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Zhang M, Wang X, Deng X, Zheng S, Zhang W, He JZ, Yu X, Feng M, Ye C. Viable but non-culturable state formation and resuscitation of different antibiotic-resistant Escherichia coli induced by UV/chlorine. WATER RESEARCH 2024; 261:122011. [PMID: 38959654 DOI: 10.1016/j.watres.2024.122011] [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: 04/13/2024] [Revised: 06/12/2024] [Accepted: 06/26/2024] [Indexed: 07/05/2024]
Abstract
The presence of "viable but nonculturable" (VBNC) state and bacterial antibiotic resistance (BAR) both pose significant threats to the safety of drinking water. However, limited data was available that explicitly addressed the contribution of bacterial VBNC state in the maintenance and propagation of BAR. Here, the VBNC state induction and resuscitation of two antibiotic-resistant Escherichia coli K12 strains, one carrying multidrug-resistant plasmid (RP4 E. coli) and the other with chromosomal mutation (RIF E. coli) were characterized by subjecting them to different doses of UV/chlorine. The results illustrated that the induction, resuscitation, and associated mechanisms of VBNC ARB exhibit variations based on resistance determinants. RP4 E. coli exhibited a higher susceptibility to enter VBNC state compared to the RIF E. coli., and most VBNC state and resuscitated RP4 E. coli retained original antibiotic resistance. While, reverse mutation in the rpoB gene was observed in VBNC state and recovered RIF E. coli strains induced by high doses of UV/chlorine treatment, leading to the loss of rifampicin resistance. According to RT-qPCR results, ARGs conferring efflux pumps appeared to play a more significant role in the VBNC state formation of RP4 E. coli and the down-regulation of rpoS gene enhanced the speed at which this plasmid-carrying ARB entered into the dormant state. As to RIF E. coli, the induction of VBNC state was supposed to be regulated by the combination of general stress response, SOS response, stringent response, and TA system. Above all, this study highlights that ARB could become VBNC state during UV/chlorine treatments and retain, in some cases, their ability to spread ARGs. Importantly, compared with chromosomal mutation-mediated ARB, both VBNC and resuscitated state ARB that carries multidrug-resistant plasmids poses more serious health risks. Our study provides insights into the relationship between the VBNC state and the propagation of BAR in drinking water systems.
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Affiliation(s)
- Menglu Zhang
- College of Environmental and Resource Science, Fujian Normal University, Fuzhou 350117, China; Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, Fujian Normal University, Fuzhou 350007, China; Fujian Sanming Forest Ecosystem National Observation and Research Station, Fujian Normal University, Sanming 365002, China; Fujian Key Laboratory of Pollution Control & Resource Reuse, Fuzhou 350117, China
| | - Xuansen Wang
- College of Environmental and Resource Science, Fujian Normal University, Fuzhou 350117, China; Fujian Key Laboratory of Pollution Control & Resource Reuse, Fuzhou 350117, China
| | - Xiaofeng Deng
- Fujian Minhuan Testing and Inspection Co., Fuzhou 350000, China
| | - Suxia Zheng
- College of Environmental and Resource Science, Fujian Normal University, Fuzhou 350117, China
| | - Weifang Zhang
- College of Environmental and Resource Science, Fujian Normal University, Fuzhou 350117, China; Fujian Key Laboratory of Pollution Control & Resource Reuse, Fuzhou 350117, China
| | - Ji-Zheng He
- Fujian Sanming Forest Ecosystem National Observation and Research Station, Fujian Normal University, Sanming 365002, China; Fujian Key Laboratory of Pollution Control & Resource Reuse, Fuzhou 350117, China
| | - Xin Yu
- Fujian Key Laboratory of Coastal Pollution Prevention and Control, College of the Environment & Ecology, Xiamen University, Xiamen, 361102, China
| | - Mingbao Feng
- Fujian Key Laboratory of Coastal Pollution Prevention and Control, College of the Environment & Ecology, Xiamen University, Xiamen, 361102, China
| | - Chengsong Ye
- Fujian Key Laboratory of Coastal Pollution Prevention and Control, College of the Environment & Ecology, Xiamen University, Xiamen, 361102, China.
