Analytical and Computational Advances, Opportunities, and Challenges in Marine Organic Biogeochemistry in an Era of “Omics”

Abstract

Advances in sampling tools, analytical methods, and data handling capabilities have been fundamental to the growth of marine organic biogeochemistry over the past four decades. There has always been a strong feedback between analytical advances and scientific advances. However, whereas advances in analytical technology were often the driving force that made possible progress in elucidating the sources and fate of organic matter in the ocean in the first decades of marine organic biogeochemistry, today process-based scientific questions should drive analytical developments. Several paradigm shifts and challenges for the future are related to the intersection between analytical progress and scientific evolution. Untargeted "molecular headhunting" for its own sake is now being subsumed into process-driven targeted investigations that ask new questions and thus require new analytical capabilities. However, there are still major gaps in characterizing the chemical composition and biochemical behavior of macromolecules, as well as in generating reference standards for relevant types of organic matter. Field-based measurements are now routinely complemented by controlled laboratory experiments and in situ rate measurements of key biogeochemical processes. And finally, the multidisciplinary investigations that are becoming more common generate large and diverse datasets, requiring innovative computational tools

Non-targeted tandem mass spectrometry enables the visualization of organic matter chemotype shifts in coastal seawater

“…New developments in MS software tools, including molecular networking, comprehensive spectral and structure databases, statistical significance estimation, as well in silico annotation and community based annotation criteria have significantly improved the annotation of MS/MS spectra (Aron et al, 2019;Dührkop et al, 2019;Horai et al, 2010;Nothias et al, 2020;Ruttkies et al, 2016;Scheubert et al, 2017;Silva et al, 2018;Steen et al, 2020;Watrous et al, 2012). These technological improvements enable the annotation of a multitude of known and unknown chemical compounds which is central for a mechanistic understanding and prediction of how human actions influence ecosystems.…”

Marine dissolved organic matter: a vast and unexplored molecular space

“…The isomeric complexity within each molecular formula may be addressed via chromatographic separation prior to mass spectrometry or by fragmentation within the MS (Hawkes et al 2018 ; Steen et al 2020 ). Chromatography and other separation techniques allow the separation of DOM fractions, though only few individual compounds have been isolated from the complex mixture (Repeta 2015 ).…”

“…2 ). NMR detects the resonance of NMR-active nuclei (i.e., 13 C, 1 H, 15 N, 31 P) in the presence of a strong magnetic field (Steen et al 2020 ). Chemical shifts from multiple nuclei are measured in two-dimensional (2D) NMR spectroscopy techniques, which allow resolution of overlapping peaks, verification of the interpretation of the chemical shifts, and identification of specific structures.…”

Lipidomics of Environmental Microbial Communities. II: Characterization Using Molecular Networking and Information Theory

“…Recent advances in the field of lipidomics, using non-targeted approaches combing with computational methods, allows for comprehensive lipidome profiling without a priori expert MS fragmentation knowledge ( Pluskal et al, 2010 ; Shevchenko and Simons, 2010 ; Han et al, 2012 ; Wörmer et al, 2014 ; Yang and Han, 2016 ; Collins et al, 2016 ; Law and Zhang, 2019 ; Steen et al, 2020 ). The combination of analytical and computational advances provides a holistic picture of the lipidome and makes it more accessible, for example for studies of microbial ecology.…”