1
|
Quintana-Bulla JI, Tonon LAC, Michaliski LF, Hajdu E, Ferreira AG, Berlinck RGS. Testacosides A-D, glycoglycerolipids produced by Microbacterium testaceum isolated from Tedania brasiliensis. Appl Microbiol Biotechnol 2024; 108:112. [PMID: 38217254 PMCID: PMC10786734 DOI: 10.1007/s00253-023-12870-0] [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: 06/09/2023] [Revised: 09/18/2023] [Accepted: 09/30/2023] [Indexed: 01/15/2024]
Abstract
Marine bacteria living in association with marine sponges have proven to be a reliable source of biologically active secondary metabolites. However, no studies have yet reported natural products from Microbacterium testaceum spp. We herein report the isolation of a M. testaceum strain from the sponge Tedania brasiliensis. Molecular networking analysis of bioactive pre-fractionated extracts from culture media of M. testaceum enabled the discovery of testacosides A-D. Analysis of spectroscopic data and chemical derivatizations allowed the identification of testacosides A-D as glycoglycerolipids bearing a 1-[α-glucopyranosyl-(1 → 3)-(α-mannopyranosyl)]-glycerol moiety connected to 12-methyltetradecanoic acid for testacoside A (1), 14-methylpentadecanoic acid for testacoside B (2), and 14-methylhexadecanoic acid for testacosides C (3) and D (4). The absolute configuration of the monosaccharide residues was determined by 1H-NMR analysis of the respective diastereomeric thiazolidine derivatives. This is the first report of natural products isolated from cultures of M. testaceum. KEY POINTS: • The first report of metabolites produced by Microbacterium testaceum. • 1-[α-Glucopyranosyl-(1 → 3)-(α-mannopyranosyl)]-glycerol lipids isolated and identified. • Microbacterium testaceum strain isolated from the sponge Tedania brasiliensis.
Collapse
Affiliation(s)
- Jairo I Quintana-Bulla
- Instituto de Química de São Carlos, Universidade de São Paulo, CP 780, CEP 13560-970, São Carlos, SP, Brazil
| | - Luciane A C Tonon
- Instituto de Química de São Carlos, Universidade de São Paulo, CP 780, CEP 13560-970, São Carlos, SP, Brazil
| | - Lamonielli F Michaliski
- Instituto de Química de São Carlos, Universidade de São Paulo, CP 780, CEP 13560-970, São Carlos, SP, Brazil
| | - Eduardo Hajdu
- Museu Nacional, Universidade Federal Do Rio de Janeiro, Quinta da Boa Vista, S/N, CEP , Rio de Janeiro, RJ, 20940-040, Brazil
| | - Antonio G Ferreira
- Departamento de Química, Universidade Federal de São Carlos, CEP , São Carlos, SP, 13565-905, Brazil
| | - Roberto G S Berlinck
- Instituto de Química de São Carlos, Universidade de São Paulo, CP 780, CEP 13560-970, São Carlos, SP, Brazil.
| |
Collapse
|
2
|
Ruocco N, Nuzzo G, Federico S, Esposito R, Gallo C, Ziaco M, Manzo E, Fontana A, Bertolino M, Zagami G, Zupo V, Sansone C, Costantini M. Potential of Polar Lipids Isolated from the Marine Sponge Haliclona ( Halichoclona) vansoesti against Melanoma. Int J Mol Sci 2024; 25:7418. [PMID: 39000524 PMCID: PMC11242152 DOI: 10.3390/ijms25137418] [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: 05/24/2024] [Revised: 07/03/2024] [Accepted: 07/03/2024] [Indexed: 07/16/2024] Open
Abstract
Marine sponges represent a good source of natural metabolites for biotechnological applications in the pharmacological, cosmeceutical, and nutraceutical fields. In the present work, we analyzed the biotechnological potential of the alien species Haliclona (Halichoclona) vansoesti de Weerdt, de Kluijver & Gomez, 1999, previously collected in the Mediterranean Sea (Faro Lake, Sicily). The bioactivity and chemical content of this species has never been investigated, and information in the literature on its Caribbean counterpart is scarce. We show that an enriched extract of H. vansoesti induced cell death in human melanoma cells with an IC50 value of 36.36 µg mL-1, by (i) triggering a pro-inflammatory response, (ii) activating extrinsic apoptosis mediated by tumor necrosis factor receptors triggering the mitochondrial apoptosis via the involvement of Bcl-2 proteins and caspase 9, and (iii) inducing a significant reduction in several proteins promoting human angiogenesis. Through orthogonal SPE fractionations, we identified two active sphingoid-based lipid classes, also characterized by nuclear magnetic resonance and mass spectrometry, as the main components of two active fractions. Overall, our findings provide the first evaluation of the anti-cancer potential of polar lipids isolated from the marine sponge H. (Halichoclona) vansoesti, which may lead to new lead compounds with biotechnological applications in the pharmaceutical field.
Collapse
Affiliation(s)
- Nadia Ruocco
- Department of Ecosustainable Marine Biotechnology, Stazione Zoologica Anton Dohrn, Calabria Marine Centre, C. da Torre Spaccata, 87071 Amendolara, Italy
| | - Genoveffa Nuzzo
- Bio-Organic Chemistry Unit, Institute of Biomolecular Chemistry CNR, Via Campi Flegrei 34, 80078 Pozzuoli, Italy
| | - Serena Federico
- Department of Ecosustainable Marine Biotechnology, Stazione Zoologica Anton Dohrn, Via Ammiraglio Ferdinando Acton, 55, 80133 Napoli, Italy
- Department of Earth, Environmental and Life Sciences, University of Genoa, Corso Europa 26, 16132 Genova, Italy
| | - Roberta Esposito
- Department of Ecosustainable Marine Biotechnology, Stazione Zoologica Anton Dohrn, Via Ammiraglio Ferdinando Acton, 55, 80133 Napoli, Italy
| | - Carmela Gallo
- Bio-Organic Chemistry Unit, Institute of Biomolecular Chemistry CNR, Via Campi Flegrei 34, 80078 Pozzuoli, Italy
| | - Marcello Ziaco
- Bio-Organic Chemistry Unit, Institute of Biomolecular Chemistry CNR, Via Campi Flegrei 34, 80078 Pozzuoli, Italy
| | - Emiliano Manzo
- Bio-Organic Chemistry Unit, Institute of Biomolecular Chemistry CNR, Via Campi Flegrei 34, 80078 Pozzuoli, Italy
| | - Angelo Fontana
- Bio-Organic Chemistry Unit, Institute of Biomolecular Chemistry CNR, Via Campi Flegrei 34, 80078 Pozzuoli, Italy
- Laboratory of Bio-Organic Chemistry and Chemical Biology, Dipartimento di Biologia, Università di Napoli "Federico II", Via Cupa Nuova Cinthia 21, 80126 Napoli, Italy
| | - Marco Bertolino
- Department of Earth, Environmental and Life Sciences, University of Genoa, Corso Europa 26, 16132 Genova, Italy
| | - Giacomo Zagami
- Department of Biological, Chemical, Pharmaceutical and Environmental Sciences, University of Messina, 98100 Messina, Italy
| | - Valerio Zupo
- Department of Ecosustainable Marine Biotechnology, Stazione Zoologica Anton Dohrn, Ischia Marine Center, 80077 Ischia, Italy
| | - Clementina Sansone
- Department of Ecosustainable Marine Biotechnology, Stazione Zoologica Anton Dohrn, Via Ammiraglio Ferdinando Acton, 55, 80133 Napoli, Italy
| | - Maria Costantini
- Department of Ecosustainable Marine Biotechnology, Stazione Zoologica Anton Dohrn, Via Ammiraglio Ferdinando Acton, 55, 80133 Napoli, Italy
| |
Collapse
|
3
|
Maslin M, Paix B, van der Windt N, Ambo-Rappe R, Debitus C, Gaertner-Mazouni N, Ho R, de Voogd NJ. Prokaryotic communities of the French Polynesian sponge Dactylospongia metachromia display a site-specific and stable diversity during an aquaculture trial. Antonie Van Leeuwenhoek 2024; 117:65. [PMID: 38602593 PMCID: PMC11008079 DOI: 10.1007/s10482-024-01962-0] [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: 03/01/2024] [Accepted: 03/28/2024] [Indexed: 04/12/2024]
Abstract
Dynamics of microbiomes through time are fundamental regarding survival and resilience of their hosts when facing environmental alterations. As for marine species with commercial applications, such as marine sponges, assessing the temporal change of prokaryotic communities allows us to better consider the adaptation of sponges to aquaculture designs. The present study aims to investigate the factors shaping the microbiome of the sponge Dactylospongia metachromia, in a context of aquaculture development in French Polynesia, Rangiroa, Tuamotu archipelago. A temporal approach targeting explants collected during farming trials revealed a relative high stability of the prokaryotic diversity, meanwhile a complementary biogeographical study confirmed a spatial specificity amongst samples at different longitudinal scales. Results from this additional spatial analysis confirmed that differences in prokaryotic communities might first be explained by environmental changes (mainly temperature and salinity), while no significant effect of the host phylogeny was observed. The core community of D. metachromia is thus characterized by a high spatiotemporal constancy, which is a good prospect for the sustainable exploitation of this species towards drug development. Indeed, a microbiome stability across locations and throughout the farming process, as evidenced by our results, should go against a negative influence of sponge translocation during in situ aquaculture.
Collapse
Affiliation(s)
- Mathilde Maslin
- Univ Polynesie Française, Ifremer, ILM, IRD, EIO UMR 241, Tahiti, French Polynesia
| | - Benoît Paix
- Naturalis Biodiversity Center, PO Box 9517, 2300 RA, Leiden, the Netherlands.
| | - Niels van der Windt
- Naturalis Biodiversity Center, PO Box 9517, 2300 RA, Leiden, the Netherlands
- Institute of Environmental Sciences (CML), Leiden University, PO Box 9518, 2300 RA, Leiden, the Netherlands
| | - Rohani Ambo-Rappe
- Faculty of Marine Science and Fisheries, Department of Marine Science, Hasanuddin University, Makassar, Indonesia
| | - Cécile Debitus
- IRD, Univ Brest, CNRS, Ifremer, LEMAR, 29280, Plouzané, France
| | | | - Raimana Ho
- Univ Polynesie Française, Ifremer, ILM, IRD, EIO UMR 241, Tahiti, French Polynesia
| | - Nicole J de Voogd
- Naturalis Biodiversity Center, PO Box 9517, 2300 RA, Leiden, the Netherlands.
- Institute of Biology (IBL), Leiden University, 2333 BE, PO Box 9505, Leiden, the Netherlands.
| |
Collapse
|
4
|
Esposito R, Federico S, Sonnessa M, Reddel S, Bertolino M, Ruocco N, Zagami G, Giovine M, Pozzolini M, Guida M, Zupo V, Costantini M. Characterizing the bacterial communities associated with Mediterranean sponges: a metataxonomic analysis. Front Microbiol 2024; 14:1295459. [PMID: 38274771 PMCID: PMC10808595 DOI: 10.3389/fmicb.2023.1295459] [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: 10/02/2023] [Accepted: 12/20/2023] [Indexed: 01/27/2024] Open
Abstract
The oceans cover over 70% of our planet, hosting a biodiversity of tremendous wealth. Sponges are one of the major ecosystem engineers on the seafloor, providing a habitat for a wide variety of species to be considered a good source of bioactive compounds. In this study, a metataxonomic approach was employed to describe the bacterial communities of the sponges collected from Faro Lake (Sicily) and Porto Paone (Gulf of Naples). Morphological analysis and amplification of the conserved molecular markers, including 18S and 28S (RNA ribosomal genes), CO1 (mitochondrial cytochrome oxidase subunit 1), and ITS (internal transcribed spacer), allowed the identification of four sponges. Metataxonomic analysis of sponges revealed a large number of amplicon sequence variants (ASVs) belonging to the phyla Proteobacteria, Cloroflexi, Dadabacteria, and Poribacteria. In particular, Myxilla (Myxilla) rosacea and Clathria (Clathria) toxivaria displayed several classes such as Alphaproteobacteria, Dehalococcoidia, Gammaproteobacteria, Cyanobacteria, and Bacteroidia. On the other hand, the sponges Ircinia oros and Cacospongia mollior hosted bacteria belonging to the classes Dadabacteriia, Anaerolineae, Acidimicrobiia, Nitrospiria, and Poribacteria. Moreover, for the first time, the presence of Rhizobiaceae bacteria was revealed in the sponge M. (Myxilla) rosacea, which was mainly associated with soil and plants and involved in biological nitrogen fixation.
