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Guo P, Du H, Mao Q, Deng Y, Wang X, Li J, Xiong B, Fan X, Wang D, Agathokleous E, Ma M. The duality of sulfate-reducing bacteria: Reducing methylmercury production in rhizosphere but enhancing accumulation in rice plants. JOURNAL OF HAZARDOUS MATERIALS 2024; 476:135049. [PMID: 38970973 DOI: 10.1016/j.jhazmat.2024.135049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Revised: 06/25/2024] [Accepted: 06/26/2024] [Indexed: 07/08/2024]
Abstract
Sulfate-reducing bacteria (SRB) are known to alter methylmercury (MeHg) production in paddy soil, but the effect of SRB on MeHg dynamics in rhizosphere and rice plants remains to be fully elucidated. The present study investigated the impact of SRB on MeHg levels in unsterilized and γ-sterilized mercury-polluted paddy soils, with the aim to close this knowledge gap. Results showed that the presence of SRB reduced MeHg production by ∼22 % and ∼17 % in the two soils, but elevated MeHg contents by approximately 55 % and 99 % in rice grains, respectively. Similar trend at smaller scales were seen in roots and shoots. SRB inoculation exerted the most profound impact on amino acid metabolism in roots, with the relative response of L-arginine positively linking to MeHg concentrations in rhizosphere. The SRB-induced enrichment of MeHg in rice plants may be interpreted by the stronger presence of endophytic nitrogen-related microbes (e.g. Methylocaldum, Hyphomicrobium and Methylocystis) and TGA transcription factors interacting with glutathione metabolism and calmodulin. Our study provides valuable insights into the complex effects of SRB inoculation on MeHg dynamics in rice ecosystems, and may help to develop strategies to effectively control MeHg accumulation in rice grains.
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Affiliation(s)
- Pan Guo
- Center of Molecular Ecophysiology (CMEP), College of Resources and Environment, Southwest University, Chongqing 400715, PR China
| | - Hongxia Du
- Chongqing Key Laboratory for Innovative Application of Genetic Technology, College of Resources and Environment, Southwest University, Chongqing 400715, PR China
| | - Qiaozhi Mao
- Center of Molecular Ecophysiology (CMEP), College of Resources and Environment, Southwest University, Chongqing 400715, PR China
| | - Yuhan Deng
- Center of Molecular Ecophysiology (CMEP), College of Resources and Environment, Southwest University, Chongqing 400715, PR China; Chongqing Key Laboratory of Agricultural Resources and Environment, College of Resources and Environment, Chongqing 400715, PR China
| | - Xun Wang
- Center of Molecular Ecophysiology (CMEP), College of Resources and Environment, Southwest University, Chongqing 400715, PR China
| | - Jing Li
- School of Chemical and Pharmaceutical Engineering, Chongqing Industry Polytechnic College, Chongqing 401120, PR China
| | - Bingcai Xiong
- Chongqing Key Laboratory for Innovative Application of Genetic Technology, College of Resources and Environment, Southwest University, Chongqing 400715, PR China
| | - Xu Fan
- Center of Molecular Ecophysiology (CMEP), College of Resources and Environment, Southwest University, Chongqing 400715, PR China
| | - Dingyong Wang
- Chongqing Key Laboratory of Agricultural Resources and Environment, College of Resources and Environment, Chongqing 400715, PR China
| | - Evgenios Agathokleous
- Department of Ecology, School of Ecology and Applied Meteorology, Nanjing University of Information Science & Technology, Nanjing 210044, PR China
| | - Ming Ma
- Center of Molecular Ecophysiology (CMEP), College of Resources and Environment, Southwest University, Chongqing 400715, PR China; Chongqing Key Laboratory of Agricultural Resources and Environment, College of Resources and Environment, Chongqing 400715, PR China.
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2
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Wang H, Zhou Q. Potential application of bioelectrochemical systems in cold environments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 927:172385. [PMID: 38604354 DOI: 10.1016/j.scitotenv.2024.172385] [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: 02/06/2024] [Revised: 03/17/2024] [Accepted: 04/08/2024] [Indexed: 04/13/2024]
Abstract
Globally, more than half of the world's regions and populations inhabit psychrophilic and seasonally cold environments. Lower temperatures can inhibit the metabolic activity of microorganisms, thereby restricting the application of traditional biological treatment technologies. Bioelectrochemical systems (BES), which combine electrochemistry and biocatalysis, can enhance the resistance of microorganisms to unfavorable environments through electrical stimulation, thus showing promising applications in low-temperature environments. In this review, we focus on the potential application of BES in such environments, given the relatively limited research in this area due to temperature limitations. We select microbial fuel cells (MFC), microbial electrolytic cells (MEC), and microbial electrosynthesis cells (MES) as the objects of analysis and compare their operational mechanisms and application fields. MFC mainly utilizes the redox potential of microorganisms during substance metabolism to generate electricity, while MEC and MES promote the degradation of refractory substances by augmenting the electrode potential with an applied voltage. Subsequently, we summarize and discuss the application of these three types of BES in low-temperature environments. MFC can be employed for environmental remediation as well as for biosensors to monitor environmental quality, while MEC and MES are primarily intended for hydrogen and methane production. Additionally, we explore the influencing factors for the application of BES in low-temperature environments, including operational parameters, electrodes and membranes, external voltage, oxygen intervention, and reaction devices. Finally, the technical, economic, and environmental feasibility analyses reveal that the application of BES in low-temperature environments has great potential for development.
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Affiliation(s)
- Hui Wang
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Qixing Zhou
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China.
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3
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Villa-Cruz V, Jaimes-Reátegui S, Alba-Cuevas JE, Zelaya-Molina LX, Jaimes-Reátegui R, Pisarchik AN. Quantifying Geobacter sulfurreducens growth: A mathematical model based on acetate concentration as an oxidizing substrate. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2024; 21:5972-5995. [PMID: 38872566 DOI: 10.3934/mbe.2024263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2024]
Abstract
We developed a mathematical model to simulate dynamics associated with the proliferation of Geobacter and ultimately optimize cellular operation by analyzing the interaction of its components. The model comprises two segments: an initial part comprising a logistic form and a subsequent segment that incorporates acetate oxidation as a saturation term for the microbial nutrient medium. Given that four parameters can be obtained by minimizing the square root of the mean square error between experimental Geobacter growth and the mathematical model, the model underscores the importance of incorporating nonlinear terms. The determined parameter values closely align with experimental data, providing insights into the mechanisms that govern Geobacter proliferation. Furthermore, the model has been transformed into a scaleless equation with only two parameters to simplify the exploration of qualitative properties. This allowed us to conduct stability analysis of the fixed point and construct a co-dimension two bifurcation diagram.
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Affiliation(s)
- Virgínia Villa-Cruz
- Centro Universitario de los Lagos, Universidad de Guadalajara, Enrique Díaz de León 1144, Colonia Paseos de la Montaña, 47460 Lagos de Moreno, Jalisco, Mexico
| | - Sumaya Jaimes-Reátegui
- Universidad Nacional Hermilio Valdizán, Av. Universitaria, 601-607, Pilco Marca, C.P. 10003, Huánuco, Perú
| | - Juana E Alba-Cuevas
- Centro Universitario de los Lagos, Universidad de Guadalajara, Enrique Díaz de León 1144, Colonia Paseos de la Montaña, 47460 Lagos de Moreno, Jalisco, Mexico
| | - Lily Xochilt Zelaya-Molina
- Centro Nacional de Recursos Genéticos, Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Boulevard de la Biodiversidad No. 400, Rancho Las Cruces, CP 47600. Tepatitlán de Morelos, Jalisco, Mexico
| | - Rider Jaimes-Reátegui
- Centro Universitario de los Lagos, Universidad de Guadalajara, Enrique Díaz de León 1144, Colonia Paseos de la Montaña, 47460 Lagos de Moreno, Jalisco, Mexico
| | - Alexander N Pisarchik
- Center for Biomedical Technology, Universidad Politécnica de Madrid, Campus de Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain
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Hidalgo-Martinez K, Giachini AJ, Schneider M, Soriano A, Baessa MP, Martins LF, de Oliveira VM. Shifts in structure and dynamics of the soil microbiome in biofuel/fuel blend-affected areas triggered by different bioremediation treatments. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:33663-33684. [PMID: 38687451 DOI: 10.1007/s11356-024-33304-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 04/09/2024] [Indexed: 05/02/2024]
Abstract
The use of biofuels has grown in the last decades as a consequence of the direct environmental impacts of fossil fuel use. Elucidating structure, diversity, species interactions, and assembly mechanisms of microbiomes is crucial for understanding the influence of environmental disturbances. However, little is known about how contamination with biofuel/petrofuel blends alters the soil microbiome. Here, we studied the dynamics in the soil microbiome structure and composition of four field areas under long-term contamination with biofuel/fossil fuel blends (ethanol 10% and gasoline 90%-E10; ethanol 25% and gasoline 75%-E25; soybean biodiesel 20% and diesel 80%-B20) submitted to different bioremediation treatments along a temporal gradient. Soil microbiomes from biodiesel-polluted areas exhibited higher richness and diversity index values and more complex microbial communities than ethanol-polluted areas. Additionally, monitored natural attenuation B20-polluted areas were less affected by perturbations caused by bioremediation treatments. As a consequence, once biostimulation was applied, the degradation was slower compared with areas previously actively treated. In soils with low diversity and richness, the impact of bioremediation treatments on the microbiomes was greater, and as a result, the hydrocarbon degradation extent was higher. The network analysis showed that all abundant keystone taxa corresponded to well-known degraders, suggesting that the abundant species are core targets for biostimulation in soil remediation processes. Altogether, these findings showed that the knowledge gained through the study of microbiomes in contaminated areas may help design and conduct optimized bioremediation approaches, paving the way for future rationalized and efficient pollutant mitigation strategies.
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Affiliation(s)
- Kelly Hidalgo-Martinez
- Divisão de Recursos Microbianos, Centro Pluridisciplinar de Pesquisas Químicas, Biológicas E Agrícolas (CPQBA), Universidade Estadual de Campinas (UNICAMP), Paulínia, SP, CEP 13148-218, Brazil.
- Programa de Pós-Graduação de Genética E Biologia Molecular, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, SP, CEP 13083-970, Brazil.
| | - Admir José Giachini
- Núcleo Ressacada de Pesquisas Em Meio Ambiente (REMA)-Department of Microbiology, Federal University of Santa Catarina (UFSC), Campus Universitário Sul da Ilha-Rua José Olímpio da Silva, 1326-Bairro Tapera, Florianópolis, SC, 88049-500, Brazil
| | - Marcio Schneider
- Núcleo Ressacada de Pesquisas Em Meio Ambiente (REMA)-Department of Microbiology, Federal University of Santa Catarina (UFSC), Campus Universitário Sul da Ilha-Rua José Olímpio da Silva, 1326-Bairro Tapera, Florianópolis, SC, 88049-500, Brazil
| | - Adriana Soriano
- PETROBRAS/R&D Center (CENPES), Cidade Universitária, Av. Horácio Macedo, Ilha Do Fundão, Rio de Janeiro, 950, ZIP 21941-915, Brazil
| | - Marcus Paulus Baessa
- PETROBRAS/R&D Center (CENPES), Cidade Universitária, Av. Horácio Macedo, Ilha Do Fundão, Rio de Janeiro, 950, ZIP 21941-915, Brazil
| | - Luiz Fernando Martins
- PETROBRAS/R&D Center (CENPES), Cidade Universitária, Av. Horácio Macedo, Ilha Do Fundão, Rio de Janeiro, 950, ZIP 21941-915, Brazil
| | - Valéria Maia de Oliveira
- Divisão de Recursos Microbianos, Centro Pluridisciplinar de Pesquisas Químicas, Biológicas E Agrícolas (CPQBA), Universidade Estadual de Campinas (UNICAMP), Paulínia, SP, CEP 13148-218, Brazil
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5
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Doolotkeldieva T, Bobusheva S, Konurbaeva M. In vitro and in vivo screening of bacterial species from contaminated soil for heavy metal biotransformation activity. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART. B, PESTICIDES, FOOD CONTAMINANTS, AND AGRICULTURAL WASTES 2024; 59:315-332. [PMID: 38676363 DOI: 10.1080/03601234.2024.2343236] [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: 04/19/2023] [Accepted: 03/30/2024] [Indexed: 04/28/2024]
Abstract
Heavy metals (HMs) are widely used in various industries. High concentrations of HMs can be severely toxic to plants, animals and humans. Microorganism-based bioremediation has shown significant potential in degrading and detoxifying specific HM contaminants. In this study, we cultivated a range of bacterial strains in liquid and solid nutrient medium containing different concentrations of different HMs to select and analyze bacteria capable of transforming HMs. The bacterial strains most resistant to selected HMs and exhibiting the ability to remove HMs from contaminated soils were identified. Then, the bacterial species capable of utilizing HMs in soil model experiments were selected, and their ability to transform HMs was evaluated. This study has also generated preliminary findings on the use of plants for further removal of HMs from soil after microbial bioremediation. Alcaligenes faecalis, Delftia tsuruhatensis and Stenotrophomonas sp. were selected for their ability to grow in and utilize HM ions at the maximum permissible concentration (MPC) and two times the MPC. Lysinibacillus fusiformis (local microflora) can be used as a universal biotransformation tool for many HM ions. Brevibacillus parabrevis has potential for the removal of lead ions, and Brevibacillus reuszeri and Bacillus safensis have potential for the removal of arsenic ions from the environment. The bacterial species have been selected for bioremediation to remove heavy metal ions from the environment.
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Affiliation(s)
| | - Saykal Bobusheva
- Plant Protection Department, Kyrgyz-Turkish Manas University, Bishkek, Kyrgyzstan
| | - Mahabat Konurbaeva
- Plant Protection Department, Kyrgyz-Turkish Manas University, Bishkek, Kyrgyzstan
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van der Waals MJ, Thornton SF, Rolfe SA, Rock L, Smith JWN, Bosma TNP, Gerritse J. Potential of stable isotope analysis to deduce anaerobic biodegradation of ethyl tert-butyl ether (ETBE) and tert-butyl alcohol (TBA) in groundwater: a review. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:16150-16163. [PMID: 38319419 PMCID: PMC10894111 DOI: 10.1007/s11356-024-32109-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 01/17/2024] [Indexed: 02/07/2024]
Abstract
Understanding anaerobic biodegradation of ether oxygenates beyond MTBE in groundwater is important, given that it is replaced by ETBE as a gasoline additive in several regions. The lack of studies demonstrating anaerobic biodegradation of ETBE, and its product TBA, reflects the relative resistance of ethers and alcohols with a tertiary carbon atom to enzymatic attack under anoxic conditions. Anaerobic ETBE- or TBA-degrading microorganisms have not been characterized. Only one field study suggested anaerobic ETBE biodegradation. Anaerobic (co)metabolism of ETBE or TBA was reported in anoxic microcosms, indicating their biodegradation potential in anoxic groundwater systems. Non-isotopic methods, such as the detection of contaminant loss, metabolites, or ETBE- and TBA-degrading bacteria are not sufficiently sensitive to track anaerobic biodegradation in situ. Compound- and position-specific stable isotope analysis provides a means to study MTBE biodegradation, but isotopic fractionation of ETBE has only been studied with a few aerobic bacteria (εC -0.7 to -1.7‰, εH -11 to -73‰) and at one anoxic field site (δ2H-ETBE +14‰). Similarly, stable carbon isotope enrichment (δ13C-TBA +6.5‰) indicated TBA biodegradation at an anoxic field site. CSIA and PSIA are promising methods to detect anaerobic ETBE and TBA biodegradation but need to be investigated further to assess their full potential at field scale.
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Affiliation(s)
- Marcelle J van der Waals
- Unit Subsurface and Groundwater Systems, Deltares, Daltonlaan 600, Utrecht, 3484 BK, The Netherlands
- Present address: KWR Water Research Institute, Groningenhaven 7, 3433 PE, Nieuwegein, The Netherlands
| | - Steven F Thornton
- Department of Civil and Structural Engineering, University of Sheffield, Mappin St, Sheffield, S1 3JD, UK
| | - Stephen A Rolfe
- School of Biosciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Luc Rock
- Shell Global Solutions International BV, Carel van Bylandtlaan 30, The Hague, 2596 HR, The Netherlands
- Present address: Shell Global Solutions (Canada) Inc, 4000 - 500 Centre Street SE, Calgary, AB, T2G 1A6, Canada
| | - Jonathan W N Smith
- Shell Global Solutions (UK) Ltd, Shell Centre, York Road, London, SE1 7NA, UK
| | - Tom N P Bosma
- Unit Subsurface and Groundwater Systems, Deltares, Daltonlaan 600, Utrecht, 3484 BK, The Netherlands
| | - Jan Gerritse
- Unit Subsurface and Groundwater Systems, Deltares, Daltonlaan 600, Utrecht, 3484 BK, The Netherlands.
