Marine environmental metabolomics studies the interactions of marine organisms with their environment using metabolomics to characterise these interactions. There are many advantages in using this method to study interactions between organisms and the environment and to assess the function and health of organisms at the molecular level. In fact, metabolomics is finding an increasing number of applications in the marine sciences. These range from understanding the response of organisms to abiotic pressure to researching the response of organisms to other biota. These interactions can be studied at different levels, from individuals to populations for more traditional eco‐physiological or ecological studies. Marine organisms have developed a high diversity of chemical defences to avoid predators and parasites. This study therefore highlights the complexity of chemical interactions in the marine environment. The research methods include 1H‐ and 13C‐NMR spectroscopy, mass spectrometry, analytical and preparative chromatography, and a multitude of bio‐assays.
Environmental metabolomics is the application of metabolomics for characterising the interactions of organisms with their environment . Marine environmental metabolomics is the application of metabolomics to characterise the interactions of marine organisms with their environment .
As Greek scholars claimed, everything is born out of struggle and need. The pressing need of organisms is to adapt to the environment or adapt the environment to the interests of the species. The survival and progress of the different living entities represent a secret driving force that harnesses metabolites to trigger sophisticated chemical interactions. Although the production of these bio‐active substances requires an enormous effort from the organism in terms of energy, the adaptive advantage gained in return is as spectacular as it is necessary for survival.
The progressive degradation of the marine environment on the other hand (animal/plant pests, pollution, etc.) leads us to the need to protect it, and to do so, we have to understand it. Scientists are increasingly clear that our understanding of the marine environment is incomplete without a deeper understanding of its metabolomics. There is even talk of a new science, although its name is not clear. Some call it chemical ecology , others ecological bio‐chemistry , and others consider it part of synecology or biocenotics. According to the principle of science itself “given enough time, only the necessary will survive”  so one can expect that the day will come when chemists and biologists will decide on the best name for it.
Coactones or semiochemicals are the compounds released by an organism which evoke a reaction in another organism of a different or the same species. When these compounds act at a distance, they are called allelochemicals, and their interaction is known as allelopathy .
Interactions can be inter‐specific or intra‐specific, depending on whether they affect individuals of different or the same species, respectively. The chemical factors that affect organisms of different species can in turn be allomones or kairomones, while the chemical factors that affect individuals of the same species can be by auto‐toxins, or pheromones .
Allomones are semiochemicals that favour the emitter, but not for the receiver. Examples in the marine environment include toxins, digestibility reducing factors, repellents, feeding deterrents, anti‐fouling compounds, escape substances, suppressors—antibiotics and cytotoxins .
Kairomones are semiochemicals that favour the receiver. Examples from the marine environment include predator attractors or substances that predators use to locate their prey, adaptation inducers, like the spine‐development factor in rotifers, warnings signals of danger or toxicity, which benefit the receiver, such as colourants that generate bright colours with characteristic designs on the most toxic animals, growth stimulators, etc. .
Pheromones are the semiochemicals released into the environment to influence behaviour or some biological function in the same species. These include sexual/social/warning/territorial marking/trace and communication pheromones . One particular and highly important case of the latter refers to migration pheromones or tele‐mediators .
Animals that are mobile or have hard shells or spines are typically not defended by noxious or toxic chemicals. This is the case of the sea urchin or the spiny lobster. Contrarily, the spotted trunkfish (
On the other hand, marine snails are strongly protected. Nudibranchs, or sea slugs as they are also known, are an example that is commonly quoted of how organisms with powerful chemical defences have little need for a physical defence like a hard shell to protect them from predators. Nudibranchs usually obtain their chemical defences from the sponges, bryozoans and sea squirts that they eat, but cases have been reported in which these are produced by
4. Repellents/feeding deterrents
Sponges are an abundant group of coral‐reef invertebrates that are very chemically rich. Recent studies have shown that many sponge chemicals effectively repel potential predators, and many of the distasteful compounds have now been isolated and structurally characterised . Bioassays are usually run to locate sponges that accumulate repellents. As an experimental methodology,
Soft fleshy seaweeds found where herbivorous fish and invertebrates abound typically deter herbivory by producing distasteful secondary metabolites.
