Special Issue "Marine Metabolomics"

A special issue of Metabolites (ISSN 2218-1989).

Deadline for manuscript submissions: closed (30 April 2017)

Special Issue Editor

Guest Editor
Dr. RuAngelie Edrada-Ebel

Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, The John Arbuthnott Building, 161 Cathedral Street, Glasgow G4 0RE, UK
Website | E-Mail
Fax: +44 141 552 2562
Interests: natural products; drug discovery; NMR spectroscopy; metabolomics

Special Issue Information

Dear Colleagues,

Metabolomics was instigated by the concepts of metabolic profiling. Metabolic profiling found its application in plant science between the late 80s and early 90s by utilising hyphenated chromatography with UV spectroscopy, mass spectrometry, and later with NMR spectroscopy targeting relevant metabolites for agricultural projects and improve food production. In the late 90s and the following decades thereafter, metabolic profiling transpired to play a central role in plant functional genomics which then evolved to be a new “omics” platform technology now known as metabolomics. With the developments in computing and data processing, it was then possible to conduct an untargeted analysis of all the metabolites.  To date, metabolomics is rapidly turning out to be the leading "omics" platform for systems biology as evidenced by almost equal ratio of the number of papers published in metabolomics alone to those published under the field of genomics, metagenomics, proteomics, transcriptomics, and lipidomics all together.  The "omics" platform has found its application in different fields of study, from biomedical analysis to plant science but only very recently in marine research with an abrupt increase in the number of publications in this field only occurring in the last three years. However, taking into consideration the number of marine metabolomics papers in comparison to the number of papers published for the "omics" platform, the ratio is quite low at approximately only 15% of entire "omics" publication in the field of marine metabolomics.

Metabolic profiling in marine research started with the introduction of photo-diode arrays along with HRFTMS detectors combined with high-performance liquid chromatography which enhanced dereplication work. By the beginning of the millennium, high-throughput sequencing was emerging and there was a shift from pure genetic research to procurement of gene function and expression. This issue will cover applications in marine ecology, biotechnology, and bioprospecting.

Dr. RuAngelie Edrada-Ebel
Guest Editor

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 papers will be 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. Metabolites is an international peer-reviewed open access quarterly 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 850 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

  • ecology
  • biotechnology
  • bioprospecting
  • dereplication
  • metabolomics profiling

Published Papers (7 papers)

View options order results:
result details:
Displaying articles 1-7
Export citation of selected articles as:

Research

Jump to: Review

Open AccessArticle The Effect of Season on the Metabolic Profile of the European Clam Ruditapes decussatus as Studied by 1H-NMR Spectroscopy
Metabolites 2017, 7(3), 36; doi:10.3390/metabo7030036
Received: 12 June 2017 / Revised: 11 July 2017 / Accepted: 24 July 2017 / Published: 26 July 2017
PDF Full-text (3383 KB) | HTML Full-text | XML Full-text
Abstract
In this study, the metabolome of Ruditapes decussatus, an economically and ecologically important marine bivalve species widely distributed in the Mediterranean region, was characterized by using proton Nuclear Magnetic Resonance (1H-NMR) spectroscopy. Significant seasonal variations in the content of carbohydrates and
[...] Read more.
In this study, the metabolome of Ruditapes decussatus, an economically and ecologically important marine bivalve species widely distributed in the Mediterranean region, was characterized by using proton Nuclear Magnetic Resonance (1H-NMR) spectroscopy. Significant seasonal variations in the content of carbohydrates and free amino acids were observed. The relative amounts of alanine and glycine were found to exhibit the same seasonal pattern as the temperature and salinity at the harvesting site. Several putative sex-specific biomarkers were also discovered. Substantial differences were found for alanine and glycine, whose relative amounts were higher in males, while acetoacetate, choline and phosphocholine were more abundant in female clams. These findings reveal novel insights into the baseline metabolism of the European clam and represent a step forward towards a comprehensive metabolic characterization of the species. Besides providing a holistic view on the prominent nutritional components, the characterization of the metabolome of this bivalve represents an important prerequisite for elucidating the underlying metabolic pathways behind the environment-organism interactions. Full article
(This article belongs to the Special Issue Marine Metabolomics)
Figures

Figure 1

Open AccessArticle Natural Product Discovery Using Planes of Principal Component Analysis in R (PoPCAR)
Metabolites 2017, 7(3), 34; doi:10.3390/metabo7030034
Received: 30 April 2017 / Revised: 20 June 2017 / Accepted: 11 July 2017 / Published: 13 July 2017
PDF Full-text (2771 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Rediscovery of known natural products hinders the discovery of new, unique scaffolds. Efforts have mostly focused on streamlining the determination of what compounds are known vs. unknown (dereplication), but an alternative strategy is to focus on what is different. Utilizing statistics and assuming
[...] Read more.
Rediscovery of known natural products hinders the discovery of new, unique scaffolds. Efforts have mostly focused on streamlining the determination of what compounds are known vs. unknown (dereplication), but an alternative strategy is to focus on what is different. Utilizing statistics and assuming that common actinobacterial metabolites are likely known, focus can be shifted away from dereplication and towards discovery. LC-MS-based principal component analysis (PCA) provides a perfect tool to distinguish unique vs. common metabolites, but the variability inherent within natural products leads to datasets that do not fit ideal standards. To simplify the analysis of PCA models, we developed a script that identifies only those masses or molecules that are unique to each strain within a group, thereby greatly reducing the number of data points to be inspected manually. Since the script is written in R, it facilitates integration with other metabolomics workflows and supports automated mass matching to databases such as Antibase. Full article
(This article belongs to the Special Issue Marine Metabolomics)
Figures