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Alabssawy AN, Hashem AH. Bioremediation of hazardous heavy metals by marine microorganisms: a recent review. Arch Microbiol 2024; 206:103. [PMID: 38358529 PMCID: PMC10869373 DOI: 10.1007/s00203-023-03793-5] [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: 10/22/2023] [Revised: 12/09/2023] [Accepted: 12/11/2023] [Indexed: 02/16/2024]
Abstract
Heavy metals (HMs) like Zn, Cu, Pb, Ni, Cd, and Hg, among others, play a role in several environmental problems. The marine environment is polluted by several contaminants, such as HMs. A variety of physico-chemical methods usually available for sanitation HMs remediation suffer from either limitation. Bioremediation is a promising way of dealing with HMs pollution. Microbes have the ability with various potencies to resist HMs tension. The current review discusses the main sources and influences of HMs, the role of marine microorganisms in HMs bioremediation, as well as the microbial mechanisms for HMs detoxification and transformation. This review paper aims to provide an overview of the bioremediation technologies that are currently available for the removal of HMs ions from industrial and urban effluent by aquatic organisms such as bacteria, fungi, and microalgae, particularly those that are isolated from marine areas. The primary goals are to outline various studies and offer helpful information about the most important aspects of the bioelimination techniques. The biotreatment practices have been primarily divided into three techniques based on this topic. They are biosorption, bioaccumulation, bioleaching, and biotransformation. This article gives the brief view on the research studies about bioremediation of HMs using marine microorganisms. The current review also deals with the critical issues and recent studies based on the HMs biodetoxification using aquatic microorganisms.
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Affiliation(s)
- Ahmed N Alabssawy
- Marine Science and Fishes Branch, Zoology Department, Faculty of Science, Al-Azhar University, Cairo, 11884, Egypt.
| | - Amr H Hashem
- Botany and Microbiology Department, Faculty of Science, Al-Azhar University, Nasr City, Cairo, 11884, Egypt.
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Cheng J, Du H, Zhou MS, Ji Y, Xie YQ, Huang HB, Zhang SH, Li F, Xiang L, Cai QY, Li YW, Li H, Li M, Zhao HM, Mo CH. Substrate-enzyme interactions and catalytic mechanism in a novel family VI esterase with dibutyl phthalate-hydrolyzing activity. ENVIRONMENT INTERNATIONAL 2023; 178:108054. [PMID: 37354883 DOI: 10.1016/j.envint.2023.108054] [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: 03/11/2023] [Revised: 05/19/2023] [Accepted: 06/17/2023] [Indexed: 06/26/2023]
Abstract
Microbial degradation has been confirmed as effective and environmentally friendly approach to remediate phthalates from the environment, and hydrolase is an effective element for contaminant degradation. In the present study, a novel dibutyl phthalate (DBP)-hydrolyzing carboxylesterase (named PS06828) from Pseudomonas sp. PS1 was heterogeneously expressed in E. coli, which was identified as a new member of the lipolytic family VI. Purified PS06828 could efficiently degrade DBP with a wide range of temperature (25-37 °C) and pH (6.5-9.0). Multi-spectroscopy methods combined with molecular docking were employed to study the interaction of PS06828 with DBP. Fluorescence and UV-visible absorption spectra revealed the simultaneous presence of static and dynamic component in the fluorescence quenching of PS06828 by DBP. Synchronous fluorescence and circular dichroism spectra showed inconspicuous alteration in micro-environmental polarity around amino acid residues but obvious increasing of α-helix and reducing of β-sheet and random coil in protein conformation. Based on the information on exact binding sites of DBP on PS06828 provided by molecular docking, the catalytic mechanism mediated by key residues (Ser113, Asp166, and His197) was proposed and subsequently confirmed by site-directed mutagenesis. The results can strengthen our mechanistic understanding of family VI esterase involved in hydrolysis of phthalic acid esters, and provide a solid foundation for further enzymatic modification.
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Affiliation(s)
- Jiliang Cheng
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Huan Du
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China; Guangzhou Customs Technology Center, No. 66 Huacheng Avenue, Tianhe District, Guangzhou, China
| | - Meng-Sha Zhou
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Yuan Ji
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - You-Qun Xie
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - He-Biao Huang
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Shu-Hui Zhang
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Fen Li
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Lei Xiang
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Quan-Ying Cai
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Yan-Wen Li
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Hui Li
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Meng Li
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Hai-Ming Zhao
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China.
| | - Ce-Hui Mo
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China.
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Tombuloglu H, Yaman C, Boudellioua I, Cevik E, Anil I, Aga O, Yaman AB, Qureshi A, Gunday ST. Metagenome analyses of microbial population in geotextile fabrics used in permeable reactor barriers for toluene biodegradation. 3 Biotech 2023; 13:40. [PMID: 36636577 PMCID: PMC9829945 DOI: 10.1007/s13205-023-03460-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 12/31/2022] [Indexed: 01/11/2023] Open
Abstract
Toluene is one of the hydrocarbons that contaminate soil and groundwater, and has a high cost to remediate, which makes it an environmental pollutant of concern. This study aimed to find bacterial distribution from nonwoven geotextile (GT) fabric specimens in a pilot-scale permeable reactive barrier (PRB). Upon 167 days of incubation with the addition of toluene, the microbial community on the GT surfaces (n = 12) was investigated by the 16S rRNA metagenome sequencing approach. According to taxonomic classification, the Proteobacteria phylum dominated the metagenomes of all the geotextile samples (80-90%). Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathway database search of the toluene degradation mechanism revealed the susceptible toluene-degrading species. For the toluene-to-benzoate degradation, the Cupriavidus genus, particularly C. gilardii, C. metallidurans, and C. taiwanensis, are likely to be functional. In addition to these species, the Novosphingobium genus was abundantly localized in the GTs, in particular Novosphingobium sp. ABRDHK2. The results suggested the biodegradation potential of these species in toluene remediation. Overall, this work sheds light on the variety of microorganisms found in the geotextile fabrics used in PRBs and the species involved in the biodegradation of toluene from several sources, including soil, sediment, and groundwater. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03460-y.
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Affiliation(s)
- Huseyin Tombuloglu
- Department of Genetics Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam, 31441 Saudi Arabia
| | - Cevat Yaman
- Environmental Engineering Department, College of Engineering, Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam, Saudi Arabia
| | - Imane Boudellioua
- Information and Computer Science Department, King Fahd University of Petroleum and Minerals, P.O. Box 2205, Dhahran, 31261 Saudi Arabia
| | - Emre Cevik
- Bioenergy Research Unit, Department of Biophysics, Institute for Research and Medical Consultations, Imam Abdulrahman Bin Faisal University, PO Box:1982, Dammam, 31441 Saudi Arabia
| | - Ismail Anil
- Environmental Engineering Department, College of Engineering, Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam, Saudi Arabia
| | - Omer Aga
- Environmental Engineering Department, College of Engineering, Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam, Saudi Arabia
| | - Ayse B. Yaman
- Environmental Engineering Department, College of Engineering, Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam, Saudi Arabia
| | - Aleem Qureshi
- Environmental Engineering Department, College of Engineering, Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam, Saudi Arabia
| | - Seyda Tugba Gunday
- Bioenergy Research Unit, Department of Biophysics, Institute for Research and Medical Consultations, Imam Abdulrahman Bin Faisal University, PO Box:1982, Dammam, 31441 Saudi Arabia
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Gao Y, Cai M, Shi K, Sun R, Liu S, Li Q, Wang X, Hua W, Qiao Y, Xue J, Xiao X. Bioaugmentation enhance the bioremediation of marine crude oil pollution: Microbial communities and metabolic pathways. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2023; 87:228-238. [PMID: 36640034 DOI: 10.2166/wst.2022.406] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Bioaugmentation is an effective strategy used to speed up the bioremediation of marine oil spills. In the present study, a highly efficient petroleum degrading bacterium (Pseudomonas aeruginosa ZS1) was applied to the bioremediation of simulated crude oil pollution in different sampling sites in the South China Sea. The metabolic pathways of ZS1 to degrade crude oil, the temporal dynamics of the microbial community response to crude oil contamination, and the biofortification process were investigated. The results showed that the abundance and diversity of the microbial community decreased sharply after the occurrence of crude oil contamination. The best degradation rate of crude oil, which was achieved in the samples from the sampling site N3 after the addition of ZS1 bacteria, was 50.94% at 50 days. C13 alkanes were totally oxidized by ZS1 in the 50 days. The degradation rate of solid n-alkanes (C18-C20) was about 70%. Based on the whole genome sequencing and the metabolites analysis of ZS1, we found that ZS1 degraded n-alkanes through the terminal oxidation pathway and aromatic compounds through the catechol pathway. This study provides data support for further research on biodegradation pathways of crude oil and contributes to the subsequent development of more reasonable bioremediation strategies.
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Affiliation(s)
- Yu Gao
- College of Safety and Environment Engineering, Shandong University of Science and Technology, Qingdao 266510, China E-mail: ; Institute of Yellow River Delta Earth Surface Processes and Ecological Integrity, Shandong University of Science and Technology, Qingdao 266510, China
| | - Mengmeng Cai
- College of Safety and Environment Engineering, Shandong University of Science and Technology, Qingdao 266510, China E-mail:
| | - Ke Shi
- College of Safety and Environment Engineering, Shandong University of Science and Technology, Qingdao 266510, China E-mail:
| | - Rui Sun
- College of Safety and Environment Engineering, Shandong University of Science and Technology, Qingdao 266510, China E-mail: ; Affiliated Hospital of Jining Medical University, Jining 272007, China
| | - Suxiang Liu
- College of Safety and Environment Engineering, Shandong University of Science and Technology, Qingdao 266510, China E-mail:
| | - Qintong Li
- Department of Applied Biosciences, Faculty of Life Sciences, Toyo University, Gunma 3740193, Japan
| | - Xiaoyan Wang
- College of Safety and Environment Engineering, Shandong University of Science and Technology, Qingdao 266510, China E-mail:
| | - Wenxin Hua
- College of Safety and Environment Engineering, Shandong University of Science and Technology, Qingdao 266510, China E-mail:
| | - Yanlu Qiao
- College of Safety and Environment Engineering, Shandong University of Science and Technology, Qingdao 266510, China E-mail: ; Institute of Yellow River Delta Earth Surface Processes and Ecological Integrity, Shandong University of Science and Technology, Qingdao 266510, China
| | - Jianliang Xue
- College of Safety and Environment Engineering, Shandong University of Science and Technology, Qingdao 266510, China E-mail: ; Institute of Yellow River Delta Earth Surface Processes and Ecological Integrity, Shandong University of Science and Technology, Qingdao 266510, China
| | - Xinfeng Xiao
- College of Safety and Environment Engineering, Shandong University of Science and Technology, Qingdao 266510, China E-mail: ; Institute of Yellow River Delta Earth Surface Processes and Ecological Integrity, Shandong University of Science and Technology, Qingdao 266510, China
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11
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Greeshma K, Kim HS, Ramanan R. The emerging potential of natural and synthetic algae-based microbiomes for heavy metal removal and recovery from wastewaters. ENVIRONMENTAL RESEARCH 2022; 215:114238. [PMID: 36108721 DOI: 10.1016/j.envres.2022.114238] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 08/20/2022] [Accepted: 08/27/2022] [Indexed: 06/15/2023]
Abstract
Heavy Metal (HM) bioremoval by microbes is a successful, environment-friendly technique, particularly at low concentrations of HMs. Studies using algae, bacteria, and fungi reveal promising capabilities in isolation and when used in consortia. Yet, few reviews have emphasized individual and collective HM removal rates and the associated mechanisms in natural or synthetic microbiomes. Besides discussing the limitations of conventional and synthetic biology approaches, this review underscores the utility of indigenous microbial taxon, i.e., algae, fungi, and bacteria, in HM removal with adsorption capacities and their synergistic role in microbiome-led studies. The detoxification mechanisms studied for certain HMs indicate distinctive removal pathways in each taxon which points to an enhanced effect when used as a microbiome. The role and higher efficacies of the designer microbiomes with complementing and mutualistic taxa are also considered, followed by recovery options for a circular bioeconomy. The citation network analysis further validates the multi-metal removal ability of microbiomes and the restricted capabilities of the individual counterparts. In precis, the study reemphasizes increased metal removal efficiencies of inter-taxon microbiomes and the mechanisms for synergistic and improved removal, eventually drawing attention to the benefits of ecological engineering approaches compared to other alternatives.
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Affiliation(s)
- Kozhumal Greeshma
- Sustainable Resources Laboratory, Department of Environmental Science, Central University of Kerala, Tejaswini Hills, Periya, Kasaragod, Kerala, 671 316, India
| | - Hee-Sik Kim
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Yuseong-gu, Daejeon, 34141, Republic of Korea; Department of Environmental Biotechnology, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), 34113, Daejeon, Republic of Korea
| | - Rishiram Ramanan
- Sustainable Resources Laboratory, Department of Environmental Science, Central University of Kerala, Tejaswini Hills, Periya, Kasaragod, Kerala, 671 316, India; Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Yuseong-gu, Daejeon, 34141, Republic of Korea.
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12
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Naz M, Benavides-Mendoza A, Tariq M, Zhou J, Wang J, Qi S, Dai Z, Du D. CRISPR/Cas9 technology as an innovative approach to enhancing the phytoremediation: Concepts and implications. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 323:116296. [PMID: 36261968 DOI: 10.1016/j.jenvman.2022.116296] [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: 07/17/2022] [Revised: 09/03/2022] [Accepted: 09/13/2022] [Indexed: 06/16/2023]
Abstract
Phytoremediation is currently an active field of research focusing chiefly on identifying and characterizing novel and high chelation action super-accumulators. In the last few years, molecular tools have been widely exploited to understand better metal absorption, translocation, cation, and tolerance mechanisms in plants. Recently more advanced CRISPR-Cas9 genome engineering technology is also employed to enhance detoxification efficiency. Further, advances in molecular science will trigger the understanding of adaptive phytoremediation ability plant production in current global warming conditions. The enhanced abilities of nucleases for genome modification can improve plant repair capabilities by modifying the genome, thereby achieving a sustainable ecosystem. The purpose of this manuscript focuses on biotechnology's fundamental principles and application to promote climate-resistant metal plants, especially the CRISPR-Cas9 genome editing system for enhancing the phytoremediation of harmful contamination and pollutants.
