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1.
Cell ; 172(6): 1336-1336.e1, 2018 03 08.
Artículo en Inglés | MEDLINE | ID: mdl-29522751

RESUMEN

Hydrocarbon-degrading bacteria are phylogenetically and physiologically diverse and employ layered strategies to sense hydrocarbons, respond transcriptionally, and then move toward an oil source. They then produce biopolymers that increase hydrocarbon bioavailability. This SnapShot highlights how these bacteria respond to and then remove hydrocarbon contaminants from the environment. To view this SnapShot, open or download the PDF.


Asunto(s)
Bacterias/metabolismo , Hidrocarburos/metabolismo , Microbiología del Suelo , Microbiología del Agua , Biodegradación Ambiental , Membrana Celular/metabolismo , Hidrocarburos/química , Hidrocarburos/clasificación , Interacciones Hidrofóbicas e Hidrofílicas , Redes y Vías Metabólicas , Modelos Biológicos , Percepción de Quorum , Tensoactivos/química , Tensoactivos/metabolismo
2.
Nature ; 631(8022): 884-890, 2024 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-39020178

RESUMEN

Plastic production reached 400 million tons in 2022 (ref. 1), with packaging and single-use plastics accounting for a substantial amount of this2. The resulting waste ends up in landfills, incineration or the environment, contributing to environmental pollution3. Shifting to biodegradable and compostable plastics is increasingly being considered as an efficient waste-management alternative4. Although polylactide (PLA) is the most widely used biosourced polymer5, its biodegradation rate under home-compost and soil conditions remains low6-8. Here we present a PLA-based plastic in which an optimized enzyme is embedded to ensure rapid biodegradation and compostability at room temperature, using a scalable industrial process. First, an 80-fold activity enhancement was achieved through structure-based rational engineering of a new hyperthermostable PLA hydrolase. Second, the enzyme was uniformly dispersed within the PLA matrix by means of a masterbatch-based melt extrusion process. The liquid enzyme formulation was incorporated in polycaprolactone, a low-melting-temperature polymer, through melt extrusion at 70 °C, forming an 'enzymated' polycaprolactone masterbatch. Masterbatch pellets were integrated into PLA by melt extrusion at 160 °C, producing an enzymated PLA film (0.02% w/w enzyme) that fully disintegrated under home-compost conditions within 20-24 weeks, meeting home-composting standards. The mechanical and degradation properties of the enzymated film were compatible with industrial packaging applications, and they remained intact during long-term storage. This innovative material not only opens new avenues for composters and biomethane production but also provides a feasible industrial solution for PLA degradation.


Asunto(s)
Plásticos Biodegradables , Biodegradación Ambiental , Enzimas Inmovilizadas , Hidrolasas , Poliésteres , Ingeniería de Proteínas , Plásticos Biodegradables/química , Plásticos Biodegradables/metabolismo , Enzimas Inmovilizadas/química , Enzimas Inmovilizadas/metabolismo , Hidrolasas/metabolismo , Hidrolasas/química , Poliésteres/química , Poliésteres/metabolismo , Suelo/química , Temperatura , Estabilidad de Enzimas , Compostaje
3.
Nature ; 601(7892): 257-262, 2022 01.
Artículo en Inglés | MEDLINE | ID: mdl-34937940

RESUMEN

The methanogenic degradation of oil hydrocarbons can proceed through syntrophic partnerships of hydrocarbon-degrading bacteria and methanogenic archaea1-3. However, recent culture-independent studies have suggested that the archaeon 'Candidatus Methanoliparum' alone can combine the degradation of long-chain alkanes with methanogenesis4,5. Here we cultured Ca. Methanoliparum from a subsurface oil reservoir. Molecular analyses revealed that Ca. Methanoliparum contains and overexpresses genes encoding alkyl-coenzyme M reductases and methyl-coenzyme M reductases, the marker genes for archaeal multicarbon alkane and methane metabolism. Incubation experiments with different substrates and mass spectrometric detection of coenzyme-M-bound intermediates confirm that Ca. Methanoliparum thrives not only on a variety of long-chain alkanes, but also on n-alkylcyclohexanes and n-alkylbenzenes with long n-alkyl (C≥13) moieties. By contrast, short-chain alkanes (such as ethane to octane) or aromatics with short alkyl chains (C≤12) were not consumed. The wide distribution of Ca. Methanoliparum4-6 in oil-rich environments indicates that this alkylotrophic methanogen may have a crucial role in the transformation of hydrocarbons into methane.


