Description: The photosynthetic and diazotrophic cyanobacterium Trichodesmium is a key contributor to marine biogeochemical cycles in the subtropical-oligotrophic oceans. Trichodesmium form colonies that harbor a distinct microbial community in comparison to the surrounding seawater. The presence of their associated bacteria can expand Trichodesmium ’s functional potential and is predicted to influence the cycling of carbon, nitrogen, phosphorus, and iron (C, N, P, and Fe). To link the bacteria associated with Trichodesmium to key functional traits and elucidate how community structure can influence nutrient cycling, we characterized Red Sea Trichodesmium colonies using metagenomics and metaproteomics. Colonies harbored bacteria that typically associate with algae and particles, such as the ubiquitous Alteromonas macleodii, but also lineages specific to Trichodesmium , such as members from the order Balneolales. The majority of associated bacteria were auxotrophic for different vitamins, indicating their dependency on vitamin production by Trichodesmium . The associated bacteria carry functional traits including siderophore biosynthesis, reduced phosphorus metabolism, and denitrification pathways. The analysis supports Trichodesmium as an active hotspot for C, N, P, Fe, and vitamin exchange. In turn, Trichodesmium may rely on associated bacteria to meet its high Fe demand as several lineages synthesize photolabile siderophores (e.g., vibrioferrin, rhizoferrin, petrobactin) which can enhance the bioavailability of particulate Fe to the entire consortium. Collectively, the results indicate that Trichodesmium colonies provide a structure where these interactions can take place. While further studies are required to clarify the exact nature of these interactions, Trichodesmium ’s reliance on particle and algae-associated bacteria and the observed redundancy of key functional traits likely underpins the resilience of Trichodesmium within an ever-changing global environment. IMPORTANCE Colonies of the cyanobacteria Trichodesmium act as a biological hotspot for the usage and recycling of key resources such as C, N, P, and Fe within an otherwise oligotrophic environment. While Trichodesmium colonies are known to interact and support a unique community of algae and particle-associated microbes, our understanding of the taxa that populate these colonies and the gene functions they encode is still limited. Characterizing the taxa and adaptive strategies that influence consortium physiology and its concomitant biogeochemistry is critical in a future ocean predicted to have increasingly resource-depleted regions. Colonies of the cyanobacteria Trichodesmium act as a biological hotspot for the usage and recycling of key resources such as C, N, P, and Fe within an otherwise oligotrophic environment. While Trichodesmium colonies are known to interact and support a unique community of algae and particle-associated microbes, our understanding of the taxa that populate these colonies and the gene functions they encode is still limited. Characterizing the taxa and adaptive strategies that influence consortium physiology and its concomitant biogeochemistry is critical in a future ocean predicted to have increasingly resource-depleted regions.

Description: The marine cyanobacterium Trichodesmium has the remarkable ability to interact with and utilize air‐borne dust as a nutrient source. However, dust may adversely affect Trichodesmium through buoyancy loss and exposure to toxic metals. Our study explored the effect of desert dust on buoyancy and mortality of natural Red Sea puff‐shaped Trichodesmium thiebautii . Sinking velocities and ability of individual colonies to stay afloat with increasing dust loads were studied in sedimentation chambers. Low dust loads of up to ∼400 ng per colony did not impact initial sinking velocity and colonies remained afloat in the chamber. Above this threshold, sinking velocity increased linearly with the colony dust load at a slope matching prediction based on Stoke's law. The potential toxicity of dust was assessed with regards to metal dissolution kinetics, differentiating between rapidly released metals, which may impact surface blooms, and gradually released metals that may impact dust‐centering colonies. Incubations with increasing dust concentrations revealed colony death, but the observed lethal dose far exceeded dust concentrations measured in coastal and open ocean systems. Removal of toxic particles as a mechanism to reduce toxicity was explored using SEM‐EDX imaging of colonies incubated with Cu‐minerals, yet observations did not support this pathway. Combining our current and former experiments, we suggest that in natural settings the nutritional benefits gained by Trichodesmium via dust collection outweigh the risks of buoyancy loss and toxicity. Our data and concepts feed into the growing recognition of the significance of dust for Trichodesmium 's ecology and subsequently to ocean productivity. Plain Language Summary Trichodesmium spp. are abundant cyanobacteria, forming extensive blooms in low latitude warm oceans, and contribute significantly to carbon (C) and nitrogen (N) fixation, recycling and export. Desert dust deposited on the ocean surface was shown to supply Trichodesmium with the scarce micronutrient iron. Spherical, millimeter‐sized colonies of Trichodesmium from different ocean basins were reported to actively accumulate dust in their cores. While dust accumulation likely helps Trichodesmium obtain nutrients, it may come at a cost. Metals released from dust may induce toxicity and the dust weight could send Trichodesmium to the ocean depth. Our experimental study with natural Red Sea colonies examined some trade‐offs of dust accumulation. Links between dust load and colony buoyancy were examined in sedimentation experiments. Toxicity thresholds for surface blooms and dust‐accumulating colonies were determined from mortality assays and dust dissolution measurements. We found that metal‐induced toxicity to Trichodesmium is unlikely at typical oceanic dust fluxes, and that dust‐containing colonies can remain buoyant. At high loads, dust weight determined the colony's sinking velocity. Our findings and concepts can be extended to additional aerosols and Trichodesmium ‐rich habitats, and may assist in assessing Trichodesmium 's distribution, ecophysiology, and contribution to C or N transport to the deep ocean. Key Points Dust collected by Trichodesmium colonies from seawater as a nutrient source may result in metal toxification and buoyancy loss At moderate dust loads, colonies kept their buoyancy, but above 400 ng, sinking velocities increased linearly with dust loads Desert dust induced Trichodesmium mortality through toxic metal release, yet the lethal dose far exceeded oceanic dust concentrations

