1
|
Yadav P, Kumari SP, Hooda S, Gupta RK, Diwan P. Comparative assessment of microbiome and resistome of influent and effluent of sewage treatment plant and common effluent treatment plant located in Delhi, India using shotgun approach. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 369:122342. [PMID: 39232318 DOI: 10.1016/j.jenvman.2024.122342] [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: 12/12/2023] [Revised: 08/09/2024] [Accepted: 08/30/2024] [Indexed: 09/06/2024]
Abstract
Antimicrobial resistance (AMR) is a significant threat that demands surveillance to identify and analyze trends of the emerging antibiotic resistance genes (ARGs) and potential microbial carriers. The influent of the wastewater treatment plants (WWTPs) reflects the microbes derived from the population and effluent being the source of dissemination of potential pathogenic microbes and AMR. The present study aimed to monitor microbial communities and antibiotic resistance genes in WWTPs employing a whole metagenome shotgun sequencing approach. The samples were collected from a sewage treatment plant (STP) and a common effluent treatment plant (CETP) in Delhi, India. The results showed the influent of STP to be rich in Bifidobacterium, Bacteroides, Escherichia, Arcobacter, and Pseudomonas residents of gut microbiota and known to cause diseases in humans and animals; whereas the CETP sample was abundant in Aeromonas, Escherichia, and Shewanella known to be involved in the degradation of different compounds. Interestingly, the effluent samples from both STPs and CETP were rich in microbial diversity, comprising organic and xenobiotic compound degrading and disease-causing bacteria, indicating the effluent being the source of dissemination of concerning bacteria to the environment. The functional profile at both sites displayed similarity with an abundance of housekeeping function genes as analyzed by Clusters of Orthologous Genes (COG), KEGG Orthology (KO), and subsystem databases. Resistome profiling by MEGARes showed the dominance of ARGs corresponding to beta-lactams having relative abundance ranging from 16% to 34% in all the metagenome datasets, followed by tetracycline (8%-16%), aminoglycosides (7%-9%), multi-drug (5%-9%), and rifampin (3%-9%). Also, AMR genes oxa, ant3-DPRIME, and rpoB, which are of clinical importance were predominantly and most prevalently present in all the samples. The presence of AMR in effluents from both types of treatment plants indicates that wastewater from both sources contributes to the spread of pathogenic bacteria and resistance genes, increasing the environmental AMR burden and therefore requires tertiary treatment before discharge. This work will facilitate further research towards the identification of suitable biomarkers for monitoring antibiotic resistance.
Collapse
Affiliation(s)
- Prerna Yadav
- Department of Microbiology, Ram Lal Anand College, University of Delhi, South Campus, New Delhi, 110021, India
| | - Shashi Prabha Kumari
- Department of Microbiology, Ram Lal Anand College, University of Delhi, South Campus, New Delhi, 110021, India
| | - Sunila Hooda
- Department of Microbiology, Ram Lal Anand College, University of Delhi, South Campus, New Delhi, 110021, India
| | - Rakesh Kumar Gupta
- Department of Microbiology, Ram Lal Anand College, University of Delhi, South Campus, New Delhi, 110021, India
| | - Prerna Diwan
- Department of Microbiology, Ram Lal Anand College, University of Delhi, South Campus, New Delhi, 110021, India.
| |
Collapse
|
2
|
Vaishnavi J, Osborne JW. Biodegradation of monocrotophos, cypermethrin & fipronil by Proteus myxofaciens VITVJ1: A plant - microbe based remediation. Heliyon 2024; 10:e37384. [PMID: 39309857 PMCID: PMC11416261 DOI: 10.1016/j.heliyon.2024.e37384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Revised: 08/30/2024] [Accepted: 09/02/2024] [Indexed: 09/25/2024] Open
Abstract
Current study was focused on the degradation of pesticides such as Monocrotophos, Cypermethrin & Fipronil (M, C & F) using phyto and rhizoremediation strategies. The isolate Proteus myxofaciens (VITVJ1) obtained from agricultural soil was capable of degrading M, C & F. The bacteria exhibited resistance to all the pesticides (M, C & F) up to 1500 ppm and was also capable of forming biofilms. The degraded products identified using Gas Chromatography-Mass Spectroscopy (GC-MS) and FTIR was further used for deriving the degradation pathway. The end product of M, C & F was acetic acid and 3-phenoxy benzoic acid which was confirmed by the presence of functional groups such as C=O and OH. Seed germination assay revealed the non-toxic nature of the degraded products with increased germination index in the treatments augmented with degraded products. The candidate genes such as opdA gene, Est gene and MnP1gene was amplified with the amplicon size of 700bp, 1200bp and 500bp respectively. P. myxofaciens not only degraded M, C & F, but was also found to be a plant growth promoting rhizobacteria. Since, it was capable of producing Indole Acetic acid (IAA), siderophore and was able to solubilize insoluble phosphate. Therefore, VITVJ1 upon augmentation to the rhizoremediation setup aided the degradation of pesticides with increase in plant growth as compared to that of the phytoremediation setup. To our knowledge this is the first study where P. myxofaciens has been effectively used for the degradation of three different classes of pesticides, which could also enhance the growth of plants and simultaneously degrade M, C & F.
Collapse
Affiliation(s)
- Jeevanandam Vaishnavi
- Department of Biosciences, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India
| | - Jabez William Osborne
- Department of Biosciences, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India
| |
Collapse
|
3
|
Zhou Y, Wang T, Wang L, Wang P, Chen F, Bhatt P, Chen S, Cui X, Yang Y, Zhang W. Microbes as carbendazim degraders: opportunity and challenge. Front Microbiol 2024; 15:1424825. [PMID: 39206363 PMCID: PMC11349639 DOI: 10.3389/fmicb.2024.1424825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Accepted: 08/02/2024] [Indexed: 09/04/2024] Open
Abstract
Carbendazim (methyl benzimidazol-2-ylcarbamate, CBZ) is a systemic benzimidazole carbamate fungicide and can be used to control a wide range of fungal diseases caused by Ascomycetes, Basidiomycetes and Deuteromycetes. It is widely used in horticulture, forestry, agriculture, preservation and gardening due to its broad spectrum and leads to its accumulation in soil and water environmental systems, which may eventually pose a potential threat to non-target organisms through the ecological chain. Therefore, the removal of carbendazim residues from the environment is an urgent problem. Currently, a number of physical and chemical treatments are effective in degrading carbendazim. As a green and efficient strategy, microbial technology has the potential to degrade carbendazim into non-toxic and environmentally acceptable metabolites, which in turn can dissipate carbendazim from the contaminated environment. To date, a number of carbendazim-degrading microbes have been isolated and reported, including, but not limited to, Bacillus, Pseudomonas, Rhodococcus, Sphingomonas, and Aeromonas. Notably, the common degradation property shared by all strains was their ability to hydrolyze carbendazim to 2-aminobenzimidazole (2-AB). The complete mineralization of the degradation products is mainly dependent on the cleavage of the imidazole and benzene rings. Additionally, the currently reported genes for carbendazim degradation are MheI and CbmA, which are responsible for breaking the ester and amide bonds, respectively. This paper reviews the toxicity, microbial degradation of carbendazim, and bioremediation techniques for carbendazim-contaminated environments. This not only summarizes and enriches the theoretical basis of microbial degradation of carbendazim, but also provides practical guidance for bioremediation of carbendazim-contaminated residues in the environment.
Collapse
Affiliation(s)
- Yi Zhou
- Key Laboratory of Sustainable Utilization of Panax Notoginseng Resources of Yunnan Province, Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Tianyue Wang
- Key Laboratory of Sustainable Utilization of Panax Notoginseng Resources of Yunnan Province, Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Liping Wang
- Key Laboratory of Sustainable Utilization of Panax Notoginseng Resources of Yunnan Province, Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Pengfei Wang
- Key Laboratory of Sustainable Utilization of Panax Notoginseng Resources of Yunnan Province, Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Feiyu Chen
- Key Laboratory of Sustainable Utilization of Panax Notoginseng Resources of Yunnan Province, Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Pankaj Bhatt
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Shaohua Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Xiuming Cui
- Key Laboratory of Sustainable Utilization of Panax Notoginseng Resources of Yunnan Province, Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Ye Yang
- Key Laboratory of Sustainable Utilization of Panax Notoginseng Resources of Yunnan Province, Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Wenping Zhang
- Key Laboratory of Sustainable Utilization of Panax Notoginseng Resources of Yunnan Province, Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China
| |
Collapse
|
4
|
Alidoosti F, Giyahchi M, Moien S, Moghimi H. Unlocking the potential of soil microbial communities for bioremediation of emerging organic contaminants: omics-based approaches. Microb Cell Fact 2024; 23:210. [PMID: 39054471 PMCID: PMC11271216 DOI: 10.1186/s12934-024-02485-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2024] [Accepted: 07/18/2024] [Indexed: 07/27/2024] Open
Abstract
The remediation of emerging contaminants presents a pressing environmental challenge, necessitating innovative approaches for effective mitigation. This review article delves into the untapped potential of soil microbial communities in the bioremediation of emerging contaminants. Bioremediation, while a promising method, often proves time-consuming and requires a deep comprehension of microbial intricacies for enhancement. Given the challenges presented by the inability to culture many of these microorganisms, conventional methods are inadequate for achieving this goal. While omics-based methods provide an innovative approach to understanding the fundamental aspects, processes, and connections among microorganisms that are essential for improving bioremediation strategies. By exploring the latest advancements in omics technologies, this review aims to shed light on how these approaches can unlock the hidden capabilities of soil microbial communities, paving the way for more efficient and sustainable remediation solutions.
Collapse
Affiliation(s)
- Fatemeh Alidoosti
- Department of Microbiology, School of Biology, College of Science, University of Tehran, Tehran, Iran
| | - Minoo Giyahchi
- Department of Microbiology, School of Biology, College of Science, University of Tehran, Tehran, Iran
| | - Shabnam Moien
- Department of Microbiology, School of Biology, College of Science, University of Tehran, Tehran, Iran
| | - Hamid Moghimi
- Department of Microbiology, School of Biology, College of Science, University of Tehran, Tehran, Iran.
| |
Collapse
|
5
|
Motovilov KA, Mostert AB. Melanin: Nature's 4th bioorganic polymer. SOFT MATTER 2024; 20:5635-5651. [PMID: 39012013 DOI: 10.1039/d4sm00491d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/17/2024]
Abstract
The pigments known as the melanins are widely recognized for their responsibility in the coloration of human skin, eyes, hair, and minimising the harmful effects of solar ultraviolet radiation. But specialists are aware that the melanins are present in all living kingdoms, barring viruses, and have functionality that extends beyond neutralizing ionising radiation. The ubiquitous presence of melanin in almost all human organs, recognized in recent years, as well as the presence of melanin in organisms that are evolutionarily distant from each other, indicate the fundamental importance of this class of material for all life forms. In this review, we argue for the need to accept melanins as the fourth primordial class of biological polymers, along with nucleic acids, proteins and polysaccharides. We consistently compare the properties of these canonical biological polymers with the properties of melanin and highlight key features that fundamentally distinguish melanins, their function and its mysteries.
Collapse
Affiliation(s)
- K A Motovilov
- Center for Photonics and 2D Materials, Moscow Institute of Physics and Technology, Institutsky Lane 9, Dolgoprudny 141701, Moscow Region, Russia.
| | - A B Mostert
- Department of Physics and Centre for Integrative Semiconductor Materials, Swansea University Bay Campus, Fabian Way, Swansea SA1 8EN, UK
| |
Collapse
|
6
|
Dan Y, Gurevich D, Gershoni O, Netti F, Adler-Abramovich L, Afriat-Jurnou L. Coupling Peptide-Based Encapsulation of Enzymes with Bacteria for Paraoxon Bioremediation. ACS APPLIED MATERIALS & INTERFACES 2024; 16:35155-35165. [PMID: 38920304 PMCID: PMC11247427 DOI: 10.1021/acsami.4c06501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/27/2024]
Abstract
The catalytic efficiency of enzymes can be harnessed as an environmentally friendly solution for decontaminating various xenobiotics and toxins. However, for some xenobiotics, several enzymatic steps are needed to obtain nontoxic products. Another challenge is the low durability and stability of many native enzymes in their purified form. Herein, we coupled peptide-based encapsulation of bacterial phosphotriesterase with soil-originated bacteria, Arthrobacter sp. 4Hβ as an efficient system capable of biodegradation of paraoxon, a neurotoxin pesticide. Specifically, recombinantly expressed and purified methyl parathion hydrolase (MPH), with high hydrolytic activity toward paraoxon, was encapsulated within peptide nanofibrils, resulting in increased shelf life and retaining ∼50% activity after 132 days since purification. Next, the addition of Arthrobacter sp. 4Hβ, capable of degrading para-nitrophenol (PNP), the hydrolysis product of paraoxon, which is still toxic, resulted in nondetectable levels of PNP. These results present an efficient one-pot system that can be further developed as an environmentally friendly solution, coupling purified enzymes and native bacteria, for pesticide bioremediation. We further suggest that this system can be tailored for different xenobiotics by encapsulating the rate-limiting key enzymes followed by their combination with environmental bacteria that can use the enzymatic step products for full degradation without the need to engineer synthetic bacteria.
Collapse
Affiliation(s)
- Yoav Dan
- Department of Oral Biology, The Goldschleger School of Dental Medicine, Faculty of Medical and Health Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
- The Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv 6997801, Israel
- The Center for the Physics and Chemistry of Living Systems, Tel Aviv University, Tel Aviv 6997801, Israel
| | - David Gurevich
- Migal-Galilee Research Institute, Kiryat Shmona 11016, Israel
| | - Ofir Gershoni
- Migal-Galilee Research Institute, Kiryat Shmona 11016, Israel
| | - Francesca Netti
- Department of Oral Biology, The Goldschleger School of Dental Medicine, Faculty of Medical and Health Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
- The Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv 6997801, Israel
- The Center for the Physics and Chemistry of Living Systems, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Lihi Adler-Abramovich
- Department of Oral Biology, The Goldschleger School of Dental Medicine, Faculty of Medical and Health Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
- The Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv 6997801, Israel
- The Center for the Physics and Chemistry of Living Systems, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Livnat Afriat-Jurnou
- Migal-Galilee Research Institute, Kiryat Shmona 11016, Israel
- The Faculty of Sciences and Technology, Tel-Hai College, Upper Galilee 1220800, Israel
| |
Collapse
|
7
|
Zou M, Zhang Q, Li F, Chen L, Qiu Y, Yin Q, Zhou S. Impacts of multiple environmental factors on soil bacterial community assembly in heavy metal polluted paddy fields. Sci Rep 2024; 14:14696. [PMID: 38926471 PMCID: PMC11208537 DOI: 10.1038/s41598-024-65678-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Accepted: 06/24/2024] [Indexed: 06/28/2024] Open
Abstract
Soil microorganisms play pivotal roles in driving essential biogeochemical processes in terrestrial ecosystems, and they are sensitive to heavy metal pollution. However, our understanding of multiple environmental factors interaction in heavy metal polluted paddy fields to shape microbial community assembly remain limited. In the current study, we used 16S rRNA amplicon sequencing to characterize the microbial community composition in paddy soils collected from a typical industry town in Taihu region, eastern China. The results revealed that Cd and Pb were the major pollutant, and Proteobacteria, Acidobacteria and Chloroflexi were the dominate indigenous bacterial phyla. Linear regression and random forest analysis demonstrated that soil pH was the most important predictor of bacterial diversity. Mantel analysis showed that bacterial community structure was mainly driven by pH, CEC, silt, sand, AK, total Cd and DTPA-Cd. The constructed bacterial co-occurrence network, utilizing a random matrix theory-based approach, exhibited non-random with scale-free and modularity features. The major modules within the networks also showed significant correlations with soil pH. Overall, our study indicated that soil physiochemical properties made predominant contribution to bacterial community diversity, structure and their association in Cd/Pb polluted paddy fields. These findings expand our knowledge of the key environmental drivers and co-occurrence patterns of bacterial community in polluted paddy fields.
