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Dos Reis JBA, Lorenzi AS, Pinho DB, Cortelo PC, do Vale HMM. The hidden treasures in endophytic fungi: a comprehensive review on the diversity of fungal bioactive metabolites, usual analytical methodologies, and applications. Arch Microbiol 2024; 206:185. [PMID: 38506928 DOI: 10.1007/s00203-024-03911-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: 01/25/2024] [Revised: 02/20/2024] [Accepted: 02/26/2024] [Indexed: 03/22/2024]
Abstract
This review provides a comprehensive overview of the key aspects of the natural metabolite production by endophytic fungi, which has attracted significant attention due to its diverse biological activities and wide range of applications. Synthesized by various fungal species, these metabolites encompass compounds with therapeutic, agricultural, and commercial significance. We delved into strategies and advancements aimed at optimizing fungal metabolite production. Fungal cultivation, especially by Aspergillus, Penicillium, and Fusarium, plays a pivotal role in metabolite biosynthesis, and researchers have explored both submerged and solid-state cultivation processes to harness the full potential of fungal species. Nutrient optimization, pH, and temperature control are critical factors in ensuring high yields of the targeted bioactive metabolites especially for scaling up processes. Analytical methods that includes High-Performance Liquid Chromatography (HPLC), Liquid Chromatography-Mass Spectrometry (LC-MS), Gas Chromatography-Mass Spectrometry (GC-MS), Nuclear Magnetic Resonance (NMR), and Mass Spectrometry (MS), are indispensable for the identification and quantification of the compounds. Moreover, genetic engineering and metabolic pathway manipulation have emerged as powerful tools to enhance metabolite production and develop novel fungal strains with increased yields. Regulation and control mechanisms at the genetic, epigenetic, and metabolic levels are explored to fine-tune the biosynthesis of fungal metabolites. Ongoing research aims to overcome the complexity of the steps involved to ensure the efficient production and utilization of fungal metabolites.
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Affiliation(s)
| | - Adriana Sturion Lorenzi
- Department of Cellular Biology, Institute of Biological Sciences, University of Brasília (UnB), Brasília, DF, Brazil
| | - Danilo Batista Pinho
- Department of Phytopathology, Institute of Biological Sciences, University of Brasília (UnB), Brasília, DF, Brazil
| | | | - Helson Mario Martins do Vale
- Department of Phytopathology, Institute of Biological Sciences, University of Brasília (UnB), Brasília, DF, Brazil
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Adouane E, Mercier C, Mamelle J, Willocquet E, Intertaglia L, Burgunter-Delamare B, Leblanc C, Rousvoal S, Lami R, Prado S. Importance of quorum sensing crosstalk in the brown alga Saccharina latissima epimicrobiome. iScience 2024; 27:109176. [PMID: 38433891 PMCID: PMC10906538 DOI: 10.1016/j.isci.2024.109176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 12/07/2023] [Accepted: 02/06/2024] [Indexed: 03/05/2024] Open
Abstract
Brown macroalgae are colonized by diverse microorganisms influencing the physiology of their host. However, cell-cell interactions within the surface microbiome (epimicrobiome) are largely unexplored, despite the significance of specific chemical mediators in maintaining host-microbiome homeostasis. In this study, by combining liquid chromatography coupled to mass spectrometry (LC-MS) analysis and bioassays, we demonstrated that the widely diverse fungal epimicrobiota of the brown alga Saccharina latissima can affect quorum sensing (QS), a type of cell-cell interaction, as well as bacterial biofilm formation. We also showed the ability of the bacterial epimicrobiota to form and inhibit biofilm growth, as well as to activate or inhibit QS pathways. Overall, we demonstrate that QS and anti-QS compounds produced by the epimicrobiota are key metabolites in these brown algal epimicrobiota communities and highlight the importance of exploring this epimicrobiome for the discovery of new bioactive compounds, including potentially anti-QS molecules with antifouling properties.
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Affiliation(s)
- Emilie Adouane
- Muséum National d’Histoire Naturelle, Unité Molécules de Communication et Adaptation des Micro-Organismes MCAM, UMR 7245, CNRS, Sorbonne Université, 75005 Paris, France
- Sorbonne Université, CNRS, UAR 3579 Laboratoire de Biodiversité et Biotechnologies Microbiennes LBBM, Observatoire Océanologique, 66650 Banyuls-sur-Mer, France
| | - Camille Mercier
- Sorbonne Université, CNRS, UAR 3579 Laboratoire de Biodiversité et Biotechnologies Microbiennes LBBM, Observatoire Océanologique, 66650 Banyuls-sur-Mer, France
| | - Jeanne Mamelle
- Sorbonne Université, CNRS, UAR 3579 Laboratoire de Biodiversité et Biotechnologies Microbiennes LBBM, Observatoire Océanologique, 66650 Banyuls-sur-Mer, France
| | - Emma Willocquet
- Sorbonne Université, CNRS, UAR 3579 Laboratoire de Biodiversité et Biotechnologies Microbiennes LBBM, Observatoire Océanologique, 66650 Banyuls-sur-Mer, France
| | - Laurent Intertaglia
- Sorbonne Université, CNRS, Bio2Mar, Observatoire Océanologique, 66650 Banyuls-sur-Mer, France
| | - Bertille Burgunter-Delamare
- Biologie Intégrative des Modèles Marins, LBI2M (Sorbonne Université/CNRS), Station Biologique de Roscoff (SBR), 29680 Roscoff, France
| | - Catherine Leblanc
- Biologie Intégrative des Modèles Marins, LBI2M (Sorbonne Université/CNRS), Station Biologique de Roscoff (SBR), 29680 Roscoff, France
| | - Sylvie Rousvoal
- Biologie Intégrative des Modèles Marins, LBI2M (Sorbonne Université/CNRS), Station Biologique de Roscoff (SBR), 29680 Roscoff, France
| | - Raphaël Lami
- Sorbonne Université, CNRS, UAR 3579 Laboratoire de Biodiversité et Biotechnologies Microbiennes LBBM, Observatoire Océanologique, 66650 Banyuls-sur-Mer, France
| | - Soizic Prado
- Muséum National d’Histoire Naturelle, Unité Molécules de Communication et Adaptation des Micro-Organismes MCAM, UMR 7245, CNRS, Sorbonne Université, 75005 Paris, France
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3
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Lee YS, Wu HC, Huang SJ, Hsiao G, Chi WC, Lee TH. Anti-inflammatory constituents from a sea anemone-derived fungus Arthrinium arundinis MA30. PHYTOCHEMISTRY 2024; 219:113998. [PMID: 38253160 DOI: 10.1016/j.phytochem.2024.113998] [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: 09/29/2023] [Revised: 01/19/2024] [Accepted: 01/19/2024] [Indexed: 01/24/2024]
Abstract
In this study, preliminary field-sampling of bioactive fungal strains and bioassay-guided selection were conducted. A number of fungal strains were isolated from sea anemones along the northeastern coast of Badouzi, Keelung, Taiwan. Among them, Arthrinium arundinis MA30 showed significant anti-inflammatory activity and was thus selected for further chemical investigation. After a series of purification and isolation using different chromatographic techniques on the fermented products of A. arundinis MA30, thirty-one compounds were identified, five of which were previously unreported, including arthrinoic acid, hexylaconitic anhydride methyl ester, (3S,8R)-8-hydroxy-3-carboxy-2-methylenenonanoic acid, and arthripenoids G and H. These compounds were subjected to comprehensive spectroscopic data analysis. Of all the isolates, 1,3,5,6-tetrahydroxy-8-methylxanthone and arthripenoid C demonstrated the most distinctive inhibitory activities against nitric oxide production in mouse microglial BV-2 cells, with their respective inhibitory rates being 71% and 81% at 10 μM concentration, and their respective IC50 values were further determined to be 5.3 ± 0.6 and 1.6 ± 0.4 μM. These compounds showed no significant cytotoxicity, and curcumin was used as a positive control in this study.
