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Quinlan, Z. A., Nelson, C. E., Koester, I., Petras, D., Nothias, L., Comstock, J., White, B. M., Aluwihare, L. I., Bailey, B. A., Carlson, C. A., Dorrestein, P. C., Haas, A. F., & Wegley Kelly, L. (2025). Microbial Community Metabolism of Coral Reef Exometabolomes Broadens the Chemodiversity of Labile Dissolved Organic Matter. Environmental Microbiology, 27(3), e70064. https://doi.org/10.1111/1462-2920.70064

McGill, L., Sleugh, T., Petrik, C., Schiff, K., McLaughlin, K., Aluwihare, L., & Semmens, B. (2024). The persistent DDT footprint of ocean disposal, and ecological controls on bioaccumulation in fishes. Proceedings of the National Academy of Sciences, 121(45), e2401500121. https://doi.org/10.1073/pnas.2401500121

Papadopoulos Lambidis, S., Schramm, T., Steuer-Lodd, K., Farrell, S., Stincone, P., Schmid, R., Koester, I., Torres, R., Dittmar, T., Aluwihare, L., Simon, C., & Petras, D. (2024). Two-Dimensional Liquid Chromatography Tandem Mass Spectrometry Untangles the Deep Metabolome of Marine Dissolved Organic Matter. Environmental Science & Technology, 58(43), 19289–19304. https://doi.org/10.1021/acs.est.4c07173

Stack, M. E., Richardot, W. H., Garcia, R., Nguyen, T., Choy, C. A., Jensen, P. R., Gutleben, J., Dodder, N. G., Aluwihare, L. I., & Hoh, E. (2024). Identification of DDT+ in Deep Ocean Sediment and Biota in the Southern California Bight. Environmental Science & Technology Letters, 11(5), 479–484. https://doi.org/10.1021/acs.estlett.4c00115

Letscher, R. T., & Aluwihare, L. I. (2024). A simple method for the quantification of amidic bioavailable dissolved organic nitrogen in seawater. Limnology and Oceanography: Methods, lom3.10622. https://doi.org/10.1002/lom3.10622

Sparagon, W. J., Arts, M. G. I., Quinlan, Z. A., Wegley Kelly, L., Koester, I., Comstock, J., Bullington, J. A., Carlson, C. A., Dorrestein, P. C., Aluwihare, L. I., Haas, A. F., & Nelson, C. E. (2024). Coral thermal stress and bleaching enrich and restructure reef microbial communities via altered organic matter exudation. Communications Biology, 7(1), 160. https://doi.org/10.1038/s42003-023-05730-0

Manck, L. E., Coale, T. H., Stephens, B. M., Forsch, K. O., Aluwihare, L. I., Dupont, C. L., Allen, A. E., & Barbeau, K. A. (2024). Iron limitation of heterotrophic bacteria in the California Current System tracks relative availability of organic carbon and iron. The ISME Journal, 18(1), wrae061. https://doi.org/10.1093/ismejo/wrae061

Bowen, J. C., Hoyt, A. M., Xu, X., Nuriman, M., Anshari, G. Z., Wahyudio, P. J., & Aluwihare, L. I. (2024). Aquatic processing enhances the loss of aged carbon from drained and burned peatlands. Global Change Biology, 30(7), e17394. https://doi.org/10.1111/gcb.17394

Bowen, J. C., Wahyudio, P. J., Anshari, G. Z., Aluwihare, L. I., & Hoyt, A. M. (2024). Canal networks regulate aquatic losses of carbon from degraded tropical peatlands. Nature Geoscience, 17(3), 213–218. https://doi.org/10.1038/s41561-024-01383-8

Swalethorp, R., Landry, M. R., Semmens, B. X., Ohman, M. D., Aluwihare, L., Chargualaf, D., & Thompson, A. R. (2023). Anchovy boom and bust linked to trophic shifts in larval diet. Nature Communications, 14(1), 7412. https://doi.org/10.1038/s41467-023-42966-0

