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Sun J, He X, LE Y, Al-Tohamy R, Ali SS. Potential applications of extremophilic bacteria in the bioremediation of extreme environments contaminated with heavy metals. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 352:120081. [PMID: 38237330 DOI: 10.1016/j.jenvman.2024.120081] [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: 11/25/2023] [Revised: 12/31/2023] [Accepted: 01/07/2024] [Indexed: 02/04/2024]
Abstract
Protecting the environment from harmful pollutants has become increasingly difficult in recent decades. The presence of heavy metal (HM) pollution poses a serious environmental hazard that requires intricate attention on a worldwide scale. Even at low concentrations, HMs have the potential to induce deleterious health effects in both humans and other living organisms. Therefore, various strategies have been proposed to address this issue, with extremophiles being a promising solution. Bacteria that exhibit resistance to metals are preferred for applications involving metal removal due to their capacity for rapid multiplication and growth. Extremophiles are a special group of microorganisms that are capable of surviving under extreme conditions such as extreme temperatures, pH levels, and high salt concentrations where other organisms cannot. Due to their unique enzymes and adaptive capabilities, extremophiles are well suited as catalysts for environmental biotechnology applications, including the bioremediation of HMs through various strategies. The mechanisms of resistance to HMs by extremophilic bacteria encompass: (i) metal exclusion by permeability barrier; (ii) extracellular metal sequestration by protein/chelator binding; (iii) intracellular sequestration of the metal by protein/chelator binding; (iv) enzymatic detoxification of a metal to a less toxic form; (v) active transport of HMs; (vi) passive tolerance; (vii) reduced metal sensitivity of cellular targets to metal ions; and (viii) morphological change of cells. This review provides comprehensive information on extremophilic bacteria and their potential roles for bioremediation, particularly in environments contaminated with HMs, which pose a threat due to their stability and persistence. Genetic engineering of extremophilic bacteria in stressed environments could help in the bioremediation of contaminated sites. Due to their unique characteristics, these organisms and their enzymes are expected to bridge the gap between biological and chemical industrial processes. However, the structure and biochemical properties of extremophilic bacteria, along with any possible long-term effects of their applications, need to be investigated further.
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Affiliation(s)
- Jianzhong Sun
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, China.
| | - Xing He
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - Yilin LE
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, China.
| | - Rania Al-Tohamy
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - Sameh S Ali
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, China; Botany Department, Faculty of Science, Tanta University, Tanta, 31527, Egypt.
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Bourhane Z, Lanzén A, Cagnon C, Ben Said O, Mahmoudi E, Coulon F, Atai E, Borja A, Cravo-Laureau C, Duran R. Microbial diversity alteration reveals biomarkers of contamination in soil-river-lake continuum. JOURNAL OF HAZARDOUS MATERIALS 2022; 421:126789. [PMID: 34365235 DOI: 10.1016/j.jhazmat.2021.126789] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 07/27/2021] [Accepted: 07/28/2021] [Indexed: 05/21/2023]
Abstract
Microbial communities inhabiting soil-water-sediment continuum in coastal areas provide important ecosystem services. Their adaptation in response to environmental stressors, particularly mitigating the impact of pollutants discharged from human activities, has been considered for the development of microbial biomonitoring tools, but their use is still in the infancy. Here, chemical and molecular (16S rRNA gene metabarcoding) approaches were combined in order to determine the impact of pollutants on microbial assemblages inhabiting the aquatic network of a soil-water-sediment continuum around the Ichkeul Lake (Tunisia), an area highly impacted by human activities. Samples were collected within the soil-river-lake continuum at three stations in dry (summer) and wet (winter) seasons. The contaminant pressure index (PI), which integrates Polycyclic aromatic hydrocarbons (PAHs), alkanes, Organochlorine pesticides (OCPs) and metal contents, and the microbial pressure index microgAMBI, based on bacterial community structure, showed significant correlation with contamination level and differences between seasons. The comparison of prokaryotic communities further revealed specific assemblages for soil, river and lake sediments. Correlation analyses identified potential "specialist" genera for the different compartments, whose abundances were correlated with the pollutant type found. Additionally, PICRUSt analysis revealed the metabolic potential for pollutant transformation or degradation of the identified "specialist" species, providing information to estimate the recovery capacity of the ecosystem. Such findings offer the possibility to define a relevant set of microbial indicators for assessing the effects of human activities on aquatic ecosystems. Microbial indicators, including the detection of "specialist" and sensitive taxa, and their functional capacity, might be useful, in combination with integrative microbial indices, to constitute accurate biomonitoring tools for the management and restoration of complex coastal aquatic systems.
