Marine dissolved organic matter: a vast and unexplored molecular space

Abstract

Marine dissolved organic matter (DOM) comprises a vast and unexplored molecular space. Most of it resided in the oceans for thousands of years. It is among the most diverse molecular mixtures known, consisting of millions of individual compounds. More than 1 Eg of this material exists on the planet. As such, it comprises a formidable source of natural products promising significant potential for new biotechnological purposes. Great emphasis has been placed on understanding the role of DOM in biogeochemical cycles and climate attenuation, its lifespan, interaction with microorganisms, as well as its molecular composition. Yet, probing DOM bioactivities is in its infancy, largely because it is technically challenging due to the chemical complexity of the material. It is of considerable interest to develop technologies capable to better discern DOM bioactivities. Modern screening technologies are opening new avenues allowing accelerated identification of bioactivities for small molecules from natural products. These methods diminish a priori the need for laborious chemical fractionation. We examine here the application of untargeted metabolomics and multiplexed high-throughput molecular-phenotypic screening techniques that are providing first insights on previously undetectable DOM bioactivities. KEY POINTS: • Marine DOM is a vast, unexplored biotechnological resource. • Untargeted bioscreening approaches are emerging for natural product screening. • Perspectives for developing bioscreening platforms for marine DOM are discussed.

Keywords: Cytological profiling; High content screening; Marine dissolved organic matter (DOM); Ultrahigh-resolution mass spectrometry; Untargeted metabolomics.

Fig. 1

A molecular universe in the ocean. This illustration depicts the molecular complexity of marine DOM. Most of this pool is chemically unidentified (big nebulous), with only 2–3% of defined chemical structures (gray squares). The representative structures of marine DOM namely carotenoids, carboxylic-rich alicyclic molecules, and fucose were extracted from Arakawa et al. (2017), Hertkorn et al. (2006), and Repeta (2015), respectively

Fig. 2

More than ten thousand molecular formulas and structural units have been identified in marine DOM. a A mass spectrum measured via ultrahigh-resolution mass spectrometry (15 T Fourier transform ion cyclotron resonance mass spectrometry, FT-ICR-MS) of the North Pacific Equatorial Intermediate Water with single asterisk indicating exemplary nominal mass (297 Da). b An HPLC–MS/MS scan of isomeric mixture peaks from Nordic Reservoir natural organic matter (NRNOM) reference material, depicting the inability to distinguish fragmentation patterns from individual isomers from a molecular mass (adapted from Hawkes et al. 2018). c An example of an assigned structure (C22H18O12) based on a riverine DOM MS/MS spectra and the METLIN database (adapted from Lu and Liu 2019). d The structural units identified by multidimensional nuclear magnetic resonance (NMR), in which each dot represents one structural feature (Hertkorn et al. 2012)

Fig. 3

Emerging bioactivity screening paradigm targeting complex mixtures. a Sample acquisition via solid-phase extraction. b First-step fractionation. c Molecular characterization of complex mixtures via ultrahigh-resolution mass spectrometry (left), tandem mass spectrometry (middle), and molecular networks (right) to characterize chemomolecular fingerprints of natural extracts. d High-content phenotypic analyses: specific inhibition of cellular processes and/or bioactivity or function (e.g., cell growth/death; cell image–based profiling; gene expression/functional analysis (transcriptomics, proteomics, metabolomics), immune/inflammatory signal analyses, cytokines) and effect on infectious process (pathogen). e Next-generation analyses (e.g., multivariate statistical analyses, machine learning, neural networks, deep learning). f Iterative fraction-by-fraction comparative analyses and selection (positive, negative, and new activities, i.e., revealed or enhanced after fractionation). g Iterative specialization process with bioactive samples. Here, analyses can be developed beyond outright binary growth inhibition/cell death–type readouts and nuanced with more sensitive/sophisticated combinatorial and/or orthogonal readouts combining, for example, cytological characteristics, and/or more subtle molecular phenotypic readouts. Single asterisk, Petras et al. (2017); double asterisks, Merder et al. (2020); triple asterisks, Aulner et al. (2019)