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Wani AK, Akhtar N, Naqash N, Rahayu F, Djajadi D, Chopra C, Singh R, Mulla SI, Sher F, Américo-Pinheiro JHP. Discovering untapped microbial communities through metagenomics for microplastic remediation: recent advances, challenges, and way forward. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023:1-24. [PMID: 36637649 PMCID: PMC9838310 DOI: 10.1007/s11356-023-25192-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 01/04/2023] [Indexed: 06/01/2023]
Abstract
Microplastics (MPs) are ubiquitous pollutants persisting almost everywhere in the environment. With the increase in anthropogenic activities, MP accumulation is increasing enormously in aquatic, marine, and terrestrial ecosystems. Owing to the slow degradation of plastics, MPs show an increased biomagnification probability of persistent, bioaccumulative, and toxic substances thereby creating a threat to environmental biota. Thus, remediation of MP-pollutants requires efficient strategies to circumvent the mobilization of contaminants leaching into the water, soil, and ultimately to human beings. Over the years, several microorganisms have been characterized by the potential to degrade different plastic polymers through enzymatic actions. Metagenomics (MGs) is an effective way to discover novel microbial communities and access their functional genetics for the exploration and characterization of plastic-degrading microbial consortia and enzymes. MGs in combination with metatranscriptomics and metabolomics approaches are a powerful tool to identify and select remediation-efficient microbes in situ. Advancement in bioinformatics and sequencing tools allows rapid screening, mining, and prediction of genes that are capable of polymer degradation. This review comprehensively summarizes the growing threat of microplastics around the world and highlights the role of MGs and computational biology in building effective response strategies for MP remediation.
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Affiliation(s)
- Atif Khurshid Wani
- School of Bioengineering and Biosciences, Lovely Professional University, Punjab, 144411, India
| | - Nahid Akhtar
- School of Bioengineering and Biosciences, Lovely Professional University, Punjab, 144411, India
| | - Nafiaah Naqash
- School of Bioengineering and Biosciences, Lovely Professional University, Punjab, 144411, India
| | - Farida Rahayu
- Research Center for Applied Microbiology, National Research and Innovation Agency, Bogor, 16911, Indonesia
| | - Djajadi Djajadi
- Research Center for Horticulture and Plantation, National Research Innovation Agency, Bogor, 16111, Indonesia
| | - Chirag Chopra
- School of Bioengineering and Biosciences, Lovely Professional University, Punjab, 144411, India
| | - Reena Singh
- School of Bioengineering and Biosciences, Lovely Professional University, Punjab, 144411, India
| | - Sikandar I Mulla
- Department of Biochemistry, School of Allied Health Sciences, REVA University, Bengaluru, 560064, Karnataka, India
| | - Farooq Sher
- Department of Engineering, School of Science and Technology, Nottingham Trent University, Nottingham, NG11 8NS, UK
| | - Juliana Heloisa Pinê Américo-Pinheiro
- Department of Forest Science, Soils and Environment, School of Agronomic Sciences, São Paulo State University (UNESP), Ave. Universitária, 3780, Botucatu, SP, 18610-034, Brazil.
- Graduate Program in Environmental Sciences, Brazil University, Street Carolina Fonseca, 584, São Paulo, SP, 08230-030, Brazil.
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2
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Lensch A, Duwenig E, Dederer HG, Kärenlampi SO, Custers R, Borg A, Wyss M. Recombinant DNA in fermentation products is of no regulatory relevance. Food Control 2022. [DOI: 10.1016/j.foodcont.2022.109170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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3
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Innard N, Chong JPJ. The challenges of monitoring and manipulating anaerobic microbial communities. BIORESOURCE TECHNOLOGY 2022; 344:126326. [PMID: 34780902 DOI: 10.1016/j.biortech.2021.126326] [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: 09/05/2021] [Revised: 11/03/2021] [Accepted: 11/09/2021] [Indexed: 06/13/2023]
Abstract
Mixed anaerobic microbial communities are a key component in valorization of waste biomass via anaerobic digestion. Similar microbial communities are important as soil and animal microbiomes and have played a critical role in shaping the planet as it is today. Understanding how individual species within communities interact with others and their environment is important for improving performance and potential applications of an inherently green technology. Here, the challenges associated with making measurements critical to assessing the status of anaerobic microbial communities are considered. How these measurements could be incorporated into control philosophies and augment the potential of anaerobic microbial communities to produce different and higher value products from waste materials are discussed. The benefits and pitfalls of current genetic and molecular approaches to measuring and manipulating anaerobic microbial communities and the challenges which should be addressed to realise the potential of this exciting technology are explored.
