetic acid (IAA) biosynthesis, trehalose production, siderophore production, acetoin synthesis, and phosphate solubilization were determined. Moreover, genes that contribute to the environmental fitness of UW4 were also observed including genes responsible for heavy metal resistance such as nickel, copper, cadmium, zinc, molybdate, cobalt, arsenate, and chromate. Whole-genome comparison with other completely sequenced Pseudomonas strains and phylogeny of four concatenated “housekeeping” genes (16S rRNA, gyrB, rpoB and rpoD) of 128 Pseudomonas strains revealed that UW4 belongs to the fluorescens group, jessenii subgroup.
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Affiliation(s)
- Jin Duan
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada.
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18
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Ray P, Girard V, Gault M, Job C, Bonneu M, Mandrand-Berthelot MA, Singh SS, Job D, Rodrigue A. Pseudomonas putida KT2440 response to nickel or cobalt induced stress by quantitative proteomics. Metallomics 2013; 5:68-79. [DOI: 10.1039/c2mt20147j] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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19
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Huang GH, Tian HH, Liu HY, Fan XW, Liang Y, Li YZ. Characterization of plant-growth-promoting effects and concurrent promotion of heavy metal accumulation in the tissues of the plants grown in the polluted soil by Burkholderia strain LD-11. INTERNATIONAL JOURNAL OF PHYTOREMEDIATION 2013; 15:991-1009. [PMID: 23819291 DOI: 10.1080/15226514.2012.751354] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Plant-growth-promoting (PGP) bacteria especially with the resistance to multiple heavy metals are helpful to phytoremediation. Further development of PGP bacteria is very necessary because of the extreme diversity of plants, soils, and heavy metal pollution. A Burkholderia sp. strain, numbered LD-11, was isolated, which showed resistances to multiple heavy metals and antibiotics. It can produce indole-3-acetic acid, 1-aminocyclopropane-1-carboxylic acid deaminase and siderophores. Inoculation with the LD-11 improved germination of seeds of the investigated vegetable plants in the presence of Cu, promoted elongation of roots and hypocotyledonary axes, enhanced the dry weights of the plants grown in the soils polluted with Cu and/or Pb, and increased activity of the soil urease and the rhizobacteria diversity. Inoculation with the LD-11 significantly enhanced Cu and/or Pb accumulation especially in the roots of the plants grown in the polluted soils. Notably, LD-11 could produce siderophores in the presence of Cu. Conclusively, the PGP effects and concurrent heavy metal accumulation in the plant tissues results from combined effects of the above-mentioned multiple factors. Cu is an important element that represses production of the siderophore by the bacteria. Phytoremediation by synergistic use of the investigated plants and the bacterial strain LD-11 is a phytoextraction process.
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Affiliation(s)
- Gui-Hai Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Key Laboratory of Ministry of Education for Microbial and Plant Genetic Engineering, Guangxi University, Nanning, Guangxi, China
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20
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Glick BR. Plant growth-promoting bacteria: mechanisms and applications. SCIENTIFICA 2012; 2012:963401. [PMID: 24278762 PMCID: PMC3820493 DOI: 10.6064/2012/963401] [Citation(s) in RCA: 869] [Impact Index Per Article: 72.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2012] [Accepted: 09/13/2012] [Indexed: 05/18/2023]
Abstract
The worldwide increases in both environmental damage and human population pressure have the unfortunate consequence that global food production may soon become insufficient to feed all of the world's people. It is therefore essential that agricultural productivity be significantly increased within the next few decades. To this end, agricultural practice is moving toward a more sustainable and environmentally friendly approach. This includes both the increasing use of transgenic plants and plant growth-promoting bacteria as a part of mainstream agricultural practice. Here, a number of the mechanisms utilized by plant growth-promoting bacteria are discussed and considered. It is envisioned that in the not too distant future, plant growth-promoting bacteria (PGPB) will begin to replace the use of chemicals in agriculture, horticulture, silviculture, and environmental cleanup strategies. While there may not be one simple strategy that can effectively promote the growth of all plants under all conditions, some of the strategies that are discussed already show great promise.
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Affiliation(s)
- Bernard R. Glick
- Department of Biology, University of Waterloo, 200 University Avenue South, Waterloo, ON, Canada N2L 3G1
- *Bernard R. Glick:
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Abstract
Nickel has long been known to be an important human toxicant, including having the ability to form carcinomas, but until recently nickel was believed to be an issue only to microorganisms living in nickel-rich serpentine soils or areas contaminated by industrial pollution. This assumption was overturned by the discovery of a nickel defense system (RcnR/RcnA) found in microorganisms that live in a wide range of environmental niches, suggesting that nickel homeostasis is a general biological concern. To date, the mechanisms of nickel toxicity in microorganisms and higher eukaryotes are poorly understood. In this review, we summarize nickel homeostasis processes used by microorganisms and highlight in vivo and in vitro effects of exposure to elevated concentrations of nickel. On the basis of this evidence we propose four mechanisms of nickel toxicity: (1) nickel replaces the essential metal of metalloproteins, (2) nickel binds to catalytic residues of non-metalloenzymes; (3) nickel binds outside the catalytic site of an enzyme to inhibit allosterically and (4) nickel indirectly causes oxidative stress.
