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Maral-Gül D, Eltem R. Evaluation of Bacillus isolates as a biological control agents against soilborne phytopathogenic fungi. Int Microbiol 2024:10.1007/s10123-024-00490-1. [PMID: 38376639 DOI: 10.1007/s10123-024-00490-1] [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: 08/03/2023] [Revised: 01/03/2024] [Accepted: 02/07/2024] [Indexed: 02/21/2024]
Abstract
Pesticides, used in agriculture to control plant diseases, pose risks to the environment and human health. To address this, there's a growing focus on biocontrol, using microorganisms instead of chemicals. In this study, we aimed to identify Bacillus isolates as potential biological control agents. We tested 1574 Bacillus isolates for antifungal effects against pathogens like Botrytis cinerea, Fusarium solani, and Rhizoctonia solani. Out of these, 77 isolates formed inhibition zones against all three pathogens. We then investigated their lytic enzyme activities (protease, chitinase, and chitosanase) and the production of antifungal metabolites (siderophore and hydrogen cyanide). Coagulase activity was also examined to estimate potential pathogenicity in humans and animals. After evaluating all mechanisms, 19 non-pathogenic Bacillus isolates with significant antifungal effects were chosen. Molecular identification revealed they belonged to B. subtilis (n = 19) strains. The 19 native Bacillus strains, demonstrating strong antifungal effects in vitro, have the potential to form the basis for biocontrol product development. This could address challenges in agricultural production, marking a crucial stride toward sustainable agriculture.
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Affiliation(s)
- Derya Maral-Gül
- Graduate School of Natural and Applied Sciences, Department of Bioengineering, Ege University, 35100, Bornova-Izmir, Türkiye.
| | - Rengin Eltem
- Faculty of Engineering, Department of Bioengineering, Ege University, Izmir, Türkiye
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2
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Chukwudulue UM, Barger N, Dubovis M, Luzzatto Knaan T. Natural Products and Pharmacological Properties of Symbiotic Bacillota (Firmicutes) of Marine Macroalgae. Mar Drugs 2023; 21:569. [PMID: 37999393 PMCID: PMC10672036 DOI: 10.3390/md21110569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 10/24/2023] [Accepted: 10/25/2023] [Indexed: 11/25/2023] Open
Abstract
The shift from the terrestrial to the marine environment to discover natural products has given rise to novel bioactive compounds, some of which have been approved for human medicine. However, the ocean, which makes up nearly three-quarters of the Earth's surface, contains macro- and microorganisms whose natural products are yet to be explored. Among these underexplored marine organisms are macroalgae and their symbiotic microbes, such as Bacillota, a phylum of mostly Gram-positive bacteria previously known as Firmicutes. Macroalgae-associated Bacillota often produce chemical compounds that protect them and their hosts from competitive and harmful rivals. Here, we summarised the natural products made by macroalgae-associated Bacillota and their pharmacological properties. We discovered that these Bacillota are efficient producers of novel biologically active molecules. However, only a few macroalgae had been investigated for chemical constituents of their Bacillota: nine brown, five red and one green algae. Thus, Bacillota, especially from the marine habitat, should be investigated for potential pharmaceutical leads. Moreover, additional diverse biological assays for the isolated molecules of macroalgae Bacillota should be implemented to expand their bioactivity profiles, as only antibacterial properties were tested for most compounds.
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Affiliation(s)
| | | | | | - Tal Luzzatto Knaan
- Department of Marine Biology, The Charney School of Marine Sciences, University of Haifa, Mount Carmel, Haifa 103301, Israel; (U.M.C.); (N.B.); (M.D.)
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3
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Zhang Y, Lin M, Qin Y, Lu H, Xu X, Gao C, Liu Y, Luo W, Luo X. Anti-Vibrio potential of natural products from marine microorganisms. Eur J Med Chem 2023; 252:115330. [PMID: 37011553 DOI: 10.1016/j.ejmech.2023.115330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 03/28/2023] [Accepted: 03/28/2023] [Indexed: 03/31/2023]
Abstract
The emergence of drug-resistant Vibrio poses a serious threat to aquaculture and human health, thus there is an urgent need for the discovery of new related antibiotics. Given that marine microorganisms (MMs) are evidenced as important sources of antibacterial natural products (NPs), great attention has been gained to the exploration of potential anti-Vibrio agents from MMs. This review summarizes the occurrence, structural diversity, and biological activities of 214 anti-Vibrio NPs isolated from MMs (from 1999 to July 2022), including 108 new compounds. They were predominantly originated from marine fungi (63%) and bacteria (30%) with great structural diversity, including polyketides, nitrogenous compounds, terpenoids, and steroids, among which polyketides account for nearly half (51%) of them. This review will shed light on the development of MMs derived NPs as potential anti-Vibrio lead compounds with promising applications in agriculture and human health.
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Iqbal S, Begum F, Rabaan AA, Aljeldah M, Al Shammari BR, Alawfi A, Alshengeti A, Sulaiman T, Khan A. Classification and Multifaceted Potential of Secondary Metabolites Produced by Bacillus subtilis Group: A Comprehensive Review. Molecules 2023; 28:molecules28030927. [PMID: 36770594 PMCID: PMC9919246 DOI: 10.3390/molecules28030927] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 12/31/2022] [Accepted: 01/04/2023] [Indexed: 01/19/2023] Open
Abstract
Despite their remarkable biosynthetic potential, Bacillus subtilis have been widely overlooked. However, their capability to withstand harsh conditions (extreme temperature, Ultraviolet (UV) and γ-radiation, and dehydration) and the promiscuous metabolites they synthesize have created increased commercial interest in them as a therapeutic agent, a food preservative, and a plant-pathogen control agent. Nevertheless, the commercial-scale availability of these metabolites is constrained due to challenges in their accessibility via synthesis and low fermentation yields. In the context of this rising in interest, we comprehensively visualized the antimicrobial peptides produced by B. subtilis and highlighted their prospective applications in various industries. Moreover, we proposed and classified these metabolites produced by the B. subtilis group based on their biosynthetic pathways and chemical structures. The biosynthetic pathway, bioactivity, and chemical structure are discussed in detail for each class. We believe that this review will spark a renewed interest in the often disregarded B. subtilis and its remarkable biosynthetic capabilities.
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Affiliation(s)
- Sajid Iqbal
- Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology (NUST), Islamabad 44000, Pakistan
- Correspondence: or
| | - Farida Begum
- Department of Biochemistry, Abdul Wali Khan University Mardan (AWKUM), Mardan 23200, Pakistan
| | - Ali A. Rabaan
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, Dhahran 31311, Saudi Arabia
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
- Department of Public Health and Nutrition, The University of Haripur, Haripur 22610, Pakistan
| | - Mohammed Aljeldah
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, University of Hafr Al Batin, Hafr Al Batin 39831, Saudi Arabia
| | - Basim R. Al Shammari
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, University of Hafr Al Batin, Hafr Al Batin 39831, Saudi Arabia
| | - Abdulsalam Alawfi
- Department of Pediatrics, College of Medicine, Taibah University, Al-Madinah 41491, Saudi Arabia
| | - Amer Alshengeti
- Department of Pediatrics, College of Medicine, Taibah University, Al-Madinah 41491, Saudi Arabia
- Department of Infection Prevention and Control, Prince Mohammad Bin Abdulaziz Hospital, National Guard Health Affairs, Al-Madinah 41491, Saudi Arabia
| | - Tarek Sulaiman
- Infectious Diseases Section, Medical Specialties Department, King Fahad Medical City, Riyadh 12231, Saudi Arabia
| | - Alam Khan
- Department of Life Sciences, Abasyn University Islamabad Campus, Islamabad 44000, Pakistan
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Iqbal S, Qasim M, Rahman H, Khan N, Paracha RZ, Bhatti MF, Javed A, Janjua HA. Genome mining, antimicrobial and plant growth-promoting potentials of halotolerant Bacillus paralicheniformis ES-1 isolated from salt mine. Mol Genet Genomics 2023; 298:79-93. [PMID: 36301366 DOI: 10.1007/s00438-022-01964-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 10/11/2022] [Indexed: 01/10/2023]
Abstract
Salinity severely affects crop yield by hindering nitrogen uptake and reducing plant growth. Plant growth-promoting bacteria (PGPB) are capable of providing cross-protection against biotic/abiotic stresses and facilitating plant growth. Genome-level knowledge of PGPB is necessary to translate the knowledge into a product as efficient biofertilizers and biocontrol agents. The current study aimed to isolate and characterize indigenous plant growth-promoting strains with the potential to promote plant growth under various stress conditions. In this regard, 72 bacterial strains were isolated from various saline-sodic soil/lakes; 19 exhibited multiple in vitro plant growth-promoting traits, including indole 3 acetic acid production, phosphate solubilization, siderophore synthesis, lytic enzymes production, biofilm formation, and antibacterial activities. To get an in-depth insight into genome composition and diversity, whole-genome sequence and genome mining of one promising Bacillus paralicheniformis strain ES-1 were performed. The strain ES-1 genome carries 12 biosynthetic gene clusters, at least six genomic islands, and four prophage regions. Genome mining identified plant growth-promoting conferring genes such as phosphate solubilization, nitrogen fixation, tryptophan production, siderophore, acetoin, butanediol, chitinase, hydrogen sulfate synthesis, chemotaxis, and motility. Comparative genome analysis indicates the region of genome plasticity which shapes the structure and function of B. paralicheniformis and plays a crucial role in habitat adaptation. The strain ES-1 has a relatively large accessory genome of 649 genes (~ 19%) and 180 unique genes. Overall, these results provide valuable insight into the bioactivity and genomic insight into B. paralicheniformis strain ES-1 with its potential use in sustainable agriculture.