Collapse
Affiliation(s)
- Mengmeng Zou
- School of Geography and Ocean Science, Nanjing University, 163 Xianlin Road, Nanjing, 210023, Jiangsu, People's Republic of China
- Key Laboratory of Coastal Zone Exploitation and Protection, Ministry of Natural Resources, Nanjing, 210024, People's Republic of China
| | - Qi Zhang
- School of Geography and Ocean Science, Nanjing University, 163 Xianlin Road, Nanjing, 210023, Jiangsu, People's Republic of China
- Key Laboratory of Coastal Zone Exploitation and Protection, Ministry of Natural Resources, Nanjing, 210024, People's Republic of China
| | - Fengchun Li
- Testing Center of Shandong Bureau of China Metallurgy and Geology, Jinan, 250014, People's Republic of China
| | - Long Chen
- School of Geography and Ocean Science, Nanjing University, 163 Xianlin Road, Nanjing, 210023, Jiangsu, People's Republic of China
- Key Laboratory of Coastal Zone Exploitation and Protection, Ministry of Natural Resources, Nanjing, 210024, People's Republic of China
| | - Yifei Qiu
- School of Geography and Ocean Science, Nanjing University, 163 Xianlin Road, Nanjing, 210023, Jiangsu, People's Republic of China
- Key Laboratory of Coastal Zone Exploitation and Protection, Ministry of Natural Resources, Nanjing, 210024, People's Republic of China
| | - Qiqi Yin
- School of Geography and Ocean Science, Nanjing University, 163 Xianlin Road, Nanjing, 210023, Jiangsu, People's Republic of China
- Key Laboratory of Coastal Zone Exploitation and Protection, Ministry of Natural Resources, Nanjing, 210024, People's Republic of China
| | - Shenglu Zhou
- School of Geography and Ocean Science, Nanjing University, 163 Xianlin Road, Nanjing, 210023, Jiangsu, People's Republic of China.
- Key Laboratory of Coastal Zone Exploitation and Protection, Ministry of Natural Resources, Nanjing, 210024, People's Republic of China.
| |
Collapse
|
8
|
Chin HS, Ravi Varadharajulu N, Lin ZH, Chen WY, Zhang ZH, Arumugam S, Lai CY, Yu SSF. Isolation, molecular identification, and genomic analysis of Mangrovibacter phragmitis strain ASIOC01 from activated sludge harboring the bioremediation prowess of glycerol and organic pollutants in high-salinity. Front Microbiol 2024; 15:1415723. [PMID: 38983623 PMCID: PMC11231211 DOI: 10.3389/fmicb.2024.1415723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Accepted: 06/04/2024] [Indexed: 07/11/2024] Open
Abstract
The physiological and genotypic characteristics of Mangrovibacter (MGB) remain largely unexplored, including their distribution and abundance within ecosystems. M. phragmitis (MPH) ASIOC01 was successfully isolated from activated sludge (AS), which was pre-enriched by adding 1,3-dichloro-2-propanol and 3-chloro-1,2-propanediol as carbon sources. The new isolate, MPH ASIOC01, exhibited resilience in a medium containing sodium chloride concentration up to 11% (with optimal growth observed at 3%) and effectively utilizing glycerol as their sole carbon source. However, species delimitation of MGBs remains challenging due to high 16S rRNA sequence similarity (greater than 99% ANI) among different MGBs. In contrast, among the housekeeping gene discrepancies, the tryptophan synthase beta chain gene can serve as a robust marker for fast species delimitation among MGBs. Furthermore, the complete genome of MPH ASIOC01 was fully sequenced and circlized as a single contig using the PacBio HiFi sequencing method. Comparative genomics revealed genes potentially associated with various phenotypic features of MGBs, such as nitrogen-fixing, phosphate-solubilizing, cellulose-digesting, Cr-reducing, and salt tolerance. Computational analysis suggested that MPH ASIOC01 may have undergone horizontal gene transfer events, possibly contributing unique traits such as antibiotic resistance. Finally, our findings also disclosed that the introduction of MPH ASIOC01 into AS can assist in the remediation of wastewater chemical oxygen demand, which was evaluated using gas chromatograph-mass spectrometry. To the best of our knowledge, this study offers the most comprehensive understanding of the phenotypic and genotypic features of MGBs to date.
Collapse
Affiliation(s)
- Hong Soon Chin
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Narendrakumar Ravi Varadharajulu
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
- Molecular Science and Technology Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan
- Department of Chemistry, National Tsing Hua University, Hsinchu, Taiwan
| | - Zhi-Han Lin
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Wen-Yu Chen
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
| | - Zong-Han Zhang
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
- Ph.D. Program in Microbial Genomics, National Chung Hsing University, Taichung City, Taiwan
| | | | - Ching-Yen Lai
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
| | - Steve S.-F. Yu
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan
- Molecular Science and Technology Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan
- Ph.D. Program in Microbial Genomics, National Chung Hsing University, Taichung City, Taiwan
| |
Collapse
|
9
|
Liao XL, Chen ZF, Liu QY, Zhou JM, Cai WX, Wang Y, Cai Z. Tissue Accumulation and Biotransformation of 6PPD-Quinone in Adult Zebrafish and Its Effects on the Intestinal Microbial Community. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:10275-10286. [PMID: 38825773 DOI: 10.1021/acs.est.4c01409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
The pronounced lethality of N-(1,3-dimethylbutyl)-N'-phenyl-p-phenylenediamine quinone (6PPD-quinone or 6PPDQ) toward specific salmonids, while sparing other fish species, has received considerable attention. However, the underlying cause of this species-specific toxicity remains unresolved. This study explored 6PPDQ toxicokinetics and intestinal microbiota composition in adult zebrafish during a 14-day exposure to environmentally realistic concentrations, followed by a 7-day recovery phase. Predominant accumulation occurred in the brain, intestine, and eyes, with the lowest levels in the liver. Six metabolites were found to undergo hydroxylation, with two additionally undergoing O-sulfonation. Semiquantitative analyses revealed that the predominant metabolite featured a hydroxy group situated on the phenyl ring adjacent to the quinone. This was further validated by assessing enzyme activity and determining in silico binding interactions. Notably, the binding affinity between 6PPDQ and zebrafish phase I and II enzymes exceeded that with the corresponding coho salmon enzymes by 1.04-1.53 times, suggesting a higher potential for 6PPDQ detoxification in tolerant species. Whole-genome sequencing revealed significant increases in the genera Nocardioides and Rhodococcus after exposure to 6PPDQ. Functional annotation and pathway enrichment analyses predicted that these two genera would be responsible for the biodegradation and metabolism of xenobiotics. These findings offer crucial data for comprehending 6PPDQ-induced species-specific toxicity.
Collapse
Affiliation(s)
- Xiao-Liang Liao
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China
| | - Zhi-Feng Chen
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China
| | - Qian-Yi Liu
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China
| | - Jia-Ming Zhou
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China
| | - Wen-Xi Cai
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China
| | - Yujie Wang
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China
| | - Zongwei Cai
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong 999077, China
| |
Collapse
|
10
|
Egbewale SO, Kumar A, Mokoena MP, Olaniran AO. Purification, characterization and three-dimensional structure prediction of multicopper oxidase Laccases from Trichoderma lixii FLU1 and Talaromyces pinophilus FLU12. Sci Rep 2024; 14:13371. [PMID: 38862560 PMCID: PMC11167041 DOI: 10.1038/s41598-024-63959-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 06/04/2024] [Indexed: 06/13/2024] Open
Abstract
Broad-spectrum biocatalysts enzymes, Laccases, have been implicated in the complete degradation of harmful pollutants into less-toxic compounds. In this study, two extracellularly produced Laccases were purified to homogeneity from two different Ascomycetes spp. Trichoderma lixii FLU1 (TlFLU1) and Talaromyces pinophilus FLU12 (TpFLU12). The purified enzymes are monomeric units, with a molecular mass of 44 kDa and 68.7 kDa for TlFLU1 and TpFLU12, respectively, on SDS-PAGE and zymogram. It reveals distinct properties beyond classic protein absorption at 270-280 nm, with TlFLU1's peak at 270 nm aligning with this typical range of type II Cu site (white Laccase), while TpFLU12's unique 600 nm peak signifies a type I Cu2+ site (blue Laccase), highlighting the diverse spectral fingerprints within the Laccase family. The Km and kcat values revealed that ABTS is the most suitable substrate as compared to 2,6-dimethoxyphenol, caffeic acid and guaiacol for both Laccases. The bioinformatics analysis revealed critical His, Ile, and Arg residues for copper binding at active sites, deviating from the traditional two His and a Cys motif in some Laccases. The predicted biological functions of the Laccases include oxidation-reduction, lignin metabolism, cellular metal ion homeostasis, phenylpropanoid catabolism, aromatic compound metabolism, cellulose metabolism, and biological adhesion. Additionally, investigation of degradation of polycyclic aromatic hydrocarbons (PAHs) by purified Laccases show significant reductions in residual concentrations of fluoranthene and anthracene after a 96-h incubation period. TlFLU1 Laccase achieved 39.0% and 44.9% transformation of fluoranthene and anthracene, respectively, while TpFLU12 Laccase achieved 47.2% and 50.0% transformation, respectively. The enzyme structure-function relationship study provided insights into the catalytic mechanism of these Laccases for possible biotechnological and industrial applications.
Collapse
Affiliation(s)
- Samson O Egbewale
- Discipline of Microbiology, School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal (Westville Campus), Durban, 4001, South Africa
| | - Ajit Kumar
- Discipline of Microbiology, School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal (Westville Campus), Durban, 4001, South Africa
| | - Mduduzi P Mokoena
- Discipline of Microbiology, School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal (Westville Campus), Durban, 4001, South Africa
- Department of Pathology, School of Medicine, University of Limpopo, Private Bag X1106, Sovenga, 0727, South Africa
| | - Ademola O Olaniran
- Discipline of Microbiology, School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal (Westville Campus), Durban, 4001, South Africa.
| |
Collapse
|
11
|
Jasińska A, Walaszczyk A, Paraszkiewicz K. Omics-Based Approaches in Research on Textile Dye Microbial Decolorization. Molecules 2024; 29:2771. [PMID: 38930836 PMCID: PMC11206425 DOI: 10.3390/molecules29122771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 06/02/2024] [Accepted: 06/07/2024] [Indexed: 06/28/2024] Open
Abstract
The development of the textile industry has negative effects on the natural environment. Cotton cultivation, dyeing fabrics, washing, and finishing require a lot of water and energy and use many chemicals. One of the most dangerous pollutants generated by the textile industry is dyes. Most of them are characterized by a complex chemical structure and an unfavorable impact on the environment. Especially azo dyes, whose decomposition by bacteria may lead to the formation of carcinogenic aromatic amines and raise a lot of concern. Using the metabolic potential of microorganisms that biodegrade dyes seems to be a promising solution for their elimination from contaminated environments. The development of omics sciences such as genomics, transcriptomics, proteomics, and metabolomics has allowed for a comprehensive approach to the processes occurring in cells. Especially multi-omics, which combines data from different biomolecular levels, providing an integrative understanding of the whole biodegradation process. Thanks to this, it is possible to elucidate the molecular basis of the mechanisms of dye biodegradation and to develop effective methods of bioremediation of dye-contaminated environments.
Collapse
Affiliation(s)
- Anna Jasińska
- Department of Industrial Microbiology and Biotechnology, Faculty of Biology and Environmental Protection, University of Lodz, 90-237 Lodz, Poland;
| | - Aleksandra Walaszczyk
- Department of Industrial Microbiology and Biotechnology, Faculty of Biology and Environmental Protection, Doctoral School of Exact and Natural Sciences, University of Lodz, 90-237 Lodz, Poland;
| | - Katarzyna Paraszkiewicz
- Department of Industrial Microbiology and Biotechnology, Faculty of Biology and Environmental Protection, University of Lodz, 90-237 Lodz, Poland;
| |
Collapse
|
12
|
Kariyawasam T, Helvig C, Petkovich M, Vriens B. Pharmaceutical removal from wastewater by introducing cytochrome P450s into microalgae. Microb Biotechnol 2024; 17:e14515. [PMID: 38925623 PMCID: PMC11197475 DOI: 10.1111/1751-7915.14515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 06/11/2024] [Indexed: 06/28/2024] Open
Abstract
Pharmaceuticals are of increasing environmental concern as they emerge and accumulate in surface- and groundwater systems around the world, endangering the overall health of aquatic ecosystems. Municipal wastewater discharge is a significant vector for pharmaceuticals and their metabolites to enter surface waters as humans incompletely absorb prescription drugs and excrete up to 50% into wastewater, which are subsequently incompletely removed during wastewater treatment. Microalgae present a promising target for improving wastewater treatment due to their ability to remove some pollutants efficiently. However, their inherent metabolic pathways limit their capacity to degrade more recalcitrant organic compounds such as pharmaceuticals. The human liver employs enzymes to break down and absorb drugs, and these enzymes are extensively researched during drug development, meaning the cytochrome P450 enzymes responsible for metabolizing each approved drug are well studied. Thus, unlocking or increasing cytochrome P450 expression in endogenous wastewater microalgae could be a cost-effective strategy to reduce pharmaceutical loads in effluents. Here, we discuss the challenges and opportunities associated with introducing cytochrome P450 enzymes into microalgae. We anticipate that cytochrome P450-engineered microalgae can serve as a new drug removal method and a sustainable solution that can upgrade wastewater treatment facilities to function as "mega livers".
Collapse
Affiliation(s)
- Thamali Kariyawasam
- Department of Geological Sciences and EngineeringQueen's UniversityKingstonOntarioCanada
- Beaty Water Research CenterQueen's UniversityKingstonOntarioCanada
| | - Christian Helvig
- Department of Biomedical EngineeringQueen's UniversityKingstonOntarioCanada
| | - Martin Petkovich
- Department of Biomedical EngineeringQueen's UniversityKingstonOntarioCanada
| | - Bas Vriens
- Department of Geological Sciences and EngineeringQueen's UniversityKingstonOntarioCanada
- Beaty Water Research CenterQueen's UniversityKingstonOntarioCanada
| |
Collapse
|
13
|
Fan M, Tan S, Wang W, Zhang X. Improvement in Salt Tolerance Ability of Pseudomonas putida KT2440. BIOLOGY 2024; 13:404. [PMID: 38927284 PMCID: PMC11200750 DOI: 10.3390/biology13060404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 05/25/2024] [Accepted: 05/29/2024] [Indexed: 06/28/2024]
Abstract
Pseudomonas putida KT2440 is a popular platform for bioremediation due to its robust tolerance to environmental stress and strong biodegradation capacity. Limited research on the salt tolerance of P. putida KT2440 has hindered its application. In this study, the strain KT2440 was tested to tolerate a maximum of 4% w/v NaCl cultured with minimal salts medium. Transcriptomic data in a high-salinity environment showed significant expression changes in genes in membrane components, redox processes, chemotaxis, and cellular catabolic processes. betB-encoding betaine-aldehyde dehydrogenase was identified from the transcriptome data to overexpress and enhance growth profile of the strain KT2440 in minimal salts medium containing 4% w/v NaCl. Meanwhile, screening for exogenous salt-tolerant genes revealed that the Na+/H+ antiporter EcnhaA from Escherichia coli significantly increased the growth of the strain KT2440 in 4% w/v NaCl. Then, co-expression of EcnhaA and betB (KT2440-EcnhaA-betB) increased the maximum salt tolerance of strain KT2440 to 5% w/v NaCl. Further addition of betaine and proline improved the salt tolerance of the engineered strain to 6% w/v NaCl. Finally, the engineered strain KT2440-EcnhaA-betB was able to degrade 56.70% of benzoic acid and 95.64% of protocatechuic acid in minimal salt medium containing 4% w/v NaCl in 48 h, while no biodegradation was observed in the normal strain KT2440 in the same conditions. However, the strain KT2440-EcnhaA-betB failed to degrade catechol in minimal salt medium containing 3% w/v NaCl. This study illustrated the improvement in the salt tolerance performance of Pseudomonas putida KT2440 and the feasibility of engineered strain KT2440 as a potential salt-tolerant bioremediation platform.
