Identification of proteins induced by polycyclic aromatic hydrocarbon and proposal of the phenanthrene catabolic pathway in Amycolatopsis tucumanensis DSM 45259

Fulvic acid enhancing pyrene biodegradation by immobilized Stenotrophomonas maltophilia: Effect and mechanism

Immobilization technology is a promising way to improve effectiveness and stability of microbial remediation for polycyclic aromatic hydrocarbons (PAHs), in which carrier material is one of key factors restricting removal efficiency. In this study, fulvic acid-wheat straw biochar (FA/WS) composites were applied for immobilization of an efficient PAHs degrading bacterium Stenotrophomonas maltophilia (SPM). FA/WS&SPM showed superior degradation capacity than free bacteria and biochar-immobilized bacteria, with the removal efficiency of pyrene (20 mg L-1) reaching 90.5 % (7 days). Transcriptome analysis revealed that FA in the carrier materials can promote transportation and degradation of pyrene, and cell growth, as well as inhibit cell apoptosis. Enzyme activity and degradation products detection showed that SPM utilized both phthalic acid and salicylic acid metabolic pathways to degrade pyrene. Practicality of FA/WS&SPM for different kinds of PAHs remediation had been verified in contaminated soil, demonstrating a great potential in the field of PAHs polluted sites remediation.

Distribution, sources, ecological risk and microbial response of polycyclic aromatic hydrocarbons in Qingdao bays, China

Bay ecosystem has garnered significant attention due to the severe threat posed by organic pollutants, particularly polycyclic aromatic hydrocarbons (PAHs). However, there is a dearth of information regarding the extent of PAHs pollutant risk and its impact on microbial communities and metabolism within this environment. In this study, the distribution, sources, ecological risk, and microbial community and metabolic response of PAHs in Jiaozhou Bay, Aoshan Bay, and Lingshan Bay in Qingdao, China were investigated. The results showed that the average concentration of ∑PAHs ranged from 120 to 614 ng/L across three bays, with Jiaozhou and Aoshan Bay exhibiting a higher risk than Lingshan Bay due to an increased concentration of high-molecular-weight PAHs. Further analysis revealed a negative correlation between dissolved organic carbon concentration and ∑PAHs concentration in water. Metagenomic analysis demonstrated that higher levels of PAHs can lead to decreased microbial diversity, while the abundance of PAHs-degrading bacteria is enhanced. Additionally, the Erythrobacter, Jannaschia and Ruegeria genera were found to have a significant correlation with low-molecular-weight PAH concentrations. In terms of microbial metabolism, higher PAH concentrations were beneficial for carbohydrate metabolic pathway but unfavorable for amino acid metabolic pathways and membrane transport pathways in natural bay environments. These findings provide a foundation for controlling PAHs pollution and offer insights into the impact of PAHs on bacterial communities and metabolism in natural bay environments.

Deciphering the recent trends in pesticide bioremediation using genome editing and multi-omics approaches: a review

Pesticide pollution in recent times has emerged as a grave environmental problem contaminating both aquatic and terrestrial ecosystems owing to their widespread use. Bioremediation using gene editing and system biology could be developed as an eco-friendly and proficient tool to remediate pesticide-contaminated sites due to its advantages and greater public acceptance over the physical and chemical methods. However, it is indispensable to understand the different aspects associated with microbial metabolism and their physiology for efficient pesticide remediation. Therefore, this review paper analyses the different gene editing tools and multi-omics methods in microbes to produce relevant evidence regarding genes, proteins and metabolites associated with pesticide remediation and the approaches to contend against pesticide-induced stress. We systematically discussed and analyzed the recent reports (2015-2022) on multi-omics methods for pesticide degradation to elucidate the mechanisms and the recent advances associated with the behaviour of microbes under diverse environmental conditions. This study envisages that CRISPR-Cas, ZFN and TALEN as gene editing tools utilizing Pseudomonas, Escherichia coli and Achromobacter sp. can be employed for remediation of chlorpyrifos, parathion-methyl, carbaryl, triphenyltin and triazophos by creating gRNA for expressing specific genes for the bioremediation. Similarly, systems biology accompanying multi-omics tactics revealed that microbial strains from Paenibacillus, Pseudomonas putida, Burkholderia cenocepacia, Rhodococcus sp. and Pencillium oxalicum are capable of degrading deltamethrin, p-nitrophenol, chlorimuron-ethyl and nicosulfuron. This review lends notable insights into the research gaps and provides potential solutions for pesticide remediation by using different microbe-assisted technologies. The inferences drawn from the current study will help researchers, ecologists, and decision-makers gain comprehensive knowledge of value and application of systems biology and gene editing in bioremediation assessments.

