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Tanvir R, Ijaz S, Sajid I, Hasnain S. Multifunctional in vitro, in silico and DFT analyses on antimicrobial BagremycinA biosynthesized by Micromonospora chokoriensis CR3 from Hieracium canadense. Sci Rep 2024; 14:10976. [PMID: 38745055 PMCID: PMC11093986 DOI: 10.1038/s41598-024-61490-9] [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: 11/19/2023] [Accepted: 05/06/2024] [Indexed: 05/16/2024] Open
Abstract
Among the actinomycetes in the rare genera, Micromonospora is of great interest since it has been shown to produce novel therapeutic compounds. Particular emphasis is now on its isolation from plants since its population from soil has been extensively explored. The strain CR3 was isolated as an endophyte from the roots of Hieracium canadense, and it was identified as Micromonospora chokoriensis through 16S gene sequencing and phylogenetic analysis. The in-vitro analysis of its extract revealed it to be active against the clinical isolates of methicillin-resistant Staphylococcus aureus (MRSA) and Candida tropicalis (15 mm). No bioactivity was observed against Gram-negative bacteria, Escherichia coli ATCC 25922, and Klebsiella pneumoniae ATCC 706003. The Micromonospora chokoriensis CR3 extract was also analyzed through the HPLC-DAD-UV-VIS resident database, and it gave a maximum match factor of 997.334 with the specialized metabolite BagremycinA (BagA). The in-silico analysis indicated that BagA strongly interacted with the active site residues of the sterol 14-α demethylase and thymidylate kinase enzymes, with the lowest binding energies of - 9.7 and - 8.3 kcal/mol, respectively. Furthermore, the normal mode analysis indicated that the interaction between these proteins and BagA was stable. The DFT quantum chemical properties depicted BagA to be reasonably reactive with a HOMO-LUMO gap of (ΔE) of 4.390 eV. BagA also passed the drug-likeness test with a synthetic accessibility score of 2.06, whereas Protox-II classified it as a class V toxicity compound with high LD50 of 2644 mg/kg. The current study reports an endophytic actinomycete, M. chokoriensis, associated with H. canadense producing the bioactive metabolite BagA with promising antimicrobial activity, which can be further modified and developed into a safe antimicrobial drug.
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Affiliation(s)
- Rabia Tanvir
- Institute of Microbiology (IOM), University of Veterinary and Animal Sciences (UVAS), Lahore, 54000, Punjab, Pakistan.
| | - Saadia Ijaz
- Department of Microbiology and Molecular Genetics, The Women University, Multan, 66000, Punjab, Pakistan
| | - Imran Sajid
- Institute of Microbiology and Molecular Genetics (IMMG), University of the Punjab, Quaid-e-Azam Campus, Lahore, 54590, Punjab, Pakistan
| | - Shahida Hasnain
- Institute of Microbiology and Molecular Genetics (IMMG), University of the Punjab, Quaid-e-Azam Campus, Lahore, 54590, Punjab, Pakistan
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Kapoore RV, Padmaperuma G, Maneein S, Vaidyanathan S. Co-culturing microbial consortia: approaches for applications in biomanufacturing and bioprocessing. Crit Rev Biotechnol 2021; 42:46-72. [PMID: 33980092 DOI: 10.1080/07388551.2021.1921691] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The application of microbial co-cultures is now recognized in the fields of biotechnology, ecology, and medicine. Understanding the biological interactions that govern the association of microorganisms would shape the way in which artificial/synthetic co-cultures or consortia are developed. The ability to accurately predict and control cell-to-cell interactions fully would be a significant enabler in synthetic biology. Co-culturing method development holds the key to strategically engineer environments in which the co-cultured microorganism can be monitored. Various approaches have been employed which aim to emulate the natural environment and gain access to the untapped natural resources emerging from cross-talk between partners. Amongst these methods are the use of a communal liquid medium for growth, use of a solid-liquid interface, membrane separation, spatial separation, and use of microfluidics systems. Maximizing the information content of interactions monitored is one of the major challenges that needs to be addressed by these designs. This review critically evaluates the significance and drawbacks of the co-culturing approaches used to this day in biotechnological applications, relevant to biomanufacturing. It is recommended that experimental results for a co-cultured species should be validated with different co-culture approaches due to variations in interactions that could exist as a result of the culturing method selected.