Collapse
Affiliation(s)
- Roberta Esposito
- Department of Ecosustainable Marine Biotechnology, Stazione Zoologica Anton Dohrn, Napoli, Italy
| | - Serena Federico
- Department of Ecosustainable Marine Biotechnology, Stazione Zoologica Anton Dohrn, Napoli, Italy
- Department of Earth, Environmental and Life Sciences, University of Genoa, Genoa, Italy
| | | | | | - Marco Bertolino
- Department of Earth, Environmental and Life Sciences, University of Genoa, Genoa, Italy
| | - Nadia Ruocco
- Department of Ecosustainable Marine Biotechnology, Stazione Zoologica Anton Dohrn, Calabria Marine Centre, Amendolara, Italy
| | - Giacomo Zagami
- Dipartimento Di Scienze Biologiche, Chimiche, Farmaceutiche Ed Ambientali, Università Di Messina, Messina, Italy
| | - Marco Giovine
- Department of Earth, Environmental and Life Sciences, University of Genoa, Genoa, Italy
| | - Marina Pozzolini
- Department of Earth, Environmental and Life Sciences, University of Genoa, Genoa, Italy
| | - Marco Guida
- Department of Biology, University of Naples Federico II, Complesso Universitario di Monte Sant'Angelo, Naples, Italy
| | - Valerio Zupo
- Department of Ecosustainable Marine Biotechnology, Stazione Zoologica Anton Dohrn, Ischia Marine Centre, Naples, Italy
| | - Maria Costantini
- Department of Ecosustainable Marine Biotechnology, Stazione Zoologica Anton Dohrn, Napoli, Italy
| |
Collapse
|
5
|
Gavriilidou A, Avcı B, Galani A, Schorn MA, Ingham CJ, Ettema TJG, Smidt H, Sipkema D. Candidatus Nemesobacterales is a sponge-specific clade of the candidate phylum Desulfobacterota adapted to a symbiotic lifestyle. THE ISME JOURNAL 2023; 17:1808-1818. [PMID: 37587369 PMCID: PMC10579324 DOI: 10.1038/s41396-023-01484-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 05/26/2023] [Accepted: 06/02/2023] [Indexed: 08/18/2023]
Abstract
Members of the candidate phylum Dadabacteria, recently reassigned to the phylum Candidatus Desulfobacterota, are cosmopolitan in the marine environment found both free-living and associated with hosts that are mainly marine sponges. Yet, these microorganisms are poorly characterized, with no cultured representatives and an ambiguous phylogenetic position in the tree of life. Here, we performed genome-centric metagenomics to elucidate their phylogenomic placement and predict the metabolism of the sponge-associated members of this lineage. Rank-based phylogenomics revealed several new species and a novel family (Candidatus Spongomicrobiaceae) within a sponge-specific order, named here Candidatus Nemesobacterales. Metabolic reconstruction suggests that Ca. Nemesobacterales are aerobic heterotrophs, capable of synthesizing most amino acids, vitamins and cofactors and degrading complex carbohydrates. We also report functional divergence between sponge- and seawater-associated metagenome-assembled genomes. Niche-specific adaptations to the sponge holobiont were evident from significantly enriched genes involved in defense mechanisms against foreign DNA and environmental stressors, host-symbiont interactions and secondary metabolite production. Fluorescence in situ hybridization gave a first glimpse of the morphology and lifestyle of a member of Ca. Desulfobacterota. Candidatus Nemesobacterales spp. were found both inside sponge cells centred around sponge nuclei and in the mesohyl of the sponge Geodia barretti. This study sheds light on the enigmatic group Ca. Nemesobacterales and their functional characteristics that reflect a symbiotic lifestyle.
Collapse
Affiliation(s)
- Asimenia Gavriilidou
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708WE, Wageningen, The Netherlands.
| | - Burak Avcı
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708WE, Wageningen, The Netherlands
| | - Anastasia Galani
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708WE, Wageningen, The Netherlands
| | - Michelle A Schorn
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708WE, Wageningen, The Netherlands
| | - Colin J Ingham
- Hoekmine BV, Verenigingstraat 36, 3515GJ, Utrecht, The Netherlands
| | - Thijs J G Ettema
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708WE, Wageningen, The Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708WE, Wageningen, The Netherlands
| | - Detmer Sipkema
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708WE, Wageningen, The Netherlands.
| |
Collapse
|
6
|
Hamoda AM, Hamdy R, Fayed B, Abouleish M, Sulaiman A, Hamad M, Soliman SSM. Evolutionary relevance of metabolite production in relation to marine sponge bacteria symbiont. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12649-3. [PMID: 37358811 DOI: 10.1007/s00253-023-12649-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 04/14/2023] [Accepted: 06/15/2023] [Indexed: 06/27/2023]
Abstract
Sponges are habitats for a diverse community of microorganisms. Sponges provide shelter, whereas microbes provide a complementary defensive mechanism. Here, a symbiotic bacterium, identified as Bacillus spp., was isolated from a marine sponge following culture enrichment. Fermentation-assisted metabolomics using thin-layer chromatography (TLC) and gas chromatography-mass spectrometry (GC-MS) indicated that marine simulated nutrition and temperature was the optimum in metabolite production represented by the highest number of metabolites and the diverse chemical classes when compared to other culture media. Following large-scale culture in potato dextrose broth (PDB) and dereplication, compound M1 was isolated and identified as octadecyl-1-(2',6'-di-tert-butyl-1'-hydroxyphenyl) propionate. M1, at screening concentrations up to 10 mg/ml, showed no activity against prokaryotic bacteria including Staphylococcus aureus and Escherichia coli, while 1 mg/ml of M1 was sufficient to cause a significant killing effect on eukaryotic cells including Candida albicans, Candida auris, and Rhizopus delemar fungi and different mammalian cells. M1 exhibited MIC50 0.97 ± 0.006 and 7.667 ± 0.079 mg/ml against C. albicans and C. auris, respectively. Like fatty acid esters, we hypothesize that M1 is stored in a less harmful form and upon pathogenic attack is hydrolyzed to a more active form as a defensive metabolite. Subsequently, [3-(3,5-di-tert-butyl-4-hydroxyphenyl)-propionic acid] (DTBPA), the hydrolysis product of M1, exhibited ~ 8-fold and 18-fold more antifungal activity than M1 against C. albicans and C. auris, respectively. These findings indicated the selectivity of that compound as a defensive metabolite towards the eukaryotic cells particularly the fungi, a major infectious agent to sponges. Metabolomic-assisted fermentation can provide a significant understanding of a triple marine-evolved interaction. KEY POINTS: • Bacillus species, closely related to uncultured Bacillus, is isolated from Gulf marine sponge • Metabolomic-assisted fermentations showed diverse metabolites • An ester with a killing effect against eukaryotes but not prokaryotes is isolated.
Collapse
Affiliation(s)
- Alshaimaa M Hamoda
- Research Institute for Medical and Health Sciences, University of Sharjah, P.O. Box 27272, Sharjah, UAE
- College of Medicine, University of Sharjah, P.O. Box 27272, Sharjah, UAE
- Department of Pharmacognosy, Faculty of Pharmacy, Assiut University, Assiut-71526, Egypt
| | - Rania Hamdy
- Research Institute for Medical and Health Sciences, University of Sharjah, P.O. Box 27272, Sharjah, UAE
- Faculty of Pharmacy, Zagazig University, Zagazig, Egypt
| | - Bahgat Fayed
- Research Institute for Medical and Health Sciences, University of Sharjah, P.O. Box 27272, Sharjah, UAE
- Chemistry of Natural and Microbial Product Department, National Research Centre, Cairo, Egypt
| | - Mohamed Abouleish
- Department of Biology, Chemistry and Environmental Sciences, College of Arts and Sciences, American University of Sharjah, P.O. Box 26666, Sharjah, UAE
| | - Ashna Sulaiman
- Research Institute for Medical and Health Sciences, University of Sharjah, P.O. Box 27272, Sharjah, UAE
| | - Mohamad Hamad
- Research Institute for Medical and Health Sciences, University of Sharjah, P.O. Box 27272, Sharjah, UAE
- Department of Medical Laboratory Sciences, Collage of Health Sciences, University of Sharjah, P.O. Box 27272, Sharjah, UAE
| | - Sameh S M Soliman
- Research Institute for Medical and Health Sciences, University of Sharjah, P.O. Box 27272, Sharjah, UAE.
- Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, P.O. Box 27272, Sharjah, UAE.
| |
Collapse
|
7
|
Bibi F, Naseer MI, Azhar EI. Exploring bioactive compounds from a symbiotic bacterial strain of Spongiobacter sp. Bioinformation 2023; 19:369-374. [PMID: 37822833 PMCID: PMC10563573 DOI: 10.6026/97320630019369] [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: 04/01/2023] [Revised: 04/30/2023] [Accepted: 04/30/2023] [Indexed: 10/13/2023] Open
Abstract
Marine sponges are a host of different symbiotic groups of bacteria playing crucial roles in the protection and survival of marine sponges. Marine symbiotic bacteria from sponges are promising sources of bioactive chemicals and are increasingly being investigated. Therefore, the present study was undertaken to analyze total compounds from active symbiotic bacterial strain from sponge, Pione vastifical. Potential bacterial strain EA276 previously isolated from P. vastifical and was identified as Spongiobacter sp. Among 57 isolates, only 42% exhibited antagonistic activity. Four major classes of bacteria were reported previously where γ-Proteobacteria, was the dominant class. From these active antagonistic bacterial isolates, a potential bacterial strain Spongiobacter sp. EA276 was selected, and total metabolites were identified using GC and LC-MS analyses. Using LC-MS analysis bioactive compounds Dichlorphenamide, Amifloxacin and Carbenicillin are identified in both positive and negative mode. Plant growth hormones, Indole-3-acetic acid and Methyl jasmonate were identified using GC-MS analysis from culture extract of strain Spongiobacter sp. EA276. Our results highlighted the significance of marine flora inhabiting sponges from the Red Sea as potential source of bioactive compounds and plant growth hormones of biological and agricultural significance.
Collapse
Affiliation(s)
- Fehmida Bibi
- Special Infectious Agents Unit-BSL3, King Fahd Medical Research Centre, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Muhammad Imran Naseer
- Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Esam Ibraheem Azhar
- Special Infectious Agents Unit-BSL3, King Fahd Medical Research Centre, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| |
Collapse
|
8
|
Davies-Coleman MT, McPhail KL, Parker-Nance S. A Quarter Century of Marine Biodiscovery in Algoa Bay, South Africa. JOURNAL OF NATURAL PRODUCTS 2023; 86:638-652. [PMID: 36853972 DOI: 10.1021/acs.jnatprod.2c00987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Algoa Bay, the largest crenulate bay on the southeastern coast of South Africa, is currently one of the most well-studied marine ecosystems in southern Africa. A plethora of endemic marine invertebrates inhabits the benthic reefs on the western edge of the Bay in close proximity to South Africa's sixth largest city. Over the past 25 years, South African marine natural products chemists, together with international collaborators from the US National Cancer Institute and other US institutions, have focused their attention on Algoa Bay's benthic marine invertebrates as a potential source of new anticancer compounds. This review commemorates a quarter of a century of marine biodiscovery in Algoa Bay and presents the structures and bioactivities of 49 new and 36 known specialized metabolites isolated from two molluscs, eight ascidians, and six sponges. Thirty-nine of these compounds were cytotoxic to cancer cells in vitro with 20 exhibiting moderate to potent cytotoxicity. Six other compounds exhibited antimicrobial activity. Foremost among the potential anticancer compounds is mandelalide A (38) from the Algoa Bay ascidian Lissoclinum species.