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Affiliation(s)
- Nathan Innard
- Department of Biology, University of York, Wentworth Way, Heslington, York YO10 5DD, UK
| | - James P J Chong
- Department of Biology, University of York, Wentworth Way, Heslington, York YO10 5DD, UK.
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4
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Huang XF, Reardon KF. Quorum-sensing molecules increase ethanol yield from Saccharomyces cerevisiae. FEMS Yeast Res 2021; 21:6424905. [PMID: 34755845 DOI: 10.1093/femsyr/foab056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 11/05/2021] [Indexed: 11/14/2022] Open
Abstract
One strategy to increase the yield of desired fermentation products is to redirect substrate carbon from biomass synthesis. Non-genetic approaches to alter metabolism may have advantages of general applicability and simple control. The goal of this study was to identify and evaluate chemicals for their ability to inhibit the growth of Saccharomyces cerevisiae while allowing ethanol production with higher yields. Eight potential growth-inhibitory chemicals were screened for their ability to reduce cell growth in 24-well plates. Effective chemicals were then evaluated in cultivations to identify those that simultaneously reduced biomass yield and increased ethanol yield. The yeast quorum-sensing molecules 2-phenylethanol, tryptophol, and tyrosol, were found to increase the ethanol yield of S. cerevisiae JAY 270. These molecules were tested with seven other yeast strains and ethanol yields of up to 15% higher were observed. The effects of 2-phenylethanol and tryptophol were also studied in bioreactor fermentations. These findings demonstrate for the first time that the ethanol yield can be improved by adding yeast quorum-sensing molecules to reduce the cell growth of S. cerevisiae, suggesting a strategy to improve the yield of ethanol and other yeast fermentation products by manipulating native biological control systems.
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Affiliation(s)
- Xing-Feng Huang
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO
| | - Kenneth F Reardon
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO
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Epis S, Varotto-Boccazzi I, Crotti E, Damiani C, Giovati L, Mandrioli M, Biggiogera M, Gabrieli P, Genchi M, Polonelli L, Daffonchio D, Favia G, Bandi C. Chimeric symbionts expressing a Wolbachia protein stimulate mosquito immunity and inhibit filarial parasite development. Commun Biol 2020; 3:105. [PMID: 32144396 PMCID: PMC7060271 DOI: 10.1038/s42003-020-0835-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 02/18/2020] [Indexed: 12/28/2022] Open
Abstract
Wolbachia can reduce the capability of mosquitoes to transmit infectious diseases to humans and is currently exploited in campaigns for the control of arboviruses, like dengue and Zika. Under the assumption that Wolbachia-mediated activation of insect immunity plays a role in the reduction of mosquito vectorial capacity, we focused our attention on the Wolbachia surface protein (WSP), a potential inductor of innate immunity. We hypothesized that the heterologous expression of this protein in gut- and tissue-associated symbionts may reduce parasite transmission. We thus engineered the mosquito bacterial symbiont Asaia to express WSP (AsaiaWSP). AsaiaWSP induced activation of the host immune response in Aedes aegypti and Anopheles stephensi mosquitoes, and inhibited the development of the heartworm parasite Dirofilaria immitis in Ae. aegypti. These results consolidate previous evidence on the immune-stimulating property of WSP and make AsaiaWSP worth of further investigations as a potential tool for the control of mosquito-borne diseases. Epis and Varotto-Boccazzi et al. show that Wolbachia surface protein (WSP) activates host innate immunity in mosquitoes, inhibiting the development of the heartworm parasite in its insect host. This study suggests the possibility that the WSP-expressing symbiont may be harnessed to control mosquito-borne diseases.
