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Huang Y, Pan A, Song Y, Deng Y, Wu ALH, Lau CSH, Zhang T. Strain-level diversity in sulfonamide biodegradation: adaptation of Paenarthrobacter to sulfonamides. ISME J 2024; 18:wrad040. [PMID: 38366247 PMCID: PMC10873849 DOI: 10.1093/ismejo/wrad040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 12/11/2023] [Accepted: 12/26/2024] [Indexed: 02/18/2024]
Abstract
The widespread occurrence of sulfonamides raises significant concerns about the evolution and spread of antibiotic resistance genes. Biodegradation represents not only a resistance mechanism but also a clean-up strategy. Meanwhile, dynamic and diverse environments could influence the cellular function of individual sulfonamide-degrading strains. Here, we present Paenarthrobacter from different origins that demonstrated diverse growth patterns and sulfonamide-degrading abilities. Generally, the degradation performance was largely associated with the number of sadA gene copies and also relied on its genotype. Based on the survey of sad genes in the public database, an independent mobilization of transposon-borne genes between chromosome and plasmid was observed. Insertions of multiple sadA genes could greatly enhance sulfonamide-degrading performance. Moreover, the sad gene cluster and sadA transposable element showed phylogenetic conservation currently, being identified only in two genera of Paenarthrobacter (Micrococcaceae) and Microbacterium (Microbacteriaceae). Meanwhile, Paenarthrobacter exhibited a high capacity for genome editing to adapt to the specific environmental niche, opening up new opportunities for bioremediation applications.
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Affiliation(s)
- Yue Huang
- Environmental Microbiome Engineering and Biotechnology Lab, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR 999077, China
| | - Anxin Pan
- Environmental Microbiome Engineering and Biotechnology Lab, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR 999077, China
| | - Ying Song
- Environmental Microbiome Engineering and Biotechnology Lab, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR 999077, China
| | - Yu Deng
- Environmental Microbiome Engineering and Biotechnology Lab, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR 999077, China
| | - Alnwick Long-Hei Wu
- Environmental Microbiome Engineering and Biotechnology Lab, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR 999077, China
| | - Colin Shiu-Hay Lau
- Environmental Microbiome Engineering and Biotechnology Lab, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR 999077, China
| | - Tong Zhang
- Environmental Microbiome Engineering and Biotechnology Lab, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR 999077, China
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El-Sabeh A, Mlesnita AM, Munteanu IT, Honceriu I, Kallabi F, Boiangiu RS, Mihasan M. Characterisation of the Paenarthrobacter nicotinovorans ATCC 49919 genome and identification of several strains harbouring a highly syntenic nic-genes cluster. BMC Genomics 2023; 24:536. [PMID: 37697273 PMCID: PMC10494377 DOI: 10.1186/s12864-023-09644-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 09/01/2023] [Indexed: 09/13/2023] Open
Abstract
BACKGROUND Paenarthrobacter nicotinovorans ATCC 49919 uses the pyridine-pathway to degrade nicotine and could provide a renewable source of precursors from nicotine-containing waste as well as a model for studying the molecular evolution of catabolic pathways and their spread by horizontal gene transfer via soil bacterial plasmids. RESULTS In the present study, the strain was sequenced using the Illumina NovaSeq 6000 and Oxford Nanopore Technology (ONT) MinION platforms. Following hybrid assembly with Unicycler, the complete genome sequence of the strain was obtained and used as reference for whole-genome-based phylogeny analyses. A total of 64 related genomes were analysed; five Arthrobacter strains showed both digital DNA-DNA hybridization and average nucleotide identity values over the species threshold when compared to P. nicotinovorans ATCC 49919. Five plasmids and two contigs belonging to Arthrobacter and Paenarthrobacter strains were shown to be virtually identical with the pAO1 plasmid of Paenarthrobacter nicotinovorans ATCC 49919. Moreover, a highly syntenic nic-genes cluster was identified on five plasmids, one contig and three chromosomes. The nic-genes cluster contains two major locally collinear blocks that appear to form a putative catabolic transposon. Although the origins of the nic-genes cluster and the putative transposon still elude us, we hypothesise here that the ATCC 49919 strain most probably evolved from Paenarthrobacter sp. YJN-D or a very closely related strain by acquiring the pAO1 megaplasmid and the nicotine degradation pathway. CONCLUSIONS The data presented here offers another snapshot into the evolution of plasmids harboured by Arthrobacter and Paenarthrobacter species and their role in the spread of metabolic traits by horizontal gene transfer among related soil bacteria.
