High-Resolution Tandem Mass Spectrometry-Based Analysis of Model Lignin-Iron Complexes: Novel Pipeline and Complex Structures.

Understanding the chemical nature of soil organic carbon (SOC) with great potential to bind iron (Fe) minerals is critical for predicting the stability of SOC. Organic ligands of Fe are among the top candidates for SOCs able to strongly sorb on Fe minerals, but most of them are still molecularly uncharacterized. To shed insights into the chemical nature of organic ligands in soil and their fate, this study developed a protocol for identifying organic ligands using ultrahigh-performance liquid chromatography-high-resolution tandem mass spectrometry (UHPLC-HRMS/MS) and metabolomic tools.

Relating Molecular Properties to the Persistence of Marine Dissolved Organic Matter with Liquid Chromatography-Ultrahigh-Resolution Mass Spectrometry.

Marine dissolved organic matter (DOM) contains a complex mixture of small molecules that eludes rapid biological degradation. Spatial and temporal variations in the abundance of DOM reflect the existence of fractions that are removed from the ocean over different time scales, ranging from seconds to millennia. However, it remains unknown whether the intrinsic chemical properties of these organic components relate to their persistence.

Natural Abundance Isotope Ratio Measurements of Organic Molecules Using 21 T FTICR MS.

Subtle variations in stable isotope ratios at natural abundance are challenging to measure but can yield critical insights into biological, physical, and geochemical processes. Well-established methods, particularly multicollector, gas-source, or plasma isotope ratio mass spectrometry, are the gold standard for stable isotope measurement, but inherent limitations in these approaches make them ill-suited to determining site-specific and multiply substituted isotopic abundances of all but a few compounds or to characterizing larger intact molecules. Fourier transform mass spectrometry, namely, Orbitrap mass spectrometry, has recently demonstrated the ability to measure natural abundance isotope ratios with chemically informative accuracy and precision.

Taxonomic distribution of metabolic functions in bacteria associated with consortia.

Colonies of the cyanobacteria act as a biological hotspot for the usage and recycling of key resources such as C, N, P, and Fe within an otherwise oligotrophic environment. While colonies are known to interact and support a unique community of algae and particle-associated microbes, our understanding of the taxa that populate these colonies and the gene functions they encode is still limited. Characterizing the taxa and adaptive strategies that influence consortium physiology and its concomitant biogeochemistry is critical in a future ocean predicted to have increasingly resource-depleted regions.

Metal Organic Complexation in Seawater: Historical Background and Future Directions.

The speciation of most biologically active trace metals in seawater is dominated by complexation by organic ligands. This review traces the history of work in this area, from the early observations that showed surprisingly poor recoveries using metal preconcentration protocols to the present day, where advances in mass spectroscopy and stable isotope geochemistry are providing new insights into the structure, origin, fate, and biogeochemical impact of organic ligands. Many long-standing hypotheses about the specific biological origin of ligands such as siderophores in seawater are finally being validated.

Quantitative Separation of Unknown Organic-Metal Complexes by Liquid Chromatography-Inductively Coupled Plasma-Mass Spectrometry.

Dissolved organic matter (DOM) is widely recognized to control the solubility and reactivity of trace metals in the environment. However, the mechanisms that govern metal-DOM complexation remain elusive, primarily due to the analytical challenge of fractionating and quantifying metal-organic species within the complex mixture of organic compounds that comprise DOM. Here, we describe a quantitative method for fractionation and element-specific detection of organic-metal complexes using liquid chromatography with online inductively coupled plasma mass spectrometry (LC-ICP-MS).

Slow Kinetics of Iron Binding to Marine Ligands in Seawater Measured by Isotope Exchange Liquid Chromatography-Inductively Coupled Plasma Mass Spectrometry.