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Affiliation(s)
- Sajid Iqbal
- Department of Industrial Biotechnology, Atta-Ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, Islamabad, Pakistan
| | - Muhammad Qasim
- Department of Microbiology, Kohat University of Science and Technology (KUST), Kohat, Pakistan
| | - Hazir Rahman
- Department of Microbiology, Abdul Wali Khan University Mardan (AWKUM), Mardan, Pakistan
| | - Naeem Khan
- Department of Agronomy, University of Florida, Gainesville, FL, 32611, USA
| | - Rehan Zafar Paracha
- School of Interdisciplinary Engineering and Science (SINES, National University of Sciences and Technology (NUST), H-12, Islamabad, Pakistan
| | - Muhammad Faraz Bhatti
- Department of Plant Biotechnology, Atta-Ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, Islamabad, Pakistan
| | - Aneela Javed
- Department of Healthcare Biotechnology, Atta-Ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, Islamabad, Pakistan
| | - Hussnain Ahmed Janjua
- Department of Industrial Biotechnology, Atta-Ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, Islamabad, Pakistan.
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Coppola D, Buonocore C, Palisse M, Tedesco P, de Pascale D. Exploring Oceans for Curative Compounds: Potential New Antimicrobial and Anti-Virulence Molecules against Pseudomonas aeruginosa. Mar Drugs 2022; 21:md21010009. [PMID: 36662182 PMCID: PMC9865402 DOI: 10.3390/md21010009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 12/16/2022] [Accepted: 12/20/2022] [Indexed: 12/28/2022] Open
Abstract
Although several antibiotics are already widely used against a large number of pathogens, the discovery of new antimicrobial compounds with new mechanisms of action is critical today in order to overcome the spreading of antimicrobial resistance among pathogen bacteria. In this regard, marine organisms represent a potential source of a wide diversity of unique secondary metabolites produced as an adaptation strategy to survive in competitive and hostile environments. Among the multidrug-resistant Gram-negative bacteria, Pseudomonas aeruginosa is undoubtedly one of the most important species due to its high intrinsic resistance to different classes of antibiotics on the market and its ability to cause serious therapeutic problems. In the present review, we first discuss the general mechanisms involved in the antibiotic resistance of P. aeruginosa. Subsequently, we list the marine molecules identified up until now showing activity against P. aeruginosa, dividing them according to whether they act as antimicrobial or anti-virulence compounds.
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Affiliation(s)
- Daniela Coppola
- Department of Ecosustainable Marine Biotechnology, Stazione Zoologica Anton Dohrn, Via Ammiraglio Ferdinando Acton 55, 80133 Naples, Italy
- Correspondence: (D.C.); (D.d.P.)
| | - Carmine Buonocore
- Department of Ecosustainable Marine Biotechnology, Stazione Zoologica Anton Dohrn, Via Ammiraglio Ferdinando Acton 55, 80133 Naples, Italy
| | - Morgan Palisse
- Département des Sciences de la Vie et de la Terre, Université de Caen Normandie, Boulevard Maréchal Juin CS, CEDEX, 14032 Caen, France
| | - Pietro Tedesco
- Department of Ecosustainable Marine Biotechnology, Stazione Zoologica Anton Dohrn, Via Ammiraglio Ferdinando Acton 55, 80133 Naples, Italy
| | - Donatella de Pascale
- Department of Ecosustainable Marine Biotechnology, Stazione Zoologica Anton Dohrn, Via Ammiraglio Ferdinando Acton 55, 80133 Naples, Italy
- Correspondence: (D.C.); (D.d.P.)
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7
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Seaweed-associated heterotrophic bacteria: are they future novel sources of antimicrobial agents against drug-resistant pathogens? Arch Microbiol 2022; 204:232. [PMID: 35355132 DOI: 10.1007/s00203-022-02835-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/06/2022] [Accepted: 03/09/2022] [Indexed: 11/02/2022]
Abstract
Emergence of multidrug-resistant microorganisms and requirements for novel antimicrobial compounds necessitate exploring newer habitats to develop potential bioactive leads. Culture-contingent analysis of heterotrophic bacterial flora from the seaweeds led to the isolation of bioactive strains possessing potential antibacterial properties against wide-ranging clinical pathogens viz., methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant Enterococcus faecalis (VREfs). Seven of the most active strains belonging to the phylum Firmicutes isolated from a brown seaweed (Phaeophyceae) Sargassum wightii exhibited spot-over-lawn assay guided inhibition zone of larger than 30 mm. Integrated phenotypic and genotypic studies have led to the characterization of the seaweed-associated bacteria particularly belonging to the phylum Firmicutes. The organic extracts of the studied bacteria exhibited promising antibacterial properties against MRSA and VREfs with minimum inhibitory concentration ranging between 6.25 and 12.50 μg/mL. Time-kill kinetic profiles of those bacteria displayed rapid bactericidal activity against both E. coli and MRSA, showing a ≥ 3log10 reduction in viable cell count than the initial. Among the studied bioactive Bacillus spp, B. tequilensis MTCC13043 and B. altiitudinis MTCC13046 were found to possess functional polyketide synthase (pks) gene (MW027664 and MW027660) that could be amplified. The outcome of amplified genes encrypting for polyketide synthase in conjunction with antibacterial activities unveiled the broad-spectrum antimicrobial activities of the marine heterotrophic Firmicutes, which could be further used against the emergent problem of antibiotic-resistant bacterial pathogens.
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8
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Antibacterial Molecules from Marine Microorganisms against Aquatic Pathogens: A Concise Review. Mar Drugs 2022; 20:md20040230. [PMID: 35447903 PMCID: PMC9027299 DOI: 10.3390/md20040230] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 03/19/2022] [Accepted: 03/24/2022] [Indexed: 02/05/2023] Open
Abstract
Antibiotic resistance and residues in aquaculture are a growing concern worldwide and consequently identifying favorable antibacterial compounds against aquatic pathogenic bacteria are gained more attention. Active compounds derived from marine microorganisms have shown great promise in this area. This review is aimed to make a comprehensive survey of anti-aquatic pathogenic bacterial compounds that were produced by marine microorganisms. A total of 79 compounds have been reported, covering literature from 1997 to 2021. The compounds are included in different structural classes such as polyketides, terpenoids, nitrogen compounds and others, and some of them present the potential to be developed into agents for the treatment of aquatic pathogenic bacteria.
