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Increasing industrialization and anthropogenic activities have resulted in the release of a wide variety of pollutants into the environment including pesticides, polycyclic aromatic hydrocarbons (PAHs), and heavy metals. These pollutants pose a serious threat to human health as well as to the ecosystem. Thus, the removal of these compounds from the environment is highly important. Mitigation of the environmental pollution caused by these pollutants via bioremediation has become a promising approach nowadays. Actinobacteria are a group of eubacteria mostly known for their ability to produce secondary metabolites. The morphological features such as spore formation, filamentous growth, higher surface area to volume ratio, and cellular mechanisms like EPS secretion, and siderophore production in Actinobacteria render higher resistance and biodegradation ability. In addition, these bacteria possess several oxidoreductase systems (oxyR, catR, furA, etc.) which help in bioremediation. Actinobacteria genera including Arthrobacter, Rhodococcus, Streptomyces, Nocardia, Microbacterium, etc. have shown great potential for the bioremediation of various pollutants. In this review, the bioremediation ability of these bacteria has been discussed in detail. The utilization of various genera of Actinobacteria for the biodegradation of organic pollutants, including pesticides and PAHs, and inorganic pollutants like heavy metals has been described. In addition, the cellular mechanisms in these microbes which help to withstand oxidative stress have been discussed. Finally, this review explores the Actinobacteria mediated strategies and recent technologies such as the utilization of mixed cultures, cell immobilization, plant-microbe interaction, utilization of biosurfactants and nanoparticles, etc., to enhance the bioremediation of various environmental pollutants., Competing Interests: Conflict of interest statement The authors declare no competing interests., (Copyright © 2023 Elsevier GmbH. All rights reserved.)

Contamination of soil and natural water bodies driven by increased organic pollutants remains a universal concern. Naturally, organic pollutants contain carcinogenic and toxic properties threatening all known life forms. The conventional physical and chemical methods employed to remove these organic pollutants ironically produce toxic and non-ecofriendly end-products. Whereas microbial-based degradation of organic pollutants provides an edge, they are usually cost-effective and take an eco-friendly approach towards remediation. Bacterial species, including Pseudomonas, Comamonas, Burkholderia, and Xanthomonas, have the unique genetic makeup to metabolically degrade toxic pollutants, conferring their survival in toxic environments. Several catabolic genes, such as alkB, xylE, catA, and nahAc, that encode enzymes and allow bacteria to degrade organic pollutants have been identified, characterized, and even engineered for better efficacy. Aerobic and anaerobic processes are followed by bacteria to metabolize aliphatic saturated and unsaturated hydrocarbons such as alkanes, cycloalkanes, aldehydes, and ethers. Bacteria use a variety of degrading pathways, including catechol, protocatechuate, gentisate, benzoate, and biphenyl, to remove aromatic organic contaminants such as polychlorinated biphenyls, polycyclic aromatic hydrocarbons, and pesticides from the environment. A better understanding of the principle, mechanisms, and genetics would be beneficial for improving the metabolic efficacy of bacteria to such ends. With a focus on comprehending the mechanisms involved in various catabolic pathways and the genetics of the biotransformation of these xenobiotic compounds, the present review offers insight into the various sources and types of known organic pollutants and their toxic effects on health and the environment., (© 2023. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Biofilm-forming and acyl homoserine lactone (AHL) synthase-positive Pseudomonas aeruginosa N6P6 was isolated from seawater after selective enrichment with two polycyclic aromatic hydrocarbons (PAHs), viz. phenanthrene and pyrene. AHL synthesis was detected qualitatively using bioreporter strains. This marine bacterium putatively synthesized N-(3-oxododecanoyl)-L-homoserine lactone and N-butyryl-L-homoserine lactone, which were identified by TLC, GC-MS, and HPLC. Two quorum sensing (QS) genes coding for AHL synthase, i.e., lasI and rhlI, were identified in the bacterium. lasI and rhlI gene expression was studied during biofilm mode of growth at different phases using quantitative real-time PCR (qRT-PCR). The expression of lasI increased with increase in biofilm growth. In contrast, the expression of rhlI decreased during log phase of biofilm growth. The changes in lasI/rhlI expression level had significant effects (P<0.05) on biofilm architecture and subsequent PAH degradation rate. Degradation of phenanthrene and pyrene by P. aeruginosa N6P6 was affected by biofilm growth and lasI expression. The respective phenanthrene degradation for 15, 24, 48, and 72 h old biofilm after 7 days was 21.5, 54.2, 85.6, and 85.7%. However, the corresponding pyrene degradation was 15, 18.28, 47.56, and 46.48%, respectively, after 7 days. A significant positive correlation (P<0.05) was observed between lasI expression and PAHs degradation. However, in the presence of tannic acid, a QS inhibitor (QSI), PAHs degradation, biofilm formation, and pyocyanin production reduced significantly which confirmed the pivotal role of QS in biodegradation of PAHs. The findings suggest that AHLs play a pivotal role during biofilm development and subsequent bioremediation of PAHs.