Genome sequencing and genomic analysis of Amycolatopsis tucumanensis DSM 45259 applicable in gray, red, and nano-biotechnology

Through the years, the genus Amycolatopsis has demonstrated its biotechnological potential. The need to clean up the environment and produce new antimicrobial molecules led to exploit promising bacterial genera such as Amycolatopsis. In this present work, we analyze the genome of the strain Amycolatopsis tucumanensis AB0 previously isolated from copper-polluted sediments. Phylogenomic and comparative analysis with the closest phylogenetic neighbor was performed. Our analysis showed the genetic potential of the strain to deal with heavy metals such as copper and mitigate oxidative stress. In addition, the ability to produce copper oxide nanoparticles and the presence of genes potentially involved in the synthesis of secondary metabolites suggest that A. tucumanensis may find utility in gray, red, and nano-biotechnology. To our knowledge, this is the first genomic analysis of an Amycolatopsis strain with potential for different biotechnological fields.

Silver nanoparticles synthesized by the heavy metal resistant strain Amycolatopsis tucumanensis and its application in controlling red strip disease in sugarcane

The production of bioethanol and sugar from sugarcane is an important economic activity in several countries. Sugarcane is susceptible to different phytopathogens. Over the last years, the red stripe disease caused by the bacterium Acidovorax avenae subsp. avenae produced significant losses in sugarcane crops. Bio-nanotechnology emerged as an eco-friendly alternative to the biosynthesis of antimicrobial molecules. The aims of this study were to (a) produce extracellular silver nanoparticles using the heavy metal resistant strain Amycolatopsis tucumanensis, (b) evaluate their antibacterial in vitro effect and (c) determine the potential of silver nanoparticles to protect sugarcane against red stripe disease.

Amycolatopsis tucumanensis synthesized spherical silver nanoparticles with an average size of 35 nm. Nanoparticles were able to control the growth of A. avenae subsp. avenae in in vitro assays. In addition, in vivo assays in sugarcane showed a control upon the red stripe disease when silver nanoparticles were applied as preventive treatment. The Disease Severity Index was 28.94% when silver nanoparticles were applied 3 days before inoculation with A. avenae subsp. avenae. To our knowledge, this is the first report of silver nanoparticles extracellularly synthesized by an Amycolatopsis strain that were able to inhibited the growth of A. avenae subsp. avenae and control the red stripe disease in sugarcane.

Determination of the metabolic pathways for degradation of naphthalene and pyrene in Amycolatopsis sp. Poz14

Polycyclic aromatic hydrocarbons (PAHs) constitute important soil contaminants derived from petroleum. Poz14 strain can degrade pyrene and naphthalene. Its genome presented 9333 genes, among them those required for PAHs degradation. By phylogenomic analysis, the strain might be assigned to Amycolatopsis nivea. The strain was grown in glucose, pyrene, and naphthalene to compare their proteomes; 180 proteins were detected in total, and 90 of them were exclusives for xenobiotic conditions. Functions enriched with the xenobiotics belonged to transcription, translation, modification of proteins and transport of inorganic ions. Enriched pathways were pentose phosphate, proteasome and RNA degradation; in contrast, in glucose were glycolysis/gluconeogenesis and glyoxylate cycle. Proteins proposed to participate in the upper PAHs degradation were multicomponent oxygenase complexes, Rieske oxygenases, and dioxygenases; in the lower pathways were ortho-cleavage of catechol, phenylacetate, phenylpropionate, benzoate, and anthranilate. The catechol dioxygenase activity was measured and found increased when the strain was grown in naphthalene. Amycolatopsis sp. Poz14 genome and proteome revealed the PAHs degradation pathways and functions helping to contend the effects of such process.

