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Alam SA, Saha P. Chemotactic response of p-nitrophenol degrading Pseudomonas asiatica strain PNPG3 through phenotypic and genome sequence-based in silico studies. 3 Biotech 2023; 13:408. [PMID: 37987023 PMCID: PMC10657342 DOI: 10.1007/s13205-023-03809-3] [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: 02/14/2023] [Accepted: 10/08/2023] [Indexed: 11/22/2023] Open
Abstract
The Pseudomonas asiatica strain PNPG3 was documented to possess chemotactic potential toward p-nitrophenol (PNP), and other nitroaromatic compounds. Initial screening with drop plate and swarm plate assays demonstrated significant movement of the strain toward the test compounds. A quantitative capillary assay revealed the highest chemotactic potential of the strain toward 4-Aminophenol (4AP), (CI: 12.33); followed by p-benzoquinone (PBQ), (CI: 6.8); and PNP, (CI: 5.33). Gene annotation revealed the presence of chemotactic genes (Che), (Methyl-accepting Proteins) MCPs, rotary motor proteins, and flagellar proteins within the genome of strain PNPG3. The chemotactic machinery of the strain PNPG3 comprised of thirteen Che genes, twenty-two MCPs, eight rotary motors, and thirty-four flagellar proteins that are involved in sensing chemoattractant. Two chemotactic gene clusters were recorded in the genome, of which the major cluster consisted of two copies of CheW, one copy of CheA, CheY, CheZ, one MotD gene, and several Fli genes. Various conserved regions and motifs were documented in them using a standard bioinformatics tool. Genes involved in the chemotaxis of strain PNPG3 were compared with three closely related strains and one distantly related strain belonging to Burkholderia sp. Considering these phenotypic and genotypic data, it can be speculated that it is metabolism-dependent chemotaxis; and that test compound activated the Che. This study indicated that strain PNPG3 could be used as a model organism for the study of the molecular mechanism of chemotaxis and bioremediation of PNP. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03809-3.
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Affiliation(s)
- Sk Aftabul Alam
- Department of Microbiology, The University of Burdwan, Golapbag, Burdwan, WB 713104 India
| | - Pradipta Saha
- Department of Microbiology, The University of Burdwan, Golapbag, Burdwan, WB 713104 India
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2
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Zou M, Wang K, Zhao J, Lu H, Yang H, Huang M, Wang L, Wang G, Huang J, Min X. DegS protease regulates the motility, chemotaxis, and colonization of Vibrio cholerae. Front Microbiol 2023; 14:1159986. [PMID: 37089576 PMCID: PMC10113495 DOI: 10.3389/fmicb.2023.1159986] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 03/14/2023] [Indexed: 04/25/2023] Open
Abstract
In bacteria, DegS protease functions as an activating factor of the σE envelope stress response system, which ultimately activates the transcription of stress response genes in the cytoplasm. On the basis of high-throughput RNA sequencing, we have previously found that degS knockout inhibits the expression of flagellum synthesis- and chemotaxis-related genes, thereby indicating that DegS may be involved in the regulation of V. cholerae motility. In this study, we examined the relationships between DegS and motility in V. cholerae. Swimming motility and chemotaxis assays revealed that degS or rpoE deletion promotes a substantial reduction in the motility and chemotaxis of V. cholerae, whereas these activities were restored in ΔdegS::degS and ΔdegSΔrseA strains, indicating that DegS is partially dependent on σE to positively regulate V. cholerae activity. Gene-act network analysis revealed that the cAMP-CRP-RpoS signaling pathway, which plays an important role in flagellar synthesis, is significantly inhibited in ΔdegS mutants, whereas in response to the overexpression of cyaA/crp and rpoS in the ΔdegS strain, the motility and chemotaxis of the ΔdegS + cyaA/crp and ΔdegS + rpoS strains were partially restored compared with the ΔdegS strain. We further demonstrated that transcription levels of the flagellar regulatory gene flhF are regulated by DegS via the cAMP-CRP-RpoS signaling pathway. Overexpression of the flhF gene in the ΔdegS strain partially restored motility and chemotaxis. In addition, suckling mouse intestinal colonization experiments indicated that the ΔdegS and ΔrpoE strains were characterized by the poor colonization of mouse intestines, whereas colonization efficacy was restored in the ΔdegSΔrseA, ΔdegS + cyaA/crp, ΔdegS + rpoS, and ΔdegS + flhF strains. Collectively, our findings indicate that DegS regulates the motility and chemotaxis of V. cholerae via the cAMP-CRP-RpoS-FlhF pathway, thereby influencing the colonization of suckling mouse intestines.
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Affiliation(s)
- Mei Zou
- Department of Laboratory Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
- School of Laboratory Medicine, Zunyi Medical University, Zunyi, Guizhou, China
| | - Kaiying Wang
- Department of Laboratory Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
- School of Laboratory Medicine, Zunyi Medical University, Zunyi, Guizhou, China
| | - Jiajun Zhao
- Department of Laboratory Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
- School of Laboratory Medicine, Zunyi Medical University, Zunyi, Guizhou, China
| | - Huifang Lu
- Department of Laboratory Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
- School of Laboratory Medicine, Zunyi Medical University, Zunyi, Guizhou, China
| | - Hui Yang
- Department of Laboratory Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
- School of Laboratory Medicine, Zunyi Medical University, Zunyi, Guizhou, China
| | - Meirong Huang
- School of Laboratory Medicine, Zunyi Medical University, Zunyi, Guizhou, China
- Department of Blood Transfusion, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
| | - Lu Wang
- Department of Laboratory Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
- School of Laboratory Medicine, Zunyi Medical University, Zunyi, Guizhou, China
| | - Guangli Wang
- Department of Laboratory Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
- School of Laboratory Medicine, Zunyi Medical University, Zunyi, Guizhou, China
| | - Jian Huang
- Department of Laboratory Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
- School of Laboratory Medicine, Zunyi Medical University, Zunyi, Guizhou, China
| | - Xun Min
- Department of Laboratory Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
- School of Laboratory Medicine, Zunyi Medical University, Zunyi, Guizhou, China
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3
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Ibrar M, Khan S, Hasan F, Yang X. Biosurfactants and chemotaxis interplay in microbial consortium-based hydrocarbons degradation. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:24391-24410. [PMID: 35061186 DOI: 10.1007/s11356-022-18492-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 12/30/2021] [Indexed: 06/14/2023]
Abstract
Hydrocarbons are routinely detected at low concentrations, despite the degrading metabolic potential of ubiquitous microorganisms. The potential drivers of hydrocarbons persistence are lower bioavailability and mass transfer limitation. Recently, bioremediation strategies have developed rapidly, but still, the solution is not resilient. Biosurfactants, known to increase bioavailability and augment biodegradation, are tightly linked to bacterial surface motility and chemotaxis, while chemotaxis help bacteria to locate aromatic compounds and increase the mass transfer. Harassing the biosurfactant production and chemotaxis properties of degrading microorganisms could be a possible approach for the complete degradation of hydrocarbons. This review provides an overview of interplay between biosurfactants and chemotaxis in bioremediation. Besides, we discuss the chemical surfactants and biosurfactant-mediated biodegradation by microbial consortium.
