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Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Marine Chemistry at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution February 2023., Marine dissolved organic matter (DOM) is an actively cycling reservoir of carbon containing thousands of unique compounds. To describe the complex dynamics that govern the biological transformation and decomposition of compounds in this molecular black box, models of DOM reactivity use chemical characteristics, as well as environmental parameters, to describe trends in the turnover time of classes of DOM. In this thesis, I describe two projects that examine hypotheses regarding the turnover of two classes of DOM. In the 1st project, I test the assumption made by the size–reactivity continuum hypothesis that high molecular weight (> 1 kDa) DOM (HMWDOM) represents a diagenetic intermediate between large labile material and small recalcitrant compounds. Size-fractions of HMWDOM were collected using size-exclusion chromatography, and the changes in MW and chemical composition of the fractions were studied using diffusion-ordered spectroscopy. The size fraction carbon isotopic values were correlated with the proportion of humic substances in the fractions. Through linear modeling, the apparent radiocarbon ages of the two major components of HMWDOM were determined to be 1-3 yrs and 2-4 kyrs, respectively. Combined with the measurements of MW distribution this work demonstrates that HMWDOM is composed of two components that have contrasting decomposition pathways in the ocean. HMWDOM cannot be treated as a single DOM pool when incorporated into models of DOM diagenesis. The 2nd project in this dissertation examines the remineralization of phosphonates, compounds with a direct C-P bond, in the lower euphotic zone using a newly developed fluorescent assay, which measures the activity of carbon-phosphorus lyase. C-P lyase activity (CLA) profiles from the North Pacific Subtropical Gyre (NPSG) showed a sharp activity maximum near the deep-chlorophyll maximum (DCM). High-resolution nutrient measurements suggest that this subsurface CLA maximum is the result of a high nitrate flu, The studies described in this dissertation were supported by the Simons Foundation (SCOPE award 329108 to D.M.K. and D.J.R.), the Gordon and Betty Moore Foundation (3794; D.M.K. and 6000; D.J.R.), and the National Science Foundation (NSF: OCE-1634080; D.J.R.) and I thank them for their support.

Significance Phosphonates are a class of phosphorus metabolites characterized by a highly stable C-P bond. Phosphonates accumulate to high concentrations in seawater, fuel a large fraction of marine methane production, and serve as a source of phosphorus to microbes inhabiting nutrient-limited regions of the oligotrophic ocean. Here, we show that 15% of all bacterioplankton in the surface ocean have genes phosphonate synthesis and that most belong to the abundant groups Prochlorococcus and SAR11. Genomic and chemical evidence suggests that phosphonates are incorporated into cell-surface phosphonoglycoproteins that may act to mitigate cell mortality by grazing and viral lysis. These results underscore the large global biogeochemical impact of relatively rare but highly expressed traits in numerically abundant groups of marine bacteria.

© The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Acker, M., Hogle, S. L., Berube, P. M., Hackl, T., Coe, A., Stepanauskas, R., Chisholm, S. W., & Repeta, D. J. Phosphonate production by marine microbes: exploring new sources and potential function. Proceedings of the National Academy of Sciences of the United States of America, 119(11), (2022): e2113386119, https://doi.org/10.1073/pnas.2113386119., Phosphonates are organophosphorus metabolites with a characteristic C-P bond. They are ubiquitous in the marine environment, their degradation broadly supports ecosystem productivity, and they are key components of the marine phosphorus (P) cycle. However, the microbial producers that sustain the large oceanic inventory of phosphonates as well as the physiological and ecological roles of phosphonates are enigmatic. Here, we show that phosphonate synthesis genes are rare but widely distributed among diverse bacteria and archaea, including Prochlorococcus and SAR11, the two major groups of bacteria in the ocean. In addition, we show that Prochlorococcus can allocate over 40% of its total cellular P-quota toward phosphonate production. However, we find no evidence that Prochlorococcus uses phosphonates for surplus P storage, and nearly all producer genomes lack the genes necessary to degrade and assimilate phosphonates. Instead, we postulate that phosphonates are associated with cell-surface glycoproteins, suggesting that phosphonates mediate ecological interactions between the cell and its surrounding environment. Our findings indicate that the oligotrophic surface ocean phosphonate pool is sustained by a relatively small fraction of the bacterioplankton cells allocating a significant portion of their P quotas toward secondary metabolism and away from growth and reproduction., This work was supported in part by grants from the NSF (OCE-1153588 and DBI-0424599 to S.W.C.; OCE-1335810 and OIA-1826734 to R.S.; and OCE-1634080 to D.J.R.), the Gordon and Betty Moore Foundation (no. 6000 to D.J.R.), and the Simons Foundation (Life Sciences Project Award IDs 337262 and 647135 to S.W.C.; 510023 to R.S.; and Simons Collaboration on Ocean Processes and Ecology [SCOPE] Award ID 329108 to S.W.C. and D.J.R.).

Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Chemical Oceanography at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution May 2022., Marine microbes require copper (Cu) for a variety of key enzymes and can therefore experience limitation when concentrations are low. However, when Cu concentrations are too high, it becomes toxic causing decreased cell growth and even cell death. Laboratory culture experiments have shown that a diverse array of microbes produce organic ligands that complex Cu (CuL) and buffer the free ion concentration, which is the most bioavailable fraction. In this way, the microbes impose a control on the speciation of Cu, decreasing the toxic effects of Cu and making seawater conditions favorable for growth. Studies have shown that CuL complexes produced in laboratory cultures have similar complexation strengths to those found in seawater samples, which suggests a biological source of CuLs in seawater where dissolved Cu is almost entirely bound by organic ligands. However, information about individual CuL complexes is lacking which limits our understanding of the sources, sinks, and cycling of dissolved Cu. In order to fill this gap in knowledge, molecular level information about CuL complexes produced in culture and found in seawater must be obtained. To investigate this, liquid chromatography (LC) was coupled to two mass spectrometers (MS), an inductively coupled plasma (ICP) MS and an electrospray ionization (ESI) MS. By using data supplied by both techniques, the molecular charateristics of CuLs were determined laboratory cultures of the marine diatom Phaeodactylum tricornutum and the cyanobacterium Synechococcus, as well as investigating the distribution of CuLs in natural seawater samples along a line from 56°N to 20°S, along 152°W through the north and central Pacific Ocean. The CuLs identified in laboratory cultures had molecular formulae and fragmentation patterns characteristic of linear tetrapyrroles, a group of organic compounds commonly found in biological systems. This identification was further supported by absorbance and nuclear magnetic resonance spectroscopy., Funding for this work was provided by the National Science Foundation Graduate Research Fellowship Program (NSF award 1122374) for providing three years of funding. Thank you to the National Science Foundation Chemical Oceanography Program (NSF award OCE-1736280 and OCE-2045223) and the Simons Collaboration on Ocean Processes and Ecology (award P49476). A portion of this work was performed at the National High Magnetic Field Laboratory in Tallahassee, Florida, which is supported through NSF DMR 11-57490, and the State of Florida.

© The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Kiang, N. Y., Swingley, W. D., Gautam, D., Broddrick, J. T., Repeta, D. J., Stolz, J. F., Blankenship, R. E., Wolf, B. M., Detweiler, A. M., Miller, K. A., Schladweiler, J. J., Lindeman, R., & Parenteau, M. N. Discovery of chlorophyll d: isolation and characterization of a far-red cyanobacterium from the original site of manning and strain (1943) at Moss Beach, California. Microorganisms, 10(4), (2022): 819, https://doi.org/10.3390/microorganisms10040819., We have isolated a chlorophyll-d-containing cyanobacterium from the intertidal field site at Moss Beach, on the coast of Central California, USA, where Manning and Strain (1943) originally discovered this far-red chlorophyll. Here, we present the cyanobacterium’s environmental description, culturing procedure, pigment composition, ultrastructure, and full genome sequence. Among cultures of far-red cyanobacteria obtained from red algae from the same site, this strain was an epiphyte on a brown macroalgae. Its Qyin vivo absorbance peak is centered at 704–705 nm, the shortest wavelength observed thus far among the various known Acaryochloris strains. Its Chl a/Chl d ratio was 0.01, with Chl d accounting for 99% of the total Chl d and Chl a mass. TEM imagery indicates the absence of phycobilisomes, corroborated by both pigment spectra and genome analysis. The Moss Beach strain codes for only a single set of genes for producing allophycocyanin. Genomic sequencing yielded a 7.25 Mbp circular chromosome and 10 circular plasmids ranging from 16 kbp to 394 kbp. We have determined that this strain shares high similarity with strain S15, an epiphyte of red algae, while its distinct gene complement and ecological niche suggest that this strain could be the closest known relative to the original Chl d source of Manning and Strain (1943). The Moss Beach strain is designated Acaryochloris sp. (marina) strain Moss Beach., N.Y.K., M.N.P. and R.E.B. were supported by the NASA Virtual Planetary Laboratory team (VPL), which was funded under NASA Astrobiology Institute Cooperative Agreement Number NNA13AA93A, and Grant Number 80NSSC18K0829. This work also benefited from participation in the NASA Nexus for Exoplanet Systems Science (NExSS) research coordination network (RCN). W.D.S, N.Y.K. and M.N.P. were also supported by a NASA Exobiology grant No. 80NSSC19K0478. J.TB. was supported by the NASA Postdoctoral Program (NPP) award number NPP168014S. N.Y.K. received training support from the NASA Goddard Space Flight Center Training Office to take the Microbial Diversity course at the Marine Biological Laboratory, Woods Hole, MA, USA.