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Affiliation(s)
- Amada El-Sabeh
- Faculty of Biology, Alexandru Ioan Cuza University of Iași, Iași, Romania
| | | | | | - Iasmina Honceriu
- Faculty of Biology, Alexandru Ioan Cuza University of Iași, Iași, Romania
| | - Fakhri Kallabi
- Faculty of Biology, Alexandru Ioan Cuza University of Iași, Iași, Romania
- Laboratory of Human Molecular Genetics, Faculty of Medicine of Sfax, University of Sfax, Sfax, Tunisia
| | | | - Marius Mihasan
- Faculty of Biology, Alexandru Ioan Cuza University of Iași, Iași, Romania.
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Wu T, Guo SZ, Zhu HZ, Yan L, Liu ZP, Li DF, Jiang CY, Corvini PFX, Shen XH, Liu SJ. The sulfonamide-resistance dihydropteroate synthase gene is crucial for efficient biodegradation of sulfamethoxazole by Paenarthrobacter species. Appl Microbiol Biotechnol 2023; 107:5813-5827. [PMID: 37439835 DOI: 10.1007/s00253-023-12679-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 06/20/2023] [Accepted: 06/30/2023] [Indexed: 07/14/2023]
Abstract
Sulfonamide antibiotics (SAs) are serious pollutants to ecosystems and environments. Previous studies showed that microbial degradation of SAs such as sulfamethoxazole (SMX) proceeds via a sad-encoded oxidative pathway, while the sulfonamide-resistant dihydropteroate synthase gene, sul, is responsible for SA resistance. However, the co-occurrence of sad and sul genes, as well as how the sul gene affects SMX degradation, was not explored. In this study, two SMX-degrading bacterial strains, SD-1 and SD-2, were cultivated from an SMX-degrading enrichment. Both strains were Paenarthrobacter species and were phylogenetically identical; however, they showed different SMX degradation activities. Specifically, strain SD-1 utilized SMX as the sole carbon and energy source for growth and was a highly efficient SMX degrader, while SD-2 did could not use SMX as a sole carbon or energy source and showed limited SMX degradation when an additional carbon source was supplied. Genome annotation, growth, enzymatic activity tests, and metabolite detection revealed that strains SD-1 and SD-2 shared a sad-encoded oxidative pathway for SMX degradation and a pathway of protocatechuate degradation. A new sulfonamide-resistant dihydropteroate synthase gene, sul918, was identified in strain SD-1, but not in SD-2. Moreover, the lack of sul918 resulted in low SMX degradation activity in strain SD-2. Genome data mining revealed the co-occurrence of sad and sul genes in efficient SMX-degrading Paenarthrobacter strains. We propose that the co-occurrence of sulfonamide-resistant dihydropteroate synthase and sad genes is crucial for efficient SMX biodegradation. KEY POINTS: • Two sulfamethoxazole-degrading strains with distinct degrading activity, Paenarthrobacter sp. SD-1 and Paenarthrobacter sp. SD-2, were isolated and identified. • Strains SD-1 and SD-2 shared a sad-encoded oxidative pathway for SMX degradation. • A new plasmid-borne SMX resistance gene (sul918) of strain SD-1 plays a crucial role in SMX degradation efficiency.
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Affiliation(s)
- Tong Wu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, 712100, Shaanxi, China
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Sheng-Zhi Guo
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, 712100, Shaanxi, China
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Hai-Zhen Zhu
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Lei Yan
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zhi-Pei Liu
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - De-Feng Li
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Cheng-Ying Jiang
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | | | - Xi-Hui Shen
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, 712100, Shaanxi, China.
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
- State Key Laboratory of Microbial Biotechnology, Shandong University, Qingdao, 266237, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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Kang Z, Yang Y, Wang C, Kang Y, Wang T, Zhu G, Han X, Yu H. Atrazine decontamination by a newly screened psychrotroph Paenarthrobacter sp. KN0901 in an aquatic system: Metabolic pathway, kinetics, and hydroponics experiment. J Hazard Mater 2023; 457:131764. [PMID: 37320906 DOI: 10.1016/j.jhazmat.2023.131764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 05/19/2023] [Accepted: 06/02/2023] [Indexed: 06/17/2023]
Abstract
Atrazine residues running off the fields and entering water resources are a major threat to food security and the ecosystem. In this study, a psychrotrophic functional strain named KN0901 to remove atrazine residues was screened. KN0901 could degrade 30 mg·L-1 atrazine in 4 days at 15ºC with 105 CFU·mL-1 incubation. The phylogenetic results showed KN0901 belonged to Paenarthrobacter sp. PCR results showed that the functional genes consist of trzN, atzB, and atzC, suggesting atrazine was transformed to cyanuric acid by KN0901. KN0901 could degrade atrazine without adding exogenous carbon and nitrogen sources. What's more, KN0901 could tolerate extreme low temperature (5ºC) and high atrazine concentration (100 mg·L-1). When growth and degradation curves were compared, the results indicated the length of lag time showed significant correlation to atrazine degradation rate. The hydroponic experiments showed that the toxicity of atrazine was significantly reduced with KN0901 treatment. The study provided an effective, economic, and eco-friendly bioremediation measure to address atrazine contamination.
