A comprehensive study of conditions of the biodegradation of a plastic additive 2,6-di-tert-butylphenol and proteomic changes in the degraderPseudomonas aeruginosasan ai

Mechanism of deltamethrin biodegradation by Brevibacillus parabrevis BCP-09 with proteomic methods

Ester-containing deltamethrin pesticides are widely used in farmland and have inevitable side effects on the biosphere and human health. Microbia have been used for efficient degradation of deltamethrin, but the related mechanism and enzyme characteristics have not been elucidated. In this study, a species Brevibacillus parabrevis BCP-09 could degrade up to 75 mg L-1 deltamethrin with a degradation efficiency of 95.41%. Proteomic and genomic methods were used to explore its degradation mechanism. Enzymes belonged to hydrolases, oxidases and aromatic compound degrading enzymes were expressed enhanced and might participate in the deltamethrin degradtion. RT-PCR experiment and enzyme activity analysis verified the degradation of deltamethrin by bacterial protein. Additionally, the formation of endospores can help strain BCP-09 resist the toxicity of deltamethrin and enhance its degradation. This study supplies a scientific evidence for the application of Brevibacillus parabrevis BCP-09 in the bioremediation of environmental pollution and enriches the resources of deltamethrin-biodegradable proteins.

Mechanistic understanding on the uptake of micro-nano plastics by plants and its phytoremediation

Contaminated soil is one of today's most difficult environmental issues, posing serious hazards to human health and the environment. Contaminants, particularly micro-nano plastics, have become more prevalent around the world, eventually ending up in the soil. Numerous studies have been conducted to investigate the interactions of micro-nano plastics in plants and agroecosystems. However, viable remediation of micro-nano plastics in soil remains limited. In this review, a powerful in situ soil remediation technology known as phytoremediation is emphasized for addressing micro-nano-plastic contamination in soil and plants. It is based on the synergistic effects of plants and the microorganisms that live in their rhizosphere. As a result, the purpose of this review is to investigate the mechanism of micro-nano plastic (MNP) uptake by plants as well as the limitations of existing MNP removal methods. Different phytoremediation options for removing micro-nano plastics from soil are also described. Phytoremediation improvements (endophytic-bacteria, hyperaccumulator species, omics investigations, and CRISPR-Cas9) have been proposed to enhance MNP degradation in agroecosystems. Finally, the limitations and future prospects of phytoremediation strategies have been highlighted in order to provide a better understanding for effective MNP decontamination from soil.

Surveillance and mitigation of soil pollution through metagenomic approaches

Soil pollution is one of the serious global threats causing risk to environment and humans. The major cause of accumulation of pollutants in soil are anthropogenic activities and some natural processes. There are several types of soil pollutants which deteriorate the quality of human life and animal health. They are recalcitrant hydrocarbon compounds, metals, antibiotics, persistent organic compounds, pesticides and different kinds of plastics. Due to the detrimental properties of pollutants present in soil on human life and ecosystem such as carcinogenic, genotoxic and mutagenic effects, alternate and effective methods to degrade the pollutants are recommended. Bioremediation is an effective and inexpensive method of biological degradation of pollutants using plants, microorganisms and fungi. With the advent of new detection methods, the identification and degradation of soil pollutants in different ecosystems were made easy. Metagenomic approaches are a boon for the identification of unculturable microorganisms and to explore the vast bioremediation potential for different pollutants. Metagenomics is a power tool to study the microbial load in polluted or contaminated land and its role in bioremediation. In addition, the negative ecosystem and health effect of pathogens, antibiotic and metal resistant genes found in the polluted area can be studied. Also, the identification of novel compounds/genes/proteins involved in the biotechnology and sustainable agriculture practices can be performed with the integration of metagenomics.