Collapse
Affiliation(s)
| | | | | | - Xuehong Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; (M.F.); (S.T.); (W.W.)
| |
Collapse
|
14
|
Du H, Cheng JL, Li ZY, Zhong HN, Wei S, Gu YJ, Yao CC, Zhang M, Cai QY, Zhao HM, Mo CH. Molecular insights into the catabolism of dibutyl phthalate in Pseudomonas aeruginosa PS1 based on biochemical and multi-omics approaches. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 926:171852. [PMID: 38518818 DOI: 10.1016/j.scitotenv.2024.171852] [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: 01/12/2024] [Revised: 03/19/2024] [Accepted: 03/19/2024] [Indexed: 03/24/2024]
Abstract
A comprehensive understanding of the molecular mechanisms underlying microbial catabolism of dibutyl phthalate (DBP) is still lacking. Here, we newly isolated a bacterial strain identified as Pseudomonas aeruginosa PS1 with high efficiency of DBP degradation. The degradation ratios of DBP at 100-1000 mg/L by this strain reached 80-99 % within 72 h without a lag phase. A rare DBP-degradation pathway containing two monobutyl phthalate-catabolism steps was proposed based on intermediates identified by HPLC-TOF-MS/MS. In combination with genomic and transcriptomic analyses, we identified 66 key genes involved in DBP biodegradation and revealed the genetic basis for a new complete catabolic pathway from DBP to Succinyl-CoA or Acetyl-CoA in the genus Pseudomonas for the first time. Notably, we found that a series of homologous genes in Pht and Pca clusters were simultaneously activated under DBP exposure and some key intermediate degradation related gene clusters including Pht, Pca, Xyl, Ben, and Cat exhibited a favorable coexisting pattern, which contributed the high-efficient DBP degradation ability and strong adaptability to this strain. Overall, these results broaden the knowledge of the catabolic diversity of DBP in microorganisms and enhance our understanding of the molecular mechanism underlying DBP biodegradation.
Collapse
Affiliation(s)
- Huan Du
- Guangzhou Customs Technology Center, No. 66 Huacheng Avenue, Tianhe District, Guangzhou 510623, China; Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China; Center for Statistical Science, Tsinghua University, Beijing 100084, China
| | - Ji-Liang Cheng
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China; Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, China
| | - Zhi-Yong Li
- Guangzhou Customs Technology Center, No. 66 Huacheng Avenue, Tianhe District, Guangzhou 510623, China
| | - Huai-Ning Zhong
- Guangzhou Customs Technology Center, No. 66 Huacheng Avenue, Tianhe District, Guangzhou 510623, China
| | - Shuang Wei
- Guangzhou Customs Technology Center, No. 66 Huacheng Avenue, Tianhe District, Guangzhou 510623, China
| | - Yu-Juan Gu
- Guangzhou Customs Technology Center, No. 66 Huacheng Avenue, Tianhe District, Guangzhou 510623, China
| | - Can-Can Yao
- Guangzhou Customs Technology Center, No. 66 Huacheng Avenue, Tianhe District, Guangzhou 510623, China
| | - Miaoyue Zhang
- Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, China
| | - Quan-Ying Cai
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Hai-Ming Zhao
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, China.
| | - Ce-Hui Mo
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| |
Collapse
|
15
|
Thakur M, Yadav V, Kumar Y, Pramanik A, Dubey KK. How to deal with xenobiotic compounds through environment friendly approach? Crit Rev Biotechnol 2024:1-20. [PMID: 38710611 DOI: 10.1080/07388551.2024.2336527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 03/13/2024] [Indexed: 05/08/2024]
Abstract
Every year, a huge amount of lethal compounds, such as synthetic dyes, pesticides, pharmaceuticals, hydrocarbons, etc. are mass produced worldwide, which negatively affect soil, air, and water quality. At present, pesticides are used very frequently to meet the requirements of modernized agriculture. The Food and Agriculture Organization of the United Nations (FAO) estimates that food production will increase by 80% by 2050 to keep up with the growing population, consequently pesticides will continue to play a role in agriculture. However, improper handling of these highly persistent chemicals leads to pollution of the environment and accumulation in food chain. These effects necessitate the development of technologies to eliminate or degrade these pollutants. Degradation of these compounds by physical and chemical processes is expensive and usually results in secondary compounds with higher toxicity. The biological strategies proposed for the degradation of these compounds are both cost-effective and eco-friendly. Microbes play an imperative role in the degradation of xenobiotic compounds that have toxic effects on the environment. This review on the fate of xenobiotic compounds in the environment presents cutting-edge insights and novel contributions in different fields. Microbial community dynamics in water bodies, genetic modification for enhanced pesticide degradation and the use of fungi for pharmaceutical removal, white-rot fungi's versatile ligninolytic enzymes and biodegradation potential are highlighted. Here we emphasize the factors influencing bioremediation, such as microbial interactions and carbon catabolism repression, along with a nuanced view of challenges and limitations. Overall, this review provides a comprehensive perspective on the bioremediation strategies.
Collapse
Affiliation(s)
- Mony Thakur
- Department of Microbiology, Central University of Haryana, Mahendergarh, India
| | - Vinod Yadav
- Department of Microbiology, Central University of Haryana, Mahendergarh, India
| | - Yatin Kumar
- Department of Microbiology, Central University of Haryana, Mahendergarh, India
| | - Avijit Pramanik
- Department of Microbiology, Central University of Haryana, Mahendergarh, India
| | | |
Collapse
|
16
|
Huang Y, Hu H, Zhang T, Wang W, Liu W, Tang H. Meta-omics assisted microbial gene and strain resources mining in contaminant environment. Eng Life Sci 2024; 24:2300207. [PMID: 38708415 PMCID: PMC11065330 DOI: 10.1002/elsc.202300207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 07/11/2023] [Accepted: 07/11/2023] [Indexed: 05/07/2024] Open
Abstract
Human activities have led to the release of various environmental pollutants, triggering ecological challenges. In situ, microbial communities in these contaminated environments are usually assumed to possess the potential capacity of pollutant degradation. However, the majority of genes and microorganisms in these environments remain uncharacterized and uncultured. The advent of meta-omics provided culture-independent solutions for exploring the functional genes and microorganisms within complex microbial communities. In this review, we highlight the applications and methodologies of meta-omics in uncovering of genes and microbes from contaminated environments. These findings may assist in future bioremediation research.
Collapse
Affiliation(s)
- Yiqun Huang
- State Key Laboratory of Microbial Metabolismand School of Life Sciences & BiotechnologyShanghai Jiao Tong UniversityShanghaiPeople's Republic of China
| | - Haiyang Hu
- State Key Laboratory of Microbial Metabolismand School of Life Sciences & BiotechnologyShanghai Jiao Tong UniversityShanghaiPeople's Republic of China
| | - Tingting Zhang
- China Tobacco Henan Industrial Co. Ltd.ZhengzhouPeople's Republic of China
| | - Weiwei Wang
- State Key Laboratory of Microbial Metabolismand School of Life Sciences & BiotechnologyShanghai Jiao Tong UniversityShanghaiPeople's Republic of China
| | - Wenzhao Liu
- China Tobacco Henan Industrial Co. Ltd.ZhengzhouPeople's Republic of China
| | - Hongzhi Tang
- State Key Laboratory of Microbial Metabolismand School of Life Sciences & BiotechnologyShanghai Jiao Tong UniversityShanghaiPeople's Republic of China
| |
Collapse
|
17
|
Peng C, Tang J, Zhou X, Zhou H, Zhang Y, Wang S, Wang W, Xiang W, Zhang Q, Yu X, Cai T. Quantitative proteomic analysis reveals the mechanism and key esterase of β-cypermethrin degradation in a bacterial strain from fermented food. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2024; 201:105858. [PMID: 38685237 DOI: 10.1016/j.pestbp.2024.105858] [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: 01/22/2024] [Revised: 03/01/2024] [Accepted: 03/07/2024] [Indexed: 05/02/2024]
Abstract
Beta-cypermethrin (β-CY) residues in food are an important threat to human health. Microorganisms can degrade β-CY residues during fermentation of fruits and vegetables, while the mechanism is not clear. In this study, a comprehensively investigate of the degradation mechanism of β-CY in a food microorganism was conducted based on proteomics analysis. The β-CY degradation bacteria Gordonia alkanivorans GH-1 was derived from fermented Pixian Doubanjiang. Its crude enzyme extract could degrade 77.11% of β-CY at a concentration of 45 mg/L within 24 h. Proteomics analysis revealed that the ester bond of β-CY is broken under the action of esterase to produce 3-phenoxy benzoic acid, which was further degraded by oxidoreductase and aromatic degrading enzyme. The up-regulation expression of oxidoreductase and esterase was confirmed by transcriptome and quantitative reverse transcription PCR. Meanwhile, the expression of esterase Est280 in Escherichia coli BL21 (DE3) resulted in a 48.43% enhancement in the degradation efficiency of β-CY, which confirmed that this enzyme was the key enzyme in the process of β-CY degradation. This study reveals the degradation mechanism of β-CY by microorganisms during food fermentation, providing a theoretical basis for the application of food microorganisms in β-CY residues.
Collapse
Affiliation(s)
- Chuanning Peng
- School of Food and Bioengineering, Xihua University, Chengdu 610039, Sichuan, People's Republic of China
| | - Jie Tang
- School of Food and Bioengineering, Xihua University, Chengdu 610039, Sichuan, People's Republic of China; Food Microbiology Key Laboratory of Sichuan Province, Xihua University, Chengdu 610039, Sichuan, China; Chongqing Key Laboratory of Speciality Food Co-Built by Sichuan and Chongqing, Xihua University, Chengdu 610039, China.
| | - Xuerui Zhou
- School of Food and Bioengineering, Xihua University, Chengdu 610039, Sichuan, People's Republic of China
| | - Hu Zhou
- School of Food and Bioengineering, Xihua University, Chengdu 610039, Sichuan, People's Republic of China
| | - Yingyue Zhang
- School of Food and Bioengineering, Xihua University, Chengdu 610039, Sichuan, People's Republic of China
| | - Su Wang
- School of Food and Bioengineering, Xihua University, Chengdu 610039, Sichuan, People's Republic of China
| | - Wanting Wang
- School of Food and Bioengineering, Xihua University, Chengdu 610039, Sichuan, People's Republic of China
| | - Wenliang Xiang
- School of Food and Bioengineering, Xihua University, Chengdu 610039, Sichuan, People's Republic of China; Food Microbiology Key Laboratory of Sichuan Province, Xihua University, Chengdu 610039, Sichuan, China
| | - Qing Zhang
- School of Food and Bioengineering, Xihua University, Chengdu 610039, Sichuan, People's Republic of China; Food Microbiology Key Laboratory of Sichuan Province, Xihua University, Chengdu 610039, Sichuan, China
| | - Xuan Yu
- School of Food and Bioengineering, Xihua University, Chengdu 610039, Sichuan, People's Republic of China; Food Microbiology Key Laboratory of Sichuan Province, Xihua University, Chengdu 610039, Sichuan, China
| | - Ting Cai
- School of Food and Bioengineering, Xihua University, Chengdu 610039, Sichuan, People's Republic of China; Food Microbiology Key Laboratory of Sichuan Province, Xihua University, Chengdu 610039, Sichuan, China
| |
Collapse
|
18
|
Harnpicharnchai P, Siriarchawatana P, Mayteeworakoon S, Ingsrisawang L, Likhitrattanapisal S, Eurwilaichitr L, Ingsriswang S. Interplay of xenobiotic-degrading and antibiotic-resistant microorganisms among the microbiome found in the air, handrail, and floor of the subway station. ENVIRONMENTAL RESEARCH 2024; 247:118269. [PMID: 38246293 DOI: 10.1016/j.envres.2024.118269] [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: 10/30/2023] [Revised: 01/11/2024] [Accepted: 01/18/2024] [Indexed: 01/23/2024]
Abstract
Investigating the quality of the subway environment, especially regarding antibiotic resistance genes (ARGs) and xenobiotics, conveys ecological and health impacts. In this study, compositions and relations of microorganisms harboring ARGs and xenobiotic degradation and metabolism genes (XDGs) in the Sukhumvit subway station (MRT-SKV) in Bangkok was assessed by analyzing the taxonomic and genetic diversity of the microbiome in the air and on the surfaces of floor and handrail. The major bacteria in the MRT-SKV (including Moraxella, which was abundant in the bioaerosol and handrail samples, and Staphylococcus, which was abundant in the bioaerosol samples) were found to contain both ARGs and XDGs. The co-abundance correlation network revealed notable relationships among bacteria harboring antibiotic resistance genes (ARGs) and xenobiotic degradation genes (XDGs). Significant associations were observed between ARGs linked to glycopeptide and fluoroquinolone resistance and genes associated with benzoate, styrene, and atrazine degradation pathways, as well as between ARGs related to cephamycin, cephalosporin, and MLS resistance and XDGs associated with the cytochrome P450-dependent drug metabolism pathway. These correlations suggested that selective pressure exerted by certain xenobiotics and antibiotics can simultaneously affect both ARGs and XDGs in the environment and should favor correlations and co-survival among ARG- and XDG-containing bacteria in the environments. The correlations may occur via shared mechanisms of resistance to both xenobiotics and antibiotics. Finally, different correlation pairs were seen in different niches (air, handrail, floor) of the subway environment or different geolocations. Thus, the relationship between ARG and XDG pairs most likely depends on the unique characteristics of the niches and on the prominent types of xenobiotics and antibiotics in the subway environment. The results indicated that interactions and connections between microbial communities can impact how they function. These microorganisms can have profound effects on accumulation of xenobiotics and ARGs in the MRT-SKV.
Collapse
Affiliation(s)
- Piyanun Harnpicharnchai
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Khlong Luang, Pathum Thani, Thailand
| | - Paopit Siriarchawatana
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Khlong Luang, Pathum Thani, Thailand
| | - Sermsiri Mayteeworakoon
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Khlong Luang, Pathum Thani, Thailand
| | - Lily Ingsrisawang
- Department of Statistics, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, Thailand
| | - Somsak Likhitrattanapisal
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Khlong Luang, Pathum Thani, Thailand
| | - Lily Eurwilaichitr
- National Energy Technology Center, National Science and Technology Development Agency, Khlong Luang, Pathum Thani, Thailand
| | - Supawadee Ingsriswang
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Khlong Luang, Pathum Thani, Thailand.
| |
Collapse
|
19
|
Rahman MU, Ullah MW, Shah JA, Sethupathy S, Bilal H, Abdikakharovich SA, Khan AU, Khan KA, Elboughdiri N, Zhu D. Harnessing the power of bacterial laccases for xenobiotic degradation in water: A 10-year overview. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 918:170498. [PMID: 38307266 DOI: 10.1016/j.scitotenv.2024.170498] [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: 08/07/2023] [Revised: 11/10/2023] [Accepted: 01/25/2024] [Indexed: 02/04/2024]
Abstract
Industrialization and population growth are leading to the production of significant amounts of sewage containing hazardous xenobiotic compounds. These compounds pose a threat to human and animal health, as well as the overall ecosystem. To combat this issue, chemical, physical, and biological techniques have been used to remove these contaminants from water bodies affected by human activity. Biotechnological methods have proven effective in utilizing microorganisms and enzymes, particularly laccases, to address this problem. Laccases possess versatile enzymatic characteristics and have shown promise in degrading different xenobiotic compounds found in municipal, industrial, and medical wastewater. Both free enzymes and crude enzyme extracts have demonstrated success in the biotransformation of these compounds. Despite these advancements, the widespread use of laccases for bioremediation and wastewater treatment faces challenges due to the complex composition, high salt concentration, and extreme pH often present in contaminated media. These factors negatively impact protein stability, recovery, and recycling processes, hindering their large-scale application. These issues can be addressed by focusing on large-scale production, resolving operation problems, and utilizing cutting-edge genetic and protein engineering techniques. Additionally, finding novel sources of laccases, understanding their biochemical properties, enhancing their catalytic activity and thermostability, and improving their production processes are crucial steps towards overcoming these limitations. By doing so, enzyme-based biological degradation processes can be improved, resulting in more efficient removal of xenobiotics from water systems. This review summarizes the latest research on bacterial laccases over the past decade. It covers the advancements in identifying their structures, characterizing their biochemical properties, exploring their modes of action, and discovering their potential applications in the biotransformation and bioremediation of xenobiotic pollutants commonly present in water sources.