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Affiliation(s)
- Sara Epis
- Department of Biosciences and Pediatric Clinical Research Center "Romeo and Enrica Invernizzi", University of Milan, Milan, Italy.,Centro Interuniversitario di Ricerca sulla Malaria/Italian Malaria Network, Milan, Italy
| | - Ilaria Varotto-Boccazzi
- Department of Biosciences and Pediatric Clinical Research Center "Romeo and Enrica Invernizzi", University of Milan, Milan, Italy.,Centro Interuniversitario di Ricerca sulla Malaria/Italian Malaria Network, Milan, Italy
| | - Elena Crotti
- Department of Food, Environmental and Nutritional Sciences, University of Milan, Milan, Italy
| | - Claudia Damiani
- Centro Interuniversitario di Ricerca sulla Malaria/Italian Malaria Network, Milan, Italy.,School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
| | - Laura Giovati
- Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Mauro Mandrioli
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Marco Biggiogera
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia, Italy
| | - Paolo Gabrieli
- Department of Biosciences and Pediatric Clinical Research Center "Romeo and Enrica Invernizzi", University of Milan, Milan, Italy.,Centro Interuniversitario di Ricerca sulla Malaria/Italian Malaria Network, Milan, Italy
| | - Marco Genchi
- Department of Veterinary Sciences, University of Parma, Parma, Italy
| | - Luciano Polonelli
- Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Daniele Daffonchio
- King Abdullah University of Science and Technology, Red Sea Research Center, Thuwal, Saudi Arabia
| | - Guido Favia
- Centro Interuniversitario di Ricerca sulla Malaria/Italian Malaria Network, Milan, Italy.,School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
| | - Claudio Bandi
- Department of Biosciences and Pediatric Clinical Research Center "Romeo and Enrica Invernizzi", University of Milan, Milan, Italy. .,Centro Interuniversitario di Ricerca sulla Malaria/Italian Malaria Network, Milan, Italy.
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Chromate reduction is expedited by bacteria engineered to produce the compatible solute trehalose. Biotechnol Lett 2013; 35:1291-6. [PMID: 23563698 DOI: 10.1007/s10529-013-1200-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Accepted: 03/28/2013] [Indexed: 10/27/2022]
Abstract
The toxicity and solubility of chromium(VI) can be decreased by certain microbes that reduce chromium(VI) to chromium(III). However, these bacteria do not escape unscathed from this process. Chromium(VI) reduction damages the essential macromolecules of living systems. Trehalose protects organisms from chemical stress but has not been tested in the context of bioremediation. We engineered bacteria to produce trehalose and found that they then reduced 1 mM chromium(VI) to chromium(III), whereas wild-type cells were only able to reduce half that amount. Thus, by providing bacteria with a biochemical defense against the side-effects of chromate reduction may be a new approach to cleaning up sites that are contaminated with high levels of chromate.
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7
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Fernández-Luqueño F, Valenzuela-Encinas C, Marsch R, Martínez-Suárez C, Vázquez-Núñez E, Dendooven L. Microbial communities to mitigate contamination of PAHs in soil--possibilities and challenges: a review. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2011; 18:12-30. [PMID: 20623198 DOI: 10.1007/s11356-010-0371-6] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2010] [Accepted: 06/23/2010] [Indexed: 05/26/2023]
Abstract
BACKGROUND, AIM, AND SCOPE Although highly diverse and specialized prokaryotic and eukaryotic microbial communities in soil degrade polycyclic aromatic hydrocarbons (PAHs), most of these are removed slowly. This review will discuss the biotechnological possibilities to increase the microbial dissipation of PAHs from soil as well as the main biological and biotechnological challenges. DISCUSSION AND CONCLUSIONS Microorganism provides effective and economically feasible solutions for soil cleanup and restoration. However, when the PAHs contamination is greater than the microbial ability to dissipate them, then applying genetically modified microorganisms might help to remove the contaminant. Nevertheless, it is necessary to have a more holistic review of the different individual reactions that are simultaneously taking place in a microbial cell and of the interactions microorganism-microorganism, microorganism-plant, microorganism-soil, and microorganisms-PAHs. PERSPECTIVES Elucidating the function of genes from the PAHs-polluted soil and the study in pure cultures of isolated PAHs-degrading organisms as well as the generation of microorganisms in the laboratory that will accelerate the dissipation of PAHs and their safe application in situ have not been studied extensively. There is a latent environmental risk when genetically engineered microorganisms are used to remedy PAHs-contaminated soil.
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Affiliation(s)
- F Fernández-Luqueño
- Renewable Energy Engineering, Universidad Tecnológica de Tulancingo, Tulancingo, Hidalgo 43642, México.