Asunto(s)
Euryarchaeota , Hidrocarburos , Metano , Alcanos/metabolismo , Biodegradación Ambiental , Euryarchaeota/enzimología , Euryarchaeota/genética , Hidrocarburos/metabolismo , Metano/metabolismo , Oxidorreductasas/metabolismo , Filogenia
4.
Proc Natl Acad Sci U S A ; 121(31): e2400525121, 2024 Jul 30.
Artículo en Inglés | MEDLINE | ID: mdl-39042683

RESUMEN

Per- and polyfluoroalkyl substances (PFAS), particularly the perfluorinated ones, are recalcitrant to biodegradation. By integrating an enrichment culture of reductive defluorination with biocompatible electrodes for the electrochemical process, a deeper defluorination of a C6-perfluorinated unsaturated PFAS was achieved compared to the biological or electrochemical system alone. Two synergies in the bioelectrochemical system were identified: i) The in-series microbial-electrochemical defluorination and ii) the electrochemically enabled microbial defluorination of intermediates. These synergies at the material-microbe interfaces surpassed the limitation of microbial defluorination and further turned the biotransformation end products into less fluorinated products, which could be less toxic and more biodegradable in the environment. This material-microbe hybrid system brings opportunities in the bioremediation of PFAS driven by renewable electricity and warrants future research on mechanistic understanding of defluorinating and electroactive microorganisms at the material-microbe interface for system optimizations.


Asunto(s)
Biodegradación Ambiental , Anaerobiosis , Halogenación , Electrodos/microbiología , Fluorocarburos/metabolismo , Fluorocarburos/química , Técnicas Electroquímicas/métodos , Bacterias/metabolismo
5.
Proc Natl Acad Sci U S A ; 121(36): e2409955121, 2024 Sep 03.
Artículo en Inglés | MEDLINE | ID: mdl-39190351

RESUMEN

Facing complex and variable emerging antibiotic pollutants, the traditional development of functional materials is a "trial-and-error" process based on physicochemical principles, where laborious steps and long timescales make it difficult to accelerate technical breakthroughs. Notably, natural biomolecular coronas derived from highly tolerant organisms under significant contamination scenarios can be used in conjunction with nanotechnology to tackling emerging contaminants of concern. Here, super worms (Tubifex tubifex) with high pollutant tolerance were integrated with nano-zero valent iron (nZVI) to effectively reduce the content of 17 antibiotics in wastewater within 7 d. Inspired by the synergistic remediation, nZVI-augmented worms were constructed as biological nanocomposites. Neither nZVI (0.3 to 3 g/L) nor worms (104 to 105 per liter) alone efficiently degraded florfenicol (FF, as a representative antibiotic), while their composite removed 87% of FF (3 µmol/L). Under antibiotic exposure, biomolecules secreted by worms formed a corona on and modified the nZVI particle surface, enabling the nano-bio interface greater functionality, including responsiveness, enrichment, and reduction. Mechanistically, FF exposure activated glucose-alanine cycle pathways that synthesize organic acids and amines as major metabolites, which were assembled into vesicles and secreted, thereby interacting with nZVI in a biologically response design strategy. Lactic acid and urea formed hydrogen bonds with FF, enriched analyte presence at the heterogeneous interface. Succinic and lactic acids corroded the nZVI passivation layer and promoted electron transfer through surface conjugation. This unique strategy highlights biomolecular coronas as a complex resource to augment nano-enabled technologies and will provide shortcuts for rational manipulation of nanomaterial surfaces with coordinated multifunctionalities.


Asunto(s)
Antibacterianos , Hierro , Antibacterianos/química , Antibacterianos/farmacología , Animales , Hierro/química , Hierro/metabolismo , Corona de Proteínas/química , Corona de Proteínas/metabolismo , Contaminantes Químicos del Agua/química , Contaminantes Químicos del Agua/metabolismo , Oligoquetos/metabolismo , Biodegradación Ambiental , Restauración y Remediación Ambiental/métodos , Nanocompuestos/química
6.
Proc Natl Acad Sci U S A ; 120(23): e2220021120, 2023 06 06.
Artículo en Inglés | MEDLINE | ID: mdl-37252959