Collapse
Affiliation(s)
- Mujeeb Ur Rahman
- Biofuels Institute, School of Emergency Management, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, PR China; Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou University of Science and Technology, Suzhou 215009, PR China
| | - Muhammad Wajid Ullah
- Biofuels Institute, School of Emergency Management, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, PR China
| | - Junaid Ali Shah
- College of Life Sciences, Jilin University, Changchun 130012, PR China; Fergana Medical Institute of Public Health Uzbekistan, Fergana 150110, Uzbekistan
| | - Sivasamy Sethupathy
- Biofuels Institute, School of Emergency Management, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, PR China; Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou University of Science and Technology, Suzhou 215009, PR China
| | - Hazart Bilal
- Department of Dermatology, The Second Affiliated Hospital of Shantou University Medical College, Shantou, PR China
| | | | - Afaq Ullah Khan
- School of Chemistry and Chemical Engineering, Jiangsu University, Zhenjiang 212013, PR China
| | - Khalid Ali Khan
- Applied College, Mahala Campus and the Unit of Bee Research and Honey Production/Research Center for Advanced Materials Science (RCAMS), King Khalid University, Abha 61413, Saudi Arabia
| | - Noureddine Elboughdiri
- Chemical Engineering Department, College of Engineering, University of Ha'il, Ha'il 81441, Saudi Arabia; Chemical Engineering Process Department, National School of Engineers Gabes, University of Gabes, Gabes 6029, Tunisia
| | - Daochen Zhu
- Biofuels Institute, School of Emergency Management, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, PR China; Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou University of Science and Technology, Suzhou 215009, PR China.
| |
Collapse
|
20
|
Farrell MV, Airkin MY, Ali TN, Altoblani ZS, Bowman CR, Diaz AAB, Faurot PF, Frausto JE, Haji SF, Hamad BA, Lively JB, Luistro DCC, Macias Y, Mathew S, McKinley KM, Nasirimoseloo S, Tran BP, Trinh AN, Shikuma NJ. Draft genome sequence of Exiguobacterium sp. strain MMG028 isolated from a salt marsh. Microbiol Resour Announc 2024; 13:e0011623. [PMID: 38358284 DOI: 10.1128/mra.00116-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 01/29/2024] [Indexed: 02/16/2024] Open
Abstract
Here, we report the draft genome sequence of Exiguobacterium sp. strain MMG028, isolated from Rose Creek, San Diego, CA, USA, assembled and analyzed by undergraduate students participating in a marine microbial genomics course. A genomic comparison suggests that MMG028 is a novel species, providing a resource for future microbiology and biotechnology investigations.
Collapse
Affiliation(s)
- Morgan V Farrell
- Department of Biology, Viral Information Institute, San Diego State University, San Diego, California, USA
| | - Mina Y Airkin
- Department of Biology, Viral Information Institute, San Diego State University, San Diego, California, USA
| | - Tatyana N Ali
- Department of Biology, Viral Information Institute, San Diego State University, San Diego, California, USA
| | - Zainalabdin S Altoblani
- Department of Biology, Viral Information Institute, San Diego State University, San Diego, California, USA
| | - Chynna R Bowman
- Department of Biology, Viral Information Institute, San Diego State University, San Diego, California, USA
| | - Abigail Anne B Diaz
- Department of Biology, Viral Information Institute, San Diego State University, San Diego, California, USA
| | - Paul F Faurot
- Department of Biology, Viral Information Institute, San Diego State University, San Diego, California, USA
| | - Joshua E Frausto
- Department of Biology, Viral Information Institute, San Diego State University, San Diego, California, USA
| | - Sazan F Haji
- Department of Biology, Viral Information Institute, San Diego State University, San Diego, California, USA
| | - Basma A Hamad
- Department of Biology, Viral Information Institute, San Diego State University, San Diego, California, USA
| | - James B Lively
- Department of Biology, Viral Information Institute, San Diego State University, San Diego, California, USA
| | - Daniella Corene C Luistro
- Department of Biology, Viral Information Institute, San Diego State University, San Diego, California, USA
| | - Yvette Macias
- Department of Biology, Viral Information Institute, San Diego State University, San Diego, California, USA
| | - Steffy Mathew
- Department of Biology, Viral Information Institute, San Diego State University, San Diego, California, USA
| | - Kayla M McKinley
- Department of Biology, Viral Information Institute, San Diego State University, San Diego, California, USA
| | - Somayeh Nasirimoseloo
- Department of Biology, Viral Information Institute, San Diego State University, San Diego, California, USA
| | - Bradley P Tran
- Department of Biology, Viral Information Institute, San Diego State University, San Diego, California, USA
| | - Amanda N Trinh
- Department of Biology, Viral Information Institute, San Diego State University, San Diego, California, USA
| | - Nicholas J Shikuma
- Department of Biology, Viral Information Institute, San Diego State University, San Diego, California, USA
| |
Collapse
|
21
|
Raj A, Kumar A, Khare PK. The looming threat of profenofos organophosphate and microbes in action for their sustainable degradation. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:14367-14387. [PMID: 38291208 DOI: 10.1007/s11356-024-32159-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 01/19/2024] [Indexed: 02/01/2024]
Abstract
Organophosphates are the most extensively used class of pesticides to deal with increasing pest diversity and produce more on limited terrestrial areas to feed the ever-expanding global population. Profenofos, an organophosphate group of non-systematic insecticides and acaricides, is used to combat aphids, cotton bollworms, tobacco budworms, beet armyworms, spider mites, and lygus bugs. Profenofos was inducted into the system as a replacement for chlorpyrifos due to its lower toxicity and half-life. It has become a significant environmental concern due to its widespread presence. It accumulates in various environmental components, contaminating food, water, and air. As a neurotoxic poison, it inhibits acetylcholinesterase receptor activity, leading to dizziness, paralysis, and pest death. It also affects other eukaryotes, such as pollinators, birds, mammals, and invertebrates, affecting ecosystem functioning. Microbes directly expose themselves to profenofos and adapt to these toxic compounds over time. Microbes use these toxic compounds as carbon and energy sources and it is a sustainable and economical method to eliminate profenofos from the environment. This article explores the studies and developments in the bioremediation of profenofos, its impact on plants, pollinators, and humans, and the policies and laws related to pesticide regulation. The goal is to raise awareness about the global threat of profenofos and the role of policymakers in managing pesticide mismanagement.
Collapse
Affiliation(s)
- Aman Raj
- Metagenomics and Secretomics Research Laboratory, Department of Botany, Dr. Harisingh Gour University (A Central University), Sagar, (M.P), -470003, India
| | - Ashwani Kumar
- Metagenomics and Secretomics Research Laboratory, Department of Botany, Dr. Harisingh Gour University (A Central University), Sagar, (M.P), -470003, India.
- Metagenomics and Secretomics Research Laboratory, Department of Botany, University of Allahabad (A Central University), Prayagraj, (UP), -211002, India.
| | - Pramod Kumar Khare
- Ecology Laboratory, Department of Botany, Dr. Harisingh Gour Vishwavidyalaya (A Central University), Madhya Pradesh, Sagar, -470003, India
| |
Collapse
|
22
|
Sillo F, Neri L, Calvo A, Zampieri E, Petruzzelli G, Ferraris I, Delledonne M, Zaldei A, Gioli B, Baraldi R, Balestrini R. Correlation between microbial communities and volatile organic compounds in an urban soil provides clues on soil quality towards sustainability of city flowerbeds. Heliyon 2024; 10:e23594. [PMID: 38205296 PMCID: PMC10776942 DOI: 10.1016/j.heliyon.2023.e23594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 12/06/2023] [Accepted: 12/07/2023] [Indexed: 01/12/2024] Open
Abstract
Soil functionality is critical to the biosphere as it provides ecosystem services relevant for a healthy planet. The soil microbial composition is significantly impacted by anthropogenic activities, including urbanization. In this context, the study of soil microorganisms associated to urban green spaces has started to be crucial toward sustainable city development. Microbes living in the soil produce and degrade volatile organic compounds (VOCs). The VOC profiles may be used to distinguish between soils with various characteristics and management practices, reflecting variations in the activity of soil microbes that use a variety of metabolic pathways. Here, a combined approach based on DNA metabarcoding and GC-MS analysis was used to evaluate the soil quality from urban flowerbeds in Prato (Tuscany, Italy) in terms of microbial biodiversity and VOC emission profiles, with the final aim of evaluating the possible correlation between composition of microbial community and VOC patterns. Results showed that VOCs in the considered soil originated from anthropic and biological activity, and significant correlations between specific microbial taxa and VOCs were detected. Overall, the study demonstrated the feasibility of the use of microbe-VOC correlation as a proxy for soil quality assessment in urban soils.
Collapse
Affiliation(s)
- Fabiano Sillo
- National Research Council, Institute for Sustainable Plant Protection, Strada delle Cacce 73, 10135 Torino, Italy
| | - Luisa Neri
- National Research Council, Institute of BioEconomy, Via P. Gobetti 101, 40129 Bologna and Via G. Caproni 8, 50145 Firenze, Italy
| | - Alice Calvo
- National Research Council, Institute for Sustainable Plant Protection, Strada delle Cacce 73, 10135 Torino, Italy
| | - Elisa Zampieri
- National Research Council, Institute for Sustainable Plant Protection, Strada delle Cacce 73, 10135 Torino, Italy
| | - Gianniantonio Petruzzelli
- National Research Council, Institute of Research on Terrestrial Ecosystems (IRET), Via Moruzzi 1, 56124 Pisa, Italy
| | - Irene Ferraris
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy
| | - Massimo Delledonne
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy
| | - Alessandro Zaldei
- National Research Council, Institute of BioEconomy, Via P. Gobetti 101, 40129 Bologna and Via G. Caproni 8, 50145 Firenze, Italy
| | - Beniamino Gioli
- National Research Council, Institute of BioEconomy, Via P. Gobetti 101, 40129 Bologna and Via G. Caproni 8, 50145 Firenze, Italy
| | - Rita Baraldi
- National Research Council, Institute of BioEconomy, Via P. Gobetti 101, 40129 Bologna and Via G. Caproni 8, 50145 Firenze, Italy
| | - Raffaella Balestrini
- National Research Council, Institute for Sustainable Plant Protection, Strada delle Cacce 73, 10135 Torino, Italy
| |
Collapse
|
23
|
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
|
24
|
Kannan P, Verma I, Banerjee B, Saleena LM. Unveiling bacterial consortium for xenobiotic biodegradation from Pichavaram mangrove forest soil: a metagenomic approach. Arch Microbiol 2023; 206:27. [PMID: 38112856 DOI: 10.1007/s00203-023-03765-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 11/17/2023] [Accepted: 11/20/2023] [Indexed: 12/21/2023]
Abstract
Pichavaram mangrove forest was established as a wetland of International Importance by Article 2.1 in April 2022 by the Ministry of Environment, Forest and Climate Change, India. Even though it is a conserved site, xenobiotic agrochemical leaching on the forest land during monsoon is inevitable. These threaten the microbial diversity in the environment. Xenobiotic degradation is achieved using bacterial consortia already acclimatised to this environment. This study aims to identify the indigenous microbial consortia able to degrade xenobiotic compounds such as fluorobenzoate, furfural, and steroids. Pichavaram mangrove metagenomic dataset was obtained by shotgun sequencing of soil DNA and processed using the automated tool SqueezeMeta. Further, the DIAMOND database provided the taxonomical classification of the microbes in each contig. With reference to the KEGG database, the selected xenobiotic degradation pathways were confirmed in the dataset. Of 1,253,029 total contigs, 1332, 72 and 1262 were involved in fluorobenzoate, furfural and steroid degradation, respectively. This study identified that microbial consortia comprising Marinobacter, Methyloceanibacter and Vibrio natriegens/Gramella sp. can degrade fluorobenzoate. While Afipia, Nitrosopumilus sp., and Phototrophicus methaneseepsis favour the degradation of furfural compound. The steroid degradation pathway possessed a plethora of bacteria belonging to the phylum Proteobacteria.
Collapse
Affiliation(s)
- Priya Kannan
- Department of Biotechnology, School of Bioengineering, College of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur, Chengalpattu District, Tamilnadu, India
| | - Ishita Verma
- Department of Biotechnology, School of Bioengineering, College of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur, Chengalpattu District, Tamilnadu, India
| | - Bhargabi Banerjee
- Department of Biotechnology, School of Bioengineering, College of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur, Chengalpattu District, Tamilnadu, India
| | - Lilly M Saleena
- Department of Biotechnology, School of Bioengineering, College of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur, Chengalpattu District, Tamilnadu, India.
| |
Collapse
|
25
|
Bhatt P, Bhatt K, Huang Y, Li J, Wu S, Chen S. Biofilm formation in xenobiotic-degrading microorganisms. Crit Rev Biotechnol 2023; 43:1129-1149. [PMID: 36170978 DOI: 10.1080/07388551.2022.2106417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 06/26/2022] [Indexed: 11/03/2022]
Abstract
The increased presence of xenobiotics affects living organisms and the environment at large on a global scale. Microbial degradation is effective for the removal of xenobiotics from the ecosystem. In natural habitats, biofilms are formed by single or multiple populations attached to biotic/abiotic surfaces and interfaces. The attachment of microbial cells to these surfaces is possible via the matrix of extracellular polymeric substances (EPSs). However, the molecular machinery underlying the development of biofilms differs depending on the microbial species. Biofilms act as biocatalysts and degrade xenobiotic compounds, thereby removing them from the environment. Quorum sensing (QS) helps with biofilm formation and is linked to the development of biofilms in natural contaminated sites. To date, scant information is available about the biofilm-mediated degradation of toxic chemicals from the environment. Therefore, we review novel insights into the impact of microbial biofilms in xenobiotic contamination remediation, the regulation of biofilms in contaminated sites, and the implications for large-scale xenobiotic compound treatment.
Collapse
Affiliation(s)
- Pankaj Bhatt
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, PR China
- Department of Agricultural & Biological Engineering, Purdue University, West Lafayette, IN, USA
| | - Kalpana Bhatt
- Department of Food Science, Purdue University, West Lafayette, IN, USA
| | - Yaohua Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, PR China
| | - Jiayi Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, PR China
| | - Siyi Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, PR China
| | - Shaohua Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, PR China
| |
Collapse
|
26
|
Ev LD, Poloni JF, Damé-Teixeira N, Arthur RA, Corralo DJ, Henz SL, DO T, Maltz M, Parolo CCF. Biofilm dysbiosis and caries activity: a surface or an individual issue? J Appl Oral Sci 2023; 31:e20230214. [PMID: 37970886 PMCID: PMC10697669 DOI: 10.1590/1678-7757-2023-0214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 08/28/2023] [Accepted: 09/19/2023] [Indexed: 11/19/2023] Open
Abstract
OBJECTIVE This study aimed to analyze the functional profile of supragingival biofilm from sound (CAs), active (CAa), and inactive (CAi) enamel caries lesions from caries-active individuals to provide insights into the diversity of biological processes regarding biofilm dysbiosis. METHODOLOGY A metatranscriptome analysis was performed in biofilm samples collected from five caries-active individuals. Total RNA was extracted, and the microbial cDNAs were obtained and sequenced (Illumina HiSeq3000). Trimmed data were submitted to the SqueezeMeta pipeline in the co-assembly mode for functional analysis and further differential gene expression analysis (DESeq2). RESULTS Bioinformatics analysis of mRNAs revealed a similar functional profile related to all analyzed conditions (CAa, CAi, and CAs). However, active and inactive surfaces share up-regulated genes (gtsA; qrtT; tqsA; pimB; EPHX1) related to virulence traits that were not overrepresented in sound surfaces. From a functional perspective, what matters most is the individual carious status rather than the surface condition. Therefore, pooling samples from various sites can be carried out using naturally developed oral biofilms but should preferably include carious surfaces. CONCLUSION Metatranscriptome data from subjects with caries activity have shown that biofilms from sound, arrested, and active lesions are similar in composition and function.