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Affiliation(s)
- Muhammad Ibrar
- Guangdong Technology Research Center for Marine Algal Bioengineering, Guangdong Key Laboratory of Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, People's Republic of China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, People's Republic of China
- Shenzhen Key Laboratory of Marine Biological Resources and Ecology Environment, College of Life Sciences and Oceanography, Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen University, Shenzhen, 518055, People's Republic of China
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, 1037 Luoyu Road, 430074, Hubei, People's Republic of China
| | - Salman Khan
- State Key Laboratory of Grassland Agro-Ecosystems, School of Life Sciences, Lanzhou University, Lanzhou, 730000, Gansu, People's Republic of China
| | - Fariha Hasan
- Department of Microbiology, Applied, Environmental and Geomicrobiology Laboratory, Quaid-I-Azam University, Islamabad, Pakistan
| | - Xuewei Yang
- Guangdong Technology Research Center for Marine Algal Bioengineering, Guangdong Key Laboratory of Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, People's Republic of China.
- Shenzhen Key Laboratory of Marine Biological Resources and Ecology Environment, College of Life Sciences and Oceanography, Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen University, Shenzhen, 518055, People's Republic of China.
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Bacillus velezensis stimulates resident rhizosphere Pseudomonas stutzeri for plant health through metabolic interactions. THE ISME JOURNAL 2022; 16:774-787. [PMID: 34593997 PMCID: PMC8483172 DOI: 10.1038/s41396-021-01125-3] [Citation(s) in RCA: 102] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 09/16/2021] [Accepted: 09/20/2021] [Indexed: 02/08/2023]
Abstract
Trophic interactions play a central role in driving microbial community assembly and function. In gut or soil ecosystems, successful inoculants are always facilitated by efficient colonization; however, the metabolite exchanges between inoculants and resident bacteria are rarely studied, particularly in the rhizosphere. Here, we used bioinformatic, genetic, transcriptomic, and metabonomic analyses to uncover syntrophic cooperation between inoculant (Bacillus velezensis SQR9) and plant-beneficial indigenous Pseudomonas stutzeri in the cucumber rhizosphere. We found that the synergistic interaction of these two species is highly environmental dependent, the emergence of syntrophic cooperation was only evident in a static nutrient-rich niche, such as pellicle biofilm in addition to the rhizosphere. Our results identified branched-chain amino acids (BCAAs) biosynthesis pathways are involved in syntrophic cooperation. Genome-scale metabolic modeling and metabolic profiling also demonstrated metabolic facilitation among the bacterial strains. In addition, biofilm matrix components from Bacillus were essential for the interaction. Importantly, the two-species consortium promoted plant growth and helped plants alleviate salt stress. In summary, we propose a mechanism in which synergic interactions between a biocontrol bacterium and a partner species promote plant health.
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Zan S, Wang J, Wang F, Li Z, Du M, Cai Y. A novel degradation mechanism of naphthenic acids by marine Pseudoalteromonas sp. JOURNAL OF HAZARDOUS MATERIALS 2022; 424:127534. [PMID: 34879524 DOI: 10.1016/j.jhazmat.2021.127534] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 10/11/2021] [Accepted: 10/14/2021] [Indexed: 06/13/2023]
Abstract
Naphthenic acids (NAs) are a persistent toxic organic pollutant that occur in different environment worldwide and cause serious threat to the ecosystem and public health. However, knowledge on the behavior and fate of NAs in marine environments still remains unknown. In this study, the degradation mechanism of NAs (cyclohexylacetic acid, CHAA) was investigated using an common indigenous marine Pseudoalteromonas sp. The results showed that CHAA could be degraded completely under aerobic condition, but could not be utilized directly under anaerobic condition. Interestingly, transcriptome and key enzyme activity results showed the CHAA degradation pathway induced under aerobic condition could still work in anaerobic condition. The degradation was activated by acetyl-CoA transferase and sequentially formed the corresponding cyclohexene, alcohol, and ketone with the assistance of related enzymes, and finally cleaved by hydroxymethylglutarate-CoA lyase. Besides, there was a positive correlation between chemotaxis and aerobic degradation genes (r = 0.976, P < 0.05), the chemotaxis would enhance bacterium movement and NAs biodegradation. It is proposed that bacterium could translocate to NAs and accomplish biodegradation from aerobic to anaerobic environments, which was a new anaerobic degradation pathway of NAs. This study provides new insights into the fate of NAs and other organic contaminants in marine environment.
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Affiliation(s)
- Shuaijun Zan
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, PR China.
| | - Jing Wang
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, PR China.
| | - Fengbo Wang
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, PR China.
| | - Zelong Li
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, PR China.
| | - Miaomiao Du
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, PR China.
| | - Yingxue Cai
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, PR China.
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A Review of the Advantages, Disadvantages and Limitations of Chemotaxis Assays for Campylobacter spp. Int J Mol Sci 2022; 23:ijms23031576. [PMID: 35163499 PMCID: PMC8836060 DOI: 10.3390/ijms23031576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 01/27/2022] [Accepted: 01/27/2022] [Indexed: 11/26/2022] Open
Abstract
Reproducible qualitative and quantitative assessment of bacterial chemotactic motility, particularly in response to chemorepellent effectors, is experimentally challenging. Here we compare several established chemotaxis assays currently used to investigate Campylobacter jejuni chemotaxis, with the aim of improving the correlation between different studies and establishing the best practices. We compare the methodologies of capillary, agar, and chamber-based assays, and discuss critical technical points, in terms of reproducibility, accuracy, and the advantages and limitations of each.
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Tahir U, Aslam F, Nawaz S, Khan UH, Yasmin A. Annotation of chemotaxis gene clusters and proteins involved in chemotaxis of Bacillus subtilis strain MB378 capable of biodecolorizing different dyes. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:3510-3520. [PMID: 34389949 DOI: 10.1007/s11356-021-15634-3] [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: 01/22/2021] [Accepted: 07/21/2021] [Indexed: 06/13/2023]
Abstract
This study explores the chemotactic potential of Bacillus subtilis MB378 against industrial dyes. Initial screening with swim plate assay showed significant movement of Bacillus subtilis MB378 towards test compounds. According to quantitative capillary assay, B. subtilis MB378 exhibited high chemotaxis potential towards Acid Orange 52 (CI: 9.52), followed by Direct Red 28 (CI: 8.39) and Basic Green 4 (CI: 5.21) in glucose-supplemented medium. Sequencing and gene annotation results evidently showed presence of chemotaxis genes and flagellar motor proteins in Bacillus subtilis draft genome. Methyl-accepting proteins (involved in chemotaxis regulation) belonged to pfam00672, pfam00072, and pfam00015 protein families. Annotated chemotaxis machinery of MB378 comprised 8 Che genes, 5 chemoreceptor genes, associated flagellar proteins, and rotary motors. Chemotaxis genes of B. subtilis MB378 were compared with genes of closely related Bacillus strains (168, WK1, and HTA426), depicting highly conserved regions showing evolutionary relation between them. Considering results of present study, it can be speculated that test compounds triggered chemotactic genes, which made these compounds bioavailable to the bacterium. Hence, the bacterium recognized and approached these compounds and facilitated biodegradation and detoxification of these compounds.
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Affiliation(s)
- Uruj Tahir
- Microbiology and Biotechnology Laboratory, Department of Environmental Sciences, Fatima Jinnah Women University, Rawalpindi, 46000, Pakistan.
- Department of Biotechnology, Fatima Jinnah Women University, Rawalpindi, 46000, Pakistan.