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Affiliation(s)
- Zhichao Kang
- Key Laboratory of Wetland Ecology and Environment, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China; College of Resources and Environment, University of Chinese Academy of Science, Beijing 101400, China
| | - Yang Yang
- Key Laboratory of Wetland Ecology and Environment, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China; College of Resources and Environment, University of Chinese Academy of Science, Beijing 101400, China
| | - Chenxu Wang
- Public Technical Service Center, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Yuanyuan Kang
- Shenzhen CAPCHEM Technology Co. Ltd., Shabo Tongfuyu Industry Zone, Pingshan New District, Shenzhen 518118, China
| | - Tianye Wang
- Key Laboratory of Wetland Ecology and Environment, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Guopeng Zhu
- Key Laboratory of Wetland Ecology and Environment, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China; College of Resources and Environment, University of Chinese Academy of Science, Beijing 101400, China
| | - Xuerong Han
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China
| | - Hongwen Yu
- Key Laboratory of Wetland Ecology and Environment, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China.
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Cao L, Zhang J, Zhao R, Deng Y, Liu J, Fu W, Lei Y, Zhang T, Li X, Li B. Genomic characterization, kinetics, and pathways of sulfamethazine biodegradation by Paenarthrobacter sp. A01. Environ Int 2019; 131:104961. [PMID: 31330364 DOI: 10.1016/j.envint.2019.104961] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 06/02/2019] [Accepted: 06/22/2019] [Indexed: 06/10/2023]
Abstract
Biodegradation is an important route for the removal of sulfamethazine (SMZ), one of the most commonly used sulfonamide antibiotics, in the environment. However, little information is known about the kinetics, products, and pathways of SMZ biodegradation owing to the complexity of its enzyme-based biotransformation processes. In this study, the SMZ-degrading strain A01 belonging to the genus Paenarthrobacter was isolated from SMZ-enriched activated sludge reactors. The bacterial cells were rod-shaped with transient branches 2.50-4.00 μm in length with most forming in a V-shaped arrangement. The genome size of Paenarthrobacter sp. A01 had a total length of 4,885,005 bp with a GC content of 63.5%, and it contained 104 contigs and 55 RNAs. The effects of pH, temperature, initial substrate concentration and additional carbon source on the biodegradation of SMZ were investigated. The results indicated that pH 6.0-7.8, 25 °C and the addition of 0.2 g/L sodium acetate favored the biodegradation, whereas a high concentration of SMZ, 500 mg/L, had an inhibitory effect. The biodegradation kinetics with SMZ as the sole carbon source or 0.2 g/L sodium acetate as the co-substrate fit the modified Gompertz model well with a correlation coefficient (R2) of 0.99. Three biodegradation pathways were proposed involving nine biodegradation products, among which C6H9N3O2S and C12H12N2 were two novel biodegradation products that have not been reported previously. Approximately 90.7% of SMZ was transformed to 2-amino-4, 6-dimethylpyrimidine. Furthermore, sad genes responsible for catabolizing sulfonamides were characterized in A01 with high similarities of 96.0%-100.0%. This study will fill the knowledge gap in the biodegradation of this ubiquitous micropollutant in the aquatic environment.
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Affiliation(s)
- Lijia Cao
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, Shenzhen, China; School of Environment, Tsinghua University, Beijing, China
| | - Jiayu Zhang
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, Shenzhen, China; School of Environment, Tsinghua University, Beijing, China
| | - Renxin Zhao
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, Shenzhen, China; School of Environment, Tsinghua University, Beijing, China; Shenzhen Engineering Research Laboratory for Sludge and Food Waste Treatment and Resource Recovery, Graduate School at Shenzhen, Tsinghua University, China
| | - Yu Deng
- Environmental Biotechnology Laboratory, The University of Hong Kong, Hong Kong, China
| | - Jie Liu
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, Shenzhen, China
| | - Wenjie Fu
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, Shenzhen, China; School of Environment, Tsinghua University, Beijing, China
| | - Yusha Lei
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, Shenzhen, China; School of Environment, Tsinghua University, Beijing, China
| | - Tong Zhang
- Environmental Biotechnology Laboratory, The University of Hong Kong, Hong Kong, China
| | - Xiaoyan Li
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, Shenzhen, China; Shenzhen Engineering Research Laboratory for Sludge and Food Waste Treatment and Resource Recovery, Graduate School at Shenzhen, Tsinghua University, China
| | - Bing Li
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, Shenzhen, China; Shenzhen Engineering Research Laboratory for Sludge and Food Waste Treatment and Resource Recovery, Graduate School at Shenzhen, Tsinghua University, China.
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