Collapse
Affiliation(s)
- Laís Daniela Ev
- Universidade Federal do Rio Grande do Sul, Faculdade de Odontologia, Departamento de Odontologia Preventiva e Social, Porto Alegre, RS, Brasil
| | - Joice Faria Poloni
- Instituto Nacional de Ciência e Tecnologia - Ciências Forense, Pontifica Universidade Católica do Rio Grande do Sul, Escola de Ciências da Saúde e da Vida, Porto Alegre, Brasil
| | - Nailê Damé-Teixeira
- Universidade de Brasília, Faculdade de Ciências da Saúde, Departamento de Odontologia, Brasília, DF, Brasil
| | - Rodrigo Alex Arthur
- Universidade Federal do Rio Grande do Sul, Faculdade de Odontologia, Departamento de Odontologia Preventiva e Social, Porto Alegre, RS, Brasil
| | - Daniela Jorge Corralo
- Universidade de Passo Fundo, Escola de Odontologia, Departamento de Odontologia, RS, Passo Fundo, Brasil
| | - Sandra Liana Henz
- Universidade Federal do Rio Grande do Sul, Faculdade de Odontologia, Departamento de Odontologia Preventiva e Social, Porto Alegre, RS, Brasil
| | - Thuy DO
- University of Leeds, School of Dentistry, Division of Oral Biology, Leeds, UK
| | - Marisa Maltz
- Universidade Federal do Rio Grande do Sul, Faculdade de Odontologia, Departamento de Odontologia Preventiva e Social, Porto Alegre, RS, Brasil
| | - Clarissa Cavalcanti Fatturi Parolo
- Universidade Federal do Rio Grande do Sul, Faculdade de Odontologia, Departamento de Odontologia Preventiva e Social, Porto Alegre, RS, Brasil
| |
Collapse
|
27
|
Gomes AFF, de Almeida LG, Cônsoli FL. Comparative Genomics of Pesticide-Degrading Enterococcus Symbionts of Spodoptera frugiperda (Lepidoptera: Noctuidae) Leads to the Identification of Two New Species and the Reappraisal of Insect-Associated Enterococcus Species. MICROBIAL ECOLOGY 2023; 86:2583-2605. [PMID: 37433981 DOI: 10.1007/s00248-023-02264-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 07/05/2023] [Indexed: 07/13/2023]
Abstract
Enterococcus species have been described as core members of the microbial community of Spodoptera frugiperda (Lepidoptera: Noctuidae) and have been previously reported as insecticide degrading agents. This study aimed to investigate the molecular composition of these microbial symbionts of S. frugiperda to better understand their association with the host and their potential for insecticide metabolization. Through phenotypic assays and comparative genomic analyses of several pesticide-degrading Enterococcus isolated from the gut of S. frugiperda larvae, we identified two new species: Enterococcus entomosocium n. sp. and Enterococcus spodopteracolus n. sp. Their identities as new species were confirmed by whole genome alignment, utilizing cut-offs of 95-96% for the average nucleotide identity (ANI) and 70% for the digital DNA: DNA hybridization (dDDH) values. The systematic positioning of these new species within the genus Enterococcus was resolved using genome-based analysis, revealing Enterococcus casseliflavus as a sister group of E. entomosocium n. sp., and Enterococcus mundtii as a sister group of E. spodopteracolus n. sp. Comparative genomic analyses of several isolates of E. entomosocium n. sp. and E. spodopteracolus n. sp. provided a better assessment of the interactions established in the symbiotic association with S. frugiperda and led to the discovery of misidentified new species of Enterococcus associated with insects. Our analyses indicated that the potential of E. entomosocium n. sp. and E. spodopteracolus n. sp. to metabolize different pesticides arises from molecular mechanisms that result in rapid evolution of new phenotypes in response to environmental stressors, in this case, the pesticides their host insect is exposed to.
Collapse
Affiliation(s)
- Ana Flávia Freitas Gomes
- Luiz de Queiroz College of Agriculture, Department of Entomology and Acarology, Insect Interactions Laboratory, University of São Paulo, Piracicaba, São Paulo, Brazil
| | - Luís Gustavo de Almeida
- Luiz de Queiroz College of Agriculture, Department of Entomology and Acarology, Insect Interactions Laboratory, University of São Paulo, Piracicaba, São Paulo, Brazil
| | - Fernando Luis Cônsoli
- Luiz de Queiroz College of Agriculture, Department of Entomology and Acarology, Insect Interactions Laboratory, University of São Paulo, Piracicaba, São Paulo, Brazil.
| |
Collapse
|
28
|
Pan L, Ding C, Deng Y, Chen H, Yang H, Wang B, Zhou Y, Wang B. Microbial degradation mechanism of historical silk revealed by proteomics and metabolomics. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2023; 15:5380-5389. [PMID: 37812415 DOI: 10.1039/d3ay01033c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Archaeological silk undergoes destructive and irreversible changes during the natural process of decay. However, in-depth studies on the influence of this biological factor are still lacking. Here, a combination of proteomics and metabolomics is proposed for the first time to explore the interaction between bacteria and historical silk during biodegradation, which provides information on changes at the molecular level of proteins and bacterial metabolites. Morphological observation revealed biofilms produced by Stenotrophomonas maltophilia and Pseudomonas alcaligenes when cultured in the stationary phase and confirmed severe deterioration of silk. Proteomics showed that S. maltophilia had an unbiased effect on silk fibroin, indicating its ability to disrupt both heavy and light chains, as well as other proteins, while P. alcaligenes showed an affinity for more disordered proteins. Analysis of bacterial metabolites showed that overall activity reduction and significant accumulation of fatty acid and phenol metabolites occurred after silk addition, suggesting that the presence of silk may inhibit the activity of an individual strain. This study provides a new insight into the microbial degradation mechanism of archaeological silk.
Collapse
Affiliation(s)
- Lindan Pan
- Institute of Textile Conservation, Zhejiang Sci-Tech University, Hangzhou 310018, China.
| | - Chuanmiao Ding
- Institute of Textile Conservation, Zhejiang Sci-Tech University, Hangzhou 310018, China.
| | - Yefeng Deng
- Institute of Textile Conservation, Zhejiang Sci-Tech University, Hangzhou 310018, China.
| | - Hao Chen
- Institute of Textile Conservation, Zhejiang Sci-Tech University, Hangzhou 310018, China.
| | - Hailiang Yang
- Key Scientific Research Base of Textile Conservation, State Administration of Cultural Heritage, China National Silk Museum, Hangzhou 310002, China
| | - Biyang Wang
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge CB2 3ER, UK
| | - Yang Zhou
- Key Scientific Research Base of Textile Conservation, State Administration of Cultural Heritage, China National Silk Museum, Hangzhou 310002, China
| | - Bing Wang
- Institute of Textile Conservation, Zhejiang Sci-Tech University, Hangzhou 310018, China.
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge CB2 3ER, UK
| |
Collapse
|
29
|
Ayub A, Ikram M, Haider A, Shahzadi I, Ul-Hamid A, Shahzadi A, Algaradah MM, Fouda AM, Nabgan W, Imran M. Enhanced Industrial Dye Degradation and Antibacterial Activity Supported by the Molecular Docking Study of Yttrium and Carbon Sphere-Doped Lanthanum Oxide Nanostructures. ACS OMEGA 2023; 8:37564-37572. [PMID: 37841132 PMCID: PMC10569003 DOI: 10.1021/acsomega.3c05938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Accepted: 09/13/2023] [Indexed: 10/17/2023]
Abstract
As the population grows, the scientific community remains focused on researching new materials, methods, and devices to ensure the availability of safe drinking water. The main aim of this research was to decrease the recombination rate of the charge carriers of La2O3 and enhance the catalytic and antimicrobial activity by employing Y/Cs- doped La2O3, respectively. In the current study, different concentrations of yttrium (Y) and a fixed amount of carbon spheres (Cs) doped into lanthanum oxide (La2O3) nanostructures (NSs) were synthesized by the coprecipitation technique. Cs are used as a cocatalyst as they have a high surface area and small size attributed to increased active sites and decreased recombination rate. Moreover, Y was further incorporated as it activates the generation of reactive oxygen species in the inhibition zone, enhancing the antibacterial activity and reducing the emission intensity. Advanced techniques were utilized to determine the structural properties, optical emission and absorption, elemental composition, and d-spacing of the synthesized samples. The reported ternary catalyst works efficiently, improving the catalytic activity and bactericidal potential. Moreover, in silico molecular docking studies, Cs-doped La2O3 and Y/Cs-doped La2O3 nanostructures toward DNA gyrase Escherichia coli showed good efficacy for antibacterial activity.
Collapse
Affiliation(s)
- Atiya Ayub
- Solar
Cell Applications Research Lab, Department of Physics, Government College University Lahore, Lahore 54000, Punjab, Pakistan
| | - Muhammad Ikram
- Solar
Cell Applications Research Lab, Department of Physics, Government College University Lahore, Lahore 54000, Punjab, Pakistan
| | - Ali Haider
- Department
of Clinical Sciences, Faculty of Veterinary and Animal Sciences, Muhammad
Nawaz Shareef, University of Agriculture, 66000 Multan, Punjab, Pakistan
| | - Iram Shahzadi
- Punjab
University College of Pharmacy, University
of the Punjab, Lahore 54000, Pakistan
| | - Anwar Ul-Hamid
- Core
Research Facilities, King Fahd University
of Petroleum & Minerals, Dhahran 31261, Saudi Arabia
| | - Anum Shahzadi
- Department
of Pharmacy, COMSATS University Islamabad,
Lahore Campus, Lahore 54000, Pakistan
| | | | - Ahmed M. Fouda
- Chemistry
Department, Faculty of Science, King Khalid
University, Abha 61413, Saudi Arabia
| | - Walid Nabgan
- Departament
d’Enginyeria Química, Universitat
Rovira i Virgili, Av
Països Catalans 26, 43007 Tarragona, Spain
| | - Muhammad Imran
- Solar
Cell Applications Research Lab, Department of Physics, Government College University Lahore, Lahore 54000, Punjab, Pakistan
| |
Collapse
|
30
|
Sharuddin SS, Ramli N, Yusoff MZM, Muhammad NAN, Ho LS, Maeda T. Insights into bacterial community metatranscriptome and metabolome in river water influenced by palm oil mill effluent final discharge. J Appl Microbiol 2023; 134:lxad219. [PMID: 37757470 DOI: 10.1093/jambio/lxad219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 09/14/2023] [Accepted: 09/22/2023] [Indexed: 09/29/2023]
Abstract
AIMS This study aimed to investigate the effect of palm oil mill effluent (POME) final discharge on the active bacterial composition, gene expression, and metabolite profiles in the receiving rivers to establish a foundation for identifying potential biomarkers for monitoring POME pollution in rivers. METHODS AND RESULTS The POME final discharge, upstream (unpolluted by POME), and downstream (effluent receiving point) parts of the rivers from two sites were physicochemically characterized. The taxonomic and gene profiles were then evaluated using de novo metatranscriptomics, while the metabolites were detected using qualitative metabolomics. A similar bacterial community structure in the POME final discharge samples from both sites was recorded, but their composition varied. Redundancy analysis showed that several families, particularly Comamonadaceae and Burkholderiaceae [Pr(>F) = 0.028], were positively correlated with biochemical oxygen demand (BOD5) and chemical oxygen demand (COD). The results also showed significant enrichment of genes regulating various metabolisms in the POME-receiving rivers, with methane, carbon fixation pathway, and amino acids among the predominant metabolisms identified (FDR < 0.05, PostFC > 4, and PPDE > 0.95). This was further validated through qualitative metabolomics, whereby amino acids were detected as the predominant metabolites. CONCLUSIONS The results suggest that genes regulating amino acid metabolism have significant potential for developing effective biomonitoring and bioremediation strategies in river water influenced by POME final discharge, fostering a sustainable palm oil industry.
Collapse
Affiliation(s)
- Siti S Sharuddin
- Department of Bioprocess Technology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, UPM Serdang, Selangor 43400, Malaysia
| | - Norhayati Ramli
- Department of Bioprocess Technology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, UPM Serdang, Selangor 43400, Malaysia
- Laboratory of Biopolymer and Derivatives, Institute of Tropical Forestry and Forest Products (INTROP), Universiti Putra Malaysia, UPM Serdang, Selangor 43400, Malaysia
| | - Mohd Z M Yusoff
- Department of Bioprocess Technology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, UPM Serdang, Selangor 43400, Malaysia
- Laboratory of Biopolymer and Derivatives, Institute of Tropical Forestry and Forest Products (INTROP), Universiti Putra Malaysia, UPM Serdang, Selangor 43400, Malaysia
| | - Nor A N Muhammad
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, UKM Bangi, Selangor 43600, Malaysia
| | - Li S Ho
- Sime Darby Plantation Technology Centre Sdn Bhd, Sime Darby Plantation, Serdang, Selangor 43400, Malaysia
| | - Toshinari Maeda
- Department of Biological Functions Engineering, Graduate School of Life Science and Systems Engineering, Kyushu Institute of Technology, 2-4 Hibikino, Wakamatsu, Kitakyushu 808-0196, Japan
| |
Collapse
|
31
|
Yeruva DK, S VM. Electrogenic engineered flow through tri-phasic wetland system for azo dye treatment: Microbial dynamics and functional metagenomics. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 334:122107. [PMID: 37369299 DOI: 10.1016/j.envpol.2023.122107] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 06/12/2023] [Accepted: 06/24/2023] [Indexed: 06/29/2023]
Abstract
Electrogenic engineered flow through tri-phasic wetland (EEFW) system based on nature-based ecological principles was studied by integrating successive biological microenvironments. The potential mechanism of the plant root-based microbial community and its functional diversity with the influence of plant-microbe-electrode synergism towards dye degradation was evaluated. The EEFW system was operated at three varied dye loads of 10, 25 and 50 mg L-1, where the results from the cumulative outlets revealed a maximum dye removal efficiency of 96%, 96.5% and 93%, respectively. Microbial community analysis depicted synergistic dependence on the plant-microbe-electrode interactions, influencing their functional diversity and metabolism towards detoxification of pollutants. The core microbial taxa enriched against the microenvironment variation were mostly associated with carbon and dye removal viz., Desulfomonile tiedjei and Rhodopseudomonas palustris in Tank 1 and Chloroflexi bacterium and Steroidobacter denitrificans in Tank 2. The degradation of polycyclic aromatic hydrocarbons, chloroalkane/chloroalkene, nitrotoluene, bisphenol, caprolactam and 1,1,1-trichloro-2,2-bis(4-chlorophenyl) ethane (DDT) were observed to be predominant in Tank 1. EEFW system could be one of the option for utilizing nature-based processes for the treatment of wastewater by self-induced bioelectrogenesis to augment process efficiency.