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Singh A, Lankapalli AK, Mendem SK, Semmler T, Ahmed N. Unraveling the evolutionary dynamics of toxin-antitoxin systems in diverse genetic lineages of Escherichia coli including the high-risk clonal complexes. mBio 2024; 15:e0302323. [PMID: 38117088 PMCID: PMC10790755 DOI: 10.1128/mbio.03023-23] [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: 11/09/2023] [Accepted: 11/15/2023] [Indexed: 12/21/2023] Open
Abstract
IMPORTANCE Large-scale genomic studies of E. coli provide an invaluable opportunity to understand how genomic fine-tuning contributes to the transition of bacterial lifestyle from being commensals to mutualists or pathogens. Within this context, through machine learning-based studies, it appears that TA systems play an important role in the classification of high-risk clonal lineages and could be attributed to their epidemiological success. Due to these profound indications and assumptions, we attempted to provide unique insights into the ordered world of TA systems at the population level by investigating the diversity and evolutionary patterns of TA genes across 19 different STs of E. coli. Further in-depth analysis of ST-specific TA structures and associated genetic coordinates holds the potential to elucidate the functional implications of TA systems in bacterial cell survival and persistence, by and large.
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Affiliation(s)
- Anuradha Singh
- Pathogen Biology Laboratory, Department of Biotechnology and Bioinformatics, University of Hyderabad, Hyderabad, Telangana State, India
| | - Aditya Kumar Lankapalli
- Department of Biology and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, United Kingdom
| | - Suresh Kumar Mendem
- Pathogen Biology Laboratory, Department of Biotechnology and Bioinformatics, University of Hyderabad, Hyderabad, Telangana State, India
| | | | - Niyaz Ahmed
- Pathogen Biology Laboratory, Department of Biotechnology and Bioinformatics, University of Hyderabad, Hyderabad, Telangana State, India
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Wang X, Kan Y, Bai K, Xu X, Chen X, Yu C, Shi J, Jiang N, Li J, Luo L. A novel double-ribonuclease toxin-antitoxin system linked to the stress response and survival of Acidovorax citrulli. Microbiol Spectr 2023; 11:e0216923. [PMID: 37819152 PMCID: PMC10714953 DOI: 10.1128/spectrum.02169-23] [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: 05/25/2023] [Accepted: 08/30/2023] [Indexed: 10/13/2023] Open
Abstract
IMPORTANCE Bacterial fruit blotch (BFB), which is caused by the seed-borne bacterium Acidovorax citrulli, is a devastating disease affecting cucurbit crops throughout the world. Although seed fermentation and treatment with disinfectants can provide effective management of BFB, they cannot completely guarantee pathogen-free seedstock, which suggests that A. citrulli is a highly stress-resistant pathogen. Toxin-antitoxin (TA) systems are common among a diverse range of bacteria and have been reported to play a role in bacterial stress response. However, there is currently much debate about the relationship between TA systems and stress response in bacteria. The current study characterized a novel TA system (Aave_1720-Aave_1719) from A. citrulli that affects both biofilm formation and survival in response to sodium hypochlorite stress. The mechanism of neutralization differed from typical TA systems as two separate mechanisms were associated with the antitoxin, which exhibited characteristics of both type II and type V TA systems. The Aave_1720-Aave_1719 system described here also constitutes the first known report of a double-ribonuclease TA system in bacteria, which expands our understanding of the range of regulatory mechanisms utilized by bacterial TA systems, providing new insight into the survival of A. citrulli in response to stress.
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Affiliation(s)
- Xudong Wang
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
- Key Laboratory of Surveillance and Management for Plant Quarantine Pests, Ministry of Agriculture and Rural Affairs, Beijing, China
- Beijing Key Laboratory of Seed Disease Testing and Control, Beijing, China
| | - Yumin Kan
- Department of Biochemistry and Cell Biology, State University of New York, Stony Brook, New York, USA
| | - Kaihong Bai
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Xiaoli Xu
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
- Key Laboratory of Surveillance and Management for Plant Quarantine Pests, Ministry of Agriculture and Rural Affairs, Beijing, China
- Beijing Key Laboratory of Seed Disease Testing and Control, Beijing, China
| | - Xing Chen
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
- Key Laboratory of Surveillance and Management for Plant Quarantine Pests, Ministry of Agriculture and Rural Affairs, Beijing, China
- Beijing Key Laboratory of Seed Disease Testing and Control, Beijing, China
| | - Chengxuan Yu
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
- Key Laboratory of Surveillance and Management for Plant Quarantine Pests, Ministry of Agriculture and Rural Affairs, Beijing, China
- Beijing Key Laboratory of Seed Disease Testing and Control, Beijing, China
| | - Jia Shi
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
- Key Laboratory of Surveillance and Management for Plant Quarantine Pests, Ministry of Agriculture and Rural Affairs, Beijing, China
- Beijing Key Laboratory of Seed Disease Testing and Control, Beijing, China
| | - Na Jiang
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
- Beijing Key Laboratory of Seed Disease Testing and Control, Beijing, China
| | - Jianqiang Li