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Affiliation(s)
- Yuen-Sing Lee
- Institute of Fisheries Science, College of Life Science, National Taiwan University, Taipei 106, Taiwan.
| | - Ho-Cheng Wu
- Graduate Institute of Pharmacognosy, College of Pharmacy, Taipei Medical University, Taipei 110, Taiwan; Ph.D. Program in Clinical Drug Development of Herbal Medicine, College of Pharmacy, Taipei Medical University, Taipei 110, Taiwan; School of Pharmacy, College of Pharmacy, Kaohsiung Medical University, Kaohsiung 807, Taiwan.
| | - Shu-Jung Huang
- Institute of Fisheries Science, College of Life Science, National Taiwan University, Taipei 106, Taiwan.
| | - George Hsiao
- Department of Pharmacology, School of Medicine, College of Medicine, Taipei Medical University, Taipei 110, Taiwan; Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei 110, Taiwan.
| | - Wei-Chiung Chi
- Department of Food Science, National Quemoy University, Kinmen 892, Taiwan.
| | - Tzong-Huei Lee
- Institute of Fisheries Science, College of Life Science, National Taiwan University, Taipei 106, Taiwan.
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Reza MZ, Oppong-Danquah E, Tasdemir D. The Impact of the Culture Regime on the Metabolome and Anti-Phytopathogenic Activity of Marine Fungal Co-Cultures. Mar Drugs 2024; 22:66. [PMID: 38393037 PMCID: PMC10890130 DOI: 10.3390/md22020066] [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: 12/22/2023] [Revised: 01/19/2024] [Accepted: 01/24/2024] [Indexed: 02/25/2024] Open
Abstract
Co-cultivation, coupled with the OSMAC approach, is considered an efficient method for expanding microbial chemical diversity through the activation of cryptic biosynthetic gene clusters (BGCs). As part of our project aiming to discover new fungal metabolites for crop protection, we previously reported five polyketides, the macrolides dendrodolides E (1) and N (2), the azaphilones spiciferinone (3) and 8α-hydroxy-spiciferinone (4), and the bis-naphtho-γ-pyrone cephalochromin (5) from the solid Potato Dextrose Agar (PDA) co-culture of two marine sediment-derived fungi, Plenodomus influorescens and Pyrenochaeta nobilis. However, some of the purified metabolites could not be tested due to their minute quantities. Here we cultivated these fungi (both axenic and co-cultures) in liquid regime using three different media, Potato Dextrose Broth (PDB), Sabouraud Dextrose Broth (SDB), and Czapek-Dox Broth (CDB), with or without shaking. The aim was to determine the most ideal co-cultivation conditions to enhance the titers of the previously isolated compounds and to produce extracts with stronger anti-phytopathogenic activity as a basis for future upscaled fermentation. Comparative metabolomics by UPLC-MS/MS-based molecular networking and manual dereplication was employed for chemical profiling and compound annotations. Liquid co-cultivation in PDB under shaking led to the strongest activity against the phytopathogen Phytophthora infestans. Except for compound 1, all target compounds were detected in the co-culture in PDB. Compounds 2 and 5 were produced in lower titers, whereas the azaphilones (3 and 4) were overexpressed in PDB compared to PDA. Notably, liquid PDB co-cultures contained meroterpenoids and depside clusters that were absent in the solid PDA co-cultures. This study demonstrates the importance of culture regime in BGC regulation and chemical diversity of fungal strains in co-culture studies.
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Affiliation(s)
- Mohammed Zawad Reza
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Product Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Wischhofstrasse 1-3, 24148 Kiel, Germany; (M.Z.R.); (E.O.-D.)
| | - Ernest Oppong-Danquah
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Product Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Wischhofstrasse 1-3, 24148 Kiel, Germany; (M.Z.R.); (E.O.-D.)
| | - Deniz Tasdemir
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Product Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Wischhofstrasse 1-3, 24148 Kiel, Germany; (M.Z.R.); (E.O.-D.)
- Faculty of Mathematics and Natural Sciences, Kiel University, Christian-Albrechts-Platz 4, 24118 Kiel, Germany
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Le Loarer A, Dufossé L, Bignon J, Frédérich M, Ledoux A, Fouillaud M, Gauvin-Bialecki A. OSMAC Method to Assess Impact of Culture Parameters on Metabolomic Diversity and Biological Activity of Marine-Derived Actinobacteria. Mar Drugs 2023; 22:23. [PMID: 38248648 PMCID: PMC10817652 DOI: 10.3390/md22010023] [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: 09/16/2023] [Revised: 12/19/2023] [Accepted: 12/22/2023] [Indexed: 01/23/2024] Open
Abstract
Actinobacteria are known for their production of bioactive specialized metabolites, but they are still under-exploited. This study uses the "One Strain Many Compounds" (OSMAC) method to explore the potential of three preselected marine-derived actinobacteria: Salinispora arenicola (SH-78) and two Micromonospora sp. strains (SH-82 and SH-57). Various parameters, including the duration of the culture and the nature of the growth medium, were modified to assess their impact on the production of specialized metabolites. This approach involved a characterization based on chemical analysis completed with the construction of molecular networks and biological testing to evaluate cytotoxic and antiplasmodial activities. The results indicated that the influence of culture parameters depended on the studied species and also varied in relation with the microbial metabolites targeted. However, common favorable parameters could be observed for all strains such as an increase in the duration of the culture or the use of the A1 medium. For Micromonospora sp. SH-82, the solid A1 medium culture over 21 days favored a greater chemical diversity. A rise in the antiplasmodial activity was observed with this culture duration, with a IC50 twice as low as for the 14-day culture. Micromonospora sp. SH-57 produced more diverse natural products in liquid culture, with approximately 54% of nodes from the molecular network specifically linked to the type of culture support. Enhanced biological activities were also observed with specific sets of parameters. Finally, for Salinispora arenicola SH-78, liquid culture allowed a greater diversity of metabolites, but intensity variations were specifically observed for some metabolites under other conditions. Notably, compounds related to staurosporine were more abundant in solid culture. Consequently, in the range of the chosen parameters, optimal conditions to enhance metabolic diversity and biological activities in these three marine-derived actinobacteria were identified, paving the way for future isolation works.