Figure 1

Open AccessArticle NMR Profiling of Metabolites in Larval and Juvenile Blue Mussels (Mytilus edulis) under Ambient and Low Salinity Conditions
Metabolites 2017, 7(3), 33; doi:10.3390/metabo7030033
Received: 29 April 2017 / Revised: 12 June 2017 / Accepted: 3 July 2017 / Published: 6 July 2017
PDF Full-text (1673 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Blue mussels (Mytilus edulis) are ecologically and economically important marine invertebrates whose populations are at risk from climate change-associated variation in their environment, such as decreased coastal salinity. Blue mussels are osmoconfomers and use components of the metabolome (free amino acids)
[...] Read more.
Blue mussels (Mytilus edulis) are ecologically and economically important marine invertebrates whose populations are at risk from climate change-associated variation in their environment, such as decreased coastal salinity. Blue mussels are osmoconfomers and use components of the metabolome (free amino acids) to help maintain osmotic balance and cellular function during low salinity exposure. However, little is known about the capacity of blue mussels during the planktonic larval stages to regulate metabolites during osmotic stress. Metabolite studies in species such as blue mussels can help improve our understanding of the species’ physiology, as well as their capacity to respond to environmental stress. We used 1D 1H nuclear magnetic resonance (NMR) and 2D total correlation spectroscopy (TOCSY) experiments to describe baseline metabolite pools in larval (veliger and pediveliger stages) and juvenile blue mussels (gill, mantle, and adductor tissues) under ambient conditions and to quantify changes in the abundance of common osmolytes in these stages during low salinity exposure. We found evidence for stage- and tissue-specific differences in the baseline metabolic profiles of blue mussels, which reflect variation in the function and morphology of each larval stage or tissue type of juveniles. These differences impacted the utilization of osmolytes during low salinity exposure, likely stemming from innate physiological variation. This study highlights the importance of foundational metabolomic studies that include multiple tissue types and developmental stages to adequately evaluate organismal responses to stress and better place these findings in a broader physiological context. Full article
(This article belongs to the Special Issue Marine Metabolomics)
Figures

Figure 1

Open AccessArticle Furanoterpene Diversity and Variability in the Marine Sponge Spongia officinalis, from Untargeted LC–MS/MS Metabolomic Profiling to Furanolactam Derivatives
Metabolites 2017, 7(2), 27; doi:10.3390/metabo7020027
Received: 14 April 2017 / Revised: 23 May 2017 / Accepted: 6 June 2017 / Published: 13 June 2017
PDF Full-text (5398 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
The Mediterranean marine sponge Spongia officinalis has been reported as a rich source of secondary metabolites and also as a bioindicator of water quality given its capacity to concentrate trace metals. In this study, we evaluated the chemical diversity within 30 S. officinalis
[...] Read more.
The Mediterranean marine sponge Spongia officinalis has been reported as a rich source of secondary metabolites and also as a bioindicator of water quality given its capacity to concentrate trace metals. In this study, we evaluated the chemical diversity within 30 S. officinalis samples collected over three years at two sites differentially impacted by anthropogenic pollutants located near Marseille (South of France). Untargeted liquid chromatography—mass spectrometry (LC–MS) metabolomic profiling (C18 LC, ESI-Q-TOF MS) combined with XCMS Online data processing and multivariate statistical analysis revealed 297 peaks assigned to at least 86 compounds. The spatio-temporal metabolite variability was mainly attributed to variations in relative content of furanoterpene derivatives. This family was further characterized through LC–MS/MS analyses in positive and negative ion modes combined with molecular networking, together with a comprehensive NMR study of isolated representatives such as demethylfurospongin-4 and furospongin-1. The MS/MS and NMR spectroscopic data led to the identification of a new furanosesterterpene, furofficin (2), as well as two derivatives with a glycinyl lactam moiety, spongialactam A (12a) and B (12b). This study illustrates the potential of untargeted LC–MS metabolomics and molecular networking to discover new natural compounds even in an extensively studied organism such as S. officinalis. It also highlights the effect of anthropogenic pollution on the chemical profiles within the sponge. Full article
(This article belongs to the Special Issue Marine Metabolomics)
Figures