Eglinton, T. I., Graven, H. D., Raymond, P. A., Trumbore, S. E., Aluwihare, L., Bard, E., Basu, S., Friedlingstein, P., Hammer, S., Lester, J., Sanderman, J., Schuur, E. A. G., Sierra, C. A., Synal, H.-A., Turnbull, J. C., & Wacker, L. (2023). Making the case for an International Decade of Radiocarbon. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, 381(2261), 20230081. https://doi.org/10.1098/rsta.2023.0081

James, B. D., Reddy, C. M., Hahn, M. E., Nelson, R. K., De Vos, A., Aluwihare, L. I., Wade, T. L., Knap, A. H., & Bera, G. (2023). Fire and Oil Led to Complex Mixtures of PAHs on Burnt and Unburnt Plastic during the M/V X-Press Pearl Disaster. ACS Environmental Au, acsenvironau.3c00011. https://doi.org/10.1021/acsenvironau.3c00011

White, M. E., Nguyen, T. B., Koester, I., Lardie Gaylord, M. C., Beman, J. M., Smith, K. L., McNichol, A. P., Beaupré, S. R., & Aluwihare, L. I. (2023). Refractory Dissolved Organic Matter has Similar Chemical Characteristics but Different Radiocarbon Signatures With Depth in the Marine Water Column. Global Biogeochemical Cycles, 37(4), e2022GB007603. https://doi.org/10.1029/2022GB007603

Quinlan, Z. A., Koester, I., Aron, A. T., Petras, D., Aluwihare, L. I., Dorrestein, P. C., Nelson, C. E., & Wegley Kelly, L. (2022). ConCISE: Consensus Annotation Propagation of Ion Features in Untargeted Tandem Mass Spectrometry Combining Molecular Networking and In Silico Metabolite Structure Prediction. Metabolites, 12(12), 1275. https://doi.org/10.3390/metabo12121275

Phillips, A. A., White, M. E., Seidel, M., Wu, F., Pavia, F. F., Kemeny, P. C., Ma, A. C., Aluwihare, L. I., Dittmar, T., & Sessions, A. L. (2022). Novel sulfur isotope analyses constrain sulfurized porewater fluxes as a minor component of marine dissolved organic matter. Proceedings of the National Academy of Sciences, 119(41), e2209152119. https://doi.org/10.1073/pnas.2209152119

White, M. E., Rafter, P. A., Stephens, B. M., Mazloff, M. R., Wankel, S. D., & Aluwihare, L. I. (2022). Stable isotopes of nitrate record effects of the 2015–2016 El Niño and diatom iron limitation on nitrogen cycling in the eastern North Pacific Ocean. Limnology and Oceanography, lno.12194. https://doi.org/10.1002/lno.12194

Lewis, S. L., Russell, L. M., Saliba, G., Quinn, P. K., Bates, T. S., Carlson, C. A., Baetge, N., Aluwihare, L. I., Boss, E., Frossard, A. A., Bell, T. G., & Behrenfeld, M. J. (2022). Characterization of Sea Surface Microlayer and Marine Aerosol Organic Composition Using STXM-NEXAFS Microscopy and FTIR Spectroscopy. ACS Earth and Space Chemistry, 6(7), 1899–1913. https://doi.org/10.1021/acsearthspacechem.2c00119

Semitsoglou-Tsiapou, S., Meador, T. B., Peng, B., & Aluwihare, L. (2022). Photochemical (UV-vis/H2O2) degradation of carotenoids: Kinetics and molecular end products. Chemosphere, 286, 11. https://doi.org/10.1016/j.chemosphere.2021.131697

Koester, I., Quinlan, Z. A., Nothias, L., White, M. E., Rabines, A., Petras, D., Brunson, J. K., Dührkop, K., Ludwig, M., Böcker, S., Azam, F., Allen, A. E., Dorrestein, P. C., & Aluwihare, L. I. (2022). Illuminating the dark metabolome of Pseudo‐nitzschia –microbiome associations. Environmental Microbiology, 24(11), 5408–5424. https://doi.org/10.1111/1462-2920.16242