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9
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Li H, Maimaitiming M, Zhou Y, Li H, Wang P, Liu Y, Schäberle TF, Liu Z, Wang CY. Discovery of Marine Natural Products as Promising Antibiotics against Pseudomonas aeruginosa. Mar Drugs 2022; 20:192. [PMID: 35323491 PMCID: PMC8954164 DOI: 10.3390/md20030192] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/02/2022] [Accepted: 03/03/2022] [Indexed: 12/29/2022] Open
Abstract
Pseudomonas aeruginosa, one of the most intractable Gram-negative bacteria, has become a public health threat due to its outer polysaccharide layer, efflux transporter system, and high level of biofilm formation, all of which contribute to multi-drug resistance. Even though it is a pathogen of the highest concern, the status of the antibiotic development pipeline is unsatisfactory. In this review, we summarize marine natural products (MNPs) isolated from marine plants, animals, and microorganisms which possess unique structures and promising antibiotic activities against P. aeruginosa. In the last decade, nearly 80 such MNPs, ranging from polyketides to alkaloids, peptides, and terpenoids, have been discovered. Representative compounds exhibited impressive in vitro anti-P. aeruginosa activities with MIC values in the single-digit nanomolar range and in vivo efficacy in infectious mouse models. For some of the compounds, the preliminary structure-activity-relationship (SAR) and anti-bacterial mechanisms of selected compounds were introduced. Compounds that can disrupt biofilm formation or membrane integrity displayed potent inhibition of multi-resistant clinical P. aeruginosa isolates and could be considered as lead compounds for future development. Challenges on how to translate hits into useful candidates for clinical development are also proposed and discussed.
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Affiliation(s)
- Haoran Li
- Institute of Evolution & Marine Biodiversity, School of Medicine and Pharmacy, College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Mireguli Maimaitiming
- Institute of Evolution & Marine Biodiversity, School of Medicine and Pharmacy, College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Yue Zhou
- Institute of Evolution & Marine Biodiversity, School of Medicine and Pharmacy, College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Huaxuan Li
- Institute of Evolution & Marine Biodiversity, School of Medicine and Pharmacy, College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Pingyuan Wang
- Institute of Evolution & Marine Biodiversity, School of Medicine and Pharmacy, College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Yang Liu
- Institute for Insect Biotechnology, Justus-Liebig-University Giessen, Ohlebergsweg 12, 35392 Giessen, Germany
| | - Till F Schäberle
- Institute for Insect Biotechnology, Justus-Liebig-University Giessen, Ohlebergsweg 12, 35392 Giessen, Germany
- Branch for Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), 35392 Giessen, Germany
- Partner Site Giessen-Marburg-Langen, German Center for Infection Research (DZIF), 35392 Giessen, Germany
| | - Zhiqing Liu
- Institute of Evolution & Marine Biodiversity, School of Medicine and Pharmacy, College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Chang-Yun Wang
- Institute of Evolution & Marine Biodiversity, School of Medicine and Pharmacy, College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
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Antibiotic-active heterotrophic Firmicutes sheltered in seaweeds: can they add new dimensions to future antimicrobial agents? Arch Microbiol 2022; 204:183. [PMID: 35179656 DOI: 10.1007/s00203-022-02784-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Revised: 01/22/2022] [Accepted: 01/28/2022] [Indexed: 11/02/2022]
Abstract
Appearance of drug-resistant microorganisms prompted researchers to unravel new environments for development of novel antimicrobial agents. Culture-supported analysis of heterotrophic bacteria associated with seaweeds yielded 152 strains, in that larger share of the isolates was embodied by Bacillus atrophaeus SHB2097 (54%), B. velezensis SHB2098 (24%), B. subtilis SHB2099 (12%), and B. amyloliquefaciens SHB20910 (10%). One of the most active strains characterized as B. atrophaeus SHB2097 (MW821482) with an inhibition zone more than 30 mm on spot-over-lawn experiment, was isolated from a seaweed Sargassum wightii, was selected for bioprospecting studies. Significant antibacterial potential was displayed by bacterial organic extract against vancomycin-resistant Enterococcus faecalis, Pseudomonas aeruginosa, methicillin-resistant Staphylococcus aureus, and Klebsiella pneumonia with minimum inhibitory concentration 6.25 µg/mL and comparable to the antibiotics ampicillin and chloramphenicol. The genes of type 1 pks (MZ222383, 700 bp) and hybrid nrps/pks (MZ222389, 1000-1400 bp) of B. atrophaeus MW821482 could be amplified. The bacterium displayed susceptibility to the commercially available antibiotic agents, and was negative for the pore-forming non-hemolytic hemolysin BL (hbl) and enterotoxin (nhe) genes, and therefore, was not pathogenic. The bacterium was found to possess genes (1000-1400 bp) involved in the biosynthesis of siderophore-class of compounds (MZ222387 and MZ222388) that showed 99% of similarity in BLAST search, and showed production of siderophore. Noteworthy antibacterial activities against clinically important pathogenic bacteria in conjunction with occurrence of genes coding for antimicrobial metabolites inferred that the marine heterotrophic bacterium B. atrophaeus SHB2097 could be used for the development of antibacterial agents against the emerging antibiotic resistance.
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Chakraborty K, Kizhakkekalam VK, Joy M. Polyketide-derived macrobrevins from marine macroalga-associated Bacillus amyloliquefaciens as promising antibacterial agents against pathogens causing nosocomial infections. PHYTOCHEMISTRY 2022; 193:112983. [PMID: 34695706 DOI: 10.1016/j.phytochem.2021.112983] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 10/06/2021] [Accepted: 10/08/2021] [Indexed: 06/13/2023]
Abstract
Marine heterotrophs are treasured bio-resources of antimicrobial metabolites, and herein we report the biosynthetic potential of Bacillus amyloliquefaciens (ex. Fukumoto) Priest et al. (Bacillaceae) strain MTCC 12713 isolated from an intertidal macroalga Kappaphycus alvarezii (Doty) L.M.Liao (Rhodophyta: Solieriaceae). The bacterium showed promising biological activities against methicillin-resistant Staphylococcus aureus and vancomycin-resistant Enterococcus faecalis. Genome mining of B. amyloliquefaciens MTCC 12713 predicted the gene clusters coding for biosynthesis of antibacterial metabolites. Bioactivity-guided purification was directed to isolate four homologous members of trans-acyltransferase polyketide synthase-derived antibiotics, which were classified as macrobrevin analogues. The compounds exhibited antibacterial activities against nosocomial pathogens, for example, methicillin-resistant S. aureus, vancomycin-resistant E. faecalis, Klebsiella pneumoniae and Pseudomonas aeruginosa with a range of MIC values from 1.56 to 6.25 μg/mL, although standard antibiotic chloramphenicol was active at 6.25-12.5 μg/mL. Conspicuously, the macrobrevin compound encompassing hexahydro-41-hydroxy-macrobrevin-31-acetate functionality, displayed considerably greater antagonistic activities against methicillin-resistant S. aureus, vancomycin-resistant E. faecalis, Vibrio parahaemolyticus, P. aeruginosa, K. pneumoniae, and Streptococcus pyogenes (MIC 1.56 μg/mL) compared to the positive controls and other macrobrevin analogues. Trans-AT polyketide synthase-stimulated biosynthetic pathway of macrobrevin compounds, through repetitive decarboxylative Claisen condensation between acetyl-S-KS domain and malonate-S-ACP units could corroborate the structural elucidation. In the genome mining study, among the 34 biosynthetic gene clusters, a hybrid trans-acyltransferase (trans-AT) pks/nrps gene cluster, which extends up to ∼81 Kb, was recognized in the genome of B. amyloliquefaciens MTCC 12713. The pks/nrps cluster revealed 46% similarity to trans-AT PKS-derived macrobrevin isolated from a mesophilic bacterium Brevibacillus sp. Leaf182 associated with the phyllosphere of the wild-type genotype of Arabidopsis thaliana. The binding positions for macrobrevins with S. aureus peptide deformylase showed docking score of larger than 14 kcal/mol, which was considerably greater than macrolactin N and actinonin (<10 kcal/mol). These present findings documented that the marine heterotrophic B. amyloliquefaciens MTCC 12713 could be used to develop prospective antibacterial agents belonging to macrobrevin analogues for biotechnological and pharmaceutical applications.
