Meta-mass shift chemical profiling of metabolomes from coral reefs

Hartmann, Aaron C.; Petras, Daniel; Quinn, Robert A.; Protsyuk, Ivan; Archer, Frederick I.; Ransome, Emma; Williams, Gareth J.; Bailey, Barbara; Vermeij, Mark J. A.; Alexandrov, Theodore; Dorrestein, Pieter C.; Rohwer, Forest

doi:10.1073/pnas.1710248114

Cited by 74 publications

(74 citation statements)

References 27 publications

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“…A number of recent studies have employed molecular networking via GNPS for analyses of natural marine DOM (Petras et al ., 2017, Hartmann et al, ) as well as cultured marine microbes (Purves et al, ; Longnecker and Kujawinski, ). Future developments may see convergence between directed experimental investigations of DOM sources and sinks with characterizations of the in situ oceanic DOM pool employing similar methodologies, thereby enabling a more integrated understanding of the production and processing of this central ocean carbon reservoir.…”

Section: Discussionmentioning

confidence: 99%

Distinct molecular signatures in dissolved organic matter produced by viral lysis of marine cyanobacteria

Coleman

Waldbauer

2018

Environmental Microbiology

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Dissolved organic matter (DOM) plays a central role in the microbial ecology and biogeochemistry of aquatic environments, yet little is known about how the mechanism of DOM release from its ultimate source, primary producer biomass, affects the molecular composition of the inputs to the dissolved pool. Here we used a model marine phytoplankton, the picocyanobacterium Synechococcus WH7803, to compare the composition of DOM released by three mechanisms: exudation, mechanical cell lysis and infection by the lytic phage S-SM1. A broad, untargeted analytical approach reveals the complexity of this freshly sourced DOM, and comparative analysis between DOM produced by the different mechanisms suggests that exudation and viral lysis are sources of unsaturated, oxygen-rich and possibly novel biomolecules. Furthermore, viral lysis of WH7803 by S-SM1 releases abundant peptides derived from specific proteolysis of the major light-harvesting protein phycoerythrin, raising the possibility that phage infection of these abundant cyanobacteria could be a significant source of high molecular weight dissolved organic nitrogen compounds.

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Section: Discussionmentioning

confidence: 99%

Distinct molecular signatures in dissolved organic matter produced by viral lysis of marine cyanobacteria

Coleman

Waldbauer

2018

Environmental Microbiology

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“…This approach paired with high acquisitions speed (>1 Hz) of state of the art instruments results in thousands of spectra per LC-MS/MS run. For a reliable data analysis and reproducible interpretation of the results, bioinformatic workflows including comprehensive databases and statistical significance estimation are crucial (da Silva et al, 2015;Böcker, 2017;Scheubert et al, 2017;Weber et al, 2017) and have been very recently employed for marine metabolomic studies Hartmann et al, 2017;Kujawinski et al, 2017;Longnecker and Kujawinski, 2017). With these new bioinformatic tools and instrumental improvements in sensitivity, acquisition speed and resolution we anticipate that the techniques used for DOM characterization will further shift toward non-targeted analyses using high-resolution LC-MS/MS that provide inventories of molecular structures in complex environmental datasets.…”

Section: Introductionmentioning

confidence: 99%

High-Resolution Liquid Chromatography Tandem Mass Spectrometry Enables Large Scale Molecular Characterization of Dissolved Organic Matter

