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Journal ArticleDOI

Horizontal 'gene drives' harness indigenous bacteria for bioremediation.

15 Sep 2020-Scientific Reports (Nature Publishing Group)-Vol. 10, Iss: 1, pp 15091
TL;DR: Pilot experiments show that vectors only persist in indigenous populations when under selection pressure, disappearing when this carbon source is removed, which could prime indigenous bacteria for degrading pollutants while providing minimal ecosystem disturbance.
Abstract: Engineering bacteria to clean-up oil spills is rapidly advancing but faces regulatory hurdles and environmental concerns. Here, we develop a new technology to harness indigenous soil microbial communities for bioremediation by flooding local populations with catabolic genes for petroleum hydrocarbon degradation. Overexpressing three enzymes (almA, xylE, p450cam) in Escherichia coli led to degradation of 60–99% of target hydrocarbon substrates. Mating experiments, fluorescence microscopy and TEM revealed indigenous bacteria could obtain these vectors from E. coli through several mechanisms of horizontal gene transfer (HGT), including conjugation and cytoplasmic exchange through nanotubes. Inoculating petroleum-polluted sediments with E. coli carrying the vector pSF-OXB15-p450camfusion showed that the E. coli cells died after five days but a variety of bacteria received and carried the vector for over 60 days after inoculation. Within 60 days, the total petroleum hydrocarbon content of the polluted soil was reduced by 46%. Pilot experiments show that vectors only persist in indigenous populations when under selection pressure, disappearing when this carbon source is removed. This approach to remediation could prime indigenous bacteria for degrading pollutants while providing minimal ecosystem disturbance.

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Citations
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Journal ArticleDOI
TL;DR: A review article as discussed by the authors discusses the biodegradation potential of microorganisms and provides insights into recent advances and omics approaches employed for the specific characterization of xenobiotic-degrading microorganisms from contaminated environments.
Abstract: Global environmental contamination with a complex mixture of xenobiotics has become a major environmental issue worldwide Many xenobiotic compounds severely impact the environment due to their high toxicity, prolonged persistence, and limited biodegradability Microbial-assisted degradation of xenobiotic compounds is considered to be the most effective and beneficial approach Microorganisms have remarkable catabolic potential, with genes, enzymes, and degradation pathways implicated in the process of biodegradation A number of microbes, including Alcaligenes, Cellulosimicrobium, Microbacterium, Micrococcus, Methanospirillum, Aeromonas, Sphingobium, Flavobacterium, Rhodococcus, Aspergillus, Penecillium, Trichoderma, Streptomyces, Rhodotorula, Candida, and Aureobasidium, have been isolated and characterized, and have shown exceptional biodegradation potential for a variety of xenobiotic contaminants from soil/water environments Microorganisms potentially utilize xenobiotic contaminants as carbon or nitrogen sources to sustain their growth and metabolic activities Diverse microbial populations survive in harsh contaminated environments, exhibiting a significant biodegradation potential to degrade and transform pollutants However, the study of such microbial populations requires a more advanced and multifaceted approach Currently, multiple advanced approaches, including metagenomics, proteomics, transcriptomics, and metabolomics, are successfully employed for the characterization of pollutant-degrading microorganisms, their metabolic machinery, novel proteins, and catabolic genes involved in the degradation process These technologies are highly sophisticated, and efficient for obtaining information about the genetic diversity and community structures of microorganisms Advanced molecular technologies used for the characterization of complex microbial communities give an in-depth understanding of their structural and functional aspects, and help to resolve issues related to the biodegradation potential of microorganisms This review article discusses the biodegradation potential of microorganisms and provides insights into recent advances and omics approaches employed for the specific characterization of xenobiotic-degrading microorganisms from contaminated environments

102 citations

Journal ArticleDOI
TL;DR: In this paper, a bioelectronic communication system that is enabled by a redox signal transduction modality to exchange information between a living cell-embedded bioelectronics interface and an engineered microbial network is developed.
Abstract: We developed a bioelectronic communication system that is enabled by a redox signal transduction modality to exchange information between a living cell-embedded bioelectronics interface and an engineered microbial network. A naturally communicating three-member microbial network is 'plugged into' an external electronic system that interrogates and controls biological function in real time. First, electrode-generated redox molecules are programmed to activate gene expression in an engineered population of electrode-attached bacterial cells, effectively creating a living transducer electrode. These cells interpret and translate electronic signals and then transmit this information biologically by producing quorum sensing molecules that are, in turn, interpreted by a planktonic coculture. The propagated molecular communication drives expression and secretion of a therapeutic peptide from one strain and simultaneously enables direct electronic feedback from the second strain, thus enabling real-time electronic verification of biological signal propagation. Overall, we show how this multifunctional bioelectronic platform, termed a BioLAN, reliably facilitates on-demand bioelectronic communication and concurrently performs programmed tasks.

