Collins James R.

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Collins

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James R.

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The molecular products and biogeochemical significance of lipid photooxidation in West Antarctic surface waters

( 2018-04) Collins, James R. ; Fredricks, Helen F. ; Bowman, Jeff S. ; Ward, Collin P. ; Moreno, Carly ; Longnecker, Krista ; Marchetti, Adrian ; Hansel, Colleen M. ; Ducklow, Hugh W. ; Van Mooy, Benjamin A. S.

The seasonal depletion of stratospheric ozone over the Southern Hemisphere allows abnormally high doses of ultraviolet radiation (UVR) to reach surface waters of the West Antarctic Peninsula (WAP) in the austral spring, creating a natural laboratory for the study of lipid photooxidation in the shallow mixed layer of the marginal ice zone. The photooxidation of lipids under such conditions has been identified as a significant source of stress to microorganisms, and short-chain fatty acids altered by photochemical processes have been found in both marine aerosols and sinking marine particle material. However, the biogeochemical impact of lipid photooxidation has not been quantitatively compared at ecosystem scale to the many other biological and abiotic processes that can transform particulate organic matter in the surface ocean. We combined results from field experiments with diverse environmental data, including high-resolution, accurate-mass HPLC-ESI-MS analysis of lipid extracts and in situ measurements of ultraviolet irradiance, to address several unresolved questions about lipid photooxidation in the marine environment. In our experiments, we used liposomes — nonliving, cell-like aggregations of lipids — to examine the photolability of various moieties of the intact polar diacylglycerol (IP-DAG) phosphatidylcholine (PC), a structural component of membranes in a broad range of microorganisms. We observed significant rates of photooxidation only when the molecule contained the polyunsaturated fatty acid (PUFA) docosahexaenoic acid (DHA). As the DHA-containing lipid was oxidized, we observed the steady ingrowth of a diversity of oxylipins and oxidized IP-DAG; our results suggest both the intact IPDAG the degradation products were amenable to heterotrophic assimilation. To complement our experiments, we used an enhanced version of a new lipidomics discovery software package to identify the lipids in water column samples and in several diatom isolates. The galactolipid digalactosyldiacylglycerol (DGDG), the sulfolipid sulfoquinovosyldiacylglycerol (SQDG) and the phospholipids PC and phosphatidylglycerol (PG) accounted for the majority of IP-DAG in the water column particulate (≥ 0.2 μm) size fraction; between 3.4 and 5.3 % of the IP-DAG contained fatty acids that were both highly polyunsaturated (i.e., each containing ≥ 5 double bonds). Using a broadband apparent quantum yield (AQY) that accounted for direct and Type I (i.e., radical-mediated) photooxidation of PUFA-containing IP-DAG, we estimated that 0.7 ± 0.2 μmol IP-DAG m-2 d-1 (0.5 ± 0.1 mg C m-2 d-1) were oxidized by photochemical processes in the mixed layer. This rate represented 4.4 % (range, 3-21 %) of the mean bacterial production rate measured in the same waters immediately following the retreat of the sea ice. Because our liposome experiments were not designed to account for oxidation by Type II photosensitized processes that often dominate in marine phytodetritus, our rate estimates may represent a sizeable underestimate of the true rate of lipid photooxidation in the water column. While production of such diverse oxidized lipids and oxylipins has been previously observed in terrestrial plants and mammals in response to biological stressors such as disease, we show here that a similar suite of molecules can be produced via an abiotic process in the environment and that the effect can be commensurate in magnitude with other ecosystem-scale biogeochemical processes.
Daily changes in phytoplankton lipidomes reveal mechanisms of energy storage in the open ocean

(Nature Publishing Group, 2018-12-05) Becker, Kevin W. ; Collins, James R. ; Durham, Bryndan P. ; Groussman, Ryan D. ; White, Angelicque E. ; Fredricks, Helen F. ; Ossolinski, Justin E. ; Repeta, Daniel J. ; Carini, Paul ; Armbrust, E. Virginia ; Van Mooy, Benjamin A. S.

