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Diversity and Biotechnological Potential of Marine Microorganisms

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A special issue of Journal of Marine Science and Engineering (ISSN 2077-1312). This special issue belongs to the section "Marine Biology".

Deadline for manuscript submissions: closed (30 July 2020) | Viewed by 34507

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Special Issue Editors

Dr. Yanis Caro

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Laboratory of Chemistry of Natural Substances and Food Sciences (LCSNSA), University of Reunion, F-97490 Sainte-Clotilde, Reunion Island, France
Interests: fermentation; industrial biotechnology; marine fungi; fungal pigments; anthraquinones; chemistry of lipids; biodiesel
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Dr. Juliana Lebeau

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Guest Editor

Laboratory of Chemistry of Natural Substances and Food Sciences (LCSNSA), University of Reunion, F-97490 Sainte-Clotilde, Reunion Island, France
Interests: fermentation biotechnology; cell cultures; gene expression; genetic engineering; biotechnology; marine fungi; pigments

Prof. Dr. Thomas Petit

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Guest Editor

Laboratory of Chemistry of Natural Substances and Food Sciences (LCSNSA), University of Reunion, F-97490 Sainte-Clotilde, Reunion Island, France
Interests: food and environmental microbiology; industrial biotechnology; yeast and fungi; fermentation

Special Issue Information

Dear Colleagues,

Marine microorganisms make up more than 90% of the sea biomass. This microflora constituted by bacteria, archaea, fungi, and viruses remains largely unexplored. The extent of marine microbial diversity has not been clearly established, but it is estimated that some 91% of species remain to be discovered. The habitat of these marine microorganisms is extremely diverse such as polar ice, deep sea, tropical sea, coral reef, marine sediments, mangroves, etc. The harsh chemical and physical conditions of the ocean have favored the production of unique bioactive compounds that differ from terrestrial microorganisms. Some of these metabolites may find biotechnological applications in different areas, including agri-horticulture, functional foods, cosmetics, nutraceuticals, and pharmaceuticals. These must be developed together with the discovery of new cultivation methods, advancements in molecular biology tools, and the implementation of sequencing programs that will help in disclosing the huge potential of these marine microorganisms.

This Special Issue welcomes scientific contributions on the following topics:

findings in marine microbial biodiversity (the identification of new marine fungal, bacterial, or microalgae species);
innovative approaches in cultivation methods;
advances in biotechnological applications of marine microbial derived products (i) such as microbial lipids, fatty acids, pigments, aromas, phenolic compounds, polysaccharides, and enzymes for food technology, and (ii) marine-derived bioactive molecules like alkaloids, terpenoids, cyclopeptides, and lactones with great potential in nutraceuticals, cosmeceuticals, or pharmaceuticals;
and genetically applied research including metagenomics, proteomics, combinatorial biosynthesis, expression systems, and bioinformatics.

Dr. Yanis Caro
Dr. Juliana Lebeau
Prof. Thomas Petit
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Journal of Marine Science and Engineering is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

marine biodiversity
marine microorganisms
marine bacteria
marine fungi
marine viruses
microalgae
microbial symbionts
marine biotechnology
marine natural products
bioactive compounds
antitumor compounds
pigments
flavors
antimicrobials

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Published Papers (7 papers)

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Research

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19 pages, 3284 KiB

Open AccessArticle

Marine Sediment-Derived Streptomyces Strain Produces Angucycline Antibiotics against Multidrug-Resistant Staphylococcus aureus Harboring SCCmec Type 1 Gene

by Edna M. Sabido, Chuckcris P. Tenebro, Angelica Faith L. Suarez, Sarah Diane C. Ong, Dana Joanne Von L. Trono, Diana S. Amago, Jose E. Evangelista, Jr., Ann Marielle Q. Reynoso, Ivy Grace M. Villalobos, Luigi Dan D. Alit, Cherryl F. Surigao, Christelle A. Villanueva, Jonel P. Saludes and Doralyn S. Dalisay