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Affiliation(s)
- Rahul Vijay Kapoore
- Department of Chemical and Biological Engineering, The University of Sheffield, Sheffield, UK.,Department of Biosciences, College of Science, Swansea University, Swansea, UK
| | - Gloria Padmaperuma
- Department of Chemical and Biological Engineering, The University of Sheffield, Sheffield, UK
| | - Supattra Maneein
- Department of Chemical and Biological Engineering, The University of Sheffield, Sheffield, UK.,Department of Pharmaceutical, Chemical & Environmental Sciences, The University of Greenwich, Kent, UK
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Buzón-Durán L, Martín-Gil J, Pérez-Lebeña E, Ruano-Rosa D, Revuelta JL, Casanova-Gascón J, Ramos-Sánchez MC, Martín-Ramos P. Antifungal Agents Based on Chitosan Oligomers, ε-polylysine and Streptomyces spp. Secondary Metabolites against Three Botryosphaeriaceae Species. Antibiotics (Basel) 2019; 8:antibiotics8030099. [PMID: 31330856 PMCID: PMC6783921 DOI: 10.3390/antibiotics8030099] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 07/16/2019] [Accepted: 07/18/2019] [Indexed: 11/16/2022] Open
Abstract
Grapevine trunk diseases (GTDs) are a major threat to the wine and grape industry. The aim of the study was to investigate the antifungal activity against Neofusicoccum parvum, Diplodia seriata, and Botryosphaeria dothidea of ε-polylysine, chitosan oligomers, their conjugates, Streptomyces rochei and S. lavendofoliae culture filtrates, and their binary mixtures with chitosan oligomers. In vitro mycelial growth inhibition tests suggest that the efficacy of these treatments, in particular those based on ε-polylysine and ε-polylysine:chitosan oligomers 1:1 w/w conjugate, against the three Botryosphaeriaceae species would be comparable to or higher than that of conventional synthetic fungicides. In the case of ε-polylysine, EC90 values as low as 227, 26.9, and 22.5 µg·mL-1 were obtained for N. parvum, D. seriata, and B. dothidea, respectively. Although the efficacy of the conjugate was slightly lower, with EC90 values of 507.5, 580.2, and 497.4 µg·mL-1, respectively, it may represent a more cost-effective option to the utilization of pure ε-polylysine. The proposed treatments may offer a viable and sustainable alternative for controlling GTDs.
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Affiliation(s)
- Laura Buzón-Durán
- Departamento de Ingeniería Agroforestal, ETSIIAA, Universidad de Valladolid, Avenida de Madrid 44, 34004 Palencia, Spain
| | - Jesús Martín-Gil
- Departamento de Ingeniería Agroforestal, ETSIIAA, Universidad de Valladolid, Avenida de Madrid 44, 34004 Palencia, Spain
| | - Eduardo Pérez-Lebeña
- Departamento de Ingeniería Agroforestal, ETSIIAA, Universidad de Valladolid, Avenida de Madrid 44, 34004 Palencia, Spain
| | - David Ruano-Rosa
- Instituto Tecnológico Agrario de Castilla y León, Unidad de Cultivos Leñosos y Hortícolas, Ctra. De Burgos km 119, Finca Zamadueñas, 47071 Valladolid, Spain
| | - José L Revuelta
- Departamento de Microbiología y Genética, Facultad de Biología, Universidad de Salamanca, Campus Miguel de Unamuno, C/ Donantes de Sangre, s/n, 37007 Salamanca, Spain
| | - José Casanova-Gascón
- Instituto Universitario de Investigación en Ciencias Ambientales de Aragón (IUCA), EPS, Universidad de Zaragoza, Carretera de Cuarte, s/n, 22071 Huesca, Spain
| | - M Carmen Ramos-Sánchez
- Servicio de Microbiología y Parasitología, Hospital Universitario Rio Hortega, SACYL, Calle Dulzaina, 2, 47012 Valladolid, Spain
| | - Pablo Martín-Ramos
- Instituto Universitario de Investigación en Ciencias Ambientales de Aragón (IUCA), EPS, Universidad de Zaragoza, Carretera de Cuarte, s/n, 22071 Huesca, Spain.
