Microbial Degradation of Contaminants of Emerging Concern: Metabolic, Genetic and Omics Insights for Enhanced Bioremediation

Overview

Journal Front Bioeng Biotechnol

Date 2024 Oct 4

PMID 39364263

Authors

Bhavik A Shah

Harshit Malhotra

Sandesh E Papade

Tushar Dhamale

Omkar P Ingale

Sravanti T Kasarlawar

Prashant S Phale

Affiliations

Soon will be listed here.

Abstract

The perpetual release of natural/synthetic pollutants into the environment poses major risks to ecological balance and human health. Amongst these, contaminants of emerging concern (CECs) are characterized by their recent introduction/detection in various niches, thereby causing significant hazards and necessitating their removal. Pharmaceuticals, plasticizers, cyanotoxins and emerging pesticides are major groups of CECs that are highly toxic and found to occur in various compartments of the biosphere. The sources of these compounds can be multipartite including industrial discharge, improper disposal, excretion of unmetabolized residues, eutrophication ., while their fate and persistence are determined by factors such as physico-chemical properties, environmental conditions, biodegradability and hydrological factors. The resultant exposure of these compounds to microbiota has imposed a selection pressure and resulted in evolution of metabolic pathways for their biotransformation and/or utilization as sole source of carbon and energy. Such microbial degradation phenotype can be exploited to clean-up CECs from the environment, offering a cost-effective and eco-friendly alternative to abiotic methods of removal, thereby mitigating their toxicity. However, efficient bioprocess development for bioremediation strategies requires extensive understanding of individual components such as pathway gene clusters, proteins/enzymes, metabolites and associated regulatory mechanisms. "Omics" and "Meta-omics" techniques aid in providing crucial insights into the complex interactions and functions of these components as well as microbial community, enabling more effective and targeted bioremediation. Aside from natural isolates, metabolic engineering approaches employ the application of genetic engineering to enhance metabolic diversity and degradation rates. The integration of omics data will further aid in developing systemic-level bioremediation and metabolic engineering strategies, thereby optimising the clean-up process. This review describes bacterial catabolic pathways, genetics, and application of omics and metabolic engineering for bioremediation of four major groups of CECs: pharmaceuticals, plasticizers, cyanotoxins, and emerging pesticides.

References

Chen F, Chen Y, Chen C, Feng L, Dong Y, Chen J . High-efficiency degradation of phthalic acid esters (PAEs) by Pseudarthrobacter defluvii E5: Performance, degradative pathway, and key genes. Sci Total Environ. 2021; 794:148719. DOI: 10.1016/j.scitotenv.2021.148719. View

Yuan M, Ding Q, Sun R, Zhang J, Yin L, Pu Y . Biodegradation of Nodularin by a Microcystin-Degrading Bacterium: Performance, Degradation Pathway, and Potential Application. Toxins (Basel). 2021; 13(11). PMC: 8618024. DOI: 10.3390/toxins13110813. View

Aris A, Shamsuddin A, Praveena S . Occurrence of 17α-ethynylestradiol (EE2) in the environment and effect on exposed biota: a review. Environ Int. 2014; 69:104-19. DOI: 10.1016/j.envint.2014.04.011. View

Fang H, Wang Y, Gao C, Yan H, Dong B, Yu Y . Isolation and characterization of Pseudomonas sp. CBW capable of degrading carbendazim. Biodegradation. 2010; 21(6):939-46. DOI: 10.1007/s10532-010-9353-0. View

Shariati S, Ebenau-Jehle C, Pourbabaee A, Alikhani H, Rodriguez-Franco M, Agne M . Degradation of dibutyl phthalate by Paenarthrobacter sp. Shss isolated from Saravan landfill, Hyrcanian Forests, Iran. Biodegradation. 2021; 33(1):59-70. PMC: 8803807. DOI: 10.1007/s10532-021-09966-7. View

Badawy S, Yang Y, Liu Y, Marawan M, Ares I, Martinez M . Toxicity induced by ciprofloxacin and enrofloxacin: oxidative stress and metabolism. Crit Rev Toxicol. 2022; 51(9):754-787. DOI: 10.1080/10408444.2021.2024496. View

