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Metabolites
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Marine Metabolomics
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Marine Metabolomics

A special issue of Metabolites (ISSN 2218-1989). This special issue belongs to the section "Environmental Metabolomics".

Deadline for manuscript submissions: closed (30 April 2017) | Viewed by 61488

Special Issue Editor

Dr. RuAngelie Edrada-Ebel

E-Mail Website
Guest Editor
Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, UK
Interests: marine natural products chemistry; secondary metabolomics; NMR- and MS-based metabolomics; marine biotechnology
Special Issues, Collections and Topics in MDPI journals

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

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Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 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

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Published Papers (7 papers)

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Research

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3383 KiB  
Article
The Effect of Season on the Metabolic Profile of the European Clam Ruditapes decussatus as Studied by 1H-NMR Spectroscopy
by Violetta Aru, Søren Balling Engelsen, Francesco Savorani, Jacopo Culurgioni, Giorgia Sarais, Giulia Atzori, Serenella Cabiddu and Flaminia Cesare Marincola
Metabolites 2017, 7(3), 36; https://doi.org/10.3390/metabo7030036 - 26 Jul 2017
Cited by 10 | Viewed by 4919
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)
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2771 KiB  
Article
Natural Product Discovery Using Planes of Principal Component Analysis in R (PoPCAR)
by Shaurya Chanana, Chris S. Thomas, Doug R. Braun, Yanpeng Hou, Thomas P. Wyche and Tim S. Bugni
Metabolites 2017, 7(3), 34; https://doi.org/10.3390/metabo7030034 - 13 Jul 2017
Cited by 25 | Viewed by 9565
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)
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1673 KiB  
Article
NMR Profiling of Metabolites in Larval and Juvenile Blue Mussels (Mytilus edulis) under Ambient and Low Salinity Conditions
by Melissa A. May, Karl D. Bishop and Paul D. Rawson
Metabolites 2017, 7(3), 33; https://doi.org/10.3390/metabo7030033 - 6 Jul 2017
Cited by 21 | Viewed by 4864
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)
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5398 KiB  
Article
Furanoterpene Diversity and Variability in the Marine Sponge Spongia officinalis, from Untargeted LC–MS/MS Metabolomic Profiling to Furanolactam Derivatives
by Cléa Bauvais, Natacha Bonneau, Alain Blond, Thierry Pérez, Marie-Lise Bourguet-Kondracki and Séverine Zirah
Metabolites 2017, 7(2), 27; https://doi.org/10.3390/metabo7020027 - 13 Jun 2017
Cited by 14 | Viewed by 6212
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)
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1909 KiB  
Article
Visualization of Microfloral Metabolism for Marine Waste Recycling
by Tatsuki Ogura, Reona Hoshino, Yasuhiro Date and Jun Kikuchi
Metabolites 2016, 6(1), 7; https://doi.org/10.3390/metabo6010007 - 27 Jan 2016
Cited by 12 | Viewed by 6884
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)
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2704 KiB  
Article
Using Molecular Networking for Microbial Secondary Metabolite Bioprospecting
by Kevin Purves, Lynsey Macintyre, Debra Brennan, Guðmundur Ó. Hreggviðsson, Eva Kuttner, Margrét E. Ásgeirsdóttir, Louise C. Young, David H. Green, Ruangelie Edrada-Ebel and Katherine R. Duncan
Metabolites 2016, 6(1), 2; https://doi.org/10.3390/metabo6010002 - 8 Jan 2016
Cited by 39 | Viewed by 12947
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)
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Review

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9505 KiB  
Review
Volatile Metabolites Emission by In Vivo Microalgae—An Overlooked Opportunity?
by Komandoor E. Achyuthan, Jason C. Harper, Ronald P. Manginell and Matthew W. Moorman
Metabolites 2017, 7(3), 39; https://doi.org/10.3390/metabo7030039 - 31 Jul 2017
Cited by 78 | Viewed by 14866
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)
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