Collapse
Affiliation(s)
- Dileep Kumar Yeruva
- Bioengineering and Environmental Science Lab, Department of Energy and Environmental Engineering, CSIR-Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad, 500 007, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Venkata Mohan S
- Bioengineering and Environmental Science Lab, Department of Energy and Environmental Engineering, CSIR-Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad, 500 007, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, 201002, India.
| |
Collapse
|
32
|
Baćmaga M, Wyszkowska J, Borowik A, Kucharski J. Bacteria, Fungi, and Enzymes in Soil Treated with Sulcotrione and Terbuthylazine. Int J Mol Sci 2023; 24:14469. [PMID: 37833917 PMCID: PMC10572980 DOI: 10.3390/ijms241914469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 09/18/2023] [Accepted: 09/22/2023] [Indexed: 10/15/2023] Open
Abstract
Soil's biological equilibrium, disturbed by the uncontrolled penetration of pesticides, can be restored by the activity of native microorganisms, which show abilities in neutralizing these xenobiotics. Therefore, this research is necessary in the search for new microorganisms used in the process of the bioremediation of contaminated soils. The aim of this study was to evaluate the effects of the herbicides, Sulcogan 300 SC, Tezosar 500 SC, and Sulcotrek 500 SC, applied to soil at the manufacturers' recommended dosage as well as 10-fold higher, on the abundance of microorganisms, the diversity and structure of bacterial and fungal communities, the activity of soil enzymes, and the growth and development of Zea mays L. It was found that herbicides in contaminating amounts stimulated the proliferation of organotrophic bacteria and inhibited the growth of fungi. Organotrophic bacteria and actinobacteria were represented by K-strategies and fungi by r-strategies. Bacteria belonging to the phylum, Actinobacteriota, represented by the genus, Cellulosimicrobium, were most abundant in the soil, while among the fungi, it was the phylum, Ascomycota, represented by the genus, Humicola and Chaetomium. The herbicides decreased urease activity while increasing arylsulfatase and acid phosphatase activity. They had a positive effect on the growth and development of Zea mays L., as evidenced by an increase in the values of the plant tolerance index (TI) and the maize leaf greenness index (SPAD). The results indicate that soil microorganisms and enzymes are suitable indicators reflecting the quality of herbicide-treated soil.
Collapse
Affiliation(s)
| | - Jadwiga Wyszkowska
- Department of Soil Science and Microbiology, Faculty of Agriculture and Forestry, University of Warmia and Mazury in Olsztyn, 10-719 Olsztyn, Poland; (M.B.); (A.B.); (J.K.)
| | | | | |
Collapse
|
33
|
De Filippis F, Bonelli M, Bruno D, Sequino G, Montali A, Reguzzoni M, Pasolli E, Savy D, Cangemi S, Cozzolino V, Tettamanti G, Ercolini D, Casartelli M, Caccia S. Plastics shape the black soldier fly larvae gut microbiome and select for biodegrading functions. MICROBIOME 2023; 11:205. [PMID: 37705113 PMCID: PMC10500907 DOI: 10.1186/s40168-023-01649-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 07/16/2023] [Indexed: 09/15/2023]
Abstract
BACKGROUND In the last few years, considerable attention has been focused on the plastic-degrading capability of insects and their gut microbiota in order to develop novel, effective, and green strategies for plastic waste management. Although many analyses based on 16S rRNA gene sequencing are available, an in-depth analysis of the insect gut microbiome to identify genes with plastic-degrading potential is still lacking. RESULTS In the present work, we aim to fill this gap using Black Soldier Fly (BSF) as insect model. BSF larvae have proven capability to efficiently bioconvert a wide variety of organic wastes but, surprisingly, have never been considered for plastic degradation. BSF larvae were reared on two widely used plastic polymers and shotgun metagenomics was exploited to evaluate if and how plastic-containing diets affect composition and functions of the gut microbial community. The high-definition picture of the BSF gut microbiome gave access for the first time to the genomes of culturable and unculturable microorganisms in the gut of insects reared on plastics and revealed that (i) plastics significantly shaped bacterial composition at species and strain level, and (ii) functions that trigger the degradation of the polymer chains, i.e., DyP-type peroxidases, multicopper oxidases, and alkane monooxygenases, were highly enriched in the metagenomes upon exposure to plastics, consistently with the evidences obtained by scanning electron microscopy and 1H nuclear magnetic resonance analyses on plastics. CONCLUSIONS In addition to highlighting that the astonishing plasticity of the microbiota composition of BSF larvae is associated with functional shifts in the insect microbiome, the present work sets the stage for exploiting BSF larvae as "bioincubators" to isolate microbial strains and enzymes for the development of innovative plastic biodegradation strategies. However, most importantly, the larvae constitute a source of enzymes to be evolved and valorized by pioneering synthetic biology approaches. Video Abstract.
Collapse
Affiliation(s)
- Francesca De Filippis
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
- Task Force on Microbiome Studies, University of Naples Federico II, Naples, Italy
| | - Marco Bonelli
- Department of Biosciences, University of Milan, Milan, Italy
| | - Daniele Bruno
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Giuseppina Sequino
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Aurora Montali
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Marcella Reguzzoni
- Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | - Edoardo Pasolli
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
- Task Force on Microbiome Studies, University of Naples Federico II, Naples, Italy
| | - Davide Savy
- Interdepartmental Research Centre of Nuclear Magnetic Resonance for the Environment, Agri-Food and New Materials (CERMANU), University of Naples Federico II, Portici, Italy
| | - Silvana Cangemi
- Interdepartmental Research Centre of Nuclear Magnetic Resonance for the Environment, Agri-Food and New Materials (CERMANU), University of Naples Federico II, Portici, Italy
| | - Vincenza Cozzolino
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
- Interdepartmental Research Centre of Nuclear Magnetic Resonance for the Environment, Agri-Food and New Materials (CERMANU), University of Naples Federico II, Portici, Italy
| | - Gianluca Tettamanti
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
- Interuniversity Center for Studies on Bioinspired Agro-Environmental Technology (BAT Center), University of Naples Federico II, Portici, Italy
| | - Danilo Ercolini
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy.
- Task Force on Microbiome Studies, University of Naples Federico II, Naples, Italy.
| | - Morena Casartelli
- Department of Biosciences, University of Milan, Milan, Italy.
- Interuniversity Center for Studies on Bioinspired Agro-Environmental Technology (BAT Center), University of Naples Federico II, Portici, Italy.
| | - Silvia Caccia
- Task Force on Microbiome Studies, University of Naples Federico II, Naples, Italy.
- Department of Biosciences, University of Milan, Milan, Italy.
| |
Collapse
|
34
|
Bharathi SD, Dilshani A, Rishivanthi S, Khaitan P, Vamsidhar A, Jacob S. Resource Recycling, Recovery, and Xenobiotic Remediation from E-wastes Through Biofilm Technology: A Review. Appl Biochem Biotechnol 2023; 195:5669-5692. [PMID: 35796946 DOI: 10.1007/s12010-022-04055-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/26/2022] [Indexed: 11/02/2022]
Abstract
Around 50 million tonnes of electronic waste has been generated globally per year, causing an environmental hazard and negative effects on human health, such as infertility and thyroid disorders in adults, endocrine and neurological damage in both animals and humans, and impaired mental and physical development in children. Out of that, only 15% is recycled each year and the remaining is disposed of in a landfill, illegally traded or burned, and treated in a sub-standard way. The processes of recycling are challenged by the presence of brominated flame retardants. The different recycling technologies such as the chemical and mechanical methods have been well studied, while the most promising approach is the biological method. The process of utilizing microbes to decontaminate and degrade a wide range of pollutants into harmless products is known as bioremediation and it is an eco-friendly, cost-effective, and sustainable method. The bioremediation process is significantly aided by biofilm communities attached to electronic waste because they promote substrate bioavailability, metabolite transfer, and cell viability, all of which accelerate bioleaching and biodegradation. Microbes existing in biofilm mode relatable to free-floating planktonic cells are advantageous of bioremediation due to their tolerant ability to environmental stress and pollutants through diverse catabolic pathways. This article discusses the harmful effects of electronic waste and its management using biological strategies especially biofilm-forming communities for resource recovery.
Collapse
Affiliation(s)
- Sundaram Deepika Bharathi
- Department of Biotechnology, School of Bioengineering, College of Engineering and Technology, Faculty of Engineering and Technology, SRM Institute of Science and Technology, SRM Nagar, Kattankulathur, Chengalpattu Dist., 603203, Tamil Nadu, India
| | - Aswin Dilshani
- Department of Biotechnology, School of Bioengineering, College of Engineering and Technology, Faculty of Engineering and Technology, SRM Institute of Science and Technology, SRM Nagar, Kattankulathur, Chengalpattu Dist., 603203, Tamil Nadu, India
| | - Srinivasan Rishivanthi
- Department of Biotechnology, School of Bioengineering, College of Engineering and Technology, Faculty of Engineering and Technology, SRM Institute of Science and Technology, SRM Nagar, Kattankulathur, Chengalpattu Dist., 603203, Tamil Nadu, India
| | - Pratham Khaitan
- Department of Biotechnology, School of Bioengineering, College of Engineering and Technology, Faculty of Engineering and Technology, SRM Institute of Science and Technology, SRM Nagar, Kattankulathur, Chengalpattu Dist., 603203, Tamil Nadu, India
| | - Adhinarayan Vamsidhar
- Department of Biotechnology, School of Bioengineering, College of Engineering and Technology, Faculty of Engineering and Technology, SRM Institute of Science and Technology, SRM Nagar, Kattankulathur, Chengalpattu Dist., 603203, Tamil Nadu, India
| | - Samuel Jacob
- Department of Biotechnology, School of Bioengineering, College of Engineering and Technology, Faculty of Engineering and Technology, SRM Institute of Science and Technology, SRM Nagar, Kattankulathur, Chengalpattu Dist., 603203, Tamil Nadu, India.
| |
Collapse
|
35
|
Jin Y, Chi J, LoMonaco K, Boon A, Gu H. Recent Review on Selected Xenobiotics and Their Impacts on Gut Microbiome and Metabolome. Trends Analyt Chem 2023; 166:117155. [PMID: 37484879 PMCID: PMC10361410 DOI: 10.1016/j.trac.2023.117155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
As it is well known, the gut is one of the primary sites in any host for xenobiotics, and the many microbial metabolites responsible for the interactions between the gut microbiome and the host. However, there is a growing concern about the negative impacts on human health induced by toxic xenobiotics. Metabolomics, broadly including lipidomics, is an emerging approach to studying thousands of metabolites in parallel. In this review, we summarized recent advancements in mass spectrometry (MS) technologies in metabolomics. In addition, we reviewed recent applications of MS-based metabolomics for the investigation of toxic effects of xenobiotics on microbial and host metabolism. It was demonstrated that metabolomics, gut microbiome profiling, and their combination have a high potential to identify metabolic and microbial markers of xenobiotic exposure and determine its mechanism. Further, there is increasing evidence supporting that reprogramming the gut microbiome could be a promising approach to the intervention of xenobiotic toxicity.
Collapse
Affiliation(s)
- Yan Jin
- Center for Translational Science, Florida International University, Port St. Lucie, FL 34987, USA
| | - Jinhua Chi
- Center for Translational Science, Florida International University, Port St. Lucie, FL 34987, USA
| | - Kaelene LoMonaco
- Center for Translational Science, Florida International University, Port St. Lucie, FL 34987, USA
| | - Alexandria Boon
- Center for Translational Science, Florida International University, Port St. Lucie, FL 34987, USA
| | - Haiwei Gu
- Center for Translational Science, Florida International University, Port St. Lucie, FL 34987, USA
| |
Collapse
|
36
|
Partipilo M, Whittaker JJ, Pontillo N, Coenradij J, Herrmann A, Guskov A, Slotboom DJ. Biochemical and structural insight into the chemical resistance and cofactor specificity of the formate dehydrogenase from Starkeya novella. FEBS J 2023; 290:4238-4255. [PMID: 37213112 DOI: 10.1111/febs.16871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 05/04/2023] [Accepted: 05/19/2023] [Indexed: 05/23/2023]
Abstract
Formate dehydrogenases (Fdhs) mediate the oxidation of formate to carbon dioxide and concomitant reduction of nicotinamide adenine dinucleotide (NAD+ ). The low cost of the substrate formate and importance of the product NADH as a cellular source of reducing power make this reaction attractive for biotechnological applications. However, the majority of Fdhs are sensitive to inactivation by thiol-modifying reagents. In this study, we report a chemically resistant Fdh (FdhSNO ) from the soil bacterium Starkeya novella strictly specific for NAD+ . We present its recombinant overproduction, purification and biochemical characterization. The mechanistic basis of chemical resistance was found to be a valine in position 255 (rather than a cysteine as in other Fdhs) preventing the inactivation by thiol-modifying compounds. To further improve the usefulness of FdhSNO as for generating reducing power, we rationally engineered the protein to reduce the coenzyme nicotinamide adenine dinucleotide phosphate (NADP+ ) with better catalytic efficiency than NAD+ . The single mutation D221Q enabled the reduction of NADP+ with a catalytic efficiency kCAT /KM of 0.4 s-1 ·mm-1 at 200 mm formate, while a quadruple mutant (A198G/D221Q/H379K/S380V) resulted in a fivefold increase in catalytic efficiency for NADP+ compared with the single mutant. We determined the cofactor-bound structure of the quadruple mutant to gain mechanistic evidence behind the improved specificity for NADP+ . Our efforts to unravel the key residues for the chemical resistance and cofactor specificity of FdhSNO may lead to wider use of this enzymatic group in a more sustainable (bio)manufacture of value-added chemicals, as for instance the biosynthesis of chiral compounds.
Collapse
Affiliation(s)
- Michele Partipilo
- Department of Biochemistry, Groningen Institute of Biomolecular Sciences & Biotechnology, University of Groningen, The Netherlands
| | - Jacob J Whittaker
- Department of Biochemistry, Groningen Institute of Biomolecular Sciences & Biotechnology, University of Groningen, The Netherlands
| | - Nicola Pontillo
- Department of Biochemistry, Groningen Institute of Biomolecular Sciences & Biotechnology, University of Groningen, The Netherlands
- Polymer Chemistry and Bioengineering, Zernike Institute for Advanced Materials, Groningen, The Netherlands
| | - Jelmer Coenradij
- Department of Biochemistry, Groningen Institute of Biomolecular Sciences & Biotechnology, University of Groningen, The Netherlands
| | - Andreas Herrmann
- Polymer Chemistry and Bioengineering, Zernike Institute for Advanced Materials, Groningen, The Netherlands
- DWI-Leibniz Institute for Interactive Materials, Aachen, Germany
- Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Germany
| | - Albert Guskov
- Department of Biochemistry, Groningen Institute of Biomolecular Sciences & Biotechnology, University of Groningen, The Netherlands
| | - Dirk Jan Slotboom
- Department of Biochemistry, Groningen Institute of Biomolecular Sciences & Biotechnology, University of Groningen, The Netherlands
| |
Collapse
|
37
|
Zaghloul HAH, El Halfawy NM. Whole genome analyses of toxicants tolerance genes of Apis mellifera gut-derived Enterococcus faecium strains. BMC Genomics 2023; 24:479. [PMID: 37620768 PMCID: PMC10463970 DOI: 10.1186/s12864-023-09590-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 08/15/2023] [Indexed: 08/26/2023] Open
Abstract
BACKGROUND Because of its social nature, the honeybee is regularly exposed to environmental toxicants such as heavy metals and xenobiotics. These toxicants are known to exert strong selective pressure on the gut microbiome's structure and diversity. For example, resistant microbial members are more likely to dominate in maintaining a stable microbiome, which is critical for bee health. Therefore, the aim of this study was to examine the Enterococcus faecium strains isolated from bee guts for their in vitro growth and tolerability to diverse heavy metals and xenobiotics. An additional aim was to analyze the genomes of E. faecium isolates to assess the molecular bases of resistance and compare them with E. faecium species isolated from other environmental sources. RESULTS The E. faecium bee isolates were able to tolerate high levels (up to 200 mg/L) of toxicants, including cadmium, zinc, benzoate, phenol and hexane. Moreover, the isolates could tolerate toluene and copper at up to 100 mg/L. The genome of E. faecium Am5, isolated from the larval stage of Apis mellifera gut, was about 2.7 Mb in size, had a GC content of 37.9% and 2,827 predicted coding sequences. Overall, the Am5 genome features were comparable with previously sequenced bee-gut isolates, E. faecium Am1, Bee9, SM21, and H7. The genomes of the bee isolates provided insight into the observed heavy metal tolerance. For example, heavy metal tolerance and/or regulation genes were present, including czcD (cobalt/zinc/cadmium resistance), cadA (exporting ATPase), cutC (cytoplasmic copper homeostasis) and zur (zinc uptake regulation). Additionally, genes associated with nine KEGG xenobiotic biodegradation pathways were detected, including γ-hexachlorocyclohexane, benzoate, biphenyl, bisphenol A, tetrachloroethene, 1,4-dichlorobenzene, ethylbenzene, trinitrotoluene and caprolactam. Interestingly, a comparative genomics study demonstrated the conservation of toxicant resistance genes across a variety of E. faecium counterparts isolated from other environmental sources such as non-human mammals, humans, avians, and marine animals. CONCLUSIONS Honeybee gut-derived E. faecium strains can tolerate a variety of heavy metals. Moreover, their genomes encode many xenobiotic biodegradation pathways. Further research is required to examine E. faecium strains potential to boost host resistance to environmental toxins.