© The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Hawco, N. J., Barone, B., Church, M. J., Babcock-Adams, L., Repeta, D. J., Wear, E. K., Foreman, R. K., Bjorkman, K. M., Bent, S., Van Mooy, B. A. S., Sheyn, U., DeLong, E. F., Acker, M., Kelly, R. L., Nelson, A., Ranieri, J., Clemente, T. M., Karl, D. M., & John, S. G. Iron depletion in the deep chlorophyll maximum: mesoscale eddies as natural iron fertilization experiments. Global Biogeochemical Cycles, 35(12), (2021): e2021GB007112, https://doi.org/10.1029/2021GB007112., In stratified oligotrophic waters, phytoplankton communities forming the deep chlorophyll maximum (DCM) are isolated from atmospheric iron sources above and remineralized iron sources below. Reduced supply leads to a minimum in dissolved iron (dFe) near 100 m, but it is unclear if iron limits growth at the DCM. Here, we propose that natural iron addition events occur regularly with the passage of mesoscale eddies, which alter the supply of dFe and other nutrients relative to the availability of light, and can be used to test for iron limitation at the DCM. This framework is applied to two eddies sampled in the North Pacific Subtropical Gyre. Observations in an anticyclonic eddy center indicated downwelling of iron-rich surface waters, leading to increased dFe at the DCM but no increase in productivity. In contrast, uplift of isopycnals within a cyclonic eddy center increased supply of both nitrate and dFe to the DCM, and led to dominance of picoeukaryotic phytoplankton. Iron addition experiments did not increase productivity in either eddy, but significant enhancement of leucine incorporation in the light was observed in the cyclonic eddy, a potential indicator of iron stress among Prochlorococcus. Rapid cycling of siderophores and low dFe:nitrate uptake ratios also indicate that a portion of the microbial community was stressed by low iron. However, near-complete nitrate drawdown in this eddy, which represents an extreme case in nutrient supply compared to nearby Hawaii Ocean Time-series observations, suggests that recycling of dFe in oligotrophic ecosystems is sufficient to avoid iron limitation in the DCM under typical conditions., The expedition and analyses were supported by the Simons Foundation SCOPE Grant 329108 to S. G. John, M. J. Church, D. J. Repeta, B. Van Mooy, E. F. DeLong, and D. M. Karl. N. J. Hawco was supported by a Simons Foundation Marine Microbial Ecology and Evolution postdoctoral fellowship (602538) and Simons Foundation grant 823167.

