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All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

SPRUCE 13C-Phospholipid Fatty Acid (13C-PLFA) Abundances, June 2014-June 2015

This data set provides the results of 13C phospholipid fatty acid analysis (13C-PLFA) of peat samples collected from ambient and experimental plots in the SPRUCE experiment site. The samples used to generate this data set were collected just prior to initiation of deep peat heating (DPH; 03 June 2014), after 3 months (09 September 2014), and after 10 months (16 June 2015). This data set includes the abundances and delta-13C isotopic signatures of individual lipids and of groups of lipids indicating total biomass, fungi, Gram-positive bacteria, Gram-negative bacteria, actinomycetes, and anaerobic bacteria. This dataset contains two files in comma separate (*.csv) format. Cores extending to 250 cm (200 cm in June 2015) were collected and subsampled at 10 cm intervals from 0 and 100 cm and 25 cm intervals below 100 cm depth. During the lipid extraction procedure, samples were pooled into the following depth increments in order to obtain sufficient material to achieve adequate lipid yield: 0-20, 20-50, 50-100, 100-150, 150-200, and 200-250cm.

actinomycetes↗
DOE OSTI2026

Blodgett 13C–labeled litter incubation 2016-2019

The dataset is from 13C-labelled (stable isotope of carbon) root-litter in-situ field incubation experiment based on the whole-soil warming experiment at the Blodgett Forest Research Station, CA, USA. The files are in both ".csv" and ".xlsx" versions, and can be opened in "maCOS numbers", and "Microsoft Excel". The files includes several sheets with all the data published in the paper: Sun, B., Zosso, C., Wiesenberg, G. L. B., Pegoraro, E., Torn, M. S., and Schmidt, M. W. I.: Warming accelerates the decomposition of root-derived hydrolysable lipids in a temperate forest and is depth- and compound class-dependent, SOIL, 11, 1077–1093, https://doi.org/10.5194/soil-11-1077-2025, 2025. This dataset includes bulk soil carbon, nitrogen, delta 13C values, the normalized concentration (to organic carbon) of hydrolysable lipids identified, the absolute concentration (normalized to bulk soil) of hydrolysable lipids, hydrolysable lipids recovery, and weighted 13C-excess of bulk soil carbon, and weighted 13C-excess of each compound class in hydrolysable lipids. These data aim to answer two research questions: 1) How will warming affect the decomposition of 13C-labelled root-litter at different depth? 2) Will the decomposition of root-derived hydrolysable lipids under warming differ among different compound classes? The experiment sites located on the foothills of the Sierra Nevada near Georgetown, CA (120°3904000W; 38°5404300 N) at 1370m above see level. The Blodgett Forest is a mixed-coniferous forest. The site has a Mediterranean climate with a mean annual air temperature of 12.5 °C and a mean annual precipitation of 1774mm.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