How humic acid and Tween80 improve the phenanthrene biodegradation efficiency: Insight from cellular characteristics and quantitative proteomics

Polycyclic aromatic hydrocarbons (PAHs) are toxic and recalcitrant pollutants, with an urgent need for bioremediation. Systematic biodegradation studies show that surfactant-mediated bioremediation is still poorly understood. Here, we investigated a comprehensive cellular response pattern of the PAH degrading strain B. subtilis ZL09-26 to (non-)green surfactants at the cellular and proteomic levels. Eight characteristic cellular factor investigations and detailed quantitative proteomics analyses were performed to understand the highly enhanced phenanthrene (PHE) degradation efficiency (2.8- to 3-fold improvement) of ZL09-26 by humic acid (HA) or Tween80. The commonly upregulated pathway and proteins (Arginine generation, LacI-family transcriptional regulator, and Lactate dehydrogenase) and various metabolic pathways (such as phenanthrene degradation upstream pathway and central carbon metabolism) jointly govern the change of cellular behaviors and improvement of PHE transport, emulsification, and degradation in a network manner. The obtained molecular knowledge empowers engineers to expand the application of surfactants in the biodegradation of PAHs and other pollutants.

Chemo-metric engineering designs for deciphering the biodegradation of polycyclic aromatic hydrocarbons

Polycyclic aromatic hydrocarbons (PAHs) are non-polar organic compounds that are omnipresent in the environment and released due to anthropogenic activities through emissions and discharges. PAHs, being xenobiotic and exerts health impacts, thus they attract serious concern by the environmentalists. The stringent regulations and the need of sustainable development urges the hunt for a technically feasible and cost-effective wastewater treatment. Although the conventional physico-chemical treatment are widely preferred, they cause secondary pollution problems and demand subsequent treatment options. This comprehensive review intends to address the (a) different PAHs and their associated toxicity, (b) the remedial strategies, particularly biodegradation. The biological wastewater treatment techniques that involve microbial systems are highly influenced by the different physio-chemical and environmental parameters. Therefore, suitable optimization techniques are prerequisite for effective functioning of the biological treatment that sustains judiciously and interpreted in a lesser time. Here we have aimed to discuss (a) different chemo-metric tools involved in the design of experiments (DoE), (b) design equations and models, (c) tools for evaluating the model's adequacy and (d) plots for graphically interpreting the chemo-metric designs. However, to best of our knowledge, this is a first review to discuss the PAHs biodegradation that are tailored by chemo-metric designs. The associated challenges, available opportunities and techno-economic aspects of PAHs degradation using chemo-metric engineering designs are explained. Additionally, the review highlights how well these DoE tools can be suited for the sustainable socio-industrial sectors. Concomitantly, the futuristic scope and prospects to undertake new areas of research exploration were emphasized to unravel the least explored chemo-metric designs.

Electrochemical performance and response of bacterial community during phenanthrene degradation in single-chamber air-cathode microbial fuel cells

Polycyclic aromatic hydrocarbons have attracted considerable attention for their carcinogenic, teratogenic, and mutagenic properties in humans. Phenanthrene is one of the most abundant polycyclic aromatic hydrocarbons in aquatic environments. In this study, different concentrations of phenanthrene were degraded by single-chamber air-cathode microbial fuel cells. The electrochemical parameter of microbial fuel cells and biofilm changes on the anode were observed. The results showed that the addition of phenanthrene reduced the power output of the microbial fuel cell which affected the process of microbial electricity generation. Meanwhile, microorganisms destroyed the original structure of phenanthrene through anaerobic metabolism, and achieved good average degradation of 94.9-98.4%. Observation of the anodic biofilm found that the microbes had tolerance to phenanthrene and the biofilm exhibited to be well-constructed. Bacterial community distribution showed a decrease in the relative abundance of Acidovorax and Aquamicrobium, whereas the relative content of the main electroactive organism, Geobacter, increased by a factor of three. The results show that it is feasible for microbial fuel cells to biodegrade phenanthrene, and provide some references for the changes of microbial community during degradation process.

Genomic analysis and proteomic response of the chromium-resistant and phenanthrene-degrading strain Streptomyces sp. MC1

AIM

Chemically disparate toxic organic and/or inorganic molecules produced by anthropogenic activities often hinder the bioremediation process. This research was conducted to understand the capacity of Streptomyces sp. MC1 to remove chemically disparate toxics such as Cr(VI) or phenanthrene.