A comprehensive proteomics analysis of the response of Pseudomonas aeruginosa to nanoceria cytotoxicity

The increased commercial use and spread of nanoceria raises concerns about the risks associated with its effects on living organisms. Although Pseudomonas aeruginosa may be ubiquitous in nature, it is largely found in locations closely linked with human activity. P. aeruginosa san ai was used as a model organism for a deeper understanding of the interaction between biomolecules of the bacteria with this intriguing nanomaterial. A comprehensive proteomics approach along with analysis of altered respiration and production of targeted/specific secondary metabolites was conducted to study the response of P. aeruginosa san ai to nanoceria. Quantitative proteomics found that proteins associated with redox homeostasis, biosynthesis of amino acids, and lipid catabolism were upregulated. Proteins from outer cellular structures were downregulated, including transporters responsible for peptides, sugars, amino acids and polyamines, and the crucial TolB protein of the Tol-Pal system, required for the structural formation of the outer membrane layer. In accordance with the altered redox homeostasis proteins, an increased amount of pyocyanin, a key redox shuttle, and the upregulation of the siderophore, pyoverdine, responsible for iron homeostasis, were found. Production of extracellular molecules, e.g. pyocyanin, pyoverdine, exopolysaccharides, lipase, and alkaline protease, was significantly increased in P. aeruginosa san ai exposed to nanoceria. Overall, nanoceria at sublethal concentrations induces profound metabolic changes in P. aeruginosa san ai and provokes increased secretion of extracellular virulence factors, revealing the powerful influence this nanomaterial has on the vital functions of the microorganism.

Proteomic response of Pseudomonas aeruginosa IIPIS-8 during rapid and efficient degradation of naphthalene

Polycyclic aromatic hydrocarbons (PAHs) are widely distributed in the ecosystem and are of significant concern due to their toxicity and mutagenicity. Bioremediation of PAHs is a popular and benign approach that ameliorates the environment. This study investigated the biodegradation and proteome response of Pseudomonas aeruginosa IIPIS-8 for two-ringed PAH: naphthalene (NAP) to understand proteome alteration during its bioremediation. Rapid biodegradation was observed up to 98 ± 1.26% and 84 ± 1.03%, respectively, for initial concentrations of 100 mg L^-1 and 500 mg L^-1 of NAP. Degradation followed first-order kinetics with rate constants of 0.12 h^-1 and 0.06 h^-1 and half-life (t_1/2) of 5.7 h and 11.3 h, respectively. Additionally, the occurrence of key ring cleavage and linear chain intermediates, 2,3,4,5,6, -pentamethyl acetophenone, 1-octanol 2-butyl, and hexadecanoic acid supported complete NAP degradation. Proteomics study of IIPIS-8 throws light on the impact of protein expression, in which 415 proteins were quantified in sequential windowed acquisition of all theoretical fragment ion mass spectra (SWATH-MS) analysis, of which 97 were found to be significantly up-regulated and 75 were significantly down-regulated by ≥ 2-fold change (p values ≤ 0.05), during the NAP degradation. The study also listed the up-regulation of several enzymes, including oxido-reductases, hydrolases, and catalases, potentially involved in NAP degradation. Overall, differential protein expression, through proteomics study, demonstrated IIPIS-8's capability to efficiently assimilate NAP in their metabolic pathways even in a high concentration of NAP.

Novel bacterial taxa in a minimal lignocellulolytic consortium and their potential for lignin and plastics transformation

The understanding and manipulation of microbial communities toward the conversion of lignocellulose and plastics are topics of interest in microbial ecology and biotechnology. In this study, the polymer-degrading capability of a minimal lignocellulolytic microbial consortium (MELMC) was explored by genome-resolved metagenomics. The MELMC was mostly composed (>90%) of three bacterial members (Pseudomonas protegens; Pristimantibacillus lignocellulolyticus gen. nov., sp. nov; and Ochrobactrum gambitense sp. nov) recognized by their high-quality metagenome-assembled genomes (MAGs). Functional annotation of these MAGs revealed that Pr. lignocellulolyticus could be involved in cellulose and xylan deconstruction, whereas Ps. protegens could catabolize lignin-derived chemical compounds. The capacity of the MELMC to transform synthetic plastics was assessed by two strategies: (i) annotation of MAGs against databases containing plastic-transforming enzymes; and (ii) predicting enzymatic activity based on chemical structural similarities between lignin- and plastics-derived chemical compounds, using Simplified Molecular-Input Line-Entry System and Tanimoto coefficients. Enzymes involved in the depolymerization of polyurethane and polybutylene adipate terephthalate were found to be encoded by Ps. protegens, which could catabolize phthalates and terephthalic acid. The axenic culture of Ps. protegens grew on polyhydroxyalkanoate (PHA) nanoparticles and might be a suitable species for the industrial production of PHAs in the context of lignin and plastic upcycling.