GLBRC Soil Yearlong Incubation 13C-SIP-Lipidomics

Data package for Lipids represent a dynamic, yet stable pool of microbially-derived soil carbon This data is published under a CC0 license. The authors encourage data reuse and request attribution by referencing the below citations for the data packages and associated manuscript. Please cite as: Rempfert KR, Bell SL, Kasanke CP, Kyle JE, Hofmockel KS. 2025. GLBRC Soil Yearlong Incubation 13C-SIP-Lipidomics. [Data Set] PNNL DataHub. doi: Rempfert KR, Bell SL, Kasanke CP, Kyle JE, Hofmockel KS. 2025. MSV000097435: GLBRC soil yearlong incubation 13C-SIP-Lipidomics [Data Set] MassIVE. doi:10.25345/C57659T3K Rempfert KR, Bell SL, Kasanke CP, Kyle JE, Hofmockel KS. 2025. Lipids represent a dynamic, yet stable pool of microbially-derived soil carbon. In Prep This data package consists of compound-specific 13C SIP-lipidomics data from a yearlong tracer incubation experiment designed to investigate microbial lipid persistence in switchgrass bioenergy crop soils. In order to explore how lipid structure may modulate the persistence of C in soil lipids, we leveraged soils from two sites (Michigan - sandy texture, Wisconsin - silty texture) operated by the U.S. Department of Energy-funded Great Lakes Bioenergy Research Center (GLBRC). These sites had comparable climates, identical management practices, but contrasting soil textures, allowing us to assess the variability of lipid accrual or degradation in soils as well as provide insight regarding the degree to which edaphic properties may regulate the retention of soil lipids. Untargeted lipidomics analyses were performed to identify 13C-labeled lipids in the soil microbiome after long-term incubation. Soils were supplemented with 100 micrograms glucose per gram dry soil (99 atom % 13C or natural abundance for paired control) and incubated; samples were collected two months and one year after glucose addition. Lipid extracts (MPLEx) were analyzed by LC-MS/MS and identified using LIQUID. Calculation of isotopic enrichment of lipids was performed by targeted approach using TarMet to quantify lipid isotopologues and IsoCorrectoR to correct for natural abundance isotopes. Contents: Data package contents reported here are the first version and contain downstream analysis files for the raw LC-MS mass spectrometry files (.mzXML) deposited at the MassIVE database repository under accession MSV000097435 (80 experimental runs; 5.85 GB) | MassIVE DOI: 10.25345/C57659T3K. Support files include the additional data download 'Read Me' file containing data descriptor information. Reported data download contents are structured for compliance with project data sharing guidelines, community standards initiatives, and sponsor stakeholder policies supporting FAIR data principles. Data processing software, analysis tools, and data workflows are listed below corresponding to the host repository long-term location. Available Data Downloads (0.3 GB): "GLBRC soil yearlong incubation 13C-SIP-Lipidomics_readme.txt" - 'Read Me' data package content file (txt) "GLBRC_DataPackage_analysis files" - Data processing files (Rmd) and saved intermediate data processing outputs (rds, csv, xlsx) "GLBRC_13C_lipidomics_dataset.xlsx" - processed data in tabular format (xlsx) Linked Software: LIQUID LC-MS Analysis Software | 10.5281/zenodo.6459462 Lipid Mini-On Software Tools | 10.5281/zenodo.1492803 pmartR Omics Statistical Software | 10.5281/zenodo.6108667 xcms (v4.3.3) TarMet (v1.1.1) IsoCorrectoR (1.24.0) Funding Acknowledgments: This research was supported by an Early Career Research Program award funded by the U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research (OBER) Genomic Science program under FWP 68292, FWP 07880 and EMSL Exploratory Research Project 51095. A portion of this work was performed in the William R. Wiley Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by OBER and located at Pacific Northwest National Laboratory (PNNL). PNNL is a multi-program national laboratory operated by Battelle for the DOE under Contract DE-AC05-76RLO1830.

Rempfert, Kaitlin R [Pacific Northwest National La↗
DOE OSTI2022

Castanha et al. 2018: Hopland Lysimeter 13C-Labeled Root Litter Decomposition Study.

The breakdown and decomposition of plant inputs are critical for nutrient cycling, soil development, and climate-ecosystem feedbacks, but uncertainties persist in how the rates and products of litter decomposition are affected by soil temperature, rhizosphere, and depth of input. To elucidate these questions we measured the effects of soil warming (+ 4 °C), rhizosphere, and depth of litter placement on the decomposition of Avena fatua (wild oat grass) root litter in a Mediterranean grassland ecosystem. Field lysimeters were subjected to three environmental treatments (heating, control, and plant removal) and three 13C-labeled root litter addition treatments (to A horizon, to B horizon, and no-addition disturbance control) for each of two harvest time points. We buried root litter in February 2014 and measured loss of 13C in CO2 from the soil surface and in leachate as dissolved organic carbon (DOC) over two growing seasons. At the end of each of the 2014 and 2015 growing seasons we recovered the 13C remaining in the soil. Loss of root litter C occurred almost entirely via heterotrophic respiration, with an estimated < 2% lost as DOC during the initial decay period. The added roots were broken down and incorporated into bulk soil material very quickly; only ~ 30% of added root was visible after 6 months. In the first growing season, decomposition occurred faster in the B than in the A horizon, the latter having greater moisture limitation. Subsequently, there was almost no further decomposition in the B horizon. After two growing seasons, less than 20% of the added root litter C remained in the A or B horizons of all environmental treatments. Heating did not stimulate decomposition, likely because it exacerbated the moisture limitation. However, while plots without plants dried down more slowly than plots with plants, their decomposition rate was not significantly greater, possibly due to the lack of rhizosphere processes such as priming. We conclude that in this Mediterranean grassland ecosystem, soil moisture, which is affected by season, depth, heating, and rhizosphere, plays a dominant role in mediating the effect of those factors on root litter decomposition, which after two seasons did not differ by depth or by treatment.The files in this dataset comprise (1) 13C-labeled litter additions made to each plot, (2) litter recovery after each of 2 growing seasons, (3) periodical soil flux measurements, (4) leachate measurements, and continuously monitored soil (5) temperature and (6) moisture.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Soil Respiration and Microbial Biomass from Soil Incubations with 13C Labeled Additions