Gorgonians, a type of soft coral, are close relatives of hard corals, but they do not have a hard calcium carbonate skeleton. Their soft texture seems to make them a target for a range of reef predators, but the many novel compounds they produce act as an effective defence to protect them from these predators. Hence, for example,
Biomass screening of a new marine‐derived strain of
This seems to suggest that the shikimic acid pathway allows fungi to produce their allomones by
5. Anti‐fouling compounds
Many sessile marine organisms are surprisingly clean given the abundance of algal spores and invertebrate larvae that could settle and grow on them. Some seaweeds and invertebrates produce compounds that deter or kill larvae and spores attempting to colonise them as a way of keeping clean. Zosteric acid
Saponins act as repellents in sea cucumbers, and many species produce these cytotoxic secondary metabolites. Despite the deterrent, they are still colonised by multiple symbiotic organisms, including the Harlequin crab,
Pheromones are secreted or excreted chemicals that trigger a social response in members of the same species. In the marine environment, there are some well‐known examples that affect behaviour or physiology: alarm pheromones, sex pheromones, etc. There are papers in the field of alarm pheromones reporting how the nudibranchs
8. Research methods
Isolating and identifying natural products requires the use of physio‐chemical fractionation and purification techniques (Figure 9). These products can be explored once enough biological matter is obtained, either from organisms collected directly from their natural habitat or using bio‐processes (fermentation, photo‐bio‐reaction) or marine aquaculture to grow them. The biomass obtained can be frozen, freeze‐dried or chemically set in a dissolvent to conserve it.
The preliminary separation techniques used in laboratories are performed with adsorption chromatography, using gravity flow columns at low or medium pressure, or using liquid‐liquid partition methods . The latter technique can be applied simply with the help of a decanting funnel, and using one of several variants, it can provide low, medium or high‐polarity fractions. This was the case of the fractions obtained from the growth medium used for
Structural elucidation using spectroscopic methods requires perfectly pure substances—crystalline, amorphous or oily. If crystals are successfully obtained, an X‐ray diffraction study could then be performed. If not, if the purified component has a non‐crystalline structure, then the literature recommends obtaining 1H‐ and 13C‐nuclear magnetic resonance spectra and mass spectra. Once we have the spectra and these are studied, the researcher proposes the structure of the component. This process requires a meticulous revision of the structures previously described in the literature.
Because of the immense number of known products, it is much easier to resort to a powerful database. In these days, many databases on the subject are available to the scientific community online, from the more conventional
Once the bibliographic background has been checked and the conclusion has been drawn that the component isolated is new, a more refined structural elucidation has to be carried out. A second high‐resolution mass spectrum (HRMS) is required for this to determine the exact molecular formula of both the molecule and the fragments of it that form in the apparatus’ injection block. With this information, the two‐dimensional structure of the new metabolite isolated can be deduced .
Obtaining the three‐dimensional structure of molecules requires high‐resolution nuclear magnetic resonance techniques. Such spectra provide data on coupling between nuclei that are close together in space and their dihedral angles, using the coupling constants
Apart from the techniques indicated above, analytical methods provide important tools in the qualitative and quantitative analysis of substances allowing us to establish their identity and the precise quantity of each component of a given mixture . Instrumental techniques include high‐resolution liquid chromatography (HPLC or UHPLC) and gas chromatography (GC). Once connected to modern mass spectrometry, these tools resolve countless analytical problems (UHPLC‐MS/MS or GC‐MS) .
9. Results and discussion
The screening of the biomass of a new marine‐derived strain of
A GC‐MS chemical screening on the biomass of a marine protist of the
The chemical constituents of the fermentation broth of the marine‐derived fungus
A recent proposal is to study
10. Conclusions and future direction
There are an estimated 22,000 known marine metabolites. Their value as potential drugs for industry—cosmetic, nutraceutical and pharmaceutical—is well documented; in fact in recent years, companies have appeared such as the Spanish company
However, only a few marine metabolites have been developed commercially. This is perhaps due to the fact that marine environmental metabolomics is scarcely 60 years old, apart from the fact that the major bio‐technology and/or pharmaceutical companies have invested very few resources in this field. But irrespective of whether or not marine metabolites have an industrial application, an understanding of their three‐dimensional chemical structures and the bio‐genetic pathways that living creatures use to produce them is already of great value in the field of marine chemical ecology.
Marine organisms use chemistry for many different purposes. The obvious objectives are to form cellular structures, genetic expression (DNA) and primary metabolism, which guarantees their basic welfare. There is also a secondary metabolism, controlled by enzymes, which is used by organisms to produce, accumulate and disseminate active biological substances into the environment that are essential for the survival of both the organism itself and others of the same or a different species.
For some time, these metabolites were classed under the definition of marine natural products (MNPs), but this definition is defective as it ignores the ecological function or role that they have. That is why more precise words such as allomone, kairomone or pheromone are increasingly applied to them, as we have explained in this chapter.
However, the future is promising, as there is an increasing awareness of the need to study the marine environment in‐depth. The proof of this is the creation of four faculties of marine sciences in Spain in recent decades, which means that there is now a bachelor's degree in marine sciences, along with a range of Masters and PhD courses that focus on the sea as their field of study. Subjects like “Chemistry of Marine Natural Products” have suddenly appeared on our syllabuses. At the same time, our students are presenting their degree/master projects or their doctoral theses on marine environmental metabolomics, all of which augers a promising future for this exciting field of science.