Pseudomonas in environmental bioremediation of hydrocarbons and phenolic compounds- key catabolic degradation enzymes and new analytical platforms for comprehensive investigation

Pollution of the environment with petroleum hydrocarbons and phenolic compounds is one of the biggest problems in the age of industrialization and high technology. Species of the genus Pseudomonas, present in almost all hydrocarbon-contaminated areas, play a particular role in biodegradation of these xenobiotics, as the genus has the potential to decompose various hydrocarbons and phenolic compounds, using them as its only source of carbon. Plasticity of carbon metabolism is one of the adaptive strategies used by Pseudomonas to survive exposure to toxic organic compounds, so a good knowledge of its mechanisms of degradation enables the development of new strategies for the treatment of pollutants in the environment. The capacity of microorganisms to metabolize aromatic compounds has contributed to the evolutionally conserved oxygenases. Regardless of the differences in structure and complexity between mono- and polycyclic aromatic hydrocarbons, all these compounds are thermodynamically stable and chemically inert, so for their decomposition, ring activation by oxygenases is crucial. Genus Pseudomonas uses several upper and lower metabolic pathways to transform and degrade hydrocarbons, phenolic compounds, and petroleum hydrocarbons. Data obtained from newly developed omics analytical platforms have enormous potential not only to facilitate our understanding of processes at the molecular level but also enable us to instigate and monitor complex biodegradations by Pseudomonas. Biotechnological application of aromatic metabolic pathways in Pseudomonas to bioremediation of environments polluted with crude oil, biovalorization of lignin for production of bioplastics, biofuel, and bio-based chemicals, as well as Pseudomonas-assisted phytoremediation are also considered.

Marine Bacteria and Omic Approaches: A Novel and Potential Repository for Bioremediation Assessment

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.

A study of the flexibility of the carbon catabolic pathways of extremophilic P. aeruginosa san ai exposed to benzoate versus glucose as sole carbon sources by multi omics analytical platform

Polyextremophilic, hydrocarbonoclastic Pseudomonas aeruginosa san ai can survive under extreme environmental challenges in the presence of a variety of pollutants such as organic solvents and hydrocarbons, particularly aromatics, heavy metals, and high pH. To date, the metabolic plasticity of the extremophilic P. aeruginosa, has not been sufficiently studied in regard to the effect of changing carbon sources. Therefore, the present study explores the carbon metabolic pathways of polyextremophilic P. aeruginosa san ai grown on sodium benzoate versus glucose and its potential for aromatic degradation. P. aeruginosa san ai removed/metabolised nearly 430 mg/L of benzoate for 48 h, demonstrating a high capacity for aromatic degradation. Comparative functional proteomics, targeted metabolomics and genomics analytical approaches were employed to study the carbon metabolism of the P. aeruginosa san ai. Functional proteomic study of selected enzymes participating in the β-ketoadipate and the Entner-Doudoroff pathways revealed a metabolic reconfiguration induced by benzoate compared to glucose. Metabolome analysis implied the existence of both catechol and protocatechuate branches of the β-ketoadipate pathway. Enzymatic study of benzoate grown cultures confirmed the activity of the ortho- catechol branch of the β-ketoadipate pathway. Even high concentrations of benzoate did not show increased stress protein synthesis, testifying to its extremophilic nature capable of surviving in harsh conditions. This ability of Pseudomonas aeruginosa san ai to efficiently degrade benzoate can provide a wide range of use of this strain in environmental and agricultural application.