Polycyclic aromatic hydrocarbons (PAHs) are persistent organic pollutants that impart several hazardous effects on the environment. Extracellular enzymes released by filamentous fungi are well-known participants in the degradation of such organic pollutants. The present study aims to determine the interaction of pyrene with Lac1 protein, coding for the extracellular laccase enzyme from Trichoderma sp. CNSC-2. Lac1 sequence analysis revealed the stable and acidic nature of the laccase enzyme. The dominance of random coils (54.8%) and extended strands (28.3%) in secondary structure defined protein flexibility. 3D homology modeling followed by validation revealed a high-quality model with 94.8% residues in the favored zone of Ramachandran plot. Molecular docking study with pyrene displayed a significant binding affinity of −7.82 kcal mol−1 with the amino acid residues at the active binding site of Lac1, indicating a strong role in pyrene binding. Trichoderma sp. CNSC-2 achieved 69.42 ± 0.4% of pyrene removal efficiency at 100 mg l−1 pyrene concentration on day 12 of incubation. Laccase activity during pyrene degradation simultaneously increased, and the highest activity was observed on day 6 of incubation. Enzyme production was found to be optimum at pH 6 (p < 0.001) and 30°C temperature (p < 0.0001). FTIR analysis showed deviation in the amide bands of laccase in the presence of pyrene, and additional peaks coinciding with pyrene metabolites were observed. The decrease in intensity of laccase due to quenching by pyrene interaction was determined by fluorescence spectroscopy. Thus, this study suggested a strong binding affinity of pyrene to the laccase active site implying the potential role of laccase enzyme from Trichoderma sp. CNSC-2 in pyrene degradation. [ABSTRACT FROM AUTHOR]

Marine environment is a dynamic habitat for survival of many microbes with unique metabolic potential. Biofilm formation benefits the marine bacteria to thrive and persist even in hostile environments. Besides, biofilm formation ability of bacteria enhances the efficiency of bioremediation of organic pollutants. In the present study, biofilm forming and polycyclic aromatic hydrocarbon (phenanthrene and pyrene) degrading bacteria were isolated and taxonomic identification was carried out by 16S rRNA gene sequencing. The isolates were able to grow on multiple aromatic hydrocarbons such as toluene, biphenyl, anthracene and naphthalene. The potential isolates were characterized by 16S rRNA gene sequencing. The isolates were identified and belong to the genera Pseudomonas, Stenotrophomonas, Paenibacillus, Alcaligenes, Sporosarcina and Lysinibacillus. Proteobacteria were found to be leading bacterial group at the pollutant sites. 75% of the isolates screened were able to establish biofilm and grow on either of aromatic hydrocarbon. This study shows the dominance of biofilm forming bacteria with ability to grow on multiple organic compounds in the marine environment. [ABSTRACT FROM AUTHOR]

