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Marine Microbial Diversity as a Source of Bioactive Natural Products

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A special issue of Marine Drugs (ISSN 1660-3397).

Deadline for manuscript submissions: closed (30 October 2019) | Viewed by 57599

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Dr. Didier Stien

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Sorbonne Université, CNRS, Laboratoire de Biodiversité et Biotechnologie Microbienne, USR3579, Observatoire Océanologique, 66650 Banyuls-sur-mer, France
Interests: natural products; metabolomics; chemical ecology; symbioses; toxicity and fate of emerging pollutants

Special Issue Information

Dear Colleagues,

The oceans and seas are the crucible of life on Earth. Living beings have evolved, adapted, and competed in these marine environments since the earliest times. From the poles to tropical lagoons, from the surface microlayer to the abyss, a large diversity of microenvironments has offered a broad range of niches for life to evolve. The consequence of these evolutionary processes are a multitude of very diverse and interwoven networks of species that use complex secondary metabolites to regulate their interactions. Marine ecosystems can therefore still be regarded as a potential, relatively underappreciated, source of unique active compounds that are yet to be discovered.

If some microorganisms can live freely in the water column, many others live in association. Sponges host microorganisms that contribute to their holometabolome, many coral species host microalgae and symbiotic prokaryotes, and many microorganisms participate in the development of interspecific biofilms covering biotic and abiotic surfaces, to name a few examples. Secondary metabolites from understudied interactions represent a novel source of compounds that by definition must be bioactive. Advances in microbial diversity analysis, natural product chemistry, metabolomics, or metabolic engineering now provide access to an unknown dimension of chemodiversity, and will allow the production of these compounds in amounts necessary for pharmaceutical development.

This Special Issue entitled “Marine Microbial Diversity as a Source of Bioactive Natural Products” focuses on the importance of the study of metabolites originating from the microbial biodiversity of marine environments, understanding the physiological and ecological roles of these microbial metabolites and their putative bioactivities, as well as the advances on the understanding and use of biosynthetic routes to guide and accelerate product development.

We plan to produce a very exciting issue that will encompass recent advances in the field (e.g., marine microbial diversity and ecology; metabolomic investigation of marine microorganisms; isolation and identification of bioactive compounds; the chemical ecology of marine microorganisms; biotechnological production of marine natural products). We look forward very much to your input.

Dr. Didier Stien
Guest Editor

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Keywords

marine microorganisms
microbial diversity
metabolomics
chemodiversity
bioactive natural products
chemical ecology
symbioses
marine and extreme environments
blue growth
marine biotechnologies

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Published Papers (11 papers)

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Editorial

Jump to: Research, Review

5 pages, 774 KiB

Open AccessEditorial

Marine Microbial Diversity as a Source of Bioactive Natural Products

by Didier Stien

Mar. Drugs 2020, 18(4), 215; https://doi.org/10.3390/md18040215 - 16 Apr 2020

Cited by 18 | Viewed by 3680

Abstract

Some 3 [...] Full article

(This article belongs to the Special Issue Marine Microbial Diversity as a Source of Bioactive Natural Products)

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Research

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15 pages, 2949 KiB

Open AccessArticle

Metabolomic Insights into Marine Phytoplankton Diversity

by Rémy Marcellin-Gros, Gwenaël Piganeau and Didier Stien

Mar. Drugs 2020, 18(2), 78; https://doi.org/10.3390/md18020078 - 25 Jan 2020

Cited by 18 | Viewed by 4356

Abstract

The democratization of sequencing technologies fostered a leap in our knowledge of the diversity of marine phytoplanktonic microalgae, revealing many previously unknown species and lineages. The evolutionary history of the diversification of microalgae can be inferred from the analysis of their genome sequences. However, the link between the DNA sequence and the associated phenotype is notoriously difficult to assess, all the more so for marine phytoplanktonic microalgae for which the lab culture and, thus, biological experimentation is very tedious. Here, we explore the potential of a high-throughput untargeted metabolomic approach to explore the phenotypic–genotypic gap in 12 marine microalgae encompassing 1.2 billion years of evolution. We identified species- and lineage-specific metabolites. We also provide evidence of a very good correlation between the molecular divergence, inferred from the DNA sequences, and the metabolomic divergence, inferred from the complete metabolomic profiles. These results provide novel insights into the potential of chemotaxonomy in marine phytoplankton and support the hypothesis of a metabolomic clock, suggesting that DNA and metabolomic profiles co-evolve. Full article