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Affiliation(s)
- Zeina Bourhane
- Université de Pau et des Pays de l'Adour, UPPA/E2S, IPREM CNRS 5254, Pau, France
| | - Anders Lanzén
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Herrera Kaia, Portualdea z/g, 20110 Pasaia, Gipuzkoa, Spain; IKERBASQUE, Basque Foundation for Science, E-48011 Bilbao, Spain
| | - Christine Cagnon
- Université de Pau et des Pays de l'Adour, UPPA/E2S, IPREM CNRS 5254, Pau, France
| | - Olfa Ben Said
- Laboratoire de Biosurveillance de l'Environnement, Faculté des Sciences de Bizerte, LBE, Tunisia
| | - Ezzeddine Mahmoudi
- Laboratoire de Biosurveillance de l'Environnement, Faculté des Sciences de Bizerte, LBE, Tunisia
| | - Frederic Coulon
- Cranfield University, School of Water, Energy and Environment, Cranfield MK430AL, UK
| | - Emmanuel Atai
- Cranfield University, School of Water, Energy and Environment, Cranfield MK430AL, UK
| | - Angel Borja
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Herrera Kaia, Portualdea z/g, 20110 Pasaia, Gipuzkoa, Spain; King Abdulaziz University, Faculty of Marine Sciences, Jeddah, Saudi Arabia
| | | | - Robert Duran
- Université de Pau et des Pays de l'Adour, UPPA/E2S, IPREM CNRS 5254, Pau, France.
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Sharma Ghimire P, Tripathee L, Zhang Q, Guo J, Ram K, Huang J, Sharma CM, Kang S. Microbial mercury methylation in the cryosphere: Progress and prospects. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 697:134150. [PMID: 32380618 DOI: 10.1016/j.scitotenv.2019.134150] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 08/20/2019] [Accepted: 08/26/2019] [Indexed: 06/11/2023]
Abstract
Mercury (Hg) is one of the most toxic heavy metals, and its cycle is mainly controlled by oxidation-reduction reactions carried out by photochemical or microbial process under suitable conditions. The deposition and accumulation of methylmercury (MeHg) in various ecosystems, including the cryospheric components such as snow, meltwater, glaciers, and ice sheet, and subsequently in the food chain pose serious health concerns for living beings. Unlike the abundance of knowledge about the processes of MeHg production over land and oceans, little is known about the sources and production/degradation rate of MeHg in cryosphere systems. In addition, processes controlling the concentration of Hg and MeHg in the cryosphere remains poorly understood, and filling this scientific gap has been challenging. Therefore, it is essential to study and review the deposition and accumulation by biological, physical, and chemical mechanisms involved in Hg methylation in the cryosphere. This review attempts to address knowledge gaps in understanding processes, especially biotic and abiotic, applicable for Hg methylation in the cryosphere. First, we focus on the variability in Hg concentration and mechanisms of Hg methylation, including physical, chemical, microbial, and biological processes, and transportation in the cryosphere. Then, we elaborate on the mechanism of redox reactions and biotic and abiotic factors controlling Hg methylation and biogeochemistry of Hg in the cryosphere. We also present possible mechanisms of Hg methylation with an emphasis on microbial transformation and molecular function to understand variability in Hg concentration in the cryosphere. Recent advancements in the genetic and physicochemical mechanisms of Hg methylation are also presented. Finally, we summarize and propose a method to study the unsolved issues of Hg methylation in the cryosphere.
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Affiliation(s)
- Prakriti Sharma Ghimire
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-environment and Resources, Chinese Academy of Sciences (CAS), Lanzhou 730000, China; Himalayan Environment Research Institute (HERI), Kathmandu, Nepal
| | - Lekhendra Tripathee
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-environment and Resources, Chinese Academy of Sciences (CAS), Lanzhou 730000, China; Himalayan Environment Research Institute (HERI), Kathmandu, Nepal.
| | - Qianggong Zhang
- Key Laboratory of Tibetan Environment Changes and Land Surface Processes, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China; CAS Center for Excellence in Tibetan Plateau Earth Sciences, Beijing 100085, China
| | - Junming Guo
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-environment and Resources, Chinese Academy of Sciences (CAS), Lanzhou 730000, China
| | - Kirpa Ram
- Institute of Environment and Sustainable Development, Banaras Hindu University, Varanasi, India
| | - Jie Huang
- CAS Center for Excellence in Tibetan Plateau Earth Sciences, Beijing 100085, China; Key Laboratory of Tibetan Environment Changes and Land Surface Processes, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Chhatra Mani Sharma
- Himalayan Environment Research Institute (HERI), Kathmandu, Nepal; Central Department of Environmental Science, Tribhuvan University, Kathmandu, Nepal
| | - Shichang Kang
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-environment and Resources, Chinese Academy of Sciences (CAS), Lanzhou 730000, China; CAS Center for Excellence in Tibetan Plateau Earth Sciences, Beijing 100085, China.