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Affiliation(s)
- Alexandre Le Loarer
- Laboratory of Chemistry and Biotechnology of Natural Products, Faculty of Sciences and Technology, University of La Réunion, 15 Avenue René Cassin, CS 92003, CEDEX 09, 97744 Saint-Denis, France; (A.L.L.); (L.D.); (M.F.)
| | - Laurent Dufossé
- Laboratory of Chemistry and Biotechnology of Natural Products, Faculty of Sciences and Technology, University of La Réunion, 15 Avenue René Cassin, CS 92003, CEDEX 09, 97744 Saint-Denis, France; (A.L.L.); (L.D.); (M.F.)
| | - Jérôme Bignon
- Institute of Chemistry of Natural Substances (ICSN), CNRS UPR 2301, Université Paris-Saclay, 1, av. de la Terrasse, 91198 Gif-sur-Yvette, France;
| | - Michel Frédérich
- Pharmacognosy Laboratory, Department of Pharmacy, Centre Interfacultaire de Recherche sur le Médicament (CIRM), University of Liège, Campus du Sart-Tilman, Quartier Hôpital, Avenue Hippocrate, 15, B36, 4000 Liege, Belgium; (M.F.); (A.L.)
| | - Allison Ledoux
- Pharmacognosy Laboratory, Department of Pharmacy, Centre Interfacultaire de Recherche sur le Médicament (CIRM), University of Liège, Campus du Sart-Tilman, Quartier Hôpital, Avenue Hippocrate, 15, B36, 4000 Liege, Belgium; (M.F.); (A.L.)
| | - Mireille Fouillaud
- Laboratory of Chemistry and Biotechnology of Natural Products, Faculty of Sciences and Technology, University of La Réunion, 15 Avenue René Cassin, CS 92003, CEDEX 09, 97744 Saint-Denis, France; (A.L.L.); (L.D.); (M.F.)
| | - Anne Gauvin-Bialecki
- Laboratory of Chemistry and Biotechnology of Natural Products, Faculty of Sciences and Technology, University of La Réunion, 15 Avenue René Cassin, CS 92003, CEDEX 09, 97744 Saint-Denis, France; (A.L.L.); (L.D.); (M.F.)
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6
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Gaudêncio SP, Bayram E, Lukić Bilela L, Cueto M, Díaz-Marrero AR, Haznedaroglu BZ, Jimenez C, Mandalakis M, Pereira F, Reyes F, Tasdemir D. Advanced Methods for Natural Products Discovery: Bioactivity Screening, Dereplication, Metabolomics Profiling, Genomic Sequencing, Databases and Informatic Tools, and Structure Elucidation. Mar Drugs 2023; 21:md21050308. [PMID: 37233502 DOI: 10.3390/md21050308] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 05/11/2023] [Accepted: 05/12/2023] [Indexed: 05/27/2023] Open
Abstract
Natural Products (NP) are essential for the discovery of novel drugs and products for numerous biotechnological applications. The NP discovery process is expensive and time-consuming, having as major hurdles dereplication (early identification of known compounds) and structure elucidation, particularly the determination of the absolute configuration of metabolites with stereogenic centers. This review comprehensively focuses on recent technological and instrumental advances, highlighting the development of methods that alleviate these obstacles, paving the way for accelerating NP discovery towards biotechnological applications. Herein, we emphasize the most innovative high-throughput tools and methods for advancing bioactivity screening, NP chemical analysis, dereplication, metabolite profiling, metabolomics, genome sequencing and/or genomics approaches, databases, bioinformatics, chemoinformatics, and three-dimensional NP structure elucidation.
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Affiliation(s)
- Susana P Gaudêncio
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, 2819-516 Caparica, Portugal
- UCIBIO-Applied Molecular Biosciences Unit, Chemistry Department, NOVA School of Science and Technology, NOVA University of Lisbon, 2819-516 Caparica, Portugal
| | - Engin Bayram
- Institute of Environmental Sciences, Room HKC-202, Hisar Campus, Bogazici University, Bebek, Istanbul 34342, Turkey
| | - Lada Lukić Bilela
- Department of Biology, Faculty of Science, University of Sarajevo, 71000 Sarajevo, Bosnia and Herzegovina
| | - Mercedes Cueto
- Instituto de Productos Naturales y Agrobiología-CSIC, 38206 La Laguna, Spain
| | - Ana R Díaz-Marrero
- Instituto de Productos Naturales y Agrobiología-CSIC, 38206 La Laguna, Spain
- Instituto Universitario de Bio-Orgánica (IUBO), Universidad de La Laguna, 38206 La Laguna, Spain
| | - Berat Z Haznedaroglu
- Institute of Environmental Sciences, Room HKC-202, Hisar Campus, Bogazici University, Bebek, Istanbul 34342, Turkey
| | - Carlos Jimenez
- CICA- Centro Interdisciplinar de Química e Bioloxía, Departamento de Química, Facultade de Ciencias, Universidade da Coruña, 15071 A Coruña, Spain
| | - Manolis Mandalakis
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, HCMR Thalassocosmos, 71500 Gournes, Crete, Greece
| | - Florbela Pereira
- LAQV, REQUIMTE, Chemistry Department, NOVA School of Science and Technology, NOVA University of Lisbon, 2819-516 Caparica, Portugal
| | - Fernando Reyes
- Fundación MEDINA, Avda. del Conocimiento 34, 18016 Armilla, Spain
| | - Deniz Tasdemir
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Am Kiel-Kanal 44, 24106 Kiel, Germany
- Faculty of Mathematics and Natural Science, Kiel University, Christian-Albrechts-Platz 4, 24118 Kiel, Germany
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Pacheco-Tapia R, Ortíz S, Jargeat P, Amasifuen C, Vansteelandt M, Haddad M. Exploration of the Production of Three Thiodiketopiperazines by an Endophytic Fungal Strain of Cophinforma mamane. Chem Biodivers 2023; 20:e202201087. [PMID: 36919620 DOI: 10.1002/cbdv.202201087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 03/10/2023] [Accepted: 03/12/2023] [Indexed: 03/16/2023]
Abstract
Endophytic fungi possess a versatile metabolism which is related to their ability to live in diverse ecological niches. While culturing under laboratory conditions, their metabolism is mainly influenced by the culture media, time of incubation and other physicochemical factors. In this study, we focused on the production of 3 thiodiketopiperazines (TDKPs) botryosulfuranols A-C produced by an endophytic strain of Cophinforma mamane isolated from the leaves of Bixa orellana L collected in the Peruvian Amazon. We studied the time-course production of botryosulfuranols A-C during 28 days and evaluated the variations in the production of secondary metabolites, including the TDKPs, produced by C. mamane in response to different culture media, light versus dark conditions and different incubation times. We observed a short time-frame production of botryosulfuranol C while its production was significantly affected by the light conditions and nutrients of the culture media. Botryosulfuranols A and B showed a similar production pattern and a similar response to culturing conditions. Molecular networking allowed us to detect three compounds related to TDKPs that will be the focus of future experiments.