J. Mar. Sci. Eng. 2020, 8(10), 734; https://doi.org/10.3390/jmse8100734 - 23 Sep 2020

Cited by 15 | Viewed by 8165

Abstract

The Philippine archipelago is geographically positioned in the tropics with rich areas of marine biodiversity. Its marine sediments harbor actinomycetes that exhibit antibacterial activity. Screening of actinomycetes isolated from marine sediments collected near the coast of Islas de Gigantes, Iloilo showed one isolate that exhibited high activity against the multidrug-resistant Staphylococcus aureus (MRSA) strain carrying the Staphylococcal Cassette Chromosome mec (SCCmec) type 1 gene, a biomarker for drug resistance. The isolate was identified as Streptomyces sp. strain DSD011 based on its 16s rRNA and protein-coding genes (atpD, recA, rpoB, and trpB) sequences, and was found to be a new species of salt-tolerant marine Streptomyces. Further, the strain harbors both non-ribosomal peptide synthetase (NRPS) and type II polyketide synthase (PKS) in its genome. The targeted chromatographic isolation and chemical investigations by Liquid Chromatography Mass Spectrometry-Time of Flight (LCMS-TOF), tandem mass spectrometry (MS/MS), and Global Natural Product Social molecular networking (GNPS) of the antibiotics produced by the strain afforded the two polycyclic aromatic polyketide angucycline glycosides, fridamycin A (1) and fridamycin D (2), which are products of type II PKS biosynthesis. Compounds 1 and 2 displayed antibacterial activity against MRSA with minimum inhibitory concentration (MIC) of 500 μg/mL and 62.5 μg/mL, respectively. These results suggest that the underexplored marine sediments near the coast of Islas de Gigantes, Iloilo offer access to undiscovered Streptomyces species that are invaluable sources of antibiotic leads. Full article

(This article belongs to the Special Issue Diversity and Biotechnological Potential of Marine Microorganisms)

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16 pages, 2528 KiB

Open AccessArticle

The Marine Sponge Petrosia ficiformis Harbors Different Cyanobacteria Strains with Potential Biotechnological Application

by Patrizia Pagliara, Amilcare Barca, Tiziano Verri and Carmela Caroppo

J. Mar. Sci. Eng. 2020, 8(9), 638; https://doi.org/10.3390/jmse8090638 - 20 Aug 2020

Cited by 11 | Viewed by 3024

Abstract

Marine cyanobacteria are a source of bioactive natural compounds, with a wide range of biotechnological applications. However, information on sponge-associated cyanobacteria are relatively scarce to date. In this paper, we carried out the morphological and molecular characterization of eight cyanobacterial strains, previously isolated from the Mediterranean sponge Petrosia ficiformis, and evaluated their biological activities on epithelial- and neuron-like cultured cells of human and murine origin. The new analysis allowed maintaining the assignment of three strains (Cyanobium sp., Leptolyngbya ectocarpi, and Synechococcus sp.), while two strains previously identified as Synechococcus sp. and Leptolyngbya sp. were assigned to Pseudanabaena spp. One strain, i.e., ITAC104, and the ITAC101 strain corresponding to Halomicronema metazoicum, shared extremely high sequence identity, practically representing two clones of the same species. Finally, for only one strain, i.e., ITAC105, assignment to a specific genus was not possible. Concerning bioactivity analyses, incubation of cyanobacterial aqueous cell supernatants induced variable responses in cultured cells, depending on cell type, with some of them showing toxic activity on human epithelial-like cells and no toxic effects on human and rat neuron-like cells. Future investigations will allow to better define the bioactive properties of these cyanobacteria strains and to understand if they can be useful for (a) therapeutic purpose(s). Full article

(This article belongs to the Special Issue Diversity and Biotechnological Potential of Marine Microorganisms)

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26 pages, 7971 KiB

Open AccessFeature PaperArticle

Effects of Antibiotics on the Bacterial Community, Metabolic Functions and Antibiotic Resistance Genes in Mariculture Sediments during Enrichment Culturing

