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Ouchene R, Zaatout N, Suzuki MT. An Overview on Nocardiopsis Species Originating From North African Biotopes as a Promising Source of Bioactive Compounds and In Silico Genome Mining Analysis of Three Sequenced Genomes. J Basic Microbiol 2024; 64:e2400046. [PMID: 38934516 DOI: 10.1002/jobm.202400046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 05/21/2024] [Accepted: 06/01/2024] [Indexed: 06/28/2024]
Abstract
Actinobacteria are renowned for their prolific production of diverse bioactive secondary metabolites. In recent years, there has been an increasing focus on exploring "rare" genera within this phylum for biodiscovery purposes, notably the Nocardiopsis genus, which will be the subject of the present study. Recognizing the absence of articles describing the research process of finding bioactive molecules from the genus Nocardiopsis in North African environments. We, therefore, present a historical overview of the discoveries of bioactive molecules of the genus Nocardiopsis originating from the region, highlighting their biological activities and associated reported molecules, providing a snapshot of the current state of the field, and offering insights into future opportunities and challenges for drug discovery. Additionally, we present a genome mining analysis of three genomes deposited in public databases that have been reported to be bioactive. A total of 36 biosynthetic gene clusters (BGCs) were identified, including those known to encode bioactive molecules. Notably, a substantial portion of the BGCs showed little to no similarity to those previously described, suggesting the possibility that the analyzed strains could be potential producers of new compounds. Further research on these genomes is essential to fully uncovering their biotechnological potential. Moving forward, we discuss the experimental designs adopted in the reported studies, as well as new avenues to guide the exploration of the Nocardiopsis genus in North Africa.
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Affiliation(s)
- Rima Ouchene
- Laboratoire de Microbiologie Appliquée (LMA), Faculté des Sciences de la Nature et de la Vie, Université de Bejaia, Bejaia, Algeria
- CNRS, Laboratoire de Biodiversité et Biotechnologies Microbiennes, LBBM, Sorbonne Université, Paris, France
| | - Nawel Zaatout
- Faculty of Natural and Life Sciences, University of Batna, Batna, Algeria
| | - Marcelino T Suzuki
- CNRS, Laboratoire de Biodiversité et Biotechnologies Microbiennes, LBBM, Sorbonne Université, Paris, France
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El-Sayed MH, Abdellatif MM, Mostafa HM, Elsehemy IA, Kobisi AENA. Biodegradation and antimicrobial capability-induced heavy metal resistance of the marine-derived actinomycetes Nocardia harenae JJB5 and Amycolatopsis marina JJB11. World J Microbiol Biotechnol 2024; 40:202. [PMID: 38743315 DOI: 10.1007/s11274-024-04006-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 04/25/2024] [Indexed: 05/16/2024]
Abstract
Currently, heavy metal-resistant (HMR) marine actinomycetes have attracted much attention worldwide due to their unique capabilities. In this study, 27 marine-derived actinomycetes were isolated from coastal beaches in the Arabian Gulf of Al-Jubail in Saudi Arabia and screened for resistance to 100 mg/L of the heavy metals Cd2+, Cr6+, Cu2+, Fe2+, Pb2+, and Ni2+ using different assay techniques. Six isolates were selected as HMRs, of which two isolates, JJB5 and JJB11, exhibited the highest maximum tolerance concentrations (200- > 300 mg/L). Both isolates were the highest among six-HMR screened for their biodegradation potential of plastics low-density polyethylene, polystyrene, and polyvinyl chloride, recording the highest weight loss (15 ± 1.22 - 65 ± 1.2%) in their thin films. They also showed the highest biodegradability of the pesticides acetamiprid, chlordane, hexachlorocyclohexane, indoxacarb and lindane, indicating promising removal capacities (95.70-100%) for acetamiprid and indoxacarb using HPLC analysis. Additionally, the cell-free filtrate (CFF) of both isolates displayed the highest antimicrobial activity among the six-HMR screened against a variety of microbial test strains, recording the highest inhibition zone diameters (13.76 ± 0.66 - 26.0 ± 1.13 mm). GC‒MS analyses of the ethyl acetate extract of their CFFs revealed the presence of diverse chemical compounds with a multitude of remarkable biological activities. Based on their spore morphology and wall-chemotype, they were assigned to the nocardioform-actinomycetes. Furthermore, their phenotypic characteristics, together with 16S rRNA gene sequencing (OR121525-OR121526), revealed them as Nocardia harenae JJB5 and Amycolatopsis marina JJB11. Our results suggest that marine HMR actinomycetes are promising candidates for various biotechnological applications.
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Affiliation(s)
- Mohamed H El-Sayed
- Department of Biology, College of Science and Arts-Rafha, Northern Border University, Arar, Saudi Arabia.