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Affiliation(s)
- Misbah Naz
- Institute of Environment and Ecology, School of the Environment and Safety Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang, 21201, Jiangsu Province, PR China
| | - Adalberto Benavides-Mendoza
- Department of Horticulture, Autonomous Agricultural University Antonio Narro, 1923 Saltillo, C.P. 25315, Mexico
| | - Muhammad Tariq
- Department of Pharmacology, Lahore Pharmacy College, 54000, Lahore, Pakistan
| | - Jianyu Zhou
- Institute of Environment and Ecology, School of the Environment and Safety Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang, 21201, Jiangsu Province, PR China
| | - Jiahao Wang
- Key Laboratory of Modern Agricultural Equipment and Technology, Ministry of Education, School of Agricultural Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang, 21201, Jiangsu Province, PR China
| | - Shanshan Qi
- Key Laboratory of Modern Agricultural Equipment and Technology, Ministry of Education, School of Agricultural Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang, 21201, Jiangsu Province, PR China
| | - Zhicong Dai
- Institute of Environment and Ecology, School of the Environment and Safety Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang, 21201, Jiangsu Province, PR China; Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou University of Science and Technology, 99 Xuefu Road, Suzhou, 215009, Jiangsu Province, PR China.
| | - Daolin Du
- Institute of Environment and Ecology, School of the Environment and Safety Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang, 21201, Jiangsu Province, PR China
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13
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Holmes DE, Zhou J, Smith JA, Wang C, Liu X, Lovley DR. Different outer membrane c-type cytochromes are involved in direct interspecies electron transfer to Geobacter or Methanosarcina species. MLIFE 2022; 1:272-286. [PMID: 38818222 PMCID: PMC10989804 DOI: 10.1002/mlf2.12037] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 07/21/2022] [Accepted: 07/26/2022] [Indexed: 06/01/2024]
Abstract
Direct interspecies electron transfer (DIET) may be most important in methanogenic environments, but mechanistic studies of DIET to date have primarily focused on cocultures in which fumarate was the terminal electron acceptor. To better understand DIET with methanogens, the transcriptome of Geobacter metallireducens during DIET-based growth with G. sulfurreducens reducing fumarate was compared with G. metallireducens grown in coculture with diverse Methanosarcina. The transcriptome of G. metallireducens cocultured with G. sulfurreducens was significantly different from those with Methanosarcina. Furthermore, the transcriptome of G. metallireducens grown with Methanosarcina barkeri, which lacks outer-surface c-type cytochromes, differed from those of G. metallireducens cocultured with M. acetivorans or M. subterranea, which have an outer-surface c-type cytochrome that serves as an electrical connect for DIET. Differences in G. metallireducens expression patterns for genes involved in extracellular electron transfer were particularly notable. Cocultures with c-type cytochrome deletion mutant strains, ∆Gmet_0930, ∆Gmet_0557 and ∆Gmet_2896, never became established with G. sulfurreducens but adapted to grow with all three Methanosarcina. Two porin-cytochrome complexes, PccF and PccG, were important for DIET; however, PccG was more important for growth with Methanosarcina. Unlike cocultures with G. sulfurreducens and M. acetivorans, electrically conductive pili were not needed for growth with M. barkeri. Shewanella oneidensis, another electroactive microbe with abundant outer-surface c-type cytochromes, did not grow via DIET. The results demonstrate that the presence of outer-surface c-type cytochromes does not necessarily confer the capacity for DIET and emphasize the impact of the electron-accepting partner on the physiology of the electron-donating DIET partner.
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Affiliation(s)
- Dawn E. Holmes
- Department of MicrobiologyUniversity of Massachusetts‐AmherstAmherstMassachusettsUSA
- Department of Physical and Biological ScienceWestern New England UniversitySpringfieldMassachusettsUSA
| | - Jinjie Zhou
- Department of MicrobiologyUniversity of Massachusetts‐AmherstAmherstMassachusettsUSA
- Institute for Advanced StudyShenzhen UniversityShenzhenChina
| | - Jessica A. Smith
- Department of MicrobiologyUniversity of Massachusetts‐AmherstAmherstMassachusettsUSA
- Department of Biomolecular SciencesCentral Connecticut State UniversityNew BritainConnecticutUSA
| | - Caiqin Wang
- Department of MicrobiologyUniversity of Massachusetts‐AmherstAmherstMassachusettsUSA
- College of EnvironmentZhejiang University of TechnologyHangzhouChina
| | - Xinying Liu
- Department of MicrobiologyUniversity of Massachusetts‐AmherstAmherstMassachusettsUSA
- College of Environmental Science and EngineeringBeijing Forestry UniversityBeijingChina
| | - Derek R. Lovley
- Department of MicrobiologyUniversity of Massachusetts‐AmherstAmherstMassachusettsUSA
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14
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Sharma P, Singh SP, Iqbal HMN, Tong YW. Omics approaches in bioremediation of environmental contaminants: An integrated approach for environmental safety and sustainability. ENVIRONMENTAL RESEARCH 2022; 211:113102. [PMID: 35300964 DOI: 10.1016/j.envres.2022.113102] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/28/2022] [Accepted: 03/07/2022] [Indexed: 02/05/2023]
Abstract
Non-degradable pollutants have emerged as a result of industrialization, population growth, and lifestyle changes, endangering human health and the environment. Bioremediation is the process of clearing hazardous contaminants with the help of microorganisms, and cost-effective approach. The low-cost and environmentally acceptable approach to removing environmental pollutants from ecosystems is microbial bioremediation. However, to execute these different bioremediation approaches successfully, this is imperative to have a complete understanding of the variables impacting the development, metabolism, dynamics, and native microbial communities' activity in polluted areas. The emergence of new technologies like next-generation sequencing, protein and metabolic profiling, and advanced bioinformatic tools have provided critical insights into microbial communities and underlying mechanisms in environmental contaminant bioremediation. These omics approaches are meta-genomics, meta-transcriptomics, meta-proteomics, and metabolomics. Moreover, the advancements in these technologies have greatly aided in determining the effectiveness and implementing microbiological bioremediation approaches. At Environmental Protection Agency (EPA)-The government placed special emphasis on exploring how molecular and "omic" technologies may be used to determine the nature, behavior, and functions of the intrinsic microbial communities present at pollution containment systems. Several omics techniques are unquestionably more informative and valuable in elucidating the mechanism of the process and identifying the essential player's involved enzymes and their regulatory elements. This review provides an overview and description of the omics platforms that have been described in recent reports on omics approaches in bioremediation and that demonstrate the effectiveness of integrated omics approaches and their novel future use.
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Affiliation(s)
- Pooja Sharma
- Environmental Research Institute, National University of Singapore, 1 Create Way, 138602, Singapore; Energy and Environmental Sustainability for Megacities (E2S2) Phase II, Campus for Research Excellence and Technological Enterprise (CREATE), 1 CREATE Way, Singapore, 138602, Singapore.
| | - Surendra Pratap Singh
- Plant Molecular Biology Laboratory, Department of Botany, Dayanand Anglo-Vedic (PG) College, Chhatrapati Shahu Ji Maharaj University, Kanpur-208001, India.
| | - Hafiz M N Iqbal
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey, 64849, Mexico.
| | - Yen Wah Tong
- Environmental Research Institute, National University of Singapore, 1 Create Way, 138602, Singapore; Energy and Environmental Sustainability for Megacities (E2S2) Phase II, Campus for Research Excellence and Technological Enterprise (CREATE), 1 CREATE Way, Singapore, 138602, Singapore; Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive, 117585, Singapore.
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15
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Maqsood Q, Hussain N, Mumtaz M, Bilal M, Iqbal HMN. Novel strategies and advancement in reducing heavy metals from the contaminated environment. Arch Microbiol 2022; 204:478. [PMID: 35831495 DOI: 10.1007/s00203-022-03087-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 06/20/2022] [Indexed: 11/27/2022]
Abstract
The most contemporary ecological issues are the dumping of unprocessed factories' effluent. As a result, there is an increasing demand for creative, practical, environmentally acceptable, and inexpensive methodologies to remediate inorganic metals (Hg, Cr, Pb, and Cd) liquidated into the atmosphere, protecting ecosystems. Latest innovations in biological metals have driven natural treatment as a viable substitute for traditional approaches in this area. To eliminate pesticide remains from soil/water sites, technologies such as oxidation, burning, adsorption, and microbial degradation have been established. Bioremediation is a more cost-effective and ecologically responsible means of removing heavy metals than conventional alternatives. As a result, microorganisms have emerged as a necessary component of methyl breakdown and detoxification via metabolic reactions and hereditary characteristics. The utmost operative variant for confiscating substantial metals commencing contaminated soil was A. niger, which had a maximum bioaccumulation efficiency of 98% (Cd) and 43% (Cr). Biosensor bacteria are both environmentally sustainable and cost-effective. As a result, microbes have a range of metal absorption processes that allow them to have higher metal biosorption capabilities. Additionally, the biosorption potential of bacterium, fungus, biofilm, and algae, inherently handled microorganisms that immobilized microbial cells for the elimination of heavy metals, was reviewed in this study. Furthermore, we discuss some of the challenges and opportunities associated with producing effective heavy metal removal techniques, such as those that employ different types of nanoparticles.
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Affiliation(s)
- Quratulain Maqsood
- Centre for Applied Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Nazim Hussain
- Centre for Applied Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Mehvish Mumtaz
- Centre for Applied Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Muhammad Bilal
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huai'an, 223003, China.
| | - Hafiz M N Iqbal
- Tecnologico de Monterrey, School of Engineering and Sciences, 64849, Monterrey, Mexico.
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16
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Hassan S, Sabreena, Khurshid Z, Bhat SA, Kumar V, Ameen F, Ganai BA. Marine Bacteria and Omic Approaches: A Novel and Potential Repository for Bioremediation Assessment. J Appl Microbiol 2022; 133:2299-2313. [PMID: 35818751 DOI: 10.1111/jam.15711] [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: 04/05/2022] [Revised: 06/15/2022] [Accepted: 07/01/2022] [Indexed: 10/17/2022]
Abstract
Marine environments accommodating diverse assortments of life constitute a great pool of differentiated natural resources. The cumulative need to remedy unpropitious effects of anthropogenic activities on estuaries, and coastal marine ecosystems has propelled the development of effective bioremediation strategies. Marine bacteria producing biosurfactants are promising agents for bio-remediating oil pollution in marine environments, making them prospective candidates for enhancing oil recovery. Molecular omics technologies are considered an emerging field of research in ecological and diversity assessment owing to their utility in environmental surveillance and bioremediation of polluted sites. A thorough literature review was undertaken to understand the applicability of different omic techniques employed for bioremediation assessment using marine bacteria. This review further establishes that for bioremediation of environmental pollutants (i.e., heavy metals, hydrocarbons, xenobiotic and numerous recalcitrant compounds), organisms isolated from marine environments can be better utilized for their removal. The literature survey shows that omics approaches can provide exemplary knowledge about microbial communities and their role in the bioremediation of environmental pollutants. This review centres on applications of marine bacteria in enhanced bioremediation, utilizing the omics approaches that can be a vital biological contrivance in environmental monitoring to tackle environmental degradation. The paper aims to identify the gaps in investigations involving marine bacteria to help researchers, ecologists, and decision-makers to develop a holistic understanding regarding their utility in bioremediation assessment.
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Affiliation(s)
- Shahnawaz Hassan
- Department of Environmental Science, University of Kashmir, India
| | - Sabreena
- Department of Environmental Science, University of Kashmir, India
| | | | | | - Vineet Kumar
- Department of Botany, Guru Ghasidas Vishwavidyalaya (A Central University), Bilaspur, Chhattisgarh-495009, India
| | - Fuad Ameen
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
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17
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Gangola S, Bhatt P, Kumar AJ, Bhandari G, Joshi S, Punetha A, Bhatt K, Rene ER. Biotechnological tools to elucidate the mechanism of pesticide degradation in the environment. CHEMOSPHERE 2022; 296:133916. [PMID: 35149016 DOI: 10.1016/j.chemosphere.2022.133916] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 12/23/2021] [Accepted: 02/05/2022] [Indexed: 06/14/2023]
Abstract
Pesticides are widely used in agriculture, households, and industries; however, they have caused severe negative effects on the environment and human health. To clean up pesticide contaminated sites, various technological strategies, i.e. physicochemical and biological, are currently being used throughout the world. Biological approaches have proven to be a viable method for decontaminating pesticide-contaminated soils and water environments. The biological process eliminates contaminants by utilizing microorganisms' catabolic ability. Pesticide degradation rates are influenced by a variety of factors, including the pesticide's structure, concentration, solubility in water, soil type, land use pattern, and microbial activity in the soil. There is currently a knowledge gap in this field of study because researchers are unable to gather collective information on the factors affecting microbial growth, metabolic pathways, optimal conditions for degradation, and genomic, transcriptomic, and proteomic changes caused by pesticide stress on the microbial communities. The use of advanced tools and omics technology in research can bridge the existing gap in our knowledge regarding the bioremediation of pesticides. This review provides new insights on the research gaps and offers potential solutions for pesticide removal from the environment through the use of various microbe-mediated technologies.
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Affiliation(s)
- Saurabh Gangola
- School of Agriculture, Graphic Era Hill University, Bhimtal, 263136, Uttarakhand, India
| | - Pankaj Bhatt
- Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642, PR China.
| | | | - Geeta Bhandari
- Department of Biosciences, Swami Rama Himalayan University, Dehradun, Uttarakhand, India
| | - Samiksha Joshi
- School of Agriculture, Graphic Era Hill University, Bhimtal, 263136, Uttarakhand, India
| | - Arjita Punetha
- Department of Environmental Science, GB Pant University of Agriculture and Technology, Pantnagar, 263145, Uttarakhand, India
| | - Kalpana Bhatt
- Department of Botany and Microbiology, Gurukul Kangri University, Haridwar, 249404, Uttarakhand, India
| | - Eldon R Rene
- Department of Water Supply, Sanitation and Environmental Engineering, IHE Delft Institute for Water Education, P. O. Box 3015, 2601 DA Delft, the Netherlands
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18
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Bacterial chemotaxis to saccharides is governed by a trade-off between sensing and uptake. Biophys J 2022; 121:2046-2059. [PMID: 35526093 DOI: 10.1016/j.bpj.2022.05.003] [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: 11/05/2021] [Revised: 04/05/2022] [Accepted: 05/03/2022] [Indexed: 11/20/2022] Open
Abstract
To swim up gradients of nutrients, E. coli senses nutrient concentrations within its periplasm. For small nutrient molecules, periplasmic concentrations typically match extracellular concentrations. However, this is not necessarily the case for saccharides, such as maltose, which are transported into the periplasm via a specific porin. Previous observations have shown that, under various conditions, E. coli limits maltoporin abundance so that, for extracellular micromolar concentrations of maltose, there are predicted to be only nanomolar concentrations of free maltose in the periplasm. Thus, in the micromolar regime, the total uptake of maltose from the external environment into the cytoplasm is limited not by the abundance of cytoplasmic transport proteins but by the abundance of maltoporins. Here we present results from experiments and modeling suggesting that this porin-limited transport enables E. coli to sense micromolar gradients of maltose despite having a high-affinity ABC transport system that is saturated at these micromolar levels. We used microfluidic assays to study chemotaxis of E. coli in various gradients of maltose and methyl-aspartate and leveraged our experimental observations to develop a mechanistic transport-and-sensing chemotaxis model. Incorporating this model into agent-based simulations, we discover a trade-off between uptake and sensing: although high-affinity transport enables higher uptake rates at low nutrient concentrations, it severely limits the range of dynamic sensing. We thus propose that E. coli may limit periplasmic uptake to increase its chemotactic sensitivity, enabling it to use maltose as an environmental cue.
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Darma A, Yang J, Zandi P, Liu J, Możdżeń K, Xia X, Sani A, Wang Y, Schnug E. Significance of Shewanella Species for the Phytoavailability and Toxicity of Arsenic-A Review. BIOLOGY 2022; 11:biology11030472. [PMID: 35336844 PMCID: PMC8944983 DOI: 10.3390/biology11030472] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 03/14/2022] [Accepted: 03/16/2022] [Indexed: 12/02/2022]
Abstract
Simple Summary The availability of some toxic heavy metals, such as arsenic (As), is related to increased human and natural activities. This type of metal availability in the environment is associated with various health and environmental issues. Such problems may arise due to direct contact with or consumption of plant products containing this metal in some of their parts. A microbial approach that employs a group of bacteria (Shewanella species) is proposed to reduce the negative consequences of the availability of this metal (As) in the environment. This innovative strategy can reduce As mobility, its spread, and uptake by plants in the environment. The benefits of this approach include its low cost and the possibility of not exposing other components of the environment to unfavourable consequences. Abstract The distribution of arsenic continues due to natural and anthropogenic activities, with varying degrees of impact on plants, animals, and the entire ecosystem. Interactions between iron (Fe) oxides, bacteria, and arsenic are significantly linked to changes in the mobility, toxicity, and availability of arsenic species in aquatic and terrestrial habitats. As a result of these changes, toxic As species become available, posing a range of threats to the entire ecosystem. This review elaborates on arsenic toxicity, the mechanisms of its bioavailability, and selected remediation strategies. The article further describes how the detoxification and methylation mechanisms used by Shewanella species could serve as a potential tool for decreasing phytoavailable As and lessening its contamination in the environment. If taken into account, this approach will provide a globally sustainable and cost-effective strategy for As remediation and more information to the literature on the unique role of this bacterial species in As remediation as opposed to conventional perception of its role as a mobiliser of As.
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Affiliation(s)
- Aminu Darma
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (A.D.); (X.X.); (Y.W.)
- Department of Biological Sciences, Faculty of Life Science, Bayero University, Kano 700006, Nigeria;
| | - Jianjun Yang
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (A.D.); (X.X.); (Y.W.)