by Meng-Qi Ye, Guan-Jun Chen and Zong-Jun Du

J. Mar. Sci. Eng. 2020, 8(8), 604; https://doi.org/10.3390/jmse8080604 - 13 Aug 2020

Cited by 5 | Viewed by 2783

Abstract

The effect of antibiotics on the diversity and functioning of indigenous microorganisms in the environment has attracted much attention. In this study, effects of exposure to six different antibiotics on the bacterial community, metabolic functions and antibiotic resistance genes (ARGs) in marine sediments during enrichment culturing were investigated. Classical culture-dependent method and high-throughput 16S rRNA gene sequencing method were both applied. In the culture-dependent analysis, the obtained 1549 isolates belonged to four phyla (Proteobacteria, Firmicutes, Bacteroidetes and Actinobacteria) and 155 genera. Proteobacteria and Firmicutes were the dominant phyla. The diversity and abundance of obtained bacteria after antibiotic processing exhibited different degrees of decrease. Enrichment culturing for different time could also affect the bacterial community composition. Some genera of bacteria were not isolated in the control group, but they could be isolated in the antibiotic-treated groups. In high-throughput 16S rRNA gene amplicon sequencing analyses, all the effective reads were clustered into 2822 OTUs at 97% similarity cutoff; they were annotated to 49 phyla, 103 class, 220 orders, 347 families, 624 genera and 1122 species. An alpha diversity analysis indicated that the community diversity and richness decreased under antibiotic exposure. The changes at the genus level were much more obvious. Only 48 genera of 129 genera were shared by all the samples. A total of 29 genera which were not detected in the initial control sample could be detected in at least one antibiotic-treated group. SIMPER analysis showed that OTU2543 and OTU1450 were the most common taxa to the dissimilarity of bacterial community between antibiotic-treated groups and the control group. OTU2034 and OUT2543 were the most contributive taxa to dissimilarity of groups incubating for different time. Metabolism was the predominant bacterial function. A total of 30 ARGs were detected in the samples. This study mainly focused on the changes of microbiota under the selective pressure of antibiotics for different time and the results demonstrated that the antibiotic could affect the bacterial diversity and richness in the marine ecosystem. Full article

(This article belongs to the Special Issue Diversity and Biotechnological Potential of Marine Microorganisms)

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17 pages, 983 KiB

Open AccessArticle

Investigation of Growth, Lipid Productivity, and Fatty Acid Profiles in Marine Bloom-Forming Dinoflagellates as Potential Feedstock for Biodiesel

by Steven Jingliang Xu, Kam-Chau Wu, Sophie Cheuk-Yan Chan, Yiu-Hung Yau, Kin-Ka Chan and Fred Wang-Fat Lee

J. Mar. Sci. Eng. 2020, 8(6), 381; https://doi.org/10.3390/jmse8060381 - 26 May 2020

Cited by 10 | Viewed by 3577

Abstract

Microalgae-based biodiesel is increasingly recognized as an alternative to crop-based biodiesel. In this study, 10 local strains of dinoflagellates collected from Hong Kong waters, including a monoculture and field sample of Scrippsiella sp. isolated from an algal bloom, were evaluated against the performance of green alga Tetraselmis suecica. The specific growth rate, biomass production, lipid productivity, and fatty acid profile were investigated. The total lipid content of isolated strains ranged from 16.2% to 32.2% of the total dry biomass, whereas palmitic acid (C16:0) and docosahexaenoic acid (DHA, C22:6n3) were dominant in the fatty acid profile. Scrippsiella sp. has a high lipid productivity (47.3 mg/L/day) and fatty acid methyl esters (FAME) content (55.2–73 mg/g dry weight (dw)), which were comparable to that in green alga T. suecica. Further, monoculture and field sampled blooming Scrippsiella sp. showed no significant difference in most parameters, suggesting the possibility of harvesting a natural algal bloom population as a mitigation strategy to harmful algal bloom and to use as biodiesel feedstock. Overall, dinoflagellate species showed a slower growth rate (0.04–0.57 day⁻¹) than most compared species (0.07–1.34 day⁻¹), likely due to a large genome size and low chlorophyll to carbon ratio. Notably, most investigated dinoflagellates were not ideal for mass biodiesel production due to the low growth rate and lipid productivity. However, a high level of polyunsaturated fatty acids (PUFA) in dinoflagellates are prospective for further studies in other biotechnological applications. Though effectively harvesting algal blooming biomass can be complex, it can be further explored as a strategy for algal bloom mitigation and potentially creating values at the advantage of natural bloom when applying harvested biomass for biodiesel and bioactive compounds extraction. Full article

(This article belongs to the Special Issue Diversity and Biotechnological Potential of Marine Microorganisms)

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15 pages, 3008 KiB

Open AccessArticle

Changes in Bacterial Communities in Seawater-Flooded Soil in the Four Years After the 2011 Tohoku Tsunami in Japan

by Ryoki Asano, Atsushi Hayakawa, Jun Fukushima, Yutaka Nakai, Yoichiro Shimura, Midori Abe and Tamio Inamoto