RESUMEN

The consistent rise of plastic pollution has stimulated interest in the development of biodegradable plastics. However, the study of polymer biodegradation has historically been limited to a small number of polymers due to costly and slow standard methods for measuring degradation, slowing new material innovation. High-throughput polymer synthesis and a high-throughput polymer biodegradation method are developed and applied to generate a biodegradation dataset for 642 chemically distinct polyesters and polycarbonates. The biodegradation assay was based on the clear-zone technique, using automation to optically observe the degradation of suspended polymer particles under the action of a single Pseudomonas lemoignei bacterial colony. Biodegradability was found to depend strongly on aliphatic repeat unit length, with chains less than 15 carbons and short side chains improving biodegradability. Aromatic backbone groups were generally detrimental to biodegradability; however, ortho- and para-substituted benzene rings in the backbone were more likely to be degradable than metasubstituted rings. Additionally, backbone ether groups improved biodegradability. While other heteroatoms did not show a clear improvement in biodegradability, they did demonstrate increases in biodegradation rates. Machine learning (ML) models were leveraged to predict biodegradability on this large dataset with accuracies over 82% using only chemical structure descriptors.


Asunto(s)
Plásticos Biodegradables , Poliésteres , Poliésteres/química , Plásticos/química , Polímeros , Biodegradación Ambiental , Proyectos de Investigación
7.
J Biol Chem ; 300(6): 107343, 2024 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-38705395

RESUMEN

Rieske nonheme iron aromatic ring-hydroxylating oxygenases (RHOs) play pivotal roles in determining the substrate preferences of polycyclic aromatic hydrocarbon (PAH) degraders. However, their potential to degrade high molecular weight PAHs (HMW-PAHs) has been relatively unexplored. NarA2B2 is an RHO derived from a thermophilic Hydrogenibacillus sp. strain N12. In this study, we have identified four "hotspot" residues (V236, Y300, W316, and L375) that may hinder the catalytic capacity of NarA2B2 when it comes to HMW-PAHs. By employing structure-guided rational enzyme engineering, we successfully modified NarA2B2, resulting in NarA2B2 variants capable of catalyzing the degradation of six different types of HMW-PAHs, including pyrene, fluoranthene, chrysene, benzo[a]anthracene, benzo[b]fluoranthene, and benzo[a]pyrene. Three representative variants, NarA2B2W316I, NarA2B2Y300F-W316I, and NarA2B2V236A-W316I-L375F, not only maintain their abilities to degrade low-molecular-weight PAHs (LMW-PAHs) but also exhibited 2 to 4 times higher degradation efficiency for HMW-PAHs in comparison to another isozyme, NarAaAb. Computational analysis of the NarA2B2 variants predicts that these modifications alter the size and hydrophobicity of the active site pocket making it more suitable for HMW-PAHs. These findings provide a comprehensive understanding of the relationship between three-dimensional structure and functionality, thereby opening up possibilities for designing improved RHOs that can be more effectively used in the bioremediation of PAHs.


Asunto(s)
Hidrocarburos Policíclicos Aromáticos , Hidrocarburos Policíclicos Aromáticos/metabolismo , Hidrocarburos Policíclicos Aromáticos/química , Peso Molecular , Proteínas Bacterianas/metabolismo , Proteínas Bacterianas/química , Proteínas Bacterianas/genética , Especificidad por Sustrato , Biodegradación Ambiental , Oxigenasas/metabolismo , Oxigenasas/química , Oxigenasas/genética , Hidroxilación
8.
Chem Rev ; 123(16): 9915-9939, 2023 08 23.
Artículo en Inglés | MEDLINE | ID: mdl-37470246

RESUMEN

Environmental concerns over waste plastics' effect on the environment are leading to the creation of biodegradable plastics. Biodegradable plastics may serve as a promising approach to manage the issue of environmental accumulation of plastic waste in the ocean and soil. Biodegradable plastics are the type of polymers that can be degraded by microorganisms into small molecules (e.g., H2O, CO2, and CH4). However, there are misconceptions surrounding biodegradable plastics. For example, the term "biodegradable" on product labeling can be misconstrued by the public to imply that the product will degrade under any environmental conditions. Such misleading information leads to consumer encouragement of excessive consumption of certain goods and increased littering of products labeled as "biodegradable". This review not only provides a comprehensive overview of the state-of-the-art biodegradable plastics but also clarifies the definitions and various terms associated with biodegradable plastics, including oxo-degradable plastics, enzyme-mediated plastics, and biodegradation agents. Analytical techniques and standard test methods to evaluate the biodegradability of polymeric materials in alignment with international standards are summarized. The review summarizes the properties and industrial applications of previously developed biodegradable plastics and then discusses how biomass-derived monomers can create new types of biodegradable polymers by utilizing their unique chemical properties from oxygen-containing functional groups. The terminology and methodologies covered in the paper provide a perspective on directions for the design of new biodegradable polymers that possess not only advanced performance for practical applications but also environmental benefits.