Cancelada, L., Torres, R. R., Luna, J. G., Dorrestein, P. C., Aluwihare, L. I., Prather, K. A., & Petras, D. (2021). Assessment of styrene-divinylbenzene polymer (PPL) solid-phase extraction and non-targeted tandem mass spectrometry for the analysis of xenobiotics in seawater. Limnology and Oceanography-Methods, 13. https://doi.org/10.1002/lom3.10470

Beman, J. M., Vargas, S. M., Wilson, J. M., Perez-Coronel, E., Karolewski, J. S., Vazquez, S., Yu, A., Cairo, A. E., White, M. E., Koester, I., Aluwihare, L. I., & Wankel, S. D. (2021). Substantial oxygen consumption by aerobic nitrite oxidation in oceanic oxygen minimum zones. Nature Communications, 12(1), 11. https://doi.org/10.1038/s41467-021-27381-7

Aron, A. T., Petras, D., Schmid, R., Gauglitz, J. M., Buttel, I., Antelo, L., Zhi, H., Nuccio, S. P., Saak, C. C., Malarney, K. P., Thines, E., Dutton, R. J., Aluwihare, L. I., Raffatellu, M., & Dorrestein, P. C. (2021). Native mass spectrometry-based metabolomics identifies metal-binding compounds. Nature Chemistry, 11. https://doi.org/10.1038/s41557-021-00803-1

Kelly, L. W., Nelson, C. E., Aluwihare, L. I., Arts, M. G. I., Dorrestein, P. C., Koester, I., Matsuda, S. B., Petras, D., Quinlan, Z. A., & Haas, A. F. (2021). Molecular commerce on coral reefs: Using metabolomics to reveal biochemical exchanges underlying holobiont biology and the ecology of coastal ecosystems. Frontiers in Marine Science, 8, 11. https://doi.org/10.3389/fmars.2021.630799

Schmid, R., Petras, D., Nothias, L. F., Wang, M. X., Aron, A. T., Jagels, A., Tsugawa, H., Rainer, J., Garcia-Aloy, M., Duhrkop, K., Korf, A., Pluskal, T., Kamenik, Z., Jarmusch, A. K., Caraballo-Rodriguez, A. M., Weldon, K. C., Nothias-Esposito, M., Aksenov, A. A., Bauermeister, A., … Dorrestein, P. C. (2021). Ion identity molecular networking for mass spectrometry-based metabolomics in the GNPS environment. Nature Communications, 12(1). https://doi.org/10.1038/s41467-021-23953-9

Petras, D., Minich, J. J., Cancelada, L. B., Torres, R. R., Kunselman, E., Wang, M. X., White, M. E., Allen, E. E., Prather, K. A., Aluwihare, L. I., & Dorrestein, P. C. (2021). Non-targeted tandem mass spectrometry enables the visualization of organic matter chemotype shifts in coastal seawater. Chemosphere, 271. https://doi.org/10.1016/j.chemosphere.2020.129450

Stephens, B. M., Opalk, K., Petras, D., Liu, S., Comstock, J., Aluwihare, L. I., Hansell, D. A., & Carlson, C. A. (2020). Organic matter composition at Ocean Station Papa affects its bioavailability, bacterioplankton growth efficiency and the responding taxa. Frontiers in Marine Science, 7. https://doi.org/10.3389/fmars.2020.590273

Ludwig, M., Nothias, L. F., Duhrkop, K., Koester, I., Fleischauer, M., Hoffmann, M. A., Petras, D., Vargas, F., Morsy, M., Aluwihare, L., Dorrestein, P. C., & Bocker, S. (2020). Database-independent molecular formula annotation using Gibbs sampling through ZODIAC. Nature Machine Intelligence, 2(10), 629-+. https://doi.org/10.1038/s42256-020-00234-6

Swalethorp, R., Aluwihare, L., Thompson, A. R., Ohman, M. D., & Landry, M. R. (2020). Errors associated with compound-specific delta N-15 analysis of amino acids in preserved fish samples purified by high-pressure liquid chromatography. Limnology and Oceanography-Methods. https://doi.org/10.1002/lom3.10359