© The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Pollara, S. B., Becker, J. W., Nunn, B. L., Boiteau, R., Repeta, D., Mudge, M. C., Downing, G., Chase, D., Harvey, E. L., & Whalen, K. E. Bacterial quorum-sensing signal arrests phytoplankton cell division and impacts virus-induced mortality. Msphere, 6(3), (2021): e00009-21, https://doi.org/10.1128/mSphere.00009-21., Interactions between phytoplankton and heterotrophic bacteria fundamentally shape marine ecosystems by controlling primary production, structuring marine food webs, mediating carbon export, and influencing global climate. Phytoplankton-bacterium interactions are facilitated by secreted compounds; however, linking these chemical signals, their mechanisms of action, and their resultant ecological consequences remains a fundamental challenge. The bacterial quorum-sensing signal 2-heptyl-4-quinolone (HHQ) induces immediate, yet reversible, cellular stasis (no cell division or mortality) in the coccolithophore Emiliania huxleyi; however, the mechanism responsible remains unknown. Using transcriptomic and proteomic approaches in combination with diagnostic biochemical and fluorescent cell-based assays, we show that HHQ exposure leads to prolonged S-phase arrest in phytoplankton coincident with the accumulation of DNA damage and a lack of repair despite the induction of the DNA damage response (DDR). While this effect is reversible, HHQ-exposed phytoplankton were also protected from viral mortality, ascribing a new role of quorum-sensing signals in regulating multitrophic interactions. Furthermore, our data demonstrate that in situ measurements of HHQ coincide with areas of enhanced micro- and nanoplankton biomass. Our results suggest bacterial communication signals as emerging players that may be one of the contributing factors that help structure complex microbial communities throughout the ocean., Funding for this work was supported by an NSF grant (OCE-1657808) awarded to K.E.W. and E.L.H. K.E.W. was also supported by a faculty research grant from Haverford College as well as funding from the Koshland Integrated Natural Science Center and Green Fund at Haverford College. E.L.H. was also supported by a Sloan Foundation research fellowship. B.L.N. was supported by an NSF grant (OCE-1633939). M.C.M. was supported by an NIH training grant (T32 HG000035). Mass spectrometry was partially supported by the University of Washington Proteomics Resource (UWPR95794). D.R. was supported by funding through the Gordon and Betty Moore Foundation (grant 6000), a Simons Collaboration for Ocean Processes and Ecology grant (329108), and an NSF grant (OCE-1736280). R.B. was supported by an NSF graduate research fellowship and an NSF grant (OCE-1829761).

Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Chemical Oceanography at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution June 2021., The existence of a marine phosphorus (P) redox cycle was recently confirmed when phosphonates, organophosphorus compounds with P in the (III) oxidation state, were found in high molecular weight dissolved organic matter. Although some features of the P redox cycle have come to light since the discovery of phosphonates, many aspects of phosphonate production, cycling and fate remain unknown. To address these gaps in our understanding, we studied phosphonate cycling in the Eastern Mediterranean Sea, a chronically P-limited basin, using 33P and enzymatic assays. We showed that phosphonate production was low but consumption was high, suggesting that phosphonate production and consumption may be spatially or temporally decoupled. We also explored phosphonate production in the model marine cyanobacterium Prochlorococcus SB. Using 31P NMR, we found Prochlorococcus SB allocates ~50% of its cellular P to phosphonates. Allocation of P to phosphonates was conserved under P-limitation, and further investigation revealed phosphonates were associated with proteins. The discovery of phosphonoproteins in Prochlorococcus SB opens new perspectives on the biochemical function of phosphonates and their role in P-cycling. Finally, we developed a new P-targeted method to characterize marine organophosphorus compounds using liquid chromatography coupled to electrospray ionization and inductively coupled plasma mass spectrometry., This work was supported by the Simons Foundation under grant numbers POP49476 and 721227 [D. Repeta], the Gordon and Betty Moore Foundation under the grant number 6000 [D. Repeta] and the National Science Foundation OCE under the grant number 1634080 [D. Repeta].

© The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Li, J., Boiteau, R. M., Babcock-Adams, L., Acker, M., Song, Z., McIlvin, M. R., & Repeta, D. J. Element-selective targeting of nutrient metabolites in environmental samples by inductively coupled plasma mass spectrometry and electrospray ionization mass spectrometry. Frontiers in Marine Science, 8, (2021): 630494, https://doi.org/10.3389/fmars.2021.630494., Metabolites that incorporate elements other than carbon, nitrogen, hydrogen and oxygen can be selectively detected by inductively coupled mass spectrometry (ICPMS). When used in parallel with chromatographic separations and conventional electrospray ionization mass spectrometry (ESIMS), ICPMS allows the analyst to quickly find, characterize and identify target metabolites that carry nutrient elements (P, S, trace metals; “nutrient metabolites”), which are of particular interest to investigations of microbial biogeochemical cycles. This approach has been applied to the study of siderophores and other trace metal organic ligands in the ocean. The original method used mass search algorithms that relied on the ratio of stable isotopologues of iron, copper and nickel to assign mass spectra collected by ESIMS to metabolites carrying these elements detected by ICPMS. However, while isotopologue-based mass assignment algorithms were highly successful in characterizing metabolites that incorporate some trace metals, they do not realize the whole potential of the ICPMS/ESIMS approach as they cannot be used to assign the molecular ions of metabolites with monoisotopic elements or elements for which the ratio of stable isotopes is not known. Here we report a revised ICPMS/ESIMS method that incorporates a number of changes to the configuration of instrument hardware that improves sensitivity of the method by a factor of 4–5, and allows for more accurate quantitation of metabolites. We also describe a new suite of mass search algorithms that can find and characterize metabolites that carry monoisotopic elements. We used the new method to identify siderophores in a laboratory culture of Vibrio cyclitrophicus and a seawater sample collected in the North Pacific Ocean, and to assign molecular ions to monoisotopic cobalt and iodine nutrient metabolites in extracts of a laboratory culture of the marine cyanobacterium Prochorococcus MIT9215., This work was generously supported by the National Science Foundation grant OCE-1829761 to RB and OCE-1356747 and -1736280 to DR. DR also received generous support from the Simons Foundation Life Sciences Project Award 49476.

© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Lin, H. T., Hsieh, C. C., Repeta, D. J., & Rappé, M. S. Sampling of basement fluids via circulation obviation retrofit kits (CORKs) for dissolved gases, fluid fixation at the seafloor, and the characterization of organic carbon. Methodsx, 7, (2020): 101033, doi:10.1016/j.mex.2020.101033., The advanced instrumented GeoMICROBE sleds (Cowen et al., 2012) facilitate the collection of hydrothermal fluids and suspended particles in the subseafloor (basaltic) basement through Circulation Obviation Retrofit Kits (CORKs) installed within boreholes of the Integrated Ocean Drilling Program. The main components of the GeoMICROBE can be converted into a mobile pumping system (MPS) that is installed on the front basket of a submersible or remotely-operated-vehicle (ROV). Here, we provide details of a hydrothermal fluid-trap used on the MPS, through which a gastight sampler can withdraw fluids. We also applied the MPS to demonstrate the value of fixing samples at the seafloor in order to determine redox-sensitive dissolved iron concentrations and speciation measurements. To make the best use of the GeoMICROBE sleds, we describe a miniature and mobile version of the GeoMICROBE sled, which permits rapid turn-over and is relatively easy for preparation and operation. Similar to GeoMICROBE sleds, the Mobile GeoMICROBE (MGM) is capable of collecting fluid samples, filtration of suspended particles, and extraction of organics. We validate this approach by demonstrating the seafloor extraction of hydrophobic organics from a large volume (247L) of hydrothermal fluids. • We describe the design of a hydrothermal fluid-trap for use with a gastight sampler, as well as the use of seafloor fixation, through ROV- or submersible assisted mobile pumping systems. • We describe the design of a Mobile GeoMICROBE (MGM) that enhances large volume hydrothermal fluid sampling, suspended particle filtration, and organic matter extraction on the seafloor. • We provide an example of organic matter extracted and characterized from hydrothermal fluids via a MGM., We dedicate this work to Dr. James P. Cowen, who had envisioned and constructed the integrated instrumentation, GeoMICROBE, to monitor the sub-basement biosphere. We thank the chief scientists, captains, crews, and science teams on board R/V Atlantis cruises AT15-35, AT15-51, AT15-66, AT18-07, MSM20-5, AT26-03, and AT26-18, and the pilots and crews of ROV Jason II and HOV Alvin. We thank our student assistants, Natalie Hamada, Kathryn Hu, Ryan Matzumoto, Everette Omori, and Fan-Chieh Chuang. This work was supported by the National Science Foundation-Microbial Observatory Project (NSF-MCB06-04014 to J. P. Cowen), Center for Dark Energy Biosphere Investigations (C-DEBI; NSF award OCE-0939564 to M. S. Rappé), NSF award OCE-1260723 (to M. S. Rappé), and the Ministry of Science and Technology of Taiwan award (MOST 105-2119-M-002-034, MOST 107-2611-M-002-002, MOST 108-2611-M-002-006, and MOST109-2611-M-002-008 to H.-T. Lin). Ministry of Education (MOE) Republic of China (Taiwan) 109L892601 to H.-T. Lin. NSF award OCE-1634080 (to D. J. Repeta), the Simons Foundation-Simons Collaboration on Ocean Processes and Ecology (SCOPE) award 329108 (to D. J. Repeta), the Gordon and Betty Moore Foundation award 6000 (to D. J. Repeta). This paper is SOEST contribution number 11121, HIMB contribution 1804 and C-DEBI contribution number 543.