Sunlight is the dominant control on phytoplankton biosynthetic activity, and darkness deprives them of their primary external energy source. Changes in the biochemical composition of phytoplankton communities over diel light cycles and attendant consequences for carbon and energy flux in environments remain poorly elucidated. Here we use lipidomic data from the North Pacific subtropical gyre to show that biosynthesis of energy-rich triacylglycerols (TAGs) by eukaryotic nanophytoplankton during the day and their subsequent consumption at night drives a large and previously uncharacterized daily carbon cycle. Diel oscillations in TAG concentration comprise 23 ± 11% of primary production by eukaryotic nanophytoplankton representing a global flux of about 2.4 Pg C yr−1. Metatranscriptomic analyses of genes required for TAG biosynthesis indicate that haptophytes and dinoflagellates are active members in TAG production. Estimates suggest that these organisms could contain as much as 40% more calories at sunset than at sunrise due to TAG production.
The remineralization of marine organic matter by diverse biological and abiotic processes

(Massachusetts Institute of Technology and Woods Hole Oceanographic Institution, 2017-02) Collins, James R.

While aerobic respiration is typically invoked as the dominant mass-balance sink for organic matter in the upper ocean, many other biological and abiotic processes can degrade particulate and dissolved substrates on globally significant scales. The relative strengths of these other remineralization processes — including mechanical mechanisms such as dissolution and disaggregation of sinking particles, and abiotic processes such as photooxidation — remain poorly constrained. In this thesis, I examine the biogeochemical significance of various alternative pathways of organic matter remineralization using a combination of field experiments, modeling approaches, geochemical analyses, and a new, high-throughput lipidomics method for identification of lipid biomarkers. I first assess the relative importance of particleattached microbial respiration compared to other processes that can degrade sinking marine particles. A hybrid methodological approach — comparison of substrate-specific respiration rates from across the North Atlantic basin with Monte Carlo-style sensitivity analyses of a simple mechanistic model — 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, questioning the conventional assumption that direct respiration dominates remineralization. I next present and demonstrate a new lipidomics method and open-source software package for discovery and identification of molecular biomarkers for organic matter degradation in large, high-mass-accuracy HPLC-ESI-MS datasets. I use the software to unambiguously identify more than 1,100 unique lipids, oxidized lipids, and oxylipins in data from cultures of the marine diatom Phaeodactylum tricornutum that were subjected to oxidative stress. Finally, I present the results of photooxidation experiments conducted with liposomes — nonliving aggregations of lipids — in natural waters of the Southern Ocean. A broadband polychromatic apparent quantum yield (AQY) is applied to estimate rates of lipid photooxidation in surface waters of the West Antarctic Peninsula, which receive seasonally elevated doses of ultraviolet radiation as a consequence of anthropogenic ozone depletion in the stratosphere. The mean daily rate of lipid photooxidation (50 ± 11 pmol IP-DAG L−1 d−1, equivalent to 31 ± 7 𝜇g C m−3 d−1) represented between 2 and 8 % of the total bacterial production observed in surface waters immediately following the retreat of the sea ice.
An autonomous, in situ light-dark bottle device for determining community respiration and net community production

( 2018-03) Collins, James R. ; Fucile, Paul D. ; McDonald, Glenn ; Ossolinski, Justin E. ; Keil, Richard G. ; Valdes, James R. ; Doney, Scott C. ; Van Mooy, Benjamin A. S.

We describe a new, autonomous, incubation-based instrument that is deployed in situ to determine rates of gross community respiration and net community production in marine and aquatic ecosystems. During deployments at a coastal pier and in the open ocean, the PHORCYS (PHOtosynthesis and Respiration Comparison-Yielding System) captured dissolved oxygen fluxes over hourly timescales that were missed by traditional methods. The instrument uses fluorescence-quenching optodes fitted into separate light and dark chambers; these are opened and closed with piston-like actuators, allowing the instrument to make multiple, independent rate estimates in the course of each deployment. Consistent with other studies in which methods purporting to measure the same metabolic processes have yielded divergent results, respiration rate estimates from the PHORCYS were systematically higher than those calculated for the same waters using a traditional two-point Winkler titration technique. However, PHORCYS estimates of gross respiration agreed generally with separate incubations in bottles fitted with optode sensor spots. An Appendix describes a new method for estimating uncertainties in metabolic rates calculated from continuous dissolved oxygen data. Multiple successful, unattended deployments of the PHORCYS represent a small step toward fully autonomous observations of community metabolism. Yet the persistence of unexplained disagreements among aquatic metabolic rate estimates — such as those we observed between rates calculated with the PHORCYS and two existing, widely-accepted bottle-based methods — suggests that a new community intercalibration effort is warranted to address lingering sources of error in these critical measurements.
Estimates of new and total productivity in central Long Island Sound from in situ measurements of nitrate and dissolved oxygen

( 2013-01) Collins, James R. ; Raymond, Peter A. ; Bohlen, Walter Franklin ; Howard-Strobel, Mary M.