Collapse
Affiliation(s)
- Michael T Davies-Coleman
- Department of Chemistry, University of the Western Cape, Bellville, 7535, South Africa and Department of Chemistry, Rhodes University, Makhanda, 6140, South Africa
| | - Kerry L McPhail
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregaon 97331, United States
| | - Shirley Parker-Nance
- South African Environmental Observation Network, Elwandle Coastal Node, Nelson Mandela University, Ocean Sciences Campus, Summerstrand, Gqeberha, 6001, South Africa
| |
Collapse
|
9
|
Conservation of Genomic Information in Multiple Displacement Amplified Low-Quantity Metagenomic Material from Marine Invertebrates. Mar Drugs 2023; 21:md21030165. [PMID: 36976214 PMCID: PMC10054348 DOI: 10.3390/md21030165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 02/21/2023] [Accepted: 02/28/2023] [Indexed: 03/06/2023] Open
Abstract
Marine invertebrate microbiomes have been a rich source of bioactive compounds and interesting genomic features. In cases where the achievable amounts of metagenomic DNA are too low for direct sequencing, multiple displacement amplification (MDA) can be used for whole genome amplification. However, MDA has known limitations which can affect the quality of the resulting genomes and metagenomes. In this study, we evaluated the conservation of biosynthetic gene clusters (BGCs) and enzymes in MDA products from low numbers of prokaryotic cells (estimated 2–850). Marine invertebrate microbiomes collected from Arctic and sub-Arctic areas served as source material. The cells were separated from the host tissue, lysed, and directly subjected to MDA. The MDA products were sequenced by Illumina sequencing. Corresponding numbers of bacteria from a set of three reference strains were treated the same way. The study demonstrated that useful information on taxonomic, BGC, and enzyme diversities was obtainable from such marginal quantities of metagenomic material. Although high levels of assembly fragmentation resulted in most BGCs being incomplete, we conclude that this genome mining approach has the potential to reveal interesting BGCs and genes from hard-to-reach biological sources.
Collapse
|
10
|
Amelia TSM, Suaberon FAC, Vad J, Fahmi ADM, Saludes JP, Bhubalan K. Recent Advances of Marine Sponge-Associated Microorganisms as a Source of Commercially Viable Natural Products. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2022; 24:492-512. [PMID: 35567600 DOI: 10.1007/s10126-022-10130-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 04/25/2022] [Indexed: 06/15/2023]
Abstract
Many industrially significant compounds have been derived from natural products in the environment. Research efforts so far have contributed to the discovery of beneficial natural products that have improved the quality of life on Earth. As one of the sources of natural products, marine sponges have been progressively recognised as microbial hotspots with reports of the sponges harbouring diverse microbial assemblages, genetic material, and metabolites with multiple industrial applications. Therefore, this paper aims at reviewing the recent literature (primarily published between 2016 and 2022) on the types and functions of natural products synthesised by sponge-associated microorganisms, thereby helping to bridge the gap between research and industrial applications. The metabolites that have been derived from sponge-associated microorganisms, mostly bacteria, fungi, and algae, have shown application prospects especially in medicine, cosmeceutical, environmental protection, and manufacturing industries. Sponge bacteria-derived natural products with medical properties harboured anticancer, antibacterial, antifungal, and antiviral functions. Efforts in re-identifying the origin of known and future sponge-sourced natural products would further clarify the roles and significance of microbes within marine sponges.
Collapse
Affiliation(s)
- Tan Suet May Amelia
- Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia
| | - Ferr Angelus C Suaberon
- Center for Natural Drug Discovery & Development (CND3), University of San Agustin, 5000, Iloilo City, Philippines
| | - Johanne Vad
- Changing Oceans Research Group, School of GeoSciences, University of Edinburgh, Edinburgh, UK
| | - Afiq Durrani Mohd Fahmi
- Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia
- Eco-Innovation Research Interest Group, Universiti Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia
| | - Jonel P Saludes
- Center for Natural Drug Discovery & Development (CND3), University of San Agustin, 5000, Iloilo City, Philippines
- Department of Chemistry, University of San Agustin, 5000, Iloilo City, Philippines
- Department of Science and Technology, Balik Scientist Program, Philippine Council for Health Research & Development (PCHRD), Bicutan, 1631, Taguig, Philippines
| | - Kesaven Bhubalan
- Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia.
- Eco-Innovation Research Interest Group, Universiti Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia.
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia.
| |
Collapse
|
11
|
Cophylogeny and convergence shape holobiont evolution in sponge-microbe symbioses. Nat Ecol Evol 2022; 6:750-762. [PMID: 35393600 DOI: 10.1038/s41559-022-01712-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 02/24/2022] [Indexed: 02/07/2023]
Abstract
Symbiotic microbial communities of sponges serve critical functions that have shaped the evolution of reef ecosystems since their origins. Symbiont abundance varies tremendously among sponges, with many species classified as either low microbial abundance (LMA) or high microbial abundance (HMA), but the evolutionary dynamics of these symbiotic states remain unknown. This study examines the LMA/HMA dichotomy across an exhaustive sampling of Caribbean sponge biodiversity and predicts that the LMA symbiotic state is the ancestral state among sponges. Conversely, HMA symbioses, consisting of more specialized microorganisms, have evolved multiple times by recruiting similar assemblages, mostly since the rise of scleractinian-dominated reefs. Additionally, HMA symbioses show stronger signals of phylosymbiosis and cophylogeny, consistent with stronger co-evolutionary interaction in these complex holobionts. These results indicate that HMA holobionts are characterized by increased endemism, metabolic dependence and chemical defences. The selective forces driving these patterns may include the concurrent increase in dissolved organic matter in reef ecosystems or the diversification of spongivorous fishes.
Collapse
|
12
|
Marine Sponge Endosymbionts: Structural and Functional Specificity of the Microbiome within
Euryspongia arenaria
Cells. Microbiol Spectr 2022; 10:e0229621. [PMID: 35499324 PMCID: PMC9241883 DOI: 10.1128/spectrum.02296-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Sponge microbiomes are typically profiled by analyzing the community DNA of whole tissues, which does not distinguish the taxa residing within sponge cells from extracellular microbes. To uncover the endosymbiotic microbiome, we separated the sponge cells to enrich the intracellular microbes. The intracellular bacterial community of sponge Euryspongia arenaria was initially assessed by amplicon sequencing, which indicated that it hosts three unique phyla not found in the extracellular and bulk tissue microbiomes. These three phyla account for 66% of the taxonomically known genera in the intracellular microbiome. The shotgun metagenomic analysis extended the taxonomic coverage to viruses and eukaryotes, revealing the most abundant signature taxa specific to the intracellular microbiome. Functional KEGG pathway annotation demonstrated that the endosymbiotic microbiome hosted the greatest number of unique gene orthologs. The pathway profiles distinguished the intra- and extracellular microbiomes from the tissue and seawater microbiomes. Carbohydrate-active enzyme analysis further discriminated each microbiome based on their representative and dominant enzyme families. One pathway involved in digestion system and family esterase had a consistently higher level in intracellular microbiome and could statistically differentiate the intracellular microbiome from the others, suggesting that triacylglycerol lipases could be the key functional component peculiar to the endosymbionts. The identified higher abundance of lipase-related eggNOG categories further supported the lipid-hydrolyzing metabolism of endosymbiotic microbiota. Pseudomonas members, reported as lipase-producing bacteria, were only in the endosymbiotic microbiome, meanwhile Pseudomonas also showed a greater abundance intracellularly. Our study aided a comprehensive sponge microbiome that demonstrated the taxonomic and functional specificity of endosymbiotic microbiota. IMPORTANCE Sponges host abundant microbial symbionts that can produce an impressive number of novel bioactive metabolites. However, knowledge on intracellular (endosymbiotic) microbiota is scarce. We characterize the composition and function of the endosymbiotic microbiome by separation of sponge cells and enrichment of intracellular microbes. We uncover a noteworthy number of taxa exclusively in the endosymbiotic microbiome. We unlock the unique pathways and enzymes of endosymbiotic taxa. This study achieves a more comprehensive sponge microbial community profile, which demonstrates the structural and functional specificity of the endosymbiotic microbiome. Our findings not only open the possibility to reveal the low abundant and the likely missed microbiota when directly sequencing the sponge bulk tissues, but also warrant future in-depth exploration within single sponge cells.
Collapse
|
13
|
Antarctic Porifera homogenates as a source of enzymes and antibacterial substances: first results. Polar Biol 2022. [DOI: 10.1007/s00300-022-03042-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
AbstractMarine Porifera (sponges) are known to produce several bioactive metabolites having a biotechnological potential, mostly derived from their bacterial symbionts; however, current knowledge on the production of metabolites such as enzymes and antibacterial molecules in sponges living in Antarctic environments is not fully exhaustive and needs further deepened investigation. The interest in discovering the broad spectrum of natural products potentially derived from species adapted to colonize extreme environments stimulates the research toward Antarctic sponge bioprospection. In this study, whole homogenates of Antarctic Demospongiae, belonging to five different species [Haliclona (Rhizoniera) sp., Haliclona (Rhizoniera) dancoi, Microxina sarai, Dendrilla antarctica, and Mycale acerata] were collected from Terra Nova Bay (Ross Sea) and examined for presence and activity of enzymes, including lysozyme, and antibacterial substances. Enzyme activities (leucine aminopeptidase, beta-glucosidase, and alkaline phosphatase) were measured using fluorogenic substrates; lysozyme content was determined on plates containing lyophilized Micrococcus lysodeikticus cell walls as a substrate. Homogenates were screened in microtiter plates for their antibacterial activity against Antarctic bacterial isolates, and the absorbance reduction was measured with a microplate reader. All homogenates exhibited proteolytic, glycolytic, and phosphatasic activities, lysozyme and antibacterial activities at near “in situ” temperature (5 °C), with some differences among the examined species. Results confirmed that Antarctic sponge homogenates are interesting sources of different bioactive substances, likely produced from associated bacterial symbionts, and that could have great potential to be used in medicine or industrial applications.
Collapse
|
14
|
Anteneh YS, Yang Q, Brown MH, Franco CMM. Factors affecting the isolation and diversity of marine sponge-associated bacteria. Appl Microbiol Biotechnol 2022; 106:1729-1744. [PMID: 35103809 PMCID: PMC8882111 DOI: 10.1007/s00253-022-11791-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 01/13/2022] [Accepted: 01/17/2022] [Indexed: 12/24/2022]
Abstract
Abstract Marine sponges are an ideal source for isolating as yet undiscovered microorganisms with some sponges having about 50% of their biomass composed of microbial symbionts. This study used a variety of approaches to investigate the culturable diversity of the sponge-associated bacterial community from samples collected from the South Australian marine environment. Twelve sponge samples were selected from two sites and their bacterial population cultivated using seven different agar media at two temperatures and three oxygen levels over 3 months. These isolates were identified using microscopic, macroscopic, and 16S rRNA gene analysis. A total of 1234 bacterial colonies were isolated which consisted of four phyla: Actinobacteria, Firmicutes, Proteobacteria, and Bacteroidetes, containing 21 genera. The diversity of the bacterial population was demonstrated to be influenced by the type of isolation medium, length of the incubation period and temperature, sponge type, and oxygen level. The findings of this study showed that marine sponges of South Australia can yield considerable bacterial culturable diversity if a comprehensive isolation strategy is implemented. Two sponges, with the highest and the lowest diversity of culturable isolates, were examined using next-generation sequencing to better profile the bacterial population. A marked difference in terms of phyla and genera was observed using culture-based and culture-independent approaches. This observed variation displays the importance of utilizing both methods to reflect a more complete picture of the microbial population of marine sponges. Key points Improved bacterial diversity due to long incubations, 2 temperatures, and 3 oxygen levels. Isolates identified by morphology, restriction digests, and 16S rRNA gene sequencing. At least 70% of culturable genera were not revealed by NGS methods.
Supplementary Information The online version contains supplementary material available at 10.1007/s00253-022-11791-8.
Collapse
Affiliation(s)
- Yitayal S Anteneh
- Medical Biotechnology, College of Medicine and Public Health, Flinders University, Bedford Park, SA, 5042, Australia.,Department of Medical Microbiology, College of Medicine, Addis Ababa University, Addis Ababa, Ethiopia.,Centre for Marine Bioproducts Development, College of Medicine and Public Health, Flinders University, Bedford Park, SA, 5042, Australia
| | - Qi Yang
- Centre for Marine Bioproducts Development, College of Medicine and Public Health, Flinders University, Bedford Park, SA, 5042, Australia.,Center for Marine Drugs, State Key Laboratory of Oncogene and Related Genes, Department of Pharmacy, School of Medicine, Renji Hospital, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Melissa H Brown
- College of Science and Engineering, Flinders University, Bedford Park, SA, 5042, Australia
| | - Christopher M M Franco
- Medical Biotechnology, College of Medicine and Public Health, Flinders University, Bedford Park, SA, 5042, Australia. .,Centre for Marine Bioproducts Development, College of Medicine and Public Health, Flinders University, Bedford Park, SA, 5042, Australia.
| |
Collapse
|
15
|
Kamel HL, Hanora A, Solyman SM. Metataxanomic, bioactivity and microbiome analysis of Red Sea marine sponges from Egypt. Mar Genomics 2021; 61:100920. [PMID: 34973527 DOI: 10.1016/j.margen.2021.100920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 12/14/2021] [Accepted: 12/14/2021] [Indexed: 10/19/2022]
Abstract
Red Sea marine sponges (phylum Porifera) and associated microorganisms harbor a wide range of microorganisms, which are considered an essential source of bioactive products. In this study, we screened both the crude extracts of Red Sea marine sponges and their associated bacterial extract for antimicrobial activity and antiviral activity. Molecular characterization of bioactive producers was performed using16S rRNA sequencing, in addition to metagenomic analysis of three representative sponges utilizing the 16S rRNA gene V3-V4 region sequencing in two different seasons. Twelve samples were collected from five different sponge species by scuba diving, and all the crude extracts of sponges showed antimicrobial activity except Negombata corticata. Moreover, 84 out of 110 bacterial isolates extracts demonstrated antimicrobial activity against at least one tested microorganism. These results revealed the bioactivity and biodiversity of the Red Sea marine invertebrates-associated bacteria. It was found that the bioactive isolates belong to several bacterial groups. The bacterial communities of Negombata magnifica, Negombata corticata, and Siphonochalina siphonella were shown with great diversity and differences in the bacterial percentage, diversity, and unique community composition at different seasons in each sponge species. Unique microenvironment for each sponge species may be linked to the production of specific bioactive product.