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Affiliation(s)
- Romina Pacheco-Tapia
- UMR 152 Pharma Dev, Université de Toulouse, IRD, UPS, France
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Sergio Ortíz
- Therapeutic Innovation Laboratory UMR CNRS 7200, Faculty of Pharmacy, Université de Strasbourg, Strasbourg, France
| | - Patricia Jargeat
- Laboratoire Evolution et Diversité Biologique UMR 5174, Université de Toulouse, CNRS, IRD, France
| | - Carlos Amasifuen
- Instituto Nacional de Innovación Agraria, Dirección de Recursos Genéticos y Biotecnología, Avenida La Molina 1981, Lima, 15024, Perú
- Present address: Epigénomique Fonctionnelle et Physiologie Moléculaire Du Diabète et Maladies Associées UMR 1283/8199, Université de Lille, Lille, France
| | | | - Mohamed Haddad
- UMR 152 Pharma Dev, Université de Toulouse, IRD, UPS, France
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Oppong-Danquah E, Miranda M, Blümel M, Tasdemir D. Bioactivity Profiling and Untargeted Metabolomics of Microbiota Associated with Mesopelagic Jellyfish Periphylla periphylla. Mar Drugs 2023; 21:md21020129. [PMID: 36827170 PMCID: PMC9958851 DOI: 10.3390/md21020129] [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: 01/20/2023] [Revised: 02/14/2023] [Accepted: 02/15/2023] [Indexed: 02/19/2023] Open
Abstract
The marine mesopelagic zone extends from water depths of 200 m to 1000 m and is home to a vast number and diversity of species. It is one of the least understood regions of the marine environment with untapped resources of pharmaceutical relevance. The mesopelagic jellyfish Periphylla periphylla is a well-known and widely distributed species in the mesopelagic zone; however, the diversity or the pharmaceutical potential of its cultivable microbiota has not been explored. In this study, we isolated microorganisms associated with the inner and outer umbrella of P. periphylla collected in Irminger Sea by a culture-dependent approach, and profiled their chemical composition and biological activities. Sixteen mostly gram-negative bacterial isolates were selected and subjected to an OSMAC cultivation regime approach using liquid and solid marine broth (MB) and glucose-yeast-malt (GYM) media. Their ethyl acetate (EtOAc) extracts were assessed for cytotoxicity and antimicrobial activity against fish and human pathogens. All, except one extract, displayed diverse levels of antimicrobial activities. Based on low IC50 values, four most bioactive gram-negative strains; Polaribacter sp. SU124, Shewanella sp. SU126, Psychrobacter sp. SU143 and Psychrobacter sp. SU137, were prioritized for an in-depth comparative and untargeted metabolomics analysis using feature-based molecular networking. Various chemical classes such as diketopiperazines, polyhydroxybutyrates (PHBs), bile acids and other lipids were putatively annotated, highlighting the biotechnological potential in P. periphylla-associated microbiota as well as gram-negative bacteria. This is the first study providing an insight into the cultivable bacterial community associated with the mesopelagic jellyfish P. periphylla and, indeed, the first to mine the metabolome and antimicrobial activities of these microorganisms.
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Affiliation(s)
- Ernest Oppong-Danquah
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Am Kiel-Kanal 44, 24106 Kiel, Germany
| | - Martina Miranda
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Am Kiel-Kanal 44, 24106 Kiel, Germany
| | - Martina Blümel
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Am Kiel-Kanal 44, 24106 Kiel, Germany
| | - Deniz Tasdemir
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Am Kiel-Kanal 44, 24106 Kiel, Germany
- Faculty of Mathematics and Natural Science, Kiel University, Christian-Albrechts-Platz 4, 24118 Kiel, Germany
- Correspondence: ; Tel.: +49-431-6004430
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9
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Chemistry and bioactivities of alkaloids isolated from marine fungi (covering 2016-2022). Fitoterapia 2023; 164:105377. [PMID: 36544299 DOI: 10.1016/j.fitote.2022.105377] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 11/24/2022] [Accepted: 11/25/2022] [Indexed: 11/29/2022]
Abstract
The ocean is a treasure house with rich resources of new chemical and biological molecules. A growing body of evidence suggests that marine fungi represent a huge and largely untapped resource of natural products that have been optimized by evolution for biological and ecological relevance. Alkaloids, the important components of natural products, have attracted much attention from medicinal and natural product chemists due to their unique structures and biological potential. The number and variety of alkaloids from marine fungi discovered in recent years maintain an upward trend. This review would give a systematic overview of the structures and bioactivities of marine fungal alkaloids obtained over the past six years and inspire the development of novel pharmaceutical agents.
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10
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Cooper C, Walker AK. Endophytic Fungi from Marine Macroalgae in Nova Scotia. Northeast Nat (Steuben) 2022. [DOI: 10.1656/045.029.0212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Caryn Cooper
- Department of Botany, University of British Columbia, 170-6371 Crescent Road, Vancouver, BC V6T 1Z2, Canada
| | - Allison K. Walker
- Department of Biology, Acadia University, 33 Westwood Avenue, Wolfville, NS B4P 2R6, Canada
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11
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Fan B, Grauso L, Li F, Scarpato S, Mangoni A, Tasdemir D. Application of Feature-Based Molecular Networking for Comparative Metabolomics and Targeted Isolation of Stereoisomers from Algicolous Fungi. Mar Drugs 2022; 20:210. [PMID: 35323509 PMCID: PMC8948805 DOI: 10.3390/md20030210] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/11/2022] [Accepted: 03/14/2022] [Indexed: 11/17/2022] Open
Abstract
Seaweed endophytic (algicolous) fungi are talented producers of bioactive natural products. We have previously isolated two strains of the endophytic fungus, Pyrenochaetopsis sp. FVE-001 and FVE-087, from the thalli of the brown alga Fucus vesiculosus. Initial chemical studies yielded four new decalinoylspirotetramic acid derivatives with antimelanoma activity, namely pyrenosetins A-C (1-3) from Pyrenochaetopsis sp. strain FVE-001, and pyrenosetin D (4) from strain FVE-087. In this study, we applied a comparative metabolomics study employing HRMS/MS based feature-based molecular networking (FB MN) on both Pyrenochaetopsis strains. A higher chemical capacity in production of decalin derivatives was observed in Pyrenochaetopsis sp. FVE-087. Notably, several decalins showed different retention times despite the same MS data and MS/MS fragmentation pattern with the previously isolated pyrenosetins, indicating they may be their stereoisomers. FB MN-based targeted isolation studies coupled with antimelanoma activity testing on the strain FVE-087 afforded two new stereoisomers, pyrenosetins E (5) and F (6). Extensive NMR spectroscopy including DFT computational studies, HR-ESIMS, and Mosher's ester method were used in the structure elucidation of compounds 5 and 6. The 3'R,5'R stereochemistry determined for compound 6 was identical to that previously reported for pyrenosetin C (3), whose stereochemistry was revised as 3'S,5'R in this study. Pyrenosetin E (5) inhibited the growth of human malignant melanoma cells (A-375) with an IC50 value of 40.9 μM, while 6 was inactive. This study points out significant variations in the chemical repertoire of two closely related fungal strains and the versatility of FB MN in identification and targeted isolation of stereoisomers. It also confirms that the little-known fungal genus Pyrenochaetopsis is a prolific source of complex decalinoylspirotetramic acid derivatives.
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Affiliation(s)
- Bicheng Fan
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Product Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Am Kiel-Kanal 44, 24106 Kiel, Germany; (B.F.); (F.L.)
| | - Laura Grauso
- Dipartimento di Agraria, Università degli Studi di Napoli Federico II, 80055 Portici, Italy;
| | - Fengjie Li
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Product Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Am Kiel-Kanal 44, 24106 Kiel, Germany; (B.F.); (F.L.)
| | - Silvia Scarpato
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, 80131 Napoli, Italy; (S.S.); (A.M.)
| | - Alfonso Mangoni
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, 80131 Napoli, Italy; (S.S.); (A.M.)
| | - Deniz Tasdemir
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Product Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Am Kiel-Kanal 44, 24106 Kiel, Germany; (B.F.); (F.L.)