Stephens, B. M., Wankel, S. D., Beman, J. M., Rabines, A. J., Allen, A. E., & Aluwihare, L. I. (2019). Euphotic zone nitrification in the California Current Ecosystem. Limnology and Oceanography. https://doi.org/10.1002/lno.11348

Stukel, M. R., Kelly, T. B., Aluwihare, L. I., Barbeau, K. A., Goericke, R., Krause, J. W., Landry, M. R., & Ohman, M. D. (2019). The Carbon:(234)Thorium ratios of sinking particles in the California current ecosystem 1: relationships with plankton ecosystem dynamics. Marine Chemistry, 212, 1–15. https://doi.org/10.1016/j.marchem.2019.01.003

Malfatti, F., Lee, C., Tinta, T., Pendergraft, M. A., Celussi, M., Zhou, Y. Y., Sultana, C. M., Rotter, A., Axson, J. L., Collins, D. B., Santander, M. V., Morales, A. L. A., Aluwihare, L. I., Riemer, N., Grassian, V. H., Azam, F., & Prather, K. A. (2019). Detection of active microbial enzymes in nascent sea spray aerosol: Implications for atmospheric chemistry and climate. Environmental Science & Technology Letters, 6(3), 171–177. https://doi.org/10.1021/acs.estlett.8b00699

Stephens, B. M., Porrachia, M., Dovel, S., Roadman, M., Goericke, R., & Aluwihare, L. I. (2018). Nonsinking Organic Matter Production in the California Current. Global Biogeochemical Cycles, 32(9), 1386–1405. https://doi.org/10.1029/2018gb005930

Paulsen, M. L., Andersson, A. J., Aluwihare, L., Cyronak, T., D’Angelo, S., Davidson, C., Elwany, H., Giddings, S. N., Page, H. N., Porrachia, M., & Schroeter, S. (2018). Temporal changes in seawater carbonate chemistry and carbon export from a Southern California estuary. Estuaries and Coasts, 41(4), 1050–1068. https://doi.org/10.1007/s12237-017-0345-8

Kharbush, J. J., Thompson, L. R., Haroon, M. F., Knight, R., & Aluwihare, L. I. (2018). Hopanoid-producing bacteria in the Red Sea include the major marine nitrite oxidizers. Fems Microbiology Ecology, 94(6). https://doi.org/10.1093/femsec/fiy063

Petras, D., Koester, I., Da Silva, R., Stephens, B. M., Haas, A. F., Nelson, C. E., Kelly, L. W., Aluwihare, L. I., & Dorrestein, P. C. (2017). High-resolution liquid chromatography tandem mass spectrometry enables large scale molecular characterization of dissolved organic matter. Frontiers in Marine Science, 4(405). https://doi.org/10.3389/fmars.2017.00405

Arakawa, N., Aluwihare, L. I., Simpson, A. J., Soong, R., Stephens, B. M., & Lane-Coplen, D. (2017). Carotenoids are the likely precursor of a significant fraction of marine dissolved organic matter. Science Advances, 3. https://doi.org/10.1126/sciadv.1602976

Hansman, R. L., Thurber, A. R., Levin, L. A., & Aluwihare, L. I. (2017). Methane fates in the benthos and water column at cold seep sites along the continental margin of Central and North America. Deep-Sea Research Part I-Oceanographic Research Papers, 120, 122–131. https://doi.org/10.1016/j.dsr.2016.12.016

Stukel, M. R., Aluwihare, L. I., Barbeau, K. A., Chekalyuk, A. M., Goericke, R., Miller, A. J., Ohman, M. D., Ruacho, A., Song, H., Stephens, B. M., & Landry, M. R. (2017). Mesoscale ocean fronts enhance carbon export due to gravitational sinking and subduction. Proceedings of the National Academy of Sciences of the United States of America, 114(6), 1252–1257. https://doi.org/10.1073/pnas.1609435114