Collapse
Affiliation(s)
- Hasnaa L Kamel
- Department of Microbiology & Immunology, College of Pharmacy, Suez Canal University, Ismailia, Egypt; Department of Microbiology & Immunology, College of Pharmacy, Sinai University, Ismailia, Egypt.
| | - Amro Hanora
- Department of Microbiology & Immunology, College of Pharmacy, Suez Canal University, Ismailia, Egypt.
| | - Samar M Solyman
- Department of Microbiology & Immunology, College of Pharmacy, Suez Canal University, Ismailia, Egypt; Department of Microbiology & Immunology, College of Pharmacy, Sinai University, Ismailia, Egypt.
| |
Collapse
|
16
|
Ansari N, Rokhbakhsh-Zamin F, Hassanshahian M, Hesni MA. The Occurrence of Crude Oil-Degrading Bacteria in Some Sponges Collected at the Persian Gulf: Ecological Importance and Biotechnological Application. Polycycl Aromat Compd 2021. [DOI: 10.1080/10406638.2021.2014529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Nasrin Ansari
- Department of Microbiology, Kerman Branch, Islamic Azad University, Kerman, Iran
| | | | - Mehdi Hassanshahian
- Department of Biology, Faculty of Sciences, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Majid Askari Hesni
- Department of Biology, Faculty of Sciences, Shahid Bahonar University of Kerman, Kerman, Iran
| |
Collapse
|
17
|
Dat TTH, Steinert G, Cuc NTK, Smidt H, Sipkema D. Bacteria Cultivated From Sponges and Bacteria Not Yet Cultivated From Sponges-A Review. Front Microbiol 2021; 12:737925. [PMID: 34867854 PMCID: PMC8634882 DOI: 10.3389/fmicb.2021.737925] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 10/18/2021] [Indexed: 12/21/2022] Open
Abstract
The application of high-throughput microbial community profiling as well as "omics" approaches unveiled high diversity and host-specificity of bacteria associated with marine sponges, which are renowned for their wide range of bioactive natural products. However, exploration and exploitation of bioactive compounds from sponge-associated bacteria have been limited because the majority of the bacteria remains recalcitrant to cultivation. In this review, we (i) discuss recent/novel cultivation techniques that have been used to isolate sponge-associated bacteria, (ii) provide an overview of bacteria isolated from sponges until 2017 and the associated culture conditions and identify the bacteria not yet cultured from sponges, and (iii) outline promising cultivation strategies for cultivating the uncultivated majority of bacteria from sponges in the future. Despite intensive cultivation attempts, the diversity of bacteria obtained through cultivation remains much lower than that seen through cultivation-independent methods, which is particularly noticeable for those taxa that were previously marked as "sponge-specific" and "sponge-enriched." This poses an urgent need for more efficient cultivation methods. Refining cultivation media and conditions based on information obtained from metagenomic datasets and cultivation under simulated natural conditions are the most promising strategies to isolate the most wanted sponge-associated bacteria.
Collapse
Affiliation(s)
- Ton That Huu Dat
- Mientrung Institute for Scientific Research, Vietnam Academy of Science and Technology, Hanoi, Vietnam
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
| | - Georg Steinert
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
| | - Nguyen Thi Kim Cuc
- Institute of Marine Biochemistry, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
| | - Detmer Sipkema
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
| |
Collapse
|
18
|
Ruocco N, Esposito R, Zagami G, Bertolino M, De Matteo S, Sonnessa M, Andreani F, Crispi S, Zupo V, Costantini M. Microbial diversity in Mediterranean sponges as revealed by metataxonomic analysis. Sci Rep 2021; 11:21151. [PMID: 34707182 PMCID: PMC8551288 DOI: 10.1038/s41598-021-00713-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 09/20/2021] [Indexed: 11/13/2022] Open
Abstract
Although the Mediterranean Sea covers approximately a 0.7% of the world's ocean area, it represents a major reservoir of marine and coastal biodiversity. Among marine organisms, sponges (Porifera) are a key component of the deep-sea benthos, widely recognized as the dominant taxon in terms of species richness, spatial coverage, and biomass. Sponges are evolutionarily ancient, sessile filter-feeders that harbor a largely diverse microbial community within their internal mesohyl matrix. In the present work, we firstly aimed at exploring the biodiversity of marine sponges from four different areas of the Mediterranean: Faro Lake in Sicily and "Porto Paone", "Secca delle fumose", "Punta San Pancrazio" in the Gulf of Naples. Eight sponge species were collected from these sites and identified by morphological analysis and amplification of several conserved molecular markers (18S and 28S RNA ribosomal genes, mitochondrial cytochrome oxidase subunit 1 and internal transcribed spacer). In order to analyze the bacterial diversity of symbiotic communities among these different sampling sites, we also performed a metataxonomic analysis through an Illumina MiSeq platform, identifying more than 1500 bacterial taxa. Amplicon Sequence Variants (ASVs) analysis revealed a great variability of the host-specific microbial communities. Our data highlight the occurrence of dominant and locally enriched microbes in the Mediterranean, together with the biotechnological potential of these sponges and their associated bacteria as sources of bioactive natural compounds.
Collapse
Affiliation(s)
- Nadia Ruocco
- grid.6401.30000 0004 1758 0806Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Roberta Esposito
- grid.6401.30000 0004 1758 0806Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy ,grid.4691.a0000 0001 0790 385XDepartment of Biology, University of Naples Federico II, Complesso Universitario Di Monte Sant’Angelo, Via Cinthia 21, 80126 Naples, Italy
| | - Giacomo Zagami
- grid.10438.3e0000 0001 2178 8421Dipartimento Di Scienze Biologiche, Chimiche, Farmaceutiche Ed Ambientali, Università Di Messina, 98100 Messina, Italy
| | - Marco Bertolino
- grid.5606.50000 0001 2151 3065DISTAV, Università Degli Studi Di Genova, Corso Europa 26, 16132 Genoa, Italy
| | - Sergio De Matteo
- grid.10438.3e0000 0001 2178 8421Dipartimento Di Scienze Biologiche, Chimiche, Farmaceutiche Ed Ambientali, Università Di Messina, 98100 Messina, Italy
| | | | | | - Stefania Crispi
- grid.6401.30000 0004 1758 0806Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy ,grid.5326.20000 0001 1940 4177Institute of Biosciences and BioResources Naples, National Research Council of Italy, Naples, Italy
| | - Valerio Zupo
- grid.6401.30000 0004 1758 0806Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Maria Costantini
- grid.6401.30000 0004 1758 0806Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| |
Collapse
|
19
|
Passarini MRZ, Moreira JVF, Gomez JAM, Bonugli-Santos RC. DNA metabarcoding of the leachate microbiota from sanitary landfill: potential for bioremediation process. Arch Microbiol 2021; 203:4847-4858. [PMID: 34228134 DOI: 10.1007/s00203-021-02471-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 06/29/2021] [Accepted: 06/30/2021] [Indexed: 01/04/2023]
Abstract
Leachate generation contains a variety of toxic compounds, and is a major problem for municipal solid waste (MSW). Microbial profile knowledge is essential to new alternatives and improvements in current treatments of these effluents. In this respect, the microbial community in the leachate from the sanitary landfill of the city of Foz do Iguaçu was analyzed. The 16S rDNA metabarcoding suggested the dominance of fermenting bacteria belonging to Firmicutes phylum, followed by Proteobacteria, Bacteroidetes, and Synergistetes. The most abundant genera were Sedimentibacter, Vulcanibacillus, and Anaerovorax. However, 60% of amplicon sequence variants (ASVs) were not classified taxonomically. In addition, an expressive abundance was attributed to the superphylum known as PVC group, little studied and with unknown scientific potential. The leachate acidogenic phase was masked in the chemical and physical analyzes. Nevertheless, it was evidenced in the metabarcoding methodology. No specifically methanogenic group was detected in significant abundance. Therefore, from bacterial community identification, a bioremediation process can be designed. Enriched culture media can be developed and targeted to the recovery of specific groups which may be involved in leachate biodegradation. What is more, the results expand the knowledge of bacterial diversity, especially from the presence of unknown genera in this habitat.
Collapse
Affiliation(s)
- Michel Rodrigo Zambrano Passarini
- Institute Latin American of Nature and Life Sciences (ILACNV), Interdisciplinary Center of Life Sciences (CICV), Federal University of Latin American Integration (UNILA), 1000 Tarquínio Joslin dos Santos Av., Jardim Universitário, Foz do Iguaçu, PR, 85870-901, Brazil
| | - João Victor Fonseca Moreira
- Institute Latin American of Nature and Life Sciences (ILACNV), Interdisciplinary Center of Life Sciences (CICV), Federal University of Latin American Integration (UNILA), 1000 Tarquínio Joslin dos Santos Av., Jardim Universitário, Foz do Iguaçu, PR, 85870-901, Brazil
| | - Jose Alejandro Morales Gomez
- Institute Latin American of Nature and Life Sciences (ILACNV), Interdisciplinary Center of Life Sciences (CICV), Federal University of Latin American Integration (UNILA), 1000 Tarquínio Joslin dos Santos Av., Jardim Universitário, Foz do Iguaçu, PR, 85870-901, Brazil
| | - Rafaella Costa Bonugli-Santos
- Institute Latin American of Nature and Life Sciences (ILACNV), Interdisciplinary Center of Life Sciences (CICV), Federal University of Latin American Integration (UNILA), 1000 Tarquínio Joslin dos Santos Av., Jardim Universitário, Foz do Iguaçu, PR, 85870-901, Brazil.
| |
Collapse
|
20
|
Jagannathan SV, Manemann EM, Rowe SE, Callender MC, Soto W. Marine Actinomycetes, New Sources of Biotechnological Products. Mar Drugs 2021; 19:365. [PMID: 34201951 PMCID: PMC8304352 DOI: 10.3390/md19070365] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 06/14/2021] [Accepted: 06/21/2021] [Indexed: 02/07/2023] Open
Abstract
The Actinomycetales order is one of great genetic and functional diversity, including diversity in the production of secondary metabolites which have uses in medical, environmental rehabilitation, and industrial applications. Secondary metabolites produced by actinomycete species are an abundant source of antibiotics, antitumor agents, anthelmintics, and antifungals. These actinomycete-derived medicines are in circulation as current treatments, but actinomycetes are also being explored as potential sources of new compounds to combat multidrug resistance in pathogenic bacteria. Actinomycetes as a potential to solve environmental concerns is another area of recent investigation, particularly their utility in the bioremediation of pesticides, toxic metals, radioactive wastes, and biofouling. Other applications include biofuels, detergents, and food preservatives/additives. Exploring other unique properties of actinomycetes will allow for a deeper understanding of this interesting taxonomic group. Combined with genetic engineering, microbial experimental evolution, and other enhancement techniques, it is reasonable to assume that the use of marine actinomycetes will continue to increase. Novel products will begin to be developed for diverse applied research purposes, including zymology and enology. This paper outlines the current knowledge of actinomycete usage in applied research, focusing on marine isolates and providing direction for future research.