- Department of Environmental Sciences, Faculty of Natural Sciences, University of Okara, Okara, 56130, Pakistan.
| | - Fozia Aslam
- Microbiology and Biotechnology Laboratory, Department of Environmental Sciences, Fatima Jinnah Women University, Rawalpindi, 46000, Pakistan
| | - Shiza Nawaz
- National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
| | - Umair Hassan Khan
- School of Agriculture and Environment, The University of Western Australia, Crawley, Perth, Australia
| | - Azra Yasmin
- Microbiology and Biotechnology Laboratory, Department of Environmental Sciences, Fatima Jinnah Women University, Rawalpindi, 46000, Pakistan
- Department of Biotechnology, Fatima Jinnah Women University, Rawalpindi, 46000, Pakistan
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8
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Zan S, Lv J, Li Z, Cai Y, Wang Z, Wang J. Genomic insights into Pseudoalteromonas sp. JSTW coping with petroleum-heavy metals combined pollution. J Basic Microbiol 2021; 61:947-957. [PMID: 34387369 DOI: 10.1002/jobm.202100156] [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: 04/21/2021] [Revised: 07/02/2021] [Accepted: 08/08/2021] [Indexed: 11/05/2022]
Abstract
Worldwide marine compound contamination by petroleum products and heavy metals is a burgeoning environmental concern. Pseudoalteromonas, prevalently distributed in marine environment, has been proven to degrade petroleum and plays an essential role in the fate of oil pollution under the combined pollution. Nevertheless, the research on the reference genes is still incomplete. Therefore, this study aims to thoroughly investigate the reference genes represented by Pseudoalteromonas sp. JSTW via whole-genome sequencing. Next-generation sequencing technology unfolded a genome of 4,026,258 bp, database including Clusters of Orthologous Groups (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) were utilized to annotate the genes and metabolic pathways conferring to petroleum hydrocarbon degradation. The results show that common alkane and aromatic hydrocarbon degradation genes (alkB, ligB, yqhD, and ladA), chemotaxis gene (MCP, cheA, cheB, pcaY, and pcaR), heavy-metal resistance, and biofilm genes (σ54, merC, pcoA, copB, etc.) were observed in whole-genome sequence (WGS) of JSTW, which indicated that strain JSTW could potentially cope with combined pollution. The degradation efficiency of naphthalene in 60 h by JSTW was 99% without Cu2+ and 67% with 400 mg L-1 Cu2+ . Comparative genome analysis revealed that genomes of Pseudoalteromonas lipolytica strain LEMB 39 and Pseudoalteromonas donghaensis strain HJ51 shared similarity with strain JSTW, suggesting they are also the potential degradater of petroleum hydrocarbons under combined pollution. Therefore, this study provides a WGS annotation and reveals the mechanism of response to combined pollution of Pseudoalteromonas sp. JSTW.
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Affiliation(s)
- Shuaijun Zan
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian, China
| | - Jingping Lv
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian, China
| | - Zelong Li
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian, China
| | - Yingxue Cai
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian, China
| | - Zongcheng Wang
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian, China
| | - Jing Wang
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian, China
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Strategic approach of multifaceted antibacterial mechanism of limonene traced in Escherichia coli. Sci Rep 2021; 11:13816. [PMID: 34226573 PMCID: PMC8257740 DOI: 10.1038/s41598-021-92843-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Accepted: 06/11/2021] [Indexed: 02/01/2023] Open
Abstract
Antibacterial potential of Limonene against Multi Drug Resistant (MDR) pathogens was studied and mechanism explored. Microscopic techniques viz. Fluorescent Microscopy (FM), Scanning Electron Microscopy (SEM), and Transmission Electron Microscopy (TEM) indicated membrane disruption, cellular leakage and cell death of Escherichia coli (E. coli) cells when treated with limonene. Leakage of intracellular proteins, lipids and nucleic acid confirmed membrane damage and disruption of cell permeability barrier. Further, release of intracellular ATP, also suggested disruption of membrane barrier. Interaction of limonene with DNA revealed its capability in unwinding of plasmid, which could eventually inhibit DNA transcription and translation. Differential expression of various proteins and enzymes involved in transport, respiration, metabolism, chemotaxis, protein synthesis confirmed the mechanistic role of limonene on their functions. Limonene thus can be a potential candidate in drug development.
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Khalid F, Hashmi MZ, Jamil N, Qadir A, Ali MI. Microbial and enzymatic degradation of PCBs from e-waste-contaminated sites: a review. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:10474-10487. [PMID: 33411303 DOI: 10.1007/s11356-020-11996-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Accepted: 12/07/2020] [Indexed: 05/21/2023]
Abstract
Electronic waste is termed as e-waste and on recycling it produces environmental pollution. Among these e-waste pollutants, polychlorinated biphenyls (PCBs) are significantly important due to ubiquitous, organic in nature and serious health and environmental hazards. PCBs are used in different electrical equipment such as in transformers and capacitors for the purposes of exchange of heat and hydraulic fluids. Bioremediation is a reassuring technology for the elimination of the PCBs from the environment. In spite of their chemical stability, there are several microbes which can bio-transform or mineralize the PCBs aerobically or anaerobically. In this review paper, our objective was to summarize the information regarding PCB-degrading enzymes and microbes. The review suggested that the most proficient PCB degraders during anaerobic condition are Dehalobacter, Dehalococcoides, and Desulfitobacterium and in aerobic condition are Burkholderia, Achromobacter, Comamonas, Ralstonia, Pseudomonas, Bacillus, and Alcaligenes etc., showing the broadest substrate among bacterial strains. Enzymes found in soil such as dehydrogenases and fluorescein diacetate (FDA) esterases have the capability to breakdown PCBs. Biphenyl upper pathway involves four enzymes: dehydrogenase (bphB), multicomponent dioxygenase (bphA, E, F, and G), second dioxygenase (bphC), hydrolase, and (bphD). Biphenyl dioxygenase is considered as the foremost enzyme used for aerobic degradation of PCBs in metabolic pathway. It has been proved that several micro-organisms are responsible for the PCB metabolization. The review provides novel strategies for e-waste-contaminated soil management.
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Affiliation(s)
- Foqia Khalid
- College of Earth and Environmental Science, University of the Punjab, Lahore, Pakistan
| | - Muhammad Zaffar Hashmi
- Department of Chemistry, COMSATS University Islamabad, Islamabad, 44000, Pakistan.
- Pakistan Academy of Science, 3-Constitution Avenue Sector G-5/2, Islamabad, Pakistan.
| | - Nadia Jamil
- College of Earth and Environmental Science, University of the Punjab, Lahore, Pakistan
| | - Abdul Qadir
- College of Earth and Environmental Science, University of the Punjab, Lahore, Pakistan
| | - Muhammad Ishtiaq Ali
- Department of Microbiology, Quaid-i-Azam University Islamabad, Islamabad, Pakistan
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Chemotaxis Towards Aromatic Compounds: Insights from Comamonas testosteroni. Int J Mol Sci 2019; 20:ijms20112701. [PMID: 31159416 PMCID: PMC6600141 DOI: 10.3390/ijms20112701] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2019] [Revised: 05/28/2019] [Accepted: 05/30/2019] [Indexed: 02/07/2023] Open
Abstract
Chemotaxis is an important physiological adaptation that allows many motile bacteria to orientate themselves for better niche adaptation. Chemotaxis is best understood in Escherichia coli. Other representative bacteria, such as Rhodobacter sphaeroides, Pseudomonas species, Helicobacter pylori, and Bacillus subtilis, also have been deeply studied and systemically summarized. These bacteria belong to α-, γ-, ε-Proteobacteria, or Firmicutes. However, β-Proteobacteria, of which many members have been identified as holding chemotactic pathways, lack a summary of chemotaxis. Comamonas testosteroni, belonging to β-Proteobacteria, grows with and chemotactically responds to a range of aromatic compounds. This paper summarizes the latest research on chemotaxis towards aromatic compounds, mainly from investigations of C. testosteroni and other Comamonas species.