This data set provides the respiration and soil microbial biomass data from a series of short and long-term laboratory incubation experiments with 13C labeled substrates to examine how plant communities (forest vs. grassland), edaphic properties, and microbial communities influence C cycling and the long-term fate of C in soil systems. Paired forest and grassland soils from four locations were incubated with 13C labeled glucose in a short-term (144 hours) study while 13C labeled cellulose was added to soils used in the long-term (729 days) study. Soil respiration, microbial biomass, and soil 13C values were monitored throughout the study. Soils were collected from paired forest and grassland locations in the following states in the United States of America: Tennessee (TN), Ohio (OH), Iowa (IA), and Missouri (MO). This dataset contains one data file in comma-separate (*.csv) format.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Analyzing Mass Spectrometry Imaging Data of 13C-Labeled Phospholipids in Camelina sativa and Thlaspi arvense (Pennycress) Embryos

The combination of 13C-isotopic labeling and mass spectrometry imaging (MSI) offers an approach to analyze metabolic flux in situ. However, combining isotopic labeling and MSI presents technical challenges ranging from sample preparation, label incorporation, data collection, and analysis. Isotopic labeling and MSI individually create large, complex data sets, and this is compounded when both methods are combined. Therefore, analyzing isotopically labeled MSI data requires streamlined procedures to support biologically meaningful interpretations. Using currently available software and techniques, here we describe a workflow to analyze 13C-labeled isotopologues of the membrane lipid and storage oil lipid intermediate―phosphatidylcholine (PC). Our results with embryos of the oilseed crops, Camelina sativa and Thlaspi arvense (pennycress), demonstrated greater 13C-isotopic labeling in the cotyledons of developing embryos compared with the embryonic axis. Greater isotopic enrichment in PC molecular species with more saturated and longer chain fatty acids suggest different flux patterns related to fatty acid desaturation and elongation pathways. The ability to evaluate MSI data of isotopically labeled plant embryos will facilitate the potential to investigate spatial aspects of metabolic flux in situ.

metabolomics↗
DOE OSTI2025

SPRUCE Air 13C and 14C Isotopes, Marcell Experimental Forest, Minnesota, 2016-2025

This data set reports 13C (carbon) and 14C signatures of air from Spruce and Peatland Responses Under Changing Environments (SPRUCE) experimental study plots located in the S1-Bog at the Marcell Experimental Forest in northern Minnesota from 2016-2025 (2016-04-13 to 2025-09-24). Air measurements were collected approximately five times throughout each active growing season beginning in 2016 and included the 10 SPRUCE experimental plots (Plots 4, 6, 8, 10, 11, 13, 16, 17, 19, and 20) two ambient co-located ambient plots (Plots 7 and 21) and a site at the Marcell Experiment Station’s S2-Bog meteorological station (MET) located 1.7 km northeast of the SPRUCE experimental site on the S1-Bog. Air samples were assessed for both 13C- and 14C-CO2 (carbon-carbon dioxide) signatures. 13C and 14C isotopic signatures can be used in end-member analysis and C-cycle models to track the movement of C within the experimental ecosystem, calculate turnover times within plant tissues, and to test mechanisms used in models. This dataset contains one data file in comma separate (*.csv) format. Additional metadata are provided: one data dictionary and a file-level metadata file in comma separate (*.csv) format and a user guide in PDF (*.pdf) format.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Methodology for the development of empirical models relating 13C NMR spectral features to fuel properties

Effective formulation of new gasoline or diesel fuels for internal combustion engines would benefit from the development of reliable models for predicting key fuel properties based on a set of molecular descriptors obtained from a single measurement. This is particularly relevant in the case of renewable fuels, where the available fuel sample quantity may be limited. In this work, we present a statistically-based methodology for building empirical models to predict multiple properties from one-dimensional 13C nuclear magnetic resonance (NMR) spectra measured on around 200 microliters of a liquid fuel. NMR spectra contain information about the molecular composition of a sample and the carbon types and molecular substructures therein. Our approach uses this information to build sparse, interpretable models, where the predicted properties are linked to specific molecular features. The approach takes into consideration the constrained nature of the features making up the one-dimensional NMR spectrum, which, after standardization, represent a relative fuel composition. We point to the limitations in interpretability that arise when building this type of empirical predictive model and suggest how these limitations may be diminished. Among the many properties important for maximizing engine performance and minimizing emissions, we build models that predict derived cetane number and distillation temperatures as these are of particular interest because of their links to fuel economy, drivability, and engine-out emissions. Results suggest that the properties of interest may be impacted by only a few of the 27 13C NMR regions represented in the data, pointing to new directions for further testing in the development of improved fuels.