Microbial capability for the degradation of chemical additives present in petroleum-based plastic products: A review on current status and perspectives

Plastic additives are present as pollutants in the environment because they are released from plastics and have been reported to be toxic to mammals. Due to this toxicity, it is crucial to develop ecofriendly tools to decontaminate the environment. Microorganisms are a promising alternative for efficient and effective plastic additive removal. This review describes the current knowledge and significant advances in the microbial degradation of plastic additives (i.e. plasticizers, flame retardants, stabilizers and antioxidants) and biotechnological research strategies that are being used to accelerate the biodegradation process of these additives. It is expected that further research supported by advances in genomics, proteomics, gene expression, enzyme immobilization, protein design, and nanotechnology can substantially increase our knowledge to enhance the enzymatic degradation efficiency, which will accelerate plastic additive degradation and establish successful and cost-effective bioremediation processes. Investigations should also address the identification of the enzymes involved in the degradation process and their catalytic mechanisms to achieve full metabolization of organopollutants (i.e. plastic additives) while avoiding harmful plastic additive biodegradation products. Microorganisms and their enzymes undoubtedly represent a potential resource for developing promising environmental biotechnologies, as they have the best systems for pollutant degradation, and their actions are essential for decontaminating the environment.

De-colourization of textile effluent using immobilized Geotrichum candidum: an insight into mycoremediation

Textile effluent is generally complicated to manage because of its extremely noxious and recalcitrant coloured compositions. Mycoremediation is an extensively used strategy for the competent degradation of hazardous pollutants present in textile effluent. Fungus could be immobilized in synthetic or natural matrices. The current study shows the decolourization of the textile effluent by 85·5 and 98·5% within 6 h using suspended and immobilized fungus, Geotrichum candidum with optimized parameters like inoculum size (5%), pH (4·5), and temperature (30°C). To maintain a high biomass of fungal population and enhance the retention of fungal strain in the contaminated sites, the fungi need to be immobilized. Hence, the fungus was immobilized naturally onto the selected inert support that is, coconut fibres by the means of adsorption, where they grew as active films on the fibres after being grown in the culture broth. The optimized process parameters of inoculum size, fibre quantity and agitation speed for immobilized G. candidum were 5%, 2·2 g l^-1 of effluent and 100 rev min^-1 respectively. High level of laccase (22 and 25 U l^-1 in suspended and immobilized fungal cells treatment respectively) was observed during the process of decolourization and it was found that decolourization was directly proportional to the laccase activity. The UV-vis, FTIR, ¹ H NMR and GC-MS analyses of treated textile industrial wastewater revealed the degradation of toxic pollutants in the textile effluent and formation of lower molecular weight intermediates. The study revealed a higher efficacy of immobilized G. candidum in comparison to suspended fungal culture, employing ligninolytic enzyme laccase, which catalyzes the degradation/transformation of aromatic dyes in the textile effluent thus decolourizing it.

Metabolomics analysis of plasma and adipose tissue samples from mice orally administered with polydextrose and correlations with cecal microbiota

Polydextrose (PDX) is a branched glucose polymer, utilized as a soluble dietary fiber. Recently, PDX was found to have hypolipidemic effects and effects on the gut microbiota. To investigate these findings more closely, a non-targeted metabolomics approach, was exploited to determine metabolic alterations in blood and epididymal adipose tissue samples that were collected from C57BL/6 mice fed with a Western diet, with or without oral administration of PDX. Metabolomic analyses revealed significant differences between PDX- and control mice, which could be due to differences in diet or due to altered microbial metabolism in the gut. Some metabolites were found in both plasma and adipose tissue, such as the bile acid derivative deoxycholic acid and the microbiome-derived tryptophan metabolite indoxyl sulfate, both of which increased by PDX. Additionally, PDX increased the levels of glycine betaine and L-carnitine in plasma samples, which correlated negatively with plasma TG and positively correlated with bacterial genera enriched in PDX mice. The results demonstrated that PDX caused differential metabolite patterns in blood and adipose tissues and that one-carbon metabolism, associated with glycine betaine and L-carnitine, and bile acid and tryptophan metabolism are associated with the hypolipidemic effects observed in mice that were given PDX.

Efficient biodegradation of petroleum n-alkanes and polycyclic aromatic hydrocarbons by polyextremophilic Pseudomonas aeruginosa san ai with multidegradative capacity

Pseudomonas aeruginosa san ai degraded individual selected petroleum compounds: n-hexadecane, n-nonadecane, fluorene, phenanthrene, and pyrene with high efficiency, at initial concentrations of 20 mg L⁻¹ and in seven days.