Collapse
Affiliation(s)
- Heba A H Zaghloul
- Department of Botany and Microbiology, Faculty of Science, Alexandria University, Moharam Bek 21511, Alexandria, Egypt
| | - Nancy M El Halfawy
- Department of Botany and Microbiology, Faculty of Science, Alexandria University, Moharam Bek 21511, Alexandria, Egypt.
| |
Collapse
|
38
|
Ascandari A, Aminu S, Safdi NEH, El Allali A, Daoud R. A bibliometric analysis of the global impact of metaproteomics research. Front Microbiol 2023; 14:1217727. [PMID: 37476667 PMCID: PMC10354264 DOI: 10.3389/fmicb.2023.1217727] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 06/20/2023] [Indexed: 07/22/2023] Open
Abstract
Background Metaproteomics is a subfield in meta-omics that is used to characterize the proteome of a microbial community. Despite its importance and the plethora of publications in different research area, scientists struggle to fully comprehend its functional impact on the study of microbiomes. In this study, bibliometric analyses are used to evaluate the current state of metaproteomic research globally as well as evaluate the specific contribution of Africa to this burgeoning research area. In this study, we use bibliometric analyses to evaluate the current state of metaproteomic research globally, identify research frontiers and hotspots, and further predict future trends in metaproteomics. The specific contribution of Africa to this research area was evaluated. Methods Relevant documents from 2004 to 2022 were extracted from the Scopus database. The documents were subjected to bibliometric analyses and visualization using VOS viewer and Biblioshiny package in R. Factors such as the trends in publication, country and institutional cooperation networks, leading scientific journals, author's productivity, and keywords analyses were conducted. The African publications were ranked using Field-Weighted Citation Impact (FWCI) scores. Results A total of 1,138 documents were included and the number of publications increased drastically from 2004 to 2022 with more publications (170) reported in 2021. In terms of publishers, Frontiers in Microbiology had the highest number of total publications (62). The United States of America (USA), Germany, China, and Canada, together with other European countries were the most productive. Institution-wise, the Helmholtz Zentrum für Umweltforschung, Germany had more publications while Max Plank Institute had the highest total collaborative link strength. Jehmlich N. was the most productive author whereas Hettich RL had the highest h-index of 63. Regarding Africa, only 2.2% of the overall publications were from the continent with more publication outputs from South Africa. More than half of the publications from the continent had an FWCI score ≥ 1. Conclusion The scientific outputs of metaproteomics are rapidly evolving with developed countries leading the way. Although Africa showed prospects for future progress, this could only be accelerated by providing funding, increased collaborations, and mentorship programs.
Collapse
Affiliation(s)
- AbdulAziz Ascandari
- African Genome Center, Mohammed VI Polytechnic University, Ben Guerir, Morocco
| | - Suleiman Aminu
- African Genome Center, Mohammed VI Polytechnic University, Ben Guerir, Morocco
- Department of Biochemistry, Ahmadu Bello University, Zaria, Nigeria
| | - Nour El Houda Safdi
- African Genome Center, Mohammed VI Polytechnic University, Ben Guerir, Morocco
| | - Achraf El Allali
- African Genome Center, Mohammed VI Polytechnic University, Ben Guerir, Morocco
| | - Rachid Daoud
- African Genome Center, Mohammed VI Polytechnic University, Ben Guerir, Morocco
| |
Collapse
|
39
|
Khan A, Chen S, Fatima S, Ahamad L, Siddiqui MA. Biotechnological Tools to Elucidate the Mechanism of Plant and Nematode Interactions. PLANTS (BASEL, SWITZERLAND) 2023; 12:2387. [PMID: 37376010 DOI: 10.3390/plants12122387] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 06/16/2023] [Accepted: 06/17/2023] [Indexed: 06/29/2023]
Abstract
Plant-parasitic nematodes (PPNs) pose a threat to global food security in both the developed and developing worlds. PPNs cause crop losses worth a total of more than USD 150 billion worldwide. The sedentary root-knot nematodes (RKNs) also cause severe damage to various agricultural crops and establish compatible relationships with a broad range of host plants. This review aims to provide a broad overview of the strategies used to identify the morpho-physiological and molecular events that occur during RKN parasitism. It describes the most current developments in the transcriptomic, proteomic, and metabolomic strategies of nematodes, which are important for understanding compatible interactions of plants and nematodes, and several strategies for enhancing plant resistance against RKNs. We will highlight recent rapid advances in molecular strategies, such as gene-silencing technologies, RNA interference (RNAi), and small interfering RNA (siRNA) effector proteins, that are leading to considerable progress in understanding the mechanism of plant-nematode interactions. We also take into account genetic engineering strategies, such as targeted genome editing techniques, the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR associated protein 9 (Cas9) (CRISPR/Cas-9) system, and quantitative trait loci (QTL), to enhance the resistance of plants against nematodes.
Collapse
Affiliation(s)
- Arshad Khan
- Department of Botany, Aligarh Muslim University, Aligarh 202002, India
| | - Shaohua Chen
- National Key Laboratory of Green Pesticide, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Saba Fatima
- Department of Botany, Aligarh Muslim University, Aligarh 202002, India
| | - Lukman Ahamad
- Department of Botany, Aligarh Muslim University, Aligarh 202002, India
| | | |
Collapse
|
40
|
Maqsood Q, Sumrin A, Waseem R, Hussain M, Imtiaz M, Hussain N. Bioengineered microbial strains for detoxification of toxic environmental pollutants. ENVIRONMENTAL RESEARCH 2023; 227:115665. [PMID: 36907340 DOI: 10.1016/j.envres.2023.115665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 03/05/2023] [Accepted: 03/08/2023] [Indexed: 05/08/2023]
Abstract
Industrialization and other anthropogenic human activities pose significant environmental risks. As a result of the hazardous pollution, numerous living organisms may suffer from undesirable diseases in their separate habitats. Bioremediation, which removes hazardous compounds from the environment using microbes or their biologically active metabolites, is one of the most successful remediation approaches. According to the United Nations Environment Program (UNEP), deteriorating soil health negatively impacts food security and human health over time. Soil health restoration is critical right now. Microbes are widely known for their importance in cleaning up toxins present in the soil, such as heavy metals, pesticides, and hydrocarbons. However, the capacity of local bacteria to digest these pollutants is limited, and the process takes an extended time. Genetically modified organisms (GMOs), whose altered metabolic pathways promote the over-secretion of a variety of proteins favorable to the bioremediation process, can speed up the breakdown process. The need for remediation procedures, degrees of soil contamination, site circumstances, broad adoptions, and numerous possibilities occurring at various cleaning stages are all studied in detail. Massive efforts to restore contaminated soils have also resulted in severe issues. This review focuses on the enzymatic removal of hazardous pollutants from the environment, such as pesticides, heavy metals, dyes, and plastics. There are also in-depth assessments of present discoveries and future plans for efficient enzymatic degradation of hazardous pollutants.
Collapse
Affiliation(s)
- Quratulain Maqsood
- Center for Applied Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Aleena Sumrin
- Center for Applied Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Rafia Waseem
- Center for Applied Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Maria Hussain
- Center for Applied Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Mehwish Imtiaz
- Center for Applied Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Nazim Hussain
- Center for Applied Molecular Biology, University of the Punjab, Lahore, Pakistan.
| |
Collapse
|
41
|
Li B, Xu D, Zhou X, Yin Y, Feng L, Liu Y, Zhang L. Environmental behaviors of emerging contaminants in freshwater ecosystem dominated by submerged plants: A review. ENVIRONMENTAL RESEARCH 2023; 227:115709. [PMID: 36933641 DOI: 10.1016/j.envres.2023.115709] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 02/25/2023] [Accepted: 03/15/2023] [Indexed: 05/08/2023]
Abstract
Persistent exposure of emerging contaminants (ECs) in freshwater ecosystem has initiated intense global concerns. Freshwater ecosystem dominated by submerged plants (SP-FES) has been widely constructed to control eutrophic water. However, the environmental behaviors (e.g. migration, transformation, and degradation) of ECs in SP-FES have rarely been concerned and summarized. This review briefly introduced the sources of ECs, the pathways of ECs entering into SP-FES, and the constituent elements of SP-FES. And then the environmental behaviors of dissolved ECs and refractory solid ECs in SP-FES were comprehensively summarized, and the feasibility of removing ECs from SP-FES was critically evaluated. Finally, the challenges and perspectives on the future development for ECs removal from SP-FES were prospected, giving possible research gaps and key directions. This review will provide theoretical and technical support for the effective removal of ECs in freshwater ecosystem, especially in SP-FES.
Collapse
Affiliation(s)
- Benhang Li
- Beijing Key Lab for Source Control Technology of Water Pollution, Engineering Research Center for Water Pollution Source Control and Eco-remediation, Beijing Forestry University, Beijing, 100083, China; School of Energy and Environmental Engineering, Hebei University of Technology, Tianjin 300401, China
| | - Dandan Xu
- Beijing Key Lab for Source Control Technology of Water Pollution, Engineering Research Center for Water Pollution Source Control and Eco-remediation, Beijing Forestry University, Beijing, 100083, China
| | - Xiaohong Zhou
- Beijing Key Lab for Source Control Technology of Water Pollution, Engineering Research Center for Water Pollution Source Control and Eco-remediation, Beijing Forestry University, Beijing, 100083, China
| | - Yijun Yin
- Beijing Key Lab for Source Control Technology of Water Pollution, Engineering Research Center for Water Pollution Source Control and Eco-remediation, Beijing Forestry University, Beijing, 100083, China
| | - Li Feng
- Beijing Key Lab for Source Control Technology of Water Pollution, Engineering Research Center for Water Pollution Source Control and Eco-remediation, Beijing Forestry University, Beijing, 100083, China
| | - Yongze Liu
- Beijing Key Lab for Source Control Technology of Water Pollution, Engineering Research Center for Water Pollution Source Control and Eco-remediation, Beijing Forestry University, Beijing, 100083, China
| | - Liqiu Zhang
- Beijing Key Lab for Source Control Technology of Water Pollution, Engineering Research Center for Water Pollution Source Control and Eco-remediation, Beijing Forestry University, Beijing, 100083, China.
| |
Collapse
|
42
|
Hassan S, Ganai BA. Deciphering the recent trends in pesticide bioremediation using genome editing and multi-omics approaches: a review. World J Microbiol Biotechnol 2023; 39:151. [PMID: 37029313 DOI: 10.1007/s11274-023-03603-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 04/03/2023] [Indexed: 04/09/2023]
Abstract
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.
Collapse
Affiliation(s)
- Shahnawaz Hassan
- Department of Environmental Science, University of Kashmir, Srinagar, 190006, India.
| | - Bashir Ahmad Ganai
- Centre of Research for Development, University of Kashmir, Srinagar, 190006, India.
| |
Collapse
|
43
|
Singh VK, Gunasekaran P, Kumari M, Krishnan D, Ramachandran VK. Animal sourced biopolymer for mitigating xenobiotics and hazardous materials. PHYSICAL SCIENCES REVIEWS 2023. [DOI: 10.1515/psr-2022-0221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2023]
Abstract
Abstract
Over the past several decades, xenobiotic chemicals have badly affected the environment including human health, ecosystem and environment. Animal-sourced biopolymers have been employed for the removal of heavy metals and organic dyes from the contaminated soil and waste waters. Animal-sourced biopolymers are biocompatible, cost-effective, eco-friendly, and sustainable in nature which make them a favorable choice for the mitigation of xenobiotic and hazardous compounds. Chitin/chitosan, collagen, gelatin, keratin, and silk fibroin-based biopolymers are the most commonly used biopolymers. This chapter reviews the current challenge faced in applying these animal-based biopolymers in eliminating/neutralizing various recalcitrant chemicals and dyes from the environment. This chapter ends with the discussion on the recent advancements and future development in the employability of these biopolymers in such environmental applications.
Collapse
Affiliation(s)
- Vipendra Kumar Singh
- School of Biosciences and Bioengineering , Indian Institute of Technology Mandi , VPO Kamand , Mandi , Himachal Pradesh , India
| | - Priya Gunasekaran
- Department of Biotechnology , College of Science and Humanities, SRM Institute of Science and Technology , Ramapuram , Chennai , Tamil Nadu , India
| | - Medha Kumari
- Brainology Research Fellow, Neuroscience and Microplastic Lab , Brainology Scientific Academy of Jharkhand , Ranchi , Jharkhand , India
| | - Dolly Krishnan
- Secretary cum Founder Director, Research Wing , Brainology Scientific Academy of Jharkhand , Ranchi , Jharkhand , India
| | - Vinoth Kumar Ramachandran
- Department of Biotechnology , College of Science and Humanities, SRM Institute of Science and Technology , Ramapuram , Chennai , Tamil Nadu , India
| |
Collapse
|
44
|
Chaudhari YS, Kumar P, Soni S, Gacem A, Kumar V, Singh S, Yadav VK, Dawane V, Piplode S, Jeon BH, Ibrahium HA, Hakami RA, Alotaibi MT, Abdellattif MH, Cabral-Pinto MMS, Yadav P, Yadav KK. An inclusive outlook on the fate and persistence of pesticides in the environment and integrated eco-technologies for their degradation. Toxicol Appl Pharmacol 2023; 466:116449. [PMID: 36924898 DOI: 10.1016/j.taap.2023.116449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 02/28/2023] [Accepted: 03/02/2023] [Indexed: 03/17/2023]
Abstract
Intensive and inefficient exploitation of pesticides through modernized agricultural practices has caused severe pesticide contamination problems to the environment and become a crucial problem over a few decades. Due to their highly toxic and persistent properties, they affect and get accumulated in non-target organisms, including microbes, algae, invertebrates, plants as well as humans, and cause severe issues. Considering pesticide problems as a significant issue, researchers have investigated several approaches to rectify the pesticide contamination problems. Several analyses have provided an extensive discussion on pesticide degradation but using specific technology for specific pesticides. However, in the middle of this time, cleaner techniques are essential for reducing pesticide contamination problems safely and environmentally friendly. As per the research findings, no single research finding provides concrete discussion on cleaner tactics for the remediation of contaminated sites. Therefore, in this review paper, we have critically discussed cleaner options for dealing with pesticide contamination problems as well as their advantages and disadvantages have also been reviewed. As evident from the literature, microbial remediation, phytoremediation, composting, and photocatalytic degradation methods are efficient and sustainable and can be used for treatment at a large scale in engineered systems and in situ. However, more study on the bio-integrated system is required which may be more effective than existing technologies.
