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.

Availability of vitamin B12 and its lower ligand intermediate α-ribazole impact prokaryotic and protist communities in oceanic systems

“…In situ concentrations of α-ribazole or lower ligand derivates are unknown. However, a mass formula matching that of α-ribazole has been detected in the exometabolome of various Rhodobacteraceae , Nitrosopumilus maritimus and in marine DOM [ 29 – 32 ] and a gene enabling transport of α-ribazole into a bacterium was identified [ 26 ]. Hence, it is highly probable that lower ligands occur in one or the other form in oceanic systems as a release product of prokaryotes and are available to and used by prokaryotes.…”

“…However, there is some information available that the lower ligand intermediate α-ribazole is present in marine waters. A molecular formula matching that of α-ribazole has been detected in marine dissolved organic matter (DOM) and within the exometabolome of several marine prokaryotes [ 29 – 32 ]. Life of the majority of marine microorganisms depends on the availability of B 12 , however only a minority of marine prokaryotes holds the genetic apparatus for its de novo synthesis.…”

The 3D ultrastructural morphology of a marine ammonia-oxidizing archaeon

“…We followed previous protocol for SCM1 cultivation, growth monitoring, and culture purity assessment (Law et al, 2021b). To ensure the absence of bacterial and organic contaminants during the long-term cultivation, we used a combination of 0.5 μg/ml Rifamycin sodium and 1 μg/ml hydrosoluble Amphotericin B.…”

A Novel Approach to Characterize the Lipidome of Marine Archaeon Nitrosopumilus maritimus by Ion Mobility Mass Spectrometry

“…1,2-diphytanoyl- sn -glycero-3-phosphocholine and 1,2-diarachidoyl-sn-glycero-3-phosphocholine were purchased from Avanti Polar Lipids (Alabama, United States), beta -L-gulopyranosyl-caldarchaetidyl-glycerol was purchased from Matreya, LLC (Pennsylvania, United States), and C46 GTGT was purchased from Pandion Laboratories LLC (Indiana, United States). Other reagents used for cell culturing and quantitative PCR assays have been described in our previous report ( Law et al, 2021 ).…”

“…Cell growth was monitored by nitrite production, and the purity of the culture was monitored by quantitative real-time PCR (qPCR) analysis ( Yu et al, 2005 ). Further details have been given in Law et al (2021) previously. Cells were harvested by filtering through a 0.22 μm Polyvinylidene Fluoride (PVDF) filter (Whatman) after reaching the stationary phase.…”