Collapse
Affiliation(s)
| | | | | | | | - William Soto
- Department of Biology, College of William & Mary, Williamsburg, VA 23185, USA; (S.V.J.); (E.M.M.); (S.E.R.); (M.C.C.)
| |
Collapse
|
21
|
Seasonal Variation in Antimicrobial Activity of Crude Extracts of Psammaplysilla sp. 1 from Phillips Reef, South Africa. Int J Microbiol 2021; 2021:7568493. [PMID: 34054965 PMCID: PMC8131155 DOI: 10.1155/2021/7568493] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 04/29/2021] [Indexed: 12/03/2022] Open
Abstract
Marine invertebrates constitute a diverse group of marine organisms beneficial to humanity due to their therapeutic significance. The marine sponge species Psammaplysilla sp. 1 was collected from Philips Reef, South Africa, over a four-season period and assayed for antimicrobial potential. The physicochemical parameters of the collection site were also recorded. The sponge crude extracts' antimicrobial activity was evaluated using an agar well diffusion assay against 5 pathogens. Phytochemical screening was conducted to identify the presence of 7 critical phytochemical groups. During the four seasons, the mean water temperature was 17.35°C ± 2.06, with autumn recording the highest (20°C) temperature. Antifungal activity was observed by Psammaplysilla sp. 1 (30 mm) against C. albicans, and this was higher than that showed by standard drugs ICZ-10 µg (15 ± 0.1 mm), FLU-15 µg (21 ± 0.2 mm), and VCZ-5 µg (17 ± 0.1 mm), respectively. Similar bioactivities were observed seasonally with Psammaplysilla sp. 1 (22 mm and 24 mm) during autumn and spring, respectively, against C. difficile while only crude extracts collected in spring showed bioactivity against C. albicans. Psammaplysilla sp. crude extracts showed broad-spectrum bioactivity against all test pathogens. DCM : ME crude extracts tested positive for the presence of 2/7 of the phytochemicals (terpenoids and flavonoids). GC-MS revealed several previously reported biologically active compounds such bicyclo[4.2.0]octa-1,3,5-trien-7-ol and phenol, 2,6-dibromo, some of which have been found in plants. This study revealed that sponge bioactivity is dependent on the season and further validated the antimicrobial potential of South African marine sponges.
Collapse
|
22
|
An Analysis of Biosynthesis Gene Clusters and Bioactivity of Marine Bacterial Symbionts. Curr Microbiol 2021; 78:2522-2533. [PMID: 34041587 DOI: 10.1007/s00284-021-02535-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Accepted: 05/05/2021] [Indexed: 01/28/2023]
Abstract
Symbiotic marine bacteria have a pivotal role in drug discovery due to the synthesis of diverse biologically potential compounds. The marine bacterial phyla proteobacteria, actinobacteria and firmicutes are commonly associated with marine macro organisms and frequently reported as dominant bioactive compound producers. They can produce biologically active compounds that possess antimicrobial, antiviral, antitumor, antibiofilm and antifouling properties. Synthesis of these bioactive compounds is controlled by a set of genes of their genomes that is known as biosynthesis gene clusters (BGCs). The development in the field of biotechnology and bioinformatics has uncovered the potential BGCs of the bacterial genome and its functions. Now-a-days researchers have focused their attention on the identification of potential BGCs for the discovery of novel bioactive compounds using advanced technology. This review highlights the marine bacterial symbionts and their BGCs which are responsible for the synthesis of bioactive compounds.
Collapse
|
23
|
Ruocco N, Esposito R, Bertolino M, Zazo G, Sonnessa M, Andreani F, Coppola D, Giordano D, Nuzzo G, Lauritano C, Fontana A, Ianora A, Verde C, Costantini M. A Metataxonomic Approach Reveals Diversified Bacterial Communities in Antarctic Sponges. Mar Drugs 2021; 19:173. [PMID: 33810171 PMCID: PMC8004616 DOI: 10.3390/md19030173] [Citation(s) in RCA: 7] [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: 01/29/2021] [Revised: 03/17/2021] [Accepted: 03/20/2021] [Indexed: 02/06/2023] Open
Abstract
Marine sponges commonly host a repertoire of bacterial-associated organisms, which significantly contribute to their health and survival by producing several anti-predatory molecules. Many of these compounds are produced by sponge-associated bacteria and represent an incredible source of novel bioactive metabolites with biotechnological relevance. Although most investigations are focused on tropical and temperate species, to date, few studies have described the composition of microbiota hosted by Antarctic sponges and the secondary metabolites that they produce. The investigation was conducted on four sponges collected from two different sites in the framework of the XXXIV Italian National Antarctic Research Program (PNRA) in November-December 2018. Collected species were characterized as Mycale (Oxymycale) acerata, Haliclona (Rhizoniera) dancoi, Hemigellius pilosus and Microxina sarai by morphological analysis of spicules and amplification of four molecular markers. Metataxonomic analysis of these four Antarctic sponges revealed a considerable abundance of Amplicon Sequence Variants (ASVs) belonging to the phyla Proteobacteria, Bacteroidetes, Actinobacteria and Verrucomicrobia. In particular, M. (Oxymycale) acerata, displayed several genera of great interest, such as Endozoicomonas, Rubritalea, Ulvibacter, Fulvivirga and Colwellia. On the other hand, the sponges H. pilosus and H. (Rhizoniera) dancoi hosted bacteria belonging to the genera Pseudhongella, Roseobacter and Bdellovibrio, whereas M. sarai was the sole species showing some strains affiliated to the genus Polaribacter. Considering that most of the bacteria identified in the present study are known to produce valuable secondary metabolites, the four Antarctic sponges could be proposed as potential tools for the discovery of novel pharmacologically active compounds.
Collapse
Affiliation(s)
- Nadia Ruocco
- Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy; (N.R.); (R.E.); (D.C.); (D.G.); (C.L.); (A.I.); (C.V.)
| | - Roberta Esposito
- Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy; (N.R.); (R.E.); (D.C.); (D.G.); (C.L.); (A.I.); (C.V.)
- Department of Biology, University of Naples Federico II, Complesso Universitario di Monte Sant’Angelo, Via Cinthia 21, 80126 Napoli, Italy
| | - Marco Bertolino
- Dipartimento di Scienze della Terra, dell’Ambiente e della Vita (DISTAV), Università degli Studi di Genova, Corso Europa 26, 16132 Genova, Italy;
| | - Gianluca Zazo
- Department of Research Infrastructure for Marine Biological Resources, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy;
| | - Michele Sonnessa
- Bio-Fab Research srl, Via Mario Beltrami, 5, 00135 Roma, Italy; (M.S.); (F.A.)
| | - Federico Andreani
- Bio-Fab Research srl, Via Mario Beltrami, 5, 00135 Roma, Italy; (M.S.); (F.A.)
| | - Daniela Coppola
- Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy; (N.R.); (R.E.); (D.C.); (D.G.); (C.L.); (A.I.); (C.V.)
- Institute of Biosciences and BioResources (IBBR), National Research Council (CNR), Via Pietro Castellino 111, 80131 Napoli, Italy
| | - Daniela Giordano
- Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy; (N.R.); (R.E.); (D.C.); (D.G.); (C.L.); (A.I.); (C.V.)
- Institute of Biosciences and BioResources (IBBR), National Research Council (CNR), Via Pietro Castellino 111, 80131 Napoli, Italy
| | - Genoveffa Nuzzo
- Consiglio Nazionale delle Ricerche, Istituto di Chimica Biomolecolare, Via Campi Flegrei 34, 80078 Pozzuoli (Napoli), Italy; (G.N.); (A.F.)
| | - Chiara Lauritano
- Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy; (N.R.); (R.E.); (D.C.); (D.G.); (C.L.); (A.I.); (C.V.)
| | - Angelo Fontana
- Consiglio Nazionale delle Ricerche, Istituto di Chimica Biomolecolare, Via Campi Flegrei 34, 80078 Pozzuoli (Napoli), Italy; (G.N.); (A.F.)
| | - Adrianna Ianora
- Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy; (N.R.); (R.E.); (D.C.); (D.G.); (C.L.); (A.I.); (C.V.)
| | - Cinzia Verde
- Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy; (N.R.); (R.E.); (D.C.); (D.G.); (C.L.); (A.I.); (C.V.)
- Institute of Biosciences and BioResources (IBBR), National Research Council (CNR), Via Pietro Castellino 111, 80131 Napoli, Italy
| | - Maria Costantini
- Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy; (N.R.); (R.E.); (D.C.); (D.G.); (C.L.); (A.I.); (C.V.)
- Institute of Biosciences and BioResources (IBBR), National Research Council (CNR), Via Pietro Castellino 111, 80131 Napoli, Italy
| |
Collapse
|
24
|
Antimicrobial Potential and Phytochemical Screening of Clathria sp. 1 and Tedania ( Tedania) stylonychaeta Sponge Crude Extracts Obtained from the South East Coast of South Africa. BIOMED RESEARCH INTERNATIONAL 2021; 2021:6697944. [PMID: 33728340 PMCID: PMC7936908 DOI: 10.1155/2021/6697944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 02/11/2021] [Accepted: 02/17/2021] [Indexed: 12/01/2022]
Abstract
Scientists have continuously searched for novel bioactive compounds to overcome the inherent problems associated with drug resistance, the evolution of unknown diseases, and the toxicity of currently used compounds. The ocean has been considered a rich source of compounds that possess unique chemical structures and novel biological capabilities. Biologically active molecules isolated from marine flora and fauna have shown significant advancement over the past century in the pharmaceutical industry. Marine natural products (MNPs) have been used as nanomedicine, cosmetics, wound healing, antimicrobial agents, anticancer agents, and anti-inflammatory agents. The physicochemical parameters of the collection site were also recorded. This study's marine sponge species were collected from Phillip's Reef, South Africa, at 12 m during the spring season. Ethyl acetate (EA) and dichloromethane : methanol (DCM : ME, 1 : 1) were used as extraction solvents. Crude extracts of the marine sponges were tested against MRSA, P. aeruginosa, C. difficile, A. fumigatus, and C. albicans. Phytochemical screening was conducted to identify seven critical phytochemical groups. A pH reading of 8.01 and a temperature of 15.45°C were recorded at the sampling site. Clathria sp. 1 and Tedania (Tedania) stylonychaeta EA crude extracts showed bioactivity against all five test pathogens. The DCM : ME crude extract of Clathria sp. 1 was the only bioactive crude extract from DCM : ME extracts. This crude extract was only bioactive against C. albicans as no activity was observed against the other four pathogens. EA crude extracts of Clathria sp. 1 yielded more significant inhibition zones against both fungal pathogens. These EA crude extracts performed better than fluconazole as inhibition zones of 35 ± 0 mm at 24 mg/ml, 31 ± 0 mm at 19 mg/ml, 31 ± 0 mm at 14.4 mg/ml, 30 ± 0 mm at 9.6 mg/ml, and 25 ± 0 mm at 7.2 mg/ml were recorded. Clathria sp. 1 crude extracts exhibited higher inhibition zones compared to Tedania (Tedania) stylonychaeta. The antibiotic imipenem (26 ± 0.7 mm at 10 μg) and ciprofloxacin (30 ± 0.3 mm at 5 μg) exhibited higher zones of inhibition than EA crude extracts of Tedania (Tedania) stylonychaeta at all test concentrations. In this study, Clathria sp. 1 was observed to have broad-spectrum bioactivity as EA crude extracts were bioactive against MRSA, P. aeruginosa, C. difficile, A. fumigatus, and C. albicans. In addition to this, the EA crude extract of Clathria sp. 1 was bacteriostatic (9.6 mg/ml). Clathria sp. 1 DCM : ME crude extract only tested positive for the presence of terpenoids. In contrast, EA crude extracts did not test positive for the existence of any of the seven phytochemicals. Our study has revealed that Tedania (Tedania) stylonychaeta and Clathria sp. 1 sponge species collected from Phillip's Reef in South Africa can produce bioactive compounds useful against bacterial and fungal species.
Collapse
|
25
|
Antibiofilm Activity of Antarctic Sponge-Associated Bacteria against Pseudomonas aeruginosa and Staphylococcus aureus. JOURNAL OF MARINE SCIENCE AND ENGINEERING 2021. [DOI: 10.3390/jmse9030243] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Bioprospecting in unusual marine environments provides an innovative approach to search novel biomolecules with antibiofilm activity. Antarctic sponge-associated bacteria belonging to Colwellia, Pseudoalteromonas, Shewanella and Winogradskyella genera were evaluated for their ability to contrast the biofilm formation by Pseudomonas aeruginosa ATCC 27853 and Staphylococcus aureus ATCC 29213, as model organisms. All strains were able to produce biofilm at both 4 and 25 °C, with the highest production being for Colwellia, Shewanella and Winogradskyella strains at 4 °C after 24 h. Antibiofilm activity of cell-free supernatants (CFSs) differed among strains and on the basis of their incubation temperature (CFSs4°C and CFSs25°C). The major activity was observed by CFSs4°C against S. aureus and CFSs25°C against P. aeruginosa, without demonstrating a bactericidal effect on their growth. Furthermore, the antibiofilm activity of crude extracts from Colwellia sp. GW185, Shewanella sp. CAL606, and Winogradskyella sp. CAL396 was also evaluated and visualized by confocal laser scanning microscopic images. Results based on the surface-coating assay and surface tension measurements suggest that CFSs and the crude extracts may act as biosurfactants inhibiting the first adhesion of P. aeruginosa and S. aureus. The CFSs and the novel biopolymers may be useful in applicative perspectives for pharmaceutical and environmental purposes.