- Department of Botany and Microbiology, Faculty of Science, Al-Azhar University, Cairo, 11884, Egypt.
| | - Muaz M Abdellatif
- Department of Biology, College of Science and Arts-Rafha, Northern Border University, Arar, Saudi Arabia
| | - Howayada M Mostafa
- Department of Chemistry, College of Science and Arts-Rafha, Northern Border University, Arar, Saudi Arabia
| | - Islam A Elsehemy
- Department of Natural and Microbial Products Chemistry, Division of Pharmaceutical and Drug Industries Research, National Research Centre, Cairo, Egypt
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Ren K, Yang X, Li J, Jin H, Gu K, Chen Y, Liu M, Luo Y, Jiang Y. Alleviating the adverse effects of Cd-Pb contamination through the application of silicon fertilizer: Enhancing soil microbial diversity and mitigating heavy metal contamination. CHEMOSPHERE 2024; 352:141414. [PMID: 38336042 DOI: 10.1016/j.chemosphere.2024.141414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 02/05/2024] [Accepted: 02/06/2024] [Indexed: 02/12/2024]
Abstract
The use of silicon fertilizer (SF) as a means of remediating cadmium (Cd) and lead (Pb) pollution has proven to be beneficial. However, the mechanism via which SF enhances soil quality and crop productivity under Cd- and Pb-contaminated soil (S) remains unclear. This study investigated the impacts of chemical fertilizer, mineral SF (MSF), and organic SF (OSF) on microbial community structure, activity of nutrient acquisition enzymes, and growth of tobacco in the presence of S condition. SF significantly reduced the contents of Cd and Pb in soil under S condition by 6.92-42.43% and increased plant height and leaf area by 15.27-81.77%. Moreover, the use of SF was observed to increase the efficiency of soil carbon and phosphorus cycling under S condition by 6.88-23.08%. Concurrently, SF was found to play a crucial role in facilitating the establishment of a complex, efficient, and interdependent molecular ecological network among soil microorganisms. In this context, Actinobacteriota, Bacteroidota, Ascomycota, and Basidiomycota were observed to be integral components of this network. SF was found to have a substantial positive impact on the metabolic functions and organismal systems of soil microorganisms. Moreover, the combined utilization of the Mantel test and partial least squares path model provided empirical evidence supporting the assertion that the administration of SF had a positive impact on both soil nutrient acquisition enzyme activity and tobacco growth, which was attributed to the enhancement of soil microbial diversity resulting from the application of SF. Furthermore, compared with MSF, OSF has advantages in reducing soil Pb and Cd content, promoting tobacco agronomic traits, increasing the number of key microbial communities, and maintaining the structural stability of microbial networks. The aforementioned findings, therefore, suggest that the OSF played a pivotal role in alleviating the adverse impacts of S, thereby demonstrating its efficacy in this particular process.
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Affiliation(s)
- Ke Ren
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming, 650021, China; College of Agronomy and Biotechnology, Southwest University / Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, 400715, China
| | - Xiongwei Yang
- College of Landscape Architecture, Southwest Forestry University, Kunming, 650224, China
| | - Jian Li
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, China
| | - Hongyan Jin
- College of Landscape Architecture, Southwest Forestry University, Kunming, 650224, China
| | - Kaiyuan Gu
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming, 650021, China; College of Agronomy and Biotechnology, Southwest University / Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, 400715, China
| | - Yi Chen
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming, 650021, China
| | - Ming Liu
- College of Agronomy and Biotechnology, Southwest University / Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, 400715, China
| | - Yigui Luo
- College of Tobacco Science, Yunnan Agricultural University, Kunming, 650031, China.
| | - Yonglei Jiang
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming, 650021, China.
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Syiemiong D, Rabha J. Unveiling nature's treasures: actinobacteria from Meghalaya's mining sites as sources of bioactive compounds. Arch Microbiol 2024; 206:64. [PMID: 38224372 DOI: 10.1007/s00203-023-03791-7] [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: 08/17/2023] [Revised: 12/08/2023] [Accepted: 12/09/2023] [Indexed: 01/16/2024]
Abstract
Coal and sillimanite mining sites present unique ecological niches favoring the growth of actinobacteria, a group of Gram-positive bacteria known for producing a wide array of bioactive compounds. Isolating these bacteria from such environments could unveil novel compounds with potential biotechnological applications. This study involved the isolation of actinobacteria from two mining sites in Meghalaya, India. The dominant genera from both sites were Streptomyces, Amycolatopsis, Nocardia, and Streptosporangium. Metabolic pathway prediction from 16S rRNA gene revealed several pathways beneficial for plant growth. Exploration of biosynthetic genes indicated a prevalence of the type-II polyketide synthase gene. Sequencing the ketosynthase-alpha domain of the gene led to predictions of various bioactive secondary metabolites. Around 44% of the isolates demonstrated antimicrobial properties, with some also displaying plant growth-promoting traits. Amycolatopsis SD-15 exhibited promising results in planta when tested on tomato plants. These findings highlight the potential of actinobacteria from Meghalaya's mining sites across medical, agricultural, and industrial domains.
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Affiliation(s)
- Debulman Syiemiong
- Department of Botany, St. Edmund's College, Shillong, 793003, India.