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Hödar C, Moreno P, di Genova A, Latorre M, Reyes-Jara A, Maass A, González M, Cambiazo V. Genome wide identification of Acidithiobacillus ferrooxidans (ATCC 23270) transcription factors and comparative analysis of ArsR and MerR metal regulators. Biometals 2011; 25:75-93. [PMID: 21830017 DOI: 10.1007/s10534-011-9484-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2011] [Accepted: 07/21/2011] [Indexed: 10/25/2022]
Abstract
Acidithiobacillus ferrooxidans is a chemolithoautotrophic acidophilic bacterium that obtains its energy from the oxidation of ferrous iron, elemental sulfur, or reduced sulfur minerals. This capability makes it of great industrial importance due to its applications in biomining. During the industrial processes, A. ferrooxidans survives to stressing circumstances in its environment, such as an extremely acidic pH and high concentration of transition metals. In order to gain insight into the organization of A. ferrooxidans regulatory networks and to provide a framework for further studies in bacterial growth under extreme conditions, we applied a genome-wide annotation procedure to identify 87 A. ferrooxidans transcription factors. We classified them into 19 families that were conserved among diverse prokaryotic phyla. Our annotation procedure revealed that A. ferrooxidans genome contains several members of the ArsR and MerR families, which are involved in metal resistance and detoxification. Analysis of their sequences revealed known and potentially new mechanism to coordinate gene-expression in response to metal availability. A. ferrooxidans inhabit some of the most metal-rich environments known, thus transcription factors identified here seem to be good candidates for functional studies in order to determine their physiological roles and to place them into A. ferrooxidans transcriptional regulatory networks.
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Affiliation(s)
- Christian Hödar
- Laboratorio de Bioinformática y Expresión Génica, INTA, Universidad de Chile, El Libano 5524, Santiago, Chile
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Takeuchi F, Negishi A, Nakamura S, Kanao T, Kamimura K, Sugio T. Existence of an iron-oxidizing bacterium Acidithiobacillus ferrooxidans resistant to organomercurial compounds. J Biosci Bioeng 2005; 99:586-91. [PMID: 16233835 DOI: 10.1263/jbb.99.586] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2005] [Accepted: 03/13/2005] [Indexed: 11/17/2022]
Abstract
Acidithiobacillus ferrooxidans MON-1 which is highly resistant to Hg2+ could grow in a ferrous sulfate medium (pH 2.5) with 0.1 microM p-chloromercuribenzoic acid (PCMB) with a lag time of 2 d. In contrast, A. ferrooxidans AP19-3 which is sensitive to Hg2+ did not grow in the medium. Nine strains of A. ferrooxidans, including seven strains of the American Type Culture Collection grew in the medium with a lag time ranging from 5 to 12 d. The resting cells of MON-1, which has NADPH-dependent mercuric reductase activity, could volatilize Hg0 when incubated in acidic water (pH 3.0) containing 0.1 microM PCMB. However, the resting cells of AP19-3, which has a similar level of NADPH-dependent mercuric reductase activity compared with MON-1, did not volatilize Hg0 from the reaction mixture with 0.1 microM PCMB. The activity level of the 11 strains of A. ferrooxidans to volatilize Hg0 from PCMB corresponded well with the level of growth inhibition by PCMB observed in the growth experiments. The resting cells of MON-1 volatilized Hg0 from phenylmercury acetate (PMA) and methylmercury chloride (MMC) as well as PCMB. The cytosol prepared from MON-1 could volatilize Hg0 from PCMB (0.015 nmol mg(-1) h(-1)), PMA (0.33 nmol mg(-1) h(-1)) and MMC (0.005 nmol mg(-1) h(-1)) in the presence of NADPH and beta-mercaptoethanol.
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Affiliation(s)
- Fumiaki Takeuchi
- Environmental Management and Safety Section, Health and Environment Center, Okayama University, 3-1-1 Tsushima-naka, Okayama 700-8530, Japan
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Dopson M, Baker-Austin C, Koppineedi PR, Bond PL. Growth in sulfidic mineral environments: metal resistance mechanisms in acidophilic micro-organisms. MICROBIOLOGY (READING, ENGLAND) 2003; 149:1959-1970. [PMID: 12904536 DOI: 10.1099/mic.0.26296-0] [Citation(s) in RCA: 255] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Acidophilic micro-organisms inhabit some of the most metal-rich environments known, including both natural and man-made ecosystems, and as such are ideal model systems for study of microbial metal resistance. Although metal resistance systems have been studied in neutrophilic micro-organisms, it is only in recent years that attention has been placed on metal resistance in acidophiles. The five metal resistance mechanisms identified in neutrophiles are also present in acidophiles, in some cases utilizing homologous proteins, but in many cases the degree of resistance is greater in acidophiles. This review summarizes the knowledge of acidophile metal resistance and presents preliminary in silico studies on a few known metal resistance systems in the sequenced acidophile genomes.
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Affiliation(s)
- Mark Dopson
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
| | - Craig Baker-Austin
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
| | - P Ram Koppineedi
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
| | - Philip L Bond
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
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Makarova KS, Wolf YI, White O, Minton K, Daly MJ. Short repeats and IS elements in the extremely radiation-resistant bacterium Deinococcus radiodurans and comparison to other bacterial species. Res Microbiol 1999; 150:711-24. [PMID: 10673009 DOI: 10.1016/s0923-2508(99)00121-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Computer analysis of the complete genome of Deinococcus radiodurans R1 has shown that the number of insertion sequences (ISs) and small noncoding repeats (SNRs) it contains is very high, and comparable with those of Escherichia coli. IS elements and several families of SNRs are described, together with their possible function in the D. radiodurans genome.
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Affiliation(s)
- K S Makarova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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