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Affiliation(s)
- Kajal Chakraborty
- Marine Bioprospecting Section of Marine Biotechnology Division, Central Marine Fisheries Research Institute, Ernakulam North, P.B. No. 1603, Cochin, Kerala State, India.
| | - Vinaya Kizhakkepatt Kizhakkekalam
- Marine Bioprospecting Section of Marine Biotechnology Division, Central Marine Fisheries Research Institute, Ernakulam North, P.B. No. 1603, Cochin, Kerala State, India; Faculty of Marine Sciences, Lakeside Campus, Cochin University of Science and Technology, Cochin, Kerala State, India
| | - Minju Joy
- Marine Bioprospecting Section of Marine Biotechnology Division, Central Marine Fisheries Research Institute, Ernakulam North, P.B. No. 1603, Cochin, Kerala State, India
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Chakraborty K, Kizhakkekalam VK, Joy M, Chakraborty RD. Novel amylomacins from seaweed-associated Bacillus amyloliquefaciens as prospective antimicrobial leads attenuating resistant bacteria. World J Microbiol Biotechnol 2021; 37:200. [PMID: 34664128 DOI: 10.1007/s11274-021-03161-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 10/01/2021] [Indexed: 11/25/2022]
Abstract
The rise in antibiotic-resistant bacterial strains prompting nosocomial infections drives the search for new bioactive substances of promising antibacterial properties. The surfaces of seaweeds are rich in heterotrophic bacteria with prospective antimicrobial substances. This study aimed to isolate antibacterial leads from a seaweed-associated bacterium. Heterotrophic Bacillus amyloliquefaciens MTCC 12716 associated with the seaweed Hypnea valentiae, was isolated and screened for antimicrobial properties against drug-resistant pathogens. The bacterial crude extract was purified and three novel amicoumacin-class of isocoumarin analogues, 11'-butyl acetate amicoumacin C (amylomacin A), 4'-hydroxy-11'-methoxyethyl carboxylate amicoumacin C (amylomacin B) and 11'-butyl amicoumacin C (amylomacin C) were isolated to homogeneity. The studied amylomacins possessed potential activities against Pseudomonas aeruginosa, vancomycin-resistant Enterococcus faecalis, Klebsiella pneumoniae, methicillin-resistant Staphylococcus aureus, and Shigella flexneri with a range of minimum inhibitory concentration values from 0.78 to 3.12 µg/mL, although standard antibiotics ampicillin and chloramphenicol were active at 6.25-25 µg/mL. Noticeably, the amylomacin compound encompassing 4'-hydroxy-11'-methoxyethyl carboxylate amicoumacin C functionality (amylomacin B), displayed considerably greater antagonistic activities against methicillin-resistant S. aureus, vancomycin-resistant E. faecalis, Vibrio parahaemolyticus, Escherichia coli, and K. pneumoniae (minimum inhibitory concentration 0.78 μg/mL) compared to the positive controls and other amylomacin analogues. Antimicrobial properties of the amylomacins, coupled with the presence of polyketide synthase-I/non-ribosomal peptide synthetase hybrid gene attributed the bacterium as a promising source of antimicrobial compounds with pharmaceutical and biotechnological applications.
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Affiliation(s)
- Kajal Chakraborty
- Marine Bioprospecting Section of Marine Biotechnology Division, Central Marine Fisheries Research Institute, Ernakulam North, P.B. No. 1603, Cochin, Kerala, 682018, India.
| | - Vinaya Kizhakkepatt Kizhakkekalam
- Marine Bioprospecting Section of Marine Biotechnology Division, Central Marine Fisheries Research Institute, Ernakulam North, P.B. No. 1603, Cochin, Kerala, 682018, India
- Faculty of Marine Sciences, Lakeside Campus, Cochin University of Science and Technology, Cochin, Kerala State, India
| | - Minju Joy
- Marine Bioprospecting Section of Marine Biotechnology Division, Central Marine Fisheries Research Institute, Ernakulam North, P.B. No. 1603, Cochin, Kerala, 682018, India
| | - Rekha Devi Chakraborty
- Crustacean Fisheries Division, Central Marine Fisheries Research Institute, Ernakulam North, P.B. No. 1603, Cochin, India
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Srinivasan R, Kannappan A, Shi C, Lin X. Marine Bacterial Secondary Metabolites: A Treasure House for Structurally Unique and Effective Antimicrobial Compounds. Mar Drugs 2021; 19:md19100530. [PMID: 34677431 PMCID: PMC8539464 DOI: 10.3390/md19100530] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 09/12/2021] [Accepted: 09/15/2021] [Indexed: 02/06/2023] Open
Abstract
The prevalence of antimicrobial resistance reduces the effectiveness of antimicrobial drugs in preventing and treating infectious diseases caused by pathogenic organisms, such as bacteria, fungi, and viruses. Because of the burgeoning growth of microbes with antimicrobial-resistant traits, there is a dire need to identify and develop novel and effective antimicrobial agents to treat infections from antimicrobial-resistant strains. The marine environment is rich in ecological biodiversity and can be regarded as an untapped resource for prospecting novel bioactive compounds. Therefore, exploring the marine environment for antimicrobial agents plays a significant role in drug development and biomedical research. Several earlier scientific investigations have proven that bacterial diversity in the marine environment represents an emerging source of structurally unique and novel antimicrobial agents. There are several reports on marine bacterial secondary metabolites, and many are pharmacologically significant and have enormous promise for developing effective antimicrobial drugs to combat microbial infections in drug-resistant pathogens. In this review, we attempt to summarize published articles from the last twenty-five years (1996–2020) on antimicrobial secondary metabolites from marine bacteria evolved in marine environments, such as marine sediment, water, fauna, and flora.
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Affiliation(s)
- Ramanathan Srinivasan
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Correspondence: (R.S.); (X.L.)
| | - Arunachalam Kannappan
- State Key Laboratory of Microbial Metabolism, MOST-USDA Joint Research Center for Food Safety, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China; (A.K.); (C.S.)
| | - Chunlei Shi
- State Key Laboratory of Microbial Metabolism, MOST-USDA Joint Research Center for Food Safety, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China; (A.K.); (C.S.)
| | - Xiangmin Lin
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Correspondence: (R.S.); (X.L.)
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Chakraborty K, Kizhakkekalam VK, Joy M, Dhara S. Difficidin class of polyketide antibiotics from marine macroalga-associated Bacillus as promising antibacterial agents. Appl Microbiol Biotechnol 2021; 105:6395-6408. [PMID: 34415389 DOI: 10.1007/s00253-021-11390-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 05/20/2021] [Accepted: 06/02/2021] [Indexed: 11/25/2022]
Abstract
A heterotrophoic Bacillus amyloliquefaciens MTCC12713 isolated from an intertidal macroalga Kappaphycus alverezii displayed promising antibacterial activities against multidrug-resistant bacteria. Genome mining of the bacterium predicted biosynthetic gene clusters coding for antibacterial secondary metabolites. Twenty-one membered macrocyclic lactones, identified as difficidin analogues bearing 6-hydroxy-8-propyl carboxylate, 9-methyl-19-propyl dicarboxylate, 6-methyl-9-propyl dicarboxylate-19-propanone, and (20-acetyl)-6-methyl-9-isopentyl dicarboxylate (compounds 1 through 4) functionalities were purified through bioassay-guided fractionation. The difficidin analogues exhibited bactericidal activities against vancomycin-resistant Enterococcus faecalis, methicillin-resistant Staphylococcus aureus, and other drug-resistant strains, such of Klebsiella pneumonia and Pseudomonas aeruginosa with the minimum inhibitory concentration of about 2-9 × 10-3 μM. A plausible enzyme-catalyzed biosynthetic pathway that is generated through addition of acrylyl initiator unit by repetitive decarboxylative Claisen condensation modules with malonate units was recognized, and their structures were corroborated with gene organization of the dif operon, which could comprehend dif A-O (~ 70 kb). Drug-likeness score for 5-ethoxy-28-methyl-(9-methyl-19-propyl dicarboxylate) difficidin (compound 2, 0.35) was greater than those of other difficidin analogues, which corroborated the potential in vitro antibacterial properties of the former. The present study demonstrated the potential of difficidin analogues for pharmaceutical and biotechnological uses against the bottleneck of emergent drug-resistant pathogens. KEY POINTS: • Difficidins were isolated from marine alga associated Bacillus amyloliquefaciens. • Whole-genome mining of bacterial genome predicted biosynthetic gene clusters. • Greater drug-likeness for difficidin 2 confirmed its potent antibacterial activity.