- Faculty of Mathematics and Natural Sciences, Kiel University, Christian-Albrechts-Platz 4, 24118 Kiel, Germany
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Abstract
BACKGROUND Marine ecosystems are hosts to a vast array of organisms, being among the most richly biodiverse locations on the planet. The study of these ecosystems is very important, as they are not only a significant source of food for the world but also have, in recent years, become a prolific source of compounds with therapeutic potential. Studies of aspects of marine life have involved diverse fields of marine science, and the use of metabolomics as an experimental approach has increased in recent years. As part of the "omics" technologies, metabolomics has been used to deepen the understanding of interactions between marine organisms and their environment at a metabolic level and to discover new metabolites produced by these organisms. AIM OF REVIEW This review provides an overview of the use of metabolomics in the study of marine organisms. It also explores the use of metabolomics tools common to other fields such as plants and human metabolomics that could potentially contribute to marine organism studies. It deals with the entire process of a metabolomic study, from sample collection considerations, metabolite extraction, analytical techniques, and data analysis. It also includes an overview of recent applications of metabolomics in fields such as marine ecology and drug discovery and future perspectives of its use in the study of marine organisms. KEY SCIENTIFIC CONCEPTS OF REVIEW The review covers all the steps involved in metabolomic studies of marine organisms including, collection, extraction methods, analytical tools, statistical analysis, and dereplication. It aims to provide insight into all aspects that a newcomer to the field should consider when undertaking marine metabolomics.
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Affiliation(s)
- Lina M Bayona
- Natural Products Laboratory, Institute of Biology, Leiden University, 2333 BE, Leiden, The Netherlands
| | - Nicole J de Voogd
- Naturalis Biodiversity Center, Marine Biodiversity, 2333 CR, Leiden, The Netherlands
- Institute of Environmental Sciences, Leiden University, 2333 CC, Leiden, The Netherlands
| | - Young Hae Choi
- Natural Products Laboratory, Institute of Biology, Leiden University, 2333 BE, Leiden, The Netherlands.
- College of Pharmacy, Kyung Hee University, 130-701, Seoul, Republic of Korea.
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Farinella VF, Kawafune ES, Tangerina MMP, Domingos HV, Costa-Lotufo LV, Ferreira MJP. OSMAC Strategy Integrated with Molecular Networking for Accessing Griseofulvin Derivatives from Endophytic Fungi of Moquiniastrum polymorphum (Asteraceae). Molecules 2021; 26:7316. [PMID: 34885898 PMCID: PMC8658887 DOI: 10.3390/molecules26237316] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/20/2021] [Accepted: 11/30/2021] [Indexed: 12/05/2022] Open
Abstract
Three endophytic fungi isolated from Moquiniastrum polymorphum (Less.) G. Sancho (Asteraceae) were cultivated using the one strain many compounds (OSMAC) strategy to evaluate the production of griseofulvin derivatives. Extracts obtained were analyzed by HPLC-MS/MS and the chromatographic and spectrometric data used to elaborate a feature-based molecular network (FBMN) through the GNPS platform. This approach allowed the observation of differences such as medium-specific and strain-specific production of griseofulvin derivatives and variations of cytotoxic activity in most extracts. To evaluate the efficiency of the OSMAC approach allied with FBMN analysis in the prospection of compounds of biotechnological interest, griseofulvin and 7-dechlorogriseofulvin were isolated, and the relative concentrations were estimated in all culture media using HPLC-UV, allowing for the inference of the best strain-medium combinations to maximize its production. Malt extract-peptone broth and Wickerham broth media produced the highest concentrations of both secondary metabolites.
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Affiliation(s)
- Victor F. Farinella
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo 05508-090, SP, Brazil; (V.F.F.); (E.S.K.); (M.M.P.T.)
| | - Eunizinis S. Kawafune
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo 05508-090, SP, Brazil; (V.F.F.); (E.S.K.); (M.M.P.T.)
| | - Marcelo M. P. Tangerina
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo 05508-090, SP, Brazil; (V.F.F.); (E.S.K.); (M.M.P.T.)
| | - Helori V. Domingos
- Departamento de Farmacologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo 05508-090, SP, Brazil; (H.V.D.); (L.V.C.-L.)
| | - Leticia V. Costa-Lotufo
- Departamento de Farmacologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo 05508-090, SP, Brazil; (H.V.D.); (L.V.C.-L.)
| | - Marcelo J. P. Ferreira
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo 05508-090, SP, Brazil; (V.F.F.); (E.S.K.); (M.M.P.T.)
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Mohamed GA, Ibrahim SRM. Untapped Potential of Marine-Associated Cladosporium Species: An Overview on Secondary Metabolites, Biotechnological Relevance, and Biological Activities. Mar Drugs 2021; 19:645. [PMID: 34822516 PMCID: PMC8622643 DOI: 10.3390/md19110645] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 11/11/2021] [Accepted: 11/16/2021] [Indexed: 12/12/2022] Open
Abstract
The marine environment is an underexplored treasure that hosts huge biodiversity of microorganisms. Marine-derived fungi are a rich source of novel metabolites with unique structural features, bioactivities, and biotechnological applications. Marine-associated Cladosporium species have attracted considerable interest because of their ability to produce a wide array of metabolites, including alkaloids, macrolides, diketopiperazines, pyrones, tetralones, sterols, phenolics, terpenes, lactones, and tetramic acid derivatives that possess versatile bioactivities. Moreover, they produce diverse enzymes with biotechnological and industrial relevance. This review gives an overview on the Cladosporium species derived from marine habitats, including their metabolites and bioactivities, as well as the industrial and biotechnological potential of these species. In the current review, 286 compounds have been listed based on the reported data from 1998 until July 2021. Moreover, more than 175 references have been cited.
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Affiliation(s)
- Gamal A. Mohamed
- Department of Natural Products and Alternative Medicine, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Sabrin R. M. Ibrahim
- Preparatory Year Program, Batterjee Medical College, Jeddah 21442, Saudi Arabia;
- Department of Pharmacognosy, Faculty of Pharmacy, Assiut University, Assiut 71526, Egypt
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Storie J, Suškevičs M, Nevzati F, Külvik M, Kuhn T, Burkhard B, Vikström S, Lehtoranta V, Riikonen S, Oinonen S. Evidence on the impact of Baltic Sea ecosystems on human health and well-being: a systematic map. ENVIRONMENTAL EVIDENCE 2021; 10:30. [PMID: 34777788 PMCID: PMC8572082 DOI: 10.1186/s13750-021-00244-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 10/12/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND While the unique marine and coastal environment of the Baltic Sea provides numerous ecosystem services, its ecosystems are under pressure due to the intensification and diversification of anthropogenic uses. This present work constitutes a systematic map of the evidence of the impacts of ecosystem services and disservices on human health and well-being. The aim is to create a better understanding of the threats of unsustainable management or the benefits of sustainable management of the Baltic Sea and the impacts these may have on the health and well-being of human populations and present these findings to policy advisors. The mapping process is described, and the characteristics of the evidence base are presented. METHODS The applied method has been previously published in a systematic map protocol. Literature searches were carried out in English considering published peer-reviewed literature from traditional scientific journals and scientific reports from the grey literature, using synthesis software. A total of 17 databases were searched. Articles were screened in stages at title and abstract stage, then full-text stage. Geographic limitations were placed on the searches in accordance with research funders call, however, watersheds that had an impact on the Baltic Sea marine and coastal regions were considered. We used the more open PEO format, where population (P) included the human populations within the marine and coastal environment of the Baltic Sea region, exposure (E) related to the Baltic Sea ecosystems services and disservices, and the outcome (O) included all aspects of human health and well-being. After full-text screening articles selected for inclusion were searched for metadata connected to bibliographic information, ecosystem services, health and well-being outcomes and policy relevance. REVIEW FINDINGS Out of 6456 hits only 460 studies discussed either health or well-being indicators to some extent. Of these, only 67 explicitly mentioned ecosystem services and health and well-being indicators. However, few in this subset engaged with the topic of ecosystem services or disservices and health and well-being in depth. Studies are increasingly relating the two concepts but currently it is mainly studies focussed on cultural ecosystem services that deal with the concept of health and well-being to a greater degree. Studies in the medical literature relating to impacts on health from exposure to the Baltic Sea did not relate their findings to ecosystem services. The database of 67 studies is attached as Additional file 5. CONCLUSIONS Ecosystem services play an important role in human health and well-being; however, we found few studies that explicitly examine these impacts in detail. Further research is needed to link the health and well-being outcomes from the Baltic Sea to the ecosystem services supplied and therefore to demonstrate the benefits and disservices provided by the Baltic Sea ecosystems to human populations. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1186/s13750-021-00244-w.