Collapse
Affiliation(s)
- Yogesh S Chaudhari
- Department of Microbiology, K. J. Somaiya College of Arts, Commerce, and Science, Kopargaon, Maharashtra 423601, India
| | - Pankaj Kumar
- Department of Environmental Science, Parul Institute of Applied Sciences, Parul University, Vadodara, Gujarat 391760, India.
| | - Sunil Soni
- School of Environment and Sustainable Development, Central University of Gujarat, Gandhinagar, Gujarat 382030, India
| | - Amel Gacem
- Department of Physics, Faculty of Sciences, University 20 Août 1955, Skikda, Algeria
| | - Vinay Kumar
- Department of Environmental Science, Babasaheb Bhimrao Ambedkar University, Lucknow, Uttar Pradesh 226025, India
| | - Snigdha Singh
- School of Environment and Sustainable Development, Central University of Gujarat, Gandhinagar, Gujarat 382030, India
| | - Virendra Kumar Yadav
- Department of Biosciences, School of Liberal Arts and Sciences, Mody University, Lakshmangarh, Sikar 332311, Rajasthan, India
| | - Vinars Dawane
- Department of Microbiology and Biotechnology, Sardar Vallabh Bhai Patel College Mandleshwar, Madhya Pradesh 451221, India
| | - Satish Piplode
- Department of Chemistry, SBS Government PG College, Pipariya, Hoshangabad, Madhya Pradesh 461775, India
| | - Byong-Hun Jeon
- Department of Earth Resources & Environmental Engineering, Hanyang University, 222-Wangsimni-ro, Seongdong-gu, Seoul 04763, Republic of Korea
| | - Hala A Ibrahium
- Biology Department, Faculty of Science, King Khalid University, Abha 61413, Saudi Arabia; Department of Semi Pilot Plant, Nuclear Materials Authority, P.O. Bo x 530, El Maadi, Egypt
| | - Rabab A Hakami
- Chemistry Department, Faculty of Science, King Khalid University, Postal Code 61413, Box number 9044, Saudi Arabia
| | - Mohammed T Alotaibi
- Department of Chemistry, Turabah University Collage, Taif University, Turabah, Saudi Arabia
| | - Magda H Abdellattif
- Department of Chemistry, College of Science, Taif University, Al-Haweiah, P. O. Box 11099, Taif 21944, Saudi Arabia
| | - Marina M S Cabral-Pinto
- Geobiotec Research Centre, Department of Geoscience, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Priyanka Yadav
- Department of Zoology, Mohammad Hasan P. G. College, Shahganj road, Jaunpur 222001, India
| | - Krishna Kumar Yadav
- Faculty of Science and Technology, Madhyanchal Professional University, Ratibad, Bhopal 462044, India; Department of Civil and Environmental Engineering, Faculty of Engineering, PSU Energy Systems Research Institute, Prince of Songkla University, Hat Yai, Songkhla 90110, Thailand.
| |
Collapse
|
45
|
Anusha P, Ragavendran C, Kamaraj C, Sangeetha K, Thesai AS, Natarajan D, Malafaia G. Eco-friendly bioremediation of pollutants from contaminated sewage wastewater using special reference bacterial strain of Bacillus cereus SDN1 and their genotoxicological assessment in Allium cepa. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 863:160935. [PMID: 36527898 DOI: 10.1016/j.scitotenv.2022.160935] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 12/08/2022] [Accepted: 12/11/2022] [Indexed: 06/17/2023]
Abstract
The present study aimed to assess the Bacillus cereus SDN1 native bacterium's ability to clean up contaminated or polluted water. The isolated bacterium was identified by its morphological and biochemical characteristics, which were then confirmed at the genus level. Furthermore, the isolated B. cereus (NCBI accession No: MW828583) was identified genomically by PCR amplifying 16 s rDNA using a universal primer. The phylogenetic analysis of the rDNA sequence was analyzed to determine the taxonomic and evolutionary profile of the isolate of the previously identified Bacillus sp. Besides, B. cereus and the bacterial consortium were treated using sewage wastewater. After 15 days of treatment, the following pollutants or chemicals were reduced: total hardness particles removal varied from 63.33 % to 67.55 %, calcium removal varied from 90 % to 93.33 %, and total nitrate decreased range from 37.77 % to 22.22 %, respectively. Electrical conductivity ranged from 1809 mS/cm to 2500 mS/cm, and pH values ranged from 6.5 to 8.95. The outcome of in-situ remediation results suggested that B. cereus has a noticeable remediation efficiency to the suspended particles. A root tip test was also used to investigate the genotoxicity of treated and untreated sewage-contaminated waters on onion (Allium cepa) root cells. The highest chromosomal aberrations and mitotic inhibition were found in roots exposed to contaminated sewage water, and their results displayed chromosome abnormalities, including disorganized, sticky chain, disturbed metaphase, chromosomal displacement in anaphase, abnormal telophase, spindle disturbances, and binucleate cells observed in A. cepa exposed to untreated contaminated water. The study can thus be applied as a biomarker to detect the genotoxic impacts of sewage water pollution on biota. Furthermore, based on an identified bacterial consortium, this work offers a low-cost and eco-favorable method for treating household effluents.
Collapse
Affiliation(s)
- Ponniah Anusha
- Department of Science and Humanities, Kongunadu College of Engineering and Technology, Tholurpatti, Trichy 621 215, Tamil Nadu, India
| | - Chinnasamy Ragavendran
- Department of Conservative Dentistry and Endodontics, Saveetha Dental College, and Hospitals, Saveetha Institute of Medical and Technical Sciences (SIMATS), Chennai 600 077, India.
| | - Chinnaperumal Kamaraj
- Interdisciplinary Institute of Indian System of Medicine (IIISM), SRM Institute of Science and Technology (SRMIST), Kattankulathur, Chennai 603 203, Tamil Nadu, India
| | - Kanagaraj Sangeetha
- Natural Drug Research Laboratory, Department of Biotechnology, School of Biosciences, Periyar University, Salem, Tamil Nadu, India
| | | | - Devarajan Natarajan
- Natural Drug Research Laboratory, Department of Biotechnology, School of Biosciences, Periyar University, Salem, Tamil Nadu, India
| | - Guilherme Malafaia
- Laboratory of Toxicology Applied to the Environment, Goiano Federal Institute, Urutaí, GO, Brazil.; Post-Graduation Program in Conservation of Cerrado Natural Resources, Goiano Federal Institute, Urutaí, GO, Brazil.; Post-Graduation Program in Ecology, Conservation, and Biodiversity, Federal University of Uberlândia, Uberlândia, MG, Brazil.; Post-Graduation Program in Biotechnology and Biodiversity, Federal University of Goiás, Goiânia, GO, Brazil..
| |
Collapse
|
46
|
Gauttam R, Eng T, Zhao Z, Ul Ain Rana Q, Simmons BA, Yoshikuni Y, Mukhopadhyay A, Singer SW. Development of genetic tools for heterologous protein expression in a pentose-utilizing environmental isolate of Pseudomonas putida. Microb Biotechnol 2023; 16:645-661. [PMID: 36691869 PMCID: PMC9948227 DOI: 10.1111/1751-7915.14205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 12/17/2022] [Indexed: 01/25/2023] Open
Abstract
Pseudomonas putida has emerged as a promising host for the conversion of biomass-derived sugars and aromatic intermediates into commercially relevant biofuels and bioproducts. Most of the strain development studies previously published have focused on P. putida KT2440, which has been engineered to produce a variety of non-native bioproducts. However, P. putida is not capable of metabolizing pentose sugars, which can constitute up to 25% of biomass hydrolysates. Related P. putida isolates that metabolize a larger fraction of biomass-derived carbon may be attractive as complementary hosts to P. putida KT2440. Here we describe genetic tool development for P. putida M2, a soil isolate that can metabolize pentose sugars. The functionality of five inducible promoter systems and 12 ribosome binding sites was assessed to regulate gene expression. The utility of these expression systems was confirmed by the production of indigoidine from C6 and C5 sugars. Chromosomal integration and expression of non-native genes was achieved by using chassis-independent recombinase-assisted genome engineering (CRAGE) for single-step gene integration of biosynthetic pathways directly into the genome of P. putida M2. These genetic tools provide a foundation to develop hosts complementary to P. putida KT2440 and expand the ability of this versatile microbial group to convert biomass to bioproducts.
Collapse
Affiliation(s)
- Rahul Gauttam
- The Joint BioEnergy Institute, Emeryville, California, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Thomas Eng
- The Joint BioEnergy Institute, Emeryville, California, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Zhiying Zhao
- Joint Genome Institute, Berkeley, California, USA.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Qurrat Ul Ain Rana
- The Joint BioEnergy Institute, Emeryville, California, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Blake A Simmons
- The Joint BioEnergy Institute, Emeryville, California, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Yasuo Yoshikuni
- Joint Genome Institute, Berkeley, California, USA.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Aindrila Mukhopadhyay
- The Joint BioEnergy Institute, Emeryville, California, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Steven W Singer
- The Joint BioEnergy Institute, Emeryville, California, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| |
Collapse
|
47
|
Bonilla JO, Callegari EA, Paez MD, Gil RA, Villegas LB. Bivalent copper ions presence triggers removal and homeostatic mechanisms in the metal-resistant microorganism Apiotrichum loubieri M12. Res Microbiol 2023; 174:104013. [PMID: 36494018 DOI: 10.1016/j.resmic.2022.104013] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 10/04/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022]
Abstract
Microorganisms, especially those habiting mining environments, are of great importance for the retention of toxic metals in the environment. This work aimed to isolate a copper removing-microorganism from sediments of an Acid Mine Drainage-affected environment and to study the cellular responses trigger by metal presence. Apiotrichum loubieri M12 was able to tolerate and remove Cu(II) from liquid culture media, reaching a 30-35% removal capacity when it was exposed to 40 μg mL-1 Cu(II) after 48 h. Analysis of the biomass exposed to the metal through SEM-EDS showed copper presence on the cell surface and variations in the proportion of other biomass constituent elements. Proteomics revealed that the presence of Cu(II) induces differential expression of intracellular proteins involved in a wide variety of metabolic processes. Interestingly, a specific response to the metal was detected in cell-free supernatants, in which copper binding proteins were identified. A large number of proteins with metal ion binding sites were detected both at intra and extracellular levels. The microorganism responds not only by adjusting intracellular protein expression, but also by adjusting expression of proteins in the extracellular space.
Collapse
Affiliation(s)
- José Oscar Bonilla
- Instituto de Química San Luis (INQUISAL), CONICET, Chacabuco 917, 5700 San Luis, Argentina; Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Chacabuco 917, 5700 San Luis, Argentina.
| | - Eduardo Alberto Callegari
- Division of Basic Biomedical Sciences Sanford School of Medicine, University of South Dakota, Vermillion, SD, USA.
| | - María Daniela Paez
- Division of Basic Biomedical Sciences Sanford School of Medicine, University of South Dakota, Vermillion, SD, USA.
| | - Raúl Andrés Gil
- Instituto de Química San Luis (INQUISAL), CONICET, Chacabuco 917, 5700 San Luis, Argentina; Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Chacabuco 917, 5700 San Luis, Argentina.
| | - Liliana Beatriz Villegas
- Instituto de Química San Luis (INQUISAL), CONICET, Chacabuco 917, 5700 San Luis, Argentina; Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Chacabuco 917, 5700 San Luis, Argentina.
| |
Collapse
|
48
|
Petroleum Hydrocarbon Catabolic Pathways as Targets for Metabolic Engineering Strategies for Enhanced Bioremediation of Crude-Oil-Contaminated Environments. FERMENTATION-BASEL 2023. [DOI: 10.3390/fermentation9020196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
Anthropogenic activities and industrial effluents are the major sources of petroleum hydrocarbon contamination in different environments. Microbe-based remediation techniques are known to be effective, inexpensive, and environmentally safe. In this review, the metabolic-target-specific pathway engineering processes used for improving the bioremediation of hydrocarbon-contaminated environments have been described. The microbiomes are characterised using environmental genomics approaches that can provide a means to determine the unique structural, functional, and metabolic pathways used by the microbial community for the degradation of contaminants. The bacterial metabolism of aromatic hydrocarbons has been explained via peripheral pathways by the catabolic actions of enzymes, such as dehydrogenases, hydrolases, oxygenases, and isomerases. We proposed that by using microbiome engineering techniques, specific pathways in an environment can be detected and manipulated as targets. Using the combination of metabolic engineering with synthetic biology, systemic biology, and evolutionary engineering approaches, highly efficient microbial strains may be utilised to facilitate the target-dependent bioprocessing and degradation of petroleum hydrocarbons. Moreover, the use of CRISPR-cas and genetic engineering methods for editing metabolic genes and modifying degradation pathways leads to the selection of recombinants that have improved degradation abilities. The idea of growing metabolically engineered microbial communities, which play a crucial role in breaking down a range of pollutants, has also been explained. However, the limitations of the in-situ implementation of genetically modified organisms pose a challenge that needs to be addressed in future research.
Collapse
|
49
|
Sun L, D'Amico DJ. Characterization of microbial community assembly on new wooden vats for use in cheese production. Food Microbiol 2023; 109:104154. [DOI: 10.1016/j.fm.2022.104154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 09/14/2022] [Accepted: 09/21/2022] [Indexed: 10/14/2022]
|
50
|
Sharma A, Song XP, Singh RK, Vaishnav A, Gupta S, Singh P, Guo DJ, Verma KK, Li YR. Impact of carbendazim on cellular growth, defence system and plant growth promoting traits of Priestia megaterium ANCB-12 isolated from sugarcane rhizosphere. Front Microbiol 2022; 13:1005942. [PMID: 36605502 PMCID: PMC9808048 DOI: 10.3389/fmicb.2022.1005942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 11/04/2022] [Indexed: 01/07/2023] Open
Abstract
Agrochemicals are consistently used in agricultural practices to protect plants from pathogens and ensure high crop production. However, their overconsumption and irregular use cause adverse impacts on soil flora and non-target beneficial microorganisms, ultimately causing a hazard to the ecosystem. Taking this into account, the present study was conducted to determine the high dosage of fungicide (carbendazim: CBZM) effects on the rhizobacteria survival, plant growth promoting trait and reactive oxygen species (ROS) scavenging antioxidant enzyme system. Thus, a multifarious plant growth promoting rhizobacteria (PGPR) isolate, ANCB-12, was obtained from the sugarcane rhizosphere through an enrichment technique. The taxonomic position of the isolated rhizobacteria was confirmed through 16S rRNA gene sequencing analysis as Priestia megaterium ANCB-12 (accession no. ON878101). Results showed that increasing concentrations of fungicide showed adverse effects on rhizobacterial cell growth and survival. In addition, cell visualization under a confocal laser scanning microscope (CLSM) revealed more oxidative stress damage in the form of ROS generation and cell membrane permeability. Furthermore, the increasing dose of CBZM gradually decreased the plant growth promoting activities of the rhizobacteria ANCB-12. For example, CBZM at a maximum 3,000 μg/ml concentration decreases the indole acetic acid (IAA) production by 91.6%, ACC deaminase by 92.3%, and siderophore production by 94.1%, respectively. Similarly, higher dose of fungicide enhanced the ROS toxicity by significantly (p < 0.05) modulating the stress-related antioxidant enzymatic biomarkers in P. megaterium ANCB-12. At a maximum 3,000 μg/ml CBZM concentration, the activity of superoxide dismutase (SOD) declined by 82.3%, catalase (CAT) by 61.4%, glutathione peroxidase (GPX) by 76.1%, and glutathione reductase (GR) by 84.8%, respectively. The results of this study showed that higher doses of the fungicide carbendazim are toxic to the cells of plant-beneficial rhizobacteria. This suggests that a recommended dose of fungicide should be made to lessen its harmful effects.
Collapse
Affiliation(s)
- Anjney Sharma
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Academy of Agricultural Sciences (GXAAS), Nanning, Guangxi, China,Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences (GXAAS), Nanning, Guangxi, China
| | - Xiu-Peng Song
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences (GXAAS), Nanning, Guangxi, China
| | - Rajesh Kumar Singh
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Academy of Agricultural Sciences (GXAAS), Nanning, Guangxi, China,Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences (GXAAS), Nanning, Guangxi, China
| | | | - Saurabh Gupta
- Department of Biotechnology, GLA University, Mathura, UP, India
| | - Pratiksha Singh
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Academy of Agricultural Sciences (GXAAS), Nanning, Guangxi, China,Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences (GXAAS), Nanning, Guangxi, China
| | - Dao-Jun Guo
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Academy of Agricultural Sciences (GXAAS), Nanning, Guangxi, China,Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences (GXAAS), Nanning, Guangxi, China,State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, Guangxi, China
| | - Krishan K. Verma
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Academy of Agricultural Sciences (GXAAS), Nanning, Guangxi, China,Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences (GXAAS), Nanning, Guangxi, China
| | - Yang-Rui Li
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Academy of Agricultural Sciences (GXAAS), Nanning, Guangxi, China,Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences (GXAAS), Nanning, Guangxi, China,State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, Guangxi, China,*Correspondence: Yang-Rui Li,
| |
Collapse
|