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Affiliation(s)
- Kajal Chakraborty
- Marine Bioprospecting Section of Marine Biotechnology Division, Central Marine Fisheries Research Institute, Ernakulam North P.O., P.B. No. 1603, Cochin, Kerala, India.
| | - Vinaya Kizhakkepatt Kizhakkekalam
- Marine Bioprospecting Section of Marine Biotechnology Division, Central Marine Fisheries Research Institute, Ernakulam North P.O., P.B. No. 1603, Cochin, Kerala, India
- Faculty of Marine Sciences, Lakeside Campus, Cochin University of Science and Technology, Cochin, Kerala, India
| | - Minju Joy
- Marine Bioprospecting Section of Marine Biotechnology Division, Central Marine Fisheries Research Institute, Ernakulam North P.O., P.B. No. 1603, Cochin, Kerala, India
| | - Shubhajit Dhara
- Marine Bioprospecting Section of Marine Biotechnology Division, Central Marine Fisheries Research Institute, Ernakulam North P.O., P.B. No. 1603, Cochin, Kerala, India
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Torres-Sánchez A, Pardo-Cacho J, López-Moreno A, Ruiz-Moreno Á, Cerk K, Aguilera M. Antimicrobial Effects of Potential Probiotics of Bacillus spp. Isolated from Human Microbiota: In Vitro and In Silico Methods. Microorganisms 2021; 9:1615. [PMID: 34442694 PMCID: PMC8399655 DOI: 10.3390/microorganisms9081615] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 07/26/2021] [Accepted: 07/26/2021] [Indexed: 12/14/2022] Open
Abstract
The variable taxa components of human gut microbiota seem to have an enormous biotechnological potential that is not yet well explored. To investigate the usefulness and applications of its biocompounds and/or bioactive substances would have a dual impact, allowing us to better understand the ecology of these microbiota consortia and to obtain resources for extended uses. Our research team has obtained a catalogue of isolated and typified strains from microbiota showing resistance to dietary contaminants and obesogens. Special attention was paid to cultivable Bacillus species as potential next-generation probiotics (NGP) together with their antimicrobial production and ecological impacts. The objective of the present work focused on bioinformatic genome data mining and phenotypic analyses for antimicrobial production. In silico methods were applied over the phylogenetically closest type strain genomes of the microbiota Bacillus spp. isolates and standardized antimicrobial production procedures were used. The main results showed partial and complete gene identification and presence of polyketide (PK) clusters on the whole genome sequences (WGS) analysed. Moreover, specific antimicrobial effects against B. cereus, B. circulans, Staphylococcus aureus, Streptococcus pyogenes, Escherichia coli, Serratia marcescens, Klebsiella spp., Pseudomonas spp., and Salmonella spp. confirmed their capacity of antimicrobial production. In conclusion, Bacillus strains isolated from human gut microbiota and taxonomic group, resistant to Bisphenols as xenobiotics type endocrine disruptors, showed parallel PKS biosynthesis and a phenotypic antimicrobial effect. This could modulate the composition of human gut microbiota and therefore its functionalities, becoming a predominant group when high contaminant exposure conditions are present.
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Affiliation(s)
- Alfonso Torres-Sánchez
- Department of Microbiology, Faculty of Pharmacy, University of Granada, Campus of Cartuja, 18071 Granada, Spain; (A.T.-S.); (J.P.-C.); (Á.R.-M.); (K.C.)
- Institute of Nutrition and Food Technology “José Mataix”, CIBM, University of Granada, Armilla, 18016 Granada, Spain
| | - Jesús Pardo-Cacho
- Department of Microbiology, Faculty of Pharmacy, University of Granada, Campus of Cartuja, 18071 Granada, Spain; (A.T.-S.); (J.P.-C.); (Á.R.-M.); (K.C.)
| | - Ana López-Moreno
- Department of Microbiology, Faculty of Pharmacy, University of Granada, Campus of Cartuja, 18071 Granada, Spain; (A.T.-S.); (J.P.-C.); (Á.R.-M.); (K.C.)
- Institute of Nutrition and Food Technology “José Mataix”, CIBM, University of Granada, Armilla, 18016 Granada, Spain
- Instituto de Investigación Biosanitaria ibs (IBS), 18012 Granada, Spain
| | - Ángel Ruiz-Moreno
- Department of Microbiology, Faculty of Pharmacy, University of Granada, Campus of Cartuja, 18071 Granada, Spain; (A.T.-S.); (J.P.-C.); (Á.R.-M.); (K.C.)
- Institute of Nutrition and Food Technology “José Mataix”, CIBM, University of Granada, Armilla, 18016 Granada, Spain
| | - Klara Cerk
- Department of Microbiology, Faculty of Pharmacy, University of Granada, Campus of Cartuja, 18071 Granada, Spain; (A.T.-S.); (J.P.-C.); (Á.R.-M.); (K.C.)
| | - Margarita Aguilera
- Department of Microbiology, Faculty of Pharmacy, University of Granada, Campus of Cartuja, 18071 Granada, Spain; (A.T.-S.); (J.P.-C.); (Á.R.-M.); (K.C.)
- Institute of Nutrition and Food Technology “José Mataix”, CIBM, University of Granada, Armilla, 18016 Granada, Spain
- Instituto de Investigación Biosanitaria ibs (IBS), 18012 Granada, Spain
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Abstract
This review covers the literature published between January and December in 2018 for marine natural products (MNPs), with 717 citations (706 for the period January to December 2018) referring to compounds isolated from marine microorganisms and phytoplankton, green, brown and red algae, sponges, cnidarians, bryozoans, molluscs, tunicates, echinoderms, mangroves and other intertidal plants and microorganisms. The emphasis is on new compounds (1554 in 469 papers for 2018), together with the relevant biological activities, source organisms and country of origin. Reviews, biosynthetic studies, first syntheses, and syntheses that led to the revision of structures or stereochemistries, have been included. The proportion of MNPs assigned absolute configuration over the last decade is also surveyed.
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Affiliation(s)
- Anthony R Carroll
- School of Environment and Science, Griffith University, Gold Coast, Australia. and Griffith Institute for Drug Discovery, Griffith University, Brisbane, Australia
| | - Brent R Copp
- School of Chemical Sciences, University of Auckland, Auckland, New Zealand
| | - Rohan A Davis
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, Australia and School of Environment and Science, Griffith University, Brisbane, Australia
| | - Robert A Keyzers
- Centre for Biodiscovery, School of Chemical and Physical Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Michèle R Prinsep
- Chemistry, School of Science, University of Waikato, Hamilton, New Zealand
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Wu T, Xiao F, Li W. Macrolactins: biological activity and biosynthesis. MARINE LIFE SCIENCE & TECHNOLOGY 2021; 3:62-68. [PMID: 37073393 PMCID: PMC10064405 DOI: 10.1007/s42995-020-00068-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 08/03/2020] [Indexed: 05/03/2023]
Abstract
Marine microorganisms have proven to be a rich source of natural products with unique structures and novel activities, due to their special living conditions. Macrolactins (MLNs), mostly produced by marine-derived microorganisms, are a group of 24-membered lactone natural products, which exhibit potent antibacterial, antifungal, antiviral, anticancer, anti-inflammatory, anti-angiogenic and other activities. Their extensive biological activities make them potential compounds for drug development. MLNs are biosynthesized via a type I polyketide synthase (PKS) pathway with different tailoring steps, such as epoxidation, glycosylation and acylation. These modification steps provide opportunities to diversify their structures by combinatorial biosynthesis strategies. This review mainly focuses on the newly discovered MLNs in the past five years, including their biological activities and relevant biosynthetic studies.