Collapse
|
26
|
Gavriilidou A, Mackenzie TA, Sánchez P, Tormo JR, Ingham C, Smidt H, Sipkema D. Bioactivity Screening and Gene-Trait Matching across Marine Sponge-Associated Bacteria. Mar Drugs 2021; 19:75. [PMID: 33573261 PMCID: PMC7912018 DOI: 10.3390/md19020075] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 01/25/2021] [Accepted: 01/26/2021] [Indexed: 12/23/2022] Open
Abstract
Marine sponges harbor diverse microbial communities that represent a significant source of natural products. In the present study, extracts of 21 sponge-associated bacteria were screened for their antimicrobial and anticancer activity, and their genomes were mined for secondary metabolite biosynthetic gene clusters (BGCs). Phylogenetic analysis assigned the strains to four major phyla in the sponge microbiome, namely Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes. Bioassays identified one extract with anti-methicillin-resistant Staphylococcus aureus (MRSA) activity, and more than 70% of the total extracts had a moderate to high cytotoxicity. The most active extracts were derived from the Proteobacteria and Actinobacteria, prominent for producing bioactive substances. The strong bioactivity potential of the aforementioned strains was also evident in the abundance of BGCs, which encoded mainly beta-lactones, bacteriocins, non-ribosomal peptide synthetases (NRPS), terpenes, and siderophores. Gene-trait matching was performed for the most active strains, aiming at linking their biosynthetic potential with the experimental results. Genetic associations were established for the anti-MRSA and cytotoxic phenotypes based on the similarity of the detected BGCs with BGCs encoding natural products with known bioactivity. Overall, our study highlights the significance of combining in vitro and in silico approaches in the search of novel natural products of pharmaceutical interest.
Collapse
Affiliation(s)
- Asimenia Gavriilidou
- Laboratory of Microbiology, Wageningen University and Research, 6708 WE Wageningen, The Netherlands; (H.S.); (D.S.)
| | - Thomas Andrew Mackenzie
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avda. del Conocimiento 34, 18016 Granada, Spain; (T.A.M.); (P.S.); (J.R.T.)
| | - Pilar Sánchez
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avda. del Conocimiento 34, 18016 Granada, Spain; (T.A.M.); (P.S.); (J.R.T.)
| | - José Ruben Tormo
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avda. del Conocimiento 34, 18016 Granada, Spain; (T.A.M.); (P.S.); (J.R.T.)
| | | | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University and Research, 6708 WE Wageningen, The Netherlands; (H.S.); (D.S.)
| | - Detmer Sipkema
- Laboratory of Microbiology, Wageningen University and Research, 6708 WE Wageningen, The Netherlands; (H.S.); (D.S.)
| |
Collapse
|
27
|
Hassanshahian M, Amirinejad N, Askarinejad Behzadi M. Crude oil pollution and biodegradation at the Persian Gulf: A comprehensive and review study. JOURNAL OF ENVIRONMENTAL HEALTH SCIENCE & ENGINEERING 2020; 18:1415-1435. [PMID: 33312652 PMCID: PMC7721969 DOI: 10.1007/s40201-020-00557-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 09/29/2020] [Indexed: 06/01/2023]
Abstract
The Persian Gulf consider as the fundamental biological marine condition between the seas. There is a different assortment of marine life forms including corals, wipes, and fish in this marine condition. Mangrove timberlands are found all through this sea-going biological system. Sullying of the Persian Gulf to oil-based goods is the principle of danger to this marine condition and this contamination can effectively affect this differing marine condition. Numerous specialists examined the result of oil contamination on Persian Gulf marine creatures including corals sponges, bivalves, and fishes. These analysts affirmed this oil contamination on the Persian Gulf significantly diminished biodiversity. Diverse microorganisms fit to consume oil-based commodities detailed by various scientists from the Persian Gulf and their capacity to the debasement of unrefined petroleum has been examined. There has additionally been little exploration of cyanobacteria, yeast, and unrefined petroleum debasing organisms in this sea-going environment. Biosurfactants are amphipathic molecules that upgrade the disintegration of oil and increment their bioavailability to corrupt microscopic organisms. Additionally, biosurfactant-producing bacteria were discovered from the Persian Gulf, and the capability to degradation of crude oil in microscale was evaluated. The current review article aims to collect the finding of various researches performed in the Persian Gulf on oil pollution and crude-oil biodegradation. It is expected that by applying biological methods in combination with mechanical and chemical methods, the hazard consequences of crude-oil contamination on this important aquatic ecosystem at the world will be mitigated and a step towards preserving this diverse marine environment.
Collapse
Affiliation(s)
- Mehdi Hassanshahian
- Department of Biology, Faculty of Sciences, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Nazanin Amirinejad
- Department of Biology, Faculty of Sciences, Shahid Bahonar University of Kerman, Kerman, Iran
| | | |
Collapse
|
28
|
Capecchi A, Reymond JL. Assigning the Origin of Microbial Natural Products by Chemical Space Map and Machine Learning. Biomolecules 2020; 10:E1385. [PMID: 32998475 PMCID: PMC7600738 DOI: 10.3390/biom10101385] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 09/22/2020] [Accepted: 09/25/2020] [Indexed: 12/20/2022] Open
Abstract
Microbial natural products (NPs) are an important source of drugs, however, their structural diversity remains poorly understood. Here we used our recently reported MinHashed Atom Pair fingerprint with diameter of four bonds (MAP4), a fingerprint suitable for molecules across very different sizes, to analyze the Natural Products Atlas (NPAtlas), a database of 25,523 NPs of bacterial or fungal origin. To visualize NPAtlas by MAP4 similarity, we used the dimensionality reduction method tree map (TMAP). The resulting interactive map organizes molecules by physico-chemical properties and compound families such as peptides and glycosides. Remarkably, the map separates bacterial and fungal NPs from one another, revealing that these two compound families are intrinsically different despite their related biosynthetic pathways. We used these differences to train a machine learning model capable of distinguishing between NPs of bacterial or fungal origin.
Collapse
Affiliation(s)
| | - Jean-Louis Reymond
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland;
| |
Collapse
|
29
|
Antimicrobial Chlorinated 3-Phenylpropanoic Acid Derivatives from the Red Sea Marine Actinomycete Streptomyces coelicolor LY001. Mar Drugs 2020; 18:md18090450. [PMID: 32867397 PMCID: PMC7551466 DOI: 10.3390/md18090450] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 08/24/2020] [Accepted: 08/25/2020] [Indexed: 11/17/2022] Open
Abstract
The actinomycete strain Streptomyces coelicolor LY001 was purified from the sponge Callyspongia siphonella. Fractionation of the antimicrobial extract of the culture of the actinomycete afforded three new natural chlorinated derivatives of 3-phenylpropanoic acid, 3-(3,5-dichloro-4-hydroxyphenyl)propanoic acid (1), 3-(3,5-dichloro-4-hydroxyphenyl)propanoic acid methyl ester (2), and 3-(3-chloro-4-hydroxyphenyl)propanoic acid (3), together with 3-phenylpropanoic acid (4), E-cinnamic acid (5), and the diketopiperazine alkaloids cyclo(l-Phe-trans-4-OH-l-Pro) (6) and cyclo(l-Phe-cis-4-OH-d-Pro) (7) were isolated. Interpretation of nuclear magnetic resonance (NMR) and high-resolution electrospray ionization mass spectrometry (HRESIMS) data of 1–7 supported their assignments. Compounds 1–3 are first candidates of the natural chlorinated phenylpropanoic acid derivatives. The production of the chlorinated derivatives of 3-phenylpropionic acid (1–3) by S. coelicolor provides insight into the biosynthetic capabilities of the marine-derived actinomycetes. Compounds 1–3 demonstrated significant and selective activities towards Escherichia. coli and Staphylococcus aureus, while Candida albicans displayed more sensitivity towards compounds 6 and 7, suggesting a selectivity effect of these compounds against C. albicans.
Collapse
|
30
|
Role of symbiosis in the discovery of novel antibiotics. J Antibiot (Tokyo) 2020; 73:490-503. [PMID: 32499556 DOI: 10.1038/s41429-020-0321-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 04/18/2020] [Accepted: 04/26/2020] [Indexed: 12/16/2022]
Abstract
Antibiotic resistance has been an ongoing challenge that has emerged almost immediately after the initial discovery of antibiotics and requires the development of innovative new antibiotics and antibiotic combinations that can effectively mitigate the development of resistance. More than 35,000 people die each year from antibiotic resistant infections in just the United States. This signifies the importance of identifying other alternatives to antibiotics for which resistance has developed. Virtually, all currently used antibiotics can trace their genesis to soil derived bacteria and fungi. The bacteria and fungi involved in symbiosis is an area that still remains widely unexplored for the discovery and development of new antibiotics. This brief review focuses on the challenges and opportunities in the application of symbiotic microbes and also provides an interesting platform that links natural product chemistry with evolutionary biology and ecology.
Collapse
|
31
|
Marine microbial natural products: the evolution of a new field of science. J Antibiot (Tokyo) 2020; 73:481-487. [PMID: 32713942 DOI: 10.1038/s41429-020-0331-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 05/21/2020] [Indexed: 12/29/2022]
|
32
|
Antimicrobial Lipids from Plants and Marine Organisms: An Overview of the Current State-of-the-Art and Future Prospects. Antibiotics (Basel) 2020; 9:antibiotics9080441. [PMID: 32722192 PMCID: PMC7459900 DOI: 10.3390/antibiotics9080441] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 07/17/2020] [Accepted: 07/22/2020] [Indexed: 02/07/2023] Open
Abstract
In the actual post-antibiotic era, novel ways of rethinking antimicrobial research approaches are more urgent than ever. Natural compounds with antimicrobial activity such as fatty acids and monoacylglycerols have been investigated for decades. Additionally, the interest in other lipid classes as antimicrobial agents is rising. This review provides an overview on the research about plant and marine lipids with potential antimicrobial activity, the methods for obtaining and analyzing these compounds, with emphasis on lipidomics, and future perspectives for bioprospection and applications for antimicrobial lipids. Lipid extracts or lipids isolated from higher plants, algae or marine invertebrates are promising molecules to inactivate a wide spectrum of microorganisms. These lipids include a variety of chemical structures. Present and future challenges in the research of antimicrobial lipids from natural origin are related to the investment and optimization of the analytical workflow based on lipidomics tools, complementary to the bioassay-guided fractionation, to identify the active compound(s). Also, further work is needed regarding the study of their mechanism of action, the structure-activity relationship, the synergistic effect with conventional antibiotics, and the eventual development of resistance to lipids, which, as far as is known, is unlikely.
Collapse
|
33
|
Sharma AR, Harunari E, Oku N, Matsuura N, Trianto A, Igarashi Y. Two antibacterial and PPARα/γ-agonistic unsaturated keto fatty acids from a coral-associated actinomycete of the genus Micrococcus. Beilstein J Org Chem 2020; 16:297-304. [PMID: 32256847 PMCID: PMC7082699 DOI: 10.3762/bjoc.16.29] [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: 11/01/2019] [Accepted: 02/14/2020] [Indexed: 01/01/2023] Open
Abstract
A pair of geometrically isomeric unsaturated keto fatty acids, (6E,8Z)- and (6E,8E)-5-oxo-6,8-tetradecadienoic acids (1 and 2), were isolated from the culture broth of an actinomycete of the genus Micrococcus, which was associated with a stony coral, Catalaphyllia sp. Their chemical structures were elucidated by spectroscopic analysis including NMR and MS, with special assistance of spin system simulation studies for the assignment of an E geometry at C8 in 2. As metabolites of microbes, compounds 1 and 2 are unprecedented in terms of bearing a 2,4-dienone system. Both 1 and 2 showed antibacterial activity against the plant pathogen Rhizobium radiobacter and the fish pathogen Tenacibaculum maritimum, with a contrasting preference that 1 is more effective to the former strain while 2 is so to the latter. In addition, compounds 1 and 2 displayed agonistic activity against peroxisome proliferator-activated receptors (PPARs) with an isoform specificity towards PPARα and PPARγ.