(This article belongs to the Special Issue Marine Microbial Diversity as a Source of Bioactive Natural Products)

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26 pages, 2625 KiB

Open AccessArticle

Fungal Diversity in Intertidal Mudflats and Abandoned Solar Salterns as a Source for Biological Resources

by Young Mok Heo, Hanbyul Lee, Kyeongwon Kim, Sun Lul Kwon, Min Young Park, Ji Eun Kang, Gyu-Hyeok Kim, Beom Seok Kim and Jae-Jin Kim

Mar. Drugs 2019, 17(11), 601; https://doi.org/10.3390/md17110601 - 23 Oct 2019

Cited by 21 | Viewed by 5119

Abstract

Intertidal zones are unique environments that are known to be ecological hot spots. In this study, sediments were collected from mudflats and decommissioned salterns on three islands in the Yellow Sea of South Korea. The diversity analysis targeted both isolates and unculturable fungi via Illumina sequencing, and the natural recovery of the abandoned salterns was assessed. The phylogeny and bioactivities of the fungal isolates were investigated. The community analysis showed that the abandoned saltern in Yongyudo has not recovered to a mudflat, while the other salterns have almost recovered. The results suggested that a period of more than 35 years may be required to return abandoned salterns to mudflats via natural restoration. Gigasporales sp. and Umbelopsis sp. were selected as the indicators of mudflats. Among the 53 isolates, 18 appeared to be candidate novel species, and 28 exhibited bioactivity. Phoma sp., Cladosporium sphaerospermum, Penicillium sp. and Pseudeurotium bakeri, and Aspergillus urmiensis showed antioxidant, tyrosinase inhibition, antifungal, and quorum-sensing inhibition activities, respectively, which has not been reported previously. This study provides reliable fungal diversity information for mudflats and abandoned salterns and shows that they are highly valuable for bioprospecting not only for novel microorganisms but also for novel bioactive compounds. Full article

(This article belongs to the Special Issue Marine Microbial Diversity as a Source of Bioactive Natural Products)

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11 pages, 1968 KiB

Open AccessArticle

Discovery of Bioactive Indole-Diketopiperazines from the Marine-Derived Fungus Penicillium brasilianum Aided by Genomic Information

by Ya-Hui Zhang, Ce Geng, Xing-Wang Zhang, Hua-Jie Zhu, Chang-Lun Shao, Fei Cao and Chang-Yun Wang

Mar. Drugs 2019, 17(9), 514; https://doi.org/10.3390/md17090514 - 1 Sep 2019

Cited by 24 | Viewed by 4676

Abstract

Identification and analysis of the whole genome of the marine-derived fungus Penicillium brasilianum HBU-136 revealed the presence of an interesting biosynthetic gene cluster (BGC) for non-ribosomal peptide synthetases (NRPS), highly homologous to the BGCs of indole-diketopiperazine derivatives. With the aid of genomic analysis, eight indole-diketopiperazines (1−8), including three new compounds, spirotryprostatin G (1), and cyclotryprostatins F and G (2 and 3), were obtained by large-scale cultivation of the fungal strain HBU-136 using rice medium with 1.0% MgCl₂. The absolute configurations of 1−3 were determined by comparison of their experimental electronic circular dichroism (ECD) with calculated ECD spectra. Selective cytotoxicities were observed for compounds 1 and 4 against HL-60 cell line with the IC₅₀ values of 6.0 and 7.9 μM, respectively, whereas 2, 3, and 5 against MCF-7 cell line with the IC₅₀ values of 7.6, 10.8, and 5.1 μM, respectively. Full article