Bacteria thrive in biofilms embedding in the three-dimensional extracellular polymeric substances (EPS). Functional Amyloid in Pseudomonas (Fap), a protein in EPS, efficiently sequesters polycyclic aromatic hydrocarbons (PAHs). Present study reports the characterization of Fap fibrils from Pseudomonas aeruginosa PFL-P1 and describes the interaction with pyrene to assess the impact on pyrene degradation. Overexpression of fap in E. coli BL21(DE3) cells significantly enhances biofilm formation (p < 0.0001) and amyloid production (p = 0.0002), particularly with pyrene. Defibrillated Fap analysis reveals FapC monomers and increased fibrillation with pyrene. Circular Dichroism (CD), Fourier Transform Infrared Spectroscopy (FTIR), and X-ray Diffraction (XRD) unveil characteristic amyloid peaks and structural changes in Fap fibrils upon pyrene exposure. 3D-EEM analysis identifies a protein-like fluorophore in Fap fibrils, exhibiting pyrene-induced fluorescence quenching. Binding constants range from 5.23 to 7.78 M−1, with ΔG of −5.10 kJ mol−1 at 298 K, indicating spontaneous and exothermic interaction driven by hydrophobic forces. Exogenous Fap fibrils substantially increased the biofilm growth and pyrene degradation by P. aeruginosa PFL-P1 from 46 % to 64 % within 7 days (p = 0.0236). GC–MS identifies diverse metabolites, implying phthalic acid pathway in pyrene degradation. This study deepens insights into structural dynamics of Fap fibrils when exposed to pyrene, offering potential application in environmental bioremediation. [Display omitted] • Functional amyloid from P. aeruginosa PFL-P1 showed increased fibrillation with pyrene. • CD, FTIR, and XRD revealed amyloid peaks and pyrene-induced structural changes. • Fap fibrils spontaneously interact with pyrene through hydrophobic forces. • Pyrene binds to Fap fibrils at multiple sites with binding constants of 5.23–7.78 M−1. • Exogenous Fap fibrils enhanced biofilm-mediated pyrene degradation from 46 % to 64 %. [ABSTRACT FROM AUTHOR]

Increasing level of polycyclic aromatic hydrocarbons (PAHs) in the environment results in environmental pollution. Microbial biofilm-mediated bioremediation has been widely used as an attractive approach to mitigate PAHs contamination in the ecosystem. Amyloid, a proteinaceous component of biofilm-associated extracellular polymeric substances (EPS), forms an integral strengthening part of the biofilm. This study aims to determine the interaction of functional amyloid in Pseudomonas (Fap) with two different PAHs (phenanthrene and pyrene). The production of amyloid by the marine bacterium Pseudomonas aeruginosa PFL-P1 was confirmed by Congo red (CR) assay, thioflavin T (ThT) staining method and amplification of fapC gene. The expression of fapC was up-regulated six folds (p < 0.0001) when phenanthrene and pyrene were used as the sole carbon source. The molecular docking of modelled FapC revealed a strong binding energy of − 7.0 and − 6.75 kcal/mol with phenanthrene and pyrene, respectively. Confocal laser scanning microscopic (CLSM) analysis indicated a significant increase in amyloid percentage during biofilm formation by P. aeruginosa PFL-P1 in the presence of phenanthrene and pyrene (p < 0.0001). The increased expression of the fapC gene and the potent hydrophobic interaction between the FapC protein and the PAH molecules suggest the essential role of this protein in PAH binding. [Display omitted] • Marine bacterium Pseudomonas aeruginosa PFL-P1 showed amyloid-producing ability. • Amyloid production increased under polycyclic aromatic hydrocarbon stress. • fapC encodes the major amyloid protein in Pseudomonas. • In silico study revealed β-sheet-rich region in the tertiary structure of FapC. • FapC was found to interact hydrophobically with polycyclic aromatic hydrocarbon. [ABSTRACT FROM AUTHOR]

