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Jiménez-Volkerink SN, Jordán M, Smidt H, Minguillón C, Vila J, Grifoll M. Metagenomic insights into the microbial cooperative networks of a benz(a)anthracene-7,12-dione degrading community from a creosote-contaminated soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 907:167832. [PMID: 37863223 DOI: 10.1016/j.scitotenv.2023.167832] [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: 07/31/2023] [Revised: 10/11/2023] [Accepted: 10/12/2023] [Indexed: 10/22/2023]
Abstract
Genotoxicity of PAH-contaminated soils can eventually increase after bioremediation due to the formation and accumulation of polar transformation products, mainly oxygenated PAHs (oxy-PAHs). Biodegradation of oxy-PAHs has been described in soils, but information on the microorganisms and mechanisms involved is still scarce. Benz(a)anthracene-7,12-dione (BaAQ), a transformation product from benz(a)anthracene frequently detected in soils, presents higher genotoxic potential than its parent PAH. Here, using sand-in-liquid microcosms we identified a specialized BaAQ-degrading subpopulation in a PAH-contaminated soil. A BaAQ-degrading microbial consortium was obtained by enrichment in sand-in-liquid cultures with BaAQ as sole carbon source, and its metagenomic analysis identified members of Sphingobium, Stenotrophomonas, Pusillimonas, Olivibacter, Pseudomonas, Achromobacter, and Hyphomicrobiales as major components. The integration of data from metabolomic and metagenomic functional gene analyses of the consortium revealed that the BaAQ metabolic pathway was initiated by Baeyer-Villiger monooxygenases (BVMOs). The presence of plasmid pANTQ-1 in the metagenomic sequences, identified in a previous multi-omic characterization of a 9,10-anthraquinone-degrading isolate recovered from the same soil, suggested the occurrence of a horizontal gene transfer event. Further metagenomic analysis of the BaAQ-degrading consortium also provided insights into the potential roles and interactions within the consortium members. Several potential auxotrophies were detected, indicating that relevant nutritional interdependencies and syntrophic associations were taking place within the community members, not only to provide suitable carbon and energy sources, but also to supply essential nutrients and cofactors. Our work confirms the essential role that BVMO may play as a detoxification mechanism to mitigate the risk posed by oxy-PAH formation during bioremediation of contaminated soils.
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Affiliation(s)
- Sara N Jiménez-Volkerink
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Av. Diagonal, 643, 08028 Barcelona, Spain
| | - Maria Jordán
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Av. Diagonal, 643, 08028 Barcelona, Spain
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708, WE, Wageningen, the Netherlands
| | - Cristina Minguillón
- Department of Nutrition, Food Science and Gastronomy, University of Barcelona, Avda. Prat de la Riba, 171, 08921 Sta. Coloma de Gramanet, Barcelona, Spain
| | - Joaquim Vila
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Av. Diagonal, 643, 08028 Barcelona, Spain.
| | - Magdalena Grifoll
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Av. Diagonal, 643, 08028 Barcelona, Spain
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Li YQ, Xin Y, Li C, Liu J, Huang T. Metagenomics-metabolomics analysis of microbial function and metabolism in petroleum-contaminated soil. Braz J Microbiol 2023:10.1007/s42770-023-01000-7. [PMID: 37162704 DOI: 10.1007/s42770-023-01000-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 04/27/2023] [Indexed: 05/11/2023] Open
Abstract
Contamination of soil by petroleum is becoming increasingly serious in the world today. However, the research on gene functional characteristics, metabolites and distribution of microbial genomes in oil-contaminated soil is limited. Considering that, metagenomic and metabonomic were used to detect microbes and metabolites in oil-contaminated soil, and the changes of functional pathways were analyzed. We found that oil pollution significantly changed the composition of soil microorganisms and metabolites, and promoted the relative abundance of Pseudoxanthomonas, Pseudomonas, Mycobacterium, Immundisolibacter, etc. The degradation of toluene, xylene, polycyclic aromatic hydrocarbon and fluorobenzoate increased in Xenobiotics biodegradation and metabolism. Key monooxygenases and dioxygenase systems were regulated to promote ring opening and degradation of aromatic hydrocarbons. Metabolite contents of polycyclic aromatic hydrocarbons (PAHs) such as 9-fluoronone and gentisic acid increased significantly. The soil microbiome degraded petroleum pollutants into small molecular substances and promoted the bioremediation of petroleum-contaminated soil. Besides, we discovered the complete degradation pathway of petroleum-contaminated soil microorganisms to generate gentisic acid from the hydroxylation of naphthalene in PAHs by salicylic acid. This study offers important insights into bioremediation of oil-contaminated soil from the aspect of molecular regulation mechanism and provides a theoretical basis for the screening of new oil degrading bacteria.