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Balaraman P, Plettner E. Chemotaxis by Pseudomonas putida (ATCC 17453) towards camphor involves cytochrome P450 cam (CYP101A1). Biochim Biophys Acta Gen Subj 2018; 1863:304-312. [PMID: 30391161 DOI: 10.1016/j.bbagen.2018.10.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 10/27/2018] [Accepted: 10/29/2018] [Indexed: 11/29/2022]
Abstract
The camphor-degrading microorganism, Pseudomonas putida strain ATCC 17453, is an aerobic, gram-negative soil bacterium that uses camphor as its sole carbon and energy source. The genes responsible for the catabolic degradation of camphor are encoded on the extra-chromosomal CAM plasmid. A monooxygenase, cytochrome P450cam, mediates hydroxylation of camphor to 5-exo-hydroxycamphor as the first and committed step in the camphor degradation pathway, requiring a dioxygen molecule (O2) from air. Under low O2 levels, P450cam catalyzes the production of borneol via an unusual reduction reaction. We have previously shown that borneol downregulates the expression of P450cam. To understand the function of P450cam and the consequences of down-regulation by borneol under low O2 conditions, we have studied chemotaxis of camphor induced and non-induced P. putida strain ATCC 17453. We have tested camphor, borneol, oxidized camphor metabolites and known bacterial attractants (d)-glucose, (d) - and (l)-glutamic acid for their elicitation chemotactic behavior. In addition, we have used 1-phenylimidazole, a P450cam inhibitor, to investigate if P450cam plays a role in the chemotactic ability of P. putida in the presence of camphor. We found that camphor, a chemoattractant, became toxic and chemorepellent when P450cam was inhibited. We have also evaluated the effect of borneol on chemotaxis and found that the bacteria chemotaxed away from camphor in the presence of borneol. This is the first report of the chemotactic behaviour of P. putida ATCC 17453 and the essential role of P450cam in this process.
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Affiliation(s)
- Priyadarshini Balaraman
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
| | - Erika Plettner
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada.
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Min J, Wang J, Chen W, Hu X. Biodegradation of 2-chloro-4-nitrophenol via a hydroxyquinol pathway by a Gram-negative bacterium, Cupriavidus sp. strain CNP-8. AMB Express 2018; 8:43. [PMID: 29560541 PMCID: PMC5861257 DOI: 10.1186/s13568-018-0574-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 03/12/2018] [Indexed: 11/21/2022] Open
Abstract
Cupriavidus sp. strain CNP-8 isolated from a pesticide-contaminated soil was able to utilize 2-chloro-4-nitrophenol (2C4NP) as a sole source of carbon, nitrogen and energy, together with the release of nitrite and chloride ions. It could degrade 2C4NP at temperatures from 20 to 40 °C and at pH values from 5 to 10, and degrade 2C4NP as high as 1.6 mM. Kinetics assay showed that biodegradation of 2C4NP followed Haldane substrate inhibition model, with the maximum specific growth rate (μmax) of 0.148/h, half saturation constant (Ks) of 0.022 mM and substrate inhibition constant (Ki) of 0.72 mM. Strain CNP-8 was proposed to degrade 2C4NP with hydroxyquinol (1,2,4-benzenetriol, BT) as the ring-cleavage substrate. The 2C4NP catabolic pathway in strain CNP-8 is significant from those reported in other Gram-negative 2C4NP utilizers. Enzymatic assay indicated that the monooxygenase initiating 2C4NP catabolism had different substrates specificity compared with previously reported 2C4NP monooxygenations. Capillary assays showed that strain CNP-8 exhibited metabolism-dependent chemotactic response toward 2C4NP at the optimum concentration of 0.5 mM with a maximum chemotaxis index of 37.5. Furthermore, microcosm studies demonstrated that strain CNP-8, especially the pre-induced cells, could remove 2C4NP rapidly from the 2C4NP-contaminated soil. Considering its adaptability to pH and temperature fluctuations and great degradation efficiency against 2C4NP, strain CNP-8 could be a promising candidate for the bioremediation of 2C4NP-contaminated sites.
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Abstract
Although the mechanism of bacterial chemotaxis has been extensively studied in enteric bacteria, the hunt for novel and atypical chemoeffectors (in enterics and distantly-related species alike) has necessitated the modification of classic chemotaxis assays to deal with recalcitrant and potentially toxic chemicals. Here, we describe detailed protocols for the quantitative and qualitative assessment of chemotaxis responses that are categorized into short-term direct population response assays and long-term metabolism-based assays that can be used to identify novel chemoeffector molecules and the specific chemoreceptors involved. We emphasize the importance of behavior-based assays to verify the biochemical and physiological relevance of newly identified chemoeffector-receptor pairs.
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Affiliation(s)
- Rebecca E Parales
- Department of Microbiology and Molecular Genetics, College of Biological Sciences, University of California, Davis, CA, USA
| | - Jayna L Ditty
- Department of Biology, College of Arts and Sciences, University of St. Thomas, St. Paul, MN, USA.
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15
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Biodegradation and chemotaxis of polychlorinated biphenyls, biphenyls, and their metabolites by Rhodococcus spp. Biodegradation 2017; 29:1-10. [DOI: 10.1007/s10532-017-9809-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 10/09/2017] [Indexed: 11/26/2022]
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16
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Gran-Scheuch A, Fuentes E, Bravo DM, Jiménez JC, Pérez-Donoso JM. Isolation and Characterization of Phenanthrene Degrading Bacteria from Diesel Fuel-Contaminated Antarctic Soils. Front Microbiol 2017; 8:1634. [PMID: 28894442 PMCID: PMC5581505 DOI: 10.3389/fmicb.2017.01634] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 08/11/2017] [Indexed: 12/03/2022] Open
Abstract
Antarctica is an attractive target for human exploration and scientific investigation, however the negative effects of human activity on this continent are long lasting and can have serious consequences on the native ecosystem. Various areas of Antarctica have been contaminated with diesel fuel, which contains harmful compounds such as heavy metals and polycyclic aromatic hydrocarbons (PAH). Bioremediation of PAHs by the activity of microorganisms is an ecological, economical, and safe decontamination approach. Since the introduction of foreign organisms into the Antarctica is prohibited, it is key to discover native bacteria that can be used for diesel bioremediation. By following the degradation of the PAH phenanthrene, we isolated 53 PAH metabolizing bacteria from diesel contaminated Antarctic soil samples, with three of these isolates exhibiting a high phenanthrene degrading capacity. In particular, the Sphingobium xenophagum D43FB isolate showed the highest phenanthrene degradation ability, generating up to 95% degradation of initial phenanthrene. D43FB can also degrade phenanthrene in the presence of its usual co-pollutant, the heavy metal cadmium, and showed the ability to grow using diesel-fuel as a sole carbon source. Microtiter plate assays and SEM analysis revealed that S. xenophagum D43FB exhibits the ability to form biofilms and can directly adhere to phenanthrene crystals. Genome sequencing analysis also revealed the presence of several genes involved in PAH degradation and heavy metal resistance in the D43FB genome. Altogether, these results demonstrate that S. xenophagum D43FB shows promising potential for its application in the bioremediation of diesel fuel contaminated-Antarctic ecosystems.