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Padmaperuma G, Kapoore RV, Gilmour DJ, Vaidyanathan S. Microbial consortia: a critical look at microalgae co-cultures for enhanced biomanufacturing. Crit Rev Biotechnol 2017; 38:690-703. [PMID: 29233009 DOI: 10.1080/07388551.2017.1390728] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Monocultures have been the preferred production route in the bio-industry, where contamination has been a major bottleneck. In nature, microorganisms usually exist as part of organized communities and consortia, gaining benefits from co-habitation, keeping invaders at bay. There is increasing interest in the use of co-cultures to tackle contamination issues, and simultaneously increase productivity and product diversity. The feasibility of extending the natural phenomenon of co-habitation to the biomanufacturing industry in the form of co-cultures requires careful and systematic consideration of several aspects. This article will critically examine and review current work on microbial co-cultures, with the intent of examining the concept and proposing a design pipeline that can be developed in a biomanufacturing context.
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Affiliation(s)
- Gloria Padmaperuma
- a ChELSI Institute, Advanced Biomanufacturing Centre, Department of Chemical and Biological Engineering , The University of Sheffield , Sheffield , UK
| | - Rahul Vijay Kapoore
- a ChELSI Institute, Advanced Biomanufacturing Centre, Department of Chemical and Biological Engineering , The University of Sheffield , Sheffield , UK
| | - Daniel James Gilmour
- b Department of Molecular Biology and Biotechnology , The University of Sheffield , Sheffield , UK
| | - Seetharaman Vaidyanathan
- a ChELSI Institute, Advanced Biomanufacturing Centre, Department of Chemical and Biological Engineering , The University of Sheffield , Sheffield , UK
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Himaman W, Thamchaipenet A, Pathom-Aree W, Duangmal K. Actinomycetes from Eucalyptus and their biological activities for controlling Eucalyptus leaf and shoot blight. Microbiol Res 2016; 188-189:42-52. [PMID: 27296961 DOI: 10.1016/j.micres.2016.04.011] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 04/22/2016] [Accepted: 04/24/2016] [Indexed: 01/13/2023]
Abstract
In Thailand, Eucalyptus plantations rapidly expand across the country. Leaf and shoot blight caused by Cryptosporiopsis eucalypti, Cylindrocladium sp. and Teratosphaeria destructans is a serious disease in Eucalyptus plantations. In this study, a total of 477 actinomycete strains were successfully isolated from roots and rhizosphere soil of Eucalyptus. Four hundred and thirty nine isolates were classified as streptomycetes and 38 isolates were non-streptomycetes. Among these isolates, 272 (57.0%), 118 (24.7%) and 241 (50.5%) isolates were antagonistic to Cryptosporiopsis eucalypti, Cylindrocladium sp. and Teratosphaeria destructans, respectively. All isolates were tested for their abilities to produce siderophores, indole acetic acid (IAA) and solubilise phosphate. Most isolates (464, 97.3%) produced siderophores. The majority of isolates (345, 72.3%) solubilised phosphate. In addition, almost half of these isolates (237, 49.7%) produced indole acetic acid. Strain EUSKR2S82 which showed the strongest inhibitory effect against all tested fungi with plant growth promoting ability was selected to test with Eucalyptus. This strain could colonize plant roots and increase Eucalyptus roots length. In a detached leaves bioassay, the disease severity of EUSKR2S82-inoculated Eucalyptus leaves was only 30% compared to 95% in the control treatment. The 16S rRNA gene sequence analysis revealed that the strain EUSKR2S82 was related to Streptomyces ramulosus NRRL-B 2714(T) (99.44% similarity). Identification of non-streptomycete isolates using 16S rRNA gene sequences classified them into 9 genera: Actinoallomurus, Actinomadura, Amycolatopsis, Cryptosporangium, Microbispora, Micromonospora, Nocardia, Nonomuraea and Pseudonocardia. It is evident that Eucalyptus tree harbored several genera of actinomycetes. The selected isolate, EUSKR2S82 showed potential as a candidate for biocontrol agent of leaf and shoot blight of Eucalyptus and to promote growth.