Asunto(s)
Plásticos Biodegradables , Plásticos Biodegradables/química , Polímeros/química , Biodegradación Ambiental , Biomasa
9.
Proc Natl Acad Sci U S A ; 119(47): e2214513119, 2022 11 22.
Artículo en Inglés | MEDLINE | ID: mdl-36375055

RESUMEN

Fungi are central to every terrestrial and many aquatic ecosystems, but the mechanisms underlying fungal tolerance to mercury, a global pollutant, remain unknown. Here, we show that the plant symbiotic fungus Metarhizium robertsii degrades methylmercury and reduces divalent mercury, decreasing mercury accumulation in plants and greatly increasing their growth in contaminated soils. M. robertsii does this by demethylating methylmercury via a methylmercury demethylase (MMD) and using a mercury ion reductase (MIR) to reduce divalent mercury to volatile elemental mercury. M. robertsii can also remove methylmercury and divalent mercury from fresh and sea water even in the absence of added nutrients. Overexpression of MMD and MIR significantly improved the ability of M. robertsii to bioremediate soil and water contaminated with methylmercury and divalent mercury. MIR homologs, and thereby divalent mercury tolerance, are widespread in fungi. In contrast, MMD homologs were patchily distributed among the few plant associates and soil fungi that were also able to demethylate methylmercury. Phylogenetic analysis suggests that fungi could have acquired methylmercury demethylase genes from bacteria via two independent horizontal gene transfer events. Heterologous expression of MMD in fungi that lack MMD homologs enabled them to demethylate methylmercury. Our work reveals the mechanisms underlying mercury tolerance in fungi, and may provide a cheap and environmentally friendly means of cleaning up mercury pollution.


Asunto(s)
Mercurio , Metarhizium , Compuestos de Metilmercurio , Biodegradación Ambiental , Agua , Mercurio/toxicidad , Filogenia , Ecosistema , Metarhizium/genética , Suelo
10.
Proc Natl Acad Sci U S A ; 119(32): e2203604119, 2022 08 09.
Artículo en Inglés | MEDLINE | ID: mdl-35917352

RESUMEN

Anthropogenic organophosphorus compounds (AOPCs), such as phosphotriesters, are used extensively as plasticizers, flame retardants, nerve agents, and pesticides. To date, only a handful of soil bacteria bearing a phosphotriesterase (PTE), the key enzyme in the AOPC degradation pathway, have been identified. Therefore, the extent to which bacteria are capable of utilizing AOPCs as a phosphorus source, and how widespread this adaptation may be, remains unclear. Marine environments with phosphorus limitation and increasing levels of pollution by AOPCs may drive the emergence of PTE activity. Here, we report the utilization of diverse AOPCs by four model marine bacteria and 17 bacterial isolates from the Mediterranean Sea and the Red Sea. To unravel the details of AOPC utilization, two PTEs from marine bacteria were isolated and characterized, with one of the enzymes belonging to a protein family that, to our knowledge, has never before been associated with PTE activity. When expressed in Escherichia coli with a phosphodiesterase, a PTE isolated from a marine bacterium enabled growth on a pesticide analog as the sole phosphorus source. Utilization of AOPCs may provide bacteria a source of phosphorus in depleted environments and offers a prospect for the bioremediation of a pervasive class of anthropogenic pollutants.


Asunto(s)
Organismos Acuáticos , Bacterias , Contaminantes Ambientales , Compuestos Organofosforados , Hidrolasas de Triéster Fosfórico , Organismos Acuáticos/enzimología , Bacterias/enzimología , Biodegradación Ambiental , Contaminantes Ambientales/metabolismo , Escherichia coli/genética , Escherichia coli/metabolismo , Océano Índico , Mar Mediterráneo , Compuestos Organofosforados/metabolismo , Hidrolasas de Triéster Fosfórico/genética , Hidrolasas de Triéster Fosfórico/metabolismo , Fósforo/metabolismo , Agua de Mar/microbiología
11.
Crit Rev Biochem Mol Biol ; 57(3): 305-332, 2022 06.
Artículo en Inglés | MEDLINE | ID: mdl-34937434