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Affiliation(s)
- Alejandro Gran-Scheuch
- Bionanotechnology and Microbiology Lab, Center for Bioinformatics and Integrative Biology, Facultad de Ciencias Biologicas, Universidad Andres BelloSantiago, Chile.,Departamento de Química Inorgánica y Analítica, Facultad de Ciencias Químicas y Farmaceuticas, Universidad de ChileSantiago, Chile
| | - Edwar Fuentes
- Departamento de Química Inorgánica y Analítica, Facultad de Ciencias Químicas y Farmaceuticas, Universidad de ChileSantiago, Chile
| | - Denisse M Bravo
- Laboratorio de Microbiología Oral, Facultad de Odontología, Universidad de ChileSantiago, Chile.,Research and Development Laboratory, uBiomeSantiago, Chile
| | - Juan Cristobal Jiménez
- Bionanotechnology and Microbiology Lab, Center for Bioinformatics and Integrative Biology, Facultad de Ciencias Biologicas, Universidad Andres BelloSantiago, Chile.,Research and Development Laboratory, uBiomeSantiago, Chile
| | - José M Pérez-Donoso
- Bionanotechnology and Microbiology Lab, Center for Bioinformatics and Integrative Biology, Facultad de Ciencias Biologicas, Universidad Andres BelloSantiago, Chile.,Research and Development Laboratory, uBiomeSantiago, Chile
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Gkorezis P, Daghio M, Franzetti A, Van Hamme JD, Sillen W, Vangronsveld J. The Interaction between Plants and Bacteria in the Remediation of Petroleum Hydrocarbons: An Environmental Perspective. Front Microbiol 2016; 7:1836. [PMID: 27917161 PMCID: PMC5116465 DOI: 10.3389/fmicb.2016.01836] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 11/01/2016] [Indexed: 11/24/2022] Open
Abstract
Widespread pollution of terrestrial ecosystems with petroleum hydrocarbons (PHCs) has generated a need for remediation and, given that many PHCs are biodegradable, bio- and phyto-remediation are often viable approaches for active and passive remediation. This review focuses on phytoremediation with particular interest on the interactions between and use of plant-associated bacteria to restore PHC polluted sites. Plant-associated bacteria include endophytic, phyllospheric, and rhizospheric bacteria, and cooperation between these bacteria and their host plants allows for greater plant survivability and treatment outcomes in contaminated sites. Bacterially driven PHC bioremediation is attributed to the presence of diverse suites of metabolic genes for aliphatic and aromatic hydrocarbons, along with a broader suite of physiological properties including biosurfactant production, biofilm formation, chemotaxis to hydrocarbons, and flexibility in cell-surface hydrophobicity. In soils impacted by PHC contamination, microbial bioremediation generally relies on the addition of high-energy electron acceptors (e.g., oxygen) and fertilization to supply limiting nutrients (e.g., nitrogen, phosphorous, potassium) in the face of excess PHC carbon. As an alternative, the addition of plants can greatly improve bioremediation rates and outcomes as plants provide microbial habitats, improve soil porosity (thereby increasing mass transfer of substrates and electron acceptors), and exchange limiting nutrients with their microbial counterparts. In return, plant-associated microorganisms improve plant growth by reducing soil toxicity through contaminant removal, producing plant growth promoting metabolites, liberating sequestered plant nutrients from soil, fixing nitrogen, and more generally establishing the foundations of soil nutrient cycling. In a practical and applied sense, the collective action of plants and their associated microorganisms is advantageous for remediation of PHC contaminated soil in terms of overall cost and success rates for in situ implementation in a diversity of environments. Mechanistically, there remain biological unknowns that present challenges for applying bio- and phyto-remediation technologies without having a deep prior understanding of individual target sites. In this review, evidence from traditional and modern omics technologies is discussed to provide a framework for plant-microbe interactions during PHC remediation. The potential for integrating multiple molecular and computational techniques to evaluate linkages between microbial communities, plant communities and ecosystem processes is explored with an eye on improving phytoremediation of PHC contaminated sites.
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Affiliation(s)
- Panagiotis Gkorezis
- Environmental Biology, Centre for Environmental Sciences, Hasselt UniversityDiepenbeek, Belgium
| | - Matteo Daghio
- Department of Environmental Sciences, University of Milano-BicoccaMilano, Italy
- Department of Biological Sciences, Thompson Rivers University, KamloopsBC, Canada
| | - Andrea Franzetti
- Department of Environmental Sciences, University of Milano-BicoccaMilano, Italy
| | | | - Wouter Sillen
- Environmental Biology, Centre for Environmental Sciences, Hasselt UniversityDiepenbeek, Belgium
| | - Jaco Vangronsveld
- Environmental Biology, Centre for Environmental Sciences, Hasselt UniversityDiepenbeek, Belgium
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18
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Mulla SI, Sun Q, Hu A, Wang Y, Ashfaq M, Eqani SAMAS, Yu CP. Evaluation of Sulfadiazine Degradation in Three Newly Isolated Pure Bacterial Cultures. PLoS One 2016; 11:e0165013. [PMID: 27755578 PMCID: PMC5068754 DOI: 10.1371/journal.pone.0165013] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 10/05/2016] [Indexed: 11/24/2022] Open
Abstract
This study is aimed to assess the biodegradation of sulfadiazine (SDZ) and characterization of heavy metal resistance in three pure bacterial cultures and also their chemotactic response towards 2-aminopyrimidine. The bacterial cultures were isolated from pig manure, activated sludge and sediment samples, by enrichment technique on SDZ (6 mg L-1). Based on the 16S rRNA gene sequence analysis, the microorganisms were identified within the genera of Paracoccus, Methylobacterium and Kribbella, which were further designated as SDZ-PM2-BSH30, SDZ-W2-SJ40 and SDZ-3S-SCL47. The three identified pure bacterial strains degraded up to 50.0, 55.2 and 60.0% of SDZ (5 mg L-1), respectively within 290 h. On the basis of quadrupole time-of-flight mass spectrometry and high performance liquid chromatography, 2-aminopyrimidine and 4-hydroxy-2-aminopyrimidine were identified as the main intermediates of SDZ biodegradation. These bacteria were also able to degrade the metabolite, 2-aminopyrimidine, of the SDZ. Furthermore, SDZ-PM2-BSH30, SDZ-W2-SJ40 and SDZ-3S-SCL47 also showed resistance to various heavy metals like copper, cadmium, chromium, cobalt, lead, nickel and zinc. Additionally, all three bacteria exhibited positive chemotaxis towards 2-aminopyrimidine based on the drop plate method and capillary assay. The results of this study advanced our understanding about the microbial degradation of SDZ, which would be useful towards the future SDZ removal in the environment.