40 citations

Journal ArticleDOI
TL;DR: In this article, the authors introduce the strategies and technologies developed in the field of synthetic biology and their applications to the construction of microbial scavengers with improved efficiency of biodegradation while minimizing the impact of genetically engineered microbes on ecosystems.

22 citations

Journal ArticleDOI
TL;DR: In this paper, a review of the biochemical pathways and molecular mechanisms of butachlor biodegradation in depth is presented, in order to provide new ideas for repairing contaminated environments.
Abstract: The herbicide butachlor has been used in huge quantities worldwide, affecting various environmental systems. Butachlor residues have been detected in soil, water, and organisms, and have been shown to be toxic to these non-target organisms. This paper briefly summarizes the toxic effects of butachlor on aquatic and terrestrial animals, including humans, and proposes the necessity of its removal from the environment. Due to long-term exposure, some animals, plants, and microorganisms have developed resistance toward butachlor, indicating that the toxicity of this herbicide can be reduced. Furthermore, we can consider removing butachlor residues from the environment by using such butachlor-resistant organisms. In particular, microbial degradation methods have attracted much attention, with about 30 kinds of butachlor-degrading microorganisms have been found, such as Fusarium solani, Novosphingobium chloroacetimidivorans, Chaetomium globosum, Pseudomonas putida, Sphingomonas chloroacetimidivorans, and Rhodococcus sp. The metabolites and degradation pathways of butachlor have been investigated. In addition, enzymes associated with butachlor degradation have been identified, including CndC1 (ferredoxin), Red1 (reductase), FdX1 (ferredoxin), FdX2 (ferredoxin), Dbo (debutoxylase), and catechol 1,2 dioxygenase. However, few reviews have focused on the microbial degradation and molecular mechanisms of butachlor. This review explores the biochemical pathways and molecular mechanisms of butachlor biodegradation in depth in order to provide new ideas for repairing butachlor-contaminated environments. • Biodegradation is a powerful tool for the removal of butachlor. • Dechlorination plays a key role in the degradation of butachlor. • Possible biochemical pathways of butachlor in the environment are described.

19 citations

Journal ArticleDOI
TL;DR: In this article, a review on the application of bio-engineered microorganisms for the restoration of soil health by degradation of various pollutants is presented, and the challenges of using GMOs in environmental application as their introduction may affect the normal microbial community in soil.
Abstract: According to the United Nations Environment Programme (UNEP), soil health is declining over the decades and it has an adverse impact on human health as well as food security. Hence, soil health restoration is a need of the hour. It is known that microorganisms play a vital role in remediation of soil pollutants like heavy metals, pesticides, hydrocarbons etc. However, the indigenous microbes have a limited capacity to degrade these pollutants and it will be a slow process. Genetically modified organisms (GMO) can catalyse the degradation process as their altered metabolic pathways lead to hyper secretions of various biomolecules that favours the bioremediation process. This review provides an overview on the application of bioengineered microorganisms for the restoration of soil health by degradation of various pollutants. It also sheds light on the challenges of using GMOs in environmental application as their introduction may affect the normal microbial community in soil. Since, soil health also refers to the potential for native organisms to survive; the possible changes in native microbial community with the introduction of GMOs are also discussed. Finally, the future prospects of using bioengineered microorganisms in the environmental engineering applications to make the soil fertile and healthy has been deciphered. With the alarming rates of soil health loss, the treatment of soil and soil health restoration needs to fastened to a greater pace and the combinatorial efforts unifying GMOs, plant growth promoting rhizobacteria and other soil amendments will provide an effective solution to soil heath restoration ten years ahead.

14 citations

References
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Journal ArticleDOI
TL;DR: The functions, properties and constituents of the EPS matrix that make biofilms the most successful forms of life on earth are described.
Abstract: The microorganisms in biofilms live in a self-produced matrix of hydrated extracellular polymeric substances (EPS) that form their immediate environment. EPS are mainly polysaccharides, proteins, nucleic acids and lipids; they provide the mechanical stability of biofilms, mediate their adhesion to surfaces and form a cohesive, three-dimensional polymer network that interconnects and transiently immobilizes biofilm cells. In addition, the biofilm matrix acts as an external digestive system by keeping extracellular enzymes close to the cells, enabling them to metabolize dissolved, colloidal and solid biopolymers. Here we describe the functions, properties and constituents of the EPS matrix that make biofilms the most successful forms of life on earth.