Figure 1

Open AccessArticle Visualization of Microfloral Metabolism for Marine Waste Recycling
Metabolites 2016, 6(1), 7; doi:10.3390/metabo6010007
Received: 30 September 2015 / Revised: 16 December 2015 / Accepted: 21 January 2016 / Published: 27 January 2016
Cited by 2 | PDF Full-text (1909 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Marine biomass including fishery products are precious protein resources for human foods and are an alternative to livestock animals in order to reduce the virtual water problem. However, a large amount of marine waste can be generated from fishery products and it is
[...] Read more.
Marine biomass including fishery products are precious protein resources for human foods and are an alternative to livestock animals in order to reduce the virtual water problem. However, a large amount of marine waste can be generated from fishery products and it is not currently recycled. We evaluated the metabolism of digested marine waste using integrated analytical methods, under anaerobic conditions and the fertilization of abandoned agricultural soils. Dynamics of fish waste digestion revealed that samples of meat and bony parts had similar dynamics under anaerobic conditions in spite of large chemical variations in input marine wastes. Abandoned agricultural soils fertilized with fish waste accumulated some amino acids derived from fish waste, and accumulation of l-arginine and l-glutamine were higher in plant seedlings. Therefore, we have proposed an analytical method to visualize metabolic dynamics for recycling of fishery waste processes. Full article
(This article belongs to the Special Issue Marine Metabolomics)
Figures

Open AccessArticle Using Molecular Networking for Microbial Secondary Metabolite Bioprospecting
Metabolites 2016, 6(1), 2; doi:10.3390/metabo6010002
Received: 23 September 2015 / Revised: 23 December 2015 / Accepted: 30 December 2015 / Published: 8 January 2016
Cited by 4 | PDF Full-text (2704 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
The oceans represent an understudied resource for the isolation of bacteria with the potential to produce novel secondary metabolites. In particular, actinomyces are well known to produce chemically diverse metabolites with a wide range of biological activities. This study characterised spore-forming bacteria from
[...] Read more.
The oceans represent an understudied resource for the isolation of bacteria with the potential to produce novel secondary metabolites. In particular, actinomyces are well known to produce chemically diverse metabolites with a wide range of biological activities. This study characterised spore-forming bacteria from both Scottish and Antarctic sediments to assess the influence of isolation location on secondary metabolite production. Due to the selective isolation method used, all 85 isolates belonged to the phyla Firmicutes and Actinobacteria, with the majority of isolates belonging to the genera Bacillus and Streptomyces. Based on morphology, thirty-eight isolates were chosen for chemical investigation. Molecular networking based on chemical profiles (HR-MS/MS) of fermentation extracts was used to compare complex metabolite extracts. The results revealed 40% and 42% of parent ions were produced by Antarctic and Scottish isolated bacteria, respectively, and only 8% of networked metabolites were shared between these locations, implying a high degree of biogeographic influence upon secondary metabolite production. The resulting molecular network contained over 3500 parent ions with a mass range of m/z 149–2558 illustrating the wealth of metabolites produced. Furthermore, seven fermentation extracts showed bioactivity against epithelial colon adenocarcinoma cells, demonstrating the potential for the discovery of novel bioactive compounds from these understudied locations. Full article
(This article belongs to the Special Issue Marine Metabolomics)

Review

Jump to: Research

Open AccessReview Volatile Metabolites Emission by In Vivo Microalgae—An Overlooked Opportunity?
Metabolites 2017, 7(3), 39; doi:10.3390/metabo7030039
Received: 28 April 2017 / Revised: 19 July 2017 / Accepted: 25 July 2017 / Published: 31 July 2017
PDF Full-text (9505 KB) | HTML Full-text | XML Full-text
Abstract
Fragrances and malodors are ubiquitous in the environment, arising from natural and artificial processes, by the generation of volatile organic compounds (VOCs). Although VOCs constitute only a fraction of the metabolites produced by an organism, the detection of VOCs has a broad range
[...] Read more.
Fragrances and malodors are ubiquitous in the environment, arising from natural and artificial processes, by the generation of volatile organic compounds (VOCs). Although VOCs constitute only a fraction of the metabolites produced by an organism, the detection of VOCs has a broad range of civilian, industrial, military, medical, and national security applications. The VOC metabolic profile of an organism has been referred to as its ‘volatilome’ (or ‘volatome’) and the study of volatilome/volatome is characterized as ‘volatilomics’, a relatively new category in the ‘omics’ arena. There is considerable literature on VOCs extracted destructively from microalgae for applications such as food, natural products chemistry, and biofuels. VOC emissions from living (in vivo) microalgae too are being increasingly appreciated as potential real-time indicators of the organism’s state of health (SoH) along with their contributions to the environment and ecology. This review summarizes VOC emissions from in vivo microalgae; tools and techniques for the collection, storage, transport, detection, and pattern analysis of VOC emissions; linking certain VOCs to biosynthetic/metabolic pathways; and the role of VOCs in microalgae growth, infochemical activities, predator-prey interactions, and general SoH. Full article
(This article belongs to the Special Issue Marine Metabolomics)
Figures

Journal Contact

MDPI AG
Metabolites Editorial Office
St. Alban-Anlage 66, 4052 Basel, Switzerland
E-Mail: 
Tel. +41 61 683 77 34
Fax: +41 61 302 89 18
Editorial Board
Contact Details Submit to Metabolites Edit a special issue Review for Metabolites
logo
loading...
Back to Top