RESUMEN

Biofilms are assemblages of bacteria embedded within a matrix of extracellular polymeric substances (EPS) attached to a substratum. The process of biofilm formation is a complex phenomenon regulated by the intracellular and intercellular signaling systems. Various secondary messenger molecules such as cyclic dimeric guanosine 3',5'-monophosphate (c-di-GMP), cyclic adenosine 3',5'-monophosphate (cAMP), and cyclic dimeric adenosine 3',5'-monophosphate (c-di-AMP) are involved in complex signaling networks to regulate biofilm development in several bacteria. Moreover, the cell to cell communication system known as Quorum Sensing (QS) also regulates biofilm formation via diverse mechanisms in various bacterial species. Bacteria often switch to the biofilm lifestyle in the presence of toxic pollutants to improve their survivability. Bacteria within a biofilm possess several advantages with regard to the degradation of harmful pollutants, such as increased protection within the biofilm to resist the toxic pollutants, synthesis of extracellular polymeric substances (EPS) that helps in the sequestration of pollutants, elevated catabolic gene expression within the biofilm microenvironment, higher cell density possessing a large pool of genetic resources, adhesion ability to a wide range of substrata, and metabolic heterogeneity. Therefore, a comprehensive account of the various factors regulating biofilm development would provide valuable insights to modulate biofilm formation for improved bioremediation practices. This review summarizes the complex regulatory networks that influence biofilm development in bacteria, with a major focus on the applications of bacterial biofilms for environmental restoration.


Asunto(s)
Proteínas Bacterianas , Contaminantes Ambientales , Adenosina/metabolismo , Bacterias/metabolismo , Proteínas Bacterianas/metabolismo , Biodegradación Ambiental , Biopelículas , Contaminantes Ambientales/metabolismo , Contaminantes Ambientales/toxicidad , Regulación Bacteriana de la Expresión Génica
12.
J Bacteriol ; 206(7): e0013624, 2024 07 25.
Artículo en Inglés | MEDLINE | ID: mdl-38975763

RESUMEN

Although members of the genus Pseudomonas share specific morphological, metabolic, and genomic traits, the diversity of niches and lifestyles adopted by the family members is vast. One species of the group, Pseudomonas putida, thrives as a colonizer of plant roots and frequently inhabits soils polluted with various types of chemical waste. Owing to a combination of historical contingencies and inherent qualities, a particular strain, P. putida KT2440, emerged time ago as an archetype of an environmental microorganism amenable to recombinant DNA technologies, which was also capable of catabolizing chemical pollutants. Later, the same bacterium progressed as a reliable platform for programming traits and activities in various biotechnological applications. This article summarizes the stepwise upgrading of P. putida KT2440 from being a system for fundamental studies on the biodegradation of aromatic compounds (especially when harboring the TOL plasmid pWW0) to its adoption as a chassis of choice in metabolic engineering and synthetic biology. Although there are remaining uncertainties about the taxonomic classification of KT2440, advanced genome editing capabilities allow us to tailor its genetic makeup to meet specific needs. This makes its traditional categorization somewhat less important, while also increasing the strain's overall value for contemporary industrial and environmental uses.


Asunto(s)
Biodegradación Ambiental , Pseudomonas putida , Microbiología del Suelo , Biología Sintética , Pseudomonas putida/genética , Pseudomonas putida/metabolismo , Biología Sintética/métodos , Ingeniería Metabólica , Plásmidos/genética
13.
Proteins ; 92(2): 302-313, 2024 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-37864384

RESUMEN

Endosulfan is an organochlorine insecticide widely used for agricultural pest control. Many nations worldwide have restricted or completely banned it due to its extreme toxicity to fish and aquatic invertebrates. Arthrobacter sp. strain KW has the ability to degrade α, ß endosulfan and its intermediate metabolite endosulfate; this degradation is associated with Ese protein, a two-component flavin-dependent monooxygenase (TC-FDM). Employing in silico tools, we obtained the 3D model of Ese protein, and our results suggest that it belongs to the Luciferase Like Monooxygenase family (LLM). Docking studies showed that the residues V59, V315, D316, and T335 interact with α-endosulfan. The residues: V59, T60, V315, D316, and T335 are implicated in the interacting site with ß-endosulfan, and the residues: H17, V315, D316, T335, N364, and Q363 participate in the interaction with endosulfate. Topological analysis of the electron density by means of the Quantum Theory of Atoms in Molecules (QTAIM) and the Non-Covalent Interaction (NCI) index reveals that the Ese-ligands complexes are formed mainly by dispersive forces, where Cl atoms have a predominant role. As Ese is a monooxygenase member, we predict the homodimer formation. However, enzymatic studies must be developed to investigate the Ese protein's enzymatic and catalytic activity.


