Structural characterization of dissolved organic matter: a review of current techniques for isolation and analysis

Minor, Elizabeth C.; Swenson, Michael M.; Mattson, Bruce; Oyler, Alan R.

doi:10.1039/c4em00062e

Cited by 208 publications

(217 citation statements)

References 175 publications

(314 reference statements)

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“…While the majority of marine metabolomics studies have involved controlled cultures, metabolite profiling has been successful with marine bacteria, microalgae, macroalgae and animals (Mopper et al, 2007;Minor et al, 2014). Metabolomics analyses of spent media from these systems have shed light on unique chemical defense mechanisms and production of secondary metabolites (Goulitquer et al, 2012).…”

Section: The Use Of Untargeted Metabolomics To Understand Dom Composimentioning

confidence: 99%

Untargeted soil metabolomics methods for analysis of extractable organic matter

Swenson

Jenkins

Bowen

et al. 2015

Soil Biology and Biochemistry

159

112

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a b s t r a c tThe cycling of soil organic matter (SOM) by microorganisms is a critical component of the global carbon cycle but remains poorly understood. There is an emerging view that much of SOM, and especially the dissolved fraction (DOM), is composed of small molecules of plant and microbial origin resulting from lysed cells and released metabolites. Unfortunately, little is known about the small molecule composition of soils and how these molecules are cycled (by microbes or plants or by adsorption to mineral surfaces). The water-extractable organic matter (WEOM) fraction is of particular interest given that this is presumably the most biologically-accessible component of SOM. Here we describe the development of a simple soil metabolomics workflow and a novel spike recovery approach using 13 C bacterial lysates to assess the types of metabolites remaining in the WEOM fraction. Soil samples were extracted with multiple mass spectrometry-compatible extraction buffers (water, 10 mM K 2 SO 4 or NH 4 HCO 3 , 10e100% methanol or isopropanol/methanol/water [3:3:2 v/v/v]) with and without prior chloroform vapor fumigation. Profiling of derivatized extracts was performed using gas chromatography/mass spectrometry (GC/MS) with 55 metabolites identified by comparing fragmentation patterns and retention times with authentic standards. As expected, fumigation, which is thought to lyse microbial cells, significantly increased the range and abundance of metabolites relative to unfumigated samples. To assess the types of microbial metabolites from lysed bacterial cells that remain in the WEOM fraction, an extract was prepared from the soil bacterium Pseudomonas stutzerii RCH2 grown on 13 C acetate. This approach produced highly labeled metabolites that were easily discriminated from the endogenous soil metabolites. Comparing the composition of the fresh bacterial extract with what was recovered following a 15 min incubation with soil revealed that only 27% of the metabolites showed >50% recovery in the WEOM. Many, especially cations (polyamines) and anions, showed <10% recovery. These represent metabolites that may be inaccessible to microbes in this environment and would be most likely to accumulate as SOM presumably due to binding with minerals and negatively-charged clay particles. This study presents a simple untargeted metabolomics workflow for extractable organic matter and an approach to estimate microbial metabolite availability in soils. These methods can be used to further our understanding of SOM and DOM composition and examine the link between metabolic pathways and microbial communities to terrestrial carbon cycling.Published by Elsevier Ltd.

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Section: The Use Of Untargeted Metabolomics To Understand Dom Composimentioning

confidence: 99%

Untargeted soil metabolomics methods for analysis of extractable organic matter

Swenson

Jenkins

Bowen

et al. 2015

Soil Biology and Biochemistry

159

112

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“…Recent applications of mass spectrometry to DOM include high-performance liquid chromatography coupled online to a mass spectrometer (Liu et al 2011, van Roosmalen et al 2010 and Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) (Minor et al 2014, Stubbins et al 2014. Electrospray ionization coupled to FT-ICR-MS has been used, for example, to characterize polar compounds associated with DOM at the molecular level during transport within a subestuary of the lower Chesapeake Bay .…”