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TL;DR: The extracellular matrix is a complex and extremely important component of all biofilms, providing architectural structure and mechanical stability to the attached population, and these intrinsic and extrinsic factors combine to produce a dynamic, heterogeneous microenvironment for the attached and enveloped cells.
Abstract: The extracellular matrix is a complex and extremely important component of all biofilms, providing architectural structure and mechanical stability to the attached population. The matrix is composed of cells, water and secreted/released extracellular macromolecules. In addition, a range of enzymic and regulatory activities can be found within the matrix. Together, these different components and activities are likely to interact and in so doing create a series of local environments within the matrix which co-exist as a functional consortium. The matrix architecture is also subject to a number of extrinsic factors, including fluctuations in nutrient and gaseous levels and fluid shear. Together, these intrinsic and extrinsic factors combine to produce a dynamic, heterogeneous microenvironment for the attached and enveloped cells.

1,810 citations

Journal ArticleDOI
TL;DR: An updated overview of petroleum hydrocarbon degradation by microorganisms under different ecosystems is presented and it is shown that many indigenous microorganisms in water and soil are capable of degrading hydrocarbon contaminants.
Abstract: One of the major environmental problems today is hydrocarbon contamination resulting from the activities related to the petrochemical industry. Accidental releases of petroleum products are of particular concern in the environment. Hydrocarbon components have been known to belong to the family of carcinogens and neurotoxic organic pollutants. Currently accepted disposal methods of incineration or burial insecure landfills can become prohibitively expensive when amounts of contaminants are large. Mechanical and chemical methods generally used to remove hydrocarbons from contaminated sites have limited effectiveness and can be expensive. Bioremediation is the promising technology for the treatment of these contaminated sites since it is cost-effective and will lead to complete mineralization. Bioremediation functions basically on biodegradation, which may refer to complete mineralization of organic contaminants into carbon dioxide, water, inorganic compounds, and cell protein or transformation of complex organic contaminants to other simpler organic compounds by biological agents like microorganisms. Many indigenous microorganisms in water and soil are capable of degrading hydrocarbon contaminants. This paper presents an updated overview of petroleum hydrocarbon degradation by microorganisms under different ecosystems.

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TL;DR: This review describes MGEs, their properties that are important in horizontal gene transfer, and current opportunities to advance MGE genomics.
Abstract: Horizontal genomics is a new field in prokaryotic biology that is focused on the analysis of DNA sequences in prokaryotic chromosomes that seem to have originated from other prokaryotes or eukaryotes. However, it is equally important to understand the agents that effect DNA movement: plasmids, bacteriophages and transposons. Although these agents occur in all prokaryotes, comprehensive genomics of the prokaryotic mobile gene pool or 'mobilome' lags behind other genomics initiatives owing to challenges that are distinct from cellular chromosomal analysis. Recent work shows promise of improved mobile genetic element (MGE) genomics and consequent opportunities to take advantage - and avoid the dangers - of these 'natural genetic engineers'. This review describes MGEs, their properties that are important in horizontal gene transfer, and current opportunities to advance MGE genomics.

1,488 citations

Journal ArticleDOI
19 Dec 2003-Science
TL;DR: The ecosystem response to the 1989 spill of oil from the Exxon Valdez into Prince William Sound, Alaska, shows that current practices for assessing ecological risks of oil in the oceans and, by extension, other toxic sources should be changed.
Abstract: The ecosystem response to the 1989 spill of oil from the Exxon Valdez into Prince William Sound, Alaska, shows that current practices for assessing ecological risks of oil in the oceans and, by extension, other toxic sources should be changed. Previously, it was assumed that impacts to populations derive almost exclusively from acute mortality. However, in the Alaskan coastal ecosystem, unexpected persistence of toxic subsurface oil and chronic exposures, even at sublethal levels, have continued to affect wildlife. Delayed population reductions and cascades of indirect effects postponed recovery. Development of ecosystem-based toxicology is required to understand and ultimately predict chronic, delayed, and indirect long-term risks and impacts.

1,387 citations


"Horizontal 'gene drives' harness in..." refers background in this paper

  • ...Future research is needed to determine (1) how long these plasmids are maintained under field conditions, (2) whether genetic mutations accumulate over time that might impact enzyme functioning, and (3) how vector-based gene drives harnessing natural processes of conjugation may affect local microbial community composition and soil metabolic functions....

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