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Affiliation(s)
- Ting Wu
- Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003 China
| | - Fei Xiao
- Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003 China
| | - Wenli Li
- Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003 China
- Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237 China
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Chakraborty K, Kizhakkekalam VK, Joy M. Chemical mining of heterotrophic Shewanella algae reveals anti-infective potential of macrocyclic polyketides against multidrug-resistant pathogens. Bioorg Chem 2020; 108:104533. [PMID: 33342567 DOI: 10.1016/j.bioorg.2020.104533] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 11/25/2020] [Accepted: 12/03/2020] [Indexed: 11/17/2022]
Abstract
Heterotrophic Gamma-proteobacterium Shewanella algae MTCC 12715, associated with an intertidal red algae Hypnea valentiae, presented broad-spectra of antibacterial activities against pathogenic bacteria bringing about nosocomial infection. Bioassay-guided fractionation of the bacterial crude extract resulted in two undescribed macrocyclic polyketide analogs, with anti-infective activities against methicillin-resistant Staphylococcus aureus and vancomycin-resistant Enterococcus faecalis (MIC 3.1-5.0 µg/mL). In order to identify the polyketide biosynthetic machinery termed type-I polyketide synthase (pks-I) encoding biologically active secondary metabolites in this strain, the ketosynthase-coding regions of DNA with ≈700 bp size, were amplified, and the partial sequence was submitted in the GenBank (accession number MH157093). The titled compounds were classified under macrocyclic polyketides bearing dodecahydropyrano-trioxacyclooctadecine-dione and trioxo-octadecahydro-1H-benzo[o]tetraoxacyclopentacosine-carboxylate functionalities. Structure-activity correlation analysis displayed that hydrophobic descriptor of the studied compounds could play a prominent role in its anti-infective property against the opportunistic pathogens. Further, in silico molecular docking studies were performed in the allosteric sites of penicillin-binding protein (PBP2a) coded by mecA genes of MRSA, and the best binding pose for each compound (docking score -8.47 kcal/mol and -9.58 kcal/mol, respectively) could be correlated with their in vitro antibacterial activities. The pks-I assisted biosynthetic pathway of macrocyclic polyketides through step-wise decarboxylative condensation initiated by malonate-acyl carrier protein corroborated their structural attributes. Chemical mining of the studied macroalgae-associated heterotrophic bacterium thus revealed the promising antagonistic properties of macrocyclic polyketides isolated from Shewanella algae MTCC 12715 against multidrug-resistant pathogens.
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Affiliation(s)
- Kajal Chakraborty
- Marine Bioprospecting Section of Marine Biotechnology Division, Central Marine Fisheries Research Institute, Ernakulam North, P.B. No. 1603, Cochin, India.
| | - Vinaya Kizhakkepatt Kizhakkekalam
- Marine Bioprospecting Section of Marine Biotechnology Division, Central Marine Fisheries Research Institute, Ernakulam North, P.B. No. 1603, Cochin, India; Faculty of Marine Sciences, Lakeside Campus, Cochin University of Science and Technology, Cochin, Kerala State, India
| | - Minju Joy
- Marine Bioprospecting Section of Marine Biotechnology Division, Central Marine Fisheries Research Institute, Ernakulam North, P.B. No. 1603, Cochin, India
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19
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Chakraborty K, Kizhakkekalam VK, Joy M. Macrocyclic polyketides with siderophore mode of action from marine heterotrophic Shewanella algae: Prospective anti-infective leads attenuate drug-resistant pathogens. J Appl Microbiol 2020; 130:1552-1570. [PMID: 33006801 DOI: 10.1111/jam.14875] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 07/19/2020] [Accepted: 09/24/2020] [Indexed: 02/01/2023]
Abstract
AIMS Biotechnological and chemical characterization of previously undescribed homologous siderophore-type macrocyclic polyketides from heterotrophic Shewanella algae Microbial Type Culture Collection (MTCC) 12715 affiliated with Rhodophycean macroalga Hypnea valentiae of marine origin, with significant anti-infective potential against drug-resistant pathogens. METHODS AND RESULTS The heterotrophic bacterial strain in symbiotic association with intertidal macroalga H. valentiae was isolated to homogeneity in a culture-dependent method and screened for bioactivities by spot-over-lawn assay. The bacterial organic extract was purified and characterized by extensive chromatographic and spectroscopic methods, respectively, and was assessed for antibacterial activities with disc diffusion and microtube dilution methods. The macrocyclic polyketide compounds exhibited wide-spectrum of anti-infective potential against clinically significant vancomycin-resistant Enterococcus faecalis (VREfs), methicillin-resistant Staphylococcus aureus (MRSA), Pseudomonas aeruginosa and Klebsiella pneumonia with minimum inhibitory concentration of about 1-3 µg ml-1 , insomuch as the antibiotics chloramphenicol and ampicillin were active at ≥6·25 µg ml-1 . The studied compounds unveiled Fe3+ chelating activity, which designated that their prospective anti-infective activities against the pathogens could be due to their siderophore mechanism of action. In support of that, the bacterium exhibited siderophore production on bioassay involving the cast upon culture agar plate, and the presence of siderophore biosynthetic gene (≈1000 bp) (MF 981936) further corroborated the inference. In silico molecular modelling with penicillin-binding protein (PBP2a) coded by mecA genes of MRSA (docking score -11·68 to -12·69 kcal mol-1 ) verified their in vitro antibacterial activities. Putative biosynthetic pathway of macrocyclic polyketides through stepwise decarboxylative condensation initiated by malonate-acyl carrier protein further validated their structural and molecular attributes. CONCLUSIONS The studied siderophore-type macrocyclic polyketides from S. algae MTCC 12715 with significant anti-infective potential could be considered as promising candidates for pharmaceutical and biotechnological applications, especially against emerging multidrug-resistant pathogens. SIGNIFICANCE AND IMPACT OF THE STUDY This study exhibited the heterotrophic bacteria in association with intertidal macroalga as propitious biological resources to biosynthesize novel antibacterial agents.
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Affiliation(s)
- K Chakraborty
- Marine Bioprospecting Section of Marine Biotechnology Division, Central Marine Fisheries Research Institute, Ernakulam North, P.B. No. 1603, Cochin, India.,Faculty of Marine Sciences, Cochin University of Science and Technology, Kerala State, Lakeside Campus, Cochin, India
| | - V K Kizhakkekalam
- Marine Bioprospecting Section of Marine Biotechnology Division, Central Marine Fisheries Research Institute, Ernakulam North, P.B. No. 1603, Cochin, India.,Faculty of Marine Sciences, Cochin University of Science and Technology, Kerala State, Lakeside Campus, Cochin, India
| | - M Joy
- Marine Bioprospecting Section of Marine Biotechnology Division, Central Marine Fisheries Research Institute, Ernakulam North, P.B. No. 1603, Cochin, India.,Faculty of Marine Sciences, Cochin University of Science and Technology, Kerala State, Lakeside Campus, Cochin, India
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Aryl-enclosed polyketides from mangrove sediment associated bacterium Bacillus amyloliquefaciens attenuating pro-inflammatory 5-lipoxygenase. Med Chem Res 2020. [DOI: 10.1007/s00044-020-02618-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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21
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Chakraborty K, Kizhakkekalam VK, Joy M, Chakraborty RD. Moving away from traditional antibiotic treatment: can macrocyclic lactones from marine macroalga-associated heterotroph be the alternatives? Appl Microbiol Biotechnol 2020; 104:7117-7130. [PMID: 32621124 DOI: 10.1007/s00253-020-10658-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 04/17/2020] [Accepted: 04/29/2020] [Indexed: 01/02/2023]
Abstract
Intertidal red algae Hypnea valentiae associated Bacillus amyloliquefaciens MTCC 12716 revealed potential inhibitory effects on the growth of drug-resistant pathogens. In the genome of B. amyloliquefaciens MTCC 12716, biosynthetic gene clusters encoding antibacterial metabolites were predicted, which might be expressed and contributed to the broad-spectrum anti-infective activity. Three homologue members of the 24-membered macrocyclic lactone family, named as bacvalactones 1-3 bearing 13-O-ethyl (1); 15-O-furanyl-13-O-isobutyl-7-O-propyl-propanoate (2); and 15-O-furanyl-13-O-isobutyl-7-O-propyl-propanoate-7,24-dimethyl (3) functionalities, were acquired through bioactivity-guided purification. The macrocyclic lactones displayed bactericidal activity against opportunistic pathogens causing nosocomial infections, for instance, methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-resistant Enterococcus faecalis (VREfs), and multidrug-resistant strains of Pseudomonas aeruginosa and Klebsiella pneumonia with MIC ≤ 3.0 μg/mL, whereas standard antibiotics ampicillin and chloramphenicol were active only at concentrations of ≥ 6.25 mg/mL. The biosynthetic pathway of macrocyclic lactones that are generated by trans-AT polyketide synthases through stepwise extension of an acetyl starter unit by eleven sequential Claisen condensations with malonyl-CoA was established, and the structures were correlated with the gene organization of the mln operon, which encompasses nine genes mln A-I (approximately 47 kb in size). The best binding poses for each compounds (1-3) with Staphylococcus aureus peptide deformylase (SaPDF) unveiled docking scores (≥ 9.70 kcal/mol) greater than that of natural peptide deformylase inhibitors, macrolactin N and actinonin (9.14 and 6.96 kcal/mol, respectively), which supported their potential in vitro bioactivities. Thus, the present work demonstrated the potential of macrocyclic lactone for biotechnological and pharmaceutical applications against emerging multidrug-resistant pathogens. Key Points •Three antibacterial bacvalactones were identified from the symbiotic bacterium. •The symbiotic bacterial genome was explored to identify the biosynthetic gene clusters. •Trans-AT pks-assisted mln biosynthetic pathway of the macrocyclic lactone was proposed. •In silicomolecular interactions of the bacvalactones with S. aureus PDF were analyzed.