- Correspondence: (J.Y.); (E.S.); Tel.: +86-010-82105996 (J.Y.)
| | - Peiman Zandi
- International Faculty of Applied Technology, Yibin University, Yibin 644600, China;
| | - Jin Liu
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100094, China;
| | - Katarzyna Możdżeń
- Institute of Biology, Pedagogical University of Krakow, Podchorążych 2 St., 30-084 Krakow, Poland;
| | - Xing Xia
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (A.D.); (X.X.); (Y.W.)
| | - Ali Sani
- Department of Biological Sciences, Faculty of Life Science, Bayero University, Kano 700006, Nigeria;
| | - Yihao Wang
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (A.D.); (X.X.); (Y.W.)
| | - Ewald Schnug
- Department of Life Sciences, Institute for Plant Biology, Technical University of Braunschweig, 38106 Braunschweig, Germany
- Correspondence: (J.Y.); (E.S.); Tel.: +86-010-82105996 (J.Y.)
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Miri S, Rasooli A, Brar SK, Rouissi T, Martel R. Biodegradation of p-xylene-a comparison of three psychrophilic Pseudomonas strains through the lens of gene expression. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:21465-21479. [PMID: 34762239 DOI: 10.1007/s11356-021-17387-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 11/02/2021] [Indexed: 05/21/2023]
Abstract
p-Xylene is considered a recalcitrant compound despite showing a similar aromatic structure to other BTEXs (benzene, toluene, ethylbenzene, xylene isomers). This study evaluated the p-xylene biodegradation potential of three psychrophilic Pseudomonas strains (Pseudomonas putida S2TR-01, Pseudomonas synxantha S2TR-20, and Pseudomonas azotoformans S2TR-09). The p-xylene metabolism-related catabolic genes (xylM, xylA, and xylE) and the corresponding regulatory genes (xylR and xylS) of the selected strains were investigated. The biodegradation results showed that the P. azotoformans S2TR-09 strain was the only strain that was able to degrade 200 mg/L p-xylene after 60 h at 15 °C. The gene expression study indicated that the xylE (encoding catechol 2,3-dioxygenase) gene represents the bottleneck in p-xylene biodegradation. A lack of xylE expression leads to the accumulation of intermediates and the inhibition of biomass production and complete carbon recovery. The activity of xylene monooxygenase and catechol 2,3-dioxygenase was significantly increased in P. azotoformans S2TR-09 (0.5 and 0.08 U/mg, respectively) in the presence of p-xylene. The expression of the ring cleavage enzyme and its encoding gene (xylE) and activator (xylS) explained the differences in the p-xylene metabolism of the isolated bacteria and can be used as a novel biomarker of efficient p-xylene biodegradation at contaminated sites.
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Affiliation(s)
- Saba Miri
- Department of Civil Engineering, Lassonde School of Engineering, York University, North York, Toronto, ON, M3J 1P3, Canada
- INRS-ETE, Université du Québec, 490, Rue de la Couronne, Québec, G1K 9A9, Canada
| | - Azadeh Rasooli
- Department of Civil Engineering, Lassonde School of Engineering, York University, North York, Toronto, ON, M3J 1P3, Canada
| | - Satinder Kaur Brar
- Department of Civil Engineering, Lassonde School of Engineering, York University, North York, Toronto, ON, M3J 1P3, Canada.
- INRS-ETE, Université du Québec, 490, Rue de la Couronne, Québec, G1K 9A9, Canada.
| | - Tarek Rouissi
- INRS-ETE, Université du Québec, 490, Rue de la Couronne, Québec, G1K 9A9, Canada
| | - Richard Martel
- INRS-ETE, Université du Québec, 490, Rue de la Couronne, Québec, G1K 9A9, Canada
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21
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Bertin PN, Crognale S, Plewniak F, Battaglia-Brunet F, Rossetti S, Mench M. Water and soil contaminated by arsenic: the use of microorganisms and plants in bioremediation. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:9462-9489. [PMID: 34859349 PMCID: PMC8783877 DOI: 10.1007/s11356-021-17817-4] [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: 02/17/2021] [Accepted: 11/23/2021] [Indexed: 04/16/2023]
Abstract
Owing to their roles in the arsenic (As) biogeochemical cycle, microorganisms and plants offer significant potential for developing innovative biotechnological applications able to remediate As pollutions. This possible use in bioremediation processes and phytomanagement is based on their ability to catalyse various biotransformation reactions leading to, e.g. the precipitation, dissolution, and sequestration of As, stabilisation in the root zone and shoot As removal. On the one hand, genomic studies of microorganisms and their communities are useful in understanding their metabolic activities and their interaction with As. On the other hand, our knowledge of molecular mechanisms and fate of As in plants has been improved by laboratory and field experiments. Such studies pave new avenues for developing environmentally friendly bioprocessing options targeting As, which worldwide represents a major risk to many ecosystems and human health.
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Affiliation(s)
- Philippe N Bertin
- Génétique Moléculaire, Génomique et Microbiologie, UMR7156 CNRS - Université de Strasbourg, Strasbourg, France.
| | - Simona Crognale
- Water Research Institute, National Research Council of Italy (IRSA - CNR), Rome, Italy
| | - Frédéric Plewniak
- Génétique Moléculaire, Génomique et Microbiologie, UMR7156 CNRS - Université de Strasbourg, Strasbourg, France
| | | | - Simona Rossetti
- Water Research Institute, National Research Council of Italy (IRSA - CNR), Rome, Italy
| | - Michel Mench
- Univ. Bordeaux, INRAE, BIOGECO, F-33615, Pessac, France
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22
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Ahmad S, Cui D, Zhong G, Liu J. Microbial Technologies Employed for Biodegradation of Neonicotinoids in the Agroecosystem. Front Microbiol 2021; 12:759439. [PMID: 34925268 PMCID: PMC8675359 DOI: 10.3389/fmicb.2021.759439] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 10/25/2021] [Indexed: 11/13/2022] Open
Abstract
Neonicotinoids are synthetic pesticides widely used for the control of various pests in agriculture throughout the world. They mainly attack the nicotinic acetylcholine receptors, generate nervous stimulation, receptor clot, paralysis and finally cause death. They are low volatile, highly soluble and have a long half-life in soil and water. Due to their extensive use, the environmental residues have immensely increased in the last two decades and caused many hazardous effects on non-target organisms, including humans. Hence, for the protection of the environment and diversity of living organism's the degradation of neonicotinoids has received widespread attention. Compared to the other methods, biological methods are considered cost-effective, eco-friendly and most efficient. In particular, the use of microbial species makes the degradation of xenobiotics more accessible fast and active due to their smaller size. Since this degradation also converts xenobiotics into less toxic substances, the various metabolic pathways for the microbial degradation of neonicotinoids have been systematically discussed. Additionally, different enzymes, genes, plasmids and proteins are also investigated here. At last, this review highlights the implementation of innovative tools, databases, multi-omics strategies and immobilization techniques of microbial cells to detect and degrade neonicotinoids in the environment.
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Affiliation(s)
- Sajjad Ahmad
- Key Laboratory of Integrated Pest Management of Crop in South China, Ministry of Agriculture and Rural Affairs, Key Laboratory of Natural Pesticide and Chemical Biology, Ministry of Education, South China Agricultural University, Guangzhou, China
| | - Dongming Cui
- Key Laboratory of Integrated Pest Management of Crop in South China, Ministry of Agriculture and Rural Affairs, Key Laboratory of Natural Pesticide and Chemical Biology, Ministry of Education, South China Agricultural University, Guangzhou, China
| | - Guohua Zhong
- Key Laboratory of Integrated Pest Management of Crop in South China, Ministry of Agriculture and Rural Affairs, Key Laboratory of Natural Pesticide and Chemical Biology, Ministry of Education, South China Agricultural University, Guangzhou, China
| | - Jie Liu
- Key Laboratory of Integrated Pest Management of Crop in South China, Ministry of Agriculture and Rural Affairs, Key Laboratory of Natural Pesticide and Chemical Biology, Ministry of Education, South China Agricultural University, Guangzhou, China
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Santos MIS, Brandão ÉCTA, Santos E, Batista MVA, Estevam CS, Alexandre MR, Fernandes MF. Pendimethalin biodegradation by soil strains of Burkholderia sp. and Methylobacterium radiotolerans. AN ACAD BRAS CIENC 2021; 93:e20210924. [PMID: 34909833 DOI: 10.1590/0001-3765202120210924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 09/24/2021] [Indexed: 11/22/2022] Open
Abstract
Pendimethalin herbicide is widely used and persists in the environment as a contaminant causing negative impacts, including for human health. Microorganisms have the capacity to remove many contaminants from the environment. Thus, the aim of this work was to evaluate the efficiency of soil bacterial species prospected by molecular modelling of cytochrome P450 in to degrade pendimethalin. Strains of Burkholderia sp. and Methylobacterium radiotolerans were cultivated in a mineral saline medium enriched with 281 mg/L pendimethalin (MSPEN) and another containing glucose 1.0 g/L as extra carbon source (MSPENGLI). Both strains were able to degrade pendimethalin under the two conditions experienced. Burkholderia sp. F7G4PR33-4 was more efficient in degrading 65% of the herbicide in MSPEN medium, with 49.3% in MSPENGLI; while Methylobacterium radiotolerans A6A1PR46-4 degraded 55.4% in MSPEN and 29.8% in MSPENGLI mediums. These findings contribute to the expansion of knowledge on the competence of isolates of these two bacterial genera in degrading herbicidal xenobiotics and biotechnological potential for pendimethalin degradation and bioremediation.
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Affiliation(s)
- Matheus I S Santos
- Departamento de Fisiologia, Universidade Federal de Sergipe, Cidade Univ. Prof. José Aloísio de Campos, Av. Marechal Rondon, s/n, Jd. Rosa Elze, 49100-000 São Cristóvão, SE, Brazil
| | - Érika C T A Brandão
- Embrapa Tabuleiros Costeiros, Av. Gov. Paulo Barreto de Menezes (Beira Mar), 3250, Jardins, 49025-040 Aracaju, SE, Brazil
| | - Ewerton Santos
- Departamento de Química, Universidade Federal de Sergipe, Cidade Univ. Prof. José Aloísio de Campos, Av. Marechal Rondon, s/n, Jd. Rosa Elze, 49100-000 São Cristóvão, SE, Brazil
| | - Marcus Vinícius A Batista
- Departamento de Biologia, Universidade Federal de Sergipe, Cidade Univ. Prof. José Aloísio de Campos, Av. Marechal Rondon, s/n, Jd. Rosa Elze, 49100-000 São Cristóvão, SE, Brazil
| | - Charles S Estevam
- Departamento de Fisiologia, Universidade Federal de Sergipe, Cidade Univ. Prof. José Aloísio de Campos, Av. Marechal Rondon, s/n, Jd. Rosa Elze, 49100-000 São Cristóvão, SE, Brazil
| | - Marcelo R Alexandre
- Departamento de Química, Universidade Federal de Sergipe, Cidade Univ. Prof. José Aloísio de Campos, Av. Marechal Rondon, s/n, Jd. Rosa Elze, 49100-000 São Cristóvão, SE, Brazil
| | - Marcelo F Fernandes
- Embrapa Tabuleiros Costeiros, Av. Gov. Paulo Barreto de Menezes (Beira Mar), 3250, Jardins, 49025-040 Aracaju, SE, Brazil
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Hu R, Zhao H, Xu X, Wang Z, Yu K, Shu L, Yan Q, Wu B, Mo C, He Z, Wang C. Bacteria-driven phthalic acid ester biodegradation: Current status and emerging opportunities. ENVIRONMENT INTERNATIONAL 2021; 154:106560. [PMID: 33866059 DOI: 10.1016/j.envint.2021.106560] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 03/15/2021] [Accepted: 04/05/2021] [Indexed: 06/12/2023]
Abstract
The extensive use of phthalic acid esters (PAEs) has led to their widespread distribution across various environments. As PAEs pose significant threats to human health, it is urgent to develop efficient strategies to eliminate them from environments. Bacteria-driven PAE biodegradation has been considered as an inexpensive yet effective strategy to restore the contaminated environments. Despite great advances in bacterial culturing and sequencing, the inherent complexity of indigenous microbial community hinders us to mechanistically understand in situ PAE biodegradation and efficiently harness the degrading power of bacteria. The synthetic microbial ecology provides us a simple and controllable model system to address this problem. In this review, we focus on the current progress of PAE biodegradation mediated by bacterial isolates and indigenous bacterial communities, and discuss the prospective of synthetic PAE-degrading bacterial communities in PAE biodegradation research. It is anticipated that the theories and approaches of synthetic microbial ecology will revolutionize the study of bacteria-driven PAE biodegradation and provide novel insights for developing effective bioremediation solutions.
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Affiliation(s)
- Ruiwen Hu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China
| | - Haiming Zhao
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Xihui Xu
- Department of Microbiology, Key Laboratory of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhigang Wang
- School of Life Science and Agriculture and Forestry, Qiqihar University, Qiqihar 161006, China
| | - Ke Yu
- School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen 518055, China
| | - Longfei Shu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China
| | - Qingyun Yan
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China
| | - Bo Wu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China
| | - Cehui Mo
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Zhili He
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China; College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Cheng Wang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China.
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25
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Silva MA, Salgueiro CA. Multistep Signaling in Nature: A Close-Up of Geobacter Chemotaxis Sensing. Int J Mol Sci 2021; 22:ijms22169034. [PMID: 34445739 PMCID: PMC8396549 DOI: 10.3390/ijms22169034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 07/30/2021] [Accepted: 08/09/2021] [Indexed: 11/23/2022] Open
Abstract
Environmental changes trigger the continuous adaptation of bacteria to ensure their survival. This is possible through a variety of signal transduction pathways involving chemoreceptors known as methyl-accepting chemotaxis proteins (MCP) that allow the microorganisms to redirect their mobility towards favorable environments. MCP are two-component regulatory (or signal transduction) systems (TCS) formed by a sensor and a response regulator domain. These domains synchronize transient protein phosphorylation and dephosphorylation events to convert the stimuli into an appropriate cellular response. In this review, the variability of TCS domains and the most common signaling mechanisms are highlighted. This is followed by the description of the overall cellular topology, classification and mechanisms of MCP. Finally, the structural and functional properties of a new family of MCP found in Geobacter sulfurreducens are revisited. This bacterium has a diverse repertoire of chemosensory systems, which represents a striking example of a survival mechanism in challenging environments. Two G. sulfurreducens MCP—GSU0582 and GSU0935—are members of a new family of chemotaxis sensor proteins containing a periplasmic PAS-like sensor domain with a c-type heme. Interestingly, the cellular location of this domain opens new routes to the understanding of the redox potential sensing signaling transduction pathways.
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Affiliation(s)
- Marta A. Silva
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, 2819-516 Caparica, Portugal;
- UCIBIO—Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, NOVA University Lisbon, 2819-516 Caparica, Portugal
| | - Carlos A. Salgueiro
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, 2819-516 Caparica, Portugal;
- UCIBIO—Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, NOVA University Lisbon, 2819-516 Caparica, Portugal
- Correspondence:
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Xu A, Zhang X, Wu S, Xu N, Huang Y, Yan X, Zhou J, Cui Z, Dong W. Pollutant Degrading Enzyme: Catalytic Mechanisms and Their Expanded Applications. Molecules 2021; 26:4751. [PMID: 34443339 PMCID: PMC8401168 DOI: 10.3390/molecules26164751] [Citation(s) in RCA: 7] [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: 06/02/2021] [Revised: 07/03/2021] [Accepted: 07/30/2021] [Indexed: 11/16/2022] Open
Abstract
The treatment of environmental pollution by microorganisms and their enzymes is an innovative and socially acceptable alternative to traditional remediation approaches. Microbial biodegradation is often characterized with high efficiency as this process is catalyzed via degrading enzymes. Various naturally isolated microorganisms were demonstrated to have considerable ability to mitigate many environmental pollutants without external intervention. However, only a small fraction of these strains are studied in detail to reveal the mechanisms at the enzyme level, which strictly limited the enhancement of the degradation efficiency. Accordingly, this review will comprehensively summarize the function of various degrading enzymes with an emphasis on catalytic mechanisms. We also inspect the expanded applications of these pollutant-degrading enzymes in industrial processes. An in-depth understanding of the catalytic mechanism of enzymes will be beneficial for exploring and exploiting more degrading enzyme resources and thus ameliorate concerns associated with the ineffective biodegradation of recalcitrant and xenobiotic contaminants with the help of gene-editing technology and synthetic biology.