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Affiliation(s)
- Winanda Himaman
- Department of Microbiology, Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand; Center for Advanced Studies in Tropical Natural Resources, NRU-KU, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
| | - Arinthip Thamchaipenet
- Department of Genetics, Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
| | - Wasu Pathom-Aree
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Kannika Duangmal
- Department of Microbiology, Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand; Center for Advanced Studies in Tropical Natural Resources, NRU-KU, Kasetsart University, Chatuchak, Bangkok 10900, Thailand.
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van der Voort M, Kempenaar M, van Driel M, Raaijmakers JM, Mendes R. Impact of soil heat on reassembly of bacterial communities in the rhizosphere microbiome and plant disease suppression. Ecol Lett 2016; 19:375-82. [PMID: 26833547 DOI: 10.1111/ele.12567] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Revised: 10/29/2015] [Accepted: 12/08/2015] [Indexed: 02/05/2023]
Abstract
The rhizosphere microbiome offers a range of ecosystem services to the plant, including nutrient acquisition and tolerance to (a)biotic stress. Here, analysing the data by Mendes et al. (2011), we show that short heat disturbances (50 or 80 °C, 1 h) of a soil suppressive to the root pathogenic fungus Rhizoctonia solani caused significant increase in alpha diversity of the rhizobacterial community and led to partial or complete loss of disease protection. A reassembly model is proposed where bacterial families that are heat tolerant and have high growth rates significantly increase in relative abundance after heat disturbance, while temperature-sensitive and slow-growing bacteria have a disadvantage. The results also pointed to a potential role of slow-growing, heat-tolerant bacterial families from Actinobacteria and Acidobacteria phyla in plant disease protection. In conclusion, short heat disturbance of soil results in rearrangement of rhizobacterial communities and this is correlated with changes in the ecosystem service disease suppression.
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Affiliation(s)
- Menno van der Voort
- Laboratory of Phytopathology, Wageningen University, Wageningen, Netherlands
| | - Marcel Kempenaar
- The Netherlands Bioinformatics Centre (NBIC), Nijmegen, Netherlands
| | - Marc van Driel
- The Netherlands Bioinformatics Centre (NBIC), Nijmegen, Netherlands
| | - Jos M Raaijmakers
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO/KNAW), Wageningen, Netherlands.,Institute of Biology, Leiden University, Wageningen, Netherlands
| | - Rodrigo Mendes
- Laboratory of Environmental Microbiology, Embrapa Environment, Jaguariuna, Brazil
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Tanvir R, Sajid I, Hasnain S, Kulik A, Grond S. Rare actinomycetes Nocardia caishijiensis and Pseudonocardia carboxydivorans as endophytes, their bioactivity and metabolites evaluation. Microbiol Res 2016; 185:22-35. [PMID: 26946375 DOI: 10.1016/j.micres.2016.01.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Revised: 11/23/2015] [Accepted: 01/20/2016] [Indexed: 11/15/2022]
Abstract
Two strains identified as Nocardia caishijiensis (SORS 64b) and Pseudonocardia carboxydivorans (AGLS 2) were isolated as endophytes from Sonchus oleraceus and Ageratum conyzoides respectively. The analysis of their extracts revealed them to be strongly bioactive. The N. caishijiensis extract gave an LC50 of 570 μg/ml(-1) in the brine shrimp cytotoxicity assay and an EC50 of 0.552 μg/ml(-1) in the DPPH antioxidant assay. Antimicrobial activity was observed against Methicillin resistant Staphlococcus aureus (MRSA) and Escherichia coli ATCC 25922 (14 mm), Klebsiella pneumoniae ATCC 706003 (13 mm), S. aureus ATCC 25923 (11 mm) and Candida tropicalis (20 mm). For the extract of P. carboxydivorans the EC50 was 0.670 μg/ml(-1) and it was observed to be more bioactive against Bacillus subtilis DSM 10 ATCC 6051 (21 mm), C. tropicalis (20 mm), S. aureus ATCC 25923 (17 mm), MRSA (17 mm), E. coli K12 (W1130) (16 mm) and Chlorella vulgaris (10 mm). The genotoxicity testing revealed a 20 mm zone of inhibition against the polA mutant strain E. coli K-12 AB 3027 suggesting damage to the DNA and polA genes. The TLC and bioautography screening revealed a diversity of active bands of medium polar and nonpolar compounds. Metabolite analysis by HPLC-DAD via UV/vis spectral screening suggested the possibility of stenothricin and bagremycin A in the mycelium extract of N. caishijiensis respectively. In the broth and mycelium extract of P. carboxydivorans borrelidin was suggested along with α-pyrone. The HPLC-MS revealed bioactive long chained amide derivatives such as 7-Octadecenamide, 9, 12 octadecandienamide. This study reports the rare actinomycetes N. caishijiensis and P. carboxydivorans as endophytes and evaluates their bioactive metabolites.