(This article belongs to the Special Issue Marine Microbial Diversity as a Source of Bioactive Natural Products)

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9 pages, 1492 KiB

Open AccessArticle

New Ophiobolin Derivatives from the Marine Fungus Aspergillus flocculosus and Their Cytotoxicities against Cancer Cells

by Byeoung-Kyu Choi, Phan Thi Hoai Trinh, Hwa-Sun Lee, Byeong-Woo Choi, Jong Soon Kang, Ngo Thi Duy Ngoc, Tran Thi Thanh Van and Hee Jae Shin

Mar. Drugs 2019, 17(6), 346; https://doi.org/10.3390/md17060346 - 11 Jun 2019

Cited by 36 | Viewed by 4884

Abstract

Five new sesterterpenes, 14,15-dehydro-6-epi-ophiobolin K (1), 14,15-dehydro- ophiobolin K (2), 14,15-dehydro-6-epi-ophiobolin G (3), 14,15-dehydro-ophiobolin G (4) and 14,15-dehydro-(Z)-14-ophiobolin G (5), together with four known ophiobolins (6–9) were isolated from the marine fungus Aspergillus flocculosus derived from the seaweed Padina sp. collected in Vietnam. The five new ophiobolins were first isolated as ophiobolin derivatives consisting of a fully unsaturated side chain. Their structures were elucidated via spectroscopic methods including 1D, 2D NMR and HR-ESIMS. The absolute configurations were determined by the comparison of chemical shifts and optical rotation values with those of known ophiobolins. All compounds (1–9) were then evaluated for their cytotoxicity against six cancer cell lines, HCT-15, NUGC-3, NCI-H23, ACHN, PC-3 and MDA-MB-231. All the compounds showed potent cytotoxicity with GI₅₀ values ranging from 0.14 to 2.01 μM. Full article

(This article belongs to the Special Issue Marine Microbial Diversity as a Source of Bioactive Natural Products)

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8 pages, 605 KiB

Open AccessArticle

Two New Spiro-Heterocyclic γ-Lactams from A Marine-Derived Aspergillus fumigatus Strain CUGBMF170049

by Xiuli Xu, Jiahui Han, Yanan Wang, Rui Lin, Haijin Yang, Jiangpeng Li, Shangzhu Wei, Steven W. Polyak and Fuhang Song

Mar. Drugs 2019, 17(5), 289; https://doi.org/10.3390/md17050289 - 14 May 2019

Cited by 13 | Viewed by 3365

Abstract

Two new spiro-heterocyclic γ-lactam derivatives, cephalimysins M (1) and N (2), were isolated from the fermentation cultures of the marine-derived fungus Aspergillus fumigatus CUGBMF17018. Two known analogues, pseurotin A (3) and FD-838 (4), as well as four previously reported helvolic acid derivatives, 16-O-propionyl-16-O-deacetylhelvolic acid (5), 6-O-propionyl-6-O-deacetylhelvolic acid (6), helvolic acid (7), and 1,2-dihydrohelvolic acid (8) were also identified. One-dimensional (1D), two-dimensional (2D) NMR, HRMS, and circular dichroism spectral analysis characterized the structures of the isolated compounds. Full article

(This article belongs to the Special Issue Marine Microbial Diversity as a Source of Bioactive Natural Products)