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
- Key Laboratory of Surveillance and Management for Plant Quarantine Pests, Ministry of Agriculture and Rural Affairs, Beijing, China
- Beijing Key Laboratory of Seed Disease Testing and Control, Beijing, China
| | - Laixin Luo
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
- Key Laboratory of Surveillance and Management for Plant Quarantine Pests, Ministry of Agriculture and Rural Affairs, Beijing, China
- Beijing Key Laboratory of Seed Disease Testing and Control, Beijing, China
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Li XL, Lv XY, Ji JB, Wang WD, Wang J, Wang C, He HB, Ben AL, Liu TL. Complete genome sequence of Nguyenibacter sp. L1, a phosphate solubilizing bacterium isolated from Lespedeza bicolor rhizosphere. Front Microbiol 2023; 14:1257442. [PMID: 38152372 PMCID: PMC10752598 DOI: 10.3389/fmicb.2023.1257442] [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: 07/12/2023] [Accepted: 11/27/2023] [Indexed: 12/29/2023] Open
Abstract
Phosphorus (P) deficiency is a predominant constraint on plant growth in acidified soils, largely due to the sequestration of P by toxic aluminum (Al) compounds. Indigenous phosphorus-solubilizing bacteria (PSBs) capable of mobilizing Al-P in these soils hold significant promise. A novel Al-P-solubilizing strain, Al-P Nguyenibacter sp. L1, was isolated from the rhizosphere soil of healthy Lespedeza bicolor plants indigenous to acidic terrains. However, our understanding of the genomic landscape of bacterial species within the genus Nguyenibacter remains in its infancy. To further explore its biotechnological potentialities, we sequenced the complete genome of this strain, employing an amalgamation of Oxford Nanopore ONT and Illumina sequencing platforms. The resultant genomic sequence of Nguyenibacter sp. L1 manifests as a singular, circular chromosome encompassing 4,294,433 nucleotides and displaying a GC content of 66.73%. The genome was found to host 3,820 protein-coding sequences, 12 rRNAs, and 55 tRNAs. Intriguingly, annotations derived from the eggNOG and KEGG databases indicate the presence of genes affiliated with phosphorus solubilization and nitrogen fixation, including iscU, glnA, and gltB/D associated with nitrogen fixation, and pqqBC associated with inorganic phosphate dissolution. Several bioactive secondary metabolite genes in the genome, including pqqCDE, phytoene synthase and squalene synthase predicted by antiSMASH. Moreover, we uncovered a complete metabolic pathway for ammonia, suggesting an ammonia-affinity property inherent to Nguyenibacter sp. L1. This study verifies the nitrogen-fixing and phosphate-dissolving abilities of Nguyenibacter sp. L1 at the molecular level through genetic screening and analysis. The insights gleaned from this study offer strategic guidance for future strain enhancement and establish a strong foundation for the potential incorporation of this bacterium into agricultural practices.
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Affiliation(s)
- Xiao Li Li
- School of Food Science, Nanjing Xiaozhuang University, Nanjing, China
| | - Xin Yang Lv
- School of Food Science, Nanjing Xiaozhuang University, Nanjing, China
| | - Jun Bin Ji
- School of Food Science, Nanjing Xiaozhuang University, Nanjing, China
| | - Wei Duo Wang
- School of Food Science, Nanjing Xiaozhuang University, Nanjing, China
| | - Ji Wang
- School of Food Science, Nanjing Xiaozhuang University, Nanjing, China
| | - Cong Wang
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, China
| | - Hai Bin He
- College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Ai Ling Ben
- School of Food Science, Nanjing Xiaozhuang University, Nanjing, China
| | - Ting Li Liu
- School of Food Science, Nanjing Xiaozhuang University, Nanjing, China
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Ming Q, Huang X, He Y, Qin L, Tang Y, Liu Y, Huang Y, Zhang H, Li P. Genome Mining and Screening for Secondary Metabolite Production in the Endophytic Fungus Dactylonectria alcacerensis CT-6. Microorganisms 2023; 11:microorganisms11040968. [PMID: 37110391 PMCID: PMC10142127 DOI: 10.3390/microorganisms11040968] [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: 03/23/2023] [Revised: 04/01/2023] [Accepted: 04/06/2023] [Indexed: 04/29/2023] Open
Abstract
Endophytic fungi are a treasure trove of natural products with great chemical diversity that is largely unexploited. As an alternative to the traditional bioactivity-guided screening approach, the genome-mining-based approach provides a new methodology for obtaining novel natural products from endophytes. In our study, the whole genome of an endophyte, Dactylonectria alcacerensis CT-6, was obtained for the first time. Genomic analysis indicated that D. alcacerensis CT-6 has one 61.8 Mb genome with a G+C content of 49.86%. Gene annotation was extensively carried out using various BLAST databases. Genome collinearity analysis revealed that D. alcacerensis CT-6 has high homology with three other strains of the Dactylonectria genus. AntiSMASH analysis displayed 45 secondary metabolite biosynthetic gene clusters (BGCs) in D. alcacerensis CT-6, and most of them were unknown and yet to be unveiled. Furthermore, only six known substances had been isolated from the fermented products of D. alcacerensis CT-6, suggesting that a great number of cryptic BGCs in D. alcacerensis CT-6 are silent and/or expressed at low levels under conventional conditions. Therefore, our study provides an important basis for further chemical study of D. alcacerensis CT-6 using the gene-mining strategy to awaken these cryptic BGCs for the production of bioactive secondary metabolites.