Pseudomonas aeruginosa is a small rod shaped Gram-negative bacterium of Gammaproteobacteria class known for its metabolic versatility. P. aeruginosa PFL-P1 was isolated from Polycyclic Aromatic Hydrocarbons (PAHs) contaminated site of Paradip Port, Odisha Coast, India. The strain showed excellent biofilm formation and could retain its ability to form biofilm grown with different PAHs in monoculture as well as co-cultures. To explore mechanistic insights of PAHs metabolism, the whole genome of the strain was sequenced. Next generation sequencing unfolded a genome size of 6,333,060 bp encoding 5857 CDSs. Gene ontology distribution assigned to a total of 2862 genes, wherein 2235 genes were allocated to biological process, 1549 genes to cellular component and 2339 genes to molecular function. A total of 318 horizontally transferred genes were identified when the genome was compared with the reference genomes of P. aeruginosa PAO1 and P. aeruginosa DSM 50071. Further comparison of P. aeruginosa PFL-P1 genome with P. putida containing TOL plasmids revealed similarities in the meta cleavage pathway employed for degradation of aromatic compounds like xylene and toluene. Gene annotation and pathway analysis unveiled 145 genes involved in xenobiotic biodegradation and metabolism. The biofilm cultures of P. aeruginosa PFL-P1 could degrade ~74% phenanthrene within 120 h while degradation increased up to ~76% in co-culture condition. GC-MS analysis indicated presence of diverse metabolites indicating the involvement of multiple pathways for one of the PAHs (phenanthrene) degradation. The strain also possesses the genetic machinery to utilize diverse toxic aromatic compounds such as naphthalene, benzoate, aminobenzoate, fluorobenzoate, toluene, xylene, styrene, atrazine, caprolactam etc. Common catabolic gene clusters such as benABCD , xylXYZ and catAB were observed within the genome of P. aeruginosa PFL-P1 which play key roles in the degradation of various toxic aromatic compounds. Image 1 • Marine biofilm forming PAH degrading bacterium Pseudomonas aeruginosa possessed a genome of 6.3 Mbp. • 145 genes accounted for conferring xenobiotic degradation ability. • 269 genes were involved in forming cellular community. • Multiple pathways were found for phenanthrene degradation. [ABSTRACT FROM AUTHOR]

Manglicolous filamentous fungi release extracellular lignolytic enzymes that can readily degrade polycyclic aromatic hydrocarbons (PAHs). The present study emphasizes the role of the extracellular enzyme in phenanthrene degradation by the manglicolous fungus Trichoderma sp. CNSC-2 isolated from the Indian Sundarban mangrove ecosystem. The removal efficiency reached 64.05 ± 0.75 % in 50 mg l−1 phenanthrene-amended mineral salt medium at pH 5.6 after 10 days of incubation. Phenanthrene removal was optimized at different pH, nutrient sources, and Cu2+ concentrations. The degradation significantly increased to 67.75 ± 4.32 % at pH 6 (P < 0.0001). The addition of Cu2+ (30 mg l−1) increased the degradation to 78.15 ± 0.36 % (P < 0.0001). The validation experiment confirmed the increase in phenanthrene degradation up to 79.9 ± 1.67 % under optimized conditions. The Lac1 and CytP 450 genes encoding for extracellular and intracellular enzymes, respectively, were identified. The GC-MS derived phenanthrene degradation metabolites, i.e., phthalic acid, isobutyl 2-pentyl ester derivative, 1, 2 benzene dicarboxylic acid, butyl 2-methyl propyl ester derivative, TMS derivative of benzoic acid and 3,5 dihydroxy benzoic acid determined two possible metabolic pathways. The laccase enzyme activity was higher in the presence of Phe+Cu2+ (P < 0.0001), indicating the enzyme induction potential of PAH and Cu2+ ions. Purified laccase had a molecular weight of 45 kDa and was highly stable at pH 4–6 and temperature 20–50 °C. The enzyme retained 47 %, 87 %, and 63 % of enzyme activity at 30 mg l−1 concentration of Pb2+, Cd2+, and Hg2+. However, laccase activity was induced by 1.37 folds in the presence of 30 mg l−1 Cu2+ concentration. Thus, the study suggests the potential role of Trichoderma sp. CNSC-2 in phenanthrene degradation. [Display omitted] • Manglicolous fungus, Trichoderma sp. CNSC-2 could remove 64 % of 50 mg l−1 phenanthrene • Phenanthrene removal was optimized under different pH, nutrient and Cu2+ concentrations • Laccase enzyme regulate the phenanthrene degradation pathways [ABSTRACT FROM AUTHOR]