J. Mar. Sci. Eng. 2020, 8(2), 76; https://doi.org/10.3390/jmse8020076 - 24 Jan 2020

Cited by 3 | Viewed by 2185

Abstract

The 2011 Tohoku tsunami had a serious impact, such as an increase in harmful substances and salinity over a large area. Herein, we evaluated transitions in bacterial communities in agricultural fields in the four years after the 2011 Tohoku tsunami. Bacterial communities were compared across four different types of soil—unflooded field (UF) soil, soil flooded for a short term (ST), soil flooded for the long term (LT), soil flooded long term and cultivated fields (LTC), and marine environmental materials (bay sediment, sea sand and sea water), using a polymerase chain reaction (PCR) and pyrosequencing of 16S ribosomal RNA genes. In the soil bacterial communities that were flooded by the 2011 Tohoku tsunami, these effects were not seen after 2013. Although the difference in bacterial communities between LT and UF became smaller during the four years, the bacterial communities in LT were different from those in UF in several ways, such as a higher tendency frequency of sulfur-oxidizing bacteria (SOB) and the presence of halotolerant SOB. Therefore, it is thought that the Tohoku tsunami affected the microbial communities in the soil for more than four years. Especially genus Halothiobacillus, which is Halotolerant SOB in flooded soils, was detected neither in unflooded soil nor in the marine environment. Therefore, it is thought that inundation by a tsunami produces a unique environment with bacterial communities to form in soil. Further, SOB structure, especially halotolerant, might serve as a good indicators of the impacts of inundation on bacterial communities in agricultural fields over the long term. Full article

(This article belongs to the Special Issue Diversity and Biotechnological Potential of Marine Microorganisms)

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Review

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47 pages, 4048 KiB

Open AccessReview

Novel Insights into the Biotechnological Production of Haematococcus pluvialis-Derived Astaxanthin: Advances and Key Challenges to Allow Its Industrial Use as Novel Food Ingredient

by Samuel Jannel, Yanis Caro, Marc Bermudes and Thomas Petit

J. Mar. Sci. Eng. 2020, 8(10), 789; https://doi.org/10.3390/jmse8100789 - 10 Oct 2020

Cited by 80 | Viewed by 9251

Abstract

Astaxanthin shows many biological activities. It has acquired a high economic potential and its current market is dominated by its synthetic form. However, due to the increase of the health and environmental concerns from consumers, natural forms are now preferred for human consumption. Haematococcus pluvialis is artificially cultured at an industrial scale to produce astaxanthin used as a dietary supplement. However, due to the high cost of its cultivation and its relatively low biomass and pigment productivities, the astaxanthin extracted from this microalga remains expensive and this has probably the consequence of slowing down its economic development in the lower added-value market such as food ingredient. In this review, we first aim to provide an overview of the chemical and biochemical properties of astaxanthin, as well as of its natural sources. We discuss its bioavailability, metabolism, and biological activities. We present a state-of-the-art of the biology and physiology of H. pluvialis, and highlight novel insights into the biotechnological processes which allow optimizing the biomass and astaxanthin productivities. We are trying to identify some lines of research that would improve the industrial sustainability and economic viability of this bio-production and to broaden the commercial potential of astaxanthin produced from H. pluvialis. Full article

(This article belongs to the Special Issue Diversity and Biotechnological Potential of Marine Microorganisms)

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20 pages, 828 KiB

Open AccessReview

The Nagoya Protocol and Its Implications on the EU Atlantic Area Countries

by Joana Martins, Diogo Cruz and Vitor Vasconcelos

J. Mar. Sci. Eng. 2020, 8(2), 92; https://doi.org/10.3390/jmse8020092 - 3 Feb 2020

Cited by 9 | Viewed by 4655

Abstract

The Nagoya Protocol on Access to Genetic Resources and Fair and Equitable Sharing of Benefits Arising from their Utilization came into force in October 2014. In the European Union (EU), new legislation had to be developed in order to apply the mandatory elements of the Protocol, namely, the Regulation (EU) Nº 511/2014 (ABS Regulation) and the Implementing Regulation (EU) 2015/1866, laying down detailed rules for the implementation of Regulation ABS with regard to the register of collection, monitor user compliance, and best practices. As a consequence, EU countries had to develop their own legislation in order to implement the Nagoya Protocol (NP), as well as the EU regulations. One important fact that distinguishes the national legislation of the EU countries is that some countries choose to control access to genetic resources (GR), while others do not apply access measures. The Atlantic Area countries in the EU share an attractive coastline with regard to the potential of their GR. In addition, the microalgae industry has been identified as a business sector with high potential. Therefore, it is important for GR users to be informed about the existing regulations and the national differences that may occur within EU countries. In this article, the origins and main content of the Nagoya Protocol are described, together with their implications at the EU level and particularly in the countries of the Atlantic Area region. As a result, a decision framework is proposed in order to support the GR users among this region. Full article

(This article belongs to the Special Issue Diversity and Biotechnological Potential of Marine Microorganisms)

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