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Affiliation(s)
- Anming Xu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, China; (A.X.); (X.Z.); (S.W.); (N.X.); (J.Z.)
| | - Xiaoxiao Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, China; (A.X.); (X.Z.); (S.W.); (N.X.); (J.Z.)
| | - Shilei Wu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, China; (A.X.); (X.Z.); (S.W.); (N.X.); (J.Z.)
| | - Ning Xu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, China; (A.X.); (X.Z.); (S.W.); (N.X.); (J.Z.)
| | - Yan Huang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; (Y.H.); (X.Y.)
| | - Xin Yan
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; (Y.H.); (X.Y.)
| | - Jie Zhou
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, China; (A.X.); (X.Z.); (S.W.); (N.X.); (J.Z.)
| | - Zhongli Cui
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; (Y.H.); (X.Y.)
| | - Weiliang Dong
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, China; (A.X.); (X.Z.); (S.W.); (N.X.); (J.Z.)
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Liang D, Xiao C, Song F, Li H, Liu R, Gao J. Complete Genome Sequence and Function Gene Identify of Prometryne-Degrading Strain Pseudomonas sp. DY-1. Microorganisms 2021; 9:microorganisms9061261. [PMID: 34200754 PMCID: PMC8230428 DOI: 10.3390/microorganisms9061261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 05/30/2021] [Accepted: 06/08/2021] [Indexed: 12/02/2022] Open
Abstract
The genus Pseudomonas is widely recognized for its potential for environmental remediation and plant growth promotion. Pseudomonas sp. DY-1 was isolated from the agricultural soil contaminated five years by prometryne, it manifested an outstanding prometryne degradation efficiency and an untapped potential for plant resistance improvement. Thus, it is meaningful to comprehend the genetic background for strain DY-1. The whole genome sequence of this strain revealed a series of environment adaptive and plant beneficial genes which involved in environmental stress response, heavy metal or metalloid resistance, nitrate dissimilatory reduction, riboflavin synthesis, and iron acquisition. Detailed analyses presented the potential of strain DY-1 for degrading various organic compounds via a homogenized pathway or the protocatechuate and catechol branches of the β-ketoadipate pathway. In addition, heterologous expression, and high efficiency liquid chromatography (HPLC) confirmed that prometryne could be oxidized by a Baeyer-Villiger monooxygenase (BVMO) encoded by a gene in the chromosome of strain DY-1. The result of gene knock-out suggested that the sulfate starvation-induced (SSI) genes in this strain might also involve in the process of prometryne degradation. These results would provide the molecular basis for the application of strain DY-1 in various fields and would contribute to the study of prometryne biodegradation mechanism as well.
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Affiliation(s)
- Dong Liang
- College of Life Science, Northeast Agricultural University, Harbin 150038, China; (D.L.); (C.X.); (H.L.)
| | - Changyixin Xiao
- College of Life Science, Northeast Agricultural University, Harbin 150038, China; (D.L.); (C.X.); (H.L.)
| | - Fuping Song
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China;
| | - Haitao Li
- College of Life Science, Northeast Agricultural University, Harbin 150038, China; (D.L.); (C.X.); (H.L.)
| | - Rongmei Liu
- College of Life Science, Northeast Agricultural University, Harbin 150038, China; (D.L.); (C.X.); (H.L.)
- Correspondence: (R.L.); (J.G.); Tel.: +86-133-5999-0992 (J.G.)
| | - Jiguo Gao
- College of Life Science, Northeast Agricultural University, Harbin 150038, China; (D.L.); (C.X.); (H.L.)
- Correspondence: (R.L.); (J.G.); Tel.: +86-133-5999-0992 (J.G.)
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Fernandes TM, Morgado L, Turner DL, Salgueiro CA. Protein Engineering of Electron Transfer Components from Electroactive Geobacter Bacteria. Antioxidants (Basel) 2021; 10:844. [PMID: 34070486 PMCID: PMC8227773 DOI: 10.3390/antiox10060844] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 05/02/2021] [Accepted: 05/20/2021] [Indexed: 01/02/2023] Open
Abstract
Electrogenic microorganisms possess unique redox biological features, being capable of transferring electrons to the cell exterior and converting highly toxic compounds into nonhazardous forms. These microorganisms have led to the development of Microbial Electrochemical Technologies (METs), which include applications in the fields of bioremediation and bioenergy production. The optimization of these technologies involves efforts from several different disciplines, ranging from microbiology to materials science. Geobacter bacteria have served as a model for understanding the mechanisms underlying the phenomenon of extracellular electron transfer, which is highly dependent on a multitude of multiheme cytochromes (MCs). MCs are, therefore, logical targets for rational protein engineering to improve the extracellular electron transfer rates of these bacteria. However, the presence of several heme groups complicates the detailed redox characterization of MCs. In this Review, the main characteristics of electroactive Geobacter bacteria, their potential to develop microbial electrochemical technologies and the main features of MCs are initially highlighted. This is followed by a detailed description of the current methodologies that assist the characterization of the functional redox networks in MCs. Finally, it is discussed how this information can be explored to design optimal Geobacter-mutated strains with improved capabilities in METs.
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Affiliation(s)
- Tomás M. Fernandes
- UCIBIO, Chemistry Department, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Campus Caparica, 2829-516 Caparica, Portugal; (T.M.F.); (L.M.)
| | - Leonor Morgado
- UCIBIO, Chemistry Department, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Campus Caparica, 2829-516 Caparica, Portugal; (T.M.F.); (L.M.)
| | - David L. Turner
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Avenida da República (EAN), 2780-157 Oeiras, Portugal;
| | - Carlos A. Salgueiro
- UCIBIO, Chemistry Department, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Campus Caparica, 2829-516 Caparica, Portugal; (T.M.F.); (L.M.)
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Singh AK, Bilal M, Iqbal HMN, Raj A. Trends in predictive biodegradation for sustainable mitigation of environmental pollutants: Recent progress and future outlook. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 770:144561. [PMID: 33736422 DOI: 10.1016/j.scitotenv.2020.144561] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 12/13/2020] [Accepted: 12/13/2020] [Indexed: 02/05/2023]
Abstract
The feasibility of in-silico techniques, together with the computational framework, has been applied to predictive bioremediation aiming to clean-up contaminants, toxicity evaluation, and possibilities for the degradation of complex recalcitrant compounds. Emerging contaminants from different industries have posed a significant hazard to the environment and public health. Given current bioremediation strategies, it is often a failure or inadequate for sustainable mitigation of hazardous pollutants. However, clear-cut vital information about biodegradation is quite incomplete from a conventional remediation techniques perspective. Lacking complete information on bio-transformed compounds leads to seeking alternative methods. Only scarce information about the transformed products and toxicity profile is available in the published literature. To fulfill this literature gap, various computational or in-silico technologies have emerged as alternating techniques, which are being recognized as in-silico approaches for bioremediation. Molecular docking, molecular dynamics simulation, and biodegradation pathways predictions are the vital part of predictive biodegradation, including the Quantitative Structure-Activity Relationship (QSAR), Quantitative structure-biodegradation relationship (QSBR) model system. Furthermore, machine learning (ML), artificial neural network (ANN), genetic algorithm (GA) based programs offer simultaneous biodegradation prediction along with toxicity and environmental fate prediction. Herein, we spotlight the feasibility of in-silico remediation approaches for various persistent, recalcitrant contaminants while traditional bioremediation fails to mitigate such pollutants. Such could be addressed by exploiting described model systems and algorithm-based programs. Furthermore, recent advances in QSAR modeling, algorithm, and dedicated biodegradation prediction system have been summarized with unique attributes.
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Affiliation(s)
- Anil Kumar Singh
- Environmental Microbiology Laboratory, Environmental Toxicology Group, CSIR-Indian Institute of Toxicology Research (CSIR-IITR), Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, Lucknow 226001, Uttar Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Muhammad Bilal
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China
| | - Hafiz M N Iqbal
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Mexico.
| | - Abhay Raj
- Environmental Microbiology Laboratory, Environmental Toxicology Group, CSIR-Indian Institute of Toxicology Research (CSIR-IITR), Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, Lucknow 226001, Uttar Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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Sharma P. Efficiency of bacteria and bacterial assisted phytoremediation of heavy metals: An update. BIORESOURCE TECHNOLOGY 2021; 328:124835. [PMID: 33618184 DOI: 10.1016/j.biortech.2021.124835] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 02/05/2021] [Accepted: 02/07/2021] [Indexed: 05/12/2023]
Abstract
The aim of this review to address the plant-associated bacteria to enhance the phytoremediation efficiency of the heavy metals from polluted sites and it is also highlighted advances for the application in wastewater treatment. Plant-associated bacteria have potential to encourage the plant growth and resistance under stress conditions. Such bacteria could enhance plant growth by controlling growth hormone, nutrition security, producing siderophore, secondary metabolites, and improving the antioxidant enzymes system. This review also explores the concepts and applications of bacteria assisted phytoremediation, addressing aspects that affect phytoremediation and pathways for restoration. Significant review issues relating to production and application of bacteria for improvement of bioremediation were established and presented for possible future research. Bacteria assisted phytoremediation is cost-effective strategy and metal sequestration mechanism that hold high metal biosorption capacities. This also takes into consideration the current state of technology implementations and proposals for prospective clean-up studies.
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Affiliation(s)
- Pooja Sharma
- Department of Environmental Microbiology, School for Environmental Sciences, Babasaheb Bhimrao Ambedkar Central University, Lucknow 226 025, Uttar Pradesh, India
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Yan J, Wang J, Villalobos Solis MI, Jin H, Chourey K, Li X, Yang Y, Yin Y, Hettich RL, Löffler FE. Respiratory Vinyl Chloride Reductive Dechlorination to Ethene in TceA-Expressing Dehalococcoides mccartyi. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:4831-4841. [PMID: 33683880 DOI: 10.1021/acs.est.0c07354] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Bioremediation of chlorinated ethenes in anoxic aquifers hinges on organohalide-respiring Dehalococcoidia expressing vinyl chloride (VC) reductive dehalogenase (RDase). The tceA gene encoding the trichloroethene-dechlorinating RDase TceA is frequently detected in contaminated groundwater but not recognized as a biomarker for VC detoxification. We demonstrate that tceA-carrying Dehalococcoides mccartyi (Dhc) strains FL2 and 195 grow with VC as an electron acceptor when sufficient vitamin B12 (B12) is provided. Strain FL2 cultures that received 50 μg L-1 B12 completely dechlorinated VC to ethene at rates of 14.80 ± 1.30 μM day-1 and attained 1.64 ± 0.11 × 108 cells per μmol of VC consumed. Strain 195 attained similar growth yields of 1.80 ± 1.00 × 108 cells per μmol of VC consumed, and both strains could be consecutively transferred with VC as the electron acceptor. Proteomic analysis demonstrated TceA expression in VC-grown strain FL2 cultures. Resequencing of the strain FL2 and strain 195 tceA genes identified non-synonymous substitutions, although their consequences for TceA function are currently unknown. The finding that Dhc strains expressing TceA respire VC can explain ethene formation at chlorinated solvent sites, where quantitative polymerase chain reaction analysis indicates that tceA dominates the RDase gene pool.
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Affiliation(s)
- Jun Yan
- Key Laboratory of Pollution Control and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, Liaoning 110016, China
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Jingjing Wang
- Key Laboratory of Pollution Control and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, Liaoning 110016, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | | | - Huijuan Jin
- Key Laboratory of Pollution Control and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, Liaoning 110016, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Karuna Chourey
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Xiuying Li
- Key Laboratory of Pollution Control and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, Liaoning 110016, China
| | - Yi Yang
- Key Laboratory of Pollution Control and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, Liaoning 110016, China
| | - Yongchao Yin
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Robert L Hettich
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Frank E Löffler
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee 37996, United States
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee 37996, United States
- Joint Institute for Biological Sciences (JIBS), Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee 37996, United States
- Department of Biosystems Engineering & Soil Science, University of Tennessee, Knoxville, Tennessee 37996, United States
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Hammerschmid D, Germani F, Drusin SI, Fagnen C, Schuster CD, Hoogewijs D, Marti MA, Venien-Bryan C, Moens L, Van Doorslaer S, Sobott F, Dewilde S. Structural modeling of a novel membrane-bound globin-coupled sensor in Geobacter sulfurreducens. Comput Struct Biotechnol J 2021; 19:1874-1888. [PMID: 33995893 PMCID: PMC8076648 DOI: 10.1016/j.csbj.2021.03.031] [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: 12/19/2020] [Revised: 03/24/2021] [Accepted: 03/24/2021] [Indexed: 12/12/2022] Open
Abstract
Globin-coupled sensors (GCS) usually consist of three domains: a sensor/globin, a linker, and a transmitter domain. The globin domain (GD), activated by ligand binding and/or redox change, induces an intramolecular signal transduction resulting in a response of the transmitter domain. Depending on the nature of the transmitter domain, GCSs can have different activities and functions, including adenylate and di-guanylate cyclase, histidine kinase activity, aerotaxis and/or oxygen sensing function. The gram-negative delta-proteobacterium Geobacter sulfurreducens expresses a protein with a GD covalently linked to a four transmembrane domain, classified, by sequence similarity, as GCS (GsGCS). While its GD is fully characterized, not so its transmembrane domain, which is rarely found in the globin superfamily. In the present work, GsGCS was characterized spectroscopically and by native ion mobility-mass spectrometry in combination with cryo-electron microscopy. Although lacking high resolution, the oligomeric state and the electron density map were valuable for further rational modeling of the full-length GsGCS structure. This model demonstrates that GsGCS forms a transmembrane domain-driven tetramer with minimal contact between the GDs and with the heme groups oriented outward. This organization makes an intramolecular signal transduction less likely. Our results, including the auto-oxidation rate and redox potential, suggest a potential role for GsGCS as redox sensor or in a membrane-bound e-/H+ transfer. As such, GsGCS might act as a player in connecting energy production to the oxidation of organic compounds and metal reduction. Database searches indicate that GDs linked to a four or seven helices transmembrane domain occur more frequently than expected.