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Affiliation(s)
- Kajal Chakraborty
- Marine Bioprospecting Section of Marine Biotechnology Division, Central Marine Fisheries Research Institute, Ernakulam North, P.B. No. 1603, Cochin, India.
| | - Vinaya Kizhakkepatt Kizhakkekalam
- Marine Bioprospecting Section of Marine Biotechnology Division, Central Marine Fisheries Research Institute, Ernakulam North, P.B. No. 1603, Cochin, India.,Faculty of Marine Sciences, Lakeside Campus, Cochin University of Science and Technology, Cochin, Kerala State, India
| | - Minju Joy
- Marine Bioprospecting Section of Marine Biotechnology Division, Central Marine Fisheries Research Institute, Ernakulam North, P.B. No. 1603, Cochin, India
| | - Rekha Devi Chakraborty
- Crustacean Fisheries Division, Central Marine Fisheries Research Institute, Ernakulam North, P.B. No. 1603, Cochin, India
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Marine macroalgae-associated heterotrophic Firmicutes and Gamma-proteobacteria: prospective anti-infective agents against multidrug resistant pathogens. Arch Microbiol 2020; 202:905-920. [DOI: 10.1007/s00203-019-01800-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 07/29/2019] [Accepted: 12/16/2019] [Indexed: 10/25/2022]
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23
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Antibacterial and antioxidant aryl-enclosed macrocyclic polyketide from intertidal macroalgae associated heterotrophic bacterium Shewanella algae. Med Chem Res 2019. [DOI: 10.1007/s00044-019-02468-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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Bacterial Consortium for Improved Maize ( Zea mays L.) Production. Microorganisms 2019; 7:microorganisms7110519. [PMID: 31683950 PMCID: PMC6920993 DOI: 10.3390/microorganisms7110519] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 10/15/2019] [Accepted: 10/22/2019] [Indexed: 11/16/2022] Open
Abstract
The ever-increasing human population is a major concern for food security. Maize is the third largest most important food crop. The major problems of cultivation arise from urbanization and land pollution. This reduces the amount of land available for agriculture. The use of chemicals in agriculture is not environmentally friendly. Thus, plant growth-promoting bacteria (PGPB) have been proposed as alternatives. This study aims to test the growth-promoting effect of maize inoculated with six indigenous PGPB isolates. These isolates were assayed for various biochemical and plant growth-promoting activities. They were also assayed for biocontrol activities. Based on the results, six isolates viz A1, A18, A29, NWU4, NWU14, and NWU198 were used to inoculate maize seeds. The inoculated seeds were tried out on the field. A randomized block design was used. PGPB used were in single, consortia of two, and three organisms. The length of the leaves, roots, and stem, plant height, numbers of leaves, and weight of 100 seeds were taken at the fourth and eighth weeks after planting. Microbial consortia increased growth parameters compared to single inoculant treatments. Thus, they can be of advantage in the eradication of low yield. They can also serve as reliable alternatives to chemical fertilizers.
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Kaspar F, Neubauer P, Gimpel M. Bioactive Secondary Metabolites from Bacillus subtilis: A Comprehensive Review. JOURNAL OF NATURAL PRODUCTS 2019; 82:2038-2053. [PMID: 31287310 DOI: 10.1021/acs.jnatprod.9b00110] [Citation(s) in RCA: 116] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Bacillus subtilis is widely underappreciated for its inherent biosynthetic potential. This report comprehensively summarizes the known bioactive secondary metabolites from B. subtilis and highlights potential applications as plant pathogen control agents, drugs, and biosurfactants. B. subtilis is well known for the production of cyclic lipopeptides exhibiting strong surfactant and antimicrobial activities, such as surfactins, iturins, and fengycins. Several polyketide-derived macrolides as well as nonribosomal peptides, dihydroisocoumarins, and linear lipopeptides with antimicrobial properties have been reported, demonstrating the biosynthetic arsenal of this bacterium. Promising efforts toward the application of B. subtilis strains and their natural products in areas of agriculture and medicine are underway. However, industrial-scale availability of these compounds is currently limited by low fermentation yields and challenging accessibility via synthesis, necessitating the development of genetically engineered strains and optimized cultivation processes. We hope that this review will attract renewed interest in this often-overlooked bacterium and its impressive biosynthetic skill set.
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Affiliation(s)
- Felix Kaspar
- Institute of Biotechnology , Technical University of Berlin , Ackerstraße 76 , 13355 Berlin , Germany
| | - Peter Neubauer
- Institute of Biotechnology , Technical University of Berlin , Ackerstraße 76 , 13355 Berlin , Germany
| | - Matthias Gimpel
- Institute of Biotechnology , Technical University of Berlin , Ackerstraße 76 , 13355 Berlin , Germany
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Marine Macrolides with Antibacterial and/or Antifungal Activity. Mar Drugs 2019; 17:md17040241. [PMID: 31018512 PMCID: PMC6520931 DOI: 10.3390/md17040241] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Revised: 04/19/2019] [Accepted: 04/19/2019] [Indexed: 12/11/2022] Open
Abstract
Currently, the increasing resistance of microorganisms to antibiotics is a serious problem. Marine organisms are the source of thousands of substances, which also have antibacterial and antifungal effects. Among them, marine macrolides are significant. In this review, the antibacterial and/or antifungal activities of 34 groups of marine macrolides are presented. Exemplary groups are chalcomycins, curvulides, halichondramides, lobophorins, macrolactins, modiolides, scytophycins, spongistatins, or zearalanones. In the paper, 74 antibiotics or their analog sets, among which 29 with antifungal activity, 25 that are antibacterial, and 20 that are both antifungal and antibacterial are summarized. Also, 36 macrolides or their sets are produced by bacteria, 18 by fungi, ten by sponges, seven by algae, two by porifera, and one by nudibranch. Moreover, the chemical structures of representatives from each of the 34 groups of these antibiotics are presented. To summarize, marine organisms are rich in natural macrolides. Some of these may be used in the future in the treatment of bacterial and fungal infections. Marine macrolides can also be potential drugs applicable against pathogens resistant to currently known antibiotics.
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Taghdisi SM, Danesh NM, Nameghi MA, Ramezani M, Alibolandi M, Abnous K. An electrochemical sensing platform based on ladder-shaped DNA structure and label-free aptamer for ultrasensitive detection of ampicillin. Biosens Bioelectron 2019; 133:230-235. [PMID: 30951983 DOI: 10.1016/j.bios.2019.03.044] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 03/20/2019] [Accepted: 03/21/2019] [Indexed: 12/27/2022]
Abstract
Herein, an electrochemical aptasensor is described for detection of ampicillin (Ampi). The sensing strategy is based on the application of a ladder-shaped DNA structure as a multi-layer physical block on the surface of gold electrode. Attributing to the electrostatic repulsion and physical prevention of the ladder-shaped DNA structure, ultrasensitive detection of Ampi was achieved with a detection limit as low as 1 pM. In the presence of Ampi, the ladder-shaped DNA structure is disassembled and detached from the electrode surface. This leads to the high access of [Fe(CN)6]3-/4- as a redox indicator to the electrode surface and a strong redox peak. The aptasensor response for Ampi detection was in the linear range from 7 pM to 100 nM with the detection limit of 1 pM. The presented analytical strategy showed its application in detecting Ampi in the spiked milk samples with satisfactory performance. This work can be easily expanded for different targets by alternating the corresponding aptamers.
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Affiliation(s)
- Seyed Mohammad Taghdisi
- Targeted Drug Delivery Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Pharmaceutical Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | | | - Morteza Alinezhad Nameghi
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohammad Ramezani
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mona Alibolandi
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Khalil Abnous
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran.