Section: Dissolved Organic Mattermentioning

confidence: 99%

“…In recent years, mass spectrometry has increased our ability to characterize DOM at the molecular level (Minor et al 2014, Stubbins et al 2014. Recent applications of mass spectrometry to DOM include high-performance liquid chromatography coupled online to a mass spectrometer (Liu et al 2011, van Roosmalen et al 2010 and Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) (Minor et al 2014, Stubbins et al 2014.…”

Section: Dissolved Organic Mattermentioning

confidence: 99%

Sources, Ages, and Alteration of Organic Matter in Estuaries

Canuel

Hardison

2016

Annu. Rev. Mar. Sci.

175

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Understanding the processes influencing the sources and fate of organic matter (OM) in estuaries is important for quantifying the contributions of carbon from land and rivers to the global carbon budget of the coastal ocean. Estuaries are sites of high OM production and processing, and understanding biogeochemical processes within these regions is key to quantifying organic carbon (Corg) budgets at the land-ocean margin. These regions provide vital ecological services, including nutrient filtration and protection from floods and storm surge, and provide habitat and nursery areas for numerous commercially important species. Human activities have modified estuarine systems over time, resulting in changes in the production, respiration, burial, and export of Corg. Corg in estuaries is derived from aquatic, terrigenous, and anthropogenic sources, with each source exhibiting a spectrum of ages and lability. The complex source and age characteristics of Corg in estuaries complicate our ability to trace OM along the river-estuary-coastal ocean continuum. This review focuses on the application of organic biomarkers and compound-specific isotope analyses to estuarine environments and on how these tools have enhanced our ability to discern natural sources of OM, trace their incorporation into food webs, and enhance understanding of the fate of Corg within estuaries and their adjacent waters.

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“…10 Different techniques have been used to gain information on the composition and the concentration of DOC. Two frequently used optical methods to characterize bulk DOC are UV-Vis spectroscopy and fluorescence spectroscopy (Minor et al, 2014).…”

Section: Introductionmentioning

confidence: 99%

Diel fluctuations of viscosity-driven riparian inflow affect streamflow DOC concentration

Schwab

Klaus

Pfister

et al. 2017

Preprint

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Abstract. Diel fluctuations of streamwater DOC concentrations are generally explained by a complex interplay of different instream processes. We measured the light absorption spectrum of water and DOC concentrations in-situ and with highfrequency by means of a UV-Vis spectrometer during 18 months at the outlet of a forested headwater catchment in 10 Luxembourg (0.45 km 2 ). We generally observed diel DOC fluctuations with a maximum in the afternoon during days thatwere not affected by rainfall-runoff events. We identified an increased inflow of terrestrial DOC to the stream in the afternoon, causing the DOC maxima in the stream. The terrestrial origin of the DOC was derived from the SUVA-254(specific UV absorbance at 254 nm) index, which is a good indicator for the aromaticity of DOC. In the studied catchment, the only possible process that can explain the diel DOC input variations towards the stream is the so-called viscosity effect. 15The water temperature in the upper parts of the riparian zone is increasing during the day, leading to a lower viscosity and therefore a higher hydraulic conductivity. Consequently, more water from areas that are rich in terrestrial DOC passes through the riparian zone and contributes to streamflow in the afternoon. We believe that not only diel instream processes, but also viscosity driven diel fluctuations of terrestrial DOC input should be considered for explaining diel DOC patterns in streams. 20Biogeosciences Discuss., https://doi

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Structural characterization of dissolved organic matter: a review of current techniques for isolation and analysis

Cited by 208 publications

References 175 publications

Untargeted soil metabolomics methods for analysis of extractable organic matter

Untargeted soil metabolomics methods for analysis of extractable organic matter

Sources, Ages, and Alteration of Organic Matter in Estuaries

Diel fluctuations of viscosity-driven riparian inflow affect streamflow DOC concentration

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