Collapse
Affiliation(s)
- Amit Raj Sharma
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Enjuro Harunari
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Naoya Oku
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Nobuyasu Matsuura
- Okayama University of Science, 1-1 Ridaicho, Okayama 700-0005, Japan
| | - Agus Trianto
- Faculty of Fisheries and Marine Sciences, Diponegoro University, Tembalang Campus, St. Prof. Soedarto SH., Semarang 50275, Central Java, Indonesia
| | - Yasuhiro Igarashi
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| |
Collapse
|
34
|
Fiore CL, Jarett JK, Steinert G, Lesser MP. Trait-Based Comparison of Coral and Sponge Microbiomes. Sci Rep 2020; 10:2340. [PMID: 32047192 PMCID: PMC7012828 DOI: 10.1038/s41598-020-59320-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 01/27/2020] [Indexed: 12/27/2022] Open
Abstract
Corals and sponges harbor diverse microbial communities that are integral to the functioning of the host. While the taxonomic diversity of their microbiomes has been well-established for corals and sponges, their functional roles are less well-understood. It is unclear if the similarities of symbiosis in an invertebrate host would result in functionally similar microbiomes, or if differences in host phylogeny and environmentally driven microhabitats within each host would shape functionally distinct communities. Here we addressed this question, using metatranscriptomic and 16S rRNA gene profiling techniques to compare the microbiomes of two host organisms from different phyla. Our results indicate functional similarity in carbon, nitrogen, and sulfur assimilation, and aerobic nitrogen cycling. Additionally, there were few statistical differences in pathway coverage or abundance between the two hosts. For example, we observed higher coverage of phosphonate and siderophore metabolic pathways in the star coral, Montastraea cavernosa, while there was higher coverage of chloroalkane metabolism in the giant barrel sponge, Xestospongia muta. Higher abundance of genes associated with carbon fixation pathways was also observed in M. cavernosa, while in X. muta there was higher abundance of fatty acid metabolic pathways. Metagenomic predictions based on 16S rRNA gene profiling analysis were similar, and there was high correlation between the metatranscriptome and metagenome predictions for both hosts. Our results highlight several metabolic pathways that exhibit functional similarity in these coral and sponge microbiomes despite the taxonomic differences between the two microbiomes, as well as potential specialization of some microbially based metabolism within each host.
Collapse
Affiliation(s)
- Cara L Fiore
- University of New Hampshire, Department of Molecular, Cellular and Biomedical Sciences, School of Marine Science and Ocean Engineering, Durham, NH, USA.
- Appalachian State University, Biology Department, Boone, NC, USA.
| | - Jessica K Jarett
- University of New Hampshire, Department of Molecular, Cellular and Biomedical Sciences, School of Marine Science and Ocean Engineering, Durham, NH, USA
- AnimalBiome, Oakland, CA, USA
| | - Georg Steinert
- Institute for Chemistry and Biology of the Marine Environment, Carl-von-Ossietzky University Oldenburg, Wilhelmshaven, Germany
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Marine Symbioses, Kiel, Germany
| | - Michael P Lesser
- University of New Hampshire, Department of Molecular, Cellular and Biomedical Sciences, School of Marine Science and Ocean Engineering, Durham, NH, USA
| |
Collapse
|
35
|
Antimicrobial activity of bacteria from marine sponge Suberea mollis and bioactive metabolites of Vibrio sp. EA348. Saudi J Biol Sci 2020; 27:1139-1147. [PMID: 32256176 PMCID: PMC7105658 DOI: 10.1016/j.sjbs.2020.02.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 01/27/2020] [Accepted: 02/01/2020] [Indexed: 11/22/2022] Open
Abstract
Discovery of potential bioactive metabolites from sponge-associated bacteria have gained attraction in recent years. The current study explores the potential of sponge (Suberea mollis) associated bacteria against bacterial and fungal pathogens. Sponge samples were collected from Red sea in Obhur region, Jeddah, Saudi Arabia. Of 29 isolated bacteria belong to four different classes i.e. Firmicutes (62%), γ-Proteobacteria (21%), α-Proteobacteria (10%) and Actinobacteria (7%). Among them nineteen (65%) bacterial strains showed antagonistic activity against oomycetes and only 3 (10%) bacterial strains were active against human pathogenic bacteria tested. Most bioactive genera include Bacillus (55%), Pseudovibrio (13%) and Ruegeria (10%). Enzyme production (protease, lipase, amylase, cellualse) was identified in 12 (41%) bacterial strains where potential strains belonging to γ-Proteobacteria and Firmicutes groups. Production of antimicrobial metabolites and hydrolysates in these bacteria suggest their potential role in sponge against pathogens. Further bioactive metabolites from selected strain of Vibrio sp. EA348 were identified using LC-MS and GC–MS analyses. We identified many active metabolites including antibiotics such as Amifloxacin and fosfomycin. Plant growth hormones including Indoleacetic acid and Gibberellin A3 and volatile organic compound such as methyl jasmonate were also detected in this strain. Our results highlighted the importance of marine bacteria inhabiting sponges as potential source of antimicrobial compounds and plant growth hormones of pharmaceutical and agricultural significance.
Collapse
|
36
|
Chaetoglobosins and azaphilones from Chaetomium globosum associated with Apostichopus japonicus. Appl Microbiol Biotechnol 2020; 104:1545-1553. [PMID: 31897521 DOI: 10.1007/s00253-019-10308-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 11/29/2019] [Accepted: 12/08/2019] [Indexed: 01/01/2023]
Abstract
Increasing attention has recently been focused on complex symbiotic associations, for instance coral and its symbionts. Sea cucumber, harboring diverse fungi, has also attracted more and more attention for their functional diversity. Here, secondary metabolites produced by Chaetomium globosum associated with sea cucumber, Apostichopus japonicus, were investigated using gene mining with third-generation sequencing technology (PacBio SMRT). Nine compounds, including one new compound cytoglobosin X (1), were isolated from cultures of Chaetomium globosum. Compound 1 was identified based on NMR data, HRESIMS, and ECD, and the absolute configurations were identified as 3S, 4R, 7S, 8R, 9R, 16S, 19S, 20S, and 23S. In an antimicrobial assay, compound 4 showed moderate activity against Staphylococcus aureus and methicillin-resistant Staphylococcus aureus with MICs of 47.3 and 94.6 μM, respectively. Our results suggest that the microbiomes associated with sea cucumber could be an important resource for biodiversity and structural novelty, and the bioactive compounds may protect the host from pathogen microbial.
Collapse
|
37
|
Impact of the Cultivation Technique on the Production of Secondary Metabolites by Chrysosporium lobatum TM-237-S5, Isolated from the Sponge Acanthella cavernosa. Mar Drugs 2019; 17:md17120678. [PMID: 31801271 PMCID: PMC6950079 DOI: 10.3390/md17120678] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 11/25/2019] [Accepted: 11/26/2019] [Indexed: 12/22/2022] Open
Abstract
The fungi Chrysosporium lobatum TM-237-S5 was isolated from the sponge Acanthella cavernosa, collected from the mesophotic coral ecosystem of the Red Sea. The strain was cultivated on a potato dextrose agar (PDA) medium, coupling solid-state fermentation and solid-state extraction (SSF/SSE) with a neutral macroreticular polymeric adsorbent XAD Amberlite resin (AMBERLITE XAD1600N). The SSF/SSE lead to high chemodiversity and productivity compared to classical submerged cultivation. Ten phenalenone related compounds were isolated and fully characterized by one-dimensional and two-dimensional NMR and HRMS. Among them, four were found to be new compounds corresponding to isoconiolactone, (-)-peniciphenalenin F, (+)-8-hydroxyscleroderodin, and (+)-8-hydroxysclerodin. It is concluded that SSF/SSE is a powerful strategy, opening a new era for the exploitation of microbial secondary metabolites.
Collapse
|
38
|
Sharma AR, Harunari E, Zhou T, Trianto A, Igarashi Y. Isolation and biosynthesis of an unsaturated fatty acid with unusual methylation pattern from a coral-associated bacterium Microbulbifer sp. Beilstein J Org Chem 2019; 15:2327-2332. [PMID: 31666867 PMCID: PMC6808205 DOI: 10.3762/bjoc.15.225] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 09/16/2019] [Indexed: 12/22/2022] Open
Abstract
(2Z,4E)-3-Methyl-2,4-decadienoic acid (1) was identified as a major metabolite from a culture extract of a marine bacterium Microbulbifer which was collected from a stony coral Porites sp. NMR-based spectroscopic analysis revealed that 1 is an unsaturated fatty acid in which a methyl group is located in an uncommon position as a natural product. Feeding experiments of 13C-labeled precursors clarified that ʟ-methionine-derived methylation takes place at the carbon which is derived from the carbonyl carbon of acetate. Compound 1 showed weak growth inhibition against Saccharomyces cerevisiae.
Collapse
Affiliation(s)
- Amit Raj Sharma
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Enjuro Harunari
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Tao Zhou
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Agus Trianto
- Faculty of Fisheries and Marine Sciences, Diponegoro University, Tembalang Campus, St. Prof. Soedarto SH., Semarang 50275, Central Java, Indonesia
| | - Yasuhiro Igarashi
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| |
Collapse
|
39
|
Antimicrobial Lavandulylated Flavonoids from a Sponge-Derived Streptomyces sp. G248 in East Vietnam Sea. Mar Drugs 2019; 17:md17090529. [PMID: 31510079 PMCID: PMC6780759 DOI: 10.3390/md17090529] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 08/30/2019] [Accepted: 09/06/2019] [Indexed: 11/18/2022] Open
Abstract
Three new lavandulylated flavonoids, (2S,2″S)-6-lavandulyl-7,4′-dimethoxy-5,2′-dihydroxylflavanone (1), (2S,2″S)-6-lavandulyl-5,7,2′,4′-tetrahydroxylflavanone (2), and (2″S)-5′-lavandulyl-2′-methoxy-2,4,4′,6′-tetrahydroxylchalcone (3), along with seven known compounds 4–10 were isolated from culture broth of Streptomyces sp. G248. Their structures were established by spectroscopic data analysis, including 1D and 2D nuclear magnetic resonance (NMR), and high-resolution electrospray ionization mass spectrometry (HR-ESI-MS). The absolute configurations of 1–3 were resolved by comparison of their experimental and calculated electronic circular dichroism spectra. Compounds 1–3 exhibited remarkable antimicrobial activity. Whereas, two known compounds 4 and 5 exhibited inhibitory activity against Mycobacterium tuberculosis H37Rv with minimum inhibitory concentration (MIC) values of 6.0 µg/mL and 11.1 µg/mL, respectively.
Collapse
|
40
|
Bibi F, Alvi SA, Al-Sofyani A, Naseer MI, Yasir M, Azhar EI. Pyrosequencing reveals sponge specific bacterial communities in marine sponges of Red Sea, Saudi Arabia. Saudi J Biol Sci 2019; 27:67-73. [PMID: 31889819 PMCID: PMC6933160 DOI: 10.1016/j.sjbs.2019.05.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 05/01/2019] [Accepted: 05/06/2019] [Indexed: 11/16/2022] Open
Abstract
Bacterial communities of marine sponges are believed to be an important partner for host survival but remain poorly studied. Sponges show difference in richness and abundance of microbial population inhabiting them. Three marine sponges belonging to the species of Pione vastifica, Siphonochalina siphonella and Suberea mollis were collected from Red sea in Jeddah and were investigated using high throughput sequencing. Highly diverse communities containing 105 OTUs were identified in S. mollis host. Only 61 and 43 OTUs were found in P. vastifica and S. siphonella respectively. We identified 10 different bacterial phyla and 31 genera using 27,356 sequences. Most of the OTUs belong to phylum Proteobacteria (29%–99%) comprising of Gammaproteobacteria, Alphaproteobacteria, and Deltaproteobacteria where later two were only detected in HMA sponge, S. mollis. A number of 16S rRNA sequences (25%) were not identified to phylum level and may be novel taxa. Richness of bacterial community and Shannon, Simpson diversity revealed that sponge S. mollis harbors high diversity compared to other two LMA sponges. Dominance of Proteobacteria in sponges may indicate an ecological significance of this phylum in the Red sea sponges. These differences in bacterial composition may be due to difference in location site or host responses to environmental conditions. To the best of our knowledge, the microbial communities of these sponges have never been studied before and this is first attempt to unravel bacterial diversity using PCR-based 454-pyrosequencing method.