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Affiliation(s)
- Yong-Quan Li
- School of Medicine, Northwest Minzu University, Lanzhou, China.
- Key Laboratory of Environmental Ecology and Population Health in Northwest Minority Areas, State Ethnic Affairs Commission, Lanzhou, China.
| | - Ying Xin
- School of Medicine, Northwest Minzu University, Lanzhou, China
| | - Caili Li
- School of Medicine, Northwest Minzu University, Lanzhou, China
| | - Jin Liu
- School of Medicine, Northwest Minzu University, Lanzhou, China
| | - Tao Huang
- School of Medicine, Northwest Minzu University, Lanzhou, China
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Das S, Najar IN, Sherpa MT, Kumar S, Sharma P, Mondal K, Tamang S, Thakur N. Baseline metagenome-assembled genome (MAG) data of Sikkim hot springs from Indian Himalayan geothermal belt (IHGB) showcasing its potential CAZymes, and sulfur-nitrogen metabolic activity. World J Microbiol Biotechnol 2023; 39:179. [PMID: 37133792 DOI: 10.1007/s11274-023-03631-2] [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: 08/25/2022] [Accepted: 04/26/2023] [Indexed: 05/04/2023]
Abstract
Here we present the construction and characterization of metagenome assembled genomes (MAGs) from two hot springs residing in the vicinity of Indian Himalayan Geothermal Belt (IHGB). A total of 78 and 7 taxonomic bins were obtained for Old Yume Samdong (OYS) and New Yume Samdong (NYS) hot springs respectively. After passing all the criteria only 21 and 4 MAGs were further studied based on the successful prediction of their 16 S rRNA. Various databases were used such as GTDB, Kaiju, EzTaxon, BLAST XY Plot and NCBI BLAST to get the taxonomic classification of various 16 S rRNA predicted MAGs. The bacterial genomes found were from both thermophilic and mesophilic bacteria among which Proteobacteria, Chloroflexi, Bacteroidetes and Firmicutes were the abundant phyla. However, in case of OYS, two genomes belonged to archaeal Methanobacterium and Methanocaldococcus. Functional characterization revealed the richness of CAZymes such as Glycosyl Transferase (GT) (56.7%), Glycoside Hydrolase (GH) (37.4%), Carbohydrate Esterase family (CE) (8.2%), and Polysaccharide Lyase (PL) (1.9%). There were negligible antibiotic resistance genes in the MAGs however, a significant heavy metal tolerance gene was found in the MAGs. Thus, it may be assumed that there is no coexistence of antibiotic and heavy metal resistance genes in these hot spring microbiomes. Since the selected hot springs possess good sulfur content thus, we also checked the presence of genes for sulfur and nitrogen metabolism. It was found that MAGs from both the hot springs possess significant number of genes related to sulfur and nitrogen metabolism.
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Affiliation(s)
- Sayak Das
- Department of Microbiology, School of Life Sciences, Sikkim University, 6th Mile, Samdur, Gangtok, Sikkim, 737102, India
- Department of Life Science and Bioinformatics, Hargobind Khurana School of Life Sciences, Assam University, Silchar, Assam, 788011, India
| | - Ishfaq Nabi Najar
- Department of Microbiology, School of Life Sciences, Sikkim University, 6th Mile, Samdur, Gangtok, Sikkim, 737102, India
| | - Mingma Thundu Sherpa
- Department of Microbiology, School of Life Sciences, Sikkim University, 6th Mile, Samdur, Gangtok, Sikkim, 737102, India
| | - Santosh Kumar
- Department of Microbiology, School of Life Sciences, Sikkim University, 6th Mile, Samdur, Gangtok, Sikkim, 737102, India
| | - Prayatna Sharma
- Department of Microbiology, School of Life Sciences, Sikkim University, 6th Mile, Samdur, Gangtok, Sikkim, 737102, India
| | - Krishnendu Mondal
- Department of Microbiology, Vidyasagar University, Midnapore, West Bengal, 721102, India
| | - Sonia Tamang
- Department of Microbiology, School of Life Sciences, Sikkim University, 6th Mile, Samdur, Gangtok, Sikkim, 737102, India
| | - Nagendra Thakur
- Department of Microbiology, School of Life Sciences, Sikkim University, 6th Mile, Samdur, Gangtok, Sikkim, 737102, India.
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