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Collins, J. R., B. R. Edwards, Helen F. Fredricks, and B. A. S. Van Mooy. LOBSTAHS: An adduct-based lipidomics strategy for discovery and identification of oxidative stress biomarkers. Analytical Chemistry 88:7154-7162; doi:10.1021/acs.analchem.6b01260

Discovery and identification of molecular biomarkers in large LC/MS datasets requires significant automation without loss of accuracy in the compound screening and annotation process. Here we describe a lipidomics workflow and open-source software package for high-throughput annotation and putative identification of lipid, oxidized lipid, and oxylipin biomarkers in high-mass-accuracy HPLC-MS data. Lipid and Oxylipin Biomarker Screening through Adduct Hierarchy Sequences, or LOBSTAHS, uses orthogonal screening criteria based on adduct ion formation patterns and other properties to identify thousands of compounds while providing the user with a confidence score for each assignment. Assignments are made from one of two customizable databases; the default databases contain 14,068 unique entries. To demonstrate the software's functionality, we screened more than 340,000 mass spectral features from an experiment in which hydrogen peroxide was used to induce oxidative stress in the marine diatom Phaeodactylum tricornutum. LOBSTAHS putatively identified 1,969 unique parent compounds in 21,869 features that survived the multi-stage screening process. While P. tricornutum maintained more than 92% of its core lipidome under oxidative stress, patterns in biomarker distribution and abundance indicated remodeling was both subtle and pervasive. Treatment with 150 μM H2O2 promoted statistically significant carbon-chain elongation across lipid classes, with the strongest elongation accompanying oxidation in moieties of monogalactosyldiacylglycerol, a lipid typically localized to the chloroplast. Oxidative stress also induced a pronounced reallocation of lipidome peak area to triacylglycerols. LOBSTAHS can be used with environmental or experimental data from a variety of systems and is freely available at

» Article: PDF
» Supporting information, including detailed instructions for reproduction of results and figures: PDF
» Software: "LOBSTAHS" R package
» Code: R scripts used for data analysis and generation of figures
» Data: Thermo .raw data files | "PtH2O2lipids" R package; processed data in xcms and LOBSTAHS objects

Collins, J. R., B. R. Edwards, K. Thamatrakoln, J. E. Ossolinski, G. R. DiTullio, K. D. Bidle, S. C. Doney, and B. A. S. Van Mooy. 2015. The multiple fates of sinking particles in the North Atlantic Ocean. Global Biogeochemical Cycles 29:1471-1494; doi:10.1002/2014GB005037

The direct respiration of sinking organic matter by attached bacteria is often invoked as the dominant sink for settling particles in the mesopelagic ocean. However, other processes, such as enzymatic solubilization and mechanical disaggregation, also contribute to particle flux attenuation by transferring organic matter to the water column. Here we use observations from the North Atlantic Ocean, coupled to sensitivity analyses of a simple model, to assess the relative importance of particle-attached microbial respiration compared to the other processes that can degrade sinking particles. The observed carbon fluxes, bacterial production rates, and respiration by water column and particle-attached microbial communities each spanned more than an order of magnitude. Rates of substrate-specific respiration on sinking particle material ranged from 0.007 ± 0.003 to 0.173 ± 0.105 day-1. A comparison of these substrate-specific respiration rates with model results suggested sinking particle material was transferred to the water column by various biological and mechanical processes nearly 3.5 times as fast as it was directly respired. This finding, coupled with strong metabolic demand imposed by measurements of water column respiration (729.3 ± 266.0 mg C m-2 d-1, on average, over the 50 to 150 m depth interval), suggested a large fraction of the organic matter evolved from sinking particles ultimately met its fate through subsequent remineralization in the water column. At three sites, we also measured very low bacterial growth efficiencies and large discrepancies between depth-integrated mesopelagic respiration and carbon inputs.

» Article: PDF
» Supplementary information: PDF
» Code: MATLAB & R scripts for model and figures | MATLAB scripts for analysis of bacterial production data
» Cruise data: KN207-1 | KN207-3

Collins, J. R., P. A. Raymond, W. F. Bohlen, and M. M. Howard-Strobel. 2013. Estimates of new and total productivity in central Long Island Sound from in situ measurements of nitrate and dissolved oxygen. Estuaries and Coasts 36:74-97; doi:10.1007/s12237-012-9560-5

Biogeochemical cycles in estuaries are regulated by a diverse set of physical and biological variables that operate over a variety of time scales. Using in situ optical sensors, we conducted a high-frequency time-series study of several biogeochemical parameters at a mooring in central Long Island Sound from May to August 2010. During this period, we documented well-defined diel cycles in nitrate concentration that were correlated to dissolved oxygen, wind stress, tidal mixing, and irradiance. By filtering the data to separate the nitrate time series into various signal components, we estimated the amount of variation that could be ascribed to each process. Primary production and surface wind stress explained 59 and 19%, respectively, of the variation in nitrate concentrations. Less frequent physical forcings, including large-magnitude wind events and spring tides, served to decouple the relationship between oxygen, nitrate, and sunlight on about one quarter of study days. Daytime nitrate minima and dissolved oxygen maxima occurred nearly simultaneously on the majority (>80 %) of days during the study period; both were strongly correlated with the daily peak in irradiance. Nighttime nitrate maxima reflected a pattern in which surface-layer stocks were depleted each afternoon and recharged the following night. Changes in nitrate concentrations were used to generate daily estimates of new primary production (182 ± 37 mg C m-2 day-1) and the ƒ ratio (0.25), i.e., the ratio of production based on nitrate to total production. These estimates, the first of their kind in Long Island Sound, were compared to values of community respiration, primary productivity, and net ecosystem metabolism, which were derived from in situ measurements of oxygen concentration. Daily averages of the three metabolic parameters were 1,660 ± 431, 2,080 ± 419, and 429 ± 203 mg C m-2 day-1, respectively. While the system remained weakly autotrophic over the duration of the study period, we observed very large day-to-day differences in the ƒ ratio and in the various metabolic parameters.

» Article: PDF
» Data: Excel files containing all data and calculations