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Key Words
- AfGcHK, Anaeromyxobacter sp. Fw109-5 GcHK
- AsFRMF, Ascaris suum FRMF-amide receptor
- AvGReg, Azotobacter vinilandii Greg
- BpGReg, Bordetella pertussis Greg
- BsHemAT, Bacillus subtilis HemAT
- CCS, collision cross section
- CIU, collision-induced unfolding
- CMC, critical micelle concentration
- CV, cyclic voltammetry
- CeGLB26, Caenorhabditis elegans globin 26
- CeGLB33, Caenorhabditis elegans globin 33
- CeGLB6, Caenorhabditis elegans globin 6
- DDM, n-dodecyl-β-d-maltoside
- DPV, differential pulse voltammetry
- EcDosC, Escherichia coli Dos with DGC activity
- FMRF, H-Phe-Met-Arg-Phe-NH2 neuropeptide
- GCS, globin-coupled sensor
- GD, globin domain
- GGDEF, Gly-Gly-Asp-Glu-Phe motive
- Gb, globin
- Geobacter sulfurreducens
- GintHb, hemoglobin from Gasterophilus intestinalis
- Globin-coupled sensor
- GsGCS, Geobacter sulfurreducens GCS
- GsGCS162, GD of GsGCS
- IM-MS, ion mobility-mass spectrometry
- LmHemAC, Leishmania major HemAC
- MaPgb, Methanosarcina acetivorans protoglobin
- MtTrHbO, Mycobacterium tuberculosis truncated hemoglobin O
- NH4OAc, ammonium acetate
- OG, n-octyl-β-d-glucopyranoside
- PDE, phosphodiesterase
- PcMb, Physether catodon myoglobin
- PccGCS, Pectobacterium carotivorum GCS
- PsiE, phosphate-starvation-inducible E
- RR, resonance Raman
- SCE, saturated calomel electrode
- SHE, standard hydrogen electrode
- SaktrHb, Streptomyces avermitilis truncated hemoglobin-antibiotic monooxygenase
- SwMb, myoglobin from sperm whale
- TD, Transmitter domain
- TmD, Transmembrane domain
- Transmembrane domain
- Transmembrane-coupled globins
- mNgb, mouse neuroglobin
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Affiliation(s)
- Dietmar Hammerschmid
- Proteinchemistry, Proteomics and Epigenetic Signalling, Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
- Biomolecular & Analytical Mass Spectrometry, Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Francesca Germani
- Proteinchemistry, Proteomics and Epigenetic Signalling, Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
| | - Salvador I. Drusin
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (FCEyN-UBA) e Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Pabellòn 2 de Ciudad Universitaria, Ciudad de Buenos Aires C1428EHA, Argentina
| | - Charline Fagnen
- Sorbonne Université, UMR 7590, CNRS, Muséum National d’Histoire Naturelle, Institut de Minéralogie, Physique des Matériaux et Cosmochimie, IMPMC, 75005 Paris, France
| | - Claudio D. Schuster
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (FCEyN-UBA) e Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Pabellòn 2 de Ciudad Universitaria, Ciudad de Buenos Aires C1428EHA, Argentina
| | - David Hoogewijs
- Section of Medicine, Department of Endocrinology, Metabolism and Cardiovascular System, University of Fribourg, Switzerland
| | - Marcelo A. Marti
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (FCEyN-UBA) e Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Pabellòn 2 de Ciudad Universitaria, Ciudad de Buenos Aires C1428EHA, Argentina
| | - Catherine Venien-Bryan
- Sorbonne Université, UMR 7590, CNRS, Muséum National d’Histoire Naturelle, Institut de Minéralogie, Physique des Matériaux et Cosmochimie, IMPMC, 75005 Paris, France
| | - Luc Moens
- Proteinchemistry, Proteomics and Epigenetic Signalling, Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
| | - Sabine Van Doorslaer
- Biophysics and Biomedical Physics, Department of Chemistry, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
| | - Frank Sobott
- Biomolecular & Analytical Mass Spectrometry, Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
- School of Molecular and Cellular Biology, University of Leeds, LS2 9JT, United Kingdom
| | - Sylvia Dewilde
- Proteinchemistry, Proteomics and Epigenetic Signalling, Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
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Lekbach Y, Liu T, Li Y, Moradi M, Dou W, Xu D, Smith JA, Lovley DR. Microbial corrosion of metals: The corrosion microbiome. Adv Microb Physiol 2021; 78:317-390. [PMID: 34147188 DOI: 10.1016/bs.ampbs.2021.01.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Microbially catalyzed corrosion of metals is a substantial economic concern. Aerobic microbes primarily enhance Fe0 oxidation through indirect mechanisms and their impact appears to be limited compared to anaerobic microbes. Several anaerobic mechanisms are known to accelerate Fe0 oxidation. Microbes can consume H2 abiotically generated from the oxidation of Fe0. Microbial H2 removal makes continued Fe0 oxidation more thermodynamically favorable. Extracellular hydrogenases further accelerate Fe0 oxidation. Organic electron shuttles such as flavins, phenazines, and possibly humic substances may replace H2 as the electron carrier between Fe0 and cells. Direct Fe0-to-microbe electron transfer is also possible. Which of these anaerobic mechanisms predominates in model pure culture isolates is typically poorly documented because of a lack of functional genetic studies. Microbial mechanisms for Fe0 oxidation may also apply to some other metals. An ultimate goal of microbial metal corrosion research is to develop molecular tools to diagnose the occurrence, mechanisms, and rates of metal corrosion to guide the implementation of the most effective mitigation strategies. A systems biology approach that includes innovative isolation and characterization methods, as well as functional genomic investigations, will be required in order to identify the diagnostic features to be gleaned from meta-omic analysis of corroding materials. A better understanding of microbial metal corrosion mechanisms is expected to lead to new corrosion mitigation strategies. The understanding of the corrosion microbiome is clearly in its infancy, but interdisciplinary electrochemical, microbiological, and molecular tools are available to make rapid progress in this field.
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Affiliation(s)
- Yassir Lekbach
- Shenyang National Laboratory for Materials Science, Northeastern University, Shenyang, China; Electrobiomaterials Institute, Key Laboratory for Anisotropy and Texture of Materials (Ministry of Education), Northeastern University, Shenyang, China
| | - Tao Liu
- College of Ocean Science and Engineering, Shanghai Maritime University, Shanghai, China
| | - Yingchao Li
- Beijing Key Laboratory of Failure, Corrosion and Protection of Oil/Gas Facility Materials, College of New Energy and Materials, China University of Petroleum-Beijing, Beijing, China
| | - Masoumeh Moradi
- Shenyang National Laboratory for Materials Science, Northeastern University, Shenyang, China; Electrobiomaterials Institute, Key Laboratory for Anisotropy and Texture of Materials (Ministry of Education), Northeastern University, Shenyang, China
| | - Wenwen Dou
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Dake Xu
- Shenyang National Laboratory for Materials Science, Northeastern University, Shenyang, China; Electrobiomaterials Institute, Key Laboratory for Anisotropy and Texture of Materials (Ministry of Education), Northeastern University, Shenyang, China.
| | - Jessica A Smith
- Department of Biomolecular Sciences, Central Connecticut State University, New Britain, CT, United States
| | - Derek R Lovley
- Electrobiomaterials Institute, Key Laboratory for Anisotropy and Texture of Materials (Ministry of Education), Northeastern University, Shenyang, China; Department of Microbiology, University of Massachusetts, Amherst, MA, United States.
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34
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Fan YY, Tang Q, Li Y, Li FH, Wu JH, Li WW, Yu HQ. Rapid and highly efficient genomic engineering with a novel iEditing device for programming versatile extracellular electron transfer of electroactive bacteria. Environ Microbiol 2021; 23:1238-1255. [PMID: 33369000 DOI: 10.1111/1462-2920.15374] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 12/19/2020] [Accepted: 12/20/2020] [Indexed: 12/17/2022]
Abstract
The advances in synthetic biology bring exciting new opportunities to reprogram microorganisms with novel functionalities for environmental applications. For real-world applications, a genetic tool that enables genetic engineering in a stably genomic inherited manner is greatly desired. In this work, we design a novel genetic device for rapid and efficient genome engineering based on the intron-encoded homing-endonuclease empowered genome editing (iEditing). The iEditing device enables rapid and efficient genome engineering in Shewanella oneidensis MR-1, the representative strain of the electroactive bacteria group. Moreover, combining with the Red or RecET recombination system, the genome-editing efficiency was greatly improved, up to approximately 100%. Significantly, the iEditing device itself is eliminated simultaneously when genome editing occurs, thereby requiring no follow-up to remove the encoding system. Then, we develop a new extracellular electron transfer (EET) engineering strategy by programming the parallel EET systems to enhance versatile EET. The engineered strains exhibit sufficiently enhanced electron output and pollutant reduction ability. Furthermore, this device has demonstrated its great potential to be extended for genome editing in other important microbes. This work provides a useful and efficient tool for the rapid generation of synthetic microorganisms for various environmental applications.
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Affiliation(s)
- Yang-Yang Fan
- CAS Key Laboratory of Urban Pollutant Conversion, School of Life Sciences, University of Science and Technology of China, Hefei, 230026, China.,Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Qiang Tang
- Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Yang Li
- CAS Key Laboratory of Urban Pollutant Conversion, School of Life Sciences, University of Science and Technology of China, Hefei, 230026, China.,Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Feng-He Li
- Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Jing-Hang Wu
- Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Wen-Wei Li
- Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Han-Qing Yu
- Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
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35
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Yang YC, Huang WS, Hu SM, Huang CW, Chiu CH, Chen HY. Synergistic and Regulatable Bioremediation Capsules Fabrication Based on Vapor-Phased Encapsulation of Bacillus Bacteria and its Regulator by Poly- p-Xylylene. Polymers (Basel) 2020; 13:polym13010041. [PMID: 33374286 PMCID: PMC7795076 DOI: 10.3390/polym13010041] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/17/2020] [Accepted: 12/22/2020] [Indexed: 02/03/2023] Open
Abstract
A regulatable bioremediation capsule material was synthesized with isolated single-strain bacteria (Bacillus species, B. CMC1) and a regulator molecule (carboxymethyl cellulose, CMC) by a vapor-phased encapsulation method with simple steps of water sublimation and poly-p-xylylene deposition in chemical vapor deposition (CVD) process. Mechanically, the capsule construct exhibited a controllable shape and dimensions, and was composed of highly biocompatible poly-p-xylylene as the matrix with homogeneously distributed bacteria and CMC molecules. Versatility of the encapsulation of the molecules at the desired concentrations was achieved in the vapor-phased sublimation and deposition fabrication process. The discovery of the fabricated capsule revealed that viable living B. CMC1 inhabited the capsule, and the capsule enhanced bacterial growth due to the materials and process used. Biologically, the encapsulated B. CMC1 demonstrated viable and functional enzyme activity for cellulase activation, and such activity was regulatable and proportional to the concentration of the decorated CMC molecules in the same capsule construct. Impressively, 13% of cellulase activity increase was realized by encapsulation of B. CMC1 by poly-p-xylylene, and a further 34% of cellulase activity increase was achieved by encapsulation of additional 2.5% CMC. Accordingly, this synergistic effectiveness of the capsule constructs was established by combining enzymatic B. CMC1 bacteria and its regulatory CMC by poly-p-xylylene encapsulation process. This reported encapsulation process exhibited other advantages, including the use of simple steps and a dry and clean process free of harmful chemicals; most importantly, the process is scalable for mass production. The present study represents a novel method to fabricate bacteria-encapsulated capsule for cellulose degradation in bioremediation that can be used in various applications, such as wastewater treatment and transforming of cellulose into glucose for biofuel production. Moreover, the concept of this vapor-phased encapsulation technology can be correspondingly used to encapsulate multiple bacteria and regulators to enhance the specific enzyme functions for degradation of various organic matters.
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Affiliation(s)
- Yen-Ching Yang
- Department of Chemical Engineering, National Taiwan University, Taipei 10617, Taiwan; (Y.-C.Y.); (S.-M.H.); (C.-W.H.)
| | - Wei-Shen Huang
- Institute of Oceanography, National Taiwan University, Taipei 10617, Taiwan;
| | - Shu-Man Hu
- Department of Chemical Engineering, National Taiwan University, Taipei 10617, Taiwan; (Y.-C.Y.); (S.-M.H.); (C.-W.H.)
| | - Chao-Wei Huang
- Department of Chemical Engineering, National Taiwan University, Taipei 10617, Taiwan; (Y.-C.Y.); (S.-M.H.); (C.-W.H.)
| | - Chih-Hao Chiu
- Department of Orthopedic Surgery, Chang Gung Memorial Hospital, Taoyuan 33378, Taiwan
- Bone and Joint Research Center, Chang Gung Memorial Hospital, Linkou 33305, Taiwan
- Correspondence: (C.-H.C.); (H.-Y.C.); Tel.: +886-2-33669476 (H.-Y.C.)
| | - Hsien-Yeh Chen
- Department of Chemical Engineering, National Taiwan University, Taipei 10617, Taiwan; (Y.-C.Y.); (S.-M.H.); (C.-W.H.)
- Molecular Imaging Center, National Taiwan University, Taipei 10617, Taiwan
- Advanced Research Center for Green Materials Science and Technology, National Taiwan University, Taipei 10617, Taiwan
- Correspondence: (C.-H.C.); (H.-Y.C.); Tel.: +886-2-33669476 (H.-Y.C.)
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Maucourt B, Vuilleumier S, Bringel F. Transcriptional regulation of organohalide pollutant utilisation in bacteria. FEMS Microbiol Rev 2020; 44:189-207. [PMID: 32011697 DOI: 10.1093/femsre/fuaa002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 01/31/2020] [Indexed: 12/13/2022] Open
Abstract
Organohalides are organic molecules formed biotically and abiotically, both naturally and through industrial production. They are usually toxic and represent a health risk for living organisms, including humans. Bacteria capable of degrading organohalides for growth express dehalogenase genes encoding enzymes that cleave carbon-halogen bonds. Such bacteria are of potential high interest for bioremediation of contaminated sites. Dehalogenase genes are often part of gene clusters that may include regulators, accessory genes and genes for transporters and other enzymes of organohalide degradation pathways. Organohalides and their degradation products affect the activity of regulatory factors, and extensive genome-wide modulation of gene expression helps dehalogenating bacteria to cope with stresses associated with dehalogenation, such as intracellular increase of halides, dehalogenase-dependent acid production, organohalide toxicity and misrouting and bottlenecks in metabolic fluxes. This review focuses on transcriptional regulation of gene clusters for dehalogenation in bacteria, as studied in laboratory experiments and in situ. The diversity in gene content, organization and regulation of such gene clusters is highlighted for representative organohalide-degrading bacteria. Selected examples illustrate a key, overlooked role of regulatory processes, often strain-specific, for efficient dehalogenation and productive growth in presence of organohalides.
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Affiliation(s)
- Bruno Maucourt
- Université de Strasbourg, UMR 7156 CNRS, Génétique Moléculaire, Génomique, Microbiologie, Strasbourg, France
| | - Stéphane Vuilleumier
- Université de Strasbourg, UMR 7156 CNRS, Génétique Moléculaire, Génomique, Microbiologie, Strasbourg, France
| | - Françoise Bringel
- Université de Strasbourg, UMR 7156 CNRS, Génétique Moléculaire, Génomique, Microbiologie, Strasbourg, France
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37
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Laczi K, Erdeiné Kis Á, Szilágyi Á, Bounedjoum N, Bodor A, Vincze GE, Kovács T, Rákhely G, Perei K. New Frontiers of Anaerobic Hydrocarbon Biodegradation in the Multi-Omics Era. Front Microbiol 2020; 11:590049. [PMID: 33304336 PMCID: PMC7701123 DOI: 10.3389/fmicb.2020.590049] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 10/26/2020] [Indexed: 12/17/2022] Open
Abstract
The accumulation of petroleum hydrocarbons in the environment substantially endangers terrestrial and aquatic ecosystems. Many microbial strains have been recognized to utilize aliphatic and aromatic hydrocarbons under aerobic conditions. Nevertheless, most of these pollutants are transferred by natural processes, including rain, into the underground anaerobic zones where their degradation is much more problematic. In oxic zones, anaerobic microenvironments can be formed as a consequence of the intensive respiratory activities of (facultative) aerobic microbes. Even though aerobic bioremediation has been well-characterized over the past few decades, ample research is yet to be done in the field of anaerobic hydrocarbon biodegradation. With the emergence of high-throughput techniques, known as omics (e.g., genomics and metagenomics), the individual biodegraders, hydrocarbon-degrading microbial communities and metabolic pathways, interactions can be described at a contaminated site. Omics approaches provide the opportunity to examine single microorganisms or microbial communities at the system level and elucidate the metabolic networks, interspecies interactions during hydrocarbon mineralization. Metatranscriptomics and metaproteomics, for example, can shed light on the active genes and proteins and functional importance of the less abundant species. Moreover, novel unculturable hydrocarbon-degrading strains and enzymes can be discovered and fit into the metabolic networks of the community. Our objective is to review the anaerobic hydrocarbon biodegradation processes, the most important hydrocarbon degraders and their diverse metabolic pathways, including the use of various terminal electron acceptors and various electron transfer processes. The review primarily focuses on the achievements obtained by the current high-throughput (multi-omics) techniques which opened new perspectives in understanding the processes at the system level including the metabolic routes of individual strains, metabolic/electric interaction of the members of microbial communities. Based on the multi-omics techniques, novel metabolic blocks can be designed and used for the construction of microbial strains/consortia for efficient removal of hydrocarbons in anaerobic zones.
