1
|
Wu J, Lv J, Zhao L, Zhao R, Gao T, Xu Q, Liu D, Yu Q, Ma F. Exploring the role of microbial proteins in controlling environmental pollutants based on molecular simulation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 905:167028. [PMID: 37704131 DOI: 10.1016/j.scitotenv.2023.167028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 09/03/2023] [Accepted: 09/10/2023] [Indexed: 09/15/2023]
Abstract
Molecular simulation has been widely used to study microbial proteins' structural composition and dynamic properties, such as volatility, flexibility, and stability at the microscopic scale. Herein, this review describes the key elements of molecular docking and molecular dynamics (MD) simulations in molecular simulation; reviews the techniques combined with molecular simulation, such as crystallography, spectroscopy, molecular biology, and machine learning, to validate simulation results and bridge information gaps in the structure, microenvironmental changes, expression mechanisms, and intensity quantification; illustrates the application of molecular simulation, in characterizing the molecular mechanisms of interaction of microbial proteins with four different types of contaminants, namely heavy metals (HMs), pesticides, dyes and emerging contaminants (ECs). Finally, the review outlines the important role of molecular simulations in the study of microbial proteins for controlling environmental contamination and provides ideas for the application of molecular simulation in screening microbial proteins and incorporating targeted mutagenesis to obtain more effective contaminant control proteins.
Collapse
Affiliation(s)
- Jieting Wu
- School of Environmental Science, Liaoning University, Shenyang 110036, China
| | - Jin Lv
- School of Environmental Science, Liaoning University, Shenyang 110036, China
| | - Lei Zhao
- State Key Laboratory of Urban Water Resources & Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Ruofan Zhao
- School of Environment, Beijing Normal University, Beijing 100875, China
| | - Tian Gao
- Key Laboratory of Integrated Regulation and Resource Development of Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing 210098, China
| | - Qi Xu
- PetroChina Fushun Petrochemical Company, Fushun 113000, China
| | - Dongbo Liu
- School of Environmental Science, Liaoning University, Shenyang 110036, China
| | - Qiqi Yu
- School of Environmental Science, Liaoning University, Shenyang 110036, China
| | - Fang Ma
- State Key Laboratory of Urban Water Resources & Environment, Harbin Institute of Technology, Harbin 150090, China.
| |
Collapse
|
2
|
Du Y, Cheng Q, Qian M, Liu Y, Wang F, Ma J, Zhang X, Lin H. Biodegradation of sulfametoxydiazine by Alcaligenes aquatillis FA: Performance, degradation pathways, and mechanisms. JOURNAL OF HAZARDOUS MATERIALS 2023; 452:131186. [PMID: 36948117 DOI: 10.1016/j.jhazmat.2023.131186] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 03/07/2023] [Accepted: 03/08/2023] [Indexed: 05/03/2023]
Abstract
This study reports the isolation and characterization of a novel bacterial strain Alcaligenes aquatillis FA with the ability to degrade sulfametoxydiazine (SMD), a commonly used sulfonamide antibiotic (SA) in livestock and poultry production. The biodegradation kinetics, pathways, and genomic background of SMD by FA were investigated. The results showed that strain FA had high specificity to degrade SMD, and was unable to effectively degrade its isomer, sulfamonomethoxine. The SMD biodegradation followed a first-order kinetic model with a rate constant of 27.39 mg·L-1·day-1 and a half-life of 5.98 days. The biodegradation pathways and detoxification processes of SMD were proposed based on the identification of its biodegradation byproducts and the biotoxicity assessment using both the ecological structure-activity relationship (ECOSAR) model and biological indicator. The involvement of novel degrading enzymes, such as dimethyllsulfone monooxygenase, 4-carboxymuconolactone decarboxylase, and 1,4-benzoquinone reductase, was inferred in the SMD biodegradation process. The presence of sul2 and dfrA genes in strain FA, which were constitutively expressed in its cells, suggests that multiple mechanisms were employed by the strain to resist SMD. This study provides new insights into the biodegradation of sulfonamide antibiotics (SAs) as it is the first to describe an SMD-degrading bacterium and its genetic information.