Asunto(s)
Arthrobacter , Insecticidas , Animales , Endosulfano/química , Endosulfano/metabolismo , Arthrobacter/metabolismo , Biodegradación Ambiental , Insecticidas/química , Insecticidas/metabolismo , Oxigenasas de Función Mixta
14.
Mol Plant Microbe Interact ; 37(7): 552-560, 2024 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-38619862

RESUMEN

Diphenyl ether herbicides are extensively utilized in agricultural systems, but their residues threaten the health of sensitive rotation crops. Functional microbial strains can degrade diphenyl ether herbicides in the rhizosphere of crops, facilitating the restoration of a healthy agricultural environment. However, the interplay between microorganisms and plants in diphenyl ether herbicides degradation remains unclear. Thus, the herbicide-degrading strain Bacillus sp. Za and the sensitive crop, maize, were employed to uncover the interaction mechanism. The degradation of diphenyl ether herbicides by strain Bacillus sp. Za was promoted by root exudates. The strain induced root exudate re-secretion in diphenyl ether herbicide-polluted maize. We further showed that root exudates enhanced the rhizosphere colonization and the biofilm biomass of strain Za, augmenting its capacity to degrade diphenyl ether herbicide. Root exudates regulated gene fliZ, which is pivotal in biofilm formation. Wild-type strain Za significantly reduced herbicide toxicity to maize compared to the ZaΔfliZ mutant. Moreover, root exudates promoted strain Za growth and chemotaxis, which was related to biofilm formation. This mutualistic relationship between the microorganisms and the plants demonstrates the significance of plant-microbe interactions in shaping diphenyl ether herbicide degradation in rhizosphere soils. [Formula: see text] The author(s) have dedicated the work to the public domain under the Creative Commons CC0 "No Rights Reserved" license by waiving all of his or her rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law, 2024.


Asunto(s)
Bacillus , Biopelículas , Herbicidas , Raíces de Plantas , Rizosfera , Zea mays , Zea mays/microbiología , Bacillus/metabolismo , Bacillus/fisiología , Herbicidas/metabolismo , Raíces de Plantas/microbiología , Biodegradación Ambiental , Exudados de Plantas/metabolismo , Éteres Fenílicos/metabolismo , Contaminantes del Suelo/metabolismo
15.
Environ Microbiol ; 26(2): e16560, 2024 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-38234207

RESUMEN

Some bacteria can degrade organic micropollutants (OMPs) as primary carbon sources. Due to typically low OMP concentrations, these bacteria may benefit from supplemental assimilation of natural substrates present in the pool of dissolved organic matter (DOM). The biodegradability of such auxiliary substrates and the impacts on OMP removal are tightly linked to biotransformation pathways. Here, we aimed to elucidate the biodegradability and effect of different DOM constituents for the carbofuran degrader Novosphingobium sp. KN65.2, using a novel approach that combines pathway prediction, laboratory experiments, and fluorescence spectroscopy. Pathway prediction suggested that ring hydroxylation reactions catalysed by Rieske-type dioxygenases and flavin-dependent monooxygenases determine the transformability of the 11 aromatic compounds used as model DOM constituents. Our approach further identified two groups with distinct transformation mechanisms amongst the four growth-supporting compounds selected for mixed substrate biodegradation experiments with the pesticide carbofuran (Group 1: 4-hydroxybenzoic acid, 4-hydroxybenzaldehyde; Group 2: p-coumaric acid, ferulic acid). Carbofuran biodegradation kinetics were stable in the presence of both Group 1 and Group 2 auxiliary substrates. However, Group 2 substrates would be preferable for bioremediation processes, as they showed constant biodegradation kinetics under different experimental conditions (pre-growing KN65.2 on carbofuran vs. DOM constituent). Furthermore, Group 2 substrates were utilisable by KN65.2 in the presence of a competitor (Pseudomonas fluorescens sp. P17). Our study thus presents a simple and cost-efficient approach that reveals mechanistic insights into OMP-DOM biodegradation.