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Affiliation(s)
- Joanna Storie
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi 1, 51006 Tartu, Estonia
| | - Monika Suškevičs
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi 1, 51006 Tartu, Estonia
| | - Fiona Nevzati
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi 1, 51006 Tartu, Estonia
| | - Mart Külvik
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi 1, 51006 Tartu, Estonia
| | - Tinka Kuhn
- Institute of Physical Geography and Landscape Ecology, Gottfried Wilhelm Leibniz University Hannover, Schneiderberg 50, 30167 Hannover, Germany
| | - Benjamin Burkhard
- Institute of Physical Geography and Landscape Ecology, Gottfried Wilhelm Leibniz University Hannover, Schneiderberg 50, 30167 Hannover, Germany
| | - Suvi Vikström
- Finnish Environment Institute, Latokartanonkaari 11, 00790 Helsinki, Finland
| | - Virpi Lehtoranta
- Finnish Environment Institute, Latokartanonkaari 11, 00790 Helsinki, Finland
| | - Simo Riikonen
- Finnish Environment Institute, Latokartanonkaari 11, 00790 Helsinki, Finland
| | - Soile Oinonen
- Finnish Environment Institute, Latokartanonkaari 11, 00790 Helsinki, Finland
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16
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Quemener M, Dayras M, Frotté N, Debaets S, Le Meur C, Barbier G, Edgcomb V, Mehiri M, Burgaud G. Highlighting the Biotechnological Potential of Deep Oceanic Crust Fungi through the Prism of Their Antimicrobial Activity. Mar Drugs 2021; 19:md19080411. [PMID: 34436250 PMCID: PMC8399467 DOI: 10.3390/md19080411] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 07/22/2021] [Accepted: 07/23/2021] [Indexed: 12/03/2022] Open
Abstract
Among the different tools to address the antibiotic resistance crisis, bioprospecting in complex uncharted habitats to detect novel microorganisms putatively producing original antimicrobial compounds can definitely increase the current therapeutic arsenal of antibiotics. Fungi from numerous habitats have been widely screened for their ability to express specific biosynthetic gene clusters (BGCs) involved in the synthesis of antimicrobial compounds. Here, a collection of unique 75 deep oceanic crust fungi was screened to evaluate their biotechnological potential through the prism of their antimicrobial activity using a polyphasic approach. After a first genetic screening to detect specific BGCs, a second step consisted of an antimicrobial screening that tested the most promising isolates against 11 microbial targets. Here, 12 fungal isolates showed at least one antibacterial and/or antifungal activity (static or lytic) against human pathogens. This analysis also revealed that Staphylococcus aureus ATCC 25923 and Enterococcus faecalis CIP A 186 were the most impacted, followed by Pseudomonas aeruginosa ATCC 27853. A specific focus on three fungal isolates allowed us to detect interesting activity of crude extracts against multidrug-resistant Staphylococcus aureus. Finally, complementary mass spectrometry (MS)-based molecular networking analyses were performed to putatively assign the fungal metabolites and raise hypotheses to link them to the observed antimicrobial activities.
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Affiliation(s)
- Maxence Quemener
- Laboratoire Universitaire de Biodiversité et Écologie Microbienne, Université de Brest, F-29280 Plouzané, France; (M.Q.); (N.F.); (S.D.); (C.L.M.); (G.B.)
| | - Marie Dayras
- Marine Natural Products Team, Institut de Chimie de Nice, UMR 7272, Université Côte d’Azur, CNRS, 06108 Nice, France; (M.D.); (M.M.)
| | - Nicolas Frotté
- Laboratoire Universitaire de Biodiversité et Écologie Microbienne, Université de Brest, F-29280 Plouzané, France; (M.Q.); (N.F.); (S.D.); (C.L.M.); (G.B.)
| | - Stella Debaets
- Laboratoire Universitaire de Biodiversité et Écologie Microbienne, Université de Brest, F-29280 Plouzané, France; (M.Q.); (N.F.); (S.D.); (C.L.M.); (G.B.)
| | - Christophe Le Meur
- Laboratoire Universitaire de Biodiversité et Écologie Microbienne, Université de Brest, F-29280 Plouzané, France; (M.Q.); (N.F.); (S.D.); (C.L.M.); (G.B.)
| | - Georges Barbier
- Laboratoire Universitaire de Biodiversité et Écologie Microbienne, Université de Brest, F-29280 Plouzané, France; (M.Q.); (N.F.); (S.D.); (C.L.M.); (G.B.)
| | - Virginia Edgcomb
- Departments of Geology and Geophysics and Biology, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA;
| | - Mohamed Mehiri
- Marine Natural Products Team, Institut de Chimie de Nice, UMR 7272, Université Côte d’Azur, CNRS, 06108 Nice, France; (M.D.); (M.M.)
| | - Gaëtan Burgaud
- Laboratoire Universitaire de Biodiversité et Écologie Microbienne, Université de Brest, F-29280 Plouzané, France; (M.Q.); (N.F.); (S.D.); (C.L.M.); (G.B.)
- Correspondence: ; Tel.: +33-290915148
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Kum E, İnce E. Genome-guided investigation of secondary metabolites produced by a potential new strain Streptomyces BA2 isolated from an endemic plant rhizosphere in Turkey. Arch Microbiol 2021; 203:2431-2438. [PMID: 33666690 DOI: 10.1007/s00203-021-02210-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 12/16/2020] [Accepted: 02/09/2021] [Indexed: 02/07/2023]
Abstract
Terrestrial actinomycetes are the important sources of secondary metabolites that serve as a major source of drugs. Recent advances in genome mining have revealed that Streptomyces genomes have a wide range of undiscovered secondary metabolite biosynthetic gene clusters. In the present study, genome mining was employed to discover biosynthetic potential of plant-associated strain Streptomyces BA2. Based on 16S rRNA gene sequencing, this strain was found to be closely related to Streptomyces durmitorensis, Streptomyces alboniger, and Streptomyces kanamyceticus with similarity of 99.71%, 99.64%, and 99.56%, respectively. The genome of BA2 contained 10.043.478 base pairs with G + C content of 69.92%. The annotation results revealed the presence of 9.056 protein coding genes, 88 tRNA and 18 rRNA genes. The dDDH and ANI values of genome sequences between strain BA2 and closely related type strains were considerably lower than the recommended threshold values. A total of 33 secondary metabolite biosynthetic gene clusters responsible for the biosynthesis of known and/or novel secondary metabolites, including non-ribosomal peptides, polyketides, terpenes, siderophores, bacteriocins, ectoines, and lassopeptides were identified. Metabolic profiling of Streptomyces sp. BA2 grown in three different culture media was determined by a non-targeted LC-MS/MS approach coupled with spectral networking. Significant bioactive natural products such as actinomycin D, desferrioxamine E, malyngamide K, and bouillonamide B were detected. Malyngamide K and bouillonamide B, known as marine cyanobacterial-derived compounds, were first reported from a Streptomyces strain in this study. Our study demonstrated the potentially novel strain Streptomyces sp. BA2 as a valuable source of new bioactive secondary metabolites.