Collapse
Affiliation(s)
- Fehmida Bibi
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, 21589, Jeddah, Saudi Arabia.,Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King AbdulAziz University, 21589, Jeddah, Saudi Arabia
| | - Sana Akhtar Alvi
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, 21589, Jeddah, Saudi Arabia
| | - Abdulmohsin Al-Sofyani
- Department of Marine Biology, Faculty of Marine Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Muhammad Imran Naseer
- Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, 21589, Jeddah, Saudi Arabia.,Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King AbdulAziz University, 21589, Jeddah, Saudi Arabia
| | - Muhammad Yasir
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, 21589, Jeddah, Saudi Arabia.,Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King AbdulAziz University, 21589, Jeddah, Saudi Arabia
| | - Esam Ibraheem Azhar
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, 21589, Jeddah, Saudi Arabia.,Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King AbdulAziz University, 21589, Jeddah, Saudi Arabia
| |
Collapse
|
41
|
Ngangbam AK, Mouatt P, Smith J, Waters DLE, Benkendorff K. Bromoperoxidase Producing Bacillus spp. Isolated from the Hypobranchial Glands of a Muricid Mollusc Are Capable of Tyrian Purple Precursor Biogenesis. Mar Drugs 2019; 17:md17050264. [PMID: 31058830 PMCID: PMC6562550 DOI: 10.3390/md17050264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 04/26/2019] [Accepted: 04/30/2019] [Indexed: 11/16/2022] Open
Abstract
The secondary metabolite Tyrian purple, also known as shellfish purple and royal purple, is a dye with historical importance for humans. The biosynthetic origin of Tyrian purple in Muricidae molluscs is not currently known. A possible role for symbiotic bacteria in the production of tyrindoxyl sulphate, the precursor to Tyrian purple stored in the Australian species, Dicathais orbita, has been proposed. This study aimed to culture bacterial symbionts from the purple producing hypobranchial gland, and screen the isolates for bromoperoxidase genes using molecular methods. The ability of bromoperoxidase positive isolates to produce the brominated indole precursor to Tyrian purple was then established by extraction of the culture, and analysis by liquid chromatography-mass spectrometry (LC-MS). In total, 32 bacterial isolates were cultured from D. orbita hypobranchial glands, using marine agar, marine agar with hypobranchial gland aqueous extracts, blood agar, thiosulphate citrate bile salts sucrose agar, and cetrimide agar at pH 7.2. These included 26 Vibrio spp., two Bacillus spp., one Phaeobacter sp., one Shewanella sp., one Halobacillus sp. and one Pseudoalteromonas sp. The two Bacillus species were the only isolates found to have coding sequences for bromoperoxidase enzymes. LC-MS analysis of the supernatant and cell pellets from the bromoperoxidase producing Bacillus spp. cultured in tryptone broth, supplemented with KBr, confirmed their ability to produce the brominated precursor to Tyrian purple, tyrindoxyl sulphate. This study supports a potential role for symbiotic Bacillus spp. in the biosynthesis of Tyrian purple.
Collapse
Affiliation(s)
- Ajit Kumar Ngangbam
- Marine Ecology Research Centre, School of Environment, Science and Engineering, Southern Cross University, Lismore, NSW 2480, Australia.
| | - Peter Mouatt
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW 2480, Australia.
| | - Joshua Smith
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW 2480, Australia.
| | - Daniel L E Waters
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW 2480, Australia.
- ARC Industrial Transformation Training Centre for Functional Grains, Charles Sturt University, Wagga, NSW 2650, Australia.
| | - Kirsten Benkendorff
- Marine Ecology Research Centre, School of Environment, Science and Engineering, Southern Cross University, Lismore, NSW 2480, Australia.
| |
Collapse
|
42
|
Mathivanan A, Ravikumar S, Selvakumar G. Bioprospecting of sponge and its symbionts: New tool for mosquitocidal & insecticidal metabolites. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2019. [DOI: 10.1016/j.bcab.2019.101158] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
|
43
|
Bickmeyer U, Thoms S, Koch F, Petety Mukagatare L, Silalahi R, Sartoris FJ. Enhancement of photosynthesis in Synechococcus bacillaris by sponge-derived Ageladine A. PLoS One 2019; 14:e0213771. [PMID: 30913222 PMCID: PMC6435135 DOI: 10.1371/journal.pone.0213771] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 02/28/2019] [Indexed: 01/25/2023] Open
Abstract
This study is a proof of concept that the sponge derived pyrrole-imidazole alkaloid Ageladine A acts as an additional light harvesting molecule for photosynthesis of symbionts of marine sponges. The absorbance of Ageladine A is in the UV range and fluoresces blue, matching the blue absorbance of chlorophyll a. A joint modeling and experimental approach demonstrates that Ageladine A increases photosynthetic O2 production of Synechococcus bacillaris WH5701 (CCMP1333), when the cells are exposed to UV light, which is marginally used for photosynthesis. Due to the presence of Ageladine A, production of O2 increased 2.54 and 3.1-fold, in the experiments and the model, respectively.
Collapse
Affiliation(s)
- Ulf Bickmeyer
- Alfred Wegener Institute Helmholtz Center for Polar and Marine Research, Department of Biosciences, Bremerhaven, Germany
- * E-mail:
| | - Silke Thoms
- Alfred Wegener Institute Helmholtz Center for Polar and Marine Research, Department of Biosciences, Bremerhaven, Germany
| | - Florian Koch
- Alfred Wegener Institute Helmholtz Center for Polar and Marine Research, Department of Biosciences, Bremerhaven, Germany
| | - Liliane Petety Mukagatare
- Alfred Wegener Institute Helmholtz Center for Polar and Marine Research, Department of Biosciences, Bremerhaven, Germany
| | - Romaston Silalahi
- Alfred Wegener Institute Helmholtz Center for Polar and Marine Research, Department of Biosciences, Bremerhaven, Germany
| | - Franz Josef Sartoris
- Alfred Wegener Institute Helmholtz Center for Polar and Marine Research, Department of Biosciences, Bremerhaven, Germany
| |
Collapse
|
44
|
Tinta T, Kogovšek T, Klun K, Malej A, Herndl GJ, Turk V. Jellyfish-Associated Microbiome in the Marine Environment: Exploring Its Biotechnological Potential. Mar Drugs 2019; 17:E94. [PMID: 30717239 PMCID: PMC6410321 DOI: 10.3390/md17020094] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 01/25/2019] [Accepted: 01/29/2019] [Indexed: 12/25/2022] Open
Abstract
Despite accumulating evidence of the importance of the jellyfish-associated microbiome to jellyfish, its potential relevance to blue biotechnology has only recently been recognized. In this review, we emphasize the biotechnological potential of host⁻microorganism systems and focus on gelatinous zooplankton as a host for the microbiome with biotechnological potential. The basic characteristics of jellyfish-associated microbial communities, the mechanisms underlying the jellyfish-microbe relationship, and the role/function of the jellyfish-associated microbiome and its biotechnological potential are reviewed. It appears that the jellyfish-associated microbiome is discrete from the microbial community in the ambient seawater, exhibiting a certain degree of specialization with some preferences for specific jellyfish taxa and for specific jellyfish populations, life stages, and body parts. In addition, different sampling approaches and methodologies to study the phylogenetic diversity of the jellyfish-associated microbiome are described and discussed. Finally, some general conclusions are drawn from the existing literature and future research directions are highlighted on the jellyfish-associated microbiome.
Collapse
Affiliation(s)
- Tinkara Tinta
- Department of Limnology and Bio-Oceanography, University of Vienna, Althanstrasse 14, A-1090 Vienna, Austria.
- Marine Biology Station Piran, National Institute of Biology, Fornače 41, 6330 Piran, Slovenia.
| | - Tjaša Kogovšek
- Marine Biology Station Piran, National Institute of Biology, Fornače 41, 6330 Piran, Slovenia.
| | - Katja Klun
- Marine Biology Station Piran, National Institute of Biology, Fornače 41, 6330 Piran, Slovenia.
| | - Alenka Malej
- Marine Biology Station Piran, National Institute of Biology, Fornače 41, 6330 Piran, Slovenia.
| | - Gerhard J Herndl
- Department of Limnology and Bio-Oceanography, University of Vienna, Althanstrasse 14, A-1090 Vienna, Austria.
- NIOZ, Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Utrecht University, 1790 AB Den Burg, The Netherlands.
| | - Valentina Turk
- Marine Biology Station Piran, National Institute of Biology, Fornače 41, 6330 Piran, Slovenia.
| |
Collapse
|
45
|
Integrated Genomic and Metabolomic Approach to the Discovery of Potential Anti-Quorum Sensing Natural Products from Microbes Associated with Marine Samples from Singapore. Mar Drugs 2019; 17:md17010072. [PMID: 30669697 PMCID: PMC6356914 DOI: 10.3390/md17010072] [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: 12/27/2018] [Revised: 01/18/2019] [Accepted: 01/20/2019] [Indexed: 12/17/2022] Open
Abstract
With 70% of the Earth's surface covered in water, the marine ecosystem offers immense opportunities for drug discovery and development. Due to the decreasing rate of novel natural product discovery from terrestrial sources in recent years, many researchers are beginning to look seaward for breakthroughs in new therapeutic agents. As part of an ongoing marine drug discovery programme in Singapore, an integrated approach of combining metabolomic and genomic techniques were initiated for uncovering novel anti-quorum sensing molecules from bacteria associated with subtidal samples collected in the Singapore Strait. Based on the culture-dependent method, a total of 102 marine bacteria strains were isolated and the identities of selected strains were established based on their 16S rRNA gene sequences. About 5% of the marine bacterial organic extracts showed quorum sensing inhibitory (QSI) activity in a dose-dependent manner based on the Pseudomonas aeruginosa QS reporter system. In addition, the extracts were subjected to mass spectrometry-based molecular networking and the genome of selected strains were analysed for known as well as new biosynthetic gene clusters. This study revealed that using integrated techniques, coupled with biological assays, can provide an effective and rapid prioritization of marine bacterial strains for downstream large-scale culturing for the purpose of isolation and structural elucidation of novel bioactive compounds.
Collapse
|
46
|
Extending the "One Strain Many Compounds" (OSMAC) Principle to Marine Microorganisms. Mar Drugs 2018; 16:md16070244. [PMID: 30041461 PMCID: PMC6070831 DOI: 10.3390/md16070244] [Citation(s) in RCA: 156] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 07/17/2018] [Accepted: 07/19/2018] [Indexed: 02/07/2023] Open
Abstract
Genomic data often highlights an inconsistency between the number of gene clusters identified using bioinformatic approaches as potentially producing secondary metabolites and the actual number of chemically characterized secondary metabolites produced by any given microorganism. Such gene clusters are generally considered as “silent”, meaning that they are not expressed under laboratory conditions. Triggering expression of these “silent” clusters could result in unlocking the chemical diversity they control, allowing the discovery of novel molecules of both medical and biotechnological interest. Therefore, both genetic and cultivation-based techniques have been developed aimed at stimulating expression of these “silent” genes. The principles behind the cultivation based approaches have been conceptualized in the “one strain many compounds” (OSMAC) framework, which underlines how a single strain can produce different molecules when grown under different environmental conditions. Parameters such as, nutrient content, temperature, and rate of aeration can be easily changed, altering the global physiology of a microbial strain and in turn significantly affecting its secondary metabolism. As a direct extension of such approaches, co-cultivation strategies and the addition of chemical elicitors have also been used as cues to activate “silent” clusters. In this review, we aim to provide a focused and comprehensive overview of these strategies as they pertain to marine microbes. Moreover, we underline how changes in some parameters which have provided important results in terrestrial microbes, but which have rarely been considered in marine microorganisms, may represent additional strategies to awaken “silent” gene clusters in marine microbes. Unfortunately, the empirical nature of the OSMAC approach forces scientists to perform extensive laboratory experiments. Nevertheless, we believe that some computation and experimental based techniques which are used in other disciplines, and which we discuss; could be effectively employed to help streamline the OSMAC based approaches. We believe that natural products discovery in marine microorganisms would be greatly aided through the integration of basic microbiological approaches, computational methods, and technological innovations, thereby helping unearth much of the as yet untapped potential of these microorganisms.
Collapse
|
47
|
Symbiotic Microbes from Marine Invertebrates: Driving a New Era of Natural Product Drug Discovery. DIVERSITY-BASEL 2017. [DOI: 10.3390/d9040049] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
|