Asunto(s)
Carbofurano , Sphingomonadaceae , Biodegradación Ambiental , Carbofurano/metabolismo , Espectrometría de Fluorescencia , Carbono/metabolismo , Compuestos Orgánicos , Sphingomonadaceae/metabolismo
16.
Environ Microbiol ; 26(6): e16658, 2024 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-38843592

RESUMEN

Plastic pollution is a vast and increasing problem that has permeated the environment, affecting all aspects of the global food web. Plastics and microplastics have spread to soil, water bodies, and even the atmosphere due to decades of use in a wide range of applications. Plastics include a variety of materials with different properties and chemical characteristics, with polyethylene being a dominant fraction. Polyethylene is also an extremely persistent compound with slow rates of photodegradation or biodegradation. In this study, we developed a method to isolate communities of microbes capable of biodegrading a polyethylene surrogate. This method allows us to study potential polyethylene degradation over much shorter time periods. Using this method, we enriched several communities of microbes that can degrade the polyethylene surrogate within weeks. We also identified specific bacterial strains with a higher propensity to degrade compounds similar to polyethylene. We provide a description of the method, the variability and efficacy of four different communities, and key strains from these communities. This method should serve as a straightforward and adaptable tool for studying polyethylene biodegradation.


Asunto(s)
Bacterias , Biodegradación Ambiental , Polietileno , Polietileno/metabolismo , Polietileno/química , Bacterias/metabolismo , Bacterias/clasificación , Bacterias/genética , Microbiota , Microbiología del Suelo
17.
Environ Microbiol ; 26(2): e16567, 2024 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-38233213

RESUMEN

Soluble di-iron monooxygenase (SDIMO) enzymes enable insertion of oxygen into diverse substrates and play significant roles in biogeochemistry, bioremediation and biocatalysis. An unusual SDIMO was detected in an earlier study in the genome of the soil organism Solimonas soli, but was not characterized. Here, we show that the S. soli SDIMO is part of a new clade, which we define as 'Group 7'; these share a conserved gene organization with alkene monooxygenases but have only low amino acid identity. The S. soli genes (named zmoABCD) could be functionally expressed in Pseudomonas putida KT2440 but not in Escherichia coli TOP10. The recombinants made epoxides from C2 C8 alkenes, preferring small linear alkenes (e.g. propene), but also epoxidating branched, carboxylated and chlorinated substrates. Enzymatic epoxidation of acrylic acid was observed for the first time. ZmoABCD oxidised the organochlorine pollutants vinyl chloride (VC) and cis-1,2-dichloroethene (cDCE), with the release of inorganic chloride from VC but not cDCE. The original host bacterium S. soli could not grow on any alkenes tested but grew well on phenol and n-octane. Further work is needed to link ZmoABCD and the other Group 7 SDIMOs to specific physiological and ecological roles.


Asunto(s)
Gammaproteobacteria , Pseudomonas putida , Cloruro de Vinilo , Oxigenasas de Función Mixta/genética , Oxigenasas de Función Mixta/metabolismo , Alquenos/metabolismo , Gammaproteobacteria/metabolismo , Biodegradación Ambiental , Pseudomonas putida/genética , Pseudomonas putida/metabolismo
18.
Biochem Biophys Res Commun ; 709: 149822, 2024 05 21.
Artículo en Inglés | MEDLINE | ID: mdl-38547604

RESUMEN

Aromatic nitriles are of considerable environmental concern, because of their hazardous impacts on the health of both humans and wildlife. In the present study, Burkholderia sp. strain BC1 was observed to be capable of utilizing toxic benzonitrile and hydroxybenzonitrile isomers singly, as sole carbon and energy sources. The results of chromatographic and spectrometric analyses in combination with oxygen uptake and enzyme activity studies, revealed the metabolism of benzonitrile as well as 2-, 3-, and 4-hydroxybenzonitriles by nitrile hydratase-amidase to the corresponding carboxylates. These carboxylates were further metabolized via central pathways, namely benzoate-catechol, salicylate-catechol, 3-hydroxybenzoate-gentisate and 4-hydroxybenzoate-protocatechute pathways in strain BC1, ultimately leading to the TCA cycle intermediates. Studies also evaluated substrate specificity profiles of both nitrile hydratase and amidase(s) involved in the denitrification of the nitriles. In addition, a few metabolic crosstalk events due to the induction of multiple operons by central metabolites were appraised in strain BC1. The present study illustrates the broad degradative potential of strain BC1, harboring diverse catabolic machinery of biotechnological importance, elucidating pathways for the assimilation of benzonitrile and that of hydroxybenzonitrile isomers for the first time.