Collapse
Affiliation(s)
- Yuqian Du
- College of Forest and Biotechnology, Zhejiang A & F University, Hangzhou 311300, China; State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Environment, Resource, Soil and Fertilizers, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Qilu Cheng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Environment, Resource, Soil and Fertilizers, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Mingrong Qian
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Interdisciplinary Research Academy, Zhejiang Shuren University, Hangzhou 310015, China
| | - Yangzhi Liu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Environment, Resource, Soil and Fertilizers, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Feng Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Environment, Resource, Soil and Fertilizers, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Junwei Ma
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Environment, Resource, Soil and Fertilizers, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Xin Zhang
- College of Forest and Biotechnology, Zhejiang A & F University, Hangzhou 311300, China.
| | - Hui Lin
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Environment, Resource, Soil and Fertilizers, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
| |
Collapse
|
3
|
Sodhi KK, Singh CK, Kumar M, Singh DK. Whole-genome sequencing of Alcaligenes sp. strain MMA: insight into the antibiotic and heavy metal resistant genes. Front Pharmacol 2023; 14:1144561. [PMID: 37251338 PMCID: PMC10213877 DOI: 10.3389/fphar.2023.1144561] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 05/02/2023] [Indexed: 05/31/2023] Open
Abstract
Introduction: A wide range of pollutants, including the likes of xenobiotics, heavy metals, and antibiotics, are characteristic of marine ecosystems. The ability of the bacteria to flourish under high metal stress favors the selection of antibiotic resistance in aquatic environments. Increased use and misuse of antibiotics in medicine, agriculture, and veterinary have posed a grave concern over antimicrobial resistance. The exposure to these heavy metals and antibiotics in the bacteria drives the evolution of antibiotic and heavy metal resistance genes. In the earlier study by the author Alcaligenes sp. MMA was involved in the removal of heavy metals and antibiotics. Alcaligenes display diverse bioremediation capabilities but remain unexplored at the level of the genome. Methods: To shed light on its genome, the Alcaligenes sp. strain MMA, was sequenced using Illumina Nova Seq sequencer, which resulted in a draft genome of 3.9 Mb. The genome annotation was done using Rapid annotation using subsystem technology (RAST). Given the spread of antimicrobial resistance and the generation of multi-drug resistant pathogens (MDR), the strain MMA was checked for potential antibiotic and heavy metal resistance genes Further, we checked for the presence of biosynthetic gene clusters in the draft genome. Results: Alcaligenes sp. strain MMA, was sequenced using Illumina Nova Seq sequencer, which resulted in a draft genome of 3.9 Mb. The RAST analysis revealed the presence of 3685 protein-coding genes, involved in the removal of antibiotics and heavy metals. Multiple metal-resistant genes and genes conferring resistance to tetracycline, beta-lactams, and fluoroquinolones were present in the draft genome. Many types of BGCs were predicted, such as siderophore. The secondary metabolites of fungi and bacteria are a rich source of novel bioactive compounds which have the potential to in new drug candidates. Discussion: The results of this study provide information on the strain MMA genome and are valuable for the researcher in further exploitation of the strain MMA for bioremediation. Moreover, whole-genome sequencing has become a useful tool to monitor the spread of antibiotic resistance, a global threat to healthcare.
Collapse
Affiliation(s)
| | | | - Mohit Kumar
- Hindu College, University of Delhi, Delhi, India
| | | |
Collapse
|
4
|
Yan L, Yan N, Gao XY, Liu Y, Liu ZP. Degradation of amoxicillin by newly isolated Bosea sp. Ads-6. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 828:154411. [PMID: 35288139 DOI: 10.1016/j.scitotenv.2022.154411] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/15/2022] [Accepted: 03/04/2022] [Indexed: 06/14/2023]
Abstract
Amoxicillin (AMX), one of the micro-amount hazardous pollutants, was frequently detected in environments, and of great risks to environments and human health. Microbial degradation is a promising method to eliminate pollutants. In this study, an efficient AMX-degrading strain, Ads-6, was isolated and characterized. Strain Ads-6, belonging to the genus Bosea, was also able to grow on AMX as the sole carbon and nitrogen source, with a removal of ~60% TOC. Ads-6 exhibited strong AMX-degrading ability at initial concentrations of 0.5-2 mM and pH 6-8. Addition of yeast extract could significantly enhance its degrading ability. Many degradation intermediates were identified by HPLC-MS, including new ones such as two phosphorylated products which were firstly defined in AMX degradation. A new AMX degradation pathway was proposed accordingly. Moreover, the results of comparative transcriptomes and proteomes revealed that β-lactamase, L, D-transpeptidase or its homologous enzymes were responsible for the initial degradation of AMX. Protocatechuate branch of the beta-ketoadipate pathway was confirmed as the downstream degradation pathway. These results in the study suggested that Ads-6 is great potential in biodegradation of antibiotics as well as in the bioremediation of contaminated environments.