METHODS AND RESULTS

Genomic, metabolic modeling and proteomic approaches were used in this study. Our results demonstrated that Streptomyces sp. MC1 has the genetic determinants to remove Cr(VI) or degrade phenanthrene. Proteomics showed that these genetic determinants were expressed. Metabolic versatility of the strain was confirmed by two metabolic models in complex and minimal media. Interestingly, our results also suggested a connection between the degradation of phenanthrene and synthesis of specialized metabolites.

CONCLUSIONS

Streptomyces sp. MC1 has the genetic and physiological potential to remove Cr(VI) or degrade phenanthrene SIGNIFICANCE AND IMPACT OF STUDY: The probability of a microorganism to survive in the presence of different contaminants depends on its genetic potential and the ability to express it. The genetic and proteomic profiles obtained for Streptomyces sp. MC1 can be recommended as model and predict if other Streptomyces strains can be used in bioremediation processes. Our work also hypothesized that intermediates of the phenanthrene degradation serve as precursors for the specialized metabolism.

Microbial Enzymes Used in Bioremediation

Emerging pollutants in nature are linked to various acute and chronic detriments in biotic components and subsequently deteriorate the ecosystem with serious hazards. Conventional methods for removing pollutants are not efficient; instead, they end up with the formation of secondary pollutants. Significant destructive impacts of pollutants are perinatal disorders, mortality, respiratory disorders, allergy, cancer, cardiovascular and mental disorders, and other harmful effects. The pollutant substrate can recognize different microbial enzymes at optimum conditions (temperature/pH/contact time/concentration) to efficiently transform them into other rather unharmful products. The most representative enzymes involved in bioremediation include cytochrome P450s, laccases, hydrolases, dehalogenases, dehydrogenases, proteases, and lipases, which have shown promising potential degradation of polymers, aromatic hydrocarbons, halogenated compounds, dyes, detergents, agrochemical compounds, etc. Such bioremediation is favored by various mechanisms such as oxidation, reduction, elimination, and ring-opening. The significant degradation of pollutants can be upgraded utilizing genetically engineered microorganisms that produce many recombinant enzymes through eco-friendly new technology. So far, few microbial enzymes have been exploited, and vast microbial diversity is still unexplored. This review would also be useful for further research to enhance the efficiency of degradation of xenobiotic pollutants, including agrochemical, microplastic, polyhalogenated compounds, and other hydrocarbons.

Changes in the fluorescence intensity, degradability, and aromaticity of organic carbon in ammonium and phenanthrene-polluted aquatic ecosystems

Mixed cultures were established by a sediment to investigate the changes in organic carbon (C) in a combined ammonium and phenanthrene biotransformation process in aquatic ecosystems. The microorganisms in the sediment demonstrated significant ammonium-N and phenanthrene biotransformation capacity with removal efficiencies of 99.96% and 99.99%, respectively. The changes in the organic C characteristics were evaluated by the fluorescence intensity, degradability (humification index (HIX) and UV absorbance at 254 nm (A₂₅₄)), aromaticity (specific UV absorbance at 254 nm (SUVA₂₅₄) and fluorescence index (FI)). Compared with C2 (the second control), the lower values of fluorescence intensity (after the 15^th d), HIX (after the 8^th d), A₂₅₄ (after the 11^th d), and SUVA₂₅₄ (after the 8^th d) and the higher FI value (after the 8^th d) in ammonium and phenanthrene-fed mixed cultures (N_PHE) suggest that aromatic structures and some condensed molecules were easier to break down in N_PHE. Similar results were obtained from Fourier transformation infrared spectroscopy (FTIR) and nuclear magnetic resonance (¹H NMR) spectra. Changes in organic C characteristics may be due to two key organisms Massilia and Azohydromonas. The biodiversity also suggested that the selective pressure of ammonium and phenanthrene is the decisive factor for changes in organic C characteristics. This study will shed light on theoretical insights into the interaction of N and aromatic compounds in aquatic ecosystems.

Mixed cultures were established by a sediment to investigate the changes in organic carbon (C) in a combined ammonium and phenanthrene biotransformation process in aquatic ecosystems.