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Affiliation(s)
- Sikandar I. Mulla
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China
| | - Qian Sun
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China
| | - Anyi Hu
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China
| | - Yuwen Wang
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China
| | - Muhammad Ashfaq
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China
| | | | - Chang-Ping Yu
- Graduate Institute of Environmental Engineering, National Taiwan University, Taipei 106, Taiwan
- * E-mail:
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Hashmi MZ, Qin Z, Yao X, Ahmed Z, Xiaomei S, Shen C, Tang X. PCBs attenuation and abundance of Dehalococcoides spp., bphC, CheA, and flic genes in typical polychlorinated biphenyl-polluted soil under floody and dry soil conditions. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:3907-3913. [PMID: 26503002 DOI: 10.1007/s11356-015-5577-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 10/07/2015] [Indexed: 06/05/2023]
Abstract
This study investigates PCBs attenuation and the abundance of active polychlorinated-degrading Dehalococcoides spp. biphenyl dioxygenase (bphC), chemotaxis (CheA), and flagellum (flic) genes in floody and dry soil conditions polluted with polychlorinated biphenyls. The results revealed that total PCBs, high chlorinated PCBs (>4 cl), and less chlorinated PCBs (<4 cl) decreased with the passage of time in floody and dry soil conditions. The reduction of total PCBs (13.87%) and less chlorinated PCBs (15.39%) was more in dry soil than floody soil, while high chlorinated PCBs showed more reduction in floody soil (8.06%) than dry soil. Dehaloccoides spp., bphC, CheA, and flic genes indicated temporal dynamics in abundance in floody and dry soil conditions. The highest abundance was 1.6 × 10(9), 3.7 × 10(4), and 3.6 × 10(2) copies in floody and 1.6 × 10(4) copies in dry soil for Dehalococcoides spp., bphC, CheA, and flic, respectively. Multivariate statistics (RDA) revealed that Dehaloccoides spp. were positively influenced by the higher chlorinated PCBs and soil physical properties, CheA gene with floody soil, flic gene with total PCBs and less chlorinated PCBs, and bphC gene was affected with moisture contents and less chlorinated PCBs. This study provides new insight in the attenuation of PCBs and the abundance of active Dehalococcoides spp. and genes in PCBs polluted soil under floody and dry soil conditions.
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Affiliation(s)
- Muhammad Zaffar Hashmi
- College of Environmental and Natural Resource Sciences, Zhejiang University, Yuhangtang Road 866, Hangzhou, 310058, Zhejiang, People's Republic of China
- Department of Meteorology, COMSATS Institute of Information Technology, Park road, Islamabad, Pakistan
- Institute of Health and Management Sciences, Green Avenue, Park Road, Islamabad, Pakistan
| | - Zhihui Qin
- College of Environmental and Natural Resource Sciences, Zhejiang University, Yuhangtang Road 866, Hangzhou, 310058, Zhejiang, People's Republic of China
| | - Xiaoyan Yao
- College of Environmental and Natural Resource Sciences, Zhejiang University, Yuhangtang Road 866, Hangzhou, 310058, Zhejiang, People's Republic of China
| | - Zulkifl Ahmed
- Department of Building and Architecture Engineering, Bahauddin Zakariya University, Multan, Pakistan
| | - Su Xiaomei
- College of Environmental and Natural Resource Sciences, Zhejiang University, Yuhangtang Road 866, Hangzhou, 310058, Zhejiang, People's Republic of China
| | - Chaofeng Shen
- College of Environmental and Natural Resource Sciences, Zhejiang University, Yuhangtang Road 866, Hangzhou, 310058, Zhejiang, People's Republic of China
| | - Xianjin Tang
- College of Environmental and Natural Resource Sciences, Zhejiang University, Yuhangtang Road 866, Hangzhou, 310058, Zhejiang, People's Republic of China.
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Abstract
Pseudomonads sense changes in the concentration of chemicals in their environment and exhibit a behavioral response mediated by flagella or pili coupled with a chemosensory system. The two known chemotaxis pathways, a flagella-mediated pathway and a putative pili-mediated system, are described in this review. Pseudomonas shows chemotaxis response toward a wide range of chemicals, and this review includes a summary of them organized by chemical structure. The assays used to measure positive and negative chemotaxis swimming and twitching Pseudomonas as well as improvements to those assays and new assays are also described. This review demonstrates that there is ample research and intellectual space for future investigators to elucidate the role of chemotaxis in important processes such as pathogenesis, bioremediation, and the bioprotection of plants and animals.
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Affiliation(s)
| | - Rebecca E Parales
- Department of Microbiology and Molecular Genetics, College of Biological Sciences, University of California, Davis, CA, USA
| | - Tino Krell
- Department of Environmental Protection, CSIC, Estacion Experimental del Zaidin, Granada, Spain
| | - Jane E Hill
- Thayer School of Engineering, Dartmouth College, Hanover, NH, USA
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21
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Metabolism Dependent Chemotaxis of Pseudomonas aeruginosa N1 Towards Anionic Detergent Sodium Dodecyl Sulfate. Indian J Microbiol 2014; 54:134-8. [PMID: 25320412 DOI: 10.1007/s12088-013-0426-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Accepted: 09/09/2013] [Indexed: 10/26/2022] Open
Abstract
Sodium dodecyl sulfate (SDS) is one of the most commonly used detergent, which exhibits excellent biocidal activity against various bacteria and fungi. It is commonly employed in many detergent formulations and is employed for disinfection purposes. It is shown to be toxic to fishes, aquatic animals and is also inhibitory to microbes and cyanobacteria. We had isolated a strain belonging to Pseudomonas aeruginosa N1, from a detergent contaminated pond situated in Varanasi city India, which was able to degrade and metabolize SDS as a source of carbon. In the present investigation, we have studied chemotactic response of this strain towards SDS. The results clearly indicate that this strain showed chemotactic response towards SDS. The nature of chemotaxis was found to be metabolism dependent as glucose grown cells showed a delayed chemotactic response towards SDS. This is first study that reported chemotaxis response for P. aeruginosa towards anionic detergent SDS.
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Darias JAR, García-Fontana C, Lugo AC, Rico-Jiménez M, Krell T. Qualitative and quantitative assays for flagellum-mediated chemotaxis. Methods Mol Biol 2014; 1149:87-97. [PMID: 24818900 DOI: 10.1007/978-1-4939-0473-0_10] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
A primary driving force during bacterial evolution was the capacity to access compounds necessary for growth and survival. Since the species of the genus Pseudomonas are characterized by metabolic versatility, these bacteria have developed chemotactic behaviors towards a wide range of different compounds. The specificity of a chemotactic response is determined by the chemoreceptor, which is at the beginning of the signaling cascade and to which chemoattractants and chemorepellents bind. The number of chemoreceptor genes of Pseudomonas species is significantly higher than the average number in motile bacteria. Although some of the receptors have been annotated with a function, the cognate signal molecules for the majority of them still need to be identified. Different qualitative and quantitative methods are presented that can be used to study flagellum-mediated taxis.