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Affiliation(s)
- Qianliang Ming
- Department of Pharmacognosy, College of Pharmacy, Army Medical University, Chongqing 400038, China
- Drug and Instrument Supervision and Inspection Station, 32339 Troops of the Chinese People's Liberation Army, Lhasa 850015, China
| | - Xiuning Huang
- Department of Pharmacognosy, College of Pharmacy, Army Medical University, Chongqing 400038, China
| | - Yimo He
- Department of Pharmacognosy, College of Pharmacy, Army Medical University, Chongqing 400038, China
| | - Lingyue Qin
- Department of Pharmacognosy, College of Pharmacy, Army Medical University, Chongqing 400038, China
| | - Yu Tang
- Department of Pharmacognosy, College of Pharmacy, Army Medical University, Chongqing 400038, China
| | - Yanxia Liu
- Department of Pharmacognosy, College of Pharmacy, Army Medical University, Chongqing 400038, China
| | - Yuting Huang
- Department of Pharmacognosy, College of Pharmacy, Army Medical University, Chongqing 400038, China
| | - Hongwei Zhang
- Drug and Instrument Supervision and Inspection Station, 32339 Troops of the Chinese People's Liberation Army, Lhasa 850015, China
| | - Peng Li
- Department of Pharmacognosy, College of Pharmacy, Army Medical University, Chongqing 400038, China
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6
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Kumar P, Rani S, Dahiya P, Kumar A, Dang AS, Suneja P. Whole genome analysis for plant growth promotion profiling of Pantoea agglomerans CPHN2, a non-rhizobial nodule endophyte. Front Microbiol 2022; 13:998821. [PMID: 36419432 PMCID: PMC9676466 DOI: 10.3389/fmicb.2022.998821] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 09/13/2022] [Indexed: 09/04/2024] Open
Abstract
Reduced agricultural production as well as issues like nutrient-depleted soils, eutrophication, and groundwater contamination have drawn attention to the use of endophyte-based bioformulations to restore soil fertility. Pantoea agglomerans CPHN2, a non-rhizobial nodule endophyte isolated from Cicer arietinum, exhibited a variety of plant growth-promoting traits. In this study, we used NextSeq500 technology to analyze whole-genome sequence information of this plant growth-promoting endophytic bacteria. The genome of P. agglomerans CPHN2 has a length of 4,839,532 bp and a G + C content of 55.2%. The whole genome comprises three different genomic fractions, comprising one circular chromosome and two circular plasmids. A comparative analysis between P. agglomerans CPHN2 and 10 genetically similar strains was performed using a bacterial pan-genome pipeline. All the predicted and annotated gene sequences for plant growth promotions (PGPs), such as phosphate solubilization, siderophore synthesis, nitrogen metabolism, and indole-3-acetic acid (IAA) of P. agglomerans CPHN2, were identified. The whole-genome analysis of P. agglomerans CPHN2 provides an insight into the mechanisms underlying PGP by endophytes and its potential applications as a biofertilizer.
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Affiliation(s)
- Pradeep Kumar
- Department of Microbiology, Maharshi Dayanand University, Rohtak, India
| | - Simran Rani
- Department of Microbiology, Maharshi Dayanand University, Rohtak, India
| | - Priyanka Dahiya
- Department of Microbiology, Maharshi Dayanand University, Rohtak, India
| | - Ajit Kumar
- Centre for Bioinformatics, Maharshi Dayanand University, Rohtak, India
| | - Amita Suneja Dang
- Centre for Medical Biotechnology, Maharshi Dayanand University, Rohtak, India
| | - Pooja Suneja
- Department of Microbiology, Maharshi Dayanand University, Rohtak, India
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