Characterization of the Exometabolome of Nitrosopumilus maritimus SCM1 by Liquid Chromatography-Ion Mobility Mass Spectrometry
- PMID: 34276593
- PMCID: PMC8281238
- DOI: 10.3389/fmicb.2021.658781
Characterization of the Exometabolome of Nitrosopumilus maritimus SCM1 by Liquid Chromatography-Ion Mobility Mass Spectrometry
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.
Copyright © 2021 Law, He, Tao and Zhang.
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
Similar articles
-
A Novel Approach to Characterize the Lipidome of Marine Archaeon Nitrosopumilus maritimus by Ion Mobility Mass Spectrometry.Front Microbiol. 2021 Dec 2;12:735878. doi: 10.3389/fmicb.2021.735878. eCollection 2021. Front Microbiol. 2021. PMID: 34925256 Free PMC article.
-
Nitrosopumilus maritimus gen. nov., sp. nov., Nitrosopumilus cobalaminigenes sp. nov., Nitrosopumilus oxyclinae sp. nov., and Nitrosopumilus ureiphilus sp. nov., four marine ammonia-oxidizing archaea of the phylum Thaumarchaeota.Int J Syst Evol Microbiol. 2017 Dec;67(12):5067-5079. doi: 10.1099/ijsem.0.002416. Epub 2017 Oct 16. Int J Syst Evol Microbiol. 2017. PMID: 29034851
-
Genome-scale metabolic model analysis indicates low energy production efficiency in marine ammonia-oxidizing archaea.AMB Express. 2018 Jun 27;8(1):106. doi: 10.1186/s13568-018-0635-y. AMB Express. 2018. PMID: 29946801 Free PMC article.
-
Nitrogen metabolism and kinetics of ammonia-oxidizing archaea.Methods Enzymol. 2011;496:465-87. doi: 10.1016/B978-0-12-386489-5.00019-1. Methods Enzymol. 2011. PMID: 21514476 Review.
-
The history of aerobic ammonia oxidizers: from the first discoveries to today.J Microbiol. 2014 Jul;52(7):537-47. doi: 10.1007/s12275-014-4114-0. Epub 2014 Jun 28. J Microbiol. 2014. PMID: 24972807 Review.
Cited by
-
A Novel Approach to Characterize the Lipidome of Marine Archaeon Nitrosopumilus maritimus by Ion Mobility Mass Spectrometry.Front Microbiol. 2021 Dec 2;12:735878. doi: 10.3389/fmicb.2021.735878. eCollection 2021. Front Microbiol. 2021. PMID: 34925256 Free PMC article.
-
Ultrastructural insights into cellular organization, energy storage and ribosomal dynamics of an ammonia-oxidizing archaeon from oligotrophic oceans.Front Microbiol. 2024 Apr 26;15:1367658. doi: 10.3389/fmicb.2024.1367658. eCollection 2024. Front Microbiol. 2024. PMID: 38737410 Free PMC article.
References
-
- 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
LinkOut - more resources
Full Text Sources