© The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Baltar, F., Bayer, B., Bednarsek, N., Deppeler, S., Escribano, R., Gonzalez, C. E., Hansman, R. L., Mishra, R. K., Moran, M. A., Repeta, D. J., Robinson, C., Sintes, E., Tamburini, C., Valentin, L. E., & Herndl, G. J. Towards integrating evolution, metabolism, and climate change studies of marine ecosystems. Trends in Ecology and Evolution. 34(11), (2019): 1022-1033, doi: 10.1016/j.tree.2019.07.003., Global environmental changes are challenging the structure and functioning of ecosystems. However, a mechanistic understanding of how global environmental changes will affect ecosystems is still lacking. The complex and interacting biological and physical processes spanning vast temporal and spatial scales that constitute an ecosystem make this a formidable problem. A unifying framework based on ecological theory, that considers fundamental and realized niches, combined with metabolic, evolutionary, and climate change studies, is needed to provide the mechanistic understanding required to evaluate and forecast the future of marine communities, ecosystems, and their services., This work arose from the international workshop IMBIZO 5: Marine biosphere research for a sustainable ocean: Linking ecosystems, future states and resource management, organized by the IMBeR (Integrated Marine Biosphere Research) Program, and held at the Woods Hole Oceanographic Institution in October 2017. In particular, this work was generated from the working group from Workshop 2: Metabolic diversity and evolution in marine biogeochemical cycling and ocean ecosystem processes. The constructive criticism of three reviewers on a previous version of the manuscript is gratefully acknowledged. F.B. was supported by a Rutherford Discovery Fellowship by the Royal Society of New Zealand. G.J.H. was supported by the Austrian Science Fund (FWF) project ARTEMIS (P28781-B21).

Dataset: Water column methane ethylene and nutrients, Concentration measurements of water column phosphate, nitrate and nitrite, dissolved organic phosphorus, methane, and ethylene from samples collected during the R/V Niel Armstrong cruise AR16 in the western North Atlantic Ocean in May 2017. Seawater was collected from Niskin bottles deployed on a rosette with a CTD. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/769203, NSF Division of Ocean Sciences (NSF OCE) OCE-1634080

© The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in O'Brien, R. E., Ridley, K. J., Canagaratna, M. R., Jayne, J. T., Croteau, P. L., Worsnop, D. R., Budisulistiorini, S. H., Surratt, J. D., Follett, C. L., Repeta, D. J., & Kroll, J. H. Ultrasonic nebulization for the elemental analysis of microgram-level samples with offline aerosol mass spectrometry. Atmospheric Measurement Techniques, 12(3), (2019):1659-1671, doi:10.5194/amt-12-1659-2019., The elemental composition of organic material in environmental samples – including atmospheric organic aerosol, dissolved organic matter, and other complex mixtures – provides insights into their sources and environmental processing. However, standard analytical techniques for measuring elemental ratios typically require large sample sizes (milligrams of material or more). Here we characterize a method for measuring elemental ratios in environmental samples, requiring only micrograms of material, using a small-volume nebulizer (SVN). The technique uses ultrasonic nebulization of samples to generate aerosol particles (100–300 nm diameter), which are then analyzed using an aerosol mass spectrometer (AMS). We demonstrate that the technique generates aerosol from complex organic mixtures with minimal changes to the elemental composition of the organic material and that quantification is possible using internal standards (e.g., NH154NO3). Sample volumes of 2–4 µL with total solution concentrations of at least 0.2 g L−1 form sufficient particle mass for elemental ratio measurement by the AMS, despite only a small fraction (∼ 0.1 %) of the sample forming fine particles after nebulization (with the remainder ending up as larger droplets). The method was applied to aerosol filter extracts from the field and laboratory, as well as to the polysaccharide fraction of dissolved organic matter (DOM) from the North Pacific Ocean. In the case of aerosol particles, the mass spectra and elemental ratios from the SVN–AMS agree with those from online AMS sampling. Similarly, for DOM, the elemental ratios determined from the SVN–AMS agree with those determined using combustion analysis. The SVN–AMS provides a platform for the rapid quantitative analysis of the elemental composition of complex organic mixtures and non-refractory inorganic salts from microgram samples with applications that include analysis of aerosol extracts and terrestrial, aquatic, and atmospheric dissolved organic mat, This work was supported by National Oceanic and Atmospheric Administration grant nos. NA13OAR4310072 and NA140AR4310132. Kelsey J. Ridley acknowledges support from the NSF Graduate Research Fellowship Program. Sri Hapsari Budisulistiorini and Jason D. Surratt acknowledges support from the U.S. Environmental Protection Agency award no. 835404, Electric Power Research Institute (EPRI), and National Oceanic and Atmospheric Administration grant no. NA13OAR4310064. Special thanks are due to David Karl and Eric Grabowski, University of Hawaii, for the CHNS elemental analysis of DOM. Daniel J. Repeta acknowledges support from the Gordan and Betty Moore Foundation award 6000 and the Simons Foundation SCOPE award 329108.