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Affiliation(s)
- Ekrem Kum
- Institute of Natural and Applied Science, Dicle University, Diyarbakır, Turkey
| | - Ebru İnce
- Department of Biology, Faculty of Science, Dicle University, Diyarbakır, Turkey.
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Genomics- and Metabolomics-Based Investigation of the Deep-Sea Sediment-Derived Yeast, Rhodotorula mucilaginosa 50-3-19/20B. Mar Drugs 2020; 19:md19010014. [PMID: 33396687 PMCID: PMC7823890 DOI: 10.3390/md19010014] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 12/14/2020] [Accepted: 12/24/2020] [Indexed: 01/10/2023] Open
Abstract
Red yeasts of the genus Rhodotorula are of great interest to the biotechnological industry due to their ability to produce valuable natural products, such as lipids and carotenoids with potential applications as surfactants, food additives, and pharmaceuticals. Herein, we explored the biosynthetic potential of R. mucilaginosa 50-3-19/20B collected from the Mid-Atlantic Ridge using modern genomics and untargeted metabolomics tools. R. mucilaginosa 50-3-19/20B exhibited anticancer activity when grown on PDA medium, while antimicrobial activity was observed when cultured on WSP-30 medium. Applying the bioactive molecular networking approach, the anticancer activity was linked to glycolipids, namely polyol esters of fatty acid (PEFA) derivatives. We purified four PEFAs (1–4) and the known methyl-2-hydroxy-3-(1H-indol-2-yl)propanoate (5). Their structures were deduced from NMR and HR-MS/MS spectra, but 1–5 showed no anticancer activity in their pure form. Illumina-based genome sequencing, de novo assembly and standard biosynthetic gene cluster (BGC) analyses were used to illustrate key components of the PEFA biosynthetic pathway. The fatty acid producing BGC3 was identified to be capable of producing precursors of PEFAs. Some Rhodotorula strains are able to convert inulin into high-yielding PEFA and cell lipid using a native exo-inulinase enzyme. The genomic locus for an exo-inulinase enzyme (g1629.t1), which plays an instrumental role in the PEFA production via the mannitol biosynthesis pathway, was identified. This is the first untargeted metabolomics study on R. mucilaginosa providing new genomic insights into PEFA biosynthesis.
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Culture-Dependent Microbiome of the Ciona intestinalis Tunic: Isolation, Bioactivity Profiling and Untargeted Metabolomics. Microorganisms 2020; 8:microorganisms8111732. [PMID: 33167375 PMCID: PMC7694362 DOI: 10.3390/microorganisms8111732] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 11/01/2020] [Accepted: 11/03/2020] [Indexed: 01/28/2023] Open
Abstract
Ascidians and their associated microbiota are prolific producers of bioactive marine natural products. Recent culture-independent studies have revealed that the tunic of the solitary ascidian Cionaintestinalis (sea vase) is colonized by a diverse bacterial community, however, the biotechnological potential of this community has remained largely unexplored. In this study, we aimed at isolating the culturable microbiota associated with the tunic of C.intestinalis collected from the North and Baltic Seas, to investigate their antimicrobial and anticancer activities, and to gain first insights into their metabolite repertoire. The tunic of the sea vase was found to harbor a rich microbial community, from which 89 bacterial and 22 fungal strains were isolated. The diversity of the tunic-associated microbiota differed from that of the ambient seawater samples, but also between sampling sites. Fungi were isolated for the first time from the tunic of Ciona. The proportion of bioactive extracts was high, since 45% of the microbial extracts inhibited the growth of human pathogenic bacteria, fungi or cancer cell lines. In a subsequent bioactivity- and metabolite profiling-based approach, seven microbial extracts were prioritized for in-depth chemical investigations. Untargeted metabolomics analyses of the selected extracts by a UPLC-MS/MS-based molecular networking approach revealed a vast chemical diversity with compounds assigned to 22 natural product families, plus many metabolites that remained unidentified. This initial study indicates that bacteria and fungi associated with the tunic of C.intestinalis represent an untapped source of putatively new marine natural products with pharmacological relevance.
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Fan B, Dewapriya P, Li F, Grauso L, Blümel M, Mangoni A, Tasdemir D. Pyrenosetin D, a New Pentacyclic Decalinoyltetramic Acid Derivative from the Algicolous Fungus Pyrenochaetopsis sp. FVE-087. Mar Drugs 2020; 18:E281. [PMID: 32466545 PMCID: PMC7344976 DOI: 10.3390/md18060281] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 05/22/2020] [Accepted: 05/24/2020] [Indexed: 12/12/2022] Open
Abstract
The fungal genus Pyrenochaetopsis is commonly found in soil, terrestrial, and marine environments, however, has received little attention as a source of bioactive secondary metabolites so far. In a recent work, we reported the isolation and characterization of three new anticancer decalinoyltetramic acid derivatives, pyrenosetins A-C, from the Baltic Fucus vesiculosus-derived endophytic fungus Pyrenochaetopsis sp. FVE-001. Herein we report a new pentacyclic decalinoylspirotetramic acid derivative, pyrenosetin D (1), along with two known decalin derivatives wakodecalines A (2) and B (3) from another endophytic strain Pyrenochaetopsis FVE-087 isolated from the same seaweed and showed anticancer activity in initial screenings. The chemical structures of the purified compounds were elucidated by comprehensive analysis of HR-ESIMS, FT-IR, [a]D, 1D and 2D NMR data coupled with DFT calculations of NMR parameters and optical rotation. Compounds 1-3 were evaluated for their anticancer and toxic potentials against the human malignant melanoma cell line (A-375) and the non-cancerous keratinocyte cell line (HaCaT). Pyrenosetin D (1) showed toxicity towards both A-375 and HaCaT cells with IC50 values of 77.5 and 39.3 μM, respectively, while 2 and 3 were inactive. This is the third chemical study performed on the fungal genus Pyrenochaetopsis and the first report of a pentacyclic decalin ring system from the fungal genus Pyrenochaetopsis.
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Affiliation(s)
- Bicheng Fan
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Am Kiel-Kanal 44, 24106 Kiel, Germany; (B.F.); (P.D.); (F.L.); (M.B.)
| | - Pradeep Dewapriya
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Am Kiel-Kanal 44, 24106 Kiel, Germany; (B.F.); (P.D.); (F.L.); (M.B.)
| | - Fengjie Li
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Am Kiel-Kanal 44, 24106 Kiel, Germany; (B.F.); (P.D.); (F.L.); (M.B.)
| | - Laura Grauso
- Dipartimento di Agraria, Università degli Studi di Napoli Federico II, via Università 100, 80055 Portici (NA), Italy;
| | - Martina Blümel
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Am Kiel-Kanal 44, 24106 Kiel, Germany; (B.F.); (P.D.); (F.L.); (M.B.)
| | - Alfonso Mangoni
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, via Domenico Montesano 49, 80131 Napoli, Italy;
| | - Deniz Tasdemir
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Am Kiel-Kanal 44, 24106 Kiel, Germany; (B.F.); (P.D.); (F.L.); (M.B.)