Effect of exogenous N-acyl homoserine lactones (AHLs) on biofilm growth, cell surface hydrophobicity, auto-aggregation and polycyclic aromatic hydrocarbons (PAHs) degradation potential of two marine Pseudomonas isolates ( Pseudomonas pseudoalcaligenes NP103 and Pseudomonas aeruginosa N6P6) were evaluated in the present study. Increased biofilm growth, auto-aggregation and swarming motility was observed in the presence of exogenous AHLs (3OC8-HSL and 3OC12-HSL) resulting in enhanced phenanthrene and pyrene degradation. P. pseudoalcaligenes NP103 biofilm was able to degrade up to 79% of phenanthrene and 49% pyrene in 7 d whereas 85.6% phenanthrene and 47.56% pyrene degradation was achieved using P. aeruginosa N6P6 biofilm. 3OC8-HSL significantly ( P < 0.05; Tukey’s HSD test) potentiated the phenanthrene and pyrene degradation by P. pseudoalcaligenes NP103 biofilm (89% and 65.5%), whereas the phenanthrene and pyrene degradation potential of P. aeruginosa N6P6 biofilm increased significantly ( P < 0.05; Tukey’s HSD test) in presence of 3OC12-HSL (97.4% and 54.39%). Furthermore, the degradation achieved by both the isolates in presence of tannic acid, a quorum sensing inhibitor (QSI), was highest in presence of 3OC12-HSL suggesting the most pronounced effect of long chain AHL in degradation of phenanthrene and pyrene. Both the isolates followed catechol pathway for PAHs degradation. The findings suggest that AHL can significantly affect the biodegradation performance specifically when bacteria are present in abundant numbers in biofilms. [ABSTRACT FROM AUTHOR]

Increased tolerance to toxic pollutants and enhanced degradation capabilities of the bacterial biofilm is often attributed to the matrix of extracellular polymeric substances (EPS). This biopolymeric matrix provides structure, stability, and shelter to the cells within a biofilm and the major constituent of this matrix is exopolysaccharides. However, the role of EPS extends beyond offering protection to the bacterial cells under stress. Bacterial EPS exhibits a double-layered structure consisting of the loosely bound EPS (LB-EPS) and the tightly bound EPS (TB-EPS). Both these EPS layers interact with noxious environmental pollutants through emulsification, solubilization, binding, precipitation, complexation, and ion exchange. Different functional groups of EPS, such as carboxyl, amide, phosphoryl, and hydroxyl, are involved in the removal of toxic pollutants from contaminated environments. Biofilm-EPS participate in several remedial functions such as sequestration of heavy metals, emulsification of petroleum hydrocarbons, binding and solubilization of polycyclic aromatic hydrocarbons (PAHs), and sorption and degradation of dyes and pesticides. Thus, bacterial biofilm and EPS present an attractive solution for decontaminating heavily polluted environments. This review discusses a comprehensive account of biofilm physiology, EPS components, and synthesis mechanisms of exopolysaccharides. The interaction mechanisms of bacterial biofilm and EPS with pollutants have been discussed in detail, and the application of biofilm-forming bacteria and associated EPS in the bioremediation of the environment has been summarized. A deeper understanding of the bacterial biofilm and EPS-mediated pollutant removal will help develop technologies for field-scale applications. [Display omitted] • Bacterial biofilm exhibits increased tolerance to toxic environments. • EPS imparts functional and mechanical stability to the biofilm. • EPS-metal interaction occurs via complexation, precipitation and ion exchange. • Biofilm-EPS enhances the bioavailability of hydrophobic pollutants to cells. • Commercialization of the technology is needed for large-scale applications. [ABSTRACT FROM AUTHOR]