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Lavecchia A, Fosso B, Engelen AH, Borin S, Manzari C, Picardi E, Pesole G, Placido A. Macroalgal microbiomes unveil a valuable genetic resource for halogen metabolism. MICROBIOME 2024; 12:47. [PMID: 38454513 PMCID: PMC10919026 DOI: 10.1186/s40168-023-01740-6] [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: 06/19/2023] [Accepted: 12/18/2023] [Indexed: 03/09/2024]
Abstract
BACKGROUND Macroalgae, especially reds (Rhodophyta Division) and browns (Phaeophyta Division), are known for producing various halogenated compounds. Yet, the reasons underlying their production and the fate of these metabolites remain largely unknown. Some theories suggest their potential antimicrobial activity and involvement in interactions between macroalgae and prokaryotes. However, detailed investigations are currently missing on how the genetic information of prokaryotic communities associated with macroalgae may influence the fate of organohalogenated molecules. RESULTS To address this challenge, we created a specialized dataset containing 161 enzymes, each with a complete enzyme commission number, known to be involved in halogen metabolism. This dataset served as a reference to annotate the corresponding genes encoded in both the metagenomic contigs and 98 metagenome-assembled genomes (MAGs) obtained from the microbiome of 2 red (Sphaerococcus coronopifolius and Asparagopsis taxiformis) and 1 brown (Halopteris scoparia) macroalgae. We detected many dehalogenation-related genes, particularly those with hydrolytic functions, suggesting their potential involvement in the degradation of a wide spectrum of halocarbons and haloaromatic molecules, including anthropogenic compounds. We uncovered an array of degradative gene functions within MAGs, spanning various bacterial orders such as Rhodobacterales, Rhizobiales, Caulobacterales, Geminicoccales, Sphingomonadales, Granulosicoccales, Microtrichales, and Pseudomonadales. Less abundant than degradative functions, we also uncovered genes associated with the biosynthesis of halogenated antimicrobial compounds and metabolites. CONCLUSION The functional data provided here contribute to understanding the still largely unexplored role of unknown prokaryotes. These findings support the hypothesis that macroalgae function as holobionts, where the metabolism of halogenated compounds might play a role in symbiogenesis and act as a possible defense mechanism against environmental chemical stressors. Furthermore, bacterial groups, previously never connected with organohalogen metabolism, e.g., Caulobacterales, Geminicoccales, Granulosicoccales, and Microtrichales, functionally characterized through MAGs reconstruction, revealed a biotechnologically relevant gene content, useful in synthetic biology, and bioprospecting applications. Video Abstract.
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Affiliation(s)
- Anna Lavecchia
- Department of Biosciences, Biotechnology and Environment, University of Bari "Aldo Moro", Via Orabona 4, Bari, 70124, Italy
| | - Bruno Fosso
- Department of Biosciences, Biotechnology and Environment, University of Bari "Aldo Moro", Via Orabona 4, Bari, 70124, Italy
| | - Aschwin H Engelen
- Center of Marine Sciences (CCMar), University of Algarve, Campus Gambelas, Faro, 8005-139, Portugal
| | - Sara Borin
- Department of Food, Environmental and Nutritional Sciences, University of Milan, Via Celoria 2, Milan, 20133, Italy
| | - Caterina Manzari
- Department of Biosciences, Biotechnology and Environment, University of Bari "Aldo Moro", Via Orabona 4, Bari, 70124, Italy
| | - Ernesto Picardi
- Department of Biosciences, Biotechnology and Environment, University of Bari "Aldo Moro", Via Orabona 4, Bari, 70124, Italy
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council of Italy, Via Giovanni Amendola, Bari, 122/O, 70126, Italy
| | - Graziano Pesole
- Department of Biosciences, Biotechnology and Environment, University of Bari "Aldo Moro", Via Orabona 4, Bari, 70124, Italy
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council of Italy, Via Giovanni Amendola, Bari, 122/O, 70126, Italy
| | - Antonio Placido
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council of Italy, Via Giovanni Amendola, Bari, 122/O, 70126, Italy.
