Biodegradation mechanism of polyesters by hydrolase from Rhodopseudomonas palustris: An in silico approach

Engineering the mangrove soil microbiome for selection of polyethylene terephthalate-transforming bacterial consortia

Mangroves are impacted by multiple environmental stressors, including sea level rise, erosion, and plastic pollution. Thus, mangrove soil may be an excellent source of as yet unknown plastic-transforming microorganisms. Here, we assess the impact of polyethylene terephthalate (PET) particles and seawater intrusion on the mangrove soil microbiome and report an enrichment culture experiment to artificially select PET-transforming microbial consortia. The analysis of metagenome-assembled genomes of two bacterial consortia revealed that PET catabolism can be performed by multiple taxa, of which particular species harbored putative novel PET-active hydrolases. A key member of these consortia (Mangrovimarina plasticivorans gen. nov., sp. nov.) was found to contain two genes encoding monohydroxyethyl terephthalate hydrolases. This study provides insights into the development of strategies for harnessing soil microbiomes, thereby advancing our understanding of the ecology and enzymology involved in microbial-mediated PET transformations in marine-associated systems.

Biodegradation: the best solution to the world problem of discarded polymers

The widespread use of polymers has made our lives increasingly convenient by offering a more convenient and dependable material. However, the challenge of efficiently decomposing these materials has resulted in a surge of polymer waste, posing environment and health risk. Currently, landfill and incineration treatment approaches have notable shortcomings, prompting a shift towards more eco-friendly and sustainable biodegradation approaches. Biodegradation primarily relies on microorganisms, with research focusing on both solitary bacterial strain and multi-strain communities for polymer biodegradation. Furthermore, directed evolution and rational design of enzyme have significantly contributed to the polymer biodegradation process. However, previous reviews often undervaluing the role of multi-strain communities. In this review, we assess the current state of these three significant fields of research, provide practical solutions to issues with polymer biodegradation, and outline potential future directions for the subject. Ultimately, biodegradation, whether facilitated by single bacteria, multi-strain communities, or engineered enzymes, now represents the most effective method for managing waste polymers.

Deconstructed Plastic Substrate Preferences of Microbial Populations from the Natural Environment

Over half of the world's plastic waste is landfilled, where it is estimated to take hundreds of years to degrade. Given the continued use and disposal of plastic products, it is vital that we develop fast and effective ways to utilize plastic waste. Here, we explore the potential of tandem chemical and biological processing to process various plastics quickly and effectively. Four samples of compost or sediment were used to set up enrichment cultures grown on mixtures of compounds, including disodium terephthalate and terephthalic acid (monomers of polyethylene terephthalate), compounds derived from the chemical deconstruction of polycarbonate, and pyrolysis oil derived from high-density polyethylene plastics. Established enrichment communities were also grown on individual substrates to investigate the substrate preferences of different taxa. Biomass harvested from the cultures was characterized using 16S rRNA gene amplicon sequencing and shotgun metagenomic sequencing. These data reveal low-diversity microbial communities structured by differences in culture inoculum, culture substrate source plastic type, and time. Microbial populations from the classes Alphaproteobacteria, Gammaproteobacteria, Actinobacteria, and Acidobacteriae were significantly enriched when grown on substrates derived from high-density polyethylene and polycarbonate. The metagenomic data contain abundant aromatic and aliphatic hydrocarbon degradation genes relevant to the biodegradation of deconstructed plastic substrates used here. We show that microbial populations from diverse environments are capable of growth on substrates derived from the chemical deconstruction or pyrolysis of multiple plastic types and that paired chemical and biological processing of plastics should be further developed for industrial applications to manage plastic waste. IMPORTANCE The durability and impermeable nature of plastics have made them a popular material for numerous applications, but these same qualities make plastics difficult to dispose of, resulting in massive amounts of accumulated plastic waste in landfills and the natural environment. Since plastic use and disposal are projected to increase in the future, novel methods to effectively break down and dispose of current and future plastic waste are desperately needed. We show that the products of chemical deconstruction or pyrolysis of plastic can successfully sustain the growth of low-diversity microbial communities. These communities were enriched from multiple environmental sources and are capable of degrading complex xenobiotic carbon compounds. This study demonstrates that tandem chemical and biological processing can be used to degrade multiple types of plastics over a relatively short period of time and may be a future avenue for the mitigation of rapidly accumulating plastic waste.

Critical effect of biodegradation on long-term microplastic weathering in sediment environments: A systematic review

Microplastic (MP) pollution in global sediment has been intensely studied and recognized as the ultimate sink for residual MPs in terrestrial and aquatic ecosystems. During MP long-term retention in sediments, plastic-degrading bacteria (i.e., Flavobacteriaceae, Bacillus, Rhodobacteraceae, and Desulfobacteraceae) can utilize those MPs as their carbon and energy sources through enzyme (hydrolase and oxidoreductase) reactions, which further alter or transform high molecular weight MP polymers into lower molecular weight biodegradation byproducts (i.e., monomers and oligomers) and release toxic additives. In other words, MPs can act as durable substrates for plastic-degrading bacteria in sediments. However, to date, the biodegradation rates of MPs in sediment environments are still poorly understood due to their limited degradation efficiency. Herein, we review the enzyme-induced biodegradation processes of MPs in sediment environments, which is important for accessing the alteration of MP properties and their potential ecological risks after undergoing long-term weathering processes. In addition, the factors associated with the MP properties (polymer type, molecular weight, crystallinity, and hydrophobicity) and sediment conditions (sediment type, temperature, pH, salinity, and oxygen content) that influence plastic degradation processes are also reviewed. The mechanisms may relate to the MP properties and sediment conditions that can influence microbial abundance, enzyme concentrations, and enzyme activities, thus altering MP biodegradation ratios. We anticipate that the observations reviewed in this study will pose a new issue to better understand the formation process, fate, and potential ecological risks associated with aged MPs in sediment environments.