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8
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de Crécy E, Metzgar D, Allen C, Pénicaud M, Lyons B, Hansen CJ, de Crécy-Lagard V. Development of a novel continuous culture device for experimental evolution of bacterial populations. Appl Microbiol Biotechnol 2007; 77:489-96. [PMID: 17896105 DOI: 10.1007/s00253-007-1168-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2007] [Revised: 08/15/2007] [Accepted: 08/15/2007] [Indexed: 10/22/2022]
Abstract
The availability of a robust and reliable continuous culture apparatus that eliminates wall growth problems would lead to many applications in the microbial field, including allowing genetically engineered strains to recover high fitness, improving biodegradation strains, and predicting likely antibiotic resistance mechanisms. We describe the design and implementation of a novel automated continuous culture machine that can be used both in time-dependent mode (similar to a chemostat) and turbidostat modes, in which wall growth is circumvented through the use of a long, variably divisible tube of growth medium. This tube can be restricted with clamps to create a mobile growth chamber region in which static portions of the tube and the associated medium are replaced together at equal rates. To functionally test the device as a tool for re-adaptation of engineered strains, we evolved a strain carrying a highly deleterious deletion of Elongation Factor P, a gene involved in translation. In 200 generations over 2 weeks of dilution cycles, the evolved strain improved in generation time by a factor of three, with no contaminations and easy manipulation.
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Affiliation(s)
- E de Crécy
- Evolugate 5745 SW 75th St #188, Gainesville, FL 32608, USA
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9
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Sayler GS, Ripp S. Field applications of genetically engineered microorganisms for bioremediation processes. Curr Opin Biotechnol 2000; 11:286-9. [PMID: 10851144 DOI: 10.1016/s0958-1669(00)00097-5] [Citation(s) in RCA: 122] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Genetically engineered microorganisms (GEMs) have shown potential for bioremediation applications in soil, groundwater, and activated sludge environments, exhibiting enhanced degradative capabilities encompassing a wide range of chemical contaminants. However, the vast majority of studies pertaining to genetically engineered microbial bioremediation are supported by laboratory-based experimental data. In general, relatively few examples of GEM applications in environmental ecosystems exist. Unfortunately, the only manner in which to fully address the competence of GEMs in bioremediation efforts is through long-term field release studies. It is therefore essential that field studies be performed to acquire the requisite information for determining the overall effectiveness and risks associated with GEM introduction into natural ecosystems.
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Affiliation(s)
- G S Sayler
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Knoxville, TN 37996, USA.
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10
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Pleiotropic effects of adaptation to a single carbon source for growth on alternative substrates. Appl Environ Microbiol 1999; 65:264-9. [PMID: 9872788 PMCID: PMC91011 DOI: 10.1128/aem.65.1.264-269.1999] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
It is frequently assumed that populations of genetically modified microorganisms will perform their intended function and then disappear from the environment due to inherent fitness disadvantages resulting from their genetic alteration. However, modified organisms used in bioremediation can be expected to adapt evolutionarily to growth on the anthropogenic substrate that they are intended to degrade. If such adaptation results in improved competitiveness for alternative, naturally occurring substrates, then this will increase the likelihood that the modified organisms will persist in the environment. In this study, bacteria capable of degrading the herbicide 2,4-dichlorophenoxyacetic acid (2,4-D) were used to test the effects of evolutionary adaptation to one substrate on fitness during growth on an alternative substrate. Twenty lineages of bacteria were allowed to evolve under abundant resource conditions on either 2,4-D or succinate as their sole carbon source. The competitiveness of each evolved line was then measured relative to that of its ancestor for growth on both substrates. Only three derived lines showed a clear drop in fitness on the alternative substrate after demonstrable adaptation to their selective substrate, while five derived lines showed significant simultaneous increases in fitness on both their selective and alternative substrates. These data demonstrate that adaptation to an anthropogenic substrate can pleiotropically increase competitiveness for an alternative natural substrate and therefore increase the likelihood that a genetically modified organism will persist in the environment.
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11
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Chang H. Genetic engineering to enhance microbial interference and related therapeutic applications. Nat Biotechnol 1996; 14:444-7. [PMID: 9630918 DOI: 10.1038/nbt0496-444] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- H Chang
- US Food and Drug Administration, Rockville, MD 20857, USA.
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