Kumar, A., Borgen, M., Aluwihare, L. I., & Fenical, W. (2017). Ozone-activated halogenation of mono- and dimethylbipyrrole in seawater. Environmental Science & Technology, 51(1), 589–595. https://doi.org/10.1021/acs.est.6b03601

Mackintosh, S. A., Dodder, N. G., Shaul, N. J., Aluwihare, L. I., Maruya, K. A., Chivers, S. J., Danil, K., Weller, D. W., & Hoh, E. (2016). Newly identified DDT-related compounds accumulating in Southern California bottlenose dolphins. Environmental Science & Technology, 50(22), 12129–12137. https://doi.org/10.1021/acs.est.6b03150

Tolar, B. B., Ross, M. J., Wallsgrove, N. J., Liu, Q., Aluwihare, L. I., Popp, B. N., & Hollibaugh, J. T. (2016). Contribution of ammonia oxidation to chemoautotrophy in Antarctic coastal waters. Isme Journal, 10(11), 2605–2619. https://doi.org/10.1038/ismej.2016.61

Kharbush, J. J., Allen, A. E., Moustafa, A., Dorrestein, P. C., & Aluwihare, L. I. (2016). Intact polar diacylglycerol biomarker lipids isolated from suspended particulate organic matter accumulating in an ultraoligotrophic water column. Organic Geochemistry, 100, 29–41. https://doi.org/10.1016/j.orggeochem.2016.07.008

Haskell, W. Z., Prokopenko, M. G., Hammond, D. E., Stanley, R. H. R., Berelson, W. M., Baronas, J. J., Fleming, J. C., & Aluwihare, L. (2016). An organic carbon budget for coastal Southern California determined by estimates of vertical nutrient flux, net community production and export. Deep-Sea Research Part I-Oceanographic Research Papers, 116, 49–76. https://doi.org/10.1016/j.dsr.2016.07.003

Moran, M. A., Kujawinski, E. B., Stubbins, A., Fatland, R., Aluwihare, L. I., Buchan, A., Crump, B. C., Dorrestein, P. C., Dyhrman, S. T., Hess, N. J., Howe, B., Longnecker, K., Medeiros, P. M., Niggemann, J., Obernosterer, I., Repeta, D. J., & Waldbauer, J. R. (2016). Deciphering ocean carbon in a changing world. Proceedings of the National Academy of Sciences of the United States of America, 113(12), 3143–3151. https://doi.org/10.1073/pnas.1514645113

Kharbush, J. J., Kejriwal, K., & Aluwihare, L. I. (2016). Distribution and abundance of hopanoid producers in low-oxygen environments of the Eastern Pacific Ocean. Microbial Ecology, 71(2), 401–408. https://doi.org/10.1007/s00248-015-0671-y

Sherwood, B. P., Shaffer, E. A., Reyes, K., Longnecker, K., Aluwihare, L. I., & Azam, F. (2015). Metabolic characterization of a model heterotrophic bacterium capable of significant chemical alteration of marine dissolved organic matter. Marine Chemistry, 177, 357–365. https://doi.org/10.1016/j.marchem.2015.06.027

Arakawa, N., & Aluwihare, L. (2015). Direct identification of diverse alicyclic terpenoids in Suwannee River fulvic acid. Environmental Science & Technology, 49(7), 4097–4105. https://doi.org/10.1021/es5055176

Agarwal, V., Li, J., Rahman, I., Borgen, M., Aluwihare, L. I., Biggs, J. S., Paul, V. J., & Moore, B. S. (2015). Complexity of naturally produced polybrominated diphenyl ethers revealed via mass spectrometry. Environmental Science & Technology, 49(3), 1339–1346. https://doi.org/10.1021/es505440j

Goldberg, S. J., Ball, G. I., Allen, B. C., Schladow, S. G., Simpson, A. J., Masoom, H., Soong, R., Graven, H. D., & Aluwihare, L. I. (2015). Refractory dissolved organic nitrogen accumulation in high-elevation lakes. Nature Communications, 6. https://doi.org/10.1038/ncomms7347