Collapse
Affiliation(s)
- Lei Yan
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ning Yan
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Xi-Yan Gao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Ying Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhi-Pei Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
| |
Collapse
|
5
|
Dos S Grignet R, Barros MGA, Panatta AAS, Bernal SPF, Ottoni JR, Passarini MRZ, da C S Gonçalves C. Medicines as an emergent contaminant: the review of microbial biodegration potential. Folia Microbiol (Praha) 2022; 67:157-174. [PMID: 34978661 DOI: 10.1007/s12223-021-00941-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 12/09/2021] [Indexed: 12/20/2022]
Abstract
Emerging environmental contaminants, such as medicine waste, are of great concern to the scientific community and to the local environmental and health departments because of their potential long-term effects and ecotoxicological risk. Besides the prolonged use of medicines for the development of modern society, the elucidation of their effect on the ecosystem is relatively recent. Medicine waste and its metabolites can, for instance, cause alterations in microbial dynamics and disturb fish behavior. Bioremediation is an efficient and eco-friendly technology that appears as a suitable alternative to conventional methods of water waste and sludge treatment and has the capacity to remove or reduce the presence of emerging contaminants. Thus, this review has the objective of compiling information on environmental contamination by common medicines and their microbial biodegradation, focusing on five therapeutic classes: analgesics, antibiotics, antidepressants, non-steroidal anti-inflammatory drugs (NSAIDs), and contraceptives. Their effects in the environment will also be analyzed, as well as the possible routes of degradation by microorganisms.
Collapse
Affiliation(s)
- Rosane Dos S Grignet
- Instituto Latino-Americano de Ciências da Vida E da Natureza, Universidade Federal da Integração Latino-Americana, Foz do Iguaçu - PR, 85870-650, Brazil
| | - Maria G A Barros
- Instituto Latino-Americano de Ciências da Vida E da Natureza, Universidade Federal da Integração Latino-Americana, Foz do Iguaçu - PR, 85870-650, Brazil
| | - Andressa A S Panatta
- Instituto Latino-Americano de Ciências da Vida E da Natureza, Universidade Federal da Integração Latino-Americana, Foz do Iguaçu - PR, 85870-650, Brazil
| | - Suzan P F Bernal
- Instituto Latino-Americano de Ciências da Vida E da Natureza, Universidade Federal da Integração Latino-Americana, Foz do Iguaçu - PR, 85870-650, Brazil
| | - Julia R Ottoni
- Instituto Latino-Americano de Ciências da Vida E da Natureza, Universidade Federal da Integração Latino-Americana, Foz do Iguaçu - PR, 85870-650, Brazil
| | - Michel R Z Passarini
- Instituto Latino-Americano de Ciências da Vida E da Natureza, Universidade Federal da Integração Latino-Americana, Foz do Iguaçu - PR, 85870-650, Brazil
| | - Caroline da C S Gonçalves
- Instituto Latino-Americano de Ciências da Vida E da Natureza, Universidade Federal da Integração Latino-Americana, Foz do Iguaçu - PR, 85870-650, Brazil.