Description: Author Posting. © The Author(s), 2015. This is the author's version of the work. It is posted here by permission of Royal Society of Chemistry for personal use, not for redistribution. The definitive version was published in Metallomics 7 (2015): 877-884, doi:10.1039/C5MT00005J.

Description: Siderophores are thought to play an important role in iron cycling in the ocean, but relatively few marine siderophores have been identified. Sensitive, high throughput methods hold promise for expediting the discovery and characterization of new siderophores produced by marine microbes. We developed a methodology for siderophore characterization that combines liquid chromatography (LC) inductively coupled plasma mass spectrometry (ICPMS) with high resolution electrospray ionization mass spectrometry (ESIMS). To demonstrate this approach, we investigated siderophore production by the marine cyanobacteria Synechococcus sp. PCC 7002. Three hydroxamate siderophores, synechobactin A-C, have been previously isolated and characterized from this strain. These compounds consist of an iron binding head group attached to a fatty acid side chain of variable length (C12, C10, and C8 respectively). In this study, we detected six iron-containing compounds in Synechococcus sp. PCC 7002 media by LC-ICPMS. To identify the molecular ions of these siderophores, we aligned the chromatographic retention times of peaks from the LC-ICPMS chromatogram with features detected from LC-ESIMS spectra using an algorithm designed to recognize metal isotope patterns. Three of these compounds corresponded to synechobactins A (614 m/z), B (586m/z), and C (558m/z). The MS2 spectra of these compounds revealed diagnostic synechobactin fragmentation patterns which were used to confirm the identity of the three unknown compounds (600, 628, and 642 m/z) as new members of the synechobactin suite with side chain lengths of 11, 13, and 14 carbons. These results demonstrate the potential of combined LCMS techniques for the identification of novel iron-organic complexes.

Description: This work was supported by the National Science Foundation program in Chemical Oceanography (OCE-1356747), and by the National Science Foundation Science and Technology Center for Microbial Oceanography Research and Education (C-MORE; DBI-0424599).

Description: 2016-03-12

Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Biogeosciences 15 (2018): 6451-6460, doi:10.5194/bg-15-6451-2018.

Description: Mercury bioaccumulation in open-ocean food webs depends on the net rate of inorganic mercury conversion to monomethylmercury in the water column. We measured significant methylation rates across large gradients in oxygen utilization in the oligotrophic central Pacific Ocean. Overall, methylation rates over 24h incubation periods were comparable to those previously published from Arctic and Mediterranean waters despite differences in productivity between these marine environments. In contrast to previous studies that have attributed Hg methylation to heterotrophic bacteria, we measured higher methylation rates in filtered water compared to unfiltered water. Furthermore, we observed enhanced demethylation of newly produced methylated mercury in incubations of unfiltered water relative to filtered water. The addition of station-specific bulk filtered particulate matter, a source of inorganic mercury substrate and other possibly influential compounds, did not stimulate sustained methylation, although transient enhancement of methylation occurred within 8h of addition. The addition of dissolved inorganic cobalt also produced dramatic, if transient, increases in mercury methylation. Our results suggest important roles for noncellular or extracellular methylation mechanisms and demethylation in determining methylated mercury concentrations in marine oligotrophic waters. Methylation and demethylation occur dynamically in the open-ocean water column, even in regions with low accumulation of methylated mercury.