Pollution caused by nanoplastics: adverse effects and mechanisms of interaction via molecular simulation

The continuous increase in the production of synthetic plastics for decades and the inadequate disposal of plastic waste have resulted in a considerable increase of these materials in aquatic environments, which has developed into a major environmental concern. In addition to conventional parameters, the relevance of the environmental monitoring of microplastics (MPs) and nanoplastics (NPs) has been highlighted by the scientific community due to the potential adverse effects these materials pose to the ecosystem as well as to human health. The literature has registered an increasing interest in understanding the mechanisms, at the molecular level, of the interaction between NPs and other compounds using molecular simulation techniques. The present review aims to: (i) summarize the force fields conventionally used to describe NPs by molecular simulations; (ii) discuss the effects of NPs in the structural and dynamical properties of biological membranes; (iii) evaluate how NPs affect the folding of proteins; (iv) discuss the mechanisms by which NPs adsorb contaminants from the environment. NPs can affect the secondary structure of proteins and change the lateral organization and diffusion of lipid membranes. As a result, they may alter the lipid digestion in the gastrointestinal system representing a risk to the assimilation of the nutrients by humans. The adsorption of contaminants on MPs and NPs can potentiate their harmful effects on human health, due to a possible synergism. Therefore, understanding the mechanisms involved in these interactions is crucial to predict dangerous combinations and outline action strategies that reduce negative impacts on ecosystems and human health. Depending on the chemical properties of contaminants and NPs, electrostatic and/or van der Waals interactions can be more relevant in explaining the adsorption process. Finally, we conclude by highlighting gaps in the literature and the critical aspects for future investigations.

Rhodopseudomonas palustris: A biotechnology chassis

Rhodopseudomonas palustris is an attractive option for biotechnical applications and industrial engineering due to its metabolic versatility and its ability to catabolize a wide variety of feedstocks and convert them to several high-value products. Given its adaptable metabolism, R. palustris has been studied and applied in an extensive variety of applications such as examining metabolic tradeoffs for environmental perturbations, biodegradation of aromatic compounds, environmental remediation, biofuel production, agricultural biostimulation, and bioelectricity production. This review provides a holistic summary of the commercial applications for R. palustris as a biotechnology chassis and suggests future perspectives for research and engineering.

Fluoroacetate dehalogenase catalyzed dehalogenation of halogenated carboxylic acids: A QM/MM approach

Dehalogenation is one of the most important reactions in environmental pollution control, for instance, the degradation of persistent organic pollutants (POPs). Recently, fluoroacetate dehalogenase (FAcD) has been reported to catalyze the dehalogenation reactions, which shows great potential in treating halogenated pollutants. Here the dehalogenation mechanism catalyzed by FAcD was fully deciphered with the aid of quantum mechanics/molecular mechanics method. The results show that FAcD catalyzed dehalogenation efficiency follows the order of defluorination > dechlorination > debromination. The corresponding Boltzmann-weighted average barriers are 10.1, 19.7, and 20.9 kcal mol^-1. Positive/negative correlations between activation barriers and structural parameters (e.g. distance and angle) for FAcD catalyzed dechlorination and debromination were established. Based on the structure-energy relationship, we propose that mutation of the binding pocket amino acids (e.g. His155, Trp156, Tyr219) to smaller proton donor amino acids (e.g. Serine, Threonine, Cysteine, Asparagine) may increase the efficiency for dechlorination and debromination. The results may of practical value for the efficient degradation of chlorined and bromined pollutants by harnessing FAcD.

D-Lactic Acid as a Metabolite: Toxicology, Diagnosis, and Detection

Two enantiomers of lactic acid exist. While L-lactic acid is a common compound of human metabolism, D-lactic acid is produced by some strains of microorganism or by some less relevant metabolic pathways. While L-lactic acid is an endogenous compound, D-lactic acid is a harmful enantiomer. Exposure to D-lactic acid can happen by various ways including contaminated food and beverages and by microbiota during some pathological states like short bowel syndrome. The exposure to D-lactic acid cannot be diagnosed because the common analytical methods are not suitable for distinguishing between the two enantiomers. In this review, pathways for D-lactic acid, pathological processes, and diagnostical and analytical methods are introduced followed by figures and tables. The current literature is summarized and discussed.

Degradation mechanism for Zearalenone ring-cleavage by Zearalenone hydrolase RmZHD: A QM/MM study

The danger of zearalenone (ZEN) as an endocrine disruptor to humans and the environment has aroused increasing attention. In this study, we implemented the quantum mechanics/molecular mechanics (QM/MM) method to investigate the degradation mechanism of ZEN hydrolase (RmZHD) toward ZEN at the atomic level. The degradation process involves two concerted reaction pathways, where the active site contains a Ser-His-Glu triplet as a proton donor. With the Boltzmann-weighted average potential barriers of 18.1 and 21.5 kcal/mol, the process undergoes proton transfer and nucleophilic-substituted ring opening to form a hydroxyl product. Non-covalent interaction analyses elucidated hydrogen bonding between key amino acids with ZEN. The electrostatic influence analysis of 16 amino acids proposes residues Asp34 and His128 as the possible mutation target for future mutation design of enzyme RmZHD. An in-depth investigation of the protein environment of RmZHD can improve the bioremediation efficiency of endocrine disrupting chemicals.