| |
Collapse
|
6
|
Vijayaraghavan P, Lourthuraj AA, Arasu MV, AbdullahAl-Dhabi N, Ravindran B, WoongChang S. Effective removal of pharmaceutical impurities and nutrients using biocatalyst from the municipal wastewater with moving bed packed reactor. ENVIRONMENTAL RESEARCH 2021; 200:111777. [PMID: 34333016 DOI: 10.1016/j.envres.2021.111777] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 07/05/2021] [Accepted: 07/22/2021] [Indexed: 06/13/2023]
Abstract
The presence of antibiotics in the wastewater is one of the important issues related to environmental management. In this study, antibiotics-degrading bacteria were screened from the enriched sewage sludge sample. Among the isolated bacterial strains, Bacillus subtilis AQ03 showed maximum antibiotic tolerance (>2000 ppm). The characterized strain B. subtilis AQ03 degraded sulfamethaoxazole and sulfamethoxine and the optimum nutrient and physical-factors were analyzed. B. subtilis AQ03 degraded 99.8 ± 1.3 % sulfamethaoxazole, and 93.3 ± 6.2 % sulfamethoxine. Sodium nitrate and ammonium chloride were improved antibiotics degradation (<90 %). The optimized conditions were maintained in a moving bed bioreactor for the removal of antibiotics and nutrients from the wastewater. The selected strain considerably produced proteases (109.4 U/mL), amylases (55.1 U/mL), cellulase (9.6 U/mL) and laccases (15.2). In moving bed reactor, sulfamethaoxazole degradation was maximum after 8 days (100 ± 1.5 %) and sulfamethoxazole (100 ± 0) was removed completely from wastewater after 10 days. In moving bed reactor, biological oxygen demand (92.1 ± 2.8 %), chemical oxygen demand (79.6 ± 1.2 %), nitrate (89.4 ± 3.9 %) and phosphate (91.8 ± 1.2) were removed from the wastewater along with antibiotics after 10 days of treatment. The findings indicate that the indigenous bacterial communities and the ability to survive in the presence of high antibiotic concentrations and xenobiotics. Moving bed bioreactor is useful for the removal of nutrients and antibiotics from wastewater.
Collapse
Affiliation(s)
| | - A Amala Lourthuraj
- Department of Biochemistry,Guru nanak College (autonomous), Velachery, Chennai, 600042, Tamil nadu, India
| | - Mariadhas Valan Arasu
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. BOX 2455, Riyadh, 11451, Saudi Arabia
| | - Naif AbdullahAl-Dhabi
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. BOX 2455, Riyadh, 11451, Saudi Arabia
| | - Balasubramani Ravindran
- Department of Environmental Energy and Engineering, Kyonggi University Youngtong-Gu, Suwon, Gyeonggi-Do, 16227, Republic of Korea
| | - Soon WoongChang
- Department of Environmental Energy and Engineering, Kyonggi University Youngtong-Gu, Suwon, Gyeonggi-Do, 16227, Republic of Korea
| |
Collapse
|
7
|
Biodegradation of Amoxicillin, Tetracyclines and Sulfonamides in Wastewater Sludge. WATER 2020. [DOI: 10.3390/w12082147] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The removal of antibiotics from the aquatic environment has received great interest. The aim of this study is to examine degradation of oxytetracycline (OTC), tetracycline (TC), chlortetracycline (CTC), amoxicillin (AMO), sulfamethazine (SMZ), sulfamethoxazole (SMX), sulfadimethoxine (SDM) in sludge. Four antibiotic-degrading bacterial strains, SF1 (Pseudmonas sp.), A12 (Pseudmonas sp.), strains B (Bacillus sp.), and SANA (Clostridium sp.), were isolated, identified and tested under aerobic and anaerobic conditions in this study. Batch experiments indicated that the addition of SF1 and A12 under aerobic conditions and the addition of B and SANA under anaerobic conditions increased the biodegradation of antibiotics in sludge. Moreover, the results of repeated addition experiments indicated that the efficiency of the biodegradation of antibiotics using the isolated bacterial strains could be maintained for three degradation cycles. Two groups of potential microbial communities associated with the aerobic and anaerobic degradation of SMX, AMO and CTC in sludge were revealed. Twenty-four reported antibiotics-degrading bacterial genera (Achromobacter, Acidovorax, Acinetobacter, Alcaligenes, Bacillus, Burkholderia, Castellaniella, Comamonas, Corynebacterium, Cupriavidus, Dechloromonas, Geobacter, Gordonia, Klebsiella, Mycobacterium, Novosphingobium, Pandoraea, Pseudomonas, Rhodococcus, Sphingomonas, Thauera, Treponema, Vibrio and Xanthobacter) were found in both the aerobic and anaerobic groups, suggesting that these 24 bacterial genera may be the major antibiotic-degrading bacteria in sludge.
Collapse
|