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9 pages, 1427 KiB

Open AccessArticle

Isolation, Identification of Carotenoid-Producing Rhodotorula sp. from Marine Environment and Optimization for Carotenoid Production

by Yanchen Zhao, Liyun Guo, Yu Xia, Xiyi Zhuang and Weihua Chu

Mar. Drugs 2019, 17(3), 161; https://doi.org/10.3390/md17030161 - 8 Mar 2019

Cited by 64 | Viewed by 8836

Abstract

Carotenoids are natural pigments found in plants and microorganisms. These important nutrients play significant roles in animal health. In contrast to plant production, the advantages of microbial fermentation of carotenoids are the lower media costs, fast growth rate of microorganisms, and the ease of culture condition control. In this study, a colony of red pigment-producing yeast, Rhodotorula sp. RY1801, was isolated from the sediment of marine environment with the potential to produce carotenoids. Optimization of carotenoid production in Rhodotorula sp. RY1801 was also discussed. The optimum conditions found for carotenoid production were as follows: temperature, 28 °C; pH 5.0; carbon source, 10 g/L glucose, nitrogen source, 10 g/L yeast extract, maximum concentration of 987 µg/L of total carotenoids was obtained. The results of this study show that the isolated yeast strain Rhodotorula sp. RY1801 can potentially be used in future as a promising microorganism for the commercial production of carotenoids. Full article

(This article belongs to the Special Issue Marine Microbial Diversity as a Source of Bioactive Natural Products)

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9 pages, 1302 KiB

Open AccessArticle

Four New Isocoumarins and a New Natural Tryptamine with Antifungal Activities from a Mangrove Endophytic Fungus Botryosphaeria ramosa L29

by Zhihui Wu, Jiaqing Chen, Xiaolin Zhang, Zelin Chen, Tong Li, Zhigang She, Weijia Ding and Chunyuan Li

Mar. Drugs 2019, 17(2), 88; https://doi.org/10.3390/md17020088 - 1 Feb 2019

Cited by 24 | Viewed by 3502

Abstract

Four new isocoumarin derivatives, botryospyrones A (1), B (2), C (3), and D (4), and a new natural tryptamine, (3aS, 8aS)-1-acetyl-1, 2, 3, 3a, 8, 8a-hexahydropyrrolo [2,3b] indol-3a-ol (5), were isolated from a marine mangrove endophytic fungus Botryosphaeria ramosa L29, obtained from the leaf of Myoporum bontioides. Their structures were elucidated using spectroscopic analysis. The absolute configurations of compounds 3, 4, and 5 were determined by comparison of their circular dichroism (CD) spectra with the calculated data. The inhibitory activities of compound 1 on Fusarium oxysporum, of compounds 2 and 3 on F. oxysporum and Fusarium graminearum, and of compound 5 on F. oxysporum, Penicillium italicum, and F. graminearum were higher than those of triadimefon, widely used as an agricultural fungicide. Compound 5 was produced after using the strategy we called “using inhibitory stress from components of the host” (UISCH), wherein (2R, 3R)-3, 5, 7-trihydroxyflavanone 3-acetate, a component of M. bontioides with weak growth inhibitory activity towards B. ramosa L29, was introduced into the culture medium. Full article

(This article belongs to the Special Issue Marine Microbial Diversity as a Source of Bioactive Natural Products)

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15 pages, 1350 KiB

Open AccessArticle

Diversity and Ecology of Marine Algicolous Arthrinium Species as a Source of Bioactive Natural Products

by Young Mok Heo, Kyeongwon Kim, Seung Mok Ryu, Sun Lul Kwon, Min Young Park, Ji Eun Kang, Joo-Hyun Hong, Young Woon Lim, Changmu Kim, Beom Seok Kim, Dongho Lee and Jae-Jin Kim

