Glycine betaine uptake and metabolism in marine microbial communities

Abstract

Summary Glycine betaine (GBT) is a compatible solute in high concentrations in marine microorganisms. As a component of labile organic matter, GBT has complex biochemical potential as a substrate for microbial use that is unconstrained in the environment. Here we determine the uptake kinetics and metabolic fate of GBT in two natural microbial communities in the North Pacific characterized by different nitrate concentrations. Dissolved GBT had maximum uptake rates of 0.36 and 0.56 nM h−1 with half‐saturation constants of 79 and 11 nM in the high nitrate and low nitrate stations respectively. During multiday incubations, most GBT taken into cells was retained as a compatible solute. Stable isotopes derived from the added GBT were also observed in other metabolites, including choline, carnitine and sarcosine, suggesting that GBT was used for biosynthesis and for catabolism to pyruvate and ammonium. Where nitrate was scarce, GBT was primarily metabolized via demethylation to glycine. Gene transcript data were consistent with SAR11 using GBT as a source of methyl groups to fuel the methionine cycle. Where nitrate concentrations were higher, more GBT was partitioned for lipid biosynthesis by both bacteria and eukaryotic phytoplankton. Our data highlight unexpected metabolic pathways and potential routes of microbial metabolite exchange.

Quantification of dissolved metabolites in environmental samples through cation‐exchange solid‐phase extraction paired with liquid chromatography–mass spectrometry

“…The concentrations of many of the compounds measured in environmental samples by CX-SPE analysis are within or close to the environmental concentration ranges reported by other studies of dissolved metabolites such as amino acids (Lee and Bada 1975;Fuhrman and Ferguson 1986;Sabadel et al 2017), TMAO (Gibb and Hatton 2004), creatine (Wawrik et al 2017), DMSP (Kiene and Slezak 2006), and arsenobetaine (Glabonjat et al 2018) (Table 1). Furthermore, the concentrations of some compounds measured for the first time using CX-SPE such as glycine betaine were of roughly the same order of magnitude (low nM) as those predicted by uptake kinetics studies (Kiene and Slezak 2006;Boysen et al 2022;Mausz et al 2022). The overall composition of the compounds in the environmental samples fit our expectations based on observed particulate metabolite pools, with the most abundant particulate metabolites also contributing significantly to the quantifiable dissolved metabolite pool.…”

“…Compounds involved in microbial adaptation to salt or other stressors (e.g., compatibles solutes such as glycine betaine or DMSP) that enable organisms to handle osmotic stress and have been documented to have high concentrations in marine phytoplankton and bacteria (Welsh 2000) are also a part of our compound library. While not exhaustive, the compound library employed in this study includes many of the most abundant compounds documented in marine particulate community metabolomes (Johnson et al 2020;Boysen et al 2021;Heal et al 2021) as are compounds that are suggested by previous work to be actively cycled and potentially abundant in marine dissolved metabolomes (Gibb and Hatton 2004;Kiene and Slezak 2006;Poretsky et al 2010;Fiore et al 2015;Sabadel et al 2017;Mayali and Weber 2018;Vorobev et al 2018;Weber et al 2020;Ferrer-Gonz alez et al 2021;Widner et al 2021;Boysen et al 2022). Our in-house library consists of 179 standards separated and analyzed using HILIC chromatography (HILIC Standards) and 70 standards separated and analyzed using RP chromatography (RP Standards) (Supporting Information Table S1).…”

“…A critical gap in understanding dissolved organic compounds is in the ability to measure polar zwitterionic compounds containing positively charged quaternary amine or sulfonium groups including dimethylsulfoniopropionate (DMSP), gonyol, dimethylsulfonioacetate (DMS‐Ac), glycine betaine, homarine, trigonelline, and trimethylamine N‐oxide (TMAO). These compounds have been identified as quantitatively important components of marine particulate metabolite pools (Johnson et al 2020; Boysen et al 2021; Heal et al 2021), are often accumulated as osmolytes to help microbes respond to osmotic stress (Welsh 2000; Gebser and Pohnert 2013; Dawson et al 2020 a , b ), mediate microbial interactions such as phytoplankton‐bacteria symbioses (Johnson et al 2016), and play important roles in the cycling of carbon and other elements (Welsh 2000; Yoch 2002; Boysen et al 2022). Many polar charged and zwitterionic compounds are largely unextractable with existing dissolved metabolomics extraction approaches and invisible to some LC–MS analytical methods, requiring the development of new metabolomics methods to study the distribution and roles of these compounds in marine systems alongside other key dissolved metabolite groups such as amino acids.…”

Chemotaxonomic patterns in intracellular metabolites of marine microbial plankton

“…Omics-based analyses that taxonomically resolve metabolic pathways using gene expression patterns have provided an important viewpoint into the microbial producers and/or consumers of particular metabolites (Aylward et al, 2015;Moran et al, 2016). Detailed studies of labile molecules like DMSP (Levine et al, 2012;Varaljay et al, 2015), methylphosphonate (Martıńez et al, 2013), 2,3-dihydroxypropane-1-sulfonate (DHPS) (Durham et al, 2019), glycine betaine (Boysen et al, 2022), and trehalose (Boysen et al, 2021) have aided in resolving the specific producers and/or consumers of these molecules in natural microbial populations through concurrent measurements of transcript and metabolite abundances. Isotope-based tools like Chip-SIP have provided highthroughput means to quantify taxon-specific incorporation of stable isotope-labeled substrates (Mayali et al, 2012).…”

Exogenous Regulators Enhance the Yield and Stress Resistance of Chlamydospores of the Biocontrol Agent Trichoderma harzianum T4

“…Glycine betaine is mainly used as an organic osmotic protector or methyl donor. In the face of various environmental stresses, cells accumulate glycine betaine [ 37 , 38 ], and more glycine betaine is used in lipid biosynthesis to maintain membrane fluidity [ 19 , 39 ]. These studies also indicate that mannitol, glycine betaine, and N-A-G are important raw materials for assembling and producing chlamydospores.…”