- Faculty of Mathematics and Natural Sciences, Kiel University, Christian-Albrechts-Platz 4, 24118 Kiel, Germany
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Oppong-Danquah E, Passaretti C, Chianese O, Blümel M, Tasdemir D. Mining the Metabolome and the Agricultural and Pharmaceutical Potential of Sea Foam-Derived Fungi. Mar Drugs 2020; 18:md18020128. [PMID: 32098306 PMCID: PMC7074149 DOI: 10.3390/md18020128] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 02/10/2020] [Accepted: 02/21/2020] [Indexed: 12/12/2022] Open
Abstract
Sea foam harbors a diverse range of fungal spores with biological and ecological relevance in marine environments. Fungi are known as the producers of secondary metabolites that are used in health and agricultural sectors, however the potentials of sea foam-derived fungi have remained unexplored. In this study, organic extracts of six foam-derived fungal isolates belonging to the genera Penicillium, Cladosporium, Emericellopsis and Plectosphaerella were investigated for their antimicrobial activity against plant and human pathogens and anticancer activity. In parallel, an untargeted metabolomics study using UPLC-QToF–MS/MS-based molecular networking (MN) was performed to unlock their chemical inventory. Penicillium strains were identified as the most prolific producers of compounds with an average of 165 parent ions per strain. In total, 49 known mycotoxins and functional metabolites were annotated to specific and ubiquitous parent ions, revealing considerable chemical diversity. This allowed the identification of putative new derivatives, such as a new analog of the antimicrobial tetrapeptide, fungisporin. Regarding bioactivity, the Penicillium sp. isolate 31.68F1B showed a strong and broad-spectrum activity against seven plant and human pathogens, with the phytopathogen Magnaporthe oryzae and the human pathogen Candida albicans being the most susceptible (IC50 values 2.2 and 6.3 µg/mL, respectively). This is the first study mining the metabolome of the sea foam-derived fungi by MS/MS-based molecular networking, and assessing their biological activities against phytopathogens.
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Affiliation(s)
- Ernest Oppong-Danquah
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Am Kiel-Kanal 44, 24106 Kiel, Germany; (E.O.-D.); (C.P.); (O.C.); (M.B.)
| | - Cristina Passaretti
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Am Kiel-Kanal 44, 24106 Kiel, Germany; (E.O.-D.); (C.P.); (O.C.); (M.B.)
| | - Orazio Chianese
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Am Kiel-Kanal 44, 24106 Kiel, Germany; (E.O.-D.); (C.P.); (O.C.); (M.B.)
| | - Martina Blümel
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Am Kiel-Kanal 44, 24106 Kiel, Germany; (E.O.-D.); (C.P.); (O.C.); (M.B.)
| | - Deniz Tasdemir
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Am Kiel-Kanal 44, 24106 Kiel, Germany; (E.O.-D.); (C.P.); (O.C.); (M.B.)
- Faculty of Mathematics and Natural Science, Kiel University, Christian-Albrechts-Platz 4, 24118 Kiel, Germany
- Correspondence: ; Tel.: +49-431-6004430
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Fan B, Dewapriya P, Li F, Blümel M, Tasdemir D. Pyrenosetins A-C, New Decalinoylspirotetramic Acid Derivatives Isolated by Bioactivity-Based Molecular Networking from the Seaweed-Derived Fungus Pyrenochaetopsis sp. FVE-001. Mar Drugs 2020; 18:E47. [PMID: 31940767 PMCID: PMC7024310 DOI: 10.3390/md18010047] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 01/07/2020] [Accepted: 01/09/2020] [Indexed: 02/07/2023] Open
Abstract
Marine algae represent a prolific source of filamentous fungi for bioprospecting. In continuation of our search for new anticancer leads from fungi derived from the brown alga Fucus vesiculosus, an endophytic Pyrenochaetopsis sp. FVE-001 was selected for an in-depth chemical analysis. The crude fungal extract inhibited several cancer cell lines in vitro, and the highest anticancer activity was tracked to its CHCl3-soluble portion. A bioactivity-based molecular networking approach was applied to C18-SPE fractions of the CHCl3 subextract to predict the bioactivity scores of metabolites in the fractions and to aid targeted purification of anticancer metabolites. This approach led to a rapid isolation of three new decalinoylspirotetramic acid derivatives, pyrenosetins A-C (1-3) and the known decalin tetramic acid phomasetin (4). The structures of the compounds were elucidated by extensive NMR, HR-ESIMS, FT-IR spectroscopy, [α]D and Mosher's ester method. Compounds 1 and 2 showed high anticancer activity against malignant melanoma cell line A-375 (IC50 values 2.8 and 6.3 μM, respectively), in line with the bioactivity predictions. This is the first study focusing on secondary metabolites of a marine-derived Pyrenochaetopsis sp. and the second investigation performed on the member of the genus Pyrenochaetopsis.
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Affiliation(s)
- Bicheng Fan
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Am Kiel-Kanal 44, 24106 Kiel, Germany; (B.F.); (P.D.); (F.L.); (M.B.)
| | - Pradeep Dewapriya
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Am Kiel-Kanal 44, 24106 Kiel, Germany; (B.F.); (P.D.); (F.L.); (M.B.)
| | - Fengjie Li
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Am Kiel-Kanal 44, 24106 Kiel, Germany; (B.F.); (P.D.); (F.L.); (M.B.)
| | - Martina Blümel
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Am Kiel-Kanal 44, 24106 Kiel, Germany; (B.F.); (P.D.); (F.L.); (M.B.)
| | - Deniz Tasdemir
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Am Kiel-Kanal 44, 24106 Kiel, Germany; (B.F.); (P.D.); (F.L.); (M.B.)
- Faculty of Mathematics and Natural Sciences, Kiel University, Christian-Albrechts-Platz 4, 24118 Kiel, Germany
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Rapid Metabolome and Bioactivity Profiling of Fungi Associated with the Leaf and Rhizosphere of the Baltic Seagrass Zostera marina. Mar Drugs 2019; 17:md17070419. [PMID: 31330983 PMCID: PMC6669648 DOI: 10.3390/md17070419] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 07/15/2019] [Accepted: 07/16/2019] [Indexed: 01/30/2023] Open
Abstract
Zostera marina (eelgrass) is a marine foundation species with key ecological roles in coastal habitats. Its bacterial microbiota has been well studied, but very little is known about its mycobiome. In this study, we have isolated and identified 13 fungal strains, dominated by Penicillium species (10 strains), from the leaf and the root rhizosphere of Baltic Z. marina. The organic extracts of the fungi that were cultured by an OSMAC (One-Strain–Many-Compounds) regime using five liquid culture media under both static and shaking conditions were investigated for their chemical and bioactivity profiles. All extracts showed strong anti-quorum sensing activity, and the majority of the Penicillium extracts displayed antimicrobial or anti-biofilm activity against Gram-negative environmental marine and human pathogens. HPLC-DAD-MS-based rapid metabolome analyses of the extracts indicated the high influence of culture conditions on the secondary metabolite (SM) profiles. Among 69 compounds detected in all Penicillium sp. extracts, 46 were successfully dereplicated. Analysis of SM relatedness in culture conditions by Hierarchical Cluster Analysis (HCA) revealed generally low similarity and showed a strong effect of medium selection on chemical profiles of Penicillium sp. This is the first study assessing both the metabolite and bioactivity profile of the fungi associated with Baltic eelgrass Z. marina.
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