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Zhu X, Yu Y, Meng W, Huang J, Su G, Zhong Y, Yu X, Sun J, Jin L, Peng P, Zhu L. Aerobic Microbial Transformation of Fluorinated Liquid Crystal Monomer: New Pathways and Mechanism. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:510-521. [PMID: 38100654 DOI: 10.1021/acs.est.3c04256] [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: 12/17/2023]
Abstract
Fluorinated liquid crystal monomers (FLCMs) have been suggested as emerging contaminants, raising global concern due to their frequent occurrence, potential toxic effects, and endurance capacity in the environment. However, the environmental fate of the FLCMs remains unknown. To fill this knowledge gap, we investigated the aerobic microbial transformation mechanisms of an important FLCM, 4-[difluoro(3,4,5-trifluorophenoxy)methyl]-3, 5-difluoro-4'-propylbiphenyl (DTMDPB), using an enrichment culture termed as BG1. Our findings revealed that 67.5 ± 2.1% of the initially added DTMDPB was transformed in 10 days under optimal conditions. A total of 14 microbial transformation products obtained due to a series of reactions (e.g., reductive defluorination, ether bond cleavage, demethylation, oxidative hydroxylation and aromatic ring opening, sulfonation, glucuronidation, O-methylation, and thiolation) were identified. Consortium BG1 harbored essential genes that could transform DTMDPB, such as dehalogenation-related genes [e.g., glutathione S-transferase gene (GST), 2-haloacid dehalogenase gene (2-HAD), nrdB, nuoC, and nuoD]; hydroxylating-related genes hcaC, ubiH, and COQ7; aromatic ring opening-related genes ligB and catE; and methyltransferase genes ubiE and ubiG. Two DTMDPB-degrading strains were isolated, which are affiliated with the genus Sphingopyxis and Agromyces. This study provides a novel insight into the microbial transformation of FLCMs. The findings of this study have important implications for the development of bioremediation strategies aimed at addressing sites contaminated with FLCMs.
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Affiliation(s)
- Xifen Zhu
- Guangdong Provincial Key Laboratory of Petrochemical Pollution Processes and Control, School of Environmental Science and Engineering, Guangdong University of Petrochemical Technology, Maoming, Guangdong 525000, China
| | - Yuanyuan Yu
- Guangdong Provincial Key Laboratory of Petrochemical Pollution Processes and Control, School of Environmental Science and Engineering, Guangdong University of Petrochemical Technology, Maoming, Guangdong 525000, China
| | - Weikun Meng
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, PR China
| | - Jiahui Huang
- Guangdong Provincial Key Laboratory of Petrochemical Pollution Processes and Control, School of Environmental Science and Engineering, Guangdong University of Petrochemical Technology, Maoming, Guangdong 525000, China
| | - Guanyong Su
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, PR China
| | - Yin Zhong
- State Key Laboratory of Organic Geochemistry, Guangdong Provincial Key Laboratory of Environmental Protection and Resources Utilization, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Wushan, Guangzhou 510640, China
| | - Xiaolong Yu
- Guangdong Provincial Key Laboratory of Petrochemical Pollution Processes and Control, School of Environmental Science and Engineering, Guangdong University of Petrochemical Technology, Maoming, Guangdong 525000, China
| | - Jianteng Sun
- Guangdong Provincial Key Laboratory of Petrochemical Pollution Processes and Control, School of Environmental Science and Engineering, Guangdong University of Petrochemical Technology, Maoming, Guangdong 525000, China
| | - Ling Jin
- Department of Civil and Environmental Engineering and Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hung Hom, Kowloon 999077, Hong Kong
| | - Ping'an Peng
- State Key Laboratory of Organic Geochemistry, Guangdong Provincial Key Laboratory of Environmental Protection and Resources Utilization, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Wushan, Guangzhou 510640, China
| | - Lizhong Zhu
- Department of Environmental Science, Zhejiang University, Hangzhou, Zhejiang 310058, China
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Ma W, Lian J, Rene ER, Zhang P, Liu X. Enhanced thyroxine removal from micro-polluted drinking water resources in a bio-electrochemical reactor amended with TiO 2@GAC particles: Efficiency, mechanism and energy consumption. ENVIRONMENTAL RESEARCH 2023; 237:116949. [PMID: 37625538 DOI: 10.1016/j.envres.2023.116949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Revised: 08/17/2023] [Accepted: 08/20/2023] [Indexed: 08/27/2023]