Description: This work was funded by the National Science Foundation in a Chemical Oceanography Program Grant (OCE-1031271) awarded to Carl H. Lamborg and Mak A. Saito and a graduate student fellowship to Kathleen M. Munson.

Description: Author Posting. © American Geophysical Union, 2012. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Paleoceanography 27 (2012): PA3227, doi:10.1029/2012PA002335.

Description: The rate of uranium accumulation in oceanic sediments from seawater is controlled by bottom water oxygen concentrations and organic carbon fluxes—two parameters that are linked to deep ocean storage of CO2. To investigate glacial-interglacial changes in what is known as authigenic U, we have developed a rapid method for its determination as a simple addition to a procedure for foraminiferal trace element analysis. Foraminiferal calcite acts as a low U substrate (U/Ca 〈 15 nmol/mol) upon which authigenic U accumulates in reducing sediments. We measured a downcore record of foraminiferal U/Ca from ODP Site 1090 in the South Atlantic and found that U/Ca ratios increase by 70–320 nmol/mol during glacial intervals. There is a significant correlation between U/Ca records of benthic and planktonic foraminiferal species and between U/Ca and bulk sediment authigenic U. These results indicate that elevated U/Ca ratios are attributable to the accumulation of authigenic U coatings in sediments. Foraminiferal Mn/Ca ratios were lower during the glacial intervals, suggesting that the observed U accumulation on the shells is not directly linked to U incorporation into secondary manganese phases. Thus, foraminiferal U/Ca ratios may provide useful information on past changes in sediment redox conditions.

Description: R.B. was funded by the Winston Churchill Foundation, and H.E. was funded by the UK Natural Environment Research Council and the European Research Council.

Description: 2013-03-08

Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution February 2016

Description: Marine microbes produce a wide variety of metal binding organic ligands that regulate the solubility and availability of biologically important metals such as iron, copper, cobalt, and zinc. In marine environments where the availability of iron limits microbial growth and carbon fixation rates, the ability to access organically bound iron confers a competitive advantage. Thus, the compounds that microbes produced to acquire iron play an important role in biogeochemical carbon and metal cycling. However, the source, abundance, and identity of these compounds are poorly understood. To investigate these processes, sensitive methodologies were developed to gain a compound-specific window into marine iron speciation by combining trace metal clean sample collection and chromatography with inductively coupled plasma mass spectrometry (LCICPMS) and electrospray ionization mass spectrometry (LC-ESIMS). Coupled with isotope pattern assisted search algorithms, these tools provide a means to quantify and isolate specific iron binding ligands from seawater and marine cultures, identify them based on their mass and fragmentation spectra, and investigate their metal binding kinetics. Using these techniques, we investigated the distribution and diversity of marine iron binding ligands. In cultures, LC-ICPMS-ESIMS was used to identify new members of siderophore classes produced by marine cyanobacteria and heterotrophic bacteria, including synechobactins and marinobactins. Applications to natural seawater samples from the Pacific Ocean revealed a wide diversity of both known and novel metal compounds that are linked to specific nutrient regimes. Ferrioxamines B, E, and G were identified in productive coastal waters near California and Peru, in oligotrophic waters of the North and South Pacific Gyre, and in association with zooplankton grazers. Siderophore concentrations were up to five-fold higher in iron-deficient offshore waters (9pM) and were dominated by amphibactins, amphiphilic siderophores that partition into cell membranes. Furthermore, synechobactins were detected within nepheloid layers along the continental shelf. These siderophores reflect adaptations that impact dissolved iron bioavailability and thus have important consequences for marine ecosystem community structures and primary productivity. The ability to map and characterize these compounds has opened new opportunities to better understand mechanisms that link metals with the microbes that use them.

Description: Thanks to the National Science Foundation Graduate Research Fellowship Program (NSF Award 0645960) for providing three years of funding. A special thanks to the National Science Foundation Chemical Oceanography Program (NSF awards OCE-01751733 and OCE-1356747) and the Gordon and Betty Moore Foundation for providing research and instrumentation funding that made this work possible. Additional support was provided by the Center for Microbial Oceanography: Research and Education (CMORE IF0424599) and the Simons Collaboration on Ocean Processes and Ecology (SCOPE).

Description: © 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.

Description: 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 the mesopelagic.

Description: 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).

Description: © 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.

Description: 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 the mesopelagic.

Description: 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.

Description: © 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.

Description: 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.

Description: 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.

Description: © 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.

Description: 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.

Description: 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).