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Affiliation(s)
- Lee Macomber
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824-4320, USA
| | - Robert P. Hausinger
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824-4320, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824-1319, USA
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do Carmo FL, dos Santos HF, Martins EF, van Elsas JD, Rosado AS, Peixoto RS. Bacterial structure and characterization of plant growth promoting and oil degrading bacteria from the rhizospheres of mangrove plants. J Microbiol 2011; 49:535-43. [DOI: 10.1007/s12275-011-0528-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2010] [Accepted: 02/24/2011] [Indexed: 10/17/2022]
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23
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Doxey AC, Cheng Z, Moffatt BA, McConkey BJ. Structural motif screening reveals a novel, conserved carbohydrate-binding surface in the pathogenesis-related protein PR-5d. BMC STRUCTURAL BIOLOGY 2010; 10:23. [PMID: 20678238 PMCID: PMC2924342 DOI: 10.1186/1472-6807-10-23] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2010] [Accepted: 08/03/2010] [Indexed: 01/10/2023]
Abstract
BACKGROUND Aromatic amino acids play a critical role in protein-glycan interactions. Clusters of surface aromatic residues and their features may therefore be useful in distinguishing glycan-binding sites as well as predicting novel glycan-binding proteins. In this work, a structural bioinformatics approach was used to screen the Protein Data Bank (PDB) for coplanar aromatic motifs similar to those found in known glycan-binding proteins. RESULTS The proteins identified in the screen were significantly associated with carbohydrate-related functions according to gene ontology (GO) enrichment analysis, and predicted motifs were found frequently within novel folds and glycan-binding sites not included in the training set. In addition to numerous binding sites predicted in structural genomics proteins of unknown function, one novel prediction was a surface motif (W34/W36/W192) in the tobacco pathogenesis-related protein, PR-5d. Phylogenetic analysis revealed that the surface motif is exclusive to a subfamily of PR-5 proteins from the Solanaceae family of plants, and is absent completely in more distant homologs. To confirm PR-5d's insoluble-polysaccharide binding activity, a cellulose-pulldown assay of tobacco proteins was performed and PR-5d was identified in the cellulose-binding fraction by mass spectrometry. CONCLUSIONS Based on the combined results, we propose that the putative binding site in PR-5d may be an evolutionary adaptation of Solanaceae plants including potato, tomato, and tobacco, towards defense against cellulose-containing pathogens such as species of the deadly oomycete genus, Phytophthora. More generally, the results demonstrate that coplanar aromatic clusters on protein surfaces are a structural signature of glycan-binding proteins, and can be used to computationally predict novel glycan-binding proteins from 3 D structure.
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Affiliation(s)
- Andrew C Doxey
- Department of Biology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada
- Department of Developmental Biology, Stanford University, Stanford, CA, 94305, USA
| | - Zhenyu Cheng
- Department of Biology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada
| | - Barbara A Moffatt
- Department of Biology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada
| | - Brendan J McConkey
- Department of Biology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada
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Sun Z, Cheng Z, Taylor CA, McConkey BJ, Thompson JE. Apoptosis induction by eIF5A1 involves activation of the intrinsic mitochondrial pathway. J Cell Physiol 2010; 223:798-809. [PMID: 20232312 DOI: 10.1002/jcp.22100] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The regulatory role of eukaryotic translation initiation factor 5A1 (eIF5A1) in apoptosis was examined using HT-29 and HeLa S3 cells. eIF5A is the only known protein to contain the unusual amino acid, hypusine, and eIF5A1 is one of two human eIF5A family members. Two observations indicated that eIF5A1 is involved in apoptosis. First, siRNA-mediated suppression of eIF5A1 resulted in inhibition of apoptosis induced by various apoptotic stimuli, and second, adenovirus-mediated over-expression of eIF5A1 strongly induced apoptotic cell death. A mutant of eIF5A1 incapable of being hypusinated also induced apoptosis when over-expressed indicating that unhypusinated eIF5A1 is the pro-apoptotic form of the protein. Over-expression of eIF5A1 or of the mutant resulted in loss of mitochondrial transmembrane potential, translocation of Bax to the mitochondria, release of cytochrome c, caspase activation, up-regulation of p53, and up-regulation of Bim, a pro-apoptotic BH3-only Bcl-2 family protein. In addition, Bim(L) and Bim(S), the pro-apoptotic alternative spliced forms of Bim, were induced in response to over-expression of eIF5A1. Thus eIF5A1 appears to induce apoptosis by activating the mitochondrial apoptotic pathway. Proteomic analyses indicated that, of 1,899 proteins detected, 131 showed significant changes in expression (P or=1.5) within 72 h of eIF5A1 up-regulation. Among these are proteins involved in translation and protein folding, transcription factors, proteins mediating proteolysis, and a variety of proteins known to be directly involved in apoptosis. These observations collectively indicate that unhypusinated eIF5A1 plays a central role in the regulation of apoptosis.
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Affiliation(s)
- Zhong Sun
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
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