Abstract
A three-dimensional bioelectrochemical system (3D-BES) with both electrocatalytic and biodegradation functions was designed and developed to enhance iodine-containing hormone removal from micro-polluted oligotrophic drinking water sources and to reduce energy consumption. Thyroxine (T4) removal efficiency was 99.0% in the 3D-BES amendment with TiO2@GAC as the particle electrodes, which was 20.5% higher than the total efficiency of single biodegradation (28.7%) plus electrochemical decomposition (49.8%). The high T4 removal efficiency was a result of biochemical synergistic degradation, enhancement of electron transfer and utilization, enrichment of functional microorganisms, and the expression of dehalogenation functional genes. The electron transfer was increased by 1.63 times in 3D-BES compared to the 2D-BES, which contributed to: (i) ∼17.8% enhancement of dehalogenation, (ii) 2.35 times enhancement of the attenuation rate, and (iii) 60% reduction in energy consumption. Moreover, the aggregation of microorganisms and the hydrophobic T4 onto TiO2@GAC shortened the transfer distance of matter and energy, which induced the degradation steps to be shortened and the toxic decay to be accelerated from T4 and its metabolites. These comprehensive functions also enhanced the 31.8% ATPase activity, 7.3% abundance of the functional reductive dehalogenation genera, and 52.3% dehalogenation genes expression for Pseudomonas, Ancylobacter, and Dehalogenimonas, which contributed to an increase in T4 removal. This work provides an environmental-friendly biochemical synergistic method for the detoxification of T4 polluted water.
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Affiliation(s)
- Weifang Ma
- College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China.
| | - Jiangru Lian
- College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China
| | - Eldon R Rene
- Department of Water Supply, Sanitation and Environmental Engineering, IHE Delft Institute for Water Education, Westvest 7, P.O. Box 3015, 2601DA, Delft, the Netherlands
| | - Panyue Zhang
- College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China
| | - Xiang Liu
- School of Environment, Tsinghua University, Beijing, 100084, China
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Kumari A, Upadhyay V, Kumar S. A critical insight into occurrence and fate of polycyclic aromatic hydrocarbons and their green remediation approaches. CHEMOSPHERE 2023; 329:138579. [PMID: 37031842 DOI: 10.1016/j.chemosphere.2023.138579] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 03/23/2023] [Accepted: 03/31/2023] [Indexed: 05/03/2023]
Abstract
Over the last century, the tremendous growth in industrial activities particularly in the sectors of pharmaceuticals, petrochemicals and the reckless application of fertilizers and insecticides has raised the contamination of polyaromatic hydrocarbons (PAHs) tremendously. For more than a decade, the main focus of environmental experts is to come up with management approaches for the clean-up of sites polluted with PAHs. These are ubiquitous in nature i.e., widely distributed in ecosystem ranging from soil, air and marine water. Most of the PAHs possess immunotoxicity, carcinogenicity and genotoxicity. Being highly soluble in lipids, they are readily absorbed into the mammalian gastro intestinal tract. They are widely distributed with marked tendency of getting localized into body fat in varied tissues. Several remediation technologies have been tested for the removal of these environmental contaminants, particularly bioremediation has turned out to be a hope as the safest and cost-effective option. Therefore, this review first discusses various sources of PAHs, their effect on human health and interactions of PAHs with soils and sediments. In this review, a holistic insight of current scenario of existing remediation technologies and how they can be improvised along with the hindrances in the path of these technologies are properly addressed.
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Affiliation(s)
- Archana Kumari
- CSIR-National Environmental Engineering Research Institute (CSIR-NEERI), Nehru Marg, Nagpur, 440020, Maharashtra, India
| | - Vidisha Upadhyay
- CSIR-National Environmental Engineering Research Institute (CSIR-NEERI), Nehru Marg, Nagpur, 440020, Maharashtra, India
| | - Sunil Kumar
- CSIR-National Environmental Engineering Research Institute (CSIR-NEERI), Nehru Marg, Nagpur, 440020, Maharashtra, India.
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