Current understanding of dissolved iron (Fe) speciation in the ocean is based on two fundamentally different approaches: electrochemical methods that measure bulk properties of a heterogeneous ligand pool and liquid chromatography mass spectrometry methods that characterize ligands at a molecular level. Here, we describe a method for simultaneously determining Fe-ligand dissociation rate constants () of suites of naturally occurring ligands in seawater by monitoring the exchange of ligand-bound Fe with Fe using liquid chromatography-inductively coupled mass spectrometry. Values of were determined for solutions of ferrichrome and ferrioxamine E.

Basin-scale biogeography of marine phytoplankton reflects cellular-scale optimization of metabolism and physiology.

Extensive microdiversity within , the most abundant marine cyanobacterium, occurs at scales from a single droplet of seawater to ocean basins. To interpret the structuring role of variations in genetic potential, as well as metabolic and physiological acclimation, we developed a mechanistic constraint-based modeling framework that incorporates the full suite of genes, proteins, metabolic reactions, pigments, and biochemical compositions of 69 sequenced isolates spanning the pangenome. Optimizing each strain to the local, observed physical and chemical environment along an Atlantic Ocean transect, we predicted variations in strain-specific patterns of growth rate, metabolic configuration, and physiological state, defining subtle niche subspaces directly attributable to differences in their encoded metabolic potential.

Soil Organic Matter Characterization by Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (FTICR MS): A Critical Review of Sample Preparation, Analysis, and Data Interpretation.

The biogeochemical cycling of soil organic matter (SOM) plays a central role in regulating soil health, water quality, carbon storage, and greenhouse gas emissions. Thus, many studies have been conducted to reveal how anthropogenic and climate variables affect carbon sequestration and nutrient cycling. Among the analytical techniques used to better understand the speciation and transformation of SOM, Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS) is the only technique that has sufficient mass resolving power to separate and accurately assign elemental compositions to individual SOM molecules.

Bacterial Quorum-Sensing Signal Arrests Phytoplankton Cell Division and Impacts Virus-Induced Mortality.

Interactions between phytoplankton and heterotrophic bacteria fundamentally shape marine ecosystems by controlling primary production, structuring marine food webs, mediating carbon export, and influencing global climate. Phytoplankton-bacterium interactions are facilitated by secreted compounds; however, linking these chemical signals, their mechanisms of action, and their resultant ecological consequences remains a fundamental challenge. The bacterial quorum-sensing signal 2-heptyl-4-quinolone (HHQ) induces immediate, yet reversible, cellular stasis (no cell division or mortality) in the coccolithophore ; however, the mechanism responsible remains unknown.

Metabolic Interactions between and Pseudomonas fluorescens under Controlled Iron-Limited Conditions.

Iron (Fe) availability has well-known effects on plant and microbial metabolism, but its effects on interspecies interactions are poorly understood. The purpose of this study was to investigate metabolite exchange between the grass strain Bd21 and the soil bacterium SBW25::gfp/lux (SBW25) during Fe limitation under axenic conditions. We compared the transcriptional profiles and root exudate metabolites of plants grown semihydroponically with and without SBW25 inoculation and Fe amendment.

Online supercritical fluid extraction mass spectrometry (SFE-LC-FTMS) for sensitive characterization of soil organic matter.

We report a novel technical approach for subcritical fluid extraction (SFE) for organic matter characterization in complex matrices such as soil. The custom platform combines on-line SFE with micro-solid phase extraction, nano liquid chromatography (LC), electrospray ionization and Fourier transform mass spectrometry (SFE-LC-FTMS). We demonstrated the utility of SFE-LC-FTMS, including results from both Orbitrap and FTICR MS, for analysis of complex mixtures of organic compounds in a solid matrix by characterizing soil organic matter in peat, a high-carbon soil.

Siderophore profiling of co-habitating soil bacteria by ultra-high resolution mass spectrometry.

The chemical structure of organic molecules profoundly impacts their interactions with metal ions and mineral phases in soils. Understanding the sources and cycling of metal-chelating compounds is therefore essential for predicting the bioavailability and transport of metals throughout terrestrial environments. Here we investigate the molecular speciation of organic molecules that solubilize trace metals in calcareous soils from Eastern Washington.