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Affiliation(s)
- Rabia Tanvir
- Department of Microbiology and Molecular Genetics, University of the Punjab, Quaid-e-Azam Campus, 54590, Lahore, Punjab, Pakistan; Institut fur Organische Chemie, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 18A, 72076, Tübingen, Germany.
| | - Imran Sajid
- Department of Microbiology and Molecular Genetics, University of the Punjab, Quaid-e-Azam Campus, 54590, Lahore, Punjab, Pakistan
| | - Shahida Hasnain
- Department of Microbiology and Molecular Genetics, University of the Punjab, Quaid-e-Azam Campus, 54590, Lahore, Punjab, Pakistan; Department of Microbiology and Molecular Genetics, The Women University, Multan, Punjab, Pakistan
| | - Andreas Kulik
- Mikrobiologie/Biotechnologie, Interfakultäres Institut für Mikrobiologie und Infektionsmedizin, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
| | - Stephanie Grond
- Institut fur Organische Chemie, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 18A, 72076, Tübingen, Germany
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Nur Azura AB, Yusoff M, Tan GYA, Jegadeesh R, Appleton DR, Vikineswary S. Streptomyces sanglieri which colonised and enhanced the growth of Elaeis guineensis Jacq. seedlings was antagonistic to Ganoderma boninense in in vitro studies. J Ind Microbiol Biotechnol 2015; 43:485-93. [PMID: 26721619 DOI: 10.1007/s10295-015-1724-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 12/15/2015] [Indexed: 12/30/2022]
Abstract
Actinomycete strain AUM 00500 was 99.5 % similar to Streptomyces sanglieri NBRC 100784(T) and was evaluated for antagonistic activity towards Ganoderma boninense, the causative fungus of basal stem rot of oil palm. The strain showed strong antifungal activity towards G. boninense in in vitro and SEM analysis showed various modes of inhibition of the fungus. Ethyl acetate extracts of single culture and inhibition zone of cross-plug culture by HPLC indicated that strain AUM 00500 produced two different antibiotics of the glutarimide group namely cycloheximide and actiphenol. In greenhouse trials, oil palm seed treated with spores of S. sanglieri strain AUM 00500 at 10(9) cfu/ml showed significant (P < 0.05) increase in oil palm seedlings growth when compared to the control. Streptomyces sanglieri strain AUM 00500 successfully colonised the epidermal surface of the roots of treated oil palm seedlings and it was recovered from root fragments plated on starch casein agar.
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Affiliation(s)
- A B Nur Azura
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia.,Mushroom Research Centre, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - M Yusoff
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - G Y A Tan
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia.,Mushroom Research Centre, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - R Jegadeesh
- Mushroom Research Centre, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - D R Appleton
- Sime Darby Technology Centre Sdn. Bhd., 1st Floor, Block B, UPM-MTDC Technology Centre III, University Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - S Vikineswary
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia. .,Mushroom Research Centre, University of Malaya, 50603, Kuala Lumpur, Malaysia.
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