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. 2021 Jul 1:12:658781.
doi: 10.3389/fmicb.2021.658781. eCollection 2021.

Characterization of the Exometabolome of Nitrosopumilus maritimus SCM1 by Liquid Chromatography-Ion Mobility Mass Spectrometry

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Characterization of the Exometabolome of Nitrosopumilus maritimus SCM1 by Liquid Chromatography-Ion Mobility Mass Spectrometry

Kai P Law et al. Front Microbiol. .

Abstract

Marine Thaumarchaeota (formerly known as the marine group I archaea) have received much research interest in recent years since these chemolithoautotrophic organisms are abundant in the subsurface ocean and oxidize ammonium to nitrite, which makes them a major contributor to the marine carbon and nitrogen cycles. However, few studies have investigated the chemical composition of their exometabolome and their contributions to the pool of dissolved organic matter (DOM) in seawater. This study exploits the recent advances in ion mobility mass spectrometry (IM-MS) and integrates this instrumental capability with bioinformatics to reassess the exometabolome of a model ammonia-oxidizing archaeon, Nitrosopumilus maritimus strain SCM1. Our method has several advantages over the conventional approach using an Orbitrap or ion cyclotron resonance mass analyzer and allows assignments or annotations of spectral features to known metabolites confidently and indiscriminately, as well as distinction of biological molecules from background organics. Consistent with the results of a previous report, the SPE-extracted exometabolome of N. maritimus is dominated by biologically active nitrogen-containing metabolites, in addition to peptides secreted extracellularly. Cobalamin and associated intermediates, including α-ribazole and α-ribazole 5'-phosphate, are major components of the SPE-extracted exometabolome of N. maritimus. This supports the proposition that Thaumarchaeota have the capacity of de novo biosynthesizing cobalamin. Other biologically significant metabolites, such as agmatidine and medicagenate, predicted by genome screening are also detected, which indicates that Thaumarchaeota have remarkable metabolic potentials, underlining their importance in driving elemental cycles critical to biological processes in the ocean.

Keywords: Nitrosopumilus maritimus; Thaumarchaeota; dissolved organic matter; exometabolome; ion mobility mass spectrometry.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

FIGURE 1
FIGURE 1
Experimental design for metabolite analysis of N. maritimus SCM1. One group of the cultures was prepared with a supplement of vitamin B12 and the other group without. Cell growth was monitored by nitrite concentration in the medium. After 15 days of culture, cells were harvested by filtering 500 ml of culture solution. The used and filtered culture medium was also collected, and the organic compounds in the medium were extracted with SPE. The other 50 ml of culture medium was used for qPCR analysis.
FIGURE 2
FIGURE 2
Pairwise comparison analysis of the total ion chromatography (TIC) of an experimental culture medium (red) and a cell-free control culture medium (blue) after PPL-SPE extraction. The net spectrum between the experimental culture medium and cell-free control culture medium is shown as a subtracted chromatography (green) that represents the SPE retained fraction of the exometabolome of N. maritimus. Data were acquired in the negative ion mode.
FIGURE 3
FIGURE 3
(A) Pairwise comparison analysis of the ion mobility conformational spaces of an experimental culture medium and (B) a cell-free control medium after PPL-SPE extraction. The major differences between the pair are shown in (C), in which light blue indicates the regions where biomolecules were produced and exported extracellularly to the culture medium, whereas yellow denotes the organics that might have been consumed or degraded over the course of the experiment. Data were acquired in the negative ion mode.
FIGURE 4
FIGURE 4
(A) The ion chromatography, (B) the mass spectrum, and (C) the ion mobility characteristics of Vitamin B12 (cobalamin). Data were acquired in the negative ion mode.
FIGURE 5
FIGURE 5
(A) PCA of the whole data set, (B) OPLS-DA of the experimental media with and without supplement of Vitamin B12, and (C) 200 permutation tests of the OPLS-DA model in (B).
FIGURE 6
FIGURE 6
CCS-mz plots of the spectral features (ions) that are statistically significantly different between the experimental and control media. (A) Features or ions that were found higher in the experimental culture media (assumed exported extracellularly), or (B) higher in the cell-free control media (assumed consumed or degraded by extra-cellular enzymes).
FIGURE 7
FIGURE 7
Ion mobility enhanced MSE (HDMSE) fragmentation spectra of the five most important putatively identified metabolites of N. maritimus, (A) agmatidine, (B) cyanocob(III)alamin, (C) cob(I)alamin, (D) α-ribazole, and (E) medicagenic acid, detected from the experimental culture medium in the negative ion mode. Fragment ions consistent with in silico fragmentation are highlighted. Inserts show the chemical structures of neutral molecules.

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References

    1. Alsufyani T., Weiss A., Wichard T. (2017). Time course exo-metabolomic profiling in the green marine macroalga Ulva (Chlorophyta) for identification of growth phase-dependent biomarkers. Mar. Drugs 15:14. 10.3390/md15010014 - DOI - PMC - PubMed
    1. Angela G., Swati D. (2019). Riboswitches in archaea. Comb. Chem. High Throughput Screen. 22 135–149. 10.2174/1386207322666190425143301 - DOI - PubMed
    1. Baran R., Bowen B. P., Northen T. R. (2011). Untargeted metabolic footprinting reveals a surprising breadth of metabolite uptake and release by Synechococcus sp. PCC 7002. Mol. Biosyst. 7 3200–3206. 10.1039/c1mb05196b - DOI - PubMed
    1. Barbosa A. J. M., Roque A. C. A. (2019). Free marine natural products databases for biotechnology and bioengineering. Biotechnol. J. 14:1800607. 10.1002/biot.201800607 - DOI - PubMed
    1. Barofsky A., Vidoudez C., Pohnert G. (2009). Metabolic profiling reveals growth stage variability in diatom exudates. Limnol. Oceanogr. Methods 7 382–390. 10.4319/lom.2009.7.382 - DOI

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