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 d-1) and the f-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 1660 ± 431, 2080 ± 419, and 429 ± 203 mg C m-2 d-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 f-ratio and in the various metabolic parameters.
The multiple fates of sinking particles in the North Atlantic Ocean

(John Wiley & Sons, 2015-09-25) Collins, James R. ; Edwards, Bethanie R. ; Thamatrakoln, Kimberlee ; Ossolinski, Justin E. ; DiTullio, Giacomo R. ; Bidle, Kay D. ; Doney, Scott C. ; Van Mooy, Benjamin A. S.

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.
Whole community metatranscriptomes and lipidomes reveal diverse responses among antarctic phytoplankton to changing ice conditions

(Frontiers Media, 2021-02-18) Bowman, Jeff S. ; Van Mooy, Benjamin A. S. ; Lowenstein, Daniel P. ; Fredricks, Helen F. ; Hansel, Colleen M. ; Gast, Rebecca J. ; Collins, James R. ; Couto, Nicole ; Ducklow, Hugh W.

The transition from winter to spring represents a major shift in the basal energy source for the Antarctic marine ecosystem from lipids and other sources of stored energy to sunlight. Because sea ice imposes a strong control on the transmission of sunlight into the water column during the polar spring, we hypothesized that the timing of the sea ice retreat influences the timing of the transition from stored energy to photosynthesis. To test the influence of sea ice on water column microbial energy utilization we took advantage of unique sea ice conditions in Arthur Harbor, an embayment near Palmer Station on the western Antarctic Peninsula, during the 2015 spring–summer seasonal transition. Over a 5-week period we sampled water from below land-fast sea ice, in the marginal ice zone at nearby Palmer Station B, and conducted an ice removal experiment with incubations of water collected below the land-fast ice. Whole-community metatranscriptomes were paired with lipidomics to better understand how lipid production and utilization was influenced by light conditions. We identified several different phytoplankton taxa that responded similarly to light by the number of genes up-regulated, and in the transcriptional complexity of this response. We applied a principal components analysis to these data to reduce their dimensionality, revealing that each of these taxa exhibited a strikingly different pattern of gene up-regulation. By correlating the changes in lipid concentration to the first principal component of log fold-change for each taxa we could make predictions about which taxa were associated with different changes in the community lipidome. We found that genes coding for the catabolism of triacylglycerol storage lipids were expressed early on in phytoplankton associated with a Fragilariopsis kerguelensis reference transcriptome. Phytoplankton associated with a Corethron pennatum reference transcriptome occupied an adjacent niche, responding favorably to higher light conditions than F. kerguelensis. Other diatom and dinoflagellate taxa had distinct transcriptional profiles and correlations to lipids, suggesting diverse ecological strategies during the polar winter–spring transition.
LOBSTAHS : an adduct-based lipidomics strategy for discovery and identification of oxidative stress biomarkers

(American Chemical Society, 2016-06-20) Collins, James R. ; Edwards, Bethanie R. ; Fredricks, Helen F. ; Van Mooy, Benjamin A. S.

Discovery and identification of molecular biomarkers in large LC/MS data sets 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 1969 unique parent compounds in 21 869 features that survived the multistage 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 https://github.com/vanmooylipidomics/LOBSTAHS.
A code of conduct is imperative for ocean carbon dioxide removal research

(Frontiers Media, 2022-05-02) Loomis, Rebecca ; Cooley, Sarah R. ; Collins, James R. ; Engler, Simon ; Suatoni, Lisa

As the impacts of rising temperatures mount and the global transition to clean energy advances only gradually, scientists and policymakers are looking towards carbon dioxide removal (CDR) methods to prevent the worst impacts of climate change. Attention has increasingly focused on ocean CDR techniques, which enhance or restore marine systems to sequester carbon. Ocean CDR research presents the risk of uncertain impacts to human and environmental welfare, yet there are no domestic regulations aimed at ensuring the safety and efficacy of this research. A code of conduct that establishes principles of responsible research, fairness, and equity is needed in this field. This article presents fifteen key components of an ocean CDR research code of conduct.
Auxiliary material for "Estimates of new and total productivity in central Long Island Sound from in situ measurements of nitrate and dissolved oxygen"

( 2013) Collins, James R. ; Raymond, Peter A. ; Bohlen, Walter Franklin ; Howard-Strobel, Mary M.

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 d-1) and the f-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 1660 ± 431, 2080 ± 419, and 429 ± 203 mg C m-2 d-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 f-ratio and in the various metabolic parameters.

Collins James R.

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