predictive models, biofuels., NMR Analysis↗
DOE OSTI2022

Hicks Pries, Sulman, et al 2018. In situ incubation of 13C-labeled litter in three soil pits at Blodgett Forest, CA from 2013 to 2016

Even though over half of the world's soil organic carbon (SOC) is stored in subsoils (>20 cm deep), and the old ages of subsoil OC indicate its cycling differs from surface SOC, there are few studies examining in situ decomposition processes in deep soils. The purpose of this dataset is to elucidate these processes. In this study we added 13C-labeled fine roots to 15, 55, and 95 cm depths of a well-characterized coniferous forest Alfisol and monitored the amount of root-derived C remaining over 6, 12, and 30 months. We recovered the root-derived C in microbial phospholipid fatty acids (PLFAs) after 6 months and in coarse (>2 mm) particulate, fine (<2 mm) particulate, and dense, mineral-associated pools after 6, 12, and 30 months. Overall, root decomposition in the first 6 months was similar among all depths but significantly diverged at 30 months with faster decomposition at 15 cm than at 95 cm. There were more fungal and Gram negative-associated PLFAs at 15 cm than at 95 cm, and 13C analysis revealed those microbial groups preferred the added root carbon to native SOC. Mineral-associations were not the cause of slower decomposition at depth because similar amounts of applied root C was recovered in the dense fraction at all depths. The largest difference among depths was in the amount of root C recovered in the coarse particulate fraction, which was greater at 95 cm (50%) than at 15 cm (15%). Slower decomposition of the particulate pool at depth likely contributed to the increase in C:N ratios and depletion of δ13C values below 60 cm depth in our soil profiles. Simulations of these soils using the CORPSE model, which incorporates microbial priming effects and mineral stabilization of SOC, reproduced patterns of particulate and mineral-associated SOC over both time and depth and suggested that a lack of priming by root exudates at depth could account for the slower decomposition rate of particulate root material. Decomposition of deep particulate SOC may increase if root exudation or dissolved OC transport to depth increases.This dataset includes (1) characterization of the soil pits prior to litter addition, (2) characterization of how the litter changed after 6, 12, and 30 months, and (3) the CORPSE model structure, parameterization, and output.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

13C-labeling reveals how membrane lipid components contribute to triacylglycerol accumulation in Chlamydomonas

Abstract Lipid metabolism in microalgae has attracted much interest due to potential utilization of lipids as feedstocks for biofuels, nutraceuticals, and other high-value compounds. Chlamydomonas reinhardtii is a model organism for characterizing the synthesis of the neutral lipid triacylglycerol (TAG), from which biodiesel is made. While much of TAG accumulation under N-deprivation is the result of de novo fatty acid (FA) synthesis, recent work has revealed that approximately one-third of FAs, especially polyunsaturated FAs (PUFAs), come from preexisting membrane lipids. Here, we used 13C-isotopic labeling and mass spectrometry to analyze the turnover of glycerol backbones, headgroups, FAs, whole molecules, and molecular fragments of individual lipids. About one-third of the glyceryl backbones in TAG are derived from preexisting membrane lipids, as are approximately one-third of FAs. The different moieties of the major galactolipids turn over synchronously, while the FAs of diacylglyceryltrimethylhomoserine (DGTS), the most abundant extraplastidial lipid, turn over independently of the rest of the molecule. The major plastidic lipid monogalactosyldiacylglycerol (MGDG), whose predominant species is 18:3α/16:4, was previously shown to be a major source of PUFAs for TAG synthesis. This study reveals that MGDG turns over as whole molecules, the 18:3α/16:4 species is present in both DAG and TAG, and the positional distribution of these PUFAs is identical in MGDG, DAG, and TAG. We conclude that headgroup removal with subsequent acylation is the mechanism by which the major MGDG species is converted to TAG during N-deprivation. This has noteworthy implications for engineering the composition of microalgal TAG for food, fuel, and other applications.

Plant Sciences↗