- Microbial Ecology Laboratory, Department of Botany, Gauhati University, Guwahati, 781014, India.
| | - Jintu Rabha
- Microbial Ecology Laboratory, Department of Botany, Gauhati University, Guwahati, 781014, India
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Rathinam AJ, Santhaseelan H, Dahms HU, Dinakaran VT, Murugaiah SG. Bioprospecting of unexplored halophilic actinobacteria against human infectious pathogens. 3 Biotech 2023; 13:398. [PMID: 37974926 PMCID: PMC10645811 DOI: 10.1007/s13205-023-03812-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 10/08/2023] [Indexed: 11/19/2023] Open
Abstract
Human pathogenic diseases received much attention recently due to their uncontrolled spread of antimicrobial resistance (AMR) which causes several threads every year. Effective alternate antimicrobials are urgently required to combat those disease causing infectious microbes. Halophilic actinobacteria revealed huge potentials and unexplored cultivable/non-cultivable actinobacterial species producing enormous antimicrobials have been proved in several genomics approaches. Potential gene clusters, PKS and NRPKS from Nocardia, Salinospora, Rhodococcus, and Streptomyces have wide range coding genes of secondary metabolites. Biosynthetic pathways identification via various approaches like genome mining, In silico, OSMAC (one strain many compound) analysis provides better identification of knowing the active metabolites using several databases like AMP, APD and CRAMPR, etc. Genome constellations of actinobacteria particularly the prediction of BGCs (Biosynthetic Gene Clusters) to mine the bioactive molecules such as pigments, biosurfactants and few enzymes have been reported for antimicrobial activity. Saltpan, saltlake, lagoon and haloalkali environment exploring potential actinobacterial strains Micromonospora, Kocuria, Pseudonocardia, and Nocardiopsis revealed several acids and ester derivatives with antimicrobial potential. Marine sediments and marine macro organisms have been found as significant population holders of potential actinobacterial strains. Deadly infectious diseases (IDs) including tuberculosis, ventilator-associated pneumonia and Candidiasis, have been targeted by halo-actinobacterial metabolites with promising results. Methicillin resistant Staphylococus aureus and virus like Encephalitic alphaviruses were potentially targeted by halophilic actinobacterial metabolites by the compound Homoseongomycin from sponge associated antinobacterium. In this review, we discuss the potential antimicrobial properties of various biomolecules extracted from the unexplored halophilic actinobacterial strains specifically against human infectious pathogens along with prospective genomic constellations.
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Affiliation(s)
- Arthur James Rathinam
- Department of Marine Science, Bharathidasan University, Tiruchirappalli, 620 024 India
| | - Henciya Santhaseelan
- Department of Marine Science, Bharathidasan University, Tiruchirappalli, 620 024 India
| | - Hans-Uwe Dahms
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, 80708 Taiwan
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Math HH, Kumar RS, Chakraborty B, Almansour AI, Perumal K, Kantli GB, Nayaka S. Antimicrobial Efficacy of 7-Hydroxyflavone Derived from Amycolatopsis sp. HSN-02 and Its Biocontrol Potential on Cercospora Leaf Spot Disease in Tomato Plants. Antibiotics (Basel) 2023; 12:1175. [PMID: 37508271 PMCID: PMC10376496 DOI: 10.3390/antibiotics12071175] [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: 05/16/2023] [Revised: 07/04/2023] [Accepted: 07/08/2023] [Indexed: 07/30/2023] Open
Abstract
The actinomycete strain HSN-02 was isolated from the soil of a mining field in the Sandur region, Bellary, Karnataka, India. According to the morphological, cultural, physiological, and biochemical characteristics and the 16S rDNA sequence analysis, the strain HSN-02 was identified as Amycolatopsis sp. The antimicrobial activity strain HSN-02 presented stable and moderate inhibitory activity against human pathogens. In pot experiments in the greenhouse, the development of Cercospora leaf spot was markedly suppressed by treatment with the purified compound from the strain HSN-02, and the control efficacy was 45.04 ± 1.30% in Septoria lycopersici-infected tomato plants. A prominent compound was obtained from the fermentation broth of the strain HSN-02 using column chromatography and HPLC. The chemical structural analyses using UV, FTIR, HR-ESI-MS, and NMR confirmed that the compound produced by the strain HSN-02 is 7-hydroxyflavone. This investigation showed the role which the actinomycete strain can play in controlling leaf spots caused by S. lycopersici to reduce treatments with chemical fungicides.
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Affiliation(s)
- Halaswamy Hire Math
- P.G. Department of Studies in Botany, Karnatak University, Dharwad 580003, Karnataka, India
| | - Raju Suresh Kumar
- Department of Chemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Bidhayak Chakraborty
- P.G. Department of Studies in Botany, Karnatak University, Dharwad 580003, Karnataka, India
| | - Abdulrahman I Almansour
- Department of Chemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Karthikeyan Perumal
- Department of Chemistry and Biochemistry, The Ohio State University, 151 W. Woodruff Ave, Columbus, OH 43210, USA
| | - Girish Babu Kantli
- Department of Life Sciences, PIAS, Parul University, Vadodara 391760, Gujarat, India
| | - Sreenivasa Nayaka
- P.G. Department of Studies in Botany, Karnatak University, Dharwad 580003, Karnataka, India
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