Asunto(s)
Burkholderia , Humanos , Nitrilos/química , Amidohidrolasas/metabolismo , Catecoles , Biodegradación Ambiental
19.
BMC Biotechnol ; 24(1): 42, 2024 Jun 19.
Artículo en Inglés | MEDLINE | ID: mdl-38898480

RESUMEN

BACKGROUND: γ-Hexachlorocyclohexane (γ-HCH), an organochlorine insecticide of anthropogenic origin, is a persistent organic pollutant (POP) that causes environmental pollution concerns worldwide. Although many γ-HCH-degrading bacterial strains are available, inoculating them directly into γ-HCH-contaminated soil is ineffective because of the low survival rate of the exogenous bacteria. Another strategy for the bioremediation of γ-HCH involves the use of transgenic plants expressing bacterial enzyme for γ-HCH degradation through phytoremediation. RESULTS: We generated transgenic Arabidopsis thaliana expressing γ-HCH dehydrochlroninase LinA from bacterium Sphingobium japonicum strain UT26. Among the transgenic Arabidopsis T2 lines, we obtained one line (A5) that expressed and accumulated LinA well. The A5-derived T3 plants showed higher tolerance to γ-HCH than the non-transformant control plants, indicating that γ-HCH is toxic for Arabidopsis thaliana and that this effect is relieved by LinA expression. The crude extract of the A5 plants showed γ-HCH degradation activity, and metabolites of γ-HCH produced by the LinA reaction were detected in the assay solution, indicating that the A5 plants accumulated the active LinA protein. In some A5 lines, the whole plant absorbed and degraded more than 99% of γ-HCH (10 ppm) in the liquid medium within 36 h. CONCLUSION: The transgenic Arabidopsis expressing active LinA absorbed and degraded γ-HCH in the liquid medium, indicating the high potential of LinA-expressing transgenic plants for the phytoremediation of environmental γ-HCH. This study marks a crucial step toward the practical use of transgenic plants for the phytoremediation of POPs.


Asunto(s)
Arabidopsis , Biodegradación Ambiental , Hexaclorociclohexano , Plantas Modificadas Genéticamente , Sphingomonadaceae , Arabidopsis/genética , Arabidopsis/metabolismo , Plantas Modificadas Genéticamente/genética , Plantas Modificadas Genéticamente/metabolismo , Hexaclorociclohexano/metabolismo , Sphingomonadaceae/genética , Sphingomonadaceae/metabolismo , Sphingomonadaceae/enzimología , Contaminantes del Suelo/metabolismo , Proteínas Bacterianas/genética , Proteínas Bacterianas/metabolismo , Liasas/genética , Liasas/metabolismo
20.
BMC Plant Biol ; 24(1): 752, 2024 Aug 06.
Artículo en Inglés | MEDLINE | ID: mdl-39103757

RESUMEN

Present study assessed the growth of two plant species and ion uptake by them grown on different proportion of industrial solid waste and garden soil. The industrial waste having high concentration of chemicals were used with garden soil at different proportion i.e. 0% (T0), 5% (T1), 10% (T2), 15% (T3) and 20% (T4). Two species namely Conocarpus erectus (alien plant) and Dodonaea viscosa (indigenous) were used as test plants in pot study. Different parameters including growth, physiology, and anatomy of plants and concentration of cations (Na+, K+, Ca2+, and Mg2+) in the plant shoot and root were measured at different time duration (initial, 1st, 2nd, 3rd and 4th month). The key objective of the study was to use these plants to establish their plantations on the barren lands where industrial solid wastes were being disposed of. C. erectus showed better growth than D. viscosa, as well as more uptake of ions. A significant increase in plant growth was observed in fourth month in T1, where plant height reached 24.5% and 46% for C. erectus and D. viscosa, respectively. At harvest, in C. erectus, no significant difference in the fresh (65-78 g) and dry weight (24-30 g) of the shoot was observed across treatments compared to the control. In D. viscosa, at the time of harvest, the fresh and dry weights of the root and shoot showed a strong, significantly decreasing pattern across T1, T2, and T3, leading to the death of the plant at T3 and T4. Further, optimum ratio of waste soil to garden soil was found as 10:90 and 20:80 to establish the plantations of D. viscosa and C. erectus, respectively in areas where such solid waste from industries are disposed. Findings can be used for the restoration of such solid waste for the sustainable management of industrial areas and their associated ecosystems.


Asunto(s)
Residuos Industriales , Brotes de la Planta/crecimiento & desarrollo , Brotes de la Planta/metabolismo , Raíces de Plantas/crecimiento & desarrollo , Raíces de Plantas/metabolismo , Sapindaceae/crecimiento & desarrollo , Sapindaceae/metabolismo , Sapindaceae/fisiología , Iones/metabolismo , Biodegradación Ambiental
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