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Affiliation(s)
- Krisztián Laczi
- Department of Biotechnology, University of Szeged, Szeged, Hungary
| | - Ágnes Erdeiné Kis
- Department of Biotechnology, University of Szeged, Szeged, Hungary.,Institute of Biophysics, Biological Research Centre, Szeged, Hungary
| | - Árpád Szilágyi
- Department of Biotechnology, University of Szeged, Szeged, Hungary
| | - Naila Bounedjoum
- Department of Biotechnology, University of Szeged, Szeged, Hungary.,Institute of Environmental and Technological Sciences, University of Szeged, Szeged, Hungary
| | - Attila Bodor
- Department of Biotechnology, University of Szeged, Szeged, Hungary.,Institute of Biophysics, Biological Research Centre, Szeged, Hungary.,Institute of Environmental and Technological Sciences, University of Szeged, Szeged, Hungary
| | | | - Tamás Kovács
- Department of Biotechnology, Nanophagetherapy Center, Enviroinvest Corporation, Pécs, Hungary
| | - Gábor Rákhely
- Department of Biotechnology, University of Szeged, Szeged, Hungary.,Institute of Biophysics, Biological Research Centre, Szeged, Hungary.,Institute of Environmental and Technological Sciences, University of Szeged, Szeged, Hungary
| | - Katalin Perei
- Department of Biotechnology, University of Szeged, Szeged, Hungary.,Institute of Environmental and Technological Sciences, University of Szeged, Szeged, Hungary
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38
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Methane Monooxygenase Gene Transcripts as Quantitative Biomarkers of Methanotrophic Activity in Methylosinus trichosporium OB3b. Appl Environ Microbiol 2020; 86:AEM.01048-20. [PMID: 32948519 DOI: 10.1128/aem.01048-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 09/10/2020] [Indexed: 01/20/2023] Open
Abstract
Methanotrophic microorganisms are characterized by their ability to oxidize methane. Globally they have a significant impact on methane emissions by attenuating net methane fluxes to the atmosphere in natural and engineered systems, though the populations are dynamic in their activity level in soils and waters. Methanotrophs oxidize methane using methane monooxygenase (MMO) enzymes, and selected subunit genes of the most common MMOs, specifically pmoA and mmoX, are used as biomarkers for the presence and abundance of populations of bacterial methanotrophs. The relative expression of these biomarker genes is dependent on copper-to-biomass ratios. Empirically derived quantitative relationships between methane oxidation biomarker transcript amounts and methanotrophic activity could facilitate determination of methane oxidation rates. In this study, pure cultures of a model type II methanotroph, Methylosinus trichosporium OB3b, were grown in hollow-fiber membrane bioreactors (HFMBR) under different steady-state methane oxidation conditions. Methanotroph biomass (DNA based) and methane oxidation biomarker mRNA transcript amounts were determined using quantitative PCR (qPCR) and reverse transcription-PCR (RT-qPCR), respectively. Under both copper-present and copper-limited conditions, per-cell pmoA mRNA transcript levels positively correlated with measured per-cell methane oxidation rates across 3 orders of magnitude. These correlations, if maintained across different methanotrophs, could prove valuable for inferring in situ oxidation rates of methanotrophs and understanding the dynamics of their impact on net methane emissions.IMPORTANCE Methanotrophs are naturally occurring microorganisms capable of oxidizing methane and have an impact on global net methane emissions. The genes pmoA and mmoX are used as biomarkers for bacterial methanotrophs. Quantitative relationships between transcript amounts of these genes and methane oxidation rates could facilitate estimation of methanotrophic activity. In this study, a strong correlation was observed between per-cell pmoA transcript levels and per-cell methane oxidation rates for pure cultures of the aerobic methanotroph M. trichosporium OB3b grown in bioreactors. If similar relationships exist across different methanotrophs, they could prove valuable for inferring in situ oxidation rates of methanotrophs and better understanding their impact on net methane emissions.
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Ferreira MR, Fernandes TM, Salgueiro CA. Thermodynamic properties of triheme cytochrome PpcF from Geobacter metallireducens reveal unprecedented functional mechanism. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2020; 1861:148271. [PMID: 32692985 DOI: 10.1016/j.bbabio.2020.148271] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 07/02/2020] [Accepted: 07/11/2020] [Indexed: 12/12/2022]
Abstract
The bacterium Geobacter metallireducens is highly efficient in long-range extracellular electron transfer, a process that relies on an efficient bridging between the cytoplasmic electron donors and the extracellular acceptors. The periplasmic triheme cytochromes are crucial players in these processes and thus the understanding of their functional mechanism is crucial to elucidate the extracellular electron transfer processes in this microorganism. The triheme cytochrome PpcF from G. metallireducens has the lowest amino acid sequence identity with the remaining cytochromes from the PpcA-family of G. sulfurreducens and G. metallireducens, making it an interesting target for structural and functional studies. In this work, we performed a detailed functional and thermodynamic characterization of cytochrome PpcF by the complementary usage of NMR and visible spectroscopic techniques. The results obtained show that the heme reduction potentials are negative, different from each other and are also modulated by the redox and redox-Bohr interactions that assure unprecedented mechanistic features to the protein. The results showed that the order of oxidation of the hemes in cytochrome PpcF is maintained in the entire physiological pH range. The considerable separation of the hemes' redox potential values facilitates a sequential transfer within the chain of redox centers in PpcF, thus assuring electron transfer directionality to the electron acceptors.
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Affiliation(s)
- Marisa R Ferreira
- UCIBIO-Requimte, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Campus Caparica, 2829-516 Caparica, Portugal
| | - Tomás M Fernandes
- UCIBIO-Requimte, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Campus Caparica, 2829-516 Caparica, Portugal
| | - Carlos A Salgueiro
- UCIBIO-Requimte, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Campus Caparica, 2829-516 Caparica, Portugal.
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Li D, Sharp JO, Drewes JE. Microbial genetic potential for xenobiotic metabolism increases with depth during biofiltration. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2020; 22:2058-2069. [PMID: 33084698 DOI: 10.1039/d0em00254b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Water infiltration into the subsurface can result in pronounced biogeochemical depth gradients. In this study, we assess metabolic potential and properties of the subsurface microbiome during water infiltration by analyzing sediments from spatially-segmented columns. Past work in these laboratory set-ups demonstrated that removal efficiencies of trace organic pollutants were enhanced by limited availability of biodegradable dissolved organic carbon (BDOC) associated with higher humic ratios and deeper sediment regions. Distinct differences were observed in the microbial community when contrasting shallow versus deeper profile sediments. Metagenomic analyses revealed that shallow sediments contained an enriched potential for bacterial growth and division processes. In contrast, deeper sediments harbored a significant increase in genes associated with the metabolism of secondary metabolites and the biotransformation of xenobiotic water pollutants. Metatranscripts further supported this trend, with increased potential for metabolic attributes associated with the biotransformation of xenobiotics and antibiotic resistance within deeper sediments. Furthermore, increasing ratios of humics in feed solutions correlated to enhanced expression of genes associated with xenobiotic biodegradation. These results provide genetic support for the interplay of dissolved organic carbon limitation and enhanced trace organic biotransformation by the subsurface microbiome.
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Affiliation(s)
- Dong Li
- NSF Engineering Research Center ReNUWIt, Department of Civil and Environmental Engineering, Colorado School of Mines, Golden, CO, USA
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Hidalgo KJ, Sierra-Garcia IN, Dellagnezze BM, de Oliveira VM. Metagenomic Insights Into the Mechanisms for Biodegradation of Polycyclic Aromatic Hydrocarbons in the Oil Supply Chain. Front Microbiol 2020; 11:561506. [PMID: 33072021 PMCID: PMC7530279 DOI: 10.3389/fmicb.2020.561506] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 08/24/2020] [Indexed: 02/01/2023] Open
Abstract
Petroleum is a very complex and diverse organic mixture. Its composition depends on reservoir location and in situ conditions and changes once crude oil is spilled into the environment, making the characteristics associated with every spill unique. Polycyclic aromatic hydrocarbons (PAHs) are common components of the crude oil and constitute a group of persistent organic pollutants. Due to their highly hydrophobic, and their low solubility tend to accumulate in soil and sediment. The process by which oil is sourced and made available for use is referred to as the oil supply chain and involves three parts: (1) upstream, (2) midstream and (3) downstream activities. As consequence from oil supply chain activities, crude oils are subjected to biodeterioration, acidification and souring, and oil spills are frequently reported affecting not only the environment, but also the economy and human resources. Different bioremediation techniques based on microbial metabolism, such as natural attenuation, bioaugmentation, biostimulation are promising approaches to minimize the environmental impact of oil spills. The rate and efficiency of this process depend on multiple factors, like pH, oxygen content, temperature, availability and concentration of the pollutants and diversity and structure of the microbial community present in the affected (contaminated) area. Emerging approaches, such as (meta-)taxonomics and (meta-)genomics bring new insights into the molecular mechanisms of PAH microbial degradation at both single species and community levels in oil reservoirs and groundwater/seawater spills. We have scrutinized the microbiological aspects of biodegradation of PAHs naturally occurring in oil upstream activities (exploration and production), and crude oil and/or by-products spills in midstream (transport and storage) and downstream (refining and distribution) activities. This work addresses PAH biodegradation in different stages of oil supply chain affecting diverse environments (groundwater, seawater, oil reservoir) focusing on genes and pathways as well as key players involved in this process. In depth understanding of the biodegradation process will provide/improve knowledge for optimizing and monitoring bioremediation in oil spills cases and/or to impair the degradation in reservoirs avoiding deterioration of crude oil quality.
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Affiliation(s)
- Kelly J. Hidalgo
- Microbial Resources Division, Research Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas (UNICAMP), Paulínia, Brazil
- Graduate Program in Genetics and Molecular Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Isabel N. Sierra-Garcia
- Microbial Resources Division, Research Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas (UNICAMP), Paulínia, Brazil
- Biology Department & Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Aveiro, Portugal
| | - Bruna M. Dellagnezze
- Microbial Resources Division, Research Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas (UNICAMP), Paulínia, Brazil
| | - Valéria Maia de Oliveira
- Microbial Resources Division, Research Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas (UNICAMP), Paulínia, Brazil
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Hidalgo KJ, Teramoto EH, Soriano AU, Valoni E, Baessa MP, Richnow HH, Vogt C, Chang HK, Oliveira VM. Taxonomic and functional diversity of the microbiome in a jet fuel contaminated site as revealed by combined application of in situ microcosms with metagenomic analysis. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 708:135152. [PMID: 31812384 DOI: 10.1016/j.scitotenv.2019.135152] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 10/21/2019] [Accepted: 10/22/2019] [Indexed: 06/10/2023]
Abstract
Natural attenuation represents all processes that govern contaminant mass removal, which mainly occurs via microbial degradation in the environment. Although this process is intrinsic its rate and efficiency depend on multiple factors. This study aimed to characterize the microbial taxonomic and functional diversity in different aquifer sediments collected in the saturated zone and in situ microcosms (BACTRAP®s) amended with hydrocarbons (13C-labeled and non-labeled benzene, toluene and naphthalene) using 16S rRNA gene and "shotgun" Illumina high throughput sequencing at a jet-fuel contaminated site. The BACTRAP®s were installed to assess hydrocarbon metabolism by native bacteria. Results indicated that Proteobacteria, Actinobacteria and Firmicutes were the most dominant phyla (~98%) in the aquifer sediment samples. Meanwhile, in the benzene- and toluene-amended BACTRAP®s the phyla Firmicutes and Proteobacteria accounted for about 90% of total community. In the naphthalene-amended BACTRAP®, members of the SR-FBR-L83 family (Order Ignavibacteriales) accounted for almost 80% of bacterial community. Functional annotation of metagenomes showed that only the sediment sample located at the source zone border and with the lowest BTEX concentration, has metabolic potential to degrade hydrocarbons aerobically. On the other hand, in situ BACTRAP®s allowed enrichment of hydrocarbon-degrading bacteria. Metagenomic data suggest that fumarate addition is the main mechanism for hydrocarbon activation of toluene. Also, indications for methylation, hydroxylation and carboxylation as activation mechanisms for benzene anaerobic conversion were found. After 120 days of exposure in the contaminated groundwater, the isotopic analysis of fatty acids extracted from BACTRAP®s demonstrated the assimilation of isotopic labeled compounds in the cells of microbes expressed by strong isotopic enrichment. We propose that the microbiota in this jet-fuel contaminated site has metabolic potential to degrade benzene and toluene by a syntrophic process, between members of the families Geobacteraceae and Peptococcaceae (genus Pelotomaculum), coupled to nitrate, iron and/or sulfate reduction.
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Affiliation(s)
- K J Hidalgo
- Graduate Program in Genetics and Molecular Biology, Institute of Biology, University of Campinas (UNICAMP), Rua Monteiro Lobato 255, Cidade Universitária, Campinas, SP. ZIP 13083-862, Brazil.
| | - E H Teramoto
- Laboratory of Basin Studies (LEBAC), São Paulo State University (UNESP), Rio Claro, Av. 24A, 1515 ZIP 13506-900, Brazil
| | - A U Soriano
- PETROBRAS/ R&D Center (CENPES), Av. Horácio Macedo, 950. ZIP 21941-915 Ilha do Fundão, Rio de Janeiro, Brazil
| | - E Valoni
- PETROBRAS/ R&D Center (CENPES), Av. Horácio Macedo, 950. ZIP 21941-915 Ilha do Fundão, Rio de Janeiro, Brazil
| | - M P Baessa
- PETROBRAS/ R&D Center (CENPES), Av. Horácio Macedo, 950. ZIP 21941-915 Ilha do Fundão, Rio de Janeiro, Brazil
| | - H H Richnow
- Department Isotope Biogeochemistry, Helmholtz Centre for Environmental Research (UFZ), Permoserstrasse 15 04318 Leipzig, Germany
| | - C Vogt
- Department Isotope Biogeochemistry, Helmholtz Centre for Environmental Research (UFZ), Permoserstrasse 15 04318 Leipzig, Germany
| | - H K Chang
- Laboratory of Basin Studies (LEBAC), São Paulo State University (UNESP), Rio Claro, Av. 24A, 1515 ZIP 13506-900, Brazil
| | - V M Oliveira
- Microbial Resources Division, Research Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas - UNICAMP, Paulínia, Brazil, Av. Alexandre Cazellato, 999, ZIP 13148-218, Brazil
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Wanner P, Aravena R, Fernandes J, BenIsrael M, Haack EA, Tsao DT, Dunfield KE, Parker BL. Assessing toluene biodegradation under temporally varying redox conditions in a fractured bedrock aquifer using stable isotope methods. WATER RESEARCH 2019; 165:114986. [PMID: 31446293 DOI: 10.1016/j.watres.2019.114986] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 08/09/2019] [Accepted: 08/13/2019] [Indexed: 06/10/2023]
Abstract
In complex hydrogeological settings little is known about the extent of temporally varying redox conditions and their effect on aromatic hydrocarbon biodegradation. This study aims to assess the impact of changing redox conditions over time on aromatic hydrocarbon biodegradation in a fractured bedrock aquifer using stable isotope methods. To that end, four snapshots of highly spatio-temporally resolved contaminant and redox sensitive species concentrations, as well as stable isotope ratio profiles, were determined over a two-years time period in summer 2016, spring 2017, fall 2017 and summer 2018 in a toluene contaminated fractured bedrock aquifer. The concentration profiles of redox sensitive species and stable isotope ratio profiles for dissolved inorganic carbon (DIC) and sulfate (δ13CDIC, δ34SSO4, δ18OSO4) revealed that the aquifer alternates between oxidising (spring 2017/summer 2018) and reducing conditions (summer 2016/fall 2017). This alternation was attributed to a stronger aquifer recharge with oxygen-rich meltwater in spring 2017/summer 2018 compared to summer 2016/fall 2017. The temporally varying redox conditions coincided with various extents of toluene biodegradation revealed by the different magnitude of heavy carbon (13C) and hydrogen (2H) isotope enrichment in toluene. This indicated that the extent of toluene biodegradation and its contribution to plume attenuation was controlled by the temporally changing redox conditions. The highest toluene biodegradation was observed in summer 2016, followed by spring 2017 and fall 2017, whereby these temporal changes in biodegradation occurred throughout the whole plume. Thus, under temporally varying recharge conditions both the core and the fringe of a contaminant plume can be replenished with terminal electron acceptors causing biodegradation in the whole plume and not only at its distal end as previously suggested by the plume fringe concept. Overall, this study highlights the importance of highly temporally resolved groundwater monitoring to capture temporally varying biodegradation rates and to accurately predict biodegradation-induced contaminant attenuation in fractured bedrock aquifers.