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Xu BH, Ye ZW, Zheng QW, Wei T, Lin JF, Guo LQ. Isolation and characterization of cyclic lipopeptides with broad-spectrum antimicrobial activity from Bacillus siamensis JFL15. 3 Biotech 2018; 8:444. [PMID: 30333946 DOI: 10.1007/s13205-018-1443-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2018] [Accepted: 09/24/2018] [Indexed: 11/26/2022] Open
Abstract
In this research, the antimicrobial substance anti-JFL15 was partially purified using a simple two-step extraction process from the cell-free supernatants of Bacillus siamensis JFL15. Anti-JFL15 exhibited a strong antibacterial activity against various multidrug-resistant aquatic bacterial pathogens, including Escherichia coli, Edwardsiella tarda, Pseudomonas aeruginosa, Aeromonas hydrophila, and Vibrio. Liquid chromatography-mass spectrometry revealed that anti-JFL15 contained eight cyclic lipopeptides belonging to two families: bacillomycin F (m/z 1056.56-1084.59) and surfactin (m/z 1007.65-1049.70) analogs. PCR analysis showed the presence of genes (i.e., sfp gene, surfactin synthetase D, fengycin synthetase B, iturin synthetase A, iturin synthetase C and bacillomycin synthetase D) involved in the biosynthesis of cyclic lipopeptides. This study is the first to identify cyclic lipopeptides from B. siamensis and use them to suppress the growth of various multidrug-resistant aquatic bacterial pathogens. Results indicated that B. siamensis JFL15 is a promising biocontrol agent for the effective and environmentally friendly control of various multidrug-resistant aquatic bacterial pathogens.
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Affiliation(s)
- Ben-Hong Xu
- 1College of Food Science and Institute of Food Biotechnology, South China Agricultural University, Guangzhou, China
- Research Center for Micro-Ecological Agent Engineering and Technology of Guangdong Province, Guangzhou, China
| | - Zhi-Wei Ye
- 1College of Food Science and Institute of Food Biotechnology, South China Agricultural University, Guangzhou, China
- Research Center for Micro-Ecological Agent Engineering and Technology of Guangdong Province, Guangzhou, China
| | - Qian-Wang Zheng
- 1College of Food Science and Institute of Food Biotechnology, South China Agricultural University, Guangzhou, China
- Research Center for Micro-Ecological Agent Engineering and Technology of Guangdong Province, Guangzhou, China
| | - Tao Wei
- 1College of Food Science and Institute of Food Biotechnology, South China Agricultural University, Guangzhou, China
- Research Center for Micro-Ecological Agent Engineering and Technology of Guangdong Province, Guangzhou, China
| | - Jun-Fang Lin
- 1College of Food Science and Institute of Food Biotechnology, South China Agricultural University, Guangzhou, China
- Research Center for Micro-Ecological Agent Engineering and Technology of Guangdong Province, Guangzhou, China
| | - Li-Qiong Guo
- 1College of Food Science and Institute of Food Biotechnology, South China Agricultural University, Guangzhou, China
- Research Center for Micro-Ecological Agent Engineering and Technology of Guangdong Province, Guangzhou, China
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Liu X, Hu M, Wang M, Song Y, Zhou N, He L, Zhang Z. Novel nanoarchitecture of Co-MOF-on-TPN-COF hybrid: Ultralowly sensitive bioplatform of electrochemical aptasensor toward ampicillin. Biosens Bioelectron 2018; 123:59-68. [PMID: 30312876 DOI: 10.1016/j.bios.2018.09.089] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 09/18/2018] [Accepted: 09/27/2018] [Indexed: 11/17/2022]
Abstract
Owning to the misuse of the antibiotics in animal husbandry and agriculture, it is highly urgent to determine the quantification of antibiotics in biological systems by the simple, sensitive, and fast method. In this work, a novel nanoarchitecture of Co-based metal-organic frameworks (Co-MOF) and terephthalonitrile-based covalent organic framework (TPN-COF) was synthesized (represented by Co-MOF@TPN-COF), followed by the exploitation as the bioplatform of non-label aptasensor for detecting the most frequently used β-lactam antibiotics, ampicillin (AMP). The new porous hybrid material of Co-MOF@TPN-COF was synthesized by adding the as-prepared TPN-COF into the Co-MOF preparation system. The multilayered Co-MOF@TPN-COF nanosheets exhibit a high specific surface area (52.64 m2 g-1), nitrogen-rich groups and excellent electrochemical activity. As a result, large amounts of aptamer strands can be bound over the Co-MOF@TPN-COF nanosheets owning to the strong π-π stacking and hydrogen bonds. When detecting AMP by the electrochemical impedance spectroscopy, the fabricated Co-MOF@TPN-COF-based aptasensor exhibits an ultra-low detection limit of 0.217 fg mL-1 within the AMP concentration from 1.0 fg mL-1 to 2.0 ng mL-1, which was superior to those previously reported in literatures. In addition, this proposed aptasensor also shows high selectivity, good reproducibility and stability, acceptable regenerability, and favorable applicability in human serum, river water and milk. Therefore, the proposed Co-MOF@TPN-COF-based aptasensor has a great promise to be applied as a powerful tool in the fields of food safety.
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Affiliation(s)
- Xiaokang Liu
- Department of Orthopedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450000, PR China
| | - Mengyao Hu
- Henan Provincial Key Laboratory of Surface and Interface Science, Zhengzhou University of Light Industry, No. 136, Science Avenue, Zhengzhou 450001, PR China
| | - Minghua Wang
- Henan Provincial Key Laboratory of Surface and Interface Science, Zhengzhou University of Light Industry, No. 136, Science Avenue, Zhengzhou 450001, PR China
| | - Yingpan Song
- Henan Provincial Key Laboratory of Surface and Interface Science, Zhengzhou University of Light Industry, No. 136, Science Avenue, Zhengzhou 450001, PR China
| | - Nan Zhou
- Department of Orthopedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450000, PR China.
| | - Linghao He
- Henan Provincial Key Laboratory of Surface and Interface Science, Zhengzhou University of Light Industry, No. 136, Science Avenue, Zhengzhou 450001, PR China
| | - Zhihong Zhang
- Henan Provincial Key Laboratory of Surface and Interface Science, Zhengzhou University of Light Industry, No. 136, Science Avenue, Zhengzhou 450001, PR China.
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Luo Y, Cheng Y, Yi J, Zhang Z, Luo Q, Zhang D, Li Y. Complete Genome Sequence of Industrial Biocontrol Strain Paenibacillus polymyxa HY96-2 and Further Analysis of Its Biocontrol Mechanism. Front Microbiol 2018; 9:1520. [PMID: 30050512 PMCID: PMC6052121 DOI: 10.3389/fmicb.2018.01520] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Accepted: 06/19/2018] [Indexed: 12/17/2022] Open
Abstract
Paenibacillus polymyxa (formerly known as Bacillus polymyxa) has been extensively studied for agricultural applications as a plant-growth-promoting rhizobacterium and is also an important biocontrol agent. Our team has developed the P. polymyxa strain HY96-2 from the tomato rhizosphere as the first microbial biopesticide based on P. polymyxa for controlling plant diseases around the world, leading to the commercialization of this microbial biopesticide in China. However, further research is essential for understanding its precise biocontrol mechanisms. In this paper, we report the complete genome sequence of HY96-2 and the results of a comparative genomic analysis between different P. polymyxa strains. The complete genome size of HY96-2 was found to be 5.75 Mb and 5207 coding sequences were predicted. HY96-2 was compared with seven other P. polymyxa strains for which complete genome sequences have been published, using phylogenetic tree, pan-genome, and nucleic acid co-linearity analysis. In addition, the genes and gene clusters involved in biofilm formation, antibiotic synthesis, and systemic resistance inducer production were compared between strain HY96-2 and two other strains, namely, SC2 and E681. The results revealed that all three of the P. polymyxa strains have the ability to control plant diseases via the mechanisms of colonization (biofilm formation), antagonism (antibiotic production), and induced resistance (systemic resistance inducer production). However, the variation of the corresponding genes or gene clusters between the three strains may lead to different antimicrobial spectra and biocontrol efficacies. Two possible pathways of biofilm formation in P. polymyxa were reported for the first time after searching the KEGG database. This study provides a scientific basis for the further optimization of the field applications and quality standards of industrial microbial biopesticides based on HY96-2. It may also serve as a reference for studying the differences in antimicrobial spectra and biocontrol capability between different biocontrol agents.
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Affiliation(s)
| | | | | | | | | | - Daojing Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Yuanguang Li
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
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