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Affiliation(s)
- José Antonio Reyes Darias
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/ Prof. Albareda 1, 18008, Granada, Spain
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Identification of CtpL as a chromosomally encoded chemoreceptor for 4-chloroaniline and catechol in Pseudomonas aeruginosa PAO1. Appl Environ Microbiol 2013; 79:7241-8. [PMID: 24038698 DOI: 10.1128/aem.02428-13] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacterial chemotaxis influences the ability of bacteria to survive and thrive in most environments, including polluted ones. Despite numerous reports of the phenotypic characterization of chemotactic bacteria, only a few molecular details of chemoreceptors for aromatic pollutants have been described. In this study, the molecular basis of chemotaxis toward an environmentally toxic chlorinated aromatic pollutant, 4-chloroaniline (4CA), was evaluated. Among the three Pseudomonas spp. tested, Pseudomonas aeruginosa PAO1 exhibited positive chemotaxis both to the nonmetabolizable 4CA, where 4-chloroacetanilide was formed as a dead-end transformation product, and to the metabolizable catechol. Molecular analysis of all 26 mutants with a disrupted methyl-accepting chemotaxis gene revealed that CtpL, a chromosomally encoded chemoreceptor, was responsible for the positive chemotactic response toward 4CA. Since CtpL has previously been described to be a major chemoreceptor for inorganic phosphate at low concentrations in PAO1, this report describes a fortuitous ability of CtpL to function toward aromatic pollutants. In addition, its regulation not only was dependent on the presence of the chemoattractant inducer but also was regulated by conditions of phosphate starvation. These results expand the range of known chemotactic transducers and their function in the environmental bacterium PAO1.
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Krell T, Lacal J, Reyes-Darias JA, Jimenez-Sanchez C, Sungthong R, Ortega-Calvo JJ. Bioavailability of pollutants and chemotaxis. Curr Opin Biotechnol 2013; 24:451-6. [DOI: 10.1016/j.copbio.2012.08.011] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Revised: 08/27/2012] [Accepted: 08/29/2012] [Indexed: 10/27/2022]
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Ditty JL, Williams KM, Keller MM, Chen GY, Liu X, Parales RE. Integrating grant-funded research into the undergraduate biology curriculum using IMG-ACT. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2013; 41:16-23. [PMID: 23382122 DOI: 10.1002/bmb.20662] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Indexed: 06/01/2023]
Abstract
It has become clear in current scientific pedagogy that the emersion of students in the scientific process in terms of designing, implementing, and analyzing experiments is imperative for their education; as such, it has been our goal to model this active learning process in the classroom and laboratory in the context of a genuine scientific question. Toward this objective, the National Science Foundation funded a collaborative research grant between a primarily undergraduate institution and a research-intensive institution to study the chemotactic responses of the bacterium Pseudomonas putida F1. As part of the project, a new Bioinformatics course was developed in which undergraduates annotate relevant regions of the P. putida F1 genome using Integrated Microbial Genomes Annotation Collaboration Toolkit, a bioinformatics interface specifically developed for undergraduate programs by the Department of Energy Joint Genome Institute. Based on annotations of putative chemotaxis genes in P. putida F1 and comparative genomics studies, undergraduate students from both institutions developed functional genomics research projects that evolved from the annotations. The purpose of this study is to describe the nature of the NSF grant, the development of the Bioinformatics lecture and wet laboratory course, and how undergraduate student involvement in the project that was initiated in the classroom has served as a springboard for independent undergraduate research projects.
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Affiliation(s)
- Jayna L Ditty
- Department of Biology, University of St. Thomas, St. Paul, MN, USA.
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Lacal J, Reyes-Darias JA, García-Fontana C, Ramos JL, Krell T. Tactic responses to pollutants and their potential to increase biodegradation efficiency. J Appl Microbiol 2012; 114:923-33. [PMID: 23163356 DOI: 10.1111/jam.12076] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Revised: 11/07/2012] [Accepted: 11/11/2012] [Indexed: 11/26/2022]
Abstract
A significant number of bacterial strains are able to use toxic aromatic hydrocarbons as carbon and energy sources. In a number of cases, the evolution of the corresponding degradation pathway was accompanied by the evolution of tactic behaviours either towards or away from these toxic carbon sources. Reports are reviewed which show that a chemoattraction to heterogeneously distributed aromatic pollutants increases the bioavailability of these compounds and their biodegradation efficiency. An extreme form of chemoattraction towards aromatic pollutants, termed 'hyperchemotaxis', was described for Pseudomonas putida DOT-T1E, which is based on the action of the plasmid-encoded McpT chemoreceptor. Cells with this phenotype were found of being able to approach and of establishing contact with undiluted crude oil samples. Although close McpT homologues are found on other degradation plasmids, the sequence of their ligand-binding domains does not share significant similarity with that of NahY, the other characterized chemoreceptor for aromatic hydrocarbons. This may suggest the existence of at least two families of chemoreceptors for aromatic pollutants. The use of receptor chimers comprising the ligand-binding region of McpT for biosensing purposes is discussed.
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Affiliation(s)
- J Lacal
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
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27
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Pandey J, Sharma NK, Khan F, Ghosh A, Oakeshott JG, Jain RK, Pandey G. Chemotaxis of Burkholderia sp. strain SJ98 towards chloronitroaromatic compounds that it can metabolise. BMC Microbiol 2012; 12:19. [PMID: 22292983 PMCID: PMC3293717 DOI: 10.1186/1471-2180-12-19] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2011] [Accepted: 02/01/2012] [Indexed: 11/10/2022] Open
Abstract
Background Burkholderia sp. strain SJ98 is known for its chemotaxis towards nitroaromatic compounds (NACs) that are either utilized as sole sources of carbon and energy or co-metabolized in the presence of alternative carbon sources. Here we test for the chemotaxis of this strain towards six chloro-nitroaromatic compounds (CNACs), namely 2-chloro-4-nitrophenol (2C4NP), 2-chloro-3-nitrophenol (2C3NP), 4-chloro-2-nitrophenol (4C2NP), 2-chloro-4-nitrobenzoate (2C4NB), 4-chloro-2-nitrobenzoate (4C2NB) and 5-chloro-2-nitrobenzoate (5C2NB), and examine its relationship to the degradation of such compounds. Results Strain SJ98 could mineralize 2C4NP, 4C2NB and 5C2NB, and co-metabolically transform 2C3NP and 2C4NB in the presence of an alternative carbon source, but was unable to transform 4C2NP under these conditions. Positive chemotaxis was only observed towards the five metabolically transformed CNACs. Moreover, the chemotaxis was induced by growth in the presence of the metabolisable CNAC. It was also competitively inhibited by the presence of nitroaromatic compounds (NACs) that it could metabolise but not by succinate or aspartate. Conclusions Burkholderia sp. strain SJ98 exhibits metabolic transformation of, and inducible chemotaxis towards CNACs. Its chemotactic responses towards these compounds are related to its previously demonstrated chemotaxis towards NACs that it can metabolise, but it is independently inducible from its chemotaxis towards succinate or aspartate.