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Affiliation(s)
- Philipp Wanner
- G360 Institute for Groundwater Research, College of Engineering and Physical Sciences, University of Guelph, 50 Stone Road East, Guelph, Ontario, N1G 2W1, Canada.
| | - Ramon Aravena
- G360 Institute for Groundwater Research, College of Engineering and Physical Sciences, University of Guelph, 50 Stone Road East, Guelph, Ontario, N1G 2W1, Canada; Department of Earth and Environmental Sciences, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada
| | - Jeremy Fernandes
- G360 Institute for Groundwater Research, College of Engineering and Physical Sciences, University of Guelph, 50 Stone Road East, Guelph, Ontario, N1G 2W1, Canada
| | - Michael BenIsrael
- School of Environmental Sciences, University of Guelph, 50 Stone Road East, Guelph, Ontario, N1G 2W1, Canada
| | - Elizabeth A Haack
- EcoMetrix Inc., 6800 Campobello Road, Mississauga, Ontario, L5N 2L8, Canada
| | - David T Tsao
- BP Corporation North America Inc, Naperville, USA
| | - Kari E Dunfield
- School of Environmental Sciences, University of Guelph, 50 Stone Road East, Guelph, Ontario, N1G 2W1, Canada
| | - Beth L Parker
- G360 Institute for Groundwater Research, College of Engineering and Physical Sciences, University of Guelph, 50 Stone Road East, Guelph, Ontario, N1G 2W1, Canada
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Palma E, Espinoza Tofalos A, Daghio M, Franzetti A, Tsiota P, Cruz Viggi C, Papini MP, Aulenta F. Bioelectrochemical treatment of groundwater containing BTEX in a continuous-flow system: Substrate interactions, microbial community analysis, and impact of sulfate as a co-contaminant. N Biotechnol 2019; 53:41-48. [DOI: 10.1016/j.nbt.2019.06.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 06/03/2019] [Accepted: 06/08/2019] [Indexed: 11/28/2022]
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Abstract
The study of electrically conductive protein nanowires in Geobacter sulfurreducens has led to new concepts for long-range extracellular electron transport, as well as for the development of sustainable conductive materials and electronic devices with novel functions. Until recently, electrically conductive pili (e-pili), assembled from the PilA pilin monomer, were the only known Geobacter protein nanowires. However, filaments comprised of the multi-heme c-type cytochrome, OmcS, are present in some preparations of G. sulfurreducens outer-surface proteins. The purpose of this review is to evaluate the available evidence on the in vivo expression of e-pili and OmcS filaments and their biological function. Abundant literature demonstrates that G. sulfurreducens expresses e-pili, which are required for long-range electron transport to Fe (III) oxides and through conductive biofilms. In contrast, there is no definitive evidence yet that wild-type G. sulfurreducens express long filaments of OmcS extending from the cells, and deleting the gene for OmcS actually increases biofilm conductivity. The literature does not support the concern that many previous studies on e-pili were mistakenly studying OmcS filaments. For example, heterologous expression of the aromatic-rich pilin monomer of Geobacter metallireducens in G. sulfurreducens increases the conductivity of individual nanowires more than 5,000-fold, whereas expression of an aromatic-poor pilin reduced conductivity more than 1,000-fold. This more than million-fold range in nanowire conductivity was achieved while maintaining the 3-nm diameter characteristic of e-pili. Purification methods that eliminate all traces of OmcS yield highly conductive e-pili, as does heterologous expression of the e-pilin monomer in microbes that do not produce OmcS or any other outer-surface cytochromes. Future studies of G. sulfurreducens expression of protein nanowires need to be cognizant of the importance of maintaining environmentally relevant growth conditions because artificial laboratory culture conditions can rapidly select against e-pili expression. Principles derived from the study of e-pili have enabled identification of non-cytochrome protein nanowires in diverse bacteria and archaea. A similar search for cytochrome appendages is warranted. Both e-pili and OmcS filaments offer design options for the synthesis of protein-based "green" electronics, which may be the primary driving force for the study of these structures in the near future.
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Affiliation(s)
- Derek R. Lovley
- Department of Microbiology, Institute for Applied Life Sciences, University of Massachusetts, Amherst, MA, United States
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Marín P, Martirani‐Von Abercron SM, Urbina L, Pacheco‐Sánchez D, Castañeda‐Cataña MA, Retegi A, Eceiza A, Marqués S. Bacterial nanocellulose production from naphthalene. Microb Biotechnol 2019; 12:662-676. [PMID: 31087504 PMCID: PMC6559018 DOI: 10.1111/1751-7915.13399] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 02/18/2019] [Accepted: 02/21/2019] [Indexed: 11/29/2022] Open
Abstract
Polycyclic aromatic compounds (PAHs) are toxic compounds that are released in the environment as a consequence of industrial activities. The restoration of PAH-polluted sites considers the use of bacteria capable of degrading aromatic compounds to carbon dioxide and water. Here we characterize a new Xanthobacteraceae strain, Starkeya sp. strain N1B, previously isolated during enrichment under microaerophilic conditions, which is capable of using naphthalene crystals as the sole carbon source. The strain produced a structured biofilm when grown on naphthalene crystals, which had the shape of a half-sphere organized over the crystal. Scanning electron microscopy (SEM) and GC-MS analysis indicated that the biofilm was essentially made of cellulose, composed of several micron-long nanofibrils of 60 nm diameter. A cellulosic biofilm was also formed when the cells grew with glucose as the carbon source. Fourier transformed infrared spectroscopy (FTIR) confirmed that the polymer was type I cellulose in both cases, although the crystallinity of the material greatly depended on the carbon source used for growth. Using genome mining and mutant analysis, we identified the genetic complements required for the transformation of naphthalene into cellulose, which seemed to have been successively acquired through horizontal gene transfer. The capacity to develop the biofilm around the crystal was found to be dispensable for growth when naphthalene was used as the carbon source, suggesting that the function of this structure is more intricate than initially thought. This is the first example of the use of toxic aromatic hydrocarbons as the carbon source for bacterial cellulose production. Application of this capacity would allow the remediation of a PAH into such a value-added polymer with multiple biotechnological usages.
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Affiliation(s)
- Patricia Marín
- Estación Experimental del ZaidínDepartment of Environmental ProtectionConsejo Superior de Investigaciones CientíficasCalle Profesor Albareda, 1Granada18008Spain
| | - Sophie Marie Martirani‐Von Abercron
- Estación Experimental del ZaidínDepartment of Environmental ProtectionConsejo Superior de Investigaciones CientíficasCalle Profesor Albareda, 1Granada18008Spain
| | - Leire Urbina
- Materials + Technologies Research Group (GMT)Department of Chemical and Environmental EngineeringFaculty of Engineering of GipuzkoaUniversity of the Basque CountryPza Europa 1Donostia‐San Sebastian20018Spain
| | - Daniel Pacheco‐Sánchez
- Estación Experimental del ZaidínDepartment of Environmental ProtectionConsejo Superior de Investigaciones CientíficasCalle Profesor Albareda, 1Granada18008Spain
| | - Mayra Alejandra Castañeda‐Cataña
- Estación Experimental del ZaidínDepartment of Environmental ProtectionConsejo Superior de Investigaciones CientíficasCalle Profesor Albareda, 1Granada18008Spain
| | - Aloña Retegi
- Materials + Technologies Research Group (GMT)Department of Chemical and Environmental EngineeringFaculty of Engineering of GipuzkoaUniversity of the Basque CountryPza Europa 1Donostia‐San Sebastian20018Spain
| | - Arantxa Eceiza
- Materials + Technologies Research Group (GMT)Department of Chemical and Environmental EngineeringFaculty of Engineering of GipuzkoaUniversity of the Basque CountryPza Europa 1Donostia‐San Sebastian20018Spain
| | - Silvia Marqués
- Estación Experimental del ZaidínDepartment of Environmental ProtectionConsejo Superior de Investigaciones CientíficasCalle Profesor Albareda, 1Granada18008Spain
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Heavner GLW, Mansfeldt CB, Wilkins MJ, Nicora CD, Debs GE, Edwards EA, Richardson RE. Detection of Organohalide-Respiring Enzyme Biomarkers at a Bioaugmented TCE-Contaminated Field Site. Front Microbiol 2019; 10:1433. [PMID: 31316484 PMCID: PMC6610324 DOI: 10.3389/fmicb.2019.01433] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 06/06/2019] [Indexed: 12/17/2022] Open
Abstract
RNA-based biomarkers have been successfully detected at field sites undergoing in situ bioremediation, but the detection of expressed enzymes is a more direct way to prove activity for a particular biocatalytic process of interest since they provide evidence of potential in situ activity rather than simply confirming presence and abundance of genes in a given population by measurement of DNA copies using qPCR. Here we successfully applied shotgun proteomics to field samples from a trichloroethene (TCE)-contaminated industrial site in southern Ontario, Canada that had been bio-augmented with the commercially available KB-1TM microbial culture. The KB-1TM culture contains multiple strains of Dehalococcoides mccartyi (D. mccartyi) as well as an organohalide respiring Geobacter species. The relative abundances of specific enzymatic proteins were subsequently compared to corresponding qPCR-derived levels of DNA and RNA biomarkers in the same samples. Samples were obtained from two wells with high hydraulic connectivity to the KB-1TM-bioaugemented enhanced in situ bioremediation system, and two control wells that showed evidence of low levels of native organohalide respiring bacteria (OHRB), Dehalococcoides and Geobacter. Enzymes involved in organohalide respiration were detected in the metaproteomes of all four field samples, as were chaperonins of D. mccartyi, chemotaxis proteins, and ATPases. The most highly expressed RDase in the bioaugmentation culture (VcrA) was the most highly detected enzyme overall in the bioaugmented groundwater samples. In one background groundwater well, we found high expression of the Geobacter pceA RDase. The DNA and RNA biomarkers detected using qPCR-based assays were a set of orthologs of Dehalococcoides reductive dehalogenases (VcrA, TceA, BvcA, dehalogenase “DET1545”), and the Ni-Fe uptake hydrogenase, HupL. Within a sample, RNA levels for key enzymes correlated with relative protein abundance. These results indicate that laboratory observations of TCE-bioremediation biomarker protein expression are recapitulated in field environmental systems and that both RNA and protein biomarker monitoring hold promise for activity monitoring of in situ populations of OHRB.
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Affiliation(s)
- Gretchen L W Heavner
- School of Civil and Environmental Engineering, Cornell University, Ithaca, NY, United States
| | - Cresten B Mansfeldt
- School of Civil and Environmental Engineering, Cornell University, Ithaca, NY, United States
| | - Michael J Wilkins
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Carrie D Nicora
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Garrett E Debs
- School of Civil and Environmental Engineering, Cornell University, Ithaca, NY, United States
| | - Elizabeth A Edwards
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada
| | - Ruth E Richardson
- School of Civil and Environmental Engineering, Cornell University, Ithaca, NY, United States
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Xia D, Yi X, Lu Y, Huang W, Xie Y, Ye H, Dang Z, Tao X, Li L, Lu G. Dissimilatory iron and sulfate reduction by native microbial communities using lactate and citrate as carbon sources and electron donors. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2019; 174:524-531. [PMID: 30861440 DOI: 10.1016/j.ecoenv.2019.03.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 03/01/2019] [Accepted: 03/01/2019] [Indexed: 05/25/2023]
Abstract
The bacterial (dissimilatory) iron and sulfate reduction (BIR and BSR) are intimately linked to the biogeochemical cycling of C, Fe, and S in acid mine drainage (AMD) environments. This study examined the response of native microbial communities to the reduction of iron and sulfate in bench experimental systems. Results showed that the reduction of ferric iron and sulfate took place when the electron acceptors coexist. Existence of Fe(III) can postpone the reduction of sulfate, but can enhance the reduction rate. Cultures grown in the presence of 10 mM iron can reach the final level of sulfate bio-reduction rate (~100%) after 35 days incubation. 16 S rDNA -based microbial community analysis revealed that the three genera Anaeromusa, Acinetobacter and Bacteroides were dominated in the ferric-reducing conditions. SRB (Desulfobulbus, Desulfosporosinus and Desulfovibrio) were dominated in the sulfate reduction process. Results in this study highlighted the highly coupled nature of C, Fe, and S biogeochemical cycles in AMD and provided insights into the potential of environmental remediation by native microbial.
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Affiliation(s)
- Di Xia
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China; South China Institute of Environmental Sciences, Ministry of Environmental Protection, (MEP), Guangzhou 510655, China
| | - Xiaoyun Yi
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China; The Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, Guangzhou 510006, China.
| | - Yang Lu
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
| | - Weilin Huang
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China; School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA
| | - Yingying Xie
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China; School of Chemistry and Environmental Engineering, Hanshan Normal University, Chaozhou 521041, China
| | - Han Ye
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
| | - Zhi Dang
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China; The Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, Guangzhou 510006, China
| | - Xueqin Tao
- College of Environmental Science and Engineering, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Li Li
- College of Environmental Science and Engineering, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Guining Lu
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China; School of Chemistry and Environmental Engineering, Hanshan Normal University, Chaozhou 521041, China.
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Determination of the magnetic properties and orientation of the heme axial ligands of PpcA from Geobacter metallireducens by paramagnetic NMR. J Inorg Biochem 2019; 198:110718. [PMID: 31153111 DOI: 10.1016/j.jinorgbio.2019.110718] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 05/09/2019] [Accepted: 05/13/2019] [Indexed: 11/22/2022]
Abstract
The rising interest in the use of Geobacter bacteria for biotechnological applications demands a deep understanding of how these bacteria are able to thrive in a variety of environments and perform extracellular electron transfer. The Geobacter metallireducens bacterium can couple the oxidation of a wide range of compounds to the reduction of several extracellular acceptors, including heavy metals, toxic organic compounds or electrode surfaces. The periplasmic c-type cytochrome PpcA from this bacterium is a member of a family composed of five periplasmic triheme cytochromes, which are important to bridge the electron transfer between the cytoplasm and the extracellular environment. To better understand the functional mechanism of PpcA it is essential to obtain structural data for this cytochrome. In this work, the geometry of the heme axial ligands, as well as the magnetic properties of the hemes were determined for the oxidized form of the cytochrome, using the 13C NMR chemical shifts of the heme α-substituents. The results were further compared with those previously obtained for the homologous cytochrome from Geobacter sulfurreducens. The orientations of the axial histidine planes and the magnetic properties of the hemes are conserved in both proteins. Overall, the results obtained allowed the definition of the orientation of the magnetic axes of PpcA from G. metallireducens, which will be used as constraints to assist the solution structure determination of the cytochrome in the oxidized form.
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Liang X, Radosevich M, Löffler F, Schaeffer SM, Zhuang J. Impact of microbial iron oxide reduction on the transport of diffusible tracers and non-diffusible nanoparticles in soils. CHEMOSPHERE 2019; 220:391-402. [PMID: 30597359 DOI: 10.1016/j.chemosphere.2018.12.165] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 11/22/2018] [Accepted: 12/22/2018] [Indexed: 06/09/2023]
Abstract
In subsurface bioremediation, electron donor addition promotes microbial Fe(III)-oxide mineral reduction that could change soil pore structure, release colloids, and alter soil surface properties. These processes in turn may impact bioremediation rates and the ultimate fate of contaminants. Columns packed with water-stable, Fe-oxide-rich soil aggregates were infused with acetate-containing artificial groundwater and operated for 20 d or 60 d inside an anoxic chamber. Soluble Fe(II) and soil colloids were detected in the effluent within one week after initiation of the acetate addition, demonstrating Fe(III)-bioreduction and colloid formation. Diffusible Br-, less diffusible 2,6-difluorobenzoate (DFBA), and non-diffusible silica-shelled silver nanoparticles (SSSNP) were used as tracers in transport experiments before and after the bioreduction. The transport of Br- was not influenced by the bioreduction. DFBA showed earlier breakthrough and less tailing after the bioreduction, suggesting alterations in flow paths and soil surface chemistry during the 20-d bioreduction treatment. Similarly, the bioreduction increased the transport of SSSNP very significantly, with mass recovery increasing from 1.7% to 25.1%. Unexpectedly, the SSSNP was completely retained in the columns when the acetate injection was extended from 20 to 60 d, while the mass recovery of DFBA decreased from 89.1% to 84.1% and Br- showed no change. The large change in the transport of SSSNP was attributed to soil aggregate breakdown and colloid release (causing mechanical straining of SSSNP) and the exposure of iron oxide surfaces previously unavailable within aggregate interiors (facilitating attachment of SSSNP). These results suggest a time-dependent fashion of microbial effect on the transport of diffusivity-varying tracers.
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Affiliation(s)
- Xiaolong Liang
- Department of Biosystems Engineering and Soil Science, The University of Tennessee, Knoxville, TN 37996, USA
| | - Mark Radosevich
- Department of Biosystems Engineering and Soil Science, The University of Tennessee, Knoxville, TN 37996, USA
| | - Frank Löffler
- Department of Biosystems Engineering and Soil Science, The University of Tennessee, Knoxville, TN 37996, USA; Department of Microbiology, Department of Civil and Environmental Engineering, Center for Environmental Biotechnology, The University of Tennessee, Knoxville, TN 37996, USA; Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Sean M Schaeffer
- Department of Biosystems Engineering and Soil Science, The University of Tennessee, Knoxville, TN 37996, USA
| | - Jie Zhuang
- Department of Biosystems Engineering and Soil Science, The University of Tennessee, Knoxville, TN 37996, USA.
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