et al. 2017

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Dissolved organic matter (DOM) is arguably one of the most complex exometabolomes on earth, and is comprised of thousands of compounds, that together contribute more than 600 × 10 15 g carbon. This reservoir is primarily the product of interactions between the upper ocean's microbial food web, yet abiotic processes that occur over millennia have also modified many of its molecules. The compounds within this reservoir play important roles in determining the rate and extent of element exchange between inorganic reservoirs and the marine biosphere, while also mediating microbe-microbe interactions. As such, there has been a widespread effort to characterize DOM using high-resolution analytical methods including nuclear magnetic resonance spectroscopy (NMR) and mass spectrometry (MS). To date, molecular information in DOM has been primarily obtained through calculated molecular formulas from exact mass. This approach has the advantage of being non-targeted, accessing the inherent complexity of DOM. Molecular structures are however still elusive and the most commonly used instruments are costly. More recently, tandem mass spectrometry has been employed to more precisely identify DOM components through comparison to library mass spectra. Here we describe a data acquisition and analysis workflow that expands the repertoire of high-resolution analytical approaches available to access the complexity of DOM molecules that are amenable to electrospray ionization (ESI) MS. We couple liquid chromatographic separation with tandem MS (LC-MS/MS) and a data analysis pipeline, that integrates peak extraction from extracted ion chromatograms (XIC), molecular formula calculation and molecular networking. This provides more precise structural characterization. Although only around 1% of detectable DOM compounds can be annotated through publicly available spectral libraries, community-wide participation in populating and annotating DOM datasets could rapidly increase the annotation rate and should be broadly encouraged. Our analysis also identifies shortcomings of the current Petras et al. LC-MS/MS Analysis of DOMdata analysis workflow that need to be addressed by the community in the future. This work will lay the foundation for an integrative, non-targeted molecular analysis of DOM which, together with next generation sequencing, meta-proteomics and physical data, will pave the way to a more comprehensive understanding of the role of DOM in structuring marine ecosystems.

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“…The structural diversity stretches from very diverse terpenes, e.g., the macfarlandines A–E ( 84 – 88 ) and briaranes ( 110 – 111 ) over peptides, e.g., kulolide ( 31 ), polyketides e.g., laulimalide ( 75 ) to complex imidazole alkaloids, e.g., 65 , 66 and the highly cytotoxic jorumycin ( 121 ), as well as structures which should be biosynthesized by mixed biosynthetic pathways like the highly cytotoxic kabiramides ( 125 , 130 – 133 ). Considering coral reef environments, it was shown that three genera of stony corals had distinct patterns of molecular relatedness, despite their high degree of taxonomic relatedness [ 202 ]. Further, it was indicated that even between individuals, different metabolomes exist, suggesting that every coral reef holobiont is a potential source of novel chemical diversity [ 202 ].…”

Section: Discussionmentioning

confidence: 99%

The Potential of Indonesian Heterobranchs Found around Bunaken Island for the Production of Bioactive Compounds

et al. 2017

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The species diversity of marine heterobranch sea slugs found on field trips around Bunaken Island (North Sulawesi, Indonesia) and adjacent islands of the Bunaken National Marine Park forms the basis of this review. In a survey performed in 2015, 80 species from 23 families were collected, including 17 new species. Only three of these have been investigated previously in studies from Indonesia. Combining species diversity with a former study from 2003 reveals in total 140 species from this locality. The diversity of bioactive compounds known and yet to be discovered from these organisms is summarized and related to the producer if known or suspected (might it be down the food chain, de novo synthesised from the slug or an associated bacterium). Additionally, the collection of microorganisms for the discovery of natural products of pharmacological interest from this hotspot of biodiversity that is presented here contains more than 50 species that have never been investigated before in regard to bioactive secondary metabolites. This highlights the great potential of the sea slugs and the associated microorganisms for the discovery of natural products of pharmacological interest from this hotspot of biodiversity.

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Meta-mass shift chemical profiling of metabolomes from coral reefs

Cited by 74 publications

References 27 publications

Distinct molecular signatures in dissolved organic matter produced by viral lysis of marine cyanobacteria

Distinct molecular signatures in dissolved organic matter produced by viral lysis of marine cyanobacteria

High-Resolution Liquid Chromatography Tandem Mass Spectrometry Enables Large Scale Molecular Characterization of Dissolved Organic Matter

The Potential of Indonesian Heterobranchs Found around Bunaken Island for the Production of Bioactive Compounds

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