© The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Bundy, R. M., Boiteau, R. M., McLean, C., Turk-Kubo, K. A., Mcllvin, M. R., Saito, M. A., Van Mooy, B. A. S., & Repeta, D. J.. Distinct siderophores contribute to iron cycling in the mesopelagic at station ALOHA. Frontiers in Marine Science, 5, (2018): 61. doi:10.3389/fmars.2018.00061., The distribution of dissolved iron (Fe), total organic Fe-binding ligands, and siderophores were measured between the surface and 400 m at Station ALOHA, a long term ecological study site in the North Pacific Subtropical Gyre. Dissolved Fe concentrations were low throughout the water column and strong organic Fe-binding ligands exceeded dissolved Fe at all depths; varying from 0.9 nmol L−1 in the surface to 1.6 nmol L−1 below 150 m. Although Fe does not appear to limit microbial production, we nevertheless found siderophores at nearly all depths, indicating some populations of microbes were responding to Fe stress. Ferrioxamine siderophores were most abundant in the upper water column, with concentrations between 0.1 and 2 pmol L−1, while a suite of amphibactins were found below 200 m with concentrations between 0.8 and 11 pmol L−1. The distinct vertical distribution of ferrioxamines and amphibactins may indicate disparate strategies for acquiring Fe from dust in the upper water column and recycled organic matter in the lower water column. Amphibactins were found to have conditional stability constants (log KcondFeL1,Fe′) ranging from 12.0 to 12.5, while ferrioxamines had much stronger conditional stability constants ranging from 14.0 to 14.4, within the range of observed L1 ligands by voltammetry. We used our data to calculate equilibrium Fe speciation at Station ALOHA to compare the relative concentration of inorganic and siderophore complexed Fe. The results indicate that the concentration of Fe bound to siderophores was up to two orders of magnitude higher than inorganic Fe, suggesting that even if less bioavailable, siderophores were nevertheless a viable pathway for Fe acquisition by microbes at our study site. Finally, we observed rapid production of ferrioxamine E by particle-associated bacteria during incubation of freshly collected sinking organic matter. Fe-limitation may therefore be a factor in regulating carbon metabolism and nutrient regeneration in t, We thank Chief Scientists Tara Clemente and Sam Wilson for leading the SCOPE Diel cruises. We also thank the Captain and crew of the R/V Ka'imikai-O-Kanaloa, as well as Paul Henderson in the Woods Hole Oceanographic Nutrient Analytical Facility for nutrient analyses. This work was funded by the Woods Hole Oceanographic Postdoctoral Fellowship for RaB, the Simons Foundation (Award 329108), and the National Science Foundation (OCE-1356747). We also thank two reviewers for helpful comments on the manuscript.