Structure Elucidation of Unknown Metabolites in Metabolomics by Combined NMR and MS/MS Prediction.

We introduce a cheminformatics approach that combines highly selective and orthogonal structure elucidation parameters; accurate mass, MS/MS (MS²), and NMR into a single analysis platform to accurately identify unknown metabolites in untargeted studies. The approach starts with an unknown LC-MS feature, and then combines the experimental MS/MS and NMR information of the unknown to effectively filter out the false positive candidate structures based on their predicted MS/MS and NMR spectra. We demonstrate the approach on a model mixture, and then we identify an uncatalogued secondary metabolite in .

Siderophore-based microbial adaptations to iron scarcity across the eastern Pacific Ocean.

Nearly all iron dissolved in the ocean is complexed by strong organic ligands of unknown composition. The effect of ligand composition on microbial iron acquisition is poorly understood, but amendment experiments using model ligands show they can facilitate or impede iron uptake depending on their identity. Here we show that siderophores, organic compounds synthesized by microbes to facilitate iron uptake, are a dynamic component of the marine ligand pool in the eastern tropical Pacific Ocean.

An extended siderophore suite from Synechococcus sp. PCC 7002 revealed by LC-ICPMS-ESIMS.

Siderophores are thought to play an important role in iron cycling in the ocean, but relatively few marine siderophores have been identified. Sensitive, high throughput methods hold promise for expediting the discovery and characterization of new siderophores produced by marine microbes. We developed a methodology for siderophore characterization that combines liquid chromatography (LC) inductively coupled plasma mass spectrometry (ICPMS) with high resolution electrospray ionization mass spectrometry (ESIMS).

Detection of iron ligands in seawater and marine cyanobacteria cultures by high-performance liquid chromatography-inductively coupled plasma-mass spectrometry.

Organic ligands dominate the speciation of iron in the ocean. Little is known, however, about the chemical composition and distribution of these compounds. Here, we describe a method to detect low concentrations of organic Fe ligands using reverse-phase high-performance liquid chromatography (HPLC) tandem multicollector inductively coupled plasma mass spectrometry.

Traditional and molecular analyses for fecal indicator bacteria in non-point source subtropical recreational marine waters.

The use of enterococci as the primary fecal indicator bacteria (FIB) for the determination of recreational water safety has been questioned, particularly in sub/tropical marine waters without known point sources of sewage. Alternative FIB (such as the Bacteroidales group) and alternative measurement methods (such as rapid molecular testing) have been proposed to supplement or replace current marine water quality testing methods which require culturing enterococci. Moreover, environmental parameters have also been proposed to supplement current monitoring programs.

Mechanisms of ZnII-activated magnetic resonance imaging agents.

We report on the mechanism of a series of Zn (II)-activated magnetic resonance contrast agents that modulate the access of water to a paramagnetic Gd (III) ion to create an increase in relaxivity upon binding of Zn (II). In the absence and presence of Zn (II), the coordination at the Gd (III) center is modulated by appended Zn (II) binding groups. These groups were systematically varied to optimize the change in coordination upon Zn (II) binding.

sAPPalpha enhances the transdifferentiation of adult bone marrow progenitor cells to neuronal phenotypes.

The remediation of neurodegeneration and cognitive decline in Alzheimer's Disease (AD) remains a challenge to basic scientists and clinicians. It has been suggested that adult bone marrow stem cells can transdifferentiate into different neuronal phenotypes. Here we demonstrate that the alpha-secretase-cleaved fragment of the amyloid precursor protein (sAPPalpha), a potent neurotrophic factor, potentiates the nerve growth factor (NGF)/retinoic acid (RA) induced transdifferentiation of bone marrow-derived adult progenitor cells (MAPCs) into neural progenitor cells and, more specifically, enhances their terminal differentiation into a cholinergic-like neuronal phenotype.