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Affiliation(s)
- Janmejay Pandey
- Institute of Microbial Technology, Sector 39A, Chandigarh 160036, India
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Plant exudates promote PCB degradation by a rhodococcal rhizobacteria. Appl Microbiol Biotechnol 2011; 95:1589-603. [PMID: 22202970 DOI: 10.1007/s00253-011-3824-z] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2011] [Revised: 12/04/2011] [Accepted: 12/07/2011] [Indexed: 10/14/2022]
Abstract
Rhodococcus erythropolis U23A is a polychlorinated biphenyl (PCB)-degrading bacterium isolated from the rhizosphere of plants grown on a PCB-contaminated soil. Strain U23A bphA exhibited 99% identity with bphA1 of Rhodococcus globerulus P6. We grew Arabidopsis thaliana in a hydroponic axenic system, collected, and concentrated the plant secondary metabolite-containing root exudates. Strain U23A exhibited a chemotactic response toward these root exudates. In a root colonizing assay, the number of cells of strain U23A associated to the plant roots (5.7 × 10⁵ CFU g⁻¹) was greater than the number remaining in the surrounding sand (4.5 × 10⁴ CFU g⁻¹). Furthermore, the exudates could support the growth of strain U23A. In a resting cell suspension assay, cells grown in a minimal medium containing Arabidopsis root exudates as sole growth substrate were able to metabolize 2,3,4'- and 2,3',4-trichlorobiphenyl. However, no significant degradation of any of congeners was observed for control cells grown on Luria-Bertani medium. Although strain U23A was unable to grow on any of the flavonoids identified in root exudates, biphenyl-induced cells metabolized flavanone, one of the major root exudate components. In addition, when used as co-substrate with sodium acetate, flavanone was as efficient as biphenyl to induce the biphenyl catabolic pathway of strain U23A. Together, these data provide supporting evidence that some rhodococci can live in soil in close association with plant roots and that root exudates can support their growth and trigger their PCB-degrading ability. This suggests that, like the flagellated Gram-negative bacteria, non-flagellated rhodococci may also play a key role in the degradation of persistent pollutants.
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Lacal J, Muñoz-Martínez F, Reyes-Darías JA, Duque E, Matilla M, Segura A, Calvo JJO, Jímenez-Sánchez C, Krell T, Ramos JL. Bacterial chemotaxis towards aromatic hydrocarbons in Pseudomonas. Environ Microbiol 2011; 13:1733-44. [DOI: 10.1111/j.1462-2920.2011.02493.x] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Tremaroli V, Fedi S, Tamburini S, Viti C, Tatti E, Ceri H, Turner RJ, Zannoni D. A histidine-kinase cheA gene of Pseudomonas pseudoalcaligens KF707 not only has a key role in chemotaxis but also affects biofilm formation and cell metabolism. BIOFOULING 2011; 27:33-46. [PMID: 21108067 DOI: 10.1080/08927014.2010.537099] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
A histidine-kinase cheA gene in Pseudomonas pseudoalcaligenes KF707 plays a central role in the regulation of metabolic responses as well as in chemotaxis. Non-chemotactic mutants harboring insertions into the cheA gene were screened for their ability to form biofilms in the Calgary biofilm device. Notably, ≥95% decrease in the number of cells attached to the polystyrene surface was observed in cheA mutants compared to the KF707 wild-type biofilm phenotype. The ability to form mature biofilms was restored to wild-type levels, providing functional copies of the KF707 cheA gene to the mutants. In addition, phenotype micro-arrays and proteomic analyses revealed that several basic metabolic activities and a few periplasmic binding proteins of cheA mutant cells differed compared to those of wild-type cells. These results are interpreted as evidence of a strong integration between chemotactic and metabolic pathways in the process of biofilm development by P. pseudoalcaligenes KF707.
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Affiliation(s)
- V Tremaroli
- Department of Biological Sciences & Biofilm Research Group, University of Calgary, Calgary, Alberta, Canada
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Tremaroli V, Vacchi Suzzi C, Fedi S, Ceri H, Zannoni D, Turner RJ. Tolerance of Pseudomonas pseudoalcaligenes KF707 to metals, polychlorobiphenyls and chlorobenzoates: effects on chemotaxis-, biofilm- and planktonic-grown cells. FEMS Microbiol Ecol 2010; 74:291-301. [PMID: 20846140 DOI: 10.1111/j.1574-6941.2010.00965.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Pseudomonas pseudoalcaligenes KF707 is a polychlorinated biphenyls (PCBs) degrader, also tolerant to several toxic metals and metalloids. The work presented here examines for the first time the chemotactic response of P. pseudoalcaligenes KF707 to biphenyl and intermediates of the PCB biodegradation pathway in the presence and absence of metals. Chemotaxis analyses showed that biphenyl, benzoic acid and chlorobenzoic acids acted as chemoattractants for KF707 cells and that metal cations such as Ni(2+) and Cu(2+) strongly affected the chemotactic response. Toxicity profiles of various metals on KF707 cells grown on succinate or biphenyl as planktonic and biofilm were determined both in the presence and in the absence of PCBs. Notably, KF707 cells from both biofilms and planktonic cultures were tolerant to high amounts (up to 0.5 g L(-1)) of Aroclor 1242, a commercial mixture of PCBs. Together, the data show that KF707 cells are chemotactic and can form a biofilm in the presence of Aroclor 1242 and specific metals. These findings provide new perspectives on the effectiveness of using PCB-degrading bacterial strains in bioremediation strategies of metal-co-contaminated sites.
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Affiliation(s)
- Valentina Tremaroli
- Department of Biology, General Microbiology Unit, University of Bologna, Bologna, Italy
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Campos VL, Valenzuela C, Yarza P, Kämpfer P, Vidal R, Zaror C, Mondaca MA, Lopez-Lopez A, Rosselló-Móra R. Pseudomonas arsenicoxydans sp nov., an arsenite-oxidizing strain isolated from the Atacama desert. Syst Appl Microbiol 2010; 33:193-7. [DOI: 10.1016/j.syapm.2010.02.007] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2010] [Revised: 02/22/2010] [Accepted: 02/23/2010] [Indexed: 11/16/2022]
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Wang G, Or D. Aqueous films limit bacterial cell motility and colony expansion on partially saturated rough surfaces. Environ Microbiol 2010; 12:1363-73. [DOI: 10.1111/j.1462-2920.2010.02180.x] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Pandey J, Chauhan A, Jain RK. Integrative approaches for assessing the ecological sustainability ofin situbioremediation. FEMS Microbiol Rev 2009; 33:324-75. [PMID: 19178567 DOI: 10.1111/j.1574-6976.2008.00133.x] [Citation(s) in RCA: 120] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
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Rudrappa T, Czymmek KJ, Paré PW, Bais HP. Root-secreted malic acid recruits beneficial soil bacteria. PLANT PHYSIOLOGY 2008; 148:1547-56. [PMID: 18820082 PMCID: PMC2577262 DOI: 10.1104/pp.108.127613] [Citation(s) in RCA: 479] [Impact Index Per Article: 29.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Beneficial soil bacteria confer immunity against a wide range of foliar diseases by activating plant defenses, thereby reducing a plant's susceptibility to pathogen attack. Although bacterial signals have been identified that activate these plant defenses, plant metabolites that elicit rhizobacterial responses have not been demonstrated. Here, we provide biochemical evidence that the tricarboxylic acid cycle intermediate L-malic acid (MA) secreted from roots of Arabidopsis (Arabidopsis thaliana) selectively signals and recruits the beneficial rhizobacterium Bacillus subtilis FB17 in a dose-dependent manner. Root secretions of L-MA are induced by the foliar pathogen Pseudomonas syringae pv tomato (Pst DC3000) and elevated levels of L-MA promote binding and biofilm formation of FB17 on Arabidopsis roots. The demonstration that roots selectively secrete L-MA and effectively signal beneficial rhizobacteria establishes a regulatory role of root metabolites in recruitment of beneficial microbes, as well as underscores the breadth and sophistication of plant-microbial interactions.
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Affiliation(s)
- Thimmaraju Rudrappa
- Department of Plant and Soil Sciences, University of Delaware, Newark, Delaware 19716, USA
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