© The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Marine Science 5 (2018): 61, doi:10.3389/fmars.2018.00061., The distribution of dissolved iron (Fe), total organic Fe-binding ligands, and siderophores were measured between the surface and 400 m at Station ALOHA, a long term ecological study site in the North Pacific Subtropical Gyre. Dissolved Fe concentrations were low throughout the water column and strong organic Fe-binding ligands exceeded dissolved Fe at all depths; varying from 0.9 nmol L−1 in the surface to 1.6 nmol L−1 below 150 m. Although Fe does not appear to limit microbial production, we nevertheless found siderophores at nearly all depths, indicating some populations of microbes were responding to Fe stress. Ferrioxamine siderophores were most abundant in the upper water column, with concentrations between 0.1 and 2 pmol L−1, while a suite of amphibactins were found below 200 m with concentrations between 0.8 and 11 pmol L−1. The distinct vertical distribution of ferrioxamines and amphibactins may indicate disparate strategies for acquiring Fe from dust in the upper water column and recycled organic matter in the lower water column. Amphibactins were found to have conditional stability constants (log KcondFeL1,Fe′) ranging from 12.0 to 12.5, while ferrioxamines had much stronger conditional stability constants ranging from 14.0 to 14.4, within the range of observed L1 ligands by voltammetry. We used our data to calculate equilibrium Fe speciation at Station ALOHA to compare the relative concentration of inorganic and siderophore complexed Fe. The results indicate that the concentration of Fe bound to siderophores was up to two orders of magnitude higher than inorganic Fe, suggesting that even if less bioavailable, siderophores were nevertheless a viable pathway for Fe acquisition by microbes at our study site. Finally, we observed rapid production of ferrioxamine E by particle-associated bacteria during incubation of freshly collected sinking organic matter. Fe-limitation may therefore be a factor in regulating carbon metabolism and nutrient regeneration in t, This work was funded by the Woods Hole Oceanographic Postdoctoral Fellowship for RaB, the Simons Foundation (Award 329108), and the National Science Foundation (OCE-1356747).

Ocean acidification (OA) threatens coral reef ecosystems by slowing calcification and enhancing dissolution of calcifying organisms and sediments. Nevertheless, multiple factors have been shown to modulate OA's impact on calcification, including the nutritional status of the coral host. In three separate experiments, we exposed juveniles of the Atlantic golf ball coral, Favia fragum, to elevated CO2 and varied nutritional (light or feeding) conditions. Juveniles reared from planulae larvae were significantly larger and produced more CaCO3 when fed, regardless of CO2 level. However, corals subjected to elevated CO2 produced less CaCO3 per mm2 regardless of feeding condition. Additionally, unfed corals reared under elevated light levels exhibited lower chlorophyll a and higher total lipid content, but light had no significant effect on coral calcification. Conversely, elevated CO2 had a significant, negative affect on calcification, regardless of light condition but no detectable effect on physiological tissue parameters. Our results indicate that the sensitivity of juvenile F. fragum calcification to OA was neither modulated by light nor by feeding, despite physiological indications of enhanced nutritional status. This suggests that corals do not necessarily divert energy to maintain calcification under high CO2, even when they have the energetic resources to do so.

© The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 8 (2017): 2117, doi:10.3389/fmicb.2017.02117., Bacterial consumption of dissolved organic matter (DOM) drives much of the movement of carbon through the oceanic food web and the global carbon cycle. Understanding complex interactions between bacteria and marine DOM remains an important challenge. We tested the hypothesis that bacterial growth and community succession would respond differently to DOM additions due to seasonal changes in phytoplankton abundance in the environment. Four mesocosm experiments were conducted that spanned the spring transitional period (August–December 2013) in surface waters of the Western Antarctic Peninsula (WAP). Each mesocosm consisted of nearshore surface seawater (50 L) incubated in the laboratory for 10 days. The addition of DOM, in the form of cell-free exudates extracted from Thalassiosira weissflogii diatom cultures led to changes in bacterial abundance, production, and community composition. The timing of each mesocosm experiment (i.e., late winter vs. late spring) influenced the magnitude and direction of bacterial changes. For example, the same DOM treatment applied at different times during the season resulted in different levels of bacterial production and different bacterial community composition. There was a mid-season shift from Collwelliaceae to Polaribacter having the greatest relative abundance after incubation. This shift corresponded to a modest but significant increase in the initial relative abundance of Polaribacter in the nearshore seawater used to set up experiments. This finding supports a new hypothesis that starting community composition, through priority effects, influenced the trajectory of community succession in response to DOM addition. As strong inter-annual variability and long-term climate change may shift the timing of WAP phytoplankton blooms, and the corresponding production of DOM exudates, this study suggests a mechanism by which different seasonal successional patterns in bacterial communities could occur., CL was partially funded by the Graduate School and the Department of Ecology and Evolutionary Biology at Brown University and the Brown University-Marine Biological Laboratory Joint Graduate Program. This material is based upon work supported by the National Science Foundation under Grant Nos. ANT-1142114 to LA-Z, OPP-0823101 and PLR-1440435 to HD, and ANT-1141993 to JR. The Gordon and Betty Moore Foundation grant 1711 supported work by DR.