Chen J, Li X, Li J, Cao J, Qiu Z, Zhao Q . Degradation of environmental endocrine disruptor di-2-ethylhexyl phthalate by a newly discovered bacterium, Microbacterium sp. strain CQ0110Y. Appl Microbiol Biotechnol. 2006; 74(3):676-82. DOI: 10.1007/s00253-006-0700-3. View

Tassoulas L, Robinson A, Martinez-Vaz B, Aukema K, Wackett L . Filling in the Gaps in Metformin Biodegradation: a New Enzyme and a Metabolic Pathway for Guanylurea. Appl Environ Microbiol. 2021; 87(11). PMC: 8208167. DOI: 10.1128/AEM.03003-20. View

Palma T, Costa M . Anaerobic biodegradation of fluoxetine using a high-performance bacterial community. Anaerobe. 2021; 68:102356. DOI: 10.1016/j.anaerobe.2021.102356. View

10.

Chang T, Lin Z, Zhang L, Liu W, Zhou Y, Ye B . Efficient biodegradation of di-(2-ethylhexyl) phthalate by a novel strain Nocardia asteroides LMB-7 isolated from electronic waste soil. Sci Rep. 2022; 12(1):15262. PMC: 9464244. DOI: 10.1038/s41598-022-19752-x. View

11.

Szewczyk R, Sobon A, Slaba M, Dlugonski J . Mechanism study of alachlor biodegradation by Paecilomyces marquandii with proteomic and metabolomic methods. J Hazard Mater. 2015; 291:52-64. DOI: 10.1016/j.jhazmat.2015.02.063. View

12.

Reis A, Kolvenbach B, Chami M, Gales L, Egas C, Corvini P . Comparative genomics reveals a novel genetic organization of the sad cluster in the sulfonamide-degrader 'Candidatus Leucobacter sulfamidivorax' strain GP. BMC Genomics. 2019; 20(1):885. PMC: 6868719. DOI: 10.1186/s12864-019-6206-z. View

13.

Ferrao-Filho A, Kozlowsky-Suzuki B . Cyanotoxins: bioaccumulation and effects on aquatic animals. Mar Drugs. 2012; 9(12):2729-2772. PMC: 3280578. DOI: 10.3390/md9122729. View

14.

Syafrudin M, Kristanti R, Yuniarto A, Hadibarata T, Rhee J, Al-Onazi W . Pesticides in Drinking Water-A Review. Int J Environ Res Public Health. 2021; 18(2). PMC: 7826868. DOI: 10.3390/ijerph18020468. View

15.

Li T, Xu Z, Zhang S, Xu J, Pan P, Zhou N . Discovery of a Ni-dependent heterohexameric metformin hydrolase. Nat Commun. 2024; 15(1):6121. PMC: 11271267. DOI: 10.1038/s41467-024-50409-7. View

16.

Sarkar J, Pal Chowdhury P, Dutta T . Complete degradation of di-n-octyl phthalate by Gordonia sp. strain Dop5. Chemosphere. 2012; 90(10):2571-7. DOI: 10.1016/j.chemosphere.2012.10.101. View

17.

Aulestia M, Flores A, Acosta-Jurado S, Santero E, Camacho E . Genetic Characterization of the Ibuprofen-Degradative Pathway of Rhizorhabdus wittichii MPO218. Appl Environ Microbiol. 2022; 88(11):e0038822. PMC: 9195938. DOI: 10.1128/aem.00388-22. View

18.

Chen G, Wang L, Wang M, Hu T . Comprehensive insights into the occurrence and toxicological issues of nodularins. Mar Pollut Bull. 2020; 162:111884. DOI: 10.1016/j.marpolbul.2020.111884. View

19.

Santer M, AJL S . Steroid metabolism by a species of Pseudomonas. II. Direct evidence for the breakdown of testosterone. J Biol Chem. 1952; 199(1):85-9. View

20.

Kim D, Thawng C, Lee K, Wellington E, Cha C . A novel sulfonamide resistance mechanism by two-component flavin-dependent monooxygenase system in sulfonamide-degrading actinobacteria. Environ Int. 2019; 127:206-215. DOI: 10.1016/j.envint.2019.03.046. View