Mar. Drugs 2018, 16(12), 508; https://doi.org/10.3390/md16120508 - 14 Dec 2018

Cited by 25 | Viewed by 5270

Abstract

In our previous study, all Arthrinium isolates from Sargassum sp. showed high bioactivities, but studies on marine Arthrinium spp. are insufficient. In this study, a phylogenetic analysis of 28 Arthrinium isolates from seaweeds and egg masses of Arctoscopus japonicus was conducted using internal transcribed spacers, nuclear large subunit rDNA, β-tubulin, and translation elongation factor region sequences, and their bioactivities were investigated. They were analyzed as 15 species, and 11 of them were found to be new species. Most of the extracts exhibited radical-scavenging activity, and some showed antifungal activities, tyrosinase inhibition, and quorum sensing inhibition. It was implied that marine algicolous Arthrinium spp. support the regulation of reactive oxygen species in symbiotic algae and protect against pathogens and bacterial biofilm formation. The antioxidant from Arthrinium sp. 10 KUC21332 was separated by bioassay-guided isolation and identified to be gentisyl alcohol, and the antioxidant of Arthrinium saccharicola KUC21221 was identical. These results demonstrate that many unexploited Arthrinium species still exist in marine environments and that they are a great source of bioactive compounds. Full article

(This article belongs to the Special Issue Marine Microbial Diversity as a Source of Bioactive Natural Products)

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9 pages, 3780 KiB

Open AccessCommunication

Geospallins A–C: New Thiodiketopiperazines with Inhibitory Activity against Angiotensin-Converting Enzyme from a Deep-Sea-Derived Fungus Geosmithia pallida FS140

by Zhang-Hua Sun, Jiangyong Gu, Wei Ye, Liang-Xi Wen, Qi-Bin Lin, Sai-Ni Li, Yu-Chan Chen, Hao-Hua Li and Wei-Min Zhang

Mar. Drugs 2018, 16(12), 464; https://doi.org/10.3390/md16120464 - 23 Nov 2018

Cited by 14 | Viewed by 3227

Abstract

Three new thiodiketopiperazines, geospallins A–C (1–3), together with nine known analogues (4–12), were isolated from the culture of the deep-sea sediment-derived fungus Geosmithia pallida FS140. Among them, geospallins A and B (1 and 2) represent rare examples of thiodiketopiperazines featuring an S-methyl group at C-10 and a tertiary hydroxyl group at C-11. Their structures were determined by high-resolution electrospray mass spectrometry (HRESIMS), spectroscopic analyses, and electronic circular dichroism (ECD) calculations. Their angiotensin-converting enzyme (ACE) inhibitory activity was reported, and geospallins A–C (1–3) showed inhibitory activity with IC₅₀ values of 29–35 µM. Full article

(This article belongs to the Special Issue Marine Microbial Diversity as a Source of Bioactive Natural Products)

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Review

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20 pages, 5407 KiB

Open AccessFeature PaperReview

The Neglected Marine Fungi, Sensu stricto, and Their Isolation for Natural Products’ Discovery

by David P. Overy, Teppo Rämä, Rylee Oosterhuis, Allison K. Walker and Ka-Lai Pang

Mar. Drugs 2019, 17(1), 42; https://doi.org/10.3390/md17010042 - 10 Jan 2019

Cited by 54 | Viewed by 9612

Abstract

Despite the rapid development of molecular techniques relevant for natural product research, culture isolates remain the primary source from which natural products chemists discover and obtain new molecules from microbial sources. Techniques for obtaining and identifying microbial isolates (such as filamentous fungi) are thus of crucial importance for a successful natural products’ discovery program. This review is presented as a “best-practices guide” to the collection and isolation of marine fungi for natural products research. Many of these practices are proven techniques used by mycologists for the isolation of a broad diversity of fungi, while others, such as the construction of marine baiting stations and the collection and processing of sea foam using dilution to extinction plating techniques, are methodological adaptations for specialized use in marine/aquatic environments. To this day, marine fungi, Sensu stricto, remain one of the few underexplored resources of natural products. Cultivability is one of the main limitations hindering the discovery of natural products from marine fungi. Through encouraged collaboration with marine mycologists and the sharing of historically proven mycological practices for the isolation of marine fungi, our goal is to provide natural products chemists with the necessary tools to explore this resource in-depth and discover new and potentially novel natural products. Full article

(This article belongs to the Special Issue Marine Microbial Diversity as a Source of Bioactive Natural Products)

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